Sample records for acid similarity matrix

  1. Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

    Directory of Open Access Journals (Sweden)

    Sette Alessandro


    Full Text Available Abstract Background Experts in peptide:MHC binding studies are often able to estimate the impact of a single residue substitution based on a heuristic understanding of amino acid similarity in an experimental context. Our aim is to quantify this measure of similarity to improve peptide:MHC binding prediction methods. This should help compensate for holes and bias in the sequence space coverage of existing peptide binding datasets. Results Here, a novel amino acid similarity matrix (PMBEC is directly derived from the binding affinity data of combinatorial peptide mixtures. Like BLOSUM62, this matrix captures well-known physicochemical properties of amino acid residues. However, PMBEC differs markedly from existing matrices in cases where residue substitution involves a reversal of electrostatic charge. To demonstrate its usefulness, we have developed a new peptide:MHC class I binding prediction method, using the matrix as a Bayesian prior. We show that the new method can compensate for missing information on specific residues in the training data. We also carried out a large-scale benchmark, and its results indicate that prediction performance of the new method is comparable to that of the best neural network based approaches for peptide:MHC class I binding. Conclusion A novel amino acid similarity matrix has been derived for peptide:MHC binding interactions. One prominent feature of the matrix is that it disfavors substitution of residues with opposite charges. Given that the matrix was derived from experimentally determined peptide:MHC binding affinity measurements, this feature is likely shared by all peptide:protein interactions. In addition, we have demonstrated the usefulness of the matrix as a Bayesian prior in an improved scoring-matrix based peptide:MHC class I prediction method. A software implementation of the method is available at:

  2. Spectral clustering based on learning similarity matrix. (United States)

    Park, Seyoung; Zhao, Hongyu; Birol, Inanc


    Single-cell RNA-sequencing (scRNA-seq) technology can generate genome-wide expression data at the single-cell levels. One important objective in scRNA-seq analysis is to cluster cells where each cluster consists of cells belonging to the same cell type based on gene expression patterns. We introduce a novel spectral clustering framework that imposes sparse structures on a target matrix. Specifically, we utilize multiple doubly stochastic similarity matrices to learn a similarity matrix, motivated by the observation that each similarity matrix can be a different informative representation of the data. We impose a sparse structure on the target matrix followed by shrinking pairwise differences of the rows in the target matrix, motivated by the fact that the target matrix should have these structures in the ideal case. We solve the proposed non-convex problem iteratively using the ADMM algorithm and show the convergence of the algorithm. We evaluate the performance of the proposed clustering method on various simulated as well as real scRNA-seq data, and show that it can identify clusters accurately and robustly. The algorithm is implemented in MATLAB. The source code can be downloaded at Supplementary data are available at Bioinformatics online.

  3. Fragmentation of extracellular matrix by hypochlorous acid

    DEFF Research Database (Denmark)

    Woods, Alan A; Davies, Michael Jonathan


    of the MPO-derived oxidant hypochlorous acid (HOCl) with extracellular matrix from vascular smooth muscle cells and healthy pig arteries has been examined. HOCl is rapidly consumed by such matrix samples, with the formation of matrix-derived chloramines or chloramides. The yield of these intermediates...... increases with HOCl dose. These materials undergo a time- and temperature-dependent decay, which parallels the release of sugar and protein components from the treated matrix, consistent with these species being important intermediates. Matrix damage is enhanced by species that increase chloramine....../chloramide decomposition, with copper and iron ions being effective catalysts, and decreased by compounds which scavenge chloramines/chloramides, or species derived from them. The effect of such matrix modifications on cellular behaviour is poorly understood, though it is known that changes in matrix materials can have...

  4. Igbo consonant confusion matrix: Issues on phonetic similarity | Eme ...

    African Journals Online (AJOL)

    This paper is on Igbo consonant confusion experiment aimed at producing an Igbo consonant confusion matrix. One hundred Igbo-speaking subjects were used for the experiment at the ratio of 1:1 for the control and experimental groups. Whereas the 28 consonants of standard Igbo were presented to the control group in ...

  5. On the definition of the effectively unpaired electron density matrix: A similarity measure approach (United States)

    Alcoba, Diego R.; Bochicchio, Roberto C.; Lain, Luis; Torre, Alicia


    The mathematical concepts of similarity and distance in metric spaces are used to relate Takatsuka et al. and Head-Gordon definitions of the effectively unpaired electron density matrix. This approach opens the possibility of new suitable definitions of this quantity to given purposes.

  6. Preparation of Coated Valproic Acid and Sodium Valproate Sustained-release Matrix Tablets. (United States)

    Phaechamud, T; Mueannoom, W; Tuntarawongsa, S; Chitrattha, S


    The aim of this research was to investigate the technique for preparation of coated valproic acid and sodium valproate sustained-release matrix tablets. Different diluents were tested and selected as the effective absorbent for oily valproic acid. Effect of the amount of absorbent and hydroxypropylmethylcellulose on drug release from valproic acid-sodium valproate matrix tablets prepared with wet granulation technique was evaluated in pH change system. Colloidal silicon dioxide effectively adsorbed liquid valproic acid during wet granulation and granule preparation. The amounts of colloidal silicon dioxide and hydroxypropylmethylcellulose employed in tablet formulations affected drug release from the tablets. The drug release was prominently sustained for over 12 h using hydroxypropylmethylcellulose-based hydrophilic matrix system. The mechanism of drug release through the matrix polymer was a diffusion control. The drug release profile of the developed matrix tablet was similar to Depakine Chrono(®), providing the values of similarity factor (f2) and difference factor (f1) of 85.56 and 2.37, respectively. Eudragit(®) L 30 D-55 was used as effective subcoating material for core matrix tablets before over coating with hydroxypropylmethylcellulose film with organic base solvent. Drug release profile of coated matrix tablet was almost similar to that of Depakine Chrono(®).

  7. Protein sequence alignment with family-specific amino acid similarity matrices (United States)


    Background Alignment of amino acid sequences by means of dynamic programming is a cornerstone sequence comparison method. The quality of alignments produced by dynamic programming critically depends on the choice of the alignment scoring function. Therefore, for a specific alignment problem one needs a way of selecting the best performing scoring function. This work is focused on the issue of finding optimized protein family- and fold-specific scoring functions for global similarity matrix-based sequence alignment. Findings I utilize a comprehensive set of reference alignments obtained from structural superposition of homologous and analogous proteins to design a quantitative statistical framework for evaluating the performance of alignment scoring functions in global pairwise sequence alignment. This framework is applied to study how existing general-purpose amino acid similarity matrices perform on individual protein families and structural folds, and to compare them to family-specific and fold-specific matrices derived in this work. I describe an adaptive alignment procedure that automatically selects an appropriate similarity matrix and optimized gap penalties based on the properties of the sequences being aligned. Conclusions The results of this work indicate that using family-specific similarity matrices significantly improves the quality of the alignment of homologous sequences over the traditional sequence alignment based on a single general-purpose similarity matrix. However, using fold-specific similarity matrices can only marginally improve sequence alignment of proteins that share the same structural fold but do not share a common evolutionary origin. The family-specific matrices derived in this work and the optimized gap penalties are available at PMID:21846354

  8. Risk Analysis and Setting Priorities in Air Traffic Control by Using a Matrix of Similarities

    Directory of Open Access Journals (Sweden)

    Lacane Monta


    Full Text Available This article considers how mathematical decision-making in Air Traffic Control could be done in order to minimize the risk of collisions. An example of how to prioritize airplanes which are in the vicinity of an airport according to their level of risk in respect to other airplanes is given by using a matrix of similarities and Euclidean metric. The analysis has shown that it is necessary to classify ATC specialists and ATC centers according to their ability to provide safe enough service using time methods and highly experienced team work.

  9. Community structure discovery method based on the Gaussian kernel similarity matrix (United States)

    Guo, Chonghui; Zhao, Haipeng


    Community structure discovery in complex networks is a popular issue, and overlapping community structure discovery in academic research has become one of the hot spots. Based on the Gaussian kernel similarity matrix and spectral bisection, this paper proposes a new community structure discovery method. First, by adjusting the Gaussian kernel parameter to change the scale of similarity, we can find the corresponding non-overlapping community structure when the value of the modularity is the largest relatively. Second, the changes of the Gaussian kernel parameter would lead to the unstable nodes jumping off, so with a slight change in method of non-overlapping community discovery, we can find the overlapping community nodes. Finally, synthetic data, karate club and political books datasets are used to test the proposed method, comparing with some other community discovery methods, to demonstrate the feasibility and effectiveness of this method.

  10. Null broadening adaptive beamforming based on covariance matrix reconstruction and similarity constraint (United States)

    Qian, Junhui; He, Zishu; Xie, Julan; Zhang, Yile


    In this paper, a procedure for the null broadening algorithm design with respect to the nonstationary interference is proposed. In contrast to previous works, we first impose nulls toward the regions of the nonstationary interference based on the reconstruction of the interference-plus-noise covariance matrix. Additionally, in order to provide a restriction on the shape of the beam pattern, a similarity constraint is enforced at the design stage. Then, the adaptive weight vector can be computed via maximizing a new signal-to-interference-plus-noise ratio (SINR) criterion subject to similarity constraint. Mathematically, the design original problem is expressed as a nonconvex fractional quadratically constrained quadratic programming (QCQP) problem with additional constraint, which can be converted into a convex optimisation problem by semidefinite programming (SDP) techniques. Finally, an optimal solution can be found by using the Charnes-Cooper transformation and the rank-one matrix decomposition theorem. Several numerical examples are performed to validate the performance of the proposed algorithm.


    Energy Technology Data Exchange (ETDEWEB)

    Lambert, D.; Koopman, D.


    Testing was completed to demonstrate the viability of the newly developed glycolic acid/formic acid flowsheet on processing in the Defense Waste Processing Facility's (DWPF) Chemical Process Cell (CPC). The Savannah River National Laboratory (SRNL) initiated a sludge matrix study to evaluate the impact of changing insoluble solid composition on the processing characteristics of slurries in DWPF. Four sludge simulants were prepared to cover two compositional ranges in the waste. The first was high iron/low aluminum versus low iron/high aluminum (referred to as HiFe or LoFe in this report). The second was high calcium-manganese/low nickel, chromium, and magnesium versus low calcium-manganese/high nickel, chromium, and magnesium (referred to as HiMn or LoMn in this report). These two options can be combined to form four distinct sludge compositions. The sludge matrix study called for testing each of these four simulants near the minimum acid required for nitrite destruction (100% acid stoichiometry) and at a second acid level that produced significant hydrogen by noble metal catalyzed decomposition of formic acid (150% acid stoichiometry). Four simulants were prepared based on the four possible combinations of the Al/Fe and Mn-Ca/Mg-Ni-Cr options. Preliminary simulant preparation work has already been documented. The four simulants were used for high and low acid testing. Eight planned experiments (GF26 to GF33) were completed to demonstrate the viability of the glycolic-formic flowsheet. Composition and physical property measurements were made on the SRAT product. Composition measurements were made on the condensate from the Mercury Water Wash Tank (MWWT), Formic Acid Vent Condenser (FAVC), ammonia scrubber and on SRAT samples pulled throughout the SRAT cycle. Updated values for formate loss and nitrite-tonitrate conversion were found that can be used in the acid calculations for future sludge matrix process simulations with the glycolic acid/formic acid

  12. Modeling of matrix acidizing process under reservoir conditions (United States)

    Turegeldieva, Karlygash; Assilbekov, Bakhytzhan; Zhapbasbayev, Uzak; Zolotukhin, Anatoly; Bekibaev, Timur; Kenzhebekov, Nurlan; Gubkin Russian State University of oil; gas Collaboration


    Effectiveness of the process depends on the parameters: well choice, geological structure of the reservoir, definition of physical and chemical properties of rocks and fluids, agent choice. There are different mathematical models of the matrix acidizing, including the two scale model. These models describe the process in the core scale and Darcy scale, i.e. in an area with dimensions of several centimeters. It leads to the main problem - how to use these models to the near wellbore scale under reservoir conditions. Some authors have increased the dimensions of the cores in numerical simulations and investigated the influence of the core dimensions to acidizing process. In this paper effort to indirectly solve this problem made. It based on boundary conditions alteration and simultaneous solution of matrix acidizing in damaged zone and reservoir fluid flow models. Furthermore in this work the criterion of the acid injection shut down for optimal breakthrough volume calculation was modified. Influence of boundary conditions on near well-bore zone treatment process was investigated. Science Committee of Ministry of Education and Science of Republic of Kazakhstan.

  13. A letter visual-similarity matrix for Latin-based alphabets

    National Research Council Canada - National Science Library

    Simpson, Ian C; Mousikou, Petroula; Montoya, Juan Manuel; Defior, Sylvia


    Indicators of letter visual similarity have been used for controlling the design of empirical and neuropsychological studies and for rigorously determining the factors that underlie reading ability...

  14. Matrix approach to dual similar associated consistency for the Shapley value

    NARCIS (Netherlands)

    Xu Genjiu, G.; Driessen, Theo; Sun, H.; Sun, H.


    In terms of the similarity of matrices, by combining the dual operator and the linear mapping with respect to Hamiache’s associated game on the game space, the Shapley value for TU-games is axiomatized as the unique value verifying dual similar associated consistency, continuity, and the inessential

  15. 5-Methoxysalicylic Acid Matrix for Ganglioside Analysis with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (United States)

    Lee, Dongkun; Cha, Sangwon


    In this note, we report that high quality ganglioside profiles with minimal loss of sialic acid residues can be obtained in the positive ion mode by using a 5-methoxysalicylic acid (MSA) matrix for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). Our results showed that MSA produced much less sialic acid losses from gangliosides than DHB, although MSA and DHB are differ only by their functional groups at their 5-positions (-OH for DHB and -OCH3 for MSA). Furthermore, our data also demonstrated that addition of an alkali metal additive was effective for simplifying ganglioside profiles, but not necessary for stabilizing glycosidic bonds of gangliosides if MSA was used as a matrix. This suggests that MALDI MS with MSA has a potential to gain additional benefits from the positive-ion mode analyses without losing performance in ganglioside profiling.

  16. Degradation of extracellular matrix by peroxynitrite/peroxynitrous acid. (United States)

    Kennett, Eleanor C; Davies, Michael J


    The extracellular matrix (ECM) provides strength and elasticity to tissues and plays a key role in regulating cell behavior; damage to this material is believed to be a major factor in many inflammatory diseases. Peroxynitrite/peroxynitrous acid, which is generated at elevated levels at sites of inflammation, is believed to play a role in ECM damage; however, the mechanisms involved are poorly understood. Here we examined the reactions of bolus peroxynitrite, and that generated in a time-dependent manner by SIN-1 decomposition, with ECM isolated from a vascular smooth muscle cell line and porcine thoracic aorta. Bolus peroxynitrite caused the release of ECM glycosaminoglycans and proteins, the formation of 3-nitroTyr, and the detection of ECM-derived radicals (by immuno-spin trapping) in a concentration-dependent manner. Release and nitration of ECM components were modulated by the local pH and bicarbonate. SIN-1 caused the release of glycosaminoglycan, but not protein, from vascular smooth muscle cell-derived ECM in a concentration-, time-, and pH-dependent manner. The data presented here suggest that peroxynitrite-mediated damage to ECM occurs via a radical-mediated pathway. These reactions may contribute to ECM damage at sites of inflammation and play a role in disease progression, including rupture of atherosclerotic lesions.

  17. Phosphoric acid as a matrix additive for MALDI MS analysis of phosphopeptides and phosphoproteins

    DEFF Research Database (Denmark)

    Kjellström, Sven; Jensen, Ole Nørregaard


    ,5-dihydroxybenzoic acid (2,5-DHB) matrix. Phosphoric acid in combination with 2,5-DHB matrix significantly enhanced phosphopeptide ion signals in MALDI mass spectra of crude peptide mixtures derived from the phosphorylated proteins alpha-casein and beta-casein. The beneficial effects of adding up to 1% phosphoric...... acid to 2,5-DHB were also observed in LC-MALDI-MS analysis of tryptic phosphopeptides of B. subtilis PrkC phosphoprotein. Finally, the mass resolution of MALDI mass spectra of intact proteins was significantly improved by using phosphoric acid in 2,5-DHB matrix....

  18. Radiolysis and Termolysis of Tetradecanoic Acid and Docosanoic Acid in Physicochemical Conditions Similar to Hydrothermal Vents (United States)

    Cruz-Castañeda, J.; Negrón-Mendoza, A.; Ramos-Bernal, S.; Colín-García, M.; Heredia, A.


    Our results show the stability of carboxylic acids against different energy sources. Additionally, the reaction products may have importance in chemical evolution, since they could function as reagents towards synthesis of other important compounds.

  19. Rheumatic Heart Disease and Myxomatous Degeneration: Differences and Similarities of Valve Damage Resulting from Autoimmune Reactions and Matrix Disorganization.

    Directory of Open Access Journals (Sweden)

    Carlo de Oliveira Martins

    Full Text Available Autoimmune inflammatory reactions leading to rheumatic fever (RF and rheumatic heart disease (RHD result from untreated Streptococcus pyogenes throat infections in individuals who exhibit genetic susceptibility. Immune effector mechanisms have been described that lead to heart tissue damage culminating in mitral and aortic valve dysfunctions. In myxomatous valve degeneration (MXD, the mitral valve is also damaged due to non-inflammatory mechanisms. Both diseases are characterized by structural valve disarray and a previous proteomic analysis of them has disclosed a distinct profile of matrix/structural proteins differentially expressed. Given their relevance in organizing valve tissue, we quantitatively evaluated the expression of vimentin, collagen VI, lumican, and vitronectin as well as performed immunohistochemical analysis of their distribution in valve tissue lesions of patients in both diseases. We identified abundant expression of two isoforms of vimentin (45 kDa, 42 kDa with reduced expression of the full-size protein (54 kDa in RHD valves. We also found increased vitronectin expression, reduced collagen VI expression and similar lumican expression between RHD and MXD valves. Immunohistochemical analysis indicated disrupted patterns of these proteins in myxomatous degeneration valves and disorganized distribution in rheumatic heart disease valves that correlated with clinical manifestations such as valve regurgitation or stenosis. Confocal microscopy analysis revealed a diverse pattern of distribution of collagen VI and lumican into RHD and MXD valves. Altogether, these results demonstrated distinct patterns of altered valve expression and tissue distribution/organization of structural/matrix proteins that play important pathophysiological roles in both valve diseases.

  20. Teichoic acid is the major polysaccharide present in the Listeria monocytogenes biofilm matrix. (United States)

    Brauge, Thomas; Sadovskaya, Irina; Faille, Christine; Benezech, Thierry; Maes, Emmanuel; Guerardel, Yann; Midelet-Bourdin, Graziella


    The aim of this study was to characterize the Listeria monocytogenes biofilm and particularly the nature of the carbohydrates in the biofilm extracellular matrix and culture supernatant versus to cell wall carbohydrates. Listeria monocytogenes serotype 1/2a and 4b strains were able to form complex biofilms embedded in an extracellular matrix. The soluble carbohydrates from biofilm extracellular matrix and culture supernatant were identified as teichoic acids, structurally identical to cell wall teichoic acids. In addition, the DSS 1130 BFA2 strain had a serotype 1/2a teichoic acid lacking N-acetyl glucosamine glycosylation due to a mutation in the lmo2550 gene. Consequently, we hypothesized that the extracellular teichoic acids in L. monocytogenes biofilms have the same origin as cell wall teichoic acid. © FEMS 2015. All rights reserved. For permissions, please e-mail:

  1. Similar, but different: structurally related azelaic acid and hexanoic acid trigger differential metabolomic and transcriptomic responses in tobacco cells. (United States)

    Djami-Tchatchou, Arnaud T; Ncube, Efficient N; Steenkamp, Paul A; Dubery, Ian A


    Plants respond to various stress stimuli by activating an enhanced broad-spectrum defensive ability. The development of novel resistance inducers represents an attractive, alternative crop protection strategy. In this regard, hexanoic acid (Hxa, a chemical elicitor) and azelaic acid (Aza, a natural signaling compound) have been proposed as inducers of plant defense, by means of a priming mechanism. Here, we investigated both the mode of action and the complementarity of Aza and Hxa as priming agents in Nicotiana tabacum cells in support of enhanced defense. Metabolomic analyses identified signatory biomarkers involved in the establishment of a pre-conditioned state following Aza and Hxa treatment. Both inducers affected the metabolomes in a similar manner and generated common biomarkers: caffeoylputrescine glycoside, cis-5-caffeoylquinic acid, feruloylglycoside, feruloyl-3-methoxytyramine glycoside and feruloyl-3-methoxytyramine conjugate. Subsequently, quantitative real time-PCR was used to investigate the expression of inducible defense response genes: phenylalanine ammonia lyase, hydroxycinnamoyl CoA quinate transferase and hydroxycinnamoyl transferase to monitor activation of the early phenylpropanoid pathway and chlorogenic acids metabolism, while ethylene response element-binding protein, small sar1 GTPase, heat shock protein 90, RAR1, SGT1, non-expressor of PR genes 1 and thioredoxin were analyzed to report on signal transduction events. Pathogenesis-related protein 1a and defensin were quantified to investigate the activation of defenses regulated by salicylic acid and jasmonic acid respectively. The qPCR results revealed differential expression kinetics and, in general (except for NPR1, Thionin and PR1a), the relative gene expression ratios observed in the Hxa-treated cells were significantly greater than the expression observed in the cells treated with Aza. The results indicate that Aza and Hxa have a similar priming effect through activation of genes

  2. Omega-3 and Omega-6 Fatty Acids Act as Inhibitors of the Matrix Metalloproteinase-2 and Matrix Metalloproteinase-9 Activity. (United States)

    Nicolai, Eleonora; Sinibaldi, Federica; Sannino, Gianpaolo; Laganà, Giuseppina; Basoli, Francesco; Licoccia, Silvia; Cozza, Paola; Santucci, Roberto; Piro, Maria Cristina


    Polyunsaturated fatty acids have been reported to play a protective role in a wide range of diseases characterized by an increased metalloproteinases (MMPs) activity. The recent finding that omega-3 and omega-6 fatty acids exert an anti-inflammatory effect in periodontal diseases has stimulated the present study, designed to determine whether such properties derive from a direct inhibitory action of these compounds on the activity of MMPs. To this issue, we investigated the effect exerted by omega-3 and omega-6 fatty acids on the activity of MMP-2 and MMP-9, two enzymes that actively participate to the destruction of the organic matrix of dentin following demineralization operated by bacteria acids. Data obtained (both in vitro and on ex-vivo teeth) reveal that omega-3 and omega-6 fatty acids inhibit the proteolytic activity of MMP-2 and MMP-9, two enzymes present in dentin. This observation is of interest since it assigns to these compounds a key role as MMPs inhibitors, and stimulates further study to better define their therapeutic potentialities in carious decay.

  3. 3-Aminoquinoline/p-coumaric acid as a MALDI matrix for glycopeptides, carbohydrates, and phosphopeptides. (United States)

    Fukuyama, Yuko; Funakoshi, Natsumi; Takeyama, Kohei; Hioki, Yusaku; Nishikaze, Takashi; Kaneshiro, Kaoru; Kawabata, Shin-Ichirou; Iwamoto, Shinichi; Tanaka, Koichi


    Glycosylation and phosphorylation are important post-translational modifications in biological processes and biomarker research. The difficulty in analyzing these modifications is mainly their low abundance and dissociation of labile regions such as sialic acids or phosphate groups. One solution in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is to improve matrices for glycopeptides, carbohydrates, and phosphopeptides by increasing the sensitivity and suppressing dissociation of the labile regions. Recently, a liquid matrix 3-aminoquinoline (3-AQ)/α-cyano-4-hydroxycinnamic acid (CHCA) (3-AQ/CHCA), introduced by Kolli et al. in 1996, has been reported to increase sensitivity for carbohydrates or phosphopeptides, but it has not been systematically evaluated for glycopeptides. In addition, 3-AQ/CHCA enhances the dissociation of labile regions. In contrast, a liquid matrix 1,1,3,3-tetramethylguanidium (TMG, G) salt of p-coumaric acid (CA) (G3CA) was reported to suppress dissociation of sulfate groups or sialic acids of carbohydrates. Here we introduce a liquid matrix 3-AQ/CA for glycopeptides, carbohydrates, and phosphopeptides. All of the analytes were detected as [M + H](+) or [M - H](-) with higher or comparable sensitivity using 3-AQ/CA compared with 3-AQ/CHCA or 2,5-dihydroxybenzoic acid (2,5-DHB). The sensitivity was increased 1- to 1000-fold using 3-AQ/CA. The dissociation of labile regions such as sialic acids or phosphate groups and the fragmentation of neutral carbohydrates were suppressed more using 3-AQ/CA than using 3-AQ/CHCA or 2,5-DHB. 3-AQ/CA was thus determined to be an effective MALDI matrix for high sensitivity and the suppression of dissociation of labile regions in glycosylation and phosphorylation analyses.

  4. New particle formation from sulfuric acid and amines: Similarities and differences between mono-, di-, and trimethylamines (United States)

    Olenius, Tinja; Halonen, Roope; Kurtén, Theo; Henschel, Henning; Kupiainen-Määttä, Oona; Ortega, Ismael K.; Vehkamäki, Hanna; Riipinen, Ilona


    Amines are organic base species that are emitted to the atmosphere from both anthropogenic and natural sources. Both theoretical and laboratory studies suggest that mono-, di-, and trimethylamines (MMA, DMA, and TMA, respectively) are capable of enhancing the initial steps of sulfuric acid-driven aerosol particle formation much more strongly than ammonia (Kurtén et al., 2008; Jen et al., 2014). Despite the potential importance for atmospheric new particle formation, quantitative estimates on the emissions and thermochemical properties of amines remain relatively uncertain. Because of this and also due to computational reasons, recent large-scale modeling studies have treated sulfuric acid-amine nucleation by introducing a single surrogate amine species, the total emissions of which combine together MMA, DMA and TMA but which resembles DMA or TMA in its various properties (e.g. Bergman et al., 2015). On the other hand, there are likely to be differences in the potentials of the three amines to enhance particle formation, causing uncertainties to the lumping approach. Systematic comparisons are needed to evaluate how to treat these species in atmospheric models and to assess what level of simplification is justifiable. In this work, we study the differences and similarities of MMA, DMA and TMA by modeling nanoparticle formation from sulfuric acid, water, and each of the three amines. We simulate molecular cluster concentrations and formation rates at boundary layer conditions with a dynamic cluster population model using quantum chemistry-based cluster evaporation rates, and study the dependence of particle formation rate on precursor vapor concentrations, temperature and relative humidity. The results suggest that for the three amines, there are differences in the nucleation mechanism and hygroscopicity of molecular clusters. However, for DMA and TMA, formation of nanometer-sized particles and its dependence on ambient conditions is roughly similar: both

  5. Study of acid solution bonding in epoxy matrix for sealed radioactive sources production

    Energy Technology Data Exchange (ETDEWEB)

    Benega, Marcos A.G.; Nagatomi, Helio R.; Rostelato, Maria Elisa C.M.; Tiezzi, Rodrigo; Rodrigues, Bruna T.; Peleias Junior, Fernando; Souza, Carla D.; Souza, Daiane C.C. de; Souza, Anderson S. de; Silva, Thais H. da, E-mail:, E-mail:, E-mail:, E-mail:, E-mail:, E-mail:, E-mail:, E-mail: [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)


    The present work aims to analyze different resin formulations. These formulations are used in the production of radioactive sealed sources that are used in many fields such as nuclear medicine; environmental analyzes, radiation detectors accuracy check, and so on. These sources can be produced with different radioisotopes and different activities, it all depending on the use they will have. Certain types of resins have the same density water. This property is appreciated when we consider that radiotracers used in nuclear medicine are applied in aqueous solutions. So the sources used for checking and calibrating equipment must have their radioisotopes sealed in a material having similar properties, thus the measures are reproducible and repetitive. The most important aspect that is brought to attention in this work is the miscibility those resins have with water. The radioisotopes for the production of the sources are supplied in an aqueous form. In case the resin and the radioisotope solution do not mix, the source will not be sturdy enough to seal the radioisotopes in its structure and the source will not be safe. There were prepared different formulations with different amounts of acid solution, and the cured formulations were analyzed by Wipe Test, DSC (Differential Splanatory Calorimetry) and also, the possible volatile aspect of the radionuclide used. All to evaluate the integrity of the sources. The obtained results were satisfactory and show that when the resin is well cured, the radioisotope remains sealed in the matrix, making it possible to produce radioactive sealed sources. (author)

  6. Multi-objective clustering technique based on k-nodes update policy and similarity matrix for mining communities in social networks (United States)

    Shang, Ronghua; Liu, Huan; Jiao, Licheng


    This paper proposes a relatively all-purpose network clustering technique based on the framework of multi-objective evolutionary algorithms, which can effectively dispose the issue of community detection in unsigned social networks, as well as in signed social networks. Firstly, we formulate a generalized similarity function to construct a similarity matrix, and then a pre-partitioning strategy is projected according to the similarity matrix. The pre-partitioning strategy merely considers nodes with high similarity values, which avoids the interference of noise nodes during the label update phase. In this way, at the initial phase of the algorithm, nodes with strong connections are fleetly gathered into sub-communities. Secondly, we elaborately devise a crossover operator, called cross-merging operator, to merge sub-communities generated by the pre-partitioning technique. Moreover, a special mutation operator, based on the similarity matrix of nodes, is implemented to adjust boundary nodes connecting different communities. Finally, to handle different types of networks, we, therefore, have presented the novel multi-objective optimization models for this issue. Through a bulk of rigorous experiments on both unsigned and signed social networks, the preeminent clustering performance illustrate that the proposed algorithm is capable of mining communities effectively.

  7. Priming of plant innate immunity by rhizobacteria and β-aminobutyric acid: differences and similarities in regulation

    NARCIS (Netherlands)

    Ent, S. van der; Hulten, M.H.A. van; Pozo, Maria J.; Czechowski, Tomasz; Udvardi, Michael K.; Pieterse, C.M.J.; Ton, J.

    Pseudomonas fluorescens WCS417r bacteria and β-aminobutyric acid can induce disease resistance in Arabidopsis, which is based on priming of defence. In this study, we examined the differences and similarities of WCS417r- and β-aminobutyric acid-induced priming. Both WCS417r and β-aminobutyric acid

  8. Degradation of matrix glycosaminoglycans by peroxynitrite/peroxynitrous acid: evidence for a hydroxyl-radical-like mechanism. (United States)

    Kennett, Eleanor C; Davies, Michael J


    The oxidant peroxynitrite/peroxynitrous acid (ONOO-/ONOOH) is generated at sites of inflammation via reaction of O2.- with .NO. Previous studies have shown that these species can oxidize cellular targets, but few data are available on damage to extracellular matrix and its components, despite evidence for matrix modification in a number of pathologies. In the current study we show that reaction of ONOO-/ONOOH with glycosaminoglycans results in extensive polymer fragmentation. Bolus authentic ONOO-/ONOOH modifies hyaluronan, heparin, and chondroitin, dermatan, and heparan sulfates, in a concentration-dependent, but O2-independent, manner. The ONOO-/ONOOH generator 3-(4-morpholinyl)sydnoneimine produces similar time- and concentration-dependent damage. These reactions generate specific polymer fragments via cleavage at disaccharide intervals. Studies at different pH values, and in the presence of bicarbonate, are consistent with ONOOH, rather than the carbonate adduct, CO3.- or ONOO-, being the source of damage. EPR spin trapping experiments have provided evidence for the formation of carbon-centered radicals on glycosaminoglycans and related monosaccharides; the similarity of these spectra to those obtained with authentic HO. is consistent with fragmentation being induced by this oxidant. These data suggest that extracellular matrix fragmentation at sites of inflammation may be due, in part, to the formation and reactions of ONOOH.

  9. Hydrogen bonded complexes of acetylene and boric acid: A matrix isolation infrared and ab initio study (United States)

    Sundararajan, K.; Ramanathan, N.; Kar, Bishnu Prasad; Viswanathan, K. S.


    The infrared spectra of the hydrogen bonded complexes of acetylene-boric acid have been investigated in solid nitrogen matrix. We have observed the 1:1 acetylene-boric acid complex in the nitrogen matrix. Formation of the complex was evidenced from the shifts in the vibrational frequencies corresponding to the modes involving the acetylene and boric acid submolecules in the complex. The structure of the complexes and the energies were computed at HF, B3LYP and MP2 levels of theory using 6-31++G ** basis sets. Only one minimum was obtained, which corresponded to a complex with both O sbnd H⋯π and C sbnd H⋯O interactions. In this complex boric acid acts as a proton donor to the acetylene π-cloud and proton acceptor to the acidic hydrogen in acetylene. The computed vibrational frequencies of acetylene-boric acid complexes at B3LYP/6-31++G ** level corroborated well with the experimental frequencies. Calculations were also performed for the higher 2:1 and 3:1 acetylene-boric acid complexes.

  10. Bovine lactoferrin binds oleic acid to form an anti-tumor complex similar to HAMLET. (United States)

    Fang, Bing; Zhang, Ming; Tian, Mai; Jiang, Lu; Guo, Hui Yuan; Ren, Fa Zheng


    α-Lactalbumin (α-LA) can bind oleic acid (OA) to form HAMLET-like complexes, which exhibited highly selective anti-tumor activity in vitro and in vivo. Considering the structural similarity to α-LA, we conjectured that lactoferrin (LF) could also bind OA to obtain a complex with anti-tumor activity. In this study, LF-OA was prepared and its activity and structural changes were compared with α-LA-OA. The anti-tumor activity was evaluated by methylene blue assay, while the apoptosis mechanism was analyzed using flow cytometry and Western blot. Structural changes of LF-OA were measured by fluorescence spectroscopy and circular dichroism. The interactions of OA with LF and α-LA were evaluated by isothermal titration calorimetry (ITC). LF-OA was obtained by heat-treatment at pH8.0 with LD50 of 4.88, 4.95 and 4.62μM for HepG2, HT29, and MCF-7 cells, respectively, all of which were 10 times higher than those of α-LA-OA. Similar to HAMLET, LF-OA induced apoptosis in tumor cells through both death receptor- and mitochondrial-mediated pathways. Exposure of tryptophan residues and the hydrophobic regions as well as the loss of tertiary structure were observed in LF-OA. Besides these similarities, LF showed different secondary structure changes when compared with α-LA, with a decrease of α-helix and β-turn and an increase of β-sheet and random coil. ITC results showed that there was a higher binding number of OA to LF than to α-LA, while both of the proteins interacted with OA through van der Waals forces and hydrogen bonds. This study provides a theoretical basis for further exploration of protein-OA complexes. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

  11. The Development of Reproducible and Selective Uric Acid Biosensor by Using Electrodeposited Polytyramine as Matrix Polymer

    Directory of Open Access Journals (Sweden)

    Manihar Situmorang


    Full Text Available A versatile method for the construction of reproducible and high selective uric acid biosensor is explained. Electrodeposited polytyramine is used as biosensor matrixes due to its compatibility to immobilize enzyme uric oxidase in the membrane electrode. The precise control over the charge passed during deposition of polytyramine allows concomitant control over the thickness of the deposited enzyme layers onto the surface of the electrode. The uric acid biosensor showed a sensitive response to uric acid with a linear calibration curve lies in the concentration range of 0.1–2.5 mM, slope 0.066 µA mM-1, and the limit detection was 0.01 mM uric acid (S/N = 3. The biosensor shown excellent reproducibility, the variation between response curves for uric acid lies between RSD 1% at low concentrations and up to RSD 6% at saturation concentration. Uric acid biosensor is free from normal interference. The biosensor showed good stability and to be applicable to determine uric acid in real samples. Analysis of uric acid in the reference standard serum samples by the biosensor method are all agreed with the real value from supplier. Standard samples were also analyzed independently by two methods: the present biosensor method and the standard UV-Vis spectrophotometry method, gave a correlation coefficient of 0.994. This result confirms that the biosensor method meets the rigid demands expected for uric acid in real samples.

  12. Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin. (United States)

    Mann, Karlheinz; Poustka, Albert J; Mann, Matthias


    Sea urchin is a major model organism for developmental biology and biomineralization research. However, identification of proteins involved in larval skeleton formation and mineralization processes in the embryo and adult, and the molecular characterization of such proteins, has just gained momentum with the sequencing of the Strongylocentrotus purpuratus genome and the introduction of high-throughput proteomics into the field. The present report contains the determination of test (shell) and tooth organic matrix phosphoproteomes. Altogether 34 phosphoproteins were identified in the biomineral organic matrices. Most phosphoproteins were specific for one compartment, only two were identified in both matrices. The sea urchin phosphoproteomes contained several obvious orthologs of mammalian proteins, such as a Src family tyrosine kinase, protein kinase C-delta 1, Dickkopf-1 and other signal transduction components, or nucleobindin. In most cases phosphorylation sites were conserved between sea urchin and mammalian proteins. However, the majority of phosphoproteins had no mammalian counterpart. The most interesting of the sea urchin-specific phosphoproteins, from the perspective of biomineralization research, was an abundant highly phosphorylated and very acidic tooth matrix protein composed of 35 very similar short sequence repeats, a predicted N-terminal secretion signal sequence, and an Asp-rich C-terminal motif, contained in [Glean3:18919]. The 64 phosphorylation sites determined represent the most comprehensive list of experimentally identified sea urchin protein phosphorylation sites at present and are an important addition to the recently analyzed Strongylocentrotus purpuratus shell and tooth proteomes. The identified phosphoproteins included a major, highly phosphorylated protein, [Glean3:18919], for which we suggest the name phosphodontin. Although not sequence-related to such highly phosphorylated acidic mammalian dental phosphoproteins as phosphoryn or

  13. Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin

    Directory of Open Access Journals (Sweden)

    Mann Matthias


    Full Text Available Abstract Background Sea urchin is a major model organism for developmental biology and biomineralization research. However, identification of proteins involved in larval skeleton formation and mineralization processes in the embryo and adult, and the molecular characterization of such proteins, has just gained momentum with the sequencing of the Strongylocentrotus purpuratus genome and the introduction of high-throughput proteomics into the field. Results The present report contains the determination of test (shell and tooth organic matrix phosphoproteomes. Altogether 34 phosphoproteins were identified in the biomineral organic matrices. Most phosphoproteins were specific for one compartment, only two were identified in both matrices. The sea urchin phosphoproteomes contained several obvious orthologs of mammalian proteins, such as a Src family tyrosine kinase, protein kinase C-delta 1, Dickkopf-1 and other signal transduction components, or nucleobindin. In most cases phosphorylation sites were conserved between sea urchin and mammalian proteins. However, the majority of phosphoproteins had no mammalian counterpart. The most interesting of the sea urchin-specific phosphoproteins, from the perspective of biomineralization research, was an abundant highly phosphorylated and very acidic tooth matrix protein composed of 35 very similar short sequence repeats, a predicted N-terminal secretion signal sequence, and an Asp-rich C-terminal motif, contained in [Glean3:18919]. Conclusions The 64 phosphorylation sites determined represent the most comprehensive list of experimentally identified sea urchin protein phosphorylation sites at present and are an important addition to the recently analyzed Strongylocentrotus purpuratus shell and tooth proteomes. The identified phosphoproteins included a major, highly phosphorylated protein, [Glean3:18919], for which we suggest the name phosphodontin. Although not sequence-related to such highly phosphorylated

  14. The Combined Influence of Hydrogel Stiffness and Matrix-Bound Hyaluronic Acid Content on Glioblastoma Invasion. (United States)

    Chen, Jee-Wei Emily; Pedron, Sara; Harley, Brendan A C


    Glioblastoma (GBM) is the most common and lethal form of brain cancer. Its high mortality is associated with its aggressive invasion throughout the brain. The heterogeneity of stiffness and hyaluronic acid (HA) content within the brain makes it difficult to study invasion in vivo. A dextran-bead assay is employed to quantify GBM invasion within HA-functionalized gelatin hydrogels. Using a library of stiffness-matched hydrogels with variable levels of matrix-bound HA, it is reported that U251 GBM invasion is enhanced in softer hydrogels but reduced in the presence of matrix-bound HA. Inhibiting HA-CD44 interactions reduces invasion, even in hydrogels lacking matrix-bound HA. Analysis of HA biosynthesis suggests that GBM cells compensate for a lack of matrix-bound HA by producing soluble HA to stimulate invasion. Together, a robust method is showed to quantify GBM invasion over long culture times to reveal the coordinated effect of matrix stiffness, immobilized HA, and compensatory HA production on GBM invasion. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. A mechanically strengthened polyacrylamide gel matrix fully compatible with electrophoresis of proteins and nucleic acids. (United States)

    Pushparajan, Charlotte; Goswami, Shailesh K; McAdam, Christopher J; Hanton, Lyall R; Dearden, Peter K; Moratti, Stephen C; Cridge, Andrew G


    Polyacrylamide gel electrophoresis is a universal tool in a biochemist's toolkit for protein and nucleic acid separation and subsequent visualisation and analysis. The standard formulation of polyacrylamide gels consists of acrylamide (ACM) monomer crosslinked with bisacrylamide (MBA) which creates a gel with excellent sieving properties but which is mechanically fragile and prone to tearing during post-electrophoresis manipulations involved in visualisation and analysis. By adding a poly(ethylene oxide) macro-crosslinker to the standard gel formulation, we have created a tough gel matrix that can be used to fractionate proteins and nucleic acids by polyacrylamide gel electrophoresis. The protein and nucleic acid resolving capabilities and performance during staining and electroblotting of the tough gel matrix rivals that of conventional acrylamide/bisacrylamide gels. The tough gel matrix is resistant to tear and remarkably elastic, capable of stretching to over four times its original length before breaking, and represents a significant improvement over standard polyacrylamide gel formulations. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  16. A novel honeycomb matrix for cell immobilization to enhance lactic acid production by Rhizopus oryzae. (United States)

    Wang, Zhen; Wang, Yuanliang; Yang, Shang-Tian; Wang, Runguang; Ren, Huiqing


    A new support matrix inspired by honeycomb was developed for cell immobilization to control fungal morphology and enhance mass transfer in bioreactor for lactic acid production by Rhizopus oryzae. The immobilization matrix composed of asterisk-shaped fibrous matrices in a honeycomb configuration provided high surface areas for cell attachment and biofilm growth. More than 90% of inoculated spores were adsorbed onto the matrices within 6-8h and after 10h there was no suspended cell in the fermentation broth, indicating a 100% immobilization efficiency. Compared to free-cell fermentation, lactic acid production increased approximately 70% (49.5 g/L vs. 29.3g/L) and fermentation time reduced 33% (48 h vs. 72 h) in shake-flasks with 80 g/L initial glucose. The immobilized-cell fermentation was evaluated for its long-term performance in a bubble-column bioreactor operated in a repeated batch mode for nine cycles in 36 days. The highest lactic acid production was 68.8 g/L, corresponding to a volumetric productivity of 0.72 g/Lh and 93.4% (w/w) lactic acid yield from consumed glucose. The overall yield and productivity were 77.6% and 0.57 g/Lh, respectively. The fermentation can be improved by increasing aeration and mixing in the bubble-column bioreactor. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  17. A novel enzyme-based acidizing system: Matrix acidizing and drilling fluid damage removal

    Energy Technology Data Exchange (ETDEWEB)

    Harris, R.E.; McKay, D.M. [Cleansorb Limited, Surrey (United Kingdom); Moses, V. [King`s College, London (United Kingdom)


    A novel acidizing process is used to increase the permeability of carbonate rock cores in the laboratory and to remove drilling fluid damage from cores and wafers. Field results show the benefits of the technology as applied both to injector and producer wells.

  18. Molecularly imprinted polymer-matrix nanocomposite for enantioselective electrochemical sensing of D- and L-aspartic acid

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Bhim Bali, E-mail:; Srivastava, Amrita; Tiwari, Mahavir Prasad


    A new molecularly imprinted polymer-matrix (titanium dioxide nanoparticle/multiwalled carbon nanotubes) nanocomposite was developed for the modification of pencil graphite electrode as an enantioselective sensing probe for aspartic acid isomers, prevalent at ultra trace level in aqueous and real samples. The nanocomposite having many shape complementary cavities was synthesized adopting surface initiated-activators regenerated by electron transfer for atom transfer radical polymerization. The proposed sensor has high stability, nanocomposite uniformity, good reproducibility, and enhanced electrocatalytic activity to respond oxidative peak current of L-aspartic acid quantitatively by differential pulse anodic stripping voltammetry, without any cross-reactivity in real samples. Under the optimized operating conditions, the L-aspartic acid imprinted modified electrode showed a wide linear response for L-aspartic acid within the concentration range 9.98–532.72 ng mL{sup −1}, with the minimum detection limit of 1.73–1.79 ng mL{sup −1} (S/N = 3) in aqueous and real samples. Almost similar stringent limit (1.79 ng mL{sup −1}) was obtained with cerebrospinal fluid which is typical for the primitive diagnosis of neurological disorders, caused by an acute depletion of L-aspartic acid biomarker, in clinical settings. Highlights: • We have adopted surface initiated-activators regenerated by electron transfer for atom transfer radical polymerization. • This approach takes advantage of the nanostructured ultrathin imprinted film. • Successful enantioselective sensing and ultratrace analysis of D- and L-aspartic acid. • Stringent detection limit without any non-specific false-positive contribution.

  19. 5-Methoxysalicylic Acid Matrix for Ganglioside Analysis with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

    National Research Council Canada - National Science Library

    Lee, Dongkun; Cha, Sangwon


    ... of gangliosides if MSA was used as a matrix. This suggests that MALDI MS with MSA has a potential to gain additional benefits from the positive-ion mode analyses without losing performance in ganglioside profiling. Graphical Abstract ᅟ

  20. Extracellular DNA and lipoteichoic acids interact with exopolysaccharides in the extracellular matrix of Streptococcus mutans biofilms. (United States)

    Castillo Pedraza, Midian C; Novais, Tatiana F; Faustoferri, Roberta C; Quivey, Robert G; Terekhov, Anton; Hamaker, Bruce R; Klein, Marlise I


    Streptococcus mutans-derived exopolysaccharides are virulence determinants in the matrix of biofilms that cause caries. Extracellular DNA (eDNA) and lipoteichoic acid (LTA) are found in cariogenic biofilms, but their functions are unclear. Therefore, strains of S. mutans carrying single deletions that would modulate matrix components were used: eDNA - ∆lytS and ∆lytT; LTA - ∆dltA and ∆dltD; and insoluble exopolysaccharide - ΔgtfB. Single-species (parental strain S. mutans UA159 or individual mutant strains) and mixed-species (UA159 or mutant strain, Actinomyces naeslundii and Streptococcus gordonii) biofilms were evaluated. Distinct amounts of matrix components were detected, depending on the inactivated gene. eDNA was found to be cooperative with exopolysaccharide in early phases, while LTA played a larger role in the later phases of biofilm development. The architecture of mutant strains biofilms was distinct (vs UA159), demonstrating that eDNA and LTA influence exopolysaccharide distribution and microcolony organization. Thus, eDNA and LTA may shape exopolysaccharide structure, affecting strategies for controlling pathogenic biofilms.

  1. 2,5-Dihydroxybenzoic acid butylamine and other ionic liquid matrixes for enhanced MALDI-MS analysis of biomolecules. (United States)

    Mank, Marko; Stahl, Bernd; Boehm, Günther


    The performance of the new ionic liquid MALDI-MS matrix 2,5-dihydroxybenzoic acid butylamine (DHBB) was assessed and compared to results obtained with the ionic liquid MALDI-MS matrixes alpha-cyano-4-hydroxycinnamic acid butylamine (CHCAB), 3,5-dimethoxycinnamic acid triethylamine (SinTri), and the frequently used solid MALDI matrixes 2,5-dihydroxybenzoic acid (DHB) and alpha-cyano-4-hydroxycinnamic acid (CHCA). The vacuum-stable, liquid consistency of ionic liquid matrix sample preparations considerably enhanced MALDI-MS analysis in terms of shot-to-shot reproducibility. Consequently, relative standard deviations serving as a measure for reproducibility of intensity-values acquired from 90 different spots on one MALDI-MS preparation were approximately one-half as high when solid DHB was replaced by the ionic liquid DHBB and eight times lower after exchange of solid CHCA by ionic liquid CHCAB. Interestingly, the ionic liquid MALDI matrix DHBB conserved the broad applicability of its solid analogue DHB, reduced MALDI induced fragmentation of monosialylated glycans and gangliosides, and was the superior ionic liquid matrix for MALDI-MS analysis of oligosaccharides and polymers, such as poly(ethylene glycol). It also worked well with glycoconjugates, peptides, and proteins; however, the tendency of DHBB to form multiple alkali adduct ions with peptides and proteins made CHCAB the ionic liquid matrix of choice for peptides. SinTri was the best ionic liquid matrix for proteins of high molecular weight, such as IgG. Furthermore, it was demonstrated for the first time that solvent properties and MALDI matrix properties of ionic liquids, such as DHBB, can be combined to enable fast, direct screening of an enzymatic reaction. This was proven by the desialylation of sialylactose with sialidase from Clostridium perfringens in the presence of diluted aqueous DHBB and subsequent direct MALDI-MS analysis of the reaction mixture.

  2. Investigation of Changing Pore Topology and Porosity During Matrix Acidizing using Different Chelating Agents (United States)

    Umer Shafiq, Mian; Khaled Ben Mahmud, Hisham; Rezaee, Reza; Testamanti, Nadia


    Core flooding acidizing experiments on sandstone/carbonate formation are usually performed in the laboratory to observe different physical phenomena and to design acidizing stimulation jobs for the field. During the tests, some key parameters are analyzed such as pore volume required for breakthrough as well as pressure. Hydrochloric acid (HCl) is commonly used in the carbonate matrix acidizing while Mud acid (HF: HCl) is usually applied during the sandstone acidizing to remove damage around the well bore. However, many problems are associated with the application of these acids, such as fast reaction, corrosion and incompatibility of HCl with some minerals (illite). To overcome these problems, chelating agents (HEDTA, EDTA and GLDA) were used in this research. Colton tight sandstone and Guelph Dolomite core samples were used in this study. The experiments usually are defined in terms of porosity, permeability, dissolution and pore topology. Effluent samples were analyzed to determine dissolved iron, sodium, potassium, calcium and other positive ions using Inductively Coupled Plasma (ICP). Meanwhile Nuclear Magnetic Resonance (NMR) was employed to determine porosity and pore structure of the core sample. Core flood experiments on Berea sandstone cores and dolomite samples with dimensions of 1.5 in × 3 in were conducted at a flow rate of 1 cc/min under 150oF temperature. NMR and porosity analysis concluded that applied chemicals are effective in creating fresh pore spaces. ICP analysis concluded that HEDTA showed good ability to chelate calcium, sodium, magnesium, potassium and iron. It can be established from the analysis that HEDTA can increase more amount of permeability as compared to other chelates.

  3. Ovocalyxin-32, a novel chicken eggshell matrix protein. isolation, amino acid sequencing, cloning, and immunocytochemical localization. (United States)

    Gautron, J; Hincke, M T; Mann, K; Panheleux, M; Bain, M; McKee, M D; Solomon, S E; Nys, Y


    The eggshell is a highly ordered structure resulting from the deposition of calcium carbonate concomitantly with an organic matrix upon the eggshell membranes. Mineralization takes place in an acellular uterine fluid, which contains the ionic and matrix precursors of the eggshell. We have identified a novel 32-kDa protein, ovocalyxin-32, which is expressed at high levels in the uterine and isthmus regions of the oviduct, and concentrated in the eggshell. Sequencing of peptides derived from the purified protein allowed expressed sequence tag sequences to be identified that were assembled to yield a full-length composite sequence whose conceptual translation product contained the complete amino acid sequence of ovocalyxin-32. Data base searches revealed that ovocalyxin-32 has limited identity (32%) to two unrelated proteins: latexin, a carboxypeptidase inhibitor expressed in the rat cerebral cortex and mast cells, and a skin protein, which is encoded by a retinoic acid receptor-responsive gene, TIG1. High level expression of ovocalyxin-32 was limited to the isthmus and uterus tissue, where immunocytochemistry at the light and electron microscope levels demonstrated that ovocalyxin-32 is secreted by surface epithelial cells. In the eggshell, ovocalyxin-32 localizes to the outer palisade layer, the vertical crystal layer, and the cuticle of the eggshell, in agreement with its demonstration by Western blotting at high levels in the uterine fluid during the termination phase of eggshell formation. Ovocalyxin-32 is therefore identified as a novel protein synthesized in the distal oviduct where hen eggshell formation occurs.

  4. Bioprocess monitoring: minimizing sample matrix effects for total protein quantification with bicinchoninic acid assay. (United States)

    Reichelt, Wieland N; Waldschitz, Daniel; Herwig, Christoph; Neutsch, Lukas


    Determining total protein content is a routine operation in many laboratories. Despite substantial work on assay optimization interferences, the widely used bicinchoninic acid (BCA) assay remains widely recognized for its robustness. Especially in the field of bioprocess engineering the inaccuracy caused by interfering substances remains hardly predictable and not well understood. Since the introduction of the assay, sample pre-treatment by trichloroacetic acid (TCA) precipitation has been indicated as necessary and sufficient to minimize interferences. However, the sample matrix in cultivation media is not only highly complex but also dynamically changing over process time in terms of qualitative and quantitative composition. A significant misestimation of the total protein concentration of bioprocess samples is often observed when following standard work-up schemes such as TCA precipitation, indicating that this step alone is not an adequate means to avoid measurement bias. Here, we propose a modification of the BCA assay, which is less influenced by sample complexity. The dynamically changing sample matrix composition of bioprocessing samples impairs the conventional approach of compensating for interfering substances via a static offset. Hence, we evaluated the use of a correction factor based on an internal spike measurement for the respective samples. Using protein spikes, the accuracy of the BCA protein quantification could be improved fivefold, taking the BCA protein quantification to a level of accuracy comparable to other, more expensive methods. This will allow reducing expensive iterations in bioprocess development to due inaccurate total protein analytics.

  5. 37% Phosphoric Acid Induced Stronger Matrix Metalloproteinase-8 Expression of the Dental Pulp than 19% Ethylene Diamine Tetraacetic Acid

    Directory of Open Access Journals (Sweden)

    Nadie Fatimatuzzahro


    Full Text Available Etching agents such as ethylene diamine tetraacetic acid (EDTA and phosphoric acid which are widely used in adhesive restoration system aimed to increase for retention of restorative materials, may act a chemical irritant that induce inflammation of dental pulp. Inflammation is a body response against irritant and infectious agents. Matrix metalloproteinase-8, the major collagenolytic enzyme, degrades collagen type 1. This enzyme is expressed in low level in normal condition, however, the expression will increase during inflammation. The purpose of the present research was to study the effect of 19% EDTA and 37% phosphoric acid application as an etching agents on the MMP-8 expression of dental pulp. Forty-five male Sprague Dawley rats were divided into 3 groups. Cavity preparation was made on the occlusal surface of maxillary first molar using a round diamond bur. 19% EDTA, 37% phosphoric acid, and distilled water were applied on the surface of the cavity of the teeth in group I, II, and III subsequently. The cavity then filed by glass ionomer cements. The rats were sacrified at 1, 3, 5, 7, and 14 days after the treatment (n=3 for each day. The specimens were then processed histologically. Immunohistochemical (IHC analysis was performed using rabbit anti rat MMP-8 polyclonal antibody to examine MMP-8 expression and HE (Hematoxylen Eosin staining to observe the number of macrophages. The results showed 37% phosphoric acid application induced stronger expression of MMP-8 and higher number of macrophages than 19% EDTA. The strongest expression of MMP-8 seems on 5 days after the treatment where the highest number of macrophages were also found.

  6. Plasmids from Food Lactic Acid Bacteria: Diversity, Similarity, and New Developments

    Directory of Open Access Journals (Sweden)

    Yanhua Cui


    Full Text Available Plasmids are widely distributed in different sources of lactic acid bacteria (LAB as self-replicating extrachromosomal genetic materials, and have received considerable attention due to their close relationship with many important functions as well as some industrially relevant characteristics of the LAB species. They are interesting with regard to the development of food-grade cloning vectors. This review summarizes new developments in the area of lactic acid bacteria plasmids and aims to provide up to date information that can be used in related future research.

  7. TG containing stearic acid, synthesized from coconut oil, exhibit lipidemic effects in rats similar to those of cocoa butter. (United States)

    Rao, Reena; Lokesh, Belur R


    Lipase-catalyzed interesterification was used to prepare structured TG from coconut oil TG by partially replacing some of the atherogenic saturated FA with stearic acid, which is known to have a neutral effect on lipid levels in the body. The level of stearic acid was increased from 4% in the native coconut oil to 40% in the structured lipids, with most of the stearic acid being incorporated into the sn-1 and sn-3 positions of TG. When structured lipids were fed to rats at a 10% level for a period of 60 d, a 15% decrease in total cholesterol and a 23% decrease in LDL cholesterol levels in the serum were observed when compared to those fed coconut oil. Similarly, the total and free cholesterol levels in the livers of the rats fed structured lipids were lowered by 31 and 36%, respectively, when compared to those fed coconut oil. The TG levels in the serum and in the liver showed decreases of 14 and 30%, respectively, in animals fed structured lipids. Rats fed cocoa butter and structured lipids having a similar amount of stearic acid had similar lipid levels in the serum and liver. These studies indicated that the atherogenic potential of coconut oil lipids can be reduced significantly by enriching them with stearic acid. This also changed the physical properties of coconut oil closer to those of cocoa butter as determined by DSC.

  8. Physical and psychological stress have similar effects on gastric acid and pepsin secretions in rat


    Ehsan Salimi; Soheila Adeli; Hedayat Sahraei; Mohammad Vahedian; Nabavizadeh Fatemeh


    Stress is one of the most important health and social problems. Previous studies have demonstrated stress influence on the clinical course of a number of gastrointestinal diseases, but its physical and psychological effects on gastric acid and pepsin secretions are largely unknown. 48 male wistar rats weighing 200-250 gr were used in this study. Animals were divided into 6 groups (n=8); Control, Physical stress, Psychological stress, L-NAME+ Physical stress and L-NAME+ Psychological stress gr...

  9. Priming of plant innate immunity by rhizobacteria and beta-aminobutyric acid: differences and similarities in regulation. (United States)

    Van der Ent, Sjoerd; Van Hulten, Marieke; Pozo, Maria J; Czechowski, Tomasz; Udvardi, Michael K; Pieterse, Corné M J; Ton, Jurriaan


    Pseudomonas fluorescens WCS417r bacteria and beta-aminobutyric acid can induce disease resistance in Arabidopsis, which is based on priming of defence. In this study, we examined the differences and similarities of WCS417r- and beta-aminobutyric acid-induced priming. Both WCS417r and beta-aminobutyric acid prime for enhanced deposition of callose-rich papillae after infection by the oomycete Hyaloperonospora arabidopsis. This priming is regulated by convergent pathways, which depend on phosphoinositide- and ABA-dependent signalling components. Conversely, induced resistance by WCS417r and beta-aminobutyric acid against the bacterial pathogen Pseudomonas syringae are controlled by distinct NPR1-dependent signalling pathways. As WCS417r and beta-aminobutyric acid prime jasmonate- and salicylate-inducible genes, respectively, we subsequently investigated the role of transcription factors. A quantitative PCR-based genome-wide screen for putative WCS417r- and beta-aminobutyric acid-responsive transcription factor genes revealed distinct sets of priming-responsive genes. Transcriptional analysis of a selection of these genes showed that they can serve as specific markers for priming. Promoter analysis of WRKY genes identified a putative cis-element that is strongly over-represented in promoters of 21 NPR1-dependent, beta-aminobutyric acid-inducible WRKY genes. Our study shows that priming of defence is regulated by different pathways, depending on the inducing agent and the challenging pathogen. Furthermore, we demonstrated that priming is associated with the enhanced expression of transcription factors.

  10. Lactic acid bacteria in dairy food: surface characterization and interactions with food matrix components. (United States)

    Burgain, J; Scher, J; Francius, G; Borges, F; Corgneau, M; Revol-Junelles, A M; Cailliez-Grimal, C; Gaiani, C


    This review gives an overview of the importance of interactions occurring in dairy matrices between Lactic Acid Bacteria and milk components. Dairy products are important sources of biological active compounds of particular relevance to human health. These compounds include immunoglobulins, whey proteins and peptides, polar lipids, and lactic acid bacteria including probiotics. A better understanding of interactions between bioactive components and their delivery matrix may successfully improve their transport to their target site of action. Pioneering research on probiotic lactic acid bacteria has mainly focused on their host effects. However, very little is known about their interaction with dairy ingredients. Such knowledge could contribute to designing new and more efficient dairy food, and to better understand relationships between milk constituents. The purpose of this review is first to provide an overview of the current knowledge about the biomolecules produced on bacterial surface and the composition of the dairy matter. In order to understand how bacteria interact with dairy molecules, adhesion mechanisms are subsequently reviewed with a special focus on the environmental conditions affecting bacterial adhesion. Methods dedicated to investigate the bacterial surface and to decipher interactions between bacteria and abiotic dairy components are also detailed. Finally, relevant industrial implications of these interactions are presented and discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Hypohalous acids contribute to renal extracellular matrix damage in experimental diabetes. (United States)

    Brown, Kyle L; Darris, Carl; Rose, Kristie Lindsey; Sanchez, Otto A; Madu, Hartman; Avance, Josh; Brooks, Nickolas; Zhang, Ming-Zhi; Fogo, Agnes; Harris, Raymond; Hudson, Billy G; Voziyan, Paul


    In diabetes, toxic oxidative pathways are triggered by persistent hyperglycemia and contribute to diabetes complications. A major proposed pathogenic mechanism is the accumulation of protein modifications that are called advanced glycation end products. However, other nonenzymatic post-translational modifications may also contribute to pathogenic protein damage in diabetes. We demonstrate that hypohalous acid-derived modifications of renal tissues and extracellular matrix (ECM) proteins are significantly elevated in experimental diabetic nephropathy. Moreover, diabetic renal ECM shows diminished binding of α1β1 integrin consistent with the modification of collagen IV by hypochlorous (HOCl) and hypobromous acids. Noncollagenous (NC1) hexamers, key connection modules of collagen IV networks, are modified via oxidation and chlorination of tryptophan and bromination of tyrosine residues. Chlorotryptophan, a relatively minor modification, has not been previously found in proteins. In the NC1 hexamers isolated from diabetic kidneys, levels of HOCl-derived oxidized and chlorinated tryptophan residues W(28) and W(192) are significantly elevated compared with nondiabetic controls. Molecular dynamics simulations predicted a more relaxed NC1 hexamer tertiary structure and diminished assembly competence in diabetes; this was confirmed using limited proteolysis and denaturation/refolding. Our results suggest that hypohalous acid-derived modifications of renal ECM, and specifically collagen IV networks, contribute to functional protein damage in diabetes. © 2015 by the American Diabetes Association. Readers may use this article as long as the work is properly cited, the use is educational and not for profit, and the work is not altered.

  12. Determination of Trace Perfluoroalkyl Carboxylic Acids in Edible Crop Matrices: Matrix Effect and Method Development. (United States)

    Xiang, Lei; Chen, Lei; Xiao, Tao; Mo, Ce-Hui; Li, Yan-Wen; Cai, Quan-Ying; Li, Hui; Zhou, Dong-Mei; Wong, Ming-Hung


    A robust method was developed for simultaneous determination of nine trace perfluoroalkyl carboxylic acids (PFCAs) in various edible crop matrices including cereal (grain), root vegetable (carrot), leafy vegetable (lettuce), and melon vegetable (pumpkin) using ultrasonic extraction followed by solid-phase extraction cleanup and high liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The varieties of extractants and cleanup cartridges, the usage of Supelclean graphitized carbon, and the matrix effect and its potential influencing factors were estimated to gain an optimal extraction procedure. The developed method presented high sensitivity and accuracy with the method detection limits and the recoveries at four fortification levels in various matrices ranging from 0.017 to 0.180 ng/g (dry weight) and from 70% to 114%, respectively. The successful application of the developed method to determine PFCAs in various crops sampled from several farms demonstrated its practicability for regular monitoring of PFCAs in real crops.

  13. Amino Acid Derivatives as New Zinc Binding Groups for the Design of Selective Matrix Metalloproteinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Mariateresa Giustiniano


    Full Text Available A number of matrix metalloproteinases (MMPs are important medicinal targets for conditions ranging from rheumatoid arthritis to cardiomyopathy, periodontal disease, liver cirrhosis, multiple sclerosis, and cancer invasion and metastasis, where they showed to have a dual role, inhibiting or promoting important processes involved in the pathology. MMPs contain a zinc (II ion in the protein active site. Small-molecule inhibitors of these metalloproteins are designed to bind directly to the active site metal ions. In an effort to devise new approaches to selective inhibitors, in this paper, we describe the synthesis and preliminary biological evaluation of amino acid derivatives as new zinc binding groups (ZBGs. The incorporation of selected metal-binding functions in more complex biphenyl sulfonamide moieties allowed the identification of one compound able to interact selectively with different MMP enzymatic isoforms.

  14. Cytocompatibility of novel extracellular matrix protein analogs of biodegradable polyester polymers derived from α-hydroxy amino acids. (United States)

    Lecht, Shimon; Cohen-Arazi, Naomi; Cohen, Gadi; Ettinger, Keren; Momic, Tatjana; Kolitz, Michal; Naamneh, Majdi; Katzhendler, Jehoshua; Domb, Abraham J; Lazarovici, Philip; Lelkes, Peter I


    One of the challenges in regenerative medicine is the development of novel biodegradable materials to build scaffolds that will support multiple cell types for tissue engineering. Here we describe the preparation, characterization, and cytocompatibility of homo- and hetero-polyesters of α-hydroxy amino acid derivatives with or without lactic acid conjugation. The polymers were prepared by a direct condensation method and characterized using gel permeation chromatography, (1)H-nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, differential scanning calorimetry, optical activity, and solubility. The surface charge of the polymers was evaluated using zeta potential measurements. The polymers were coated onto glass cover slips followed by characterization using nano-surface profiler, thin film reflectometry, and atomic force microscopy (AFM). Their interaction with endothelial and neuronal cells was assessed using adhesion, proliferation, and differentiation assays. Of the characterized polymers, Poly-HOVal-LA, but not Poly-(D)HOPhe, significantly augmented nerve growth factor (NGF)-induced neuronal differentiation of the PC12 pheochromcytoma cells. In contrast, Poly-HOLeu increased by 20% the adhesion of endothelial cells, but did not affect PC12 cell differentiation. NGF-induced Erk1/2 phosphorylation in PC12 cells grown on the different polymers was similar to the effect observed for cells cultured on collagen type I. While no significant association could be established between charge and the differentiative/proliferative properties of the polymers, AFM analysis indicated augmentation of NGF-induced neuronal differentiation on smooth polymer surfaces. We conclude that overall selective cytocompatibility and bioactivity might render α-hydroxy amino acid polymers useful as extracellular matrix-mimicking materials for tissue engineering.

  15. In vitro toxicity of carbon nanotubes, nano-graphite and carbon black, similar impacts of acid functionalization. (United States)

    Figarol, Agathe; Pourchez, Jérémie; Boudard, Delphine; Forest, Valérie; Akono, Céline; Tulliani, Jean-Marc; Lecompte, Jean-Pierre; Cottier, Michèle; Bernache-Assollant, Didier; Grosseau, Philippe


    Carbon nanotubes (CNT) and nano-graphite (NG) are graphene-based nanomaterials which share exceptional physicochemical properties, but whose health impacts are unfortunately still not well understood. On the other hand, carbon black (CB) is a conventional and widely studied material. The comparison of these three carbon-based nanomaterials is thus of great interest to improve our understanding of their toxicity. An acid functionalization was carried out on CNT, NG and CB so that, after a thorough characterization, their impacts on RAW 264.7 macrophages could be compared for a similar surface chemistry (15 to 120 μg·mL(-1) nanomaterials, 90-min to 24-h contact). Functionalized nanomaterials triggered a weak cytotoxicity similar to the pristine nanomaterials. Acid functionalization increased the pro-inflammatory response except for CB which did not trigger any TNF-α production before or after functionalization, and seemed to strongly decrease the oxidative stress. The toxicological impact of acid functionalization appeared thus to follow a similar trend whatever the carbon-based nanomaterial. At equivalent dose expressed in surface and equivalent surface chemistry, the toxicological responses from murine macrophages to NG were higher than for CNT and CB. It seemed to correspond to the hypothesis of a platelet and fiber paradigm. Copyright © 2015. Published by Elsevier Ltd.

  16. [Effects of extracts of Dragon's blood on fibroblast proliferation and extracellular matrix hyaluronic acid]. (United States)

    Li, Dan; Hui, Rui; Hu, Yongwu; Han, Yan; Guo, Shuzhong


    To investigate the effects of Dragon' s blood extract on proliferation and secret extracellular matrix function of fibroblasts in vitro. Dragon' s blood was extracted by chloroform, acetoacetic ester, alcohol. Human fibroblast were cultured in vitro in media containing gradient dilutions of Dragon' s blood extracts (0.002, 0.02, 0.2, 2, 20 mg/ml) , which was followed by cell proliferation assessed with MTT assay on 0, 12, 24, 36, 48, 60, 72 h. Under the optimal concentration, the cell growth curves were drawn and the flow cytometry (FCM) was used to determine the changes of cell cycle. On 0, 12, 24, 36, 48, 60, 72 h, the concentration of hyaluronic acid in the supernatant of fibroblast culture was measured by radioimmunoassay. 0.2-2 mg/ml Dragon' s blood extracts enhanced the proliferation of fibroblasts in a dose-dependent manner. 2 mg/ml was the optimal dilution of Dragon's blood extract, and it increased the ratio of S cells in cell cycle [(25.80 ± 3.10)%] than control group [(7.50 ± 0.70)%, P < 0.01]. From 12 h to 72 h, in 2 mg/ml Dragon's blood group, concentration of Hyaluronic acid secreted by fibroblasts gradually increased, but were less than control (P < 0.01). Dragon's blood acetoacetic ester extract improved the proliferation of cultured human fibroblasts in vitro, might be beneficial to promote wound healing.

  17. Omega-3 fatty acid supplementation decreases matrix metalloproteinase-9 production in relapsing-remitting multiple sclerosis (United States)

    Shinto, L.; Marracci, G.; Baldauf-Wagner, S.; Strehlow, A.; Yadav, V.; Stuber, L.; Bourdette, D.


    Objectives The primary objective was to evaluate the effect of omega-3 fatty acids (omega-3 FA) on matrix metalloproteinase-9 (MMP-9) production by immune cells in multiple sclerosis (MS). Quality of life, fatty acid levels, and safety were also evaluated. Materials and Methods Ten participants with relapsing-remitting MS (RRMS) received omega-3 FA supplementation (9.6 grams/day fish oil) in an open-label study. Participants were evaluated at four time points, baseline, after 1-month of omega-3 FA supplementation, after 3-months of omega-3 FA supplementation, and after a 3-month wash out. Results Immune cell secretion of MMP-9 decreased by 58% after 3-months of omega-3 FA supplementation when compared to baseline levels (p < 0.01). This effect was coupled with a significant increase in omega-3 FA levels in red blood cell membranes. Conclusions Omega-3 FA significantly decreased MMP-9 levels in RRMS and may act as immune-modulator that has potential therapeutic benefit in MS patients. PMID:19171471

  18. Secreted protein acidic and rich in cysteine is a matrix scavenger chaperone.

    Directory of Open Access Journals (Sweden)

    Alexandre Chlenski

    Full Text Available Secreted Protein Acidic and Rich in Cysteine (SPARC is one of the major non-structural proteins of the extracellular matrix (ECM in remodeling tissues. The functional significance of SPARC is emphasized by its origin in the first multicellular organisms and its high degree of evolutionary conservation. Although SPARC has been shown to act as a critical modulator of ECM remodeling with profound effects on tissue physiology and architecture, no plausible molecular mechanism of its action has been proposed. In the present study, we demonstrate that SPARC mediates the disassembly and degradation of ECM networks by functioning as a matricellular chaperone. While it has low affinity to its targets inside the cells where the Ca(2+ concentrations are low, high extracellular concentrations of Ca(2+ activate binding to multiple ECM proteins, including collagens. We demonstrated that in vitro, this leads to the inhibition of collagen I fibrillogenesis and disassembly of pre-formed collagen I fibrils by SPARC at high Ca(2+ concentrations. In cell culture, exogenous SPARC was internalized by the fibroblast cells in a time- and concentration-dependent manner. Pulse-chase assay further revealed that internalized SPARC is quickly released outside the cell, demonstrating that SPARC shuttles between the cell and ECM. Fluorescently labeled collagen I, fibronectin, vitronectin, and laminin were co-internalized with SPARC by fibroblasts, and semi-quantitative Western blot showed that SPARC mediates internalization of collagen I. Using a novel 3-dimensional model of fluorescent ECM networks pre-deposited by live fibroblasts, we demonstrated that degradation of ECM depends on the chaperone activity of SPARC. These results indicate that SPARC may represent a new class of scavenger chaperones, which mediate ECM degradation, remodeling and repair by disassembling ECM networks and shuttling ECM proteins into the cell. Further understanding of this mechanism may provide

  19. The inhibitory effect of polyvinylphosphonic acid on functional matrix metalloproteinase activities in human demineralized dentin. (United States)

    Tezvergil-Mutluay, Arzu; Agee, Kelli A; Hoshika, Tomohiro; Tay, Franklin R; Pashley, David H


    This study has examined the use of polyvinylphosphonic acid (PVPA) as a potential matrix metalloproteinase (MMP) inhibitor and how brief cross-linking of demineralized dentin matrix that did not affect its mechanical properties enhanced the anti-MMP activity of PVPA. The anti-MMP potential of five PVPA concentrations (100-3000 microgml(-1)) was initially screened using a rhMMP-9 colorimetic assay. Demineralized dentin beams were treated with the same five concentrations of PVPA to collagen and then aged for 30 days in a calcium- and zinc-containing medium. The changes in modulus of elasticity, loss of dry mass and dissolution of collagen peptides were measured via three-point bending, precision weighing and hydroxyproline assay, respectively. All tested PVPA concentrations were highly effective (P<0.05) in inhibiting MMP-9. Ageing in the incubation medium did not significantly alter the modulus of elasticity of the five PVPA treatment groups. Conversely, aged dentin beams from the control group exhibited a significant decline in their modulus of elasticity (P<0.05) over time. Mass loss from the dentin beams and the corresponding increase in hydroxyproline in the medium in the five PVPA treatment groups were significantly lower than for the control (P<0.05). PVPA is a potent inhibitor of endogenous MMP activities in demineralized dentin. It may be used as an alternative to chlorhexidine to prevent collagen degradation within hybrid layers to extend the longevity of resin-dentin bonds. 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  20. Effects of spray-drying on w/o/w multiple emulsions prepared from a stearic acid matrix

    CSIR Research Space (South Africa)

    Mlalila, N


    Full Text Available The goal of this study was to explore the effects of spray-drying on w/o/w double emulsions of methyltestosterone (MT) loaded in a stearic acid matrix. MT-loaded nanoparticles were formulated by a water-in-oil-in-water emulsion technique using 50...

  1. Evaluation of Influence of Various Polymers on Dissolution and Phase Behavior of Carbamazepine-Succinic Acid Cocrystal in Matrix Tablets. (United States)

    Ullah, Majeed; Ullah, Hanif; Murtaza, Ghulam; Mahmood, Qaisar; Hussain, Izhar


    The aim of current study was to explore the influence of three commonly used polymers, that is, cellulosics and noncellulosics, for example, Methocel K4M, Kollidon VA/64, and Soluplus, on the phase disproportionation and drug release profile of carbamazepine-succinic acid (CBZ-SUC) cocrystal at varying drug to polymer ratios (1 : 1 to 1 : 0.25) in matrix tablets. The polymorphic phase disproportionation during in-depth dissolution studies of CBZ-SUC cocrystals and its crystalline properties were scrutinized by X-ray powder diffractrometry and Raman spectroscopy. The percent drug release from HPMC formulations (CSH) showed inverse relation with the concentration of polymer; that is, drug release increased with decrease in polymer concentration. On contrary, direct relation was observed between percent drug release and polymer concentrations of Kollidon VA 64/Soluplus (CSK, CSS). At similar polymer concentration, drug release from pure carbamazepine was slightly lower with HPMC formulations than that of cocrystal; however, opposite trend in release rate was observed with Kollidon VA/64 and Soluplus. The significant increase in dissolution rate of cocrystal occurred with Kollidon VA/64 and Soluplus at higher polymer concentration. Moreover, no phase change took place in Methocel and Kollidon formulations. No tablet residue was left for Soluplus formulation so the impact of polymer on cocrystal integrity cannot be predicted.

  2. Evaluation of Influence of Various Polymers on Dissolution and Phase Behavior of Carbamazepine-Succinic Acid Cocrystal in Matrix Tablets

    Directory of Open Access Journals (Sweden)

    Majeed Ullah


    Full Text Available The aim of current study was to explore the influence of three commonly used polymers, that is, cellulosics and noncellulosics, for example, Methocel K4M, Kollidon VA/64, and Soluplus, on the phase disproportionation and drug release profile of carbamazepine-succinic acid (CBZ-SUC cocrystal at varying drug to polymer ratios (1 : 1 to 1 : 0.25 in matrix tablets. The polymorphic phase disproportionation during in-depth dissolution studies of CBZ-SUC cocrystals and its crystalline properties were scrutinized by X-ray powder diffractrometry and Raman spectroscopy. The percent drug release from HPMC formulations (CSH showed inverse relation with the concentration of polymer; that is, drug release increased with decrease in polymer concentration. On contrary, direct relation was observed between percent drug release and polymer concentrations of Kollidon VA 64/Soluplus (CSK, CSS. At similar polymer concentration, drug release from pure carbamazepine was slightly lower with HPMC formulations than that of cocrystal; however, opposite trend in release rate was observed with Kollidon VA/64 and Soluplus. The significant increase in dissolution rate of cocrystal occurred with Kollidon VA/64 and Soluplus at higher polymer concentration. Moreover, no phase change took place in Methocel and Kollidon formulations. No tablet residue was left for Soluplus formulation so the impact of polymer on cocrystal integrity cannot be predicted.

  3. Hyaluronic acid based hydroxamate and conjugates with biologically active amines: In vitro effect on matrix metalloproteinase-2. (United States)

    Ponedel'kina, Irina Yu; Gaskarova, Aigul R; Khaybrakhmanova, Elvira A; Lukina, Elena S; Odinokov, Victor N


    In this study, water soluble hyaluronic acid (HA) based hydroxamate and conjugates with biologically active amines and hydrazides such as p- and o-aminophenols, anthranilic, 4- and 5-aminosalicylic acids, nicotinic, N-benzylnicotinic and isonicotinic hydrazides, p-aminobenzenesulfonamide (Streptocide), p-aminobenzoic acid diethylaminoethyl ester (Procaine), and 4-amino-2,3-dimethyl-1-phenyl-3-pyrazolin-5-one (4-aminoantipyrene) were examined as matrix metalloproteinase-2 inhibitors (MMPIs). In a dose of 0.27-270μM, the most efficient MMPIs were HA conjugates with o-aminophenol=4-aminoantipyrine>4-aminosalicylic acid>5-aminosalicylic acid. Conjugates with Streptocide, Procaine and HA hydroxamate showed 40-50% inhibitory effect at all used concentrations. Conjugates with anthranilic acid and isonicotinic hydrazide (Isoniazid) in a dose of 0.27μM inhibited enzyme activity by ∼70%, but with the concentration increase their inhibitory effect was decreased. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Dentin matrix components extracted with phosphoric acid enhance cell proliferation and mineralization. (United States)

    Salehi, Satin; Cooper, Paul; Smith, Anthony; Ferracane, Jack


    Acids, such as those used in adhesive dentistry, have been shown to solubilize bioactive molecules from dentin. These dentin matrix components (DMC) may promote cell proliferation and differentiation, and ultimately contribute to dentin regeneration. The objective of this study was to evaluate the potential for varying concentrations of DMC extracted from human dentin by phosphoric acid of a range of pHs to stimulate proliferation and mineralization of two different cultured pulp cell populations. DMC were solubilized from powdered human dentin (7 days - 4°C) by phosphoric acid of pH 1, 3, and 5 and also, EDTA. Extracts were dialyzed for 7 days against distilled water and lyophilized. Undifferentiated mouse dental pulp cells (OD-21) and cells of the odontoblast-like cell line (MDPC-23) were seeded in six-well plates (1×10(5)) and cultured for 24h in DMEM (Dulbecco's modified Eagle's medium) containing 10% (v/v) FBS (fetal bovine serum). The cells were washed with serum-free medium and then treated with different concentrations of DMC (0.01, 0.1, 1.0 and 10.0μg/ml) daily in serum free medium for 7 days. After 3, 5 (MDPC-23 only), and 7 days of treatment, cell proliferation was measured using 10vol% Alamar blue solution, which was added to each well for 1h. Cell numbers were first measured by cell counting (Trypan blue; n=5) and Alamar blue fluorescence to validate the assay, which was then used for the subsequent assessments of proliferation. Mineralization was assessed by Alizarin Red S assay after 12 days exposure to DMC (n=5). Controls were media-only (DMEM) and dexamethasone (DEX; positive control). Results were analysed by ANOVA/Tukey's (p≤0.05). There was a linear correlation between cell counts and Alamar blue fluorescence (R(2)>0.96 for both cell types) , verifying the validity of the Alamar blue assay for these cell types. In general, there was a dose-dependent trend for enhanced cell proliferation with higher concentration of DMC for both cell lines

  5. Salvianolic acid A, a novel matrix metalloproteinase-9 inhibitor, prevents cardiac remodeling in spontaneously hypertensive rats. (United States)

    Jiang, Baohong; Li, Defang; Deng, Yanping; Teng, Fukang; Chen, Jing; Xue, Song; Kong, Xiangqian; Luo, Cheng; Shen, Xu; Jiang, Hualiang; Xu, Feng; Yang, Wengang; Yin, Jun; Wang, Yanhui; Chen, Hui; Wu, Wanying; Liu, Xuan; Guo, De-an


    Cardiac fibrosis is a deleterious consequence of hypertension which may further advance to heart failure and increased matrix metalloproteinase-9 (MMP-9) contributes to the underlying mechanism. Therefore, new therapeutic strategies to attenuate the effects of MMP-9 are urgently needed. In the present study, we characterize salvianolic acid A (SalA) as a novel MMP-9 inhibitor at molecular, cellular and animal level. We expressed a truncated form of MMP-9 which contains only the catalytic domain (MMP-9 CD), and used this active protein for enzymatic kinetic analysis and Biacore detection. Data generated from these assays indicated that SalA functioned as the strongest competitive inhibitor of MMP-9 among 7 phenolic acids from Salvia miltiorrhiza. In neonatal cardiac fibroblast, SalA inhibited fibroblast migration, blocked myofibroblast transformation, inhibited secretion of intercellular adhesion molecule (ICAM), interleukin-6 (IL-6) and soluble vascular cell adhesion molecule-1 (sVCAM-1) as well as collagen induced by MMP-9 CD. Functional effects of SalA inhibition on MMP-9 was further confirmed in cultured cardiac H9c2 cell overexpressing MMP-9 in vitro and in heart of spontaneously hypertensive rats (SHR) in vivo. Moreover, SalA treatment in SHR resulted in decreased heart fibrosis and attenuated heart hypertrophy. These results indicated that SalA is a novel inhibitor of MMP-9, thus playing an inhibitory role in hypertensive fibrosis. Further studies to develop SalA and its analogues for their potential clinical application of cardioprotection are warranted.

  6. Hyaluronic acid-hydroxyapatite nanocomposite hydrogels for enhanced biophysical and biological performance in a dermal matrix. (United States)

    Jeong, Seol-Ha; Fan, Yingfang; Cheon, Kwang-Hee; Baek, Jaeuk; Kim, Sukwha; Kim, Hyoun-Ee


    A hyaluronic acid (HAc)-hydroxyapatite (HAp) nanocomposite (HAc-nanoHAp) hydrogel was fabricated through an in situ precipitation process for mechanical and biological enhancement as a soft tissue augmentation product. In this study, these composite hydrogel fillers were analyzed from three different perspectives and compared with pure HAc hydrogel for soft tissue augmentation application: (1) rheological behaviors, (2) in vivo lateral diffusion under mouse skin, and (3) wrinkle improvement in a photo-aged mouse model. HAc-nanoHAp provided great improvement to wrinkles because of its higher stiffness and gel cohesiveness in comparison with that of pure HAc. HAc-nanoHAp also presented great enhancement in strengthening the dermal matrix by stimulating the synthesis of collagen and elastin. Thus, HAc-nanoHAp filler has great potential as a soft tissue augmentation product, improving the biophysical and biological performance in skin tissue. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 3315-3325, 2017. © 2017 Wiley Periodicals, Inc.

  7. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

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    Naughton Thomas J


    Full Text Available Abstract Background In recent years, model based approaches such as maximum likelihood have become the methods of choice for constructing phylogenies. A number of authors have shown the importance of using adequate substitution models in order to produce accurate phylogenies. In the past, many empirical models of amino acid substitution have been derived using a variety of different methods and protein datasets. These matrices are normally used as surrogates, rather than deriving the maximum likelihood model from the dataset being examined. With few exceptions, selection between alternative matrices has been carried out in an ad hoc manner. Results We start by highlighting the potential dangers of arbitrarily choosing protein models by demonstrating an empirical example where a single alignment can produce two topologically different and strongly supported phylogenies using two different arbitrarily-chosen amino acid substitution models. We demonstrate that in simple simulations, statistical methods of model selection are indeed robust and likely to be useful for protein model selection. We have investigated patterns of amino acid substitution among homologous sequences from the three Domains of life and our results show that no single amino acid matrix is optimal for any of the datasets. Perhaps most interestingly, we demonstrate that for two large datasets derived from the proteobacteria and archaea, one of the most favored models in both datasets is a model that was originally derived from retroviral Pol proteins. Conclusion This demonstrates that choosing protein models based on their source or method of construction may not be appropriate.

  8. Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates. (United States)

    Sydykova, Dariya K; Wilke, Claus O


    Site-specific evolutionary rates can be estimated from codon sequences or from amino-acid sequences. For codon sequences, the most popular methods use some variation of the dN∕dS ratio. For amino-acid sequences, one widely-used method is called Rate4Site, and it assigns a relative conservation score to each site in an alignment. How site-wise dN∕dS values relate to Rate4Site scores is not known. Here we elucidate the relationship between these two rate measurements. We simulate sequences with known dN∕dS, using either dN∕dS models or mutation-selection models for simulation. We then infer Rate4Site scores on the simulated alignments, and we compare those scores to either true or inferred dN∕dS values on the same alignments. We find that Rate4Site scores generally correlate well with true dN∕dS, and the correlation strengths increase in alignments with greater sequence divergence and more taxa. Moreover, Rate4Site scores correlate very well with inferred (as opposed to true) dN∕dS values, even for small alignments with little divergence. Finally, we verify this relationship between Rate4Site and dN∕dS in a variety of empirical datasets. We conclude that codon-level and amino-acid-level analysis frameworks are directly comparable and yield very similar inferences.

  9. Effects of ultraviolet irradiation on bonding strength between Co-Cr alloy and citric acid-crosslinked gelatin matrix. (United States)

    Inoue, Motoki; Sasaki, Makoto; Katada, Yasuyuki; Taguchi, Tetsushi


    Novel techniques for creating a strong bond between polymeric matrices and biometals are required. We immobilized polymeric matrices on the surface of biometal for drug-eluting stents through covalent bond. We performed to improve the bonding strength between a cobalt-chromium alloy and a citric acid-crosslinked gelatin matrix by ultraviolet irradiation on the surface of cobalt-chromium alloy. The ultraviolet irradiation effectively generated hydroxyl groups on the surface of the alloy. The bonding strength between the gelatin matrix and the alloy before ultraviolet irradiation was 0.38 ± 0.02 MPa, whereas it increased to 0.48 ± 0.02 MPa after ultraviolet irradiation. Surface analysis showed that the citric acid derivatives occurred on the surface of the cobalt-chromium alloy through ester bond. Therefore, ester bond formation between the citric acid derivatives active esters and the hydroxyl groups on the cobalt-chromium alloy contributed to the enhanced bonding strength. Ultraviolet irradiation and subsequent immobilization of a gelatin matrix using citric acid derivatives is thus an effective way to functionalize biometal surfaces.

  10. Adhesion dynamics of porcine esophageal fibroblasts on extracellular matrix protein-functionalized poly(lactic acid). (United States)

    Cai, Ning; Gong, Yingxue; Chian, Kerm Sin; Chan, Vincent; Liao, Kin


    Effective attachment of esophageal cells on biomaterials is one important requirement in designing engineered esophagus substitute for esophageal cancer treatment. In this study, poly(lactic acid) (PLA) was subjected to surface modification by coupling extracellular matrix (ECM) proteins on its surface to promote cell adhesion. Two typical ECM proteins, collagen type I (COL) and fibronectin (FN), were immobilized on the PLA surface with the aid of glutaraldehyde as a cross linker between aminolyzed PLA and ECM proteins. By using confocal reflectance interference contrast microscopy (C-RICM) integrating with phase contrast microscopy, the long-term adhesion dynamics of porcine esophageal fibroblasts (PEFs) on four types of surfaces (unmodified PLA, PLA-COOH, PLA-COL and PLA-FN) was investigated during 24 h of culture. It is demonstrated by C-RICM results that PEFs form strong adhesion contact on all four types of surfaces at different stages of cell seeding. Among the four surfaces, PEFs on the PLA-FN surface reach the maximum adhesion energy (9.5 x 10(-7) J m(-2)) in the shortest time (20 min) during the initial stage of cell seeding. After adhesion energy reaches the maximum value, PEFs maintain their highly deformed geometries till they reached a steady state after 20 h of culture. F-actin immunostaining results show that the evolvement of spatial organization of F-actin is tightly correlated with the formation of adhesion contact and cell spreading. Furthermore, the cell attachment ratio of PEFs on PLA in 2 h is only 26% compared with 88% on PLA-FN, 73% on PLA-COL and 36% on PLA-COOH. All the results demonstrate the effect of surface functionalization on the biophysical responses of PEFs in cell adhesion. Fibronectin-immobilized PLA demonstrates promising potential for application as an engineered esophagus substitute.

  11. Humic acids as both matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and adsorbent for magnetic solid phase extraction. (United States)

    Zhao, Qin; Xu, Jing; Yin, Jia; Feng, Yu-Qi


    In the present study, humic acids (HAs) were applied as both a matrix for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and an adsorbent of magnetic solid phase extraction (MSPE) for the first time. As natural macromolecule compounds, HAs are inherently highly functionalized and contain laser energy absorbing-transferring aromatic structures. This special molecular structure made HAs a good candidate for use as a MALDI matrix in small molecule analysis. At the same time, due to its good adsorption ability, HAs was prepared as MSPE adsorbent via a simple co-mixing method, in which the commercially available HAs were directly mixed with Fe3O4 magnetic nanoparticles (MNPs) in a mortar and grinded evenly and completely. In this process, MNPs were physically wrapped and adhered to tiny HAs leading to the formation of magnetic HAs (MHAs). To verify the bi-function of the MHAs, Rhodamine B (RdB) was chosen as model compound. Our results show that the combination of MHAs-based MSPE and MALDI-TOF-MS can provide a rapid and sensitive method for the determination of RdB in chili oil. The whole analytical procedure could be completed within 30 min for simultaneous determination of more than 20 samples, and the limit of quantitation for RdB was found to be 0.02 μg/g. The recoveries in chili oil were in the range 73.8-81.5% with the RSDs less than 21.3% (intraday) and 20.3% (interday). The proposed strategy has potential applications for high-throughput analysis of small molecules in complex samples. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Similarities Across Mars: Acidic Fluids at Both Meridiani Planum and Gale Crater in the Formation of Magnesium-Nickel Sulfates (United States)

    Yen, A. S.; Ming, D. W.; Gellert, R.; Mittlefehldt, D. W.; Vaniman, D. T.; Thompson, L. M.; Morris, R. V.; Clark, B. C.; Arvidson, R. E.


    In-situ identification of sulfates at the martian surface by the Mars Exploration Rovers and the Mars Science Laboratory have included calcium sulfates with various states of hydration (gypsum, bassanite, anhydrite), iron sulfates of likely fumarolic origin, massive deposits of iron hydroxysulfates indicative of an acidic history, and minor occurrences of magnesium sulfates. Recent measurements by the Opportunity and Curiosity Alpha Particle X-ray Spectrometers (APXS) have indicated the presence of Ni-substituted Mg-sulfates at the Meridiani Planum and Gale Crater landing sites. The Opportunity rover has traversed nearly 43 km and is currently exploring the impact breccias of the rim of Endeavour crater, near a location where signatures of aqueous alteration have been established from orbit. APXS analyses of subsurface materials excavated by a rover wheel show clear evidence for a Mg(Ni)-sulfate with Mg:Ni 100:1 (molar). On the other side of the planet, Curiosity is continuing its climb up Mount Sharp after driving 13 km since landing. Over the last 4 km of the traverse, there have been multiple chemical analyses of erosionally-resistant nodules and dendritic features in a finely laminated mudstone unit which also indicate Mg(Ni)-sulfate (Mg:Ni 30:1, molar). The geologic settings for the Endeavour rim and the Mount Sharp mudstones are clearly different, but similar formation conditions for these sulfates may be possible. Ni(2+) readily substitutes for Mg(2+) in a variety of geochemical processes due to their comparable ionic radii. The availability of soluble Ni at the time of Mg-sulfate precipitation suggests acidic solutions. The fluids responsible for alteration in the Endeavour rim and for the formation of nodules in Gale mudstones may have had similar chemical characteristics at the time the Mg-sulfates were formed.

  13. Similarities Across Mars: Acidic Fluids at Both Meridiani Planum and Gale Crater in the Formation of Magnesium-Nickel Sulfates (United States)

    Yen, Albert S.; Ming, Douglas W.; Gellert, Ralf; Mittlefehldt, David W.; Vaniman, David T.; Thompson, Lucy M.; Morris, Richard V.; Clark, Benton C.; Arvidson, Raymond


    In-situ identification of sulfates at the martian surface by the Mars Exploration Rovers and the Mars Science Laboratory have included calcium sulfates with various states of hydration (gypsum, bassanite, anhydrite), iron sulfates of likely fumarolic origin, massive deposits of iron hydroxysulfates indicative of an acidic history, and minor occurrences of magnesium sulfates. Recent measurements by the Opportunity and Curiosity Alpha Particle X-ray Spectrometers (APXS) have indicated the presence of Ni-substituted Mg-sulfates at the Meridiani Planum and Gale Crater landing sites. The Opportunity rover has traversed nearly 43 km and is currently exploring the impact breccias of the rim of Endeavour crater, near a location where signatures of aqueous alteration have been established from orbit. APXS analyses of subsurface materials excavated by a rover wheel show clear evidence for a Mg(Ni)-sulfate with Mg:Ni (is) approximately 100:1 (molar). On the other side of the planet, Curiosity is continuing its climb up Mount Sharp after driving (is) approximately 13 km since landing. Over the last 4 km of the traverse, there have been multiple chemical analyses of erosionally-resistant nodules and dendritic features in a finely laminated mudstone unit which also indicate Mg(Ni)-sulfate (Mg:Ni (is) approximately 30:1, molar). The geologic settings for the Endeavour rim and the Mount Sharp mudstones are clearly different, but similar formation conditions for these sulfates may be possible. Ni(2+) readily substitutes for Mg(2+) in a variety of geochemical processes due to their comparable ionic radii. The availability of soluble Ni at the time of Mg-sulfate precipitation suggests acidic solutions. The fluids responsible for alteration in the Endeavour rim and for the formation of nodules in Gale mudstones may have had similar chemical characteristics at the time the Mg-sulfates were formed.

  14. Rapid HPLC analysis of amino acids and biogenic amines in wines during fermentation and evaluation of matrix effect. (United States)

    Wang, Ya-Qin; Ye, Dong-Qing; Zhu, Bao-Qing; Wu, Guang-Feng; Duan, Chang-Qing


    A rapid HPLC method has been developed for the simultaneous determination of 23 amino acids, 10 biogenic amines and the ammonium ion in wine. Samples were pre-column derivatised with diethyl ethoxymethylenemalonate and separated using reversed-phase HPLC within 30 min. The matrix effect was evaluated when measuring samples taken from different stages of fermentation. Most compounds showed no obvious matrix effect, whereas proline, ethanolamine and spermine had remarkably different responses to variable concentrations of sugar. High concentrations of sugar affected the pH of the derivatisation reaction system; proline, ethanolamine and spermine derivatives were sensitive to this effect. Matrix-matched calibration was used for the quantification of these compounds. Validation of the method showed that it was accurate, reproducible and efficient for the simultaneous determination of amino acids and biogenic amines in wines during fermentation. As a specific application of the method, red wine samples taken from different stages of fermentation were analysed. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Furoic and mefenamic acids as new matrices for matrix assisted laser desorption/ionization-(MALDI)-mass spectrometry. (United States)

    Abdelhamid, Hani Nasser; Wu, Hui-Fen


    The present study introduces two novel organic matrices for matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) for the analysis of small molecules. The first matrix is "2-amino-4,5-diphenylfuran-3-carboxylic acid" (also called furoic acid, FA) which was synthesized and then characterized by ultraviolet (UV), infrared (FTIR), nuclear magnetic resonance NMR ((1)H and (13)C) and mass spectrometry. The compound has organic semiconductor properties and exhibits intense UV-absorption which is suitable for the UV-MALDI laser (N2 laser, 337 nm). The second matrix is mefenamic acid (MA). The two matrices can be successfully applied for various classes of compounds including adenosine-5'-triphosphate (ATP, 0.5 µL(10.0 nmol)), spectinomycin (spect, 0.5 µL(14.0 nmol)), glutathione (GSH, 0.5 µL(9.0 nmol)), sulfamethazole (SMT, 0.5 µL(2.0 nmol)) and mixture of peptides gramicidin D (GD, 0.5µL (9.0 nmol)). The two matrices can effectively absorb the laser energy, resulting in excellent desorption/ionization of small molecules. The new matrices offer a significant enhancement of ionization, less fragmentation, few interferences, nice reproducibility, and excellent stability under vacuum. Theoretical calculations of the physical parameters demonstrated increase in polarizability, molar volume and refractivity than the conventional organic matrices which can effectively enhance the proton transfer reactions between the matrices with the analyte molecules. While the reduction in density, surface tension and index of refraction can enhance homogeneity between the two new matrices with the analytes. Due to the sublimation energy of mefenamic acid is (1.2 times) higher than that of the DHB, it is more stable to be used in the vacuum. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Similar PAH fate in anaerobic digesters inoculated with three microbial communities accumulating either volatile fatty acids or methane.

    Directory of Open Access Journals (Sweden)

    Florence Braun

    Full Text Available Urban sludge produced on wastewater treatment plants are often contaminated by organic pollutants such as polycyclic aromatic hydrocarbons (PAH. Their removal under methanogenic conditions was already reported, but the factors influencing this removal remain unclear. Here, we determined the influence of microbial communities on PAH removal under controlled physico-chemical conditions. Twelve mesophilic anaerobic digesters were inoculated with three microbial communities extracted from ecosystems with contrasting pollution histories: a PAH contaminated soil, a PCB contaminated sediment and a low contaminated anaerobic sludge. These anaerobic digesters were operated during 100 days in continuous mode. A sterilised activated sludge, spiked with 13 PAH at concentrations usually encountered in full-scale wastewater treatment plants, was used as substrate. The dry matter and volatile solid degradation, the biogas production rate and composition, the volatile fatty acids (VFA production and the PAH removals were monitored. Bacterial and archaeal communities were compared in abundance (qPCR, in community structure (SSCP fingerprinting and in dominant microbial species (454-pyrosequencing. The bioreactors inoculated with the community extracted from low contaminated anaerobic sludge showed the greater methane production. The PAH removals ranged from 10% to 30%, respectively, for high and low molecular weight PAH, whatever the inoculums tested, and were highly correlated with the dry matter and volatile solid removals. The microbial community structure and diversity differed with the inoculum source; this difference was maintained after the 100 days of digestion. However, the PAH removal was not correlated to these diverse structures and diversities. We hence obtained three functional stable consortia with two contrasted metabolic activities, and three different pictures of microbial diversity, but similar PAH and matter removals. These results confirm

  17. Effect of pioglitazone, quercetin and hydroxy citric acid on extracellular matrix components in experimentally induced non-alcoholic steatohepatitis. (United States)

    Mohan, Surapaneni Krishna; Veeraraghavan, Vishnu Priya; Jainu, Mallika


    Non-alcoholic steatohepatitis (NASH), is an important component of Non-alcoholic fatty liver disease (NAFLD) spectrum, which progresses to the end stage liver disease, if not diagnosed and treated properly. The disproportionate production of pro- and anti-inflammatory adipokines secreted from fat contributes to the pathogenesis of NASH. In this study, the comparative effect of pioglitazone, quercetin and hydroxy citric acid on extracellular matrix (ECM) component levels were studied in experimentally induced NASH. The experimental protocol consists of using 48 male Wister rats, which were divided into 8 groups. The levels of hyaluronic acid, leptin and adiponectin were monitored in experimental NASH. The experimental NASH rats treated with pioglitazone showed significant decrease in the levels of hyaluronic acid and significant increase in adiponectin levels when compared to experimentally induced NASH group, but did not show any effect on the levels of leptin. Contrary to these two drugs, viz. pioglitazone and hydroxy citric acid, the group treated with quercetin showed significant decrease in the levels of hyaluronic acid and leptin and significant decrease in adiponectin levels compared with that of experimentally induced NASH NASH group, offering maximum protection against NASH. Considering our findings, it could be concluded that quercetin may offer maximum protection against NASH by significantly increasing the levels of adiponectin, when compared to pioglitazone and hydroxy citric acid.

  18. Chamazulene carboxylic acid and matricin: a natural profen and its natural prodrug, identified through similarity to synthetic drug substances. (United States)

    Ramadan, Mai; Goeters, Susanne; Watzer, Bernhard; Krause, Eva; Lohmann, Klaus; Bauer, Rudolf; Hempel, Bernd; Imming, Peter


    Chamazulene carboxylic acid (1) is a natural profen with anti-inflammatory activity and a degradation product of proazulenic sesquiterpene lactones, e.g., matricin. Both 1 and proazulenes occur in chamomile (Matricaria recutita), yarrow (Achillea millefolium), and a few other Asteraceae species. It was isolated in improved yields, characterized physicochemically, and found to be an inhibitor of cyclooxygenase-2, but not of cyclooxygenase-1. It had anti-inflammatory activity in several animal models with local and systemic application. When human volunteers were given matricin orally, plasma levels of 1 were found to be in the micromolar range. Matricin was converted to 1 in artificial gastric fluid, but not in artificial intestinal fluid. Matricin and the yarrow proazulenes are proposed to be anti-inflammatory through conversion to 1. Intriguingly, the biological activity of the natural compound 1 was found because of its similarity to fully synthetic drug substances. This is the reverse process of the common lead function of natural compounds in drug discovery.

  19. Matrix-assisted laser desorption/ionisation mass spectrometry of transfer ribonucleic acids isolated from yeast. (United States)

    Gruic-Sovulj, I; Lüdemann, H C; Hillenkamp, F; Weygand-Durasevic, I; Kucan, Z; Peter-Katalinic, J


    tRNATyr and tRNASer purified from bulk brewer's yeast tRNA were subjected to analysis by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. Choosing a mixture of 2,4,6- and 2,3,4-trihydroxy-acetophenone and diammonium citrate as matrix a mass resolution of up to 220 (FWHM) was achieved in the linear mode of operation. Cation adduct suppression by addition of cation exchange beads and a chelating agent (CDTA) is shown to substantially improve mass resolution for this class of molecules. PMID:9108172

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

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


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

  1. Effects of the matrix and intramolecular interactions on the stability of the higher-energy conformers of 2-fluorobenzoic acid (United States)

    Kuş, Nihal; Fausto, Rui


    DFT(B3LYP)/6-311++G(d,p) calculations on 2-fluorobenzoic acid (2FBA) show that the molecule has four conformers: two low energy conformers (forms I and II) with the carboxylic acid group assuming the cis configuration (O=C—O—H dihedral equal to 0°) and two higher-energy conformers (III, IV) with a trans carboxylic group configuration. Isolation of 2FBA monomers in argon or nitrogen matrices allows for the efficient trapping of both low-energy conformers. Narrowband selective near-IR (NIR) excitation of the 2νOH mode of I in both argon and N2 matrices leads to its efficient conversion into conformer III, which is stabilized by an intramolecular O—H...F interaction. On the other hand, upon identical selective vibrational excitation of II no changes could be noticed in the argon matrix spectra, while experiments carried out on N2 matrices showed conversion of II into III. In conformer IV (the expected direct product resulting from NIR excitation of II), the stabilizing O—H...F interaction existing in III is replaced by an O—H...H repulsive interaction, which leads to a barrier separating this form from II that is about one third of that separating III from I. Under these circumstances, once formed by vibrational excitation of II, conformer IV can easily convert to the reactant species by fast tunneling, justifying the apparent inefficiency of the II → IV conversion upon vibrational excitation of II in an argon matrix. On the other hand, the stabilization of the initially formed conformer IV by the N2 matrix (due to OH...N2 interactions) allows this species to survive long enough to allow the IV → III over-the-barrier conversion to be competitive with the IV → II tunneling, justifying the observed net conversion of the NIR excited conformer II into form III in N2 matrix. These results demonstrate as the intramolecular local topology may decisively influence the intrinsic kinetic stability of different conformers of the same molecule. They are also a

  2. Similar effect of sodium nitroprusside and acetylsalicylic acid on antioxidant system improvement in mouse liver but not in the brain. (United States)

    Wróbel, Maria; Góralska, Joanna; Jurkowska, Halina; Sura, Piotr


    The aim of the present study was to analyze the relative antioxidant effects of acetylsalicylic acid (ASA) and sodium nitroprusside (SNP) in mouse liver and brain. The activity of rhodanese, 3-mercaptopyruvate sulfurtransferase (MPST) and γ-cystathionase (CSE), functioning as antioxidant proteins and capable of producing H2S, was investigated in mouse liver and brain after intraperitoneal once a day administration of sodium nitroprusside (5 mg/kg body weight) or acetylsalicylic acid (500 mg/kg body weight) continued for 5 days. The tissues were homogenized and then the obtained supernatants were used for further determinations. At the same time, the levels of sulfane sulfur, reduced and oxidized glutathione, cysteine, cystine, and cystathionine were also studied in these tissues. Both ASA and SNP show a statistically significant increase of sulfurtransferases activities in liver. The mechanism of action of sodium nitroprusside appears to consist in liberation of nitric oxide (NO), an important signaling molecule in the mammalian body. SNP also releases cyanide ions, which are converted in the liver to thiocyanate by the enzyme rhodanese and/or MPST and/or γ-cystathionase - the activities of all the enzymes were elevated in reaction to SNP. The action of γ-cystathionase is dependent upon converting cystathionine to cysteine, a precursor of the major cellular antioxidant, glutathione. Under oxidizing conditions, an increase in cystathionine β-synthase activity might indirectly result in an increase in the antioxidant glutathione level; this was reflected by the increased GSH/GSSG ratio in the liver, but not in the brain, where a trace activity of γ-cystathionase is normally detected. The results of the present investigations show that ASA and SNP may stimulate the GSH-dependent antioxidant system and protect liver cells from oxidative stress. An increased activity of the H2S-producing enzymes and the increased GSH/GSSG ratio may lead to an elevated level of H2

  3. Pore formation mechanism of porous poly(DL-lactic acid) matrix membrane

    Energy Technology Data Exchange (ETDEWEB)

    Phaechamud, Thawatchai, E-mail:; Chitrattha, Sasiprapa, E-mail:


    Porous PLA structure has been widely used in cell transplantation, drug carrier and wound dressing. The porous structure can be controlled depending on the choice of the polymer, solvent, nonsolvent and preparation parameters. In this study, the porous PLA matrix membranes were prepared by adding PEG 400 in PLA solution using dichloromethane (DCM) as solvent prior to casting. The influence of other liquids as co-solvent on pore formation and the structural change during membrane formation were evaluated. The co-solvents affected both porous topography and mechanical properties of PLA membrane. The porous matrix were produced when the non-solvent of PLA was used as co-solvent. Cryo-SEM micrographs revealed that PEG 400 still remained in the PLA porous matrix membrane. From the tracking of the structural change during film formation, the PLA–PEG solution changed into porous structure by liquid liquid phase separation and solidification processes, respectively. Thermogravimetric analysis revealed that PLA–PEG in DCM solution exhibited the two-step of weight loss, the first step occurred from DCM evaporation and the second step occurred from the degradation of PLA–PEG matrix. The liquid–liquid phase separation and solidification started when the amount of DCM was higher than PEG 400 for 2.67 folds and DCM amount was equal to that of PEG 400, respectively. These results could clarify the pore formation mechanism of porous PLA membrane and will be useful for the further investigation and application. - Highlights: • Pore formation mechanism of PLA matrix membrane inducing by PEG 400 addition was investigated. • Cryo-scanning electron microscopy revealed the embedded PEG 400 in matrix membrane. • Tracking of structural change during membrane formation with stereomicroscope and thermogravimetric analysis could explain the pore formation mechanism. • Liquid-liquid phase separation of PLA-PEG 400 solution started when the amount of dichloromethane remained 2

  4. Mixed matrix membranes for process intensification in electrodialysis of amino acids

    NARCIS (Netherlands)

    Kattan Readi, O.M.; Rolevink, Hendrikus H.M.; Nijmeijer, Dorothea C.


    BACKGROUND Amino acids are valuable intermediates in the biobased economy for the production of chemicals. Electro-membrane processes combined with enzymatic modification have been investigated as an alternative technology for the fractionation of a mixture of amino acids with almost identical

  5. Analysis of the relationship between genomic GC Content and patterns of base usage, codon usage and amino acid usage in prokaryotes: similar GC content adopts similar compositional frequencies regardless of the phylogenetic lineages.

    Directory of Open Access Journals (Sweden)

    Hui-Qi Zhou

    Full Text Available The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. These genomes had GC contents that ranged from 13.5% to 74.9%. We analyzed the distance of base frequencies at the three codon positions, codon frequencies, and amino acid compositions across genomes with respect to the differences in the GC content of these prokaryotic species. We found that although the phylogenetic lineages were remote among some species, a similar genomic GC content forced them to adopt similar base usage patterns at the three codon positions, codon usage patterns, and amino acid usage patterns. Our work demonstrates that in prokaryotic genomes: a base usage, codon usage, and amino acid usage change with GC content with a linear correlation; b the distance of each usage has a linear correlation with the GC content difference; and c GC content is more essential than phylogenetic lineage in determining base usage, codon usage, and amino acid usage. This work is exceptional in that we adopted intuitively graphic methods for all analyses, and we used these analyses to examine as many as 2670 prokaryotes. We hope that this work is helpful for understanding common features in the organization of microbial genomes.

  6. Investigating the use of coupling agents to improve the interfacial properties between a resorbable phosphate glass and polylactic acid matrix. (United States)

    Hasan, Muhammad Sami; Ahmed, Ifty; Parsons, Andrew J; Rudd, Chris D; Walker, Gavin S; Scotchford, Colin A


    Eight different chemicals were investigated as potential candidate coupling agents for phosphate glass fibre reinforced polylactic acid composites. Evidence of reaction of the coupling agents with phosphate glass and their effect on surface wettability and glass degradation were studied along with their principle role of improving the interface between glass reinforcement and polymer matrix. It was found that, with an optimal amount of coupling agent on the surface of the glass/polymer, interfacial shear strength improved by a factor of 5. Evidence of covalent bonding between agent and glass was found for three of the coupling agents investigated, namely: 3-aminopropyltriethoxysilane; etidronic acid and hexamethylene diisocyanate. These three coupling agents also improved the interfacial shear strength and increased the hydrophobicity of the glass surface. It is expected that this would provide an improvement in the macroscopic properties of full-scale composites fabricated from the same materials which may also help to retain these properties for the desired length of time by retarding the breakdown of the fibre/matrix interface within these composites.

  7. Matrix metalloproteinase-7 regulates cleavage of pro-nerve growth factor and is neuroprotective following kainic acid-induced seizures. (United States)

    Le, Audrey P; Friedman, Wilma J


    The neurotrophin nerve growth factor (NGF) regulates neuronal growth, differentiation, and survival during development. However, the precursor of NGF, proNGF, is a potent apoptotic ligand for the p75 neurotrophin receptor (p75(NTR))-sortilin complex. The mechanisms that regulate cleavage of proNGF, therefore, are critical determinants of whether this factor promotes neuronal survival or death. In this study, we demonstrate that, following kainic acid-induced seizures, the proNGF processing enzyme matrix metalloproteinase 7 (MMP-7) and its inhibitor TIMP-1 (tissue inhibitor of matrix metalloproteinase 1) are regulated in a manner that prevents proneurotrophin cleavage and leads to increased proNGF in the extracellular milieu. Furthermore, we demonstrate both in vitro and in vivo that exogenous MMP-7 enhances proNGF cleavage and provides neuroprotection following kainic acid treatment. These data demonstrate that increased extracellular proNGF levels following seizures are stabilized by altered MMP-7 enzymatic activity, leading to increased neuronal death via activation of p75(NTR).

  8. Phenotypic stability, matrix elaboration and functional maturation of nucleus pulposus cells encapsulated in photocrosslinkable hyaluronic acid hydrogels. (United States)

    Kim, Dong Hwa; Martin, John T; Elliott, Dawn M; Smith, Lachlan J; Mauck, Robert L


    Degradation of the nucleus pulposus (NP) is an early hallmark of intervertebral disc degeneration. The capacity for endogenous regeneration in the NP is limited due to the low cellularity and poor nutrient and vascular supply. Towards restoring the NP, a number of biomaterials have been explored for cell delivery. These materials must support the NP cell phenotype while promoting the elaboration of an NP-like extracellular matrix in the shortest possible time. Our previous work with chondrocytes and mesenchymal stem cells demonstrated that hydrogels based on hyaluronic acid (HA) are effective at promoting matrix production and the development of functional material properties. However, this material has not been evaluated in the context of NP cells. Therefore, to test this material for NP regeneration, bovine NP cells were encapsulated in 1%w/vol HA hydrogels at either a low seeding density (20×10(6)cellsml(-1)) or a high seeding density (60×10(6)cellsml(-1)), and constructs were cultured over an 8week period. These NP cell-laden HA hydrogels showed functional matrix accumulation, with increasing matrix content and mechanical properties with time in culture at both seeding densities. Furthermore, encapsulated cells showed NP-specific gene expression profiles that were significantly higher than expanded NP cells prior to encapsulation, suggesting a restoration of phenotype. Interestingly, these levels were higher at the lower seeding density compared to the higher seeding density. These findings support the use of HA-based hydrogels for NP tissue engineering and cellular therapies directed at restoration or replacement of the endogenous NP. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  9. Effect of food matrix microstructure on stomach emptying rate and apparent ileal fatty acid digestibility of almond lipids. (United States)

    Gallier, Sophie; Rutherfurd, Shane M; Moughan, Paul J; Singh, Harjinder


    Almond lipids can be consumed in different forms such as nuts, oil-in-water emulsions or oil. The stomach emptying rate (SER) of almond lipids (0.2 g of fat per 2 mL of almond lipid suspension) as a function of the food matrix was studied using magnetic resonance spectroscopy based on the stomach emptying of a marker (AlCl3-6H2O) in the growing rat. Chyme and digesta samples were collected following serial gavaging (0.2 g of fat per 2 mL of almond lipid suspension) to study microstructural changes and determine the apparent ileal digestibility of almond fatty acids as a function of the native food matrix. The T(1/2) for the stomach emptying of crushed whole almonds and almond cream (194 ± 17 min and 185 ± 19 min, respectively) were not different (P > 0.05) from that of a gastric-stable Tween-oil emulsion (197 ± 19 min). The T(1/2) values for a sodium caseinate (NaCas)-oil emulsion (145 ± 11 min) and a gastric-unstable Span-oil emulsion (135 ± 7 min) were different (P almond milk and oil emptied at an intermediate rate (157 ± 9 min and 172 ± 11 min, respectively). Extensively coalesced emulsions under gastric conditions (almond oil, almond cream and Span-oil) had lower (P almond milk, NaCas-oil and Tween-oil emulsions (91.0%, 92.2%, 92.1% and 88.7%, respectively). The original food matrix and structural changes occurring within the gastrointestinal tract had an impact on SER and ileal fatty acid digestibility of the almond preparations.

  10. [Effects of hyaluronic acid on biomechanic performance of porcine acellular dermal matrix plus thin skin autograft after transplantation]. (United States)

    Zhao, Jing-yu; Chai, Jia-ke; Song, Hui-feng; Xu, Ming-huo


    To explore the effects of hyaluronic acid (HA) on biomechanical properties for porcine acellular dermal matrix (PADM) plus thin skin autograft after transplantation. The dorsa of 10 Japanese white rabbits were symmetrically divided into four areas of A-D by random grouping. Full-thickness skin defects were created in Groups A-C while Group D was blank with normal skin. Operations were performed in Group A: implant with HA + PADM + thin skin autografts, Group B: implant with PADM + thin skin autografts and Group C: skin autografts group. Histological examination of specimen was performed at Day 56 postoperatively. And the biomechanical properties such as relaxation and stress-strain properties of grafts were recorded. The structure of PADM was found to be basically intact by hematoxylin and eosin E dyeing in Groups A and B. In Group A, dense fiber structure could be observed. Lots of regularly arranged collagenous fibers and new blood capillaries were grown into the dermal matrix with sparsely distributed inflammatory cells. In Group B, acellular dermal matrix became clustered with a small amount of invaded fibroblasts. And there was a high expression of inflammatory cells. The biomechanic performances of transplanted skin were: Group A's curve was mostly close to that of Group D's, Group B's curve was the most further from that of Group D's (P = 0.001) and Group C's curve stayed between Groups A and B. Under the same strain, the stress of Groups A-D was (87 ± 8), (115 ± 9), (63 ± 7) and (81 ± 4) kPa respectively. No significant difference of stress existed between these two groups (P = 0.838). There was significant difference of stress between Groups B/C and D (P = 0.001 and P = 0.009). Topical hyaluronic acid may be used to enhance the biomechanics performances of transplanted skin.

  11. Graphene nanoplatelets based matrix solid-phase dispersion microextraction for phenolic acids by ultrahigh performance liquid chromatography with electrochemical detection. (United States)

    Peng, Li-Qing; Yi, Ling; Yang, Qiu-Cheng; Cao, Jun; Du, Li-Jing; Zhang, Qi-Dong


    A simple, rapid and eco-friendly approach based on matrix solid-phase dispersion microextraction (MSPDM) followed by ultrahigh performance liquid chromatography coupled with electrochemical detection (UHPLC-ECD) was presented for the microextraction and determination of six phenolic acids in a plant preparation (Danshen tablets). The parameters that influenced the extraction performance of phenolic acids were investigated and optimized. The optimal MSPDM conditions were determined as follows: sorbent, using graphene nanoplatelets with sample/sorbent ratio of 1:1, grinding time set at 60 s, and 0.2 mL of water as elution solvent. Under the optimum conditions, the validation experiments indicated that the proposed method exhibited good linearity (r2 ≥ 0.9991), excellent precision (RSD ≤ 4.57%), and satisfactory recoveries (82.34-98.34%). The limits of detection were from 1.19 to 4.62 ng/mL for six phenolic acids. Compared with other reported methods, this proposal required less sample, solvent and extraction time. Consequently, the proposed method was successfully used to the extraction and determination of phenolic acids in Danshen tablets.

  12. Nonlinear optical studies on 4-(ferrocenylmethylimino)-2-hydroxy-benzoic acid thin films deposited by matrix-assisted pulsed laser evaporation (MAPLE)

    Energy Technology Data Exchange (ETDEWEB)

    Matei, Andreea [INFLPR - National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Str., Magurele RO-077125, Bucharest (Romania); Marinescu, Maria, E-mail: [UB - University of Bucharest, Faculty of Chemistry, 90-92 Şoseaua Panduri, Sector 5, RO-010184, Bucharest (Romania); Constantinescu, Catalin, E-mail: [INFLPR - National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Str., Magurele RO-077125, Bucharest (Romania); Ion, Valentin; Mitu, Bogdana [INFLPR - National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Str., Magurele RO-077125, Bucharest (Romania); Ionita, Iulian [INFLPR - National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Str., Magurele RO-077125, Bucharest (Romania); UB - University of Bucharest, Faculty of Physics, 405 Atomistilor Str., Magurele RO-077125, Bucharest (Romania); Dinescu, Maria [INFLPR - National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Str., Magurele RO-077125, Bucharest (Romania); Emandi, Ana [INFLPR - National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Str., Magurele RO-077125, Bucharest (Romania); UB - University of Bucharest, Faculty of Chemistry, 90-92 Şoseaua Panduri, Sector 5, RO-010184, Bucharest (Romania)


    Graphical abstract: - Highlights: • A newly synthesized ferrocene-derivative exhibits SHG potential. • Matrix-assisted pulsed laser evaporation is employed for thin film fabrication. • The optical properties of the films are investigated, presented and discussed. • At maximum laser output power, the SHG signal is strongly influenced by thin film thickness. - Abstract: We present results on a new, laboratory synthesized ferrocene-derivative, i.e. 4-(ferrocenylmethylimino)-2-hydroxy-benzoic acid. Thin films with controlled thickness are deposited by matrix-assisted pulsed laser evaporation (MAPLE), on quartz and silicon substrates, with the aim of evaluating the nonlinear optical properties for potential optoelectronic applications. Dimethyl sulfoxide was used as matrix, with 1% wt. concentration of the guest compound. The frozen target is irradiated by using a Nd:YAG laser (4ω/266 nm, 7 ns pulse duration, 10 Hz repetition rate), at low fluences ranging from 0.1 to 1 J/cm{sup 2}. Atomic force microscopy (AFM) and scanning electron microscopy (SEM) are used to probe the surface morphology of the films. Fourier transform infrared (FTIR) and Raman spectroscopy reveal similar structure of the thin film material when compared to the starting material. The optical properties of the thin films are investigated by spectroscopic-ellipsometry (SE), and the refractive index dependence with respect to temperature is studied. The second harmonic generation (SHG) potential is assessed by using a femtosecond Ti:sapphire laser (800 nm, 60–100 fs pulse duration, 80 MHz repetition rate), at 200 mW maximum output power, revealing that the SHG signal intensity is strongly influenced by the films’ thickness.

  13. Understanding the similarities and differences between ozone and peroxone in the degradation of naphthenic acids: Comparative performance for potential treatment. (United States)

    Meshref, Mohamed N A; Klamerth, Nikolaus; Islam, Md Shahinoor; McPhedran, Kerry N; Gamal El-Din, Mohamed


    Ozonation at high doses is a costly treatment for oil sands process-affected water (OSPW) naphthenic acids (NAs) degradation. To decrease costs and limit doses, different peroxone (hydrogen peroxide/ozone; H2O2:O3) processes using mild-ozone doses of 30 and 50 mg/L were investigated. The degradation efficiency of Ox-NAs (classical (O2-NAs) + oxidized NAs) improved from 58% at 30 mg/L ozone to 59%, 63% and 76% at peroxone (1:1), 50 mg/L ozone, and peroxone (1:2), respectively. Suppressing the hydroxyl radical (•OH) pathway by adding tert-butyl alcohol did significantly reduce the degradation in all treatments, while molecular ozone contribution was around 50% and 34% for O2-NAs and Ox-NAs, respectively. Structure reactivity toward degradation was observed with degradation increase for both O2-NAs and Ox-NAs with increase of both carbon (n) and hydrogen deficiency/or |-Z| numbers in all treatments. However, the combined effect of n and Z showed specific insights and differences between ozone and peroxone treatments. The degradation pathway for |-Z|≥10 isomers in ozone treatments through molecular ozone was significant compared to •OH. Though peroxone (1:2) highly reduced the fluorophore organics and toxicity to Vibrio fischeri, the best oxidant utilization in the degradation of O2-NAs (mg/L) per ozone dose (mg/L) was observed in the peroxone (1:1) (0.91) and 30 mg/L ozone treatments (0.92). At n = 9-11, peroxone (1:1) had similar or enhanced effect on the O2-NAs degradation compared to 50 mg/L ozone. Enhancing •OH pathway through peroxone versus ozone may be an effective OSPW treatment that will allow its safe release into receiving environments with marginal cost addition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Quantitative analysis of highly similar salvianolic acids with 1H qNMR for quality control of traditional Chinese medicinal preparation Salvianolate Lyophilized Injection. (United States)

    Chen, Xialin; Guo, Yujie; Hu, Yuanjia; Yu, Boyang; Qi, Jin


    Salvianolate Lyophilized Injection (SLI), a traditional Chinese medicinal (TCM) preparation which is used to treat stroke, is composed of multiple salvianolic acids from the aqueous extracts of Salvia miltiorrhiza, and includes mainly protocatechualdehyde, rosmarinic acid, salvianolic acid B, salvianolic acid D, salvianolic acid E, diastereomer of salvianolic acid E, salvianolic acid Y, lithospermic acid and diastereomer of lithospermic acid. It is difficult to quantitatively control the quality of SLI using traditional high performance liquid chromatography due to the highly similar structure of these constituents including three pairs of diastereomers and the lack of commercial resources for most of these constituents as standards. Thus, a highly reproducible, fast, accurate and simple (1)H quantitative nuclear magnetic resonance (qNMR) method without the need for calibration curves and complex computation was established by optimizing the solvent system and acquisition parameters to simultaneously determine the nine salvianolic acids and mannitol in SLI. This method was validated and successfully used to determine 10 batches of SLI and the qNMR data were further analyzed with a vector including angle cosine and the partial least squares method for the quality control of SLI. The results indicated that qNMR can be used as a routine method for the quality control of SLI and may have potential in the quantification of diastereomers in other TCM preparations. Copyright © 2016. Published by Elsevier B.V.

  15. Studies Related to the Oregon State University High Temperature Test Facility: Scaling, the Validation Matrix, and Similarities to the Modular High Temperature Gas-Cooled Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Richard R. Schultz; Paul D. Bayless; Richard W. Johnson; William T. Taitano; James R. Wolf; Glenn E. McCreery


    The Oregon State University (OSU) High Temperature Test Facility (HTTF) is an integral experimental facility that will be constructed on the OSU campus in Corvallis, Oregon. The HTTF project was initiated, by the U.S. Nuclear Regulatory Commission (NRC), on September 5, 2008 as Task 4 of the 5 year High Temperature Gas Reactor Cooperative Agreement via NRC Contract 04-08-138. Until August, 2010, when a DOE contract was initiated to fund additional capabilities for the HTTF project, all of the funding support for the HTTF was provided by the NRC via their cooperative agreement. The U.S. Department of Energy (DOE) began their involvement with the HTTF project in late 2009 via the Next Generation Nuclear Plant project. Because the NRC interests in HTTF experiments were only centered on the depressurized conduction cooldown (DCC) scenario, NGNP involvement focused on expanding the experimental envelope of the HTTF to include steady-state operations and also the pressurized conduction cooldown (PCC). Since DOE has incorporated the HTTF as an ingredient in the NGNP thermal-fluids validation program, several important outcomes should be noted: 1. The reference prismatic reactor design, that serves as the basis for scaling the HTTF, became the modular high temperature gas-cooled reactor (MHTGR). The MHTGR has also been chosen as the reference design for all of the other NGNP thermal-fluid experiments. 2. The NGNP validation matrix is being planned using the same scaling strategy that has been implemented to design the HTTF, i.e., the hierarchical two-tiered scaling methodology developed by Zuber in 1991. Using this approach a preliminary validation matrix has been designed that integrates the HTTF experiments with the other experiments planned for the NGNP thermal-fluids verification and validation project. 3. Initial analyses showed that the inherent power capability of the OSU infrastructure, which only allowed a total operational facility power capability of 0.6 MW, is

  16. Analysis of low molecular weight acids by negative mode matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. (United States)

    Shroff, Rohit; Muck, Alexander; Svatos, Ales


    Free 9-aminoacridine base is demonstrated to be a suitable matrix for negative mode matrix-assisted laser desorption/ionization time-of-flight mass spectrometric (MALDI-TOFMS) analysis of a wide range of low molecular weight organic acids including aliphatic (from acetic to palmitic acid), aromatic acids, phytohormones (e.g. jasmonic and salicylic acids), and amino acids. Low limits of quantitation in the femtomolar range (jasmonic - 250 fmol; caffeic - 160 fmol and salicylic - 12.5 fmol) and linear detector response over two concentration orders in the pico- and femtomolar range are extremely encouraging for the direct study of such acids in complex biological matrices. Copyright (c) 2007 John Wiley & Sons, Ltd.

  17. FTIR Studies of the Photochemistry of Deuterated Formic Acid in a Parahydrogen Matrix (United States)

    Anderson, David T.


    We report new FTIR studies of the 193 nm photochemistry of deuterated formic acid (DCOOD) trapped in parahydrogen matrices. In our 2011 preliminary report, we showed the 193 nm in situ photolysis of formic acid (HCOOH) produces small amounts of HCO and HOCO and that after the laser is turned off, we observe continued slow growth in the HOCO radical for up to 10 hours after photolysis. At that time we were unsure of the detailed chemical mechanism by which the HOCO continues to grow after photolysis, but we suspected it had to do with reactions of mobile H-atoms with the HCOOH precursor that remains at significant concentrations after photolysis under these conditions. The present deuterated formic acid photolysis studies provide strong circumstantial evidence that H-atom reactions with formic acid are the source of the continued HOCO growth. Further, variable-temperature kinetic studies conducted with the deuterated formic acid sample show a strong inverse temperature dependence to the reaction kinetics. Essentially, the reaction that leads to HOCO growth only occurs at temperatures below 2.4 K. We are currently trying to model the kinetics using standard methods and the most recent analysis will be presented at the meeting. David T. Anderson, Leif O. Paulson, 66th Ohio State University International Symposium on Molecular Spectroscopy, talk FE02 (2011).

  18. Preparation of Acid-Resistant Microcapsules with Shell-Matrix Structure to Enhance Stability of Streptococcus Thermophilus IFFI 6038. (United States)

    Zhou, Huan Bin; Chen, Jiashu; Li, Shunyi; Zhang, Jianpan; Zhu, Chun E; Ran, Hao; Luo, Meihua; Pan, Xin; Hu, Haiyan; Wu, Chuanbin


    Microencapsulation is an effective technology used to protect probiotics against harsh conditions. Extrusion is a commonly used microencapsulation method utilized to prepare probiotics microcapsules that is regarded as economical and simple to operate. This research aims to prepare acid-resistant probiotic microcapsules with high viability after freeze-drying and optimized storage stability. Streptococcus thermophilus IFFI 6038 (IFFI 6038) cells were mixed with trehalose and alginate to fabricate microcapsules using extrusion. These capsules were subsequently coated with chitosan to obtain chitosan-trehalose-alginate microcapsules with shell-matrix structure. Chitosan-alginate microcapsules (without trehalose) were also prepared using the same method. The characteristics of the microcapsules were observed by measuring the freeze-dried viability, acid resistance, and long-term storage stability of the cells. The viable count of IFFI 6038 in the chitosan-trehalose-alginate microcapsules was 8.34 ± 0.30 log CFU g -1 after freeze-drying (lyophilization), which was nearly 1 log units g -1 greater than the chitosan-alginate microcapsules. The viability of IFFI 6038 in the chitosan-trehalose-alginate microcapsules was 6.45 ± 0.09 log CFU g -1 after 120 min of treatment in simulated gastric juices, while the chitosan-alginate microcapsules only measured 4.82 ± 0.22 log CFU g -1 . The results of the long-term storage stability assay indicated that the viability of IFFI 6038 in chitosan-trehalose-alginate microcapsules was higher than in chitosan-alginate microcapsules after storage at 25 °C. Trehalose played an important role in the stability of IFFI 6038 during storage. The novel shell-matrix chitosan-trehalose-alginate microcapsules showed optimal stability and acid resistance, demonstrating their potential as a delivery vehicle to transport probiotics. © 2017 Institute of Food Technologists®.

  19. Local effect of zoledronic acid on new bone formation in posterolateral spinal fusion with demineralized bone matrix in a murine model. (United States)

    Zwolak, Pawel; Farei-Campagna, Jan; Jentzsch, Thorsten; von Rechenberg, Brigitte; Werner, Clément M


    Posterolateral spinal fusion is a common orthopaedic surgery performed to treat degenerative and traumatic deformities of the spinal column. In posteriolateral spinal fusion, different osteoinductive demineralized bone matrix products have been previously investigated. We evaluated the effect of locally applied zoledronic acid in combination with commercially available demineralized bone matrix putty on new bone formation in posterolateral spinal fusion in a murine in vivo model. A posterolateral sacral spine fusion in murine model was used to evaluate the new bone formation. We used the sacral spine fusion model to model the clinical situation in which a bone graft or demineralized bone matrix is applied after dorsal instrumentation of the spine. In our study, group 1 received decortications only (n = 10), group 2 received decortication, and absorbable collagen sponge carrier, group 3 received decortication and absorbable collagen sponge carrier with zoledronic acid in dose 10 µg, group 4 received demineralized bone matrix putty (DBM putty) plus decortication (n = 10), and group 5 received DBM putty, decortication and locally applied zoledronic acid in dose 10 µg. Imaging was performed using MicroCT for new bone formation assessment. Also, murine spines were harvested for histopathological analysis 10 weeks after surgery. The surgery performed through midline posterior approach was reproducible. In group with decortication alone there was no new bone formation. Application of demineralized bone matrix putty alone produced new bone formation which bridged the S1-S4 laminae. Local application of zoledronic acid to demineralized bone matrix putty resulted in significant increase of new bone formation as compared to demineralized bone matrix putty group alone. A single local application of zoledronic acid with DBM putty during posterolateral fusion in sacral murine spine model increased significantly new bone formation in situ in our model. Therefore, our

  20. Stearic acid and high molecular weight PEO as matrix for the highly water soluble metoprolol tartrate in continuous twin-screw melt granulation. (United States)

    Monteyne, Tinne; Adriaensens, Peter; Brouckaert, Davinia; Remon, Jean-Paul; Vervaet, Chris; De Beer, Thomas


    Granules with release-sustaining properties were developed by twin screw hot melt granulation (HMG) using a combination of stearic acid (SA) and high molecular weight polyethylene oxide (PEO) as matrix for a highly water soluble model drug, metoprolol tartrate (MPT). Earlier studies demonstrated that mixing molten SA and PEO resulted in hydrogen bond formation between hydroxyl groups of fatty acid molecules and ether groups in PEO chains. These molecular interactions might be beneficial in order to elevate the sustained release effect of drugs from a SA/PEO matrix. This study aims to investigate the continuous twin screw melt granulation technique to study the impact of a SA/PEO matrix on the dissolution rate of a highly water soluble drug (MPT). Decreasing the SA/PEO ratio improved the release-sustaining properties of the matrix. The solid state of the granules was characterized using differential scanning calorimetry (DSC), nuclear magnetic resonance (NMR), X-ray diffraction (XRD), Raman spectroscopy, Fourier transform infrared (FTIR) and near infrared chemical imaging (NIR-CI) in order to understand the dissolution behavior. The results revealed a preferential interaction of the MPT molecules with stearic acid impeding the PEO to form hydrogen bonds with the stearic acid chains. However, this allowed the PEO chains to recrystallize inside the stearic acid matrix after granulation, hence, elevating the release-sustaining characteristics of the formulation. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. Identification of Protein–Protein Interactions via a Novel Matrix-Based Sequence Representation Model with Amino Acid Contact Information

    Directory of Open Access Journals (Sweden)

    Yijie Ding


    Full Text Available Identification of protein–protein interactions (PPIs is a difficult and important problem in biology. Since experimental methods for predicting PPIs are both expensive and time-consuming, many computational methods have been developed to predict PPIs and interaction networks, which can be used to complement experimental approaches. However, these methods have limitations to overcome. They need a large number of homology proteins or literature to be applied in their method. In this paper, we propose a novel matrix-based protein sequence representation approach to predict PPIs, using an ensemble learning method for classification. We construct the matrix of Amino Acid Contact (AAC, based on the statistical analysis of residue-pairing frequencies in a database of 6323 protein–protein complexes. We first represent the protein sequence as a Substitution Matrix Representation (SMR matrix. Then, the feature vector is extracted by applying algorithms of Histogram of Oriented Gradient (HOG and Singular Value Decomposition (SVD on the SMR matrix. Finally, we feed the feature vector into a Random Forest (RF for judging interaction pairs and non-interaction pairs. Our method is applied to several PPI datasets to evaluate its performance. On the S . c e r e v i s i a e dataset, our method achieves 94 . 83 % accuracy and 92 . 40 % sensitivity. Compared with existing methods, and the accuracy of our method is increased by 0 . 11 percentage points. On the H . p y l o r i dataset, our method achieves 89 . 06 % accuracy and 88 . 15 % sensitivity, the accuracy of our method is increased by 0 . 76 % . On the H u m a n PPI dataset, our method achieves 97 . 60 % accuracy and 96 . 37 % sensitivity, and the accuracy of our method is increased by 1 . 30 % . In addition, we test our method on a very important PPI network, and it achieves 92 . 71 % accuracy. In the Wnt-related network, the accuracy of our method is increased by 16 . 67 % . The source code and all

  2. Spectrophotometric method for fast quantification of ascorbic acid and dehydroascorbic acid in simple matrix for kinetics measurements. (United States)

    Gómez Ruiz, Braulio; Roux, Stéphanie; Courtois, Francis; Bonazzi, Catherine


    A simple, rapid and reliable method was developed for quantifying ascorbic (AA) and dehydroascorbic (DHAA) acids and validated in 20mM malate buffer (pH 3.8). It consists in a spectrophotometric measurement of AA, either directly on the solution added with metaphosphoric acid or after reduction of DHAA into AA by dithiothreitol. This method was developed with real time measurement of reactions kinetics in bulk reactors in mind, and was checked in terms of linearity, limits of detection and quantification, fidelity and accuracy. The linearity was found satisfactory on the range of 0-6.95mM with limits of detection and quantification of 0.236mM and 0.467mM, respectively. The method was found acceptable in terms of fidelity and accuracy with a coefficient of variation for repeatability and reproducibility below 6% for AA and below 15% for DHAA, and with a recovery range of 97-102% for AA and 88-112% for DHAA. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Effects of spray-drying on w/o/w multiple emulsions prepared from a stearic acid matrix (United States)

    Mlalila, Nichrous; Swai, Hulda; Kalombo, Lonji; Hilonga, Askwar


    The goal of this study was to explore the effects of spray-drying on w/o/w double emulsions of methyltestosterone (MT) loaded in a stearic acid matrix. MT-loaded nanoparticles were formulated by a water-in-oil-in-water emulsion technique using 50, 75, and 100 mg of stearic acid, 2% and 3% w/v polyvinyl alcohol, 5% w/v lactose, and 0.2% w/v chitosan. The emulsions were immediately spray-dried based on an optimized model of inlet temperature and pump rate, and characterized for optimized responses with regard to particle size, polydispersity index, and zeta potential, for both emulsion and powder samples. Dynamic light scattering analysis shown that the nanoparticles increased in size with increasing concentrations of polyvinyl alcohol and stearic acid. Scanning electron microscopy indicated that the MT-loaded nanoparticles were spherical in shape, had a smooth surface, and were in an amorphous state, which was confirmed by differential scanning calorimetry. These MT-loaded nanoparticles are a promising candidate carrier for the delivery of MT; however, further studies are needed in order to establish the stability of the system and the cargo release profile under normal conditions of use. PMID:25489238

  4. Promoting extracellular matrix remodeling via ascorbic acid enhances the survival of primary ovarian follicles encapsulated in alginate hydrogels. (United States)

    Tagler, David; Makanji, Yogeshwar; Tu, Tao; Bernabé, Beatriz Peñalver; Lee, Raymond; Zhu, Jie; Kniazeva, Ekaterina; Hornick, Jessica E; Woodruff, Teresa K; Shea, Lonnie D


    The in vitro growth of ovarian follicles is an emerging technology for fertility preservation. Various strategies support the culture of secondary and multilayer follicles from various species including mice, non-human primate, and human; however, the culture of early stage (primary and primordial) follicles, which are more abundant in the ovary and survive cryopreservation, has been limited. Hydrogel-encapsulating follicle culture systems that employed feeder cells, such as mouse embryonic fibroblasts (MEFs), stimulated the growth of primary follicles (70-80 µm); yet, survival was low and smaller follicles (ascorbic acid based on its role in extracellular matrix (ECM) deposition/remodeling for other applications. The selection of ascorbic acid was further supported by a microarray analysis that suggested a decrease in mRNA levels of enzymes within the ascorbate pathway between primordial, primary, and secondary follicles. The supplementation of ascorbic acid (50 µg/mL) significantly enhanced the survival of primary follicles (<80 µm) cultured in alginate hydrogels, which coincided with improved structural integrity. Follicles developed antral cavities and increased to diameters exceeding 250 µm. Consistent with improved structural integrity, the gene/protein expression of ECM and cell adhesion molecules was significantly changed. This research supports the notion that modifying the culture environment (medium components) can substantially enhance the survival and growth of early stage follicles. © 2013 Wiley Periodicals, Inc.

  5. Rosmarinic acid induces rabbit articular chondrocyte differentiation by decreases matrix metalloproteinase-13 and inflammation by upregulating cyclooxygenase-2 expression. (United States)

    Eo, Seong-Hui; Kim, Song Ja


    Matrix metalloproteinases (MMPs) are known to play an important role in the degradation of the extracellular matrix and the pathological progression of osteoarthritis (OA). The natural polyphenolic compound rosmarinic acid (Ros. A) has been shown to suppress the inhibitory activity of matrix metalloproteinases (MMPs). However, the effects of Ros. A on OA have not been investigated. In the current study, primary articular chondrocytes were cultured from rabbit articular cartilage and treated with Ros. A. Phenotypic characterization was performed by western blotting to assess specific markers, prostaglandin E2 (PGE2) assays, and alcian blue staining to measure sulfated-proteoglycan production. We report that in rabbit articular chondrocytes, Ros. A increased type II collagen, sulfated-proteoglycan, cyclooxygenase-2 (COX-2), and PGE2 production in a dose- and time-dependent manner. Furthermore, Ros. A suppressed the expression of MMP-13. In addition, treatment with Ros A activated extracellular signal-regulated kinase (ERK)-1/2 and p38 kinase signaling pathways. Inhibition of MMP-13 enhanced Ros. A-induced type II collagen expression and sulfated-proteoglycan synthesis but COX-2 and PGE2 production were unchanged. Ros. A-mediated up-regulation of ERK phosphorylation was abolished by the MEK inhibitor, PD98059, which prevented induction of the associated inflammatory response. Inhibition of p38 kinase with SB203580 enhanced the increase in type II collagen expression via Ros. A-mediated down-regulation of MMP-13. Results suggest that ERK-1/2 regulates Ros. A-induced inflammation and that p38 regulates differentiation by inhibiting MMP-13 in rabbit articular chondrocytes.

  6. In vitro dissolution study of acetylsalicylic acid solid dispersions. Tunable drug release allowed by the choice of polymer matrix. (United States)

    Policianova, Olivia; Brus, Jiri; Hruby, Martin; Urbanova, Martina


    Abstract Due to their high versatility and diverse excipient options, solid dispersions (SDs) are an elegant choice for the formulation of active pharmaceutical ingredients with inconvenient solubility. Four distinct types of polymers with different physicochemical properties [polyvinylpyrrolidone, poly[N-(2-hydroxypropyl)-metacrylamide], poly(2-ethyl-2-oxazoline), and polyethylene glycol] and variable molecular weights were compared to investigate the influence of the polymer matrix on drug release. To probe the extent of intercomponent interactions, acetylsalicylic acid (ASA) was used as a model active substance. Controlled drug release was demonstrated for all four types of polymer-ASA SDs created by the freeze-drying method. While the polyethylene glycol-ASA SD exhibited an increased dissolution rate, the other polymer-ASA systems exhibited significantly reduced drug dissolution kinetics compared to free ASA. Furthermore, in contrast to physical mixtures, the prepared SDs all exhibited zero-order dissolution kinetics for ASA. The dissolution rate was strongly dependent on the molecular weight of the polymer. These results demonstrate that the type of SD may be controlled by the chemical constitutions of the polymers and that appropriate selection of the molecular weight of the polymer matrix enables finely tuned drug release over a wide range of dissolution rates.

  7. R-matrix calculation of low-energy electron collisions with phosphoric acid

    Energy Technology Data Exchange (ETDEWEB)

    Bryjko, Lilianna; Van Mourik, Tanja [School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST (United Kingdom); Dora, Amar; Tennyson, Jonathan, E-mail: [Department of Physics and Astronomy, University College London, Gower St, London WC1E 6BT (United Kingdom)


    Electron collision calculations are performed on two conformers of H{sub 3}PO{sub 4}, a weakly dipolar form with all OH groups pointing up and a strongly dipolar form where one OH group points down. Strong evidence is found for a broad shape resonance at about 7 eV for both conformers, although the precise parameters of this resonance are sensitive to the details of the target wavefunction used. Ten-state close-coupling calculations suggest the presence of very narrow Feshbach resonances in a similar energy region. Again both conformers behave similarly. Elastic and electronically inelastic cross sections are calculated for both conformers.

  8. The Effects of Various Amendments on Trace Element Stabilization in Acidic, Neutral, and Alkali Soil with Similar Pollution Index. (United States)

    Kim, Min-Suk; Min, Hyun-Gi; Lee, Sang-Hwan; Kim, Jeong-Gyu


    Many studies have examined the application of soil amendments, including pH change-induced immobilizers, adsorbents, and organic materials, for soil remediation. This study evaluated the effects of various amendments on trace element stabilization and phytotoxicity, depending on the initial soil pH in acid, neutral, and alkali conditions. As in all types of soils, Fe and Ca were well stabilized on adsorption sites. There was an effect from pH control or adsorption mechanisms on the stabilization of cationic trace elements from inorganic amendments in acidic and neutral soil. Furthermore, acid mine drainage sludge has shown great potential for stabilizing most trace elements. In a phytotoxicity test, the ratio of the bioavailable fraction to the pseudo-total fraction significantly affected the uptake of trace elements by bok choy. While inorganic amendments efficiently decreased the bioavailability of trace elements, significant effects from organic amendments were not noticeable due to the short-term cultivation period. Therefore, the application of organic amendments for stabilizing trace elements in agricultural soil requires further study.

  9. The Effects of Various Amendments on Trace Element Stabilization in Acidic, Neutral, and Alkali Soil with Similar Pollution Index.

    Directory of Open Access Journals (Sweden)

    Min-Suk Kim

    Full Text Available Many studies have examined the application of soil amendments, including pH change-induced immobilizers, adsorbents, and organic materials, for soil remediation. This study evaluated the effects of various amendments on trace element stabilization and phytotoxicity, depending on the initial soil pH in acid, neutral, and alkali conditions. As in all types of soils, Fe and Ca were well stabilized on adsorption sites. There was an effect from pH control or adsorption mechanisms on the stabilization of cationic trace elements from inorganic amendments in acidic and neutral soil. Furthermore, acid mine drainage sludge has shown great potential for stabilizing most trace elements. In a phytotoxicity test, the ratio of the bioavailable fraction to the pseudo-total fraction significantly affected the uptake of trace elements by bok choy. While inorganic amendments efficiently decreased the bioavailability of trace elements, significant effects from organic amendments were not noticeable due to the short-term cultivation period. Therefore, the application of organic amendments for stabilizing trace elements in agricultural soil requires further study.

  10. Oxidative stress-induced apoptosis and matrix loss of chondrocytes is inhibited by eicosapentaenoic acid. (United States)

    Sakata, Shuhei; Hayashi, Shinya; Fujishiro, Takaaki; Kawakita, Kohei; Kanzaki, Noriyuki; Hashimoto, Shingo; Iwasa, Kenjiro; Chinzei, Nobuaki; Kihara, Shinsuke; Haneda, Masahiko; Ueha, Takeshi; Nishiyama, Takayuki; Kuroda, Ryosuke; Kurosaka, Masahiro


    Eicosapentaenoic acid (EPA) is an antioxidant and n-3 polyunsaturated fatty acid that reduces the production of inflammatory cytokines. We evaluated the role of EPA in chondrocyte apoptosis and degeneration. Normal human chondrocytes were treated with EPA and sodium nitroprusside (SNP). Expression of metalloproteinases (MMPs) was detected by real-time polymerase chain reaction (PCR) and that of apoptosis-related proteins was detected by western blotting. Chondrocyte apoptosis was detected by flow cytometry. C57BL/6J mice were used for the detection of MMP expression by immunohistochemistry and for investigation of chondrocyte apoptosis. EPA inhibited SNP-induced chondrocyte apoptosis, caspase 3 and poly(ADP-ribose) polymerase cleavage, phosphorylation of p38 MAPK and p53, and expression of MMP3 and MMP13. Intra-articular injection of EPA prevented the progression of osteoarthritis (OA) by inhibiting MMP13 expression and chondrocyte apoptosis. EPA treatment can control oxidative stress-induced OA progression, and thus may be a new approach for OA therapy. © 2014 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  11. In Vitro and In Silico Studies of Immobilized Xylanase on Zeolite Matrix Activated with Hydrochloric Acid

    Directory of Open Access Journals (Sweden)

    Janatun Na’imah


    Full Text Available Xylanase is a hydrolase enzyme that can hydrolyze hemicellulose into xilo-oligosaccharide and xylose. This research is aimed to investigate the in vitro and in silico xylanase (isolated from the fungus Trichoderma viride immobilized on the zeolite matrix activated with HCl 0.4 M solution. The study was performed using in silico docking molecular methods to investigate the interaction between the xylanase primarily to its ligand. Xylanase activity was determined by reducing sugar produced (xylose by 1 mL of enzyme per minute. The optimum conditions of immobilized xylanase were measured according to the time agitation and concentration of xylanase. The time variation agitation used were 1, 2, 3, 4, and 5 hours, while variations in the concentrations of a xylanase used were 11.500, 15.653, 20.444, 25.875, and 31.944 mg/mL. The optimum conditions of immobilized xylanase was obtained in the shaking time for 3 hours at a concentration of xylanase 15.653 mg/mL and immobilized xylanase activity generated at 46.755 μg.g-1.min-1. Immobilized xylanase activity was greater than the purified xylanase (15.976 μg.mL-1.min-1. These results were due to the cofactors Al (AlO4 and Si (SiO4 of zeolite was able to increase the kinetic energy caused the reaction rate between xylanase with the larger substrates. Cofactor also increased the kinetic energy and can enhance the rate of reaction between a xylanase with its substrate, in order to give greater activity. Immobilized xylanase was stable and its reusability as much as 6 times which afforded the activity 21.331 μg.g-1.min-1 and the efficiency of 56.77%.

  12. Use of stirred tanks for studying matrix effects caused by inorganic acids, easily ionized elements and organic solvents in inductively coupled plasma atomic emission spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Paredes, Eduardo [Departamento de Quimica Analitica, Nutricion y Bromatologia, University of Alicante, 03080 Alicante (Spain); Maestre, Salvador E. [Departamento de Quimica Analitica, Nutricion y Bromatologia, University of Alicante, 03080 Alicante (Spain); Todoli, Jose L. [Departamento de Quimica Analitica, Nutricion y Bromatologia, University of Alicante, 03080 Alicante (Spain)]. E-mail:


    A stirred tank was used for the first time to elucidate the mechanism responsible for inductively coupled plasma atomic emission spectroscopy (ICP-AES) matrix effects caused by inorganic, acids and easily ionized elements (EIEs), as well as organic, ethanol and acetic acid, compounds. In order to gradually increase the matrix concentration, a matrix solution was introduced inside a stirred container (tank) initially filled with an aqueous multielement standard. PolyTetraFluoroEthylene (PTFE) tubing was used to deliver the resulting solution to the liquid sample introduction system. Matrix concentration ranged from 0 to 2 mol l{sup -1} in the case of inorganic acids (i.e., nitric, sulfuric, hydrochloric and a mixture of them), from 0 to about 2500 mg l{sup -1} for EIEs (i.e., sodium, calcium and mixtures of both) and from 0% to 15%, w/w for organic compounds. Up to 40-50 different solutions were prepared and measured in a period of time shorter than 6-7 min. This investigation was carried out in terms of emission intensity and tertiary aerosols characteristics. The experimental setup used in the present work allowed to thoroughly study the effect of matrix concentration on analytical signal. Generally speaking, the experiments concerning tertiary aerosol characterization revealed that, in the case of inorganic acids and EIEs, the mechanism responsible for changes in aerosol characteristics was the droplet fission. In contrast, for organic matrices it was found that the interference was caused by a change in both aerosol transport and plasma thermal characteristics. The extent of the interferences caused by organic as well as inorganic compounds was compared for a set of 14 emission lines through a wide range of matrix concentrations. With a stirred tank, it is possible to choose an efficient internal standard for any given matrix composition. The time required to complete this procedure was shorter than 7 min.

  13. Detection of single amino acid mutation in human breast cancer by disordered plasmonic self-similar chain

    KAUST Repository

    Coluccio, M. L.


    Control of the architecture and electromagnetic behavior of nanostructures offers the possibility of designing and fabricating sensors that, owing to their intrinsic behavior, provide solutions to new problems in various fields. We show detection of peptides in multicomponent mixtures derived from human samples for early diagnosis of breast cancer. The architecture of sensors is based on a matrix array where pixels constitute a plasmonic device showing a strong electric field enhancement localized in an area of a few square nanometers. The method allows detection of single point mutations in peptides composing the BRCA1 protein. The sensitivity demonstrated falls in the picomolar (10−12 M) range. The success of this approach is a result of accurate design and fabrication control. The residual roughness introduced by fabrication was taken into account in optical modeling and was a further contributing factor in plasmon localization, increasing the sensitivity and selectivity of the sensors. This methodology developed for breast cancer detection can be considered a general strategy that is applicable to various pathologies and other chemical analytical cases where complex mixtures have to be resolved in their constitutive components.

  14. Amino acids supply in culture media is not a limiting factor in the matrix synthesis of engineered cartilage tissue (United States)

    Ng, K. W.; DeFrancis, J. G.; Kugler, L. E.; Kelly, T.-A. N.; Ho, M. M.; O’Conor, C. J.; Ateshian, G. A.; Hung, C. T.


    Summary Increased amino acid supplementation (0.5×, 1.0×, and 5.0× recommended concentrations or additional proline) was hypothesized to increase the collagen content in engineered cartilage. No significant differences were found between groups in matrix content or dynamic modulus. Control constructs possessed the highest compressive Young’s modulus on day 42. On day 42, compared to controls, decreased type II collagen was found with 0.5×, 1.0×, and 5.0× supplementation and significantly increased DNA content found in 1.0× and 5.0×. No effects were observed on these measures with added proline. These results lead us to reject our hypothesis and indicate that the low collagen synthesis in engineered cartilage is not due to a limited supply of amino acids in media but may require a further stimulatory signal. The results of this study also highlight the impact that culture environment can play on the development of engineered cartilage. PMID:17713744

  15. Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire

    DEFF Research Database (Denmark)

    Pletscher-Frankild, Sune; de Boer, Rob J.; Lund, Ole


    Background: Cytotoxic T cell (CTL) cross-reactivity is believed to play a pivotal role in generating immune responses but the extent and mechanisms of CTL cross-reactivity remain largely unknown. Several studies suggest that CTL clones can recognize highly diverse peptides, some sharing no obvious...... sequence identity. The emerging realization in the field is that T cell receptors (TcR) recognize multiple distinct ligands. Principal Findings: First, we analyzed peptide scans of the HIV epitope SLFNTVATL (SFL9) and found that TCR specificity is position dependent and that biochemically similar amino...... to demonstrate that seemingly distinct T cell epitopes, i.e., ones with low sequence identity, are in fact more biochemically similar than expected. Additionally, an analysis of HIV immunogenicity data with our model showed that CTLs have the tendency to respond mostly to peptides that do not resemble self...

  16. Safety and performance of cohesive polydensified matrix hyaluronic acid fillers with lidocaine in the clinical setting – an open-label, multicenter study

    Directory of Open Access Journals (Sweden)

    Kühne U


    Full Text Available Ulrich Kühne,1 Jørgen Esmann,2 Dennis von Heimburg,3 Matthias Imhof,1 Petra Weissenberger,4 Gerhard Sattler,5 On behalf of the BALIA Study Group 1Aesthetische Dermatologie im Medico Palais, Bad Soden, Germany; 2Jørgen Esmann Aps, Hellerup, Denmark; 3Praxisklinik Kaiserplatz, Frankfurt am Main, Germany; 4Corporate Clinical Research, Merz Pharmaceuticals GmbH, Frankfurt am Main, Germany; 5Rosenparkklinik GmbH, Darmstadt, Germany Abstract: Cohesive polydensified matrix (CPM® hyaluronic acid fillers are now available with or without lidocaine. The aim of this study was to investigate the safety and performance of CPM® fillers with lidocaine in the clinical setting. In an open-label, prospective, postmarketing study, 108 patients from seven sites in Germany and Denmark were treated with one or more lidocaine-containing CPM® fillers. Performance was assessed using the Merz Aesthetics Scales® (MAS. Pain was rated on an 11-point visual analog scale. Patients’ and physicians’ satisfaction as well as adverse events were recorded. Improvements of ≥1-point on MAS immediately after and 17 days posttreatment were observed in ~90% of patients compared with baseline. All investigators assessed ejection force, product positioning, and performance as similar or superior to the respective nonlidocaine products. Overall, 94% of investigators were satisfied with the esthetic outcomes and were willing to continue using the products. All patients except one were satisfied with the results, and all were willing to repeat the treatment. Mean pain scores were low during (<3.0 and after injection (<0.6. Except for one case of bruising, all adverse events were mild to moderate. CPM® fillers with lidocaine are safe and effective for a wide range of esthetic facial indications. Keywords: cohesive polydensified matrix, dermal fillers, Belotero, Esthélis, Fortélis, Modélis

  17. Vesiculoviral matrix (M) protein occupies nucleic acid binding site at nucleoporin pair (Rae1∙Nup98)

    Energy Technology Data Exchange (ETDEWEB)

    Quan, Beili; Seo, Hyuk-Soo; Blobel, Günter; Ren, Yi [Rockefeller


    mRNA export factor 1 (Rae1) and nucleoporin 98 (Nup98) are host cell targets for the matrix (M) protein of vesicular stomatitis virus (VSV). How Rae1 functions in mRNA export and how M protein targets both Rae1 and Nup98 are not understood at the molecular level. To obtain structural insights, we assembled a 1:1:1 complex of M•Rae1•Nup98 and established a crystal structure at 3.15-Å resolution. We found that the M protein contacts the Rae1•Nup98 heterodimer principally by two protrusions projecting from the globular domain of M like a finger and thumb. Both projections clamp to the side of the β-propeller of Rae1, with the finger also contacting Nup98. The most prominent feature of the finger is highly conserved Methionine 51 (Met51) with upstream and downstream acidic residues. The complementary surface on Rae1 displays a deep hydrophobic pocket, into which Met51 fastens like a bolt, and a groove of basic residues on either side, which bond to the acidic residues of the finger. Notably, the M protein competed for in vitro binding of various oligonucleotides to Rae1•Nup98. We localized this competing activity of M to its finger using a synthetic peptide. Collectively, our data suggest that Rae1 serves as a binding protein for the phosphate backbone of any nucleic acid and that the finger of M mimics this ligand. In the context of mRNA export, we propose that a given mRNA segment, after having been deproteinated by helicase, is transiently reproteinated by Nup98-tethered Rae1. We suggest that such repetitive cycles provide cytoplasmic stopover sites required for ratcheting mRNA across the nuclear pore.

  18. Effects of spray-drying on w/o/w multiple emulsions prepared from a stearic acid matrix

    Directory of Open Access Journals (Sweden)

    Mlalila N


    Full Text Available Nichrous Mlalila,1 Hulda Swai,2 Lonji Kalombo,2 Askwar Hilonga3 1School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania; 2Materials Science and Manufacturing, Council for Scientific and Industrial Research, Pretoria, South Africa; 3Department of Materials Science and Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania Abstract: The goal of this study was to explore the effects of spray-drying on w/o/w double emulsions of methyltestosterone (MT loaded in a stearic acid matrix. MT-loaded nanoparticles were formulated by a water-in-oil-in-water emulsion technique using 50, 75, and 100 mg of stearic acid, 2% and 3% w/v polyvinyl alcohol, 5% w/v lactose, and 0.2% w/v chitosan. The emulsions were immediately spray-dried based on an optimized model of inlet temperature and pump rate, and characterized for optimized responses with regard to particle size, polydispersity index, and zeta potential, for both emulsion and powder samples. Dynamic light scattering analysis shown that the nanoparticles increased in size with increasing concentrations of polyvinyl alcohol and stearic acid. Scanning electron microscopy indicated that the MT-loaded nanoparticles were spherical in shape, had a smooth surface, and were in an amorphous state, which was confirmed by differential scanning calorimetry. These MT-loaded nanoparticles are a promising candidate carrier for the delivery of MT; however, further studies are needed in order to establish the stability of the system and the cargo release profile under normal conditions of use. Keywords: double emulsions, nanoparticles, pump rate, spray-drying, testosterone

  19. Effect of the medium on intramolecular H-atom tunneling: cis-trans conversion of formic acid in solid matrixes of noble gases. (United States)

    Trakhtenberg, Leonid I; Fokeyev, Anatoly A; Zyubin, Alexander S; Mebel, Alexander M; Lin, S H


    Intramolecular tunneling of a hydrogen atom in formic acid at low temperatures has been studied theoretically on the basis of quantum-chemical modeling of HCOOH@Nb(12) clusters. Three noble matrixes (Ar, Kr, and Xe) are considered. Energetic and geometric parameters as well as vibrational frequencies for the formic acid in cis and trans configurations surrounded by 12 Nb atoms are calculated within the frame of the MP2 approach with extended basis sets. The rate constant of HCOOH cis-trans conversion is analyzed by taking into account matrix reorganization and the change of HCOOH position in the cluster. The matrix reorganization is considered within the Debye model of lattice vibrations, whereas the external motion of HCOOH in the cluster is treated using the Einstein model of solids. It has been shown that the literature experimental data on the cis to trans tunneling reaction in the formic acid can be accounted for within the proposed mechanism, which describes the matrix reorganization and the change of the HCOOH position in the noble gas matrix, with fitting parameters of the suggested theoretical model attaining reasonable values.

  20. Study on the Fouling Behavior of Polyethylene and Silica Nanoparticles Mixed Matrix Membranes in Filtration of Humic Acid Solution

    Directory of Open Access Journals (Sweden)

    Ali Akbari


    Full Text Available Because most contaminants in water create strong interactions with hydrophobic surfaces, there are usually problems such as flux decline and pore blocking in polyethylene (PE membranes due to irreversible adsorption of foulants on their intrinsic hydrophobic surface. Therefore, in this work, attempts were made to improve the properties of PE membranes in terms of water flux and membrane fouling resistance by dispersion of silica nanoparticles (NPs. First, NPs were synthesized by sol-gel method at two concentrations of ammonia (0.5 and 1 mol/L. The synthesized NPs with smaller size were used to fabricate the mixed matrix PE membranes containing 0, 0.5, 1 and 2 wt% NPs. FE-SEM and EDX analyses were employed to evaluate the morphology and structure of the fabricated membranes and confirmed the presence of NPs in the membranes matrix. The results of pure water flux test revealed that the membrane containing 1 wt% NPs displayed the maximum flux of 30 L/m2.h. Furthermore, the performance and fouling behaviors of membranes during filtration of humic acid solution, one of the most important contaminants of water resources, were studied using a classical fouling model. Fouling mechanism analysis showed that for neat and NPs-embedded membranes containing 0.5 and 2 wt% NPs, the best fit of the data was obtained by cake layer formation as well as the intermediate blocking mechanisms. However, the best fit of the experimental data of NPs-embedded membrane containing 1 wt% occurred with only cake layer formation mechanism. The investigation on membrane fouling resistance showed that 1 wt% NPs-embedded membrane displayed 58% maximum flux recovery and 52% reversibility to total fouling ratio, respectively.

  1. Effect of phosphate-based glass fibre surface properties on thermally produced poly(lactic acid) matrix composites. (United States)

    Mohammadi, Maziar Shah; Ahmed, Ifty; Muja, Naser; Rudd, Christopher D; Bureau, Martin N; Nazhat, Showan N


    Incorporation of soluble bioactive glass fibres into biodegradable polymers is an interesting approach for bone repair and regeneration. However, the glass composition and its surface properties significantly affect the nature of the fibre-matrix interface and composite properties. Herein, the effect of Si and Fe on the surface properties of calcium containing phosphate based glasses (PGs) in the system (50P(2)O(5)-40CaO-(10-x)SiO(2)-xFe(2)O(3), where x = 0, 5 and 10 mol.%) were investigated. Contact angle measurements revealed a higher surface energy, and surface polarity as well as increased hydrophilicity for Si doped PG which may account for the presence of surface hydroxyl groups. Two PG formulations, 50P(2)O(5)-40CaO-10Fe(2)O(3) (Fe10) and 50P(2)O(5)-40CaO-5Fe(2)O(3)-5SiO(2) (Fe5Si5), were melt drawn into fibres and randomly incorporated into poly(lactic acid) (PLA) produced by melt processing. The ageing in deionised water (DW), mechanical property changes in phosphate buffered saline (PBS) and cytocompatibility properties of these composites were investigated. In contrast to Fe10 and as a consequence of the higher surface energy and polarity of Fe5Si5, its incorporation into PLA led to increased inorganic/organic interaction indicated by a reduction in the carbonyl group of the matrix. PLA chain scission was confirmed by a greater reduction in its molecular weight in PLA-Fe5Si5 composites. In DW, the dissolution rate of PLA-Fe5Si5 was significantly higher than that of PLA-Fe10. Dissolution of the glass fibres resulted in the formation of channels within the matrix. Initial flexural strength was significantly increased through PGF incorporation. After PBS ageing, the reduction in mechanical properties was greater for PLA-Fe5Si5 compared to PLA-Fe10. MC3T3-E1 preosteoblasts seeded onto PG discs, PLA and PLA-PGF composites were evaluated for up to 7 days indicating that the materials were generally cytocompatible. In addition, cell alignment along the PGF

  2. Delivery of a foreign epitope by sharing amino acid residues with the carrier matrix. (United States)

    Cheong, Wan-Shoo; Drummer, Heidi Edelgard; Netter, Hans-Jürgen


    A broad range of structural viral proteins has the ability to assemble into virus-like particles (VLPs). Under the condition that modified subunits are still competent to assemble into VLPs, they are epitope delivery platforms suitable for vaccination purposes. The insertion of foreign sequences can be detrimental for the formation of chimeric VLPs as a result of misfolded subunit proteins. Hence, a strategy was adopted to screen for locations allowing the use of shared residues between the wildtype subunit sequence and the foreign insert. The insertion of a cysteine-containing sequence of hepatitis C virus (HCV) envelope protein 2 (E2) without adding an additional cysteine residue retained the ability of recombinant small hepatitis B surface antigen (HBsAg-S) to form secretion competent VLPs. A cysteine residue shared by the insert and the template protein avoided the formation of non-native disulfide bonds, and allowed the formation of VLPs. The chimeric HBsAg-S VLPs were similar to wildtype VLPs in density exposing the inserted foreign epitope and being immunogenic. Overall, the use of shared sequences between the insert and the subunit will facilitate the design of chimeric VLPs carrying multiple epitopes.

  3. The Expression of Bone Morphogenetic Protein 2 and Matrix Metalloproteinase 2 through Retinoic Acid Receptor Beta Induced by All-Trans Retinoic Acid in Cultured ARPE-19 Cells.

    Directory of Open Access Journals (Sweden)

    Zhenya Gao

    Full Text Available All-trans retinoic acid (ATRA plays an important role in ocular development. Previous studies found that retinoic acid could influence the metabolism of scleral remodeling by promoting retinal pigment epithelium (RPE cells to secrete secondary signaling factors. The purpose of this study was to investigate whether retinoic acid affected secretion of bone morphogenetic protein 2 (BMP-2 and matrix metalloproteinase 2 (MMP-2 and to explore the signaling pathway of retinoic acid in cultured acute retinal pigment epithelial 19 (ARPE-19 cells.The effects of ATRA (concentrations from 10-9 to 10-5 mol/l on the expression of retinoic acid receptors (RARs in ARPE-19 cells were examined at the mRNA and protein levels using reverse transcription-polymerase chain reaction (RT-PCR and western blot assay, respectively. The effects of treating ARPE-19 cells with ATRA concentrations ranging from 10-9 to 10-5 mol/l for 24 h and 48 h or with 10-6mol/l ATRA at different times ranging from 6h to 72h were assessed using real-time quantitative PCR (qPCR and enzyme-linked immunosorbent assay (ELISA. The contribution of RARβ-induced activation of ARPE-19 cells was confirmed using LE135, an antagonist of RARβ.RARβ mRNA levels significantly increased in the ARPE-19 cells treated with ATRA for 24h and 48h. These increases in RARβ mRNA levels were dose dependent (at concentrations of 10-9 to 10-5 mol/l with a maximum effect observed at 10-6 mol/l. There were no significant changes in the mRNA levels of RARα and RARγ. Western blot assay revealed that RARβ protein levels were increased significantly in a time-dependent manner in ARPE-19 cells treated with 10-6 mol/l ATRA from 12 h to 72 h, with a marked increase observed at 24 h and 48 h. The upregulation of RARβ and the ATRA-induced secretion in ARPE-19 cells could be inhibited by the RARβ antagonist LE135.ATRA induced upregulation of RARβ in ARPE-19 cells and stimulated these cells to secrete BMP-2 and MMP-2.

  4. High-sensitivity matrix-assisted laser desorption/ionization Fourier transform mass spectrometry analyses of small carbohydrates and amino acids using oxidized carbon nanotubes prepared by chemical vapor deposition as matrix. (United States)

    Wang, Cui-hong; Li, Jian; Yao, Sheng-jun; Guo, Yin-long; Xia, Xing-hua


    In matrix-assisted laser desorption/ionization (MALDI) Fourier transform mass spectrometry (FTMS) analyses of small oligosaccharides and amino acids, high sensitivities for oligosaccharides (10 fmol) were obtained by introducing oxidized carbon nanotubes (CNTs) with short and open-end structure as valuable matrix. The CNTs were deposited in porous anodic alumina (PAA) templates by chemical vapor deposition. Transmission electron microscopy (TEM) images show that those CNTs include low levels of amorphous carbon. Thus, the background interference signals generally caused by amorphous carbon powder in CNTs can be reduced effectively. Experiments also confirmed that the FTMS signal intensity of CNTs prepared in PAA template is much lower than that of commercial multi-wall carbon nanotubes (MCNTs). Moreover, the purified process for CNTs with mixed acid (H2SO4 and HNO3) also contributed to the minimization of background. Intense signals corresponding to alkali cation adduct of neutral carbohydrates and amino acids have been acquired. In addition, reliable quantitative analyses for urine and corn root were also achieved successfully. The present work will open a new way to the application of oxidized CNTs as an effective matrix in MALDI MS research.

  5. Anti-inflammatory Chitosan/Poly-γ-glutamic acid nanoparticles control inflammation while remodeling extracellular matrix in degenerated intervertebral disc. (United States)

    Teixeira, Graciosa Q; Leite Pereira, Catarina; Castro, Flávia; Ferreira, Joana R; Gomez-Lazaro, Maria; Aguiar, Paulo; Barbosa, Mário A; Neidlinger-Wilke, Cornelia; Goncalves, Raquel M


    Intervertebral disc (IVD) degeneration is one of the most common causes of low back pain (LBP), the leading disorder in terms of years lived with disability. Inflammation can play a role in LPB, while impairs IVD regeneration. In spite of this, different inflammatory targets have been purposed in the context of IVD regeneration. Anti-inflammatory nanoparticles (NPs) of Chitosan and Poly-(γ-glutamic acid) with a non-steroidal anti-inflammatory drug, diclofenac (Df), were previously shown to counteract a pro-inflammatory response of human macrophages. Here, the effect of intradiscal injection of Df-NPs in degenerated IVD was evaluated. For that, Df-NPs were injected in a bovine IVD organ culture in pro-inflammatory/degenerative conditions, upon stimulation with needle-puncture and interleukin (IL)-1β. Df-NPs were internalized by IVD cells, down-regulating IL-6, IL-8, MMP1 and MMP3, and decreasing PGE2 production, compared with IL-1β-stimulated IVD punches. Interestingly, at the same time, Df-NPs promoted an up-regulation of extracellular matrix (ECM) proteins, namely collagen type II and aggrecan. Allover, this study suggests that IVD treatment with Df-NPs not only reduces inflammation, but also delays and/or decreases ECM degradation, opening perspectives to new intradiscal therapies for IVD degeneration, based on the modulation of inflammation. Degeneration of the IVD is an age-related progressive process considered to be the major cause of spine disorders. The pro-inflammatory environment and biomechanics of the degenerated IVD is a challenge for regenerative therapies. The novelty of this work is the intradiscal injection of an anti-inflammatory therapy based on Chitosan (Ch)/Poly-(γ-glutamic acid) (γ-PGA) nanoparticles (NPs) with an anti-inflammatory drug (diclofenac, Df), previously developed by us. This drug delivery system was tested in a pro-inflammatory/degenerative intervertebral disc ex vivo model. The main findings support the success of an anti

  6. So different and still so similar: The plant compound rosmarinic acid mimics bacterial homoserine lactone quorum sensing signals. (United States)

    Corral-Lugo, Andrés; Daddaoua, Abdelali; Ortega, Alvaro; Espinosa-Urgel, Manuel; Krell, Tino


    Apart from inter-bacteria communication quorum sensing (QS) mechanisms also enable inter-domain interactions. To interfere with bacterial QS, plants were found to secrete compounds; most of which of unknown identity. We have identified the plant compound rosmarinic acid (RA) to modulate Pseudomonas aeruginosa QS by binding to the RhlR QS regulator. RA was found to be a homoserine-lactone (HSL) mimic that caused agonistic effects on transcription, resulting ultimately in a stimulation of several RhlR controlled phenotypes like virulence factor synthesis or biofilm formation. Our study was initiated by in silico screening of an RhlR model with compound libraries, demonstrating that this approach is suitable to tackle a major bottleneck in signal transduction research, which is the identification of sensor protein ligands. Previous work has shown that plant compounds interfere with the function of orphan QS regulators. Our study demonstrates that this has not necessarily to be the case since RhlR forms a functional pair with the RhlI synthase. A wide range of structurally dissimilar compounds have been found to mimic HSLs suggesting that this class of QS regulators is characterized by a significant plasticity in the recognition of effector molecules. Further research will show to what extent RA impacts on QS mechanisms of other bacteria.

  7. Amniotic Fluid or Its Fatty Acids Produce Actions Similar to Diazepam on Lateral Septal Neurons Firing Rate

    Directory of Open Access Journals (Sweden)

    Ana G. Gutiérrez-García


    Full Text Available Human amniotic fluid (AF contains eight fatty acids (FATs, and both produce anxiolytic-like effects in adult rats and appetitive responses in human newborns. The medial amygdala and lateral septal nucleus function are related to social behavior, but the action of AF or its FATs in this circuit is known. We obtained 267 single-unit extracellular recordings in Wistar rats treated with vehicle (1 mL, s.c.; n=12, human AF (1 mL, s.c.; n=12, a FAT mixture (1 mL, s.c.; n=13, diazepam (1 mg/kg, i.p.; n=11, and fluoxetine (1 mg/kg, p.o.; n=12. Compared with the vehicle group, the spontaneous septal firing rate in the AF, FAT mixture, and diazepam groups was the lowest and in the fluoxetine group the highest. Cumulative peristimulus histograms indicated that the significant change in septal firing occurred only in the AF and FAT mixture groups and exclusively in those neurons that increased their firing rate during amygdala stimulation. We conclude that human AF and its FATs produce actions comparable to anxiolytic drugs and are able to modify the responsivity of a circuit involved in social behavior, suggesting facilitation of social recognition processes by maternal-fetal fluids.

  8. Amniotic Fluid or Its Fatty Acids Produce Actions Similar to Diazepam on Lateral Septal Neurons Firing Rate (United States)

    Gutiérrez-García, Ana G.; Vásquez-Hernández, Diana Idania


    Human amniotic fluid (AF) contains eight fatty acids (FATs), and both produce anxiolytic-like effects in adult rats and appetitive responses in human newborns. The medial amygdala and lateral septal nucleus function are related to social behavior, but the action of AF or its FATs in this circuit is known. We obtained 267 single-unit extracellular recordings in Wistar rats treated with vehicle (1 mL, s.c.; n = 12), human AF (1 mL, s.c.; n = 12), a FAT mixture (1 mL, s.c.; n = 13), diazepam (1 mg/kg, i.p.; n = 11), and fluoxetine (1 mg/kg, p.o.; n = 12). Compared with the vehicle group, the spontaneous septal firing rate in the AF, FAT mixture, and diazepam groups was the lowest and in the fluoxetine group the highest. Cumulative peristimulus histograms indicated that the significant change in septal firing occurred only in the AF and FAT mixture groups and exclusively in those neurons that increased their firing rate during amygdala stimulation. We conclude that human AF and its FATs produce actions comparable to anxiolytic drugs and are able to modify the responsivity of a circuit involved in social behavior, suggesting facilitation of social recognition processes by maternal-fetal fluids. PMID:23864826

  9. Influence of vaginal bacteria and D- and L-lactic acid isomers on vaginal extracellular matrix metalloproteinase inducer: implications for protection against upper genital tract infections. (United States)

    Witkin, Steven S; Mendes-Soares, Helena; Linhares, Iara M; Jayaram, Aswathi; Ledger, William J; Forney, Larry J


    We evaluated levels of vaginal extracellular matrix metalloproteinase inducer (EMMPRIN) and matrix metalloproteinase (MMP-8) in vaginal secretions in relation to the composition of vaginal bacterial communities and D- and L-lactic acid levels. The composition of vaginal bacterial communities in 46 women was determined by pyrosequencing the V1 to V3 region of 16S rRNA genes. Lactobacilli were dominant in 71.3% of the women, followed by Gardnerella (17.4%), Streptococcus (8.7%), and Enterococcus (2.2%). Of the lactobacillus-dominated communities, 51.5% were dominated by Lactobacillus crispatus, 36.4% by Lactobacillus iners, and 6.1% each by Lactobacillus gasseri and Lactobacillus jensenii. Concentrations of L-lactic acid were slightly higher in lactobacillus-dominated vaginal samples, but most differences were not statistically significant. D-Lactic acid levels were higher in samples containing L. crispatus than in those with L. iners (Plactic acid in vaginal communities dominated by species of lactobacilli was in concordance with the proportions found in axenic cultures of the various species grown in vitro. Levels of L-lactic acid (Plactic acid to D-lactic acid (P=0.0060), but not concentrations of D-lactic acid, were also correlated with EMMPRIN concentrations. Moreover, vaginal concentrations of EMMPRIN and MMP-8 levels were highly correlated (Plactic acid isomers in the vagina may influence the extent of local EMMPRIN production and subsequent induction of MMP-8. The expression of these proteins may help determine the ability of bacteria to transverse the cervix and initiate upper genital tract infections. A large proportion of preterm births (>50%) result from infections caused by bacteria originating in the vagina, which requires that they traverse the cervix. Factors that influence susceptibility to these infections are not well understood; however, there is evidence that matrix metalloproteinase (MMP-8) is known to alter the integrity of the cervix. In this

  10. The composition of acids in bitumen and in products from saponification of kerogen: Investigation of their role as connecting kerogen and mineral matrix

    Energy Technology Data Exchange (ETDEWEB)

    Razvigorova, M.; Budinova, T.; Tsyntsarski, B.; Petrova, B. [Bulgarian Academy of Sciences, Institute of Organic Chemistry, 1113 Sofia, Acad. Bonchev Str., bl. 9 (Bulgaria); Ekinci, E. [ISIK University, Kumbaba Mevkii, 34980 Istanbul (Turkey); Atakul, H. [Istanbul Technical University, Department of Chemical Engineering, Maslak, 34469 Istanbul (Turkey)


    In order to obtain more information and to understand the nature of relation between organic and mineral matter in oil shales, the compositions of soluble bitumen fractions obtained by extraction from Bulgarian oil shales before and after demineralization with 10% HCl, concentrated HF, and a HF/HCl mixture were investigated. The four extracts were quantitatively examined by IR and {sup 1}H NMR spectroscopy. The investigation of isolated acidic material of the bitumen fractions showed that the fatty acids are present in bitumen fractions as free acids, esters and salts. The amount of free acids in bitumen is very small. The dominant part of bitumen acids is associated with mineral components of the oil shales as well as part of them is included in the mineral matrix, and can be separated only after deep demineralization. The kerogen of the oil shales, obtained after separation of the bitumen fractions and mineral components, was subjected to saponification in order to determine the amount of acids, bound as esters to the kerogen matrix. The major components found were n-carboxylic, {alpha},{omega}-di-carboxylic, and aromatic acids. The connection of kerogen with mineral components is accomplished by the participation of carboxylic and complicated ester bonds. Experimental data for the composition of bitumen acids give evidence that algae and terrestrial materials are initial sources in the formation of soluble organic matter of Bulgarian oil shale. (author)

  11. Mixed matrix membranes with HF acid etched ZSM-5 for ethanol/water separation: Preparation and pervaporation performance (United States)

    Zhan, Xia; Lu, Juan; Tan, Tingting; Li, Jiding


    The mixed matrix membranes (MMMs) were prepared from crosslinked PDMS incorporated with HF acid etched ZSM-5. ZSM-5 zeolite was etched with a series of HF aqueous-acetone solution and characterized by SEM, BET, XRD and FT-IR. It was found that HF etching process was very effective for removing organic impurities in zeolite and micro-pores were observed out of the surface of zeolite particles, which enhanced the hydrophobicity and surface roughness of ZSM-5 successfully. Both tensile strength and swelling resistance of ZSM-5/PDMS MMMs increased with the rising concentration of HF solution, which can mainly be attributed to the improved zeolite-PDMS interfacial adhesion resulted from the intrusion of PDMS into micro-pores out of the ZSM-5 surface. Subsequently, the sorption experiment was performed with the results suggesting preferential sorption of ethanol by MMMs. Moreover, the sorption selectivity of ZSM-5/PDMS MMMs increased notably as the concentration of HF solution increased. The pervaporation performance of ethanol/water mixtures using MMMs was also investigated in detail. The MMMs filled with etched ZSM-5 showed much better selectivity than that filled with non-etched ones, with a little expense of permeability. It was found that with the same zeolite loading, increasing the HF acid concentration in etching process enhanced the zeolite-PDMS interfacial adhesion which promoted the ethanol selectivity of MMMs, while depressed the total permeation flux a little. In addition, both ethanol permeation and the selectivity increased with an increase of the zeolite loading from 10% to 30%. Nevertheless, excessive zeolite loading or decreasing thickness of selective layer led to the poor selectivity to ethanol. A decline of the ethanol selectivity was also observed as the feed ethanol concentration as well as feed temperature increased.

  12. Analysis of acidic carbohydrates as their quaternary ammonium or phosphonium salts by matrix-assisted laser desorption/ionization mass spectrometry. (United States)

    Ueki, Masaaki; Yamaguchi, Miyuki


    New two-component systems using quaternary ammonium or phosphonium salts as a co-matrix have been developed for the analysis of acidic carbohydrates by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). In the analysis of the sodium salt of heparin disaccharide I-S, the combination of 2-amino-5-nitropyridine with tetraphenylphosphonium bromide gave the best result. In the analysis of gangliosides containing the sialic acid moiety, the combination of 2,4,6-trihydroxyacetophenone with dimethyldipalmitylammonium bromide was determined to be the system of choice. Under optimum conditions all acidic carbohydrates gave molecular ions in the form of [M(Q(n))-Q]-, where M(Q(n)) is the molecular mass of a molecule containing n molecules of quaternary ions as salt.

  13. Doehlert matrix design for optimization of the determination of bound deoxynivalenol in barley grain with trifluoroacetic acid (TFA). (United States)

    Zhou, Bing; Li, Yin; Gillespie, James; He, Guo-Qing; Horsley, Richard; Schwarz, Paul


    Fusarium head blight (FHB) is an impediment to barley production in many regions of the world. Tricothecene toxins, associated with FHB-infected grain, particularly, deoxynivalenol (DON), pose a serious threat to human and animal health. Recent research has suggested that a portion of the DON present on grain is bound and escapes detection through conventional determination. The objective of this study was to optimize a method for determination of nonextractable DON in barley grain using trifluoroacetic acid (TFA). A Doehlert matrix design was performed to determine the optimal conditions for time, temperature, and TFA concentration. These conditions were treated with 1.25 N TFA in 86:14 acetontrile/water for 54 min at 133 degrees C. Cleanup, derivatization, and determination of DON by a gas chromatography electron capture detector (GC-ECD) was as normal. Treatment of the test sample resulted in the release of an additional 58% DON under the optimized conditions and an increase of 9-88% in a set of verification samples.

  14. Predict protein structural class for low-similarity sequences by evolutionary difference information into the general form of Chou's pseudo amino acid composition. (United States)

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang


    Knowledge of protein structural class plays an important role in characterizing the overall folding type of a given protein. At present, it is still a challenge to extract sequence information solely using protein sequence for protein structural class prediction with low similarity sequence in the current computational biology. In this study, a novel sequence representation method is proposed based on position specific scoring matrix for protein structural class prediction. By defined evolutionary difference formula, varying length proteins are expressed as uniform dimensional vectors, which can represent evolutionary difference information between the adjacent residues of a given protein. To perform and evaluate the proposed method, support vector machine and jackknife tests are employed on three widely used datasets, 25PDB, 1189 and 640 datasets with sequence similarity lower than 25%, 40% and 25%, respectively. Comparison of our results with the previous methods shows that our method may provide a promising method to predict protein structural class especially for low-similarity sequences. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Similar eicosapentaenoic acid and docosahexaenoic acid plasma levels achieved with fish oil or krill oil in a randomized double-blind four-week bioavailability study. (United States)

    Yurko-Mauro, Karin; Kralovec, Jaroslav; Bailey-Hall, Eileen; Smeberg, Vanessa; Stark, Jeffrey G; Salem, Norman


    Long-chain n-3 polyunsaturated fatty acids (LC n-3-PUFA), docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) provide multiple health benefits for heart, brain and eyes. However, consumption of fatty fish, the main source of LC n-3-PUFAs is low in Western countries. Intakes of LC n-3-PUFA can be increased by taking dietary supplements, such as fish oil, algal oil, or krill oil. Recently, conflicting information was published on the relative bioavailability of these omega-3 supplements. A few studies suggested that the phospholipid form (krill) is better absorbed than the fish oil ethyl ester (EE) or triglyceride (TG) forms. Yet studies did not match the doses administered nor the concentrations of DHA and EPA per supplement across such comparisons, leading to questionable conclusions. This study was designed to compare the oral bioavailability of the same dose of both EPA and DHA in fish oil-EE vs. fish oil-TG vs. krill oil in plasma at the end of a four-week supplementation. Sixty-six healthy adults (n = 22/arm) were enrolled in a double blind, randomized, three-treatment, multi-dose, parallel study. Subjects were supplemented with a 1.3 g/d dose of EPA + DHA (approximately 816 mg/d EPA + 522 mg/d DHA, regardless of formulation) for 28 consecutive days, as either fish oil-EE, fish oil-TG or krill oil capsules (6 caps/day). Plasma and red blood cell (RBC) samples were collected at baseline (pre-dose on Day 1) and at 4, 8, 12, 48, 72, 336, and 672 h. Total plasma EPA + DHA levels at Week 4 (Hour 672) were measured as the primary endpoint. No significant differences in total plasma EPA + DHA at 672 h were observed between fish oil-EE (mean = 90.9 ± 41 ug/mL), fish oil-TG (mean = 108 ± 40 ug/mL), and krill oil (mean = 118.5 ± 48 ug/mL), p = 0.052 and bioavailability differed by oil and krill oil products when matched for dose, EPA, and DHA concentrations in this four week study, indicating comparable oral bioavailability irrespective of formulation

  16. Effect of natural antioxidants in Spanish salchichón elaborated with encapsulated n-3 long chain fatty acids in konjac glucomannan matrix. (United States)

    Munekata, P E S; Domínguez, R; Franco, D; Bermúdez, R; Trindade, M A; Lorenzo, Jose M


    The effect of natural antioxidants on physicochemical properties, lipid and protein oxidation, volatile compounds and free fatty acids (FFA) were determined in Spanish salchichón enriched with n-3 fatty acids encapsulated and stabilized in konjac matrix. Phenolic compounds of beer residue extract (BRE), chestnut leaves extract (CLE) and peanut skin extract (PSE) were also identified and quantified. Five batches of salchichón were prepared: control (CON, without antioxidants), butylated hydroxytoluene (BHT), BRE, CLE and PSE. The main phenolic compounds were catechin and benzoic acid for BRE, gallic acid and catechin for CLE and catechin and protocatechuic acid for PSE. Statistical analysis did not show significant differences on chemical composition among treatments. Reductions in luminosity (Pantioxidants. Finally, the inclusion of antioxidants (P<0.001) decreased the hexanal content, whereas the FFA content increased by the addition of natural extracts. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. The effects of omega-3 Fatty acids on matrix metalloproteinase-9 production and cell migration in human immune cells: implications for multiple sclerosis. (United States)

    Shinto, Lynne; Marracci, Gail; Bumgarner, Lauren; Yadav, Vijayshree


    In multiple sclerosis (MS), compromised blood-brain barrier (BBB) integrity contributes to inflammatory T cell migration into the central nervous system. Matrix metalloproteinase-9 (MMP-9) is associated with BBB disruption and subsequent T cell migration into the CNS. The aim of this paper was to evaluate the effects of omega-3 fatty acids on MMP-9 levels and T cell migration. Peripheral blood mononuclear cells (PBMC) from healthy controls were pretreated with two types of omega-3 fatty acids, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). Cell supernatants were used to determine MMP-9 protein and activity levels. Jurkat cells were pretreated with EPA and DHA and were added to fibronectin-coated transwells to measure T cell migration. EPA and DHA significantly decreased MMP-9 protein levels, MMP-9 activity, and significantly inhibited human T cell migration. The data suggest that omega-3 fatty acids may benefit patients with multiple sclerosis by modulating immune cell production of MMP-9.

  18. Brain docosahexaenoic acid (DHA levels of young rats are related to alpha-linolenic acid (ALA levels and fat matrix of the diet: impact of dairy fat*

    Directory of Open Access Journals (Sweden)

    Delplanque Bernadette


    Full Text Available Dososahexaenoate (DHA is highly concentrated in mammalian nervous and visual systems and its deficiency during gestation, lactation and early life, could have dramatic impacts on brain functions and mental health. Achieving an appropriate DHA status in the neonatal brain is an important goal of neonatal nutrition. We evaluated how a-linolenic acid (ALA provided by different dietary fat matrices improved DHA content in the brains of both young male and female rats. Young rats born from dams fed during gestation and lactation with a low ALA diet (0.4% of fatty acids were subjected for 6 weeks after weaning to an anhydrous dairy fat blend-based diet that provided 1.5% ALA or to a palm oil blend-based diet that provided the same ALA level: either 1.5% ALA or 1.5% ALA and 0.12% DHA with 0.4% arachidonic acid (ARA. With each diet the n-6/ n-3 ratio was similar (10 to follow the values generally recommended for infant formula. Fatty acids analysis in whole brain showed that 1.5% ALA dairy fat blend was superior to both 1.5% ALA palm-oil blends, supplemented or not with dietary DHA, for increasing brain DHA. Females compared to males had significantly higher brain DHA with the 1.5% ALA palm-blend diet, but the dietary supplementation with DHA smoothed the differences by a specific increase of males DHA brain. In conclusion, dairy fat blend enriched with ALA appear to be an interesting strategy for achieving optimal DHA levels in the brain of post-weaning rats. Inclusion of dairy fat in infant formulas should be reconsidered.

  19. Rock specific hydraulic fracturing and matrix acidizing to enhance a geothermal system — Concepts and field results (United States)

    Zimmermann, Günter; Blöcher, Guido; Reinicke, Andreas; Brandt, Wulf


    treatment, a total of 100 ton of high strength proppants was injected with 500 m 3 of cross-linked gel. The subsequent production test in conjunction with flowmeter logging showed an improvement of productivity by a factor of more than 4. Due to assumed residual drilling mud (constituents: calcite, dolomite, and aragonite) in the near-wellbore vicinity, an acid matrix stimulation was performed thereafter using a coil tubing unit. The following nitrogen lift test demonstrated another increase of productivity by 30-50% to an overall increase by a factor of 5.5-6.2.

  20. Detection of Amine Impurity and Quality Assessment of the MALDI Matrix α-Cyano-4-Hydroxy-Cinnamic Acid for Peptide Analysis in the amol Range (United States)

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


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

  1. Wound healing effects of collagen-laminin dermal matrix impregnated with resveratrol loaded hyaluronic acid-DPPC microparticles in diabetic rats. (United States)

    Gokce, Evren H; Tuncay Tanrıverdi, Sakine; Eroglu, Ipek; Tsapis, Nicolas; Gokce, Goksel; Tekmen, Isıl; Fattal, Elias; Ozer, Ozgen


    An alternative formulation for the treatment of diabetic foot wounds that heal slowly is a requirement in pharmaceutical field. The aim of this study was to develop a dermal matrix consisting of skin proteins and lipids with an antioxidant that will enhance healing and balance the oxidative stress in the diabetic wound area due to the high levels of glucose. Thus a novel three dimensional collagen-laminin porous dermal matrix was developed by lyophilization. Resveratrol-loaded hyaluronic acid and dipalmitoylphosphatidylcholine microparticles were combined with this dermal matrix. Characterization, in vitro release, microbiological and in vivo studies were performed. Spherical microparticles were obtained with a high RSV encapsulation efficacy. The microparticles were well dispersed in the dermal matrix from the surface to deeper layers. Collagenase degraded dermal matrix, however the addition of RSV loaded microparticles delayed the degradation time. The release of RSV was sustained and reached 70% after 6h. Histological changes and antioxidant parameters in different treatment groups were investigated in full-thickness excision diabetic rat model. Collagen fibers were intense and improved by the presence of formulation without any signs of inflammation. The highest healing score was obtained with the dermal matrix impregnated with RSV-microparticles with an increased antioxidant activity. Collagen-laminin dermal matrix with RSV microparticles was synergistically effective due to presence of skin components in the formulation and controlled release achieved. This combination is a safe and promising option for the treatment of diabetic wounds requiring long recovery. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Cohesive Polydensified Matrix® hyaluronic acid volumizer injected for cheek augmentation has additional positive effect on nasolabial folds

    Directory of Open Access Journals (Sweden)

    Gauglitz G


    Full Text Available Gerd Gauglitz,1 Stephanie Steckmeier,1 Julian Pötschke,2 Hannah Schwaiger,1 1Department of Dermatology and Allergy, Ludwig-Maximilian University, Munich, Germany; 2Department of Plastic and Hand Surgery, Klinikum St Georg gGmbH, Leipzig, Germany Purpose: Cohesive Polydensified Matrix® hyaluronic acid (CPM-HA volumizer has been used successfully for several years to reverse biometric volume loss during facial aging. This observational study explored the additive effect on nasolabial folds when CPM-HA volumizer is injected into the neighboring cheek area.Patients and methods: In this open-label, prospective, postmarketing noninterventional study, 18 adult patients seeking esthetic enhancement of the lateral cheek hollows and cheekbone area were injected with CPM-HA volumizer integrated with lidocaine (CPM-HA-VL in the upper or lower cheek area. Safety and performance of CPM-HA-VL up to 12 months after injection with follow-up visits at week 4 and month 3, 6, and 12 were assessed. The primary endpoint was improvement of cheek fullness on the validated Merz Aesthetics Scales. Additionally, changes in nasolabial folds were quantified using a phaseshift rapid in vivo measurement of skin optical three-dimensional (3D in vivo measurement device. Results: Patients (94.4% female, median age 52 years, age range 39–69 years were injected with a mean volume of 2.5±1.1 mL CPM-HA-VL per side. Immediately after injection, mean severity for upper and lower cheek fullness assessed on the validated MAS improved from 2.5±0.6 and 2.8±0.5, respectively, to 1.0±0.0, and remained unchanged through month 12. Improvement in relation to baseline was attested on the Global Aesthetics Improvement Scale for all assessments. Compared with baseline, the following assessments offered a statistical significance in the reduction of wrinkle depth of nasolabial folds (maximum depth reduction by 30.4% at 3 months according to optical 3D in vivo measurements. Pain during

  3. Matrix metalloproteinase-9 induces cardiac fibroblast migration, collagen and cytokine secretion: inhibition by salvianolic acid B from Salvia miltiorrhiza. (United States)

    Wang, Yanhui; Xu, Feng; Chen, Jing; Shen, Xu; Deng, Yanping; Xu, Lingling; Yin, Jun; Chen, Hui; Teng, Fukang; Liu, Xuan; Wu, Wanying; Jiang, Baohong; Guo, De-an


    Cardiac fibroblasts play the key role in cardiac function and matrix metalloproteinases-9 (MMP-9) is a well known contributor to the development of myocardial remodeling. However, the direct regulation of MMP-9 on the function of cardiac fibroblasts and the underlying mechanism are far from elucidation. In the present research, recombinant protein encoding catalytic domain of MMP-9 (MMP-9 CD) was constructed and the function of neonatal cardiac fibroblasts was investigated by cell proliferation assay, migration assay, picrosirius red assay, multiplex cytokine assay and fibroblast phenotype detection. 200 nM MMP-9 CD stimulated cardiac fibroblasts migration (169.4±22.5% versus 100±0%, p<0.01), increased collagen synthesis (1.5±0.2 fold, p<0.05), up-regulated the secretion of ICAM (574.0±40.1 versus 268.5±8.6pg/ml, p<0.01), TNF-α (192.6±11.0 versus 14.4±1.8pg/ml, p<0.001), IL-6 (1500.9±70.2 versus 323.4±40.6pg/ml, p<0.001) and sVCAM-1 (30.3±4.3 versus 7.0±0.1 pg/ml, p<0.05) and down-regulated VEGF (436.5±148.9 versus 1034.3±28.1 pg/ml, p<0.05) significantly with modest effects on proliferation. Accompanying with these regulations, transition of fibroblasts to myofibroblast was confirmed by immunofluorescent stain of α-smooth muscle actin (α-SMA) with MMP-9 CD treatment. Furthermore, salvianolic acid B (SalB) inhibited the effects of MMP-9 CD significantly. In conclusion, our results provide evidence for a direct influence of MMP-9 on cardiac fibroblast migration, collagen and cytokine secretion, which can be attenuated by SalB. Copyright © 2011 Elsevier GmbH. All rights reserved.

  4. Effect of acid or alkaline catalyst and of different capping agents on the optical properties of CdS nanoparticles incorporated within a diureasil hybrid matrix (United States)

    Gonçalves, Luis F. F. F.; Silva, Carlos J. R.; Kanodarwala, Fehmida K.; Stride, John A.; Pereira, Mario R.


    CdS nanoparticles (NPs) were synthesized using colloidal methods and incorporated within a diureasil hybrid matrix. The surface capping of the CdS NPs by 3-mercaptopropyltrimethoxysilane (MPTMS) and 3-aminopropyltrimethoxysilane (APTMS) organic ligands during the incorporation of the NPs within the hybrid matrix has been investigated. The matrix is based on poly(ethylene oxide)/poly(propylene oxide) chains grafted to a siliceous skeleton through urea bonds and was produced by sol-gel process. Both alkaline and acidic catalysis of the sol-gel reaction were used to evaluate the effect of each organic ligand on the optical properties of the CdS NPs. The hybrid materials were characterized by absorption, steady-state and time-resolved photoluminescence spectroscopy and High Resolution Transmission Electron Microscopy (HR-TEM). The preservation of the optical properties of the CdS NPs within the diureasil hybrids was dependent on the experimental conditions used. Both organic ligands (APTMS and MPTMS) demonstrated to be crucial in avoiding the increase of size distribution and clustering of the NPs within the hybrid matrix. The use of organic ligands was also shown to influence the level of interaction between the hybrid host and the CdS NPs. The CdS NPs showed large Stokes shifts and long average lifetimes, both in colloidal solution and in the xerogels, due to the origin of the PL emission in surface states. The CdS NPs capped with MPTMS have lower PL lifetimes compared to the other xerogel samples but still larger than the CdS NPs in the original colloidal solution. An increase in PL lifetimes of the NPs after their incorporation within the hybrid matrix is related to interaction between the NPs and the hybrid host matrix.

  5. A biotin-drug extraction and acid dissociation (BEAD) procedure to eliminate matrix and drug interference in a protein complex anti-drug antibody (ADA) isotype specific assay. (United States)

    Niu, Hongmei; Klem, Thomas; Yang, Jinsong; Qiu, Yongchang; Pan, Luying


    Monitoring anti-drug antibody (ADA) responses in patients receiving protein therapeutics treatment is an important safety assessment for regulatory agencies, drug manufacturers, clinicians and patients. Recombinant human IGF-1/IGFBP-3 (rhIGF-1/rhIGFBP-3) is a 1:1 formulation of naturally occurring protein complex. The individual IGF-1 and IGFBP-3 proteins have multiple binding partners in serum matrix with high binding affinity to each other, which presents challenges in ADA assay development. We have developed a biotin-drug extraction with acid dissociation (BEAD) procedure followed by an electrochemiluminescence (ECL) direct assay to overcome matrix and drug interference. The method utilizes two step acid dissociation and excess biotin-drug to extract total ADA, which are further captured by soluble biotin-drug and detected in an ECL semi-homogeneous direct assay format. The pre-treatment method effectively eliminates interference by serum matrix and free drug, and enhances assay sensitivity. The assays passed acceptance criteria for all validation parameters, and have been used for clinical sample Ab testing. This method principle exemplifies a new approach for anti-isotype ADA assays, and could be an effective strategy for neutralizing antibody (NAb), pharmacokinetic (PK) and biomarker analysis in need of overcoming interference factors. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium. (United States)

    Shishkov, Alexander; Bogacheva, Elena; Fedorova, Natalia; Ksenofontov, Alexander; Badun, Gennadii; Radyukhin, Victor; Lukashina, Elena; Serebryakova, Marina; Dolgov, Alexey; Chulichkov, Alexey; Dobrov, Evgeny; Baratova, Lyudmila


    The structure of the C-terminal domain of the influenza virus A matrix M1 protein, for which X-ray diffraction data were still missing, was studied in acidic solution. Matrix M1 protein was bombarded with thermally-activated tritium atoms, and the resulting intramolecular distribution of the tritium label was analyzed to assess the steric accessibility of the amino acid residues in this protein. This technique revealed that interdomain loops and the C-terminal domain of the protein are the most accessible to labeling with tritium atoms. A model of the spatial arrangement of the C-terminal domain of matrix M1 protein was generated using rosetta software adjusted to the data obtained by tritium planigraphy experiments. This model suggests that the C-terminal domain is an almost flat layer with a three-α-helical structure. To explain the high level of tritium label incorporation into the C-terminal domain of the M1 protein in an acidic solution, we also used independent experimental approaches (CD spectroscopy, limited proteolysis and MALDI-TOF MS analysis of the proteolysis products, dynamic light scattering and analytical ultracentrifugation), as well as multiple computational algorithms, to analyse the intrinsic protein disorder. Taken together, the results obtained in the present study indicate that the C-terminal domain is weakly structured. We hypothesize that the specific 3D structural peculiarities of the M1 protein revealed in acidic pH solution allow the protein greater structural flexibility and enable it to interact effectively with the components of the host cell. © 2011 The Authors Journal compilation © 2011 FEBS.

  7. Ammonia-treated N-(1-naphthyl) ethylenediamine dihydrochloride as a novel matrix for rapid quantitative and qualitative determination of serum free fatty acids by matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yaping [Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005 (China); Wang, Yanmin [Department of Clinical Laboratory, Heze Municipal Hospital, Shandong (China); Guo, Shuai; Guo, Yumei; Liu, Hui [Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005 (China); Li, Zhili, E-mail: [Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005 (China)


    Graphical abstract: -- Highlights: •A novel MALDI matrix for the detection of serum free fatty acids is ammonia-treated N-(1-naphthyl) ethylenediamine dihydrochloride. •Multiple point internal standard calibration curves were constructed for nine FFAs, respectively, with excellent correlation coefficients between 0.991 and 0.999. •The MALDI-MS approach was used to rapidly differentiate the patients with and without hyperglycemia and healthy controls. -- Abstract: The blood free fatty acids (FFAs), which provide energy to the cell and act as substrates in the synthesis of fats, lipoproteins, liposaccharides, and eicosanoids, involve in a number of important physiological processes. In the present study, matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS) with ammonia-treated N-(1-naphthyl) ethylenediamine dihydrochloride (ATNEDC) as a novel MALDI matrix in a negative ion mode was employed to directly quantify serum FFAs. Multiple point internal standard calibration curves between the concentration ratios of individual fatty acids to internal standard (IS, C{sub 17:0}) versus their corresponding intensity ratios were constructed for C{sub 14:0}, C{sub 16:1}, C{sub 16:0}, C{sub 18:0}, C{sub 18:1}, C{sub 18:2}, C{sub 18:3}, C{sub 20:4}, and C{sub 22:6}, respectively, in their mixture, with correlation coefficients between 0.991 and 0.999 and limits of detection (LODs) between 0.2 and 5.4 μM, along with the linear dynamic range of more than two orders of magnitude. The results indicate that the multiple point internal standard calibration could reduce the impact of ion suppression and improve quantification accuracy in the MALDI mode. The quantitative results of nine FFAs from 339 serum samples, including 161 healthy controls, 118 patients with hyperglycemia and 60 patients without hyperglycemia show that FFAs levels in hyperglycemic patient sera are significantly higher than those in healthy

  8. Simultaneous determination of bromate, chlorite and haloacetic acids by two-dimensional matrix elimination ion chromatography with coupled conventional and capillary columns. (United States)

    Teh, Hui Boon; Li, Sam Fong Yau


    A new, highly sensitive and reliable two-dimensional matrix elimination ion chromatography (IC) method was developed for simultaneous detection of bromate, chlorite and five haloacetic acids. This method combined the conventional IC in first dimension with capillary IC in the second dimension coupled with suppressed conductivity detection. The first dimension utilizes a high capacity column to partially resolve matrix from target analytes. By optimizing the cut window, the target analytes were selectively cut and trapped in a trap column through the use of a six-port valve, while the separated matrix were diverted to waste. The trapped target analytes were delivered on to the capillary column for further separation and detection. Temperature programming was used to improve selectivity in second dimension column to obtain complete resolution of the target analytes. Compared to the performance of one-dimensional IC, the two-dimensional approach resulted in a significant increase in sensitivity for all target analytes with limit of detection ranging from 0.30 to 0.64μg/L and provided more reliable analysis due to second column confirmation. Good linearity was obtained for all the target analytes with correlation coefficients >0.998. The proposed method was successfully applied to the determination of oxyhalides and haloacetic acids in various matrices with recoveries ranging from 90 to 116% and RSD less than 6.1%. The method allows direct injection of samples and the use of columns with different selectivity, thus significantly reduces the level of false positive results. The method is fully automated and simple, making it practical for routine monitoring of water quality. The satisfactory results also demonstrated that the two-dimensional matrix elimination method coupled with capillary IC is a promising approach for detection of trace substances in complex matrices. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Folic Acid Modulates Matrix Metalloproteinase-2 Expression, Alleviates Neuropathic Pain, and Improves Functional Recovery in Spinal Cord-Injured Rats (United States)

    Miranpuri, Gurwattan S.; Meethal, Sivan Vadakkadath; Sampene, Emmanuel; Chopra, Abhishek; Buttar, Seah; Nacht, Carrie; Moreno, Neydis; Patel, Kush; Liu, Lisa; Singh, Anupama; Singh, Chandra K.; Hariharan, Nithya; Iskandar, Bermans; Resnick, Daniel K.


    Background The molecular underpinnings of spinal cord injury (SCI) associated with neuropathic pain (NP) are unknown. Recent studies have demonstrated that matrix metalloproteinases (MMPs) such as MMP2 play a critical role in inducing NP following SCI. Promoter methylation of MMPs is known to suppress their transcription and reduce NP. In this context, it has been shown in rodents that folic acid (FA), an FDA approved dietary supplement and key methyl donor in the central nervous system (CNS), increases axonal regeneration and repair of injured CNS in part via methylation. Purpose Based on above observations, in this study, we test whether FA could decrease MMP2 expression and thereby decrease SCI-induced NP. Methods Sprague-Dawley male rats weighing 250–270 g received contusion spinal cord injuries (cSCIs) with a custom spinal cord impactor device that drops a 10 g weight from a height of 12.5 mm. The injured rats received either i.p. injections of FA (80 µg/kg) or water (control) 3 days prior and 17 days post-cSCI (mid phase) or for 3 days pre-cSCI and 14 days post-cSCI ending on the 42nd day of cSCI (late phase). The functional neurological deficits due to cSCI were then assessed by Basso, Beattie, and Bresnahan (BBB) scores either on post-impaction days 0 through 18 post-cSCI (mid phase) or on days 0, 2, 7, 14, 21, 28, 35, and 42 (late phase). Baseline measurements were taken the day before starting treatments. Thermal hyperalgesia (TH) testing for pain was performed on 4 days pre-cSCI (baseline data) and on days 18, 21, 28, 35, and 42 post-cSCI. Following TH testing, animals were euthanized and spinal cords harvested for MMP-2 expression analysis. Result The FA-treated groups showed higher BBB scores during mid phase (day 18) and in late phase (day 42) of injury compared to controls, suggesting enhanced functional recovery. There is a transient decline in TH in animals from the FA-treated group compared to controls when tested on days 18, 21, 28, and 35

  10. Influence of the composition of hydroxypropyl cellulose/maleic acid-alt-styrene copolymer blends on their properties as matrix for drug release

    Directory of Open Access Journals (Sweden)


    Full Text Available Poly(carboxylic acid-polysaccharide compositions have been found suitable for obtaining drug formulations with controlled release, most formulations being therapeutically efficacious, stable, and non-irritant. The influence of the characteristics of the aqueous solutions from which the polymer matrix is prepared (i.e. the total concentration of polymer in solutions and the mixing ratio between the partners, hydroxypropyl cellulose, HPC and maleic acid-alternating-styrene copolymer, MAc-alt-S on the kinetics of some drugs release in acidic environment (pH = 2 has been followed by ‘in vitro’ dissolution tests. It has been established that the kinetics of procaine hydrochloride release from HPC/MAc-alt-S matrix depends on its composition; the diffusion exponent, n is close to 0.5 for matrices where one of the components is in large excess and n~0.02 for middle composition range. The lower value of diffusion exponent for middle composition range could be caused by the so called ‘burst effect’, therefore the kinetic evaluation is difficult.

  11. Ammonia-treated N-(1-naphthyl) ethylenediamine dihydrochloride as a novel matrix for rapid quantitative and qualitative determination of serum free fatty acids by matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry. (United States)

    Zhang, Yaping; Wang, Yanmin; Guo, Shuai; Guo, Yumei; Liu, Hui; Li, Zhili


    The blood free fatty acids (FFAs), which provide energy to the cell and act as substrates in the synthesis of fats, lipoproteins, liposaccharides, and eicosanoids, involve in a number of important physiological processes. In the present study, matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS) with ammonia-treated N-(1-naphthyl) ethylenediamine dihydrochloride (ATNEDC) as a novel MALDI matrix in a negative ion mode was employed to directly quantify serum FFAs. Multiple point internal standard calibration curves between the concentration ratios of individual fatty acids to internal standard (IS, C17:0) versus their corresponding intensity ratios were constructed for C14:0, C16:1, C16:0, C18:0, C18:1, C18:2, C18:3, C20:4, and C22:6, respectively, in their mixture, with correlation coefficients between 0.991 and 0.999 and limits of detection (LODs) between 0.2 and 5.4μM, along with the linear dynamic range of more than two orders of magnitude. The results indicate that the multiple point internal standard calibration could reduce the impact of ion suppression and improve quantification accuracy in the MALDI mode. The quantitative results of nine FFAs from 339 serum samples, including 161 healthy controls, 118 patients with hyperglycemia and 60 patients without hyperglycemia show that FFAs levels in hyperglycemic patient sera are significantly higher than those in healthy controls and patients without hyperglycemia, and elevated FFA levels are also associated with increased levels of fasting blood glucose (FBG) in hyperglycemic patient sera. Serum FFAs were identified on the basis of the observed accurate molecular masses and reliable isotope distributions obtained by MALDI-FTICR MS. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. The Effects of Omega-3 Fatty Acids on Matrix Metalloproteinase-9 Production and Cell Migration in Human Immune Cells: Implications for Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Lynne Shinto


    Full Text Available In multiple sclerosis (MS, compromised blood-brain barrier (BBB integrity contributes to inflammatory T cell migration into the central nervous system. Matrix metalloproteinase-9 (MMP-9 is associated with BBB disruption and subsequent T cell migration into the CNS. The aim of this paper was to evaluate the effects of omega-3 fatty acids on MMP-9 levels and T cell migration. Peripheral blood mononuclear cells (PBMC from healthy controls were pretreated with two types of omega-3 fatty acids, eicosapentaenoic acid (EPA, and docosahexaenoic acid (DHA. Cell supernatants were used to determine MMP-9 protein and activity levels. Jurkat cells were pretreated with EPA and DHA and were added to fibronectin-coated transwells to measure T cell migration. EPA and DHA significantly decreased MMP-9 protein levels, MMP-9 activity, and significantly inhibited human T cell migration. The data suggest that omega-3 fatty acids may benefit patients with multiple sclerosis by modulating immune cell production of MMP-9.

  13. RARα2 and PML-RAR similarities in the control of basal and retinoic acid induced myeloid maturation of acute myeloid leukemia cells (United States)

    Gianni, Maurizio; Fratelli, Maddalena; Bolis, Marco; Kurosaki, Mami; Zanetti, Adriana; Paroni, Gabriela; Rambaldi, Alessandro; Borleri, Gianmaria; Rochette-Egly, Cecile; Terao, Mineko; Garattini, Enrico


    Treatment of acute promyelocytic leukemia (APL) with all-trans retinoic acid (ATRA) is the first example of targeted therapy. In fact, the oncogenic fusion-protein (PML-RAR) typical of this leukemia contains the retinoid-nuclear-receptor RARα. PML-RAR is responsible for the differentiation block of the leukemic blast. Besides PML-RAR, two endogenous RARα proteins are present in APL blasts, i.e. RARα1 and RARα2. We developed different cell populations characterized by PML-RAR, RARα2 and RARα1 knock-down in the APL-derived NB4 cell-line. Unexpectedly, silencing of PML-RAR and RARα2 results in similar increases in the constitutive expression of several granulocytic differentiation markers. This is accompanied by enhanced expression of the same granulocytic markers upon exposure of the NB4 blasts to ATRA. Silencing of PML-RAR and RARα2 causes also similar perturbations in the whole genome gene-expression profiles of vehicle and ATRA treated NB4 cells. Unlike PML-RAR and RARα2, RARα1 knock-down blocks ATRA-dependent induction of several granulocytic differentiation markers. Many of the effects on myeloid differentiation are confirmed by over-expression of RARα2 in NB4 cells. RARα2 action on myeloid differentiation does not require the presence of PML-RAR, as it is recapitulated also upon knock-down in PML-RAR-negative HL-60 cells. Thus, relative to RARα1, PML-RAR and RARα2 exert opposite effects on APL-cell differentiation. These contrasting actions may be related to the fact that both PML-RAR and RARα2 interact with and inhibit the transcriptional activity of RARα1. The interaction surface is located in the carboxy-terminal domain containing the D/E/F regions and it is influenced by phosphorylation of Ser-369 of RARα1. PMID:27419624

  14. Effects of dietary palmitoleic acid on plasma lipoprotein profile and aortic cholesterol accumulation are similar to those of other unsaturated fatty acids in the F1B golden Syrian hamster. (United States)

    Matthan, Nirupa R; Dillard, Alice; Lecker, Jaime L; Ip, Blanche; Lichtenstein, Alice H


    The lower susceptibility of palmitoleic acid (16:1) to oxidation compared to PUFA may confer functional advantages with respect to finding acceptable alternatives to partially hydrogenated fats, but limited data are available on its effect on cardiovascular risk factors. This study investigated the effect of diets (10% fat, 0.1% cholesterol, wt:wt) enriched with macadamia [monounsaturated fatty acid (MUFA)16:1], palm (SFA,16:0), canola (MUFA,18:1), or safflower (PUFA,18:2) oils on lipoprotein profiles and aortic cholesterol accumulation in F1B Golden Syrian hamsters (n = 16/group). After 12 wk, 8 hamsters in each group were killed (phase 1). The remaining hamsters fed palm oil were changed to a diet containing coconut oil, while hamsters in the other diet groups continued on their original diets for an additional 6 wk (phase 2). With minor exceptions, the time course and dietary SFA source did not alter the study outcomes. Macadamia oil-fed hamsters had lower non-HDL cholesterol and triglyceride concentrations compared with the palm and coconut oil-fed hamsters and higher HDL-cholesterol compared with the coconut, canola, and safflower oil-fed hamsters. The aortic cholesterol concentration was not affected by dietary fat type. The hepatic cholesterol concentration was higher in the unsaturated compared with the saturated oil-fed hamsters. RBC membrane and aortic cholesteryl ester, triglyceride, and phospholipid fatty acid profiles reflected that of the dietary oil. These data suggest that an oil relatively high in palmitoleic acid does not adversely affect plasma lipoprotein profiles or aortic cholesterol accumulation and was similar to other unsaturated fatty acid-rich oils.

  15. Effects of Dietary Palmitoleic Acid on Plasma Lipoprotein Profile and Aortic Cholesterol Accumulation Are Similar to Those of Other Unsaturated Fatty Acids in the F1B Golden Syrian Hamster 1–3 (United States)

    Matthan, Nirupa R.; Dillard, Alice; Lecker, Jaime L.; Ip, Blanche; Lichtenstein, Alice H.


    The lower susceptibility of palmitoleic acid (16:1) to oxidation compared to PUFA may confer functional advantages with respect to finding acceptable alternatives to partially hydrogenated fats, but limited data are available on its effect on cardiovascular risk factors. This study investigated the effect of diets (10% fat, 0.1% cholesterol, wt:wt) enriched with macadamia [monounsaturated fatty acid (MUFA)16:1], palm (SFA,16:0), canola (MUFA,18:1), or safflower (PUFA,18:2) oils on lipoprotein profiles and aortic cholesterol accumulation in F1B Golden Syrian hamsters (n = 16/group). After 12 wk, 8 hamsters in each group were killed (phase 1). The remaining hamsters fed palm oil were changed to a diet containing coconut oil, while hamsters in the other diet groups continued on their original diets for an additional 6 wk (phase 2). With minor exceptions, the time course and dietary SFA source did not alter the study outcomes. Macadamia oil-fed hamsters had lower non-HDL cholesterol and triglyceride concentrations compared with the palm and coconut oil-fed hamsters and higher HDL-cholesterol compared with the coconut, canola, and safflower oil-fed hamsters. The aortic cholesterol concentration was not affected by dietary fat type. The hepatic cholesterol concentration was higher in the unsaturated compared with the saturated oil-fed hamsters. RBC membrane and aortic cholesteryl ester, triglyceride, and phospholipid fatty acid profiles reflected that of the dietary oil. These data suggest that an oil relatively high in palmitoleic acid does not adversely affect plasma lipoprotein profiles or aortic cholesterol accumulation and was similar to other unsaturated fatty acid-rich oils. PMID:19106316

  16. Grain-based versus alfalfa-based subacute ruminal acidosis induction experiments: Similarities and differences between changes in milk fatty acids. (United States)

    Colman, E; Khafipour, E; Vlaeminck, B; De Baets, B; Plaizier, J C; Fievez, V


    Subacute ruminal acidosis (SARA) is one of the most important metabolic disorders, traditionally characterized by low rumen pH, which might be induced by an increase in the dietary proportion of grains as well as by a reduction of structural fiber. Both approaches were used in earlier published experiments in which SARA was induced by replacing part of the ration by a grain mixture or alfalfa hay by alfalfa pellets. The main differences between both experiments were the presence of blood lipopolysaccharide and Escherichia coli and associated effects on the rumen microbial population in the rumen of grain-based induced SARA animals as well as a great amount of quickly fermentable carbohydrates in the grain-based SARA induction experiment. Both induction approaches changed rumen pH although the pH decrease was more substantial in the alfalfa-based SARA induction protocol. The goal of the current analysis was to assess whether both acidosis induction approaches provoked similar shifts in the milk fatty acid (FA) profile. Similar changes of the odd- and branched-chain FA and the C18 biohydrogenation intermediates were observed in the alfalfa-based SARA induction experiment and the grain-based SARA induction experiment, although they were more pronounced in the former. The proportion of trans-10 C18:1 in the last week of the alfalfa-based induction experiment was 6 times higher than the proportion measured during the control week. The main difference between both induction experiments under similar rumen pH changes was the decreasing sum of iso FA during the grain-based SARA induction experiment whereas the sum of iso FA remained stable during the alfalfa-based SARA induction experiment. The cellulolytic bacterial community seemed to be negatively affected by either the presence of E. coli and the associated lipopolysaccharide accumulation in the rumen or by the amount of starch and quickly fermentable carbohydrates in the diet. In general, changes in the milk FA


    Energy Technology Data Exchange (ETDEWEB)

    Lambert, D.; Stone, M.; Newell, J.; Best, D.


    Savannah River Remediation (SRR) is evaluating changes to its current DWPF flowsheet to improve processing cycle times. This will enable the facility to support higher canister production while maximizing waste loading. Higher throughput is needed in the CPC since the installation of the bubblers into the melter has increased melt rate. Due to the significant maintenance required for the DWPF gas chromatographs (GC) and the potential for production of flammable quantities of hydrogen, reducing or eliminating the amount of formic acid used in the CPC is being developed. Earlier work at Savannah River National Laboratory has shown that replacing formic acid with an 80:20 molar blend of glycolic and formic acids has the potential to remove mercury in the SRAT without any significant catalytic hydrogen generation. This report summarizes the research completed to determine the feasibility of processing without formic acid. In earlier development of the glycolic-formic acid flowsheet, one run (GF8) was completed without formic acid. It is of particular interest that mercury was successfully removed in GF8, no formic acid at 125% stoichiometry. Glycolic acid did not show the ability to reduce mercury to elemental mercury in initial screening studies, which is why previous testing focused on using the formic/glycolic blend. The objective of the testing detailed in this document is to determine the viability of the nitric-glycolic acid flowsheet in processing sludge over a wide compositional range as requested by DWPF. This work was performed under the guidance of Task Technical and Quality Assurance Plan (TT and QAP). The details regarding the simulant preparation and analysis have been documented previously.

  18. Influence of seeding density and extracellular matrix on bile Acid transport and mrp4 expression in sandwich-cultured mouse hepatocytes. (United States)

    Swift, Brandon; Brouwer, Kim L R


    This study was undertaken to examine the influence of seeding density, extracellular matrix and days in culture on bile acid transport proteins and hepatobiliary disposition of the model bile acid taurocholate. Mouse hepatocytes were cultured in a sandwich configuration on six-well Biocoat plates with an overlay of Matrigel (BC/MG) or gelled-collagen (BC/GC) for 3 or 4 days at seeding densities of 1.0, 1.25, or 1.5 x 10(6) cells/well. The lower seeding densities of 1.0 and 1.25 x 10(6) cells/well resulted in good hepatocyte morphology and bile canalicular network formation, as visualized by 5-(and 6)-carboxy-2',7'-dichlorofluorescein accumulation. In general, taurocholate cellular accumulation tended to increase as a function of seeding density in BC/GC; cellular accumulation was significantly increased in hepatocytes cultured in BC/MG compared to BC/GC at the same seeding density on both days 3 and 4 of culture. In general, in vitro intrinsic biliary clearance of taurocholate was increased at higher seeding densities. Levels of bile acid transport proteins on days 3 and 4 were not markedly influenced by seeding density or extracellular matrix except for multidrug resistance protein 4 (Mrp4), which was inversely related to seeding density. Mrp4 levels decreased approximately 2- to 3-fold between seeding densities of 1.0 x 10(6) and 1.25 x 10(6) cells/well regardless of extracellular matrix; an additional approximately 3- to 5-fold decrease in Mrp4 protein was noted in BC/GC between seeding densities of 1.25 x 10(6) and 1.5 x 10(6) cells/well. Results suggest that seeding density, extracellular matrix and days in culture profoundly influence Mrp4 expression in sandwich-cultured mouse hepatocytes. Primary mouse hepatocytes seeded in a BC/MG configuration at densities of 1.25 x 10(6) cells/well and 1.0 x 10(6), and cultured for 3 days, yielded optimal transport based on the probes studied. This work demonstrates the applicability of the sandwich-cultured model to

  19. Mixed-matrix membranes with enhanced antifouling activity: probing the surface-tailoring potential of Tiron and chromotropic acid for nano-TiO2. (United States)

    Pal, Avishek; Dey, T K; Debnath, A K; Bhushan, Bharat; Sahu, A K; Bindal, R C; Kar, Soumitra


    Mixed-matrix membranes (MMMs) were developed by impregnating organofunctionalized nanoadditives within fouling-susceptible polysulfone matrix following the non-solvent induced phase separation (NIPS) method. The facile functionalization of nanoparticles of anatase TiO2 (nano-TiO2) by using two different organoligands, viz. Tiron and chromotropic acid, was carried out to obtain organofunctionalized nanoadditives, FT-nano-TiO2 and FC-nano-TiO2, respectively. The structural features of nanoadditives were evaluated by X-ray diffraction, X-ray photoelectron spectroscopy, Raman and Fourier transform infrared spectroscopy, which established that Tiron leads to the blending of chelating and bridging bidentate geometries for FT-nano-TiO2, whereas chromotropic acid produces bridging bidentate as well as monodentate geometries for FC-nano-TiO2. The surface chemistry of the studied membranes, polysulfone (Psf): FT-nano-TiO2 UF and Psf: FC-nano-TiO2 UF, was profoundly influenced by the benign distributions of the nanoadditives enriched with distinctly charged sites ([Formula: see text]), as evidenced by superior morphology, improved topography, enhanced surface hydrophilicity and altered electrokinetic features. The membranes exhibited enhanced solvent throughputs, viz. 3500-4000 and 3400-4300 LMD at 1 bar of transmembrane pressure, without significant compromise in their rejection attributes. The flux recovery ratios and fouling resistive behaviours of MMMs towards bovine serum albumin indicated that the nanoadditives could impart stable and appreciable antifouling activity, potentially aiding in a sustainable ultrafiltration performance.

  20. Mixed-matrix membranes with enhanced antifouling activity: probing the surface-tailoring potential of Tiron and chromotropic acid for nano-TiO2 (United States)

    Pal, Avishek; Dey, T. K.; Debnath, A. K.; Bhushan, Bharat; Sahu, A. K.; Bindal, R. C.; Kar, Soumitra


    Mixed-matrix membranes (MMMs) were developed by impregnating organofunctionalized nanoadditives within fouling-susceptible polysulfone matrix following the non-solvent induced phase separation (NIPS) method. The facile functionalization of nanoparticles of anatase TiO2 (nano-TiO2) by using two different organoligands, viz. Tiron and chromotropic acid, was carried out to obtain organofunctionalized nanoadditives, FT-nano-TiO2 and FC-nano-TiO2, respectively. The structural features of nanoadditives were evaluated by X-ray diffraction, X-ray photoelectron spectroscopy, Raman and Fourier transform infrared spectroscopy, which established that Tiron leads to the blending of chelating and bridging bidentate geometries for FT-nano-TiO2, whereas chromotropic acid produces bridging bidentate as well as monodentate geometries for FC-nano-TiO2. The surface chemistry of the studied membranes, polysulfone (Psf): FT-nano-TiO2 UF and Psf: FC-nano-TiO2 UF, was profoundly influenced by the benign distributions of the nanoadditives enriched with distinctly charged sites (-SO3 -H+ ), as evidenced by superior morphology, improved topography, enhanced surface hydrophilicity and altered electrokinetic features. The membranes exhibited enhanced solvent throughputs, viz. 3500-4000 and 3400-4300 LMD at 1 bar of transmembrane pressure, without significant compromise in their rejection attributes. The flux recovery ratios and fouling resistive behaviours of MMMs towards bovine serum albumin indicated that the nanoadditives could impart stable and appreciable antifouling activity, potentially aiding in a sustainable ultrafiltration performance.

  1. Effect of pioglitazone, quercetin and hydroxy citric acid on extracellular matrix components in experimentally induced non-alcoholic steatohepatitis

    Directory of Open Access Journals (Sweden)

    Surapaneni Krishna Mohan


    Results:The experimental NASH rats treated with pioglitazone showed significant decrease in the levels of hyaluronic acid and significant increase in adiponectin levels when compared to experimentally induced NASH group, but did not show any effect on the levels of leptin. Contrary to these two drugs, viz. pioglitazone and hydroxy citric acid, the group treated with quercetin showedsignificant decrease in the levels of hyaluronic acid and leptin and significant decrease in adiponectin levels compared with that of experimentally induced NASH NASH group, offering maximum protection against NASH. Conclusion: Considering our findings, it could be concluded that quercetin may offer maximum protection against NASH by significantly increasing the levels of adiponectin, when compared to pioglitazone and hydroxy citric acid.

  2. Similar effect of revascularization on technetium-99 m sestamibi and 15-(p-iodophenyl)pentadecanoic acid uptake in myocardial infarction patiients

    Energy Technology Data Exchange (ETDEWEB)

    Bendel, S.; Kettunen, R.; Hartikainen, J.; Remes, J. [Department of Medicine, Kuopio University Hospital, Kuopio (Finland); Vanninen, E.; Yang, J.; Kuikka, J. [Department of Clinical Physiology, Kuopio University Hospital, Kuopio (Finland); Huikuri, H. [Department of Medicine, Oulu University Hospital, Oulu (Finland)


    To study its usefulness as a tracer for assessment of the perfusion and viability of myocardium, 15-(p-iodophenyl)pentadecanoic acid (IPPA) was compared with technetium-99m sestamibi (MIBI). Dual-tracer single-photon emission tomography rest imaging was performed no more than 2 months before and 3 months after coronary artery bypass grafting in 28 patients with previous anterior (n=13) or inferior (n=15) infarction. The size of MIBI and IPPA defects decreased from 14%{+-}12% and 13%{+-}9% to 10%{+-}11% and 9%{+-}7%, respectively (P<0.001 for both). The MIBI uptake increased in the infarct zones from 35%{+-}11% to 43%{+-}8% (P<0.001), and in the peri-infarct zones from 50%{+-}11% to 55%{+-}10% (P<0.05). The IPPA uptake increased in the infarct zones from 37%{+-}11% to 44%{+-}13% (P<0.001), and in the peri-infarct zones from 51%{+-}11% to 57%{+-}12% (P<0.05). In nine patients with improved regional echocardiographic wall motion score after bypass surgery, the pre-operative uptake values of both MIBI and IPPA in the infarct and peri-infarct zones were on average slightly but not significantly higher than in 19 patients with no observed improvement in regional wall motion score. In patients with improved regional wall motion, the MIBI scans and the IPPA scans showed (non-significant) decreases in defect size and increases in infarct and peri-infarct zone uptake after bypass surgery. Similar (in some cases significant) changes were observed in the patients without improvement in wall motion. Thus IPPA and MIBI provided similar information about perfusion and viability in pre- and postoperative evaluation of patients with clinically evident myocardial infarction and with normal global ejection fraction. Regardless of the tracer used, the resolution capability of the dual-tracer method with a rest imaging protocol was not sufficient to differentiate viable from non-viable infarction defects in unselected individual patients with a normal ejection fraction. (orig.)

  3. Beneficial effects of retinoic acid on extracellular matrix degradation and attachment behaviour in follicular thyroid carcinoma cell lines

    NARCIS (Netherlands)

    Havekes, B.; Schröder van der Elst, J. P.; van der Pluijm, G.; Goslings, B. M.; Romijn, J. A.; Smit, J. W.


    The prognosis of patients with metastasised follicular thyroid carcinoma (FTC) is limited, necessitating the search for new treatment options. Beneficial effects of retinoids have been suggested in thyroid cancer and the present study was performed to investigate the effects of retinoic acid (RA) on

  4. Profiling the Fatty Acids Content of Ornamental Camellia Seeds Cultivated in Galicia by an Optimized Matrix Solid-Phase Dispersion Extraction

    Directory of Open Access Journals (Sweden)

    Carmen Garcia-Jares


    Full Text Available Camellia (genus of flowering plants of fam. Theaceae is one of the main crops in Asia, where tea and oil from leaves and seeds have been utilized for thousands of years. This plant is excellently adapted to the climate and soil of Galicia (northwestern Spain and northern Portugal where it is grown not only as an ornamental plant, but to be evaluated as a source of bioactive compounds. In this work, the main fatty acids were extracted from Camellia seeds of four varieties of Camellia: sasanqua, reticulata, japonica and sinensis, by means of matrix-solid phase dispersion (MSPD, and analyzed by gas chromatography (GC with MS detection of the corresponding methyl esters. MSPD constitutes an efficient and greener alternative to conventional extraction techniques, moreover if it is combined with the use of green solvents such as limonene. The optimization of the MSPD extraction procedure has been conducted using a multivariate approach based on strategies of experimental design, which enabled the simultaneous evaluation of the factors influencing the extraction efficiency as well as interactions between factors. The optimized method was applied to characterize the fatty acids profiles of four Camellia varieties seeds, allowing us to compare their fatty acid composition.

  5. Profiling the Fatty Acids Content of Ornamental Camellia Seeds Cultivated in Galicia by an Optimized Matrix Solid-Phase Dispersion Extraction. (United States)

    Garcia-Jares, Carmen; Sanchez-Nande, Marta; Lamas, Juan Pablo; Lores, Marta


    Camellia (genus of flowering plants of fam. Theaceae ) is one of the main crops in Asia, where tea and oil from leaves and seeds have been utilized for thousands of years. This plant is excellently adapted to the climate and soil of Galicia (northwestern Spain) and northern Portugal where it is grown not only as an ornamental plant, but to be evaluated as a source of bioactive compounds. In this work, the main fatty acids were extracted from Camellia seeds of four varieties of Camellia : sasanqua , reticulata , japonica and sinensis , by means of matrix-solid phase dispersion (MSPD), and analyzed by gas chromatography (GC) with MS detection of the corresponding methyl esters. MSPD constitutes an efficient and greener alternative to conventional extraction techniques, moreover if it is combined with the use of green solvents such as limonene. The optimization of the MSPD extraction procedure has been conducted using a multivariate approach based on strategies of experimental design, which enabled the simultaneous evaluation of the factors influencing the extraction efficiency as well as interactions between factors. The optimized method was applied to characterize the fatty acids profiles of four Camellia varieties seeds, allowing us to compare their fatty acid composition.

  6. A simple method for the determination of glyphosate and aminomethylphosphonic acid in seawater matrix with high performance liquid chromatography and fluorescence detection. (United States)

    Wang, Shu; Liu, Baomin; Yuan, Dongxing; Ma, Jian


    Glyphosate (GLYP) is an important herbicide which is also used as the phosphorus source for marine organisms. The wide applications of GLYP can lead to its accumulation in oceans and coastal waters, thus creating environmental issues. However, there is limited methods for detection of GLYP and its degradation product, aminomethylphosphonic acid (AMPA) in saline samples. Therefore, a simple and fast method for the quantification of GLYP and AMPA in seawater matrix has been developed based on the derivatization with 9-fluorenylmethylchloroformate (FMOC-Cl), separation with high performance liquid chromatography (HPLC) and detection with fluorescence detector (FLD). In order to maximize sensitivity, the derivatization procedure was carefully optimized regarding concentration of FMOC-Cl, volume of borate buffer, pH of borate buffer, mixing and derivatization time. The derivatization reaction could be completed within 30min in seawater samples without any additional clean-up or desalting steps. Under the optimized conditions, the developed HPLC method showed a wide linear response (up to several mg/L, R 2 >0.99). The limits of detection were 0.60μg/L and 0.30μg/L for GLYP and AMPA in seawater matrix, respectively. The relative standard deviation was 14.0% for GLYP (1.00mg/L) and 3.1% for AMPA (100μg/L) in saline samples with three different operators (n=24). This method was applied to determine the concentration of GLYP and AMPA in seawater culture media and the recovery data indicated minimal matrix interference. Due to its simplicity, high reproducibility and successful application in seawater culture media analysis, this method is a potentially useful analytical technique for both marine research and environmental science. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. A Similarity Search Using Molecular Topological Graphs

    Directory of Open Access Journals (Sweden)

    Yoshifumi Fukunishi


    Full Text Available A molecular similarity measure has been developed using molecular topological graphs and atomic partial charges. Two kinds of topological graphs were used. One is the ordinary adjacency matrix and the other is a matrix which represents the minimum path length between two atoms of the molecule. The ordinary adjacency matrix is suitable to compare the local structures of molecules such as functional groups, and the other matrix is suitable to compare the global structures of molecules. The combination of these two matrices gave a similarity measure. This method was applied to in silico drug screening, and the results showed that it was effective as a similarity measure.

  8. Adaptive Calcified Matrix Response of Dental Pulp to Bacterial Invasion Is Associated with Establishment of a Network of Glial Fibrillary Acidic Protein+/Glutamine Synthetase+ Cells (United States)

    Farahani, Ramin M.; Nguyen, Ky-Anh; Simonian, Mary; Hunter, Neil


    We report evidence for anatomical and functional changes of dental pulp in response to bacterial invasion through dentin that parallel responses to noxious stimuli reported in neural crest-derived sensory tissues. Sections of resin-embedded carious adult molar teeth were prepared for immunohistochemistry, in situ hybridization, ultrastructural analysis, and microdissection to extract mRNA for quantitative analyses. In odontoblasts adjacent to the leading edge of bacterial invasion in carious teeth, expression levels of the gene encoding dentin sialo-protein were 16-fold greater than in odontoblasts of healthy teeth, reducing progressively with distance from this site of the carious lesion. In contrast, gene expression for dentin matrix protein-1 by odontoblasts was completely suppressed in carious teeth relative to healthy teeth. These changes in gene expression were related to a gradient of deposited reactionary dentin that displayed a highly modified structure. In carious teeth, interodontoblastic dentin sialo-protein− cells expressing glutamine synthetase (GS) showed up-regulation of glial fibrillary acidic protein (GFAP). These cells extended processes that associated with odontoblasts. Furthermore, connexin 43 established a linkage between adjacent GFAP+/GS+ cells in carious teeth only. These findings indicate an adaptive pulpal response to encroaching caries that includes the deposition of modified, calcified, dentin matrix associated with networks of GFAP+/GS+ interodontoblastic cells. A regulatory role for the networks of GFAP+/GS+ cells is proposed, mediated by the secretion of glutamate to modulate odontoblastic response. PMID:20802180

  9. Tissue inhibitor of matrix metalloproteinases-1 loaded poly(lactic-co-glycolic acid) nanoparticles for delivery across the blood–brain barrier (United States)

    Chaturvedi, Mayank; Molino, Yves; Sreedhar, Bojja; Khrestchatisky, Michel; Kaczmarek, Leszek


    Aim The aim of this study was to develop poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) for delivery of a protein – tissue inhibitor of matrix metalloproteinases 1 (TIMP-1) – across the blood–brain barrier (BBB) to inhibit deleterious matrix metalloproteinases (MMPs). Materials and methods The NPs were formulated by multiple-emulsion solvent-evaporation, and for enhancing BBB penetration, they were coated with polysorbate 80 (Ps80). We compared Ps80-coated and uncoated NPs for their toxicity, binding, and BBB penetration on primary rat brain capillary endothelial cell cultures and the rat brain endothelial 4 cell line. These studies were followed by in vivo studies for brain delivery of these NPs. Results Results showed that neither Ps80-coated nor uncoated NPs caused significant opening of the BBB, and essentially they were nontoxic. NPs without Ps80 coating had more binding to endothelial cells compared to Ps80-coated NPs. Penetration studies showed that TIMP-1 NPs + Ps80 had 11.21%±1.35% penetration, whereas TIMP-1 alone and TIMP-1 NPs without Ps80 coating did not cross the endothelial monolayer. In vivo studies indicated BBB penetration of intravenously injected TIMP-1 NPs + Ps80. Conclusion The study demonstrated that Ps80 coating of NPs does not cause significant toxic effects to endothelial cells and that it can be used to enhance the delivery of protein across endothelial cell barriers, both in vitro and in vivo. PMID:24531257

  10. Tissue inhibitor of matrix metalloproteinases-1 loaded poly(lactic-co-glycolic acid) nanoparticles for delivery across the blood-brain barrier. (United States)

    Chaturvedi, Mayank; Molino, Yves; Sreedhar, Bojja; Khrestchatisky, Michel; Kaczmarek, Leszek


    The aim of this study was to develop poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) for delivery of a protein - tissue inhibitor of matrix metalloproteinases 1 (TIMP-1) - across the blood-brain barrier (BBB) to inhibit deleterious matrix metalloproteinases (MMPs). The NPs were formulated by multiple-emulsion solvent-evaporation, and for enhancing BBB penetration, they were coated with polysorbate 80 (Ps80). We compared Ps80-coated and uncoated NPs for their toxicity, binding, and BBB penetration on primary rat brain capillary endothelial cell cultures and the rat brain endothelial 4 cell line. These studies were followed by in vivo studies for brain delivery of these NPs. Results showed that neither Ps80-coated nor uncoated NPs caused significant opening of the BBB, and essentially they were nontoxic. NPs without Ps80 coating had more binding to endothelial cells compared to Ps80-coated NPs. Penetration studies showed that TIMP-1 NPs + Ps80 had 11.21%± 1.35% penetration, whereas TIMP-1 alone and TIMP-1 NPs without Ps80 coating did not cross the endothelial monolayer. In vivo studies indicated BBB penetration of intravenously injected TIMP-1 NPs + Ps80. The study demonstrated that Ps80 coating of NPs does not cause significant toxic effects to endothelial cells and that it can be used to enhance the delivery of protein across endothelial cell barriers, both in vitro and in vivo.

  11. Room Temperature Consolidation of a Porous Poly(lactic-co-glycolic acid Matrix by the Addition of Maltose to the Water-in-Oil Emulsion

    Directory of Open Access Journals (Sweden)

    Eliana Esposito


    Full Text Available In composite materials made of polymer matrices and micro-nano dispersed compartments, the morphology of the dispersed phase can strongly affect several features of the final material, including stability, loading efficiency, and kinetic release of the embedded molecules. Such a polymer matrix composite can be obtained through the consolidation of the continuous polymer phase of a water-in-oil (W/O emulsion. Here, we show that the morphology of the dispersed phase in a poly(lactic-co-glycolic acid, PLGA matrix can be optimized by combining an effective mild temperature drying process with the addition of maltose as a densifying compound for the water phase of the emulsion. The influence of this addition on final stability and consequent optimal pore distribution was theoretically and experimentally confirmed. Samples were analyzed in terms of morphology on dried flat substrates and in terms of rheology and interfacial tension at the liquid state. While an increase of interfacial tension was found following the addition of maltose, the lower difference in density between the two emulsion phases coming from the addition of maltose allowed us to estimate a reduced creaming tendency confirmed by the experimental observations. Rheological measurements also confirmed an improved elastic behavior for the maltose-containing emulsion.

  12. Mixed-matrix membranes with enhanced antifouling activity: probing the surface-tailoring potential of Tiron and chromotropic acid for nano-TiO2 (United States)

    Pal, Avishek; Dey, T. K.; Debnath, A. K.; Bhushan, Bharat; Sahu, A. K.; Bindal, R. C.


    Mixed-matrix membranes (MMMs) were developed by impregnating organofunctionalized nanoadditives within fouling-susceptible polysulfone matrix following the non-solvent induced phase separation (NIPS) method. The facile functionalization of nanoparticles of anatase TiO2 (nano-TiO2) by using two different organoligands, viz. Tiron and chromotropic acid, was carried out to obtain organofunctionalized nanoadditives, FT-nano-TiO2 and FC-nano-TiO2, respectively. The structural features of nanoadditives were evaluated by X-ray diffraction, X-ray photoelectron spectroscopy, Raman and Fourier transform infrared spectroscopy, which established that Tiron leads to the blending of chelating and bridging bidentate geometries for FT-nano-TiO2, whereas chromotropic acid produces bridging bidentate as well as monodentate geometries for FC-nano-TiO2. The surface chemistry of the studied membranes, polysulfone (Psf): FT-nano-TiO2 UF and Psf: FC-nano-TiO2 UF, was profoundly influenced by the benign distributions of the nanoadditives enriched with distinctly charged sites (−SO3−H+), as evidenced by superior morphology, improved topography, enhanced surface hydrophilicity and altered electrokinetic features. The membranes exhibited enhanced solvent throughputs, viz. 3500–4000 and 3400–4300 LMD at 1 bar of transmembrane pressure, without significant compromise in their rejection attributes. The flux recovery ratios and fouling resistive behaviours of MMMs towards bovine serum albumin indicated that the nanoadditives could impart stable and appreciable antifouling activity, potentially aiding in a sustainable ultrafiltration performance. PMID:28989744

  13. Matrix theory

    CERN Document Server

    Franklin, Joel N


    Mathematically rigorous introduction covers vector and matrix norms, the condition-number of a matrix, positive and irreducible matrices, much more. Only elementary algebra and calculus required. Includes problem-solving exercises. 1968 edition.

  14. Amino Acid substitutions in matrix, fusion and hemagglutinin proteins of wild measles virus for adaptation to vero cells. (United States)

    Xin, Ji Yi; Ihara, Toshiaki; Komase, Katsuhiro; Nakayama, Tetsuo


    Wild-type measles virus (MV) is isolated in B95a but not in Vero cells. Through an adaptation process of wild-type MV to Vero cells, several amino acid substitutions were reported. Six strains were adapted to Vero cells and membrane (M), fusion (F) and hemagglutinin (H) genes were sequenced. Cell fusion was assessed and recombinant MVs were constructed, having wild-type H or M gene with or without mutations. No F gene substitution was noted. Amino-acid substitutions at positions 481 from Asn to Tyr (N481Y) and 546 from Ser to Gly (S546G) were observed in the H protein. Glu at position 89 of the M protein was substituted for Gly (E89G) and two mutations were noted at positions 62 (S62R) and 83 (S83P) in M protein. Recombinant viruses with mutation(s) detected in Vero-adapted strains induced a cytopathic effect and grew well in Vero cells, but those with the wild type did not. Recombinant viruses with mutation(s) demonstrated lower viral growth in B95a cells. Substitutions of E89G, S62R and S83P of the M protein were newly observed through adaptation to Vero cells, besides the mutations described in previous reports, with varying adaptation for each strain. Copyright © 2011 S. Karger AG, Basel.

  15. Novel chenodeoxycholic acid-sodium alginate matrix in the microencapsulation of the potential antidiabetic drug, probucol. An in vitro study. (United States)

    Mooranian, Armin; Negrulj, Rebecca; Mikov, Momir; Golocorbin-Kon, Svetlana; Arfuso, Frank; Al-Salami, Hani


    We previously designed, developed and characterized a novel microencapsulated formulation as a platform for the targeted delivery of Probucol (PB) in an animal model of Type 2 Diabetes. The objective of this study is to optimize this platform by incorporating Chenodeoxycholic acid (CDCA), a bile acid with good permeation-enhancing properties, and examine its effect in vitro. Using sodium alginate (SA), we prepared PB-SA (control) and PB-CDCA-SA (test) microcapsules. CDCA resulted in better structural and surface characteristics, uniform morphology, and stable chemical and thermal profiles, while size and rheological parameters remained unchanged. PB-CDCA-SA microcapsules showed good excipients' compatibilities, as evidenced by differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy, scanning electron microscopy and energy dispersive X-ray spectroscopy studies. CDCA reduced microcapsule swelling at pH 7.8 at both 37 °C and 25 °C and improved PB-release. CDCA improved the characteristics and release properties of PB-microcapsules and may have potential in the targeted oral delivery of PB.

  16. Glycolic Acid peels/azelaic Acid 20% cream combination and low potency triple combination lead to similar reduction in melasma severity in ethnic skin: results of a randomized controlled study. (United States)

    Mahajan, Rahul; Kanwar, Amrinder Jit; Parsad, Davinder; Kumaran, Muthu Sendhil; Sharma, Reena


    Numerous therapeutic options have been tried in the management of melasma. This prospective randomized study was planned to assess the efficacy of low potency triple combination (TC) cream (TC-hydroquinone 2%/tretinoin 0.05%/fluocinolone 0.01%) versus glycolic acid (GA) peels/azelaic acid (AA) 20% cream (GA/AA) combination in melasma. Forty patients with melasma were recruited into this study and randomized into two groups. Group A consisting 20 patients received TC cream once a day for night time application for 3 months. Group B comprising of 20 patients received GA/AA 20% cream combination for 3 months. The disease severity was monitored with digital photography, melasma area and severity index (MASI) score, which was calculated at baseline, 6 weeks and 12 weeks, and visual analog scale (VAS) score, which was calculated at baseline and 12 weeks. Of 40 patients, 38 were completed the study. A significant reduction in MASI and VAS was recorded after 6 weeks and 12 weeks of treatment in both groups A and B (P = 0.001). However, there was no significant difference in the mean MASI scores between the two groups at baseline, 6 weeks and 12 weeks. Similarly, there was no difference in the mean VAS scores between the two groups at baseline and 12 weeks. Four patients in group A and 3 in group B experienced adverse effects such as irritation, dryness, and photosensitivity. Both low potency TC cream and GA/AA 20% cream combination are effective in treating melasma among Indian patients.

  17. Application of a simple column-switching ion chromatography technique for removal of matrix interferences and sensitive fluorescence determination of acidic compounds (pharmaceutical drugs) in complex samples. (United States)

    Muhammad, Nadeem; Subhani, Qamar; Wang, Fenglian; Guo, Dandan; Zhao, Qiming; Wu, Shuchao; Zhu, Yan


    This work illustrates the introduction of a simple, rugged and flexible column-switching ion chromatography (IC) technique for an automated on-line QuEChERS extracted samples extracts washing followed by sensitive fluorescence (FLD) determination of five acidic pharmaceutical drugs namely; clofibric acid (CLO), ibuprofen (IBU), aspirin (ASP), naproxen (NAP) and flurobrofen (FLU) in three complex samples (spinach, apple and hospital sewage sludge). An old anion exchange column IonPac ® AS11-HC was utilized as a pre-treatment column for on-line washing of inorganic and organic interferences followed by isocratic separation of five acidic drugs with another anion exchange IonPac ® AS12A analytical column by exploiting the column-switching technique. This novel method exhibited good linearity with correlation coefficients (r 2 ) for all drugs were in the range 0.976-0.996. The limit of detection and quantification of all five acidic drugs were in the range 0.024μg/kg to 8.70μg/kg and 0.082μg/kg to 0.029mg/kg, respectively, and better recoveries in the range 81.17-112.5% with percentage relative standard deviations (RSDs) less than 17.8% were obtained. This on-line sample pre-treatment method showed minimum matrix effect in the range of 0.87-1.25 except for aspirin. This simple rugged and flexible column-switching system required only 28min for maximum elimination of matrices and interferences in three complex samples extracts, isocratic separation of five acidic drugs and for the continuous regeneration of pre-treatment column prior to every subsequent analysis. Finally, this simple automated IC system was appeared so rugged and flexible, which can eliminate and wash out most of interference, impurities and matrices in complex samples, simply by adjusting the NaOH and acetonitrile concentration in washing mobile phase with maximum recoveries of acidic analytes of interest. Copyright © 2017. Published by Elsevier B.V.

  18. The application of chitosan/collagen/hyaluronic acid sponge cross-linked by dialdehyde starch addition as a matrix for calcium phosphate in situ precipitation. (United States)

    Kaczmarek, B; Sionkowska, A; Osyczka, A M


    Scaffolds based on chitosan, collagen and hyaluronic acid, cross-linked by dialdehyde starch were obtained through the freeze-drying method. The porous structures were used as matrixes for calcium phosphate in situ precipitation. Composites were characterized by different analyses, e.g. infrared spectroscopy, SEM images, porosity, density, and mechanical tests. Moreover, an examination involving the energy dispersive X-ray spectroscopic method was carried out for the calcium and phosphorus ratio determination. In addition, the adhesion and proliferation of human osteosarcoma SaOS-2 cells were examined on the obtained scaffolds. The results showed that the properties of the scaffolds based on chitosan, collagen, and hyaluronic acid can be modified by dialdehyde starch addition. The mechanical parameters (i.e. compressive modulus and maximum compressive force), porosity, and density of the material were improved. Calcium phosphate was deposited in the scaffolds at the Ca/P ratio ∼2. SEM images showed the homogeneous structure, with interconnected pores. The cross-linker addition and an inorganic compound precipitation improved the biocompatibility of the scaffolds. The obtained materials can provide the support required in tissue engineering and regenerative medicine. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Antioxidative activity of 3,4-dihydroxyplienylacetic acid and α-tocopherol on the triglyceride matrix of olive oil. Effect of acidity.

    Directory of Open Access Journals (Sweden)

    Blekas, Georgios


    Full Text Available Minor constituents of virgin olive oil are important for the remarkable stability of the oil in autoxidation, but the exact role and the extent to which each antioxidant factor contributes to the total antioxidant effect has not been thoroughly Investigated. In this study the role of α-tocopherol is explored at various acidity levels and at low concentrations of ortho-diphenols. A substrate of olive oil triacylglycerols devoid of prooxidant or antioxidant constituents was prepared from refined olive oil by column chromatography To tills substrate, slightly oxidized, the additives (oleic acid, 3,4-dihydroxyphenylacetic acid and α-tocopherol were added and the stability was assessed by periodical measurements of peroxide values. It was found that free fatty adds reduce mainly the protective activity of the ortho-diphenol. It is also concluded that α-tocopherol has a synergistic effect with the ortho-diphenols and contributes significantly to the retardation of peroxide formation. This is Important for oils poor in ortho-diphenols.

    Los constituyentes menores del aceite de oliva virgen son importantes para la notable estabilidad del aceite en la autooxidación, pero el papel exacto y el alcance con que cada factor antioxidante contribuye al efecto antioxidante total no ha sido investigado a fondo. En este estudio el papel del α-tocoferol es examinado a varios niveles de acidez y a baja concentraciones de o-difenoles. Un sustrato de triacilgliceroles de aceite de oliva desprovisto de constituyentes prooxidantes o antioxidantes fue preparado a partir de aceite de oliva refinado mediante cromatografía en columna. A este sustrato, un poco oxidado, los aditivos (ácido oleico, ácido 3,4-dihidroxifenilacético y α-tocoferol fueron añadidos y la estabilidad fue calculada mediante medidas periódicas del índice de peróxido. Se encontró que los ácidos grasos libres reducen principalmente la actividad protectora de los orto-difenoles. Se

  20. The remarkable similarity between the acid-base properties of ISFETs and proteins and the consequences for the design of ISFET biosensors

    NARCIS (Netherlands)

    Bergveld, Piet; van Hal, R.E.G.; van Hal, R.E.G.; Eijkel, Jan C.T.


    Studying the acid-base properties of protein molecules led us to reconsider the operational mechanism of ISFETs. Based on the site-dissociation model, applied to the amphoteric metal oxide gate materials used in ISFETs, the sensitivity of ISFETs is described in terms of the intrinsic buffer capacity

  1. Long- and Medium-Chain Fatty Acids Induce Insulin Resistance to a Similar Extent in Humans Despite Marked Differences in Muscle Fat Accumulation

    NARCIS (Netherlands)

    Hoeks, J.; Mensink, M.R.; Hesselink, M.K.C.; Ekroos, K.; Schrauwen, P.


    Context: Animal studies revealed that medium-chain fatty acids (MCFA), due to their metabolic characteristics, are not stored in skeletal muscle and may therefore not give rise to potentially hazardous lipid species impeding insulin signaling. Objective: We here hypothesized that infusion of

  2. Hyaluronic acid fillers with cohesive polydensified matrix for soft-tissue augmentation and rejuvenation: a literature review

    Directory of Open Access Journals (Sweden)

    Prasetyo AD


    Full Text Available Adri D Prasetyo,1 Welf Prager,2 Mark G Rubin,3 Ernesto A Moretti,4 Andreas Nikolis5 1Rejuva Skin & Beauty, Surabaya, Indonesia; 2Prager & Partner, Hamburg, Germany; 3University of California, San Diego, CA, USA; 4Gamma Health Group, Sanatorio Los Arroyos, Santa Fe, Republic of Argentina; 5Victoria Park Clinical Research Centre, Westmount, QC, Canada Background: Cohesive monophasic polydensified fillers show unique viscoelastic properties and variable density of hyaluronic acid, allowing for a homogeneous tissue integration and distribution of the material.Objective: The aim of this paper was to review the clinical data regarding the performance, tolerability, and safety of the Belotero® fillers for soft-tissue augmentation and rejuvenation.Methods: A literature search was performed up until May 31, 2015 to identify all relevant articles on Belotero® fillers (Basic/Balance, Hydro, Soft, Intense, Volume and equivalent products (Esthélis®, Mesolis®, Fortélis®, Modélis®.Results: This comprehensive review included 26 papers. Findings from three randomized controlled trials showed a greater reduction in nasolabial fold severity with Belotero® Basic/Balance than with collagen (at 8, 12, 16, and 24 weeks, n=118 and Restylane® (at 4 weeks, n=40, and higher patient satisfaction with Belotero® Intense than with Perlane® (at 2 weeks, n=20. With Belotero® Basic/Balance, an improvement of at least 1 point on the severity scale can be expected in ~80% of patients 1–6 months after injection, with an effect still visible at 8–12 months. Positive findings were also reported with Belotero® Volume (no reduction in hyaluronic acid volume at 12 months, as demonstrated by magnetic resonance imaging, Soft (improvement in the esthetic outcomes when used in a sequential approach, and Hydro (improvement in skin appearance in all patients. The most common adverse effects were mild-to-moderate erythema, edema, and hematoma, most of which were

  3. Side-effects of domestication: cultivated legume seeds contain similar tocopherols and fatty acids but less carotenoids than their wild counterparts. (United States)

    Fernández-Marín, Beatriz; Milla, Rubén; Martín-Robles, Nieves; Arc, Erwann; Kranner, Ilse; Becerril, José María; García-Plazaola, José Ignacio


    Lipophilic antioxidants play dual key roles in edible seeds (i) as preservatives of cell integrity and seed viability by preventing the oxidation of fats, and (ii) as essential nutrients for human and animal life stock. It has been well documented that plant domestication and post-domestication evolution frequently resulted in increased seed size and palatability, and reduced seed dormancy. Nevertheless, and surprisingly, it is poorly understood how agricultural selection and cultivation affected the physiological fitness and the nutritional quality of seeds. Fabaceae have the greatest number of crop species of all plant families, and most of them are cultivated for their highly nutritious edible seeds. Here, we evaluate whether evolution of plants under cultivation has altered the integrated system formed by membranes (fatty acids) and lipophilic antioxidants (carotenoids and tocopherols), in the ten most economically important grain legumes and their closest wild relatives, i.e.: Arachis (peanut), Cicer (chickpea), Glycine (soybean), Lathyrus(vetch), Lens (lentil), Lupinus (lupin), Phaseolus (bean), Pisum (pea), Vicia (faba bean) and Vigna (cowpea). Unexpectedly, we found that following domestication, the contents of carotenoids, including lutein and zeaxanthin, decreased in all ten species (total carotenoid content decreased 48% in average). Furthermore, the composition of carotenoids changed, whereby some carotenoids were lost in most of the crops. An undirected change in the contents of tocopherols and fatty acids was found, with contents increasing in some species and decreasing in others, independently of the changes in carotenoids. In some species, polyunsaturated fatty acids (linolenic acid especially), α-tocopherol and γ-tocopherol decreased following domestication. The changes in carotenoids, tocopherols and fatty acids are likely side-effects of the selection for other desired traits such as the loss of seed dormancy and dispersal mechanisms, and

  4. Discovery of dehydroabietic acid sulfonamide based derivatives as selective matrix metalloproteinases inactivators that inhibit cell migration and proliferation. (United States)

    Huang, Ri-Zhen; Liang, Gui-Bin; Huang, Xiao-Chao; Zhang, Bin; Zhou, Mei-Mei; Liao, Zhi-Xin; Wang, Heng-Shan


    A series of dehydroabietic acid (DHAA) dipeptide derivatives containing the sulfonamide moiety were designed, synthesized and evaluated for inhibition of MMPs as well as the effects of in vitro cell migration. These compounds exhibited relatively good inhibition activity against MMPs with IC50 values in low micromolar range. A docking study of the most active compound 8k revealed key interactions between 8k and MMP-3 in which the sulfonamide moiety and the dipeptide group were important for improving activity. It is noteworthy that further antitumor activity screening revealed that some compounds exhibited better inhibitory activity than the commercial anticancer drug 5-FU. In particular, compound 8k appeared to be the most potent compound against the HepG2 cell line, at least partly, by inhibition of the activity of MMP-3 and apoptosis induction. The treatment of HepG2 cells with compound 8k resulted in inhibition of in vitro cell migration through wound healing assay and G1 phase of cell cycle arrested. In addition, 8k-induced apoptosis was significantly facilitated in HepG2 cells. Thus, we conclude that DHAA dipeptide derivatives containing the sulfonamide moiety may be the potential MMPs inhibitors with the ability to suppress cells migration. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  5. Analysis of residual trifluoroacetic acid in a phosphate-buffered saline matrix by ion chromatography with suppressed conductivity detection. (United States)

    Fernando, P N; McLean, M A; Egwu, I N; deGuzman, E; Weyker, C


    As part of the formulation of a cell-based pharmaceutical product, cells were harvested from mice and incubated in a cocktail containing cell culture media and high levels of trifluoroacetic acid (TFA). The cells were washed with a phosphate-buffered saline solution to remove residual cell culture media and other reagents before the cells were infused back into the mice from which they originated. Because of the potentially toxic nature of the TFA, the cells were washed multiple times and the final wash was monitored for residual TFA in order to demonstrate the efficient removal of the reagent before the cell product could be reintroduced into the test animal. This report describes the method that was developed incorporating anion-exchange chromatography with suppressed conductivity detection for the analysis of residual TFA (down to 50 ng/ml) in the presence of high concentrations of phosphate and chloride interferences. The ultimate sensitivity of the method was improved by selectively removing halide anions using a silver cartridge before sample analysis. The method proved to be rugged and reproducible enough to be validated and used to monitor residual TFA levels in cell washes in support of an acute toxicological study. Results demonstrating the method's sensitivity, selectivity, precision and linearity were reported.

  6. Higher Spin Matrix Models

    Directory of Open Access Journals (Sweden)

    Mauricio Valenzuela


    Full Text Available We propose a hybrid class of theories for higher spin gravity and matrix models, i.e., which handle simultaneously higher spin gravity fields and matrix models. The construction is similar to Vasiliev’s higher spin gravity, but part of the equations of motion are provided by the action principle of a matrix model. In particular, we construct a higher spin (gravity matrix model related to type IIB matrix models/string theory that have a well defined classical limit, and which is compatible with higher spin gravity in A d S space. As it has been suggested that higher spin gravity should be related to string theory in a high energy (tensionless regime, and, therefore to M-Theory, we expect that our construction will be useful to explore concrete connections.

  7. Lysophosphatidic Acid Is Associated with Atherosclerotic Plaque Instability by Regulating NF-κB Dependent Matrix Metalloproteinase-9 Expression via LPA2 in Macrophages

    Directory of Open Access Journals (Sweden)

    Xi Chen


    Full Text Available Lysophosphatidic acid (LPA, one of the simplest phospholipid signaling molecules, participates in formation and disruption of atherosclerotic plaque. Matrix metalloproteinases (MMPs contribute to atherosclerotic plaque rupture by involving in extracellular matrix (ECM degradation and then thinning fibrous cap. Our previous study demonstrated that macrophage-derived MMP-9 was associated with coronary plaque instability, but the relationship between LPA and MMP-9 remains unclear. The present work therefore aimed at elucidating association between LPA and MMP-9 and the regulation mechanism of LPA on MMP-9 in macrophages. We found that plasma LPA and MMP-9 levels were correlated positively (r = 0.31, P < 0.05 and both elevated significantly in patients with acute myocardial infarct (AMI. Consistent with peripheral blood levels, histochemical staining indicated that autotaxin (ATX, LPA-producing ectoenzyme, and MMP-9 were expressed frequently in the necrotic core and fibrous cap of human unstable plaques, which might increase the instability of plaque. Experiments in vitro were done with THP-1-derived macrophages and showed that LPA enhanced the expression, secretion and activity of MMP-9 in a time- and dose-dependent manner. Induction of LPA on pro-MMP-9 and active-MMP-9 was confirmed in human peripheral blood monocyte-derived macrophages. PDTC, NF-κB inhibitor, but not inhibitor of AP-1 and PPARγ, effectively prevented LPA-induced MMP-9 expression and NF-κB p65 siRNA decreased MMP-9 transcription, confirming that LPA might induce MMP-9 elevation by activating NF-κB pathway. In addition, knockdown of LPA2 attenuated LPA-induced MMP-9 expression and nucleus p65 levels. These findings revealed that LPA upregulated the expression of MMP-9 through activating NF-κB pathway in the LPA2 dependent manner, hence blocking LPA receptors signaling may provide therapeutic strategy to target plaque destabilization.

  8. Ethyl group as matrix modifier and inducer of ordered domains in hybrid xerogels synthesised in acidic media using ethyltriethoxysilane (ETEOS) and tetraethoxysilane (TEOS) as precursors

    Energy Technology Data Exchange (ETDEWEB)

    Rios, Xabier; Moriones, Paula; Echeverría, Jesús C. [Departamento de Química Aplicada, Universidad Pública de Navarra, Campus Arrosadía, 31006 Pamplona (Spain); Luquin, Asunción; Laguna, Mariano [Instituto de Síntesis Química y Catálisis Homogénea (CSIC), Departamento de Química Inorgánica. Universidad de Zaragoza (Spain); Garrido, Julián J., E-mail: [Departamento de Química Aplicada, Universidad Pública de Navarra, Campus Arrosadía, 31006 Pamplona (Spain)


    Hybrid silica xerogels favourably combine the properties of organic and inorganic components in one material; consequently these materials are useful for multiple applications. The versatility and mild synthetic conditions provided by the sol-gel process are ideal for the synthesis of hybrid materials. The specific aims of this study were to synthesise hybrid xerogels in acidic media using tetraethoxysilane (TEOS) and ethyltriethoxysilane (ETEOS) as silica precursors, and to assess the role of the ethyl group as a matrix modifier and inducer of ordered domains in xerogels. All xerogels were synthesised at pH 4.5, at 60 °C, with 1:4.75:5.5 TEOS:EtOH:H{sub 2}O molar ratio. Gelation time exponentially increased with the ETEOS molar ratio. Incorporation of the ethyl groups into the structure of xerogels reduced cross-linking, increased the average siloxane bond length, and promoted the formation of ordered domains. As a result, a transition from Q{sup n} to T{sup n} signals detected in the {sup 29}Si NMR spectra, the Si–O structural band in the FTIR spectra shifted to lower wavelength, and a new peak in the XRD pattern at 2θ < 10° appeared in the XRD patterns. Mass spectroscopy detected fragments with high numbers of silicon atoms and a polymeric distribution. - Graphical abstract: Display Omitted - Highlights: • Hybrid xerogels were synthesised for ETEOS/TEOS mixtures up to 80% ETEOS. • The gelification time exponentially increased with ETEOS content. • FTIR, XRD and MAS NMR demonstrated the presence of ethyl groups into xerogels. • For ETEOS contents ≤30%, ethyl group acted as matrix modifier. • For ETEOS contents ≥30%, ethyl groups induced the formation of ordered domains.

  9. 2,5-dihydroxybenzoic acid salts for matrix-assisted laser desorption/ionization time-of-flight mass spectrometric lipid analysis: simplified spectra interpretation and insights into gas-phase fragmentation. (United States)

    Jaskolla, Thorsten W; Onischke, Kristin; Schiller, Jürgen


    In the last decades the interest in lipids as important components of membranes has considerably increased. Nowadays, lipids are often routinely analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In this regard, many relevant aspects are so far unknown, e.g., gas-phase stabilities, adduct formation and fragmentation. To fill this gap, MALDI matrix salts are presented which allow for simplified lipid analysis and elucidation of the underlying gas-phase fragmentation mechanisms. MALDI-TOF MS was used due to its beneficial properties for lipid investigations, e.g., high sensitivity, simple sample preparations, and a high tolerance to contaminants. The lipid hydrolysis, ionization and fragmentation properties of synthesized near neutral Na(+) and NH4 (+) salts of the commonly used MALDI matrix 2,5-dihydroxybenzoic acid were compared to that of DHB free acid itself as well as to base addition to DHB during dried-droplet sample preparation. Many lipid classes such as sterols, triacylglycerols, phosphatidylcholines and -ethanolamines undergo initial protonation with subsequent prompt partial up to quantitative fragmentation when analyzed with classical acidic matrices by MALDI-TOF MS. Neutral matrix salts can prevent initial analyte fragmentation by suppression of analyte protonation. Additionally, intramolecular gas-phase fragmentation reactions can be inhibited due to analyte stabilization by cation chelation. Base addition during sample preparation leads not only to in situ generation of matrix salts but also to analyte hydrolysis. Neutral DHB salts avoid separation of lipid species into several ionization states when used as matrices in MALDI-TOF MS. This allows for simplified lipid spectra interpretation. Due to the high cationization efficiency of DHB matrix salts, certain lipid classes become detectable which cannot be analyzed easily using standard acidic DHB. Copyright © 2014 John Wiley & Sons, Ltd.

  10. Acute cold and exercise training up-regulate similar aspects of fatty acid transport and catabolism in house sparrows (Passer domesticus). (United States)

    Zhang, Yufeng; Carter, Travis; Eyster, Kathleen; Swanson, David L


    Summit maximum thermoregulatory metabolic rate (Msum) and maximum exercise metabolic rate (MMR) both increase in response to acute cold or exercise training in birds. Because lipids are the main fuel supporting both thermogenesis and exercise in birds, adjustments to lipid transport and catabolic capacities may support elevated energy demands from cold and exercise training. To examine a potential mechanistic role for lipid transport and catabolism in organismal cross-training effects (exercise effects on both exercise and thermogenesis, and vice versa), we measured enzyme activities and mRNA and protein expression in pectoralis muscle for several key steps of lipid transport and catabolism pathways in house sparrows (Passer domesticus) during acute exercise and cold training. Both training protocols elevated pectoralis protein levels of fatty acid translocase (FAT/CD36), cytosolic fatty acid-binding protein, and citrate synthase (CS) activity. However, mRNA expression of FAT/CD36 and both mRNA and protein expression of plasma membrane fatty acid-binding protein did not change for either training group. CS activities in supracoracoideus, leg and heart, and carnitine palmitoyl transferase (CPT) and β-hydroxyacyl CoA-dehydrogenase activities in all muscles did not vary significantly with either training protocol. Both Msum and MMR were significantly positively correlated with CPT and CS activities. These data suggest that up-regulation of trans-sarcolemmal and intramyocyte lipid transport capacities and cellular metabolic intensities, along with previously documented increases in body and pectoralis muscle masses and pectoralis myostatin (a muscle growth inhibitor) levels, are common mechanisms underlying the training effects of both exercise and shivering in birds. © 2015. Published by The Company of Biologists Ltd.

  11. RAR?2 and PML-RAR similarities in the control of basal and retinoic acid induced myeloid maturation of acute myeloid leukemia cells


    Gianni, M; Fratelli, M.; Bolis, M.; Kurosaki, M; Zanetti, A.; Paroni, G.; Rambaldi, A; Borleri, G.; Rochette-Egly, C; Terao, M; Garattini, E


    Treatment of acute promyelocytic leukemia (APL) with all-trans retinoic acid (ATRA) is the first example of targeted therapy. In fact, the oncogenic fusion-protein (PML-RAR) typical of this leukemia contains the retinoid-nuclear-receptor RAR?. PML-RAR is responsible for the differentiation block of the leukemic blast. Besides PML-RAR, two endogenous RAR? proteins are present in APL blasts, i.e. RAR?1 and RAR?2. We developed different cell populations characterized by PML-RAR, RAR?2 and RAR?1 ...

  12. Similarities and Differences Between “Proactive” and “Passive” Stress-Coping Rats in Responses to Sucrose, NaCl, Citric Acid, and Quinine (United States)


    A stress-coping style describes a set of behavioral and physiological measures that characterize an individual’s response to stressful stimuli. It would follow that different stress-coping styles are associated with differential sensitivity for taste stimuli. Animals with stress-coping characteristics better suited to an environment in which new foods are more frequently encountered may show enhanced orosensitivity to cues that signal toxins and/or nutritional value. Here, rats were categorized as “proactive” or “passive” based on results from a defensive burying test. Next, the brief-access taste procedure was used to compare unconditioned licking responses to a concentration array of compounds that humans describe as “sweet” (sucrose), “salty” (NaCl), “sour” (citric acid), and “bitter” (quinine) across the 2 groups. Both groups displayed concentration-dependent lick responses to sucrose, NaCl, citric acid, and quinine. The passive group initiated significantly fewer trials to sucrose than the proactive rats, but the groups did not significantly differ in trial initiation for the other 3 test compounds. Thus, differences in food intake, body weight, and glucose homeostasis between the stress-coping styles are not likely driven by alterations in orosensory responsivity. However, the current findings lend support to the hypothesis that the 2 groups differ in reward-related signaling mechanisms. PMID:24510916

  13. Multi-imaging of Cytokinin and Abscisic Acid on the Roots of Rice (Oryza sativa) Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry. (United States)

    Shiono, Katsuhiro; Hashizaki, Riho; Nakanishi, Toyofumi; Sakai, Tatsuko; Yamamoto, Takushi; Ogata, Koretsugu; Harada, Ken-Ichi; Ohtani, Hajime; Katano, Hajime; Taira, Shu


    Plant hormones act as important signaling molecules that regulate responses to abiotic stress as well as plant growth and development. Because their concentrations of hormones control the physiological responses in the target tissue, it is important to know the distributions and concentrations in the tissues. However, it is difficult to determine the hormone concentration on the plant tissue as a result of the limitations of conventional methods. Here, we report the first multi-imaging of two plant hormones, one of cytokinin [i.e., trans-zeatin (tZ)] and abscisic acid (ABA) using a new technology, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) imaging. Protonated signals of tZ (m/z 220.1) and ABA (m/z 265.3) were chosen on longitudinal sections of rice roots for MS imaging. tZ was broadly distributed about 40 mm behind the root apex but was barely detectable at the apex, whereas ABA was mainly detected at the root apex. Multi-imaging using MALDI-TOF-MS enabled the visualization of the localization and quantification of plant hormones. Thus, this tool is applicable to a wide range of plant species growing under various environmental conditions.

  14. Detection of melamine in a human renal uric acid stone by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). (United States)

    Liu, Chia-Chu; Wu, Chia-Fang; Shiea, Jentaie; Cho, Yi-Tzu; Hsieh, Tusty-Jiuan; Chou, Yii-Her; Chen, Bai-Hsiun; Huang, Shu-Pin; Wu, Wen-Jeng; Shen, Jung-Tsung; Chang, Mei-Yu; Huang, Chun-Hsiung; Chang, Ai-Wen; Wu, Ming-Tsang


    The link between melamine-contaminated daily foodstuffs and urolithiasis formation has drawn an international concern. However, detection of melamine levels in urine may not completely represent external melamine exposure. Thus, finding an additional analytical method for the study of environmental melamine exposure and its adverse effect in humans is crucial. Eleven adult patients diagnosed with uric acid urolithiasis were retrospectively analyzed. Melamine levels in their overnight one-spot urine samples were measured by a triple quadrupole liquid chromatography tandem mass spectrometry (LC-MS/MS). The compositions of stone samples were analyzed by the Fourier transform infrared (FTIR) spectrophotometer and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Seven (63.6%) out of 11 patients had detectable melamine levels in their urine specimens (method of detection limit: 0.8 ng/ml). Three patients (27.3%) were highly suspected of having melamine-containing urolithiasis in FTIR spectra. In one of those three cases who still had available stored stone specimens, MALDI-TOF MS further confirmed melamine components in this male patient's stone specimens. In contrast, his urinary melamine level was below the detection limit by LC-MS/MS. Direct analysis of melamine in the composition of urolithiasis by MALDI-TOF MS can be an additional analytical method to evaluate for external melamine exposure. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Quantitation of lysergic acid diethylamide in urine using atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry. (United States)

    Cui, Meng; McCooeye, Margaret A; Fraser, Catharine; Mester, Zoltán


    A quantitative method was developed for analysis of lysergic acid diethylamide (LSD) in urine using atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry (AP MALDI-ITMS). Following solid-phase extraction of LSD from urine samples, extracts were analyzed by AP MALDI-ITMS. The identity of LSD was confirmed by fragmentation of the [M + H](+) ion using tandem mass spectrometry. The quantification of LSD was achieved using stable-isotope-labeled LSD (LSD-d(3)) as the internal standard. The [M + H](+) ion fragmented to produce a dominant fragment ion, which was used for a selected reaction monitoring (SRM) method for quantitative analysis of LSD. SRM was compared with selected ion monitoring and produced a wider linear range and lower limit of quantification. For SRM analysis of samples of LSD spiked in urine, the calibration curve was linear in the range of 1-100 ng/mL with a coefficient of determination, r(2), of 0.9917. This assay was used to determine LSD in urine samples and the AP MALDI-MS results were comparable to the HPLC/ ESI-MS results.

  16. In vitro effect of caffeic acid phenethyl ester on matrix metalloproteinases (MMP-1 and MMP-9) and their inhibitor (TIMP-1) in lipopolysaccharide-activated human monocytes. (United States)

    Vilela, Polyana das Graças Figueiredo; de Oliveira, Jonatas Rafael; de Barros, Patrícia Pimentel; Leão, Mariella Vieira Pereira; de Oliveira, Luciane Dias; Jorge, Antonio Olavo Cardoso


    The role of matrix metalloproteinases (MMPs) in tissue degradation has become evident in many diseases and great interest therefore exists in the pharmacological control of the activity of these enzymes. This study evaluated the effect of caffeic acid phenethyl ester (CAPE) on the production of MMPs and their inhibitor (TIMP) in monocytes activated by lipopolysaccharide (LPS). The human monocytic cell line (THP-1) was treated with non-cytotoxic concentrations of CAPE (10 and 60μM) combined with 1μg/mL of LPS. The gene expression of MMP-1, MMP-9 and TIMP-1 was evaluated by quantitative real-time polymerase chain reaction. The protein secretion into the culture medium was assessed via enzyme-linked immunosorbent assay and the gelatinolytic activity of MMP-9 by zymography. CAPE, especially at the highest concentration, down-regulated MMP-1 and MMP-9 gene expression but up-regulated the gene expression of TIMP-1. Furthermore, CAPE reduced the secreted protein level of MMP-1 and MMP-9 as well as the gelatinolytic activity of MMP-9. CAPE was able to inhibit the gene expression, production and the activity of MMPs induced by LPS and also increased the gene expression of TIMP-1. The present observations suggest that CAPE exerted a positive effect on the regulatory mechanism between MMPs and TIMP, which is important for the control of different diseases. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Effect of SiC weight percentage on tribological properties of Al-SiC metal matrix composites under acid environment

    Directory of Open Access Journals (Sweden)

    Smrutiranjan Pradhan


    Full Text Available In this paper, Al-SiC MMCs reinforced with different weight percentages of SiC content (5 wt.%, 7.5 wt.% and 10 wt.% are fabricated through the liquid stir casting method. The effect of weight percentage of SiC on friction and wear properties of Al-SiC MMC is investigated. Tribological tests are conducted under acid environment in a pin-on-disk tribotester by varying the design parameters (applied normal load and sliding speed while the duration of each experiment is kept constant for 30 minutes. It is seen from the result that wear increases with increase in applied load and sliding speed but friction coefficient shows a decreasing trend with increase in load. The addition of SiC reinforcement increases the wear resistance of the metal matrix composite. The scanning electron microscope (SEM and energy dispersive X-Ray (EDX technique are used to analyse the wear mechanism of worn surface. From the microstructure study, it is seen that adhesive, abrasive and corrosive wear mechanisms are present for removal of material from the Al-SiC MMCs.

  18. Insight into the heterogeneous adsorption of humic acid fluorescent components on multi-walled carbon nanotubes by excitation-emission matrix and parallel factor analysis. (United States)

    Yang, Chenghu; Liu, Yangzhi; Cen, Qiulin; Zhu, Yaxian; Zhang, Yong


    The heterogeneous adsorption behavior of commercial humic acid (HA) on pristine and functionalized multi-walled carbon nanotubes (MWCNTs) was investigated by fluorescence excitation-emission matrix and parallel factor (EEM- PARAFAC) analysis. The kinetics, isotherms, thermodynamics and mechanisms of adsorption of HA fluorescent components onto MWCNTs were the focus of the present study. Three humic-like fluorescent components were distinguished, including one carboxylic-like fluorophore C1 (λex/λem= (250, 310) nm/428nm), and two phenolic-like fluorophores, C2 (λex/λem= (300, 460) nm/552nm) and C3 (λex/λem= (270, 375) nm/520nm). The Lagergren pseudo-second-order model can be used to describe the adsorption kinetics of the HA fluorescent components. In addition, both the Freundlich and Langmuir models can be suitably employed to describe the adsorption of the HA fluorescent components onto MWCNTs with significantly high correlation coefficients (R2> 0.94, Pfluorescent components to MWCNTs was clearly observed. The adsorption mechanism suggested that the π-π electron donor-acceptor (EDA) interaction played an important role in the interaction between HA fluorescent components and the three MWCNTs. Furthermore, the values of the thermodynamic parameters, including the Gibbs free energy change (ΔG°), enthalpy change (ΔH°) and entropy change (ΔS°), showed that the adsorption of the HA fluorescent components on MWCNTs was spontaneous and exothermic. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Serotonin-Sensitive Adenylate Cyclase in Neural Tissue and Its Similarity to the Serotonin Receptor: A Possible Site of Action of Lysergic Acid Diethylamide (United States)

    Nathanson, James A.; Greengard, Paul


    An adenylate cyclase (EC that is activated specifically by low concentrations of serotonin has been identified in homogenates of the thoracic ganglia of an insect nervous system. The activation of this enzyme by serotonin was selectively inhibited by extremely low concentrations of D-lysergic acid diethylamide (LSD), 2-bromo-LSD, and cyproheptadine, agents which are known to block certain serotonin receptors in vivo. The inhibition was competitive with respect to serotonin, and the calculated inhibitory constant of LSD for this serotonin-sensitive adenylate cyclase was 5 nM. The data are consistent with a model in which the serotonin receptor of neural tissue is intimately associated with a serotonin-sensitive adenylate cyclase which mediates serotonergic neurotransmission. The results are also compatible with the possibility that some of the physiological effects of LSD may be mediated through interaction with serotonin-sensitive adenylate cyclase. PMID:4595572

  20. Novel highly thermostable endolysin from Thermus scotoductus MAT2119 bacteriophage Ph2119 with amino acid sequence similarity to eukaryotic peptidoglycan recognition proteins. (United States)

    Plotka, Magdalena; Kaczorowska, Anna-Karina; Stefanska, Aleksandra; Morzywolek, Agnieszka; Fridjonsson, Olafur H; Dunin-Horkawicz, Stanislaw; Kozlowski, Lukasz; Hreggvidsson, Gudmundur O; Kristjansson, Jakob K; Dabrowski, Slawomir; Bujnicki, Janusz M; Kaczorowski, Tadeusz


    In this study, we present the discovery and characterization of a highly thermostable endolysin from bacteriophage Ph2119 infecting Thermus strain MAT2119 isolated from geothermal areas in Iceland. Nucleotide sequence analysis of the 16S rRNA gene affiliated the strain with the species Thermus scotoductus. Bioinformatics analysis has allowed identification in the genome of phage 2119 of an open reading frame (468 bp in length) coding for a 155-amino-acid basic protein with an Mr of 17,555. Ph2119 endolysin does not resemble any known thermophilic phage lytic enzymes. Instead, it has conserved amino acid residues (His(30), Tyr(58), His(132), and Cys(140)) that form a Zn(2+) binding site characteristic of T3 and T7 lysozymes, as well as eukaryotic peptidoglycan recognition proteins, which directly bind to, but also may destroy, bacterial peptidoglycan. The purified enzyme shows high lytic activity toward thermophiles, i.e., T. scotoductus (100%), Thermus thermophilus (100%), and Thermus flavus (99%), and also, to a lesser extent, toward mesophilic Gram-negative bacteria, i.e., Escherichia coli (34%), Serratia marcescens (28%), Pseudomonas fluorescens (13%), and Salmonella enterica serovar Panama (10%). The enzyme has shown no activity against a number of Gram-positive bacteria analyzed, with the exception of Deinococcus radiodurans (25%) and Bacillus cereus (15%). Ph2119 endolysin was found to be highly thermostable: it retains approximately 87% of its lytic activity after 6 h of incubation at 95°C. The optimum temperature range for the enzyme activity is 50°C to 78°C. The enzyme exhibits lytic activity in the pH range of 6 to 10 (maximum at pH 7.5 to 8.0) and is also active in the presence of up to 500 mM NaCl.

  1. Matrix calculus

    CERN Document Server

    Bodewig, E


    Matrix Calculus, Second Revised and Enlarged Edition focuses on systematic calculation with the building blocks of a matrix and rows and columns, shunning the use of individual elements. The publication first offers information on vectors, matrices, further applications, measures of the magnitude of a matrix, and forms. The text then examines eigenvalues and exact solutions, including the characteristic equation, eigenrows, extremum properties of the eigenvalues, bounds for the eigenvalues, elementary divisors, and bounds for the determinant. The text ponders on approximate solutions, as well

  2. A putative carbohydrate-binding domain of the lactose-binding Cytisus sessilifolius anti-H(O) lectin has a similar amino acid sequence to that of the L-fucose-binding Ulex europaeus anti-H(O) lectin. (United States)

    Konami, Y; Yamamoto, K; Osawa, T; Irimura, T


    The complete amino acid sequence of a lactose-binding Cytisus sessilifolius anti-H(O) lectin II (CSA-II) was determined using a protein sequencer. After digestion of CSA-II with endoproteinase Lys-C or Asp-N, the resulting peptides were purified by reversed-phase high performance liquid chromatography (HPLC) and then subjected to sequence analysis. Comparison of the complete amino acid sequence of CSA-II with the sequences of other leguminous seed lectins revealed regions of extensive homology. The amino acid sequence of a putative carbohydrate-binding domain of CSA-II was found to be similar to those of several anti-H(O) leguminous lectins, especially to that of the L-fucose-binding Ulex europaeus lectin I (UEA-I).

  3. Pork meat increases iron absorption from a 5-day fully controlled diet when compared to a vegetarian diet with similar vitamin C and phytic acid content. (United States)

    Bach Kristensen, Mette; Hels, Ole; Morberg, Catrine; Marving, Jens; Bügel, Susanne; Tetens, Inge


    Meat increases absorption of non-haem iron in single-meal studies. The aim of the present study was to investigate, over a 5 d period, the potential increasing effect of consumption of pork meat in a whole diet on the fractional absorption of non-haem iron and the total absorption of iron, when compared to a vegetarian diet. A randomised cross-over design with 3 x 5 d whole-diet periods with diets containing Danish-produced meat, Polish-produced meat or a vegetarian diet was conducted. Nineteen healthy female subjects completed the study. All main meals in the meat diets contained 60 g of pork meat and all diets had high phytic acid content (1250 mumol/d). All main meals were extrinsically labelled with the radioactive isotope (59)Fe and absorption of iron was measured in a whole body counter. The non-haem iron absorption from the Danish meat diet was significantly higher compared to the vegetarian diet (P=0.031). The mean fractional absorption of non-haem iron was 7.9 (se1.1), 6.8 (se 1.0) and 5.3 (se 0.6) % for the Danish and Polish meat diets and vegetarian diet, respectively. Total absorption of iron was higher for both meat diets compared to the vegetarian diet (Danish meat diet: P=0.006, Polish meat diet: P=0.003). The absorption ratios of the present study were well in accordance with absorption ratios estimated using algorithms on iron bioavailability. Neither the meat diets nor the vegetarian diets fulfilled the estimated daily requirements of absorbed iron in spite of a meat intake of 180 g/d in the meat diets.

  4. Amino acid properties conserved in molecular evolution.

    Directory of Open Access Journals (Sweden)

    Witold R Rudnicki

    Full Text Available That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.

  5. Matrix metalloproteinase (MMP-9 in cancer-associated fibroblasts (CAFs is suppressed by omega-3 polyunsaturated fatty acids in vitro and in vivo.

    Directory of Open Access Journals (Sweden)

    Ayumi Taguchi

    Full Text Available Cancer associated fibroblasts (CAFs are responsible for tumor growth, angiogenesis, invasion, and metastasis. Matrix metalloproteinase (MMP-9 secreted from cancer stroma populated by CAFs is a prerequisite for cancer angiogenesis and metastasis. Omega-3 polyunsaturated fatty acids (omega-3 PUFA have been reported to have anti-tumor effects on diverse types of malignancies. Fat-1 mice, which can convert omega-6 to omega-3 PUFA independent of diet, are useful to investigate the functions of endogenous omega-3 PUFA. To examine the effect of omega-3 PUFA on tumorigenesis, TC-1 cells, a murine epithelial cell line immortalized by human papillomavirus (HPV oncogenes, were injected subcutaneously into fat-1 or wild type mice. Tumor growth and angiogenesis of the TC-1 tumor were significantly suppressed in fat-1 compared to wild type mice. cDNA microarray of the tumors derived from fat-1 and wild type mice revealed that MMP-9 is downregulated in fat-1 mice. Immunohistochemical study demonstrated immunoreactivity for MMP-9 in the tumor stromal fibroblasts was diffusely positive in wild type whereas focal in fat-1 mice. MMP-9 was expressed in primary cultured fibroblasts isolated from fat-1 and wild type mice but was not expressed in TC-1 cells. Co-culture of fibroblasts with TC-1 cells enhanced the expression and the proteinase activity of MMP-9, although the protease activity of MMP-9 in fat-1-derived fibroblasts was lower than that in wild type fibroblasts. Our data suggests that omega-3 PUFAs suppress MMP-9 induction and tumor angiogenesis. These findings may provide insight into mechanisms by which omega-3 PUFAs exert anti-tumor effects by modulating tumor microenvironment.

  6. Effect of All-Trans Retinoic Acid (ATRA against expression of Matrix Metalloproteinase-2 (MMP-2 in model mice (Rattus norvegicus periodontitis

    Directory of Open Access Journals (Sweden)

    Ilma Soraya


    Full Text Available Introduction: Periodontitis is a condition of inflammation of the tooth supporting tissues generally caused by bacteria Phorphyromonas gingivalis (Pg. and is usually characterized by the occurrence of the alveolar bone resorption. Matrix metalloproteinase-2 (MMP-2 is an enzyme that plays an important role in inflammatory conditions. All-trans retinoic acid (ATRA is a metabolite of vitamin A which plays a role in healing the inflamed tissue and maintain the immune system. The purpose of this study was to determine the effect of ATRA on the expression of MMP-2 in mouse models Rattus norvegicus of periodontitis. Methods: Experimental laboratory by using post test only with control group design. This study used 25 male Wistar mice (Rattus norvegicus that divided into 5 groups. Group 1 (G1 is a group of healthy mice, group 2 (G2 is a group of sick mice as induced periodontitis without treatment, group 3 (G3 is a group of periodontitis mice treated with 5 mg/kg dose of ATRA, group 4 (G4 is a group of periodontitis mice treated with 10 mg/kg dose of ATRA, group 5 (G5 is a group of periodontitis mice treated with 20 mg/kg dose of ATRA. Periodontitis induction was induced by Pg. bacteria every 3 days for 28 days and followed by administration of ATRA for 7 days. Expression of MMP-2 from gingival tissues and periodontal ligament was obtained by immunohistochemical methods. Results were analyzed using the Shapiro-Wilk Test and Mann-Whitney Test. Results: The results showed there were significant differences in the positive area of MMP-2 and MMP-2 color intensity (p < 0.05 between groups. Conclusion: ATRA dose of 20 mg/kg is the most effective dose in inhibiting the expression of MMP-2 in mice models of periodontitis when compared with the dose on other groups.

  7. [Progress on matrix metalloproteinase inhibitors]. (United States)

    Lingling, Jia; Qianbing, Wan


    Continuing advances in dentin bonding technology and adhesives revolutionized bonding of resin-based composite restorations. However, hybrid layers created by contemporary dentin adhesives present imperfect durability, and degradation of collagen matrix by endogenous enzymes is a significant factor causing destruction of hybrid layers. Bond durability can be improved by using enzyme inhibitors to prevent collagen degradation and to preserve integrity of collagen matrix. This review summarizes progress on matrix metalloproteinase inhibitors (including chlorhexidine, ethylenediaminetetraacetic acid, quaternary ammonium salt, tetracycline and its derivatives, hydroxamic acid inhibitors, bisphosphonate derivative, and cross-linking agents) and suggests prospects for these compounds.

  8. N-phosphorylation labeling for analysis of twenty natural amino acids and small peptides by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. (United States)

    Gao, Xiang; Bi, Xin; Wei, Juntong; Peng, Zhimin; Liu, Hongxia; Jiang, Yuyang; Wei, Wei; Cai, Zongwei


    N-phosphorylation labeling was utilized to analyze the low molecular weight compounds by using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A wide range of natural amino acids and short peptides was successfully analyzed by MALDI-TOF MS without matrix background interferences. The N-phosphorylation labeling reaction was carried out easily within 30 min in a one-pot reaction under mild reaction conditions. The phosphoryl derivatization reaction is a global labeling approach with high selectivity and high specificity with targeting only on the N-terminal and ε-amino group of Lys. The incorporation of a neutral phosphoryl group with high gas-phase affinity of protons not only improves the ionization efficiency of target molecules and simultaneously decreases the ion suppression effects in MALDI-TOF MS analysis, but also greatly reduces or eliminates the matrix background interferences by suppressing the matrix signals and increasing the molecular weight of the targeted compounds. By applying the N-phosphorylation labeling approach, many amino acids could be detected in serum samples by using MALDI-TOF MS.

  9. Clustering of ingredients with amino acid composition similar to the nutritional requirement of Nile tilapia Agrupamento de ingredientes com composição de aminoácidos similar à exigência nutricional da tilápia do Nilo

    Directory of Open Access Journals (Sweden)

    Álvaro José de Almeida Bicudo


    Full Text Available The search for balanced diets, which may elicit improved growth of fish, requires appropriate selection of available protein sources. This study aims at clustering feedstuffs according to amino acid profile, determining which ones show essential amino acids (EAA profiles closer to the ideal dietary amino acids requirements of Nile tilapia (Oreochromis niloticus, and studying the relationship among amino acids feedstuffs groups. Tabled data on EAA more cystine and tyrosine, in relation to lysine contents, of 40 feedstuffs ordinarily used to formulate fish diets were studied. Feedstuffs were grouped according to amino acids profile by cluster analysis of Euclidean distances. The principal components analysis was used to determine the relationship among amino acids in each feedstuff group. Three groups of ingredients were parted and two ingredients, low tannin sorghum and corn gluten meal 60%, did not go with any group. Dietary amino acids requirements of Nile tilapia were similar to the amino acid profile of 22 feedstuffs. The principal component analysis explained with three principal components more than 75% of total variance of amino acids in three feedstuff groups. Therefore, until additional, detailed information on amino acids availability of different ingredients is consolidated, total amino acids profiles will continue to be important information to select and use conventional or surrogate ingredients for formulating and processing feeds for tilapia.A busca de uma ração balanceada, que proporcione maior crescimento aos peixes, passa pela escolha adequada das fontes protéicas disponíveis. Este estudo teve por objetivo agrupar alimentos de acordo com o perfil de aminoácidos essenciais, determinando quais mostram perfis mais próximos do requerimento da tilápia do Nilo (Oreochromis niloticus, e estudar a relação entre os aminoácidos dentro dos agrupamentos obtidos. Foram utilizadas composições de aminoácidos em relação ao conte

  10. Different preparations of natural and recombinant human interleukin-6 (IFN-beta 2, BSF-2) similarly stimulate acute phase protein synthesis and uptake of alpha-aminoisobutyric acid by cultured rat hepatocytes. (United States)

    Bereta, J; Kurdowska, A; Koj, A; Hirano, T; Kishimoto, T; Content, J; Fiers, W; Van Damme, J; Gauldie, J


    1. Rat hepatocytes were cultured for 2 days in Williams E medium containing 1 microM insulin and dexamethasone. 2. Production of five plasma proteins was determined by electroimmunoassay in the media, and amino acid uptake was measured by [alpha-14C]aminoisobutyric acid accumulation in hepatocytes. 3. Supernatants from rat peritoneal macrophages and IL-6/IFN-beta 2/BSF-2 obtained from four different laboratories similarly stimulated synthesis of fibrinogen, alpha 1-cysteine proteinase inhibitor and alpha 2-macroglobulin, as well as [14C]-accumulation in cultured hepatocytes. 4. It is concluded that IL-6 is the principal hepatocyte stimulating factor responsible for typical features of the acute phase response of liver cells.

  11. Mining Diagnostic Assessment Data for Concept Similarity (United States)

    Madhyastha, Tara; Hunt, Earl


    This paper introduces a method for mining multiple-choice assessment data for similarity of the concepts represented by the multiple choice responses. The resulting similarity matrix can be used to visualize the distance between concepts in a lower-dimensional space. This gives an instructor a visualization of the relative difficulty of concepts…

  12. Microencapsulated krill and tuna oil blend raises plasma long-chain n-3 polyunsaturated fatty acid levels compared to tuna oil with similar increases in ileal contractility in rats. (United States)

    Patten, Glen S; Sanguansri, Luz; Augustin, Mary Ann; Abeywardena, Mahinda Y; Bird, Anthony R; Patch, Craig S; Belobrajdic, Damien P


    Long-chain n-3 polyunsaturated fatty acids (LC n-3 PUFA) may be more bioavailable from krill oil compared to fish oil due to their phospholipid structure. We tested whether a microencapsulated krill and tuna oil blend (ME-TOKO) provided greater LC n-3 PUFA bioavailability, improved blood lipid profiles and increased intestinal contractility compared to microencapsulated tuna oil (ME-TO). Rats were divided into three groups to receive isocaloric diets containing ME-TO, ME-TOKO and microencapsulated olive oil (ME-OO) at 0.3 or 2 g/100 g for 4 weeks. Final body and organ weights, feed intake and waste output were similar. ME-TOKO rats had higher plasma total LC n-3 PUFA levels compared to ME-TO, but liver LC n-3 PUFA levels and plasma triglyceride and cholesterol levels were similar in non-fasted rats. Diets containing 2% ME-TO and ME-TOKO also showed similar increases in ileal contractility. In summary, ME-TO bioavailability of LC n-3 PUFA was similar to ME-TOKO.

  13. Fluorescent water soluble polymers for isozyme-selective interactions with matrix metalloproteinase-9. (United States)

    Dutta, Rinku; Scott, Michael D; Haldar, Manas K; Ganguly, Bratati; Srivastava, D K; Friesner, Daniel L; Mallik, Sanku


    Matrix metalloproteinases (MMPs) are overexpressed in various pathological conditions, including cancers. Although these isozymes have similar active sites, the patterns of exposed amino acids on their surfaces are different. Herein, we report the synthesis and molecular interactions of two water soluble, fluorescent polymers which demonstrate selective interactions with MMP-9 compared to MMP-7 and -10. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Inequalities involving upper bounds for certain matrix operators

    Indian Academy of Sciences (India)

    Copson and Hilbert matrix operators, which are recently considered in [5] and [6] and similar to that in [10]. Keywords. Inequality; norm; summability matrix; Hausdorff matrix; Hilbert matrix; weighted sequence space; Lorentz sequence space. 1. Introduction. We study the norm of a certain matrix operator on lp(w) and Lorentz ...

  15. Microcrystalline cellulose based matrix solid phase dispersion microextration for isomeric triterpenoid acids in loquat leaves by ultrahigh-performance liquid chromatography and quadrupole time-of-flight mass spectrometry. (United States)

    Cao, Jun; Peng, Li-Qing; Xu, Jing-Jing


    An analytical procedure based on matrix solid phase dispersion (MSPD) microextration and ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry was developed for the determination of isomeric triterpenoid acids (maslinic acid, corosolic acid, oleanolic acid and ursolic acid) in loquat leaves. Microcrystalline cellulose was used for the first time as a solid sorbent in MSPD microextration. Compared with the traditional extraction methods, the proposed method possessed the advantages of shorter extraction time, and lower consumption of sample, sorbent and organic solvent. The MSPD parameters that influenced the extraction efficiency of isomeric analytes were investigated and optimized in detail. Under the optimized conditions, good linearity was obtained with correlation coefficients higher than 0.9990. The limits of detection and quantification were 19.6-51.6μg/kg and 65.3-171.8μg/kg, respectively. Meanwhile, the recoveries obtained for all the analytes were ranging from 90.1% to 107.5%. Finally, the optimized method was successfully applied for analyzing these isomeric acids in loquat leaves samples obtained from different cultivated areas. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. alpha-Lipoic acid modulates extracellular matrix and angiogenesis gene expression in non-healing wounds treated with hyperbaric oxygen therapy

    Czech Academy of Sciences Publication Activity Database

    Alleva, R.; Tomasetti, M.; Sartini, D.; Emanuelli, M.; Nasole, E.; Di Donato, F.; Borghi, B.; Santarelli, L.; Neužil, Jiří


    Roč. 14, 3-4 (2008), s. 175-183 ISSN 1076-1551 Institutional research plan: CEZ:AV0Z50520514; CEZ:AV0Z50520701 Keywords : angiogenesis mediators * wound repair * matrix metalloproteinase expression Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.411, year: 2008

  17. Protein-protein interaction based on pairwise similarity

    Directory of Open Access Journals (Sweden)

    Zaki Nazar


    Full Text Available Abstract Background Protein-protein interaction (PPI is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines. Results To assess the ability of the proposed method to recognize the difference between "interacted" and "non-interacted" proteins pairs, we applied it on different datasets from the available yeast saccharomyces cerevisiae protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction. Conclusion Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.

  18. Matrix analysis

    CERN Document Server

    Bhatia, Rajendra


    A good part of matrix theory is functional analytic in spirit. This statement can be turned around. There are many problems in operator theory, where most of the complexities and subtleties are present in the finite-dimensional case. My purpose in writing this book is to present a systematic treatment of methods that are useful in the study of such problems. This book is intended for use as a text for upper division and gradu­ ate courses. Courses based on parts of the material have been given by me at the Indian Statistical Institute and at the University of Toronto (in collaboration with Chandler Davis). The book should also be useful as a reference for research workers in linear algebra, operator theory, mathe­ matical physics and numerical analysis. A possible subtitle of this book could be Matrix Inequalities. A reader who works through the book should expect to become proficient in the art of deriving such inequalities. Other authors have compared this art to that of cutting diamonds. One first has to...

  19. Preparation of high efficiency and low carry-over immobilized enzymatic reactor with methacrylic acid-silica hybrid monolith as matrix for on-line protein digestion. (United States)

    Yuan, Huiming; Zhang, Lihua; Zhang, Yukui


    In this work, a novel kind of organic-silica hybrid monolith based immobilized enzymatic reactor (IMER) was developed. The monolithic support was prepared by a single step "one-pot" strategy via the polycondensation of tetramethoxysilane and vinyltrimethoxysilane and in situ copolymerization of methacrylic acid and vinyl group on the precondensed siloxanes with ammonium persulfate as the thermal initiator. Subsequently, the monolith was activated by N-(3-dimethylaminopropyl) - N'-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS), followed by the modification of branched polyethylenimine (PEI) to improve the hydrophilicity. Finally, after activated by EDC and NHS, trypsin was covalently immobilized onto the monolithic support. The performance of such a microreactor was evaluated by the in sequence digestion of bovine serum albumin (BSA) and myoglobin, followed by MALDI-TOF-MS analysis. Compared to those obtained by traditional in-solution digestion, not only higher sequence coverages for BSA (74±1.4% vs. 59.5±2.7%, n=6) and myoglobin (93±3% vs. 81±4.5%, n=6) were obtained, but also the digestion time was shortened from 24h to 2.5 min, demonstrating the high digestion efficiency of such an IMER. The carry-over of these two proteins on the IMER was investigated, and peptides from BSA could not be found in mass spectrum of myoglobin digests, attributed to the good hydrophilicity of our developed monolithic support. Moreover, the dynamic concentration range for protein digestion was proved to be four orders of magnitude, and the IMER could endure at least 7-day consecutive usage. Furthermore, such an IMER was coupled with nano-RPLC-ESI/MS/MS for the analysis of extracted proteins from Escherichia coli. Compared to formerly reported silica hybrid monolith based IMER and the traditional in-solution counterpart, by our developed IMER, although the identified protein number was similar, the identified distinct peptide number was improved by 7% and 25% respectively

  20. Graphite supported preparation (GSP) of α-cyano-4-hydroxycinnamic acid (CHCA) for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) for peptides and proteins. (United States)

    Gorka, Jan; Bahr, Ute; Karas, Michael


    Graphite as MALDI matrix or in combination with other substances has been reported in recent years. Here, we demonstrate that graphite can be used as target coating supporting the crystallization of the α-cyano-4-hydroxycinnamic acid matrix. A conventional dried-droplet preparation of matrix and analyte solution on a graphite-coated metal target leads to a thin, uniform layer of cubic crystals with about 1 μm edge length. Commercially available graphite powder of 1-2 μm particle size is gently wiped over the target using a cotton Q-tip, leading to an ultra-thin, not-visible film. This surface modification considerably improves analysis of peptides and proteins for MALDI MS using conventional dried-droplet preparation. Compared with untreated targets, the signal intensities of standard peptides are up to eight times higher when using the graphite supported crystallization. The relative standard deviation in peak area of angiotensin II for sample amounts between 1 and 50 fmol is reduced to about 15 % compared with 45 % for untreated sample holders. For a quantification of 1 fmol of the peptide using an internal standard the coefficient of variation is reduced to 3.5 % from 8 %. The new graphite supported preparation (GSP) protocol is very simple and does not require any technical nor manual skills. All standard solvents for peptides and proteins can be used.

  1. Domain similarity based orthology detection. (United States)

    Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M; Bornberg-Bauer, Erich


    Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationally feasible in a reasonable amount of time. We propose to speed up the detection of orthologous proteins by using strings of domains to characterize the proteins. We present two new protein similarity measures, a cosine and a maximal weight matching score based on domain content similarity, and new software, named porthoDom. The qualities of the cosine and the maximal weight matching similarity measures are compared against curated datasets. The measures show that domain content similarities are able to correctly group proteins into their families. Accordingly, the cosine similarity measure is used inside porthoDom, the wrapper developed for proteinortho. porthoDom makes use of domain content similarity measures to group proteins together before searching for orthologs. By using domains instead of amino acid sequences, the reduction of the search space decreases the computational complexity of an all-against-all sequence comparison. We demonstrate that representing and comparing proteins as strings of discrete domains, i.e. as a concatenation of their unique identifiers, allows a drastic simplification of search space. porthoDom has the advantage of speeding up orthology detection while maintaining a degree of accuracy similar to proteinortho. The implementation of porthoDom is released using python and C++ languages and is available under the GNU GPL licence 3 at .

  2. Temperature-dependent Henry's law constants of 4-alkyl-branched chain fatty acids and 3-methylindole in an oil-air matrix and analysis of volatiles in lamb fat using selected ion flow tube mass spectrometry (SIFT-MS). (United States)

    Castada, Hardy Z; Polentz, Victoria; Barringer, Sheryl; Wick, Macdonald


    4-Alkyl-branched chain fatty acids and 3-methylindole are characteristic flavor compounds associated with sheep meat. Determining their partitioning behavior between the gas and condensed phase and ultimately developing a correlation between the compound's headspace concentration and sensory descriptive grouping are important for high throughput characterization and grading classification. The headspace concentrations of 3-methylindole, 4-methyloctanoic acid, 4-ethyloctanoic acid, and 4-methylnonanoic acid above corn oil-based standard solutions, and lamb fat samples were measured using selected ion flow tube-mass spectrometry (SIFT-MS). The standard solutions were equilibrated at 80, 100, 110 and 125(o) C while the fat samples were equilibrated at 125(o) C. Statistical evaluation, linear and polynomial regression analyses were performed to establish the compound-specific and temperature-dependent Henry's law constants, enthalpy (∆H) and entropy (∆S) of phase changes. The Henry's law constants (kH(cp) ) were calculated from the regression analysis with a high degree of confidence (p 0.99). The kH(cp) increased with increase in equilibrium temperature. The empirical calculation of the ∆H and ∆S at different temperatures confirmed the temperature-dependence of the Henry's law constants. The headspace concentrations of the lamb-flavor compounds were determined above actual lamb fat samples and the corresponding condensed phase concentrations were successfully derived. The temperature-dependent Henry's law constants, ∆H, and ∆S of phase changes for 3-methylindole, 4-methyloctanoic acid, 4-ethyloctanoic acid, and 4-methylnonanoic acid in an air-oil matrix were empirically derived. The effectiveness of SIFT-MS for the direct, real-time, and rapid determination of key flavor compounds in lamb fat samples was established. This article is protected by copyright. All rights reserved.

  3. Revisiting amino acid substitution matrices for identifying distantly related proteins. (United States)

    Yamada, Kazunori; Tomii, Kentaro


    Although many amino acid substitution matrices have been developed, it has not been well understood which is the best for similarity searches, especially for remote homology detection. Therefore, we collected information related to existing matrices, condensed it and derived a novel matrix that can detect more remote homology than ever. Using principal component analysis with existing matrices and benchmarks, we developed a novel matrix, which we designate as MIQS. The detection performance of MIQS is validated and compared with that of existing general purpose matrices using SSEARCH with optimized gap penalties for each matrix. Results show that MIQS is able to detect more remote homology than the existing matrices on an independent dataset. In addition, the performance of our developed matrix was superior to that of CS-BLAST, which was a novel similarity search method with no amino acid matrix. We also evaluated the alignment quality of matrices and methods, which revealed that MIQS shows higher alignment sensitivity than that with the existing matrix series and CS-BLAST. Fundamentally, these results are expected to constitute good proof of the availability and/or importance of amino acid matrices in sequence analysis. Moreover, with our developed matrix, sophisticated similarity search methods such as sequence-profile and profile-profile comparison methods can be improved further. Newly developed matrices and datasets used for this study are available at

  4. Application of fractional factorial design and Doehlert matrix in the optimization of experimental variables associated with the ultrasonic-assisted acid digestion of chocolate samples for aluminum determination by atomic absorption spectrometry. (United States)

    Jalbani, Nusrat; Kazi, Tasneem Gul; Jamali, Muhammad Khan; Arain, Muhammad Balal; Afridi, Hassan Imran; Sheerazi, Syed T; Ansari, Rehana


    A simple and rapid method based on ultrasound energy is described for the determination of aluminum (AI) in complex matrixes of chocolate and candy samples by electrothermal atomic absorption spectrometry. The optimization strategy was carried out using multivariate methodologies. Five variables (temperature of the ultrasonic bath; exposure time to ultrasound energy; volumes of 2 acid mixtures, HNO3-H2SO4-H2O2 (1 + 1 + 1) and HNO3-H2O2 (1 + 1); and sample mass) were considered as factors in the optimization process. Interactions between analytical factors and their optimal levels were investigated using fractional factorial and Doehlert matrix designs. Validation of the ultrasonic-assisted acid digestion procedure was performed against standard reference materials, milk powder (SRM 8435) and wheat flour (SRM 1567a). The proposed procedure allowed Al determination with a detection limit of 2.3 microg/L (signal-to-noise = 3) and a precision, calculated as relative standard deviation, of 2.2% for a set of 10 measurements of certified samples. The recovery of Al by the proposed procedure was close to 100%, and no significant difference at the 95% confidence level was found between determined and certified values of Al. The proposed procedure was applied to the determination of Al in chocolate and candy samples. The results indicated that cocoa-based chocolates have higher contents of Al than milk- and sugar-based chocolates and candies.

  5. Quantitative determination of nicotinic acid in micro liter volume of urine sample by drop-to-drop solvent microextraction coupled to matrix assisted laser desorption/ionization mass spectrometry. (United States)

    Shrivas, Kamlesh; Patel, Devesh Kumar


    Drop-to-drop solvent microextraction (DDSME) coupled with matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS) for quantitative determination of nicotinic acid in one drop of urine sample has been proposed. All parameters, such as type of organic solvent, extraction time, exposure volume solvent, pH of the sample solution that affecting the separation and preconcentration of nicotinic acid were investigated. Under the optimal conditions, the detection limit of the method was 20 ng mL(-1) and the relative standard deviations (RSD) for determination of the nicotinic acid were in the range of 8.0-12.5%. The calculated calibration curves gave linearity in the range of 80-1000 ng mL(-1). The main advantages of the proposed method are simple, fast, and small amount of sample solution is used for separation and preconcentration of nicotinic acid. This method could be also useful for the analysis of other interested analytes in small volume of biological samples, like plasma, saliva and urine, where the availability of samples are limited. Copyright © 2010 Elsevier B.V. All rights reserved.

  6. Similarity transformations of MAPs

    Directory of Open Access Journals (Sweden)

    Andersen Allan T.


    Full Text Available We introduce the notion of similar Markovian Arrival Processes (MAPs and show that the event stationary point processes related to two similar MAPs are stochastically equivalent. This holds true for the time stationary point processes too. We show that several well known stochastical equivalences as e.g. that between the H 2 renewal process and the Interrupted Poisson Process (IPP can be expressed by the similarity transformations of MAPs. In the appendix the valid region of similarity transformations for two-state MAPs is characterized.

  7. Similarity after Goodman

    NARCIS (Netherlands)

    Decock, L.B.; Douven, I.


    In a famous critique, Goodman dismissed similarity as a slippery and both philosophically and scientifically useless notion. We revisit his critique in the light of important recent work on similarity in psychology and cognitive science. Specifically, we use Tversky's influential set-theoretic

  8. Judgments of brand similarity

    NARCIS (Netherlands)

    Bijmolt, THA; Wedel, M; Pieters, RGM; DeSarbo, WS

    This paper provides empirical insight into the way consumers make pairwise similarity judgments between brands, and how familiarity with the brands, serial position of the pair in a sequence, and the presentation format affect these judgments. Within the similarity judgment process both the

  9. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji


    Full Text Available The topic of identifying the similarity of graphs was considered as highly recommended research field in the Web semantic, artificial intelligence, the shape recognition and information research. One of the fundamental problems of graph databases is finding similar graphs to a graph query. Existing approaches dealing with this problem are usually based on the nodes and arcs of the two graphs, regardless of parental semantic links. For instance, a common connection is not identified as being part of the similarity of two graphs in cases like two graphs without common concepts, the measure of similarity based on the union of two graphs, or the one based on the notion of maximum common sub-graph (SCM, or the distance of edition of graphs. This leads to an inadequate situation in the context of information research. To overcome this problem, we suggest a new measure of similarity between graphs, based on the similarity measure of Wu and Palmer. We have shown that this new measure satisfies the properties of a measure of similarities and we applied this new measure on examples. The results show that our measure provides a run time with a gain of time compared to existing approaches. In addition, we compared the relevance of the similarity values obtained, it appears that this new graphs measure is advantageous and  offers a contribution to solving the problem mentioned above.

  10. New Similarity Functions

    DEFF Research Database (Denmark)

    Yazdani, Hossein; Ortiz-Arroyo, Daniel; Kwasnicka, Halina


    spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets......In data science, there are important parameters that affect the accuracy of the algorithms used. Some of these parameters are: the type of data objects, the membership assignments, and distance or similarity functions. This paper discusses similarity functions as fundamental elements in membership...... assignments. The paper introduces Weighted Feature Distance (WFD), and Prioritized Weighted Feature Distance (PWFD), two new distance functions that take into account the diversity in feature spaces. WFD functions perform better in supervised and unsupervised methods by comparing data objects on their feature...

  11. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore


    Full Text Available Computational measures of semantic similarity between geographic terms provide valuable support across geographic information retrieval, data mining, and information integration. To date, a wide variety of approaches to geo-semantic similarity have been devised. A judgment of similarity is not intrinsically right or wrong, but obtains a certain degree of cognitive plausibility, depending on how closely it mimics human behavior. Thus selecting the most appropriate measure for a specific task is a significant challenge. To address this issue, we make an analogy between computational similarity measures and soliciting domain expert opinions, which incorporate a subjective set of beliefs, perceptions, hypotheses, and epistemic biases. Following this analogy, we define the semantic similarity ensemble (SSE as a composition of different similarity measures, acting as a panel of experts having to reach a decision on the semantic similarity of a set of geographic terms. The approach is evaluated in comparison to human judgments, and results indicate that an SSE performs better than the average of its parts. Although the best member tends to outperform the ensemble, all ensembles outperform the average performance of each ensemble's member. Hence, in contexts where the best measure is unknown, the ensemble provides a more cognitively plausible approach.

  12. Additive Similarity Trees (United States)

    Sattath, Shmuel; Tversky, Amos


    Tree representations of similarity data are investigated. Hierarchical clustering is critically examined, and a more general procedure, called the additive tree, is presented. The additive tree representation is then compared to multidimensional scaling. (Author/JKS)

  13. Gender similarities and differences. (United States)

    Hyde, Janet Shibley


    Whether men and women are fundamentally different or similar has been debated for more than a century. This review summarizes major theories designed to explain gender differences: evolutionary theories, cognitive social learning theory, sociocultural theory, and expectancy-value theory. The gender similarities hypothesis raises the possibility of theorizing gender similarities. Statistical methods for the analysis of gender differences and similarities are reviewed, including effect sizes, meta-analysis, taxometric analysis, and equivalence testing. Then, relying mainly on evidence from meta-analyses, gender differences are reviewed in cognitive performance (e.g., math performance), personality and social behaviors (e.g., temperament, emotions, aggression, and leadership), and psychological well-being. The evidence on gender differences in variance is summarized. The final sections explore applications of intersectionality and directions for future research.

  14. Potassium cation affinities of matrix assisted laser desorption ionization matrices determined by threshold collision-induced dissociation: application to benzoic acid derivatives. (United States)

    Chinthaka, S D M; Rodgers, M T


    Threshold collision-induced dissociation of K+(xBA) complexes with xenon is studied using guided ion beam mass spectrometry. The xBA ligands studied include benzoic acid and all of the mono- and dihydroxy-substituted benzoic acids: 2-, 3-, and 4-hydroxybenzoic acid and 2,3-, 2,4-, 2,5-, 2,6-, 3,4-, and 3,5-dihydroxybenzoic acid. In all cases, the primary product corresponds to endothermic loss of the intact xBA ligand. The cross section thresholds are interpreted to yield 0 and 298 K bond dissociation energies (BDEs) for K+-xBA after accounting for the effects of multiple ion-neutral collisions, the kinetic and internal energy distributions of the reactants, and dissociation lifetimes. Density functional theory calculations at the B3LYP/6-31G* level of theory are used to determine the structures of the xBA ligands and their complexes with K+. Theoretical BDEs are determined from single-point energy calculations at the B3LYP/6-311+G(2d,2p) and MP2(full)/6-311+G(2d,2p) levels using B3LYP/6-31G* optimized geometries. Four favorable binding modes for the K+(xBA) complexes are found. In all complexes to an xBA ligand that does not have a 2-hydroxyl substituent, the most favorable binding mode corresponds to a single interaction with the carbonyl oxygen atom. Formation of a 4-membered ring via chelation interactions with both oxygen atoms of the carboxylic acid group is found to be the most favorable binding mode for all of the 2-hydroxy-substituted systems except K+(2,3-dihydroxybenzoic acid). In these complexes, a hydrogen-bonding interaction between the hydrogen atom of the carboxylic acid moiety and the oxygen atom of the 2-hydroxy substituent provides additional stabilization. Formation of a 5-membered chelation ring via interaction of K+ with the oxygen atoms of adjacent hydroxyl substituents is also favorable and corresponds to the ground-state geometry for the K+(23DHBA) complex. Formation of a 6-membered chelation ring via interaction of K+ with the carbonyl and

  15. Degradation of extracellular matrix by larvae of Schistosoma mansoni. I. Degradation by cercariae as a model for initial parasite invasion of host

    Energy Technology Data Exchange (ETDEWEB)

    McKerrow, J.H.; Keene, W.E.; Jeong, K.H.; Werb, Z.


    The ability of cercariae of Schistosoma mansoni to degrade a model extracellular connective tissue matrix produced by rat vascular smooth muscle cells in culture was investigated. In this model, connective tissue macromolecules are present in the interactive framework that characterizes their structure in vivo. Cercariae were stimulated to degrade the matrix by skin lipid or linoleic acid. At the maximally stimulating concentration of linoleic acid (25 2/), 68% of the total matrix was degraded, including 57% of the glycoprotein, 79% of the elastin, and 8% of the collagen. Degradation of matrix was inhibited by ..cap alpha../sub 1/-proteinase inhibitor and soybean trypsin inhibitor. Ethylenediaminetetraacetic acid inhibited degradation by unstimulated but not linoleic acid-stimulated cercariae. Preacetabular gland secretions collected from cercariae also degraded the matrix with an activity 86% of that of live cercariae. Preacetabular gland proteolytic activity was also inhibited by ..cap alpha../sub 1/-proteinase inhibitor, soybean trypsin inhibitor, and ethylenediaminetetraacetic acid. The similar characteristics of matrix degradation by both live cercariae and cercarial preacetabular gland secretions support the idea that a proteinase secreted from cercarial preacetabular glands facilitates invasion of skin and connective tissue by these larvae. Degradation of elastin and glycoprotein constituentes of extracellular matrix is probably essential for skin penetration.

  16. Composite glycerol/graphite/aromatic acid matrices for thin-layer chromatography/matrix-assisted laser desorption/ionization mass spectrometry of heterocyclic compounds. (United States)

    Esparza, Cesar; Borisov, R S; Varlamov, A V; Zaikin, V G


    New composite matrices have been suggested for the analysis of mixtures of different synthetic organic compounds (N-containing heterocycles and erectile dysfunction drugs) by thin layer chromatography/matrix-assisted laser desorption ionization time-of-flight mass spectrometry (TLC/MALDI-TOF). Different mixtures of classical MALDI matrices and graphite particles dispersed in glycerol were used for the registration of MALDI mass spectra directly from TLC plates after analytes separation. In most of cases, the mass spectra possessed [M+H](+) ions; however, for some analytes only [M+Na](+) and [M+K](+) ions were observed. These ions have been used to generate visualized TLC chromatograms. The described approach increases the desorption/ionization efficiencies of analytes separated by TLC, prevent spot blurring, simplifies and decrease time for sample preparation. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Integral edge seals for phosphoric acid fuel cells (United States)

    Granata, Jr., Samuel J. (Inventor); Woodle, Boyd M. (Inventor); Dunyak, Thomas J. (Inventor)


    A phosphoric acid fuel cell having integral edge seals formed by an elastomer permeating an outer peripheral band contiguous with the outer peripheral edges of the cathode and anode assemblies and the matrix to form an integral edge seal which is reliable, easy to manufacture and has creep characteristics similar to the anode, cathode and matrix assemblies inboard of the seals to assure good electrical contact throughout the life of the fuel cell.

  18. Improved method for the analysis of organic acids and new derivatization of alcohols in complex natural aqueous matrixes: application to wine and apple vinegar. (United States)

    Giumanini, A G; Verardo, G; Della Martina, D; Toniutti, N


    An improvement in the procedure for investigation of organic acids and a new derivatization method, amenable to gas chromatographic-mass spectrometric detection of alcohols, are presented. The latter is based on the formation of phenacetyl esters. The simultaneous application of the two methods also allows data to be obtained on some volatile neutrals present in complex natural aqueous fluids. Application to wine and cider vinegars allowed detection of a number of previously unreported components, among which are interesting partially esterified polycarboxylic esters.

  19. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom


    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field...... of action. It is theorized that to meet this challenge organizations may substitute increased similarity on one core dimension for increased idiosyncrasy on another, but only after a certain level of isomorphism is reached. Results of quantitative analyses support this theory and show that an inverse U...

  20. Oxidizing gel formulation for nuclear decontamination: rheological and acidic properties of the organic matrix and its ozonolysis; Formulation d'un gel oxydant a matrice organique applicable a la decontamination nucleaire: proprietes rheologiques, acido-basiques et ozonolyse de la matrice

    Energy Technology Data Exchange (ETDEWEB)

    Rouy, E


    An acidic and oxidizing gel was formulated with a purely organic matrix, xanthan gum, at low concentrations (1 to 2 wt %). This polymer gel was investigated in various media (aqueous, acidic and ceric) by means of rheology: shear thinning behaviour, thixotropy, yield stress... Evidences of unexpected rheological properties in highly concentrated media show that xanthan is quite convenient for industrial projection of this type of gel on metallic walls in nuclear plants, notwithstanding its time-limited resistance to oxidation (about a few hours). Complexation mechanisms between ceric species and polar sites of the polymer led us to characterise acidic properties of our xanthan sample by potentiometric titration and {sup 1}H NMR techniques. The matrix was finally treated by ozonolysis to suppress organic residues, as required to handle nuclear wastes. In acidic medium, ozonolysis of the gel was achieved successfully while in acidic and ceric medium this process showed limited efficiency, needing further investigation to be clarified. (author)

  1. Incremental Similarity and Turbulence

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole E.; Hedevang, Emil; Schmiegel, Jürgen

    This paper discusses the mathematical representation of an empirically observed phenomenon, referred to as Incremental Similarity. We discuss this feature from the viewpoint of stochastic processes and present a variety of non-trivial examples, including those that are of relevance for turbulence...

  2. Analysis of complex phthalic acid based polyesters by the combination of size exclusion chromatography and matrix-assisted laser desorption/ionization mass spectrometry. (United States)

    Pretorius, Nadine O; Rode, Karsten; Simpson, Jaylin M; Pasch, Harald


    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used in conjunction with size exclusion chromatography (SEC) to investigate a model polyester system based on phthalic anhydride-1,2-propylene glycol. The polyesters were synthesized with a 30% molar excess of glycol, with kinetic samples being removed during different intervals of the polyesterification reaction. SEC was used to track the course of the reaction by determining the molecular weight and molecular weight distributions before subsequent off-line coupling with MALDI-TOF MS as a selective detection method to determine the chemical composition, identify the functionality type distributions as well as assist in assigning structural conformations. Mass spectrometry analysis proved to be a highly effective tool to facilitate the identification of the narrowly dispersed fractions obtained from the chromatographic separations as well as serve as a core method to investigate the heterogeneous nature of the bulk kinetic samples. Through the hyphenation of these sophisticated polymer characterization techniques, information on the molecular heterogeneity of the model polyesters, showing a complex variety of possible distributions, was obtained. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Anti-inflammatory potential of a malleable matrix composed of fermented whey proteins and lactic acid bacteria in an atopic dermatitis model

    Directory of Open Access Journals (Sweden)

    Dupont Claude


    Full Text Available Abstract Background Over the last 10 years, whey proteins have received considerable attention in the area of functional foods and nutraceuticals. In this paper, a novel fermented whey protein-based product described as a gel-like Malleable Protein Matrix (MPM has been tested for its anti-inflammatory activity. Preliminary in vitro results have already indicated that MPM could exert such an anti-inflammatory activity. Methods The systemic anti-inflammatory activity of the MPM was explored using the oxazolone-induced atopic contact dermatitis mouse model (ACD. Parameters including ear thickness, side effects as well as neutrophil extravasation were monitored. Results In the ACD model, the MPM exhibited an anti-inflammatory effect comparable to that of hydrocortisone (positive control. Mice fed with MPM showed strong reduction of the ear inflammation while no side effects, as compared to hydrocortisone, were observed. The MPM seemed to reduce neutrophil extravasation in tissue as evidenced by blood polymorphonuclear cells and ear myeloperoxidase content. Conclusion The anti-inflammatory activity demonstrated in the ACD model suggests that the mechanism of action of the MPM is different than that of hydrocortisone and could become a relevant product for people suffering from dermatological manifestations associated with immune dysfunctions such as allergies, eczema, dermatitis, and autoimmune diseases.

  4. Tracking the composition and transformation of humic and fulvic acids during vermicomposting of sewage sludge by elemental analysis and fluorescence excitation-emission matrix. (United States)

    Zhang, Jie; Lv, Baoyi; Xing, Meiyan; Yang, Jian


    Sewage sludge (T1) and the mixture of sewage sludge and cattle dung (T2) were vermicomposted with Eisenia fetida, respectively. The transformation of humic acid (HA) and fulvic acid (FA) extracted from these two treatments were evaluated by a series of chemical and spectroscopic methods. Results indicated that the vermicomposting decreased pH, TOC, and C/N ratio, and increased EC, total extractable C, and HA contents. The FA content in treatment T1 was increased significantly, and only slight increasing was observed in treatment T2. Moreover, vermicomposting decreased H content, C/N ratio, proteinaceous and carbohydrates components, and increased the N content, C/H ratio, aromatic compounds and polycondensation structures in HA and FA. In addition, fluorescence spectra and fluorescence regional integration indicated that protein-like groups were degraded and HA compounds were formed. Furthermore, the addition of cattle dung enhanced the humification process and improved the HA quality in spite of no significant effect on the FA. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Clinical and radiographic evaluation of copolymerized Polylactic/polyglycolic acids as a bone filler in combination with a cellular dermal matrix graft around immediate implants (United States)

    Soliman, Mahitab M.; Zaki, Azza Abdulrahman; El Gazaerly, Hanaa Mohamed; Shemmrani, Ammar Al; Sorour, Abd El Latif


    Objective This study was conducted to evaluate clinically and radiographically the use of a cellular dermal matrix allograft (Alloderm) in combination with PLA/PGA (Fisiograft) around immediate implants. Materials and Methods Fourteen patients were included in this study, three patients received two implants, total of seventeen implants were placed. Periapical radiographs and orthopantomographs were taken. The selected teeth were extracted atraumatically after the reflection of full thickness flaps. One-piece Zimmer implants were placed immediately into the sockets. Weeks from implantation, radiographic evaluation was made at 6 Fisiograft in powder form was placed in the osseous defects around the implants. The implants were immediately restored with provisional crowns free from occlusion. Patients were clinically evaluated at 3, 6, and 14 months after loading which was done after 6 weeks from implantation. Radiographic evaluation was made at 6 and 14 months from implant placement. Results showed that immediate implantation was successful in sixteen out of seventeen implants, clinical parameters regarding plaque index, gingival index, there was a slight decrease through the follow-up periods from 3 to 14 months but it was non-significant, while there was a significant decrease in the probing depth. Radiographically there was a significant increase in the bone density from 6 to 14 months post loading, while the vertical bone defect was significantly decreased. The fisiograft functioned well as space maker and scaffolding material. The Alloderm performed well as a membrane to be used in association with immediate implants and it has a good potentiality for increasing the width of the keratinized gingiva, which is an important feature for implant esthetics. Conclusion the combination technique between the bone graft and the membrane proved to be successful to overcome dehiscence and osseous defects around immediate implants. PMID:25780357

  6. More Similar Than Different

    DEFF Research Database (Denmark)

    Pedersen, Mogens Jin


    What role do employee features play into the success of different personnel management practices for serving high performance? Using data from a randomized survey experiment among 5,982 individuals of all ages, this article examines how gender conditions the compliance effects of different...... incentive treatments—each relating to the basic content of distinct types of personnel management practices. The findings show that males and females are more similar than different in terms of the incentive treatments’ effects: Significant average effects are found for three out of five incentive...

  7. Towards Google matrix of brain

    Energy Technology Data Exchange (ETDEWEB)

    Shepelyansky, D.L., E-mail: [Laboratoire de Physique Theorique (IRSAMC), Universite de Toulouse, UPS, F-31062 Toulouse (France); LPT - IRSAMC, CNRS, F-31062 Toulouse (France); Zhirov, O.V. [Budker Institute of Nuclear Physics, 630090 Novosibirsk (Russian Federation)


    We apply the approach of the Google matrix, used in computer science and World Wide Web, to description of properties of neuronal networks. The Google matrix G is constructed on the basis of neuronal network of a brain model discussed in PNAS 105 (2008) 3593. We show that the spectrum of eigenvalues of G has a gapless structure with long living relaxation modes. The PageRank of the network becomes delocalized for certain values of the Google damping factor {alpha}. The properties of other eigenstates are also analyzed. We discuss further parallels and similarities between the World Wide Web and neuronal networks.

  8. Poly(DL-lactic acid) as a direct compression excipient in controlled release tablets - Part I. Compaction behaviour and release characteristics of poly(DL-lactic acid) matrix tablets

    NARCIS (Netherlands)

    Steendam, R; Lerk, CF


    High-molecular weight poly(DL-lactic acid) (PDLA, M-v 85000) was applied as a direct compression excipient in controlled release tablets. PDLA powders with good flowing properties were obtained by milling pre-cooled PDLA granules. Apparent yield pressure values ranged from 44 to 71 MPa for

  9. Similar or different?

    DEFF Research Database (Denmark)

    Cornér, Solveig; Pyhältö, Kirsi; Peltonen, Jouni


    experienced by PhD students within the same discipline. This study explores the support experiences of 381 PhD students within the humanities and social sciences from three research-intensive universities in Denmark (n=145) and Finland (n=236). The mixed methods design was utilized. The data were collected...... counter partners, whereas the Finnish students perceived lower levels of instrumental support than the Danish students. The findings imply that seemingly similar contexts hold valid differences in experienced social support and educational strategies at the PhD level.......Previous research has identified researcher community and supervisory support as key determinants of the doctoral journey contributing to students’ persistence and robustness. However, we still know little about cross-cultural variation in the researcher community and supervisory support...

  10. Affinity Propagation Clustering Using Path Based Similarity

    Directory of Open Access Journals (Sweden)

    Yuan Jiang


    Full Text Available Clustering is a fundamental task in data mining. Affinity propagation clustering (APC is an effective and efficient clustering technique that has been applied in various domains. APC iteratively propagates information between affinity samples, updates the responsibility matrix and availability matrix, and employs these matrices to choose cluster centers (or exemplars of respective clusters. However, since it mainly uses negative Euclidean distance between exemplars and samples as the similarity between them, it is difficult to identify clusters with complex structure. Therefore, the performance of APC deteriorates on samples distributed with complex structure. To mitigate this problem, we propose an improved APC based on a path-based similarity (APC-PS. APC-PS firstly utilizes negative Euclidean distance to find exemplars of clusters. Then, it employs the path-based similarity to measure the similarity between exemplars and samples, and to explore the underlying structure of clusters. Next, it assigns non-exemplar samples to their respective clusters via that similarity. Our empirical study on synthetic and UCI datasets shows that the proposed APC-PS significantly outperforms original APC and other related approaches.

  11. MALDI Matrix Research for Biopolymers (United States)

    Fukuyama, Yuko


    Matrices are necessary materials for ionizing analytes in matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). The choice of a matrix appropriate for each analyte controls the analyses. Thus, in some cases, development or improvement of matrices can become a tool for solving problems. This paper reviews MALDI matrix research that the author has conducted in the recent decade. It describes glycopeptide, carbohydrate, or phosphopeptide analyses using 2,5-dihydroxybenzoic acid (2,5-DHB), 1,1,3,3-tetramethylguanidinium (TMG) salts of p-coumaric acid (CA) (G3CA), 3-aminoquinoline (3-AQ)/α-cyano-4-hydroxycinnamic acid (CHCA) (3-AQ/CHCA) or 3-AQ/CA and gengeral peptide, peptide containing disulfide bonds or hydrophobic peptide analyses using butylamine salt of CHCA (CHCAB), 1,5-diaminonaphthalene (1,5-DAN), octyl 2,5-dihydroxybenzoate (alkylated dihydroxybenzoate, ADHB), or 1-(2,4,6-trihydroxyphenyl)octan-1-one (alkylated trihydroxyacetophenone, ATHAP). PMID:26819908

  12. New 1:1 and 2:1 salts in the `DL-norvaline-maleic acid' system as an example of assembling various crystal structures from similar supramolecular building blocks. (United States)

    Arkhipov, Sergey G; Losev, Evgeniy A; Boldyreva, Elena V


    Molecular salts and cocrystals of amino acids have potential applications as molecular materials with nonlinear optical, ferroelectric, piezoelectric, and other various target physical properties. The wide choice of amino acids and coformers makes it possible to design various crystal structures. The amino acid-maleic acid system provides a perfect example of a rich variety of crystal structures with different stoichiometries, symmetries and packing motifs built from the molecular building blocks, which are either exactly the same, or differ merely by protonation or as optical isomers. The present paper reports the crystal structures of two new salts of the DL-norvaline-maleic acid system with 1:1 and 2:1 stoichiometries, namely DL-norvalinium hydrogen maleate, C5H12NO2+·C4H3O4-, (I), and DL-norvalinium hydrogen maleate-DL-norvaline, C5H12NO2+·C4H3O4-·C5H11NO2, (II). These are the first examples of molecular salts of DL-norvaline with an organic anion. The crystal structure of (I) has the same C22(12) structure-forming motif which is common for hydrogen maleates of amino acids. The structure of (II) has dimeric cations. Of special interest is that the single crystals of (I) which are originally formed on crystallization from aqueous solution transform into single crystals of (II) if stored in the mother liquor for several hours.

  13. Sunlight assisted synthesis of silver nanoparticles in zeolite matrix and study of its application on electrochemical detection of dopamine and uric acid in urine samples. (United States)

    Meenakshi, S; Devi, S; Pandian, K; Devendiran, R; Selvaraj, M


    Sunlight assisted reduction of silver ions were accomplished for the synthesis of silver nanoparticles incorporated within the mesoporous silicate framework of zeolite Y. The zeolite-Y and AgNP/Zeo-Y were characterized by field emission scanning electron microscopy, transmission electron microscopy, N2 adsorption-desorption BET isotherm and X-ray diffraction techniques. The incorporation of silver nanoparticles within the porous framework was further confirmed by cyclic voltammetry and electrochemical impedance spectroscopy. An enhanced electrocatalytic oxidation of biologically important molecules like dopamine and uric acid using AgNP/Zeo-Y modified glassy carbon electrode has been developed. A simultaneous oxidation of DA and UA peaks were obtained at +0.31V and +0.43V (vs. Ag/AgCl) using AgNP/Zeo-Y/GCE under the optimum experimental condition. A well-resolved peak potential window (~120mV) for the oxidation of both DA and UA were observed at AgNP/Zeo-Y/GCE system. The calibration curves for DA and UA were obtained within the dynamic linear range of 0.02×10(-6) to 0.18×10(-6)M (R(2)=0.9899) and 0.05×10(-6) to 0.7×10(-6)M (R(2)=0.9996) and the detection limits were found to be 1.6×10(-8)M and 2.51×10(-8)M by using differential pulse voltammetry (DPV) method. The proposed method was successfully applied for the determination of both DA and UA in human urine samples with a related standard deviation was <3%, and n=5 using the standard addition method. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Matrix completion by deep matrix factorization. (United States)

    Fan, Jicong; Cheng, Jieyu


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

  15. Diagnosis using nail matrix. (United States)

    Richert, Bertrand; Caucanas, Marie; André, Josette


    Diagnosing nail matrix diseases requires knowledge of the nail matrix function and anatomy. This allows recognition of the clinical manifestations and assessment of potential surgical risk. Nail signs depend on the location within the matrix (proximal or distal) and the intensity, duration, and extent of the insult. Proximal matrix involvement includes nail surface irregularities (longitudinal lines, transverse lines, roughness of the nail surface, pitting, and superficial brittleness), whereas distal matrix insult induces longitudinal or transverse chromonychia. Clinical signs are described and their main causes are listed to enable readers to diagnose matrix disease from the nail's clinical features. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Comparative proteomics of matrix fractions between pimpled and normal chicken eggshells. (United States)

    Liu, Zhangguo; Song, Lingzi; Lu, Lizhi; Zhang, Xianfu; Zhang, Fuming; Wang, Kehua; Linhardt, Robert J


    Eggshell matrix can be dissociated into three matrix fractions: acid-insoluble matrix (M1), water-insoluble matrix (M2) and acid-water facultative-soluble matrix (M3). Matrix fractions from pimpled and normal eggshells were compared using label-free proteomic method to understand the differences among three matrix fractions and the proteins involved with eggshell quality. A total of 738 and 600 proteins were identified in the pimpled and normal calcified eggshells, respectively. Both eggshells showed a combined proteomic inventory of 769 proteins. In the same type of eggshell, a high similarity was present in the proteomes of three matrix fractions. These triply overlapped common proteins formed the predominant contributor to proteomic abundance in the matrix fractions. In each matrix fraction and between both eggshell models, normal and pimpled eggshells, a majority of the proteomes of the fractions were commonly observed. Forty-two common major proteins (iBAQ-derived abundance ≥0.095% of proteomic abundance) were identified throughout the three matrix fractions and these proteins might act as backbone constituents in chicken eggshell matrix. Finally, using 1.75-fold as up-regulated and using 0.57-fold as down-regulated cutoff values, twenty-five differential major proteins were screened and they all negatively influence and none showed any effect on eggshell quality. Overall, we uncovered the characteristics of proteomics of three eggshell matrix fractions and identified candidate proteins influencing eggshell quality. The next research on differential proteins will uncover the potential mechanisms underlying how proteins affect eggshell quality. It was reported that the proteins in an eggshell can be divided into insoluble and soluble proteins. The insoluble proteins are thought to be an inter-mineral matrix and acts as a structural framework, while the soluble proteins are thought as intra-mineral matrix that are embedded within the crystal during

  17. Development of C60-based labeling reagents for the determination of low-molecular-weight compounds by matrix assisted laser desorption ionization mass (I): Determination of amino acids in microliter biofluids. (United States)

    Wu, Pin; Xiao, Hua-Ming; Ding, Jun; Deng, Qian-Yun; Zheng, Fang; Feng, Yu-Qi


    Quantification of low molecular weight compounds (C60 labeling-MALDI MS strategy was proposed for the fast, sensitive and reliable determination of amino acids (AAs) in biofluids. An N-hydroxysuccinimide functionalized C60 was synthesized as the labeling reagent and added as an 880 Da tag to AAs; a carboxyl acid containing C60 was employed as the internal standards to normalize MS variations. This solved the inherent problems of MALDI MS for small molecule analysis. The entire analytical procedure-which consisted of simple protein precipitation and 10 min of derivatization in a microwave prior to the MALDI MS analysis-could be accomplished within 20 min with high throughput and great sample matrix tolerance. AA quantification showed good linearity from 0.7 to 70.0 μM with correlation coefficients (R) larger than 0.9954. The limits of detection were 70.0-300.0 fmol. Good reproducibility and reliability of the method were demonstrated by intra-day and inter-day precision with relative standard deviations less than 13.8%, and the recovery in biofluid ranged from 80.4% to 106.8%. This approach could be used in 1 μL of urine, serum, plasma, whole blood, and cerebrospinal fluid. Most importantly, the C60 labeling strategy is a universal approach for MALDI MS analysis of various LMW compounds because functionalized C60 is now available on demand. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. The Matrix Cookbook

    DEFF Research Database (Denmark)

    Petersen, Kaare Brandt; Pedersen, Michael Syskind

    Matrix identities, relations and approximations. A desktop reference for quick overview of mathematics of matrices.......Matrix identities, relations and approximations. A desktop reference for quick overview of mathematics of matrices....

  19. Matrix differentiation formulas (United States)

    Usikov, D. A.; Tkhabisimov, D. K.


    A compact differentiation technique (without using indexes) is developed for scalar functions that depend on complex matrix arguments which are combined by operations of complex conjugation, transposition, addition, multiplication, matrix inversion and taking the direct product. The differentiation apparatus is developed in order to simplify the solution of extremum problems of scalar functions of matrix arguments.

  20. Matrix with Prescribed Eigenvectors (United States)

    Ahmad, Faiz


    It is a routine matter for undergraduates to find eigenvalues and eigenvectors of a given matrix. But the converse problem of finding a matrix with prescribed eigenvalues and eigenvectors is rarely discussed in elementary texts on linear algebra. This problem is related to the "spectral" decomposition of a matrix and has important technical…

  1. Matrix Effects and Interferences of Different Citrus Fruit Coextractives in Pesticide Residue Analysis Using Ultrahigh-Performance Liquid Chromatography-High-Resolution Mass Spectrometry. (United States)

    Besil, Natalia; Cesio, Verónica; Heinzen, Horacio; Fernandez-Alba, Amadeo R


    The matrix effects of ethyl acetate extracts from seven different citrus fruits on the determination of 80 pesticide residues using liquid chromatography coupled to high-resolution time-of-flight mass spectrometry (UHPLC-(ESI)-HR-TOF) at 4 GHz resolution mode were studied. Only 20% of the evaluated pesticides showed noticeable matrix effects (ME) due to coelution with natural products between tR = 3 and 11 min. Principal component analysis (PCA) of the detected coextractives grouped the mandarins and the orange varieties, but separated lemon, oranges, and mandarins from each other. Matrix effects were different among species but similar between varieties, forcing the determination of pesticide residues through matrix-matched calibration curves with the same fruit. Twenty-three natural products (synephrine, naringin, poncirin, glycosides of hesperitin, limonin, nomilin, and a few fatty acids, among others) were identified in the analyzed extracts. Twelve of the identified compounds coeluted with 28 of the pesticides under study, causing different matrix effects.

  2. Performance of a growth-no growth model for Listeria monocytogenes developed for mayonnaise-based salads: influence of strain variability, food matrix, inoculation level, and presence of sorbic and benzoic acid. (United States)

    Vermeulen, A; Smigic, N; Rajkovic, A; Gysemans, K; Bernaerts, K; Geeraerd, A; Van Impe, J; Debevere, J; Devlieghere, F


    A previously developed growth-no growth model for Listeria monocytogenes, based on nutrient broth data and describing the influence of water activity (a(w)), pH, and acetic acid concentrations, was validated (i) for a variety of L. monocytogenes strains and (ii) in a laboratory-made, mayonnaise-based surimi salad (as an example of a mayonnaise-based salad). In these challenge tests, the influence of the inoculation level was tested as well. Also, the influence of chemical preservatives on the growth probability of L. monocytogenes in mayonnaise-based salads was determined. To evaluate the growth-no growth model performance on the validation data, four quantitative criteria are determined: concordance index, % correct predictions, % fail-dangerous, and % fail-safe. First, the growth probability of 11 L. monocytogenes strains, not used for model development, was assessed in nutrient broth under conditions within the interpolation region. Experimental results were compared with model predictions. Second, the growth-no growth model was assessed in a laboratory-made, sterile, mayonnaise-based surimi salad to identify a possible model completeness error related to the food matrix, making use of the above-mentioned validation criteria. Finally, the effect on L. monocytogenes of common chemical preservatives (sorbic and benzoic acid) at different concentrations under conditions typical of mayonnaise-based salads was determined. The study showed that the growth-no growth zone was properly predicted and consistent for all L. monocytogenes strains. A larger prediction error was observed under conditions within the transition zone between growth-no growth. However, in all cases, the classification between no growth (P = 0) and any growth (P > 0) occurred properly, which is most important for the food industry, where outgrowth needs to be prevented in all instances. The results in the sterile mayonnaise-based salad showed again that the growth-no growth zone was well predicted

  3. Nanocrystal doped matrixes (United States)

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


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

  4. The extracellular-matrix-retaining cyanobacterium Nostoc verrucosum accumulates trehalose, but is sensitive to desiccation. (United States)

    Sakamoto, Toshio; Kumihashi, Keisuke; Kunita, Shinpei; Masaura, Takuya; Inoue-Sakamoto, Kaori; Yamaguchi, Masaaki


    The aquatic cyanobacterium Nostoc verrucosum forms macroscopic colonies, which consist of both cellular filaments and massive extracellular matrix material. In this study, the physiological features of N. verrucosum were investigated and compared with those of the anhydrobiotic cyanobacterium Nostoc commune. Nostoc verrucosum cells were sensitive to desiccation, but tolerant of freeze-thawing treatment in terms of both cell viability and photosynthetic O(2) evolution. Natural colonies of these cyanobacteria contained similar levels of chlorophyll a, carotenoids, the UV-absorbing pigments scytonemin and mycosporine-like amino acids, and uronic acid [a component of extracellular polysaccharides (EPS)]. EPS from both N. verrucosum and N. commune indicated low acidity and a high affinity for divalent cations, although their sugar compositions differed. The WspA protein, known to be a major component of the extracellular matrix of N. commune, was detected in N. verrucosum. Desiccation caused similarly high levels of trehalose accumulation in both cyanobacteria. Although previously considered relevant to anhydrobiosis in the terrestrial cyanobacterium N. commune, the data presented here suggest that extracellular matrix production and trehalose accumulation are not enough for standing extreme desiccation in N. verrucosum. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  5. Nuclear Matrix Proteins in Human Colon Cancer (United States)

    Keesee, Susan K.; Meneghini, Marc D.; Szaro, Robert P.; Wu, Ying-Jye


    The nuclear matrix is the nonchromatin scaffolding of the nucleus. This structure confers nuclear shape, organizes chromatin, and appears to contain important regulatory proteins. Tissue specific nuclear matrix proteins have been found in the rat, mouse, and human. In this study we compared high-resolution two-dimensional gel electropherograms of nuclear matrix protein patterns found in human colon tumors with those from normal colon epithelia. Tumors were obtained from 18 patients undergoing partial colectomy for adenocarcinoma of the colon and compared with tissue from 10 normal colons. We have identified at least six proteins which were present in 18 of 18 colon tumors and 0 of 10 normal tissues, as well as four proteins present in 0 of 18 tumors and in 10 of 10 normal tissues. These data, which corroborate similar findings of cancer-specific nuclear matrix proteins in prostate and breast, suggest that nuclear matrix proteins may serve as important markers for at least some types of cancer.

  6. Comparison of peptide nucleic acid fluorescence in situ hybridization assays with culture-based matrix-assisted laser desorption/ionization-time of flight mass spectrometry for the identification of bacteria and yeasts from blood cultures and cerebrospinal fluid cultures. (United States)

    Calderaro, A; Martinelli, M; Motta, F; Larini, S; Arcangeletti, M C; Medici, M C; Chezzi, C; De Conto, F


    Peptide nucleic acid fluorescence in situ hybridization (PNA FISH) is a molecular diagnostic tool for the rapid detection of pathogens directly from liquid media. The aim of this study was to prospectively evaluate PNA FISH assays in comparison with culture-based matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) identification, as a reference method, for both blood and cerebrospinal fluid (CSF) cultures, during a 1-year investigation. On the basis of the Gram stain microscopy results, four different PNA FISH commercially available assays were used ('Staphylococcus aureus/CNS', 'Enterococcus faecalis/OE', 'GNR Traffic Light' and 'Yeasts Traffic Light' PNA FISH assays, AdvanDx). The four PNA FISH assays were applied to 956 positive blood cultures (921 for bacteria and 35 for yeasts) and 11 CSF cultures. Among the 921 blood samples positive for bacteria, PNA FISH gave concordant results with MALDI-TOF MS in 908/921 (98.64%) samples, showing an agreement of 99.4% in the case of monomicrobial infections. As regards yeasts, the PNA FISH assay showed a 100% agreement with the result obtained by MALDI-TOF MS. When PNA FISH assays were tested on the 11 CSF cultures, the results agreed with the reference method in all cases (100%). PNA FISH assays provided species identification at least one work-day before the MALDI-TOF MS culture-based identification. PNA FISH assays showed an excellent efficacy in the prompt identification of main pathogens, yielding a significant reduction in reporting time and leading to more appropriate patient management and therapy in cases of sepsis and severe infections. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

  7. Comparison of the Bruker Biotyper and VITEK MS Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Systems Using a Formic Acid Extraction Method to Identify Common and Uncommon Yeast Isolates. (United States)

    Lee, Hyun Seung; Shin, Jong Hee; Choi, Min Ji; Won, Eun Jeong; Kee, Seung Jung; Kim, Soo Hyun; Shin, Myung Geun; Suh, Soon Pal


    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows rapid and accurate identification of clinical yeast isolates. In-tube formic acid/acetonitrile (FA/ACN) extraction is recommended prior to the analysis with MALDI Biotyper, but the direct on-plate FA extraction is simpler. We compared the Biotyper with the VITEK MS for the identification of various clinically relevant yeast species, focusing on the use of the FA extraction method. We analyzed 309 clinical isolates of 42 yeast species (four common Candida species, Cryptococcus neoformans, and 37 uncommon yeast species) using the Biotyper and VITEK MS systems. FA extraction was used initially for all isolates. If 'no identification' result was obtained following the initial FA extraction, these samples were then retested by using FA (both systems, additive FA) or FA/ACN (Biotyper only, additive FA/ACN) extraction. These results were compared with those obtained by sequence-based identification. Both systems correctly identified all 158 isolates of the four common Candida species after the initial FA extraction. The Biotyper correctly identified 8.7%, 30.4%, and 100% of 23 C. neoformans isolates after performing initial FA, additive FA, and FA/ACN extractions, respectively, while VITEK MS identified all C. neoformans isolates after the initial FA extraction. Both systems had comparable identification rates of 37 uncommon yeast species (128 isolates), following the initial FA (Biotyper, 74.2%; VITEK MS, 73.4%) or additive FA (Biotyper, 82.0%; VITEK MS, 73.4%). The identification rate of most common and uncommon yeast isolates is comparable between simple FA extraction/Biotyper method and VITEK MS methods, but FA/ACN extraction is necessary for C. neoformans identification by Biotyper.

  8. A clean-up technology for the simultaneous determination of lysophosphatidic acid and sphingosine-1-phosphate by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a phosphate-capture molecule, Phos-tag. (United States)

    Morishige, Jun-ichi; Urikura, Mai; Takagi, Haruko; Hirano, Kaoru; Koike, Tohru; Tanaka, Tamotsu; Satouchi, Kiyoshi


    Lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P) are growth factor-like lipids having a phosphate group. The concentrations of these mediator lipids in blood are considered to be potential biomarkers for early detection of cancer or vascular diseases. Here, we report a method for simultaneous determination of LPA and S1P using Phos-tag, a zinc complex that specifically binds to a phosphate-monoester group. Although both LPA and S1P are hydrophilic compounds, we found that they acquire hydrophobic properties when they form complexes with Phos-tag. Based on this finding, we developed a method for the enrichment of LPA and S1P from biological samples. The first partition in a two-phase solvent system consisting of chloroform/methanol/water (1:1:0.9, v/v/v) is conducted for the removal of lipids. LPA and S1P are specifically extracted as Phos-tag complexes at the second partition by adding Phos-tag. The Phos-tag complexes of LPA and S1P are detectable by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and quantifiable based on the relative intensities of ions using 17:0 LPA and C17 S1P as internal standards. The protocol was validated by analyses of these mediator lipids in calf serum, a rat brain and a lung. The clean-up protocol is rapid, requires neither thin-layer chromatography (TLC) nor liquid chromatography (LC), and is applicable to both blood and solid tissue samples. We believe that our protocol will be useful for a routine analysis of LPA and S1P in many clinical samples. 2010 John Wiley & Sons, Ltd.

  9. A Comparative Study of the Application of Fluorescence Excitation-Emission Matrices Combined with Parallel Factor Analysis and Nonnegative Matrix Factorization in the Analysis of Zn Complexation by Humic Acids. (United States)

    Boguta, Patrycja; Pieczywek, Piotr M; Sokołowska, Zofia


    The main aim of this study was the application of excitation-emission fluorescence matrices (EEMs) combined with two decomposition methods: parallel factor analysis (PARAFAC) and nonnegative matrix factorization (NMF) to study the interaction mechanisms between humic acids (HAs) and Zn(II) over a wide concentration range (0-50 mg·dm-3). The influence of HA properties on Zn(II) complexation was also investigated. Stability constants, quenching degree and complexation capacity were estimated for binding sites found in raw EEM, EEM-PARAFAC and EEM-NMF data using mathematical models. A combination of EEM fluorescence analysis with one of the proposed decomposition methods enabled separation of overlapping binding sites and yielded more accurate calculations of the binding parameters. PARAFAC and NMF processing allowed finding binding sites invisible in a few raw EEM datasets as well as finding totally new maxima attributed to structures of the lowest humification. Decomposed data showed an increase in Zn complexation with an increase in humification, aromaticity and molecular weight of HAs. EEM-PARAFAC analysis also revealed that the most stable compounds were formed by structures containing the highest amounts of nitrogen. The content of oxygen-functional groups did not influence the binding parameters, mainly due to fact of higher competition of metal cation with protons. EEM spectra coupled with NMF and especially PARAFAC processing gave more adequate assessments of interactions as compared to raw EEM data and should be especially recommended for modeling of complexation processes where the fluorescence intensities (FI) changes are weak or where the processes are interfered with by the presence of other fluorophores.

  10. Determination of spatial distribution of melamine-cyanuric acid crystals in rat kidney tissue by histology and imaging matrix-assisted laser desorption/ionization quadrupole time-of-flight mass spectrometry. (United States)

    Kim, Chae-Wook; Yun, Jun-Won; Bae, Il-Hong; Lee, Joon-Seok; Kang, Hyun-Jin; Joo, Kyung-Mi; Jeong, Hye-Jin; Chung, Jin-Ho; Park, Young-Ho; Lim, Kyung-Min


    After the outbreak of acute renal failure associated with melamine-contaminated pet food, many attempts have been made to uncover the mechanism underlying the renal toxicity caused by melamine and melamine-related compounds. Using rat models, we investigated the renal crystal formation following the ingestion of a melamine-cyanuric acid mixture (M+CA, 1:1) to gain insight into the M+CA-induced renal toxicity. M+CA did not induce toxicity in precision-cut kidney slices, suggesting that M+CA does not have a direct nephrotoxicity. On the contrary, oral administration of M+CA for 3 days induced nephrotoxicity as determined by increased serum blood urea nitrogen and creatinine, reduced creatinine clearance, and enlarged kidneys in the animals treated with 50 mg/kg M+CA (melamine, 25 mg/kg, and cyanuric acid, 25 mg/kg; 2 of 10 animals) and 100 mg/kg M+CA (9 of 9 animals). While urine crystals were found in all animals treated with M+CA (25-100 mg/kg), histological examination revealed that renal crystals could be observed only in the kidneys of animals showing signs of nephrotoxicity. Remarkably, at 50 mg/kg M+CA, crystals were observed mainly in the medulla region of the kidney, while at 100 mg/kg, crystals were disseminated throughout the cortex and medulla regions. To further investigate the crystal formation by M+CA, matrix-assisted laser desorption/ionization quadrupole time-of-flight (MALDI-Q-TOF) imaging mass spectrometry detecting melamine distribution through monitoring the product ion (m/z 85, M + H) from melamine (m/z 127, M + H) was developed to directly obtain the image of melamine distribution in the kidney. The distribution image of melamine in kidney tissue confirmed that dense points of melamine were located only in the medulla region at 50 mg/kg M+CA, while at 100 mg/kg, they were disseminated widely from the cortex to medulla. These results demonstrated that M+CA ingestion could lead to crystal formation in kidney tubules along the osmotic gradient and

  11. Cell-matrix adhesion. (United States)

    Berrier, Allison L; Yamada, Kenneth M


    The complex interactions of cells with extracellular matrix (ECM) play crucial roles in mediating and regulating many processes, including cell adhesion, migration, and signaling during morphogenesis, tissue homeostasis, wound healing, and tumorigenesis. Many of these interactions involve transmembrane integrin receptors. Integrins cluster in specific cell-matrix adhesions to provide dynamic links between extracellular and intracellular environments by bi-directional signaling and by organizing the ECM and intracellular cytoskeletal and signaling molecules. This mini review discusses these interconnections, including the roles of matrix properties such as composition, three-dimensionality, and porosity, the bi-directional functions of cellular contractility and matrix rigidity, and cell signaling. The review concludes by speculating on the application of this knowledge of cell-matrix interactions in the formation of cell adhesions, assembly of matrix, migration, and tumorigenesis to potential future therapeutic approaches. 2007 Wiley-Liss, Inc.

  12. Parallelism in matrix computations

    CERN Document Server

    Gallopoulos, Efstratios; Sameh, Ahmed H


    This book is primarily intended as a research monograph that could also be used in graduate courses for the design of parallel algorithms in matrix computations. It assumes general but not extensive knowledge of numerical linear algebra, parallel architectures, and parallel programming paradigms. The book consists of four parts: (I) Basics; (II) Dense and Special Matrix Computations; (III) Sparse Matrix Computations; and (IV) Matrix functions and characteristics. Part I deals with parallel programming paradigms and fundamental kernels, including reordering schemes for sparse matrices. Part II is devoted to dense matrix computations such as parallel algorithms for solving linear systems, linear least squares, the symmetric algebraic eigenvalue problem, and the singular-value decomposition. It also deals with the development of parallel algorithms for special linear systems such as banded ,Vandermonde ,Toeplitz ,and block Toeplitz systems. Part III addresses sparse matrix computations: (a) the development of pa...

  13. Quasiclassical Random Matrix Theory


    Prange, R. E.


    We directly combine ideas of the quasiclassical approximation with random matrix theory and apply them to the study of the spectrum, in particular to the two-level correlator. Bogomolny's transfer operator T, quasiclassically an NxN unitary matrix, is considered to be a random matrix. Rather than rejecting all knowledge of the system, except for its symmetry, [as with Dyson's circular unitary ensemble], we choose an ensemble which incorporates the knowledge of the shortest periodic orbits, th...

  14. Multiscale characterization of chemical–mechanical interactions between polymer fibers and cementitious matrix

    Energy Technology Data Exchange (ETDEWEB)

    Hernández-Cruz, Daniel; Hargis, Craig W.; Bae, Sungchul; Itty, Pierre A.; Meral, Cagla; Dominowski, Jolee; Radler, Michael J.; Kilcoyne, David A.; Monteiro, Paulo J. M.


    Together with a series of mechanical tests, the interactions and potential bonding between polymeric fibers and cementitious materials were studied using scanning transmission X-ray microscopy (STXM) and microtomography (lCT). Experimental results showed that these techniques have great potential to characterize the polymer fiber-hydrated cement-paste matrix interface, as well as differentiating the chemistry of the two components of a bi-polymer (hybrid) fiber the polypropylene core and the ethylene acrylic acid copolymer sheath. Similarly, chemical interactions between the hybrid fiber and the cement hydration products were observed, indicating the chemical bonding between the sheath and the hardened cement paste matrix. Microtomography allowed visualization of the performance of the samples, and the distribution and orientation of the two types of fiber in mortar. Beam flexure tests confirmed improved tensile strength of mixes containing hybrid fibers, and expansion bar tests showed similar reductions in expansion for the polypropylene and hybrid fiber mortar bars.

  15. Application of Similarity in Fault Diagnosis of Power Electronics Circuits (United States)

    Rongjie, Wang; Yiju, Zhan; Meiqian, Chen; Haifeng, Zhou; Kewei, Guo

    A method of fault diagnosis was proposed for power electronics circuits based on S transforms similarity. At first, the standard module time-frequency matrixes of S transforms for all fault signals were constructed, then the similarity of fault signals' module time-frequency matrixes to standard module time-frequency matrixes were calculated, and according to the principle of maximum similarity, the faults were diagnosed. The simulation result of fault diagnosis of a thyristor in a three-phase full-bridge controlled rectifier shows that the method can accurately diagnose faults and locate the fault element for power electronics circuits, and it has excellent performance for noise robustness and calculation complexity, thus it also has good practical engineering value in the solution to the fault problems for power electronics circuits.

  16. Patience of matrix games

    DEFF Research Database (Denmark)

    Hansen, Kristoffer Arnsfelt; Ibsen-Jensen, Rasmus; Podolskii, Vladimir V.


    For matrix games we study how small nonzero probability must be used in optimal strategies. We show that for image win–lose–draw games (i.e. image matrix games) nonzero probabilities smaller than image are never needed. We also construct an explicit image win–lose game such that the unique optimal...

  17. Fuzzy risk matrix. (United States)

    Markowski, Adam S; Mannan, M Sam


    A risk matrix is a mechanism to characterize and rank process risks that are typically identified through one or more multifunctional reviews (e.g., process hazard analysis, audits, or incident investigation). This paper describes a procedure for developing a fuzzy risk matrix that may be used for emerging fuzzy logic applications in different safety analyses (e.g., LOPA). The fuzzification of frequency and severity of the consequences of the incident scenario are described which are basic inputs for fuzzy risk matrix. Subsequently using different design of risk matrix, fuzzy rules are established enabling the development of fuzzy risk matrices. Three types of fuzzy risk matrix have been developed (low-cost, standard, and high-cost), and using a distillation column case study, the effect of the design on final defuzzified risk index is demonstrated.

  18. Involvement of extracellular matrix constituents in breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    Lochter, Andre; Bissell, Mina J


    It has recently been established that the extracellular matrix is required for normal functional differentiation of mammary epithelia not only in culture, but also in vivo. The mechanisms by which extracellular matrix affects differentiation, as well as the nature of extracellular matrix constituents which have major impacts on mammary gland function, have only now begun to be dissected. The intricate variety of extracellular matrix-mediated events and the remarkable degree of plasticity of extracellular matrix structure and composition at virtually all times during ontogeny, make such studies difficult. Similarly, during carcinogenesis, the extracellular matrix undergoes gross alterations, the consequences of which are not yet precisely understood. Nevertheless, an increasing amount of data suggests that the extracellular matrix and extracellular matrix-receptors might participate in the control of most, if not all, of the successive stages of breast tumors, from appearance to progression and metastasis.

  19. Wavy-walled bioreactor supports increased cell proliferation and matrix deposition in engineered cartilage constructs. (United States)

    Bueno, Ericka M; Bilgen, Bahar; Barabino, Gilda A


    Hydrodynamic forces in bioreactors can decisively influence extracellular matrix deposition in engineered cartilage constructs. In the present study, the reduced fluid shear, high-axial mixing environment provided by a wavy-walled bioreactor was exploited in the cultivation of cartilage constructs using polyglycolic acid scaffolds seeded with bovine articular chondrocytes. Increased growth as defined by weight, cell proliferation and extracellular matrix deposition was observed in cartilage constructs from wavy-walled bioreactors in comparison with those from spinner flasks cultured under the same conditions. The wet weight composition of 4-week constructs from the wavy-walled bioreactor was similar to that of spinner flask constructs, but the former were 60% heavier due to equally higher incorporation of extracellular matrix and 30% higher cell population. It is most likely that increased construct matrix incorporation was a result of increased mitotic activity of chondrocytes cultured in the environment of the wavy-walled bioreactor. A layer of elongated cells embedded in type I collagen formed at the periphery of wavy-walled bioreactor and spinner flask constructs, possibly as a response to local shear forces. On the basis of the robustness and reproducibility of the extracellular matrix composition of cartilage constructs, the wavy-walled bioreactor demonstrated promise as an experimental cartilage tissue-engineering vessel. Increased construct growth in the wavy-walled bioreactor may lead to enhanced mechanical properties and expedited in vitro cultivation.

  20. Characteristics of global organic matrix in normal and pimpled chicken eggshells. (United States)

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


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

  1. Matrix diffusion coefficients in volcanic rocks at the Nevada test site: Influence of matrix porosity, matrix permeability, and fracture coating minerals (United States)

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


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

  2. Physical characterization and kinetic modelling of matrix tablets of ...

    African Journals Online (AJOL)

    Purpose: To design controlled release ketorolac tromethamol (KT) matrix tablets for increased drug bioavailability. Methods: Waxes (Compritol® ATO 888, Precirol® ATO 5 and stearic acid - SA) and polymers (hydroxypropyl methylcellulose - HPMC and xanthan gum - XG) were used in the preparation of the matrix tablets at ...

  3. A toolbox for representational similarity analysis.

    Directory of Open Access Journals (Sweden)

    Hamed Nili


    Full Text Available Neuronal population codes are increasingly being investigated with multivariate pattern-information analyses. A key challenge is to use measured brain-activity patterns to test computational models of brain information processing. One approach to this problem is representational similarity analysis (RSA, which characterizes a representation in a brain or computational model by the distance matrix of the response patterns elicited by a set of stimuli. The representational distance matrix encapsulates what distinctions between stimuli are emphasized and what distinctions are de-emphasized in the representation. A model is tested by comparing the representational distance matrix it predicts to that of a measured brain region. RSA also enables us to compare representations between stages of processing within a given brain or model, between brain and behavioral data, and between individuals and species. Here, we introduce a Matlab toolbox for RSA. The toolbox supports an analysis approach that is simultaneously data- and hypothesis-driven. It is designed to help integrate a wide range of computational models into the analysis of multichannel brain-activity measurements as provided by modern functional imaging and neuronal recording techniques. Tools for visualization and inference enable the user to relate sets of models to sets of brain regions and to statistically test and compare the models using nonparametric inference methods. The toolbox supports searchlight-based RSA, to continuously map a measured brain volume in search of a neuronal population code with a specific geometry. Finally, we introduce the linear-discriminant t value as a measure of representational discriminability that bridges the gap between linear decoding analyses and RSA. In order to demonstrate the capabilities of the toolbox, we apply it to both simulated and real fMRI data. The key functions are equally applicable to other modalities of brain-activity measurement. The

  4. Elementary matrix theory

    CERN Document Server

    Eves, Howard


    The usefulness of matrix theory as a tool in disciplines ranging from quantum mechanics to psychometrics is widely recognized, and courses in matrix theory are increasingly a standard part of the undergraduate curriculum.This outstanding text offers an unusual introduction to matrix theory at the undergraduate level. Unlike most texts dealing with the topic, which tend to remain on an abstract level, Dr. Eves' book employs a concrete elementary approach, avoiding abstraction until the final chapter. This practical method renders the text especially accessible to students of physics, engineeri


    Directory of Open Access Journals (Sweden)

    Q. X. Xu


    Full Text Available The semantic similarities are important in concept definition, recognition, categorization, interpretation, and integration. Many semantic similarity models have been established to evaluate semantic similarities of objects or/and concepts. To find out the suitability and performance of different models in evaluating concept similarities, we make a comparison of four main types of models in this paper: the geometric model, the feature model, the network model, and the transformational model. Fundamental principles and main characteristics of these models are introduced and compared firstly. Land use and land cover concepts of NLCD92 are employed as examples in the case study. The results demonstrate that correlations between these models are very high for a possible reason that all these models are designed to simulate the similarity judgement of human mind.

  6. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman


    Full Text Available In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemmingfrom its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problemat hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, bysurveying established results and new developments in the theory and methods of similarity-preservingassociative lookup and dimensionality reduction — critical components of many cognitive functions, aswell as of intelligent data management in computer vision. We focus in particular on the growing familyof algorithms that support associative memory by performing hashing that respects local similarity, andon the uses of similarity in representing structured objects and scenes. Insofar as these similarity-basedideas and methods are useful in cognitive modeling and in AI applications, they should be included inthe core conceptual toolkit of computational neuroscience.

  7. Pesticide-Exposure Matrix (United States)

    The "Pesticide-exposure Matrix" was developed to help epidemiologists and other researchers identify the active ingredients to which people were likely exposed when their homes and gardens were treated for pests in past years.

  8. Tendon functional extracellular matrix. (United States)

    Screen, Hazel R C; Berk, David E; Kadler, Karl E; Ramirez, Francesco; Young, Marian F


    This article is one of a series, summarizing views expressed at the Orthopaedic Research Society New Frontiers in Tendon Research Conference. This particular article reviews the three workshops held under the "Functional Extracellular Matrix" stream. The workshops focused on the roles of the tendon extracellular matrix, such as performing the mechanical functions of tendon, creating the local cell environment, and providing cellular cues. Tendon is a complex network of matrix and cells, and its biological functions are influenced by widely varying extrinsic and intrinsic factors such as age, nutrition, exercise levels, and biomechanics. Consequently, tendon adapts dynamically during development, aging, and injury. The workshop discussions identified research directions associated with understanding cell-matrix interactions to be of prime importance for developing novel strategies to target tendon healing or repair. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

  9. Matrix Big Brunch


    Bedford, J; Papageorgakis, C.; Rodriguez-Gomez, D.; Ward, J.


    Following the holographic description of linear dilaton null Cosmologies with a Big Bang in terms of Matrix String Theory put forward by Craps, Sethi and Verlinde, we propose an extended background describing a Universe including both Big Bang and Big Crunch singularities. This belongs to a class of exact string backgrounds and is perturbative in the string coupling far away from the singularities, both of which can be resolved using Matrix String Theory. We provide a simple theory capable of...

  10. The Matrix Organization Revisited

    DEFF Research Database (Denmark)

    Gattiker, Urs E.; Ulhøi, John Parm


    This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively).......This paper gives a short overview of matrix structure and technology management. It outlines some of the characteristics and also points out that many organizations may actualy be hybrids (i.e. mix several ways of organizing to allocate resorces effectively)....

  11. Matrix comparison, Part 2

    DEFF Research Database (Denmark)

    Schneider, Jesper Wiborg; Borlund, Pia


    The present two-part article introduces matrix comparison as a formal means for evaluation purposes in informetric studies such as cocitation analysis. In the first part, the motivation behind introducing matrix comparison to informetric studies, as well as two important issues influencing such c...... and Procrustes analysis can be used as statistical validation tools in informetric studies and thus help choosing suitable proximity measures....

  12. Hacking the Matrix. (United States)

    Czerwinski, Michael; Spence, Jason R


    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.

  13. Similarly shaped letters evoke similar colors in grapheme-color synesthesia. (United States)

    Brang, David; Rouw, Romke; Ramachandran, V S; Coulson, Seana


    Grapheme-color synesthesia is a neurological condition in which viewing numbers or letters (graphemes) results in the concurrent sensation of color. While the anatomical substrates underlying this experience are well understood, little research to date has investigated factors influencing the particular colors associated with particular graphemes or how synesthesia occurs developmentally. A recent suggestion of such an interaction has been proposed in the cascaded cross-tuning (CCT) model of synesthesia, which posits that in synesthetes connections between grapheme regions and color area V4 participate in a competitive activation process, with synesthetic colors arising during the component-stage of grapheme processing. This model more directly suggests that graphemes sharing similar component features (lines, curves, etc.) should accordingly activate more similar synesthetic colors. To test this proposal, we created and regressed synesthetic color-similarity matrices for each of 52 synesthetes against a letter-confusability matrix, an unbiased measure of visual similarity among graphemes. Results of synesthetes' grapheme-color correspondences indeed revealed that more similarly shaped graphemes corresponded with more similar synesthetic colors, with stronger effects observed in individuals with more intense synesthetic experiences (projector synesthetes). These results support the CCT model of synesthesia, implicate early perceptual mechanisms as driving factors in the elicitation of synesthetic hues, and further highlight the relationship between conceptual and perceptual factors in this phenomenon. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Dynamic similarity in erosional processes (United States)

    Scheidegger, A.E.


    A study is made of the dynamic similarity conditions obtaining in a variety of erosional processes. The pertinent equations for each type of process are written in dimensionless form; the similarity conditions can then easily be deduced. The processes treated are: raindrop action, slope evolution and river erosion. ?? 1963 Istituto Geofisico Italiano.

  15. Random matrix approach to categorical data analysis (United States)

    Patil, Aashay; Santhanam, M. S.


    Correlation and similarity measures are widely used in all the areas of sciences and social sciences. Often the variables are not numbers but are instead qualitative descriptors called categorical data. We define and study similarity matrix, as a measure of similarity, for the case of categorical data. This is of interest due to a deluge of categorical data, such as movie ratings, top-10 rankings, and data from social media, in the public domain that require analysis. We show that the statistical properties of the spectra of similarity matrices, constructed from categorical data, follow random matrix predictions with the dominant eigenvalue being an exception. We demonstrate this approach by applying it to the data for Indian general elections and sea level pressures in the North Atlantic ocean.

  16. Renewing the respect for similarity. (United States)

    Edelman, Shimon; Shahbazi, Reza


    In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemming from its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problem at hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, by surveying established results and new developments in the theory and methods of similarity-preserving associative lookup and dimensionality reduction-critical components of many cognitive functions, as well as of intelligent data management in computer vision. We focus in particular on the growing family of algorithms that support associative memory by performing hashing that respects local similarity, and on the uses of similarity in representing structured objects and scenes. Insofar as these similarity-based ideas and methods are useful in cognitive modeling and in AI applications, they should be included in the core conceptual toolkit of computational neuroscience. In support of this stance, the present paper (1) offers a discussion of conceptual, mathematical, computational, and empirical aspects of similarity, as applied to the problems of visual object and scene representation, recognition, and interpretation, (2) mentions some key computational problems arising in attempts to put similarity to use, along with their possible solutions, (3) briefly states a previously developed similarity-based framework for visual object representation, the Chorus of Prototypes, along with the empirical support it enjoys, (4) presents new mathematical insights into the effectiveness of this framework, derived from its relationship to locality-sensitive hashing (LSH) and to concomitant statistics, (5) introduces a new model, the Chorus of Relational Descriptors (ChoRD), that extends this framework to scene representation and interpretation, (6) describes its implementation and testing, and finally (7) suggests possible directions in which the present research program can be

  17. Changes in matrix phosphorylation during bovine dentin development. (United States)

    Verdelis, Kostas; Lukashova, Lyudmilla; Yamauchi, Mitsuo; Atsawasuwan, Peter; Wright, John T; Peterson, Margaret G E; Jha, Divya; Boskey, Adele L


    Phosphorylation of the organic matrix proteins of dentin is important for the initiation of mineralization, but its relevance in later mineralization stages is controversial. The objective of this study was to analyze changes in the total matrix phosphate content during dentin development and to identify their origin. Amino acid and total matrix phosphate analyses of microdissected developing mantle and circumpulpal fetal bovine dentin specimens were performed. The amino acid composition showed few changes during mantle and circumpulpal dentin maturation. However, the total matrix phosphate content showed a significant, positive correlation with tissue maturation in both mantle and circumpulpal dentin, with a two- and a three-fold increase, respectively, being observed. The data indicate that changes occur in the pattern of phosphorylation of matrix proteins during dentin maturation, which we suggest may play a functional role in later stages of tooth mineralization.

  18. The normalization of occurrence and Co-occurrence matrices in bibliometrics using Cosine similarities and Ochiai coefficients

    NARCIS (Netherlands)

    Zhou, Q.; Leydesdorff, L.


    We prove that Ochiai similarity of the co-occurrence matrix is equal to cosine similarity in the underlying occurrence matrix. Neither the cosine nor the Pearson correlation should be used for the normalization of co-occurrence matrices because the similarity is then normalized twice, and therefore

  19. Self-similar aftershock rates

    CERN Document Server

    Davidsen, Jörn


    In many important systems exhibiting crackling noise --- intermittent avalanche-like relaxation response with power-law and, thus, self-similar distributed event sizes --- the "laws" for the rate of activity after large events are not consistent with the overall self-similar behavior expected on theoretical grounds. This is in particular true for the case of seismicity and a satisfying solution to this paradox has remained outstanding. Here, we propose a generalized description of the aftershock rates which is both self-similar and consistent with all other known self-similar features. Comparing our theoretical predictions with high resolution earthquake data from Southern California we find excellent agreement, providing in particular clear evidence for a unified description of aftershocks and foreshocks. This may offer an improved way of time-dependent seismic hazard assessment and earthquake forecasting.

  20. 2matrix: A Utility for Indel Coding and Phylogenetic Matrix Concatenation

    Directory of Open Access Journals (Sweden)

    Nelson R. Salinas


    Full Text Available Premise of the study: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel events in sequence alignments and concatenate data sets. Methods and Results: A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs. Conclusions: 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License open source license (

  1. An Algebraic Relation between Consimilarity and Similarity of Quaternion Matrices and Applications

    Directory of Open Access Journals (Sweden)

    Tongsong Jiang


    Full Text Available This paper, by means of complex representation of a quaternion matrix, discusses the consimilarity of quaternion matrices, and obtains a relation between consimilarity and similarity of quaternion matrices. It sets up an algebraic bridge between consimilarity and similarity, and turns the theory of consimilarity of quaternion matrices into that of ordinary similarity of complex matrices. This paper also gives algebraic methods for finding coneigenvalues and coneigenvectors of quaternion matrices by means of complex representation of a quaternion matrix.

  2. Method of similarity for cavitation

    Energy Technology Data Exchange (ETDEWEB)

    Espanet, L.; Tekatlian, A.; Barbier, D. [CEA/Cadarache, Dept. d' Etudes des Combustibles (DEC), 13 - Saint-Paul-lez-Durance (France); Gouin, H. [Aix-Marseille-3 Univ., 13 - Marseille (France). Laboratoire de Modelisation en Mecanique et Thermodynamique


    The knowledge of possible cavitation in subassembly nozzles of the fast reactor core implies the realization of a fluid dynamic model test. We propose a method of similarity based on the non-dimensionalization of the equation of motion for viscous capillarity fluid issued from the Cahn and Hilliard model. Taking into account the dissolved gas effect, a condition of compatibility is determined. This condition must be respected by the fluid in experiment, along with the scaling between the two similar flows. (author)

  3. Self-Similar Isentropic Implosions

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, M.; Amable, L.


    The self-similar compression of an isentropic spherical gas pellet Is analyzed for large values of the ratio of the final to initial densities. An asymptotic analysis provides the solution corresponding to a prescribed value of the final density when it is high. In addition an approximate solution is given when the specific heat ratio is not constant. The time evolution of the pressure on the outer surface leading to the self-similar solutions, is calculated for large density ratios. (Author)

  4. Matrix Information Geometry

    CERN Document Server

    Bhatia, Rajendra


    This book is an outcome of the Indo-French Workshop on Matrix Information Geometries (MIG): Applications in Sensor and Cognitive Systems Engineering, which was held in Ecole Polytechnique and Thales Research and Technology Center, Palaiseau, France, in February 23-25, 2011. The workshop was generously funded by the Indo-French Centre for the Promotion of Advanced Research (IFCPAR).  During the event, 22 renowned invited french or indian speakers gave lectures on their areas of expertise within the field of matrix analysis or processing. From these talks, a total of 17 original contribution or state-of-the-art chapters have been assembled in this volume. All articles were thoroughly peer-reviewed and improved, according to the suggestions of the international referees. The 17 contributions presented  are organized in three parts: (1) State-of-the-art surveys & original matrix theory work, (2) Advanced matrix theory for radar processing, and (3) Matrix-based signal processing applications.  

  5. [Biochemical, structural and biomechanical features of human scleral matrix in primary open-angle glaucoma]. (United States)

    Iomdina, E N; Ignat'eva, N Iu; Danilov, N A; Arutiunian, L L; Kiseleva, O A; Nazarenko, L A


    The goal of the investigation was to study the changes of scleral matrix collagen in progressing primary open-angle glaucoma (POAG). In scleral samples of 16 patients aged 52-81 years with different stages of POAG amino acid composition, collagen content and cross-linking ratio characterizing tissue rigidity were estimated. Collagen I was found to be the dominant type in sclera of glaucomatous and normal eyes, though as POAG progressing the content and cross-linking increase, that underlies the scleral rigidity increase and permeability decrease. Similar ratio of collagen cross-linking with age and glaucoma progression give evidence of specific pathologic changes of the dominant matrix component, that may be one of significant pathogenic factor of POAG.

  6. Google matrix analysis of DNA sequences. (United States)

    Kandiah, Vivek; Shepelyansky, Dima L


    For DNA sequences of various species we construct the Google matrix [Formula: see text] of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power law with the exponent being close to those of outgoing links in such scale-free networks as the World Wide Web (WWW). At the same time the sum of ingoing matrix elements is characterized by the exponent being significantly larger than those typical for WWW networks. This results in a slow algebraic decay of the PageRank probability determined by the distribution of ingoing elements. The spectrum of [Formula: see text] is characterized by a large gap leading to a rapid relaxation process on the DNA sequence networks. We introduce the PageRank proximity correlator between different species which determines their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google matrix are also discussed. Our results establish scale-free features of DNA sequence networks showing their similarities and distinctions with the WWW and linguistic networks.

  7. Google matrix analysis of DNA sequences.

    Directory of Open Access Journals (Sweden)

    Vivek Kandiah

    Full Text Available For DNA sequences of various species we construct the Google matrix [Formula: see text] of Markov transitions between nearby words composed of several letters. The statistical distribution of matrix elements of this matrix is shown to be described by a power law with the exponent being close to those of outgoing links in such scale-free networks as the World Wide Web (WWW. At the same time the sum of ingoing matrix elements is characterized by the exponent being significantly larger than those typical for WWW networks. This results in a slow algebraic decay of the PageRank probability determined by the distribution of ingoing elements. The spectrum of [Formula: see text] is characterized by a large gap leading to a rapid relaxation process on the DNA sequence networks. We introduce the PageRank proximity correlator between different species which determines their statistical similarity from the view point of Markov chains. The properties of other eigenstates of the Google matrix are also discussed. Our results establish scale-free features of DNA sequence networks showing their similarities and distinctions with the WWW and linguistic networks.

  8. MATLAB matrix algebra

    CERN Document Server

    Pérez López, César


    MATLAB is a high-level language and environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications. The language, tools, and built-in math functions enable you to explore multiple approaches and reach a solution faster than with spreadsheets or traditional programming languages, such as C/C++ or Java. MATLAB Matrix Algebra introduces you to the MATLAB language with practical hands-on instructions and results, allowing you to quickly achieve your goals. Starting with a look at symbolic and numeric variables, with an emphasis on vector and matrix variables, you will go on to examine functions and operations that support vectors and matrices as arguments, including those based on analytic parent functions. Computational methods for finding eigenvalues and eigenvectors of matrices are detailed, leading to various matrix decompositions. Applications such as change of bases, the classification of quadratic forms and ...

  9. Dynamic Matrix Rank

    DEFF Research Database (Denmark)

    Frandsen, Gudmund Skovbjerg; Frandsen, Peter Frands


    We consider maintaining information about the rank of a matrix under changes of the entries. For n×n matrices, we show an upper bound of O(n1.575) arithmetic operations and a lower bound of Ω(n) arithmetic operations per element change. The upper bound is valid when changing up to O(n0.575) entries...... in a single column of the matrix. We also give an algorithm that maintains the rank using O(n2) arithmetic operations per rank one update. These bounds appear to be the first nontrivial bounds for the problem. The upper bounds are valid for arbitrary fields, whereas the lower bound is valid for algebraically...... closed fields. The upper bound for element updates uses fast rectangular matrix multiplication, and the lower bound involves further development of an earlier technique for proving lower bounds for dynamic computation of rational functions....

  10. Matrix interdiction problem

    Energy Technology Data Exchange (ETDEWEB)

    Pan, Feng [Los Alamos National Laboratory; Kasiviswanathan, Shiva [Los Alamos National Laboratory


    In the matrix interdiction problem, a real-valued matrix and an integer k is given. The objective is to remove k columns such that the sum over all rows of the maximum entry in each row is minimized. This combinatorial problem is closely related to bipartite network interdiction problem which can be applied to prioritize the border checkpoints in order to minimize the probability that an adversary can successfully cross the border. After introducing the matrix interdiction problem, we will prove the problem is NP-hard, and even NP-hard to approximate with an additive n{gamma} factor for a fixed constant {gamma}. We also present an algorithm for this problem that achieves a factor of (n-k) mUltiplicative approximation ratio.

  11. Control of extracellular matrix assembly by syndecan-2 proteoglycan

    DEFF Research Database (Denmark)

    Klass, C M; Couchman, J R; Woods, A


    Extracellular matrix (ECM) deposition and organization is maintained by transmembrane signaling and integrins play major roles. We now show that a second transmembrane component, syndecan-2 heparan sulfate proteoglycan, is pivotal in matrix assembly. Chinese Hamster Ovary (CHO) cells were stably...... transfected with full length (S2) or truncated syndecan-2 lacking the C-terminal 14 amino acids of the cytoplasmic domain (S2deltaS). No differences in the amount of matrix assembly were noted with S2 cells, but those expressing S2deltaS could not assemble laminin or fibronectin into a fibrillar matrix....... The loss of matrix formation was not caused by a failure to synthesize or externalize ECM components as determined by metabolic labeling or due to differences in surface expression of alpha5 or beta1 integrin. The matrix assembly defect was at the cell surface, since S2deltaS cells also lost the ability...

  12. Matrixed business support comparison study.

    Energy Technology Data Exchange (ETDEWEB)

    Parsons, Josh D.


    The Matrixed Business Support Comparison Study reviewed the current matrixed Chief Financial Officer (CFO) division staff models at Sandia National Laboratories. There were two primary drivers of this analysis: (1) the increasing number of financial staff matrixed to mission customers and (2) the desire to further understand the matrix process and the opportunities and challenges it creates.

  13. Elementary matrix algebra

    CERN Document Server

    Hohn, Franz E


    This complete and coherent exposition, complemented by numerous illustrative examples, offers readers a text that can teach by itself. Fully rigorous in its treatment, it offers a mathematically sound sequencing of topics. The work starts with the most basic laws of matrix algebra and progresses to the sweep-out process for obtaining the complete solution of any given system of linear equations - homogeneous or nonhomogeneous - and the role of matrix algebra in the presentation of useful geometric ideas, techniques, and terminology.Other subjects include the complete treatment of the structur

  14. Complex matrix model duality

    Energy Technology Data Exchange (ETDEWEB)

    Brown, T.W.


    The same complex matrix model calculates both tachyon scattering for the c=1 non-critical string at the self-dual radius and certain correlation functions of half-BPS operators in N=4 super- Yang-Mills. It is dual to another complex matrix model where the couplings of the first model are encoded in the Kontsevich-like variables of the second. The duality between the theories is mirrored by the duality of their Feynman diagrams. Analogously to the Hermitian Kontsevich- Penner model, the correlation functions of the second model can be written as sums over discrete points in subspaces of the moduli space of punctured Riemann surfaces. (orig.)

  15. Conversation level syntax similarity metric. (United States)

    Boghrati, Reihane; Hoover, Joe; Johnson, Kate M; Garten, Justin; Dehghani, Morteza


    The syntax and semantics of human language can illuminate many individual psychological differences and important dimensions of social interaction. Accordingly, psychological and psycholinguistic research has begun incorporating sophisticated representations of semantic content to better understand the connection between word choice and psychological processes. In this work we introduce ConversAtion level Syntax SImilarity Metric (CASSIM), a novel method for calculating conversation-level syntax similarity. CASSIM estimates the syntax similarity between conversations by automatically generating syntactical representations of the sentences in conversation, estimating the structural differences between them, and calculating an optimized estimate of the conversation-level syntax similarity. After introducing and explaining this method, we report results from two method validation experiments (Study 1) and conduct a series of analyses with CASSIM to investigate syntax accommodation in social media discourse (Study 2). We run the same experiments using two well-known existing syntactic metrics, LSM and Coh-Metrix, and compare their results to CASSIM. Overall, our results indicate that CASSIM is able to reliably measure syntax similarity and to provide robust evidence of syntax accommodation within social media discourse.

  16. Visualizing multiple word similarity measures. (United States)

    Kievit-Kylar, Brent; Jones, Michael N


    Although many recent advances have taken place in corpus-based tools, the techniques used to guide exploration and evaluation of these systems have advanced little. Typically, the plausibility of a semantic space is explored by sampling the nearest neighbors to a target word and evaluating the neighborhood on the basis of the modeler's intuition. Tools for visualization of these large-scale similarity spaces are nearly nonexistent. We present a new open-source tool to plot and visualize semantic spaces, thereby allowing researchers to rapidly explore patterns in visual data that describe the statistical relations between words. Words are visualized as nodes, and word similarities are shown as directed edges of varying strengths. The "Word-2-Word" visualization environment allows for easy manipulation of graph data to test word similarity measures on their own or in comparisons between multiple similarity metrics. The system contains a large library of statistical relationship models, along with an interface to teach them from various language sources. The modularity of the visualization environment allows for quick insertion of new similarity measures so as to compare new corpus-based metrics against the current state of the art. The software is available at

  17. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico


    Face recognition has several applications, including security, such as (authentication and identification of device users and criminal suspects), and in medicine (corrective surgery and diagnosis). Facial recognition programs rely on algorithms that can compare and compute the similarity between two sets of images. This eBook explains some of the similarity measures used in facial recognition systems in a single volume. Readers will learn about various measures including Minkowski distances, Mahalanobis distances, Hansdorff distances, cosine-based distances, among other methods. The book also summarizes errors that may occur in face recognition methods. Computer scientists "facing face" and looking to select and test different methods of computing similarities will benefit from this book. The book is also useful tool for students undertaking computer vision courses.

  18. Kolmogorov's Lagrangian similarity law revisited (United States)

    Barjona, Manuel; da Silva, Carlos B.


    Kolmogorov's similarity turbulence theory in a Lagrangian frame is assessed with new direct numerical simulations of isotropic turbulence with and without hyperviscosity, which attain higher Reynolds numbers than previously available. It is demonstrated that hyperviscous simulations can be used to accurately predict the second order Lagrangian velocity structure function (LVSF-2) in the inertial range, by using an original new procedure. The results strongly support Kolmogorov's Lagrangian similarity assumption and allow the universal constant of LVSF-2 to be computed with a new level of confidence with C0=7.4 ±0.2 .

  19. Design and Evaluation of an Oral Floating Matrix Tablet of ...

    African Journals Online (AJOL)

    Purpose: To develop floating matrix tablets of salbutamol sulphate using ethyl cellulose and acrycoat S-100 as polymers, and sodium bicarbonate, citric acid and tartaric acid as gas generating agents. Methods: Twenty four formulations were prepared and segregated into four major categories, A to D. The floating tablets ...

  20. Protein structure similarity from principle component correlation analysis

    Directory of Open Access Journals (Sweden)

    Chou James


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

  1. Extracellular matrix remodeling and matrix metalloproteinases (ajMMP-2 like and ajMMP-16 like) characterization during intestine regeneration of sea cucumber Apostichopus japonicus. (United States)

    Miao, Ting; Wan, Zixuan; Sun, Lina; Li, Xiaoni; Xing, Lili; Bai, Yucen; Wang, Fang; Yang, Hongsheng


    Remodeling of extracellular matrix (ECM) regulated by matrix metalloproteinases (MMPs) is essential for tissue regeneration. In the present study, we used immunohistochemistry (IHC) techniques against ECM components to reveal changes of ECM during intestine regeneration of Apostichopus japonicus. The expression of collagen I and laminin reduced apparently from the eviscerated intestine, while fibronectin exhibited continuous expression in all regeneration stages observed. Meanwhile, we cloned two MMP genes from A. japonicus by RACE PCR. The full-length cDNA of ajMMP-2 like is 2733bp and contains a predicted open reading frame (ORF) of 1716bp encoding 572 amino acids. The full-length cDNA of ajMMP-16 like is 2705bp and contains an ORF of 1452bp encoding 484 amino acids. The predicted protein sequences of each MMP contain two conserved domains, ZnMc_MMP and HX. Homology and phylogenetic analysis revealed that ajMMP-2 like and ajMMP-16 like share high sequence similarity with MMP-2 and MMP-16 from Strongylocentrotus purpuratus, respectively. Then we investigated spatio-temporal expression of ajMMP-2 like and ajMMP-16 like during different regeneration stages by qRT-PCR and IHC. The expression pattern of them showed a roughly opposite trend from that of ECM components. According to our results, a fibronectin-dominate temporary matrix is created in intestine regeneration, and it might provide structural integrity for matrix and promote cell movement. We also hypothesize that ajMMP-2 like and ajMMP-16 like could accelerate cell migration and regulate interaction between ECM components and growth factors. This work provides new evidence of ECM and MMPs involvement in sea cucumber regeneration. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Matrix relation algebras

    NARCIS (Netherlands)

    el Bachraoui, M.; van de Vel, M.L.J.


    Square matrices over a relation algebra are relation algebras in a natural way. We show that for fixed n, these algebras can be characterized as reducts of some richer kind of algebra. Hence for fixed n, the class of n × n matrix relation algebras has a first-order characterization. As a

  3. Kernelized Bayesian Matrix Factorization. (United States)

    Gönen, Mehmet; Kaski, Samuel


    We extend kernelized matrix factorization with a full-Bayesian treatment and with an ability to work with multiple side information sources expressed as different kernels. Kernels have been introduced to integrate side information about the rows and columns, which is necessary for making out-of-matrix predictions. We discuss specifically binary output matrices but extensions to realvalued matrices are straightforward. We extend the state of the art in two key aspects: (i) A full-conjugate probabilistic formulation of the kernelized matrix factorization enables an efficient variational approximation, whereas full-Bayesian treatments are not computationally feasible in the earlier approaches. (ii) Multiple side information sources are included, treated as different kernels in multiple kernel learning which additionally reveals which side sources are informative. We then show that the framework can also be used for supervised and semi-supervised multilabel classification and multi-output regression, by considering samples and outputs as the domains where matrix factorization operates. Our method outperforms alternatives in predicting drug-protein interactions on two data sets. On multilabel classification, our algorithm obtains the lowest Hamming losses on 10 out of 14 data sets compared to five state-of-the-art multilabel classification algorithms. We finally show that the proposed approach outperforms alternatives in multi-output regression experiments on a yeast cell cycle data set.

  4. A random matrix analysis

    Indian Academy of Sciences (India)

    chaos to galaxies. We demonstrate the applicability of random matrix theory for networks by pro- viding a new dimension to complex systems research. We show that in spite of huge differences ... as mentioned earlier, different types of networks can be constructed based on the nature of connections. For example,.

  5. Constructing the matrix (United States)

    Elliott, John


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

  6. Revisiting Inter-Genre Similarity

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Gouyon, Fabien


    We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...

  7. Interfaces between a fibre and its matrix

    DEFF Research Database (Denmark)

    Lilholt, Hans; Sørensen, Bent F.


    The interface between a fibre and its matrix represents an important element in the characterization and exploitation of composite materials. Both theoretical models and analyses of experimental data have been presented in the literature since modern composite were developed and many experiments......, the interfacial energy [J/m2], the interfacial frictional shear stress [MPa] and the mismatch strain [-] between fibre and matrix. The model has been used for the different modes of fibre pull-out and fibre fragmentation. In this paper it is demonstrated that the governing equations for the experimental...... parameters (applied load, debond length and relative fibre/matrix displacement) are rather similar for these test modes. A simplified analysis allows the direct determination of the three interface parameters from two plots for the experimental data. The complete analysis is demonstrated for steel fibres...

  8. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper


    a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single....... However, instead of examining individual conformations it is in many cases more relevant to analyse ensembles of conformations that have been obtained either through experiments or from methods such as molecular dynamics simulations. We here present three approaches that can be used to compare......Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations...

  9. Improved collaborative filtering recommendation algorithm of similarity measure (United States)

    Zhang, Baofu; Yuan, Baoping


    The Collaborative filtering recommendation algorithm is one of the most widely used recommendation algorithm in personalized recommender systems. The key is to find the nearest neighbor set of the active user by using similarity measure. However, the methods of traditional similarity measure mainly focus on the similarity of user common rating items, but ignore the relationship between the user common rating items and all items the user rates. And because rating matrix is very sparse, traditional collaborative filtering recommendation algorithm is not high efficiency. In order to obtain better accuracy, based on the consideration of common preference between users, the difference of rating scale and score of common items, this paper presents an improved similarity measure method, and based on this method, a collaborative filtering recommendation algorithm based on similarity improvement is proposed. Experimental results show that the algorithm can effectively improve the quality of recommendation, thus alleviate the impact of data sparseness.

  10. Redesigning Triangular Dense Matrix Computations on GPUs

    KAUST Repository

    Charara, Ali


    A new implementation of the triangular matrix-matrix multiplication (TRMM) and the triangular solve (TRSM) kernels are described on GPU hardware accelerators. Although part of the Level 3 BLAS family, these highly computationally intensive kernels fail to achieve the percentage of the theoretical peak performance on GPUs that one would expect when running kernels with similar surface-to-volume ratio on hardware accelerators, i.e., the standard matrix-matrix multiplication (GEMM). The authors propose adopting a recursive formulation, which enriches the TRMM and TRSM inner structures with GEMM calls and, therefore, reduces memory traffic while increasing the level of concurrency. The new implementation enables efficient use of the GPU memory hierarchy and mitigates the latency overhead, to run at the speed of the higher cache levels. Performance comparisons show up to eightfold and twofold speedups for large dense matrix sizes, against the existing state-of-the-art TRMM and TRSM implementations from NVIDIA cuBLAS, respectively, across various GPU generations. Once integrated into high-level Cholesky-based dense linear algebra algorithms, the performance impact on the overall applications demonstrates up to fourfold and twofold speedups, against the equivalent native implementations, linked with cuBLAS TRMM and TRSM kernels, respectively. The new TRMM/TRSM kernel implementations are part of the open-source KBLAS software library ( and are lined up for integration into the NVIDIA cuBLAS library in the upcoming v8.0 release.

  11. Matrix rigidity regulates microtubule network polarization in migration. (United States)

    Raab, Matthew; Discher, Dennis E


    The microtubule organizing center (MTOC) frequently polarizes to a position in front of the nucleus during cell migration, but recent work has shown conflicting evidence for MTOC location in migratory polarized cells. Here, we show that subcellular localization of the MTOC is modulated by extracellular matrix stiffness. In scratch wound assays as well as single cell migration of mesenchymal stem cells (MSCs) the MTOC appears randomly positioned when cells are migrating on soft matrix, whereas on stiff matrix the MTOC is in front of the nucleus. The bulk of the microtubule density is also equally likely to be in front of or behind the nucleus on soft matrix, but it is polarized in front of the nucleus on stiff matrix. This occurred during cell migration with cells in interphase. During cytokinesis, the centrosomes polarize on either side of the chromosomes even on soft matrix, with MIIB localized strongly in the cleavage furrow which depolarizes only on soft matrix as cells exit cytokinesis. When cells are immobilized on micro-patterns printed on the top of substrates of different stiffness, MIIB polarized if the matrix was sufficiently stiff similar to results with migrating cells. However, the MTOC was randomly positioned with respect to the nucleus independent of matrix stiffness. We deduce that cell migration is necessary to orient the MTOC in front of the nucleus and that matrix stiffness helps to drive cell polarization during migration. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences

    National Research Council Canada - National Science Library

    Campanella, James J; Bitincka, Ledion; Smalley, John


    .... We have developed MatGAT (Matrix Global Alignment Tool), a simple, easy to use computer application that generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data...

  13. Matrix groups for undergraduates

    CERN Document Server

    Tapp, Kristopher


    Matrix groups touch an enormous spectrum of the mathematical arena. This textbook brings them into the undergraduate curriculum. It makes an excellent one-semester course for students familiar with linear and abstract algebra and prepares them for a graduate course on Lie groups. Matrix Groups for Undergraduates is concrete and example-driven, with geometric motivation and rigorous proofs. The story begins and ends with the rotations of a globe. In between, the author combines rigor and intuition to describe the basic objects of Lie theory: Lie algebras, matrix exponentiation, Lie brackets, maximal tori, homogeneous spaces, and roots. This second edition includes two new chapters that allow for an easier transition to the general theory of Lie groups. From reviews of the First Edition: This book could be used as an excellent textbook for a one semester course at university and it will prepare students for a graduate course on Lie groups, Lie algebras, etc. … The book combines an intuitive style of writing w...

  14. Extracellular matrix structure. (United States)

    Theocharis, Achilleas D; Skandalis, Spyros S; Gialeli, Chrysostomi; Karamanos, Nikos K


    Extracellular matrix (ECM) is a non-cellular three-dimensional macromolecular network composed of collagens, proteoglycans/glycosaminoglycans, elastin, fibronectin, laminins, and several other glycoproteins. Matrix components bind each other as well as cell adhesion receptors forming a complex network into which cells reside in all tissues and organs. Cell surface receptors transduce signals into cells from ECM, which regulate diverse cellular functions, such as survival, growth, migration, and differentiation, and are vital for maintaining normal homeostasis. ECM is a highly dynamic structural network that continuously undergoes remodeling mediated by several matrix-degrading enzymes during normal and pathological conditions. Deregulation of ECM composition and structure is associated with the development and progression of several pathologic conditions. This article emphasizes in the complex ECM structure as to provide a better understanding of its dynamic structural and functional multipotency. Where relevant, the implication of the various families of ECM macromolecules in health and disease is also presented. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. Localization of an O-glycosylated site in the recombinant barley alpha-amylase 1 produced in yeast and correction of the amino acid sequence using matrix-assisted laser desorption/ionization mass spectrometry of peptide mixtures

    DEFF Research Database (Denmark)

    Andersen, Jens S.; Søgaard, M; Svensson, B


    degradation of two selected peptides isolated from the endoproteinase Lys-C digest corrected the sequence to be Val instead of Ala in position 284 and confirmed the O-glycosylation. These results demonstrate that the direct peptide mixture analysis by MALDI-MS is a rapid and sensitive method for protein......Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of peptide mixtures was used to characterize recombinant barley alpha-amylase 1, produced in yeast. Three peptide mixtures were generated by cleavage with CNBr, digestion with endoproteinase Lys-C and Asp-N, respectively...

  16. Caries correlates strongly to salivary levels of matrix metalloproteinase-8

    DEFF Research Database (Denmark)

    Hedenbjörk-Lager, Anders; Bjørndal, Lars; Gustafsson, Anders


    The caries process in dentin involves the degradation of both mineral and organic matrix. The demineralization has been demonstrated to be caused by bacterial acids. However, the collagen degradation is considered to be initiated by endogenous proteolytic enzymes, mainly collagenolytic matrix...... determined using a chair-side kit. Subjects with manifest caries lesions presented with elevated levels of MMP-8 (p plaque index (p = 0.05) compared with subjects without manifest caries. Multiple linear regression analysis...

  17. Nano-fillers to tune Young's modulus of silicone matrix (United States)

    Xia, Lijin; Xu, Zhonghua; Sun, Leming; Caveney, Patrick M.; Zhang, Mingjun


    In this study, we investigated nanoparticles, nanofibers, and nanoclays for their filler effects on tuning the Young's modulus of silicone matrix, a material with broad in vivo applications. Nano-fillers with different shapes, sizes, and surface properties were added into silicone matrix, and then their filler effects were evaluated through experimental studies. It was found that spherical nanoparticles could clearly improve Young's modulus of the silicone matrix, while nanoclays and carbon nanofibers had limited effects. Smaller spherical nanoparticles were better in performance compared to larger nanoparticles. In addition, enhanced distribution of the nanoparticles in the matrix has been observed to improve the filler effect. In order to minimize toxicity of the nanoparticles for in vivo applications, spherical nanoparticles coated with amine, acid, or hydroxide groups were also investigated, but they were found only to diminish the filler effect of nanoparticles. This study demonstrated that spherical nanoparticles could serve as fillers to tune Young's modulus of silicone matrix for potential applications in medicine.

  18. Molecular cloning and characterization of lustrin A, a matrix protein from shell and pearl nacre of Haliotis rufescens. (United States)

    Shen, X; Belcher, A M; Hansma, P K; Stucky, G D; Morse, D E


    A specialized extracellular matrix of proteins and polysaccharides controls the morphology and packing of calcium carbonate crystals and becomes occluded within the mineralized composite during formation of the molluscan shell and pearl. We have cloned and characterized the cDNA coding for Lustrin A, a newly described matrix protein from the nacreous layer of the shell and pearl produced by the abalone, Haliotis rufescens, a marine gastropod mollusc. The full-length cDNA is 4,439 base pairs (bp) long and contains an open reading frame coding for 1,428 amino acids. The deduced amino acid sequence reveals a highly modular structure with a high proportion of Ser (16%), Pro (14%), Gly (13%), and Cys (9%). The protein contains ten highly conserved cysteine-rich domains interspersed by eight proline-rich domains; a glycine- and serine-rich domain lies between the two cysteine-rich domains nearest the C terminus, and these are followed by a basic domain and a C-terminal domain that is highly similar to known protease inhibitors. The glycine- and serine-rich domain and at least one of the proline-rich domains show sequence similarity to proteins of two extracellular matrix superfamilies (one of which also is involved in the mineralized matrixes of bone, dentin, and avian eggshell). The arrangement of alternating cysteine-rich domains and proline-rich domains is strikingly similar to that found in frustulins, the proteins that are integral to the silicified cell wall of diatoms. Its modular structure suggests that Lustrin A is a multifunctional protein, whereas the occurrence of related sequences suggest it is a member of a multiprotein family.

  19. Assembly and development of the Pseudomonas aeruginosa biofilm matrix.

    Directory of Open Access Journals (Sweden)

    Luyan Ma


    Full Text Available 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.

  20. A note on matrix differentiation


    Kowal, Pawel


    This paper presents a set of rules for matrix differentiation with respect to a vector of parameters, using the flattered representation of derivatives, i.e. in form of a matrix. We also introduce a new set of Kronecker tensor products of matrices. Finally we consider a problem of differentiating matrix determinant, trace and inverse.

  1. Optimal neighborhood indexing for protein similarity search. (United States)

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu


    Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  2. NMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein

    Directory of Open Access Journals (Sweden)

    Lola A. Brown


    Full Text Available Membrane targeting by the Gag proteins of the human immunodeficiency viruses (HIV types-1 and -2 is mediated by Gag’s N-terminally myristylated matrix (MA domain and is dependent on cellular phosphatidylinositol-4,5-bisphosphate [PI(4,5P2]. To determine if other lentiviruses employ a similar membrane targeting mechanism, we initiated studies of the feline immunodeficiency virus (FIV, a widespread feline pathogen with potential utility for development of human therapeutics. Bacterial co-translational myristylation was facilitated by mutation of two amino acids near the amino-terminus of the protein (Q5A/G6S; myrMAQ5A/G6S. These substitutions did not affect virus assembly or release from transfected cells. NMR studies revealed that the myristyl group is buried within a hydrophobic pocket in a manner that is structurally similar to that observed for the myristylated HIV-1 protein. Comparisons with a recent crystal structure of the unmyristylated FIV protein [myr(-MA] indicate that only small changes in helix orientation are required to accommodate the sequestered myr group. Depletion of PI(4,5P2 from the plasma membrane of FIV-infected CRFK cells inhibited production of FIV particles, indicating that, like HIV, FIV hijacks the PI(4,5P2 cellular signaling system to direct intracellular Gag trafficking during virus assembly.

  3. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  4. The cellulose resource matrix. (United States)

    Keijsers, Edwin R P; Yılmaz, Gülden; van Dam, Jan E G


    The emerging biobased economy is causing shifts from mineral fossil oil based resources towards renewable resources. Because of market mechanisms, current and new industries utilising renewable commodities, will attempt to secure their supply of resources. Cellulose is among these commodities, where large scale competition can be expected and already is observed for the traditional industries such as the paper industry. Cellulose and lignocellulosic raw materials (like wood and non-wood fibre crops) are being utilised in many industrial sectors. Due to the initiated transition towards biobased economy, these raw materials are intensively investigated also for new applications such as 2nd generation biofuels and 'green' chemicals and materials production (Clark, 2007; Lange, 2007; Petrus & Noordermeer, 2006; Ragauskas et al., 2006; Regalbuto, 2009). As lignocellulosic raw materials are available in variable quantities and qualities, unnecessary competition can be avoided via the choice of suitable raw materials for a target application. For example, utilisation of cellulose as carbohydrate source for ethanol production (Kabir Kazi et al., 2010) avoids the discussed competition with easier digestible carbohydrates (sugars, starch) deprived from the food supply chain. Also for cellulose use as a biopolymer several different competing markets can be distinguished. It is clear that these applications and markets will be influenced by large volume shifts. The world will have to reckon with the increase of competition and feedstock shortage (land use/biodiversity) (van Dam, de Klerk-Engels, Struik, & Rabbinge, 2005). It is of interest - in the context of sustainable development of the bioeconomy - to categorize the already available and emerging lignocellulosic resources in a matrix structure. When composing such "cellulose resource matrix" attention should be given to the quality aspects as well as to the available quantities and practical possibilities of processing the

  5. Random matrix theory

    CERN Document Server

    Deift, Percy


    This book features a unified derivation of the mathematical theory of the three classical types of invariant random matrix ensembles-orthogonal, unitary, and symplectic. The authors follow the approach of Tracy and Widom, but the exposition here contains a substantial amount of additional material, in particular, facts from functional analysis and the theory of Pfaffians. The main result in the book is a proof of universality for orthogonal and symplectic ensembles corresponding to generalized Gaussian type weights following the authors' prior work. New, quantitative error estimates are derive

  6. Matrix Encryption Scheme

    Directory of Open Access Journals (Sweden)

    Abdelhakim Chillali


    Full Text Available In classical cryptography, the Hill cipher is a polygraphic substitution cipher based on linear algebra. In this work, we proposed a new problem applicable to the public key cryptography, based on the Matrices, called “Matrix discrete logarithm problem”, it uses certain elements formed by matrices whose coefficients are elements in a finite field. We have constructed an abelian group and, for the cryptographic part in this unreliable group, we then perform the computation corresponding to the algebraic equations, Returning the encrypted result to a receiver. Upon receipt of the result, the receiver can retrieve the sender’s clear message by performing the inverse calculation.

  7. Matrix string partition function

    CERN Document Server

    Kostov, Ivan K; Kostov, Ivan K.; Vanhove, Pierre


    We evaluate quasiclassically the Ramond partition function of Euclidean D=10 U(N) super Yang-Mills theory reduced to a two-dimensional torus. The result can be interpreted in terms of free strings wrapping the space-time torus, as expected from the point of view of Matrix string theory. We demonstrate that, when extrapolated to the ultraviolet limit (small area of the torus), the quasiclassical expressions reproduce exactly the recently obtained expression for the partition of the completely reduced SYM theory, including the overall numerical factor. This is an evidence that our quasiclassical calculation might be exact.

  8. Matrix vector analysis

    CERN Document Server

    Eisenman, Richard L


    This outstanding text and reference applies matrix ideas to vector methods, using physical ideas to illustrate and motivate mathematical concepts but employing a mathematical continuity of development rather than a physical approach. The author, who taught at the U.S. Air Force Academy, dispenses with the artificial barrier between vectors and matrices--and more generally, between pure and applied mathematics.Motivated examples introduce each idea, with interpretations of physical, algebraic, and geometric contexts, in addition to generalizations to theorems that reflect the essential structur

  9. Matrix algebra for linear models

    CERN Document Server

    Gruber, Marvin H J


    Matrix methods have evolved from a tool for expressing statistical problems to an indispensable part of the development, understanding, and use of various types of complex statistical analyses. This evolution has made matrix methods a vital part of statistical education. Traditionally, matrix methods are taught in courses on everything from regression analysis to stochastic processes, thus creating a fractured view of the topic. Matrix Algebra for Linear Models offers readers a unique, unified view of matrix analysis theory (where and when necessary), methods, and their applications. Written f

  10. Alaska, Gulf spills share similarities

    Energy Technology Data Exchange (ETDEWEB)

    Usher, D. (Marine Pollution Control Co., Detroit, MI (United States))

    The accidental Exxon Valdez oil spill in Alaska and the deliberate dumping of crude oil into the Persian Gulf as a tactic of war contain both glaring differences and surprising similarities. Public reaction and public response was much greater to the Exxon Valdez spill in pristine Prince William Sound than to the war-related tragedy in the Persian Gulf. More than 12,000 workers helped in the Alaskan cleanup; only 350 have been involved in Kuwait. But in both instances, environmental damages appear to be less than anticipated. Natures highly effective self-cleansing action is primarily responsible for minimizing the damages. One positive action growing out of the two incidents is increased international cooperation and participation in oil-spill clean-up efforts. In 1990, in the aftermath of the Exxon Valdez spill, 94 nations signed an international accord on cooperation in future spills. The spills can be historic environmental landmarks leading to creation of more sophisticated response systems worldwide.

  11. GUMBOS matrices of variable hydrophobicity for matrix-assisted laser desorption/ionization mass spectrometry. (United States)

    Al Ghafly, Hashim; Siraj, Noureen; Das, Susmita; Regmi, Bishnu P; Magut, Paul K S; Galpothdeniya, Waduge Indika S; Murray, Kermit K; Warner, Isiah M


    Detection of hydrophobic peptides remains a major obstacle for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This stems from the fact that most matrices for MALDI are hydrophilic and therefore have low affinities for hydrophobic peptides. Herein, 1-aminopyrene (AP) and AP-derived group of uniform materials based on organic salts (GUMBOS) as novel matrices for MALDI-MS analyses of peptides were investigated for hydrophobic and hydrophilic peptides. A number of solid-phase AP-based GUMBOS are synthesized with variable hydrophobicity simply by changing the counterions. Structures were confirmed by use of (1)H NMR and electrospray ionization mass spectrometry (ESI-MS). 1-Octanol/water partition coefficients (Ko/w) were used to measure the hydrophobicity of the matrices. A dried-droplet method was used for sample preparation. All spectra were obtained using a MALDI-TOF mass spectrometer in positive ion reflectron mode. A series of AP-based GUMBOS was synthesized including [AP][chloride] ([AP][Cl]), [AP][ascorbate] ([AP][Asc]) and [AP][bis(trifluoromethane)sulfonimide] ([AP][NTf2]). The relative hydrophobicities of these compounds and α-cyano-4-hydroxycinnamic acid (CHCA, a common MALDI matrix) indicated that AP-based GUMBOS can be tuned to be much more hydrophobic than CHCA. A clear trend is observed between the signal intensities of hydrophobic peptides and hydrophobicity of the matrix. MALDI matrices of GUMBOS with tunable hydrophobicities are easily obtained simply by varying the counterion. We have found that hydrophobic matrix materials are very effective for MALDI determination of hydrophobic peptides and, similarly, the more hydrophilic peptides displayed greater intensity in the more hydrophilic matrix. Copyright © 2014 John Wiley & Sons, Ltd.

  12. Interpolymer complexation between copovidone and carbopol and its effect on drug release from matrix tablets. (United States)

    Zhang, Feng; Meng, Fan; Wang, Zhi Yuan; Na, Watson


    The interaction between copovidone and Carbopol 907 is pH dependent. When the pH of an aqueous solution fell below pH 4.5, a water-insoluble complex began to form and precipitate. This complex resulted from a hydrogen-bond-induced interaction between the carboxylic groups in Carbopol 907 and the carbonyl groups of N-vinylpyrrolidone repeat units in copovidone. Consisting of these two polymers at an approximate 1:1 weight ratio, the complex was an amorphous material with a glass transition temperature of 157 °C. The interpolymer complexation in situ was applied to modify drug release properties of Carbopol 907-based theophylline matrix tablets. The effect of copovidone on drug release was dependent on the pH of the dissolution medium. In a 0.1 N hydrochloride acid solution at pH 1.2 and 50 mM acetate buffer at pH 4.0, an insoluble tablet matrix was formed as a result of the in situ interpolymer complexation, and theophylline was released therefore via Fickian diffusion. In a 50 mM phosphate buffer at pH 6.8, drug release from the matrix tablets was still impacted by the in situ interpolymer complexation because of the low-pH microenvironment induced by Carbopol 907. As a result, drug release rate of the matrix tablet containing both polymers at pH 6.8 was slower than that of the matrix tablets containing individual polymers. We observed similar drug release rates at both pH 1.2 and pH 6.8 between tablets containing the physical blend of these two polymers and tablets containing preformed interpolymer complexes.

  13. Statistical meaning of the differential Mueller matrix of depolarizing homogeneous media. (United States)

    Ossikovski, Razvigor; Arteaga, Oriol


    By applying the statistical definition of a depolarizing Mueller matrix we formally derive and physically interpret the differential matrix of a depolarizing homogeneous medium. The depolarization phenomenon being a direct consequence of the fluctuations of the six elementary polarization properties of the medium, the differential matrix contains the mean values and the variances of the properties, thus fully describing those from a statistical viewpoint. Similarly, the reduced coherency matrix associated with the G-symmetric component of the differential matrix has an immediate physical interpretation as being the covariance matrix of the three basic groups of polarization properties. The formal developments are illustrated on experimental examples.

  14. Matrix isolation infrared spectra of OH··· π Hydrogen bonded ...

    Indian Academy of Sciences (India)

    Mid infrared spectra of two O–H· · · π hydrogen-bonded binary complexes of acetic acid (AA) and trifluoroacetic acid (F₃AA) with benzene (Bz) have been measured by isolating the complexes in an argon matrix at ∼8 K. In a matrix isolation condition, the O–H stretching fundamentals (νO−H) of the carboxylic acid groups of ...

  15. Newborn screening by matrix-assisted laser desorption/ionization mass spectrometry based on parylene-matrix chip. (United States)

    Kim, Jo-Il; Noh, Joo-Yoon; Kim, Mira; Park, Jong-Min; Song, Hyun-Woo; Kang, Min-Jung; Pyun, Jae-Chul


    Newborn screening for diagnosis of phenylketonuria, homocystinuria, and maple syrup urine disease have been conducted by analyzing the concentration of target amino acids using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) based on parylene-matrix chip. Parylene-matrix chip was applied to MALDI-ToF MS analysis reducing the matrix peaks significantly at low mass-to-charge ratio range (m/z mass spectrometric analysis showing 13.3 to 45% of extraction efficiency. Calibration curves for diagnosis of neonatal metabolic disorders were obtained by analyzing methanol-extracted serum spiked with target amino acids using MALDI-ToF MS. They showed good linearity (R2 > 0.98) and the LODs were ranging from 9.0 to 22.9 μg/mL. Effect of proteins in serum was estimated by comparing MALDI-ToF mass spectra of amino acids-spiked serum before and after the methanol extraction. Interference of other amino acids on analysis of target analyte was determined to be insignificant. From these results, MALDI-ToF MS based on parylene-matrix chip could be applicable to medical diagnosis of neonatal metabolic disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

    Directory of Open Access Journals (Sweden)

    Žel Jana


    Full Text Available Abstract Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was

  17. Structure of the catalytic domain of the Tannerella forsythia matrix metallopeptidase karilysin in complex with a tetrapeptidic inhibitor

    DEFF Research Database (Denmark)

    Guevara, Tibisay; Ksiazek, Miroslaw; Skottrup, Peter Durand


    Karilysin is the only metallopeptidase identified as a virulence factor in the odontopathogen Tannerella forsythia owing to its deleterious effect on the host immune response during bacterial infection. The very close structural and sequence-based similarity of its catalytic domain (Kly18......) to matrix metalloproteinases suggests that karilysin was acquired by horizontal gene transfer from an animal host. Previous studies by phage display identified peptides with the consensus sequence XWFPXXXGGG (single-letter amino-acid codes; X represents any residue) as karilysin inhibitors with low...

  18. Ceramic matrix and resin matrix composites: A comparison (United States)

    Hurwitz, Frances I.


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

  19. Ceramic matrix and resin matrix composites - A comparison (United States)

    Hurwitz, Frances I.


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

  20. Boric acid and boronic acids inhibition of pigeonpea urease. (United States)

    Reddy, K Ravi Charan; Kayastha, Arvind M


    Urease from the seeds of pigeonpea was competitively inhibited by boric acid, butylboronic acid, phenylboronic acid, and 4-bromophenylboronic acid; 4-bromophenylboronic acid being the strongest inhibitor, followed by boric acid > butylboronic acid > phenylboronic acid, respectively. Urease inhibition by boric acid is maximal at acidic pH (5.0) and minimal at alkaline pH (10.0), i.e., the trigonal planar B(OH)3 form is a more effective inhibitor than the tetrahedral B(OH)4 -anionic form. Similarly, the anionic form of phenylboronic acid was least inhibiting in nature.

  1. Investigation of full similarity of images digitized with stenocamera

    Directory of Open Access Journals (Sweden)

    Radvilė Budrytė


    Full Text Available In technical photography, there are cases with requirement to keep full similarity among the object and its reflection. Due to the aberration of optical systems used in photography tools, unambiguous and precise application of projecting geometry rules becomes impossible. The problem remains in digital photography with traditional optical devices and image processing with software tools is complicated due to the both insensitivity of image matrixes and the lack of suitable correction algorithms. The study has shown that the best results can be obtained by using stenocamera and sensitive photographic film. New digital image retrieval method, obtained by combining classical stenocamera tool with digital web camera matrix is described in this paper.

  2. The mechanism of ascorbic acid-induced differentiation of ATDC5 chondrogenic cells (United States)

    Temu, Tecla M.; Wu, Ke-Ying; Gruppuso, Philip A.


    The ATDC5 cell line exhibits a multistep process of chondrogenic differentiation analogous to that observed during endochondral bone formation. Previous investigators have induced ATDC5 cells to differentiate by exposing them to insulin at high concentrations. We have observed spontaneous differentiation of ATDC5 cells maintained in ascorbic acid-containing α-MEM. A comparison of the differentiation events in response to high-dose insulin vs. ascorbic acid showed similar expression patterns of key genes, including collagen II, Runx2, Sox9, Indian hedgehog, and collagen X. We took advantage of the action of ascorbic acid to examine signaling events associated with differentiation. In contrast to high-dose insulin, which downregulates both IGF-I and insulin receptors, there were only minimal changes in the abundance of these receptors during ascorbic acid-induced differentiation. Furthermore, ascorbic acid exposure was associated with ERK activation, and ERK inhibition attenuated ascorbic acid-induced differentiation. This was in contrast to the inhibitory effect of ERK activation during IGF-I-induced differentiation. Inhibition of collagen formation with a proline analog markedly attenuated the differentiating effect of ascorbic acid on ATDC5 cells. When plates were conditioned with ATDC5 cells exposed to ascorbic acid, ATDC5 cells were able to differentiate in the absence of ascorbic acid. Our results indicate that matrix formation early in the differentiation process is essential for ascorbic acid-induced ATDC5 differentiation. We conclude that ascorbic acid can promote the differentiation of ATDC5 cells by promoting the formation of collagenous matrix and that matrix formation mediates activation of the ERK signaling pathway, which promotes the differentiation program. PMID:20530736

  3. Google matrix of Twitter (United States)

    Frahm, K. M.; Shepelyansky, D. L.


    We construct the Google matrix of the entire Twitter network, dated by July 2009, and analyze its spectrum and eigenstate properties including the PageRank and CheiRank vectors and 2DRanking of all nodes. Our studies show much stronger inter-connectivity between top PageRank nodes for the Twitter network compared to the networks of Wikipedia and British Universities studied previously. Our analysis allows to locate the top Twitter users which control the information flow on the network. We argue that this small fraction of the whole number of users, which can be viewed as the social network elite, plays the dominant role in the process of opinion formation on the network.

  4. Matrix membranes and integrability

    Energy Technology Data Exchange (ETDEWEB)

    Zachos, C. [Argonne National Lab., IL (United States); Fairlie, D. [University of Durham (United Kingdom). Dept. of Mathematical Sciences; Curtright, T. [University of Miami, Coral Gables, FL (United States). Dept. of Physics


    This is a pedagogical digest of results reported in Curtright, Fairlie, {ampersand} Zachos 1997, and an explicit implementation of Euler`s construction for the solution of the Poisson Bracket dual Nahm equation. But it does not cover 9 and 10-dimensional systems, and subsequent progress on them Fairlie 1997. Cubic interactions are considered in 3 and 7 space dimensions, respectively, for bosonic membranes in Poisson Bracket form. Their symmetries and vacuum configurations are explored. Their associated first order equations are transformed to Nahm`s equations, and are hence seen to be integrable, for the 3-dimensional case, by virtue of the explicit Lax pair provided. Most constructions introduced also apply to matrix commutator or Moyal Bracket analogs.

  5. Light cone matrix product

    Energy Technology Data Exchange (ETDEWEB)

    Hastings, Matthew B [Los Alamos National Laboratory


    We show how to combine the light-cone and matrix product algorithms to simulate quantum systems far from equilibrium for long times. For the case of the XXZ spin chain at {Delta} = 0.5, we simulate to a time of {approx} 22.5. While part of the long simulation time is due to the use of the light-cone method, we also describe a modification of the infinite time-evolving bond decimation algorithm with improved numerical stability, and we describe how to incorporate symmetry into this algorithm. While statistical sampling error means that we are not yet able to make a definite statement, the behavior of the simulation at long times indicates the appearance of either 'revivals' in the order parameter as predicted by Hastings and Levitov (e-print arXiv:0806.4283) or of a distinct shoulder in the decay of the order parameter.

  6. Google matrix, dynamical attractors, and Ulam networks. (United States)

    Shepelyansky, D L; Zhirov, O V


    We study the properties of the Google matrix generated by a coarse-grained Perron-Frobenius operator of the Chirikov typical map with dissipation. The finite-size matrix approximant of this operator is constructed by the Ulam method. This method applied to the simple dynamical model generates directed Ulam networks with approximate scale-free scaling and characteristics being in certain features similar to those of the world wide web with approximate scale-free degree distributions as well as two characteristics similar to the web: a power-law decay in PageRank that mirrors the decay of PageRank on the world wide web and a sensitivity to the value alpha in PageRank. The simple dynamical attractors play here the role of popular websites with a strong concentration of PageRank. A variation in the Google parameter alpha or other parameters of the dynamical map can drive the PageRank of the Google matrix to a delocalized phase with a strange attractor where the Google search becomes inefficient.

  7. Collagen in the spicule organic matrix of the gorgonian Leptogorgia virgulata (United States)

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


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

  8. Affinity Propagation Clustering Using Path Based Similarity


    Yuan Jiang; Yuliang Liao; Guoxian Yu


    Clustering is a fundamental task in data mining. Affinity propagation clustering (APC) is an effective and efficient clustering technique that has been applied in various domains. APC iteratively propagates information between affinity samples, updates the responsibility matrix and availability matrix, and employs these matrices to choose cluster centers (or exemplars) of respective clusters. However, since it mainly uses negative Euclidean distance between exemplars and samples as the simila...

  9. Density Functional Approach and Random Matrix Theory in Proteogenesis (United States)

    Yamanaka, Masanori


    We study the energy-level statistics of amino acids by random matrix theory. The molecular orbital and the Kohn-Sham orbital energies are calculated using ab initio and density-functional formalisms for 20 different amino acids. To generate statistical data, we performed a multipoint calculation on 10000 molecular structures produced via a molecular dynamics simulation. For the valence orbitals, the energy-level statistics exhibit repulsion, but the universality in the random matrix cannot be determined. For the unoccupied orbitals, the energy-level statistics indicate an intermediate distribution between the Gaussian orthogonal ensemble and the semi-Poisson statistics for all 20 different amino acids. These amino acids are considered to be in a type of critical state.

  10. Matrix metalloproteinases in myasthenia gravis. (United States)

    Helgeland, Geir; Petzold, Axel; Luckman, Steven Paul; Gilhus, Nils Erik; Plant, Gordon T; Romi, Fredrik Robert


    Myasthenia gravis (MG) is an autoimmune disease with weakness in striated musculature due to anti-acetylcholine receptor (AChR) antibodies or muscle specific kinase at the neuromuscular junction. A subgroup of patients has periocular symptoms only; ocular MG (OMG). Matrix metalloproteinases (MMP) are increased in several autoimmune diseases, including generalized MG (GMG), and have been suggested to play a role in immune cell infiltration, basement membrane breakdown and autoimmune pathogenesis. Total levels of MMP2, MMP3 and MMP9 were measured in serum by ELISA. The MG patients had increased serum levels of MMP2 (median values 200.7 vs. 159.7 ng/ml, p < 0.001) and MMP9 (median values 629.6 vs. 386.4 ng/ml, p < 0.001) compared to controls. A subgroup of patients had increased MMP3 concentration (p = 0.001). The differences were not dependent on presence of AChR antibodies. No difference was observed between GMG and OMG patients with regard to MMP2 (p = 0.598), MMP3 (p = 0.450) and MMP9 (p = 0.271). The increased MMP levels in our MG patients group and the lack of dependence on anti-AChR antibodies suggest that MMP2, MMP3 and MMP9 play a role in the development of MG. The similarities between GMG and OMG support OMG as a systemic disease. Copyright © 2011 S. Karger AG, Basel.

  11. Homolumo Gap and Matrix Model

    CERN Document Server

    Andric, I; Jurman, D; Nielsen, H B


    We discuss a dynamical matrix model by which probability distribution is associated with Gaussian ensembles from random matrix theory. We interpret the matrix M as a Hamiltonian representing interaction of a bosonic system with a single fermion. We show that a system of second-quantized fermions influences the ground state of the whole system by producing a gap between the highest occupied eigenvalue and the lowest unoccupied eigenvalue.

  12. Generalized Framework for Similarity Measure of Time Series

    Directory of Open Access Journals (Sweden)

    Hongsheng Yin


    Full Text Available Currently, there is no definitive and uniform description for the similarity of time series, which results in difficulties for relevant research on this topic. In this paper, we propose a generalized framework to measure the similarity of time series. In this generalized framework, whether the time series is univariable or multivariable, and linear transformed or nonlinear transformed, the similarity of time series is uniformly defined using norms of vectors or matrices. The definitions of the similarity of time series in the original space and the transformed space are proved to be equivalent. Furthermore, we also extend the theory on similarity of univariable time series to multivariable time series. We present some experimental results on published time series datasets tested with the proposed similarity measure function of time series. Through the proofs and experiments, it can be claimed that the similarity measure functions of linear multivariable time series based on the norm distance of covariance matrix and nonlinear multivariable time series based on kernel function are reasonable and practical.

  13. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms. (United States)

    Klein, Marlise I; Hwang, Geelsu; Santos, Paulo H S; Campanella, Osvaldo H; Koo, Hyun


    Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA, and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria. The EPS-rich matrix provides mechanical stability/cohesiveness and facilitates the creation of highly acidic microenvironments, which are critical for the pathogenesis of dental caries. In parallel, S. mutans also releases eDNA and LTA, which can contribute with matrix development. eDNA enhances EPS (glucan) synthesis locally, increasing the adhesion of S. mutans to saliva-coated apatitic surfaces and the assembly of highly cohesive biofilms. eDNA and other extracellular substances, acting in concert with EPS, may impact the functional properties of the matrix and the virulence of cariogenic biofilms. Enhanced understanding about the assembly principles of the matrix may lead to efficacious approaches to control biofilm-related diseases.

  14. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms

    Directory of Open Access Journals (Sweden)

    Marlise eKlein


    Full Text Available Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS, eDNA and lipoteichoic acid (LTA. EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria. The EPS-rich matrix provides mechanical stability/cohesiveness and facilitates the creation of highly acidic microenvironments, which are critical for the pathogenesis of dental caries. In parallel, S. mutans also releases eDNA and LTA, which can contribute with matrix development. eDNA enhances EPS (glucan synthesis locally, increasing the adhesion of S. mutans to saliva-coated apatitic surfaces and the assembly of highly cohesive biofilms. eDNA and other extracellular substances, acting in concert with EPS, may impact the functional properties of the matrix and the virulence of cariogenic biofilms. Enhanced understanding about the assembly principles of the matrix may lead to efficacious approaches to control biofilm-related diseases.

  15. A Novel Matrix Protein Hic31 from the Prismatic Layer of Hyriopsis Cumingii Displays a Collagen-Like Structure.

    Directory of Open Access Journals (Sweden)

    Xiaojun Liu

    Full Text Available In this study, we clone and characterize a novel matrix protein, hic31, from the mantle of Hyriopsis cumingii. The amino acid composition of hic31 consists of a high proportion of Glycine residues (26.67%. Tissue expression detection by RT-PCR indicates that hic31 is expressed specifically at the mantle edge. In situ hybridization results reveals strong signals from the dorsal epithelial cells of the outer fold at the mantle edge, and weak signals from inner epithelial cells of the same fold, indicating that hic31 is a prismatic-layer matrix protein. Although BLASTP results identify no shared homology with other shell-matrix proteins or any other known proteins, the hic31 tertiary structure is similar to that of collagen I, alpha 1 and alpha 2. It has been well proved that collagen forms the basic organic frameworks in way of collagen fibrils and minerals present within or outside of these fibrils. Therefore, hic31 might be a framework-matrix protein involved in the prismatic-layer biomineralization. Besides, the gene expression of hic31 increase in the early stages of pearl sac development, indicating that hic31 may play important roles in biomineralization of the pearl prismatic layer.

  16. MALDI-MS analysis and theoretical evaluation of olanzapine as a UV laser desorption ionization (LDI) matrix. (United States)

    Musharraf, Syed Ghulam; Ameer, Mariam; Ali, Arslan


    Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) being soft ionization technique, has become a method of choice for high-throughput analysis of proteins and peptides. In this study, we have explored the potential of atypical anti-psychotic drug olanzapine (OLZ) as a matrix for MALDI-MS analysis of peptides aided with the theoretical studies. Seven small peptides were employed as target analytes to check performance of olanzapine and compared with conventional MALDI matrix α-cyano-4-hydroxycinnamic acid (HCCA). All peptides were successfully detected when olanzapine was used as a matrix. Moreover, peptides angiotensin Ι and angiotensin ΙΙ were detected with better S/N ratio and resolution with this method as compared to their analysis by HCCA. Computational studies were performed to determine the thermochemical properties of olanzapine in order to further evaluate its similarity to MALDI matrices which were found in good agreement with the data of existing MALDI matrices. Copyright © 2016. Published by Elsevier B.V.

  17. Random matrix theory for underwater sound propagation (United States)

    Hegewisch, K. C.; Tomsovic, S.


    Ocean acoustic propagation can be formulated as a wave guide with a weakly random medium generating multiple scattering. Twenty years ago, this was recognized as a quantum chaos problem, and yet random matrix theory, one pillar of quantum or wave chaos studies, has never been introduced into the subject. The modes of the wave guide provide a representation for the propagation, which in the parabolic approximation is unitary. Scattering induced by the ocean's internal waves leads to a power-law random banded unitary matrix ensemble for long-range deep-ocean acoustic propagation. The ensemble has similarities, but differs, from those introduced for studying the Anderson metal-insulator transition. The resulting long-range propagation ensemble statistics agree well with those of full wave propagation using the parabolic equation.

  18. Diffraction efficiency behavior of photopolymer based on P(MMA-co-MAA) copolymer matrix (United States)

    Kim, Won Sun; Jeong, Yong-Cheol; Park, Jung-Ki; Shin, Chang-Won; Nam-Kim


    New acrylamide-based photopolymers with poly(methyl methacrylate-co-methacrylic acid) as a polymer matrix were prepared and their optical properties including diffraction efficiency and optical transparency were investigated. As the content of methacrylic acid unit was increased, the phase stability of photopolymer was enhanced, while the diffraction efficiency decreased. The enhancement in phase stability is explained in terms of miscibility enhancement between the polymer matrix and photopolymerizable components, and the decrease in diffraction efficiency is mainly attributed to the inhibition of diffusion of acryl amide probably due to the hydrogen bonding induced between polymer matrix and acrylamide with the increase of the acid content.

  19. Synthesis and Characterization of Long-Chain Tartaric Acid Diamides as Novel Ceramide-Like Compounds

    Directory of Open Access Journals (Sweden)

    Krisztina Takács-Novák


    Full Text Available Ceramides play a crucial role in the barrier function of the skin as well as in transmembrane signaling. In this study long aliphatic chain tartaric acid diamides able to replace ceramides in an in vitro model of the stratum corneum lipid matrix due to their similar physico-chemical properties were synthesized from diacetoxysuccinic anhydride in four steps. Their pro-apoptotic effect on fibroblast cells was also investigated.

  20. Modeling of the degradation of poly(ethylene glycol)-co-(lactic acid)-dimethacrylate hydrogels


    Diederich, Vincent E.G.; Villiger, Thomas; Storti, Giuseppe; Lattuada, Marco


    Because of their similarity with extracellular matrix, hydrogels are ideal substrates for cell growth. Hydrogels made of synthetic polymers are excellent alternatives to natural ones and offer the key advantage of precisely controllable degradation times. In this work, hydrogels have been prepared from modified poly(ethylene glycol) macromonomers, functionalized on both ends first with a few lactic acid units, and then with methacrylate groups. A library of hydrogels has been prepared us...

  1. Matrix Depot: an extensible test matrix collection for Julia

    Directory of Open Access Journals (Sweden)

    Weijian Zhang


    Full Text Available Matrix Depot is a Julia software package that provides easy access to a large and diverse collection of test matrices. Its novelty is threefold. First, it is extensible by the user, and so can be adapted to include the user’s own test problems. In doing so, it facilitates experimentation and makes it easier to carry out reproducible research. Second, it amalgamates in a single framework two different types of existing matrix collections, comprising parametrized test matrices (including Hansen’s set of regularization test problems and Higham’s Test Matrix Toolbox and real-life sparse matrix data (giving access to the University of Florida sparse matrix collection. Third, it fully exploits the Julia language. It uses multiple dispatch to help provide a simple interface and, in particular, to allow matrices to be generated in any of the numeric data types supported by the language.

  2. Ceramic matrix composite article and process of fabricating a ceramic matrix composite article (United States)

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


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

  3. Matrix models with Penner interaction inspired by interacting ...

    Indian Academy of Sciences (India)


    Jan 29, 2015 ... An additional dependence of the structure combinatorics factor on (related to the size of the matrix and the interaction strength) is obtained. This factor has a strong effect on the structure combinatorics in the low regime. Databases are scanned for real ribonucleic acid (RNA) structures and pairing ...

  4. Identification of formation scales and design of compatible matrix ...

    African Journals Online (AJOL)

    The fluid systems as indicated in this work had been successfully implemented in the field for stimulation operations in the Niger Delta of Nigeria. Keyword: Formation scales, crude oil, matrix acidizing fluids, wellbore, formation pressure. International Journal of Natural and Applied Sciences, 5(4): 329-333, 2009 ...

  5. An Application of Matrix Multiplication

    Indian Academy of Sciences (India)

    IAS Admin

    linguistics, graph theory applications to biological networks, social networks, electrical engineering. We are well aware of the ever increasing impor- tance of graphical and matrix representations in applications to several day-to-day real life prob- lems. The interconnectedness of the notion of graph, matrix, probability, limits, ...

  6. Matrix Methods to Analytic Geometry. (United States)

    Bandy, C.


    The use of basis matrix methods to rotate axes is detailed. It is felt that persons who have need to rotate axes often will find that the matrix method saves considerable work. One drawback is that most students first learning to rotate axes will not yet have studied linear algebra. (MP)

  7. How to Study a Matrix (United States)

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


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

  8. Developments in Random Matrix Theory


    Snaith, N. C.; Forrester, P. J.; Verbaarschot, J. J. M.


    In this preface to the Journal of Physics A, Special Edition on Random Matrix Theory, we give a review of the main historical developments of random matrix theory. A short summary of the papers that appear in this special edition is also given.

  9. QCD and random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, A.D. [Niels Bohr Inst., Copenhagen (Denmark)


    Chiral random matrix theory has recently been shown to provide a tool useful for both modeling chiral symmetry restoration in QCD and for providing analytic descriptions of the microscopic spectral content of lattice gauge simulations. The basic ideas of chiral random matrix theory and some recent results are discussed. (orig.) 24 refs.

  10. Quantum mechanics in matrix form

    CERN Document Server

    Ludyk, Günter


    This book gives an introduction to quantum mechanics with the matrix method. Heisenberg's matrix mechanics is described in detail. The fundamental equations are derived by algebraic methods using matrix calculus. Only a brief description of Schrödinger's wave mechanics is given (in most books exclusively treated), to show their equivalence to Heisenberg's matrix  method. In the first part the historical development of Quantum theory by Planck, Bohr and Sommerfeld is sketched, followed by the ideas and methods of Heisenberg, Born and Jordan. Then Pauli's spin and exclusion principles are treated. Pauli's exclusion principle leads to the structure of atoms. Finally, Dirac´s relativistic quantum mechanics is shortly presented. Matrices and matrix equations are today easy to handle when implementing numerical algorithms using standard software as MAPLE and Mathematica.

  11. Machining of Metal Matrix Composites

    CERN Document Server


    Machining of Metal Matrix Composites provides the fundamentals and recent advances in the study of machining of metal matrix composites (MMCs). Each chapter is written by an international expert in this important field of research. Machining of Metal Matrix Composites gives the reader information on machining of MMCs with a special emphasis on aluminium matrix composites. Chapter 1 provides the mechanics and modelling of chip formation for traditional machining processes. Chapter 2 is dedicated to surface integrity when machining MMCs. Chapter 3 describes the machinability aspects of MMCs. Chapter 4 contains information on traditional machining processes and Chapter 5 is dedicated to the grinding of MMCs. Chapter 6 describes the dry cutting of MMCs with SiC particulate reinforcement. Finally, Chapter 7 is dedicated to computational methods and optimization in the machining of MMCs. Machining of Metal Matrix Composites can serve as a useful reference for academics, manufacturing and materials researchers, manu...

  12. Assembly of Fibronectin Extracellular Matrix (United States)

    Singh, Purva; Carraher, Cara; Schwarzbauer, Jean E.


    In the process of matrix assembly, multivalent extracellular matrix (ECM) proteins are induced to self-associate and to interact with other ECM proteins to form fibrillar networks. Matrix assembly is usually initiated by ECM glycoproteins binding to cell surface receptors, such as fibronectin (FN) dimers binding to α5β1 integrin. Receptor binding stimulates FN self-association mediated by the N-terminal assembly domain and organizes the actin cytoskeleton to promote cell contractility. FN conformational changes expose additional binding sites that participate in fibril formation and in conversion of fibrils into a stabilized, insoluble form. Once assembled, the FN matrix impacts tissue organization by contributing to the assembly of other ECM proteins. Here, we describe the major steps, molecular interactions, and cellular mechanisms involved in assembling FN dimers into fibrillar matrix while highlighting important issues and major questions that require further investigation. PMID:20690820

  13. On the employment of lambda carrageenan in a matrix system. III. Optimization of a lambda carrageenan-HPMC hydrophilic matrix

    NARCIS (Netherlands)

    Bonferoni, MC; Rossi, S; Ferrari, F; Bertoni, M; Bolhuis, GK; Caramella, C


    The lambda carrageenan/HPMC ratio in matrix tablets has been optimized in order to obtain pH-independent release profiles of chlorpheniramine maleate, a freely soluble drug. Release profiles in acidic (pH 1.2) and neutral (pH 6.8) media were fitted according to the Weibull and the power law models.

  14. Quantitative analysis of biopolymers by matrix-assisted laser desorption

    Energy Technology Data Exchange (ETDEWEB)

    Tang, K.; Allman, S.L.; Jones, R.B.; Chen, C.H. (Oak Ridge National Lab., TN (United States))


    During the past few years, major efforts have been made to use mass spectrometry to measure biopolymers because of the great potential benefit to biological and medical research. Although the theoretical details of laser desorption and ionization mechanisms of MALDI are not yet fully understood, several models have been presented to explain the production of large biopolymer ions. In brief, it is very difficult to obtain reliable measurements of the absolute quantity of analytes by MALDI. If MALDI is going to become a routine analytical tool, it is obvious that quantitative measurement capability must be pursued. Oligonucleotides and protein samples used in this work were purchased from commercial sources. Nicotinic acid was used as matrix for both types of biopolymers. From this experiment, it is seen that it is difficult to obtain absolute quantitative measurements of biopolymers using MALDI. However, internal calibration with molecules having similar chemical properties can be used to resolve these difficulties. Chemical reactions between biopolymers must be avoided to prevent the destruction of the analyte materials. 10 refs., 8 figs.

  15. Matrix-assisted laser desorption/ionization mass spectrometric analysis of aliphatic biodegradable photoluminescent polymers using new ionic liquid matrices. (United States)

    Serrano, Carlos A; Zhang, Yi; Yang, Jian; Schug, Kevin A


    In this study, two novel ionic liquid matrices (ILMs), N,N-diisopropylethylammonium 3-oxocoumarate and N,N-diisopropylethylammonium dihydroxymonooxoacetophenoate, were tested for the structural elucidation of recently developed aliphatic biodegradable polymers by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The polymers, formed by a condensation reaction of three components, citric acid, octane diol, and an amino acid, are fluorescent, but the exact mechanism behind their luminescent properties has not been fully elucidated. In the original studies, which introduced the polymer class (J. Yang et al., Proc. Natl. Acad. Sci. USA 2009, 106, 10086-10091), a hyper-conjugated cyclic structure was proposed as the source for the photoluminescent behavior. With the use of the two new ILMs, we present evidence that supports the presence of the proposed cyclization product. In addition, the new ILMs, when compared with a previously established ILM, N,N-diisopropylethylammonium α-cyano-3-hydroxycinnimate, provided similar signal intensities and maintained similar spectral profiles. This research also established that the new ILMs provided good spot-to-spot reproducibility and high ionization efficiency compared with corresponding crystalline matrix preparations. Many polymer features revealed through the use of the ILMs could not be observed with crystalline matrices. Ultimately, the new ILMs highlighted the composition of the synthetic polymers, as well as the loss of water that was expected for the formation of the proposed cyclic structure on the polymer backbone. Copyright © 2011 John Wiley & Sons, Ltd.

  16. A metal ion charged mixed matrix membrane for selective adsorption of hemoglobin

    NARCIS (Netherlands)

    Tetala, K.K.R.; Skrzypek, Katarzyna; Levisson, M.; Stamatialis, Dimitrios


    In this work, we developed a mixed matrix membrane by incorporating 20–40 μm size iminodiacetic acid modified immobeads within porous Ethylene vinyl alcohol (EVAL) polymer matrix. The MMM were charged with copper ions for selective adsorption of bovine hemoglobin in presence of bovine serum albumin.

  17. A metal ion charged mixed matrix membrane for selective adsorption of hemoglobin

    NARCIS (Netherlands)

    Tetala, K.K.R.; Skrzypek, K.; Levisson, M.; Stamatialis, D.F.


    In this work, we developed a mixed matrix membrane by incorporating 20–40 µm size iminodiacetic acid modified immobeads within porous Ethylene vinyl alcohol (EVAL) polymer matrix. The MMM were charged with copper ions for selective adsorption of bovine hemoglobin in presence of bovine serum albumin.

  18. Self-assembled composite matrix in a hierarchical 3-D scaffold for bone tissue engineering

    DEFF Research Database (Denmark)

    Chen, Muwan; Le, Dang Quang Svend; Baatrup, Anette


    MSC seeding efficiency, proliferation, distribution and differentiation. Porous PCL meshes prepared by fused deposition modeling (FDM) were embedded in matrix of hyaluronic acid, methylated collagen and terpolymer via polyelectrolyte complex coacervation. Scaffolds were cultured statically and dynamically...

  19. ABCD Matrix Method a Case Study

    CERN Document Server

    Seidov, Zakir F; Yahalom, Asher


    In the Israeli Electrostatic Accelerator FEL, the distance between the accelerator's end and the wiggler's entrance is about 2.1 m, and 1.4 MeV electron beam is transported through this space using four similar quadrupoles (FODO-channel). The transfer matrix method (ABCD matrix method) was used for simulating the beam transport, a set of programs is written in the several programming languages (MATHEMATICA, MATLAB, MATCAD, MAPLE) and reasonable agreement is demonstrated between experimental results and simulations. Comparison of ABCD matrix method with the direct "numerical experiments" using EGUN, ELOP, and GPT programs with and without taking into account the space-charge effects showed the agreement to be good enough as well. Also the inverse problem of finding emittance of the electron beam at the S1 screen position (before FODO-channel), by using the spot image at S2 screen position (after FODO-channel) as function of quad currents, is considered. Spot and beam at both screens are described as tilted eel...

  20. Typicality in random matrix product states (United States)

    Garnerone, Silvano; de Oliveira, Thiago R.; Zanardi, Paolo


    Recent results suggest that the use of ensembles in statistical mechanics may not be necessary for isolated systems, since typically the states of the Hilbert space would have properties similar to those of the ensemble. Nevertheless, it is often argued that most of the states of the Hilbert space are nonphysical and not good descriptions of realistic systems. Therefore, to better understand the actual power of typicality it is important to ask if it is also a property of a set of physically relevant states. Here we address this issue, studying if and how typicality emerges in the set of matrix product states. We show analytically that typicality occurs for the expectation value of subsystems’ observables when the rank of the matrix product state scales polynomially with the size of the system with a power greater than 2. We illustrate this result numerically and present some indications that typicality may appear already for a linear scaling of the rank of the matrix product state.

  1. New pole placement algorithm - Polynomial matrix approach (United States)

    Shafai, B.; Keel, L. H.


    A simple and direct pole-placement algorithm is introduced for dynamical systems having a block companion matrix A. The algorithm utilizes well-established properties of matrix polynomials. Pole placement is achieved by appropriately assigning coefficient matrices of the corresponding matrix polynomial. This involves only matrix additions and multiplications without requiring matrix inversion. A numerical example is given for the purpose of illustration.

  2. Bioreporter pseudomonas fluorescens HK44 immobilized in a silica matrix

    Directory of Open Access Journals (Sweden)

    Trogl J.


    Full Text Available The bioluminescent bioreporter Pseudomonas fluorescens HK44, the whole cell bacterial biosensor that responds to naphthalene and its metabolites via the production of visible light, was immobilized into a silica matrix by the sol-gel technique. The bioluminescence intensities were measured in the maximum of the bioluminescence band at X = 500 nm. The immobilized cells (>105 cells per g silica matrix produced light after induction by salicylate (cone. > 10 g/l, naphthalene and aminobenzoic acid. The bioluminescence intensities induced by 2,3-dihydroxynaphthalene 3-hydroxybenzoic acid and 4-hydroxybenzoic acid were comparable to a negative control. The cells in the silica layers on glass slides produced light in response to the presence of an inductor at least 8 months after immobilization, and >50 induction cycles. The results showed that these test slides could be used as assays for the multiple determination of water pollution.

  3. Hadronic matrix elements for Kaons

    Energy Technology Data Exchange (ETDEWEB)

    Bijnens, Johan [Department of Theoretical Physics 2, Lund University, Soelvegatan 14A, S-22362 Lund (Sweden); Gamiz, Elvira [CAFPE and Departamento de Fisica Teorica y del Cosmos, Universidad de Granada Campus de Fuente Nueva, E-18002 Granada (Spain); Prades, Joaquim [CAFPE and Departamento de Fisica Teorica y del Cosmos, Universidad de Granada Campus de Fuente Nueva, E-18002 Granada (Spain)


    We review some work done by us calculating matrix elements for Kaons. Emphasis is put on the matrix elements which are relevant to predict non-leptonic Kaon CP violating observables. In particular, we recall our results for the B{sub K} parameter which governs the K{sup 0}-K{sup 0} mixing and update our results for {epsilon}'inK including estimated all-higher-order CHPT corrections and the new results from recent analytical calculations of the {delta}itI = 3/2 component. Some comments on future prospects on calculating matrix elements for Kaons are also added.

  4. Fish otolith biomineralization process: first investigations about organic matrix and growth of Triglidae (Scorpaeniformes otoliths

    Directory of Open Access Journals (Sweden)

    Stefano Montanini


    Full Text Available Otolith formation involves rhythmic variations in the deposition and size of organic matrix framework and carbonate crystals, resulting in the formation of macroscopic translucent and opaque rings and microscopic zonations (growth increments (Morales Nin, 2000. As in most biominerals, the otolith matrix forms only 2-3 % of its weight, but it is admitted that it has a considerable importance in the otolith crystallization processes of nucleation, growth, orientation and growth control. The goal of this study is to characterize the matrix protein composition in the otoliths of Triglidae (Scorpaeniformes as a first step to understand molecular mechanisms of otolith formation according to biology and ecology of the species. In particular 500 sagittal otoliths from six gurnard species were analysed: Chelidonichthys cuculus, C. lucerna, Eutrigla gurnardus, Lepidotrigla cavillone, L. dieuzeidei and Trigloporus lastoviza. Protein contents were estimated by Bradford method and the urea 8 M extracts were loaded into a polyacrylamide gel, separated by SDS page and detected by Silver staining (Sigma followed the protocol of Borelli et al. (2001 with some modifications regarding protein precipitation that was enhanced by using TCA, trichloroacetic acid, 100% w/v. The urea soluble fractions revealed a unique large band around 50-55 kDa. Another common clear band was visible at the top of the separating gel (proteins >300/350 kDa unable to enter into the pores of polyacrylamide gels (12%. The complexity of the protein mixtures was investigated by 2-D electrophoresis (Gel TGX 4-20%; proteins were separated on the basis of both isoelectric point (pI and molecular size. A common protein pattern of 50-75 kDa were found in all gurnards showing a similar composition of organic matter even if the 2-D maps of otolith samples showed specie-specific variation in acid protein fractions in all the pairwise comparison. This result confirmed that the amino acid composition

  5. IMP: A Message-Passing Algorithmfor Matrix Completion

    CERN Document Server

    Kim, Byung-Hak; Pfister, Henry D


    A new message-passing (MP) method is considered for the matrix completion problem associated with recommender systems. We attack the problem using a (generative) factor graph model that is related to a probabilistic low-rank matrix factorization. Based on the model, we propose a new algorithm, termed IMP, for the recovery of a data matrix from incomplete observations. The algorithm is based on a clustering followed by inference via MP (IMP). The algorithm is compared with a number of other matrix completion algorithms on real collaborative filtering (e.g., Netflix) data matrices. Our results show that, while many methods perform similarly with a large number of revealed entries, the IMP algorithm outperforms all others when the fraction of observed entries is small. This is helpful because it reduces the well-known cold-start problem associated with collaborative filtering (CF) systems in practice.


    Directory of Open Access Journals (Sweden)

    Anatoly Beletsky


    Full Text Available The methods of construction of matrix formation the secret protocols legalized subscribers of public communications networks encryption keys. Based key exchange protocols laid asymmetric cryptography algorithms. The solution involves the calculation of one-way functions and is based on the use of generalized Galois arrays of isomorphism relationship with forming elements, and depending on the selected irreducible polynomial generating matrix. A simple method for constructing generalized Galois matrix by the method of filling the diagonal. In order to eliminate the isomorphism of Galois arrays and their constituent elements, limiting the possibility of building one-way functions, Galois matrix subjected to similarity transformation carried out by means of permutation matrices. The variant of the organization of the algebraic attacks on encryption keys sharing protocols and discusses options for easing the consequences of an attack.

  7. Reducing Actinide Production Using Inert Matrix Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Deinert, Mark [Colorado School of Mines, Golden, CO (United States)


    The environmental and geopolitical problems that surround nuclear power stem largely from the longlived transuranic isotopes of Am, Cm, Np and Pu that are contained in spent nuclear fuel. New methods for transmuting these elements into more benign forms are needed. Current research efforts focus largely on the development of fast burner reactors, because it has been shown that they could dramatically reduce the accumulation of transuranics. However, despite five decades of effort, fast reactors have yet to achieve industrial viability. A critical limitation to this, and other such strategies, is that they require a type of spent fuel reprocessing that can efficiently separate all of the transuranics from the fission products with which they are mixed. Unfortunately, the technology for doing this on an industrial scale is still in development. In this project, we explore a strategy for transmutation that can be deployed using existing, current generation reactors and reprocessing systems. We show that use of an inert matrix fuel to recycle transuranics in a conventional pressurized water reactor could reduce overall production of these materials by an amount that is similar to what is achievable using proposed fast reactor cycles. Furthermore, we show that these transuranic reductions can be achieved even if the fission products are carried into the inert matrix fuel along with the transuranics, bypassing the critical separations hurdle described above. The implications of these findings are significant, because they imply that inert matrix fuel could be made directly from the material streams produced by the commercially available PUREX process. Zirconium dioxide would be an ideal choice of inert matrix in this context because it is known to form a stable solid solution with both fission products and transuranics.

  8. Production and characterization of bacterial cellulose membranes with hyaluronic acid from chicken comb. (United States)

    de Oliveira, Sabrina Alves; da Silva, Bruno Campos; Riegel-Vidotti, Izabel Cristina; Urbano, Alexandre; de Sousa Faria-Tischer, Paula Cristina; Tischer, Cesar Augusto


    The bacterial cellulose (BC), from Gluconacetobacter hansenii, is a biofilm with a high degree of crystallinity that can be used for therapeutic purposes and as a candidate for healing wounds. Hyaluronic acid (HA) is a constitutive polysaccharide found in the extracellular matrix and is a material used in tissue engineering and scaffolding for tissue regeneration. In this study, polymeric composites were produced in presence of hyaluronic acid isolated from chicken comb on different days of fermentation, specifically on the first (BCHA-SABT0) and third day (BCHA-SABT3) of fermentation. The structural characteristics, thermal stability and molar mass of hyaluronic acid from chicken comb were evaluated. Native membrane and polymeric composites were characterized with respect to their morphology and crystallinity. The optimized process of extraction and purification of hyaluronic acid resulted in low molar mass hyaluronic acid with structural characteristics similar to the standard commercial hyaluronic acid. The results demonstrate that the polymeric composites (BC/HA-SAB) can be produced in situ. The membranes produced on the third day presented better incorporation of HA-SAB between cellulose microfiber, resulting in membranes with higher thermal stability, higher roughness and lower crystallinity. The biocompatiblily of bacterial cellulose and the importance of hyaluronic acid as a component of extracellular matrix qualify the polymeric composites as promising biomaterials for tissue engineering. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. GoM Diet Matrix (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set was taken from CRD 08-18 at the NEFSC. Specifically, the Gulf of Maine diet matrix was developed for the EMAX exercise described in that center...

  10. Newtonian M(atrix) cosmology (United States)

    Álvarez, Enrique; Meessen, Patrick


    A Newtonian matrix cosmology, corresponding to the Banks, Fischler, Shenker and Susskind model of eleven-dimensional M-theory in the infinite momentum frame as a supersymmetric (0+1) M(atrix) model is constructed. Interesting new results are obtained, such as the existence of (much sought for in the past) static solutions. The possible interpretation of the off-diagonal entries as a background geometry is also briefly discussed.

  11. Superstatistics in Random Matrix Theory


    Abul-Magd, A. Y.


    Random matrix theory (RMT) provides a successful model for quantum systems, whose classical counterpart has a chaotic dynamics. It is based on two assumptions: (1) matrix-element independence, and (2) base invariance. Last decade witnessed several attempts to extend RMT to describe quantum systems with mixed regular-chaotic dynamics. Most of the proposed generalizations keep the first assumption and violate the second. Recently, several authors presented other versions of the theory that keep...

  12. Matrix analysis of electrical machinery

    CERN Document Server

    Hancock, N N


    Matrix Analysis of Electrical Machinery, Second Edition is a 14-chapter edition that covers the systematic analysis of electrical machinery performance. This edition discusses the principles of various mathematical operations and their application to electrical machinery performance calculations. The introductory chapters deal with the matrix representation of algebraic equations and their application to static electrical networks. The following chapters describe the fundamentals of different transformers and rotating machines and present torque analysis in terms of the currents based on the p

  13. Quasi-normal modes from non-commutative matrix dynamics (United States)

    Aprile, Francesco; Sanfilippo, Francesco


    We explore similarities between the process of relaxation in the BMN matrix model and the physics of black holes in AdS/CFT. Focusing on Dyson-fluid solutions of the matrix model, we perform numerical simulations of the real time dynamics of the system. By quenching the equilibrium distribution we study quasi-normal oscillations of scalar single trace observables, we isolate the lowest quasi-normal mode, and we determine its frequencies as function of the energy. Considering the BMN matrix model as a truncation of N=4 SYM, we also compute the frequencies of the quasi-normal modes of the dual scalar fields in the AdS5-Schwarzschild background. We compare the results, and we finda surprising similarity.

  14. Method to measure soil matrix infiltration in forest soil (United States)

    Zhang, Jing; Lei, Tingwu; Qu, Liqin; Chen, Ping; Gao, Xiaofeng; Chen, Chao; Yuan, Lili; Zhang, Manliang; Su, Guangxu


    Infiltration of water into forest soil commonly involves infiltration through the matrix body and preferential passages. Determining the matrix infiltration process is important in partitioning water infiltrating into the soil through the soil body and macropores to evaluate the effects of soil and water conservation practices on hillslope hydrology and watershed sedimentation. A new method that employs a double-ring infiltrometer was applied in this study to determine the matrix infiltration process in forest soil. Field experiments were conducted in a forest field on the Loess Plateau at Tianshui Soil and Water Conservation Experimental Station. Nylon cloth was placed on the soil surface in the inner ring and between the inner and outer rings of infiltrometers. A thin layer of fine sands were placed onto the nylon cloth to shelter the macropores and ensure that water infiltrates the soil through the matrix only. Brilliant Blue tracers were applied to examine the exclusion of preferential flow occurrences in the measured soil body. The infiltration process was measured, computed, and recorded through procedures similar to those of conventional methods. Horizontal and vertical soil profiles were excavated to check the success of the experiment and ensure that preferential flow did not occur in the measured soil column and that infiltration was only through the soil matrix. The infiltration processes of the replicates of five plots were roughly the same, thereby indicating the feasibility of the methodology to measure soil matrix infiltration. The measured infiltration curves effectively explained the transient process of soil matrix infiltration. Philip and Kostiakov models fitted the measured data well, and all the coefficients of determination were greater than 0.9. The wetted soil bodies through excavations did not present evidence of preferential flow. Therefore, the proposed method can determine the infiltration process through the forest soil matrix. This

  15. The matrix metalloproteinase in larynx cancer

    Directory of Open Access Journals (Sweden)

    Weronika Lucas Grzelczyk


    Full Text Available One of the most common carcinoma occurring in the head and neck is laryngeal cancer. Despite the rapid scientific advances in medicine the prognosis for patients with such type of disease is not satisfying. In the last few years matrix metalloproteinases ‑ MMPs and their tissue inhibitors – TIMPs, mostly MMP‑2 and MMP‑9, arouses a great interest, especially in the process of carcinogenesis. It seems that their impact in the formation and development of laryngeal cancer is significant. MMPs a group of zinc‑ and calcium‑ dependent endopeptidases play crucial role extracellular matrix collagen degradation. That are enzymes, that degrade and the basement membrane by facilitating tumor growth, cell migration and tumor invasion. They are implicated in metastasis and angiogenesis potentiate within the tumor. Clear tendency was observed towards the higher MMPs and TIMPs expression in larynx cancer than in the stroma. Recent studies show correlations between increased MMP‑2 gene expression in the tumor tissue and clinical status, histopathological grading and metastases occurrence. The similar MMP2 over expression dependence were found on tumor recurrence and survival. Many authors pointed out, significant higher MMP‑2 expression as a potential marker of tumor invasiveness and worse prognosis in patients with larynx cancer. However, association of MMP 9 gene expression with laryngeal cancer clinicopathological features and survival of patients are ambiguous. Although, numerous researches show that this relationship does exists. Similar correlations could be found in TIMPs, but further studies are necessary because of small amount of literature.

  16. Asthma and COPD: Differences and Similarities (United States)

    ... and COPD: differences and similarities Share | Asthma and COPD: Differences and Similarities This article has been reviewed ... or you could have Chronic Obstructive Pulmonary Disease (COPD) , such as emphysema or chronic bronchitis. Because asthma ...

  17. Acid retention with reduced glomerular filtration rate increases urine biomarkers of kidney and bone injury. (United States)

    Wesson, Donald E; Pruszynski, Jessica; Cai, Wendy; Simoni, Jan


    Diets high in acid of developed societies that do not cause metabolic acidosis in patients with chronic kidney disease nevertheless appear to cause acid retention with associated morbidity, particularly in those with reduced glomerular filtration rate. Here we used a rat 2/3 nephrectomy model of chronic kidney disease to study induction and maintenance of acid retention and its consequences on indicators of kidney and bone injury. Dietary acid was increased in animals eating base-producing soy protein with acid-producing casein and in casein-eating animals with added ammonium chloride. Using microdialysis to measure the kidney cortical acid content, we found that nephrectomized animals had greater acid retention than sham-operated animals when both ate the soy diet. Each increment in dietary acid further increased acid retention more in nephrectomized than in sham rats. Nephrectomized and sham animals achieved similar steady-state daily urine net acid excretion in response to increments in dietary acid but nephrectomized animals took longer to do so, contributing to greater acid retention that was maintained until the increased dietary acid was stopped. Acid retention was associated with increased urine excretion of both N-acetyl-β-D-glucosaminidase and deoxypyridinoline, greater in nephrectomized than control rats, consistent with kidney tubulointerstitial and bone matrix injury, respectively. Greater acid retention in nephrectomized than control animals was induced by a slower increase in urinary net acid excretion rate in response to the increment in dietary acid and also maintained until the dietary acid increment was stopped. Thus, acid retention increased biomarkers of kidney and bone injury in the urine, supporting untoward consequences to these two tissues. Copyright © 2016 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.

  18. Acetylene terminated matrix resins (United States)

    Goldfarb, I. J.; Lee, Y. C.; Arnold, F. E.; Helminiak, T. E.


    The synthesis of resins with terminal acetylene groups has provided a promising technology to yield high performance structural materials. Because these resins cure through an addition reaction, no volatile by-products are produced during the processing. The cured products have high thermal stability and good properties retention after exposure to humidity. Resins with a wide variety of different chemical structures between the terminal acetylene groups are synthesized and their mechanical properties studied. The ability of the acetylene cured polymers to give good mechanical properties is demonstrated by the resins with quinoxaline structures. Processibility of these resins can be manipulated by varying the chain length between the acetylene groups or by blending in different amounts of reactive deluents. Processing conditions similar to the state-of-the-art epoxy can be attained by using backbone structures like ether-sulfone or bis-phenol-A. The wide range of mechanical properties and processing conditions attainable by this class of resins should allow them to be used in a wide variety of applications.

  19. MF Calculator: A Web-Based Application for Analyzing Similarity

    Directory of Open Access Journals (Sweden)

    Célia Maria Dias Sales


    Full Text Available This paper presents the metric-frequency calculator (MF Calculator, an online application to analyze similarity. The MF Calculator implements a metric-frequency similarity algorithm for the quantitative assessment of similarity in ill-structured data sets. It is widely applicable as it can be used with nominal, ordinal, or interval data when there is little prior control over the variables to be observed regarding number or content. The MF Calculator generates a proximity matrix in CSV, XML or DOC format that can be used as input to traditional statistical techniques such as hierarchical clustering, additive trees, or multidimensional scaling. The MF Calculator also displays a graphical representation of outputs using additive similarity trees. A simulated example illustrates the implementation of the MF calculator. An additional example with real data is presented, in order to illustrate the potential of combining the MF Calculator with cluster analysis. The MF Calculator is a user-friendly tool available free of charge. It can be accessed from, and it can be used by non-experts from a wide range of social sciences.

  20. 7 CFR 51.1997 - Similar type. (United States)


    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar type. 51.1997 Section 51.1997 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... Standards for Grades of Filberts in the Shell 1 Definitions § 51.1997 Similar type. Similar type means that...

  1. Molecular quantum similarity using conceptual DFT descriptors

    Indian Academy of Sciences (India)

    This paper reports a Molecular Quantum Similarity study for a set of congeneric steroid molecules, using as basic similarity descriptors electron density ρ (r), shape function (r), the Fukui functions +(r) and -(r) and local softness +(r) and -(r). Correlations are investigated between similarity indices for each couple of ...

  2. Mixed-matrix membrane adsorbers for protein separation

    NARCIS (Netherlands)

    Avramescu, M.E.; Borneman, Zandrie; Wessling, Matthias


    The separation of two similarly sized proteins, bovine serum albumin (BSA) and bovine hemoglobin (Hb) was carried out using a new type of ion-exchange mixed-matrix adsorber membranes. The adsorber membranes were prepared by incorporation of various types of Lewatit ion-exchange resins into an

  3. Imaging MALDI mass spectrometry using an oscillating capillary nebulizer matrix coating system and its application to analysis of lipids in brain from a mouse model of Tay-Sachs/Sandhoff disease. (United States)

    Chen, Yanfeng; Allegood, Jeremy; Liu, Ying; Wang, Elaine; Cachón-Gonzalez, Begoña; Cox, Timothy M; Merrill, Alfred H; Sullards, M Cameron


    The quality of tissue imaging by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) depends on the effectiveness of the matrix deposition, especially for lipids that may dissolve in the solvent used for the matrix application. This article describes the use of an oscillating capillary nebulizer (OCN) to spray small droplets of matrix aerosol onto the sample surface for improved matrix homogeneity, reduced crystal size, and controlled solvent effects. This system was then applied to the analysis of histological slices of brains from mice with homozygous disruption of the hexb gene (hexb-/-), a model of Tay-Sachs and Sandhoff disease, versus the functionally normal heterozygote (hexb+/-) by imaging MALDI-MS. This allowed profiling and localization of many different lipid species, and of particular interest, ganglioside GM2, asialo-GM2 (GA2), and sulfatides (ST). The presence of these compounds was confirmed by analysis of brain extracts using electrospray ionization in conjunction with tandem mass spectrometry (MS/MS). The major fatty acid of the ceramide backbone of both GM2 and GA2 was identified as stearic acid (18:0) versus nervonic acid (24:1) for ST by both tissue-imaging MS and ESI-MS/MS. GM2 and GA2 were highly elevated in hexb-/- and were both localized in the granular cell region of the cerebellum. ST, however, was localized mainly in myelinated fiber (white matter) region of the cerebellum as well as in the brain stem with a relatively uniform distribution and had similar relative signal intensity for both hexb+/- and hexb-/- brain. It was also observed that there were distinct localizations for numerous other lipid subclasses; hence, imaging MALDI-MS could be used for "lipidomic" studies. These results illustrate the usefulness of tissue-imaging MALDI-MS with matrix deposition by OCN for histologic comparison of lipids in tissues such as brains from this mouse model of Tay-Sachs and Sandhoff disease.

  4. Urinary bladder extracellular matrix hydrogels and matrix-bound vesicles differentially regulate central nervous system neuron viability and axon growth and branching. (United States)

    Faust, Anne; Kandakatla, Apoorva; van der Merwe, Yolandi; Ren, Tanchen; Huleihel, Luai; Hussey, George; Naranjo, Juan Diego; Johnson, Scott; Badylak, Stephen; Steketee, Michael


    Central nervous system neurons often degenerate after trauma due to the inflammatory innate immune response to injury, which can lead to neuronal cell death, scarring, and permanently lost neurologic function. Extracellular matrix bioscaffolds, derived by decellularizing healthy tissues, have been widely used in both preclinical and clinical studies to promote positive tissue remodeling, including neurogenesis, in numerous tissues, with extracellular matrix from homologous tissues often inducing more positive responses. Extracellular matrix hydrogels are liquid at room temperature and enable minimally invasive extracellular matrix injections into central nervous system tissues, before gelation at 37℃. However, few studies have analyzed how extracellular matrix hydrogels influence primary central nervous system neuron survival and growth, and whether central nervous system and non-central nervous system extracellular matrix specificity is critical to neuronal responses. Urinary bladder extracellular matrix hydrogels increase both primary hippocampal neuron survival and neurite growth to similar or even greater extents, suggesting extracellular matrix from non-homologous tissue sources, such as urinary bladder matrix-extracellular matrix, may be a more economical and safer alternative to developing central nervous system extracellular matrices for central nervous system applications. Additionally, we show matrix-bound vesicles derived from urinary bladder extracellular matrix are endocytosed by hippocampal neurons and positively regulate primary hippocampal neuron neurite growth. Matrix-bound vesicles carry protein and RNA cargos, including noncoding RNAs and miRNAs that map to the human genome and are known to regulate cellular processes. Thus, urinary bladder matrix-bound vesicles provide natural and transfectable cargoes which offer new experimental tools and therapeutic applications to study and treat central nervous system neuron injury.

  5. [Antioxidant properties of the pollen exine polymer matrix]. (United States)

    Smirnova, A V; Timoffev, K N; Breĭgina, M A; Matveeva, N P; Ermakov, I P


    The antioxidant properties of exine polymer matrix which forms the outer layer of pollen grain wall were studied. The main component of this matrix is sporopollenin - a unique biopolymer resistant to mechanical and chemical damage. The samples of isolated exine, purified from soluble compounds, were studied with EPR using stable nitroxyl radical TEMPO and DMPO spin trap. At the same time, we analyzed changes in fluorescence of DCFH which detected ROS in the solution. It has been established that exine effectively reduces TEMPO radical and eliminates hydroxyl radical. Also, the fluorometric analysis demonstrated that the exine eliminated H2O2, and this ability significantly decreased after treatment of exine with feruloyl esterase or mild alkaline hydrolysis (1M NaOH), i.e. after hydrolysis of hydroxycinnamic acid esters. After harsh hydrolysis (4M NaOH, 170 degrees C) of ethers bonds a large amount of hydroxycinnamic acids has been released, and exines have lost their antioxidant capacity almost completely. The obtained results point to the ability of extracellular polymer matrix of the exine to eliminate free radicals and H2O2 during crucial periods of male gametophyte development. The participation of ferulic acid and, possibly, of other hydroxycinnamic acids of sporopollenin in these processes has been demonstrated.

  6. High fidelity visualization of cell-to-cell variation and temporal dynamics in nascent extracellular matrix formation (United States)

    McLeod, Claire M.; Mauck, Robert L.


    Extracellular matrix dynamics are key to tissue morphogenesis, homeostasis, injury, and repair. The spatiotemporal organization of this matrix has profound biological implications, but is challenging to monitor using standard techniques. Here, we address these challenges by using noncanonical amino acid tagging to fluorescently label extracellular matrix synthesized in the presence of bio-orthogonal methionine analogs. This strategy labels matrix proteins with high resolution, without compromising their distribution or mechanical function. We demonstrate that the organization and temporal dynamics of the proteinaceous matrix depend on the biophysical features of the microenvironment, including the biomaterial scaffold and the niche constructed by cells themselves. Pulse labeling experiments reveal that, in immature constructs, nascent matrix is highly fibrous and interdigitates with pre-existing matrix, while in more developed constructs, nascent matrix lacks fibrous organization and is retained in the immediate pericellular space. Inhibition of collagen crosslinking increases matrix synthesis, but compromises matrix organization. Finally, these data demonstrate marked cell-to-cell heterogeneity amongst both chondrocytes and mesenchymal stem cells undergoing chondrogenesis. Collectively, these results introduce fluorescent noncanonical amino acid tagging as a strategy to investigate spatiotemporal matrix organization, and demonstrate its ability to identify differences in phenotype, microenvironment, and matrix assembly at the single cell level. PMID:27941914

  7. Matrix factorizations and elliptic fibrations

    Directory of Open Access Journals (Sweden)

    Harun Omer


    Full Text Available I use matrix factorizations to describe branes at simple singularities of elliptic fibrations. Each node of the corresponding Dynkin diagrams of the ADE-type singularities is associated with one indecomposable matrix factorization which can be deformed into one or more factorizations of lower rank. Branes with internal fluxes arise naturally as bound states of the indecomposable factorizations. Describing branes in such a way avoids the need to resolve singularities. This paper looks at gauge group breaking from E8 fibers down to SU(5 fibers due to the relevance of such fibrations for local F-theory GUT models. A purpose of this paper is to understand how the deformations of the singularity are understood in terms of its matrix factorizations. By systematically factorizing the elliptic fiber equation, this paper discusses geometries which are relevant for building semi-realistic local models. In the process it becomes evident that breaking patterns which are identical at the level of the Kodaira type of the fibers can be inequivalent at the level of matrix factorizations. Therefore the matrix factorization picture supplements information which the conventional less detailed descriptions lack.

  8. Grouping miRNAs of similar functions via weighted information content of gene ontology. (United States)

    Lan, Chaowang; Chen, Qingfeng; Li, Jinyan


    Regulation mechanisms between miRNAs and genes are complicated. To accomplish a biological function, a miRNA may regulate multiple target genes, and similarly a target gene may be regulated by multiple miRNAs. Wet-lab knowledge of co-regulating miRNAs is limited. This work introduces a computational method to group miRNAs of similar functions to identify co-regulating miRNAsfrom a similarity matrix of miRNAs. We define a novel information content of gene ontology (GO) to measure similarity between two sets of GO graphs corresponding to the two sets of target genes of two miRNAs. This between-graph similarity is then transferred as a functional similarity between the two miRNAs. Our definition of the information content is based on the size of a GO term's descendants, but adjusted by a weight derived from its depth level and the GO relationships at its path to the root node or to the most informative common ancestor (MICA). Further, a self-tuning technique and the eigenvalues of the normalized Laplacian matrix are applied to determine the optimal parameters for the spectral clustering of the similarity matrix of the miRNAs. Experimental results demonstrate that our method has better clustering performance than the existing edge-based, node-based or hybrid methods. Our method has also demonstrated a novel usefulness for the function annotation of new miRNAs, as reported in the detailed case studies.

  9. Magnesium Matrix Composite Foams—Density, Mechanical Properties, and Applications

    Directory of Open Access Journals (Sweden)

    Kyu Cho


    Full Text Available Potential of widespread industrial applications of magnesium has been realized in recent years. A variety of magnesium alloy matrix composites are now being studied for mechanical properties. Since magnesium is the lightest structural metal, it can replace aluminum in existing applications for further weight savings. This review presents an overview of hollow particle filled magnesium matrix syntactic composite foams. Fly ash cenospheres are the most commonly used hollow particles for such applications. Fly ash cenospheres primarily have alumino-silicate composition and contain a large number of trace elements, which makes it challenging to study the interfacial reactions and microstructure in these composites. Microstructures of commonly studied AZ and ZC series magnesium alloys and their syntactic foams are discussed. Although only a few studies are available on these materials because of the nascent stage of this field, a comparison with similar aluminum matrix syntactic foams has provided insight into the properties and weight saving potential of magnesium matrix composites. Analysis shows that the magnesium matrix syntactic foams have higher yield strength at the same level of density compared to most other metal matrix syntactic foams. The comparison can guide future work and set goals that need to be achieved through materials selection and processing method development.

  10. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji


    Self-similar processes have been widely used in modeling real-world phenomena occurring in environmetrics, network traffic, image processing, and stock pricing, to name but a few. The estimation of the degree of self-similarity has been studied extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi-self-similarity for a random field indexed in higher dimensions. If self-similarity is not rejected, our test provides a set of estimated self-similarity indexes. The key is to test stationarity of the inverse Lamperti transformations of the process. The inverse Lamperti transformation of a self-similar process is a strongly stationary process, revealing a theoretical connection between the two processes. To demonstrate the capability of our test, we test self-similarity of fractional Brownian motions and sheets, their time deformations and mixtures with Gaussian white noise, and the generalized Cauchy family. We also apply the self-similarity test to real data: annual minimum water levels of the Nile River, network traffic records, and surface heights of food wrappings. © 2016, International Biometric Society.

  11. Similarity increases altruistic punishment in humans. (United States)

    Mussweiler, Thomas; Ockenfels, Axel


    Humans are attracted to similar others. As a consequence, social networks are homogeneous in sociodemographic, intrapersonal, and other characteristics--a principle called homophily. Despite abundant evidence showing the importance of interpersonal similarity and homophily for human relationships, their behavioral correlates and cognitive foundations are poorly understood. Here, we show that perceived similarity substantially increases altruistic punishment, a key mechanism underlying human cooperation. We induced (dis)similarity perception by manipulating basic cognitive mechanisms in an economic cooperation game that included a punishment phase. We found that similarity-focused participants were more willing to punish others' uncooperative behavior. This influence of similarity is not explained by group identity, which has the opposite effect on altruistic punishment. Our findings demonstrate that pure similarity promotes reciprocity in ways known to encourage cooperation. At the same time, the increased willingness to punish norm violations among similarity-focused participants provides a rationale for why similar people are more likely to build stable social relationships. Finally, our findings show that altruistic punishment is differentially involved in encouraging cooperation under pure similarity vs. in-group conditions.

  12. Organic matrix composition and ultrastructure of eggshell: a comparative study. (United States)

    Panheleux, M; Bain, M; Fernandez, M S; Morales, I; Gautron, J; Arias, J L; Solomon, S E; Hincke, M; Nys, Y


    1. The avian eggshell is a biomineralised composite ceramic consisting of calcium carbonate embedded in an organic matrix. Matrix components are supposed to be involved in the control of mineralisation, crystallographic texture and biomechanical properties of eggshell. 2. The structure and eggshell matrix composition of various domesticated bird species were compared to gain insight into the universality of the eggshell mineralisation process. 3. The SDS-PAGE profiles of soluble eggshell matrix were specific within groups of birds (a: laying hen, breeder hen, quail, pheasant and possibly turkey; b: guinea fowl; c: duck and goose) but some of the protein bands were common to all groups. 4. Analogies between species were confirmed by Western blotting using hen protein antibodies. Ovocleidin-17 (OC-17) and ovalbumin were revealed in all species (except quail for OC-17). Lysozyme was present only in hen eggshell. Another egg white protein: ovotransferrin showed a positive signal in hens, turkey and quail. Osteopontin was observed in laying and breeder hens and quail. 5. Different proteoglycans were localised to discrete regions within the eggshell. Dermatan sulphate was observed within the matrix of the calcified shell of all species except quail which contained chondroitin-6-sulfate. Keratan sulphate was observed in mammillary bodies of breeder and laying hen, quail, pheasant and turkey while chondroitin sulphate was also present in guinea fowl and duck. 6. The general structural organisation of the different avian eggshells was similar but specific differences were observed in the ultrastructure of the mammillary layer. Species of the same taxonomic family could be grouped according to their structural analogies: breeder hen, turkey and pheasant resembled that of the domestic fowl. Guinea fowl was unique. Goose and duck were quite similar with large and confluent mammillary bodies. 7. Some matrix components are therefore common to eggshells of various species but

  13. Lectures on matrix field theory

    CERN Document Server

    Ydri, Badis


    These lecture notes provide a systematic introduction to matrix models of quantum field theories with non-commutative and fuzzy geometries. The book initially focuses on the matrix formulation of non-commutative and fuzzy spaces, followed by a description of the non-perturbative treatment of the corresponding field theories. As an example, the phase structure of non-commutative phi-four theory is treated in great detail, with a separate chapter on the multitrace approach. The last chapter offers a general introduction to non-commutative gauge theories, while two appendices round out the text. Primarily written as a self-study guide for postgraduate students – with the aim of pedagogically introducing them to key analytical and numerical tools, as well as useful physical models in applications – these lecture notes will also benefit experienced researchers by providing a reference guide to the fundamentals of non-commutative field theory with an emphasis on matrix models and fuzzy geometries.

  14. Matrix formalism of synchrobetatron coupling

    Directory of Open Access Journals (Sweden)

    Xiaobiao Huang


    Full Text Available In this paper we present a complete linear synchrobetatron coupling formalism by studying the transfer matrix which describes linear horizontal and longitudinal motions. With the technique established in the linear horizontal-vertical coupling study [D. Sagan and D. Rubin, Phys. Rev. ST Accel. Beams 2, 074001 (1999PRABFM1098-440210.1103/PhysRevSTAB.2.074001], we found a transformation to block diagonalize the transfer matrix and decouple the betatron motion and the synchrotron motion. By separating the usual dispersion term from the horizontal coordinate first, we were able to obtain analytic expressions of the transformation under reasonable approximations. We also obtained the perturbations to the betatron tune and the Courant-Snyder functions. The closed-orbit changes due to finite energy gains at rf cavities and radiation energy losses were studied by the 5×5 extended transfer matrix with the fifth column describing kicks in the 4-dimension phase space.

  15. Supersymmetry in random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Kieburg, Mario


    I study the applications of supersymmetry in random matrix theory. I generalize the supersymmetry method and develop three new approaches to calculate eigenvalue correlation functions. These correlation functions are averages over ratios of characteristic polynomials. In the first part of this thesis, I derive a relation between integrals over anti-commuting variables (Grassmann variables) and differential operators with respect to commuting variables. With this relation I rederive Cauchy- like integral theorems. As a new application I trace the supermatrix Bessel function back to a product of two ordinary matrix Bessel functions. In the second part, I apply the generalized Hubbard-Stratonovich transformation to arbitrary rotation invariant ensembles of real symmetric and Hermitian self-dual matrices. This extends the approach for unitarily rotation invariant matrix ensembles. For the k-point correlation functions I derive supersymmetric integral expressions in a unifying way. I prove the equivalence between the generalized Hubbard-Stratonovich transformation and the superbosonization formula. Moreover, I develop an alternative mapping from ordinary space to superspace. After comparing the results of this approach with the other two supersymmetry methods, I obtain explicit functional expressions for the probability densities in superspace. If the probability density of the matrix ensemble factorizes, then the generating functions exhibit determinantal and Pfaffian structures. For some matrix ensembles this was already shown with help of other approaches. I show that these structures appear by a purely algebraic manipulation. In this new approach I use structures naturally appearing in superspace. I derive determinantal and Pfaffian structures for three types of integrals without actually mapping onto superspace. These three types of integrals are quite general and, thus, they are applicable to a broad class of matrix ensembles. (orig.)

  16. A Protein Involved in the Assembly of an Extracellular Calcium Storage Matrix* (United States)

    Glazer, Lilah; Shechter, Assaf; Tom, Moshe; Yudkovski, Yana; Weil, Simy; Aflalo, Eliahu David; Pamuru, Ramachandra Reddy; Khalaila, Isam; Bentov, Shmuel; Berman, Amir; Sagi, Amir


    Gastroliths, the calcium storage organs of crustaceans, consist of chitin-protein-mineral complexes in which the mineral component is stabilized amorphous calcium carbonate. To date, only three proteins, GAP 65, gastrolith matrix protein (GAMP), and orchestin, have been identified in gastroliths. Here, we report a novel protein, GAP 10, isolated from the gastrolith of the crayfish Cherax quadricarinatus and specifically expressed in its gastrolith disc. The encoding gene was cloned by partial sequencing of the protein extracted from the gastrolith matrix. Based on an assembled microarray cDNA chip, GAP 10 transcripts were found to be highly (12-fold) up-regulated in premolt gastrolith disc and significantly down-regulated in the hypodermis at the same molt stage. The deduced protein sequence of GAP 10 lacks chitin-binding domains and does not show homology to known proteins in the GenBankTM data base. It does, however, have an amino acid composition that has similarity to proteins extracted from invertebrate and ascidian-calcified extracellular matrices. The GAP 10 sequence contains a predicted signal peptide and predicted phosphorylation sites. In addition, the protein is phosphorylated and exhibits calcium-binding ability. Repeated daily injections of GAP 10 double strand RNA to premolt C. quadricarinatus resulted in a prolonged premolt stage and in the development of gastroliths with irregularly rough surfaces. These findings suggest that GAP 10 may be involved in the assembly of the gastrolith chitin-protein-mineral complex, particularly in the deposition of amorphous calcium carbonate. PMID:20150428

  17. Trends in global warming and evolution of matrix protein 2 family from influenza A virus. (United States)

    Yan, Shao-Min; Wu, Guang


    The global warming is an important factor affecting the biological evolution, and the influenza is an important disease that threatens humans with possible epidemics or pandemics. In this study, we attempted to analyze the trends in global warming and evolution of matrix protein 2 family from influenza A virus, because this protein is a target of anti-flu drug, and its mutation would have significant effect on the resistance to anti-flu drugs. The evolution of matrix protein 2 of influenza A virus from 1959 to 2008 was defined using the unpredictable portion of amino-acid pair predictability. Then the trend in this evolution was compared with the trend in the global temperature, the temperature in north and south hemispheres, and the temperature in influenza A virus sampling site, and species carrying influenza A virus. The results showed the similar trends in global warming and in evolution of M2 proteins although we could not correlate them at this stage of study. The study suggested the potential impact of global warming on the evolution of proteins from influenza A virus.

  18. Symmetries and Interactions in Matrix String Theory

    NARCIS (Netherlands)

    Hacquebord, F.H.


    This PhD-thesis reviews matrix string theory and recent developments therein. The emphasis is put on symmetries, interactions and scattering processes in the matrix model. We start with an introduction to matrix string theory and a review of the orbifold model that flows out of matrix string theory

  19. Properties of the matrix A-XY

    NARCIS (Netherlands)

    Steerneman, A.G.M.; van Perlo -ten Kleij, Frederieke


    The main topic of this paper is the matrix V = A - XY*, where A is a nonsingular complex k x k matrix and X and Y are k x p complex matrices of full column rank. Because properties of the matrix V can be derived from those of the matrix Q = I - XY*, we will consider in particular the case where A =

  20. An elementary formula for computing shape derivatives of EFIE system matrix


    Kataja, Juhani; Toivanen, Jukka I.


    We derive analytical shape derivative formulas of the system matrix representing electric field integral equation discretized with Raviart-Thomas basis functions. The arising integrals are easy to compute with similar methods as the entries of the original system matrix. The results are compared to derivatives computed with automatic differentiation technique and finite differences, and are found to be in excellent agreement.

  1. Polychoric/Tetrachoric Matrix or Pearson Matrix? A methodological study

    Directory of Open Access Journals (Sweden)

    Dominguez Lara, Sergio Alexis


    Full Text Available The use of product-moment correlation of Pearson is common in most studies in factor analysis in psychology, but it is known that this statistic is only applicable when the variables related are in interval scale and normally distributed, and when are used in ordinal data may to produce a distorted correlation matrix . Thus is a suitable option using polychoric/tetrachoric matrices in item-level factor analysis when the items are in level measurement nominal or ordinal. The aim of this study was to show the differences in the KMO, Bartlett`s Test and Determinant of the Matrix, percentage of variance explained and factor loadings in depression trait scale of Depression Inventory Trait - State and the Neuroticism dimension of the short form of the Eysenck Personality Questionnaire -Revised, regarding the use of matrices polychoric/tetrachoric matrices and Pearson. These instruments was analyzed with different extraction methods (Maximum Likelihood, Minimum Rank Factor Analysis, Unweighted Least Squares and Principal Components, keeping constant the rotation method Promin were analyzed. Were observed differences regarding sample adequacy measures, as well as with respect to the explained variance and the factor loadings, for solutions having as polychoric/tetrachoric matrix. So it can be concluded that the polychoric / tetrachoric matrix give better results than Pearson matrices when it comes to item-level factor analysis using different methods.

  2. Bridging Database Applications and Declarative Similarity Matching


    Andrade Ribeiro, Leonardo; Schneider, Natália Cristina; de Souza Inácio, Andrei; Wagner, Harley Michel; von Wangenheim, Aldo


    Effective manipulation of string data is of fundamental importance to modern database applications. Very often, textual inconsistencies render equality comparisons meaningless and strings have to be matched in terms of their similarity. Previous work has proposed techniques to express similarity operations using declarative SQL statements. However, the non-trivial issue of embedding similarity support into object-oriented applications has received little attention. Particularly, declarative s...

  3. Evaluation of hydrophilic matrix tablets based on Carbopol(®) 971P and low-viscosity sodium alginate for pH-independent controlled drug release. (United States)

    Al-Zoubi, Nizar M; AlKhatib, Hatim S; Obeidat, Wasfy M


    The aim of this study was to evaluate matrix tablets containing different ratios of Carbopol(®) 971P (CP) to low-viscosity sodium alginate (SA) and assess their suitability for pH-independent controlled drug release. Two processing methods (physical mixing, PM and spray-drying, SD) were applied before compaction and the release from corresponding matrices was compared. The release from CP-SA PM matrices was also investigated using three model drugs (paracetamol, salicylic acid, and verapamil HCl) and two dissolution media (0.1 N HCl or phosphate buffer, pH = 6.8), and the release rate, mechanism, and pH-dependence were characterized by fitting of Higuchi and Peppas models, and evaluation of similarity factor. Furthermore, swelling behavior of CP-SA matrix tablets was studied for evaluating its impact on drug release. The processing method (SD or PM) markedly affected the drug release from CP-SA matrices. ANOVA tests showed significant effects of the CP:SA ratio and drug type on the release rate (expressed by the constant, K(H), from Higuchi model) and of the dissolution medium on the release mechanism (expressed by the exponent, n, from Peppas model). Similarity factor (f₂) indicated that the CP:SA ratios ≥ 25:75 and ≥ 50:50 were suitable for pH-independent release of paracetamol and salicylic acid, respectively, although for verapamil HCl, the matrix with low CP:SA ratio (0:100) showed remarkably reduced pH-dependence of release. Swelling parameters (water uptake and mass loss) were significantly changed with experimental variables (CP:SA ratio, medium, and time) and were in good correlation with drug release. Matrix tablets based on CP and SA form a potentially useful versatile system for pH-independent controlled drug release.

  4. Integrating Triangle and Jaccard similarities for recommendation (United States)

    Sun, Shuang-Bo; Zhang, Zhi-Heng; Dong, Xin-Ling; Zhang, Heng-Ru; Li, Tong-Jun; Zhang, Lin


    This paper proposes a new measure for recommendation through integrating Triangle and Jaccard similarities. The Triangle similarity considers both the length and the angle of rating vectors between them, while the Jaccard similarity considers non co-rating users. We compare the new similarity measure with eight state-of-the-art ones on four popular datasets under the leave-one-out scenario. Results show that the new measure outperforms all the counterparts in terms of the mean absolute error and the root mean square error. PMID:28817692

  5. Stress Corrosion Cracking in Polymer Matrix Glass Fiber Composites (United States)

    Kosak, Jonathan

    With the use of Polymer Matrix Glass Fiber Composites ever expanding, understanding conditions that lead to failure before expected service life is of increasing importance. Stress Corrosion Cracking (SCC) has proven to be one such example of conditions found in use in high voltage transmission line applications that leads to brittle fracture of polymer matrix composites. SCC has been proven to be the result of acid buildup on the lines due to corona discharges and water buildup. This acid leaches minerals from the fibers, leading to fracture at low loads and service life. In order to combat this problem, efforts are being made to determine which composites have greater resistance to SCC. This study was used to create a methodology to monitor for damage during SCC and classify damage by mechanism type (matrix cracking and fiber breaking) by using 4-point SCC bend testing, 3-point bend testing, a forward predictive model, unique post processing techniques, and microscopy. This would allow a classification in composite resistance to SCC as well as create a methodology for future research in this field. Concluding this study, only matrix cracking was able to be fully classified, however, a methodology was developed for future experimentation.

  6. Evolution of Nuclear Many-Body Forces with the Similarity Renormalization Group


    Jurgenson, E. D.; Navratil, P.; Furnstahl, R. J.


    The first practical method to evolve many-body nuclear forces to softened form using the Similarity Renormalization Group (SRG) in a harmonic oscillator basis is demonstrated. When applied to He4 calculations, the two- and three-body oscillator matrix elements yield rapid convergence of the ground-state energy with a small net contribution of the induced four-body force.

  7. Matrix acidification in carbonate reservoirs; Acidificacoes matriciais em reservatorios carbonaticos

    Energy Technology Data Exchange (ETDEWEB)

    Martins, Marcio de Oliveira [Petroleo Brasileiro S.A. (PETROBRAS), Rio de Janeiro, RJ (Brazil)


    Carbonate reservoirs are characterized by great diversity of its properties, including permeability and porosity. When submitted to matrix acidification, if no effort is employed, acid will tend to consume carbonates where permeability and porosity are higher, further increasing conductivity of these sites and also increasing permeability and porosity contrast existing before acid effects on formation. That would give limited production as result of small effective producer zone extent, with probable underutilization of potential reservoirs productivity. To overcome this effect and to achieve greater coverage of treatments, divergence techniques should be applied, including associations of them. This paper presents divergence techniques performed in matrix acidification of Campos and Espirito Santo basins wells, which represent great structural diversity and, as consequence, a significant range of situations. Formations tests results are analyzed to verify diversion systems effectiveness, and how they contribute to the growth of productive potential. (author)

  8. Random matrix theory and multivariate statistics


    Diaz-Garcia, Jose A.; Jáimez, Ramon Gutiérrez


    Some tools and ideas are interchanged between random matrix theory and multivariate statistics. In the context of the random matrix theory, classes of spherical and generalised Wishart random matrix ensemble, containing as particular cases the classical random matrix ensembles, are proposed. Some properties of these classes of ensemble are analysed. In addition, the random matrix ensemble approach is extended and a unified theory proposed for the study of distributions for real normed divisio...

  9. Matrix theory selected topics and useful results

    CERN Document Server

    Mehta, Madan Lal


    Matrices and operations on matrices ; determinants ; elementary operations on matrices (continued) ; eigenvalues and eigenvectors, diagonalization of normal matrices ; functions of a matrix ; positive definiteness, various polar forms of a matrix ; special matrices ; matrices with quaternion elements ; inequalities ; generalised inverse of a matrix ; domain of values of a matrix, location and dispersion of eigenvalues ; symmetric functions ; integration over matrix variables ; permanents of doubly stochastic matrices ; infinite matrices ; Alexander matrices, knot polynomials, torsion numbers.

  10. Solution of the weighted symmetric similarity transformations based on quaternions (United States)

    Mercan, H.; Akyilmaz, O.; Aydin, C.


    A new method through Gauss-Helmert model of adjustment is presented for the solution of the similarity transformations, either 3D or 2D, in the frame of errors-in-variables (EIV) model. EIV model assumes that all the variables in the mathematical model are contaminated by random errors. Total least squares estimation technique may be used to solve the EIV model. Accounting for the heteroscedastic uncertainty both in the target and the source coordinates, that is the more common and general case in practice, leads to a more realistic estimation of the transformation parameters. The presented algorithm can handle the heteroscedastic transformation problems, i.e., positions of the both target and the source points may have full covariance matrices. Therefore, there is no limitation such as the isotropic or the homogenous accuracy for the reference point coordinates. The developed algorithm takes the advantage of the quaternion definition which uniquely represents a 3D rotation matrix. The transformation parameters: scale, translations, and the quaternion (so that the rotation matrix) along with their covariances, are iteratively estimated with rapid convergence. Moreover, prior least squares (LS) estimation of the unknown transformation parameters is not required to start the iterations. We also show that the developed method can also be used to estimate the 2D similarity transformation parameters by simply treating the problem as a 3D transformation problem with zero (0) values assigned for the z-components of both target and source points. The efficiency of the new algorithm is presented with the numerical examples and comparisons with the results of the previous studies which use the same data set. Simulation experiments for the evaluation and comparison of the proposed and the conventional weighted LS (WLS) method is also presented.

  11. Factors Involved in Extracellular Matrix Turnover in Human Derived Cardiomyocytes

    Directory of Open Access Journals (Sweden)

    Gregori Casals


    Full Text Available Background: The molecular mechanisms by which myocardial ischemia translates into ventricular remodeling remain unclear. Methods: We investigated whether hypoxia and proinflammatory cytokines are specific inducers of remodeling signals in an in vitro model of cultured adult human ventricular myocytes (AC16 cells. Results:Hypoxia modified the ratio of matrix remodeling factors by increasing the aminoterminal propeptide of type III procollagen (PIIINP and reducing tissue inhibitor of matrix metalloproteinase type 1 (TIMP-1 secretion in AC16 cells. These effects, however, were not associated with either modifications in expression of matrix metalloproteinase type 2, collagen-I or metalloproteinase activity. Hypoxia does, actually increase the production of the cardiac antifibrogenic growth factors, Apelin and VEGF, through an Hypoxia Inducible Factor type 1-dependent mechanism. Concerning proinflammatory signaling pathways, IL1β emerged as a powerful inducer of matrix turnover, since it significantly enhanced PIIINP, TIMP-1 and hyaluronic acid production and increased metalloproteinase activity. In contrast, TNFα did not modify matrix turnover but markedly induced the production of Apelin and VEGF. Conclusion: Hypoxia and increased TNFα activity likely exert cardioprotective actions by activating the cardiac antifibrogenic factors Apelin and VEGF. In contrast, IL1β is a strong promoter of interstitial collagen remodeling that may contribute to ventricular dilation and heart failure in the ischemic myocardium.

  12. Learning deep similarity in fundus photography (United States)

    Chudzik, Piotr; Al-Diri, Bashir; Caliva, Francesco; Ometto, Giovanni; Hunter, Andrew


    Similarity learning is one of the most fundamental tasks in image analysis. The ability to extract similar images in the medical domain as part of content-based image retrieval (CBIR) systems has been researched for many years. The vast majority of methods used in CBIR systems are based on hand-crafted feature descriptors. The approximation of a similarity mapping for medical images is difficult due to the big variety of pixel-level structures of interest. In fundus photography (FP) analysis, a subtle difference in e.g. lesions and vessels shape and size can result in a different diagnosis. In this work, we demonstrated how to learn a similarity function for image patches derived directly from FP image data without the need of manually designed feature descriptors. We used a convolutional neural network (CNN) with a novel architecture adapted for similarity learning to accomplish this task. Furthermore, we explored and studied multiple CNN architectures. We show that our method can approximate the similarity between FP patches more efficiently and accurately than the state-of- the-art feature descriptors, including SIFT and SURF using a publicly available dataset. Finally, we observe that our approach, which is purely data-driven, learns that features such as vessels calibre and orientation are important discriminative factors, which resembles the way how humans reason about similarity. To the best of authors knowledge, this is the first attempt to approximate a visual similarity mapping in FP.

  13. Similarity Structure of Wave-Collapse

    DEFF Research Database (Denmark)

    Rypdal, Kristoffer; Juul Rasmussen, Jens; Thomsen, Kenneth


    Similarity transformations of the cubic Schrödinger equation (CSE) are investigated. The transformations are used to remove the explicit time variation in the CSE and reduce it to differential equations in the spatial variables only. Two different methods for similarity reduction are employed and...

  14. Similarity indices I: what do they measure.

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, J.W.


    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities.

  15. Outsourced similarity search on metric data assets

    DEFF Research Database (Denmark)

    Yiu, Man Lung; Assent, Ira; Jensen, Christian Søndergaard


    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example...

  16. Some Effects of Similarity Self-Disclosure (United States)

    Murphy, Kevin C.; Strong, Stanley R.


    College males were interviewed about how college had altered their friendships, values, and plans. The interviewers diclosed experiences and feelings similar to those revealed by the students. Results support Byrne's Law of Similarity in generating interpersonal attraction in the interview and suggest that the timing of self-disclosures is…

  17. The purification and partial characterization of bone resorptive polypeptides from bovine bone matrix. (United States)

    Hill, P A; Reynolds, J J; Meikle, M C


    Matrix proteins were extracted from bovine cortical bone with EDTA/Tris-HCl under non-dissociative conditions at neutral pH. Four distinct bone resorptive proteins with molecular masses of 14, 25, 29 and 40 kDa were purified and partially characterized using an in vitro neonatal mouse calvarial assay and a growth factor assay using BALB/c/3T3 cells. The 14 kDa protein was purified by anion exchange chromatography (Mono Q) and gel filtration (Superdex 75HR) using FPLC (fast protein liquid chromatography); this factor stimulated the proliferation of MCF-7 human breast cancer cells, a bioassay which is specific for the insulin-like growth factors (IGFs). The 25, 29 and 40 kDa proteins were purified by sequential chromatography as follows: anion-exchange (Mono Q), heparin-Sepharose, hydroxyapatite, concanavalin A-Sepharose, phenyl-Superose, reversed phase high performance liquid chromatography (HPLC) and sodium dodecylsulfate polyacrylamide gelelectrophoresis (SDS-PAGE). The 25 kDa protein was identified as TGF-beta by its inhibitory effect on the proliferation of mink lung cells. The 40 kDa protein enhanced the formation of multinucleate tartrate-resistant acid phosphatase positive cells in a murine bone marrow differentiation assay, but was without effect in an isolated osteoclast assay and had no growth factor activity; this protein is likely to be a colony stimulating factor. The 29 kDa protein was also without growth factor activity; it was, however, able to stimulate bone resorption in the isolated osteoclast assay, suggesting a direct action in osteoclast function. The 29 and 40 kDa proteins may be osteoblast gene products that have been sequestrated by the bone matrix in a similar fashion to TGF-beta and the IGFs. This is the first report of proteins isolated from bone matrix which directly stimulate osteoclast differentiation and activity.

  18. CD44 Promotes Inflammation and Extracellular Matrix Production During Arteriovenous Fistula Maturation. (United States)

    Kuwahara, Go; Hashimoto, Takuya; Tsuneki, Masayuki; Yamamoto, Kota; Assi, Roland; Foster, Trenton R; Hanisch, Jesse J; Bai, Hualong; Hu, Haidi; Protack, Clinton D; Hall, Michael R; Schardt, John S; Jay, Steven M; Madri, Joseph A; Kodama, Shohta; Dardik, Alan


    Arteriovenous fistulae (AVF) remain the optimal conduit for hemodialysis access but continue to demonstrate poor patency and poor rates of maturation. We hypothesized that CD44, a widely expressed cellular adhesion molecule that serves as a major receptor for extracellular matrix components, promotes wall thickening and extracellular matrix deposition during AVF maturation. AVF were created via needle puncture in wild-type C57BL/6J and CD44 knockout mice. CD44 mRNA and protein expression was increased in wild-type AVF. CD44 knockout mice showed no increase in AVF wall thickness (8.9 versus 26.8 μm; P=0.0114), collagen density, and hyaluronic acid density, but similar elastin density when compared with control AVF. CD44 knockout mice also showed no increase in vascular cell adhesion molecule-1 expression, intercellular adhesion molecule-1 expression, and monocyte chemoattractant protein-1 expression in the AVF compared with controls; there were also no increased M2 macrophage markers (transglutaminase-2: 81.5-fold, P=0.0015; interleukin-10: 7.6-fold, P=0.0450) in CD44 knockout mice. Delivery of monocyte chemoattractant protein-1 to CD44 knockout mice rescued the phenotype with thicker AVF walls (27.2 versus 14.7 μm; P=0.0306), increased collagen density (2.4-fold; P=0.0432), and increased number of M2 macrophages (2.1-fold; P=0.0335). CD44 promotes accumulation of M2 macrophages, extracellular matrix deposition, and wall thickening during AVF maturation. These data show the association of M2 macrophages with wall thickening during AVF maturation and suggest that enhancing CD44 activity may be a strategy to increase AVF maturation. © 2017 American Heart Association, Inc.

  19. Correlation between social proximity and mobility similarity. (United States)

    Fan, Chao; Liu, Yiding; Huang, Junming; Rong, Zhihai; Zhou, Tao


    Human behaviors exhibit ubiquitous correlations in many aspects, such as individual and collective levels, temporal and spatial dimensions, content, social and geographical layers. With rich Internet data of online behaviors becoming available, it attracts academic interests to explore human mobility similarity from the perspective of social network proximity. Existent analysis shows a strong correlation between online social proximity and offline mobility similarity, namely, mobile records between friends are significantly more similar than between strangers, and those between friends with common neighbors are even more similar. We argue the importance of the number and diversity of common friends, with a counter intuitive finding that the number of common friends has no positive impact on mobility similarity while the diversity plays a key role, disagreeing with previous studies. Our analysis provides a novel view for better understanding the coupling between human online and offline behaviors, and will help model and predict human behaviors based on social proximity.

  20. Similarity and a Duality for Fullerenes

    Directory of Open Access Journals (Sweden)

    Jennifer J. Edmond


    Full Text Available Fullerenes are molecules of carbon that are modeled by trivalent plane graphs with only pentagonal and hexagonal faces. Scaling up a fullerene gives a notion of similarity, and fullerenes are partitioned into similarity classes. In this expository article, we illustrate how the values of two important fullerene parameters can be deduced for all fullerenes in a similarity class by computing the values of these parameters for just the three smallest representatives of that class. In addition, it turns out that there is a natural duality theory for similarity classes of fullerenes based on one of the most important fullerene construction techniques: leapfrog construction. The literature on fullerenes is very extensive, and since this is a general interest journal, we will summarize and illustrate the fundamental results that we will need to develop similarity and this duality.

  1. Regularization in Matrix Relevance Learning

    NARCIS (Netherlands)

    Schneider, Petra; Bunte, Kerstin; Stiekema, Han; Hammer, Barbara; Villmann, Thomas; Biehl, Michael

    A In this paper, we present a regularization technique to extend recently proposed matrix learning schemes in learning vector quantization (LVQ). These learning algorithms extend the concept of adaptive distance measures in LVQ to the use of relevance matrices. In general, metric learning can

  2. Parallel Sparse Matrix - Vector Product

    DEFF Research Database (Denmark)

    Alexandersen, Joe; Lazarov, Boyan Stefanov; Dammann, Bernd

    This technical report contains a case study of a sparse matrix-vector product routine, implemented for parallel execution on a compute cluster with both pure MPI and hybrid MPI-OpenMP solutions. C++ classes for sparse data types were developed and the report shows how these class can be used...

  3. Supersymmetry in Random Matrix Theory


    Guhr, Thomas


    Supersymmetry is nowadays indispensable for many problems in Random Matrix Theory. It is presented here with an emphasis on conceptual and structural issues. An introduction to supermathematics is given. The Hubbard-Stratonovich transformation as well as its generalization and superbosonization are explained. The supersymmetric non-linear sigma model, Brownian motion in superspace and the color-flavor transformation are discussed.

  4. The COMPADRE Plant Matrix Database

    DEFF Research Database (Denmark)


    COMPADRE contains demographic information on hundreds of plant species. The data in COMPADRE are in the form of matrix population models and our goal is to make these publicly available to facilitate their use for research and teaching purposes. COMPADRE is an open-access database. We only request...

  5. Open Membranes in Matrix Theory


    Li, Miao


    We discuss how to construct open membranes in the recently proposed matrix model of M theory. In order to sustain an open membrane, two boundary terms are needed in the construction. These boundary terms are available in the system of the longitudinal five-branes and D0-branes.

  6. Hyper-systolic matrix multiplication

    NARCIS (Netherlands)

    Lippert, Th.; Petkov, N.; Palazzari, P.; Schilling, K.

    A novel parallel algorithm for matrix multiplication is presented. It is based on a 1-D hyper-systolic processor abstraction. The procedure can be implemented on all types of parallel systems. (C) 2001 Elsevier Science B,V. All rights reserved.

  7. Bilateral matrix-exponential distributions

    DEFF Research Database (Denmark)

    Bladt, Mogens; Esparza, Luz Judith R; Nielsen, Bo Friis


    In this article we define the classes of bilateral and multivariate bilateral matrix-exponential distributions. These distributions have support on the entire real space and have rational moment-generating functions. These distributions extend the class of bilateral phasetype distributions of [1]...

  8. Extracellular matrix and wound healing. (United States)

    Maquart, F X; Monboisse, J C


    Extracellular matrix has been known for a long time as an architectural support for the tissues. Many recent data, however, have shown that extracellular matrix macromolecules (collagens, elastin, glycosaminoglycans, proteoglycans and connective tissue glycoproteins) are able to regulate many important cell functions, such as proliferation, migration, protein synthesis or degradation, apoptosis, etc., making them able to play an important role in the wound repair process. Not only the intact macromolecules but some of their specific domains, that we called "Matrikines", are also able to regulate many cell activities. In this article, we will summarize main findings showing the effects of extracellular matrix macromolecules and matrikines on connective tissue and epithelial cells, particularly in skin, and their potential implication in the wound healing process. These examples show that extracellular matrix macromolecules or some of their specific domains may play a major role in wound healing. Better knowledge of these interactions may suggest new therapeutic targets in wound healing defects. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  9. Unravelling the nuclear matrix proteome

    DEFF Research Database (Denmark)

    Albrethsen, Jakob; Knol, Jaco C; Jimenez, Connie R


    The nuclear matrix (NM) model posits the presence of a protein/RNA scaffold that spans the mammalian nucleus. The NM proteins are involved in basic nuclear function and are a promising source of protein biomarkers for cancer. Importantly, the NM proteome is operationally defined as the proteins...

  10. Discriminant projective non-negative matrix factorization.

    Directory of Open Access Journals (Sweden)

    Naiyang Guan

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

  11. Reprocessability of molybdenum and magnesia based inert matrix fuels

    Directory of Open Access Journals (Sweden)

    Ebert Elena L.


    Full Text Available This work focuses on the reprocessability of metallic 92Mo and ceramic MgO, which is under investigation for (Pu,MA-oxide (MA = minor actinide fuel within a metallic 92Mo matrix (CERMET and a ceramic MgO matrix (CERCER. Magnesium oxide and molybdenum reference samples have been fabricated by powder metallurgy. The dissolution of the matrices was studied as a function of HNO3 concentration (1-7 mol/L and temperature (25-90°C. The rate of dissolution of magnesium oxide and metallic molybdenum increased with temperature. While the MgO rate was independent of the acid concentration (1-7 mol/L, the rate of dissolution of Mo increased with acid concentration. However, the dissolution of Mo at high temperatures and nitric acid concentrations was accompanied by precipitation of MoO3. The extraction of uranium, americium, and europium in the presence of macro amounts of Mo and Mg was studied by three different extraction agents: tri-n-butylphosphate (TBP, N,Nʹ-dimethyl-N,Nʹ-dioctylhexylethoxymalonamide (DMDOHEMA, and N,N,N’,N’- -tetraoctyldiglycolamide (TODGA. With TBP no extraction of Mo and Mg occurred. Both matrix materials are partly extracted by DMDOHEMA. Magnesium is not extracted by TODGA (D < 0.1, but a weak extraction of Mo is observed at low Mo concentration.

  12. Pericellular interphotoreceptor matrix dictates outer retina critical surface tension. (United States)

    Gonzalez-Fernandez, Federico; Fornalik, Mark; Garlipp, Mary Alice; Gonzalez-Fernandez, Priscilla; Sung, Dongjin; Meyer, Anne; Baier, Robert


    Retinal detachments create two pathological surfaces, the surface of the outer neural retinal, and an apical retinal-pigmented epithelium (RPE) surface. The physicochemical properties of these two new surfaces are poorly understood. At a molecular level little is known how detachments form, how to optimize reattachment, or prevent extension of the detachment. A major limitation is lack of information about the biophysical consequences of the retina-RPE separation. The primary challenge is determining the molecular properties of the pathological interface surfaces. Here, using detached bovine retina, we show that this hurdle can be overcome through a combination of biophysical and ultrastructural approaches. The outer surface of freshly detached bovine neural retina, and isolated molecular components of the outer retina were subjected to: 1) Contact angle goniometry to determine the critical surface tension of the outer retinal surface, isolated insoluble interphotoreceptor matrix (IPM) and purified interphotoreceptor retinoid binding protein (IRBP); 2) Multiple attenuated internal reflectance infrared (MAIR-IR) spectroscopy was used to characterize the molecular composition of the retinal surface. MAIR-IR depth penetration was established through ellipsometric measurement of barium-stearate films. Light microscopy, immunohistochemistry and electron microscopy defined the structures probed spectroscopically. Furthermore, the data were correlated to IR spectra of docosahexaenoic acid, hyaluronan, chondroitin-6-sulfate and IRBP, and imaging by IR-microscopy. We found that the retinal critical surface tension is 24 mN/m, similar to isolated insoluble IPM and lower than IRBP. Barium-stearate calibration studies established that the MAIR-IR spectroscopy penetration depth was 0.2 μm. Ultrastructural observations and MAIR-IR studies of isolated outer retina components determined that the pericellular IPM coating the outer retinal surface is primarily responsible for

  13. An immunofluorescence assay for extracellular matrix components highlights the role of epithelial cells in producing a stable, fibrillar extracellular matrix

    Directory of Open Access Journals (Sweden)

    Omar S. Qureshi


    Full Text Available Activated fibroblasts are considered major drivers of fibrotic disease progression through the production of excessive extracellular matrix (ECM in response to signals from damaged epithelial and inflammatory cells. Nevertheless, epithelial cells are capable of expressing components of the ECM, cross-linking enzymes that increase its stability and are sensitive to factors involved in the early stages of fibrosis. We therefore wanted to test the hypothesis that epithelial cells can deposit ECM in response to stimulation in a comparable manner to fibroblasts. We performed immunofluorescence analysis of components of stable, mature extracellular matrix produced by primary human renal proximal tubular epithelial cells and renal fibroblasts in response to cytokine stimulation. Whilst fibroblasts produced a higher basal level of extracellular matrix components, epithelial cells were able to deposit significant levels of fibronectin, collagen I, III and IV in response to cytokine stimulation. In response to hypoxia, epithelial cells showed an increase in collagen IV deposition but not in response to the acute stress stimuli aristolochic acid or hydrogen peroxide. When epithelial cells were in co-culture with fibroblasts we observed significant increases in the level of matrix deposition which could be reduced by transforming growth factor beta (TGF-β blockade. Our results highlight the role of epithelial cells acting as efficient producers of stable extracellular matrix which could contribute to renal tubule thickening in fibrosis.

  14. An immunofluorescence assay for extracellular matrix components highlights the role of epithelial cells in producing a stable, fibrillar extracellular matrix. (United States)

    Qureshi, Omar S; Bon, Hélène; Twomey, Breda; Holdsworth, Gill; Ford, Kirsty; Bergin, Marianne; Huang, Linghong; Muzylak, Mariusz; Healy, Louise J; Hurdowar, Vanessa; Johnson, Timothy S


    Activated fibroblasts are considered major drivers of fibrotic disease progression through the production of excessive extracellular matrix (ECM) in response to signals from damaged epithelial and inflammatory cells. Nevertheless, epithelial cells are capable of expressing components of the ECM, cross-linking enzymes that increase its stability and are sensitive to factors involved in the early stages of fibrosis. We therefore wanted to test the hypothesis that epithelial cells can deposit ECM in response to stimulation in a comparable manner to fibroblasts. We performed immunofluorescence analysis of components of stable, mature extracellular matrix produced by primary human renal proximal tubular epithelial cells and renal fibroblasts in response to cytokine stimulation. Whilst fibroblasts produced a higher basal level of extracellular matrix components, epithelial cells were able to deposit significant levels of fibronectin, collagen I, III and IV in response to cytokine stimulation. In response to hypoxia, epithelial cells showed an increase in collagen IV deposition but not in response to the acute stress stimuli aristolochic acid or hydrogen peroxide. When epithelial cells were in co-culture with fibroblasts we observed significant increases in the level of matrix deposition which could be reduced by transforming growth factor beta (TGF-β) blockade. Our results highlight the role of epithelial cells acting as efficient producers of stable extracellular matrix which could contribute to renal tubule thickening in fibrosis. © 2017. Published by The Company of Biologists Ltd.

  15. Transmission line matrix model for ultrasonic imaging (United States)

    Ciocan, Razvan; Ida, Nathan; Driscoll, Diana


    A transmission-line matrix (TLM) model was developed to simulate the ultrasound propagation in the multi-layer structures. The spatial resolution of the proposed model is better than tenth wavelength. The numerical modeling is carried-out for frequencies that are usually used in ultrasound imagery (3.5 - 25MHz). The acoustic impedance profile of multi-layer structures considered are similar to those found in nondestructive evaluation and in medical imaging. The structures modeled are: brazed joints, stomach and colon walls. Structures with artificial flaws are also modeled. A comparison between real images and numerical generated ones is provided for each considered structure. Both frequency and time domain responses are obtained from the structures under investigation. Both single and array transducer techniques are modeled and their performances are evaluated for the proposed structures. Different shapes for the incident pulse are considered in numerically generated images.

  16. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar


    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users\\' intuition about model similarity, and to support complex model searches in databases.

  17. Two perspectives on similarity between words (United States)

    Frisch, Stefan A.


    This presentation examines the similarity between words from both bottom up (phonetic) and top down (phonological/psycholinguistic) perspectives. From the phonological perspective, the influence of structure on similarity is explored using metalinguistic acceptability judgments for multisyllabic nonwords. Results from an experiment suggest that subjects try to align novel words with known words in order to maximize similarities while minimizing dissimilarities. This finding parallels results from psychology on similarity judgments for visual scenes. From the phonetic perspective, the influence of similar gestures on speech error rates is examined using ultrasound measurement of tongue position. In a pilot experiment, subjects, produced tongue twisters containing words where onset and vowel phonemes had similar gestures (e.g., tip, comb) and where the onset and vowel had dissimilar gestures (e.g., tube, keep). Preliminary results suggest that misarticulations are more frequent in the context of dissimilar gestures (e.g., in the tongue twister tip cape keep tape, error rates are higher for /k/ than /t/). These errors appear to be gestural interactions rather than errors at the phonemic or featural level of phonological spellout. Together, these two experiments indicate that similarity relations between words are found at multiple levels, any which are potentially relevant to the structure of phonological systems.

  18. Electrostatic Similarity Determination Using Multiresolution Analysis. (United States)

    Hakkoymaz, Huseyin; Kieslich, Chris A; Jr, Ronald D Gorham; Gunopulos, Dimitrios; Morikis, Dimitrios


    Molecular similarity is an important tool in protein and drug design for analyzing the quantitative relationships between physicochemical properties of two molecules. We present a family of similarity measures which exploits the ability of wavelet transformation to analyze the spectral components of physicochemical properties and suggests a sensitive way for measuring similarities of biological molecules. In order to investigate how effective wavelet-based similarity measures were against conventional measures, we defined several patterns which involve scalar or topological changes in the distribution of electrostatic properties. The wavelet-based measures were more successful in discriminating these patterns in contrast to the current state-of-art similarity measures. We also present the validity of wavelet-based similarity measures through the hierarchical clustering of two protein datasets consisting of families of homologous domains and alanine scan mutants. This type of similarity analysis is useful for protein structure-function studies and protein design. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Measure of Node Similarity in Multilayer Networks.

    Directory of Open Access Journals (Sweden)

    Anders Mollgaard

    Full Text Available The weight of links in a network is often related to the similarity of the nodes. Here, we introduce a simple tunable measure for analysing the similarity of nodes across different link weights. In particular, we use the measure to analyze homophily in a group of 659 freshman students at a large university. Our analysis is based on data obtained using smartphones equipped with custom data collection software, complemented by questionnaire-based data. The network of social contacts is represented as a weighted multilayer network constructed from different channels of telecommunication as well as data on face-to-face contacts. We find that even strongly connected individuals are not more similar with respect to basic personality traits than randomly chosen pairs of individuals. In contrast, several socio-demographics variables have a significant degree of similarity. We further observe that similarity might be present in one layer of the multilayer network and simultaneously be absent in the other layers. For a variable such as gender, our measure reveals a transition from similarity between nodes connected with links of relatively low weight to dis-similarity for the nodes connected by the strongest links. We finally analyze the overlap between layers in the network for different levels of acquaintanceships.

  20. Trajectory similarity join in spatial networks

    KAUST Repository

    Shang, Shuo


    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider the case of trajectory similarity join (TS-Join), where the objects are trajectories of vehicles moving in road networks. Thus, given two sets of trajectories and a threshold θ, the TS-Join returns all pairs of trajectories from the two sets with similarity above θ. This join targets applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm\\'s per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

  1. Similarity and Decay Laws of Momentumless Wakes. (United States)


    Naval Sea Systems Command , Code NSEA—03133. -‘ F 9 —2— 26 May 1977 SN : j ep SIMILARITY AND DECAY LAWS OF MOMENTUI’ILESS WAKE S by Samuel Ilassid...and this neg lect will have to be justified a posteriori. Now, one seeks self-similar solutions of the type: k = Xh(ri) c = Ee(n) Ud = UDf (n) ~ = where...0 9x r 3r L6 c Again, seeking self-similar solutions of the type: k = Kh(ti) c = Ee(ri) Ud = UDf (n) r~ = (6.4) and letting 2 2 = 1 (6.5)E L one

  2. Similarity-based pattern analysis and recognition

    CERN Document Server

    Pelillo, Marcello


    This accessible text/reference presents a coherent overview of the emerging field of non-Euclidean similarity learning. The book presents a broad range of perspectives on similarity-based pattern analysis and recognition methods, from purely theoretical challenges to practical, real-world applications. The coverage includes both supervised and unsupervised learning paradigms, as well as generative and discriminative models. Topics and features: explores the origination and causes of non-Euclidean (dis)similarity measures, and how they influence the performance of traditional classification alg

  3. Specialisation of extracellular matrix for function in tendons and ligaments (United States)

    Birch, Helen L.; Thorpe, Chavaunne T.; Rumian, Adam P.


    Summary Tendons and ligaments are similar structures in terms of their composition, organisation and mechanical properties. The distinction between them stems from their anatomical location; tendons form a link between muscle and bone while ligaments link bones to bones. A range of overlapping functions can be assigned to tendon and ligaments and each structure has specific mechanical properties which appear to be suited for particular in vivo function. The extracellular matrix in tendon and ligament varies in accordance with function, providing appropriate mechanical properties. The most useful framework in which to consider extracellular matrix differences therefore is that of function rather than anatomical location. In this review we discuss what is known about the relationship between functional requirements, structural properties from molecular to gross level, cellular gene expression and matrix turnover. The relevance of this information is considered by reviewing clinical aspects of tendon and ligament repair and reconstructive procedures. PMID:23885341

  4. Matrix metalloproteinases in fish biology and matrix turnover. (United States)

    Pedersen, Mona E; Vuong, Tram T; Rønning, Sissel B; Kolset, Svein O


    Matrix metalloproteinases have important functions for tissue turnover in fish, with relevance both for the fish industry and molecular and cellular research on embryology, inflammation and tissue repair. These metalloproteinases have been studied in different fish types, subjected to both aquaculture and experimental conditions. This review highlights studies on these metalloproteinases in relation to both fish quality and health and further, the future importance of fish for basic research studies. Copyright © 2015. Published by Elsevier B.V.

  5. In-depth, high-accuracy proteomics of sea urchin tooth organic matrix

    Directory of Open Access Journals (Sweden)

    Mann Matthias


    Full Text Available Abstract Background The organic matrix contained in biominerals plays an important role in regulating mineralization and in determining biomineral properties. However, most components of biomineral matrices remain unknown at present. In sea urchin tooth, which is an important model for developmental biology and biomineralization, only few matrix components have been identified. The recent publication of the Strongylocentrotus purpuratus genome sequence rendered possible not only the identification of genes potentially coding for matrix proteins, but also the direct identification of proteins contained in matrices of skeletal elements by in-depth, high-accuracy proteomic analysis. Results We identified 138 proteins in the matrix of tooth powder. Only 56 of these proteins were previously identified in the matrices of test (shell and spine. Among the novel components was an interesting group of five proteins containing alanine- and proline-rich neutral or basic motifs separated by acidic glycine-rich motifs. In addition, four of the five proteins contained either one or two predicted Kazal protease inhibitor domains. The major components of tooth matrix were however largely identical to the set of spicule matrix proteins and MSP130-related proteins identified in test (shell and spine matrix. Comparison of the matrices of crushed teeth to intact teeth revealed a marked dilution of known intracrystalline matrix proteins and a concomitant increase in some intracellular proteins. Conclusion This report presents the most comprehensive list of sea urchin tooth matrix proteins available at present. The complex mixture of proteins identified may reflect many different aspects of the mineralization process. A comparison between intact tooth matrix, presumably containing odontoblast remnants, and crushed tooth matrix served to differentiate between matrix components and possible contributions of cellular remnants. Because LC-MS/MS-based methods directly

  6. Outsourced similarity search on metric data assets

    KAUST Repository

    Yiu, Man Lung


    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying it to the service provider for similarity queries on the transformed data. Our techniques provide interesting trade-offs between query cost and accuracy. They are then further extended to offer an intuitive privacy guarantee. Empirical studies with real data demonstrate that the techniques are capable of offering privacy while enabling efficient and accurate processing of similarity queries.

  7. Distances and similarities in intuitionistic fuzzy sets

    CERN Document Server

    Szmidt, Eulalia


    This book presents the state-of-the-art in theory and practice regarding similarity and distance measures for intuitionistic fuzzy sets. Quantifying similarity and distances is crucial for many applications, e.g. data mining, machine learning, decision making, and control. The work provides readers with a comprehensive set of theoretical concepts and practical tools for both defining and determining similarity between intuitionistic fuzzy sets. It describes an automatic algorithm for deriving intuitionistic fuzzy sets from data, which can aid in the analysis of information in large databases. The book also discusses other important applications, e.g. the use of similarity measures to evaluate the extent of agreement between experts in the context of decision making.

  8. Comparing methods for single paragraph similarity analysis. (United States)

    Stone, Benjamin; Dennis, Simon; Kwantes, Peter J


    The focus of this paper is two-fold. First, similarities generated from six semantic models were compared to human ratings of paragraph similarity on two datasets-23 World Entertainment News Network paragraphs and 50 ABC newswire paragraphs. Contrary to findings on smaller textual units such as word associations (Griffiths, Tenenbaum, & Steyvers, 2007), our results suggest that when single paragraphs are compared, simple nonreductive models (word overlap and vector space) can provide better similarity estimates than more complex models (LSA, Topic Model, SpNMF, and CSM). Second, various methods of corpus creation were explored to facilitate the semantic models' similarity estimates. Removing numeric and single characters, and also truncating document length improved performance. Automated construction of smaller Wikipedia-based corpora proved to be very effective, even improving upon the performance of corpora that had been chosen for the domain. Model performance was further improved by augmenting corpora with dataset paragraphs. Copyright © 2010 Cognitive Science Society, Inc.

  9. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Parrado-Hernandez, Emilio; Meng, Anders

    Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...... for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation....

  10. Abundance estimation of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh


    Full Text Available This paper evaluates a spectral unmixing method for estimating the partial abundance of spectrally similar minerals in complex mixtures. The method requires formulation of a linear function of individual spectra of individual minerals. The first...

  11. In situ analysis of plant tissue underivatized carbohydrates and on-probe enzymatic degraded starch by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry by using carbon nanotubes as matrix. (United States)

    Gholipour, Yousef; Nonami, Hiroshi; Erra-Balsells, Rosa


    Underivatized carbohydrates of tulip bulb and leaf tissues were characterized in situ by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) by using carbon nanotubes (CNTs) as matrix. Two sample preparation methods--(i) depositing CNTs on the fresh tissue slices placed on the probe and (ii) locating semitransparent tissues on a dried layer of CNTs on the probe--were examined. Furthermore, practicability of in situ starch analysis by MALDI-TOF MS was examined by detection of glucose originated from on-probe amyloglucosidase-catalyzed degradation of starch on the tissue surface. Besides, CNTs could efficiently desorb/ionize natural mono-, di-, and oligosaccharides extracted from tulip bulb tissues as well as glucose resulting from starch enzymatic degradation in vitro. These results were compared with those obtained by in situ MALDI-TOF MS analysis of similar tissues. Positive ion mode showed superior signal reproducibility. CNTs deposited under semitransparent tissue could also desorb/ionize neutral carbohydrates, leading to nearly complete elimination of matrix cluster signals but with an increase in tissue-originated signals. Furthermore, several experiments were carried out to compare the efficiency of 2,5-dihydroxybenzoic acid, nor-harmane, alpha-cyano-4-hydroxycinnamic acid, and CNTs as matrices for MALDI of neutral carbohydrates from the intact plant tissue surface and for enzymatic tissue starch degradation; these results are discussed in brief. Among matrices studied, the lowest laser power was needed to acquire carbohydrate signals with high signal-to-noise ratio and resolution when CNTs were used.

  12. On distributional assumptions and whitened cosine similarities

    DEFF Research Database (Denmark)

    Loog, Marco


    Recently, an interpretation of the whitened cosine similarity measure as a Bayes decision rule was proposed (C. Liu, "The Bayes Decision Rule Induced Similarity Measures,'' IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 29, no. 6, pp. 1086-1090, June 2007. This communication makes...... the observation that some of the distributional assumptions made to derive this measure are very restrictive and, considered simultaneously, even inconsistent....

  13. Privacy-preserving matching of similar patients. (United States)

    Vatsalan, Dinusha; Christen, Peter


    The identification of similar entities represented by records in different databases has drawn considerable attention in many application areas, including in the health domain. One important type of entity matching application that is vital for quality healthcare analytics is the identification of similar patients, known as similar patient matching. A key component of identifying similar records is the calculation of similarity of the values in attributes (fields) between these records. Due to increasing privacy and confidentiality concerns, using the actual attribute values of patient records to identify similar records across different organizations is becoming non-trivial because the attributes in such records often contain highly sensitive information such as personal and medical details of patients. Therefore, the matching needs to be based on masked (encoded) values while being effective and efficient to allow matching of large databases. Bloom filter encoding has widely been used as an efficient masking technique for privacy-preserving matching of string and categorical values. However, no work on Bloom filter-based masking of numerical data, such as integer (e.g. age), floating point (e.g. body mass index), and modulus (numbers wrap around upon reaching a certain value, e.g. date and time), which are commonly required in the health domain, has been presented in the literature. We propose a framework with novel methods for masking numerical data using Bloom filters, thereby facilitating the calculation of similarities between records. We conduct an empirical study on publicly available real-world datasets which shows that our framework provides efficient masking and achieves similar matching accuracy compared to the matching of actual unencoded patient records. Copyright © 2015 Elsevier Inc. All rights reserved.

  14. Similarity search processing. Paralelization and indexing technologies.

    Directory of Open Access Journals (Sweden)

    Eder Dos Santos


    The next Scientific-Technical Report addresses the similarity search and the implementation of metric structures on parallel environments. It also presents the state of the art related to similarity search on metric structures and parallelism technologies. Comparative analysis are also proposed, seeking to identify the behavior of a set of metric spaces and metric structures over processing platforms multicore-based and GPU-based.

  15. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung


    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  16. Transformation Matrix for Time Discretization Based on Tustin’s Method

    Directory of Open Access Journals (Sweden)

    Yiming Jiang


    Full Text Available This paper studies rules in transformation of transfer function through time discretization. A method of using transformation matrix to realize bilinear transform (also known as Tustin’s method is presented. This method can be described as the conversion between the coefficients of transfer functions, which are expressed as transform by certain matrix. For a polynomial of degree n, the corresponding transformation matrix of order n exists and is unique. Furthermore, the transformation matrix can be decomposed into an upper triangular matrix multiplied with another lower triangular matrix. And both have obvious regularity. The proposed method can achieve rapid bilinear transform used in automatic design of digital filter. The result of numerical simulation verifies the correctness of the theoretical results. Moreover, it also can be extended to other similar problems. Example in the last throws light on this point.

  17. Tracing the evolution of nuclear forces under the similarity renormalization group

    Directory of Open Access Journals (Sweden)

    Calvin W. Johnson


    Full Text Available I examine the evolution of nuclear forces under the similarity renormalization group (SRG using traces of the many-body configuration-space Hamiltonian. While SRG is often said to “soften” the nuclear interaction, I provide numerical examples which paint a complementary point of view: the primary effect of SRG, using the kinetic energy as the generator of the evolution, is to shift downward the diagonal matrix elements in the model space, while the off-diagonal elements undergo significantly smaller changes. By employing traces, I argue that this is a very natural outcome as one diagonalizes a matrix, and helps one to understand the success of SRG.

  18. Random Vector and Matrix Theories: A Renormalization Group Approach (United States)

    Zinn-Justin, Jean


    Random matrices in the large N expansion and the so-called double scaling limit can be used as toy models for quantum gravity: 2D quantum gravity coupled to conformal matter. This has generated a tremendous expansion of random matrix theory, tackled with increasingly sophisticated mathematical methods and number of matrix models have been solved exactly. However, the somewhat paradoxical situation is that either models can be solved exactly or little can be said. Since the solved models display critical points and universal properties, it is tempting to use renormalization group ideas to determine universal properties, without solving models explicitly. Initiated by Br\\'ezin and Zinn-Justin, the approach has led to encouraging results, first for matrix integrals and then quantum mechanics with matrices, but has not yet become a universal tool as initially hoped. In particular, general quantum field theories with matrix fields require more detailed investigations. To better understand some of the encountered difficulties, we first apply analogous ideas to the simpler O(N) symmetric vector models, models that can be solved quite generally in the large N limit. Unlike other attempts, our method is a close extension of Br\\'ezin and Zinn-Justin. Discussing vector and matrix models with similar approximation scheme, we notice that in all cases (vector and matrix integrals, vector and matrix path integrals in the local approximation), at leading order, non-trivial fixed points satisfy the same universal algebraic equation, and this is the main result of this work. However, its precise meaning and role have still to be better understood.

  19. Cross-linked matrix rigidity and soluble retinoids synergize in nuclear lamina regulation of stem cell differentiation. (United States)

    Ivanovska, Irena L; Swift, Joe; Spinler, Kyle; Dingal, Dave; Cho, Sangkyun; Discher, Dennis E


    Synergistic cues from extracellular matrix and soluble factors are often obscure in differentiation. Here the rigidity of cross-linked collagen synergizes with retinoids in the osteogenesis of human marrow mesenchymal stem cells (MSCs). Collagen nanofilms serve as a model matrix that MSCs can easily deform unless the film is enzymatically cross-linked, which promotes the spreading of cells and the stiffening of nuclei as both actomyosin assembly and nucleoskeletal lamin-A increase. Expression of lamin-A is known to be controlled by retinoic acid receptor (RAR) transcription factors, but soft matrix prevents any response to any retinoids. Rigid matrix is needed to induce rapid nuclear accumulation of the RARG isoform and for RARG-specific antagonist to increase or maintain expression of lamin-A as well as for RARG-agonist to repress expression. A progerin allele of lamin-A is regulated in the same manner in iPSC-derived MSCs. Rigid matrices are further required for eventual expression of osteogenic markers, and RARG-antagonist strongly drives lamin-A-dependent osteogenesis on rigid substrates, with pretreated xenografts calcifying in vivo to a similar extent as native bone. Proteomics-detected targets of mechanosensitive lamin-A and retinoids underscore the convergent synergy of insoluble and soluble cues in differentiation. © 2017 Ivanovska et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (

  20. Differentiation of Streptococcus pneumoniae conjunctivitis outbreak isolates by matrix-assisted laser desorption ionization-time of flight mass spectrometry. (United States)

    Williamson, Yulanda M; Moura, Hercules; Woolfitt, Adrian R; Pirkle, James L; Barr, John R; Carvalho, Maria Da Gloria; Ades, Edwin P; Carlone, George M; Sampson, Jacquelyn S


    Streptococcus pneumoniae (pneumococcus [Pnc]) is a causative agent of many infectious diseases, including pneumonia, septicemia, otitis media, and conjunctivitis. There have been documented conjunctivitis outbreaks in which nontypeable (NT), nonencapsulated Pnc has been identified as the etiological agent. The use of mass spectrometry to comparatively and differentially analyze protein and peptide profiles of whole-cell microorganisms remains somewhat uncharted. In this report, we discuss a comparative proteomic analysis between NT S. pneumoniae conjunctivitis outbreak strains (cPnc) and other known typeable or NT pneumococcal and streptococcal isolates (including Pnc TIGR4 and R6, Streptococcus oralis, Streptococcus mitis, Streptococcus pseudopneumoniae, and Streptococcus pyogenes) and nonstreptococcal isolates (including Escherichia coli, Enterococcus faecalis, and Staphylococcus aureus) as controls. cPnc cells and controls were grown to mid-log phase, harvested, and subsequently treated with a 10% trifluoroacetic acid-sinapinic acid matrix mixture. Protein and peptide fragments of the whole-cell bacterial isolate-matrix combinations ranging in size from 2 to 14 kDa were evaluated by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Additionally Random Forest analytical tools and dendrogramic representations (Genesis) suggested similarities and clustered the isolates into distinct clonal groups, respectively. Also, a peak list of protein and peptide masses was obtained and compared to a known Pnc protein mass library, in which a peptide common and unique to cPnc isolates was tentatively identified. Information gained from this study will lead to the identification and validation of proteins that are commonly and exclusively expressed in cPnc strains which could potentially be used as a biomarker in the rapid diagnosis of pneumococcal conjunctivitis.