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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

    Sette Alessandro

    2009-11-01

    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: http://www.mhc-pathway.net/smmpmbec.

  2. Ultrastructure of a hyaluronic acid matrix

    Hadler, Nortin M.; Dourmashkin, Robert R; Nermut, Milan V.; Williams, Lynn D.

    1982-01-01

    Freeze-etch replicas of a hylauronic acid matrix were visualized by electron microscopy. In water a coarse branching fibrillar network of hyaluronic acid aggregates was seen. The high solvent permeability of this matrix suggests that the spaces observed are relatively devoid of unaggregated polymer. Addition of calcium disordered the matrix, resulting in a more dispersed felt of polymer.

  3. Sparse similarity matrix learning for visual object retrieval

    Yan, Z.; Yu, Y.

    2013-01-01

    Tf-idf weighting scheme is adopted by state-of-the-art object retrieval systems to reflect the difference in discriminability between visual words. However, we argue it is only suboptimal by noting that tf-idf weighting scheme does not take quantization error into account and exploit word correlation. We view tf-idf weights as an example of diagonal Mahalanobis-type similarity matrix and generalize it into a sparse one by selectively activating off-diagonal elements. Our goal is to separate s...

  4. Wavelet matrix transform for time-series similarity measurement

    HU Zhi-kun; XU Fei; GUI Wei-hua; YANG Chun-hua

    2009-01-01

    A time-series similarity measurement method based on wavelet and matrix transform was proposed, and its anti-noise ability, sensitivity and accuracy were discussed. The time-series sequences were compressed into wavelet subspace, and sample feature vector and orthogonal basics of sample time-series sequences were obtained by K-L transform. Then the inner product transform was carried out to project analyzed time-series sequence into orthogonal basics to gain analyzed feature vectors. The similarity was calculated between sample feature vector and analyzed feature vector by the Euclid distance. Taking fault wave of power electronic devices for example, the experimental results show that the proposed method has low dimension of feature vector, the anti-noise ability of proposed method is 30 times as large as that of plain wavelet method, the sensitivity of proposed method is 1/3 as large as that of plain wavelet method, and the accuracy of proposed method is higher than that of the wavelet singular value decomposition method. The proposed method can be applied in similarity matching and indexing for lager time series databases.

  5. Fragmentation of extracellular matrix by hypochlorous acid

    Woods, Alan A; Davies, Michael Jonathan

    2003-01-01

    /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...

  6. Preparation of coated valproic acid and sodium valproate sustained-release matrix tablets

    Phaechamud T

    2010-01-01

    Full Text Available 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. Oil-free hyaluronic acid matrix for serial femtosecond crystallography

    Sugahara, Michihiro; Song, Changyong; Suzuki, Mamoru; Masuda, Tetsuya; Inoue, Shigeyuki; Nakane, Takanori; Yumoto, Fumiaki; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Numata, Keiji; Iwata, So

    2016-04-01

    The grease matrix was originally introduced as a microcrystal-carrier for serial femtosecond crystallography and has been expanded to applications for various types of proteins, including membrane proteins. However, the grease-based matrix has limited application for oil-sensitive proteins. Here we introduce a grease-free, water-based hyaluronic acid matrix. Applications for proteinase K and lysozyme proteins were able to produce electron density maps at 2.3-Å resolution.

  8. Hyaluronic acid changes of the extracellular matrix in colon carcinoma

    Arab MR.; Allahyari A.; Sargolzaie Aval F.; Rafighdoost H; Karimi M

    2007-01-01

    Background: The extracellular matrix is a complex three-dimensional network of proteins and glycosaminoglycans, which have important roles in cellular physiology and cell-cell and cell-extracellular matrix interactions. Any changes in the extracellular matrix of tumors may be implicated in cellular transformation and metastasis. The aim of the present study was to identify changes in the hyaluronic acid of the stroma of colonic carcinoma.Methods: Paraffin blocks of 30 patients with colon carc...

  9. Oil-free hyaluronic acid matrix for serial femtosecond crystallography

    Michihiro Sugahara; Changyong Song; Mamoru Suzuki; Tetsuya Masuda; Shigeyuki Inoue; Takanori Nakane; Fumiaki Yumoto; Eriko Nango; Rie Tanaka; Kensuke Tono; Yasumasa Joti; Takashi Kameshima; Takaki Hatsui; Makina Yabashi; Osamu Nureki

    2016-01-01

    The grease matrix was originally introduced as a microcrystal-carrier for serial femtosecond crystallography and has been expanded to applications for various types of proteins, including membrane proteins. However, the grease-based matrix has limited application for oil-sensitive proteins. Here we introduce a grease-free, water-based hyaluronic acid matrix. Applications for proteinase K and lysozyme proteins were able to produce electron density maps at 2.3-Å resolution.

  10. Matrix member for containing fuel cell acid electrolyte

    A matrix member for carrying the acid electrolyte of a fuel cell comprised of a first layer containing a carbon material and a second layer containing a silicon carbide material. A further matrix member is disclosed wherein the mean pore size of the member is substantially equal to or less than that mean pore size of at least one of the fuel cell electrodes

  11. Analysis of amino acids network based on distance matrix

    Ali, Tazid; Akhtar, Adil; Gohain, Nisha

    2016-06-01

    In this paper we have constructed a distance matrix of the amino acids. The distance is defined based on the relative evolutionary importance of the base position of the corresponding codons. From this distance matrix a network of the amino acids is obtained. We have argued that this network depicts the evolutionary pattern of the amino acids. To examine the relative importance of the amino acids with respect to this network we have discussed different measures of centrality. We have also investigated the correlation coefficients between different measures of centrality. Further we have explored clustering coefficient as well as degree of distribution.

  12. One Shot Detection with Laplacian Object and Fast Matrix Cosine Similarity.

    Biswas, Sujoy Kumar; Milanfar, Peyman

    2016-03-01

    One shot, generic object detection involves searching for a single query object in a larger target image. Relevant approaches have benefited from features that typically model the local similarity patterns. In this paper, we combine local similarity (encoded by local descriptors) with a global context (i.e., a graph structure) of pairwise affinities among the local descriptors, embedding the query descriptors into a low dimensional but discriminatory subspace. Unlike principal components that preserve global structure of feature space, we actually seek a linear approximation to the Laplacian eigenmap that permits us a locality preserving embedding of high dimensional region descriptors. Our second contribution is an accelerated but exact computation of matrix cosine similarity as the decision rule for detection, obviating the computationally expensive sliding window search. We leverage the power of Fourier transform combined with integral image to achieve superior runtime efficiency that allows us to test multiple hypotheses (for pose estimation) within a reasonably short time. Our approach to one shot detection is training-free, and experiments on the standard data sets confirm the efficacy of our model. Besides, low computation cost of the proposed (codebook-free) object detector facilitates rather straightforward query detection in large data sets including movie videos. PMID:27046497

  13. Similarity matrix analysis and divergence measures for statistical detection of unknown deterministic signals hidden in additive noise

    This Letter proposes an algorithm to detect an unknown deterministic signal hidden in additive white Gaussian noise. The detector is based on recurrence analysis. It compares the distribution of the similarity matrix coefficients of the measured signal with an analytic expression of the distribution expected in the noise-only case. This comparison is achieved using divergence measures. Performance analysis based on the receiver operating characteristics shows that the proposed detector outperforms the energy detector, giving a probability of detection 10% to 50% higher, and has a similar performance to that of a sub-optimal filter detector. - Highlights: • We model the distribution of the similarity matrix coefficients of a Gaussian noise. • We use divergence measures for goodness-of-fit test between a model and measured data. • We distinguish deterministic signal and Gaussian noise with similarity matrix analysis. • Similarity matrix analysis outperforms energy detector

  14. Similarity matrix analysis and divergence measures for statistical detection of unknown deterministic signals hidden in additive noise

    Le Bot, O., E-mail: lebotol@gmail.com [Univ. Grenoble Alpes, GIPSA-Lab, F-38000 Grenoble (France); CNRS, GIPSA-Lab, F-38000 Grenoble (France); Mars, J.I. [Univ. Grenoble Alpes, GIPSA-Lab, F-38000 Grenoble (France); CNRS, GIPSA-Lab, F-38000 Grenoble (France); Gervaise, C. [Univ. Grenoble Alpes, GIPSA-Lab, F-38000 Grenoble (France); CNRS, GIPSA-Lab, F-38000 Grenoble (France); Chaire CHORUS, Foundation of Grenoble Institute of Technology, 46 Avenue Félix Viallet, 38031 Grenoble Cedex 1 (France)

    2015-10-23

    This Letter proposes an algorithm to detect an unknown deterministic signal hidden in additive white Gaussian noise. The detector is based on recurrence analysis. It compares the distribution of the similarity matrix coefficients of the measured signal with an analytic expression of the distribution expected in the noise-only case. This comparison is achieved using divergence measures. Performance analysis based on the receiver operating characteristics shows that the proposed detector outperforms the energy detector, giving a probability of detection 10% to 50% higher, and has a similar performance to that of a sub-optimal filter detector. - Highlights: • We model the distribution of the similarity matrix coefficients of a Gaussian noise. • We use divergence measures for goodness-of-fit test between a model and measured data. • We distinguish deterministic signal and Gaussian noise with similarity matrix analysis. • Similarity matrix analysis outperforms energy detector.

  15. Mechanical Properties of Tannic-acid-treated Dentin Matrix

    Bedran-Russo, A.K.B.; Yoo, K.J.; Ema, K.C.; Pashley, D.H.

    2009-01-01

    Dentin collagen is a major component of the hybrid layer, and its stability may have a great impact on the properties of adhesive interfaces. We tested the hypothesis that the use of tannic acid (TA), a collagen cross-linking agent, may affect the mechanical properties and stability of the dentin matrix. The present study evaluated the effects of different concentrations of TA on the modulus of elasticity and enzymatic degradation of dentin matrix. Hence, the effect of TA pre-treatment on res...

  16. Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage.

    John Lightfield

    Full Text Available The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both gram negative and gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by AT-rich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant of the codon and amino acid usage patterns observed in bacterial genomes. These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome.

  17. GLYCOLIC-FORMIC ACID FLOWSHEET SLUDGE MATRIX STUDY

    Lambert, D.; Koopman, D.

    2011-06-30

    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

  18. Anacardic Acid Inhibits the Catalytic Activity of Matrix Metalloproteinase-2 and Matrix Metalloproteinase-9

    Omanakuttan, Athira; Nambiar, Jyotsna; Harris, Rodney M.; Bose, Chinchu; Pandurangan, Nanjan; Varghese, Rebu K.; Kumar, Geetha B.; Tainer, John A; Banerji, Asoke; Perry, J. Jefferson P.; Nair, Bipin G

    2012-01-01

    Cashew nut shell liquid (CNSL) has been used in traditional medicine for the treatment of a wide variety of pathophysiological conditions. To further define the mechanism of CNSL action, we investigated the effect of cashew nut shell extract (CNSE) on two matrix metalloproteinases, MMP-2/gelatinase A and MMP-9/gelatinase B, which are known to have critical roles in several disease states. We observed that the major constituent of CNSE, anacardic acid, markedly inhibited the gelatinase activit...

  19. Thermoluminescence and the origin of the dark matrix of Fayetteville and similar meteorites

    Haq, M.; Hasan, F. A.; Sears, D. W. G.; Moore, C. B.; Lewis, C. F.

    1989-06-01

    The paper presents measurements of the induced thermoluminescence properties and carbon contents of the dark matrix and light clasts of six regolith breccias. For all of the meteorites, the dark matrix has a lower mean thermoluminescence sensitivity than the light clasts; the extent of the difference depends on the meteorite. The data suggest the formation of the dark matrix by comminution of the light clasts with the addition of a component, perhaps CM-like chondrites, with thermoluminescence properties distinct from those of ordinary chondrites.

  20. Hyaluronic acid changes of the extracellular matrix in colon carcinoma

    Arab MR.

    2007-10-01

    Full Text Available Background: The extracellular matrix is a complex three-dimensional network of proteins and glycosaminoglycans, which have important roles in cellular physiology and cell-cell and cell-extracellular matrix interactions. Any changes in the extracellular matrix of tumors may be implicated in cellular transformation and metastasis. The aim of the present study was to identify changes in the hyaluronic acid of the stroma of colonic carcinoma.Methods: Paraffin blocks of 30 patients with colon carcinoma (10 patients at each histological grade were chosen from the pathology file of Khatam-Al-Anbia Hospital in Zahedan, Iran. Tissue sections (5-6 micrometers thick were stained with hematoxylin-eosin and the alcian blue critical electrolyte concentration histochemical technique at pH=5.8. The intensity of the staining in each section was graded as 1, 2 or 3, referring to low, moderate or severe staining reactivities, respectively. Statistical data was analyzed with nonparametric tests by SPSS (ver. 10 and histopathological reports were prepared.Results: The results of this study showed that there is a good correlation between histopathological grading and staining intensity of tumoral stroma for hyaluronic acid (p<0.005. Analysis using the Mann Whitney test revealed significant differences between staining grades 1 and 3 and grades 2 and 3 (p<0.005 and p<0.002, respectively, although there was no significant difference between staining grades 1 and 2 for hyaluronic acid.Conclusions: The difference in staining intensity of the stroma in colon carcinoma is a result of different amounts of hyaluronic acid in stroma, indicating that increased levels of hyaluronic acid are associated with the invasion and metastasis of neoplastic cells.

  1. Anacardic acid inhibits the catalytic activity of matrix metalloproteinase-2 and matrix metalloproteinase-9.

    Omanakuttan, Athira; Nambiar, Jyotsna; Harris, Rodney M; Bose, Chinchu; Pandurangan, Nanjan; Varghese, Rebu K; Kumar, Geetha B; Tainer, John A; Banerji, Asoke; Perry, J Jefferson P; Nair, Bipin G

    2012-10-01

    Cashew nut shell liquid (CNSL) has been used in traditional medicine for the treatment of a wide variety of pathophysiological conditions. To further define the mechanism of CNSL action, we investigated the effect of cashew nut shell extract (CNSE) on two matrix metalloproteinases, MMP-2/gelatinase A and MMP-9/gelatinase B, which are known to have critical roles in several disease states. We observed that the major constituent of CNSE, anacardic acid, markedly inhibited the gelatinase activity of 3T3-L1 cells. Our gelatin zymography studies on these two secreted gelatinases, present in the conditioned media from 3T3-L1 cells, established that anacardic acid directly inhibited the catalytic activities of both MMP-2 and MMP-9. Our docking studies suggested that anacardic acid binds into the MMP-2/9 active site, with the carboxylate group of anacardic acid chelating the catalytic zinc ion and forming a hydrogen bond to a key catalytic glutamate side chain and the C15 aliphatic group being accommodated within the relatively large S1' pocket of these gelatinases. In agreement with the docking results, our fluorescence-based studies on the recombinant MMP-2 catalytic core domain demonstrated that anacardic acid directly inhibits substrate peptide cleavage in a dose-dependent manner, with an IC₅₀ of 11.11 μM. In addition, our gelatinase zymography and fluorescence data confirmed that the cardol-cardanol mixture, salicylic acid, and aspirin, all of which lack key functional groups present in anacardic acid, are much weaker MMP-2/MMP-9 inhibitors. Our results provide the first evidence for inhibition of gelatinase catalytic activity by anacardic acid, providing a novel template for drug discovery and a molecular mechanism potentially involved in CNSL therapeutic action. PMID:22745359

  2. Matrix models with Penner interaction inspired by interacting ribonucleic acid

    Pradeep Bhadola; N Deo

    2015-02-01

    The Penner interaction known in studies of moduli space of punctured Riemann surfaces is introduced and studied in the context of random matrix model of homo RNA. An analytic derivation of the generating function is given and the corresponding partition function is derived numerically. 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 information for these RNA structures is computationally extracted. Then the genus is calculated for every structure and plotted as a function of length. The genus distribution function is compared with the prediction from the nonlinear (NL) model. The specific heat and distribution of structure with temperature calculated from the NL model shows that the NL inter-action is biased towards planar structures. The second derivative of specific heat changes phase from a double peaked function for small to a single peak for large . Detailed analysis reveals the presence of the double peak only for genus 0 structures, the higher genii behave normally with . Comparable behaviour is found in studies involving interactions of RNA with osmolytes and monovalent cations in unfolding experiments.

  3. Stabilization of amorphous calcium carbonate by phosphate rich organic matrix proteins and by single phosphoamino acids.

    Bentov, Shmuel; Weil, Simy; Glazer, Lilah; Sagi, Amir; Berman, Amir

    2010-08-01

    Stable amorphous calcium carbonate (ACC) is a unique material produced naturally exclusively as a biomineral. It was demonstrated that proteins extracted from biogenic stable ACC induce and stabilize synthetic ACC in vitro. Polyphosphate molecules were similarly shown to induce amorphous calcium carbonate formation in vitro. Accordingly, we tested the hypothesis that biogenic ACC induction and stabilization is mediated by the phosphorylated residues of phosphoproteins. We show that extracellular organic matrix extracted from gastroliths of the red claw crayfish Cherax quadricarinatus induce stable ACC formation in vitro. The proteinaceous fraction of this organic matrix is highly phosphorylated and is incorporated into the ACC mineral phase during precipitation. We have identified the major phosphoproteins of the organic matrix and showed that they have high calcium binding capacity. Based on the above, in vitro precipitation experiments with single phosphoamino acids were performed, indicating that phosphoserine or phosphothreonine alone can induce the formation of highly stable ACC. The results indicate that phosphoproteins may play a major role in the control of ACC formation and stabilization and that their phosphoamino acid moieties are key components in this process. PMID:20416381

  4. 5-Methoxysalicylic Acid Matrix for Ganglioside Analysis with Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

    Lee, Dongkun; Cha, Sangwon

    2015-03-01

    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.

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

    Kjellström, Sven; Jensen, Ole Nørregaard

    2004-01-01

    ,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....

  6. The Influence of Matrix Size on Statistical Properties of Co-Occurrence and Limiting Similarity Null Models.

    Lavender, Thomas Michael; Schamp, Brandon S; Lamb, Eric G

    2016-01-01

    Null models exploring species co-occurrence and trait-based limiting similarity are increasingly used to explore the influence of competition on community assembly; however, assessments of common models have not thoroughly explored the influence of variation in matrix size on error rates, in spite of the fact that studies have explored community matrices that vary considerably in size. To determine how smaller matrices, which are of greatest concern, perform statistically, we generated biologically realistic presence-absence matrices ranging in size from 3-50 species and sites, as well as associated trait matrices. We examined co-occurrence tests using the C-Score statistic and independent swap algorithm. For trait-based limiting similarity null models, we used the mean nearest neighbour trait distance (NN) and the standard deviation of nearest neighbour distances (SDNN) as test statistics, and considered two common randomization algorithms: abundance independent trait shuffling (AITS), and abundance weighted trait shuffling (AWTS). Matrices as small as three × three resulted in acceptable type I error rates (p ) was associated with increased type I error rates, particularly for matrices with fewer than eight species. Type I error rates increased for limiting similarity tests using the AWTS randomization scheme when community matrices contained more than 35 sites; a similar randomization used in null models of phylogenetic dispersion has previously been viewed as robust. Notwithstanding other potential deficiencies related to the use of small matrices to represent communities, the application of both classes of null model should be restricted to matrices with 10 or more species to avoid the possibility of type II errors. Additionally, researchers should restrict the use of the AWTS randomization to matrices with fewer than 35 sites to avoid type I errors when testing for trait-based limiting similarity. The AITS randomization scheme performed better in terms of

  7. Development of gliclazide matrix tablets from pure and blended mixture of glyceryl monostearate and stearic acid

    Hussain, Talib; Saeed, Tariq; Mumtaz, Ahmed M.; Jamshaid, Muhammad; Aamir, Muhammad N.; Abbas, Khizar; Javaid, Zeshan; Awais, Azeema

    2011-01-01

    The present study was undertaken to evaluate the effect of glyceryl monostearate (GMS) and stearic acid (SA) on the release profile of gliclazide from the matrix. Matrix tablets for the controlled delivery of gliclazide were prepared by hot melt method using pure and blended mixture of glyceryl monostearate and stearic acid in different drug to polymer and polymer to polymer ratios. In vitro release characteristics of gliclazide from these hydrophobic matrices were studied over 8 h in phospha...

  8. Amino Acids Analysis by MALDI Mass Spectrometry Using Carbon Nanotube as Matrix

    张菁; 王昊阳; 郭寅龙

    2005-01-01

    Twenty common amino acids have been analyzed successfully by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) using carbon nanotubes as matrix. From the spectra, little or no background interference or fragmentation of the analytes has been observed. This method was also applied to the analysis of amino acid mixture successfully. Carbon nanotubes have some features such as large surface area to disperse the analyte molecules sufficiently and prevent the sample aggregation and strong ultraviolet absorption to transfer energy easily to the analyte molecules. The present method has potential application for the rapid and sensitive analysis of amino acids and their mixture.

  9. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities.

    Henrissat, B; Bairoch, A

    1993-01-01

    301 glycosyl hydrolases and related enzymes corresponding to 39 EC entries of the I.U.B. classification system have been classified into 35 families on the basis of amino-acid-sequence similarities [Henrissat (1991) Biochem. J. 280, 309-316]. Approximately half of the families were found to be monospecific (containing only one EC number), whereas the other half were found to be polyspecific (containing at least two EC numbers). A > 60% increase in sequence data for glycosyl hydrolases (181 additional enzymes or enzyme domains sequences have since become available) allowed us to update the classification not only by the addition of more members to already identified families, but also by the finding of ten new families. On the basis of a comparison of 482 sequences corresponding to 52 EC entries, 45 families, out of which 22 are polyspecific, can now be defined. This classification has been implemented in the SWISS-PROT protein sequence data bank. PMID:8352747

  10. Influence of Organic Acids on Diltiazem HCl Release Kinetics from Hydroxypropyl Methyl Cellulose Matrix Tablets.

    Sateesha, Sb; Rajamma, Aj; Narode, Mk; Vyas, Bd

    2010-07-01

    The matrix tablets of diltiazem hydrochloride were prepared by direct compression using hydroxypropyl methyl cellulose (HPMC) and various amounts (2.5%, 5.0%, 10% and 20%) of citric acid, malic acid and succinic acid. The characterization of physical mixture of drug and organic acids was performed by Infra-red spectroscopy. An organic acid was incorporated to set up a system bringing about gradual release of this drug. The influence of organic acids on the release rate were described by the Peppas equation: M (t) /M(∞) = Kt (n) and Higuchi's equation: Q (t) = K(1)t(1/2). The addition of organic acids and the pH value of medium could notably influence the dissolution behavior and mechanism of drug-release from matrices. Increasing amounts of organic acid produced an increase in drug release rate, which showed a good linear relationship between contents of organic acid and drug accumulate release (%) in phosphate buffer, pH 7.4. The drug release increased significantly (P < 0.05) with use of succinic acid in tablet formulation. Increasing amounts of succinic acid above 10% produced decreasing values of n and increasing values of k, in a linear relationship, which indicated there was a burst release of drug from the matrix. Optimized formulations are found to be stable upon 3-month study. PMID:21042476

  11. Bovine lactoferrin binds oleic acid to form an anti-tumor complex similar to HAMLET.

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

    2014-04-01

    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. PMID:24368211

  12. Design of Cell-Matrix Interactions in Hyaluronic Acid Hydrogel Scaffolds

    Lam, Jonathan; Truong, Norman F.; Segura, Tatiana

    2013-01-01

    The design of hyaluronic acid-based hydrogel scaffolds to elicit highly controlled and tunable cell response and behavior is a major field of interest in developing tissue engineering and regenerative medicine applications. This review will begin with an overview of the biological context of hyaluronic acid, knowledge needed to better understand how to engineer cell-matrix interactions in the scaffolds via the incorporation of different types of signals in order to direct and control cell beh...

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

    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)

  14. Fluorescence Excitation-Emission Matrix Characterization of a Commercial Humic Acid

    傅平青; 吴丰昌; 刘丛强

    2004-01-01

    Excitation-emission matrix fluorescence spectroscopy (EEM) has been widely used to elucidate the origin and structure of humic substances in natural environments. Due to its high sensitivity, good selectivity and non-destructive advantage, the EEM was applied to characterizing a commercial Fluka humic acid (FHA). The results showed that the EEMs of FHA has several Ex/Em peaks. Ionic strength (0-0.05 mol/L KClO-4) exerted little effect on the fluorescence properties of FHA, while the concentrations (5-100 mg/L) of FHA and pH (2-12) had significant effects. A red shift in the longer wavelength peak region was observed when the concentrations or pH values increased. The fluorescence intensity increased with increasing pH, but slightly decreased in the case of pH=5.0. The protonation constants (lgK'-HL) of peak B were calculated to be 3.57 and 3.13, indicating that peak B was due to carboxyl groups. The r-(A/B) values range from 0.61 to 2.59. A strong linear relationship between r-(A/B) and pH was also observed. This indicates that the fluorescence peaks A and B posses similar inherent fluorescence characteristics.

  15. Matrix solid-phase dispersion for the liquid chromatographic determination of phenolic acids in Melissa officinalis.

    Ziaková, Alica; Brandsteterová, Eva; Blahová, Eva

    2003-01-01

    Matrix solid-phase dispersion (MSPD) was used for sample preparation of plant material (Melissa officinalis, Lemon Balm) prior to liquid chromatography of rosmarinic, caffeic and protocatechuic acids, phenolic compounds present in this herb. Different MSPD sorbents and various elution agents were tested and the optimal extraction conditions determined with the aim to obtain extraction recoveries greater than 90% for all analytes. PMID:12568390

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

    Mann Matthias

    2010-02-01

    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

  17. Correction of tear trough deformity with a cohesive polydensified matrix hyaluronic acid: a case series

    Huber-Vorländer J; Kürten M

    2015-01-01

    Jürgen Huber-Vorländer, Martin KürtenFort Malakoff Klinik, Mainz, GermanyAbstract: The tear trough or infraorbital hollow is a challenging area to treat, and only a few fillers are suitable for this delicate area. We report on a European case series of six subjects with mild to severe tear troughs who received treatment with cohesive polydensified matrix (CPM®) technology hyaluronic acid gel (Belotero® Balance). The product was injected as small depo...

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

    Yanhua Cui

    2015-06-01

    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.

  19. Ascorbic acid glycation of lens proteins produces UVA sensitizers similar to those in human lens

    Soluble calf lens proteins were extensively glycated during a 4 week incubation with ascorbic acid in the presence of oxygen. Amino acids analysis of the dialyzed proteins removed at weekly intervals showed an increasing loss of lysine, arginine and histidine, consistent with the extensive protein cross-linking observed. Irradiation of the dialyzed samples with UVA light (1.0 kJ/cm2 total illumination through a 338 nm cutoff filter) caused an increasing loss of tryptophan, an additional loss of histidine and the production of micromolar concentrations of hydrogen peroxide. No alteration in amino acid content and no photolytic effects were seen in proteins incubated without ascorbic acid in proteins incubated with glucose for 4 weeks. The rate of hydrogen peroxide formation was linear with each glycated sample with a maximum production of 25 nmol/mg protein illuminated. The possibility that the sensitizer activity was due to an ascorbate-induced oxidation of tryptophan was eliminated by the presence of a heavy metal ion chelator during the incubation and by showing equivalent effects with ascorbate-incubated ribonuclease A, which is devoid of tryptophan. The ascorbate-incubated samples displayed increasing absorbance at wavelengths above 300 nm and increasing fluorescence (340/430) as glycation proceeded. The spectra of the 4 week glycated proteins were identical to those obtained with a solubilized water-insoluble fraction from human lens, which is known to have UVA sensitizer activity. (Author)

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

    Ehsan Salimi

    2011-05-01

    Full Text Available 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 groups. In this study, electrical shock generated in a communication box was used as physical shock and the emotional stress was as psychological stress.Gastric juice was collected by washout technique. Acid output was also measured by digital titrator. Gastric pepsin and nitric oxide (NO metabolites were quantified using Anson and Griess micro assay methods respectively.Basal and stimulated gastric acid and pepsin in physical and psychological stress groups were significantly more than others. NO metabolites level of gastric tissue in physical and psychological stress groups (286.9 ± 5.8, 287.7 ± 5.7 μmol/gr weight wet tissue, respectively were significantly more than other groups. But no significant differences among basal and stimulated gastric acid, pepsin and NO metabolites level were seen in physical and psychological stress groups.

  1. Correction of tear trough deformity with a cohesive polydensified matrix hyaluronic acid: a case series

    Huber-Vorländer J

    2015-06-01

    Full Text Available Jürgen Huber-Vorländer, Martin KürtenFort Malakoff Klinik, Mainz, GermanyAbstract: The tear trough or infraorbital hollow is a challenging area to treat, and only a few fillers are suitable for this delicate area. We report on a European case series of six subjects with mild to severe tear troughs who received treatment with cohesive polydensified matrix (CPM® technology hyaluronic acid gel (Belotero® Balance. The product was injected as small depots (up to ten small boli 0.2 mL maximum each per side at the supraperiosteal level along or below the orbital rim. Follow-up visits took place at 1, 3, 6, and 9 months after injection for independent evaluation of the clinical effect using the Merz Aesthetics Scale™ for infraorbital hollows and the Global Aesthetic Improvement Scale. Adverse events were also recorded. Mean hollowness scores were considerably improved compared with baseline in all subjects. In all women, the improvements remained throughout the 9-month study, with none reverting to their baseline score. Subjects’ satisfaction with treatment was very high throughout the study, and all women stated that they would repeat treatment with the same product. The CPM hyaluronic acid gel was well tolerated. CPM hyaluronic acid gel is a safe and effective treatment for the tear trough area.Keywords: Belotero® Balance, cohesive polydensified matrix (CPM®, hyaluronic acid, infraorbital hollow, tear trough

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

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

    1995-12-31

    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.

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

    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−1, with the minimum detection limit of 1.73–1.79 ng mL−1 (S/N = 3) in aqueous and real samples. Almost similar stringent limit (1.79 ng mL−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

  4. Arsenic speciation and identification of monomethylarsonous acid and monomethylthioarsonic acid in a complex matrix.

    Yathavakilla, Santha Ketavarapu V; Fricke, Michael; Creed, Patricia A; Heitkemper, Douglas T; Shockey, Nohora V; Schwegel, Carol; Caruso, Joseph A; Creed, John T

    2008-02-01

    Anion-exchange chromatography was utilized for speciation of arsenite (As(III)), arsenate (As(V)), dimethylarsinic acid (DMA(V)), monomethylarsonic acid (MMA(V)), monomethylarsonous acid (MMA(III)), and the new As species monomethylthioarsonic acid (MMTA), using inductively coupled plasma mass spectrometric (ICPMS) detection. MMA(III) and MMTA were identified for the first time in freeze-dried carrot samples that were collected over 25 years ago as part of a joint U.S. EPA, U.S. FDA, and USDA study on trace elements in agricultural crops. The discovery of MMA(III) and MMTA in terrestrial foods necessitated the analytical characterization of synthetic standards of both species, which were used for standard addition in carrot extracts. The negative ion mode, high-resolution electrospray mass spectrometry (HR-ESI-MS) data produced molecular ions of m/z 122.9418 and 154.9152 for MMA(III) and MMTA, respectively. However, ESI-MS was not sensitive enough to directly identify MMA(III) and MMTA in the carrot extracts. Therefore, to further substantiate the identification of MMA(III) and MMTA, two additional separations using an Ion-120 column were developed using the more sensitive ICPMS detection. The first separation used 20 mM tetramethylammonium hydroxide at pH 12.2 with MMA(III) eluting in less than 7 min. In the second separation, MMTA eluted at 11.2 min by utilizing 40 mM ammonium carbonate at pH 9.0. Oxidation of MMA(III) and MMTA to MMA(V) with hydrogen peroxide was observed for standards and carrot extracts alike. Several samples of carrots collected from local markets in 2006 were also analyzed and found to contain low levels of inorganic arsenic species. PMID:18181583

  5. Mechanism of drug release from poly(L-lactic acid) matrix containing acidic or neutral drugs.

    Miyajima, M; Koshika, A; Okada, J; Ikeda, M

    1999-08-01

    The release profiles of acidic and neutral drugs from poly(L-lactic acid) [P(L)LA] matrices were investigated to reveal their release mechanism. Cylindrical matrices (rods; 10 mmx1 mm diameter) were prepared by the heat compression method. The acidic and neutral drugs investigated were dissolved in the P(L)LA rods. It was found that the release profiles consisted of two sequential stages. At the first release stage, P(L)LA remained in an amorphous state and the drugs diffused through the hydrated matrices. At the second release stage, P(L)LA transformed to a semicrystalline state and the drugs diffused through water-filled micropores developed by polymer crystallization. In addition, the drugs were also found to precipitate out as crystals in the rods, resulting in a transformation of the rods into drug-dispersed matrices. On the basis of these findings, we derived a modified diffusion equation for the drug release at the second stage. This equation showed good fits to the release profiles of these drugs. Furthermore, the availability of the derived equation was supported by the acceleration in the fractional drug release rate noted both with decreases in the drug content in the rod and increases in the pH of the medium. PMID:10425326

  6. Efficiency of Gas-Phase Ion Formation in Matrix-Assisted Laser Desorption Ionization with 2,5-Dihydroxybenzoic Acid as Matrix

    Numbers of matrix- and analyte-derived ions and their sum in matrix-assisted laser desorption ionization (MALDI) of a peptide were measured using 2,5-dihydroxybenzoic acid (DHB) as matrix. As for MALDI with α-cyano-4-hydroxy cinnamic acid as matrix, the sum was independent of the peptide concentration in the solid sample, or was the same as that of pure DHB. This suggested that the matrix ion was the primary ion and that the peptide ion was generated by matrix-to-peptide proton transfer. Experimental ionization efficiencies of 10-5-10-4 for peptides and 10-8-10-7 for matrices are far smaller than 10.3-10.1 for peptides and 10-5-10-3 for matrices speculated by Hillenkamp and Karas. Number of gas-phase ions generated by MALDI was unaffected by laser wavelength or pulse energy. This suggests that the main role of photo-absorption in MALDI is not in generating ions via a multi-photon process but in ablating materials in a solid sample to the gas phase

  7. Structure and expression of an unusually acidic matrix protein of pearl oyster shells

    We report identification and characterization of the unusually acidic molluscan shell matrix protein Aspein, which may have important roles in calcium carbonate biomineralization. The Aspein gene (aspein) encodes a sequence of 413 amino acids, including a high proportion of Asp (60.4%), Gly (16.0%), and Ser (13.2%), and the predicted isoelectric point is 1.45; this is the most acidic of all the molluscan shell matrix proteins sequenced so far, or probably even of all known proteins on earth. The main body of Aspein is occupied by (Asp)2-10 sequences punctuated with Ser-Gly dipeptides. RT-PCR demonstrated that the transcript of aspein is expressed at the outer edge of the mantle, corresponding to the calcitic prismatic layer, but not at the inner part of the mantle, corresponding to the aragonitic nacreous layer. Our findings and previous in vitro experiments taken together suggest that Aspein is responsible for directed formation of calcite in the shell of the pearl oyster Pinctada fucata

  8. 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

    Zhenya Gao; Lijun Huo; Dongmei Cui; Xiao Yang; Junwen Zeng

    2016-01-01

    Purpose 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 cu...

  9. Inhibition of matrix metalloproteinases expression in human dental pulp cells by all-trans retinoic acid

    Kim, Jin Man; Kang, Sang Wook; Shin, Su-Mi; Su Kim, Duck; Choi, Kyong-Kyu; Kim, Eun-Cheol; Kim, Sun-Young

    2013-01-01

    All-trans retinoic acid (ATRA) inhibits matrix metalloproteinase (MMP)-2 and MMP-9 in synovial fibroblasts, skin fibroblasts, bronchoalveolar lavage cells and cancer cells, but activates MMP-9 in neuroblast and leukemia cells. Very little is known regarding whether ATRA can activate or inhibit MMPs in human dental pulp cells (HDPCs). The purpose of this study was to determine the effects of ATRA on the production and secretion of MMP-2 and -9 in HDPCs. The productions and messenger RNA (mRNA)...

  10. CPAG: software for leveraging pleiotropy in GWAS to reveal similarity between human traits links plasma fatty acids and intestinal inflammation.

    Wang, Liuyang; Oehlers, Stefan H; Espenschied, Scott T; Rawls, John F; Tobin, David M; Ko, Dennis C

    2015-01-01

    Meta-analyses of genome-wide association studies (GWAS) have demonstrated that the same genetic variants can be associated with multiple diseases and other complex traits. We present software called CPAG (Cross-Phenotype Analysis of GWAS) to look for similarities between 700 traits, build trees with informative clusters, and highlight underlying pathways. Clusters are consistent with pre-defined groups and literature-based validation but also reveal novel connections. We report similarity between plasma palmitoleic acid and Crohn's disease and find that specific fatty acids exacerbate enterocolitis in zebrafish. CPAG will become increasingly powerful as more genetic variants are uncovered, leading to a deeper understanding of complex traits. CPAG is freely available at www.sourceforge.net/projects/CPAG/. PMID:26374098

  11. Experimental study of foam flow through Berea Sandstone with applications to foam diversion in matrix acidizing

    Parlar, M.; Parris, M.D.; Jasinski, R.J.; Robert, J.A.

    1995-12-31

    The results of a series of dual (diversion) and single core foam experiments followed by liquid injection in unfired Berea sandstone cores are reported at high rates relevant to matrix acidizing. The sensitivity of the results to surfactant type and concentration, foam and post-foam liquid injection rates, permeability, temperature and presence of oil are discussed. Surfactant type, preflush and foam slug sites are identified as critical parameters for subsequent liquid diversion into low-permeability regions. In contrast to EOR processes, surfactant adsorption is shown to be beneficial for diversion. At low liquid rates and high foam qualities relevant to EOR, foam at steady-state is found to behave as a Newtonian fluid with respect to liquid rate provided that the gas rate is above a critical rate. At high liquid rates and low qualities a shear-thinning behavior is observed. Pressure gradient during post-foam liquid injection is found to be independent of both foam and subsequent liquid rates, and to depend only on permeability for fixed surfactant chemistry. The entrance effects noted in foam literature are found to be more pronounced at high permeabilities and intermediate injection rates. Potential mechanisms as to why foam diversion in matrix acidizing works in the field are also discussed.

  12. Function of all-trans retinoic acid observation on similar myopia changes in cultivated rabbit retinal pigment epithelium and relation with myopia relevant factors.

    Xing, Bin

    2016-03-01

    To observe the role of all-trans retinoic acid (ATRA) during the similar myopia changes of cultured rabbit retinal pigment epithelium (RPE) cells, as well as the variation changes and relationships with myopic correlation factors such as hepatocyte growth factor (HGF) and matrix metalloprateinase-2 (MMP-2). Rabbit RPE cells of primary generation were selected and cultured to fifth generation by subculture. Then the morphology of RPE cells were observed and cell vitality was analyzed by using the Trypan blue reject test. The expressions of HGF and MMP-2 in RPE cells were tested by using an immunobistochemistry method. The HGF concentration in RPE cell culture fluid was detected by applying enzyme-linked immunosorbnent assay (ELISA). As the ATRA concentration enhanced and action time prolonged, the survival rate of RPE cells was reduced, but the expressions of HGF and MMP-2 increased, so did the secretion of HGF. ATRA concentration with no less than 5nM/ml was able to induce the growth inhibition of RPE cells and the decrease in survival rate, which was similar to the changes in RPE cells in myopia. With the actin of ATRA, the expressions of HGF and MMP-2 increased in RPE cells, with more distinct in HGF increase. PMID:27113312

  13. Correction of Tear Trough Deformity With a Cohesive Polydensified Matrix Hyaluronic Acid: A Case Series.

    Huber-Vorländer, Jürgen; Kürten, Martin

    2015-01-01

    The tear trough or infraorbital hollow is a challenging area to treat, and only a few fillers are suitable for this delicate area. We report on a European case series of six subjects with mild to severe tear troughs who received treatment with cohesive polydensified matrix (CPM®) technology hyaluronic acid gel (Belotero® Balance). The product was injected as small depots (up to ten small boli 0.2 mL maximum each per side) at the supraperiosteal level along or below the orbital rim. Follow-up visits took place at 1, 3, 6, and 9 months after injection for independent evaluation of the clinical effect using the Merz Aesthetics Scale™ for infraorbital hollows and the Global Aesthetic Improvement Scale. Adverse events were also recorded. Mean hollowness scores were considerably improved compared with baseline in all subjects. In all women, the improvements remained throughout the 9-month study, with none reverting to their baseline score. Subjects' satisfaction with treatment was very high throughout the study, and all women stated that they would repeat treatment with the same product. The CPM hyaluronic acid gel was well tolerated. CPM hyaluronic acid gel is a safe and effective treatment for the tear trough area. PMID:26605822

  14. Lactic acid bacteria in dairy food: surface characterization and interactions with food matrix components.

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

    2014-11-01

    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. PMID:25277266

  15. The shell matrix of the freshwater mussel Unio pictorum (Paleoheterodonta, Unionoida). Involvement of acidic polysaccharides from glycoproteins in nacre mineralization.

    Marie, Benjamin; Luquet, Gilles; Pais De Barros, Jean-Paul; Guichard, Nathalie; Morel, Sylvain; Alcaraz, Gérard; Bollache, Loïc; Marin, Frédéric

    2007-06-01

    Among molluscs, the shell biomineralization process is controlled by a set of extracellular macromolecular components secreted by the calcifying mantle. In spite of several studies, these components are mainly known in bivalves from only few members of pteriomorph groups. In the present case, we investigated the biochemical properties of the aragonitic shell of the freshwater bivalve Unio pictorum (Paleoheterodonta, Unionoida). Analysis of the amino acid composition reveals a high amount of glycine, aspartate and alanine in the acid-soluble extract, whereas the acid-insoluble one is rich in alanine and glycine. Monosaccharidic analysis indicates that the insoluble matrix comprises a high amount of glucosamine. Furthermore, a high ratio of the carbohydrates of the soluble matrix is sulfated. Electrophoretic analysis of the acid-soluble matrix revealed discrete bands. Stains-All, Alcian Blue, periodic acid/Schiff and autoradiography with (45)Ca after electrophoretic separation revealed three major polyanionic calcium-binding glycoproteins, which exhibit an apparent molecular mass of 95, 50 and 29 kDa, respectively. Two-dimensional gel electrophoresis shows that these bands, provisionally named P95, P50 and P29, are composed of numerous isoforms, the majority of which have acidic isoelectric points. Chemical deglycosylation of the matrix with trifluoromethanesulfonic acid induces a drastic shift of both the apparent molecular mass and the isoelectric point of these matrix components. This treatment induces also a modification of the shape of CaCO(3) crystals grown in vitro and a loss of the calcium-binding ability of two of the main matrix proteins (P95 and P50). Our findings strongly suggest that post-translational modifications display important functions in mollusc shell calcification. PMID:17488282

  16. Patterns of some extracellular matrix gene expression are similar in cells from cleft lip-palate patients and in human palatal fibroblasts exposed to diazepam in culture

    Prenatal exposure to diazepam, a prototype sedative drug that belongs to Benzodiazepines, can lead to orofacial clefting in human newborns. By using real-time PCR, in the present study we investigated whether diazepam elicits gene expression alterations in extracellular matrix (ECM) components, growth factors and gamma-aminobutyric acid receptor (GABRB3), implicated in the coordinate regulation of palate development. Palate fibroblasts were treated with diazepam (Dz-N fibroblasts) and compared to cleft lip-palate (CLP) fibroblasts obtained from patients with no known exposure to diazepam or other teratogens. Untreated fibroblasts from non-CLP patients were used as control. The results showed significant convergences in gene expression pattern of collagens, fibromodulin, vitronectin, tenascin C, integrins and metalloprotease MMP13 between Dz-N and CLP fibroblasts. Among the growth factors, constitutive Fibroblast Growth Factor 2 (FGF2) was greatly enhanced in Dz-N and CLP fibroblasts and associated with a higher reduction of FGF receptor. Transforming Growth Factor beta 3 (TGFβ3) resulted up-regulated in CLP fibroblasts and decreased in Dz-N fibroblasts. We found phenotypic differences exhibited by Dz-N and CLP fibroblasts in GABRB3 gene regulation, so further studies are necessary to determine whether GABAergic system could be involved in the development of diazepam mediated CLP phenotype. Taken together the results elucidate the molecular mechanisms underlying possible toxicology effects induced by diazepam. Counselling of women on the safety of diazepam exposure is clinically important, also for the forensic consequences

  17. Oxidizing gel formulation for nuclear decontamination: rheological and acidic properties of the organic matrix and its ozonolysis

    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 1H 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)

  18. Supercritical fluid extraction of uranium from nitric acid medium and tissue paper matrix

    Supercritical fluid extraction (SFE) is a novel technique for metal ion extraction, which offers a promising alternate to the conventional extraction process. The technique has advantage of minimization of radioactive liquid waste. In the present study, supercritical CO2 containing small amount of TBP/TOPO as co-solvent were employed for uranium extraction. Uranium extraction efficiency of ∼ 98% was achievable from nitric acid medium employing TBP as co-solvent. However, uranium could be extracted to nearly same extent with lesser amount (1 ml) of TOPO. In SFE of uranium from tissue paper matrix extraction efficiency of 70% was obtained with TBP as co-solvent. Whereas nearly complete uranium extraction (∼99%) was achievable from tissue paper with TOPO as co-solvent. (author)

  19. Effect of citric acid and polymer blend on characteristics of ofloxacin floating matrix tablets by factorial design

    Bera, Hriday; Mandal, Bivash; Sinha, Chandrima; Dey, Sanjoy K.; Bera, Rammohan; Ghosh, Lakshmi K.

    2011-01-01

    The present investigation deals with the development of floating matrix tablet containing Ofloxacin, to prolong the gastric residence time, thereby effective in eradication of Helicobacter pylori from the gastric mucosa. A 32 factorial design was employed to formulate floating matrix tablet selecting polymer blend ratio [hydroxypropyl methylcellulose (HPMC) / sodium carboxymethylcellulose (SCMC)] and content of citric acid as independent variables. Time required for 50 % of drug release (t50 ...

  20. Science of Hyaluronic Acid Beyond Filling: Fibroblasts and Their Response to the Extracellular Matrix.

    Landau, Marina; Fagien, Steven

    2015-11-01

    Loss of viscoelasticity is one of the primarily signs of skin aging, followed by appearance of visible wrinkles. Hyaluronic acid (HA)-based fillers are widely used to fill wrinkles and compensate for volume loss. Recent clinical observations demonstrate persistence of the filling effect longer than the biological availability of the filler. Stimulation of new collagen by cross-linked HA and up-regulation of elastin have been suggested as possible explanation to this observation and have been supported experimentally. Cross-linked HA substitutes for fragmented collagen in restoring extracellular matrix required for normal activity of fibroblasts, such as collagen and elastin production. To restore extracellular matrix efficiently, serial monthly treatments are required. Boosting of facial and nonfacial skin through fibroblast activation is a new indication for HA-based products. Injectable HA has also been recently registered in Europe as agents specific for the improvement of skin quality (Restylane Skinboosters). Further explanation of the possible mechanisms supported by long-term clinical examples is presented herein. PMID:26441098

  1. Effects of Monocarboxylic Acid Addition on Crystallization of Calcium Phosphate in a Hydrogel Matrix

    In biomineralization, it is thought that water-soluble organic substances control crystal growth of minerals in hard tissues. The roles of organic substances are not well understood, because the biomineralization process is established by complicated parameters. Crystal growth in hydrogel matrixes can be regarded as simplified model system of biomineralization. In the present study, we investigated the effects of propionic acid (Pro) on crystalline phases and crystal morphologies of calcium phosphate formed in polymeric hydrogel matrixes as the model system of biomineralization. Crystalline phase of the precipitates was octacalcium phosphate (OCP) with spherical shape regardless of Pro concentrations. The fibrous crystals formed under the condition without addition of Pro. The crystal morphologies composing spherical crystals were changed from fibrous to plate-like shape with increasing Pro concentrations. Generally, OCP crystal has plate-like shape exposing (100) face, which calcium ions exist on. Therefore, crystal growth rate of [100] direction of OCP was decreased by Pro adsorbed on (100) face. As a result, crystal morphology composing spherulite became plate-like shape with increasing Pro concentrations.

  2. Similarities Across Mars: Acidic Fluids at Both Meridiani Planum and Gale Crater in the Formation of Magnesium-Nickel Sulfates

    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

    2016-01-01

    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.

  3. Rapid HPLC analysis of amino acids and biogenic amines in wines during fermentation and evaluation of matrix effect.

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

    2014-11-15

    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. PMID:24912689

  4. Hyaluronic acid based hydroxamate and conjugates with biologically active amines: In vitro effect on matrix metalloproteinase-2.

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

    2016-06-25

    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. PMID:27083788

  5. Similar peptides from two beta cell autoantigens, proinsulin and glutamic acid decarboxylase, stimulate T cells of individuals at risk for insulin-dependent diabetes.

    Rudy, G; N. Stone; Harrison, L C; Colman, P. G.; McNair, P; Brusic, V.; French, M. B.; Honeyman, M. C.; Tait, B.; Lew, A M

    1995-01-01

    BACKGROUND: Insulin (1) and glutamic acid decarboxylase (GAD) (2) are both autoantigens in insulin-dependent diabetes mellitus (IDDM), but no molecular mechanism has been proposed for their association. We have identified a 13 amino acid peptide of proinsulin (amino acids 24-36) that bears marked similarity to a peptide of GAD65 (amino acids 506-518) (G. Rudy, unpublished). In order to test the hypothesis that this region of similarity is implicated in the pathogenesis of IDDM, we assayed T c...

  6. Intra- and intermolecular hydrogen bonding in formohydroxamic acid complexes with water and ammonia: infrared matrix isolation and theoretical study

    SaIdyka, Magdalena [Faculty of Chemistry, University of WrocIaw, Joliot-Curie 14, 50-383 WrocIaw (Poland); Mielke, Zofia [Faculty of Chemistry, University of WrocIaw, Joliot-Curie 14, 50-383 WrocIaw (Poland)]. E-mail: zm@wchuwr.chem.uni.wroc.pl

    2005-01-10

    The complexes of formohydroxamic acid with water and ammonia have been studied using FTIR matrix isolation spectroscopy and MP2 calculations with a 6-311++G(2d,2p) basis set. The analysis of the experimental spectra of the HCONHOH/H{sub 2}O(NH{sub 3})/Ar matrixes indicates formation of strongly hydrogen-bonded complexes in which the NH group of formohydroxamic acid acts as a proton donor toward the oxygen atom of water or the nitrogen atom of ammonia. The NH stretching vibration of formohydroxamic acid exhibits 150 cm{sup -1} red shift in the complex with water and 443 cm{sup -1} red shift in the complex with ammonia as compared to the NH stretch of the HCONHOH monomer. The theoretical calculations indicate stability of five isomers for the water complex and three isomers for the ammonia complex. The most stable are the cyclic structures in which the water or ammonia molecules are inserted within the intramolecular hydrogen bond of the formohydroxamic acid molecule and act as proton donors for the CO group and proton acceptors for the OH group of the formohydroxamic acid molecule. In spite of their stability the cyclic structures have not been observed in the matrixes which indicates high energy barrier for their formation, the reaction of complex formation is under kinetic and not thermodynamic control.

  7. Extracellular matrix assembly in extreme acidic eukaryotic biofilms and their possible implications in heavy metal adsorption

    To evaluate the importance of the extracellular matrix in relation to heavy metal binding capacity in extreme acidic environments, the extracellular polymeric substances (EPS) composition of 12 biofilms isolated from Rio Tinto (SW, Spain) was analyzed. Each biofilm was composed mainly by one or two species of eukaryotes, although other microorganisms were present. EPS ranged from 130 to 439 mg g-1 biofilm dry weight, representing between 15% and the 40% of the total biofilm dry weight (DW). Statistically significant differences (p -1 dry weight; 10% to 30% of the total biofilm dry weight. Capsular EPS ranged from 50 to 318 mg g-1 dry weight; 5% to 30% of the total biofilm dry weight. Seven of the 12 biofilms showed higher amounts of capsular than colloidal EPS (p -1 biofilm dry weight, reaching up to 16% of the total composition. In general, the heavy metal composition of the EPS extracted from the biofilms closely resembled the metal composition of the water from which the biofilms were collected

  8. Inhibition of matrix metalloproteinases expression in human dental pulp cells by all-trans retinoic acid

    Jin Man Kim; Sang Wook Kang; Su-Mi Shin; Duck Su Kim; Kyong-Kyu Choi; Eun-Cheol Kim; Sun-Young Kim

    2014-01-01

    All-trans retinoic acid (ATRA) inhibits matrix metalloproteinase (MMP)-2 and MMP-9 in synovial fibroblasts, skin fibroblasts, bronchoalveolar lavage cells and cancer cells, but activates MMP-9 in neuroblast and leukemia cells. Very little is known regarding whether ATRA can activate or inhibit MMPs in human dental pulp cells (HDPCs). The purpose of this study was to determine the effects of ATRA on the production and secretion of MMP-2 and-9 in HDPCs. The productions and messenger RNA (mRNA) expressions of MMP-2 and-9 were accessed by gelatin zymography and real-time polymerase chain reaction (PCR), respectively. ATRA was found to decrease MMP-2 level in a dose-dependent manner. Significant reduction in MMP-2 mRNA expression was also observed in HDPCs treated with 25 mmol?L21 ATRA. However, HDPCs treated with ATRA had no effect on the pattern of MMP-9 produced or secreted in either cell extracts or conditioned medium fractions. Taken together, ATRA had an inhibitory effect on MMP-2 expression in HDPCs, which suggests that ATRA could be a candidate as a medicament which could control the inflammation of pulp tissue in vital pulp therapy and regenerative endodontics.

  9. Electrochemical biosensing platform using hydrogel prepared from ferrocene modified amino acid as highly efficient immobilization matrix.

    Qu, Fengli; Zhang, Yi; Rasooly, Avraham; Yang, Minghui

    2014-01-21

    To increase the loading of glucose oxidase (GOx) and simplify glucose biosensor fabrication, hydrogel prepared from ferrocene (Fc) modified amino acid phenylalanine (Phe, F) was utilized for the incorporation of GOx. The synthesized hydrogel displays good biocompatibility and contains a significant number of Fc moieties, which can be considered as an ideal matrix to immobilize enzymes for the preparation of mediator-based biosensors. The hydrogel was studied by scanning electron microscopy, which indicated that it was composed of nanofibers with a diameter of around 50-100 nm and length extended to 1 mm. With the addition of GOx into the hydrogel and by directly dropping the resulting biocomposite onto the electrode surface, a glucose biosensor, that displays good performance due to improved enzyme loading and efficient electron transfer, can be simply constructed. The favorable network structure and good biocompatibility of the hydrogel could effectively avoid enzyme leakage and maintain the bioactivity of the enzymes, which resulted in good stability of the biosensor. The biosensor was utilized for the detection of glucose in blood samples with results comparable to those obtained from the hospital. The hydrogel as a functional component of an amperometric biosensor has implications for future development of biosensors and for clinical applications. PMID:24383679

  10. Possible evidence of amide bond formation between sinapinic acid and lysine-containing bacterial proteins by matrix-assisted laser desorption/ionization (MALDI) at 355 nm

    We previously reported the apparent formation of matrix adducts of 3,5-dimethoxy-4-hydroxy-cinnamic acid (sinapinic acid or SA) via covalent attachment to disulfide bond-containing proteins (HdeA, HdeB and YbgS) from bacterial cell lysates ionized by matrix-assisted laser desorption/ionization (MALD...

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

    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

  12. Protective effect of naringin on 3-nitropropionic acid-induced neurodegeneration through the modulation of matrix metalloproteinases and glial fibrillary acidic protein.

    Gopinath, Kulasekaran; Sudhandiran, Ganapasam

    2016-01-01

    Naringin (4',5,7-trihydroxy-flavonone-7-rhamnoglucoside), a flavonone present in grapefruit, has recently been reported to protect against neurodegeration, induced with 3-nitropropionic acid (3-NP), through its antioxidant, anti-inflammatory, and antiapoptotic properties. This study used a rat model of 3-NP-induced neurodegeneration to investigate the neuroprotective effects of naringin exerted by modulating the expression of matrix metalloproteinases and glial fibrillary acidic protein. Neurodegeneration was induced with 3-NP (10 mg/kg body mass, by intraperitoneal injection) once a day for 2 weeks, and induced rats were treated with naringin (80 mg/kg body mass, by oral gavage, once a day for 2 weeks). Naringin ameliorated the motor abnormalities caused by 3-NP, and reduced blood-brain barrier dysfunction by decreasing the expression of matrix metalloproteinases 2 and 9, along with increasing the expression of the tissue inhibitors of metalloproteinases 1 and 2 in 3-NP-induced rats. Further, naringin reduced 3-NP-induced neuroinflammation by decreasing the expression of nuclear factor-kappa B and glial fibrillary acidic protein. Thus, naringin exerts protective effects against 3-NP-induced neurodegeneration by ameliorating the expressions of matrix metalloproteinases and glial fibrillary acidic protein. PMID:26544788

  13. Delivery of Polyunsaturated Fatty Acids from a Glycerol Polyester Matrix with Anti-oxidant Properties

    Awareness of the health benefits associated with the polyunsaturated acids such as alpha linolenic (ALA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA), has generated interest in formulating foods and dietary supplements with these compounds. However, the highly unsaturated structure o...

  14. Purification of a tartrate-resistant acid phosphatase (TrACP) from bovine cortical bone matrix

    It has been previously demonstrated that a partially purified bovine skeletal TrACP showed protein phosphatase (P'ase) activity that was specific for phosphotyrosyl (Ptyr) proteins. They have now purified TrACP activity from bovine cortical bone matrix to apparent homogeneity. The purification procedures included CM-Sepharose ion-exchange, cellulose phosphate affinity, sephacryl S-300 gel filtration and phenyl sepharose affinity chromatographies. Overall yield was > 25% and purification was approximately 2000-fold with a specific activity of 8.15 umol pNPP hydrolyzed/min/mg protein at 370C. The purified enzyme was judged to be homogeneous based on: (i) appearance as a single protein band on SDS-PAGE (silver staining technique) and (ii) distribution analysis of radioiodinated purified TrACP after SDS-PAGE revealing one band of radioactivity at the same positions as the TrACP protein band. M.W. of TrACP was 34,600 as assessed by gel filtration and 32,500 by SDS-PAGE, suggesting that bovine skeletal TrACP exists as active monomer. Analysis of the purified TrACP by isoelectric focusing showed at least 9 bands of enzyme activities with pIs between 4 and 5, indicating micro-heterogenecity. Substrate specificity analyses revealed that the purified TrACP also hydrolyzed nucleotide tri- and di-phosphates, but not monophosphates or other low M.W. phosphoryl esters, and was also capable of hydrolyzing phosphotyrosine (Tyr(P)) and Ptyr proteins with little activity toward other phosphoamino acids or phosphoseryl proteins. Optimal pH was 5.5 for TrACP activity, 6.0 for Tyr(P) P'ase activity and 7.0 for Ptyr protein P'ase activity. Results of these studies represent the first purification of a skeletal TrACP to apparent homogeneity

  15. Case study of the effectiveness of nitrogen foam and water-zone diverting agents in multistage matrix acid treatments

    Several oil wells producing water have been stimulated successfully with multistages of mud acid, nitrogen foam, and water-zone diverting agents. This procedure has improved well performance significantly while having little or no effect on post-treatment water production. The diverters' effectiveness was analyzed with radioactive tracers, gamma spectroscopy logs, and surface pressure equipment. Results indicate that water-ozone diverters and nitrogen foam are effective diverters when used in matrix acid stimulations. Case histories and associated data are included in this paper

  16. Wnt/β-Catenin and Retinoic Acid Receptor Signaling Pathways Interact to Regulate Chondrocyte Function and Matrix Turnover*

    Yasuhara, Rika; Yuasa, Takahito; Williams, Julie A.; Byers, Stephen W.; Shah, Salim; Pacifici, Maurizio; Iwamoto, Masahiro; Enomoto-Iwamoto, Motomi

    2009-01-01

    Activation of the Wnt/β-catenin and retinoid signaling pathways is known to tilt cartilage matrix homeostasis toward catabolism. Here, we investigated possible interactions between these pathways. We found that all-trans-retinoic acid (RA) treatment of mouse epiphyseal chondrocytes in culture did increase Wnt/β-catenin signaling in the absence or presence of exogenous Wnt3a, as revealed by lymphoid enhancer factor/T-cell factor/β-catenin reporter activity and β-catenin nuclear accumulation. T...

  17. Synthesis of silica coated zinc oxide–poly(ethylene-co-acrylic acid) matrix and its UV shielding evaluation

    Graphical abstract: - Highlights: • Well layer thickness controlled silica shell was made on ZnO nanoparticles. • PEAA, an interfacial agent is used to make nanocomposite–polymer matrix by twin-screw extruder. • Si-ZnO/PEAA matrix is highly stable and UV protective as compared to ZnO/PEAA matrix. • Nanoparticle embedded polymer matrix is suggested to make UV shielding fabrics with Nylon4. - Abstract: Silica coated zinc oxide nanoparticles (Si-ZnO NPs) (7 nm thick) were synthesized successfully and melt blended with poly(ethylene-co-acrylic acid) (PEAA resin) to improving ultraviolet (UV) shielding of zinc oxide nanoparticles (ZnO NPs). The photostability of both the ZnO NPs and Si-ZnO NPs were analyzed by the difference in photoluminescence (PL) and by methylene blue (MB) degradation. Photo-degradation studies confirmed that Si-ZnO NPs are highly photostable compared to ZnO NPs. The melt blended matrices were characterized by field emission scanning electron microscopy interfaced with energy dispersive X-ray spectroscopy (FE-SEM-EDX). The UV shielding property was analyzed from the transmittance spectra of UV–visible (UV–vis) spectroscopy. The results confirmed fine dispersion of thick Si-ZnO NPs in the entire resin matrix. Moreover, the Si-ZnO/PEAA showed about 97% UV shielding properties than the ZnO/PEAA

  18. Synthesis of silica coated zinc oxide–poly(ethylene-co-acrylic acid) matrix and its UV shielding evaluation

    Ramasamy, Mohankandhasamy [Division of Bionanotechnology, Gachon University, Seongnam 461-701 (Korea, Republic of); Kim, Yu Jun; Gao, Haiyan [Department of Polymer Engineering, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Yi, Dong Kee, E-mail: vitalis@mju.ac.kr [Department of Chemistry, Myongji University, Yongin 449-728 (Korea, Republic of); An, Jeong Ho, E-mail: jhahn1us@skku.edu [Department of Polymer Engineering, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2014-03-01

    Graphical abstract: - Highlights: • Well layer thickness controlled silica shell was made on ZnO nanoparticles. • PEAA, an interfacial agent is used to make nanocomposite–polymer matrix by twin-screw extruder. • Si-ZnO/PEAA matrix is highly stable and UV protective as compared to ZnO/PEAA matrix. • Nanoparticle embedded polymer matrix is suggested to make UV shielding fabrics with Nylon4. - Abstract: Silica coated zinc oxide nanoparticles (Si-ZnO NPs) (7 nm thick) were synthesized successfully and melt blended with poly(ethylene-co-acrylic acid) (PEAA resin) to improving ultraviolet (UV) shielding of zinc oxide nanoparticles (ZnO NPs). The photostability of both the ZnO NPs and Si-ZnO NPs were analyzed by the difference in photoluminescence (PL) and by methylene blue (MB) degradation. Photo-degradation studies confirmed that Si-ZnO NPs are highly photostable compared to ZnO NPs. The melt blended matrices were characterized by field emission scanning electron microscopy interfaced with energy dispersive X-ray spectroscopy (FE-SEM-EDX). The UV shielding property was analyzed from the transmittance spectra of UV–visible (UV–vis) spectroscopy. The results confirmed fine dispersion of thick Si-ZnO NPs in the entire resin matrix. Moreover, the Si-ZnO/PEAA showed about 97% UV shielding properties than the ZnO/PEAA.

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

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

    2015-08-19

    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. PMID:26343436

  20. 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.

    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.

  1. Radiation-induced transformations of matrix-isolated formic acid: evidence for the HCOOH → HOCO + H channel.

    Ryazantsev, Sergey V; Feldman, Vladimir I

    2015-11-11

    The effect of X-ray irradiation on the isolated formic acid molecules (HCOOH) in solid noble gas matrices (Xe, Kr, Ar, and Ne) at very low temperatures (6 K) was first studied by FTIR spectroscopy. Carbon oxides (CO and CO2) and hydrocarboxyl radicals (HOCO) have been detected as the principal degradation products. The formation of HOCO radicals represents a primary dissociation channel for formic acid, which was not reported previously under UV photolysis in solids. This reaction can be explained by the involvement of the recombination-induced excited states, which are not populated in photolysis. The effects of the matrix and the absorbed dose on the product formation were studied in detail and possible mechanisms are discussed with particular attention to the difference between radiolysis and UV-photolysis of the matrix-isolated formic acid. The results obtained provide a new insight into the effects of high-energy impact on the simplest carboxylic acid with possible implications to the astrochemical problems, in particular, the prebiotic evolution in the interstellar medium. PMID:26524429

  2. Electrochemical sensor for dopamine based on imprinted silica matrix-poly(aniline boronic acid) hybrid as recognition element.

    Li, Jian; Zhang, Ning; Sun, Qingqing; Bai, Zhanming; Zheng, Jianbin

    2016-10-01

    A novel imprinted silica matrix-poly(aniline boronic acid) hybrid for electrochemical detection of dopamine (DA) was developed. Boronic acid functionalized conducting polymer was electrochemically prepared on Au electrode. The number of covalent binding sites toward DA templates was controlled by potential cycles. A precursory sol solution of ammonium fluorosilicate (as cross-linking monomer) containing DA was spin-coated on the polymer modified electrode. Under NH3 atmosphere, the hydroxyl ions were generated in the solution and catalyzed the hydrolysis of fluorosilicate to form silica matrix. After this aqueous sol-gel process, an inorganic framework around the DA template was formed and the imprinted hybrid for DA was also produced. As revealed by scanning electron microscopy, UV-vis spectroscopy and cyclic voltammetry characterization, DA was embedded in the imprinted hybrid successfully. The affinity and selectivity of the imprinted hybrid were also characterized by cyclic voltammetry. The imprinted hybrid showed higher affinity for DA than that for epinephrine, and little or no affinity for ascorbic acid and uric acid due to the combined effects of covalent interaction, cavities matching and electrostatic repulsion. The imprinted hybrid sensor exhibited a quick response (within 5min) to DA in the concentration range from 0.05 to 500μmolL(-1) with a detection limit of 0.018μmolL(-1). The prepared sensor was also applied to detect DA in real samples with a satisfactory result. PMID:27474321

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

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

    2016-05-30

    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. PMID:26970983

  4. Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead

    Ropo, Matti; Baldauf, Carsten

    2016-01-01

    We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca$^{2+}$, Ba$^{2+}$, Sr$^{2+}$, Cd$^{2+}$, Pb$^{2+}$, and Hg$^{2+}$. The underlying data set consists of 45,892 first-principles predicted conformers with relative energies up to about 4 eV (about 400kJ/mol). We show that only very few distinct backbone structures of isolated amino acids and their dipeptides emerge as lowest-energy conformers. The isolated amino acids predominantly adopt structures that involve an acidic proton shared between the carboxy and amino function. Dipeptides adopt one of two intramolecular-hydrogen bonded conformations C$_5$ or equatorial C$_7$. Upon complexation with a divalent cation, the accessible conformational space shrinks and intramolecular hydrogen bonding is prevented due to strong electrostatic interaction of backbone and side chain functional groups with cations. Clear correlations emerge from the binding energies of the six divalent ...

  5. Matrix metalloproteinase-13 mediated degradation of hyaluronic acid-based matrices orchestrates stem cell engraftment through vascular integration.

    Jha, Amit K; Tharp, Kevin M; Browne, Shane; Ye, Jianqin; Stahl, Andreas; Yeghiazarians, Yerem; Healy, Kevin E

    2016-05-01

    A critical design parameter for the function of synthetic extracellular matrices is to synchronize the gradual cell-mediated degradation of the matrix with the endogenous secretion of natural extracellular matrix (ECM) (e.g., creeping substitution). In hyaluronic acid (HyA)-based hydrogel matrices, we have investigated the effects of peptide crosslinkers with different matrix metalloproteinases (MMP) sensitivities on network degradation and neovascularization in vivo. The HyA hydrogel matrices consisted of cell adhesive peptides, heparin for both the presentation of exogenous and sequestration of endogenously synthesized growth factors, and MMP cleavable peptide linkages (i.e., QPQGLAK, GPLGMHGK, and GPLGLSLGK). Sca1(+)/CD45(-)/CD34(+)/CD44(+) cardiac progenitor cells (CPCs) cultured in the matrices with the slowly degradable QPQGLAK hydrogels supported the highest production of MMP-2, MMP-9, MMP-13, VEGF165, and a range of angiogenesis related proteins. Hydrogels with QPQGLAK crosslinks supported prolonged retention of these proteins via heparin within the matrix, stimulating rapid vascular development, and anastomosis with the host vasculature when implanted in the murine hindlimb. PMID:26967648

  6. Strategies for the elimination of matrix effects in the LC-MS/MS analysis of the lipophilic toxins okadaic acid and azaspiracid-1 in molluscan shellfish

    Kilcoyne, Jane; Fux, Elie

    2010-01-01

    Considerable efforts are being made worldwide to replace in vivo assays with instrumental methods of analysis for the monitoring of marine biotoxins in shellfish. Analysis of these compounds by the preferred technique of LC-MS/MS is challenged by matrix effects associated with shellfish tissue components. In methods validation, assessment of matrix interferences is imperative to ensure the accuracy of analytical results. We evaluated matrix interferences in the analysis of okadaic acid (OA)...

  7. Using reduced amino acid composition to predict defensin family and subfamily: Integrating similarity measure and structural alphabet.

    Zuo, Yong-Chun; Li, Qian-Zhong

    2009-10-01

    Defensins are essentially ancient natural antibiotics with potent activity extending from lower organisms to humans. They can inhibit the growth or virulence of micro-organisms directly or indirectly enhance the host's immune system. The successful prediction of defensin peptides will provide very useful information and insights for the basic research of defensins. In this study, by selecting the N-peptide composition of reduced amino acid alphabet (RAAA) obtained from structural alphabet named Protein Blocks as the feature parameters, the increment of diversity (ID) is firstly developed to predict defensins family and subfamily. The jackknife test based on 2-peptide composition of reduced amino acid alphabet (RAAA) with 13 reduced amino acids shows that the overall accuracy of prediction are 91.36% for defensin family, and 94.21% for defensin subfamily. The results indicate that ID_RAAA is a simple and efficient prediction method for defensin peptides. PMID:19591890

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

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

    2015-01-01

    Background 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 s...

  9. A new matrix metalloproteinase-9 inhibitor 3,4-dihydroxycinnamic acid (caffeic acid) from methanol extract of Euonymus alatus: isolation and structure determination

    In a previous paper [Cha, B.Y., Park, C.J., Lee, D.G., Lee, Y.C., Kim, D.W., Kim, J.D., Seo, W.G., Moon, S.K., Kim, C.H., 2003. Inhibitory effect of methanol extract from Euonymus alatus on matrix metalloproteinase-9, J. Ethnopharm. 85, 163-167], methanol extracts prepared from stems of Euonymus alatus showed a strong inhibitory effect of matrix metalloproteinase (MMP)-9 activity, which is known to be involved in tumor cell invasion and metastasis, in a concentration-dependent manner on zymography. Assay guided fractionation led to the isolation of a caffeic acid (CA) as the compound responsible for the anti-MMP-9 activity. CA was finally obtained by reversed-phase HPLC, and its structure was elucidated by fast atom bombardment mass spectrometry and tandem mass spectrometry. The purified CA inhibited MMP-9 activity with the IC50 of 10-20 nM

  10. Acid-base-driven matrix-assisted mass spectrometry for targeted metabolomics

    Shroff, R.; Rulíšek, Lubomír; Doubský, J.; Svatoš, Aleš

    2009-01-01

    Roč. 106, č. 25 (2009), s. 10092-10096. ISSN 0027-8424 R&D Projects: GA MŠk LC512 Institutional research plan: CEZ:AV0Z40550506 Keywords : clinical diagnostic * matrix design * positive/negative ions * MALDI Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 9.432, year: 2009

  11. Diglycolamic acid anchored on polyamine matrix for the mutual separation of Eu(III) and Am(III)

    Diglycolamic acid was anchored on a polyamine matrix and the product (PA-DGAH) was characterized by ion-exchange capacity measurement, TG-DTA and FT-IR spectroscopy. The extraction behavior of Am(III) and Eu(III) in PA-DGAH was studied from dilute nitric acid medium to examine the feasibility using the anchored adsorbent for their mutual separation. The effect of various parameters such as the duration of equilibration, concentration of europium, nitric acid and diethylenetriaminepentaacetic acid (DTPA) in aqueous phase on the distribution coefficient (Kd) of Am(III) and Eu(III) was studied. The distribution coefficient decreased with increase in the concentration of nitric acid. Rapid extraction of metal ions in the initial stages of equilibration followed by the establishment of equilibrium occurred within 4 h. The data on the rate of uptake of Am(III) and Eu(III) were fitted into pseudo-first order and pseudo-second order rate equation. The extraction isotherm was fitted to Langmuir and Freundlich adsorption models and the apparent europium extraction capacity was determined. The mechanism of extraction was elucidated and the conditions needed for efficient separation of Am(III) from Eu(III) was optimized using DTPA. The study indicated the possibility of using PA-DGAH for the separation of Eu(III) from Am(III) with high separation factors.

  12. Diglycolamic acid anchored on polyamine matrix for the mutual separation of Eu(III) and Am(III)

    Suneesh, A.S.; Syamala, K.V.; Venkatesan, K.A.; Antony, M.P.; Vasudeva Rao, P.R. [Indira Gandhi Centre for Atomic Research, Kalpakkam (India). Fuel Chemistry Div.

    2016-04-01

    Diglycolamic acid was anchored on a polyamine matrix and the product (PA-DGAH) was characterized by ion-exchange capacity measurement, TG-DTA and FT-IR spectroscopy. The extraction behavior of Am(III) and Eu(III) in PA-DGAH was studied from dilute nitric acid medium to examine the feasibility using the anchored adsorbent for their mutual separation. The effect of various parameters such as the duration of equilibration, concentration of europium, nitric acid and diethylenetriaminepentaacetic acid (DTPA) in aqueous phase on the distribution coefficient (K{sub d}) of Am(III) and Eu(III) was studied. The distribution coefficient decreased with increase in the concentration of nitric acid. Rapid extraction of metal ions in the initial stages of equilibration followed by the establishment of equilibrium occurred within 4 h. The data on the rate of uptake of Am(III) and Eu(III) were fitted into pseudo-first order and pseudo-second order rate equation. The extraction isotherm was fitted to Langmuir and Freundlich adsorption models and the apparent europium extraction capacity was determined. The mechanism of extraction was elucidated and the conditions needed for efficient separation of Am(III) from Eu(III) was optimized using DTPA. The study indicated the possibility of using PA-DGAH for the separation of Eu(III) from Am(III) with high separation factors.

  13. Unitary Congruence and Unitary Similarity for Quaternion Matrix%四元数矩阵的酉相合与酉相似

    蔡永裕; 黄礼平

    2009-01-01

    This paper discusses the unitary congruence of quaternion matrices, the uni-tary congruence of quaternion matrices is natural extension of the complex unitary congruence of complex matrices and has many good properties. Since unitary congruence of quaternion matrices is in connection with unitary similarity of quaternion matrices, we also discuss some properties of the unitary similarity of quaternion matrices.%本文讨论了四元数矩阵的酉相合,四元数矩阵的酉相合是复矩阵的复酉相合的自然推广,并且它有许多好的性质.由于四元数矩阵的酉相合与酉相似有着密切联系,本文还讨论了四元数矩阵的酉相似的一些性质.

  14. Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

    McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

    2016-05-01

    Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

  15. Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides.

    McMillen, Chelsea L; Wright, Patience M; Cassady, Carolyn J

    2016-05-01

    Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides. Graphical Abstract ᅟ. PMID:26864792

  16. Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

    McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

    2016-02-01

    Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

  17. Factorial analysis of matrix effects in analysis of yttrium and uranium in phosphoric acid by ICP-AES

    Wet process phosphoric acid (WPA) is used for simultaneous extraction of uranium and rare earth by D2EHPA+TBP system. WPA consists of rare earths (RE), U, Fe, V, Al, Ca, SO42-, F- and PO43- apart from other minor elements. Matrix elements present in WPA interfere in the analysis of uranium and rare earths. Standard addition methods were developed for determination of yttrium and uranium in WPA using ICP-AES (JY Ultima 2). As an alternative to standard addition method, analysis of Y and U in WPA using phosphoric acid standards was investigated. The effect of phosphate, iron, aluminium and magnesium ions on the analysis of Y and U in WPA was studied using factorial design method. (author)

  18. 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

    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

  19. 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

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

    2010-09-01

    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

  20. Biosynthesis of monoterpenoids in higher plants. The biosynthetic pathway leading to the monoterpenoids from amino acids with a carbon-skeleton similar to mevalonic acid

    Tange, K. (Hiroshima Univ. (Japan). Faculty of Science)

    1981-09-01

    Radioisotopically labeled L-valine, DL-alanine, sodium acetate, and DL-mevalonic acid were incorporated into linalool by the intact plant of Cinnamomum camphora Sieb. var. linalooliferum Fujita and into geraniol and citronellol by that of Pelargonium roseum Bourbon. The uptake of leucine and valine resulted in the preferential location of the radioactivity on the 3,3-dimethylallyl pyrophosphate-derived moiety of these acyclic monoterpenoids, whereas the uptake of alanine resulted in the preferential location on the isopentenyl pyrophosphate-derived moiety, much as in the cases of mevalonic acid and sodium acetate. A biosynthetic pathway leading to the monoterpenoids from the amino acids is discussed.

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

    Matei, Andreea; Marinescu, Maria; Constantinescu, Catalin; Ion, Valentin; Mitu, Bogdana; Ionita, Iulian; Dinescu, Maria; Emandi, Ana

    2016-06-01

    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/cm2. 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.

  2. Effect of food matrix microstructure on stomach emptying rate and apparent ileal fatty acid digestibility of almond lipids.

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

    2014-10-01

    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 almonds, almond cream and Tween-oil emulsion, while 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 almonds, 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. PMID:25066699

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

    Coluccio, M. L.

    2015-09-04

    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.

  4. Matrix Domain Modulates HIV-1 Gag's Nucleic Acid Chaperone Activity via Inositol Phosphate Binding ▿

    Jones, Christopher P.; Datta, Siddhartha A.K.; Rein, Alan; Rouzina, Ioulia; Musier-Forsyth, Karin

    2010-01-01

    Retroviruses replicate by reverse transcribing their single-stranded RNA genomes into double-stranded DNA using specific cellular tRNAs to prime cDNA synthesis. In HIV-1, human tRNA3Lys serves as the primer and is packaged into virions during assembly. The viral Gag protein is believed to chaperone tRNA3Lys placement onto the genomic RNA primer binding site; however, the timing and possible regulation of this event are currently unknown. Composed of the matrix (MA), capsid (CA), nucleocapsid ...

  5. Spectrophotometric method for fast quantification of ascorbic acid and dehydroascorbic acid in simple matrix for kinetics measurements.

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

    2016-11-15

    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. PMID:27283671

  6. Isotachophoretic determination of basic amino acids: arginine, histidine and lysine in real matrix

    Herrmannová, Michaela; Křivánková, Ludmila; Bartoš, M.; Vytřas, K.

    Pardubice: Univezita Pardubice, 2006 - (Blattná, J.; Horna, A.; Zima, T.). s. 199-200 ISBN 80-7194-855-1. [Vitamins 2006. International Conference /6./. Health Ingredients Metabolism Analysis.. 10.09.2006-16.09.2006, Pardubice] R&D Projects: GA ČR GA203/05/2106 Keywords : isotachophoresis * amino acid Subject RIV: CB - Analytical Chemistry, Separation

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

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

    2014-01-01

    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

  8. Oleanolic acid acetate inhibits rheumatoid arthritis by modulating T cell immune responses and matrix-degrading enzymes.

    Choi, Jin Kyeong; Kim, Sung-Wan; Kim, Duk-Sil; Lee, Jong Yeong; Lee, Soyoung; Oh, Hyun-Mee; Ha, Yeong Su; Yoo, Jeongsoo; Park, Pil-Hoon; Shin, Tae-Yong; Kwon, Taeg Kyu; Rho, Mun-Chual; Kim, Sang-Hyun

    2016-01-01

    Rheumatoid arthritis (RA) is a chronic autoimmune disease associated with a combination of synovium joint inflammation, synovium hyperplasia, and destruction of cartilage and bone. Oleanolic acid acetate (OAA), a compound isolated from Vigna angularis, has been known to possess pharmacological activities, including anti-inflammation and anti-bone destruction. In this study, we investigated the effects of OAA on RA and the underlying mechanisms of action by using a type-II collagen-induced arthritis (CIA) mouse model and tumor necrosis factor (TNF)-α-stimulated RA synovial fibroblasts. Oral administration of OAA decreased the clinical arthritis symptoms, paw thickness, histologic and radiologic changes, and serum total and anti-type II collagen IgG, IgG1, and IgG2a levels. OAA administration reduced Th1/Th17 phenotype CD4(+) T lymphocyte expansions and inflammatory cytokine productions in T cell activated draining lymph nodes and spleen. OAA reduced the expression and production of inflammatory mediators, such as cytokines and matrix metalloproteinase (MMP)-1/3, in the ankle joint tissue and RA synovial fibroblasts by down-regulating Akt, mitogen-activated protein kinases, and nuclear factor-κB. Our results clearly support that OAA plays a therapeutic role in RA pathogenesis by modulating helper T cell immune responses and matrix-degrading enzymes. The immunosuppressive effects of OAA were comparable to dexamethasone and ketoprofen. We provide evidences that OAA could be a potential therapeutic candidate for RA. PMID:26570984

  9. Modal Similarity

    Vigo , Dr. Ronaldo

    2009-01-01

    Just as Boolean rules define Boolean categories, the Boolean operators define higher-order Boolean categories referred to as modal categories. We examine the similarity order between these categories and the standard category of logical identity (i.e. the modal category defined by the biconditional or equivalence operator). Our goal is 4-fold: first, to introduce a similarity measure for determining this similarity order; second, to show that such a measure is a good predictor of the similari...

  10. Web Similarity

    Cohen, Andrew; Vitányi, Paul

    2015-01-01

    Normalized web distance (NWD) is a similarity or normalized semantic distance based on the World Wide Web or any other large electronic database, for instance Wikipedia, and a search engine that returns reliable aggregate page counts. For sets of search terms the NWD gives a similarity on a scale from 0 (identical) to 1 (completely different). The NWD approximates the similarity according to all (upper semi)computable properties. We develop the theory and give applications. The derivation of ...

  11. Low pressure process for continuous fiber reinforced polyamic acid resin matrix composite laminates

    Druyun, Darleen A. (Inventor); Hou, Tan-Hung (Inventor); Kidder, Paul W. (Inventor); Reddy, Rakasi M. (Inventor); Baucom, Robert M. (Inventor)

    1994-01-01

    A low pressure processor was developed for preparing a well-consolidated polyimide composite laminate. Prepreg plies were formed from unidirectional fibers and a polyamic acid resin solution. Molding stops were placed at the sides of a matched metal die mold. The prepreg plies were cut shorter than the length of the mold in the in-plane lateral direction and were stacked between the molding stops to a height which was higher than the molding stops. The plies were then compressed to the height of the stops and heated to allow the volatiles to escape and to start the imidization reaction. After removing the stops from the mold, the heat was increased and 0 - 500 psi was applied to complete the imidization reaction. The heat and pressure were further increased to form a consolidated polyimide composite laminate.

  12. Eicosapentaenoic acid inhibits TNF-α-induced matrix metalloproteinase-9 expression in human keratinocytes, HaCaT cells

    Eicosapentaenoic acid (EPA) is an omega-3 (ω-3) polyunsaturated fatty acid (PUFA), which has anti-inflammatory and anti-cancer properties. Some reports have demonstrated that EPA inhibits NF-κB activation induced by tumor necrosis factor (TNF)-α or lipopolysaccharide (LPS) in various cells. However, its detailed mode of action is unclear. In this report, we investigated whether EPA inhibits the expression of TNF-α-induced matrix metalloproteinases (MMP)-9 in human immortalized keratinocytes (HaCaT). TNF-α induced MMP-9 expression by NF-κB-dependent pathway. Pretreatment of EPA inhibited TNF-α-induced MMP-9 expression and p65 phosphorylation. However, EPA could not affect IκB-α phosphorylation, nuclear translocation of p65, and DNA binding activity of NF-κB. EPA inhibited TNF-α-induced p65 phosphorylation through p38 and Akt inhibition and this inhibition was IKKα-dependent event. Taken together, we demonstrate that EPA inhibits TNF-α-induced MMP-9 expression through inhibition of p38 and Akt activation

  13. 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

    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: jose.todoli@ua.es

    2006-03-15

    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.

  14. 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

    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-1 in the case of inorganic acids (i.e., nitric, sulfuric, hydrochloric and a mixture of them), from 0 to about 2500 mg l-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

  15. The Carboxyl-Terminal Amino Acids Render Pro-Human LC3B Migration Similar to Lipidated LC3B in SDS-PAGE

    Wang, Wei; Chen, Zhixia; Billiar, Timothy R; Michael T. Stang; GAO, WENTAO

    2013-01-01

    LC3 is widely used marker for macroautophagy assays. After translation pro-LC3 is processed by Atg4 to expose C-terminal glycine residue for downstream conjugation reactions to accomplish the conversion of LC3-I to LC3-II. SDS-PAGE based Western blot (Wb) is generally utilized to quantify LC3-II levels where the LC3-I band migrates slower than LC3-II. We found that pro-human LC3B migrated at similar rate as LC3B-II in SDS-PAGE. The carboxyl-terminal five amino acids, particularly Lysine122 an...

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

    Mlalila N

    2014-12-01

    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

  17. Porous poly(DL-lactic acid) matrix film with antimicrobial activities for wound dressing application.

    Chitrattha, Sasiprapa; Phaechamud, Thawatchai

    2016-01-01

    Poly(lactic acid) (PLA) is polymeric biomaterial that has been used for wound dressing due to its biodegradability and biocompatibility. However, PLA has some limitations including poor toughness, low degradation rate and high hydrophobicity. The aim of this study is to develop an antibiotic drug-loaded PLA porous film as wound dressing with antibacterial activity. PLA porous film was fabricated by temperature change technique using solvent casting method. Polyethylene glycol (PEG) 400 was added for improving the pore interconnectivity of film. Gentamicin sulfate (GS) or metronidazole (MZ) was incorporated into PLA porous films. PLA containing PEG 400 exhibited the more amorphous form than plain PLA film and contained 55.31 ± 2.85% porosity and 20 μm of the pore size which significantly improved the water vapor transmission rate, oxygen transmission rate, degradation rate and percentage of drug release, respectively. Drug-loaded porous films efficiently inhibited the bacteria growth. GS-loaded film inhibited Staphylococcus aureus, Proteus mirabilis, Pseudomonas aeruginosa, whereas MZ-loaded film inhibited Bacteroides fragilis and the sustainable antibacterial activity was attained for 7 days. PMID:26478412

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

    Lynne Shinto; Gail Marracci; Lauren Bumgarner; Vijayshree Yadav

    2011-01-01

    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...

  19. OMEGA-3 fatty acids contribute to plaque stability differentially affecting the release of matrix metalloproteinases and tissue inhibitors of metalloproteinases by human monocytes/macrophages in culture

    Massaro, Marika; Scoditti, Egeria; Carluccio, Maria Annunziata; Storelli, Carlo; Distante, Alessandro; Martines, Giuseppe

    2008-01-01

    Objectives. High intakes of omega-3 fatty acids has been associated with protection from plaque rupture. The secretion of metalloproteinases (MMPs) by macrophages is believed to play a key role in matrix degradation underlying plaque instability. Conversely, tissue inhibitors of metalloproteinases (TIMPs) would contribute to plaque stability. We therefore studied the effects of omega-3 fatty acids on the release and activity of MMPs and TIMPs in cultured human monocytoid cells. Methods. Human...

  20. Potential Effects of Caffeic Acid in Suppression of Matrix Metalloproteinases Activities in Irradiated Rats

    Great Number of researches on the potential role of antioxidant nutrients and phenolic compounds in the prevention of chronic diseases has been accumulated over the past several decades. Despite this effort, there is much that remains uncertain. Bio markers research in this field has the potential to help fill the gaps in current knowledge. The present study was designed to evaluate, in one aspect, the probable direction expression of proteolytic enzymes as indices for gamma-irradiation-induced oxidative stress and their relationship, in other aspect with one antioxidant micro nutrient phenolic compound: caffeic acid (CA). Sprague Dawley male albino rats were administrated CA intraperitoneally (i.p.) 10 μmol/ kg body wt/ day for 8 consecutive days pre irradiation exposure (fractionated doses, instalment as 1 Gy every day up to total dose of 8 Gy). The treatment was continued for 15 successive days following irradiation processing. Quantitative assay of gelatinolytic zymo graphic analysis of serum and hepatic tissues showed that exposure to gamma-rays yields a marked significant increase in the activities of both latent and active MMP-9 (92 and 86 kDa), respectively, and both latent and active MMP-2 (72 and 66 kDa), respectively. Administration of CA significantly decreased the activities of MMP-2 and MMP-9 in gamma-irradiated rats. Conclusion: the present findings demonstrated that irradiation-exposure leads to enhancement of enzymatic activities of MMP-2 and MMP-9 in their inactive and active forms in the serum and liver. Meanwhile, administration of CA exhibits protective effects in gamma-irradiated rats through down-regulation of MMP-2 and MMP-9 activities

  1. SmMYC2a and SmMYC2b played similar but irreplaceable roles in regulating the biosynthesis of tanshinones and phenolic acids in Salvia miltiorrhiza.

    Zhou, Yangyun; Sun, Wei; Chen, Junfeng; Tan, Hexin; Xiao, Ying; Li, Qing; Ji, Qian; Gao, Shouhong; Chen, Li; Chen, Shilin; Zhang, Lei; Chen, Wansheng

    2016-01-01

    Salvia miltiorrhiza Bunge, which contains tanshinones and phenolic acids as major classes of bioactive components, is one of the most widely used herbs in traditional Chinese medicine. Production of tanshinones and phenolic acids is enhanced by methyl jasmonate (MeJA). Transcription factor MYC2 is the switch of jasmontes signaling in plants. Here, we focused on two novel JA-inducible genes in S. miltiorrhiza, designated as SmMYC2a and SmMYC2b, which were localized in the nucleus. SmMYC2a and SmMYC2b were also discovered to interact with SmJAZ1 and SmJAZ2, implying that the two MYC2s might function as direct targets of JAZ proteins. Ectopic RNA interference (RNAi)-mediated knockdown experiments suggested that SmMYC2a/b affected multiple genes in tanshinone and phenolic acid biosynthetic pathway. Besides, the accumulation of tanshinones and phenolic acids was impaired by the loss of function in SmMYC2a/b. Meanwhile, SmMYC2a could bind with an E-box motif within SmHCT6 and SmCYP98A14 promoters, while SmMYC2b bound with an E-box motif within SmCYP98A14 promoter, through which the regulation of phenolic acid biosynthetic pathway might achieve. Together, these results suggest that SmMYC2a and SmMYC2b are JAZ-interacting transcription factors that positively regulate the biosynthesis of tanshinones and Sal B with similar but irreplaceable effects. PMID:26947390

  2. 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.

    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.

  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

    Gao, Zhenya; Huo, Lijun; Cui, Dongmei; Yang, Xiao; Zeng, Junwen

    2016-01-01

    Purpose 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. Methods 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. Results 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. Conclusion ATRA induced upregulation of RARβ in ARPE-19 cells and stimulated

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

    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)

    2008-11-03

    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)

  5. Influence of purified multiwalled carbon nanotubes on the mechanical and morphological behavior in poly (L-lactic acid) matrix.

    Leal, C V; Martinez, D S T; Más, B A; Alves, O L; Duek, E A R

    2016-06-01

    Poly (L-latic acid) (PLLA) is a bioresorbable polymer widely used as a biomaterial, but its fragility can limit its use. An alternative is to produce polymer nanocomposites, which can enhance the mechanical properties of polymeric matrix, resulting in a material with differentiated properties. In this work, PLLA based nanocomposites containing 0.25, 0.5 and 1.0wt% of purified multiwalled carbon nanotubes (p-MWCNTs) were prepared by the solvent casting method. The morphology and mechanical properties results show an improvement in strain at break for 0.25 and 0.5wt% p-MWCNTs and an increase in stiffness and elastic modulus for all compositions. Nanocomposites presented a p-MWCNTs agglomeration; however, there was a good stress transfer between PLLA and p-MWCNTs, which was confirmed by the increase in the hardness and elastic modulus. Atomic force microscopy analysis indicated an increase in roughness after nanotube addition. The in vitro biological study showed that PLLA/p-MWCNTs nanocomposites are cytocompatible with osteoblasts cells. The capacity of PLLA nanocomposites to stimulate osteogenesis was investigated by alkaline phosphatase (ALP) activity assay. Higher ALP activity was found on osteoblasts cultured on nanocomposites with 0.25 and 0.5wt% p-MWCNT compared to neat PLLA, confirming that PLLA cytocompatibility was improved on these compositions. Finally, our results showed that by a simple and inexpensive solvent casting method, it is possible to manufacture biofunctional nanocomposites devices with potential for orthopedic applications. PMID:27038896

  6. 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*

    Delplanque Bernadette

    2011-11-01

    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.

  7. Anti-acids lead to immunological and morphological changes in the intestine of BALB/c mice similar to human food allergy.

    Pali-Schöll, Isabella; Yildirim, Ali O; Ackermann, Ute; Knauer, Tanja; Becker, Christoph; Garn, Holger; Renz, Harald; Jensen-Jarolim, Erika; Fehrenbach, Heinz

    2008-08-01

    We have shown that anti-acid medication for treating dyspeptic disorders can block protein digestion and induce a higher risk for food sensitization. This mechanism was confirmed in human and animal studies on the humoral as well as the cellular level. Here we aimed to investigate the outcome of the treatment with the anti-acid drug sucralfate on the intestine in our murine model, assuming that morphological and immunological changes will occur. BALB/c mice were fed codfish extract plus sucralfate. Antibodies were examined in ELISA, RBL assay and Western blot. Quantitative morphological analysis of the intestine was performed by design-based stereology, focussing on epithelium, lamina propria, smooth muscle, eosinophils and CD3(+) cells. Histological analyses were performed after H&E-, PAS- and Congo red-staining, while immune histochemistry was done for detection of CD3(+) cells. Codfish-specific IgE and its activity in RBL assay confirmed the Th2-response after treatment with sucralfate. The reactivity pattern of murine IgE in Western blot was similar to allergic patients' IgE. Histological examination showed more slender villi in the duodenum, and increased goblet cell mucus in the cecum after sucralfate treatment. Stereological analyses of the intestine revealed higher eosinophil/CD3(+) ratios, decreased mean thickness of the epithelium of duodenum and cecum, and thinner smooth muscle cell layer in the colon of food allergic mice. Anti-acid treatment with sucralfate induces changes in the structure of epithelium and villi, and an increase in eosinophils and mucus-producing cells in the intestine. Therefore, this medication leads to sensitization against food with changes typical for food allergy also in the intestine. PMID:18524557

  8. Reduction of Inflammatory Responses and Enhancement of Extracellular Matrix Formation by Vanillin-Incorporated Poly(Lactic-co-Glycolic Acid) Scaffolds

    Lee, Yujung; Kwon, JeongIl; Khang, Gilson; Lee, Dongwon

    2012-01-01

    Vanillin is one of the major components of vanilla, a commonly used flavoring agent and preservative and is known to exert potent antioxidant and anti-inflammatory activities. In this work, vanillin-incorporated poly(lactic-co-glycolic acid) (PLGA) films and scaffolds were fabricated to evaluate the effects of vanillin on the inflammatory responses and extracellular matrix (ECM) formation in vitro and in vivo. The incorporation of vanillin to PLGA films induced hydrophilic nature, resulting i...

  9. Perfluorooctanoic acid enhances colorectal cancer DLD-1 cells invasiveness through activating NF-κB mediated matrix metalloproteinase-2/-9 expression

    Miao, Chen; Ma, Jun; Zhang, Yajie; Chu, Yimin; Li, Ji; Kuai, Rong; Wang, Saiyu; Peng, Haixia

    2015-01-01

    Objective: Perfluorooctanoic acid (PFOA) is widely used in consumer products and detected in human serum. Our study meant to elucidate the uncovered molecular mechanisms underlying the PFOA induced colorectal cancer cell DLD-1 invasion and matrix metalloproteinases (MMP) expression. Methods and results: Trans-well filter assay appeared that PFOA treatment stimulated DLD-1 cells invasion significantly. Meanwhile, the results of luciferase reporter, quantitative real-time PCR, western blotting,...

  10. AN AMPEROMETRIC BIOSENSOR BASED ON COVALENT IMMOBILIZATION OF ASCORBATE OXIDASE ON BIOCOMPATIABLE AND LOW-TOXIC POLY(THIOPHENE-3-ACETIC ACID) MATRIX

    Dong Li; Yang-ping Wen; Jing-kun Xu; Hao-hua He; Ming Liu

    2012-01-01

    The biocompatiable and low-toxic poly(thiophene-3-acetic acid) (PTAA) matrix was successfully electrosynthesized in ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6) in comparison with the electrosynthesis of PTAA matrix in acetonitrile (ACN).Ascorbate oxidase (AO) was used as a model for the development and application of biosensor.Vitamin C (VC) biosensors were facilely fabricated by the covalent immobilization of AO molecules on PTAA matrices electrosynthesized in ACN containing tetrabutylammonium tetrafluoroborate and BmimPF6,respectively.Electrochemical impedance spectroscopy,scanning electron microscopy and FTIR spectroscopy indicated that AO molecules were covalently immobilized on PTAA matrices.Parameters of the as-obtained biosensors such as working potential,pH and temperature have been optimized.The amperometric biosensor based on PTAA matrix electrosynthesized in BmimPF6 exhibited wider linear range,lower detection limit,higher sensitivity and bioaffinity,and better operational and storage stability than that electrosynthesized in ACN under optimal conditions.The as-obtained biosensor based on PTAA matrix electrosynthesized in BmimPF6 was employed for the detection of VC content in commercial juices,and the result was close to the data given by manufacturers.Excellent results indicate that the PTAA matrix electrosynthesized in ionic liquid is a promising platform for the covalent immobilization of biologically-active species and the development of biosensors.

  11. Biofilm Matrix Proteins

    Fong, Jiunn N. C.; Yildiz, Fitnat H.

    2015-01-01

    Proteinaceous components of the biofilm matrix include secreted extracellular proteins, cell surface adhesins and protein subunits of cell appendages such as flagella and pili. Biofilm matrix proteins play diverse roles in biofilm formation and dissolution. They are involved in attaching cells to surfaces, stabilizing the biofilm matrix via interactions with exopolysaccharide and nucleic acid components, developing three-dimensional biofilm architectures, and dissolving biofilm matrix via enz...

  12. Modeling and optimizing the design of matrix treatments in carbonate reservoirs with self-diverting acid systems

    Application of a self-diverting-acid based on viscoelastic surfactant (SDVA) is a promising technology for improving the efficacy of acid treatment in oil and gas-bearing carbonate reservoirs. In this study, we present a mathematical model for assessing SDVA flow and reaction with carbonate rock using the SDVA rheological characteristics. The model calculates the technological parameters for acidizing operations and the prediction of well productivity after acid treatment, in addition to technical and economic optimization of the acidizing process by modeling different acid treatment options with varying volumes, injection rates, process fluids stages and initial economic scenarios

  13. Effect of acid or alkaline catalyst and of different capping agents on the optical properties of CdS nanoparticles incorporated within a diureasil hybrid matrix

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

    2015-11-01

    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.

  14. Thermal conductivity and acid dissolution behavior of MgO-ZrO 2 ceramics for use in LWR inert matrix fuel

    Medvedev, P. G.; Lambregts, M. J.; Meyer, M. K.

    2006-02-01

    Dual-phase MgO-ZrO 2 ceramics are proposed for use in inert matrix fuel for disposition of plutonium and minor actinides in existing light water reactors. The concept for use of this composite material was developed with the intent to capitalize on the known advantages of the composite's constituents: high thermal conductivity of MgO, and stability of ZrO 2 in LWR coolant. The study presented in this paper addressed the thermal conductivity and nitric acid solubility of MgO-ZrO 2 ceramics. Thermal analysis, based on experimental and analytical techniques, established that the product of all investigated compositions has the thermal conductivity superior to that of UO 2. Nitric acid dissolution experiments showed that only the free MgO phase dissolves in the nitric acid, leaving behind a porous pellet consisting of a ZrO 2-based solid solution.

  15. Matrix-based three-dimensional culture of buffalo mammary epithelial cells showed higher induction of genes related to milk protein and fatty acid metabolism.

    Shandilya, Umesh K; Sharma, Ankita; Sodhi, Monika; Kapila, Neha; Kishore, Amit; Mohanty, Ashok; Kataria, Ranjit; Malakar, Dhruva; Mukesh, Manishi

    2016-02-01

    Demanding transcriptomic studies in livestock animal species could be replaced by good in vitro models mimicking the function of mammary gland. Mammary epithelial cells (MEC) are the functional unit of the mammary gland. Extracellular matrix is known to be a key factor providing normal homeostasis in three-dimensional (3D) environment as important signals are lost when cells are cultured in two-dimensional (2D) environment. The aims of this study were to establish a buffalo mammary epithelial cells (BMECs) in 3D culture using extracellular matrix and to determine whether such a 3D culture model has different expression pattern than 2D counterpart. The purified MEC generated after several passages were used to establish 3D culture using Geltrex matrix. The expression of milk casein genes viz., alpha S1-casein (CSN1S1), alpha S2-casein (CSN1S2), beta-casein (CSN2), kappa-casein (CSN3); and fatty acid metabolism genes viz., butyrophilin (BTN1A1), glycerol-3-phosphate acyltransferase (GPAM), fatty acid-binding protein 3 (FABP3), and stearoyl-CoA desaturase (SCD) was assessed in 3D culture in comparison to traditional monolayer culture using qRT-PCR. Notable morphological differences were observed for BMECs grown in 3D culture in comparison to 2D culture. Morphologically, epithelial structures grown in Geltrex matrix (3D) environment showed enhanced functional differentiation in comparison to 2D culture. In 3D culture, lumen and dome-like structures were formed by day 5, whereas polarized acinus-like structure were formed within 15 days of culturing. The expression data showed higher mRNA induction of milk casein and fatty acid metabolism genes in 10-day-old 3D BMECs culture in comparison to 2D monolayer culture. The result suggests that 3D organization of epithelial cells has favorable effect on induction of milk and fatty acid metabolism-related genes. Therefore, matrix-based 3D culture of MEC that recapitulate the structural and functional context of normal tissues

  16. Determination of Iron in Layered Crystal Sodium Disilicate and Sodium Silicate by Flame Atomic Absorption Spectrometry with Boric Acid as a Matrix Modifier

    Zhi Hua WANG; Min CAI; Shu Jun WANG

    2006-01-01

    The effects of matrix silicate and experimental conditions on the determination of iron in flame atomic absorption spectrometry (FAAS) were investigated. It was found that boric acid as a matrix modifier obviously eliminated silicate interference. Under the optimum operating conditions, the determination results of iron in layered crystal sodium disilicate and sodium silicate samples by FAAS were satisfactory. The linear range of calibration curve is 0-10.5 μg.mL-1, the relative standard deviation of method is 1.2%-2.2%, the recovery of added iron is 96.0%-101%, the of iron of the standard curve method, standard addition calibration and colorimetry method was the same, but the first has the merits of rapid sample preparation, reduced contamination risks and fast analysis.

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

    2009-05-01

    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.

  18. Effects of caffeic acid phenethyl ester on matrix molecules and angiogenetic and anti-angiogenetic factors in gastric cancer cells cultured on different substrates.

    Kosova, F; Kurt, F O; Olmez, E; Tuğlu, I; Arı, Z

    2016-01-01

    Migration, invasion, metastasis and angiogenesis associated with cancer depend on the surrounding microenvironment. Angiogenesis, the growth of new capillaries, is a regulator of cancer growth and a useful target for cancer therapy. We examined matrix protein interactions in a gastric cancer cell culture that was treated with different doses of caffeic acid (3,4-dihydroxycinnamic acid) phenethyl ester (CAPE). We also investigated the relations among the levels of vascular endothelial growth factor (VEGF), matrix metalloproteinase-9 (MMP-9), endostatin (ES) and trombospondin-1 (TSP-1). Cytotoxity of CAPE was measured using the 3-(4,5-dmethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) assay. We examined the behavior of cells on laminin and collagen I coated surfaces in response to the angiogenic effect of these matrix molecules. We examined the protein alterations of these matrix molecules immunohistochemically and measured the levels of VEGF, MMP-9, ES and TSP-1 using the ELISA test. We showed that application of CAPE to the gastric cancer cell line on tissue culture plastic, laminin and collagen I significantly decreased the VEGF and MMP-9 protein levels. We found that TSP-1 levels were increased significantly in the gastric cancer cells after application of CAPE. The protein levels of gastric cancer cells also were increased significantly when tissue was cultured on laminin and collagen I. Application of CAPE to cells on laminin or collagen I coated surfaces significantly increased all of the proteins except ES. ES levels were increased on the collagen I covered surfaces, but the laminin surface decreased the levels of ES significantly. We demonstrated the beneficial effect of CAPE on a gastric cancer cell line including inhibition of proliferation and induction of some proteins that might be related to decreased angiogenesis. PMID:26523612

  19. 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

    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: lizhili@ibms.pumc.edu.cn [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)

    2013-09-10

    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

  20. Characterization and quantitative amino acids analysis of analgesic peptides in cinobufacini injection by size exclusion chromatography, matrix-assisted laser desorption/ionization time of flight mass spectrometry and gas chromatography mass spectrometry.

    Wu, Xu; Si, Nan; Bo, Gao; Hu, Hao; Yang, Jian; Bian, Baolin; Zhao, Hai Yu; Wang, Hongjie

    2015-01-01

    Cinobufacini injection that comes from the water extract of Bufo bufo gargarizans Cantor skin is widely used for cancer treatment in China. Peptide is one of its major types of constituents, however the biological effects and content of this injection are little reported. In present study, the analgesic effect of peptides was determined and evaluated by in-vivo models. To characterize and quantitatively analyze these peptides, a reliable and efficient method combining size exclusion chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with amino acid analysis was developed. The peptides presented as a series of analogs with similar molecular weights mostly ranging from 2 to 8 kDa. The amino acid analysis by gas chromatography mass spectrometry (GC-MS) was developed to determine both free and combined amino acids (FAA and CAA) in cinobufacini injection. This method achieved good linearity (R(2) , 0.9909-0.9999) and low limit of detection and quantification. FAA and CAA samples were efficiently analyzed by modified Phenomenex EZ: faast procedure. For the sample analysis, the method showed good repeatability (relative standard deviation, RSD ≤ 10%). For most FAA and CAA the mean recoveries were >80% with RSD <10%. The GC-MS based method is useful for quality assurance of both FAA and CAA in cinobufacini injection. PMID:24924921

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

    Lynne Shinto

    2011-01-01

    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.

  2. All-trans retinoic acid regulates the expression of the extracellular matrix protein fibulin-1 in the guinea pig sclera and human scleral fibroblasts

    Li, Chuanxu; McFadden, Sally A.; Morgan, Ian; Cui, Dongmei; Hu, Jianmin; Wan, Wenjuan; Zeng, Junwen

    2010-01-01

    Purpose Fibulin-1 (FBLN1) mRNA is expressed in human sclera and is an important adhesion modulatory protein that can affect cell–matrix interactions and tissue remodeling. Scleral remodeling is influenced by all-trans retinoic acid (RA). Our purpose was to confirm the presence of fibulin-1 protein in guinea pig sclera and investigate the effect of RA on the expression of fibulin-1 in guinea pig sclera in vivo and in cultured human scleral fibroblasts (HSFs). Methods Confocal fluorescence micr...

  3. GLYCOLIC-NITRIC ACID FLOWSHEET DEMONSTRATION OF THE DWPF CHEMICAL PROCESSING CELL WITH MATRIX SIMULANTS AND SUPERNATE

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

    2012-05-07

    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.

  4. Distribution in microbial genomes of genes similar to lodA and goxA which encode a novel family of quinoproteins with amino acid oxidase activity

    Campillo-Brocal, Jonatan C; Chacón-Verdú, María Dolores; Lucas-Elío, Patricia; Sánchez-Amat, Antonio

    2015-01-01

    Background L-Amino acid oxidases (LAOs) have been generally described as flavoproteins that oxidize amino acids releasing the corresponding ketoacid, ammonium and hydrogen peroxide. The generation of hydrogen peroxide gives to these enzymes antimicrobial characteristics. They are involved in processes such as biofilm development and microbial competition. LAOs are of great biotechnological interest in different applications such as the design of biosensors, biotransformations and biomedicine....

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

    Surapaneni Krishna Mohan

    2015-08-01

    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.

  6. A Similarity Search Using Molecular Topological Graphs

    2009-01-01

    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 comb...

  7. A Similarity Search Using Molecular Topological Graphs

    Yoshifumi Fukunishi

    2009-01-01

    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. Properties and mechanisms of drug release from matrix tablets containing poly(ethylene oxide) and poly(acrylic acid) as release retardants.

    Zhang, Feng; Meng, Fan; Lubach, Joseph; Koleng, Joseph; Watson, N A

    2016-08-01

    The interactions between poly(ethylene oxide) (PEO) and poly(acrylic acid) (PAA) in aqueous medium at pH 6.8 were investigated in the current study. We have also studied the effect of interpolymer interactions and various formulation variables, including the molecular weight of PEO, the ratio between PEO and PAA, the crystallinity of PEO, and the presence of an acidifying agent, on the release of theophylline from matrix tablets containing both PEO and PAA as release retardants. At pH 6.8, the synergy in solution viscosity between PEO and PAA as the result of ion-dipole interaction was observed in this study. The release of theophylline from the matrix tablets containing physical mixtures of PEO and PAA was found to be a function of dissolution medium pH because of the pH-dependent interactions between these two polymers. Because of the formation of water insoluble interpolymer complex between PEO and PAA in aqueous medium at pH below 4.0, the release of theophylline was independent of PEO molecular weight and was controlled by Fickian diffusion mechanism in 0.01N hydrochloric acid solution. In comparison, the drug release was a function of PEO molecular weight and followed the anomalous transport mechanism in phosphate buffer pH 6.8. The presence of PAA exerted opposite effects on the release of theophylline in phosphate buffer pH 6.8. In one aspect, theophylline release was accelerated because the erosion of PAA was much faster than that of PEO at pH6.8. On the opposite aspect, theophylline release was slowed down because of the formation of insoluble complex inside the gel layer as the result of the acidic microenvironment induced by PAA, and the increase in the viscosity of the gel layer as the result of the synergy between PEO and PAA. These two opposite effects offset each other. As a result, the release of theophylline remained statistically the same even when 75% PEO in the formulation was replaced with PAA. In phosphate buffer pH 6.8, the release of

  9. Nucleotide sequence of the beta-cyclodextrin glucanotransferase gene of alkalophilic Bacillus sp. strain 1011 and similarity of its amino acid sequence to those of alpha-amylases.

    Kimura, K.; Kataoka, S; Ishii, Y; Takano, T.; Yamane, K

    1987-01-01

    The nucleotide sequence of the gene for cyclodextrin glucanotransferase of alkalophilic Bacillus sp. strain 1011 was determined. The deduced amino acid sequence at the NH2-terminal side of the enzyme showed a high homology with the sequences of alpha-amylase in the three regions which constitutes the active centers of alpha-amylases.

  10. Investigation of interaction preferences in protein-nucleic acid complexes by the evaluation of interaction energy matrix of amino acid-base pairs

    Jakubec, Dávid; Vondrášek, Jiří

    Praha: Ústav organické chemie a biochemie AV ČR, 2016. s. 68. ISBN 978-80-86241-55-5. [Prague Protein Spring Meeting 2016: Proteins and their Design /4./. 05.05.2016-08.05.2016, Praha] Institutional support: RVO:61388963 Keywords : protein-nucleic acid complexes * interaction energy Subject RIV: CF - Physical ; Theoretical Chemistry

  11. Unifying bacteria from decaying wood with various ubiquitous Gibbsiella species as G. acetica sp. nov. based on nucleotide sequence similarities and their acetic acid secretion.

    Geider, Klaus; Gernold, Marina; Jock, Susanne; Wensing, Annette; Völksch, Beate; Gross, Jürgen; Spiteller, Dieter

    2015-12-01

    Bacteria were isolated from necrotic apple and pear tree tissue and from dead wood in Germany and Austria as well as from pear tree exudate in China. They were selected for growth at 37 °C, screened for levan production and then characterized as Gram-negative, facultatively anaerobic rods. Nucleotide sequences from 16S rRNA genes, the housekeeping genes dnaJ, gyrB, recA and rpoB alignments, BLAST searches and phenotypic data confirmed by MALDI-TOF analysis showed that these bacteria belong to the genus Gibbsiella and resembled strains isolated from diseased oaks in Britain and Spain. Gibbsiella-specific PCR primers were designed from the proline isomerase and the levansucrase genes. Acid secretion was investigated by screening for halo formation on calcium carbonate agar and the compound identified by NMR as acetic acid. Its production by Gibbsiella spp. strains was also determined in culture supernatants by GC/MS analysis after derivatization with pentafluorobenzyl bromide. Some strains were differentiated by the PFGE patterns of SpeI digests and by sequence analyses of the lsc and the ppiD genes, and the Chinese Gibbsiella strain was most divergent. The newly investigated bacteria as well as Gibbsiella querinecans, Gibbsiella dentisursi and Gibbsiella papilionis, isolated in Britain, Spain, Korea and Japan, are taxonomically related Enterobacteriaceae, tolerate and secrete acetic acid. We therefore propose to unify them in the species Gibbsiella acetica sp. nov. PMID:26071988

  12. Beta-oxidation of 1-[14C]-17-[131I]-iodoheptadecanoic acid following intracoronary injection in humans results in similar release of both tracers

    Radioiodine labelled 17-iodo-heptadecanoic acid (IHA) is used for non-invasive study of myocardial metabolism in coronary heart disease and cardiomyopathy. In five patients undergoing coronary sinus catheterization, a mixture of about 40 kBg of [123I] NaI was injected into the left coronary artery. During the following 15-min period, frequent blood samples were taken from the aorta and the coronary sinus. In the aqueous phase of the venous blood, 14CO2 and inorganic 131I appeared nearly in parallel, with a peak time of 4-5 min. Moreover, there was no significant back diffusion of IHA and no significant non-specific deiodination detectable. There was myocardial retention of inorganic iodide (123I) injected into the left coronary artery. The data strongly support the premise that lipid turnover through β-oxidation is the rate-limiting step in the externally measured release of iodide after IHA injection, provided that recirculating inorganic radioactive iodide is corrected for. In addition, 15 volunteers were studied using [11C]palmitic acid and [123I]IHA using PET and dynamic planar camera scintigraphy with iodide correction. There was no significant difference between the mean values of the elimination half-times, and also no significant correlation between half-times of both fatty acids for single individuals. (orig.)

  13. In vitro dissolution study of acetylsalicylic acid solid dispersions. Tunable drug release allowed by the choice of polymer matrix

    Policianová, Olivia; Brus, Jiří; Hrubý, Martin; Urbanová, Martina

    2015-01-01

    Roč. 20, č. 8 (2015), s. 935-940. ISSN 1083-7450 R&D Projects: GA ČR(CZ) GA14-03636S; GA ČR GPP106/11/P426 Grant ostatní: AV ČR(CZ) M200501201 Institutional support: RVO:61389013 Keywords : acetylsallicylic acid * controlled drug release * polymers Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.202, year: 2014

  14. Gallic acid abolishes the EGFR/Src/Akt/Erk-mediated expression of matrix metalloproteinase-9 in MCF-7 breast cancer cells.

    Chen, Ying-Jung; Lin, Ku-Nan; Jhang, Li-Mei; Huang, Chia-Hui; Lee, Yuan-Chin; Chang, Long-Sen

    2016-05-25

    Several studies have revealed that natural compounds are valuable resources to develop novel agents against dysregulation of the EGF/EGFR-mediated matrix metalloproteinase-9 (MMP-9) expression in cancer cells. In view of the findings that EGF/EGFR-mediated MMP-9 expression is closely related to invasion and metastasis of breast cancer. To determine the beneficial effects of gallic acid on the suppression of breast cancer metastasis, we explored the effect of gallic acid on MMP-9 expression in EGF-treated MCF-7 breast cancer cells. Treatment with EGF up-regulated MMP-9 mRNA and protein levels in MCF-7 cells. EGF treatment induced phosphorylation of EGFR and elicited Src activation, subsequently promoting Akt/NFκB (p65) and ERK/c-Jun phosphorylation in MCF-7 cells. Activation of Akt/p65 and ERK/c-Jun was responsible for the MMP-9 up-regulation in EGF-treated cells. Gallic acid repressed the EGF-induced activation of EGFR and Src; furthermore, inactivation of Akt/p65 and ERK/c-Jun was a result of the inhibitory effect of gallic acid on the EGF-induced MMP-9 up-regulation. Over-expression of constitutively active Akt and MEK1 or over-expression of constitutively active Src eradicated the inhibitory effect of gallic acid on the EGF-induced MMP-9 up-regulation. A chromosome conformation capture assay showed that EGF induced a chromosomal loop formation in the MMP-9 promoter via NFκB/p65 and AP-1/c-Jun activation. Treatment with gallic acid, EGFR inhibitor, or Src inhibitor reduced DNA looping. Taken together, our data suggest that gallic acid inhibits the activation of EGFR/Src-mediated Akt and ERK, leading to reduced levels of p65/c-Jun-mediated DNA looping and thus inhibiting MMP-9 expression in EGF-treated MCF-7 cells. PMID:27087131

  15. A study on chemical separation of 55Fe, 59Ni, 63Ni, 90Sr and 94Nb in boric acid matrix

    Several radionuclides are considered as an object of the assesment to develop a scaling factor and a periodical verification method which are needed for the evaluation of radionuclide inventory of concentration bottoms from nuclear power plants in Korea. A selective separation of 55Fe, 59Ni, 63Ni, 90Sr and 94Nb which should be recovered individually for the radioactivity measurement was described in detail. Sorption and desorption behaviours of ion exchange and extraction chromatographic resins for Fe, Ni, Sr, Nb and co-existing metal ions in boric acid matrix were investigated using simulated concentration bottom dissolved solutions. Separation conditions available for the sequential recovery of the metal ions from a single sample were optimized to minimize a discharge of radioactive wastes produced through the analytical process and the radiation exposure to analysts. Their recovery yields were measured with reliability

  16. Conversion of NfsA, the Major Escherichia coli Nitroreductase, to a Flavin Reductase with an Activity Similar to That of Frp, a Flavin Reductase in Vibrio harveyi, by a Single Amino Acid Substitution

    Zenno, Shuhei; Kobori, Toshiro; Tanokura, Masaru; Saigo, Kaoru

    1998-01-01

    NfsA is the major oxygen-insensitive nitroreductase of Escherichia coli, similar in amino acid sequence to Frp, a flavin reductase of Vibrio harveyi. Here, we show that a single amino acid substitution at position 99, which may destroy three hydrogen bonds in the putative active center, transforms NfsA from a nitroreductase into a flavin reductase that is as active as the authentic Frp and a tartrazine reductase that is 30-fold more active than wild-type NfsA. PMID:9440535

  17. Characterization of radiation-induced damage to nucleic acid constituents by matrix-assisted laser desorption FTMS

    Ionizing radiation causes DNA damage that can result in strand breaks as well as base and sugar modifications, and may lead to mutations and ultimately, cell death. It is necessary to determine both the identities and abundances of the radiation-induced products in order to probe the nature of DNA damage in these cases. Previous research in this area has focused on the use of GC-MS techniques for the separation and identification of radiation products. However, because these biomolecules are polar, non-volatile species, it is necessary to derivatize these compounds prior to analysis. This sample preparation step may distort the sample by creating compounds that were not generated by the radiation event. In order to circumvent this problem, matrix-assisted laser desorption FTMS is being developed for the direct examination of products generated by x-ray irradiation of aqueous nucelotide solutions. No hydrolysis or derivatization is necessary in this case, and products ranging from nucleic bases to small oligonucleotides can be simultaneously examined. The ion manipulation and accurate mass measurement of FTMS should provide detailed structural information for picomole quantities of these products. In particular, collisional dissociation experiments will used to probe compound structures in an effort to differentiate isomers

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

    Blekas, Georgios

    1998-02-01

    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

  19. Improving thermal stability and light fastness of Acid Red 114 by incorporating its anions in a ZnAl-layered double hydroxides matrix

    Haifeng Zhu; Liren Wang; Pinggui Tang; Yongjun Feng; Dianqing Li

    2012-01-01

    Incorporation of anions of Acid Red 114 dye (1,3-naphthalenedisulfonic acid,8-[2-[3,3'-dimethyl-4'-[2-[4-[[(4-methylphenyl)sulfonyl]oxy] phenyl]diazenyl] [1,1'-biphenyl]-4-yl]diazenyl]-7-hydroxy-,disodium salt) (denoted as NPDA) into ZnAl-layered double hydroxides (LDHs) has been carried out by an anionexchange method in an effort to improve their thermal stability and light fastness.After intercalation of NPDA anions,the interlayer distance of the LDHs increases from 0.87 to 2.18nm,confirming their incorporation into the interlayer galleries of the LDHs host.Infrared spectroscopy and thermogravimetric analysis revealed the presence of host-guest interactions between LDHs layers and NPDA anions.The thermal stability of NPDA and ZnAl-NPDA-LDHs was compared by thermogravimetric-differential thermal analysis,UV-visible spectroscopy and infrared spectroscopy.It was found that the thermal stability of NPDA anions was markedly improved by incorporation into the ZnAl-LDHs matrix,while the light fastness was also enhanced.

  20. Synergistic Chondroprotective Effect of α-Tocopherol, Ascorbic Acid, and Selenium as well as Glucosamine and Chondroitin on Oxidant Induced Cell Death and Inhibition of Matrix Metalloproteinase-3—Studies in Cultured Chondrocytes

    Anne-Christi Graeser

    2009-12-01

    Full Text Available Overproduction of reactive oxygen species and impaired antioxidant defence accompanied by chronic inflammatory processes may impair joint health. Pro-inflammatory cytokines such as interleukin-1β (IL-1β and tumor necrosis factor alpha (TNF-α stimulate the expression of metalloproteinases which degrade the extracellular matrix. Little is known regarding the potential synergistic effects of natural compounds such as α-tocopherol (α-toc, ascorbic acid (AA and selenium (Se on oxidant induced cell death. Furthermore studies regarding the metalloproteinase-3 inhibitory activity of glucosamine sulfate (GS and chondroitin sulfate (CS are scarce. Therefore we have studied the effect of α-toc (0.1–2.5 µmol/L, AA (10–50 µmol/L and Se (1–50 nmol/L on t-butyl hydroperoxide (t-BHP, 100–500 µmol/L-induced cell death in SW1353 chondrocytes. Furthermore we have determined the effect of GS and CS alone (100–500 µmol/L each and in combination on MMP3 mRNA levels and MMP3 secretion in IL-1β stimulated chondrocytes. A combination of α-toc, AA, and Se was more potent in counteracting t-BHP-induced cytotoxicity as compared to the single compounds. Similarly a combination of CS and GS was more effective in inhibiting MMP3 gene expression and secretion than the single components. The inhibition of MMP3 secretion due to GS plus CS was accompanied by a decrease in TNF-α production. Combining natural compounds such as α-toc, AA, and Se as well as GS and CS seems to be a promising strategy to combat oxidative stress and cytokine induced matrix degradation in chondrocytes.

  1. Selective extraction of U(VI), Th(IV), and La(III) from acidic matrix solutions and environmental samples using chemically modified Amberlite XAD-16 resin

    A new grafted polymer has been developed by the chemical modification of Amberlite XAD-16 (AXAD-16) polymeric matrix with [(2-dihydroxyarsinoylphenylamino)methyl]phosphonic acid (AXAD-16-AsP). The modified polymer was characterized by a combination of 13C CPMAS and 31P solid-state NMR, Fourier transform-NIR-FIR-Raman spectroscopy, CHNPS elemental analysis, and thermogravimetric analysis (TGA). The distribution studies for the extraction of U(VI), Th(IV), and La(III) from acidic solutions were performed using an AXAD-16-AsP-packed chromatographic column. The influences of various physiochemical parameters on analyte recovery were optimized by both static and dynamic methods. Accordingly, even under high acidities (>4 M), good distribution ratio (D) values (102-104) were achieved for all the analytes. Metal ion desorption was effective using 1 mol L-1 (NH4)2CO3. From kinetic studies, a time duration of -1 for U(VI); 0.47, 0.39, and 1.40 mmol g-1 for Th(IV); and 1.44, 1.48, and 1.12 mmol g-1 for La(III), in the presence of 2 mol L-1 HNO3, 2 mol L-1 HCl, and under pH conditions, respectively. The analyte selectivity of the grafted polymer was tested in terms of interfering species tolerance studies. The system showed an enrichment factor of 365, 300, and 270 for U(VI), Th(IV), and La(III), and the limit of analyte detection was in the range of 18-23 ng mL-1. The practical applicability of the polymer was tested with synthetic nuclear spent fuel and seawater mixtures, natural water, and geological samples. The RSD of the total analytical procedure was within 4.9%, thus confirming the reliability of the developed method. (orig.)

  2. 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

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

    2015-01-01

    Background : Numerous therapeutic options have been tried in the management of melasma. Aims and Objectives : 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. Materials and Methods: Forty patients with melasma were recruited into this study and randomized into two groups. Group A...

  3. Matrix tablets based on thiolated poly(acrylic acid): pH-dependent variation in disintegration and mucoadhesion.

    Guggi, Davide; Marschütz, Michaela K; Bernkop-Schnürch, Andreas

    2004-04-15

    This study examined the influence of the pH on the mucoadhesive and cohesive properties of polyarcylic acid (PAA) and thiolated PAA. The pH of PAA (molecular mass: 450 kDa) and of a corresponding PAA-cysteine conjugate was adjusted to 3, 4, 5, 6, 7 and 8. The amount of immobilised thiol groups and disulfide bonds was determined via Ellman's reagent. Tablets were compressed out of each pH-batch of both thiolated and unmodified PAA and the swelling behaviour, the disintegration time and the mucoadhesiveness were evaluated. The amount of thiol/disulfide groups per gram thiolated PAA of pH 3 and pH 8 was determined to be 332 +/- 94 micromol and 162 +/- 46 micromol, respectively. The thiolated PAA tablets displayed a minimum four-fold higher water uptake compared to unmodified PAA tablets. A faster and higher water uptake of both polymer types was observed above pH 5. Thiolated polymer tablets showed a 3-20-fold more prolonged disintegration time than unmodified PAA tablets. The cohesiveness of PAA-cysteine conjugate increased at higher pH, whereas the unmodified PAA behaved inversely. A 3-7-fold stronger mucoadhesiveness was observed for the PAA-cysteine conjugate tablets compared to unmodified PAA tablets. For both thiolated and unmodified polymer the mucoadhesiveness was 2-4-fold enhanced below pH 5. The difference in mucoadhesion between the two polymer types was most pronounced at these lower pH values. In this study substantial information regarding the pH-dependence of mucoadhesion and cohesion of unmodified polyacrylates and of thiolated polyacrylates is provided, representing helpful basic information for an ameliorated deployment of these polymers. PMID:15072786

  4. Alpha-amylase from germinating soybean (Glycine max) seeds--purification, characterization and sequential similarity of conserved and catalytic amino acid residues.

    Kumari, Arpana; Singh, Vinay Kumar; Fitter, Jörg; Polen, Tino; Kayastha, Arvind M

    2010-10-01

    Starch hydrolyzing amylase from germinated soybeans seeds (Glycine max) has been purified 400-fold to electrophoretic homogeneity with a final specific activity of 384 units/mg. SDS-PAGE of the final preparation revealed a single protein band of 100 kDa, whereas molecular mass was determined to be 84 kDa by MALDI-TOF and gel filtration on Superdex-200 (FPLC). The enzyme exhibited maximum activity at pH 5.5 and a pI value of 4.85. The energy of activation was determined to be 6.09 kcal/mol in the temperature range 25-85 degrees C. Apparent Michaelis constant (K(m)((app))) for starch was 0.71 mg/mL and turnover number (k(cat)) was 280 s(-1) in 50 mM sodium acetate buffer, pH 5.5. Thermal inactivation studies at 85 degrees C showed first-order kinetics with rate constant (k) equal to 0.0063 min(-1). Soybean alpha-amylase showed high specificity for its primary substrate starch. High similarity of soybean alpha-amylase with known amylases suggests that this alpha-amylase belongs to glycosyl hydrolase family 13. Cereal alpha-amylases have gained importance due to their compatibility for biotechnological applications. Wide availability and easy purification protocol make soybean as an attractive alternative for plant alpha-amylase. Soybean can be used as commercially viable source of alpha-amylase for various industrial applications. PMID:20655076

  5. 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

    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:H2O 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 Qn to Tn signals detected in the 29Si 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

  6. Tailoring of the titanium surface by preparing cardiovascular endothelial extracellular matrix layer on the hyaluronic acid micro-pattern for improving biocompatibility.

    Li, Jingan; Zhang, Kun; Wu, Juejue; Zhang, Lijuan; Yang, Ping; Tu, Qiufen; Huang, Nan

    2015-04-01

    It has been proved that high molecular weight hyaluronic acid (HMW-HA, 1×10(6) Da) micro-strips on titanium (Ti) surface can elongate the human vascular endothelial cell (EC) morphology, subsequently enhance endothelial extracellular matrix (ECM) deposition in our previous work. The HMW-HA micro-strips were anticipated to possess good hemocompatibility and EC compatibility simultaneously. However, the single HMW-HA micro-strips on Ti substrate showed bad hemocompatibility. To solve this problem, a method combining HA micro-pattern and EC decellularization was developed, and the endothelial extracellular matrix layer on the HA micro-pattern (ECM/HAP) showed excellent hemocompatibility and endothelial progenitor cells (EPCs) compatibility (cell number: 14.3±0.5×10(5) cells/cm2>2.2±0.7×10(5) cells/cm2 on ECM/TiOH, 7.5±1.3×10(5) cells/cm2 on TiOH, 3.4±0.9×10(5) cells/cm2 on TiOH/HAP and 3.6±1.2×10(5) cells/cm2 on Ti). We also found that the ECM/HAP coating could significantly inhibit the excessive proliferation of smooth muscle cells (SMCs) (cck-8 absorption: 0.25±0.06coating can be used to build the bionic human endothelial ECM on the biomaterials surface, which might provide a potential and effective method for surface modification of cardiovascular devices. PMID:25684737

  7. ZmPUMP encodes a fully functional monocot plant uncoupling mitochondrial protein whose affinity to fatty acid is increased with the introduction of a His pair at the second matrix loop

    Uncoupling proteins (UCPs) are specialized mitochondrial transporter proteins that uncouple respiration from ATP synthesis. In this study, cDNA encoding maize uncoupling protein (ZmPUMP) was expressed in Escherichia coli and recombinant ZmPUMP reconstituted in liposomes. ZmPUMP activity was associated with a linoleic acid (LA)-mediated H+ efflux with K m of 56.36 ± 0.27 μM and V max of 66.9 μmol H+ min-1 (mg prot)-1. LA-mediated H+ fluxes were sensitive to ATP inhibition with K i of 2.61 ± 0.36 mM (at pH 7.2), a value similar to those for dicot UCPs. ZmPUMP was also used to investigate the importance of a histidine pair present in the second matrix loop of mammalian UCP1 and absent in plant UCPs. ZmPUMP with introduced His pair (Lys155His and Ala157His) displayed a 1.55-fold increase in LA-affinity while its activity remained unchanged. Our data indicate conserved properties of plant UCPs and suggest an enhancing but not essential role of the histidine pair in proton transport mechanism

  8. Amino acid properties conserved in molecular evolution.

    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.

  9. Matrix Isolation Infrared Spectroscopy of an O-H···π Hydrogen-Bonded Complex between Formic Acid and Benzene.

    Banerjee, Pujarini; Bhattacharya, Indrani; Chakraborty, Tapas

    2016-05-26

    Mid-infrared spectra of an O-H···π hydrogen-bonded 1:1 complex between formic acid and benzene were measured by isolating the complex in an argon matrix at a temperature of 8 K. The O-H stretching fundamental of formic acid (νO-H) undergoes a red shift of 120 cm(-1), which is the largest among the known π-hydrogen bonded complexes of an O-H donor with respect to benzene as acceptor. Electronic structure theory methods were used extensively to suggest a suitable geometry of the complex that is consistent with a recent study performed at CCSD(T)/CBS level by Zhao et al. (J. Chem. Theory Comput. 2009, 5, 2726-2733), as well as with the measured IR spectral shifts of the present study. It has been determined that density functional theory (DFT) D functionals as well as parametrized DFT functionals like M06-2X, in conjunction with modestly sized basis sets like 6-31G (d, p), are sufficient for correct predictions of the spectral shifts observed in our measurement and also for reproducing the value of the binding energy reported by Zhao et al. We also verified that these low-cost methods are sufficient in predicting the νO-H spectral shifts of an analogous O-H···π hydrogen-bonded complex between phenol and benzene. However, some inconsistencies with respect to shifts of νO-H arise when diffuse functions are included in the basis sets, and the origin of this anomaly is shown to lie in the predicted geometry of the complex. Natural bond orbital (NBO) and atoms-in-molecule (AIM) analyses were performed to correlate the spectral behavior of the complex with its geometric parameters. PMID:27163753

  10. Perfluorooctanoic acid enhances colorectal cancer DLD-1 cells invasiveness through activating NF-κB mediated matrix metalloproteinase-2/-9 expression

    Miao, Chen; Ma, Jun; Zhang, Yajie; Chu, Yimin; Li, Ji; Kuai, Rong; Wang, Saiyu; Peng, Haixia

    2015-01-01

    Objective: Perfluorooctanoic acid (PFOA) is widely used in consumer products and detected in human serum. Our study meant to elucidate the uncovered molecular mechanisms underlying the PFOA induced colorectal cancer cell DLD-1 invasion and matrix metalloproteinases (MMP) expression. Methods and results: Trans-well filter assay appeared that PFOA treatment stimulated DLD-1 cells invasion significantly. Meanwhile, the results of luciferase reporter, quantitative real-time PCR, western blotting, and gelatin zymography showed that PFOA induced MMP-2/-9 expression and enzyme activation levels consistently (P PFOA could enhance nuclear factor kappaB (NF-κB) activity by stimulating NF-κB translocation into nuclear in DLD-1 cells. Furthermore, JSH-23, a well-known NF-κB inhibitor, could reverse the PFOA induced colorectal cancer cell invasion and MMP-2/-9 expression. Conclusions: Our study confirmed that PFOA could induce colorectal cancer cell DLD-1 invasive ability and MMP-2/-9 expression through activating NF-κB, which deserves more concerns on environmental pollutant-resulted public health risk. PMID:26617761

  11. Matrix string interactions

    Periwal, Vipul; Tafjord, Oyvind

    1998-01-01

    String configurations have been identified in compactified Matrix theory at vanishing string coupling. We show how the interactions of these strings are determined by the Yang-Mills gauge field on the worldsheet. At finite string coupling, this suggests the underlying dynamics is not well-approximated as a theory of strings. This may explain why string perturbation theory diverges badly, while Matrix string perturbation theory presumably has a perturbative expansion with properties similar to...

  12. Sinapinic acid-directed synthesis of gold nanoclusters and their application to quantitative matrix-assisted laser desorption/ionization mass spectrometry

    Chen, Tzu-Heng; Yu, Cheng-Ju; Tseng, Wei-Lung

    2014-01-01

    Core etching of gold nanoparticles (AuNPs) into smaller-sized clusters is a classic method for fabricating gold nanoclusters (AuNCs). The top down-based synthesis of AuNCs includes two steps: (i) reducing the Au3+ precursor solution to generate AuNPs in the presence of protecting ligands and (ii) core etching of the formed AuNPs into the AuNCs via ligand exchange. For the first time, this paper describes a one-step approach for preparing AuNCs using a top down approach. The sinapinic acid (SA)-induced formation of the AuNCs involved a three-step reaction process. First, large AuNPs (>200 nm) were quickly formed after mixing SA and the Au3+ precursor solution. Second, excess SA molecules self-assembled on the NP surface, and large AuNPs were etched to small AuNPs via electrostatic repulsion between the neighboring SA molecules. Finally, SA-induced core etching of the AuNPs resulted in the formation of the AuNCs within 70 min. Furthermore, we showed that the presence of the AuNCs in SA was capable of suppressing crystal growth and eliminating the coffee-ring effect. Thus, proteins can be successfully quantified using the SA-AuNCs as matrices for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Compared with using SA as matrices, the SA-AuNCs offered substantial advantages for improving shot-to-shot reproducibility and enhancing the ionization efficiency of proteins.Core etching of gold nanoparticles (AuNPs) into smaller-sized clusters is a classic method for fabricating gold nanoclusters (AuNCs). The top down-based synthesis of AuNCs includes two steps: (i) reducing the Au3+ precursor solution to generate AuNPs in the presence of protecting ligands and (ii) core etching of the formed AuNPs into the AuNCs via ligand exchange. For the first time, this paper describes a one-step approach for preparing AuNCs using a top down approach. The sinapinic acid (SA)-induced formation of the AuNCs involved a three-step reaction process. First, large

  13. Sinapinic acid-directed synthesis of gold nanoclusters and their application to quantitative matrix-assisted laser desorption/ionization mass spectrometry.

    Chen, Tzu-Heng; Yu, Cheng-Ju; Tseng, Wei-Lung

    2014-01-01

    Core etching of gold nanoparticles (AuNPs) into smaller-sized clusters is a classic method for fabricating gold nanoclusters (AuNCs). The top down-based synthesis of AuNCs includes two steps: (i) reducing the Au(3+) precursor solution to generate AuNPs in the presence of protecting ligands and (ii) core etching of the formed AuNPs into the AuNCs via ligand exchange. For the first time, this paper describes a one-step approach for preparing AuNCs using a top down approach. The sinapinic acid (SA)-induced formation of the AuNCs involved a three-step reaction process. First, large AuNPs (>200 nm) were quickly formed after mixing SA and the Au(3+) precursor solution. Second, excess SA molecules self-assembled on the NP surface, and large AuNPs were etched to small AuNPs via electrostatic repulsion between the neighboring SA molecules. Finally, SA-induced core etching of the AuNPs resulted in the formation of the AuNCs within 70 min. Furthermore, we showed that the presence of the AuNCs in SA was capable of suppressing crystal growth and eliminating the coffee-ring effect. Thus, proteins can be successfully quantified using the SA-AuNCs as matrices for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Compared with using SA as matrices, the SA-AuNCs offered substantial advantages for improving shot-to-shot reproducibility and enhancing the ionization efficiency of proteins. PMID:24288017

  14. All-trans retinoic acid regulates the expression of the extracellular matrix protein fibulin-1 in the guinea pig sclera and human scleral fibroblasts

    Li, Chuanxu; McFadden, Sally A.; Morgan, Ian; Cui, Dongmei; Hu, Jianmin; Wan, Wenjuan

    2010-01-01

    Purpose Fibulin-1 (FBLN1) mRNA is expressed in human sclera and is an important adhesion modulatory protein that can affect cell–matrix interactions and tissue remodeling. Scleral remodeling is influenced by all-trans retinoic acid (RA). Our purpose was to confirm the presence of fibulin-1 protein in guinea pig sclera and investigate the effect of RA on the expression of fibulin-1 in guinea pig sclera in vivo and in cultured human scleral fibroblasts (HSFs). Methods Confocal fluorescence microscopy was used to study fibulin-1 and aggrecan expression and localization in sclera from control guinea pigs and in animals given RA by daily gavage from 4 to 8 days of age. The effects of RA (from 10−9 to 10−5 M) on fibulin-1 expression in HSFs were observed by immunohistochemistry and assayed by real-time PCR and western blot analysis. Results Fibulin-1 protein expression was detected by confocal fluorescence microscopy in guinea pig sclera and in cultured HSFs. Upregulation of fibulin-1 in scleral tissue was observed after feeding with RA. In vitro, the level of Fbln1 mRNA was increased after treatment of HSFs with RA (at concentrations of 10−8 to 10−6 M; p<0.001), with a maximum effect at 10−7 M. Fibulin-1 protein levels were significantly increased after treatment of HSFs with 10−7 M of RA for 24 or 48 h (p<0.05). Conclusions Fibulin-1 protein was expressed in guinea pig sclera and cultured HSFs. Expression was regulated by RA, a molecule known to be involved in the regulation of eye growth. Further studies on the role of fibulin-1 in the regulation of eye growth, including during the development of myopia, are therefore warranted. PMID:20405022

  15. Channel matrix, measurement matrix and collapsed matrix in teleportation

    Zha, Xin-Wei; Qi, Jian-Xia; Song, Hai-Yang

    2014-01-01

    In this paper, two kinds of coefficient matrixes (channel matrix, measurement matrix)associated with the pure state for teleportation are presented, the general relation among channel matrix, measurement matrix and collapsed matrix is obtained. In addition, a criterion for teleportation that the number of coefficient of an unknown state is determined by the rank of the collapsed matrix is given.

  16. The matrix theory S matrix

    Plefka, J. C.; Serone, M.; Waldron, A.K.

    1998-01-01

    The technology required for eikonal scattering amplitude calculations in Matrix theory is developed. Using the entire supersymmetric completion of the v^4/r^7 Matrix theory potential we compute the graviton-graviton scattering amplitude and find agreement with eleven dimensional supergravity at tree level.

  17. Tamibarotene-loaded citric acid-crosslinked alkali-treated collagen matrix as a coating material for a drug-eluting stent

    Motoki Inoue, Mariko Takayanagi, Katsuhito Fujiu, Ichiro Manabe, Ryozo Nagai and Tetsushi Taguchi

    2012-01-01

    Full Text Available Tamibarotene-loaded biodegradable matrices with antithrombogenic and drug-releasing properties were prepared in a crosslinking reaction between amino groups of alkali-treated collagen (AlCol and active ester groups of trisuccinimidyl citrate. The resulting matrices were characterized by their residual amino group concentrations, swelling ratios and thermal, antithrombogenic and drug-releasing properties. It was clarified that the addition of tamibarotene does not inhibit matrix formation. After immersion in water, the swelling ratio of a matrix became lower than that prior to immersion. Thermal analysis indicated that AlCol interacted with tamibarotene. The addition of tamibarotene to the matrix did not influence the antithrombogenic property of the resulting matrix. A matrix with a high crosslinking density had a prolonged tamibarotene elution time. These results demonstrate that tamibarotene-loaded matrices have great potential as a coating material for drug-eluting stents.

  18. Matrix calculus

    Bodewig, E

    1959-01-01

    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

  19. A toolbox for representational similarity analysis.

    Hamed Nili; Cai Wingfield; Alexander Walther; Li Su; William Marslen-Wilson; Nikolaus Kriegeskorte

    2014-01-01

    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 enca...

  20. A toolbox for representational similarity analysis

    Nili, Hamed; Wingfield, Cai; Walther, Alexander; Su, Li; Marslen-Wilson, William; KRIEGESKORTE, Nikolaus

    2014-01-01

    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 enca...

  1. Textual Spatial Cosine Similarity

    Crocetti, Giancarlo

    2015-01-01

    When dealing with document similarity many methods exist today, like cosine similarity. More complex methods are also available based on the semantic analysis of textual information, which are computationally expensive and rarely used in the real time feeding of content as in enterprise-wide search environments. To address these real-time constraints, we developed a new measure of document similarity called Textual Spatial Cosine Similarity, which is able to detect similitude at the semantic ...

  2. Protein-protein interaction based on pairwise similarity

    Zaki Nazar

    2009-05-01

    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.

  3. Sequence-specific nucleic acid mobility using a reversible block copolymer gel matrix and DNA amphiphiles (lipid-DNA) in capillary and microfluidic electrophoretic separations.

    Wagler, Patrick; Minero, Gabriel Antonio S; Tangen, Uwe; de Vries, Jan Willem; Prusty, Deepak; Kwak, Minseok; Herrmann, Andreas; McCaskill, John S

    2015-10-01

    Reversible noncovalent but sequence-dependent attachment of DNA to gels is shown to allow programmable mobility processing of DNA populations. The covalent attachment of DNA oligomers to polyacrylamide gels using acrydite-modified oligonucleotides has enabled sequence-specific mobility assays for DNA in gel electrophoresis: sequences binding to the immobilized DNA are delayed in their migration. Such a system has been used for example to construct complex DNA filters facilitating DNA computations. However, these gels are formed irreversibly and the choice of immobilized sequences is made once off during fabrication. In this work, we demonstrate the reversible self-assembly of gels combined with amphiphilic DNA molecules, which exhibit hydrophobic hydrocarbon chains attached to the nucleobase. This amphiphilic DNA, which we term lipid-DNA, is synthesized in advance and is blended into a block copolymer gel to induce sequence-dependent DNA retention during electrophoresis. Furthermore, we demonstrate and characterize the programmable mobility shift of matching DNA in such reversible gels both in thin films and microchannels using microelectrode arrays. Such sequence selective separation may be employed to select nucleic acid sequences of similar length from a mixture via local electronics, a basic functionality that can be employed in novel electronic chemical cell designs and other DNA information-processing systems. PMID:26095642

  4. Approximate similarity search

    Amato, Giuseppe

    2000-01-01

    Similarity searching is fundamental in various application areas. Recently it has attracted much attention in the database community because of the growing need to deal with large volume of data. Consequently, efficiency has become a matter of concern in design. Although much has been done to develop structures able to perform fast similarity search, results are still not satisfactory, and more research is needed. The performance of similarity search for complex features deteriorates and does...

  5. Clustering by Pattern Similarity

    Hai-xun Wang; Jian Pei

    2008-01-01

    The task of clustering is to identify classes of similar objects among a set of objects. The definition of similarity varies from one clustering model to another. However, in most of these models the concept of similarity is often based on such metrics as Manhattan distance, Euclidean distance or other Lp distances. In other words, similar objects must have close values in at least a set of dimensions. In this paper, we explore a more general type of similarity. Under the pCluster model we proposed, two objects are similar if they exhibit a coherent pattern on a subset of dimensions. The new similarity concept models a wide range of applications. For instance, in DNA microarray analysis, the expression levels of two genes may rise and fall synchronously in response to a set of environmental stimuli. Although the magnitude of their expression levels may not be close, the patterns they exhibit can be very much alike. Discovery of such clusters of genes is essential in revealing significant connections in gene regulatory networks. E-commerce applications, such as collaborative filtering, can also benefit from the new model, because it is able to capture not only the closeness of values of certain leading indicators but also the closeness of (purchasing, browsing, etc.) patterns exhibited by the customers. In addition to the novel similarity model, this paper also introduces an effective and efficient algorithm to detect such clusters, and we perform tests on several real and synthetic data sets to show its performance.

  6. Media segmentation using self-similarity decomposition

    Foote, Jonathan T.; Cooper, Matthew L.

    2003-01-01

    We present a framework for analyzing the structure of digital media streams. Though our methods work for video, text, and audio, we concentrate on detecting the structure of digital music files. In the first step, spectral data is used to construct a similarity matrix calculated from inter-frame spectral similarity.The digital audio can be robustly segmented by correlating a kernel along the diagonal of the similarity matrix. Once segmented, spectral statistics of each segment are computed. In the second step,segments are clustered based on the self-similarity of their statistics. This reveals the structure of the digital music in a set of segment boundaries and labels. Finally, the music is summarized by selecting clusters with repeated segments throughout the piece. The summaries can be customized for various applications based on the structure of the original music.

  7. The semantic similarity ensemble

    Andrea Ballatore

    2013-12-01

    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.

  8. Matrix effects in plasma desorption mass spectrometry

    Bouchonnet, Stephane; Hoppilliard, Yannik; Mauriac, Christine

    1993-07-01

    In Plasma Desorption (PD) Mass Spectrometry, valine/matrix mixtures have been studied in order to specify the influence of a matrix during the desorption-ionization (DI) of volume. The different matrices used were carboxylic acids (barbituric acid, 2-chloronicotinic acid, 3-chloropropionic acid, cysteine, pentafluorobenzoic acid, picric acid, sinapinic acid) and CsI, an inorganic salt. Three effects are proposed to explain the influence of each matrix on the DI of valine: a physical effect, a chemical effect and a (de)cationization effect. Thermodynamic diagrams are proposed to explain each effect. Each matrix gives either a specific effect or a superimposition of effects. The concentration effect of matrices is also studied.

  9. Stability of similarity measurements for bipartite networks

    Liu, Jian-Guo; Pan, Xue; Guo, Qiang; Zhou, Tao

    2015-01-01

    Similarity is a fundamental measure in network analyses and machine learning algorithms, with wide applications ranging from personalized recommendation to socio-economic dynamics. We argue that an effective similarity measurement should guarantee the stability even under some information loss. With six bipartite networks, we investigate the stabilities of fifteen similarity measurements by comparing the similarity matrixes of two data samples which are randomly divided from original data sets. Results show that, the fifteen measurements can be well classified into three clusters according to their stabilities, and measurements in the same cluster have similar mathematical definitions. In addition, we develop a top-$n$-stability method for personalized recommendation, and find that the unstable similarities would recommend false information to users, and the performance of recommendation would be largely improved by using stable similarity measurements. This work provides a novel dimension to analyze and eval...

  10. Gender similarities and differences.

    Hyde, Janet Shibley

    2014-01-01

    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. PMID:23808917

  11. Identification of Fatty Acids, Phospholipids, and Their Oxidation Products Using Matrix-Assisted Laser Desorption Ionization Mass Spectrometry and Electrospray Ionization Mass Spectrometry

    Harmon, Christopher W.; Mang, Stephen A.; Greaves, John; Finlayson-Pitts, Barbara J.

    2010-01-01

    Electrospray ionization mass spectrometry (ESI-MS) and matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) have found increasing application in the analysis of biological samples. Using these techniques to solve problems in analytical chemistry should be an essential component of the training of undergraduate chemists. We…

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

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

    2008-01-01

    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

  13. The Reciprocal Pascal Matrix

    Richardson, Thomas M.

    2014-01-01

    The reciprocal Pascal matrix is the Hadamard inverse of the symmetric Pascal matrix. We show that the ordinary matrix inverse of the reciprocal Pascal matrix has integer elements. The proof uses two factorizations of the matrix of super Catalan numbers.

  14. Constructive Similarity of Soils

    Koudelka, Petr

    Singapore : Design, CRC a iTEK CMS Web solutions, 2012 - (Phoon, K.; Beer, M.; Quek, S.; Pang, S.), s. 206-211 ISBN 978-981-07-2218-0. [APS on Structural Reliability and Its Application – Sustainable Civil Infrastructures /5./. Singapore (SG), 23.05.2012-25.05.2012] Grant ostatní: GA ČR(CZ) GAP105/11/1160 Institutional support: RVO:68378297 Keywords : model similarity * database of soil properties * soil similarity characteristic * statistical analysis * ultimate limit states Subject RIV: JM - Building Engineering

  15. Cognitive residues of similarity

    OToole, Stephanie; Keane, Mark T.

    2013-01-01

    What are the cognitive after-effects of making a similarity judgement? What, cognitively, is left behind and what effect might these residues have on subsequent processing? In this paper, we probe for such after-effects using a visual search task, performed after a task in which pictures of real-world objects were compared. So, target objects were first presented in a comparison task (e.g., rate the similarity of this object to another) thus, presumably, modifying some of their features befor...

  16. Similarity of molecular shape.

    Meyer, A Y; Richards, W G

    1991-10-01

    The similarity of one molecule to another has usually been defined in terms of electron densities or electrostatic potentials or fields. Here it is expressed as a function of the molecular shape. Formulations of similarity (S) reduce to very simple forms, thus rendering the computerised calculation straightforward and fast. 'Elements of similarity' are identified, in the same spirit as 'elements of chirality', except that the former are understood to be variable rather than present-or-absent. Methods are presented which bypass the time-consuming mathematical optimisation of the relative orientation of the molecules. Numerical results are presented and examined, with emphasis on the similarity of isomers. At the extreme, enantiomeric pairs are considered, where it is the dissimilarity (D = 1 - S) that is of consequence. We argue that chiral molecules can be graded by dissimilarity, and show that D is the shape-analog of the 'chirality coefficient', with the simple form of the former opening up numerical access to the latter. PMID:1770379

  17. The Qualitative Similarity Hypothesis

    Paul, Peter V.; Lee, Chongmin

    2010-01-01

    Evidence is presented for the qualitative similarity hypothesis (QSH) with respect to children and adolescents who are d/Deaf or hard of hearing. The primary focus is on the development of English language and literacy skills, and some information is provided on the acquisition of English as a second language. The QSH is briefly discussed within…

  18. A novel protein distance matrix based on the minimum arc-length between two amino-acid residues on the surface of a globular protein.

    Hall, Damien; Li, Songling; Yamashita, Kazuo; Azuma, Ryuzo; Carver, John A; Standley, Daron M

    2014-06-01

    We present a novel protein distance matrix based on the minimum line of arc between two points on the surface of a protein. Two methods for calculating this distance matrix are developed and contrasted. The first method, which we have called TOPOL, is an approximate rule based algorithm consisting of successive rounds of vector addition. The second method is adapted from the graph theoretic approach of Dijkstra. Both procedures are demonstrated using cytochrome c, a 12,500 Da protein, as a test case. In respect to computational speed and accuracy the TOPOL procedure compares favorably against the more complex method based on shortest path enumeration over a surface manifold grid. Some potential uses of the algorithmic approaches and calculated surface protein distance measurement are discussed. PMID:24589301

  19. Corrosion of ceramic matrix composites

    Scanu, T. (ONERA-OM, 92 Chatillon (France) LASIR, CNRS, 94 Thiais (France)); Colomban, P. (ONERA-OM, 92 Chatillon (France) LASIR, CNRS, 94 Thiais (France))

    1993-11-01

    Air stable ceramic matrix composites are promising for thermostructural applications such as aircraft engine parts. Turbine parts are subject to both sulphuric acid and sodium molten salts corrosion due to sulphate traces in engine fuel and to the NaCl air content. The chemical stability is a very important criterion but this point has not received much attention to date. We report here a study of acidic and sodium corrosion of various aluminosilicate matrices : LAS matrices (Li[sub 2]OAl[sub 2]O[sub 3]2-6SiO[sub 2],nP[sub 2]O[sub 5]) in the amorphous, [beta] eucryptite and [beta] spodumene forms, BAS matrix (BaOAl[sub 2]O[sub 3]2SiO[sub 2]) in the form of monoclinic and hexagonal celsian, NASICON matrix (Na[sub 3]Zr[sub 2]Si[sub 2]PO[sub 12]) and mullite matrix. Microstructure damages and ion exchange have been analysed by X-ray diffraction, IR absorption, scanning electron microscopy and Raman microprobe. Drastic corrosion is observed for [beta] spodumene containing composites with the formation of strong hydrogen bond or with the cell expansion due to Li/Na[sup +] exchange. Medium acidic attack occurs for glassy LAS, [beta] eucryptite, BAS and NASICON matrix composites. On the other hand, [beta] eucryptite, NASICON and monoclinic celsian resist to alkaline melts. Mullite matrix composites are never corroded. (orig.).

  20. Corrosion of ceramic matrix composites

    Air stable ceramic matrix composites are promising for thermostructural applications such as aircraft engine parts. Turbine parts are subject to both sulphuric acid and sodium molten salts corrosion due to sulphate traces in engine fuel and to the NaCl air content. The chemical stability is a very important criterion but this point has not received much attention to date. We report here a study of acidic and sodium corrosion of various aluminosilicate matrices : LAS matrices (Li2OAl2O32-6SiO2,nP2O5) in the amorphous, β eucryptite and β spodumene forms, BAS matrix (BaOAl2O32SiO2) in the form of monoclinic and hexagonal celsian, NASICON matrix (Na3Zr2Si2PO12) and mullite matrix. Microstructure damages and ion exchange have been analysed by X-ray diffraction, IR absorption, scanning electron microscopy and Raman microprobe. Drastic corrosion is observed for β spodumene containing composites with the formation of strong hydrogen bond or with the cell expansion due to Li/Na+ exchange. Medium acidic attack occurs for glassy LAS, β eucryptite, BAS and NASICON matrix composites. On the other hand, β eucryptite, NASICON and monoclinic celsian resist to alkaline melts. Mullite matrix composites are never corroded. (orig.)

  1. Limiting Similarity Revisited

    Szabo, P; Meszena, G.

    2005-01-01

    We reinvestigate the validity of the limiting similarity principle via numerical simulations of the Lotka-Volterra model. A Gaussian competition kernel is employed to describe decreasing competition with increasing difference in a one-dimensional phenotype variable. The simulations are initiated by a large number of species, evenly distributed along the phenotype axis. Exceptionally, the Gaussian carrying capacity supports coexistence of all species, initially present. In case of any other, d...

  2. Compression-based similarity

    Vitányi, Paul

    2011-01-01

    First we consider pair-wise distances for literal objects consisting of finite binary files. These files are taken to contain all of their meaning, like genomes or books. The distances are based on compression of the objects concerned, normalized, and can be viewed as similarity distances. Second, we consider pair-wise distances between names of objects, like "red" or "christianity." In this case the distances are based on searches of the Internet. Such a search can be performed by any search...

  3. Matrix analysis

    Bhatia, Rajendra

    1997-01-01

    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...

  4. Matrix pentagons

    Belitsky, A V

    2016-01-01

    The Operator Product Expansion for null polygonal Wilson loop in planar maximally supersymmetric Yang-Mills theory runs systematically in terms of multiparticle pentagon transitions which encode the physics of excitations propagating on the color flux tube ending on the sides of the four-dimensional contour. Their dynamics was unravelled in the past several years and culminated in a complete description of pentagons as an exact function of the 't Hooft coupling. In this paper we provide a solution for the last building block in this program, the SU(4) matrix structure arising from internal symmetry indices of scalars and fermions. This is achieved by a recursive solution of the Mirror and Watson equations obeyed by the so-called singlet pentagons and fixing the form of the twisted component in their tensor decomposition. The non-singlet, or charged, pentagons are deduced from these by a limiting procedure.

  5. The qualitative similarity hypothesis.

    Paul, Peter V; Lee, Chongmin

    2010-01-01

    Evidence is presented for the qualitative similarity hypothesis (QSH) with respect to children and adolescents who are d/Deaf or hard of hearing. The primary focus is on the development of English language and literacy skills, and some information is provided on the acquisition of English as a second language. The QSH is briefly discussed within the purview of two groups of cognitive models: those that emphasize the cognitive development of individuals and those that pertain to disciplinary or knowledge structures. It is argued that the QSH has scientific merit with implications for classroom instruction. Future research should examine the validity of the QSH in other disciplines such as mathematics and science and should include perspectives from social as well as cognitive models. PMID:20415280

  6. Self Similar Optical Fiber

    Lai, Zheng-Xuan

    This research proposes Self Similar optical fiber (SSF) as a new type of optical fiber. It has a special core that consists of self similar structure. Such a structure is obtained by following the formula for generating iterated function systems (IFS) in Fractal Theory. The resulted SSF can be viewed as a true fractal object in optical fibers. In addition, the method of fabricating SSF makes it possible to generate desired structures exponentially in numbers, whereas it also allows lower scale units in the structure to be reduced in size exponentially. The invention of SSF is expected to greatly ease the production of optical fiber when a large number of small hollow structures are needed in the core of the optical fiber. This dissertation will analyze the core structure of SSF based on fractal theory. Possible properties from the structural characteristics and the corresponding applications are explained. Four SSF samples were obtained through actual fabrication in a laboratory environment. Different from traditional conductive heating fabrication system, I used an in-house designed furnace that incorporated a radiation heating method, and was equipped with automated temperature control system. The obtained samples were examined through spectrum tests. Results from the tests showed that SSF does have the optical property of delivering light in a certain wavelength range. However, SSF as a new type of optical fiber requires a systematic research to find out the theory that explains its structure and the associated optical properties. The fabrication and quality of SSF also needs to be improved for product deployment. As a start of this extensive research, this dissertation work opens the door to a very promising new area in optical fiber research.

  7. Extraction of scandium by liquid and introduced into polymeric matrix of solid extractant tributylphosphate from hydrochloric acid solutions according to 31P and 45Sc NMR data

    Scandium extraction from 8M HCl solutions by 100% TBP, 50% TBP solution in CCl4 and solid extractant containing 50% TBP has been studied. It is shown that in the course of extraction by TBP solution in CCl4 less polar complexes prevail, which have a smaller number of H2O molecules, while in 100% TBP - polar forms with the charge from 1+ to 3+ and a greater number of H2O molecules. Complexes in solid extractant - TBP occupy an intermediate position. The observed difference in scandium extraction is explained by the change in the composition of the complexes extracted brought about by solvent and solid extractant polymeric matrix effect. Refs. 21, figs. 5, tabs. 2

  8. Image fusion using bi-directional similarity

    Bai, Chunshan; Luo, Xiaoyan

    2015-05-01

    Infrared images are widely used in the practical applications to capture abundant information. However, it is still challenging to enhance the infrared image by the visual image. In this paper, we propose an effective method using bidirectional similarity. In the proposed method, we aim to find an optimal solution from many feasible solutions without introducing intermediate image. We employ some priori constraints to meet the requirements of image fusion which can be detailed to preserve both good characteristics in the infrared image and spatial information in the visual image. In the iterative step, we use the matrix with the square of the difference between images to integrate the image holding most information. We call this matrix the bidirectional similarity distance. By the bidirectional similarity distance, we can get the transitive images. Then, we fuse the images according to the weight. Experimental results show that, compared to the traditional image fusion algorithm, fusion images from bidirectional similarity fusion algorithm have greatly improved in the subjective vision, entropy, structural similarity index measurement. We believe that the proposed scheme can have a wide applications.

  9. Distance and Similarity Measures for Soft Sets

    Kharal, Athar

    2010-01-01

    In [P. Majumdar, S. K. Samanta, Similarity measure of soft sets, New Mathematics and Natural Computation 4(1)(2008) 1-12], the authors use matrix representation based distances of soft sets to introduce matching function and distance based similarity measures. We first give counterexamples to show that their Definition 2.7 and Lemma 3.5(3) contain errors, then improve their Lemma 4.4 making it a corllary of our result. The fundamental assumption of Majumdar et al has been shown to be flawed. This motivates us to introduce set operations based measures. We present a case (Example 28) where Majumdar-Samanta similarity measure produces an erroneous result but the measure proposed herein decides correctly. Several properties of the new measures have been presented and finally the new similarity measures have been applied to the problem of financial diagnosis of firms.

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

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

    1983-01-01

    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 ..mu..g/cm/sup 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.

  11. 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

    Rouy, E

    2003-10-15

    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)

  12. H-Bonding of Sulfuric Acid with Its Decomposition Products: An Infrared Matrix Isolation and Computational Study of the H2SO4·H2O·SO3 Complex.

    Rozenberg, Mark; Loewenschuss, Aharon; Nielsen, Claus J

    2016-05-26

    The FTIR matrix isolation spectra of H2SO4 vapors show a group of bands with synchronous growth of their relative intensities which is independent of the water species content of the matrix layer. Their frequency positions indicate that the species they represent is H-bonded and composed of all three components (H2SO4, H2O, and SO3) involved in the vapor decomposition equilibrium of the acid molecule. Structure, stabilization energies, and vibrational frequencies of several H-bonded complexes between these components were considered in B3LYP calculations employing Dunning's correlation-consistent aug-cc-pVTZ basis sets. Correlations between spectral shifts, bond lengths, and H-bond energies were also considered. The best fitting complex is a ring structured 1:1:1 H2SO4·H2O·SO3. The indications are that the complex is formed in the vapor phase and not after deposition. The atmospheric significance may be in its ability to serve as a H-bonding nucleation center even without the presence of additional contaminants. PMID:27135379

  13. Tracking the composition and transformation of humic and fulvic acids during vermicomposting of sewage sludge by elemental analysis and fluorescence excitation-emission matrix.

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

    2015-05-01

    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. PMID:25736580

  14. SOLVENT EFFECT ON EXTRACTION OF GALLIC ACID FROM AMALAKI CHURNA (EMBLICA OFFICINALIS Gaertn. TO REDUCE MATRIX EFFECT USING HPTLC AND UV-SPECTROSCOPY WITH 12 DIFFERENT NATURE SOLVENTS

    Sukla V.J.

    2012-06-01

    Full Text Available Standardization of Ayurvedic formulations is an important aspect for research in Indian medicine. In this era every Pharma company prefer to use pure extract of component for production of best product in short period of time. The literature survey reveals that no work has been reported for solvent selection of extraction of Ayurvedic drugs. Amalaki is one of the most useable ayurveda drug. So, the present study was selected with an aim to select solvent for extraction of component of interest. Standard for evaluating quality of Amalaki churna by employing various physico-chemical parameters. For solvent selection 12 different nature solvents are selected for extraction. Polar solvent selected are Water, Di methylsulfoxide (DMSO, Ethylene glycol, Acetonitrile, Di methyl formeamide (DMF and Methanol. Non polar solvents are Acetone, Acetic acid, Ethyl acetate, Chloroform, Di ethylether and Toluene. Extraction was done by maceration method. Results are taken by chromatographic and spectrophotometric methods. In observation component was easily extracted with less interfering component in non polar solvent. Gallic acid is component of interest for Amalaki and it is well extracted in Di ethyl ether as per result of chromatography and spectroscopy. Conclusion is that selection of solvent for extraction as per their component of interest from material.

  15. Permutation-like Matrix Groups with a Maximal Cycle of Prime Square Length

    DENG, GUODONG; Fan, Yun

    2013-01-01

    A matrix group is said to be permutation-like if any matrix of the group is similar to a permutation matrix. G. Cigler proved that, if a permutation-like matrix group contains a normal cyclic subgroup which is generated by a maximal cycle and the matrix dimension is a prime, then the group is similar to a permutation matrix group. This paper extends the result to the case where the matrix dimension is a square of a prime.

  16. Riemann Zeta Matrix Function

    Kargın, Levent; Kurt, Veli

    2015-01-01

    In this study, obtaining the matrix analog of the Euler's reflection formula for the classical gamma function we expand the domain of the gamma matrix function and give a infinite product expansion of sinπxP.  Furthermore we define Riemann zeta matrix function and evaluate some other matrix integrals. We prove a functional equation for Riemann zeta matrix function.

  17. Orthogonal Matrix in Cryptography

    Santana, Yeray Cachon

    2014-01-01

    In this work is proposed a method using orthogonal matrix transform properties to encrypt and decrypt a message. It will be showed how to use matrix functions to create complex encryptions. Because orthogonal matrix are always diagonalizable on R, and the exponential of a diagonal matrix is easy to compute, the exponential of orthogonal matrix will be used to encrypt text messages.

  18. Neu1 sialidase and matrix metalloproteinase-9 cross-talk regulates nucleic acid-induced endosomal TOLL-like receptor-7 and -9 activation, cellular signaling and pro-inflammatory responses.

    Abdulkhalek, Samar; Szewczuk, Myron R

    2013-11-01

    The precise mechanism(s) by which intracellular TOLL-like receptors (TLRs) become activated by their ligands remains unclear. Here, we report a molecular organizational G-protein coupled receptor (GPCR) signaling platform to potentiate a novel mammalian neuraminidase-1 (Neu1) and matrix metalloproteinase-9 (MMP-9) cross-talk in alliance with neuromedin B GPCR, all of which form a tripartite complex with TLR-7 and -9. siRNA silencing Neu1, MMP-9 and neuromedin-B GPCR in RAW-blue macrophage cells significantly reduced TLR7 imiquimod- and TLR9 ODN1826-induced NF-κB (NF-κB-pSer(536)) activity. Tamiflu, specific MMP-9 inhibitor, neuromedin B receptor specific antagonist BIM23127, and the selective inhibitor of whole heterotrimeric G-protein complex BIM-46174 significantly block nucleic acid-induced TLR-7 and -9 MyD88 recruitment, NF-κB activation and proinflammatory TNFα and MCP-1 cytokine responses. For the first time, Neu1 clearly plays a central role in mediating nucleic acid-induced intracellular TLR activation, and the interactions involving NMBR-MMP9-Neu1 cross-talk constitute a novel intracellular TLR signaling platform that is essential for NF-κB activation and pro-inflammatory responses. PMID:23827939

  19. Stabilization of nonlinear systems by similarity transformations

    Irina E. Zuber

    1998-01-01

    Full Text Available For a system x˙=A(x+b(xu, u(x=s∗(xx, x∈ℝn, where the pair (A(x,b(x is given, we obtain the feedback vector s(x to stabilize the corresponding closed loop system. For an arbitrarily chosen constant vector g, a sufficient condition of the existence and an explicit form of a similarity transformation T(A(x,b(x,g is established. The latter transforms matrix A(x into the Frobenius matrix, vector b(x into g, and an unknown feedback vector s(x into the first unit vector. The boundaries of A˜(y,g are determined by the boundaries of {∂kA(x∂xk,∂kb(x∂xk}, k=0,n−1¯. The stabilization of the transformed system is subject to the choice of the constant vector g.

  20. 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.

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

    2016-12-01

    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. PMID:27612692

  1. Matrix Theory over the Complex Quaternion Algebra

    Tian, Yongge

    2000-01-01

    We present in this paper some fundamental tools for developing matrix analysis over the complex quaternion algebra. As applications, we consider generalized inverses, eigenvalues and eigenvectors, similarity, determinants of complex quaternion matrices, and so on.

  2. Towards Google matrix of brain

    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 α. The properties of other eigenstates are also analyzed. We discuss further parallels and similarities between the World Wide Web and neuronal networks.

  3. Multivariate Time Series Similarity Searching

    Jimin Wang; Yuelong Zhu; Shijin Li; Dingsheng Wan; Pengcheng Zhang

    2014-01-01

    Multivariate time series (MTS) datasets are very common in various financial, multimedia, and hydrological fields. In this paper, a dimension-combination method is proposed to search similar sequences for MTS. Firstly, the similarity of single-dimension series is calculated; then the overall similarity of the MTS is obtained by synthesizing each of the single-dimension similarity based on weighted BORDA voting method. The dimension-combination method could use the existing similarity searchin...

  4. Corrosion of ceramic matrix composites

    Scanu, T.; Colomban, Ph.

    1993-01-01

    Air stable ceramic matrix composites are promising for thermostructural applications such as aircraft engine parts. Turbine parts are subject to both sulphuric acid and sodium molten salts corrosion due to sulphate traces in engine fuel and to the NaCl air content. The chemical stability is a very important criterion but this point has not received much attention to date. We report here a study of acidic and sodium corrosion of various aluminosilicate matrices : LAS matrices (Li2OAl2O32-6SiO2...

  5. Web Search Results Summarization Using Similarity Assessment

    Sawant V.V.

    2014-06-01

    Full Text Available Now day’s internet has become part of our life, the WWW is most important service of internet because it allows presenting information such as document, imaging etc. The WWW grows rapidly and caters to a diversified levels and categories of users. For user specified results web search results are extracted. Millions of information pouring online, users has no time to surf the contents completely .Moreover the information available is repeated or duplicated in nature. This issue has created the necessity to restructure the search results that could yield results summarized. The proposed approach comprises of different feature extraction of web pages. Web page visual similarity assessment has been employed to address the problems in different fields including phishing, web archiving, web search engine etc. In this approach, initially by enters user query the number of search results get stored. The Earth Mover's Distance is used to assessment of web page visual similarity, in this technique take the web page as a low resolution image, create signature of that web page image with color and co-ordinate features .Calculate the distance between web pages by applying EMD method. Compute the Layout Similarity value by using tag comparison algorithm and template comparison algorithm. Textual similarity is computed by using cosine similarity, and hyperlink analysis is performed to compute outward links. The final similarity value is calculated by fusion of layout, text, hyperlink and EMD value. Once the similarity matrix is found clustering is employed with the help of connected component. Finally group of similar web pages i.e. summarized results get displayed to user. Experiment conducted to demonstrate the effectiveness of four methods to generate summarized result on different web pages and user queries also.

  6. New approach for distinguishing the similarity of links

    Jianyun XIANG; Maozhong GE; Zhiping WANG

    2008-01-01

    Based on the problem of distinguishing the similarity of links in the regenerative innovation design of a kinematic chain, a new approach using the standard power matrix of the adjacent matrix is presented in this paper. The implementation of the approach is illustrated with an example. This method solves the technically baffling problem in mechanism type synthesis and reduced redundant design scheme, and raises the reliability and the efficiency of the regenerative innova-tion design of the kinematic chain.

  7. A mouse 3T6 fibroblast cell culture model for the study of normal and protein-engineered collagen synthesis and deposition into the extracellular matrix.

    Lamandé, S R; Bateman, J F

    1993-07-01

    Mouse 3T6 fibroblasts deposited an organized collagenous extracellular matrix during long-term culture in the presence of ascorbic acid. The matrix produced by the cells had a similar distribution of collagen types as the mouse dermal matrix, comprising predominantly type I with smaller amounts of types III and V collagens. By day 8 of culture more than 70% of the collagen in the 3T6 matrix was involved in covalent crosslinkages and required pepsin digestion for extraction. Incorporation of NaB3H4 into reducible crosslinks and aldehydes directly demonstrated the involvement of the alpha 1 (I)CB6 and alpha 2(I)CB3.5 in crosslinks. The pattern of reducible crosslinks in the in vitro 3T6 matrix was similar to that in mouse skin suggesting a comparable fibril organization. Processing of procollagen to collagen occurred efficiently throughout the culture period and the rate of collagen production was unaltered during 15 days of culture, indicating that the development of a collagenous matrix does not directly play a role in procollagen processing or biosynthetic regulation. The existence of a preformed matrix did however, increase the efficiency with which newly synthesised collagen was incorporated into the pericellular matrix. At day 0, when there was no measurable matrix present, 29% of the collagen synthesised was deposited, while by day 15, 88% of the collagen was laid down in the matrix. The development of this 3T6 culture system, where collagen is efficiently incorporated into an organized extracellular matrix, will facilitate detailed studies on matrix organization and regulation and provide a system in which protein-engineered mutant collagens can be expressed to determine their effects on the production of a functional extracellular matrix. PMID:8412990

  8. Functional Similarity and Interpersonal Attraction.

    Neimeyer, Greg J.; Neimeyer, Robert A.

    1981-01-01

    Students participated in dyadic disclosure exercises over a five-week period. Results indicated members of high functional similarity dyads evidenced greater attraction to one another than did members of low functional similarity dyads. "Friendship" pairs of male undergraduates displayed greater functional similarity than did "nominal" pairs from…

  9. A matrix lower bound

    Grcar, Joseph F.

    2002-02-04

    A matrix lower bound is defined that generalizes ideas apparently due to S. Banach and J. von Neumann. The matrix lower bound has a natural interpretation in functional analysis, and it satisfies many of the properties that von Neumann stated for it in a restricted case. Applications for the matrix lower bound are demonstrated in several areas. In linear algebra, the matrix lower bound of a full rank matrix equals the distance to the set of rank-deficient matrices. In numerical analysis, the ratio of the matrix norm to the matrix lower bound is a condition number for all consistent systems of linear equations. In optimization theory, the matrix lower bound suggests an identity for a class of min-max problems. In real analysis, a recursive construction that depends on the matrix lower bound shows that the level sets of continuously differential functions lie asymptotically near those of their tangents.

  10. Lithium/Valproic acid combination and L-glutamate induce similar pattern of changes in the expression of miR-30a-5p in SH-SY5Y neuroblastoma cells.

    Croce, Nicoletta; Bernardini, Sergio; Caltagirone, Carlo; Angelucci, Francesco

    2014-12-01

    It has been proposed that Lithium (Li) and valproic acid (VPA) may be useful to treat neurodegenerative disorders because they protect neurons against excitotoxic insults both in vitro and in vivo models. Moreover, these two drugs may exert their effects by regulating microRNAs (miRNAs), single-stranded and non-coding RNAs able to control gene expression. A subset of the miR-30a family (miR-30a-5p) is involved in the fine-tuning of neuroprotective molecules such as the neurotrophin brain-derived neurotrophic factor (BDNF). Thus, there is the possibility that Li and VPA may alter miR-30a-5p and in turn affect BDNF production. However, data on miR-30a-5p levels in presence of Li and VPA and/or a neurotoxic insult are not yet available. Thus, the aim of this study was to investigate whether exposure to Li and VPA may influence miR-30a-5p expression in an in vitro model of neurodegeneration generated by the exposure of a human neuroblastoma cell line (SH-SY5Y) to neurotoxic concentration of L-glutamate. The results showed that both L-glutamate and Li-VPA caused an increase in miR-30a-5p expression at 24 h of incubation and a decrease at 48 h. Moreover, Li-VPA alone caused a decrease in miR-30a-5p expression also in cells not exposed to the toxic effect of glutamate. These data indicate that changes in miR-30a-5p expression induced by Li-VPA are not related to the cytoprotective action of BDNF and suggest alternative function for this miR. These findings also indicate that miRNA changes are present in in vitro models of neurodegeneration, although the significance of these changes warrants further investigation. PMID:25149854

  11. Adjoint Fermion Matrix Models

    Makeenko, Yu.; Zarembo, K.

    1993-01-01

    We study fermionic one-matrix, two-matrix and $D$-dimensional gauge invariant matrix models. In all cases we derive loop equations which unambiguously determine the large-$N$ solution. For the one-matrix case the solution is obtained for an arbitrary interaction potential and turns out to be equivalent to the one for the Hermitean one-matrix model with a logarithmic potential and, therefore, belongs to the same universality class. The explicit solutions for the fermionic two-matrix and $D$-di...

  12. Characterization of organic matrix extracted from fresh water pearls

    Ma Yufei; Gao Yonghua; Feng Qingling, E-mail: biomater@mail.tsinghua.edu.cn

    2011-10-10

    Aragonite pearl and vaterite pearl from cultured Hyriopsis cumingii in Zhuji (Zhejiang province, China) were chosen for the study. The matrix proteins were extracted using water and weak acid, and classified as water soluble matrix (WSM), acid soluble matrix (ASM) and acid insoluble matrix (AIM). The proteins from both pearls were characterized by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), X-ray diffraction (XRD) and Fourier transformation infrared spectra (FTIR). The results showed that, AIM of aragonite pearl and vaterite pearl had an ordered structure of {alpha}-helix. ASM conformations of these two pearls were different from each other. WSM differed the most between these two pearls. - Research Highlights: {yields} We use a specific method for extracting matrix proteins from aragonite pearl and vaterite pearl respectively. {yields} The matrix proteins are extracted by water and weak acid, and classified as water soluble matrix (WSM), acid soluble matrix (ASM) and acid insoluble matrix (AIM). {yields} AIM of aragonite pearl and vaterite pearl have an ordered structure. ASM conformations of the two pearls are different from each other. WSM differ the most between these two pearls.

  13. Characterization of organic matrix extracted from fresh water pearls

    Aragonite pearl and vaterite pearl from cultured Hyriopsis cumingii in Zhuji (Zhejiang province, China) were chosen for the study. The matrix proteins were extracted using water and weak acid, and classified as water soluble matrix (WSM), acid soluble matrix (ASM) and acid insoluble matrix (AIM). The proteins from both pearls were characterized by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), X-ray diffraction (XRD) and Fourier transformation infrared spectra (FTIR). The results showed that, AIM of aragonite pearl and vaterite pearl had an ordered structure of α-helix. ASM conformations of these two pearls were different from each other. WSM differed the most between these two pearls. - Research Highlights: → We use a specific method for extracting matrix proteins from aragonite pearl and vaterite pearl respectively. → The matrix proteins are extracted by water and weak acid, and classified as water soluble matrix (WSM), acid soluble matrix (ASM) and acid insoluble matrix (AIM). → AIM of aragonite pearl and vaterite pearl have an ordered structure. ASM conformations of the two pearls are different from each other. WSM differ the most between these two pearls.

  14. Investigation of redox activities of soil humic acids using 3D excitation emission matrix fluorescence spectroscopy%基于三维荧光光谱特征研究土壤腐殖质氧化还原特性

    姜杰; 李黎; 孙国新

    2012-01-01

    Humic substances serve as electron shuttles in the soil environment. They not only stimulate the element migration, but also accelerate containment degradation and environment remediation. In this study, a standard humic acid and two extracted humic acids from soil samples were reduced by H2, and three-dimensional excitation emission matrix fluorescence spectroscopy (3DEEM) was employed to characterize these humic acids. The results of 3DEEMs revealed the differences between native and reduced humic acids. Fluorescence peak intensity of humic acids in the reduced state was lower than those in the natural state, which can be explained by the changes of chemical structures of humic acids, such as the loss of π-π bonds. As a model compound of quinone groups in humic acids, benzoquinone reduction and 3DEEM analysis were carried out under the same conditions. It was observed that there was a decrease of fluorescence with benzoquinone reduction. Potassium ferricyanide method was used to measure the reducing capacity of native extracted humic acids, which was found to be 0. 998 and 0. 465 meq. g-1 C for Yingtan and Taoyuan soils, respectively. Electron accepting capacities of humic acids were 3. 384 and 1.187 meq-g 1 C for Yingtan and Taoyuan soils, respectively. Determination of electron accepting capacities, quantification of redox-active functional groups and prediction of redox reaction processes in soil are all important applications of 3 DEEM in the investigation of humic acid redox-activities.%以国际腐殖质协会腐殖酸和实验室提纯腐殖酸为研究对象,发现被H2还原前后腐殖酸的三维荧光光谱明显不同,但有共同的变化趋势:还原态腐殖酸的三维荧光光谱图的波峰荧光强度均明显低于还原前,说明腐殖酸还原过程有类似π-π化学键断开的结构变化.对苯醌是腐殖酸氧化还原醌基官能团的代表化合物,将其还原前后与腐殖酸还原前后的荧光光

  15. A COMPARISON OF SEMANTIC SIMILARITY MODELS IN EVALUATING CONCEPT SIMILARITY

    Q. X. Xu

    2012-08-01

    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.

  16. Modification of natural matrix lac-bagasse for matrix composite films

    Nurhayati, Nanik Dwi; Widjaya, Karna; Triyono

    2016-02-01

    Material technology continues to be developed in order to a material that is more efficient with composite technology is a combination of two or more materials to obtain the desired material properties. The objective of this research was to modification and characterize the natural matrix lac-bagasse as composite films. The first step, natural matrix lac was changed from solid to liquid using an ethanol as a solvent so the matrix homogenly. Natural matrix lac was modified by adding citric acid with concentration variation. Secondly, the bagasse delignification using acid hydrolysis method. The composite films natural matrix lac-bagasse were prepared with optimum modified the addition citric acid 5% (v/v) and delignification bagasse optimum at 1,5% (v/v) in hot press at 80°C 6 Kg/cm-1. Thirdly, composite films without and with modification were characterized functional group analysis using FTIR spectrophotometer and mechanical properties using Universal Testing Machine. The result of research showed natural matrix lac can be modified by reaction with citric acid. FTIR spectra showed without and with modification had functional groups wide absorption 3448 cm-1 group -OH, C=O ester strong on 1712 cm-1 and the methylene group -CH2 on absorption 1465 cm-1. The mechanical properties showed tensile strength 0,55 MPa and elongation at break of 0,95 %. So that composite films natural matrix lac can be made with reinforcement bagasse for material application.

  17. Learning Multi-modal Similarity

    McFee, Brian

    2010-01-01

    In many applications involving multi-media data, the definition of similarity between items is integral to several key tasks, e.g., nearest-neighbor retrieval, classification, and recommendation. Data in such regimes typically exhibits multiple modalities, such as acoustic and visual content of video. Integrating such heterogeneous data to form a holistic similarity space is therefore a key challenge to be overcome in many real-world applications. We present a novel multiple kernel learning technique for integrating heterogeneous data into a single, unified similarity space. Our algorithm learns an optimal ensemble of kernel transfor- mations which conform to measurements of human perceptual similarity, as expressed by relative comparisons. To cope with the ubiquitous problems of subjectivity and inconsistency in multi- media similarity, we develop graph-based techniques to filter similarity measurements, resulting in a simplified and robust training procedure.

  18. Roget's Thesaurus and Semantic Similarity

    Jarmasz, Mario; Szpakowicz, Stan

    2012-01-01

    We have implemented a system that measures semantic similarity using a computerized 1987 Roget's Thesaurus, and evaluated it by performing a few typical tests. We compare the results of these tests with those produced by WordNet-based similarity measures. One of the benchmarks is Miller and Charles' list of 30 noun pairs to which human judges had assigned similarity measures. We correlate these measures with those computed by several NLP systems. The 30 pairs can be traced back to Rubenstein ...

  19. The Matrix Cookbook

    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....

  20. Matrix metalloproteinases and epileptogenesis

    Ikonomidou, Chrysanthy

    2014-01-01

    Matrix metalloproteinases are vital drivers of synaptic remodeling in health and disease. It is suggested that at early stages of epileptogenesis, inhibition of matrix metalloproteinases may help ameliorate cell death, aberrant network rewiring, and neuroinflammation and prevent development of epilepsy.

  1. Fatigue testing and damage development in continuous fiber reinforced metal matrix composites

    Johnson, W. S.

    1989-01-01

    A general overview of the fatigue behavior of metal matrix composites (MMC) is presented. The first objective is to present experimental procedures and techniques for conducting a meaningful fatigue test to detect and quantify fatigue damage in MMC. These techniques include interpretation of stress-strain responses, acid etching of the matrix, edge replicas of the specimen under load, radiography, and micrographs of the failure surfaces. In addition, the paper will show how stiffness loss in continuous fiber reinforced metal matrix composites can be a useful parameter for detecting fatigue damage initiation and accumulation. Second, numerous examples of how fatigue damage can initiate and grow in various MMC are given. Depending on the relative fatigue behavior of the fiber and matrix, and the interface properties, the failure modes of MMC can be grouped into four categories: (1) matrix dominated, (2) fiber dominated, (3) self-similar damage growth, and (4) fiber/matrix interfacial failures. These four types of damage will be discussed and illustrated by examples with the emphasis on the fatigue of unnotched laminates.

  2. Fatigue testing and damage development in continuous fiber reinforced metal matrix composites

    Johnson, W. S.

    1988-01-01

    A general overview of the fatigue behavior of metal matrix composites (MMC) is presented. The first objective is to present experimental procedures and techniques for conducting a meaningful fatigue test to detect and quantify fatigue damage in MMC. These techniques include interpretation of stress-strain responses, acid etching of the matrix, edge replicas of the specimen under load, radiography, and micrographs of the failure surfaces. In addition, the paper will show how stiffness loss in continuous fiber reinforced metal matrix composites can be a useful parameter for detecting fatigue damage initiation and accumulation. Second, numerous examples of how fatigue damage can initiate and grow in various MMC are given. Depending on the relative fatigue behavior of the fiber and matrix, and the interface properties, the failure modes of MMC can be grouped into four categories: (1) matrix dominated, (2) fiber dominated, (3) self-similar damage growth, and (4) fiber/matrix interfacial failures. These four types of damage will be discussed and illustrated by examples with the emphasis on the fatigue of unnotched laminates.

  3. Matrix Tile Analysis

    Givoni, Inmar; Cheung, Vincent; Frey, Brendan J.

    2012-01-01

    Many tasks require finding groups of elements in a matrix of numbers, symbols or class likelihoods. One approach is to use efficient bi- or tri-linear factorization techniques including PCA, ICA, sparse matrix factorization and plaid analysis. These techniques are not appropriate when addition and multiplication of matrix elements are not sensibly defined. More directly, methods like bi-clustering can be used to classify matrix elements, but these methods make the overly-restrictive assumptio...

  4. Matrix Order Differintegration

    Naber, Mark

    2003-01-01

    The Riemann-Liouville formula for fractional derivatives and integrals (differintegration) is used to derive formulae for matrix order derivatives and integrals. That is, the parameter for integration and differentiation is allowed to assume matrix values. It is found that the computation of derivatives and integrals to matrix order is well defined for any square matrix over the complex numbers. Some properties are worked out for special classes of matrices. It is hoped that this new formalis...

  5. Matrix partitions of digraphs

    Schell, David George

    2008-01-01

    The matrix partition problem has been of recent interest in graph theory. Matrix partitions generalize the study of graph colourings and homomorphisms. Many well-known graph partition problems can be stated in terms of matrices. For example skew partitions, split partitions, homogeneous sets, clique-cutsets, stable-cutsets and k-colourings can all be modeled as matrix partitions. For each matrix partition problem there is an equivalent trigraph H-colouring problem. We show a ‘dichotomy’ for t...

  6. Matrix with Prescribed Eigenvectors

    Ahmad, Faiz

    2011-01-01

    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…

  7. SPIC: A novel similarity metric for comparing transcription factor binding site motifs based on information contents

    Zhang, Shaoqiang; Zhou, Xiguo; Du, Chuanbin; Su, Zhengchang

    2013-01-01

    Background Discovering transcription factor binding sites (TFBS) is one of primary challenges to decipher complex gene regulatory networks encrypted in a genome. A set of short DNA sequences identified by a transcription factor (TF) is known as a motif, which can be expressed accurately in matrix form such as a position-specific scoring matrix (PSSM) and a position frequency matrix. Very frequently, we need to query a motif in a database of motifs by seeking its similar motifs, merge similar ...

  8. Personalized recommendation with corrected similarity

    Personalized recommendation has attracted a surge of interdisciplinary research. Especially, similarity-based methods in applications of real recommendation systems have achieved great success. However, the computations of similarities are overestimated or underestimated, in particular because of the defective strategy of unidirectional similarity estimation. In this paper, we solve this drawback by leveraging mutual correction of forward and backward similarity estimations, and propose a new personalized recommendation index, i.e., corrected similarity based inference (CSI). Through extensive experiments on four benchmark datasets, the results show a greater improvement of CSI in comparison with these mainstream baselines. And a detailed analysis is presented to unveil and understand the origin of such difference between CSI and mainstream indices. (paper)

  9. Bosonic Matrix Theory and Matrix Dbranes

    Chaudhuri, S

    2002-01-01

    We develop new tools for an in-depth investigation of our recent proposal for Matrix Theory. We construct the anomaly-free and finite planar continuum limit of the ground state with SO(2^{13}) symmetry matching with the tadpole and tachyon free IR stable high temperature ground state of the open and closed bosonic string. The correspondence between large N limits and spacetime effective actions is demonstrated more generally for an arbitrary D25brane ground state which might include brane-antibrane pairs or NS-branes and which need not have an action formulation. Closure of the finite N matrix Lorentz algebra nevertheless requires that such a ground state is simultaneously charged under all even rank antisymmetric matrix potentials. Additional invariance under the gauge symmetry mediated by the one-form matrix potential requires a ground state charged under the full spectrum of antisymmetric (p+1)-form matrix potentials with p taking any integer value less than 26. Matrix Dbrane democracy has a beautiful larg...

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

    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.

    2014-04-01

    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.

  11. Nanocrystal doped matrixes

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

    2010-01-12

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

  12. Fast and secure similarity search in high dimensional space

    Furon, Teddy; Jégou, Hervé; Amsaleg, Laurent; Mathon, Benjamin

    2013-01-01

    Similarity search in high dimensional space database is split into two worlds: i) fast, scalable, and approximate search algorithms which are not secure, and ii) search protocols based on secure computation which are not scalable. This paper presents a one-way privacy protocol that lies in between these two worlds. Approximate metrics for the cosine similarity allows speed. Elements of large random matrix theory provides security evidences if the size of the database is not too big with respe...

  13. Fatigue damage criteria - Matrix, fibers and interfaces of continuous fiber reinforced metal matrix composites

    Johnson, W. S.

    1988-01-01

    Continuous fiber reinforced metal matrix composites (MMC) are projected for use in high temperature, stiffness critical parts that will be subjected to cyclic loadings. Depending on the relative fatigue behavior of the fiber and matrix, and the interface properties, the failure modes of MMC can be grouped into four catagories: (1) matrix dominated, (2) fiber dominated, (3) self-similar damage growth, and (4) fiber/matrix interfacial failures. These four types of damage are discussed and illustrated by examples. The emphasis is on the fatigue of unnotched laminates.

  14. Self-similar aftershock rates

    Davidsen, Jörn

    2016-01-01

    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.

  15. Ranking and clustering of search results: Analysis of Similarity graph

    Shevchuk, Ksenia Alexander

    2008-01-01

    Evaluate the clustering of the similarity matrix and confirm that it is high. Compare the ranking results of the eigenvector ranking and the Link Popularity ranking and confirm for the high clustered graph the correlation between those is larger than for the low clustered graph.

  16. Learning Multi-modal Similarity

    McFee, Brian; Lanckriet, Gert

    2010-01-01

    In many applications involving multi-media data, the definition of similarity between items is integral to several key tasks, e.g., nearest-neighbor retrieval, classification, and recommendation. Data in such regimes typically exhibits multiple modalities, such as acoustic and visual content of video. Integrating such heterogeneous data to form a holistic similarity space is therefore a key challenge to be overcome in many real-world applications. We present a novel multiple kernel learning t...

  17. Similarity measures for protein ensembles

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    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...... 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...

  18. SELF-SIMILAR TRAFFIC GENERATOR

    Linawati Linawati; I Made Suartika

    2009-01-01

    Network traffic generator can be produced using OPNET. OPNET generates the traffic as explicit traffic or background traffic. This paper demonstrates generating traffic in OPNET 7.0 as background traffic. The traffi generator that was simulated is self-similar traffic with different Hurst parameter. The simulation results proved that OPNET with background traffic function can be as a qualified self-similar traffic generator. These results can help in investigating and analysing network perfor...

  19. Molecular similarity of MDR inhibitors

    Simon Gibbons; Mire Zloh

    2004-01-01

    Abstract: The molecular similarity of multidrug resistance (MDR) inhibitors was evaluated using the point centred atom charge approach in an attempt to find some common features of structurally unrelated inhibitors. A series of inhibitors of bacterial MDR were studied and there is a high similarity between these in terms of their shape, presence and orientation of aromatic ring moieties. A comparison of the lipophilic properties of these molecules has also been conducted suggesting that this ...

  20. HOW DISSIMILARLY SIMILAR ARE BIOSIMILARS?

    Ramshankar Vijayalakshmi; Kesavan Sabitha; Krishnamurthy Arvind

    2012-01-01

    Recently Biopharmaceuticals are the new chemotherapeutical agents that are called as “Biosimilars” or “follow on protein products” by the European Medicines Agency (EMA) and the American regulatory agencies (Food and Drug Administration) respectively. Biosimilars are extremely similar to the reference molecule but not identical, however close their similarities may be. A regulatory framework is therefore in place to assess the application for marketing authorisation of biosimilars. When a bi...

  1. Method of similarity for cavitation

    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)

  2. Supervised Learning with Similarity Functions

    Kar, Purushottam; Jain, Prateek

    2012-01-01

    We address the problem of general supervised learning when data can only be accessed through an (indefinite) similarity function between data points. Existing work on learning with indefinite kernels has concentrated solely on binary/multi-class classification problems. We propose a model that is generic enough to handle any supervised learning task and also subsumes the model previously proposed for classification. We give a "goodness" criterion for similarity functions w.r.t. a given superv...

  3. Representation is representation of similarities.

    Edelman, S

    1998-08-01

    Advanced perceptual systems are faced with the problem of securing a principled (ideally, veridical) relationship between the world and its internal representation. I propose a unified approach to visual representation, addressing the need for superordinate and basic-level categorization and for the identification of specific instances of familiar categories. According to the proposed theory, a shape is represented internally by the responses of a small number of tuned modules, each broadly selective for some reference shape, whose similarity to the stimulus it measures. This amounts to embedding the stimulus in a low-dimensional proximal shape space spanned by the outputs of the active modules. This shape space supports representations of distal shape similarities that are veridical as Shepard's (1968) second-order isomorphisms (i.e., correspondence between distal and proximal similarities among shapes, rather than between distal shapes and their proximal representations). Representation in terms of similarities to reference shapes supports processing (e.g., discrimination) of shapes that are radically different from the reference ones, without the need for the computationally problematic decomposition into parts required by other theories. Furthermore, a general expression for similarity between two stimuli, based on comparisons to reference shapes, can be used to derive models of perceived similarity ranging from continuous, symmetric, and hierarchical ones, as in multidimensional scaling (Shepard 1980), to discrete and nonhierarchical ones, as in the general contrast models (Shepard & Arabie 1979; Tversky 1977). PMID:10097019

  4. The symmetries of the system matrix and propagator matrix for anisotropic media and of the system matrix forperiodically layered media

    Xu, Guo-Ming; Ni, Si-Dao

    1998-11-01

    The `auxiliary' symmetry properties of the system matrix (symmetry with respect to the trailing diagonal) for a general anisotropic dissipative medium and the special form for a monoclinic medium are revealed by rearranging the motion-stress vector. The propagator matrix of a single-layer general anisotropic dissipative medium is also shown to have auxiliary symmetry. For the multilayered case, a relatively simple matrix method is utilized to obtain the inverse of the propagator matrix. Further, Woodhouse's inverse of the propagator matrix for a transversely isotropic medium is extended in a clearer form to handle the monoclinic symmetric medium. The properties of a periodic layer system are studied through its system matrix Aly , which is computed from the propagator matrix P. The matrix Aly is then compared with Aeq , the system matrix for the long-wavelength equivalent medium of the periodic isotropic layers. Then we can find how the periodic layered medium departs from its long-wavelength equivalent medium when the wavelength decreases. In our numerical example, the results show that, when λ/D decreases to 6-8, the components of the two matrices will depart from each other. The component ratio of these two matrices increases to its maximum (more than 15 in our numerical test) when λ/D is reduced to 2.3, and then oscillates with λ/D when it is further reduced. The eigenvalues of the system matrix Aly show that the velocities of P and S waves decrease when λ/D is reduced from 6-8 and reach their minimum values when λ/D is reduced to 2.3 and then oscillate afterwards. We compute the time shifts between the peaks of the transmitted waves and the incident waves. The resulting velocity curves show a similar variation to those computed from the eigenvalues of the system matrix Aly , but on a smaller scale. This can be explained by the spectrum width of the incident waves.

  5. Corrosion of Titanium Matrix Composites

    Covino, B.S., Jr.; Alman, D.E.

    2002-09-22

    The corrosion behavior of unalloyed Ti and titanium matrix composites containing up to 20 vol% of TiC or TiB{sub 2} was determined in deaerated 2 wt% HCl at 50, 70, and 90 degrees C. Corrosion rates were calculated from corrosion currents determined by extrapolation of the tafel slopes. All curves exhibited active-passive behavior but no transpassive region. Corrosion rates for Ti + TiC composites were similar to those for unalloyed Ti except at 90 degrees C where the composites were slightly higher. Corrosion rates for Ti + TiB{sub 2} composites were generally higher than those for unalloyed Ti and increased with higher concentrations of TiB{sub 2}. XRD and SEM-EDS analyses showed that the TiC reinforcement did not react with the Ti matrix during fabrication while the TiB{sub 2} reacted to form a TiB phase.

  6. Parallelism in matrix computations

    Gallopoulos, Efstratios; Sameh, Ahmed H

    2016-01-01

    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...

  7. Similarity measures for face recognition

    Vezzetti, Enrico

    2015-01-01

    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.

  8. Melvin Matrix Models

    Motl, L

    2001-01-01

    In this short note we construct the DLCQ description of the flux seven-branes in type IIA string theory and discuss its basic properties. The matrix model involves dipole fields. We explain the relation of this nonlocal matrix model to various orbifolds. We also give a spacetime interpretation of the Seiberg-Witten-like map, proposed in a different context first by Bergman and Ganor, that converts this matrix model to a local, highly nonlinear theory.

  9. Modular Matrix Models

    He, Y.; Jejjala, V.

    2003-01-01

    Inspired by a formal resemblance of certain q-expansions of modular forms and the master field formalism of matrix models in terms of Cuntz operators, we construct a Hermitian one-matrix model, which we dub the ``modular matrix model.'' Together with an N=1 gauge theory and a special Calabi-Yau geometry, we find a modular matrix model that naturally encodes the Klein elliptic j-invariant, and hence, by Moonshine, the irreducible representations of the Fischer-Griess Monster group.

  10. Study of matrix effects produced by inorganic species in inductively coupled plasma atomic emission spectrometry with several spray chambers

    In the present work, the influence of the spray chamber design on the matrix effects was investigated in Inductively Coupled Plasma Atomic Emission Spectrometry (ICP-AES). The study was carried out in terms of aerosol drop size distribution and emission signal. Solutions of two inorganic acids and salts were employed to characterize the extent of the matrix effects throughout this work. Several spray chambers. a double-pass (Scott - type), a conventional cyclonic, and two low-volume cyclonic - type spray chambers (i.e., Cinnabar, and Genie) were used in order to evaluate the matrix effects produced by nitric and sulphuric acid solutions. A glass concentric pneumatic micro nebulizer (Atom Mist) was used in conjunction with all four chambers. When nitric or sulphuric acid solutions were nebulized, the double pass spray chamber registered noticeable changes in the drop size distribution. The low-volume spray chambers, in turn, afforded changes in the aerosol drop size distributions similar to the conventional cyclonic one. The matrix effects on the signal were reduced with all three cyclonic spray chambers with respect to the double pass one. Concerning the effect of inorganic salts, the results obtained with a High Efficiency Nebulizer (HEN) coupled to a double pass spray chamber and to a cyclonic type one revealed several issues: (i) the matrix effects were more severe at low liquid and gas flow rates; (ii) as for inorganic acids, the use of a cyclonic spray chamber led to a mitigation of the matrix effects with respect to a double pass spray chamber. (author)

  11. Similarity Analysis and Modeling in Mobile Societies: The Missing Link

    Thakur, Gautam; Hsu, Wei-Jen

    2010-01-01

    A new generation of "behavior-aware" delay tolerant networks is emerging in what may define future mobile social networks. With the introduction of novel behavior-aware protocols, services and architectures, there is a pressing need to understand and realistically model mobile users behavioral characteristics, their similarity and clustering. Such models are essential for the analysis, performance evaluation, and simulation of future DTNs. This paper addresses issues related to mobile user similarity, its definition, analysis and modeling. To define similarity, we adopt a behavioral-profile based on users location preferences using their on-line association matrix and its SVD, then calculate the behavioral distance to capture user similarity. This measures the difference of the major spatio-temporal behavioral trends and can be used to cluster users into similarity groups or communities. We then analyze and contrast similarity distributions of mobile user populations in two settings: (i) based on real measure...

  12. Similarity Measures for Comparing Biclusterings.

    Horta, Danilo; Campello, Ricardo J G B

    2014-01-01

    The comparison of ordinary partitions of a set of objects is well established in the clustering literature, which comprehends several studies on the analysis of the properties of similarity measures for comparing partitions. However, similarity measures for clusterings are not readily applicable to biclusterings, since each bicluster is a tuple of two sets (of rows and columns), whereas a cluster is only a single set (of rows). Some biclustering similarity measures have been defined as minor contributions in papers which primarily report on proposals and evaluation of biclustering algorithms or comparative analyses of biclustering algorithms. The consequence is that some desirable properties of such measures have been overlooked in the literature. We review 14 biclustering similarity measures. We define eight desirable properties of a biclustering measure, discuss their importance, and prove which properties each of the reviewed measures has. We show examples drawn and inspired from important studies in which several biclustering measures convey misleading evaluations due to the absence of one or more of the discussed properties. We also advocate the use of a more general comparison approach that is based on the idea of transforming the original problem of comparing biclusterings into an equivalent problem of comparing clustering partitions with overlapping clusters. PMID:26356865

  13. Approaches to Sequence Similarity Representation

    Sokolov, Artem; Rachkovskij, Dmitri

    2006-01-01

    We discuss several approaches to similarity preserving coding of symbol sequences and possible connections of their distributed versions to metric embeddings. Interpreting sequence representation methods with embeddings can help develop an approach to their analysis and may lead to discovering useful properties.

  14. A square from similar rectangles

    Dorichenko, Sergey; Skopenkov, Mikhail

    2013-01-01

    In the present popular science paper we determine when a square can be dissected into rectangles similar to a given rectangle. The approach to the question is based on a physical interpretation using electrical networks. Only secondary school background is assumed in the paper.

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

    Tongsong Jiang

    2014-01-01

    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.

  16. HOW DISSIMILARLY SIMILAR ARE BIOSIMILARS?

    Ramshankar Vijayalakshmi

    2012-05-01

    Full Text Available Recently Biopharmaceuticals are the new chemotherapeutical agents that are called as “Biosimilars” or “follow on protein products” by the European Medicines Agency (EMA and the American regulatory agencies (Food and Drug Administration respectively. Biosimilars are extremely similar to the reference molecule but not identical, however close their similarities may be. A regulatory framework is therefore in place to assess the application for marketing authorisation of biosimilars. When a biosimilar is similar to the reference biopharmaceutical in terms of safety, quality, and efficacy, it can be registered. It is important to document data from clinical trials with a view of similar safety and efficacy. If the development time for a generic medicine is around 3 years, a biosimilar takes about 6-9 years. Generic medicines need to demonstrate bioequivalence only unlike biosimilars that need to conduct phase I and Phase III clinical trials. In this review, different biosimilars that are already being used successfully in the field on Oncology is discussed. Their similarity, differences and guidelines to be followed before a clinically informed decision to be taken, is discussed. More importantly the regulatory guidelines that are operational in India with a work flow of making a biosimilar with relevant dos and dont’s are discussed. For a large populous country like India, where with improved treatments in all sectors including oncology, our ageing population is increasing. For the health care of this sector, we need more newer, cheaper and effective biosimilars in the market. It becomes therefore important to understand the regulatory guidelines and steps to come up with more biosimilars for the existing population and also more information is mandatory for the practicing clinicians to translate these effectively into clinical practice.

  17. Study of ionization process of matrix molecules in matrix-assisted laser desorption ionization

    Highlights: ► Proton transfer and adduction reaction of matrix in MALDI were studied. ► Hydroxyl group forming intramolecular hydrogen bond was related to the ionization. ► Intramolecular proton transfer in the electronic excited state was the initial step. ► Non-volatile analytes stabilized protonated matrix in the ground state. ► A possible mechanism, “analyte support mechanism”, has been proposed. - Abstract: Proton transfer and adduction reaction of matrix molecules in matrix-assisted laser desorption ionization were studied. By using 2,4,6-trihydroxyacetophenone (THAP), 2,5-dihydroxybenzoic acid (DHBA), and their related compounds in which the position of a hydroxyl group is different, it was clarified that a hydroxyl group forming an intramolecular hydrogen bond is related to the ionization of matrix molecules. Intramolecular proton transfer in the electronic excited state of the matrix and subsequent proton adduction from a surrounding solvent to the charge-separated matrix are the initial steps for the ionization of matrix molecules. Nanosecond pump–probe NIR–UV mass spectrometry confirmed that the existence of analyte molecules having large dipole moment in their structures is necessary for the stabilization of [matrix + H]+ in the electronic ground state

  18. The shell organic matrix of the crossed lamellar queen conch shell (Strombus gigas).

    Osuna-Mascaró, Antonio; Cruz-Bustos, Teresa; Benhamada, Sana; Guichard, Nathalie; Marie, Benjamin; Plasseraud, Laurent; Corneillat, Marion; Alcaraz, Gérard; Checa, Antonio; Marin, Frédéric

    2014-02-01

    In molluscs, the shell organic matrix comprises a large set of biomineral-occluded proteins, glycoproteins and polysaccharides that are secreted by the calcifying mantle epithelium, and are supposed to display several functions related to the synthesis of the shell. In the present paper, we have characterized biochemically the shell matrix associated to the crossed-lamellar structure of the giant queen conch Strombus gigas. The acid-soluble (ASM) and acid-insoluble (AIM) matrices represent an extremely minor fraction of the shell. Both are constituted of polydisperse and of few discrete proteins among which three fractions, obtained by preparative SDS-PAGE and named 1P3, 2P3 and 3P3, are dominant and were further characterized. Compared to other matrices, the acid-soluble matrix is weakly glycosylated (3%) and among the discrete components, only 3P3 seems noticeably glycosylated. The monosaccharide composition of the ASM shows that mannose represents the main monosaccharide. To our knowledge, this is the first report of a high ratio of this sugar in a skeletal matrix. Furthermore, the ASM interacts with the in vitro crystallization of calcium carbonate, but this interaction is moderate. It differs from that of the isolated 1P3 fraction but is similar to that of the 2P3 and 3P3 fractions. At last, antibodies developed from the 3P3 fraction were used to localize this fraction within the shell by immunogold. This study is the first one aiming at characterizing the organic matrix associated to the crossed-lamellar structure of the queen conch shell. PMID:24291423

  19. Influence of complexing agents on the mechanical performances of the cement conditioning matrix

    Taking in consideration the fact that the conditioning technology of radioactive wastes foresee to include the sludge resulted from the chemical treatment of radioactive liquid effluents into cement matrix, is possible, during a long period of disposal because of the interaction between the complexing agents used and the matter, the cement matrix to be degraded, fact that can allow the radionuclide migration from the disposed container. The studies performed until now have as object to establish the upper level concentration of some decontamination solutions as citric acid, tartaric acid, oxalic acid , ammonium oxalate and sodium citrate which can be contained in the cement conditioning matrix, and do not affect its mechanical performances. Each of the complexing agents used in this paper has his own 'personality ', and influence the rheological and mechanical properties of the mixture . The results show that concentration under 0,5% doesn't influence negatively the mechanical performances, the obtained results being similarly with those obtained for the standard cement paste. (author)

  20. Conditional targeting of medium spiny neurons in the striatal matrix

    Björn eReinius

    2015-03-01

    Full Text Available The striatum serves as the main input to the basal ganglia, and is key for the regulation of motor behaviors, compulsion, addiction, and various cognitive and emotional states. Its deterioration is associated with degenerative disorders such as Huntington’s diseases. Despite its apparent anatomical uniformity, it consists of intermingled cell populations, which have precluded straightforward anatomical sub-classifications adhering to functional dissections. Approximately 95% of the striatal neurons are inhibitory projection neurons termed medium spiny neurons (MSNs. They are commonly classified according to their expression of either dopamine receptor D1 or D2, which also determines their axonal projection patterns constituting the direct and indirect pathway in the basal ganglia. Immunohistochemical patterns have further indicated compartmentalization of the striatum to the striosomes and the surrounding matrix, which integrate MSNs of both the D1 and D2 type. Here, we present a transgenic mouse line, Gpr101-Cre, with Cre recombinase activity localized to matrix D1 and D2 MSNs. Using two Gpr101-Cre founder lines with different degrees of expression in the striatum, we conditionally deleted the vesicular inhibitory amino acid transporter (VIAAT, responsible for storage of GABA and glycine in synaptic vesicles. Partial ablation of VIAAT (in ~36% of MSNs resulted in elevated locomotor activity compared to control mice, when provoked with the monoamine reuptake inhibitor cocaine. Near complete targeting of matrix MSNs led to profoundly changed motor behaviors, which increased in severity as the mice aged. Moreover, these mice had exaggerated muscle rigidity, retarded growth, increased rate of spontaneous deaths, and defective memory. Therefore, our data provide a link between dysfunctional GABA signaling of matrix MSNs to specific behavioral alterations, which are similar to the symptoms of Huntington’s disease.

  1. [Modern polymers in matrix tablets technology].

    Zimmer, Łukasz; Kasperek, Regina; Poleszak, Ewa

    2014-01-01

    Matrix tablets are the most popular method of oral drug administration, and polymeric materials have been used broadly in matrix formulations to modify and modulate drug release rate. The main goal of the system is to extend drug release profiles to maintain a constant in vivo plasma drug concentration and a consistent pharmacological effect. Polymeric matrix tablets offer a great potential as oral controlled drug delivery systems. Cellulose derivatives, like hydroxypropyl methylcellulose (HPMC) are often used as matrix formers. However, also other types of polymers can be used for this purpose including: Kollidon SR, acrylic acid polymers such as Eudragits and Carbopols. Nevertheless, polymers of natural origin like: carragens, chitosan and alginates widely used in the food and cosmetics industry are now coming to the fore of pharmaceutical research and are used in matrix tablets technology. Modern polymers allow to obtain matrix tablets by 3D printing, which enables to develop new formulation types. In this paper, the polymers used in matrix tablets technology and examples of their applications were described. PMID:25739125

  2. Protein structure similarity from principle component correlation analysis

    Chou James

    2006-01-01

    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

  3. Matrix metalloproteinases and epileptogenesis.

    Ikonomidou, Chrysanthy

    2014-12-01

    Matrix metalloproteinases are vital drivers of synaptic remodeling in health and disease. It is suggested that at early stages of epileptogenesis, inhibition of matrix metalloproteinases may help ameliorate cell death, aberrant network rewiring, and neuroinflammation and prevent development of epilepsy. PMID:26567100

  4. Retrieval of similar chess positions

    Ganguly, Debasis; LEVELING, JOHANNES; Jones, Gareth J.F.

    2014-01-01

    We address the problem of retrieving chess game positions similar to a given query position from a collection of archived chess games. We investigate this problem from an information retrieval (IR) perspective. The advantage of our proposed IR-based approach is that it allows using the standard inverted organization of stored chess positions, leading to an ecient retrieval. Moreover, in contrast to retrieving exactly identical board positions, the IR-based approach is able to provide approxim...

  5. Scaling Group Testing Similarity Search

    Iscen, Ahmet; Amsaleg, Laurent; Furon, Teddy

    2016-01-01

    The large dimensionality of modern image feature vectors, up to thousands of dimensions, is challenging the high dimensional indexing techniques. Traditional approaches fail at returning good quality results within a response time that is usable in practice. However, similarity search techniques inspired by the group testing framework have recently been proposed in an attempt to specifically defeat the curse of dimensionality. Yet, group testing does not scale and fails at indexing very large...

  6. SPATIO-TEXTUAL SIMILARITY JOIN

    Ch Shylaja and Supreethi K.P

    2015-07-01

    Full Text Available Data mining is the process of discovering interesting patterns and knowledge from large amounts of data. Spatial databases store large space related data, such as maps, preprocessed remote sensing or medical imaging data. Modern mobile phones and mobile devices are equipped with GPS devices; this is the reason for the Location based services to gain significant attention. These Location based services generate large amounts of spatio- textual data which contain both spatial location and textual description. The spatiotextual objects have different representations because of deviations in GPS or due to different user descriptions. This calls for the need of efficient methods to integrate spatio-textual data. Spatio-textual similarity join meets this need. Spatio-textual similarity join: Given two sets of spatio-textual data, it finds all the similar pairs. Filter and refine framework will be developed to device the algorithms. The prefix filter technique will be extended to generate spatial and textual signatures and inverted indexes will be built on top of these signatures. Candidate pairs will be found using these indexes. Finally the candidate pairs will be refined to get the result. MBR-prefix based signature will be used to prune dissimilar objects. Hybrid signature will be used to support spatial and textual pruning simultaneously.

  7. Roget's Thesaurus and Semantic Similarity

    Jarmasz, Mario

    2012-01-01

    We have implemented a system that measures semantic similarity using a computerized 1987 Roget's Thesaurus, and evaluated it by performing a few typical tests. We compare the results of these tests with those produced by WordNet-based similarity measures. One of the benchmarks is Miller and Charles' list of 30 noun pairs to which human judges had assigned similarity measures. We correlate these measures with those computed by several NLP systems. The 30 pairs can be traced back to Rubenstein and Goodenough's 65 pairs, which we have also studied. Our Roget's-based system gets correlations of .878 for the smaller and .818 for the larger list of noun pairs; this is quite close to the .885 that Resnik obtained when he employed humans to replicate the Miller and Charles experiment. We further evaluate our measure by using Roget's and WordNet to answer 80 TOEFL, 50 ESL and 300 Reader's Digest questions: the correct synonym must be selected amongst a group of four words. Our system gets 78.75%, 82.00% and 74.33% of ...

  8. Involvement of extracellular matrix constituents in breast cancer

    Lochter, Andre; Bissell, Mina J

    1995-06-01

    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.

  9. Matrix comparison, Part 2

    Schneider, Jesper Wiborg; Borlund, Pia

    2007-01-01

    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...... comparisons, matrix generation, and the composition of proximity measures, are introduced and discussed. In this second part, the authors introduce and thoroughly demonstrate two related matrix comparison techniques the Mantel test and Procrustes analysis, respectively. These techniques can compare and...... evaluate the degree of monotonicity between different proximity measures or their ordination results. In common with these techniques is the application of permutation procedures to test hypotheses about matrix resemblances. The choice of technique is related to the validation at hand. In the case of the...

  10. Time rate collision matrix

    The collision integral terms in Boltzmann equation are reformulated numerically leading to the substitution of the multiple integrals with a multiplicative matrix of the two colliding species velocity distribution functions which varies with the differential collision cross section. A matrix of lower rank may be constructed when one of the distribution functions is specified, in which case the matrix elements represent kinetic transition probabilities in the velocity space and the multiplication of the time rate collision matrix with the unknown velocity distribution function expresses the time rate of change of the distribution. The collision matrix may be used to describe the time evolution of systems in nonequilibrium conditions, to evaluate the rate of momentum and energy transfer between given species, or to generate validity criteria for linearized kinetic equations

  11. Double coincidence matrix

    To increase the accuracy of discrimination of true coincidences against the background of accidental ones, circuit has been developed which operates on the principle of dynamic equalization of resolution times of two coincidence circuits. The flowsheet of a 4x6 double-coincidence matrix is given. The principal elements of the matrix are commutators and output signal shapers. The matrix uses 138-series microcircuits. The resolution time of coincidence circuits is 10 ns, the dead time is 25 ns. The results of testing the matrix during experiments under conditions of a high background of accidental coincidences (70-90%) have shown that the accuracy of discrimination of true coincidences with the help of the double-coincidence matrix approximates the accuracy of time-to-digital converters within the limits of the statistical accuracy

  12. Fuzzy vulnerability matrix

    The so-called vulnerability matrix is used in the evaluation part of the probabilistic safety assessment for a nuclear power plant, during the containment event trees calculations. This matrix is established from what is knows as Numerical Categories for Engineering Judgement. This matrix is usually established with numerical values obtained with traditional arithmetic using the set theory. The representation of this matrix with fuzzy numbers is much more adequate, due to the fact that the Numerical Categories for Engineering Judgement are better represented with linguistic variables, such as 'highly probable', 'probable', 'impossible', etc. In the present paper a methodology to obtain a Fuzzy Vulnerability Matrix is presented, starting from the recommendations on the Numerical Categories for Engineering Judgement. (author)

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

    Hedenbjörk-Lager, Anders; Bjørndal, Lars; Gustafsson, Anders; Sorsa, Timo; Tjäderhane, Leo; Åkerman, Sigvard; Ericson, Dan

    2015-01-01

    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...

  14. Measurement of Similarity for Spatial Directions Between Areal Objects

    DING Hong; GUO Qingsheng; DU Xiaohu

    2004-01-01

    Similarity for spatial directions plays an important role in GIS. In this paper, the conventional approaches are analyzed. Based on raster data areal objects, the authors propose two new methods for measuring similarity among spatial directions. One is to measure the similarity among spatial directions based on the features of raster data and the changes of distances between spatial objects, the other is to measure the similarity among spatial directions according to the variation of each raster cell centroid angle. The two methods overcome the complexity of measuring similarity among spatial directions with direction matrix model and solve the limitation of small changes in direction. The two methods are simple and have broader applicability.

  15. Mechanisms for similarity based cooperation

    Traulsen, A.

    2008-06-01

    Cooperation based on similarity has been discussed since Richard Dawkins introduced the term “green beard” effect. In these models, individuals cooperate based on an aribtrary signal (or tag) such as the famous green beard. Here, two different models for such tag based cooperation are analysed. As neutral drift is important in both models, a finite population framework is applied. The first model, which we term “cooperative tags” considers a situation in which groups of cooperators are formed by some joint signal. Defectors adopting the signal and exploiting the group can lead to a breakdown of cooperation. In this case, conditions are derived under which the average abundance of the more cooperative strategy exceeds 50%. The second model considers a situation in which individuals start defecting towards others that are not similar to them. This situation is termed “defective tags”. It is shown that in this case, individuals using tags to cooperate exclusively with their own kind dominate over unconditional cooperators.

  16. Random matrix approach to categorical data analysis

    Patil, Aashay; Santhanam, M. S.

    2015-09-01

    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.

  17. Biocompatible 3D Matrix with Antimicrobial Properties

    Alberto Ion

    2016-01-01

    Full Text Available The aim of this study was to develop, characterize and assess the biological activity of a new regenerative 3D matrix with antimicrobial properties, based on collagen (COLL, hydroxyapatite (HAp, β-cyclodextrin (β-CD and usnic acid (UA. The prepared 3D matrix was characterized by Scanning Electron Microscopy (SEM, Fourier Transform Infrared Microscopy (FT-IRM, Transmission Electron Microscopy (TEM, and X-ray Diffraction (XRD. In vitro qualitative and quantitative analyses performed on cultured diploid cells demonstrated that the 3D matrix is biocompatible, allowing the normal development and growth of MG-63 osteoblast-like cells and exhibited an antimicrobial effect, especially on the Staphylococcus aureus strain, explained by the particular higher inhibitory activity of usnic acid (UA against Gram positive bacterial strains. Our data strongly recommend the obtained 3D matrix to be used as a successful alternative for the fabrication of three dimensional (3D anti-infective regeneration matrix for bone tissue engineering.

  18. Patience of matrix games

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

    2013-01-01

    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...... strategy uses a nonzero probability as small as image. This is done by constructing an explicit image nonsingular image matrix, for which the inverse has only nonnegative entries and where some of the entries are of value image....

  19. Faces of matrix models

    Morozov, A

    2012-01-01

    Partition functions of eigenvalue matrix models possess a number of very different descriptions: as matrix integrals, as solutions to linear and non-linear equations, as tau-functions of integrable hierarchies and as special-geometry prepotentials, as result of the action of W-operators and of various recursions on elementary input data, as gluing of certain elementary building blocks. All this explains the central role of such matrix models in modern mathematical physics: they provide the basic "special functions" to express the answers and relations between them, and they serve as a dream model of what one should try to achieve in any other field.

  20. Quivers from Matrix Factorizations

    Aspinwall, Paul S

    2010-01-01

    We discuss how matrix factorizations offer a practical method of computing the quiver and associated superpotential for a hypersurface singularity. This method also yields explicit geometrical interpretations of D-branes (i.e., quiver representations) on a resolution given in terms of Grassmannians. As an example we analyze some non-toric singularities which are resolved by a single CP1 but have "length" greater than one. These examples have a much richer structure than conifolds. A picture is proposed that relates matrix factorizations in Landau-Ginzburg theories to the way that matrix factorizations are used in this paper to perform noncommutative resolutions.

  1. Elementary matrix theory

    Eves, Howard

    1980-01-01

    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

  2. N-matrix completion problem

    Araújo, C. Mendes; Juan R. Torregrosa; Urbano, Ana M.

    2003-01-01

    An n x n matrix is called an N-matrix if all principal minors are negative. In this paper, we are interested in N-matrix completion problems, that is, when a partial N-matrix hás an N-matrix completion. In general, a combinatorially or non-combinatorially symmetric partial N-matrix does not have an N-matrix completion. Here we prove that a combinatorially symmetric partial N-matrix has an N-matrix completion if the graph of its specified entries is a 1-chordal graph. We also prove that there ...

  3. Oligomerization and polymerization of the filovirus matrix protein VP40

    The matrix protein VP40 from Ebola virus plays an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotein particle complex. Here we show that the N-terminal domain of VP40 folds into a mixture of two different oligomeric states in vitro, namely hexameric and octameric ringlike structures, as detected by gel filtration chromatography, chemical cross-linking, and electron microscopy. Octamer formation depends largely on the interaction with nucleic acids, which in turn confers in vitro SDS resistance. Refolding experiments with a nucleic acid free N-terminal domain preparation reveal a mostly dimeric form of VP40, which is transformed into an SDS resistant octamer upon incubation with E. coli nucleic acids. In addition, we demonstrate that the N-terminal domain of Marburg virus VP40 also folds into ringlike structures, similar to Ebola virus VP40. Interestingly, Marburg virus VP40 rings reveal a high tendency to polymerize into rods composed of stacked rings. These results may suggest distinct roles for different oligomeric forms of VP40 in the filovirus life cycle

  4. Evaluation of New Diagnostic Biomarkers in Pediatric Sepsis: Matrix Metalloproteinase-9, Tissue Inhibitor of Metalloproteinase-1, Mid-Regional Pro-Atrial Natriuretic Peptide, and Adipocyte Fatty-Acid Binding Protein.

    Mashael F Alqahtani

    Full Text Available Elevated plasma concentrations of matrix metalloproteinase-9 (MMP-9, tissue inhibitor of metalloproteinase-1 (TIMP-1, mid-regional pro-atrial natriuretic peptide (mrProANP, and adipocyte fatty-acid-binding proteins (A-FaBPs have been investigated as biomarkers for sepsis or detection of acute neurological injuries in adults, but not children. We carried out a single-center, prospective observational study to determine if these measures could serve as biomarkers to identify children with sepsis. A secondary aim was to determine if these biomarkers could identify children with neurologic complications of sepsis. A total of 90 patients ≤ 18 years-old were included in this study. 30 with severe sepsis or septic shock were compared to 30 age-matched febrile and 30 age-matched healthy controls. Serial measurements of each biomarker were obtained, beginning on day 1 of ICU admission. In septic patients, MMP9-/TIMP-1 ratios (Median, IQR, n were reduced on day 1 (0.024, 0.004-0.174, 13, day 2 (0.020, 0.002-0.109, 10, and day 3 (0.018, 0.003-0.058, 23 compared with febrile (0.705, 0.187-1.778, 22 and healthy (0.7, 0.4-1.2, 29 (p< 0.05 controls. A-FaBP and mrProANP (Median, IQR ng/mL, n were elevated in septic patients compared to control groups on first 2 days after admission to the PICU (p <0.05. The area under the curve (AUC for MMP-9/TIMP-1 ratio, mrProANP, and A-FaBP to distinguish septic patients from healthy controls were 0.96, 0.99, and 0.76, respectively. MMP-9/TIMP-1 ratio was inversely and mrProANP was directly related to PIM-2, PELOD, and ICU and hospital LOS (p<0.05. A-FaBP level was associated with PELOD, hospital and ICU length of stay (p<0.05. MMP-9/TIMP-1 ratio associated with poor Glasgow Outcome Score (p<0.05. A-FaBP levels in septic patients with neurological dysfunction (29.3, 17.2-54.6, 7 were significantly increased compared to septic patients without neurological dysfunction (14.6, 13.3-20.6, 11. MMP-9/TIMP-1 ratios were

  5. Matrix-Free Approximate Equilibration

    Bradley, Andrew M.; Murray, Walter

    2011-01-01

    The condition number of a diagonally scaled matrix, for appropriately chosen scaling matrices, is often less than that of the original. Equilibration scales a matrix so that the scaled matrix's row and column norms are equal. Scaling can be approximate. We develop approximate equilibration algorithms for nonsymmetric and symmetric matrices having signed elements that access a matrix only by matrix-vector products.

  6. A Text Similarity Matrix Operation-Based Classification Algorithm for Large-scale Unstructured Complaint Data%一种基于文本相似度矩阵运算的非结构化海量投诉数据分类算法

    李青; 陈阳; 谢浩然; 蒙圣光

    2012-01-01

    With the fast development of the Internet and information technology nowadays, the growth of the volume of unstructured data is exponential. In particular, the prevalence of the Web 2. 0 network community further enlarges the growth tendency. Therefore, how to manage and organize large-scale unstructured data effectively, so as to facilitate end-user information access, becomes an urgent and important research topic. In this paper, based on the text of unstructured data modeling and text similarity, the existing large-scale unstructured data classification algorithms are surveyed and discussed, and they are applied to a China Mobile user complaint data classification system. Upon the latter, the effectiveness of processing the complaint data is shown to have been much improved, and the usage of our proposed classification algorithm and system architecture is verified.%随着互联网和信息技术的日新月异,非结构化数据量有呈几何级数增长的趋势.尤其是Web 2.0网络社区的流行与火爆,使得增长趋势得到了进一步的加速.因此,面对海量的非结构化数据,如何有效地管理和组织它们,以便于终端用户进行信息存取,成为了一个迫在眉睫的重要研究课题.本文通过对非结构化数据的文本的建模和文本相似度比较,对于大规模非结构化数据的分类算法进行了讨论和研究,并将此算法应用到了中国移动的投诉数据分类系统中.在系统实施后,非常有效地提高了投诉数据的处理效率,从而印证所提出分类算法及系统框架的有效性.

  7. Performance Indexes: Similarities and Differences

    André Machado Caldeira

    2013-06-01

    Full Text Available The investor of today is more rigorous on monitoring a financial assets portfolio. He no longer thinks only in terms of the expected return (one dimension, but in terms of risk-return (two dimensions. Thus new perception is more complex, since the risk measurement can vary according to anyone’s perception; some use the standard deviation for that, others disagree with this measure by proposing others. In addition to this difficulty, there is the problem of how to consider these two dimensions. The objective of this essay is to study the main performance indexes through an empirical study in order to verify the differences and similarities for some of the selected assets. One performance index proposed in Caldeira (2005 shall be included in this analysis.

  8. Features Based Text Similarity Detection

    Kent, Chow Kok

    2010-01-01

    As the Internet help us cross cultural border by providing different information, plagiarism issue is bound to arise. As a result, plagiarism detection becomes more demanding in overcoming this issue. Different plagiarism detection tools have been developed based on various detection techniques. Nowadays, fingerprint matching technique plays an important role in those detection tools. However, in handling some large content articles, there are some weaknesses in fingerprint matching technique especially in space and time consumption issue. In this paper, we propose a new approach to detect plagiarism which integrates the use of fingerprint matching technique with four key features to assist in the detection process. These proposed features are capable to choose the main point or key sentence in the articles to be compared. Those selected sentence will be undergo the fingerprint matching process in order to detect the similarity between the sentences. Hence, time and space usage for the comparison process is r...

  9. Semantically enabled image similarity search

    Casterline, May V.; Emerick, Timothy; Sadeghi, Kolia; Gosse, C. A.; Bartlett, Brent; Casey, Jason

    2015-05-01

    Georeferenced data of various modalities are increasingly available for intelligence and commercial use, however effectively exploiting these sources demands a unified data space capable of capturing the unique contribution of each input. This work presents a suite of software tools for representing geospatial vector data and overhead imagery in a shared high-dimension vector or embedding" space that supports fused learning and similarity search across dissimilar modalities. While the approach is suitable for fusing arbitrary input types, including free text, the present work exploits the obvious but computationally difficult relationship between GIS and overhead imagery. GIS is comprised of temporally-smoothed but information-limited content of a GIS, while overhead imagery provides an information-rich but temporally-limited perspective. This processing framework includes some important extensions of concepts in literature but, more critically, presents a means to accomplish them as a unified framework at scale on commodity cloud architectures.

  10. ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates

    Michael Römer; Linus Backert; Johannes Eichner; Andreas Zell

    2014-01-01

    We present a new tool for hepatocarcinogenicity evaluation of drug candidates in rodents. ToxDBScan is a web tool offering quick and easy similarity screening of new drug candidates against two large-scale public databases, which contain expression profiles for substances with known carcinogenic profiles: TG-GATEs and DrugMatrix. ToxDBScan uses a set similarity score that computes the putative similarity based on similar expression of genes to identify chemicals with similar genotoxic and hep...

  11. Ion-to-Neutral Ratios and Thermal Proton Transfer in Matrix-Assisted Laser Desorption/Ionization

    Lu, I.-Chung; Chu, Kuan Yu; Lin, Chih-Yuan; Wu, Shang-Yun; Dyakov, Yuri A.; Chen, Jien-Lian; Gray-Weale, Angus; Lee, Yuan-Tseh; Ni, Chi-Kung

    2015-07-01

    The ion-to-neutral ratios of four commonly used solid matrices, α-cyano-4-hydroxycinnamic acid (CHCA), 2,5-dihydroxybenzoic acid (2,5-DHB), sinapinic acid (SA), and ferulic acid (FA) in matrix-assisted laser desorption/ionization (MALDI) at 355 nm are reported. Ions are measured using a time-of-flight mass spectrometer combined with a time-sliced ion imaging detector. Neutrals are measured using a rotatable quadrupole mass spectrometer. The ion-to-neutral ratios of CHCA are three orders of magnitude larger than those of the other matrices at the same laser fluence. The ion-to-neutral ratios predicted using the thermal proton transfer model are similar to the experimental measurements, indicating that thermal proton transfer reactions play a major role in generating ions in ultraviolet-MALDI.

  12. Pesticide-Exposure Matrix

    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.

  13. The Hill Interaction Matrix

    Hill, William Fawcett

    1971-01-01

    Leadership style, group composition, and group development are simultaneously quantified through the use of the matrix. It represents an attempt to objectify the art of group therapy. Comment by Richard C. Rank follows. (Author)

  14. 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

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

    1994-01-01

    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, and...

  15. The Matrix Organization Revisited

    Gattiker, Urs E.; Ulhøi, John Parm

    1999-01-01

    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)....

  16. Matrix Big Brunch

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

    2007-01-01

    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...

  17. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    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.

  18. Detection of HOCl-mediated protein oxidation products in the extracellular matrix of human atherosclerotic plaques

    Woods, Alan A; Linton, Stuart M; Davies, Michael Jonathan

    2003-01-01

    83-96% of the total oxidized protein side-chain products detected in these plaques. Oxidation of matrix components extracted from healthy artery tissue, and model proteins, with reagent HOCl is shown to give rise to a similar pattern of products to those detected in advanced human lesions. The......Oxidation is believed to play a role in atherosclerosis. Oxidized lipids, sterols and proteins have been detected in early, intermediate and advanced human lesions at elevated levels. The spectrum of oxidized side-chain products detected on proteins from homogenates of advanced human lesions has...... material obtained from advanced human atherosclerotic lesions are shown to contain elevated levels of oxidized amino acids [3,4-dihydroxyphenylalanine (DOPA), di-tyrosine, 2-hydroxyphenylalanine ( o-Tyr)] when compared with healthy (human and pig) arterial tissue. These matrix-derived materials account for...

  19. Bosonic Matrix Theory and Matrix Dbranes

    Chaudhuri, Shyamoli

    2002-01-01

    We develop new tools for an in-depth study of our recent proposal for Matrix Theory. We construct the anomaly-free and finite planar continuum limit of the ground state with SO(2^{13}) symmetry matching with the tadpole and tachyon free IR stable high temperature ground state of the open and closed bosonic string. The correspondence between large N limits and spacetime effective actions is demonstrated more generally for an arbitrary D25brane ground state which might include brane-antibrane p...

  20. Alaska, Gulf spills share similarities

    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

  1. Relativistic Self-similar Disks

    Cai, M J; Cai, Mike J.; Shu, Frank H.

    2002-01-01

    We formulate and solve by semi-analytic means the axisymmetric equilibria of relativistic self-similar disks of infinitesimal vertical thickness. These disks are supported in the horizontal directions against their self-gravity by a combination of isothermal (two-dimensional) pressure and a flat rotation curve. The dragging of inertial frames restricts possible solutions to rotation speeds that are always less than 0.438 times the speed of light, a result first obtained by Lynden-Bell and Pineault in 1978 for a cold disk. We show that prograde circular orbits of massive test particles exist and are stable for all of our model disks, but retrograde circular orbits cannot be maintained with particle velocities less than the speed of light once the disk develops an ergoregion. We also compute photon trajectories, planar and non-planar, in the resulting spacetime, for disks with and without ergoregions. We find that all photon orbits, except for a set of measure zero, tend to be focused by the gravity of the flat...

  2. Matricial bridges for "Matrix algebras converge to the sphere"

    Rieffel, Marc A.

    2015-01-01

    In the high-energy quantum-physics literature one finds statements such as "matrix algebras converge to the sphere". Earlier I provided a general setting for understanding such statements, in which the matrix algebras are viewed as quantum metric spaces, and convergence is with respect to a quantum Gromov-Hausdorff-type distance. In the present paper, as preparation of discussing similar statements for convergence of "vector bundles" over matrix algebras to vector bundles over spaces, we intr...

  3. Symmetries of the 2D magnetic particle imaging system matrix

    In magnetic particle imaging (MPI), the relation between the particle distribution and the measurement signal can be described by a linear system of equations. For 1D imaging, it can be shown that the system matrix can be expressed as a product of a convolution matrix and a Chebyshev transformation matrix. For multidimensional imaging, the structure of the MPI system matrix is not yet fully explored as the sampling trajectory complicates the physical model. It has been experimentally found that the MPI system matrix rows have symmetries and look similar to the tensor products of Chebyshev polynomials. In this work we will mathematically prove that the 2D MPI system matrix has symmetries that can be used for matrix compression. (paper)

  4. One anlytic form for four branches of the ABCD matrix

    Baskal, S

    2010-01-01

    It is not always possible to diagonalize the optical $ABCD$ matrix, but it can be brought into one of the four Wigner matrices by a similarity transformation. It is shown that the four Wigner matrices can be combined into one matrix with four branches. This result is illustrated in terms of optical activities, laser cavities, and multilayer optics.

  5. Matrix Information Geometry

    Bhatia, Rajendra

    2013-01-01

    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.  

  6. Influence of complexing agents on the mechanical performances of the cement conditioning matrix

    the mechanical strength, checking the strength of compression at 90 days and the adequate density in comparison with the standard test characteristics of the samples prepared with drinking water and distilled water. The strength of compression was done using hydraulic presses; - the influence of the citric acid, sodium citrate and ammonium oxalate solution concentrations on the strength of compression at the age of 60 and 90 days; - for all the mixtures used in this paper, the setting times were established by using the Vicat device outlining the specific time of set curves characterized by setting beginning, setting interval and setting ending. The best results were obtained for the ammonium oxalate, sodium citrate and citric acid for which the results are almost similarly with the standard cement matrix sample values. By comparing the results obtained after 28, 60, 90 and 240 days, it was found that for concentrations of solutions used for decontamination comprised between 0.25% and 0.5% the mechanical performances are similarly with those obtained for reference cement matrix samples. From the test interpretation, the final conclusion is that in the case in which after the decontamination process, radioactive wastes containing one of these decontamination solutions with a concentration higher than the value of 0.5% are obtained, it is necessary to reduce the concentration by a pre-treatment process applied to the radioactive wastes before cementing. (authors)

  7. Permutation-like Matrix Groups with a Maximal Cycle of Power of Odd Prime Length

    Deng, Guodong; Yun FAN

    2015-01-01

    If every element of a matrix group is similar to a permutation matrix, then it is called a permutation-like matrix group. References [4] and [5] showed that, if a permutation-like matrix group contains a maximal cycle of length equal to a prime or a square of a prime and the maximal cycle generates a normal subgroup, then it is similar to a permutation matrix group. In this paper, we prove that if a permutation-like matrix group contains a maximal cycle of length equal to any power of any odd...

  8. Permutation-like Matrix Groups with a Maximal Cycle of Length Power of Two

    Deng, Guodong; Yun FAN

    2016-01-01

    If every element of a matrix group is similar to a permutation matrix, then it is called a permutation-like matrix group. References [4], [5] and [6] showed that, if a permutation-like matrix group contains a maximal cycle such that the maximal cycle generates a normal subgroup and the length of the maximal cycle equals to a prime, or a square of a prime, or a power of an odd prime, then the permutation-like matrix group is similar to a permutation matrix group. In this paper, we prove that i...

  9. Identification of the nuclear matrix and chromosome scaffold in dinoflagellate Crypthecodinium cohnii

    CAISHUTAO; CONGMEIZENG; 等

    1992-01-01

    Dinolflagellate is one of the primitive eukaryotes,whose nucleus may represent one of the transition stages from prokaryotic nucleoid to typical eukaryotic nucleus,Using selective extraction together with embeddment-free section and whole mount electron microscopy,a delicate nuclear matrix filament network was shown,for the first time,in dinoflagellate Crypthecodinium cohnii nucleus,Chromosome residues are connected with nuclear matrix filaments to form a complete network spreading over the nucleus,Moreover,we demonstrated that the dinoflagellate chromosome retains a protein scafflod after the depletion of DNA and soluble proteins.This scaffold preserves the characterstic morphology of the chromosome.Two dimensional electrophoreses indicated that the nuclear matrix and chromosome scaffold are mainly composed of acidic proteins.Our results demonstrated that a framework similar th the nuclear matrix and chromosome scaffold in mammalian cells appears in this primitive eukaryote,suggesting that these structures may have been originated from the early stages of eukaryote evolution.

  10. Matrix interdiction problem

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

    2010-01-01

    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. Dynamic Matrix Rank

    Frandsen, Gudmund Skovbjerg; Frandsen, Peter Frands

    2009-01-01

    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....

  12. MATLAB matrix algebra

    Pérez López, César

    2014-01-01

    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 ...

  13. Influence of Binder in Iron Matrix Composites

    The ability to use iron and its alloys as the matrix material in composite systems is of great importance because it is the most widely used metallic material with a variety of commercially available steel grades [1]. The aim of this study is to investigate the influence of binder in particulate iron based metal matrix composites. There are four types of binder that were used in this study; Stearic Acid, Gummi Arabisch, Polyvinyl alcohol 15000 MW and Polyvinyl alcohol 22000 MW. Six different weight percentage of each binder was prepared to produce the composite materials using powder metallurgy (P/M) route; consists of dry mixing, uniaxially compacting at 750 MPa and vacuum sintering at 1100 deg. C for two hours. Their characterization included a study of density, porosity, hardness and microstructure. Results indicate that MMC was affected by the binder and stearic acid as a binder produced better properties of the composite.

  14. DIY Bertin Matrix

    Perin, Charles; Le Goc, Mathieu; Di Vozzo, Romain; Fekete, Jean-Daniel; Dragicevic, Pierre

    2015-01-01

    In this paper, we relate the iterative fabrication of a physical Bertin Matrix. Jacques Bertin designed and refined such devices over 10 years (1970–1980) and five iterations of what he called Dominos 1–5. For the purpose of an exhibit dedicated to Bertin's work during VIS 2014 in Paris, we designed an improved version of such device by leveraging modern fabrication possibilities and in particular a laser cutter. We describe the process, iterations and improvements of our matrix, and report l...

  15. A nonsupersymmetric matrix orbifold

    Banks, Tom; Motl, Lubos

    1999-01-01

    We construct the matrix description for a twisted version of the IIA string theory on S^1 with fermions antiperiodic around a spatial circle. The result is a 2+1-dimensional U(N) x U(N) nonsupersymmetric Yang-Mills theory with fermionic matter transforming in the (N,Nbar). The two U(N)'s are exchanged if one goes around a twisted circle of the worldvolume. Relations with Type 0 theories are explored and we find Type 0 matrix string limits of our gauge theory. We argue however that most of the...

  16. Complex matrix model duality

    Brown, T.W.

    2010-11-15

    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.)

  17. Complex matrix model duality

    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.)

  18. Reduced Google matrix

    Frahm, K M

    2016-01-01

    Using parallels with the quantum scattering theory, developed for processes in nuclear and mesoscopic physics and quantum chaos, we construct a reduced Google matrix $G_R$ which describes the properties and interactions of a certain subset of selected nodes belonging to a much larger directed network. The matrix $G_R$ takes into account effective interactions between subset nodes by all their indirect links via the whole network. We argue that this approach gives new possibilities to analyze effective interactions in a group of nodes embedded in a large directed networks. Possible efficient numerical methods for the practical computation of $G_R$ are also described.

  19. Elementary matrix algebra

    Hohn, Franz E

    2012-01-01

    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

  20. Matrixed business support comparison study.

    Parsons, Josh D.

    2004-11-01

    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.

  1. Inequalities Involving Upper Bounds for Certain Matrix Operators

    R Lashkaripour; D Foroutannia

    2006-08-01

    In this paper, we considered the problem of finding the upper bound Hausdorff matrix operator from sequence spaces $l_p(v)$ (or $d(v,p)$) into $l_p(w)$ (or $d(w, p)$). Also we considered the upper bound problem for matrix operators from $d(v,1)$ into $d(w,1)$, and matrix operators from $e(w,∞)$ into $e(v,∞)$, and deduce upper bound for Cesaro, Copson and Hilbert matrix operators, which are recently considered in [5] and [6] and similar to that in [10].

  2. Research on the Connection Bias of Amino Acids Based on Probability Transition Matrix%基于概率转移矩阵的氨基酸连接偏好性研究

    张堃; 唐旭清

    2012-01-01

    在Markov模型的基础上,提出了状态空间上合并映射的概念,以及合并过程下转移概率的计算方法.在已有氨基酸分类方法的基础上,结合Markov模型的概率转移矩阵,对氨基酸连接的偏好性进行了研究.结果表明:同一家族的蛋白质序列的氨基酸连接具有一定的偏好性,这种偏好性与氨基酸的分类有关,从而进一步说明了分类的科学性,同时这种偏好性对氨基酸序列的预测具有一定的作用.%In this manuscript, a novel concept of lumping map and a computing method of the transition probability in lumped process were suggested based on Markov model, to investigate the connection bias of amino acids. The results demonstrated that the connection of amino acids had a particular preference which was related to the classification of amino acids, and further verified the scientific of the classification of amino acids. At the same time, the preference would give some help for the prediction of amino acids sequence.

  3. Matrix model holography

    Ortiz, Thomas; Samtleben, Henning; Tsimpis, Dimitrios

    2014-01-01

    We set up the formalism of holographic renormalization for the matter-coupled two-dimensional maximal supergravity that captures the low-lying fluctuations around the non-conformal D0-brane near-horizon geometry. As an application we compute holographically one- and two-point functions of the BFSS matrix quantum mechanics and its supersymmetric $SO(3)\\times SO(6)$ deformation.

  4. Event matrix system

    The number of background events in nuclear and particle physics experiments which use multiwire proportional chambers can be extremely high. Using a computer to resolve these events results in a high deadtime for the experiment. A fast matrix system for decreasing the number of background events is described in this report. 4 figures

  5. Matrix Synthesis and Characterization

    1984-01-01

    The role of NASA in the area of composite material synthesis; evaluation techniques; prediction analysis techniques; solvent-resistant tough composite matrix; resistance to paint strippers; acceptable processing temperature and pressure for thermoplastics; and the role of computer modeling and fiber interface improvement were discussed.

  6. Generalized Framework for Similarity Measure of Time Series

    Hongsheng Yin

    2014-01-01

    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.

  7. 导入透明质酸猪脱细胞真皮基质的刺激性及致敏性研究%Skin irritation and sensitization of swine acellular dermal matrix treated with hyaluronic acid

    宁少南; 赵筱卓; 王慧英; 张国安

    2012-01-01

    Objective To evaluate the skin irritation and sensitization potential of the swine acellular dermal matrix treated with hyaluronic acid (SADM-HA).Methods (1) Skin irritation test.Twelve New Zealand rabbits were divided into SADM-HA group,allogeneic skin group,and (human) xeno-skin group according to the random number table,with 4 rabbits in each group.Four test sites were designed on the back of each rabbit.Two test sites of each rabbit in the three groups were covered with SADM-HA,allogeneic skin,and xeno-skin,respectively.Another test site was covered with gauze containing 200 g/L sodium dodecyl sulfate solution as positive control.The last test site was covered with gauze containing normal saline as negative control.The primary irritation index and cumulative irritation index of each material were calculated.(2) Skin closed-patch test.Sixty guinea pigs were used.Fifty-four guinea pigs were divided into SADM-HA group,allogeneic skin group,and (human) xeno-skin group according to the random number table,with 18 guinea pigs in each group.Twelve guinea pigs in each of the three groups were correspondingly induced and stimulated by SADM-HA,allogeneic skin,and xeno-skin,with 6 guinea pigs in each group treated with ethanol-soaked gauze to serve as negative control.The remaining 6 guinea pigs were treated with gauze containing 25% α-hexylcinnamaldehyde ethanol solution as positive control.The rating scales of Magnusson and Kligman were used to grade the condition of skin after being treated with above-mentioned materials to evaluate skin sensitivity to them at post stimulation hour 24 and 48.Data were processed with the nonparametric test of independent samples.Results (1) In the skin irritation test,the primary irritation indexes of the three dressings in SADM-HA group,allogeneic skin group,and xeno-skin group were respectively-0.04,0.13,and 0.08.The cumulative irritation indexes of the three dressings in SADM-HA group,allogeneic skin group,and xeno-skin group were

  8. r-BlockPermutation Factor Circulant Matrix and Inverse Matrix

    SUN Ji zhong; QIN Keyun; Hu, Yan

    2012-01-01

    The concept of r-block permutation factor circulant matrix is presented. The characteristics of r-block permutation factor circulant matrix are discussed by Kronecker. The interchange ability of r-block permutation factor circulant matrix has been demonstrated, that is AB=BA. The calculation method of matrix determinant and the sufficient condition of nonsingular matrix based on the diagonalization of circulant matrices are given. Finally, the method of inverse matrix is given in r-blo...

  9. Dependency Similarity, Attraction and Perceived Happiness.

    Pandey, Janak

    1978-01-01

    Subjects were asked to evaluate either a similar personality or a dissimilar personality. Subjects rated similar others more positively than dissimilar others and, additionally, perceived similar others as more helpful and sympathetic than dissimilar others. (Author)

  10. NMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein

    Lola A. Brown

    2015-04-01

    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.

  11. Ostwald ripening of the matrix phase surrounding dispersoids

    Self-similar coarsening of particles dispersed in a matrix is well known experimentally and theoretically as Ostwald ripening. In this paper we present experimental and numerical material on Cu-Co dispersions looking for the inverse effect: Does the copper matrix surrounding cobalt particles also coarsen self-similar during liquid phase sintering as the particles do? The experimental investigations were performed with Cu-Co alloys of various volume fractions of solid phase (0.25 to 0.7). Green compacts of both elemental powders were sintered at 1473 K for times between 5 minutes and 70 hours. The coarsening of the matrix was analysed in plane section of the specimens. The experimental results show that the matrix coarsens self-similar. A numerical modelling is presented clarifying the experimental results. (orig.)

  12. Intranuclear targeting of AML/CBFα regulatory factors to nuclear matrix-associated transcriptional domains

    Zeng, Congmei; McNeil, Sandra; Pockwinse, Shirwin; Nickerson, Jeffrey; Shopland, Lindsay; Lawrence, Jeanne B.; Penman, Sheldon; Hiebert, Scott; Lian, Jane B.; van Wijnen, André J.; Stein, Janet L.; Stein, Gary S.

    1998-01-01

    The AML/CBFα runt transcription factors are key regulators of hematopoietic and bone tissue-specific gene expression. These factors contain a 31-amino acid nuclear matrix targeting signal that supports association with the nuclear matrix. We determined that the AML/CBFα factors must bind to the nuclear matrix to exert control of transcription. Fusing the nuclear matrix targeting signal to the GAL4 DNA binding domain transactivates a genomically integrated GAL4 responsive reporter gene. These ...

  13. A nonsupersymmetric matrix orbifold

    Banks, T; Banks, Tom; Motl, Lubos

    2000-01-01

    We construct the matrix description for a twisted version of the IIA string theory on S^1 with fermions antiperiodic around a spatial circle. The result is a 2+1-dimensional U(N) x U(N) nonsupersymmetric Yang-Mills theory with fermionic matter transforming in the (N,Nbar). The two U(N)'s are exchanged if one goes around a twisted circle of the worldvolume. Relations with Type 0 theories are explored and we find Type 0 matrix string limits of our gauge theory. We argue however that most of these results are falsified by the absence of SUSY nonrenormalization theorems and that the models do not in fact have a sensible Lorentz invariant space time interpretation.

  14. XRF matrix corrections

    Full text: In order to obtain meaningful analytical information from an X-Ray Fluorescence spectrometer, it is necessary to correlate measured intensity values with sample concentrations. The ability to do this to a desired level of precision depends on taking care of a number of variables which influence measured intensity values. These variables include: the sample, which needs to be homogeneous, flat and critically thick to the analyte lines used for measurement; the spectrometer, which needs to perform any mechanical movements in a highly reproducible manner; the time taken to measure an analyte line, and the software, which needs to take care of detector dead-time, the contribution of background to the measured signal, the effects of line overlaps and matrix (absorption and enhancement) effects. This presentation will address commonly used correction procedures for matrix effects and their relative success in achieving their objective. Copyright (2002) Australian X-ray Analytical Association Inc

  15. Paths correlation matrix.

    Qian, Weixian; Zhou, Xiaojun; Lu, Yingcheng; Xu, Jiang

    2015-09-15

    Both the Jones and Mueller matrices encounter difficulties when physically modeling mixed materials or rough surfaces due to the complexity of light-matter interactions. To address these issues, we derived a matrix called the paths correlation matrix (PCM), which is a probabilistic mixture of Jones matrices of every light propagation path. Because PCM is related to actual light propagation paths, it is well suited for physical modeling. Experiments were performed, and the reflection PCM of a mixture of polypropylene and graphite was measured. The PCM of the mixed sample was accurately decomposed into pure polypropylene's single reflection, pure graphite's single reflection, and depolarization caused by multiple reflections, which is consistent with the theoretical derivation. Reflection parameters of rough surface can be calculated from PCM decomposition, and the results fit well with the theoretical calculations provided by the Fresnel equations. These theoretical and experimental analyses verify that PCM is an efficient way to physically model light-matter interactions. PMID:26371930

  16. Extended Matrix Variate Hypergeometric Functions and Matrix Variate Distributions

    Daya K. Nagar; Raúl Alejandro Morán-Vásquez; Gupta, Arjun K.

    2015-01-01

    Hypergeometric functions of matrix arguments occur frequently in multivariate statistical analysis. In this paper, we define and study extended forms of Gauss and confluent hypergeometric functions of matrix arguments and show that they occur naturally in statistical distribution theory.

  17. Inside the NIKE matrix

    BRENNER, BARBARA; Bodo B. Schlegelmilch; Ambos, Björn

    2013-01-01

    This case describes how Nike, a consumer goods company with an ever expanding portfolio and a tremendous brand value, manages the tradeoff between local responsiveness and global integration. In particular, the case highlights Nike's organizational structure that consists of a global matrix organization that is replicated at a regional level for the European market. While this organizational structure allows Nike to respond to local consumer tastes it also ensures that the company benefits f...

  18. 图的无号Laplace矩阵的最大特征值%On the Largest Eigenvalue of Signless Laplacian Matrix of a Graph

    谭尚旺; 王兴科

    2009-01-01

    The signless Laplacian matrix of a graph is the sum of its diagonal matrix of vertex degrees and its adjacency matrix. Li and Feng gave some basic results on the largest eigenvalue and characteristic polynomial of adjacency matrix of a graph in 1979. In this paper, we translate these results into the signless Laplacian matrix of a graph and obtain the similar results.

  19. The matrix Euler-Fermat theorem

    We prove many congruences for binomial and multinomial coefficients as well as for the coefficients of the Girard-Newton formula in the theory of symmetric functions. These congruences also imply congruences (modulo powers of primes) for the traces of various powers of matrices with integer elements. We thus have an extension of the matrix Fermat theorem similar to Euler's extension of the numerical little Fermat theorem

  20. Infinite matrix products and the representation the gamma matrix function

    J.-C. Cortés; Jódar, L.; Francisco J. Solís; Roberto Ku-Carrillo

    2015-01-01

    We introduce infinite matrix products including some of their main properties and convergence results. We apply them in order to extend to the matrix scenario the definition of the scalar gamma function given by an infinite product due to Weierstrass. A limit representation of the matrix gamma function is also provided.

  1. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms

    Klein, Marlise I.; Hwang, Geelsu; Santos, Paulo H. S.; Campanella, Osvaldo H.; Koo, Hyun

    2015-01-01

    Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA, and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria...

  2. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms

    Marlise eKlein; Geelsu eHwang; Paulo eSantos; Osvaldo eCampanella; Hyun eKoo

    2015-01-01

    Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria....

  3. Synthesis and Characterization of Long-Chain Tartaric Acid Diamides as Novel Ceramide-Like Compounds

    Krisztina Takács-Novák

    2010-02-01

    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.

  4. Novel additives for the separation of organic acids by ion-pair chromatography

    2010-01-01

    This paper proposes the use of novel surfactant additives for the separation of organic acids by ion-pair chromatography and studies the influences of surfactants on the chromatographic separation behaviors.Researches have been carried out on both silica gel matrix and polymer supporters in order to compare the two ordinary kinds of stationary phases,and the phenomenon is similar. Separation is based on differences in the stabilities of analyte-additive complexes in solution.Retention times of analytes c...

  5. Versatile matrix for constructing enzyme-based biosensors.

    Wang, Zhaohao; Luo, Xi; Wan, Qijin; Wu, Kangbing; Yang, Nianjun

    2014-10-01

    A versatile matrix was fabricated and utilized as a universal interface for the construction of enzyme-based biosensors. This matrix was formed on the gold electrode via combining self-assembled monolayer of 2,3-dimercaptosuccinic acid with gold nanoparticles. Gold nanoparticles were electrochemically deposited. Electrochemistry of three redox enzymes (catalase, glucose oxidase, and horseradish peroxidase) was investigated on such a matrix. The electrocatalytic monitoring of hydrogen peroxide and glucose was conducted on this matrix after being coated with those enzymes. On them the monitoring of hydrogen peroxide and glucose shows rapid response times, wide linear working ranges, low detection limits, and high enzymatic affinities. This matrix is thus a versatile and suitable platform to develop highly sensitive enzyme-based biosensors. PMID:25208242

  6. Matrix Completions and Chordal Graphs

    Kenneth John HARRISON

    2003-01-01

    In a matrix-completion problem the aim is to specifiy the missing entries of a matrix inorder to produce a matrix with particular properties. In this paper we survey results concerning matrix-completion problems where we look for completions of various types for partial matrices supported ona given pattern. We see that thc existence of completions of the required type often depends on thechordal properties of graphs associated with the pattern.

  7. Assembly and development of the Pseudomonas aeruginosa biofilm matrix.

    Luyan Ma

    2009-03-01

    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.

  8. The cellulose resource matrix.

    Keijsers, Edwin R P; Yılmaz, Gülden; van Dam, Jan E G

    2013-03-01

    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

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

    Tongsong Jiang; Xuehan Cheng; Sitao Ling

    2014-01-01

    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 matri...

  10. Sublimation as a Method of Matrix Application for Mass Spectrometric Imaging

    Hankin, Joseph A.; Barkley, Robert M.; Murphy, Robert C.

    2007-01-01

    Common organic MALDI matrices, 2,5-dihydroxybenzoic acid, 3,5-dimethoxy-4-hydroxycinnamic acid, and alpha-cyano-4-hydroxy-cinnamic acid were found to undergo sublimation without decomposition under conditions of reduced pressure and elevated temperature. This solid to vapor phase transition was exploited to apply MALDI matrix onto tissue samples over a broad surface in a solvent-free application for mass spectrometric imaging. Sublimation of matrix produced an even layer of small crystals acr...

  11. Matrix vector analysis

    Eisenman, Richard L

    2005-01-01

    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

  12. Investigating Boolean Matrix Factorization

    Snášel, V.; Platoš, J.; Krömer, P.; Húsek, Dušan; Neruda, Roman; Frolov, A. A.

    - : ACM, 2008 - (Ding, C.; Li, T.; Zhu, S.), s. 18-25 ISBN 978-1-60558-307-5. [DMMT'08. Workshop in Conjunction with SIGKDD 2008 /14./. Las Vegas (US), 24.08.2008-24.08.2008] Institutional research plan: CEZ:AV0Z10300504 Keywords : Boolean factor analysis * nonnegative matrix factorization * neural networks * information retrieval * data mining * binary data Subject RIV: BB - Applied Statistics, Operational Research http://users.cs.fiu.edu/~taoli/kdd08-workshop/DMMT08-Proceedings.pdf

  13. Matrix string partition function

    Kostov, Ivan K; Kostov, Ivan K.; Vanhove, Pierre

    1998-01-01

    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.

  14. Matrix algebra for linear models

    Gruber, Marvin H J

    2013-01-01

    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

  15. Hierarchical Matrix Techniques on Massively Parallel Computers

    Izadi, Mohammad

    2012-01-01

    Hierarchical matrix (H-matrix) techniques can be used to efficiently treat dense matrices. With an H-matrix, the storage requirements and performing all fundamental operations, namely matrix-vector multiplication, matrix-matrix multiplication and matrix inversion can be done in almost linear complexity. In this work, we tried to gain even further speedup for the H-matrix arithmetic by utilizing multiple processors. Our approach towards an H-matrix distribution relies on the s...

  16. Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

    Žel Jana

    2006-08-01

    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. Asthma and COPD: Differences and Similarities

    ... 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 ...

  18. Characterization of supercapacitors matrix

    This paper treats supercapacitors matrix characterization. In order to cut off transient power peaks and to compensate for the intrinsic limitations in embedded sources, the use of supercapacitors as a storage system is quite suitable, because of their appropriate electrical characteristics (huge capacitance, small series resistance, high specific energy, high specific power), direct storage (energy ready for use), and easy control by power electronic conversion. This use requires supercapacitors modules where several cells connected in serial and/or in parallel, thus a bypass system to balance the charging or the discharging of supercapacitors is required. In the matrix of supercapacitors, six elements of three parallel BCAP0350 supercapacitors in serial connections have been considered. This topology permits to reduce the number of the bypass circuits and it can work in degraded mode. Actually, it allows the system to have more reliability by providing power continually to the load even when there are one or more cells failed. Simulation and experimental results are presented and discussed.

  19. Modeling Pathological Speech Perception From Data With Similarity Labels.

    Berisha, Visar; Liss, Julie; Sandoval, Steven; Utianski, Rene; Spanias, Andreas

    2014-05-01

    The current state of the art in judging pathological speech intelligibility is subjective assessment performed by trained speech pathologists (SLP). These tests, however, are inconsistent, costly and, oftentimes suffer from poor intra- and inter-judge reliability. As such, consistent, reliable, and perceptually-relevant objective evaluations of pathological speech are critical. Here, we propose a data-driven approach to this problem. We propose new cost functions for examining data from a series of experiments, whereby we ask certified SLPs to rate pathological speech along the perceptual dimensions that contribute to decreased intelligibility. We consider qualitative feedback from SLPs in the form of comparisons similar to statements "Is Speaker A's rhythm more similar to Speaker B or Speaker C?" Data of this form is common in behavioral research, but is different from the traditional data structures expected in supervised (data matrix + class labels) or unsupervised (data matrix) machine learning. The proposed method identifies relevant acoustic features that correlate with the ordinal data collected during the experiment. Using these features, we show that we are able to develop objective measures of the speech signal degradation that correlate well with SLP responses. PMID:25435817

  20. Shape Similarity Measures of Linear Entities

    2002-01-01

    The essential of feature matching technology lies in how to measure the similarity of spatial entities.Among all the possible similarity measures,the shape similarity measure is one of the most important measures because it is easy to collect the necessary parameters and it is also well matched with the human intuition.In this paper a new shape similarity measure of linear entities based on the differences of direction change along each line is presented and its effectiveness is illustrated.

  1. Learning Good Edit Similarities with Generalization Guarantees

    Bellet, Aurélien; Habrard, Amaury; Sebban, Marc

    2011-01-01

    Similarity and distance functions are essential to many learning algorithms, thus training them has attracted a lot of interest. When it comes to dealing with structured data (e.g., strings or trees), edit similarities are widely used, and there exists a few methods for learning them. However, these methods offer no theoretical guarantee as to the generalization performance and discriminative power of the resulting similarities. Recently, a theory of learning with good similarity functions wa...

  2. Composing Measures for Computing Text Similarity

    Bär, Daniel; Zesch, Torsten; Gurevych, Iryna

    2015-01-01

    We present a comprehensive study of computing similarity between texts. We start from the observation that while the concept of similarity is well grounded in psychology, text similarity is much less well-defined in the natural language processing community. We thus define the notion of text similarity and distinguish it from related tasks such as textual entailment and near-duplicate detection. We then identify multiple text dimensions, i.e. characteristics inherent to texts that can be used...

  3. Appropriate Similarity Measures for Author Cocitation Analysis

    van Eck, Nees Jan; Waltman, Ludo

    2007-01-01

    textabstractWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not ...

  4. Representation Independent Proximity and Similarity Search

    Chodpathumwan, Yodsawalai; Aleyasin, Amirhossein; Termehchy, Arash; Sun, Yizhou

    2015-01-01

    Finding similar or strongly related entities in a graph database is a fundamental problem in data management and analytics with applications in similarity query processing, entity resolution, and pattern matching. Similarity search algorithms usually leverage the structural properties of the data graph to quantify the degree of similarity or relevance between entities. Nevertheless, the same information can be represented in many different structures and the structural properties observed ove...

  5. Similarity Structure of Wave-Collapse

    Rypdal, Kristoffer; Juul Rasmussen, Jens; Thomsen, Kenneth

    1985-01-01

    the significance of similarity in the evolution of a collapsing wave packet is investigated. Numerical solutions in radial symmetry demonstrate that the similarity behaviour is local in space and time, and that some similarity solutions must be classified as improper solutions. The nature of the...

  6. Optical Characterization of Chemically Etched Nano porous Silicon Embedded in Sol-Gel Matrix

    Nano porous (NPs) silicon fabricated by chemical etching process in HF acid was first separated in tetrahydrofuran (THF) solvent and then incorporated into SiO2 matrix. The matrix was prepared by sol gel process in which dimethylformamide (DMF) was used as drying chemical control additive (DCCA) to form crack-free dried sample. We examined the optical properties of NPs in three medium which are solvent, sol, and dried sol gel. Our observations reveal that absorption spectra of NPs silicon in THF are modified with respect to the spectra in sol gel. Significant stability in PL of NPs silicon in the sol gel is observed. Influence of matrix environment on peaks of NPs is also discussed. Surface morphology is characterized by field emission scanning electron microscopy (FESEM) which shows that the NPs silicon in THF is similar to the sol gel but becomes aggregation particle to particle. Presence of Si nanoparticles in THF and sol is confirmed by Transmission electron microscopy (TEM). The NPs silicons have mono dispersive and high crystalline nature with spherical shape of around 5 nm in sizes.

  7. Immunoinformatics and Similarity Analysis of House Dust Mite Tropomyosin

    Mohammad Mehdi Ranjbar; Sedigheh Nabian; Nayeb Ali Ahmadi; Khodayar Ghorban; Alireza Sazmand; Maryam Dadmanesh; Seyed Hossein Hekmatimoghaddam

    2015-01-01

    Background: Dermatophagoides farinae and Dermatophagoides pteronyssinus are house dust mites (HDM) that they cause severe asthma and allergic symptoms. Tropomyosin protein plays an important role in mentioned immune and allergic reactions to HDMs. Here, tropomyosin protein from Dermatophagoides spp. was comprehensively screened in silico for its allergenicity, antigenicity and similarity/conservation.Materials and Methods: The amino acid sequences of D. farinae tropomyosin, D. pteronyssinus a...

  8. Mechanical performance evaluation of bionanocomposites with polymeric matrix of poly(lactic acid)-PLA and organo clay; Avaliacao do comprtamento mecanico de bionanocompositos com patriz polimerica de poli(acido latico)-PLA e argila organofilica

    Cavalcanti, Shirley N.; Melo, Tomas J.A. de; Araujo, Edcleide M.; Oliveira, Akidauana D.A.; Lima, Jessica C.C., E-mail: shirleynobre@gmail.com [Universidade Federal de Campina Grande - UFCG - Dept. de Engenharia de Materiais, Campina Grande, PB (Brazil)

    2011-07-01

    The aim of this study is to evaluate the influence of ethylene/methyl acrylate (EMA) and ethylene/glycidyl methacrylate (E-GMA) copolymers and organoclay on the mechanical properties of polymer PLA-poly (lactic acid), from the system PLA / organoclay. The clay was organophilized with the ionic surfactant praepagem and the mixtures were prepared in a modular twin screw extruder. The behavior of bionanocomposites was evaluated by tensile and impact tests. The results of FTIR and DR-X indicated that the process was efficient organophilization. The mechanical properties showed that the elastic modulus and tensile strength of bionanocomposites obtained decreased compared to PLA. On the other hand there was a gain for resistance to impact, for all systems except for system PLA/OMMT. (author)

  9. Matricial bridges for "Matrix algebras converge to the sphere"

    Rieffel, Marc A

    2015-01-01

    In the high-energy quantum-physics literature one finds statements such as "matrix algebras converge to the sphere". Earlier I provided a general setting for understanding such statements, in which the matrix algebras are viewed as quantum metric spaces, and convergence is with respect to a quantum Gromov-Hausdorff-type distance. In the present paper, as preparation of discussing similar statements for convergence of "vector bundles" over matrix algebras to vector bundles over spaces, we introduce and study suitable matrix-norms for matrix algebras and spaces. Very recently Latremoliere introduced an improved quantum Gromov-Hausdorff-type distance between quantum metric spaces. We use it throughout this paper. To facilitate the calculations we introduce and develop a general notion of "bridges with conditional expectations".

  10. Code Similarity on High Level Programs

    Bernal, M Miron; Nazuno, J Figueroa

    2007-01-01

    This paper presents a new approach for code similarity on High Level programs. Our technique is based on Fast Dynamic Time Warping, that builds a warp path or points relation with local restrictions. The source code is represented into Time Series using the operators inside programming languages that makes possible the comparison. This makes possible subsequence detection that represent similar code instructions. In contrast with other code similarity algorithms, we do not make features extraction. The experiments show that two source codes are similar when their respective Time Series are similar.

  11. Determination of precious metals in ceramic matrix

    Complete text of publication follows. The recycling of the platinum group metals (PGM) especially from spent automobile catalytic converters increases steadily in importance, due to growing demand for, and exhausted resources of, PGM. The use of expensive PGM in catalyst production has fostered the development of an accurate method of determination of PGM in spent catalysts. Catalyst sample preparation by microwave extraction with acids (instead of successful but complex fire assay to recover the PGM from the interfering matrix) was attempted to avoid the spectral interferences resulting of matrix components during ICP-OES analysis. Different spent catalyst samples based mainly on AlO3 and SiO2 containing Pt and Pd were analysed by ICP-OES and, for comparison, ICP-MS to check if the extraction was complete. The components of the matrix of catalyst samples were identified with EDXRF. Several intense emission lines for Pt, Pd and Rh were selected for the detailed investigation of the samples. The measurement method was adjusted in several steps as external standard calibration, bracketing method and standard addition. The optimized measurement method of ICP-OES was applied to BAM reference material of spent automotive catalysts with cordierite basis. Due to many spectral interferences from the sample matrix it is not possible to determine precisely the PGM in automotive catalysts without extracting from the matrix. Microwave extraction is not as effective as fire assay, but provides fast analysis for less demanding applications. The authors gratefully acknowledge the support by Norddeutsche Affinerie and BAM, which provided the samples used in this work.

  12. Pretreatment and integrated analysis of spectral data reveal seaweed similarities based on chemical diversity.

    Wei, Feifei; Ito, Kengo; Sakata, Kenji; Date, Yasuhiro; Kikuchi, Jun

    2015-03-01

    Extracting useful information from high dimensionality and large data sets is a major challenge for data-driven approaches. The present study was aimed at developing novel integrated analytical strategies for comprehensively characterizing seaweed similarities based on chemical diversity. The chemical compositions of 107 seaweed and 2 seagrass samples were analyzed using multiple techniques, including Fourier transform infrared (FT-IR) and solid- and solution-state nuclear magnetic resonance (NMR) spectroscopy, thermogravimetry-differential thermal analysis (TG-DTA), inductively coupled plasma-optical emission spectrometry (ICP-OES), CHNS/O total elemental analysis, and isotope ratio mass spectrometry (IR-MS). The spectral data were preprocessed using non-negative matrix factorization (NMF) and NMF combined with multivariate curve resolution-alternating least-squares (MCR-ALS) methods in order to separate individual component information from the overlapping and/or broad spectral peaks. Integrated analysis of the preprocessed chemical data demonstrated distinct discrimination of differential seaweed species. Further network analysis revealed a close correlation between the heavy metal elements and characteristic components of brown algae, such as cellulose, alginic acid, and sulfated mucopolysaccharides, providing a componential basis for its metal-sorbing potential. These results suggest that this integrated analytical strategy is useful for extracting and identifying the chemical characteristics of diverse seaweeds based on large chemical data sets, particularly complicated overlapping spectral data. PMID:25647718

  13. Ceramic matrix and resin matrix composites - A comparison

    Hurwitz, Frances I.

    1987-01-01

    The underlying theory of continuous fiber reinforcement of ceramic matrix and resin matrix composites, their fabrication, microstructure, physical and mechanical properties are contrasted. The growing use of organometallic polymers as precursors to ceramic matrices is discussed as a means of providing low temperature processing capability without the fiber degradation encountered with more conventional ceramic processing techniques. Examples of ceramic matrix composites derived from particulate-filled, high char yield polymers and silsesquioxane precursors are provided.

  14. Ceramic matrix and resin matrix composites: A comparison

    Hurwitz, Frances I.

    1987-01-01

    The underlying theory of continuous fiber reinforcement of ceramic matrix and resin matrix composites, their fabrication, microstructure, physical and mechanical properties are contrasted. The growing use of organometallic polymers as precursors to ceramic matrices is discussed as a means of providing low temperature processing capability without the fiber degradation encountered with more conventional ceramic processing techniques. Examples of ceramic matrix composites derived from particulate-filled, high char yield polymers and silsesquioxane precursors are provided.

  15. Proteins in similarity relationship with the cluster - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Full Text Available Gclust Server Proteins in similarity relationship with the cluster Data detail Data name Proteins in similarity relationship with the...stered sequence of 95 organisms species, but not clustered. The data are given in... stated in ... Amino acid sequences of predicted proteins and their annotation for 9...t Us Proteins in similarity relationship with the cluster - Gclust Server | LSDB Archive ...

  16. Voltage and current spectra for matrix power converters

    Cox, Stephen M.; Creagh, Stephen C.

    2009-01-01

    Matrix power converters are used for transforming one alternating-current power supply to another, with different peak voltage and frequency. There are three input lines, with sinusoidally varying voltages which are 120◦ out of phase one from another, and the output is to be delivered as a similar three-phase supply. The matrix converter switches rapidly, to connect each output line in sequence to each of the input lines in an attempt to synthesize the prescribed output voltages. The switchin...

  17. Induced Elastic Matrix Deposition Within Three-Dimensional Collagen Scaffolds

    Venkataraman, Lavanya; Ramamurthi, Anand

    2011-01-01

    The structural stability of a cyclically distending elastic artery and the healthy functioning of vascular smooth muscle cells (SMCs) within are maintained by the presence of an intact elastic matrix and its principal protein, elastin. The accelerated degradation of the elastic matrix, which occurs in several vascular diseases, coupled with the poor ability of adult SMCs to regenerate lost elastin, can therefore adversely impact vascular homeostasis. Similarly, efforts to tissue engineer elas...

  18. Grewia polysaccharide as a pharmaceutical excipient in matrix tablets

    Nep, Elijah I.; Barbara R. Conway

    2011-01-01

    Matrix-based tablets using different concentrations of grewia gum, and the model drug ibuprofen, were prepared using a wet granulation technique. Similar formulations were also prepared using HPMC, guar gum or ethyl cellulose as the polymer matrix. In addition to tablet properties, swelling and erosion of tablets and kinetics of drug release were also investigated. In vitro drug release studies, in phosphate buffer (pH 7.2) using USP type II apparatus, revealed that grewia gum at concentratio...

  19. The Gram Matrix of a PT-symmetric Quantum System

    Weigert, S

    2003-01-01

    The eigenstates of a diagonalizable PT-symmetric Hamiltonian satisfy unconventional completeness and orthonormality relations. These relations reflect the properties of a pair of bi-orthonormal bases associated with non-hermitean diagonalizable operators. In a similar vein, such a dual pair of bases is shown to possess, in the presence of PT symmetry, a Gram matrix of a particular structure: its inverse is obtained by simply swapping the signs of some its matrix elements.

  20. Light cone matrix product

    Hastings, Matthew B [Los Alamos National Laboratory

    2009-01-01

    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.

  1. Challenging the CSCW matrix

    Jørnø, Rasmus Leth Vergmann; Gynther, Karsten; Christensen, Ove

    2014-01-01

    useful information, we question whether the axis of time and space comprising the matrix pertains to relevant defining properties of the tools, technology or learning environments to which they are applied. Subsequently we offer an example of an Adobe Connect e-learning session as an illustration of a...... an appropriate unit of analysis and that categories of such practices can be established by an axis of articulation work and an axis of the codification needed to express and coordinate knowledge and work efforts. Keywords: E-learning; distance education; synchronous; distributed; assemblages...... different approach to learning situations based on the idea that tools, technology and learning environments are media through which participants simultaneously acquire proficiency to articulate and gain a perspective in order to decode what is going on. To effectively interact online, we contend that both...

  2. Hyaluronan: A Matrix Component

    Rügheimer, Louise

    2008-09-01

    The glucosaminoglycan hyaluronan is a key component of the extracellular matrix. It is a large, negatively charged molecule that can act as an ion exchange reservoir for positive ions. Hyaluronan is involved in renomedullary water handling through its water-binding capacity. In the renal medulla, the main source for hyaluronan production is the renomedullary interstitial cells. Hyaluronan synthases are found in the inner part of the plasma membrane and polymerize hyaluronan chains which are extruded into the extracellular space. Hyaluronidases are a family of enzymes involved in the degradation of hyaluronan. They have a wide range of properties, including differences in size, inhibitor sensitivities, catalytic mechanisms, substrate specificities and pH optima.

  3. A matrix big bang

    The light-like linear dilaton background represents a particularly simple time-dependent 1/2 BPS solution of critical type-IIA superstring theory in ten dimensions. Its lift to M-theory, as well as its Einstein frame metric, are singular in the sense that the geometry is geodesically incomplete and the Riemann tensor diverges along a light-like subspace of codimension one. We study this background as a model for a big bang type singularity in string theory/M-theory. We construct the dual Matrix theory description in terms of a (1+1)-d supersymmetric Yang-Mills theory on a time-dependent world-sheet given by the Milne orbifold of (1+1)-d Minkowski space. Our model provides a framework in which the physics of the singularity appears to be under control

  4. A Matrix Big Bang

    Craps, B; Verlinde, E; Craps, Ben; Sethi, Savdeep; Verlinde, Erik

    2005-01-01

    The light-like linear dilaton background represents a particularly simple time-dependent 1/2 BPS solution of critical type IIA superstring theory in ten dimensions. Its lift to M-theory, as well as its Einstein frame metric, are singular in the sense that the geometry is geodesically incomplete and the Riemann tensor diverges along a light-like subspace of codimension one. We study this background as a model for a big bang type singularity in string theory/M-theory. We construct the dual Matrix theory description in terms of a (1+1)-d supersymmetric Yang-Mills theory on a time-dependent world-sheet given by the Milne orbifold of (1+1)-d Minkowski space. Our model provides a framework in which the physics of the singularity appears to be under control.

  5. Matrix Quantization of Turbulence

    Floratos, Emmanuel

    2011-01-01

    Based on our recent work on Quantum Nambu Mechanics $\\cite{af2}$, we provide an explicit quantization of the Lorenz chaotic attractor through the introduction of Non-commutative phase space coordinates as Hermitian $ N \\times N $ matrices in $ R^{3}$. For the volume preserving part, they satisfy the commutation relations induced by one of the two Nambu Hamiltonians, the second one generating a unique time evolution. Dissipation is incorporated quantum mechanically in a self-consistent way having the correct classical limit without the introduction of external degrees of freedom. Due to its volume phase space contraction it violates the quantum commutation relations. We demonstrate that the Heisenberg-Nambu evolution equations for the Matrix Lorenz system develop fast decoherence to N independent Lorenz attractors. On the other hand there is a weak dissipation regime, where the quantum mechanical properties of the volume preserving non-dissipative sector survive for long times.

  6. Atomic resolution structure of Moloney murine leukemia virus matrix protein and its relationship to other retroviral matrix proteins.

    Riffel, Nico; Harlos, Karl; Iourin, Oleg; Rao, Zihe; Kingsman, Alan; Stuart, David; Fry, Elizabeth

    2002-12-01

    Matrix proteins associated with the viral membrane are important in the formation of the viral particle and in virus maturation. The 1.0 A crystal structure of the ecotropic Gammaretrovirus Moloney murine leukemia virus (M-MuLV) matrix protein reveals the conserved topology of other retroviral matrix proteins, despite undetectable sequence similarity. The N terminus (normally myristylated) is exposed and adjacent to a basic surface patch, features likely to contribute to membrane binding. The four proteins in the asymmetric unit make varied contacts. The M-MuLV matrix structure is intermediate, between those of the lentiviruses and other retroviruses. The protein fold appears to be maintained, in part, by the conservation of side chain packing, which may provide a useful tool for searching for weak distant similarities in proteins. PMID:12467570

  7. Inhibition of Macrophage Migration Inhibitory Factor Protects against Inflammation and Matrix Deposition in Kidney Tissues after Injury

    Lu, Hong; Bai, Yongyu; Wu, Lianfeng; Hong, Weilong; Liang, Yong; Chen, Bicheng; Bai, Yongheng

    2016-01-01

    Background. Macrophage migration inhibitory factor (MIF) is an important immunoregulatory cytokine involved in inflammation, which may be one important reason resulting in matrix deposition in renal tissues after injury. However, the underlying mechanisms have not yet been elucidated. Methods and Results. We uncovered a crucial role of MIF in inflammation and collagen deposition in vivo and in vitro. In rats, ureteral obstruction induced tubular injury, matrix accumulation, and inflammatory cell infiltration. Additionally, enhanced MIF levels in the obstructed kidneys were closely related to the increasing numbers of CD68-positive macrophages. These obstruction-induced injuries can be relieved by recanalization, consequently resulting in downregulated expression of MIF and its receptor CD74. Similarly, ischemia reperfusion induced renal injury, and it was accompanied by elevated MIF levels and macrophages infiltration. In cultured tubular epithelial cells (TECs), aristolochic acid (AA) promoted matrix production and increased MIF expression, as well as the release of macrophage-related factors. Inhibition of MIF with an antagonist ISO-1 resulted in the abolishment of these genotypes in AA-treated TECs. Conclusion. MIF plays an important role in macrophage-related inflammation and matrix deposition in kidney tissues following injury. MIF as a specific inhibitor may have therapeutic potential for patients with inflammatory and fibrotic kidney diseases.

  8. A Novel Matrix Protein Hic31 from the Prismatic Layer of Hyriopsis Cumingii Displays a Collagen-Like Structure.

    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.

  9. Studying of Semantic Similarity Methods in Ontology

    Vahideh Reshadat

    2012-06-01

    Full Text Available Humans are able to easily judge if a pair of concepts are related in some way. Understanding of how humans are able to perform this task is not easy. Semantic similarity denotes computing the similarity between concepts, having the same meaning or related information, which are not necessarily lexically similar. Semantic similarity between concepts plays an important role in Semantic Web, knowledge sharing, Web mining, semantic sense understanding and text summarization. This also is an important problem in Natural Language Processing and Information Retrieval Researches. These techniques are becoming important components of most of the Information Retrieval (IR, Information Extraction (IE and other intelligent knowledge based systems. Therefore it has received considerable attention in the literature. Ontology has a good hierarchical structure of concepts. In the ontology, semantic information can be realized through the semantic relationship of concepts. Ontology-based semantic similarity techniques can estimate the semantic similarity between two hierarchically expressed concepts in a given ontology or taxonomy. Semantic similarity is usually computed by mapping concepts to ontology and by examining their relationships in it. The most popular semantic similarity methods are implemented and evaluated using WordNet and MeSH. Several algorithmic approaches for computing semantic similarity have been proposed. This paper discusses the various approaches used for identifying semantically similar concepts in ontology.

  10. Collagen in the spicule organic matrix of the gorgonian Leptogorgia virgulata

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

    1990-01-01

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

  11. Hyaluronic acid regulates normal intestinal and colonic growth in mice

    Riehl, Terrence E.; Ee, Xueping; Stenson, William F

    2012-01-01

    Hyaluronic acid (HA), a component of the extracellular matrix, affects gastrointestinal epithelial proliferation in injury models, but its role in normal growth is unknown. We sought to determine the effects of exogenous HA on intestinal and colonic growth by intraperitoneal injection of HA twice a week into C57BL/6 mice from 3 to 8 wk of age. Similarly, to determine the effects of endogenous HA on intestinal and colonic growth, we administered PEP-1, a peptide that blocks the binding of HA t...

  12. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms.

    Klein, Marlise I; Hwang, Geelsu; Santos, Paulo H S; Campanella, Osvaldo H; Koo, Hyun

    2015-01-01

    Biofilms are highly structured microbial communities that are enmeshed in a self-produced extracellular matrix. Within the complex oral microbiome, Streptococcus mutans is a major producer of extracellular polymeric substances including exopolysaccharides (EPS), eDNA, and lipoteichoic acid (LTA). EPS produced by S. mutans-derived exoenzymes promote local accumulation of microbes on the teeth, while forming a spatially heterogeneous and diffusion-limiting matrix that protects embedded bacteria. The EPS-rich matrix provides mechanical stability/cohesiveness and facilitates the creation of highly acidic microenvironments, which are critical for the pathogenesis of dental caries. In parallel, S. mutans also releases eDNA and LTA, which can contribute with matrix development. eDNA enhances EPS (glucan) synthesis locally, increasing the adhesion of S. mutans to saliva-coated apatitic surfaces and the assembly of highly cohesive biofilms. eDNA and other extracellular substances, acting in concert with EPS, may impact the functional properties of the matrix and the virulence of cariogenic biofilms. Enhanced understanding about the assembly principles of the matrix may lead to efficacious approaches to control biofilm-related diseases. PMID:25763359

  13. Streptococcus mutans-derived extracellular matrix in cariogenic oral biofilms

    Marlise eKlein

    2015-02-01

    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.

  14. Good edit similarity learning by loss minimization

    Bellet, Aurélien; Habrard, Amaury; Sebban, Marc

    2012-01-01

    Similarity functions are a fundamental component of many learning algorithms. When dealing with string or tree-structured data, edit distancebased measures are widely used, and there exists a few methods for learning them from data. However, these methods offer no theoretical guarantee as to the generalization ability and discriminative power of the learned similarities. In this paper, we propose a loss minimization-based edit similarity learning approach, called GESL. It is driven by the not...

  15. Dark matter halo's and self similarity

    Alard, C.

    2012-01-01

    This papers explores the self similar solutions of the Vlasov-Poisson system and their relation to the gravitational collapse of dynamically cold systems. Analytic solutions are derived for power law potential in one dimension, and extensions of these solutions in three dimensions are proposed. Next the self similarity of the collapse of cold dynamical systems is investigated numerically. The fold system in phase space is consistent with analytic self similar solutions, the solutions present ...

  16. Learning music similarity from relative user ratings

    Wolff, D.; Weyde, T.

    2013-01-01

    Computational modelling of music similarity is an increasingly important part of personalisation and optimisation in music information retrieval and research in music perception and cognition. The use of relative similarity ratings is a new and promising approach to modelling similarity that avoids well known problems with absolute ratings. In this article, we use relative ratings from the MagnaTagATune dataset with new and existing variants of state-of-the-art algorithms and provide the firs...

  17. Secure sketch search for document similarity

    Örencik, Cengiz; Orencik, Cengiz; Alewiwi, Mahmoud Khaled; SAVAŞ, Erkay; Savas, Erkay

    2015-01-01

    Document similarity search is an important problem that has many applications especially in outsourced data. With the wide spread of cloud computing, users tend to outsource their data to remote servers which are not necessarily trusted. This leads to the problem of protecting the privacy of sensitive data. We design and implement two secure similarity search schemes for textual documents utilizing locality sensitive hashing techniques for cosine similarity. While the first one provides very ...

  18. Similarity and a Duality for Fullerenes

    Jennifer J. Edmond; Graver, Jack E.

    2015-01-01

    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, i...

  19. Molecular quantum similarity using conceptual DFT descriptors

    Patrick Bultinck; Ramon carbó-dorca

    2005-09-01

    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 descriptors used and compared to assess whether these different descriptors sample different information and to investigate what information is revealed by each descriptor.

  20. Quadruplet-Wise Image Similarity Learning

    Law M.T.; Thome N.; Cord M.

    2013-01-01

    International audience This paper introduces a novel similarity learning frame-work. Working with inequality constraints involving quadruplets of images, our approach aims at efficiently modeling similarity from rich or complex semantic label relationships. From these quadruplet-wise constraints, we propose a similarity learning framework relying on a con-vex optimization scheme. We then study how our metric learning scheme can exploit specific class relationships, such as class ranking (r...

  1. Efficient Authentication of Outsourced String Similarity Search

    Dong, Boxiang; Wang, Hui

    2016-01-01

    Cloud computing enables the outsourcing of big data analytics, where a third party server is responsible for data storage and processing. In this paper, we consider the outsourcing model that provides string similarity search as the service. In particular, given a similarity search query, the service provider returns all strings from the outsourced dataset that are similar to the query string. A major security concern of the outsourcing paradigm is to authenticate whether the service provider...

  2. Biosequence Similarity Search on the Mercury System

    Krishnamurthy, Praveen; Buhler, Jeremy; Chamberlain, Roger; Franklin, Mark; Gyang, Kwame; Jacob, Arpith; Lancaster, Joseph

    2007-01-01

    Biosequence similarity search is an important application in modern molecular biology. Search algorithms aim to identify sets of sequences whose extensional similarity suggests a common evolutionary origin or function. The most widely used similarity search tool for biosequences is BLAST, a program designed to compare query sequences to a database. Here, we present the design of BLASTN, the version of BLAST that searches DNA sequences, on the Mercury system, an architecture that supports high...

  3. Persistent Homology and Partial Similarity of Shapes

    Di Fabio, Barbara; Landi, Claudia

    2011-01-01

    The ability to perform shape retrieval based not only on full similarity, but also partial similarity is a key property for any content-based search engine. We prove that persistence diagrams can reveal a partial similarity between two shapes by showing a common subset of points. This can be explained using the Mayer-Vietoris formulas that we develop for ordinary, relative and extended persistent homology. An experiment outlines the potential of persistence diagrams as shape descriptors in re...

  4. Cluster Tree Based Hybrid Document Similarity Measure

    M. Varshana Devi

    2015-10-01

    Full Text Available similarity measure is established to measure the hybrid similarity. In cluster tree, the hybrid similarity measure can be calculated for the random data even it may not be the co-occurred and generate different views. Different views of tree can be combined and choose the one which is significant in cost. A method is proposed to combine the multiple views. Multiple views are represented by different distance measures into a single cluster. Comparing the cluster tree based hybrid similarity with the traditional statistical methods it gives the better feasibility for intelligent based search. It helps in improving the dimensionality reduction and semantic analysis.

  5. A Matrix Model for WZW

    Dorey, Nick; Turner, Carl

    2016-01-01

    We study a U(N) gauged matrix quantum mechanics which, in the large N limit, is closely related to the chiral WZW conformal field theory. This manifests itself in two ways. First, we construct the left-moving Kac-Moody algebra from matrix degrees of freedom. Secondly, we compute the partition function of the matrix model in terms of Schur and Kostka polynomials and show that, in the large $N$ limit, it coincides with the partition function of the WZW model. This same matrix model was recently shown to describe non-Abelian quantum Hall states and the relationship to the WZW model can be understood in this framework.

  6. A matrix model for WZW

    Dorey, Nick; Tong, David; Turner, Carl

    2016-08-01

    We study a U( N) gauged matrix quantum mechanics which, in the large N limit, is closely related to the chiral WZW conformal field theory. This manifests itself in two ways. First, we construct the left-moving Kac-Moody algebra from matrix degrees of freedom. Secondly, we compute the partition function of the matrix model in terms of Schur and Kostka polynomials and show that, in the large N limit, it coincides with the partition function of the WZW model. This same matrix model was recently shown to describe non-Abelian quantum Hall states and the relationship to the WZW model can be understood in this framework.

  7. Clay matrix voltammetry

    Document available in extended abstract form only. In many countries, it is planned that the long life highly radioactive nuclear spent fuel will be stored in deep argillaceous rocks. The sites selected for this purpose are anoxic and satisfy several recommendations as mechanical stability, low permeability and low redox potential. Pyrite (FeS2), iron(II) carbonate, iron(II) bearing clays and organic matter that are present in very small amounts (about 1% w:w) in soils play a major role in their reactivity and are considered today as responsible for the low redox potential values of these sites. In this communication, we describe an electrochemical technique derived from 'Salt matrix voltammetry' and allowing the almost in-situ voltammetric characterization of air-sensitive samples of soils after the only addition of the minimum humidity required for electrolytic conduction. Figure 1 shows the principle of the developed technique. It consists in the entrapment of the clay sample between a graphite working electrode and a silver counter/quasi-reference electrode. The sample was previously humidified by passing a water saturated inert gas through the electrochemical cell. The technique leads to well-defined voltammetric responses of the electro-active components of the clays. Figure 2 shows a typical voltammogram relative to a Callovo-Oxfordian argillite sample from Bure, the French place planned for the underground nuclear waste disposal. During the direct scan, one can clearly distinguish the anodic voltammetric signals for the oxidation of the iron (II) species associated with the clay and the oxidation of pyrite. The reverse scan displays a small cathodic signal for the reduction of iron (III) associated with the clay that demonstrates that the majority of the previously oxidized iron (II) species were transformed into iron (III) oxides reducible at lower potentials. When a second voltammetric cycle is performed, one can notice that the signal for iron (II

  8. Matrix Product Operators, Matrix Product States, and ab initio Density Matrix Renormalization Group algorithms

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

    2016-01-01

    Current descriptions of the ab initio DMRG algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab-initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational par...

  9. Similarity indices I: what do they measure

    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

  10. Similarity indices I: what do they measure.

    Johnston, J.W.

    1976-11-01

    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.

  11. Perceived Similarity, Proactive Adjustment, and Organizational Socialization

    Kammeyer-Mueller, John D.; Livingston, Beth A.; Liao, Hui

    2011-01-01

    The present study explores how perceived demographic and attitudinal similarity can influence proactive behavior among organizational newcomers. We propose that newcomers who perceive themselves as similar to their co-workers will be more willing to seek new information or build relationships, which in turn will lead to better long-term…

  12. Outsourced similarity search on metric data assets

    Yiu, Man Lung; Assent, Ira; Jensen, Christian Søndergaard;

    2012-01-01

    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...

  13. Some Effects of Similarity Self-Disclosure

    Murphy, Kevin C.; Strong, Stanley R.

    1972-01-01

    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…

  14. Quaternionic Salkowski Curves and Similar Curves

    Önder, Mehmet

    2012-01-01

    In this paper, we give the definitions and characterizations of spatial quaternionic Salkowski, anti-Salkowski and similar curves. We show that quaternionic Salkowski and anti-Salkowski curves are quaternionic slant helices. Moreover, we obtain that the families of quaternionic Salkowski and anti-Salkowski curves form the families of quaternionic similar curves.

  15. Similarity Measures for Boolean Search Request Formulations.

    Radecki, Tadeusz

    1982-01-01

    Proposes a means for determining the similarity between search request formulations in online information retrieval systems, and discusses the use of similarity measures for clustering search formulations and document files in such systems. Experimental results using the proposed methods are presented in three tables. A reference list is provided.…

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

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

    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 to...

  17. Corrosion Behavior of Ti-Based In Situ Dendrite-Reinforced Metallic Glass Matrix Composites in Various Solutions

    Yang, F.; Tian, H. F.; Lan, A. D.; Zhou, H. F.; Wang, B. C.; Yang, H. J.; Qiao, J. W.

    2015-06-01

    The electrochemical corrosion behaviors of Ti40Zr24V12Cu5Be19 in situ dendrite-reinforced metallic glass matrix composites (MGMCs) were investigated by potentiodynamic polarization experiments and electrochemical impedance spectroscopy in acidic, salty, and alkaline solutions. Ti40Zr24V12Cu5Be19 in situ dendrite-reinforced MGMCs have an impressive corrosion resistance in strong acidic environment, while their performance was not so great in strong alkaline environment. Further immersion test in same solutions revealed similar chemical corrosion behaviors. XRD and SEM examinations were conducted to check the structure and surface modification of the material during the corrosion process. EDS test indicated that the amorphous matrices, which show excellent corrosion resistance, have a considerable composition variation from its crystalline dendrites counterpart.

  18. Measure of Node Similarity in Multilayer Networks

    Mollgaard, Anders; Dammeyer, Jesper; Jensen, Mogens H; Lehmann, Sune; Mathiesen, Joachim

    2016-01-01

    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...

  19. Semantic Similarity Calculation of Chinese Word

    Liqiang Pan

    2014-08-01

    Full Text Available This paper puts forward a two layers computing method to calculate semantic similarity of Chinese word. Firstly, using Latent Dirichlet Allocation (LDA subject model to generate subject spatial domain. Then mapping word into topic space and forming topic distribution which is used to calculate semantic similarity of word(the first layer computing. Finally, using semantic dictionary "HowNet" to deeply excavate semantic similarity of word (the second layer computing. This method not only overcomes the problem that it’s not specific enough merely using LDA to calculate semantic similarity of word, but also solves the problems such as new words (haven’t been added in dictionary and without considering specific context when calculating semantic similarity based on semantic dictionary "HowNet". By experimental comparison, this thesis proves feasibility,availability and advantages of the calculation method.

  20. Similarity and a Duality for Fullerenes

    Jennifer J. Edmond

    2015-11-01

    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. Criteria for dynamic similarity in bouncing gaits.

    Bullimore, Sharon R; Donelan, J Maxwell

    2008-01-21

    Animals of different sizes tend to move in a dynamically similar manner when travelling at speeds corresponding to equal values of a dimensionless parameter (DP) called the Froude number. Consequently, the Froude number has been widely used for defining equivalent speeds and predicting speeds of locomotion by extinct species and on other planets. However, experiments using simulated reduced gravity have demonstrated that equality of the Froude number does not guarantee dynamic similarity. This has cast doubt upon the usefulness of the Froude number in locomotion research. Here we use dimensional analysis of the planar spring-mass model, combined with Buckingham's Pi-Theorem, to demonstrate that four DPs must be equal for dynamic similarity in bouncing gaits such as trotting, hopping and bipedal running. This can be reduced to three DPs by applying the constraint of maintaining a constant average speed of locomotion. Sensitivity analysis indicates that all of these DPs are important for predicting dynamic similarity. We show that the reason humans do not run in a dynamically similar manner at equal Froude number in different levels of simulated reduced gravity is that dimensionless leg stiffness decreases as gravity increases. The reason that the Froude number can predict dynamic similarity in Earth gravity is that dimensionless leg stiffness and dimensionless vertical landing speed are both independent of size. In conclusion, although equal Froude number is not sufficient for dynamic similarity, it is a necessary condition. Therefore, to detect fundamental differences in locomotion, animals of different sizes should be compared at equal Froude number, so that they can be as close to dynamic similarity as possible. More generally, the concept of dynamic similarity provides a powerful framework within which similarities and differences in locomotion can be interpreted. PMID:17983630

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

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

    2016-01-12

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

  3. Cosmology and the S-matrix

    Bousso, Raphael

    2005-01-25

    We study conditions for the existence of asymptotic observables in cosmology. With the exception of de Sitter space, the thermal properties of accelerating universes permit arbitrarily long observations, and guarantee the production of accessible states of arbitrarily large entropy. This suggests that some asymptotic observables may exist, despite the presence of an event horizon. Comparison with decelerating universes shows surprising similarities: Neither type suffers from the limitations encountered in de Sitter space, such as thermalization and boundedness of entropy. However, we argue that no realistic cosmology permits the global observations associated with an S-matrix.

  4. Nil-clean matrix rings

    S. Breaz; Călugăreanu, G.; Danchev, P.; Micu, T.

    2013-01-01

    We characterize the nil clean matrix rings over fields. As a by product, it is proved that the full matrix rings with coefficients in commutative nil-clean rings are nil-clean, and we obtain a complete characterization of the finite rank Abelian groups with nil clean endomorphism ring and the Abelian groups with strongly nil clean endomorphism ring, respectively.

  5. How to Study a Matrix

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

    2012-01-01

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

  6. Matrix Analysis of Tracer Transport

    Mills, Peter

    2015-01-01

    We review matrix methods as applied to tracer transport. Because tracer transport is linear, matrix methods are an ideal fit for the problem. In particular, solutions of linear, first-order systems of ordinary differential equations (ODEs) are reviewed as well as special properties of these solutions. Detailed derivations are included

  7. Two-photon ionization thresholds of matrix-assisted laser desorption/ionization matrix clusters.

    Lin, Q; Knochenmuss, R

    2001-01-01

    Direct two-photon ionization of the matrix has been considered a likely primary ionization mechanism in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. This mechanism requires that the vertical ionization threshold of matrix materials be below twice the laser photon energy. Because dimers and larger aggregates may be numerous in the early stages of the MALDI plume expansion, their ionization thresholds are important as well. We have used two-color two-photon ionization to determine the ionization thresholds of jet cooled clusters of an important matrix, 2,5-dihydroxy benzoic acid (DHB), and mixed clusters with the thermal decomposition product of DHB, hydroquinone. The thresholds of the clusters were reduced by only a few tenths of an eV compared to the monomers, to an apparent limit of 7.82 eV for pure DHB clusters. None of the investigated clusters can be directly ionized by two nitrogen laser photons (7.36 eV), and the ionization efficiency at the thresholds is low. PMID:11507754

  8. Measure of Node Similarity in Multilayer Networks.

    Mollgaard, Anders; Zettler, Ingo; Dammeyer, Jesper; Jensen, Mogens H; Lehmann, Sune; Mathiesen, Joachim

    2016-01-01

    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. PMID:27300084

  9. Efficient Privacy Preserving Protocols for Similarity Join

    Bilal Hawashin

    2012-04-01

    Full Text Available During the similarity join process, one or more sources may not allow sharing its data with other sources. In this case, a privacy preserving similarity join is required. We showed in our previous work [4] that using long attributes, such as paper abstracts, movie summaries, product descriptions, and user feedbacks, could improve the similarity join accuracy using supervised learning. However, the existing secure protocols for similarity join methods can not be used to join sources using these long attributes. Moreover, the majority of the existing privacy‐preserving protocols do not consider the semantic similarities during the similarity join process. In this paper, we introduce a secure efficient protocol to semantically join sources when the join attributes are long attributes. We provide two secure protocols for both scenarios when a training set exists and when there is no available training set. Furthermore, we introduced the multi‐label supervised secure protocol and the expandable supervised secure protocol. Results show that our protocols can efficiently join sources using the long attributes by considering the semantic relationships among the long string values. Therefore, it improves the overall secure similarity join performance.

  10. Notions of similarity for computational biology models

    Waltemath, Dagmar

    2016-03-21

    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.

  11. The baryonic self similarity of dark matter

    Alard, C., E-mail: alard@iap.fr [Institut d' Astrophysique de Paris, 98bis boulevard Arago, F-75014 Paris (France)

    2014-06-20

    The cosmological simulations indicates that dark matter halos have specific self-similar properties. However, the halo similarity is affected by the baryonic feedback. By using momentum-driven winds as a model to represent the baryon feedback, an equilibrium condition is derived which directly implies the emergence of a new type of similarity. The new self-similar solution has constant acceleration at a reference radius for both dark matter and baryons. This model receives strong support from the observations of galaxies. The new self-similar properties imply that the total acceleration at larger distances is scale-free, the transition between the dark matter and baryons dominated regime occurs at a constant acceleration, and the maximum amplitude of the velocity curve at larger distances is proportional to M {sup 1/4}. These results demonstrate that this self-similar model is consistent with the basics of modified Newtonian dynamics (MOND) phenomenology. In agreement with the observations, the coincidence between the self-similar model and MOND breaks at the scale of clusters of galaxies. Some numerical experiments show that the behavior of the density near the origin is closely approximated by a Einasto profile.

  12. Florid pustular dermatitis of breast: A case report on a unusual complication from acellular dermal matrix use

    Justin James

    2016-01-01

    Conclusion: Pustular dermatitis like presentation can be associated with acelluar dermal matrix use and should be considered in similar clinical presentations, since this can avoid unnecessary surgical procedures.

  13. Mechanisms controlling fatigue damage development in continuous fiber reinforced metal matrix composites

    Johnson, W. S.

    1989-01-01

    Damage in continuous fiber reinforced metal matrix composite materials can be quite complex since there are a number of different constituents (fiber, matrix, and the fiber/matrix interface) that can fail. Multidirectional lay-ups have an even greater number of possible damage orientations and mechanisms. Based on the simplifying assumption of equivalent constituent strain states in the absence of damage, a strain based failure criteria may be applied to determine when and where initial damage will occur. Based on the relative strain to fatigue failure of the fiber and matrix, the possible damage mechanisms of an MMC can be grouped into three categories: (1) matrix dominated, (2) fiber dominated, and (3) self-similar damage growth. A fourth type of damage development, fiber/matrix interface failure, is dependent on the relative strength of the fiber/matrix interface and the matrix yield strength. These four types of damage are discussed and illustrated by examples.

  14. Machining of Metal Matrix Composites

    2012-01-01

    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...

  15. Multivariate Matrix-Exponential Distributions

    Bladt, Mogens; Nielsen, Bo Friis

    2010-01-01

    In this article we consider the distributions of non-negative random vectors with a joint rational Laplace transform, i.e., a fraction between two multi-dimensional polynomials. These distributions are in the univariate case known as matrix-exponential distributions, since their densities can be...... written as linear combinations of the elements in the exponential of a matrix. For this reason we shall refer to multivariate distributions with rational Laplace transform as multivariate matrix-exponential distributions (MVME). The marginal distributions of an MVME are univariate matrix......-exponential distributions. We prove a characterization that states that a distribution is an MVME distribution if and only if all non-negative, non-null linear combinations of the coordinates have a univariate matrix-exponential distribution. This theorem is analog to a well-known characterization theorem for the...

  16. Network structure of phonographic market with characteristic similarities between musicians

    Buda, Andrzej

    2012-01-01

    We investigate relations between best selling artists in last decade on phonographic market and from perspective of listeners by using the Social Network Analyzes. Starting network is obtained from the matrix of correlations between the world's best selling artists by considering the synchronous time evolution of weekly record sales. This method reveals the structure of phonographic market, but we claim that it has no impact on people who see relationship between artists and music genres. We compare 'sale' (based on correlation of record sales) or 'popularity' (based on data mining of the record charts) networks with 'similarity' (obtained mainly from survey within music experts opinion) and find no significant relations. We postulate that non-laminar phenomena on this specific market introduce turbulence to how people view relations of artists.

  17. New beginnings for matrix metalloproteinase inhibitors: identification of high-affinity zinc-binding groups.

    Puerta, David T; Lewis, Jana A; Cohen, Seth M

    2004-07-14

    In an effort to identify promising non-hydroxamate inhibitors of matrix metalloproteinases (MMPs), several new zinc-binding groups (ZBGs) based on pyrone, pyrothione, hydroxypyridinone, and hydroxypyridinethione chelators have been examined. Structural studies with tris(pyrazolyl)borate model complexes show that these ligands bind to the MMP active site zinc(II) ion in a bidentate fashion, similar to that found with hydroxamate-based inhibitors. Fluorescence- and colorimetric-based enzyme assays have been used to determine the IC50 values for these ZBGs against MMP-3; mixed O,S-donor ligands were found to be remarkably potent, with IC50 values as much as 700-fold lower than that found for acetohydroxamic acid. Inhibitory activity was found to parallel metal binding affinity as determined in titrations with model complexes. These results demonstrate that MPIs based on new ZBGs are feasible and may indeed improve the overall performance of inhibitors designed against these important medicinal targets. PMID:15237990

  18. Similarity-based pattern analysis and recognition

    Pelillo, Marcello

    2013-01-01

    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

  19. Convex Sparse Matrix Factorizations

    Bach, Francis; Ponce, Jean

    2008-01-01

    We present a convex formulation of dictionary learning for sparse signal decomposition. Convexity is obtained by replacing the usual explicit upper bound on the dictionary size by a convex rank-reducing term similar to the trace norm. In particular, our formulation introduces an explicit trade-off between size and sparsity of the decomposition of rectangular matrices. Using a large set of synthetic examples, we compare the estimation abilities of the convex and non-convex approaches, showing that while the convex formulation has a single local minimum, this may lead in some cases to performance which is inferior to the local minima of the non-convex formulation.

  20. Fish otolith biomineralization process: first investigations about organic matrix and growth of Triglidae (Scorpaeniformes otoliths

    Stefano Montanini

    2015-11-01

    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

  1. 维甲酸对大鼠高氧肺损伤的保护机制及其与调控丝裂原活化蛋白激酶的关系%Retinoic acid diminished the expression of lung tissue matrix metalioproteinase-2 and matrix metalioproteinase-9 in hyperoxia-exposed premature rats through regulating mitogen-activated protein kinases

    李文斌; 常立文; 容志惠; 刘汉楚; 张谦慎; 陈红兵; 祝华平; 卢红艳; 王华

    2008-01-01

    目的 探讨维甲酸(RA)对高氧肺损伤保护作用机制及其与调控丝裂原活化蛋白激酶(MAPKs)关系.方法 建立高氧(85%)暴露早产SD大鼠肺损伤模型,运用RT-PCR方法检测基质金属蛋白酶2,9(MMP-2、-9)mRNA表达,采用明胶酶谱法检测MMP-2和MMP-9酶原及活酶表达,采用Western blot技术检测磷酸化和非磷酸化总的ERK1/2、JNK1/2和038蛋白质表达.结果 与空气组比较,高氧暴露4、7、14 d,MMP-2和MMP-9 mRNA的表达均显著提高(P均<0.01),MMP-2活酶(除4 d外)、MMP-9酶原及活酶的表达明显上调(P<0.05或P<0.01),磷酸化ERK1/2、JNK1/2和p38表达显著增加(P均<0.01);与高氧组比较,4、7、14 d时,RA明显下调高氧暴露后MMP-2(除14d外)、MMP.9 mRNA的表达(P<0.01或P<0.05),不同程度降低MMP-2活酶、MMP.9酶原及活酶的表达和显著下调磷酸化JNK1/2、038水平,进一步上调磷酸化ERK1/2表达.结论 高氧暴露显著提高MMP-2和MMP-9表达,是造成肺损伤的重要因素;JNK1/2和p38信号途径可能参与了高氧暴露下早产大鼠肺组织MMP-2和MMP-9的表达调控;RA可通过降低JNK1/2和p38磷酸化水平,抑制MMP-2和MMP-9的高表达和活化,从而发挥高氧肺损伤保护作用.%Objective To further investigate the protective effect of retinoic acid (RA) on hyperoxia ieduced lung iniury and the role of RA as a modulator on mitogen-activated protein kinases (MAPKs).Methods Establishment of hypemxia(85%)induced lung injury model of premature SpragueDawley (SD) rats:21 d gestational age SD rat's fetuses (term=22 d)were delivered by hysterectomy.Within 12-24 h after birth,the premature rat pups were randomly divided into 4 groups:Group I,airexposed control group;Group Ⅱ,hyperoxia-exposed group;Group Ⅲ,air plus RA-exposed group,Group Ⅳ,hypemxia plus RA-exposed group.Group Ⅰ and Ⅲ were remained in room air,and group Ⅱ and Ⅳ were placed in 85% oxygen.The pups in Group Ⅲ and Ⅳ were injected with RA (500 μg/kg,every day

  2. Matrix ALPS: Accelerated Low Rank and Sparse Matrix Reconstruction

    Kyrillidis, Anastasios

    2012-01-01

    We propose Matrix ALPS for recovering a sparse plus low-rank decomposition of a matrix given its corrupted and incomplete linear measurements. Our approach is a first-order projected gradient method over non-convex sets, and it exploits a well-known memory-based acceleration technique. We theoretically characterize the convergence properties of Matrix ALPS using the stable embedding properties of the linear measurement operator. We then numerically illustrate that our algorithm outperforms the existing convex as well as non-convex state-of-the-art algorithms in computational efficiency without sacrificing stability.

  3. Interpersonal attraction and personality: what is attractive--self similarity, ideal similarity, complementarity or attachment security?

    Klohnen, Eva C; Luo, Shanhong

    2003-10-01

    Little is known about whether personality characteristics influence initial attraction. Because adult attachment differences influence a broad range of relationship processes, the authors examined their role in 3 experimental attraction studies. The authors tested four major attraction hypotheses--self similarity, ideal-self similarity, complementarity, and attachment security--and examined both actual and perceptual factors. Replicated analyses across samples, designs, and manipulations showed that actual security and self similarity predicted attraction. With regard to perceptual factors, ideal similarity, self similarity, and security all were significant predictors. Whereas perceptual ideal and self similarity had incremental predictive power, perceptual security's effects were subsumed by perceptual ideal similarity. Perceptual self similarity fully mediated actual attachment similarity effects, whereas ideal similarity was only a partial mediator. PMID:14561124

  4. Self-assembled composite matrix in a hierarchical 3-D scaffold for bone tissue engineering

    Chen, Muwan; Le, Dang Quang Svend; Baatrup, Anette;

    2011-01-01

    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 in...

  5. Discovering Music Structure via Similarity Fusion

    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....

  6. HYPOTHESIS TESTING WITH THE SIMILARITY INDEX

    Mulltilocus DNA fingerprinting methods have been used extensively to address genetic issues in wildlife populations. Hypotheses concerning population subdivision and differing levels of diversity can be addressed through the use of the similarity index (S), a band-sharing coeffic...

  7. Bilateral Trade Flows and Income Distribution Similarity

    2016-01-01

    Current models of bilateral trade neglect the effects of income distribution. This paper addresses the issue by accounting for non-homothetic consumer preferences and hence investigating the role of income distribution in the context of the gravity model of trade. A theoretically justified gravity model is estimated for disaggregated trade data (Dollar volume is used as dependent variable) using a sample of 104 exporters and 108 importers for 1980–2003 to achieve two main goals. We define and calculate new measures of income distribution similarity and empirically confirm that greater similarity of income distribution between countries implies more trade. Using distribution-based measures as a proxy for demand similarities in gravity models, we find consistent and robust support for the hypothesis that countries with more similar income-distributions trade more with each other. The hypothesis is also confirmed at disaggregated level for differentiated product categories. PMID:27137462

  8. Correlation between social proximity and mobility similarity

    Fan, Chao; Huang, Junming; Rong, Zhihai; Zhou, Tao

    2016-01-01

    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 similari- ty, 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 com- mon 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...

  9. Learning content similarity for music recommendation

    McFee, Brian; Lanckriet, Gert

    2011-01-01

    Many tasks in music information retrieval, such as recommendation, and playlist generation for online radio, fall naturally into the query-by-example setting, wherein a user queries the system by providing a song, and the system responds with a list of relevant or similar song recommendations. Such applications ultimately depend on the notion of similarity between items to produce high-quality results. Current state-of-the-art systems employ collaborative filter methods to represent musical items, effectively comparing items in terms of their constituent users. While collaborative filter techniques perform well when historical data is available for each item, their reliance on historical data impedes performance on novel or unpopular items. To combat this problem, practitioners rely on content-based similarity, which naturally extends to novel items, but is typically out-performed by collaborative filter methods. In this article, we propose a method for optimizing contentbased similarity by learning from a sa...

  10. Integrated Semantic Similarity Model Based on Ontology

    LIU Ya-Jun; ZHAO Yun

    2004-01-01

    To solve the problem of the inadequacy of semantic processing in the intelligent question answering system, an integrated semantic similarity model which calculates the semantic similarity using the geometric distance and information content is presented in this paper.With the help of interrelationship between concepts, the information content of concepts and the strength of the edges in the ontology network, we can calculate the semantic similarity between two concepts and provide information for the further calculation of the semantic similarity between user's question and answers in knowlegdge base.The results of the experiments on the prototype have shown that the semantic problem in natural language processing can also be solved with the help of the knowledge and the abundant semantic information in ontology.More than 90% accuracy with less than 50 ms average searching time in the intelligent question answering prototype system based on ontology has been reached.The result is very satisfied.

  11. Bilateral Trade Flows and Income Distribution Similarity.

    Martínez-Zarzoso, Inmaculada; Vollmer, Sebastian

    2016-01-01

    Current models of bilateral trade neglect the effects of income distribution. This paper addresses the issue by accounting for non-homothetic consumer preferences and hence investigating the role of income distribution in the context of the gravity model of trade. A theoretically justified gravity model is estimated for disaggregated trade data (Dollar volume is used as dependent variable) using a sample of 104 exporters and 108 importers for 1980-2003 to achieve two main goals. We define and calculate new measures of income distribution similarity and empirically confirm that greater similarity of income distribution between countries implies more trade. Using distribution-based measures as a proxy for demand similarities in gravity models, we find consistent and robust support for the hypothesis that countries with more similar income-distributions trade more with each other. The hypothesis is also confirmed at disaggregated level for differentiated product categories. PMID:27137462

  12. Distances and similarities in intuitionistic fuzzy sets

    Szmidt, Eulalia

    2014-01-01

    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.

  13. Interpersonal Congruency, Attitude Similarity, and Interpersonal Attraction

    Touhey, John C.

    1975-01-01

    As no experimental study has examined the effects of congruency on attraction, the present investigation orthogonally varied attitude similarity and interpersonal congruency in order to compare the two independent variables as determinants of interpersonal attraction. (Author/RK)

  14. Outsourced similarity search on metric data assets

    Yiu, Man Lung

    2012-02-01

    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.

  15. Notes on Mayer expansions and matrix models

    Mayer cluster expansion is an important tool in statistical physics to evaluate grand canonical partition functions. It has recently been applied to the Nekrasov instanton partition function of N=2 4d gauge theories. The associated canonical model involves coupled integrations that take the form of a generalized matrix model. It can be studied with the standard techniques of matrix models, in particular collective field theory and loop equations. In the first part of these notes, we explain how the results of collective field theory can be derived from the cluster expansion. The equalities between free energies at first orders is explained by the discrete Laplace transform relating canonical and grand canonical models. In a second part, we study the canonical loop equations and associate them with similar relations on the grand canonical side. It leads to relate the multi-point densities, fundamental objects of the matrix model, to the generating functions of multi-rooted clusters. Finally, a method is proposed to derive loop equations directly on the grand canonical model

  16. Two-way migration between similar countries

    Kreickemeier, Udo; Wrona, Jens

    2011-01-01

    We develop a model to explain two-way migration of high-skilled individuals between countries that are similar in their economic characteristics. High-skilled migration is explained by a combination of two features: In both countries there is a continuum of workers with differing abilities, which are private knowledge, and the production technology gives incentives to firms for hiring workers of similar ability. In the presence on migration cost, high-skilled workers self-select into the grou...

  17. Privacy-preserving matching of similar patients.

    Vatsalan, Dinusha; Christen, Peter

    2016-02-01

    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. PMID:26707453

  18. Protein structural similarity search by Ramachandran codes

    Chang Chih-Hung

    2007-08-01

    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.

  19. Limit theorems for self-similar tilings

    Bufetov, Alexander I

    2012-01-01

    We study deviation of ergodic averages for dynamical systems given by self-similar tilings on the plane and in higher dimensions. The main object of our paper is a special family of finitely-additive measures for our systems. An asymptotic formula is given for ergodic integrals in terms of these finitely-additive measures, and, as a corollary, limit theorems are obtained for dynamical systems given by self-similar tilings.

  20. Some more similarities between Peirce and Skinner

    Moxley, Roy A

    2002-01-01

    C. S. Peirce is noted for pioneering a variety of views, and the case is made here for the similarities and parallels between his views and B. F. Skinner's radical behaviorism. In addition to parallels previously noted, these similarities include an advancement of experimental science, a behavioral psychology, a shift from nominalism to realism, an opposition to positivism, a selectionist account for strengthening behavior, the importance of a community of selves, a recursive approach to meth...

  1. Computing Similarity Dependencies with Pattern Structures

    Baixeries, Jaume; Kaytoue, Mehdi; Napoli, Amedeo

    2013-01-01

    Functional dependencies provide valuable knowledge on the relations between the attributes of a data table. To extend their use, generalizations have been proposed, among which purity and approximate dependencies. After discussing those generalizations, we provide an alternative definition, the similarity dependencies, to handle a similarity relation between data-values, hence un-crisping the basic definition of functional dependencies. This work is rooted in formal concept analysis, and we s...

  2. A probabilistic approach to melodic similarity

    Bernabeu Briones, José Francisco; CALERA RUBIO, JORGE; Iñesta Quereda, José Manuel; Rizo Valero, David

    2009-01-01

    Melodic similarity is an important research topic in music information retrieval. The representation of symbolic music by means of trees has proven to be suitable in melodic similarity computation, because they are able to code rhythm in their structure leaving only pitch representations as a degree of freedom for coding. In order to compare trees, different edit distances have been previously used. In this paper, stochastic k-testable tree-models, formerly used in other domains like structur...

  3. Learning semantic similarity for very short texts

    De Boom, Cedric; Van Canneyt, Steven; Bohez, Steven; Demeester, Thomas; Dhoedt, Bart

    2015-01-01

    Levering data on social media, such as Twitter and Facebook, requires information retrieval algorithms to become able to relate very short text fragments to each other. Traditional text similarity methods such as tf-idf cosine-similarity, based on word overlap, mostly fail to produce good results in this case, since word overlap is little or non-existent. Recently, distributed word representations, or word embeddings, have been shown to successfully allow words to match on the semantic level....

  4. Protein structural similarity search by Ramachandran codes

    Chang Chih-Hung; Huang Po-Jung; Lo Wei-Cheng; Lyu Ping-Chiang

    2007-01-01

    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 ai...

  5. Mobile P2P Fast Similarity Search

    Bocek, T; Hecht, F. V.; Hausheer, D; Hunt, E; Stiller, B.

    2009-01-01

    In informal data sharing environments, misspellings cause problems for data indexing and retrieval. This is even more pronounced in mobile environments, in which devices with limited input devices are used. In a mobile environment, similarity search algorithms for finding misspelled data need to account for limited CPU and bandwidth. This demo shows P2P fast similarity search (P2PFastSS) running on mobile phones and laptops that is tailored to uncertain data entry and use...

  6. Similarity Theory of Withdrawn Water Temperature Experiment

    Yunpeng Han; Xueping Gao

    2015-01-01

    Selective withdrawal from a thermal stratified reservoir has been widely utilized in managing reservoir water withdrawal. Besides theoretical analysis and numerical simulation, model test was also necessary in studying the temperature of withdrawn water. However, information on the similarity theory of the withdrawn water temperature model remains lacking. Considering flow features of selective withdrawal, the similarity theory of the withdrawn water temperature model was analyzed theoretical...

  7. SIMILARITY NETWORK FOR SEMANTIC WEB SERVICES SUBSTITUTION

    Cherifi, Chantal

    2013-01-01

    Web services substitution is one of the most challenging tasks for automating the composition process of multiple Web services. It aims to improve performances and to deal efficiently with Web services failures. Many existing solutions have approached the problem through classification of substitutable Web services. To go a step further, we propose in this paper a network based approach where nodes are Web services operations and links join similar operations. Four similarity measures based o...

  8. Scalable Similarity Matching in Streaming Time Series

    Marascu, Alice; Ali Khan, Suleiman; Palpanas, Themis

    2011-01-01

    Nowadays online monitoring of data streams is essential in many real life applications, like sensor network monitoring, manufacturing process control, and video surveillance. One major problem in this area is the online identification of streaming sequences similar to a predefined set of pattern-sequences. In this paper, we present a novel solution that extends the state of the art both in terms of effectiveness and efficiency. We propose the first online similarity matching algorithm based o...

  9. Activity-relevant similarity values for fingerprints and implications for similarity searching

    Swarit Jasial; Ye Hu; Martin Vogt; Jürgen Bajorath

    2016-01-01

    A largely unsolved problem in chemoinformatics is the issue of how calculated compound similarity relates to activity similarity, which is central to many applications. In general, activity relationships are predicted from calculated similarity values. However, there is no solid scientific foundation to bridge between calculated molecular and observed activity similarity. Accordingly, the success rate of identifying new active compounds by similarity searching is limited. Although various att...

  10. Bioreporter pseudomonas fluorescens HK44 immobilized in a silica matrix

    Trogl J.

    2003-01-01

    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.

  11. The matrix of inspiration

    Oehlmann, Dietmar; Ohlmann, Odile M.; Danzebrink, Hans U.

    2005-04-01

    perform this exchange, as a matrix, understood as source, of new ideas.

  12. Containment Code Validation Matrix

    The Committee on the Safety of Nuclear Installations (CSNI) formed the CCVM (Containment Code Validation Matrix) task group in 2002. The objective of this group was to define a basic set of available experiments for code validation, covering the range of containment (ex-vessel) phenomena expected in the course of light and heavy water reactor design basis accidents and beyond design basis accidents/severe accidents. It was to consider phenomena relevant to pressurised heavy water reactor (PHWR), pressurised water reactor (PWR) and boiling water reactor (BWR) designs of Western origin as well as of Eastern European VVER types. This work would complement the two existing CSNI validation matrices for thermal hydraulic code validation (NEA/CSNI/R(1993)14) and In-vessel core degradation (NEA/CSNI/R(2001)21). The report initially provides a brief overview of the main features of a PWR, BWR, CANDU and VVER reactors. It also provides an overview of the ex-vessel corium retention (core catcher). It then provides a general overview of the accident progression for light water and heavy water reactors. The main focus is to capture most of the phenomena and safety systems employed in these reactor types and to highlight the differences. This CCVM contains a description of 127 phenomena, broken down into 6 categories: - Containment Thermal-hydraulics Phenomena; - Hydrogen Behaviour (Combustion, Mitigation and Generation) Phenomena; - Aerosol and Fission Product Behaviour Phenomena; - Iodine Chemistry Phenomena; - Core Melt Distribution and Behaviour in Containment Phenomena; - Systems Phenomena. A synopsis is provided for each phenomenon, including a description, references for further information, significance for DBA and SA/BDBA and a list of experiments that may be used for code validation. The report identified 213 experiments, broken down into the same six categories (as done for the phenomena). An experiment synopsis is provided for each test. Along with a test description

  13. Capillary zone electrophoresis of humic acids from the American continent.

    Pacheco, Maria de Lourdes; Havel, Josef

    2002-01-01

    A multicomponent background electrolyte (BGE) was developed and its composition optimized using artificial neural networks (ANN). The optimal BGE composition was found to be 90 mM boric acid, 115 mM Tris, and 0.75 mM EDTA (pH 8.4). A separation voltage of 20 kV, 20 degrees C and detection at 210 nm were used. The method was applied to characterize several humic acids originating from various countries of the American continent: soil (Argentina), peat (Brazil), leonardite (Guatemala and Mexico) and coal (United States). Comparison with humic acids of International Humic Substances Society (IHSS) standard samples was also done. Well reproducible electropherograms showing a relatively high number of peaks were obtained. Characterization of the samples by elemental analysis and UV spectrophotometry was also done. In spite of the very different origins, the similarities between humic acids are high and by matrix assisted desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry it was shown that most of the m/z patterns are the same in all humic acids. This means that humic acids of different origin have the same structural units or that they contain the same components. PMID:11840535

  14. The Effects of Extracellular Matrix on Tissue Engineering Construction of Cartilage in Vitro

    YU Li; LI Fa-tao; TANG Ming-qiao; YAN Wei-qun

    2006-01-01

    The effects of various cartilage extracellular matrix on the construction of rabbit growth plate cartilage tissue in vitro were studied. The results show that collagen, proteoglycan and hyaluronic acid can promote the growth of cultured chondrocytes but the effects of various cartilage extracellular matrix(ECM)on chondrocyte differentiation are different. Collagen can promote the hypertrophy of chondrocytes while proteoglycan and hyaluronic acid inhibit the transition of mature chondrocytes into hypertrophied chondrocytes.

  15. IMP: A Message-Passing Algorithmfor Matrix Completion

    Kim, Byung-Hak; Pfister, Henry D

    2010-01-01

    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.

  16. The transfer matrix approach to circular graphene quantum dots

    Chau Nguyen, H.; Nguyen, Nhung T. T.; Nguyen, V. Lien

    2016-07-01

    We adapt the transfer matrix (T-matrix) method originally designed for one-dimensional quantum mechanical problems to solve the circularly symmetric two-dimensional problem of graphene quantum dots. Similar to one-dimensional problems, we show that the generalized T-matrix contains rich information about the physical properties of these quantum dots. In particular, it is shown that the spectral equations for bound states as well as quasi-bound states of a circular graphene quantum dot and related quantities such as the local density of states and the scattering coefficients are all expressed exactly in terms of the T-matrix for the radial confinement potential. As an example, we use the developed formalism to analyse physical aspects of a graphene quantum dot induced by a trapezoidal radial potential. Among the obtained results, it is in particular suggested that the thermal fluctuations and electrostatic disorders may appear as an obstacle to controlling the valley polarization of Dirac electrons.

  17. Manufacturing Titanium Metal Matrix Composites by Consolidating Matrix Coated Fibres

    Hua-Xin PENG

    2005-01-01

    Titanium metal matrix composites (TiMMCs) reinforced by continuous silicon carbide fibres are being developed for aerospace applications. TiMMCs manufactured by the consolidation of matrix-coated fibre (MCF) method offer optimum properties because of the resulting uniform fibre distribution, minimum fibre damage and fibre volume fraction control. In this paper, the consolidation of Ti-6Al-4V matrix-coated SiC fibres during vacuum hot pressing has been investigated. Experiments were carried out on multi-ply MCFs under vacuum hot pressing (VHP). In contrast to most of existing studies, the fibre arrangement has been carefully controlled either in square or hexagonal arraysthroughout the consolidated sample. This has enabled the dynamic consolidation behaviour of MCFs to be demonstrated by eliminating the fibre re-arrangement during the VHP process. The microstructural evolution of the matrix coating was reported and the deformation mechanisms involved were discussed.

  18. Random matrix approach to multivariate categorical data analysis

    Patil, Aashay

    2015-01-01

    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 those from random matrix theory. We demonstrate this approach by applying it to the data of Indian general elections and sea level pressures in North Atlantic ocean.

  19. Identifying mechanistic similarities in drug responses

    Zhao, C.

    2012-05-15

    Motivation: In early drug development, it would be beneficial to be able to identify those dynamic patterns of gene response that indicate that drugs targeting a particular gene will be likely or not to elicit the desired response. One approach would be to quantitate the degree of similarity between the responses that cells show when exposed to drugs, so that consistencies in the regulation of cellular response processes that produce success or failure can be more readily identified.Results: We track drug response using fluorescent proteins as transcription activity reporters. Our basic assumption is that drugs inducing very similar alteration in transcriptional regulation will produce similar temporal trajectories on many of the reporter proteins and hence be identified as having similarities in their mechanisms of action (MOA). The main body of this work is devoted to characterizing similarity in temporal trajectories/signals. To do so, we must first identify the key points that determine mechanistic similarity between two drug responses. Directly comparing points on the two signals is unrealistic, as it cannot handle delays and speed variations on the time axis. Hence, to capture the similarities between reporter responses, we develop an alignment algorithm that is robust to noise, time delays and is able to find all the contiguous parts of signals centered about a core alignment (reflecting a core mechanism in drug response). Applying the proposed algorithm to a range of real drug experiments shows that the result agrees well with the prior drug MOA knowledge. © The Author 2012. Published by Oxford University Press. All rights reserved.

  20. Boost matrix converters in clean energy systems

    Karaman, Ekrem

    This dissertation describes an investigation of novel power electronic converters, based on the ultra-sparse matrix topology and characterized by the minimum number of semiconductor switches. The Z-source, Quasi Z-source, Series Z-source and Switched-inductor Z-source networks were originally proposed for boosting the output voltage of power electronic inverters. These ideas were extended here on three-phase to three-phase and three-phase to single-phase indirect matrix converters. For the three-phase to three-phase matrix converters, the Z-source networks are placed between the three-switch input rectifier stage and the output six-switch inverter stage. A brief shoot-through state produces the voltage boost. An optimal pulse width modulation technique was developed to achieve high boosting capability and minimum switching losses in the converter. For the three-phase to single-phase matrix converters, those networks are placed similarly. For control purposes, a new modulation technique has been developed. As an example application, the proposed converters constitute a viable alternative to the existing solutions in residential wind-energy systems, where a low-voltage variable-speed generator feeds power to the higher-voltage fixed-frequency grid. Comprehensive analytical derivations and simulation results were carried out to investigate the operation of the proposed converters. Performance of the proposed converters was then compared between each other as well as with conventional converters. The operation of the converters was experimentally validated using a laboratory prototype.