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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

    Directory of Open Access Journals (Sweden)

    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. Wavelet matrix transform for time-series similarity measurement

    Institute of Scientific and Technical Information of China (English)

    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.

  3. Similarity

    Science.gov (United States)

    Apostol, Tom M. (Editor)

    1990-01-01

    In this 'Project Mathematics! series, sponsored by the California Institute for Technology (CalTech), the mathematical concept of similarity is presented. he history of and real life applications are discussed using actual film footage and computer animation. Terms used and various concepts of size, shape, ratio, area, and volume are demonstrated. The similarity of polygons, solids, congruent triangles, internal ratios, perimeters, and line segments using the previous mentioned concepts are shown.

  4. Paper Similarity Detection Method Based on Distance Matrix Model with Row-Column Order Penalty Factor

    Directory of Open Access Journals (Sweden)

    Jun Li

    2014-08-01

    Full Text Available Paper similarity detection depends on grammatical and semantic analysis, word segmentation, similarity detection, document summarization and other technologies, involving multiple disciplines. However, there are some problems in the existing main detection models, such as incomplete segmentation preprocessing specification, impact of the semantic orders on detection, near-synonym evaluation, difficulties in paper backtrack and etc. Therefore, this paper presents a two-step segmentation model of special identifier and Sharpley value specific to above problems, which can improve segmentation accuracy. In the aspect of similarity comparison, a distance matrix model with row-column order penalty factor is proposed, which recognizes new words through search engine exponent. This model integrates the characteristics of vector detection, hamming distance and the longest common substring and carries out detection specific to near-synonyms, word deletion and changes in word order by redefining distance matrix and adding ordinal measures, making sentence similarity detection in terms of semantics and backbone word segmentation more effective. Compared with the traditional paper similarity retrieval, the present method has advantages in accuracy of word segmentation, low computation, reliability and high efficiency, which is of great academic significance in word segmentation, similarity detection and document summarization.

  5. Fragmentation of extracellular matrix by hypochlorous acid

    DEFF Research Database (Denmark)

    Woods, Alan A; Davies, Michael Jonathan

    2003-01-01

    The interaction of extracellular matrix with cells regulates their adhesion, migration and proliferation, and it is believed that damage to vascular matrix components is a factor in the development of atherosclerosis. Evidence has been provided for a role for the haem enzyme MPO (myeloperoxidase...

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

    Directory of Open Access Journals (Sweden)

    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

    Science.gov (United States)

    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. Community structure discovery method based on the Gaussian kernel similarity matrix

    Science.gov (United States)

    Guo, Chonghui; Zhao, Haipeng

    2012-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. A New Jacobian Matrix Method for Assessing Similarity between Critical Experiments and Real Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Yun, Sunghwan; Kim, Sang Ji [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-05-15

    For a metal fueled Sodium-cooled Fast Reactor (SFR), innovative reactors such as Prototype Gen-IV Sodium cooled Fast Reactor (PGSFR), unfortunately, experiment data from an operating reactor are unavailable because there are few operating reactors in the world. Hence, a critical experiment is the only way to obtain meaningful experiment data for the target core. However, there is a considerable geometrical difference between the critical assembly for a critical experiment and the target core. The neutron characteristics of a system are influenced by the geometrical difference. A number of researches have been performed to confirm the similarity between a critical experiment and a real reactor using a conventional representativity factor. The conventional representativity factor defined as S{sup T}{sub E}US{sub R} √S{sup T}{sub E}US{sub E}, √S{sup T}{sub R}US{sub R} provides insight of similarity between two sensitivity vectors for cross sections, but it did not provide a quantitative value. Hence, up to now, the influence of geometrical difference to the reactivity is believed to be negligible. In this paper, a new Jacobian matrix method is proposed to provide a quantitative error for geometrical differences between two systems. In this method, reactivity of the critical assembly is decomposed into phenomenon-based reactivity and geometry-based reactivity. The reactivity is then transformed into a target core geometry using a Jacobian matrix. Then, non-linearity of two different systems can be derived by comparing the transformed reactivity with the original reactivity of the target core. The maximum error of the transformed reactivity can be used as an additional uncertainty of the geometrical difference.

  11. GLYCOLIC-FORMIC ACID FLOWSHEET SLUDGE MATRIX STUDY

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Science.gov (United States)

    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.

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

    Indian Academy of Sciences (India)

    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.

  14. MALDI mechanism of dihydroxybenzoic acid isomers: desorption of neutral matrix and analyte.

    Science.gov (United States)

    Liang, Chi Wei; Lee, Chih Hao; Lin, Yu-Jiun; Lee, Yuan Tseh; Ni, Chi Kung

    2013-05-01

    Angular resolved velocity distributions of laser desorbed neutral matrices (dihydroxybenzoic acids, DHB) and analytes (tryptophan) embedded in these matrices were investigated at 322 nm by a modified crossed molecular beam apparatus. Desorbed ions generated from MALDI were measured by a time-of-flight mass spectrometer. Desorptions of neutral matrix and analyte from 2,3-DHB, 2,4-DHB, 2,5-DHB, 2,6-DHB, and 3,5--DHB at 322 nm have similar properties, but the ion intensities are in the order 2,3DHB ≅ 2,6-DHB > 2,5-DHB ≅ 2,4-DHB > 3,5-DHB. It indicates that the combination of various parameters related to neutral species, including absorption coefficient, sublimation energy, contact of analyte and matrix in crystal, and plume dynamics of desorbed species are not crucial in the determination of MALDI process for DHB isomers. The difference of matrix activity of DHB isomers at this wavelength must result from the other properties, like the excited state lifetime, proton affinity, gas-phase basicity, acidity, ionization energy, or the other properties related to the primary reactions in ion generation.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    Thomas Michael Lavender

    Full Text Available 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

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

    Science.gov (United States)

    Martins, Carlo de Oliveira; Demarchi, Lea; Ferreira, Frederico Moraes; Pomerantzeff, Pablo Maria Alberto; Brandao, Carlos; Sampaio, Roney Orismar; Spina, Guilherme Sobreira; Kalil, Jorge; Cunha-Neto, Edecio

    2017-01-01

    Autoimmune inflammatory reactions leading to rheumatic fever (RF) and rheumatic heart disease (RHD) result from untreated Streptococcus pyogenes throat infections in individuals who exhibit genetic susceptibility. Immune effector mechanisms have been described that lead to heart tissue damage culminating in mitral and aortic valve dysfunctions. In myxomatous valve degeneration (MXD), the mitral valve is also damaged due to non-inflammatory mechanisms. Both diseases are characterized by structural valve disarray and a previous proteomic analysis of them has disclosed a distinct profile of matrix/structural proteins differentially expressed. Given their relevance in organizing valve tissue, we quantitatively evaluated the expression of vimentin, collagen VI, lumican, and vitronectin as well as performed immunohistochemical analysis of their distribution in valve tissue lesions of patients in both diseases. We identified abundant expression of two isoforms of vimentin (45 kDa, 42 kDa) with reduced expression of the full-size protein (54 kDa) in RHD valves. We also found increased vitronectin expression, reduced collagen VI expression and similar lumican expression between RHD and MXD valves. Immunohistochemical analysis indicated disrupted patterns of these proteins in myxomatous degeneration valves and disorganized distribution in rheumatic heart disease valves that correlated with clinical manifestations such as valve regurgitation or stenosis. Confocal microscopy analysis revealed a diverse pattern of distribution of collagen VI and lumican into RHD and MXD valves. Altogether, these results demonstrated distinct patterns of altered valve expression and tissue distribution/organization of structural/matrix proteins that play important pathophysiological roles in both valve diseases. PMID:28121998

  18. Volutin granules of Eimeria parasites are acidic compartments and have physiological and structural characteristics similar to acidocalcisomes

    Science.gov (United States)

    Medeiros, Lia Carolina Soares; Gomes, Fabio; Maciel, Luis Renato Maia; Seabra, Sergio Henrique; Docampo, Roberto; Moreno, Silvia; Plattner, Helmut; Hentschel, Joachim; Kawazoe, Urara; Barrabin, Hector; de Souza, Wanderley; DaMatta, Renato Augusto; Miranda, Kildare

    2012-01-01

    The structural organization of parasites has been the subject of investigation by many groups and has lead to the identification of structures and metabolic pathways that may represent targets for anti-parasitic drugs. A specific group of organelles named acidocalcisomes has been identified in a number of organisms, including the apicomplexan parasites such as Toxoplasma and Plasmodium, where they have been shown to be involved in cation homeostasis, polyphosphate metabolism, and osmoregulation. Their structural counterparts in the apicomplexan parasite Eimeria have not been fully characterized. In this work, the ultrastructural and chemical properties of acidocalcisomes in Eimeria were characterized. Electron microscopy analysis of Eimeria parasites showed the dense organelles called volutin granules similar to acidocalcisomes. Immunolocalization of the vacuolar proton pyrophosphatase, considered as a marker for acidocalcisomes, showed labeling in vesicles of size and distribution similar to the dense organelles seen by electron microscopy. Spectrophotometric measurements of the kinetics of proton uptake showed a vacuolar proton pyrophosphatase activity. X-ray mapping revealed significant amounts of Na, Mg, P, K, Ca, and Zn in their matrix. The results suggest that volutin granules of Eimeria parasites are acidic, dense organelles and possess structural and chemical properties analogous to those of other acidocalcisomes, suggesting a similar functional role in these parasites. PMID:21699625

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

    DEFF Research Database (Denmark)

    Kjellström, Sven; Jensen, Ole Nørregaard

    2004-01-01

    Phosphopeptides are often detected with low efficiency by MALDI MS analysis of peptide mixtures. In an effort to improve the phosphopeptide ion response in MALDI MS, we investigated the effects of adding low concentrations of organic and inorganic acids during peptide sample preparation in 2......,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....

  20. Citric Acid Capped Iron Oxide Nanoparticles as an Effective MALDI Matrix for Polymers

    Science.gov (United States)

    Liang, Qiaoli; Sherwood, Jennifer; Macher, Thomas; Wilson, Joseph M.; Bao, Yuping; Cassady, Carolyn J.

    2016-12-01

    A new matrix-assisted laser desorption ionization (MALDI) mass spectrometry matrix is proposed for molecular mass determination of polymers. This matrix contains an iron oxide nanoparticle (NP) core with citric acid (CA) molecules covalently bound to the surface. With the assistance of additives, the particulate nature of NPs allows the matrix to mix uniformly with polar or nonpolar polymer layers and promotes ionization, which may simplify matrix selection and sample preparation procedures. Several distinctively different polymer classes (polyethyleneglycol (PEG), polywax/polyethylene, perfluoropolyether, and polydimethylsiloxane) are effectively detected by the water or methanol dispersed NPCA matrix with NaCl, NaOH, LiOH, or AgNO3 as additives. Furtheremore, successful quantitative measurements of PEG1000 using polypropylene glycol 1000 as an internal standard are demonstrated.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  2. Novel amino acids indices based on quantum topological molecular similarity and their application to QSAR study of peptides.

    Science.gov (United States)

    Hemmateenejad, Bahram; Yousefinejad, Saeed; Mehdipour, Ahmad Reza

    2011-04-01

    A new source of amino acid (AA) indices based on quantum topological molecular similarity (QTMS) descriptors has been proposed for use in QSAR study of peptides. For each bond of the chemical structure of AA, eight electronic properties were calculated using the approaches of bond critical point and theory of atom in molecule. Thus, for each molecule a data matrix of QTMS descriptors (having information from both topology and electronic features) were calculated. Using four different criterion based on principal component analysis of the QTMS data matrices, four different sets of AA indices were generated. The indices were used as the input variables for QSAR study (employing genetic algorithm-partial least squares) of three peptides' data sets, namely, angiotensin-converting enzyme inhibitors, bactericidal peptides and the peptides binding to the HLA-A*0201 molecule. The obtained models had better prediction ability or a comparable one with respect to the previously reported models. In addition, by using the proposed indices and analysis of the variable important in projection, the active site of the peptides which plays a significant role in the biological activity of interest, was identified.

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

    Science.gov (United States)

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

    2014-04-04

    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.

  4. 3-Aminoquinoline/p-coumaric acid as a MALDI matrix for glycopeptides, carbohydrates, and phosphopeptides.

    Science.gov (United States)

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

    2014-02-18

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Benega, Marcos A.G.; Nagatomi, Helio R.; Rostelato, Maria Elisa C.M.; Tiezzi, Rodrigo; Rodrigues, Bruna T.; Peleias Junior, Fernando; Souza, Carla D.; Souza, Daiane C.C. de; Souza, Anderson S. de; Silva, Thais H. da, E-mail: carladdsouza@yahoo.com.br, E-mail: marcosagbenega@gmail.com, E-mail: hrnagato@ipen.br, E-mail: elisaros@ipen.br, E-mail: rktiezzi@gmail.com, E-mail: bteigarodrigues@gmail.com, E-mail: fernandopeleias@gmail.com, E-mail: dcsouza@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2014-07-01

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

  6. Matrix isolation infrared spectra of O-H· · · π Hydrogen bonded complexes of Acetic acid and Trifluoroacetic acid with Benzene

    Indian Academy of Sciences (India)

    PUJARINI BANERJEE; INDRANI BHATTACHARYA; TAPAS CHAKRABORTY

    2016-10-01

    Mid infrared spectra of two O–H· · · π hydrogen-bonded binary complexes of acetic acid (AA) and trifluoroacetic acid (F₃AA) with benzene (Bz) have been measured by isolating the complexes in an argon matrix at ∼8 K. In a matrix isolation condition, the O–H stretching fundamentals (νO−H) of the carboxylic acid groups of the two molecules are observed to have almost the same value. However, the spectral red-shifts of νO−H bands of the two acids on complexation with Bz are largely different, 90 and 150 cm⁻¹ for AA and F₃AA, respectively. Thus, the O–H bond weakening of the two acids upon binding with Bz in a non-interacting environment follows the sequence of their ionic dissociation tendencies (pKa) in aqueous media. Furthermore, ΔνO−H of the latter complex is the largest among the known π-hydrogen bonded binary complexes of prototypical O–H donors reported so far with respect to Bz as acceptor. It is also observed that the spectral shifts (ΔνO−H) of phenol-Bz and carboxylic acid-Bz complexes show similar dependence on the acidity factor (pKa). Electronic structure theory has been used to suggest suitable geometries of the complexes that are consistent with the measured IR spectral changes. Calculation at MP2/6-311++G (d, p) level predicts a T-shaped geometry for both AA-Bz and F₃AA-Bz complexes, and the corresponding binding energies are 3.0 and 4.5 kcal/mol, respectively. Natural Bond Orbital (NBO) analysis has been performed to correlate the observed spectral behavior of the complexes with the electronic structure parameters.

  7. Inactivation of Matrix-bound MMPs by Cross-linking Agents in Acid Etched Dentin

    Science.gov (United States)

    Scheffel, Débora Lopes Salles; Hebling, Josimeri; Scheffel, Régis Henke; Agee, Kelly A.; Turco, Gianluca; de Souza Costa, Carlos Alberto; Pashley, David H.

    2014-01-01

    Objectives Published TEM analysis of in vivo resin-dentin bonds shows that in 44 months almost 70% of collagen fibrils from the hybrid layer disappear. Matrix metalloproteinases (MMPs) play an important role in that process and are thought to be the main factor responsible for the solubitization of dentin collagen. Therefore, this study aimed to evaluate the inactivation of matrix-bound MMPs by carbodiimide (EDC) or proanthocyanidin (PA) both cross-linking agents, or the MMP-inhibitor, chlorhexidine (CHX), on acid-etched dentin using a simplified MMP assay method. Methods Dentin beams (1×1×6mm) were obtained from mid-coronal dentin of sound third molars and randomly divided into 6 groups (G) according to the dentin treatment: G1: Deionized water (control), G2: 0.1M EDC, G3: 0.5M EDC, G4: 0.5M EDC+35% HEMA, G5: 5% Proanthocyanidin (PA) and G6: 2% CHX. The beams were etched for 15s with 37% phosphoric acid, rinsed and then immersed for 60s in one of the treatment solutions. The total MMP activity of dentin was analyzed for 1 h by colorimetric assay (Sensolyte). Data were submitted to Wilcoxon non-parametric test and Mann-Whitney tests (p>0.05). Results All experimental cross-linking solutions significantly reduced MMP activity compared to control, except 0.1M EDC (53.6% ±16.1). No difference was observed between cross-linking agents and 2% CHX 0.5M EDC + 35% HEMA (92.3% ±8.0) was similar to 0.5M EDC (89.1% ±6.4), 5% PA (100.8% ±10.9) and 2% CHX (83.4% ±10.9). Conclusion Dentin treatment with cross-linking agents is effective to significantly reduce MMP activity. Mixing 0.5M EDC and 35% HEMA did not influence EDC inhibitor potential. PMID:23786610

  8. Weighted augmented Jacobian matrix with a variable coefficient method for kinematics mapping of space teleoperation based on human-robot motion similarity

    Science.gov (United States)

    Shi, Zhong; Huang, Xuexiang; Hu, Tianjian; Tan, Qian; Hou, Yuzhuo

    2016-10-01

    Space teleoperation is an important space technology, and human-robot motion similarity can improve the flexibility and intuition of space teleoperation. This paper aims to obtain an appropriate kinematics mapping method of coupled Cartesian-joint space for space teleoperation. First, the coupled Cartesian-joint similarity principles concerning kinematics differences are defined. Then, a novel weighted augmented Jacobian matrix with a variable coefficient (WAJM-VC) method for kinematics mapping is proposed. The Jacobian matrix is augmented to achieve a global similarity of human-robot motion. A clamping weighted least norm scheme is introduced to achieve local optimizations, and the operating ratio coefficient is variable to pursue similarity in the elbow joint. Similarity in Cartesian space and the property of joint constraint satisfaction is analysed to determine the damping factor and clamping velocity. Finally, a teleoperation system based on human motion capture is established, and the experimental results indicate that the proposed WAJM-VC method can improve the flexibility and intuition of space teleoperation to complete complex space tasks.

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

    Science.gov (United States)

    Prasad, Bhim Bali; Srivastava, Amrita; Tiwari, Mahavir Prasad

    2013-10-01

    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.

  10. Effect of uric acid on gentamicin-induced nephrotoxicity in rats - role of matrix metalloproteinases 2 and 9.

    Science.gov (United States)

    Romero, Freddy; Pérez, Mariela; Chávez, Maribel; Parra, Gustavo; Durante, Paula

    2009-12-01

    In this work, we aimed to study the effect of uric acid on gentamicin-induced nephrotoxicity. Male Sprague-Dawley rats were assigned to one of six groups (six rats each) which received intraperitoneal injections for 9 days: (S) saline; (UA) Uric acid alone; (G) Gentamicin alone; (G + UA) Gentamicin + uric acid; (G rec) Gentamicin recovery and (G + UA rec) Gentamicin + uric acid recovery. In (G rec) and (G + UA rec), rats recovered for 7 days after the last injection. Urine and blood samples were taken on day 0 and at the end of every stage. Kidneys were harvested for histological scoring, determination of renal malondialdehyde (MDA), zymography and western blots for matrix metalloprotease (MMP)-2 and MMP-9. Uric acid alone did not provoke changes in biochemical and histological parameters when compared to controls. Gentamicin alone increased significantly plasma creatinine and blood urea nitrogen and caused a moderate histological damage. When combined with uric acid, these conditions worsened. MMP-9 activity and expression was decreased in rats from group G + UA as compared with rats from group G, while activity of MMP-2 was similarly increased in both groups when compared to controls. The increase in renal MDA induced by gentamicin was not altered when it was combined with uric acid. During the recovery stage, all biochemical parameters returned to normal levels, though a trend for delay of tubular damage recovery was observed in group G + UA rec when compared with group G rec. The results indicate that uric acid worsens gentamicin-induced nephrotoxicity. The mechanism is likely to implicate down-regulation of MMP-9.

  11. Poly(lactic-co-glycolic acid) matrix incorporated with nisin as a novel antimicrobial biomaterial.

    Science.gov (United States)

    Correia, Rafaela Coelho; Jozala, Angela Faustino; Martins, Kelly Fernanda; Penna, Thereza Christina Vessoni; Duek, Eliana Aparecida de Rezende; Rangel-Yagui, Carlota de Oliveira; Lopes, André Moreni

    2015-04-01

    The use of poly(lactic-co-glycolic acid) (PLGA) matrix as a biomolecule carrier has been receiving great attention due to its potential therapeutic application. In this context, we investigated the PLGA matrix capacity to incorporate nisin, an antimicrobial peptide capable of inhibiting the growth of Gram-positive bacteria and bacterial spores germination. Nisin-incorporated PLGA matrices were evaluated based on the inhibitory effect against the nisin-bioindicator Lactobacillus sakei. Additionally, the PLGA-nisin matrix stability over an 8-months period was investigated, as well as the nisin release profile. For the incorporation conditions, we observed that a 5 h incorporation time, at 30 °C, with 250 μg/mL nisin solution in PBS buffer pH 4.5, resulted in the highest inhibitory activity of 2.70 logAU/mL. The PLGA-nisin matrix was found to be relatively stable and showed sustained drug delivery, with continuous release of nisin for 2 weeks. Therefore, PLGA-nisin matrix is could be used as a novel antimicrobial delivery system and an alternative to antibiotics incorporated into PLGA matrices.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. TG containing stearic acid, synthesized from coconut oil, exhibit lipidemic effects in rats similar to those of cocoa butter.

    Science.gov (United States)

    Rao, Reena; Lokesh, Belur R

    2003-09-01

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

  14. [Similarities, differences and agonisms of pleiotropic effects of statins and omega-3 fatty acids].

    Science.gov (United States)

    Villalobos, Maria E; Sánchez-Muniz, F J; Acín, Maria T; Vaquero, Maria P; Higueras, F J; Bastida, S

    2010-01-01

    This paper compares the pleiotropic effects of statins and omega-3 fatty acids (n-3 PUFA) in treating and preventing cardiovascular disease (CVD) and deals with the possible interactions of those compounds. Statins represent one of the most important discoveries to have been made in the field of cardiovascular medicine in recent decades. Their beneficial cardiovascular effects, which have reduced the number of fatal events in patients with atherosclerosis, encompass more than their ability to lower cholesterol levels. The pleiotropic effects of statins involve their anti-inflammatory and antiplatelet properties and their ability to normalize endothelial function. In addition, these drugs may display antiarrhythmic activity, improve insulin sensitivity and counteract hypertension and obesity. The low rate of coronary disease documented in Eskimos corroborates the cardioprotective effects of the n-3 PUFA eicosapentaenoic (EPA) and docosahexaenoic acids beyond their hypolipemic effects. The reduction of CVD-related deaths attributable to the action of α-linolenic fatty acid appears to be related to its strong antiarrhythmic properties. In addition, as a precursor of EPA and this last fatty acid of thromboxane A3, prostacyclin I3, serie-3 prostaglandines and serie 5-leukotrines and inhibitor/modulator of thromboxane A2, prostacyclin I2, serie-2 prostaglandines and serie 4-leukotrienes formation, the α-linolenic acid may reduce inflammation and thrombogenesis. As results of some studies suggest that the combined use of statins and n-3 PUFA improves cardiovascular protection and reduces the CVD-related mortality rate; the paper also reviews the possible synergism between both groups of compounds on CVD treatment and concludes that clear benefits may be obtained.

  15. Plasma and erythrocyte fatty acids reflect intakes of saturated and n-6 PUFA within a similar time frame.

    Science.gov (United States)

    Hodson, Leanne; Eyles, Helen C; McLachlan, Kirsten J; Bell, Melanie L; Green, Timothy J; Skeaff, C Murray

    2014-01-01

    Erythrocytes, compared with plasma, are considered more robust markers of n-3 (ω-3) polyunsaturated fatty acid (PUFA) intake, because dietary-induced change in fatty acid (FA) composition takes longer to complete. The extent to which this applies to intakes of saturated fatty acid (SFA) or n-6 PUFA is unclear. We compared the pattern of change over time in the fatty acid composition of plasma, erythrocyte, buccal cell, and adipose tissue lipids when changing between diets high in SFA or n-6 PUFA. Twenty-four (n = 7 male) healthy participants were instructed to consume either an SFA-rich (18% energy) or n-6 PUFA-rich (10% energy) diet for 8 wk before crossing over, without washout, to the alternate diet. The FA composition of plasma triacylglycerol (TG), nonesterified FAs, cholesterol ester, total phospholipids, erythrocyte total phospholipids, erythrocyte phosphatidylcholine, and buccal cell total phospholipids was measured every 2 wk and adipose tissue TG every 4 wk during the 16-wk intervention. Linoleic acid composition of plasma, erythrocyte, and buccal cell lipids increased (P acid composition of plasma and erythrocyte lipids; however, the pentadecanoic acid composition of buccal cell lipids did not differ between the diet periods. There were no differences in linoleic or pentadecanoic acid composition of adipose tissue TG. These results suggest plasma and erythrocyte FAs reflect intakes of SFA and n-6 PUFA over a similar period of time.

  16. Effect of Matrix Modification on Durability of Cementitious Composites in an Acid Rain Environment

    Institute of Scientific and Technical Information of China (English)

    HE Kui; YANG Hui; LU Zhenbao; JIA Fangfang; WANG Erpo; DONG Quanxiao

    2014-01-01

    The durability of silane-modified mortar, a cementitious composite, in acid rain environment was investigated given its extensive usage as a structural material. The results indicated that the addition of silane decreased the compressive strength of the cementitious composite. Wetting angle was increased by incorporating silane into the matrix. Decrease in both water absorption ability and coefficient of capillary suction confirmed hydrophobicity as induced by silane addition. Results of mechanical testing, scanning electron microscopy and X-ray diffraction showed that the sulfuric acid resistance of mortar was enhanced by silane. Based on these results, it is revealed that silane addition inhibits the diffusion of water, and consequently, sulfate ion diffusion rate decreases, thereby resulting in reduction in the rate of corrosion of cementitious composites by sulfuric acid.

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

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kyung Man; Ahn, Sung Hee; Bae, Yong Jin; Kim, Myung Soo [Seoul National Univ., Seoul (Korea, Republic of)

    2013-03-15

    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{sup -5}-10{sup -4} for peptides and 10{sup -8}-10{sup -7} for matrices are far smaller than 10.3-10.1 for peptides and 10{sup -5}-10{sup -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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Bhim Bali, E-mail: prof.bbpd@yahoo.com; Srivastava, Amrita; Tiwari, Mahavir Prasad

    2013-10-15

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  20. A novel phytase with sequence similarity to purple acid phosphatases is expressed in cotyledons of germinating soybean seedlings.

    Science.gov (United States)

    Hegeman, C E; Grabau, E A

    2001-08-01

    Phytic acid (myo-inositol hexakisphosphate) is the major storage form of phosphorus in plant seeds. During germination, stored reserves are used as a source of nutrients by the plant seedling. Phytic acid is degraded by the activity of phytases to yield inositol and free phosphate. Due to the lack of phytases in the non-ruminant digestive tract, monogastric animals cannot utilize dietary phytic acid and it is excreted into manure. High phytic acid content in manure results in elevated phosphorus levels in soil and water and accompanying environmental concerns. The use of phytases to degrade seed phytic acid has potential for reducing the negative environmental impact of livestock production. A phytase was purified to electrophoretic homogeneity from cotyledons of germinated soybeans (Glycine max L. Merr.). Peptide sequence data generated from the purified enzyme facilitated the cloning of the phytase sequence (GmPhy) employing a polymerase chain reaction strategy. The introduction of GmPhy into soybean tissue culture resulted in increased phytase activity in transformed cells, which confirmed the identity of the phytase gene. It is surprising that the soybean phytase was unrelated to previously characterized microbial or maize (Zea mays) phytases, which were classified as histidine acid phosphatases. The soybean phytase sequence exhibited a high degree of similarity to purple acid phosphatases, a class of metallophosphoesterases.

  1. Matrix influence on derivatization and ionization processes during selenoamino acid liquid chromatography electrospray ionization mass spectrometric analysis.

    Science.gov (United States)

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

    2014-04-01

    Considering the importance of derivatization in LC/ESI/MS analysis, the objective of this work was to develop a method for evaluation of matrix effect that would discriminate between matrix effect due to the derivatization reaction yield and from the ESI. Four derivatization reagents (TAHS, DEEMM, DNS, FMOC-Cl) were studied with respect to matrix effects using two selenoamino acids and onion matrix as model system. A novel method for assessing matrix effects of LC/ESI/MS analyses involving derivatization is proposed, named herein post-derivatization spiking, that allows evaluating effect of matrix on ESI ionization without derivatization reaction yield contribution. The proposed post-derivatization spiking method allowed to demonstrate that the reason of reduced analytical signal can be signal suppression in ESI (as in case of DNS derivatives with matrix effects 38-99%), alteration of derivatization reaction yield (TAHS, matrix effects 92-113%, but reaction yields 20-50%) or both (FMOC-Cl, matrix effects 28-88% and reaction yields 50-70%). In case of DEEMM derivatives, matrix reduces reaction yield but enhances ESI/MS signal. A method for matrix effect evaluation was developed. It was also confirmed that matrix effects can be reduced by dilution.

  2. Use of a similarity index based on microbial fatty acid (MFA) analysis to monitor biological wastewater treatment systems.

    Science.gov (United States)

    Son, K S; Hall, E R

    2003-09-01

    Estimating the stability of microbial community structures may be useful in advanced biological wastewater treatment system design and operation. In this research, a monitoring method using fatty acid profiles was evaluated for detecting changes in microbial community structures. For the evaluation, the operating parameters such as pH, organic loading, and chlorine addition were varied in two identical laboratory scale conventional activated sludge systems. A similarity index based on microbial fatty acid analysis was used to express the stability of microbial community structures in the systems. Experiments using a model microbial community showed that microbial compositions changed daily even under constant operating conditions and that the rate of change increased under dynamic operating conditions. Substrate changes brought about a relatively large change in a microbial community structure, eventually resulting in a very different microbial community. After only 7 days following a substrate change in a lab-scale bioreactor, the biomass exhibited only 45% similarity to the original structure. The analysis of microbial fatty acids conveys additional information, in that it could be used for the calculation of biomass concentrations in a wastewater treatment system if microbial fatty acid analyses are executed on a routine basis as a monitoring tool for biological wastewater treatment systems. The total fatty acid concentrations were about 0.61% of the biomass concentration as mixed liquor volatile suspended solid concentrations in this research.

  3. In vitro toxicity of carbon nanotubes, nano-graphite and carbon black, similar impacts of acid functionalization.

    Science.gov (United States)

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

    2015-12-25

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

  4. 谱聚类图像分割中相似度矩阵构造研究%Research on Similarity Matrix Structure in Spectral Clustering Image Segmentation

    Institute of Scientific and Technical Information of China (English)

    李扬; 陆璐; 崔红霞

    2016-01-01

    In recent years,spectral clustering algorithm is widely used in the field of image segmentation,and the structure of the similarity matrix is the key of it. When the color images are segmented by traditional spectral clustering algorithm,the only one of color space and distance calculation formula is usually used to construct similarity matrix. The influence of the segmentation results established on the dif-ferent color space and distance calculation formula is neglected,which leads to many limitations of spectral clustering algorithm. To solve this problem,using the formula of Euclidean distance,cosine distance and chi square distance,the different similarity matrices are estab-lished on RGB and HSV color space. The best segmentation construction method of the similarity matrix is obtained by analysis and com-parison of the effect of different construction methods. The effectiveness of spectral clustering algorithm for segmenting color images is improved. By calculating the accuracy of image segmentation results and the performance evaluation index of precision and recall,the reli-ability and accuracy of the experiment are verified.%近年来谱聚类算法广泛应用于图像分割领域,而相似度矩阵的构造是谱聚类算法的关键。通常传统的谱聚类算法分割彩色图像时,仅采用一种颜色空间和距离计算公式构造相似度矩阵,而忽略了不同的颜色空间和距离计算公式构造的相似度矩阵对分割结果的影响,导致谱聚类算法有诸多的局限性。针对这个问题,文中分别采用RGB和HSV颜色空间,以及分别在两种颜色空间下使用欧氏距离、余弦距离和卡方距离公式,建立不同的相似度矩阵。分析比较不同构造方法的分割效果,得出了最优分割效果的相似度矩阵构造方法,提高了应用谱聚类算法分割彩色图像的有效性。通过计算性能评价指标查准率和查全率以及分割结果的准确率,验证

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

    Directory of Open Access Journals (Sweden)

    Nadie Fatimatuzzahro

    2014-11-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Aguilera, Angeles [Centro de Astrobiologia (INTA-CSIC), Carretera de Ajalvir Km 4, Torrejon de Ardoz, 28850 Madrid (Spain)], E-mail: aguileraba@inta.es; Souza-Egipsy, Virginia [Centro de Astrobiologia (INTA-CSIC), Carretera de Ajalvir Km 4, Torrejon de Ardoz, 28850 Madrid (Spain); San Martin-Uriz, Patxi [Centro de Biologia Molecular (UAM-CSIC), Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Amils, Ricardo [Centro de Astrobiologia (INTA-CSIC), Carretera de Ajalvir Km 4, Torrejon de Ardoz, 28850 Madrid (Spain); Centro de Biologia Molecular (UAM-CSIC), Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain)

    2008-07-30

    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{sup -1} biofilm dry weight, representing between 15% and the 40% of the total biofilm dry weight (DW). Statistically significant differences (p < 0.05) were found in the amount of total EPS extracted from biofilms dominated by the same organism at different sampling points. The amount of EPS varied among different biofilms collected from the same sampling location. Colloidal EPS ranged from 42 to 313 mg g{sup -1} dry weight; 10% to 30% of the total biofilm dry weight. Capsular EPS ranged from 50 to 318 mg g{sup -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 < 0.05). Total amount of EPS decreased when total cell numbers and pH increased. There was a positive correlation between EPS concentration and heavy metal concentration in the water. Observations by low temperature scanning electron microscopy (LTSEM) revealed the mineral adsorption in the matrix of EPS and onto the cell walls. EPS in all biofilms were primarily composed of carbohydrates, heavy metals and humic acid, plus small quantities of proteins and DNA. After carbohydrates, heavy metals were the second main constituents of the extracellular matrix. Their total concentrations ranged from 3 to 32 mg g{sup -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.

  7. 4-Chloro-α-cyanocinnamic acid is an efficient soft matrix for cyanocobalamin detection in foodstuffs by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS).

    Science.gov (United States)

    Calvano, Cosima Damiana; Ventura, Giovanni; Palmisano, Francesco; Cataldi, Tommaso R I

    2016-09-01

    4-Chloro-α-cyanocinnamic acid (ClCCA) is a very useful matrix able to give the protonated adduct [M+H](+) of intact cyanocobalamin (CNCbl) as the base peak (m/z 1355.58) in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS). The only fragment observed is [M-CN + H](+•) formed through the facile (•) CN neutral loss reflecting the fairly low Co-C bond energy. All other investigated proton transfer matrices, including α-cyano-4-hydroxycinnamic acid, para-nitroaniline and 2,5-dihydroxybenzoic acid, give rise to a complete decyanation of CNCbl with concomitant formation of [M-CN + H](+•) , [M-CN + Na](+•) and [M-CN + K](+•) adducts at m/z 1329.57, 1351.55 and 1367.51, respectively. Depending on the matrix used, a variable degree of fragmentation involving the α-side axial ligand was observed. A plausible explanation of the specific behaviour of 4-chloro-α-cyanocinnamic acid as a soft matrix is discussed. Tandem mass spectra of both [M + H](+) and [M-CN + H](+•) ions were obtained and product ions successfully assigned. The possibility of detecting the protonated adduct of intact CNCbl was exploited in foodstuff samples such as cow milk and hen egg yolk by MALDI tandem MS upon sample extraction. We believe that our data provide strong basis for the application of MALDI tandem MS in the qualitative analysis of natural CNCbl, including fish, liver and meat samples. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Molecular surface area based predictive models for the adsorption and diffusion of disperse dyes in polylactic acid matrix.

    Science.gov (United States)

    Xu, Suxin; Chen, Jiangang; Wang, Bijia; Yang, Yiqi

    2015-11-15

    Two predictive models were presented for the adsorption affinities and diffusion coefficients of disperse dyes in polylactic acid matrix. Quantitative structure-sorption behavior relationship would not only provide insights into sorption process, but also enable rational engineering for desired properties. The thermodynamic and kinetic parameters for three disperse dyes were measured. The predictive model for adsorption affinity was based on two linear relationships derived by interpreting the experimental measurements with molecular structural parameters and compensation effect: ΔH° vs. dye size and ΔS° vs. ΔH°. Similarly, the predictive model for diffusion coefficient was based on two derived linear relationships: activation energy of diffusion vs. dye size and logarithm of pre-exponential factor vs. activation energy of diffusion. The only required parameters for both models are temperature and solvent accessible surface area of the dye molecule. These two predictive models were validated by testing the adsorption and diffusion properties of new disperse dyes. The models offer fairly good predictive ability. The linkage between structural parameter of disperse dyes and sorption behaviors might be generalized and extended to other similar polymer-penetrant systems.

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

    Science.gov (United States)

    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.

  10. Hypohalous acids contribute to renal extracellular matrix damage in experimental diabetes.

    Science.gov (United States)

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

    2015-06-01

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

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

    Science.gov (United States)

    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.

  12. Utilizing cell-matrix interactions to modulate gene transfer to stem cells inside hyaluronic acid hydrogels.

    Science.gov (United States)

    Gojgini, Shiva; Tokatlian, Talar; Segura, Tatiana

    2011-10-01

    The effective delivery of DNA locally would increase the applicability of gene therapy in tissue regeneration, where diseased tissue is to be repaired in situ. One promising approach is to use hydrogel scaffolds to encapsulate and deliver plasmid DNA in the form of nanoparticles to the diseased tissue, so that cells infiltrating the scaffold are transfected to induce regeneration. This study focuses on the design of a DNA nanoparticle-loaded hydrogel scaffold. In particular, this study focuses on understanding how cell-matrix interactions affect gene transfer to adult stem cells cultured inside matrix metalloproteinase (MMP) degradable hyaluronic acid (HA) hydrogel scaffolds. HA was cross-linked to form a hydrogel material using a MMP degradable peptide and Michael addition chemistry. Gene transfer inside these hydrogel materials was assessed as a function of polyplex nitrogen to phosphate ratio (N/P = 5 to 12), matrix stiffness (100-1700 Pa), RGD (Arg-Gly-Asp) concentration (10-400 μM), and RGD presentation (0.2-4.7 RGDs per HA molecule). All variables were found to affect gene transfer to mouse mensenchymal stem cells culture inside the DNA loaded hydrogels. As expected, higher N/P ratios lead to higher gene transfer efficiency but also higher toxicity; softer hydrogels resulted in higher transgene expression than stiffer hydrogels, and an intermediate RGD concentration and RGD clustering resulted in higher transgene expression. We believe that the knowledge gained through this in vitro model can be utilized to design better scaffold-mediated gene delivery for local gene therapy.

  13. Synthesis and Characterization of Terbium-Trimesic Acid Luminescent Complex in Polyvinylpyrrolidone Matrix

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Tb(Ⅲ)-trimesic acid (TMA) luminescent complexes were synthesized in the polyvinylpyrrolidone (PVP) matrix. The elemental analysis, inductively coupled plasma-atomic emission spectroscopy (ICP-AES) and fourier-transform infrared spectroscopy (FT-IR) indicated that its chemical constitution is PVP/Tb(MTA)·4H2O. The XRD patterns showed that the complex is a new kind of crystal. The TEM image indicates that the complex is rod shaped. The rod diameter is about 200 nm, and the length ranges from hundred of nanometer to a few micrometers. In addition, the dispersity is better. TG-DTA curves indicate that the complex is thermally stable before 463 ℃. Photoluminescence analysis indicates that the complex emits Tb3+ characteristic luminescence under ultraviolet excitation.

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

    Directory of Open Access Journals (Sweden)

    Mariateresa Giustiniano

    2013-01-01

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

  15. Modified hydroxypropyl methyl cellulose: Efficient matrix for controlled release of 5-amino salicylic acid.

    Science.gov (United States)

    Das, Raghunath; Pal, Sagar

    2015-01-01

    Hydroxypropyl methyl cellulose has been modified by grafting synthetic polyacrylamide chains [g-HPMC (M)] in presence of microwave irradiation, which has used as carrier for controlled release of 5-amino salicylic acid (5-ASA). The FTIR and UV-vis-NIR studies reveal the excellent compatibility between g-HPMC (M) and 5-ASA. Field emission scanning electron microscopy (FESEM) and UV-vis-NIR analyses suggest that physical interaction predominates between the drug and matrix. % equilibrium swelling ratio (% ESR) of g-HPMC (M) decreased with addition of salt solutions and follow the order: Na(+)>K(+)>Mg(2+)>Ca(2+)>Al(3+). The in vitro 5-ASA release studies indicate that g-HPMC (M) delivers the drug preferentially in colonic region in more sustained way than that of HPMC. The 5-ASA release follows first order kinetics and non-Fickian diffusion mechanism. These favorable features make the graft copolymer a potential matrix for colon specific delivery of 5-ASA.

  16. The inhibitory effect of polyvinylphosphonic acid on functional matrix metalloproteinase activities in human demineralized dentin.

    Science.gov (United States)

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

    2010-10-01

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

  17. Fluorometric quantification of polyphosphate in environmental plankton samples: extraction protocols, matrix effects, and nucleic acid interference.

    Science.gov (United States)

    Martin, Patrick; Van Mooy, Benjamin A S

    2013-01-01

    Polyphosphate (polyP) is a ubiquitous biochemical with many cellular functions and comprises an important environmental phosphorus pool. However, methodological challenges have hampered routine quantification of polyP in environmental samples. We tested 15 protocols to extract inorganic polyphosphate from natural marine samples and cultured cyanobacteria for fluorometric quantification with 4',6-diamidino-2-phenylindole (DAPI) without prior purification. A combination of brief boiling and digestion with proteinase K was superior to all other protocols, including other enzymatic digestions and neutral or alkaline leaches. However, three successive extractions were required to extract all polyP. Standard addition revealed matrix effects that differed between sample types, causing polyP to be over- or underestimated by up to 50% in the samples tested here. Although previous studies judged that the presence of DNA would not complicate fluorometric quantification of polyP with DAPI, we show that RNA can cause significant interference at the wavelengths used to measure polyP. Importantly, treating samples with DNase and RNase before proteinase K digestion reduced fluorescence by up to 57%. We measured particulate polyP along a North Pacific coastal-to-open ocean transect and show that particulate polyP concentrations increased toward the open ocean. While our final method is optimized for marine particulate matter, different environmental sample types may need to be assessed for matrix effects, extraction efficiency, and nucleic acid interference.

  18. Cytocompatibility of novel extracellular matrix protein analogs of biodegradable polyester polymers derived from α-hydroxy amino acids.

    Science.gov (United States)

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

    2014-01-01

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

  19. Continuous propionic acid production with Propionibacterium acidipropionici immobilized in a novel xylan hydrogel matrix.

    Science.gov (United States)

    Wallenius, Janne; Pahimanolis, Nikolaos; Zoppe, Justin; Kilpeläinen, Petri; Master, Emma; Ilvesniemi, Hannu; Seppälä, Jukka; Eerikäinen, Tero; Ojamo, Heikki

    2015-12-01

    The cell immobilization potential of a novel xylan based disulfide-crosslinked hydrogel matrix reinforced with cellulose nanocrystals was studied with continuous cultivation of Propionibacterium acidipropionici using various dilution rates. The cells were immobilized to hydrogel beads suspended freely in the fermentation broth or else packed into a column connected to a stirred tank reactor. The maximum propionic acid productivity for the combined stirred tank and column was 0.88gL(-1)h(-1) and the maximum productivity for the column was determined to be 1.39gL(-1)h(-1). The maximum propionic acid titer for the combined system was 13.9gL(-1) with a dilution rate of 0.06h(-1). Dry cell density of 99.7gL(-1) was obtained within the column packed with hydrogel beads and productivity of 1.02gL(-1)h(-1) was maintained in the column even with the high circulation rate of 3.37h(-1).

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

    Directory of Open Access Journals (Sweden)

    Alexandre Chlenski

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

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

    Directory of Open Access Journals (Sweden)

    Majeed Ullah

    2015-01-01

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

  2. Characterizing the release of different composition of dissolved organic matter in soil under acid rain leaching using three-dimensional excitation-emission matrix spectroscopy.

    Science.gov (United States)

    Liu, Li; Song, Cunyi; Yan, Zengguang; Li, Fasheng

    2009-09-01

    Although excitation-emission matrix spectroscopy (EEMS) has been widely used to characterize dissolved organic matter (DOM), there has no report that EEMS has been used to study the effects of acid rain on DOM and its composition in soil. In this work, we employed three-dimensional EEMS to characterize the compositions of DOM leached by simulated acid rain from red soil. The red soil was subjected to leaching of simulated acid rain of different acidity, and the leached DOM presented five main peaks in its EEMS: peak-A, related to humic acid-like (HA-like) material, at Ex/Em of 310-330/395-420nm; peak-B, related to UV fulvic acid-like (FA-like) material, at Ex/Em of 230-280/400-435nm; peak-C and peak-D, both related to microbial byproduct-like material, at Ex/Em of 250-280/335-355nm and 260-280/290-320nm, respectively; and peak-E, related to simple aromatic proteins, at Ex/Em of 210-240/290-340nm. EEMS analysis results indicated that most DOM could be lost from red soil in the early phase of acid rain leaching. In addition to the effects of the pH of acid rain, the loss of DOM also depended on the properties of its compositions and the solubility of their complexes with aluminum. HA-like and microbial byproduct-like materials could be more easily released from red soil by acid rain at both higher pH (4.5 and 5.6) and lower pH (2.5 and 3) than that at middle pH (3.5). On the contrary, FA-like material lost in a similar manner under the action of different acid rains with pH ranging from 2.5 to 5.6.

  3. Striking similarities are exhibited by two small Epstein-Barr virus-encoded ribonucleic acids and the adenovirus-associated ribonucleic acids VAI and VAII

    Energy Technology Data Exchange (ETDEWEB)

    Rosa, M.D.; Gottlieb, E.; Lerner, M.R.; Steitz, J.A.

    1981-09-01

    The nucleotide sequence of the region of the Epstein-Barr virus genome that specified two small ribonucleic acids (RNAs), EBER 1 and EBER 2, has been determined. Both of these RNAs are encoded by the right-hand 1,000 base pairs of the EcoRI J fragment of EBV deoxyribonucleic acid. EBER 1 is 166 (167) nucleotides long and EBER 2 is 172 +- 1 nucleotides long; the heterogeneity resides at the 3' termini. The EBER genes are separated by 161 base pairs and are transcribed from the same deoxyribonucleic acid strand. In vitro, both EBER genes can be transcribed by RNA polymerase III; sequences homologous to previously identified RNA polymerase III intragenic transcription control regions are present. Striking similarities are therefore apparent both between the EBERs and the two adenovirus-associated RNAs, VAI and VAII, and between the regions of the two viral genomes that specify these small RNAs. We have shown that VAII RNA as well as VAI RNA and the EBERs exist in ribonucleoprotein complexes which are precipitable by anti-La antibodies associated with systemic lupus erythematosus. Finally the authors have demonstrated that the binding of protein(s) from uninfected cells confers antigenicity on each of the four virus-encoded small RNAs.

  4. Similarity of the yellow chromophores isolated from human cataracts with those from ascorbic acid-modified calf lens proteins: evidence for ascorbic acid glycation during cataract formation.

    Science.gov (United States)

    Cheng, R; Lin, B; Lee, K W; Ortwerth, B J

    2001-07-27

    Chromatographic evidence supporting the similarity of the yellow chromophores isolated from aged human and brunescent cataract lenses and calf lens proteins ascorbylated in vitro is presented. The water-insoluble fraction from early stage brunescent cataract lenses was solubilized by sonication (WISS) and digested with a battery of proteolytic enzymes under argon to prevent oxidation. Also, calf lens proteins were incubated with ascorbic acid for 4 weeks in air and submitted to the same digestion. The percent hydrolysis of the proteins to amino acids was approximately 90% in every case. The content of yellow chromophores was 90, 130 and 250 A(330) units/g protein for normal human WISS, cataract WISS and ascorbate-modified bovine lens proteins respectively. Aliquots equivalent to 2.0 g of digested protein were subjected to size-exclusion chromatography on a Bio-Gel P-2 column. Six peaks were obtained for both preparations and pooled. Side by side thin-layer chromatography (TLC) of each peak showed very similar R(f) values for the long wavelength-absorbing fluorophores. Glycation with [U-(14)C]ascorbic acid, followed by digestion and Bio-Gel P-2 chromatography, showed that the incorporated radioactivity co-eluted with the A(330)-absorbing peaks, and that most of the fluorescent bands were labeled after TLC. Peaks 2 and 3 from the P-2 were further fractionated by preparative Prodigy C-18 reversed-phase high-performance liquid chromatography. Two major A(330)-absorbing peaks were seen in peak 2 isolated from human cataract lenses and 5 peaks in fraction 3, all of which eluted at the same retention times as those from ascorbic acid glycated calf lens proteins. HPLC fractionation of P-2 peaks 4, 5 and 6 showed many A(330)-absorbing peaks from the cataract WISS, only some of which were identical to the asorbylated proteins. The major fluorophores, however, were present in both preparations. These data provide new evidence to support the hypothesis that the yellow

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

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    Baohong Jiang

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

  6. Salvianolic Acid A, a Novel Matrix Metalloproteinase-9 Inhibitor, Prevents Cardiac Remodeling in Spontaneously Hypertensive Rats

    Science.gov (United States)

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

    2013-01-01

    Cardiac fibrosis is a deleterious consequence of hypertension which may further advance to heart failure and increased matrix metalloproteinase-9 (MMP-9) contributes to the underlying mechanism. Therefore, new therapeutic strategies to attenuate the effects of MMP-9 are urgently needed. In the present study, we characterize salvianolic acid A (SalA) as a novel MMP-9 inhibitor at molecular, cellular and animal level. We expressed a truncated form of MMP-9 which contains only the catalytic domain (MMP-9 CD), and used this active protein for enzymatic kinetic analysis and Biacore detection. Data generated from these assays indicated that SalA functioned as the strongest competitive inhibitor of MMP-9 among 7 phenolic acids from Salvia miltiorrhiza. In neonatal cardiac fibroblast, SalA inhibited fibroblast migration, blocked myofibroblast transformation, inhibited secretion of intercellular adhesion molecule (ICAM), interleukin-6 (IL-6) and soluble vascular cell adhesion molecule-1 (sVCAM-1) as well as collagen induced by MMP-9 CD. Functional effects of SalA inhibition on MMP-9 was further confirmed in cultured cardiac H9c2 cell overexpressing MMP-9 in vitro and in heart of spontaneously hypertensive rats (SHR) in vivo. Moreover, SalA treatment in SHR resulted in decreased heart fibrosis and attenuated heart hypertrophy. These results indicated that SalA is a novel inhibitor of MMP-9, thus playing an inhibitory role in hypertensive fibrosis. Further studies to develop SalA and its analogues for their potential clinical application of cardioprotection are warranted. PMID:23533637

  7. Hydrophobic silica nanoparticles as reinforcing filler for poly (lactic acid polymer matrix

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    Pilić Branka M.

    2016-01-01

    Full Text Available Properties of poly (lactic acid (PLA and its nanocomposites, with silica nanoparticles (SiO2, as filler were investigated. Neat PLA films and PLA films with different percentage of hydrophobic fumed silica nanoparticles (0.2, 0.5, 1, 2, 3 and 5 wt. % were prepared by solution casting method. Several tools were used to characterize the influence of different silica content on crystalline behavior, and thermal, mechanical and barrier properties of PLA/SiO2 nanocomposites. Results from scanning electron microscope (SEM showed that the nanocomposite preparation and selection of specific hydrophobic spherical nano filler provide a good dispersion of the silica nanoparticles in the PLA matrix. Addition of silica nanoparticles improved mechanical properties, the most significant improvement being observed for lowest silica content (0.2wt.%. Barrier properties were improved for all measured gases at all loadings of silica nanoparticles. The degree of crystallinity for PLA slightly increased by adding 0.2 and 0.5 wt. % of nano filler. [Projekat Ministarstva nauke Republike Srbije, br. III46001

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

    Institute of Scientific and Technical Information of China (English)

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

    Science.gov (United States)

    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...

  10. A rapid food screener ranks potential renal acid load of renal stone formers similarly to a diet history questionnaire.

    Science.gov (United States)

    Trinchieri, Alberto

    2013-02-01

    Dietary acid load was reported to be inversely related to urinary citrate excretion. The calcium renal stone formers (RSFs) should be recommended to lower their dietary potential renal acid load (PRAL) to reduce stone recurrence. Reduction of dietary PRAL also showed a promising role for the prevention of other metabolic diseases. However, clinicians often fail to provide nutritional screening and counseling due to lack of simple tools to obtain a reliable dietary history. A one-page food screener (LAKE score) was recently designed to obtain a reliable measure of dietary PRAL in short time. We report the testing of such an instrument in the evaluation of PRAL: in a population of 135 healthy subjects (60 males, 75 females; age range 18-73), living in the area of Milan, Italy. Each participant received both the one-page LAKE food screener and an extensive 24-h dietary questionnaire. We examined agreement between the LAKE food screener scores, and estimates of PRAL and other nutrients produced by the computerized processing of thorough 24-h dietary histories. Spearman rank order correlation coefficient (r > 0.50) showed that LAKE score ranked subjects quite well with respect to dietary PRAL. LAKE positive subscore ranked patients with respect to dietary intake of total protein (r = 0.642) and phosphate (r = 0.648). We also obtained an excellent correlation of LAKE negative subscore with potassium intake (r = -0.531) and vitamin C (r = -0.554) as estimated by 24 h recalls. The LAKE score ranked patients similar to the estimates of 24-h dietary recalls, used as the "gold standard" for the evaluation of dietary PRAL. This rapid, simple and inexpensive food screener for the evaluation of dietary PRAL could provide a "snapshot" of the diet of the RSFs to allow an immediate feedback to the patient during office consultation.

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

    Directory of Open Access Journals (Sweden)

    Florence Braun

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

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

    Science.gov (United States)

    Braun, Florence; Hamelin, Jérôme; Bonnafous, Anaïs; Delgenès, Nadine; Steyer, Jean-Philippe; Patureau, Dominique

    2015-01-01

    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 that PAH removal

  13. Effects of ultraviolet irradiation on bonding strength between Co-Cr alloy and citric acid-crosslinked gelatin matrix.

    Science.gov (United States)

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

    2014-02-01

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

  14. Effect of Phosphoric Acid on the Degradation of Human Dentin Matrix

    Science.gov (United States)

    Tezvergil-Mutluay, A.; Mutluay, M.; Seseogullari-Dirihan, R.; Agee, K.A.; Key, W.O.; Scheffel, D.L.S.; Breschi, L.; Mazzoni, A.; Tjäderhane, L.; Nishitani, Y.; Tay, F.R.; Pashley, D.H.

    2013-01-01

    This study determined if dentin proteases are denatured by phosphoric acid (PA) used in etch-and-rinse dentin adhesives. Dentin beams were completely demineralized with EDTA for 30 days. We “acid-etched” experimental groups by exposing the demineralized dentin beams to 1, 10, or 37 mass% PA for 15 sec or 15 min. Control beams were not exposed to PA but were incubated in simulated body fluid for 3 days to assay their total endogenous telopeptidase activity, by their ability to solubilize C-terminal crosslinked telopeptides ICTP and CTX from insoluble dentin collagen. Control beams released 6.1 ± 0.8 ng ICTP and 0.6 ± 0.1 ng CTX/mg dry-wt/3 days. Positive control beams pre-incubated in p-aminophenylmercuric acetate, a compound known to activate proMMPs, released about the same amount of ICTP peptides, but released significantly less CTX. Beams immersed in 1, 10, or 37 mass% PA for 15 sec or 15 min released amounts of ICTP and CTX similar to that released by the controls (p > 0.05). Beams incubated in galardin, an MMP inhibitor, or E-64, a cathepsin inhibitor, blocked most of the release of ICTP and CTX, respectively. It is concluded that PA does not denature endogenous MMP and cathepsin activities of dentin matrices. PMID:23103634

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

    Energy Technology Data Exchange (ETDEWEB)

    Cai Ning; Gong Yingxue; Chan, Vincent; Liao Kin [School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 639798 (Singapore); Chian, Kerm Sin [School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore 639798 (Singapore)], E-mail: askliao@ntu.edu.sg

    2008-03-01

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

  16. A novel acidic matrix protein, PfN44, stabilizes magnesium calcite to inhibit the crystallization of aragonite.

    Science.gov (United States)

    Pan, Cong; Fang, Dong; Xu, Guangrui; Liang, Jian; Zhang, Guiyou; Wang, Hongzhong; Xie, Liping; Zhang, Rongqing

    2014-01-31

    Magnesium is widely used to control calcium carbonate deposition in the shell of pearl oysters. Matrix proteins in the shell are responsible for nucleation and growth of calcium carbonate crystals. However, there is no direct evidence supporting a connection between matrix proteins and magnesium. Here, we identified a novel acidic matrix protein named PfN44 that affected aragonite formation in the shell of the pearl oyster Pinctada fucata. Using immunogold labeling assays, we found PfN44 in both the nacreous and prismatic layers. In shell repair, PfN44 was repressed, whereas other matrix proteins were up-regulated. Disturbing the function of PfN44 by RNAi led to the deposition of porous nacreous tablets with overgrowth of crystals in the nacreous layer. By in vitro circular dichroism spectra and fluorescence quenching, we found that PfN44 bound to both calcium and magnesium with a stronger affinity for magnesium. During in vitro calcium carbonate crystallization and calcification of amorphous calcium carbonate, PfN44 regulated the magnesium content of crystalline carbonate polymorphs and stabilized magnesium calcite to inhibit aragonite deposition. Taken together, our results suggested that by stabilizing magnesium calcite to inhibit aragonite deposition, PfN44 participated in P. fucata shell formation. These observations extend our understanding of the connections between matrix proteins and magnesium.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Directory of Open Access Journals (Sweden)

    Hui-Qi Zhou

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

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

    Science.gov (United States)

    Abdelhamid, Hani Nasser; Wu, Hui-Fen

    2013-10-15

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

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

    CERN Document Server

    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 ...

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

    Science.gov (United States)

    Ropo, M.; Blum, V.; Baldauf, C.

    2016-11-01

    We derive structural and binding energy trends for twenty amino acids, their dipeptides, and their interactions with the divalent cations Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+. The underlying data set consists of more than 45,000 first-principles predicted conformers with relative energies up to ~4 eV (~400 kJ/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 C5 or . 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 ions with amino acids and dipeptides. Cd2+ and Hg2+ show the largest binding energies–a potential correlation with their known high acute toxicities. Ca2+ and Pb2+ reveal almost identical binding energies across the entire series of amino acids and dipeptides. This observation validates past indications that ion-mimicry of calcium and lead should play an important role in a toxicological context.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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

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

    Science.gov (United States)

    Zhang, Lichao; Zhao, Xiqiang; Kong, Liang

    2014-08-21

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

  4. Bioavailability of magnesium from inorganic and organic compounds is similar in rats fed a high phytic acid diet.

    Science.gov (United States)

    Bertinato, Jesse; Plouffe, Louise J; Lavergne, Christopher; Ly, Catherine

    2014-01-01

    A large section of the North American population is not meeting recommended intakes for magnesium (Mg). Supplementation and consumption of Mg-fortified foods are ways to increase intake. Currently, information on Mg bioavailability from different compounds and their efficacy in improving Mg status is scant. This study compared the relative ability of inorganic and organic Mg compounds to preserve the Mg status of rats when fed at amounts insufficient to retain optimal Mg status. Male Sprague-Dawley rats (n=12/diet group) were fed one of eight test diets supplemented with phytic acid (5 g/kg diet) and low levels of Mg (155 mg elemental Mg/kg diet) from Mg oxide, Mg sulphate, Mg chloride, Mg citrate, Mg gluconate, Mg orotate, Mg malate or ethylenediaminetetraacetic acid disodium Mg salt for five weeks. Rats were also fed three control diets that did not contain added phytic acid but were supplemented with 500 (NMgO, normal), 155 (LMgO, low) or 80 (DMgO, deficient) mg of Mg per kg diet as Mg oxide. Mg concentrations in femur, serum and urine showed a graded decrease in rats fed the control diets with lower Mg. Mg concentrations did not differ (P≥0.05) between rats fed the different test diets. Addition of phytic acid to the diet did not affect the Mg status of the rats. The results indicate that any differences in the Mg bioavailability of the compounds were small and physiologically irrelevant.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Science.gov (United States)

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

    2016-01-01

    Many studies have examined the application of soil amendments, including pH change-induced immobilizers, adsorbents, and organic materials, for soil remediation. This study evaluated the effects of various amendments on trace element stabilization and phytotoxicity, depending on the initial soil pH in acid, neutral, and alkali conditions. As in all types of soils, Fe and Ca were well stabilized on adsorption sites. There was an effect from pH control or adsorption mechanisms on the stabilization of cationic trace elements from inorganic amendments in acidic and neutral soil. Furthermore, acid mine drainage sludge has shown great potential for stabilizing most trace elements. In a phytotoxicity test, the ratio of the bioavailable fraction to the pseudo-total fraction significantly affected the uptake of trace elements by bok choy. While inorganic amendments efficiently decreased the bioavailability of trace elements, significant effects from organic amendments were not noticeable due to the short-term cultivation period. Therefore, the application of organic amendments for stabilizing trace elements in agricultural soil requires further study. PMID:27835687

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

    Science.gov (United States)

    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.

  8. Conformers of β-aminoisobutyric acid probed by jet-cooled microwave and matrix isolation infrared spectroscopic techniques

    Science.gov (United States)

    Kuş, N.; Sharma, A.; Peña, I.; Bermúdez, M. C.; Cabezas, C.; Alonso, J. L.; Fausto, R.

    2013-04-01

    β-aminoisobutyric acid (BAIBA) has been studied in isolation conditions: in the gas phase and trapped into a cryogenic N2 matrix. A solid sample of the compound was vaporized by laser ablation and investigated through their rotational spectra in a supersonic expansion using two different spectroscopic techniques: broadband chirped pulse Fourier transform microwave spectroscopy and conventional molecular beam Fourier transform microwave spectroscopy. Four conformers with structures of two types could be successfully identified by comparison of the experimental rotational and 14N nuclear quadruple coupling constants with those predicted theoretically: type A, bearing an OH⋯N intramolecular hydrogen bond and its carboxylic group in the trans geometry (H-O-C=O dihedral ˜180°), and type B, having an NH⋯O bond and the cis arrangement of the carboxylic group. These two types of conformers could also be trapped from the gas phase into a cryogenic N2 matrix and probed by Fourier transform infrared (IR) spectroscopy. In situ irradiation of BAIBA isolated in N2 matrix of type B conformers using near-IR radiation tuned at the frequency of the O-H stretching 1st overtone (˜6930 cm-1) of these forms allowed to selectively convert them into type A conformers and into a new type of conformers of higher energy (type D) bearing an NH⋯O=C bond and a O-H "free" trans carboxylic group.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Investigating the use of coupling agents to improve the interfacial properties between a resorbable phosphate glass and polylactic acid matrix.

    Science.gov (United States)

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

    2013-09-01

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

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

    KAUST Repository

    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.

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

    Science.gov (United States)

    Coluccio, Maria Laura; Gentile, Francesco; Das, Gobind; Nicastri, Annalisa; Perri, Angela Mena; Candeloro, Patrizio; Perozziello, Gerardo; Proietti Zaccaria, Remo; Gongora, Juan Sebastian Totero; Alrasheed, Salma; Fratalocchi, Andrea; Limongi, Tania; Cuda, Giovanni; Di Fabrizio, Enzo

    2015-09-01

    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.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

  14. Similarity in microbial amino acid uptake in surface waters of the North and South Atlantic (sub-)tropical gyres

    Science.gov (United States)

    Hill, Polly G.; Mary, Isabelle; Purdie, Duncan A.; Zubkov, Mikhail V.

    2011-12-01

    The Earth’s most extensive biomes - the oceanic subtropical gyres - are considered to be expanding with current surface ocean warming. Although it is well established that microbial communities control gyre biogeochemistry, comparisons of their metabolic activities between gyres are limited. In order to estimate metabolic activities including production of microbial communities, the uptake rates of amino acids leucine, methionine and tyrosine at ambient concentrations were estimated in surface waters of the Atlantic Ocean using radioisotopically labelled tracers. Data were acquired during six research cruises covering main oceanic provinces herein termed: North and South Atlantic Gyres, Bermuda Atlantic Time-series Study site (BATS), Equatorial region, and Mauritanian Upwelling (off Cape Blanc). Data were divided between provinces, the extents of which were identified by ocean colour data, in order to achieve provincial mean uptake rates. Leucine and methionine uptake rates did not differ between sampling periods, and were comparable between the North and South subtropical gyres. Furthermore, variation in uptake rates measured throughout the two oligotrophic gyres, where sampling covered ∼4 × 10 6 km 2, was considerably lower than that measured within the Mauritanian Upwelling and Equatorial regions, and even at the BATS site. Tyrosine was generally the slowest of the amino acids to be taken up, however, it was assimilated faster than methionine within the Mauritanian Upwelling region. Thus, we propose that one value for leucine (12.6 ± 3.2 pmol L -1 h -1) and methionine (10.0 ± 3.3 pmol L -1 h -1) uptake could be applied to the oligotrophic subtropical gyres of the Atlantic Ocean. However, with the significantly lower uptake rates observed at the BATS site, we would not advise extrapolation to the Sargasso Sea.

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

    Science.gov (United States)

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

    2016-10-15

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

  16. Structure of isothiocyanic acid dimers. Theoretical and FTIR matrix isolation studies

    Science.gov (United States)

    Krupa, Justyna; Wierzejewska, Maria

    2016-05-01

    A quantum mechanical study of the potential energy surface for the HNCS dimer is reported. The calculations were performed using DFT and ab initio MP2 methods. The most stable is a cyclic form with a double N-H⋯S interaction and the interaction energy in the range of 16.91-18.92 kJ mol-1. An open HNCS dimer bound by the N-H⋯N hydrogen bond is by ca 3.3-5.1 kJ mol-1 less stable. Experimental FTIR matrix isolation studies of HNCS/N2 system show that exclusively less stable open dimer is formed in solid nitrogen. Possible reasons for the observed discrepancy between theory and experiment are discussed.

  17. Promoting extracellular matrix remodeling via ascorbic acid enhances the survival of primary ovarian follicles encapsulated in alginate hydrogels.

    Science.gov (United States)

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

    2014-07-01

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

  18. Preparation and luminescence properties of europium complex with a-naphthylacetic acid incorporated in silica matrix by sol-gel method

    Institute of Scientific and Technical Information of China (English)

    陈野; 蔡伟民; 孙晓君; 崔丹; 于英宁

    2004-01-01

    Europium ternary complex of Eu (NNA)3(NNA=o-naphthylacetic acid) was embedded in silica matrix at different ratios by sol-gel method. The luminescence properties of silica composites were studied by comparing them with those of corresponding pure complex by means of excitation, emission spectra and lifetimes. The fluorescence lifetime was prolonged when the pure complex was incorporated in silica matrix. The relative fluorescence intensity and fluorescence lifetimes increased simultaneously with the increase of Eu(NNA)3.

  19. Web Similarity

    NARCIS (Netherlands)

    Cohen, A.R.; Vitányi, P.M.B.

    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 fr

  20. Towards Acid-Tolerated Ethanol Dehydration: Chitosan-Based Mixed Matrix Membranes Containing Cyano-Bridged Coordination Polymer Nanoparticles.

    Science.gov (United States)

    Wu, C-W; Kang, Chao-Hsiang; Lin, Yi-Feng; Tung, Kuo-Lun; Deng, Yu-Heng; Ahamad, Tansir; Alshehri, Saad M; Suzuki, Norihiro; Yamauchi, Yusuke

    2016-04-01

    Prussian blue (PB) nanoparticles, one of many cyano-bridged coordination polymers, are successfully incorporated into chitosan (CS) polymer to prepare PB/CS mixed matrix membranes (MMMs). The PB nanoparticles are uniformly distributed in the MMMs without the collapse of the original PB structure. As-prepared PB/CS MMMs are used for ethanol dehydration at 25 °C in the pervaporation process. The effect of loading PB in CS matrix on pervaporation performance is carefully investigated. The PB/CS membrane with 30 wt% PB loading shows the best performance with a permeate flux of 614 g. m-2 . h-1 and a separation factor of 1472. The pervaporation using our PB/CS membranes exhibits outstanding performance in comparison with the previously reported CS-based membranes and MMMs. Furthermore, the addition of PB allows PB/CS MMMs to be tolerant of acidic environment. The present work demonstrates good pervaporation performance of PB/CS MMMs for the separation of an ethanol/water (90:10 in wt%) solution. Our new system provides an opportunity for dehydration of bioethanol in the future.

  1. Similarity Judgment of Product Structure Based on Non negative Matrix Factorization and Its Applications%基于非负矩阵分解的产品结构相似性判断及其应用

    Institute of Scientific and Technical Information of China (English)

    徐新胜; 王诚; 肖颖

    2016-01-01

    为了快速发现可重用产品结构,提出了基于非负矩阵分解的产品结构相似性判断方法。通过将产品结构邻接矩阵转化为邻接向量,构建包含全部结构信息的库矩阵;利用 Multiplicative Updates (MU)算法对库矩阵进行非负矩阵分解,实现以低维空间向量描述的产品结构;在此基础上,通过计算低维向量的欧氏距离,可以判断产品结构之间的相似性;最后通过实例对所提出原理和方法进行了验证,结果表明,该方法比目前的相似性判断方法更高效。%In order to find reusable product structure promptly,an approach of measuring the similarity among product structures was proposed based on non�negative matrix factorization.A comG prehensive matrix which containsed all structures was constructed on the basic of adj acent vectors that were transformed from the adj acent matrices of product structures.The non�negative matrix factorizaG tion for the comprehensive matrix was implemented based on Multiplicative Updates(MU)algorithm. Then all product structures might be described in low dimensional space.On the basis of these,the similarity between two product structures could be measured by calculating the Euclidean distance aG mong these low dimensional vectors.Finally,an example was presented to verify the principles and methods mentioned above.The results show that the proposed methodologies are more effective than those of the existing methods.

  2. PECM: prediction of extracellular matrix proteins using the concept of Chou's pseudo amino acid composition.

    Science.gov (United States)

    Zhang, Jian; Sun, Pingping; Zhao, Xiaowei; Ma, Zhiqiang

    2014-12-21

    The extracellular matrix proteins (ECMs) are widely found in the tissues of multicellular organisms. They consist of various secreted proteins, mainly polysaccharides and glycoproteins. The ECMs involve the exchange of materials and information between resident cells and the external environment. Accurate identification of ECMs is a significant step in understanding the evolution of cancer as well as promises wide range of potential applications in therapeutic targets or diagnostic markers. In this paper, an accurate computational method named PECM is proposed for identifying ECMs. Here, we explore various sequence-derived discriminative features including evolutionary information, predicted secondary structure, and physicochemical properties. Rather than simply combining the features which may bring information redundancy and unwanted noises, we use Fisher-Markov selector and incremental feature selection approach to search the optimal feature subsets. Then, we train our model by the technique of support vector machine (SVM). PECM achieves good prediction performance with the ACC scores about 86% and 90% on testing and independent datasets, which are competitive with the state-of-the-art ECMs prediction tools. A web-server named PECM which implements the proposed approach is freely available at http://59.73.198.144:8088/PECM/.

  3. Matrix effect on serum uric acid determination%血清尿酸测定的基质效应

    Institute of Scientific and Technical Information of China (English)

    张江涛; 王冬环; 张传宝; 曾洁; 马嵘; 赵海舰; 周伟燕; 张天娇; 闫颖; 胡翠华; 汪静

    2016-01-01

    Objective To evaluate the matrix effect of 21 samples (sera and processed materials) on 13 routine determination systems in serum uric acid determination. Methods Determinations were performed according to the health industry standard WS/T356-2011. Isotope dilution liquid chromatography tandem mass spectrometry (ID-LC/MS/MS)was used as comparison method,and 13 kinds of uric acid kits(enzymic assay) were chosen as evaluation method with HITACHI 7180 analyzer. The 21 samples included 4 calibrators,5 kinds of external quality assessment(EQA) samples,6 kinds of quality control materials,3 processed materials (1 kind of spine serum and 2 kinds of liquid solutions),1 kind of standard reference material(SRM) 909c from the National Institute of Standards and Technology (NIST)and 2 kinds of the External Quality Assessment Scheme for Reference Laboratories in Laboratory Medicine (RELA)samples from the International Federation of Clinical Chemistry and Laboratory Medicine(IFCC). A total of 40 fresh frozen sera and the 21 samples were analyzed by comparison method and evaluation method. The results obtained by the 2 methods were analyzed by linear regression analysis. Two-tailed 95% confidence intervals for Y predictive value were computed,and the matrix effect of sera and processed materials was evaluated. Results A total of 5 kinds of evaluation samples (2 EQA samples,1 SRM 909c and 2 RELA samples)from fresh or lyophilized sera showed no matrix effect in all routine methods. Two calibrators (Landau and Dirui) showed matrix effect in 1 routine method. Of 5 EQA samples,except for fresh sera used for trueness verification,other lyophilized sera showed matrix effect in most routine methods. The 4 of 6 quality control materials showed no matrix effect,and 2 quality control materials with high values showed negative matrix effect. Conclusions Fresh serum is a reliable sample and could be used in SRM and quality control material preparation and EQA. Some calibrators could

  4. Enhanced visualization of small peptides absorbed in rat small intestine by phytic-acid-aided matrix-assisted laser desorption/ionization-imaging mass spectrometry.

    Science.gov (United States)

    Hong, Seong-Min; Tanaka, Mitsuru; Yoshii, Saori; Mine, Yoshinori; Matsui, Toshiro

    2013-11-05

    Enhanced visualization of small peptides absorbed through a rat intestinal membrane was achieved by matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-IMS) with the aid of phytic acid as a matrix additive. Penetrants through intestinal peptide transporter 1, i.e., glycyl-sarcosine (Gly-Sar, 147.1 m/z) and antihypertensive dipeptide, Val-Tyr (281.2 m/z), were chosen for MALDI-IMS. The signal-to-noise (S/N) ratios of dipeptides Gly-Sar and Val-Tyr were seen to increase by 2.4- and 8.0-fold, respectively, when using a 2',4',6'-trihydroxyacetophenone (THAP) matrix containing 5.0 mM phytic acid, instead of the THAP matrix alone. Owing to the phytic-acid-aided MALDI-IMS method, Gly-Sar and Val-Tyr absorbed in the rat intestinal membrane were successfully visualized. The proposed imaging method also provided useful information on intestinal peptide absorption; to some extent, Val-Tyr was rapidly hydrolyzed to Tyr by peptidases located at the intestinal microvillus during the absorption process. In conclusion, the strongly acidic additive, phytic acid, is beneficial for enhancing the visualization of small peptides using MALDI-IMS, owing to the suppression of ionization-interfering salts in the tissue.

  5. Fluorescence Properties of Eu3+/Gd3+/Citric Acid Mixed Complexes Doping in Silicon Rubber Matrix

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Series of doped rare earth complexes-EuxGd(1-x)(CA)3·nH2O (CA=citric acid) were synthesized. Some characterizations were taken for these complexes. The experimental results shows that the doped rare earth complexes have the best fluorescence property when the ratio of Eu and Gd is from 0.7 to 0.3. Silicon rubber-based composites were prepared by mechanical blending the EuxGd(1-x)(CA)3·nH2O and silicon rubber. Then, the fluorescent property of the composites was studied. It is found that the fluorescence intensity of the composites increase linearly with the contents of the rare earth complexes increasing.

  6. The effectiveness of matrix cauterization with trichloroacetic acid in the treatment of ingrown toenails.

    Science.gov (United States)

    Terzi, Erdinc; Guvenc, Ulas; Türsen, Belma; Kaya, Tamer İrfan; Erdem, Teoman; Türsen, Ümit

    2015-01-01

    Ingrown toenail is an often painful clinical condition that usually affects the big toe. Chemical matricectomy with phenol has a low recurrence rate and good cosmetic results. However, it produces extensive tissue destruction that can result in drainage and delayed healing. Alternatives such as sodium hydroxide and trichloroacetic acid (TCA) have therefore come into vogue. A total of 39 patients with 56 ingrown toenail edges underwent chemical matricectomy with 90% TCA after partial nail avulsion. In most of the patients, adverse effects such as postoperative pain and drainage were minimal. One patient who underwent matricectomy had recurrence in a single nail edge (1.8%) at 12 months follow-up. No recurrence was observed among 38 patients during the mean follow-up period. This was considered to be statistically significant (P < 0.001). Partial nail avulsion followed by TCA matricectomy is a safe, simple, and effective method with low rates of postoperative morbidity and high rates of success.

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

    Energy Technology Data Exchange (ETDEWEB)

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

  8. Inositol phosphates compete with nucleic acids for binding to bovine leukemia virus matrix protein: implications for deltaretroviral assembly.

    Science.gov (United States)

    Qualley, Dominic F; Lackey, Crystal M; Paterson, Justin P

    2013-08-01

    The matrix (MA) domain of retroviral Gag proteins plays a crucial role in virion assembly. In human immunodeficiency virus type 1 (HIV-1), a lentivirus, the presence of phosphatidylinositol-(4,5)-bisphosphate triggers a conformational change allowing the MA domain to bind the plasma membrane (PM). In this study, the MA protein from bovine leukemia virus (BLV) was used to investigate the mechanism of viral Gag binding to the membrane during replication of a deltaretrovirus. Fluorescence spectroscopy was used to measure the binding affinity of MA for two RNA constructs derived from the BLV genome as well as for single-stranded DNA (ssDNA). The importance of electrostatic interactions and the ability of inositol hexakisphosphate (IP6) to compete with nucleic acids for binding to MA were also investigated. Our data show that IP6 effectively competes with RNA and DNA for BLV MA binding, while [NaCl] of greater than 100 mM is required to produce any observable effect on DNA-MA binding. These results suggest that BLV assembly may be highly dependent on the specific interaction of the MA domain with components of the PM, as observed previously with HIV-1. The mode of MA binding to nucleic acids and the implications for BLV assembly are discussed.

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

    Directory of Open Access Journals (Sweden)

    Kühne U

    2016-10-01

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

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

    Directory of Open Access Journals (Sweden)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-01

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

  12. The effectiveness of matrix cauterization with trichloroacetic acid in the treatment of ingrown toenails

    Directory of Open Access Journals (Sweden)

    Erdinc Terzi

    2015-01-01

    Full Text Available Ingrown toenail is an often painful clinical condition that usually affects the big toe. Chemical matricectomy with phenol has a low recurrence rate and good cosmetic results. However, it produces extensive tissue destruction that can result in drainage and delayed healing. Alternatives such as sodium hydroxide and trichloroacetic acid (TCA have therefore come into vogue. A total of 39 patients with 56 ingrown toenail edges underwent chemical matricectomy with 90% TCA after partial nail avulsion. In most of the patients, adverse effects such as postoperative pain and drainage were minimal. One patient who underwent matricectomy had recurrence in a single nail edge (1.8% at 12 months follow-up. No recurrence was observed among 38 patients during the mean follow-up period. This was considered to be statistically significant (P < 0.001. Partial nail avulsion followed by TCA matricectomy is a safe, simple, and effective method with low rates of postoperative morbidity and high rates of success.

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

    Science.gov (United States)

    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.

  14. Docosahexaenoic acid suppresses breast cancer cell metastasis by targeting matrix-metalloproteinases

    Science.gov (United States)

    Shin, Soyeon; Kim, Soyeon; Heo, Jun-Young; Kweon, Gi-Ryang; Wu, Tong; Park, Jong-Il; Lim, Kyu

    2016-01-01

    Breast cancer is one of the most prevalent cancers in women, and nearly half of breast cancer patients develop distant metastatic disease after therapy. Despite the significant advances that have been achieved in understanding breast cancer metastasis in the past decades, metastatic cancer is still hard to cure. Here, we demonstrated an anti-cancer mechanism of docosahexaenoic acid (DHA) that suppressed lung metastasis in breast cancer. DHA could inhibit proliferation and invasion of breast cancer cells in vitro, and this was mainly through blocking Cox-2-PGE2-NF-κB-MMPs cascades. DHA treatment significantly decreased Cox-2 and NF-κB expression as well as nuclear translocation of NF-κB in MDA-MB-231 cells. In addition, DHA also reduced NF-κB binding to DNA which may lead to inactivation of MMPs. Moreover, in vivo studies using Fat-1 transgenic mice showed remarkable decrease of tumor growth and metastasis to EO771 cells to lung in DHA-rich environment. In conclusion, DHA attenuated breast cancer progression and lung metastasis in part through suppressing MMPs, and these findings suggest chemoprevention and potential therapeutic strategy to overcome malignant breast cancer. PMID:27363023

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

    OpenAIRE

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

    2016-01-01

    Granules with release-sustaining properties were developed by twin screw hot melt granulation (HMG) using a combination of stearic acid (SA) and high molecular weight polyethylene oxide (PEO) as matrix for a highly water soluble model drug, metoprolol tartrate (MPT). Earlier studies demonstrated that mixing molten SA and PEO resulted in hydrogen bond formation between hydroxyl groups of fatty acid molecules and ether groups in PEO chains. These molecular interactions might be beneficial in or...

  16. Delivery of a foreign epitope by sharing amino acid residues with the carrier matrix.

    Science.gov (United States)

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

    2009-06-01

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

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

    Science.gov (United States)

    Kühne, Ulrich; Esmann, Jørgen; von Heimburg, Dennis; Imhof, Matthias; Weissenberger, Petra; Sattler, Gerhard

    2016-01-01

    Cohesive polydensified matrix (CPM®) hyaluronic acid fillers are now available with or without lidocaine. The aim of this study was to investigate the safety and performance of CPM® fillers with lidocaine in the clinical setting. In an open-label, prospective, postmarketing study, 108 patients from seven sites in Germany and Denmark were treated with one or more lidocaine-containing CPM® fillers. Performance was assessed using the Merz Aesthetics Scales® (MAS). Pain was rated on an 11-point visual analog scale. Patients’ and physicians’ satisfaction as well as adverse events were recorded. Improvements of ≥1-point on MAS immediately after and 17 days posttreatment were observed in ~90% of patients compared with baseline. All investigators assessed ejection force, product positioning, and performance as similar or superior to the respective nonlidocaine products. Overall, 94% of investigators were satisfied with the esthetic outcomes and were willing to continue using the products. All patients except one were satisfied with the results, and all were willing to repeat the treatment. Mean pain scores were low during (<3.0) and after injection (<0.6). Except for one case of bruising, all adverse events were mild to moderate. CPM® fillers with lidocaine are safe and effective for a wide range of esthetic facial indications. PMID:27799807

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

    Directory of Open Access Journals (Sweden)

    Zhenya Gao

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

  19. Thimet oligopeptidase: similarity to 'soluble angiotensin II-binding protein' and some corrections to the published amino acid sequence of the rat testis enzyme.

    Science.gov (United States)

    McKie, N; Dando, P M; Rawlings, N D; Barrett, A J

    1993-01-01

    The deduced amino acid sequence of pig liver soluble angiotensin II-binding protein [Sugiura, Hagiwara and Hirose (1992) J. Biol. Chem. 267, 18067-18072] is similar over most of its length to that reported for rat testis thimet oligopeptidase (EC 3.4.24.15) by Pierotti, Dong, Glucksman, Orlowski and Roberts [(1990) (Biochemistry 29, 10323-10329]. We have found that homogeneous rat testis thimet oligopeptidase binds angiotensin II with the same distinctive characteristics as the pig liver protein. Analysis of the nucleotide sequences reported for the two proteins pointed to the likelihood that sequencing errors had caused two segments of the amino acid sequence of the rat protein to be translated out of frame, and re-sequencing of selected parts of the clone (kindly provided by the previous authors) confirmed this. The revised deduced amino acid sequence of rat thimet oligopeptidase contains 687 residues, representing a protein of 78,308 Da, and is more closely related to those of the pig liver protein and other known homologues of thimet oligopeptidase than that described previously. Images Figure 1 PMID:8216239

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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)

  1. Similarity Scaling

    Science.gov (United States)

    Schnack, Dalton D.

    In Lecture 10, we introduced a non-dimensional parameter called the Lundquist number, denoted by S. This is just one of many non-dimensional parameters that can appear in the formulations of both hydrodynamics and MHD. These generally express the ratio of the time scale associated with some dissipative process to the time scale associated with either wave propagation or transport by flow. These are important because they define regions in parameter space that separate flows with different physical characteristics. All flows that have the same non-dimensional parameters behave in the same way. This property is called similarity scaling.

  2. Populations of carbonic acid isomers at 210 K from a fast two-electron reduced-density matrix theory.

    Science.gov (United States)

    Schwerdtfeger, Christine A; Mazziotti, David A

    2011-11-03

    Parametrization of the 2-electron reduced density matrix (2-RDM) rather than the many-electron wave function yields a new family of electronic-structure methods that are faster and more accurate than traditional coupled electron-pair methods including coupled cluster with single and double excitations. Deriving the parametrization from N-representability conditions generates a 2-RDM that captures significant correlation from triple and higher-order excitations at the cost of double excitations. We apply the parametric 2-RDM method to confirm recent experiments determining the relative thermodynamic populations of the cis-cis and cis-trans isomers of carbonic acid. In 2010 Bernard et al. showed by infrared spectroscopy that the populations of cis-cis and cis-trans isomers have a 10:1 ratio at 210 K. By use of the parametric 2-RDM method, we predict a 8:1 ratio at 210 K. Comparable ab initio methods overestimate the stability of the cis-cis isomer with 24:1 and 21:1 ratios. These 2-RDM-based methods promise to have significant applications throughout chemistry.

  3. Stiffness of hyaluronic acid gels containing liver extracellular matrix supports human hepatocyte function and alters cell morphology.

    Science.gov (United States)

    Deegan, Daniel B; Zimmerman, Cynthia; Skardal, Aleksander; Atala, Anthony; Shupe, Thomas D

    2015-03-01

    Tissue engineering and cell based liver therapies have utilized primary hepatocytes with limited success due to the failure of hepatocytes to maintain their phenotype in vitro. In order to overcome this challenge, hyaluronic acid (HA) cell culture substrates were formulated to closely mimic the composition and stiffness of the normal liver cellular microenvironment. The stiffness of the substrate was modulated by adjusting HA hydrogel crosslinking. Additionally, the repertoire of bioactive molecules within the HA substrate was bolstered by supplementation with normal liver extracellular matrix (ECM). Primary human hepatocyte viability and phenotype were determined over a narrow physiologically relevant range of substrate stiffnesses from 600 to 4600Pa in both the presence and absence of liver ECM. Cell attachment, viability, and organization of the actin cytoskeleton improved with increased stiffness up to 4600Pa. These differences were not evident in earlier time points or substrates containing only HA. However, gene expression for the hepatocyte markers hepatocyte nuclear factor 4 alpha (HNF4α) and albumin significantly decreased on the 4600Pa stiffness at day 7 indicating that cells may not have maintained their phenotype long-term at this stiffness. Function, as measured by albumin secretion, varied with both stiffness and time in culture and peaked at day 7 at the 1200Pa stiffness, slightly below the stiffness of normal liver ECM at 3000Pa. Overall, gel stiffness affected primary human hepatocyte cell adhesion, functional marker expression, and morphological characteristics dependent on both the presence of liver ECM in gel substrates and time in culture.

  4. Matrix Thermalization

    CERN Document Server

    Craps, Ben; Nguyen, Kévin

    2016-01-01

    Matrix quantum mechanics offers an attractive environment for discussing gravitational holography, in which both sides of the holographic duality are well-defined. Similarly to higher-dimensional implementations of holography, collapsing shell solutions in the gravitational bulk correspond in this setting to thermalization processes in the dual quantum mechanical theory. We construct an explicit, fully nonlinear supergravity solution describing a generic collapsing dilaton shell, specify the holographic renormalization prescriptions necessary for computing the relevant boundary observables, and apply them to evaluating thermalizing two-point correlation functions in the dual matrix theory.

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

    Directory of Open Access Journals (Sweden)

    Delplanque Bernadette

    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.

  6. Salvianolic acid B functioned as a competitive inhibitor of matrix metalloproteinase-9 and efficiently prevented cardiac remodeling

    Science.gov (United States)

    2010-01-01

    Background Infarct-induced left ventricular (LV) remodeling is a deleterious consequence after acute myocardial infarction (MI) which may further advance to congestive heart failure. Therefore, new therapeutic strategies to attenuate the effects of LV remodeling are urgently needed. Salvianolic acid B (SalB) from Salviae mitiorrhizae, which has been widely used in China for the treatment of cardiovascular diseases, is a potential candidate for therapeutic intervention of LV remodeling targeting matrix metalloproteinase-9 (MMP-9). Results Molecular modeling and LIGPLOT analysis revealed in silico docking of SalB at the catalytic site of MMP-9. Following this lead, we expressed truncated MMP-9 which contains only the catalytic domain, and used this active protein for in-gel gelatin zymography, enzymatic analysis, and SalB binding by Biacore. Data generated from these assays indicated that SalB functioned as a competitive inhibitor of MMP-9. In our rat model for cardiac remodeling, western blot, echocardiography, hemodynamic measurement and histopathological detection were used to detect the effects and mechanism of SalB on cardio-protection. Our results showed that in MI rat, SalB selectively inhibited MMP-9 activities without affecting MMP-9 expression while no effect of SalB was seen on MMP-2. Moreover, SalB treatment in MI rat could efficiently increase left ventricle wall thickness, improve heart contractility, and decrease heart fibrosis. Conclusions As a competitive inhibitor of MMP-9, SalB presents significant effects on preventing LV structural damage and preserving cardiac function. Further studies to develop SalB and its analogues for their potential for cardioprotection in clinic are warranted. PMID:20735854

  7. Rock specific hydraulic fracturing and matrix acidizing to enhance a geothermal system — Concepts and field results

    Science.gov (United States)

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

    2011-04-01

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

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

    OpenAIRE

    Chaturvedi M.; Molino Y; Sreedhar B; Khrestchatisky M; Kaczmarek L

    2014-01-01

    Mayank Chaturvedi,1 Yves Molino,2 Bojja Sreedhar,3 Michel Khrestchatisky,4 Leszek Kaczmarek1 1Laboratory of Neurobiology, Nencki Institute, Warsaw, Poland; 2Vect-Horus, Marseille, France; 3Indian Institute of Chemical Technology, Hyderabad, India; 4Aix-Marseille Université, CNRS, NICN, UMR7259, Marseille, France Aim: The aim of this study was to develop poly(lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) for delivery of a protein – tissue inhibitor of matrix metallo...

  9. Matrix-elimination with steam distillation for determination of short-chain fatty acids in hypersaline waters from pre-salt layer by ion-exclusion chromatography.

    Science.gov (United States)

    Ferreira, Fernanda N; Carneiro, Manuel C; Vaitsman, Delmo S; Pontes, Fernanda V M; Monteiro, Maria Inês C; Silva, Lílian Irene D da; Neto, Arnaldo Alcover

    2012-02-03

    A method for determination of formic, acetic, propionic and butyric acids in hypersaline waters by ion-exclusion chromatography (IEC), using steam distillation to eliminate matrix-interference, was developed. The steam distillation variables such as type of solution to collect the distillate, distillation time and volume of the 50% v/v H₂SO₄ solution were optimized. The effect of the addition of NaCl different concentrations to the calibration standards on the carboxylic acid recovery was also investigated. Detection limits of 0.2, 0.5, 0.3 and 1.5 mg L⁻¹ were obtained for formic, acetic, propionic and butyric acids, respectively. Produced waters from petroleum reservoirs in the Brazilian pre-salt layer containing about 19% m/v of NaCl were analyzed. Good recoveries (99-108%) were obtained for all acids in spiked produced water samples.

  10. Interactions between cadmium and lead with acidic soils: Experimental evidence of similar adsorption patterns for a wide range of metal concentrations and the implications of metal migration

    Energy Technology Data Exchange (ETDEWEB)

    Pokrovsky, O.S. [GET-CNRS-UPS-IRD-UMR 5563, 14, Avenue Edouard Belin, 31400 Toulouse (France); Probst, A., E-mail: anne.probst@ensat.fr [Universite de Toulouse, INPT, UPS, EcoLab (Laboratoire Ecologie fonctionnelle et Environnement), ENSAT, Avenue de l' Agrobiopole, 31326 Castanet-Tolosan (France); CNRS, EcoLab, 31326 Castanet-Tolosan (France); Leviel, E. [GET-CNRS-UPS-IRD-UMR 5563, 14, Avenue Edouard Belin, 31400 Toulouse (France); Liao, B. [International College, Central South University of Forestry and Technology, Changsha 410004 (China)

    2012-01-15

    Highlights: Black-Right-Pointing-Pointer Adsorption experiments of Cd and Pb in acid soils (China, France). Black-Right-Pointing-Pointer Large pH conditions and large range of metal concentrations were considered. Black-Right-Pointing-Pointer Similar dependencies between metals concentration in solution and metal adsorbed on the surface were predicted using Langmuir and Freundlich equations and surface complexation model (SCM). Black-Right-Pointing-Pointer No competition between Cd and Pb detected at pH 5. Black-Right-Pointing-Pointer Metal adsorption capacity is two orders of magnitude higher than limit value for soil protection. - Abstract: The importance of high- and low-affinity surface sites for cadmium and lead adsorption in typical European and Asian soils was investigated. Adsorption experiments on surface and deep horizons of acidic brown (Vosges, France) and red loess soils (Hunan, China) were performed at 25 Degree-Sign C as a function of the pH (3.5-8) and a large range of metal concentrations in solution (10{sup -9}-10{sup -4} mol l{sup -1}). We studied the adsorption kinetics using a Cd{sup 2+}-selective electrode and desorption experiments as a function of the solid/solution ratio and pH. At a constant solution pH, all samples exhibited similar maximal adsorption capacities (4.0 {+-} 0.5 {mu}mol/g Cd and 20 {+-} 2 {mu}mol/g Pb). A constant slope of adsorbed-dissolved concentration dependence was valid over 5 orders of magnitude of metal concentrations. Universal Langmuir and Freundlich equations and the SCM formalism described the adsorption isotherms and the pH-dependent adsorption edge over very broad ranges of metal concentrations, indicating no high- or low-affinity sites for metal binding at the soil surface under these experimental conditions. At pH 5, Cd and Pb did not compete, in accordance with the SCM. The metal adsorption ability exceeded the value for soil protection by two orders of magnitude, but only critical load guarantees soil

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

    Science.gov (United States)

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

    2009-02-01

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

  12. Determination of the fatty acid composition of saponified vegetable oils using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

    Science.gov (United States)

    Ayorinde, F O; Garvin, K; Saeed, K

    2000-01-01

    A method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) for the determination of the fatty acid composition of vegetable oils is described and illustrated with the analysis of palm kernel oil, palm oil, olive oil, canola oil, soybean oil, vernonia oil, and castor oil. Solutions of the saponified oils, mixed with the matrix, meso-tetrakis(pentafluorophenyl)porphyrin, provided reproducible MALDI-TOF spectra in which the ions were dominated by sodiated sodium carboxylates [RCOONa + Na]+. Thus, palm kernel oil was found to contain capric acid, lauric acid, myristic acid, palmitic acid, oleic acid, and stearic acid. Palm oil had a fatty acid profile including palmitic, linoleic, oleic, and stearic. The relative percentages of the fatty acids in olive oil were palmitoleic (1.2 +/- 0.5), palmitic (10.9 +/- 0.8), linoleic (0.6 +/- 0.1), linoleic (16.5 +/- 0.8), and oleic (70.5 +/- 1.2). For soybean oil, the relative percentages were: palmitoleic (0.4 +/- 0.4), palmitic (6.0 +/- 1.3), linolenic (14.5 +/- 1.8), linoleic (50.1 +/- 4.0), oleic (26.1 +/- 1.2), and stearic (2.2 +/- 0.7). This method was also applied to the analysis of two commercial soap formulations. The first soap gave a fatty acid profile that included: lauric (19.4% +/- 0.8), myristic (9.6% +/- 0.5), palmitoleic (1.9% +/- 0.3), palmitic (16.3% +/- 0.9), linoleic (5.6% +/- 0.4), oleic (37.1% +/- 0.8), and stearic (10.1% +/- 0.7) and that of the second soap was: lauric (9.3% +/- 0.3), myristic (3.8% +/- 0.5), palmitoleic (3.1% +/- 0.8), palmitic (19.4% +/- 0.8), linoleic (4.9% +/- 0.7), oleic (49.5% +/- 1.1), and stearic (10.0% +/- 0.9). The MALDI-TOFMS method described in this communication is simpler and less time-consuming than the established transesterification method that is coupled with analysis by gas chromatography/mass spectrometry (GC/MS). The new method could be used routinely to determine the qualitative fatty acid composition of vegetable oils

  13. Comparative researches on two direct transmethylation without prior extraction methods for fatty acids analysis in vegetal matrix with low fat content

    Directory of Open Access Journals (Sweden)

    Harmanescu Monica

    2012-01-01

    Full Text Available Abstract Background The aim of our work was to compare two methods, both based on direct transmethylation with different reagents, BF3/MeOH (boron trifluoride in methanol or HCl/MeOH (hydrochloride acid in methanol, in acid catalysis, without prior extraction, to find the fast, non-expensive but enough precise method for 9 principal fatty acids (lauric, myristic, palmitic, stearic, oleic, linoleic, linolenic, arahidic and behenic acids analysis in vegetal matrix with low fat content (forage from grassland, for nutrition and agrochemical studies. Results Comparatively, between the average values obtained for all analysed fatty acids by the two methods based on direct transmethylation without prior extraction no significantly difference was identified (p > 0.05. The results of fatty acids for the same forage sample were more closely to their average value, being more homogenous for BF3/MeOH than HCl/MeOH, because of the better accuracy and repeatability of this method. Method that uses BF3/MeOH reagent produces small amounts of interfering compounds than the method using HCl/MeOH reagent, results reflected by the better statistical parameters. Conclusion The fast and non-expensive BF3/methanol method was applied with good accuracy and sensitivity for the determination of free or combined fatty acids (saturated and unsaturated in forage matrix with low fat content from grassland. Also, the final extract obtained by this method, poorer in interfering compounds, is safer to protect the injector and column from contamination with heavy or non-volatile compounds formed by transmethylation reactions.

  14. Self-similarity Driven Demosaicking

    Directory of Open Access Journals (Sweden)

    Antoni Buades

    2011-06-01

    Full Text Available Digital cameras record only one color component per pixel, red, green or blue. Demosaicking is the process by which one can infer a whole color matrix from such a matrix of values, thus interpolating the two missing color values per pixel. In this article we propose a demosaicking method based on the property of non-local self-similarity of images.

  15. Thermoreversible copolymer gels for extracellular matrix.

    Science.gov (United States)

    Vernon, B; Kim, S W; Bae, Y H

    2000-07-01

    To improve the properties of a reversible synthetic extracellular matrix based on a thermally reversible polymer, copolymers of N-isopropylacrylamide and acrylic acid were prepared in benzene with varying contents of acrylic acid (0 to 3%) and the thermal properties were evaluated. The poly(N-isopropylacrylamide) and copolymers made with acrylic acid had molecular weights from 0.8 to 1.7 x10(6) D. Differential scanning calorimetry (DSC) showed the high-molecular-weight acrylic acid copolymers had similar onset temperatures to the homopolymers, but the peak width was considerably increased with increasing acrylic acid content. DSC and cloud point measurements showed that polymers with 0 to 3% acrylic acid exhibit a lower critical solution temperature (LCST) transition between 30 degrees and 37 degrees C. In swelling studies, the homopolymer showed significant syneresis at temperatures above 31 degrees C. Copolymers with 1 and 1.5% showed syneresis beginning at 32 degrees and 37 degrees C, respectively. At 37 degrees C the copolymers with 1.5-3% acrylic acid showed little or no syneresis. Due to the high water content and a transition near physiologic conditions (below 37 degrees C), the polymers with 1.5-2.0% acrylic acid exhibited properties that would be useful in the development of a refillable synthetic extracellular matrix. Such a matrix could be applied to several cell types, including islets of Langerhans, for a biohybrid artificial pancreas.

  16. Spatial structure peculiarities of influenza A virus matrix M1 protein in an acidic solution that simulates the internal lysosomal medium.

    Science.gov (United States)

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

    2011-12-01

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

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

    Institute of Scientific and Technical Information of China (English)

    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.

  18. Simultaneous determination of bromate, chlorite and haloacetic acids by two-dimensional matrix elimination ion chromatography with coupled conventional and capillary columns.

    Science.gov (United States)

    Teh, Hui Boon; Li, Sam Fong Yau

    2015-02-27

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

  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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yaping [Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005 (China); Wang, Yanmin [Department of Clinical Laboratory, Heze Municipal Hospital, Shandong (China); Guo, Shuai; Guo, Yumei; Liu, Hui [Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005 (China); Li, Zhili, E-mail: 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. Influence of the composition of hydroxypropyl cellulose/maleic acid-alt-styrene copolymer blends on their properties as matrix for drug release

    Directory of Open Access Journals (Sweden)

    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.

  1. On-Tissue Derivatization via Electrospray Deposition for Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging of Endogenous Fatty Acids in Rat Brain Tissues.

    Science.gov (United States)

    Wu, Qian; Comi, Troy J; Li, Bin; Rubakhin, Stanislav S; Sweedler, Jonathan V

    2016-06-07

    Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) is used for the multiplex detection and characterization of diverse analytes over a wide mass range directly from tissues. However, analyte coverage with MALDI MSI is typically limited to the more abundant compounds, which have m/z values that are distinct from MALDI matrix-related ions. On-tissue analyte derivatization addresses these issues by selectively tagging functional groups specific to a class of analytes, while simultaneously changing their molecular masses and improving their desorption and ionization efficiency. We evaluated electrospray deposition of liquid-phase derivatization agents as a means of on-tissue analyte derivatization using 2-picolylamine; we were able to detect a range of endogenous fatty acids with MALDI MSI. When compared with airbrush application, electrospray led to a 3-fold improvement in detection limits and decreased analyte delocalization. Six fatty acids were detected and visualized from rat cerebrum tissue using a MALDI MSI instrument operating in positive mode. MALDI MSI of the hippocampal area allowed targeted fatty acid analysis of the dentate gyrus granule cell layer and the CA1 pyramidal layer with a 20-μm pixel width, without degrading the localization of other lipids during liquid-phase analyte derivatization.

  2. Effect of solvent on drug release and a spray-coated matrix of a sirolimus-eluting stent coated with poly(lactic-co-glycolic acid).

    Science.gov (United States)

    Choi, Jiyeon; Jang, Bu Nam; Park, Bang Ju; Joung, Yoon Ki; Han, Dong Keun

    2014-08-26

    Sirolimus (SRL) release from the biodegradable poly(l-lactic-co-glycolic acid) (PLGA) matrix was investigated for the application of drug-eluting stents (DES). In particular, this study focused on whether various organic solvents affect the interaction between SRL and PLGA and the formation of microstructures during ultrasonic coating. The SRL-loaded PLGA coated by tetrahydrofuran or acetone showed a significant initial burst, whereas that from acetonitrile was constantly released during a period of 21 days. On the basis of these results, the interactions at the molecular level of SRL with the polymer matrix were estimated according to various organic solvents. Although the topographies of the coated surface were obviously different, the correlation between surface roughness and SRL release was very poor. Irrespective of organic solvents, FT-IR data showed significantly weak SRL-PLGA interactions. From the result of wide-angle X-ray diffraction, it was confirmed that SRL was dispersed in an amorphous state in the polymer matrix after ultrasonic coating. The glass-transition temperature was also influenced by organic solvents, resulting in a plasticizing effect. The particle size of SRL appeared to determine the release profile from the PLGA matrix, which was the combination of diffusion and polymer degradation at an SRL size of more than 800 nm and the Fickian release at that of less than 300 nm. Therefore, organic solvents can lead to a heterogeneous microstructure in the SRL-loaded PLGA matrix, which is at or near the surface, consisting of aggregated drug- and polymer-rich regions. It is expected that the drug release can be controlled by physicochemical properties of organic solvents, and this study can be used effectively for localized drug release in biomedical devices such as drug-eluting stents.

  3. A Similarity Search Using Molecular Topological Graphs

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    Lynne Shinto

    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.

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

    Science.gov (United States)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. Community Detection by Neighborhood Similarity

    Institute of Scientific and Technical Information of China (English)

    LIU Xu; XIE Zheng; YI Dong-Yun

    2012-01-01

    Detection of the community structure in a network is important for understanding the structure and dynamics of the network.By exploring the neighborhood of vertices,a local similarity metric is proposed,which can be quickly computed.The resulting similarity matrix retains the same support as the adjacency matrix.Based on local similarity,an agglomerative hierarchical clustering algorithm is proposed for community detection.The algorithm is implemented by an efficient max-heap data structure and runs in nearly linear time,thus is capable of dealing with large sparse networks with tens of thousands of nodes.Experiments on synthesized and real-world networks demonstrate that our method is efficient to detect community structures,and the proposed metric is the most suitable one among all the tested similarity indices.%Detection of the community structure in a network is important for understanding the structure and dynamics of the network. By exploring the neighborhood of vertices, a local similarity metric is proposed, which can be quickly computed. The resulting similarity matrix retains the same support as the adjacency matrix. Based on local similarity, an agglomerative hierarchical clustering algorithm is proposed for community detection. The algorithm is implemented by an efficient max-heap data structure and runs in nearly linear time, thus is capable of dealing with large sparse networks with tens of thousands of nodes. Experiments on synthesized and real-world networks demonstrate that our method is efficient to detect community structures, and the proposed metric is the most suitable one among all the tested similarity indices.

  8. Assessment of antimicrobial resistance transfer between lactic acid bacteria and potential foodborne pathogens using in vitro methods and mating in a food matrix.

    Science.gov (United States)

    Toomey, Niamh; Monaghan, Aine; Fanning, Séamus; Bolton, Declan J

    2009-10-01

    The transferability of antimicrobial resistance from lactic acid bacteria (LAB) to potential pathogenic strains was studied using in vitro methods and mating in a food matrix. Five LAB donors containing either erythromycin or tetracycline resistance markers on transferable elements were conjugally mated with LAB (Enterococcus faecalis, Lactococcus lactis) and pathogenic strains (Listeria spp., Salmonella ssp., Staphylococcus aureus, and Escherichia coli). In vitro transfer experiments were carried out with the donors and recipients using both the filter and plate mating methods. The food matrix consisted of fermented whole milk (fermented with the LAB donors) with the pathogenic recipients added as contaminants during the production process. All transconjugants were confirmed by phenotypic and molecular methods. Erythromycin resistance transfer from LAB strains to Listeria spp. was observed using both in vitro mating methods at high transfer frequencies of up to 5.1 x 10(-4) transconjugants per recipient. Also, high frequency transfer (ranging from 2.7 x 10(-8) up to 1.1 x 10(-3) transconjugants per recipient) of both erythromycin and tetracycline-resistance was observed between LAB species using in vitro methods. No resistance transfer was observed to Salmonella spp., Staphylococcus aureus, and E. coli. The only conjugal transfer observed in the fermented milk matrix was for tetracycline resistance between two LAB strains (at a transfer frequency of 2.6 x 10(-7) transconjugants per recipients). This study demonstrates the transfer of antimicrobial resistance from LAB to Listeria spp. using in vitro methods and also the transfer of resistance between LAB species in a food matrix. It highlights the involvement of LAB as a potential source of resistance determinants that may be disseminated between LAB and pathogenic strains including Listeria spp. Furthermore, it indicates that food matrices such as fermented milks may provide a suitable environment to support gene

  9. 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

    Science.gov (United States)

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

    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 consisting 20 patients received TC cream once a day for night time application for 3 months. Group B comprising of 20 patients received GA/AA 20% cream combination for 3 months. The disease severity was monitored with digital photography, melasma area and severity index (MASI) score, which was calculated at baseline, 6 weeks and 12 weeks, and visual analog scale (VAS) score, which was calculated at baseline and 12 weeks. Results: Of 40 patients, 38 were completed the study. A significant reduction in MASI and VAS was recorded after 6 weeks and 12 weeks of treatment in both groups A and B (P = 0.001). However, there was no significant difference in the mean MASI scores between the two groups at baseline, 6 weeks and 12 weeks. Similarly, there was no difference in the mean VAS scores between the two groups at baseline and 12 weeks. Four patients in group A and 3 in group B experienced adverse effects such as irritation, dryness, and photosensitivity. Conclusion: Both low potency TC cream and GA/AA 20% cream combination are effective in treating melasma among Indian patients. PMID:25814702

  10. Trace anion determination in concentrated hydrofluoric acid solutions by two-dimensional ion chromatography I. Matrix elimination by ion-exclusion chromatography.

    Science.gov (United States)

    Vermeiren, Koen

    2005-08-26

    Since years, ion exclusion chromatography (ICE) has been the standard method to separate strong acid analyte anions from concentrated weak acid matrices such as hydrofluoric acid (HF). In this work, the commercially available IonPac ICE-AS 1 column was used to separate trace levels of chloride, nitrate, sulfate and phosphate from HF solutions at 20% (w/w). The efficiency of the separation was studied in more detail using techniques such as ion chromatography (IC), inductively coupled plasma optical emission spectrometry (ICP-OES) and ICP-mass spectrometry (ICP-MS). For 20% (w/w) HF solutions and at a water carrier flow-rate of 0.50 ml/min, the cut window was set from 8.5 to 14.5 min. Under these conditions, analyte recoveries of better than 90% were obtained for chloride, nitrate and sulfate, but only about 75% for phosphate. The HF rejection efficiency was better than 99.9%. It was found that the ICP techniques, measuring total element levels and not species, yielded significantly higher recoveries for phosphorus and sulfur compared to IC. Evidence will be given that part of the added phosphorus (approximately 15% for an addition of 10 mg PO4/kg) is present as mono-fluorophosphoric acid (H2FPO3). In the case of sulfate, the difference between IC and ICP-MS could be attributed to an important matrix effect from the residual HF concentration.

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

    Science.gov (United States)

    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

  12. Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein

    DEFF Research Database (Denmark)

    Rinza, Tomás Rocha; Sneskov, Kristian; Christiansen, Ove;

    2011-01-01

    Using advanced QM/MM methods, the surprisingly negligible shift of the lowest-lying bright electronic excitation of the deprotonated p-coumaric acid (pCA−) within the photoactive yellow protein (PYP) is shown to stem from a subtle balance between hypsochromic and bathochromic effects. More...

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

    NARCIS (Netherlands)

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

    2012-01-01

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

  14. In vitro toxicity of carbon nanotubes, nano-graphite and carbon black, similar impacts of acid functionalization

    OpenAIRE

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

    2015-01-01

    International audience; Carbon nanotubes (CNT) and nano-graphite (NG) are graphene-based nanomaterials which share exceptional physicochemical properties, but whose health impacts are unfortunately still not well understood. On the other hand, carbon black (CB) is a conventional and widely studied material. The comparison of these three carbon-based nanomaterials is thus of great interest to improve our understanding of their toxicity. An acid functionalization was carried out on CNT, NG and ...

  15. 改性乳酸菌微胶囊壁材的研究进展%Research Progress on Modified Matrix of Lactic Acid Bacteria Microcapsule

    Institute of Scientific and Technical Information of China (English)

    刘媛; 孙也; 李淑雅; 王晶; 王艳萍

    2016-01-01

    乳酸菌微胶囊所用壁材主要为生物相容性良好的天然高分子材料.然而天然材料的结构种类有限,不能持续地提高微胶囊对乳酸菌活菌数量的保护作用.改性壁材可以根据用途对原有材料进行结构改造,在保持良好生物相容性的前提下,赋予壁材更好的保护功能.该文综述了国内外改性微胶囊壁材在乳酸菌微胶囊化方面的研究进展.%Biocompatible natural polymer materials are mainly uesd as the matrix of lactic acid bacteria micro-capsule. However, the protective effect on the viability of lactic acid bateria could not be consistently improved becasue of the limited structure of natural materials. Modified polymers with good biocompatibility and better protective effect could be obtained by modifying the original materials according to the application purpose. This paper reviewed the research progress of some modified polymer materials for lactic acid bacteria microencapsu-lation.

  16. A simple method for the determination of glyphosate and aminomethylphosphonic acid in seawater matrix with high performance liquid chromatography and fluorescence detection.

    Science.gov (United States)

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

    2016-12-01

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

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

    Science.gov (United States)

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

    2015-12-01

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

  18. Identification of daidzein as a ligand of retinoic acid receptor that suppresses expression of matrix metalloproteinase-9 in HaCaT cells.

    Science.gov (United States)

    Oh, Hyeon-Jeong; Kang, Young-Gyu; Na, Tae-Young; Kim, Hyeon-Ji; Park, Jun Seong; Cho, Won-Jea; Lee, Mi-Ock

    2013-08-25

    Retinoids have been used as therapeutics for diverse skin diseases, but their side effects limit clinical usage. Here, we report that extracts of two soybeans, Glycine max and Rhynchosia nulubilis, and their ethyl acetate fractions increased the transcriptional activity of retinoic acid receptors (RARs), and that daidzin and genistin were the major constituents of the active fractions. Daidzin and its aglycone, daidzein, induced transcriptional activity of RAR and RARγ. FRET analysis demonstrated that daidzein, but not daidzin, bound both RAR and RARγ with EC50 values of 28μM and 40μM, respectively. Daidzein increased expression of mRNA of RARγ through direct binding of RAR and recruitment of p300 to the RARγ2 promoter. Further, mRNA and gelatinolytic activity of matrix metalloproteinase-9 were decreased by daidzein in HaCaT cells. Together, these results indicate that daidzein functions as a ligand of RAR that could be a candidate therapeutic for skin diseases.

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

    Directory of Open Access Journals (Sweden)

    Eliana Esposito

    2016-05-01

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

  20. Cloud point extraction of plutonium in environmental matrixes coupled to ICPMS and α spectrometry in highly acidic conditions.

    Science.gov (United States)

    Labrecque, Charles; Whitty-Léveillé, Laurence; Larivière, Dominic

    2013-11-01

    A new cloud point extraction procedure has been developed for the quantification of plutonium(IV) in environmental samples. The separation procedure can be either coupled to inductively coupled plasma mass spectrometry (ICPMS) or α spectrometry for plutonium quantification. The method uses a combination of selective ligand (P,P'-di(2-ethylhexyl) methanediphosphonic acid (H2DEH[MDP])) and micelle shielding by bromine formation to enable quantitative extraction of Pu in highly acidic solutions. Cross-optimization of all parameters (nonionic and ionic surfactant, chelating agent, bromate, bromide, and pH) led to optimal of the extraction conditions. Figures of merit of the method for the detection using α spectrometry and ICPMS are reported (limit of detection, limit of quantification, minimal detectable activity, and recovery). Quantitative extractions (>95%) were obtained for a wide variety of aqueous and digested samples (synthetic urine, wastewater, drinking water, seawater, and soil samples). The method features the first successful coupling between α spectrometry and cloud point extraction and is the first demonstration of CPE suitability with metaborate fusion as a sample preparation approach, techniques used extensively in nuclear industries.

  1. Rational design of two bpy-bridged 3D and 2D Co(II) open frameworks with similar amino-acid-based Schiff bases.

    Science.gov (United States)

    Li, Zong-Ze; Du, Lin; Zhou, Jie; Zhu, Ming-Rong; Qian, Fen-Hua; Liu, Jing; Chen, Peng; Zhao, Qi-Hua

    2012-12-21

    Two novel bpy-bridged Co(II) Schiff base complexes have been synthesized by the hydro(solvo)thermal reactions of corresponding amino-acid-based Schiff bases, bpy and Co(NO(3))(2)·6H(2)O. The following formulae identify the two complexes: {[Co(napala)(bpy)(0.5)]·H(2)O}(n) (1) and [Co(napgly)(bpy)(0.5)](n) (2) [H(2)napala = N-(2-hydroxy-1-naphthylmethylidene)-D/L-alanine, H(2)napgly = N-(2-hydroxy-1-naphthylmethylidene)-glycine and bpy = 4,4'-bipyridine]. These two compounds have been characterized using single-crystal X-ray diffraction, infrared, powder X-ray diffraction, thermogravimetric analysis, optical spectra analysis, and magnetic measurement. Complex 1 features an unprecedented threefold interpenetrated diamond network based on the fan-shaped Co(II)(4)(μ(2)-napala)(4) molecular square node and bpy linker, which represents the first example of 3D framework among the amino-acid-based Schiff base complexes with salicylaldehyde or its derivatives. In 2, adjacent Co(II) ions are bridged by μ(2)-napgly(2-) to form left- and right-handed [Co(II)(μ(2)-napgly)](n) helical chains. These two types of helical chains are sustained alternately by a symmetrical bpy co-ligand into a 2D grid-based layer. The solid-state fluorescence of complexes 1 and 2 are quenched almost completely compared with free mixed-ligands at room temperature. Moreover, magnetic studies show the dominant antiferromagnetic coupling between the Co(II) centers mediated by the syn-anti-COO(-)-bridges in both complexes.

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

    Science.gov (United States)

    Prasetyo, Adri D; Prager, Welf; Rubin, Mark G; Moretti, Ernesto A; Nikolis, Andreas

    2016-01-01

    Background Cohesive monophasic polydensified fillers show unique viscoelastic properties and variable density of hyaluronic acid, allowing for a homogeneous tissue integration and distribution of the material. Objective The aim of this paper was to review the clinical data regarding the performance, tolerability, and safety of the Belotero® fillers for soft-tissue augmentation and rejuvenation. Methods A literature search was performed up until May 31, 2015 to identify all relevant articles on Belotero® fillers (Basic/Balance, Hydro, Soft, Intense, Volume) and equivalent products (Esthélis®, Mesolis®, Fortélis®, Modélis®). Results This comprehensive review included 26 papers. Findings from three randomized controlled trials showed a greater reduction in nasolabial fold severity with Belotero® Basic/Balance than with collagen (at 8, 12, 16, and 24 weeks, n=118) and Restylane® (at 4 weeks, n=40), and higher patient satisfaction with Belotero® Intense than with Perlane® (at 2 weeks, n=20). With Belotero® Basic/Balance, an improvement of at least 1 point on the severity scale can be expected in ~80% of patients 1–6 months after injection, with an effect still visible at 8–12 months. Positive findings were also reported with Belotero® Volume (no reduction in hyaluronic acid volume at 12 months, as demonstrated by magnetic resonance imaging), Soft (improvement in the esthetic outcomes when used in a sequential approach), and Hydro (improvement in skin appearance in all patients). The most common adverse effects were mild-to-moderate erythema, edema, and hematoma, most of which were temporary. There were no reports of Tyndall effect, nodules, granulomas, or tissue necrosis. Conclusion Clinical evidence indicates sustainable esthetic effects, good safety profile, and long-term tolerability of the Belotero® fillers, particularly Belotero® Basic/Balance and Intense. PMID:27660479

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

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Directory of Open Access Journals (Sweden)

    Blekas, Georgios

    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

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

    Directory of Open Access Journals (Sweden)

    Prasetyo AD

    2016-09-01

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

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Chaturvedi M

    2014-01-01

    Full Text Available Mayank Chaturvedi,1 Yves Molino,2 Bojja Sreedhar,3 Michel Khrestchatisky,4 Leszek Kaczmarek1 1Laboratory of Neurobiology, Nencki Institute, Warsaw, Poland; 2Vect-Horus, Marseille, France; 3Indian Institute of Chemical Technology, Hyderabad, India; 4Aix-Marseille Université, CNRS, NICN, UMR7259, Marseille, France Aim: The aim of this study was to develop poly(lactic-co-glycolic acid (PLGA nanoparticles (NPs for delivery of a protein – tissue inhibitor of matrix metalloproteinases 1 (TIMP-1 – across the blood–brain barrier (BBB to inhibit deleterious matrix metalloproteinases (MMPs. Materials and methods: The NPs were formulated by multiple-emulsion solvent-evaporation, and for enhancing BBB penetration, they were coated with polysorbate 80 (Ps80. We compared Ps80-coated and uncoated NPs for their toxicity, binding, and BBB penetration on primary rat brain capillary endothelial cell cultures and the rat brain endothelial 4 cell line. These studies were followed by in vivo studies for brain delivery of these NPs. Results: Results showed that neither Ps80-coated nor uncoated NPs caused significant opening of the BBB, and essentially they were nontoxic. NPs without Ps80 coating had more binding to endothelial cells compared to Ps80-coated NPs. Penetration studies showed that TIMP-1 NPs + Ps80 had 11.21%±1.35% penetration, whereas TIMP-1 alone and TIMP-1 NPs without Ps80 coating did not cross the endothelial monolayer. In vivo studies indicated BBB penetration of intravenously injected TIMP-1 NPs + Ps80. Conclusion: The study demonstrated that Ps80 coating of NPs does not cause significant toxic effects to endothelial cells and that it can be used to enhance the delivery of protein across endothelial cell barriers, both in vitro and in vivo. Keywords: PLGA nanoparticles, drug delivery, protein delivery, sustained release, brain delivery, BBB penetration, RBCEC culture

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

    Science.gov (United States)

    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.

  9. Amino acid properties conserved in molecular evolution.

    Directory of Open Access Journals (Sweden)

    Witold R Rudnicki

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

  10. Incorporation of a lauric acid-conjugated GRGDS peptide directly into the matrix of a poly(carbonate-urea)urethane polymer for use in cardiovascular bypass graft applications.

    Science.gov (United States)

    Kidane, Asmeret G; Punshon, Geoffrey; Salacinski, Henryk J; Ramesh, Bala; Dooley, Audrey; Olbrich, Michael; Heitz, Johannes; Hamilton, George; Seifalian, Alexander M

    2006-12-01

    Gly-Arg-Gly-Asp-Ser (GRGDS) was modified by conjugation to lauric acid (LA) to facilitate incorporation into the matrix of a poly(carbonate-urea)urethane (PCU) used in vascular bypass grafts. GRGDS and LA-GRGDS were synthesized using solid phase Fmoc chemistry and characterized by high performance liquid chromatography and Fourier transform infrared spectroscopy. LA-GRGDS was passively coated and incorporated as nanoparticle dispersion on the PCU films. Biocompatibility of the modified surfaces was investigated. Endothelial cells seeded on LA-GRGDS coated and incorporated PCU showed after 48 h and 72 h a significant (p < 0.05) increase in metabolism compared with unmodified PCU. The platelet adhesion and hemolysis studies showed that the modification of PCU had no adverse effect. In conclusion, LA-conjugated RGD derivatives, such as LA-GRGDS, that permit solubility into solvents used in solvent casting methodologies should have wide applicability in polymer development for use in coronary, vascular, and dialysis bypass grafts, and furthermore scaffolds utilized for tissue regeneration and tissue engineering.

  11. Reduction of inflammatory responses and enhancement of extracellular matrix formation by vanillin-incorporated poly(lactic-co-glycolic acid) scaffolds.

    Science.gov (United States)

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

    2012-10-01

    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 in the higher cell attachment and proliferation than the pure PLGA film. Vanillin also reduced the generation of reactive oxygen species (ROS) in cells cultured on the pure PLGA film and significantly inhibited the PLGA-induced inflammatory responses in vivo, evidenced by the reduced accumulation of inflammatory cells and thinner fibrous capsules. The effects of vanillin on the ECM formation were evaluated using annulus fibrous (AF) cell-seeded porous PLGA/vanillin scaffolds. PLGA/vanillin scaffolds elicited the more production of glycosaminoglycan and collagen than the pure PLGA scaffold, in a concentration-dependent manner. Based on the low level of inflammatory responses and enhanced ECM formation, vanillin-incorporated PLGA constructs make them promising candidates in the future biomedical applications.

  12. Improvement of reproducibility and sensitivity by reducing matrix effect in micellar electrokinetic chromatography for determination of amino acids in turtle jelly.

    Science.gov (United States)

    Li, Lin-Qiu; Cai, Yue; Yang, Mei; Shen, Qing; Yu, Ka-Ming; Cheung, Hon-Yeung

    2015-05-01

    Matrix effect (ME) is commonly seen in electrophoretic separation, but this phenomenon lacks any systematic study. Our work aimed to find out the relationship between separation efficiency and current, and then figure out an effective, simple, and economic solution to overcome the negative impact of ME. This present study showed that small amount of NaCl (≤0.005 mg/mL) in the sample had no impact on the separation but enhanced the sensitivity. However, when concentration of NaCl increased above 0.005 mg/mL, it alleviated the separation efficiency, sensitivity, and migration time. Besides, increasing NaCl concentration resulted in increasing turning point. The study of relationship of current and NaCl concentration indicated that when the TP of a sample is higher than 62.36 μA, desalination is necessary. Since the reported desalination methods are either expensive or complicated, we developed a simple and economic method by simply adding 12 times (volume) of chloroform/methanol (2:1, v/v) into the sample. When applied this method to turtle jelly, the number of theoretical plate (N) of 20 amino acids got up to threefold enhancement.

  13. Caffeic Acid Phenethyl Ester Inhibits Oral Cancer Cell Metastasis by Regulating Matrix Metalloproteinase-2 and the Mitogen-Activated Protein Kinase Pathway

    Directory of Open Access Journals (Sweden)

    Chih-Yu Peng

    2012-01-01

    Full Text Available Caffeic acid phenethyl ester (CAPE, an active component extracted from honeybee hives, exhibits anti-inflammatory and anticancer activities. However, the molecular mechanism by which CAPE affects oral cancer cell metastasis has yet to be elucidated. In this study, we investigated the potential mechanisms underlying the effects of CAPE on the invasive ability of SCC-9 oral cancer cells. Results showed that CAPE attenuated SCC-9 cell migration and invasion at noncytotoxic concentrations (0 μM to 40 μM. Western blot and gelatin zymography analysis findings further indicated that CAPE downregulated matrix metalloproteinase-2 (MMP-2 protein expression and inhibited its enzymatic activity. CAPE exerted its inhibitory effects on MMP-2 expression and activity by upregulating tissue inhibitor of metalloproteinase-2 (TIMP-2 and potently decreased migration by reducing focal adhesion kinase (FAK phosphorylation and the activation of its downstream signaling molecules p38/MAPK and JNK. These data indicate that CAPE could potentially be used as a chemoagent to prevent oral cancer metastasis.

  14. Interference-free determination of indole-3-acetic acid in two real systems using second-order calibration method coupled with excitation-emission matrix fluorescence.

    Science.gov (United States)

    Yan, Xiu-Fang; Wu, Hai-Long; Qing, Xiang-Dong; Sun, Yan-Mei; Yu, Ru-Qin

    2014-01-01

    In this work, a simple and practicable method that combines excitation-emission matrix (EEMs) fluorescence with a second-order calibration method based on parallel factor analysis-alternative least-squares (PARAFAC-ALS) algorithm was developed for the direct interference-free determination of indole-3-acetic acid (IAA) in two real systems, coconut water (CW) and coconut milk (CM). Although the excitation and emission profiles of IAA heavily overlapped with that of unknown interferents in the complex real systems, the actual contents and satisfactory recoveries were still obtained successfully. The contents of IAA in CW and CM were 10.8 ± 0.3 and 4.9 ± 0.2 μg mL(-1), respectively, which were consistent with those reported by LC-MS/MS assays in the reference material. The average spike recoveries of IAA in the validation set based on CW and CM were 102.1 ± 3.2 and 98.0 ± 1.9%, respectively. In addition, routine experiments were performed for establishing the validity of the assay to internationally accepted criteria.

  15. Mining Diagnostic Assessment Data for Concept Similarity

    Science.gov (United States)

    Madhyastha, Tara; Hunt, Earl

    2009-01-01

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

  16. A multi-matrix HILIC-MS/MS method for the quantitation of endogenous small molecule neurological biomarker N-acetyl aspartic acid (NAA).

    Science.gov (United States)

    Sangaraju, Dewakar; Shahidi-Latham, Sheerin K; Burgess, Braydon L; Dean, Brian; Ding, Xiao

    2017-03-14

    A multi-matrix hydrophilic interaction liquid chromatography tandem mass spectrometric method (HILIC-MS/MS) was developed for the quantitation of N-Acetyl Aspartic acid (NAA) using stable isotope labeled internal standard, D3-NAA in various biological matrices such as human plasma, human CSF, mouse plasma, brain and spinal cord. A high throughput 96-well plate format supported liquid extraction (SLE) procedure was developed and used for sample preparation. Mass spectrometric analysis of NAA was performed using selected reaction monitoring transitions in positive electrospray ionization mode. As NAA is endogenously present, a surrogate matrix approach was used for quantitation of NAA and the method was qualified over linear calibration curve range of 0.01-10μg/mL. Intra and inter assay precision indicated by percent relative standard deviation (%RSD) was less than 7.1% for low, medium, medium high and high QCs. The accuracy of the method ranged from 92.6-107.0% of nominal concentration for within-run and between-run for the same QCs. Extraction recovery of NAA and D3-NAA was greater than 76%. Stability of NAA was established in the above biological matrices under bench top (RT, 5h), freeze thaw (-20±10°C, 3 cycles) and moues/human plasma sample collection (Wet ice, RT) conditions. HILIC-MS/MS method was then used to quantify and compare the NAA levels in human plasma and CSF of ALS patients versus control human subjects. NAA CSF levels in control human subjects (73.3±31.0ng/mL,N=10) were found to be slightly higher than ALS patients (46.1±22.6ng/mL, N=10) (P=0.04). No differences were observed in NAA plasma levels in human control subjects (49.7±13.8ng/mL,N=9) as compared to ALS patients (49.6±8.1ng/mL, N=10) (P=0.983). NAA endogenous concentrations in mouse plasma, brain and spinal cord were found to be 243.8±56.8ng/mL (N=6), 1029.8±115.2μg/g tissue weight (N=5) and 487.6±178.4μg/g tissue weight (N=5) respectively.

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

    Science.gov (United States)

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

    2013-07-16

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

  18. Matrix theory of gravitation

    CERN Document Server

    Koehler, Wolfgang

    2011-01-01

    A new classical theory of gravitation within the framework of general relativity is presented. It is based on a matrix formulation of four-dimensional Riemann-spaces and uses no artificial fields or adjustable parameters. The geometrical stress-energy tensor is derived from a matrix-trace Lagrangian, which is not equivalent to the curvature scalar R. To enable a direct comparison with the Einstein-theory a tetrad formalism is utilized, which shows similarities to teleparallel gravitation theories, but uses complex tetrads. Matrix theory might solve a 27-year-old, fundamental problem of those theories (sec. 4.1). For the standard test cases (PPN scheme, Schwarzschild-solution) no differences to the Einstein-theory are found. However, the matrix theory exhibits novel, interesting vacuum solutions.

  19. Clustering with Weighted Hyperlink and Sub Similarity Matrix

    Institute of Scientific and Technical Information of China (English)

    WU Ping; SONG Han-tao; ZHANG Li-ping; WU Zheng-yu

    2006-01-01

    A web page clustering algorithm called PageCluster and the improved algorithm ImPageCluster solving overlapping are proposed. These methods not only take the web structure and page hyperlink into account,but also consider the importance of each page which is described as in-weight and out-weight. Compared with the traditional clustering methods, the experiments show that the runtimes of the proposed algorithms are less with the improved accuracies.

  20. Matrix calculus

    CERN Document Server

    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

  1. EMRE Is a Matrix Ca(2+) Sensor that Governs Gatekeeping of the Mitochondrial Ca(2+) Uniporter.

    Science.gov (United States)

    Vais, Horia; Mallilankaraman, Karthik; Mak, Don-On Daniel; Hoff, Henry; Payne, Riley; Tanis, Jessica E; Foskett, J Kevin

    2016-01-26

    The mitochondrial uniporter (MCU) is an ion channel that mediates Ca(2+) uptake into the matrix to regulate metabolism, cell death, and cytoplasmic Ca(2+) signaling. Matrix Ca(2+) concentration is similar to that in cytoplasm, despite an enormous driving force for entry, but the mechanisms that prevent mitochondrial Ca(2+) overload are unclear. Here, we show that MCU channel activity is governed by matrix Ca(2+) concentration through EMRE. Deletion or charge neutralization of its matrix-localized acidic C terminus abolishes matrix Ca(2+) inhibition of MCU Ca(2+) currents, resulting in MCU channel activation, enhanced mitochondrial Ca(2+) uptake, and constitutively elevated matrix Ca(2+) concentration. EMRE-dependent regulation of MCU channel activity requires intermembrane space-localized MICU1, MICU2, and cytoplasmic Ca(2+). Thus, mitochondria are protected from Ca(2+) depletion and Ca(2+) overload by a unique molecular complex that involves Ca(2+) sensors on both sides of the inner mitochondrial membrane, coupled through EMRE.

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

    Directory of Open Access Journals (Sweden)

    Ayumi Taguchi

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

  3. Comparison of cellular effects of starch-coated SPIONs and poly(lactic-co-glycolic acid) matrix nanoparticles on human monocytes

    Science.gov (United States)

    Gonnissen, Dominik; Qu, Ying; Langer, Klaus; Öztürk, Cengiz; Zhao, Yuliang; Chen, Chunying; Seebohm, Guiscard; Düfer, Martina; Fuchs, Harald; Galla, Hans-Joachim; Riehemann, Kristina

    2016-01-01

    Within the last years, progress has been made in the knowledge of the properties of medically used nanoparticles and their toxic effects, but still, little is known about their influence on cellular processes of immune cells. The aim of our comparative study was to present the influence of two different nanoparticle types on subcellular processes of primary monocytes and the leukemic monocyte cell line MM6. We used core-shell starch-coated superparamagnetic iron oxide nanoparticles (SPIONs) and matrix poly(lactic-co-glycolic acid) (PLGA) nanoparticles for our experiments. In addition to typical biocompatibility testing like the detection of necrosis or secretion of interleukins (ILs), we investigated the impact of these nanoparticles on the actin cytoskeleton and the two voltage-gated potassium channels Kv1.3 and Kv7.1. Induction of necrosis was not seen for PLGA nanoparticles and SPIONs in primary monocytes and MM6 cells. Likewise, no alteration in secretion of IL-1β and IL-10 was detected under the same experimental conditions. In contrast, IL-6 secretion was exclusively downregulated in primary monocytes after contact with both nanoparticles. Two-electrode voltage clamp experiments revealed that both nanoparticles reduce currents of the aforementioned potassium channels. The two nanoparticles differed significantly in their impact on the actin cytoskeleton, demonstrated via atomic force microscopy elasticity measurement and phalloidin staining. While SPIONs led to the disruption of the respective cytoskeleton, PLGA did not show any influence in both experimental setups. The difference in the effects on ion channels and the actin cytoskeleton suggests that nanoparticles affect these subcellular components via different pathways. Our data indicate that the alteration of the cytoskeleton and the effect on ion channels are new parameters that describe the influence of nanoparticles on cells. The results are highly relevant for medical application and further

  4. Salvianolic Acid B Down-regulates Matrix Metalloproteinase-9 Activity and Expression in Tumor Necrosis Factor-α-induced Human Coronary Artery Endothelial Cells

    Institute of Scientific and Technical Information of China (English)

    Le Ma; Yun-Qian Guan; Zhong-Dong Du

    2015-01-01

    Background:Salvianolic acid B (Sal B) is a bioactive water-soluble compound of Salviae miltiorrhizae,a traditional herbal medicine that has been used clinically tor the treatment of cardiovascular diseases.This study sought to evaluate the effect of Sal B on matrix metalloproteinase-9 (MMP-9) and on the underlying mechanisms in tumor necrosis factor-α (TNF-α)-activated human coronary artery endothelial cells (HCAECs),a cell model of Kawasaki disease.Methods:HCAECs were pretreated with 1 l0 μmol/L of Sal B,and then stimulated by TNF-α at different time points.The protein expression and activity of MMP-9 were determined by Western blot assay and gelatin zymogram assay,respectively.Nuclear factor-κB (NF-κB) activation was detected with immunofluorescence,electrophoretic mobility shift assay,and Western blot assay.Protein expression levels of mitogen-activated protein kinase (c-Jun N-terminal kinase [JNK],extra-cellular signal-regulated kinase [ERK],and p38) were determined by Western blot assay.Results:After HCAECs were exposed to TNF-α,1-10 μtmol/L Sal B significantly inhibited TNF-α-induced MMP-9 expression and activity.Furthermore,Sal B significantly decreased IκBα phosphorylation and p65 nuclear translocation in HCAECs stimulated with TNF-α for 30 min.In addition,Sal B decreased the phosphorylation of JNK and ERK1/2 proteins in cells treated with TNF-α for 10 min.Conclusions:The data suggested that Sal B suppressed TNF-α-induced MMP-9 expression and activity by blocking the activation of NF-κB,JNK,and ERK1/2 signaling pathways.

  5. Protein-protein interaction based on pairwise similarity

    Directory of Open Access Journals (Sweden)

    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.

  6. Similarity transformations of MAPs

    Directory of Open Access Journals (Sweden)

    Andersen Allan T.

    1999-01-01

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

  7. New Similarity Functions

    DEFF Research Database (Denmark)

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

    2016-01-01

    In data science, there are important parameters that affect the accuracy of the algorithms used. Some of these parameters are: the type of data objects, the membership assignments, and distance or similarity functions. This paper discusses similarity functions as fundamental elements in membership...

  8. Clustering by Pattern Similarity

    Institute of Scientific and Technical Information of China (English)

    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.

  9. Judgments of brand similarity

    NARCIS (Netherlands)

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

    1998-01-01

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

  10. New Similarity Functions

    DEFF Research Database (Denmark)

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

    2016-01-01

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

  11. Similar component analysis

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hong; WANG Xin; LI Junwei; CAO Xianguang

    2006-01-01

    A new unsupervised feature extraction method called similar component analysis (SCA) is proposed in this paper. SCA method has a self-aggregation property that the data objects will move towards each other to form clusters through SCA theoretically,which can reveal the inherent pattern of similarity hidden in the dataset. The inputs of SCA are just the pairwise similarities of the dataset,which makes it easier for time series analysis due to the variable length of the time series. Our experimental results on many problems have verified the effectiveness of SCA on some engineering application.

  12. Stability of similarity measurements for bipartite networks

    CERN Document Server

    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...

  13. Liquid chromatography/electrospray ionization/isotopic dilution mass spectrometry analysis of n-(phosphonomethyl) glycine and mass spectrometry analysis of aminomethyl phosphonic acid in environmental water and vegetation matrixes.

    Science.gov (United States)

    Grey, L; Nguyen, B; Yang, P

    2001-01-01

    A liquid chromatography/electrospray/mass spectrometry (LC/ES/MS) method was developed for the analysis of glyphosate (n-phosphonomethyl glycine) and its metabolite, aminomethyl phosphonic acid (AMPA) using isotope-labelled glyphosate as a method surrogate. Optimized parameters were achieved to derivatize glyphosate and AMPA using 9-fluorenylmethyl chloroformate (FMOC-Cl) in borate buffer prior to a reversed-phase LC analysis. Method spike recovery data obtained using laboratory and real world sample matrixes indicated an excellent correlation between the recovery of the native and isotope-labelled glyphosate. Hence, the first performance-based, isotope dilution MS method with superior precision, accuracy, and data quality was developed for the analysis of glyphosate. There was, however, no observable correlation between the isotope-labelled glyphosate and AMPA. Thus, the use of this procedure for the accurate analysis of AMPA was not supported. Method detection limits established using standard U.S. Environmental Protection Agency protocol were 0.06 and 0.30 microg/L, respectively, for glyphosate and AMPA in water matrixes and 0.11 and 0.53 microg/g, respectively, in vegetation matrixes. Problems, solutions, and the method performance data related to the analysis of chlorine-treated drinking water samples are discussed. Applying this method to other environmental matrixes, e.g., soil, with minimum modifications is possible, assuring accurate, multimedia studies of glyphosate concentration in the environment and the delivery of useful multimedia information for regulatory applications.

  14. Gender similarities and differences.

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-11-11

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

  16. Matrix inequalities

    CERN Document Server

    Zhan, Xingzhi

    2002-01-01

    The main purpose of this monograph is to report on recent developments in the field of matrix inequalities, with emphasis on useful techniques and ingenious ideas. Among other results this book contains the affirmative solutions of eight conjectures. Many theorems unify or sharpen previous inequalities. The author's aim is to streamline the ideas in the literature. The book can be read by research workers, graduate students and advanced undergraduates.

  17. Comparison of cellular effects of starch-coated SPIONs and poly(lactic-co-glycolic acid matrix nanoparticles on human monocytes

    Directory of Open Access Journals (Sweden)

    Gonnissen D

    2016-10-01

    Full Text Available Dominik Gonnissen,1 Ying Qu,1,2 Klaus Langer,3 Cengiz Öztürk,4 Yuliang Zhao,2 Chunying Chen,2 Guiscard Seebohm,5 Martina Düfer,6 Harald Fuchs,1 Hans-Joachim Galla,7 Kristina Riehemann11Center for Nanotechnology, Institute of Physics, University of Münster, Münster, Germany; 2National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, People’s Republic of China; 3Institute of Pharmaceutical Technology and Biopharmacy, University of Münster, Münster, 4chemicell GmbH, Berlin, 5Department of Cardiovascular Medicine, Institute for Genetics of Heart Diseases, University Hospital Münster, 6Department of Pharmacology, Institute of Pharmaceutical and Medicinal Chemistry, 7Department of Cell Biology/Biophysics, Institute of Biochemistry, University of Münster, Münster, GermanyAbstract: Within the last years, progress has been made in the knowledge of the properties of medically used nanoparticles and their toxic effects, but still, little is known about their influence on cellular processes of immune cells. The aim of our comparative study was to present the influence of two different nanoparticle types on subcellular processes of primary monocytes and the leukemic monocyte cell line MM6. We used core-shell starch-coated superparamagnetic iron oxide nanoparticles (SPIONs and matrix poly(lactic-co-glycolic acid (PLGA nanoparticles for our experiments. In addition to typical biocompatibility testing like the detection of necrosis or secretion of interleukins (ILs, we investigated the impact of these nanoparticles on the actin cytoskeleton and the two voltage-gated potassium channels Kv1.3 and Kv7.1. Induction of necrosis was not seen for PLGA nanoparticles and SPIONs in primary monocytes and MM6 cells. Likewise, no alteration in secretion of IL-1β and IL-10 was detected under the same experimental conditions. In contrast, IL-6 secretion was exclusively downregulated in primary monocytes after contact with both

  18. Compression-based Similarity

    CERN Document Server

    Vitanyi, Paul M B

    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 engine that returns aggregate page counts. We can extract a code length from the numbers returned, use the same formula as before, and derive a similarity or relative semantics between names for objects. The theory is based on Kolmogorov complexity. We test both similarities extensively experimentally.

  19. Segmentation Similarity and Agreement

    CERN Document Server

    Fournier, Chris

    2012-01-01

    We propose a new segmentation evaluation metric, called segmentation similarity (S), that quantifies the similarity between two segmentations as the proportion of boundaries that are not transformed when comparing them using edit distance, essentially using edit distance as a penalty function and scaling penalties by segmentation size. We propose several adapted inter-annotator agreement coefficients which use S that are suitable for segmentation. We show that S is configurable enough to suit a wide variety of segmentation evaluations, and is an improvement upon the state of the art. We also propose using inter-annotator agreement coefficients to evaluate automatic segmenters in terms of human performance.

  20. Folic acid

    Science.gov (United States)

    ... taking folic acid by itself, or with L-carnitine a compound similar to an amino acid from ... levels. It is not clear if folic acid supplementation reduces hearing loss in people with normal folate ...

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

    Science.gov (United States)

    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…

  2. A Prenatal Multiple Micronutrient Supplement Produces Higher Maternal Vitamin B-12 Concentrations and Similar Folate, Ferritin, and Zinc Concentrations as the Standard 60-mg Iron Plus 400-μg Folic Acid Supplement in Rural Bangladeshi Women12

    Science.gov (United States)

    Rahman, Anisur; Raqib, Rubhana; Lönnerdal, Bo; Ekström, Eva-Charlotte

    2016-01-01

    Background: The effects of prenatal food and micronutrient supplementation on maternal micronutrient status are not well known. Objective: We compared the efficacy and effectiveness of 3 different micronutrient supplements on maternal micronutrient status when combined with food supplementation. Methods: In the MINIMat (Maternal and Infant Nutrition Intervention, Matlab) trial in Bangladesh, 4436 pregnant women were randomly assigned to daily intake of 3 types of micronutrient capsules: 30 mg Fe and 400 μg folic acid (Fe30F), 60 mg Fe and 400 μg folic acid (Fe60F), or multiple micronutrient supplements (MMNs) combined with early (week 9 of pregnancy) or usual (week 20 of pregnancy) food supplementation in a 2 by 3 factorial design. Plasma concentrations of vitamin B-12, folate, ferritin, and zinc were analyzed before the start of micronutrient supplementation (week 14) and at week 30 of pregnancy in 641 randomly selected women. An electronic monitoring device was used to measure the number of capsules taken. The effectiveness of food and micronutrient regimens as well as efficacy per capsule in maternal micronutrient status were analyzed by ANOVA and general linear models. Results: At week 30 of pregnancy, women in the MMN group had higher geometric mean concentrations of vitamin B-12 than women in the Fe60F group (119 compared with 101 pmol/L, respectively); no other differences in effectiveness of micronutrient and food regimens were observed. A dose-response relation between the number of capsules taken and concentrations of folate and ferritin was observed for all micronutrient supplements. Fe30F had lower efficacy per capsule in increasing ferritin concentrations within the first tertile of capsule intake than did Fe60F and MMNs. Because ferritin reached a plateau for all types of micronutrient supplements, there was no difference between the regimens in their effectiveness. Conclusion: Compared with Fe60F, MMNs produced higher maternal vitamin B-12 and

  3. Matrix analysis

    CERN Document Server

    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. Empirical codon substitution matrix

    Directory of Open Access Journals (Sweden)

    Gonnet Gaston H

    2005-06-01

    Full Text Available Abstract Background Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. Results A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons. Conclusion The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios.

  5. IR spectrum of CH3CN-BF3 in solid neon: matrix effects on the structure of a Lewis acid-base complex.

    Science.gov (United States)

    Eigner, Audrey A; Rohde, John A; Knutson, Christopher C; Phillips, James A

    2007-02-15

    We have observed several IR bands of CH3CN-BF3 in neon and nitrogen matrices. For the 11B isotopomer in neon matrices, we observed the BF3 symmetric deformation band (nu7) as a doublet at 600 and 603 cm(-1), the BF3 symmetric stretching band (nu6) as a doublet at 833 and 838 cm(-1), the BF3 asymmetric stretching mode (nu13) at 1281 cm(-1) (partially obscured), and the C-N stretching mode (nu2) as a doublet at 2352 and 2356 cm(-1). The nitrogen matrix data are largely consistent with those reported recently, though we do propose a refinement of one band assignment. Comparisons of the frequencies of a few key, structurally sensitive vibrational modes either observed in various condensed-phase environments or calculated for two minimum-energy gas-phase structures indicate that inert matrix media significantly alter the structural properties of CH3CN-BF3. Specifically, the B-N dative bond compresses relative to the gas phase and other concomitant changes occur as well. Furthermore, the frequency shifts depict structural changes that occur across the various matrix hosts in a manner that largely parallels the degree of stabilization offered by these inert media.

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

    Science.gov (United States)

    Gorka, Jan; Bahr, Ute; Karas, Michael

    2012-11-01

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

  7. More Similar Than Different

    DEFF Research Database (Denmark)

    Pedersen, Mogens Jin

    2015-01-01

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

  8. Similar dissection of sets

    CERN Document Server

    Akiyama, Shigeki; Okazaki, Ryotaro; Steiner, Wolfgang; Thuswaldner, Jörg

    2010-01-01

    In 1994, Martin Gardner stated a set of questions concerning the dissection of a square or an equilateral triangle in three similar parts. Meanwhile, Gardner's questions have been generalized and some of them are already solved. In the present paper, we solve more of his questions and treat them in a much more general context. Let $D\\subset \\mathbb{R}^d$ be a given set and let $f_1,...,f_k$ be injective continuous mappings. Does there exist a set $X$ such that $D = X \\cup f_1(X) \\cup ... \\cup f_k(X)$ is satisfied with a non-overlapping union? We prove that such a set $X$ exists for certain choices of $D$ and $\\{f_1,...,f_k\\}$. The solutions $X$ often turn out to be attractors of iterated function systems with condensation in the sense of Barnsley. Coming back to Gardner's setting, we use our theory to prove that an equilateral triangle can be dissected in three similar copies whose areas have ratio $1:1:a$ for $a \\ge (3+\\sqrt{5})/2$.

  9. Matrix pentagons

    CERN Document Server

    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.

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

    Science.gov (United States)

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

    2017-04-01

    Quantification of low molecular weight compounds (<800 Da) using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI MS) is challenging due to the matrix signal interference at low m/z region and poor reproducibility of MS responses. In this study, a C60 labeling-MALDI MS strategy was proposed for the fast, sensitive and reliable determination of amino acids (AAs) in biofluids. An N-hydroxysuccinimide functionalized C60 was synthesized as the labeling reagent and added as an 880 Da tag to AAs; a carboxyl acid containing C60 was employed as the internal standards to normalize MS variations. This solved the inherent problems of MALDI MS for small molecule analysis. The entire analytical procedure-which consisted of simple protein precipitation and 10 min of derivatization in a microwave prior to the MALDI MS analysis-could be accomplished within 20 min with high throughput and great sample matrix tolerance. AA quantification showed good linearity from 0.7 to 70.0 μM with correlation coefficients (R) larger than 0.9954. The limits of detection were 70.0-300.0 fmol. Good reproducibility and reliability of the method were demonstrated by intra-day and inter-day precision with relative standard deviations less than 13.8%, and the recovery in biofluid ranged from 80.4% to 106.8%. This approach could be used in 1 μL of urine, serum, plasma, whole blood, and cerebrospinal fluid. Most importantly, the C60 labeling strategy is a universal approach for MALDI MS analysis of various LMW compounds because functionalized C60 is now available on demand.

  11. New strategy for the determination of gliadins in maize- or rice-based foods matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: fractionation of gliadins from maize or rice prolamins by acidic treatment.

    Science.gov (United States)

    Hernando, Alberto; Valdes, Israel; Méndez, Enrique

    2003-08-01

    A procedure for determining small quantities of gliadins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) in gluten-free foods containing relatively large amounts of prolamin proteins from maize or rice is described. We report for the first time that gliadins, the ethanol-soluble wheat prolamin fraction, can be quantitatively solubilized in 1.0 M acetic acid, while the corresponding ethanol-soluble maize or rice prolamin fraction remains insoluble in acetic acid. We describe a methodology for the detection of gliadins in maize and rice foods based on a two-step procedure of extraction (60% aqueous ethanol followed by 1 M acetic acid). Subsequent MALDI-TOFMS analysis of the resulting acidic extract from these gluten-free foods clearly confirms the presence of a typical mass pattern corresponding to gliadin components, ranging from 30 to 45 kDa. Depending on the percentages of maize or rice flours employed in the elaboration of these foods, the combined procedure enables levels of gliadins from 100 to 400 ppm to be detected. The efficiency of this combined procedure corroborates enzyme-linked immunosorbent assay data for a large number of maize/rice gluten-free foods by means of direct visualization of the characteristic gliadin mass pattern in maize or rice foods.

  12. Similarity transformed semiclassical dynamics

    Science.gov (United States)

    Van Voorhis, Troy; Heller, Eric J.

    2003-12-01

    In this article, we employ a recently discovered criterion for selecting important contributions to the semiclassical coherent state propagator [T. Van Voorhis and E. J. Heller, Phys. Rev. A 66, 050501 (2002)] to study the dynamics of many dimensional problems. We show that the dynamics are governed by a similarity transformed version of the standard classical Hamiltonian. In this light, our selection criterion amounts to using trajectories generated with the untransformed Hamiltonian as approximate initial conditions for the transformed boundary value problem. We apply the new selection scheme to some multidimensional Henon-Heiles problems and compare our results to those obtained with the more sophisticated Herman-Kluk approach. We find that the present technique gives near-quantitative agreement with the the standard results, but that the amount of computational effort is less than Herman-Kluk requires even when sophisticated integral smoothing techniques are employed in the latter.

  13. Integral edge seals for phosphoric acid fuel cells

    Science.gov (United States)

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

    1992-01-01

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

  14. Distance and Similarity Measures for Soft Sets

    CERN Document Server

    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.

  15. Repression by H-NS of genes required for the biosynthesis of the Vibrio cholerae biofilm matrix is modulated by the second messenger cyclic diguanylic acid.

    Science.gov (United States)

    Ayala, Julio C; Wang, Hongxia; Silva, Anisia J; Benitez, Jorge A

    2015-08-01

    Expression of Vibrio cholerae genes required for the biosynthesis of exopolysacchide (vps) and protein (rbm) components of the biofilm matrix is enhanced by cyclic diguanylate (c-di-GMP). In a previous study, we reported that the histone-like nucleoid structuring (H-NS) protein represses the transcription of vpsA, vpsL and vpsT. Here we demonstrate that the regulator VpsT can disrupt repressive H-NS nucleoprotein complexes at the vpsA and vpsL promoters in the presence of c-di-GMP, while H-NS could disrupt the VpsT-promoter complexes in the absence of c-di-GMP. Chromatin immunoprecipitation-Seq showed a remarkable trend for H-NS to cluster at loci involved in biofilm development such as the rbmABCDEF genes. We show that the antagonistic relationship between VpsT and H-NS regulates the expression of the rbmABCDEF cluster. Epistasis analysis demonstrated that VpsT functions as an antirepressor at the rbmA/F, vpsU and vpsA/L promoters. Deletion of vpsT increased H-NS occupancy at these promoters while increasing the c-di-GMP pool had the opposite effect and included the vpsT promoter. The negative effect of c-di-GMP on H-NS occupancy at the vpsT promoter required the regulator VpsR. These results demonstrate that c-di-GMP activates the transcription of genes required for the biosynthesis of the biofilm matrix by triggering a coordinated VpsR- and VpsT-dependent H-NS antirepression cascade.

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

    Science.gov (United States)

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

    2017-01-01

    Molecular salts and cocrystals of amino acids have potential applications as molecular materials with nonlinear optical, ferroelectric, piezoelectric, and other various target physical properties. The wide choice of amino acids and coformers makes it possible to design various crystal structures. The amino acid-maleic acid system provides a perfect example of a rich variety of crystal structures with different stoichiometries, symmetries and packing motifs built from the molecular building blocks, which are either exactly the same, or differ merely by protonation or as optical isomers. The present paper reports the crystal structures of two new salts of the DL-norvaline-maleic acid system with 1:1 and 2:1 stoichiometries, namely DL-norvalinium hydrogen maleate, C5H12NO2(+)·C4H3O4(-), (I), and DL-norvalinium hydrogen maleate-DL-norvaline, C5H12NO2(+)·C4H3O4(-)·C5H11NO2, (II). These are the first examples of molecular salts of DL-norvaline with an organic anion. The crystal structure of (I) has the same C2(2)(12) structure-forming motif which is common for hydrogen maleates of amino acids. The structure of (II) has dimeric cations. Of special interest is that the single crystals of (I) which are originally formed on crystallization from aqueous solution transform into single crystals of (II) if stored in the mother liquor for several hours.

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

    Science.gov (United States)

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

    2001-06-01

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

  18. Riemann Zeta Matrix Function

    OpenAIRE

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Rouy, E

    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)

  20. Rapid ion-exchange matrix removal for a decrease of detection limits in the analysis of salt-rich reservoir waters for fluorobenzoic acids by liquid chromatography coupled with tandem mass spectrometry.

    Science.gov (United States)

    Kubica, Paweł; Vacchina, Véronique; Wasilewski, Tomasz; Reynaud, Stéphanie; Szpunar, Joanna; Lobinski, Ryszard

    2017-02-01

    A matrix removal procedure with ion-exchange resin prior to analysis for 18 fluorinated benzoic acids (FBAs) tracers in saline (>25% salt) reservoir water was optimized. The elimination of >98% of salt and the simultaneous matrix sample cleanup allowed the direct analysis using the supernatant by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). This resulted in a gain in detection limits for most of the tracers in comparison with the reference method (direct analysis after minimum required dilution). The limits of detection (LODs) were in the range of 0.01-0.15 ng/ml and compared to other studies the developed method provided comparable limits of detection and advantage of simplified and shorter sample preparation. The presented method offers a considerable gain in simplicity and analysis time. Recoveries for all the tracers reached 80-100%, except for 2-FBA and 2,6-dFBA for which they were ca. 60%. The low recoveries were corrected by the use of five isotopically labeled internal standards. The method was validated by the analysis of spiked samples and by an independent comparison of the results with those obtained by solid-phase extraction LC-MS/MS method.

  1. Stabilization of nonlinear systems by similarity transformations

    Directory of Open Access Journals (Sweden)

    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.

  2. 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

    Directory of Open Access Journals (Sweden)

    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.

  3. Estimating similarity of XML Schemas using path similarity measure

    Directory of Open Access Journals (Sweden)

    Veena Trivedi

    2012-07-01

    Full Text Available In this paper, an attempt has been made to develop an algorithm which estimates the similarity for XML Schemas using multiple similarity measures. For performing the task, the XML Schema element information has been represented in the form of string and four different similarity measure approaches have been employed. To further improve the similarity measure, an overall similarity measure has also been calculated. The approach used in this paper is a distinguished one, as it calculates the similarity between two XML schemas using four approaches and gives an integrated values for the similarity measure. Keywords-componen

  4. The incorporation of water-soluble gel matrix into bile acid-based microcapsules for the delivery of viable β-cells of the pancreas, in diabetes treatment: biocompatibility and functionality studies.

    Science.gov (United States)

    Mooranian, Armin; Negrulj, Rebecca; Al-Salami, Hani

    2016-02-01

    In recent studies, we microencapsulated pancreatic β-cells using sodium alginate (SA) and poly-L-ornithine (PLO) and the bile acid, ursodeoxycholic acid (UDCA), and tested the morphology and cell viability post-microencapsulation. Cell viability was low probably due to limited strength of the microcapsules. This study aimed to assess a β-cell delivery system which consists of UDCA-based microcapsules incorporated with water-soluble gel matrix. The polyelectrolytes, water-soluble gel (WSG), polystyrenic sulphate (PSS), PLO and polyallylamine (PAA) at ratios 4:1:1:2.5 with or without 4% UDCA, were incorporated into our microcapsules, and cell viability, metabolic profile, cell functionality, insulin production, levels of inflammation, microcapsule morphology, cellular distribution, UDCA partitioning, biocompatibility, thermal and chemical stabilities and the microencapsulation efficiency were examined. The incorporation of UDCA with PSS, PAA and WSG enhanced cell viability per microcapsule (p < 0.05), cellular metabolic profile (p < 0.01) and insulin production (p < 0.01); reduced the inflammatory release TNF-α (p < 0.01), INF-gamma (p < 0.01) and interleukin-6 (IL-6) (p < 0.01); and ceased the production of IL-1β. UDCA, PSS, PAA and WSG addition did not change the microencapsulation efficiency and resulted in biocompatible microcapsules. Our designed microcapsules showed good morphology and desirable insulin production, cell functionality and reduced inflammatory profile suggesting potential applications in diabetes.

  5. Study on HPMC-stearic acid as matrix for capsaicin transdermal gel%辅料羟丙基甲基纤维素-硬脂酸作为辣椒素透皮凝胶基质的研究

    Institute of Scientific and Technical Information of China (English)

    陈小云; 张振海; 胡琴; 蒋艳荣; 贾晓斌

    2013-01-01

    Objective To evaluate the applicability of hydroxypropyl methyl cellulose (HPMC)-stearic acid as matrix for capsaicin transdermal gel and to optimize the formula. Methods HPMC-stearic acid was added as the matrix for the preparation of capsaicin transdermal gel, the formula was optimized by orthogonal design and its permeation ability in vitro and stability were investigated. Results The prepared gel was white translucent colloid. The best formula optimized by orthogonal test was 1% HPMC-stearic acid, 15% propylene glycol, and 10% glycerol, and the cumulative permeation quantity in vitro at 12 h was 275.45 μg/cm2. Conclusion The capsaicin transdermal gel has good stability and percutaneous permeability, which may be a promising new dosage form for transdermal delivery of capsaicin.%目的 评价辅料羟丙基甲基纤维素-硬脂酸(HPMC-硬脂酸)作为辣椒素透皮凝胶基质的适用性,并对制剂处方进行优化.方法 以HPMC-硬脂酸为基质制备了辣椒素透皮凝胶,通过正交设计试验,对基质处方进行优化,并考察其体外经皮渗透性能和稳定性.结果 所制备的凝胶为白色半透明胶体,正交试验筛选出的优化处方组成为1% HPMC-硬脂酸、15%丙二醇、10%甘油,辣椒素12h累积渗透量为275.45 μg/cm2.结论 以HPMC-硬脂酸为基质制备的辣椒素凝胶性质稳定,具有良好的适用性和经皮渗透性能,有望成为辣椒素的新型透皮给药制剂.

  6. Efficacy of Ruby Dot Matrix Laser Combined with Tranexamic Acid Tablets in the Treatment of Melasma%红宝石点阵激光联合氨甲环酸治疗黄褐斑临床观察

    Institute of Scientific and Technical Information of China (English)

    张璃; 林孝华; 唐东阳

    2012-01-01

    Objective To observe the clinical therapeutic efficacy of ruby dot matrix laser combined with tranexamic acid tablets in the treatment of melasma. Methods Laser treatment; choice dot matrix pattern, with energy density from 2. 5mJ/mm to 3. 5mJ/mm . Everyone accepted treatment twice one month. One course included 4 times of treatment. Everyone accepted only one course treatment. Tranexamic acid tablets treatment; Everyone was given tranexamic acid tablets 500mg per day, 2 months as 1 course. Everyone accepted 3 courses treatment. The severity and the area of melasma was assessed by two dermatologists using the melasma area severity index ( MASI). At regular in tervals the degree of improvement in pigmentation was reassessed with MASI scores. Effect appearance, recurrence, side-effects were also recorded. Results The 120 patients were followed for 6 ~ 12 months after treatment. 118 patients(98. 33% ) appeared the varying degree facial pigmentation loss. 5 cases(4. 17% ) was cured thoroughly, 74 cases(61.67% ) were cured better than before obviously. And in 39 cases treated for effective. The efficiency was 65. 84%. 37 patients (30. 83% ) showed clinical effect at the half-month treatment, 52 patients (43. 33%) showed clinical effect after one month treatment. Furthermore, only 8 patients(6. 67% ) had recurrences. There were no obvious side-effects of the treatment except a hypomenorrhea in 7 patients. Conclusion Ruby dot matrix laser combined with tranexamic acid tablets is a novel therapy, which is safe and effective in the treatment of melasma.%目的 对红宝石点阵激光联合氨甲环酸片治疗黄褐斑进行临床疗效观察.方法 激光治疗:采用点阵模式,能量密度2.5 ~ 3.5J/cm2,每隔2周治疗1次,2个月为1个疗程;同时口服氨甲环酸片500mg,1次/d,2个月为1个疗程,连续治疗3个疗程;对患者进行黄褐斑皮损面积和严重程度指数(MASI)评分,采用自身治疗前/后对照法进行疗效观察,记录起效

  7. Effect of encapsulation in the anion receptor pocket of sub-domain IIA of human serum albumin on the modulation of pKa of warfarin and structurally similar acidic guests: a possible implication on biological activity.

    Science.gov (United States)

    Datta, Shubhashis; Halder, Mintu

    2014-01-05

    Supramolecular and bio-supramolecular host assisted pKa shift of biologically relevant acidic guests, warfarin and coumarin 343, has been monitored using both steady-state and time resolved fluorescence spectroscopy. The anion receptors present in sub-domain IIA of human serum albumin (HSA) stabilize the anionic form of the guest and thereby shift pKa towards acidic range. On the other hand, the preferential binding of the neutral form of guests in the non-polar hydrophobic cavity of β-cyclodextrin results in up-shifted pKa. This shifting of pKa of drugs like warfarin, etc., whose therapeutic activity depends on the position of the acid-base equilibrium in human system, is of great importance in pharmacokinetics. The release of the active form of such drugs from macrocyclic carrier and subsequent distribution through the carrier protein should depend on the modulation of the overall pKa window brought about by the encapsulation in these hosts. Present work also suggests that properly optimized encapsulation in appropriate receptor pocket can enhance the bioavailability of drugs. This work also opens up the possibility to use HSA as encapsulator, instead of traditional cyclodextrins or other polymeric hosts, since such system may overcome toxicity as well as biocompatibility issues.

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

    NARCIS (Netherlands)

    Steendam, R; Lerk, CF

    1998-01-01

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

  9. Towards Google matrix of brain

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-12

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

  10. Mapping of the human dentin matrix acidic phosphoprotein gene (DMP1) to the dentinogenesis imperfecta type II critical region at chromosome 4q21

    Energy Technology Data Exchange (ETDEWEB)

    Aplin, H.M.; Hirst, K.L.; Crosby, A.H.; Dixon, M.J. [Univ. of Manchester (United Kingdom)

    1995-11-20

    Dentinogenesis imperfecta type II (DGI1) is an autosomal dominant disorder of dentin formation, which has been mapped to human chromosome 4q12-q21. The region most likely to contain the DGI1 locus is a 3.2-cM region surrounding the osteopontin (SPP1) locus. Recently, a novel dentin-specific acidic phosphoprotein (dmp1) has been cloned in the rat and mapped to mouse chromosome 5q21. In the current investigation, we have isolated a cosmid containing the human DMP1 gene. The isolation of a short tandem repeat polymorphism at this locus has allowed us to map the DMP1 locus to human chromosome 4q21 and demonstrate that it is tightly linked to DGI1 in two families (Z{sub max} = 11.01, {theta} = 0.001). The creation of a yeast artificial chromosome contig around SPP1 has further allowed us to demonstrate that DMP1 is located within 150 kb of the bone sialoprotein and 490 kb of the SPP1 loci, respectively. DMP1 is therefore a strong candidate for the DGI1 locus. 12 refs., 2 figs., 1 tab.

  11. Web Search Results Summarization Using Similarity Assessment

    Directory of Open Access Journals (Sweden)

    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.

  12. New approach for distinguishing the similarity of links

    Institute of Scientific and Technical Information of China (English)

    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.

  13. Role-based similarity in directed networks

    CERN Document Server

    Cooper, Kathryn

    2010-01-01

    The widespread relevance of increasingly complex networks requires methods to extract meaningful coarse-grained representations of such systems. For undirected graphs, standard community detection methods use criteria largely based on density of connections to provide such representations. We propose a method for grouping nodes in directed networks based on the role of the nodes in the network, understood in terms of patterns of incoming and outgoing flows. The role groupings are obtained through the clustering of a similarity matrix, formed by the distances between feature vectors that contain the number of in and out paths of all lengths for each node. Hence nodes operating in a similar flow environment are grouped together although they may not themselves be densely connected. Our method, which includes a scale factor that reveals robust groupings based on increasingly global structure, provides an alternative criterion to uncover structure in networks where there is an implicit flow transfer in the system...

  14. MALDI Matrix Research for Biopolymers

    Science.gov (United States)

    Fukuyama, Yuko

    2015-01-01

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

  15. On Geometry and Matrix Models

    CERN Document Server

    Dijkgraaf, R; Dijkgraaf, Robbert; Vafa, Cumrun

    2002-01-01

    We point out two extensions of the relation between matrix models, topological strings and N=1 supersymmetric gauge theories. First, we note that by considering double scaling limits of unitary matrix models one can obtain large N duals of the local Calabi-Yau geometries that engineer N=2 gauge theories. In particular, a double scaling limit of the Gross-Witten one-plaquette lattice model gives the SU(2) Seiberg-Witten solution, including its induced gravitational corrections. Secondly, we point out that the effective superpotential terms for N=1 ADE quiver gauge theories is similarly computed by large multi-matrix models, that have been considered in the context of ADE minimal models on random surfaces. The associated spectral curves are multiple branched covers obtained as Virasoro and W-constraints of the partition function.

  16. On geometry and matrix models

    Science.gov (United States)

    Dijkgraaf, Robbert; Vafa, Cumrun

    2002-11-01

    We point out two extensions of the relation between matrix models, topological strings and N=1 supersymmetric gauge theories. First, we note that by considering double scaling limits of unitary matrix models one can obtain large- N duals of the local Calabi-Yau geometries that engineer N=2 gauge theories. In particular, a double scaling limit of the Gross-Witten one-plaquette lattice model gives the SU(2) Seiberg-Witten solution, including its induced gravitational corrections. Secondly, we point out that the effective superpotential terms for N=1 ADE quiver gauge theories is similarly computed by large- N multi-matrix models, that have been considered in the context of ADE minimal models on random surfaces. The associated spectral curves are multiple branched covers obtained as Virasoro and W-constraints of the partition function.

  17. On geometry and matrix models

    Energy Technology Data Exchange (ETDEWEB)

    Dijkgraaf, Robbert E-mail: rhd@science.uva.nl; Vafa, Cumrun

    2002-11-11

    We point out two extensions of the relation between matrix models, topological strings and N=1 supersymmetric gauge theories. First, we note that by considering double scaling limits of unitary matrix models one can obtain large-N duals of the local Calabi-Yau geometries that engineer N=2 gauge theories. In particular, a double scaling limit of the Gross-Witten one-plaquette lattice model gives the SU(2) Seiberg-Witten solution, including its induced gravitational corrections. Secondly, we point out that the effective superpotential terms for N=1 ADE quiver gauge theories is similarly computed by large-N multi-matrix models, that have been considered in the context of ADE minimal models on random surfaces. The associated spectral curves are multiple branched covers obtained as Virasoro and W-constraints of the partition function.

  18. Analysis of proteinaceous components of the organic matrix of endoskeletal sclerites from the alcyonarian Lobophytum crassum.

    Science.gov (United States)

    Rahman, M Azizur; Isa, Y; Takemura, A; Uehara, T

    2006-03-01

    The mesoglea of alcyonarians is occupied by an abundance of minute calcitic sclerites. The sclerites of the alcyonarian Lobophytum crassum contain a water-soluble organic matrix comprising 0.48% of the sclerite weight and a water-insoluble fraction comprising 1.15% of the sclerite weight. Analysis of proteinaceous components in the soluble fraction shows a particularly high content of aspartic acid, followed by alanine, glycine, and glutamate. Aspartic acid, glycine, alanine, and glutamate are the most abundant residues in the insoluble fraction. In both cases, the fractions show the highest concentration of aspartic acid from the total proteins. In an in vitro assay, we show that the matrix proteins extracted from the calcitic sclerites induce the formation of amorphous calcium carbonate prior to its transformation into the calcitic crystalline form. We also show scanning electron micrographs of the rhombohedral calcite crystals used as template, the protein imprinted with these crystals. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of both matrices shows the protein fractions at 67 and 48 kDa. The soluble matrix shows two additional faint bands. Both fractions stain for a carbohydrate at 67 kDa, indicating a glycoprotein at this molecular weight. A newly derived protein sequence was subjected to bioinformatics analysis involving identification of similarities to other acidic proteins. The identification of these proteins in alcyonarian endoskeletal sclerites emphasizes the fundamental importance of such acidic proteins and sheds more light on the functions of these proteins in the processes of biocalcification.

  19. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    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 conformatio...

  20. Bioavailability of long-chain omega-3 fatty acids.

    Science.gov (United States)

    Schuchardt, Jan Philipp; Hahn, Andreas

    2013-07-01

    Supplements have reached a prominent role in improving the supply of long-chain omega-3 fatty acids, such as Eicosapentaenoic acid (EPA 20:5n-3) and Docosahexaenoic acid (DHA 22:6n-3). Similar to other nutrients, the availability of omega-3 fatty acids is highly variable and determined by numerous factors. However, the question of omega-3 fatty acids bioavailability has long been disregarded, which may have contributed to the neutral or negative results concerning their effects in several studies. This review provides an overview of the influence of chemical binding form (free fatty acids bound in ethylesters, triacylglycerides or phospholipids), matrix effects (capsule ingestion with concomitant intake of food, fat content in food) or galenic form (i.e. microencapsulation, emulsification) on the bioavailability of omega-3 fatty acids. There is a need to systematically investigate the bioavailability of omega-3 fatty acids formulations, which might be a key to designing more effective studies in the future.

  1. Functional Similarity and Interpersonal Attraction.

    Science.gov (United States)

    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…

  2. Similitudes, diferencias y agonismos en los efectos pleiotrópicos de las estatinas y los ácidos grasos omega-3 Similarities, differences and agonisms of pleiotropic effects of statins and omega-3 fatty acids

    Directory of Open Access Journals (Sweden)

    M.ª E. Villalobos

    2010-12-01

    grupos de compuestos en el tratamiento de CVD y se concluye que pueden obtenerse claros beneficios.This paper compares the pleiotropic effects of statins and omega-3 fatty acids (n-3 PUFA in treating and preventing cardiovascular disease (CVD and deals with the possible interactions of those compounds. Statins represent one of the most important discoveries to have been made in the field of cardiovascular medicine in recent decades. Their beneficial cardiovascular effects, which have reduced the number of fatal events in patients with atherosclerosis, encompass more than their ability to lower cholesterol levels. The pleiotropic effects of statins involve their anti-inflammatory and antiplatelet properties and their ability to normalize endothelial function. In addition, these drugs may display antiarrhythmic activity, improve insulin sensitivity and counteract hypertension and obesity. The low rate of coronary disease documented in Eskimos corroborates the cardioprotective effects of the n-3 PUFA eicosapentaenoic (EPA and docosahexaenoic acids beyond their hypolipemic effects. The reduction of CVD-related deaths attributable to the action of α-linolenic fatty acid appears to be related to its strong antiarrhythmic properties. In addition, as a precursor of EPA and this last fatty acid of thromboxane A3, prostacyclin I3, serie-3 prostaglandines and serie 5-leukotrines and inhibitor/modulator of thromboxane A2, prostacyclin I2, serie-2 prostaglandines and serie 4-leukotrienes formation, the α-linolenic acid may reduce inflammation and thrombogenesis. As results of some studies suggest that the combined use of statins and n-3 PUFA improves cardiovascular protection and reduces the CVD-related mortality rate; the paper also reviews the possible synergism between both groups of compounds on CVD treatment and concludes that clear benefits may be obtained.

  3. 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.

    Science.gov (United States)

    Alqahtani, Mashael F; Smith, Craig M; Weiss, Scott L; Dawson, Susan; Ralay Ranaivo, Hantamalala; Wainwright, Mark S

    2016-01-01

    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) (psepsis.

  4. Alteration of the interconversion of pyruvate and malate in the plastid or cytosol of ripening tomato fruit invokes diverse consequences on sugar but similar effects on cellular organic acid, metabolism, and transitory starch accumulation.

    Science.gov (United States)

    Osorio, Sonia; Vallarino, José G; Szecowka, Marek; Ufaz, Shai; Tzin, Vered; Angelovici, Ruthie; Galili, Gad; Fernie, Alisdair R

    2013-02-01

    The aim of this work was to investigate the effect of decreased cytosolic phosphoenolpyruvate carboxykinase (PEPCK) and plastidic NADP-dependent malic enzyme (ME) on tomato (Solanum lycopersicum) ripening. Transgenic tomato plants with strongly reduced levels of PEPCK and plastidic NADP-ME were generated by RNA interference gene silencing under the control of a ripening-specific E8 promoter. While these genetic modifications had relatively little effect on the total fruit yield and size, they had strong effects on fruit metabolism. Both transformants were characterized by lower levels of starch at breaker stage. Analysis of the activation state of ADP-glucose pyrophosphorylase correlated with the decrease of starch in both transformants, which suggests that it is due to an altered cellular redox status. Moreover, metabolic profiling and feeding experiments involving positionally labeled glucoses of fruits lacking in plastidic NADP-ME and cytosolic PEPCK activities revealed differential changes in overall respiration rates and tricarboxylic acid (TCA) cycle flux. Inactivation of cytosolic PEPCK affected the respiration rate, which suggests that an excess of oxaloacetate is converted to aspartate and reintroduced in the TCA cycle via 2-oxoglutarate/glutamate. On the other hand, the plastidic NADP-ME antisense lines were characterized by no changes in respiration rates and TCA cycle flux, which together with increases of pyruvate kinase and phosphoenolpyruvate carboxylase activities indicate that pyruvate is supplied through these enzymes to the TCA cycle. These results are discussed in the context of current models of the importance of malate during tomato fruit ripening.

  5. Preparation of bioconjugates by solid-phase conjugation to ion exchange matrix-adsorbed carrier proteins

    DEFF Research Database (Denmark)

    Houen, G.; Olsen, D.T.; Hansen, P.R.;

    2003-01-01

    A solid-phase conjugation method utilizing carrier protein bound to an ion exchange matrix was developed. Ovalbumin was adsorbed to an anion exchange matrix using a batch procedure, and the immobilized protein was then derivatized with iodoacetic acid N-hydroxysuccinimid ester. The activated......, and immunization experiments with the eluted conjugates showed that the more substituted conjugates gave rise to the highest titers of glutathione antibodies. Direct immunization with the conjugates adsorbed to the ion exchange matrix was possible and gave rise to high titers of glutathione antibodies. Conjugates...... of ovalbumin and various peptides were prepared in a similar manner and used for production of peptide antisera by direct immunization with the conjugates bound to the ion exchanger. Advantages of the method are its solid-phase nature, allowing fast and efficient reactions and intermediate washings...

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

    Directory of Open Access Journals (Sweden)

    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.

  7. a Comparison of Semantic Similarity Models in Evaluating Concept Similarity

    Science.gov (United States)

    Xu, Q. X.; Shi, W. Z.

    2012-08-01

    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.

  8. The Matrix Cookbook

    DEFF Research Database (Denmark)

    Petersen, Kaare Brandt; Pedersen, Michael Syskind

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

  9. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

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

  10. EMRE Is a Matrix Ca2+ Sensor that Governs Gatekeeping of the Mitochondrial Ca2+ Uniporter

    Directory of Open Access Journals (Sweden)

    Horia Vais

    2016-01-01

    Full Text Available The mitochondrial uniporter (MCU is an ion channel that mediates Ca2+ uptake into the matrix to regulate metabolism, cell death, and cytoplasmic Ca2+ signaling. Matrix Ca2+ concentration is similar to that in cytoplasm, despite an enormous driving force for entry, but the mechanisms that prevent mitochondrial Ca2+ overload are unclear. Here, we show that MCU channel activity is governed by matrix Ca2+ concentration through EMRE. Deletion or charge neutralization of its matrix-localized acidic C terminus abolishes matrix Ca2+ inhibition of MCU Ca2+ currents, resulting in MCU channel activation, enhanced mitochondrial Ca2+ uptake, and constitutively elevated matrix Ca2+ concentration. EMRE-dependent regulation of MCU channel activity requires intermembrane space-localized MICU1, MICU2, and cytoplasmic Ca2+. Thus, mitochondria are protected from Ca2+ depletion and Ca2+ overload by a unique molecular complex that involves Ca2+ sensors on both sides of the inner mitochondrial membrane, coupled through EMRE.

  11. Amino acid similarities and divergences in the small surface proteins of genotype C hepatitis B viruses between nucleos(t)ide analogue-naïve and lamivudine-treated patients with chronic hepatitis B.

    Science.gov (United States)

    Ding, Hai; Liu, Baoming; Zhao, Chengyu; Yang, Jingxian; Yan, Chunhui; Yan, Ling; Zhuang, Hui; Li, Tong

    2014-02-01

    Entire C-genotype small hepatitis B surface (SHBs) sequences were isolated from 139 nucleos(t)ide analogues (NA)-naïve and 74 lamivudine (LMV)-treated chronic hepatitis B (CHB) patients. The conservation and variability of total 226 amino acids (AAs) within the sequences were determined individually, revealing significant higher mutant isolate rate and mutation frequency in LMV-treated cohort than those in the NA-naïve one (P=0.009 and 0.0001, respectively). Three absolutely conserved fragments (s16-s19, s176-s181 and s185-s188) and seven moderately conserved regions (a few AA sites acquiring increased variability after LMV-treatment) were identified. The significant mutation rate increase after LMV-treatment occurred primarily in major hydrophilic region (except 'a' determinant) and transmembrane domain 3/4, but not in other upstream functional regions of SHBs. With little influence on immune escape-associated mutation frequencies within 'a' determinant, LMV-monotherapy significantly induced classical LMVr-associated mirror changes sE164D/rtV173L, sI195M/rtM204V and sW196L/S/rtM204I, as well as non-classical ones sG44E/rtS53N, sT47K/A/rtH55R/Q and sW182stop/rtV191I outside 'a' determinant. Interestingly, another newly-identified truncation mutation sC69stop/rtS78T decreased from 7.91% (11/139) in NA-naïve cohort to 2.70% (2/74) in LMV-treated one. Altogether, the altered AA conservation and diversity in SHBs sequences after LMV-treatment in genotype-C HBV infection might shed new insights into how LMV-therapy affects the SHBs variant evolution and its antigenicity.

  12. Similarity Learning of Manifold Data.

    Science.gov (United States)

    Chen, Si-Bao; Ding, Chris H Q; Luo, Bin

    2015-09-01

    Without constructing adjacency graph for neighborhood, we propose a method to learn similarity among sample points of manifold in Laplacian embedding (LE) based on adding constraints of linear reconstruction and least absolute shrinkage and selection operator type minimization. Two algorithms and corresponding analyses are presented to learn similarity for mix-signed and nonnegative data respectively. The similarity learning method is further extended to kernel spaces. The experiments on both synthetic and real world benchmark data sets demonstrate that the proposed LE with new similarity has better visualization and achieves higher accuracy in classification.

  13. RECOGNITION OF STRUCTURE SIMILARITIES IN PROTEINS

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Protein fold structure is more conserved than its amino acid sequence and closely associated with biological function,so calculating the similarity of protein structures is a fundamental problem in structural biology and plays a key role in protein fold classification,fold function inference,and protein structure prediction.Large progress has been made in recent years in this field and many methods for considering structural similarity have been proposed,including methods for protein structure compar-ison,retrieval of protein structures from databases,and ligand binding site comparison.Most of those methods can be available on the World Wide Web,but evaluation of all the methods is still a hard problem.This paper summarizes some popular methods and latest methods for structure similarities,including structure alignment,protein structure retrieval,and ligand binding site alignment.

  14. Matrix with Prescribed Eigenvectors

    Science.gov (United States)

    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…

  15. A toolbox for representational similarity analysis.

    Directory of Open Access Journals (Sweden)

    Hamed Nili

    2014-04-01

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

  16. Dynamic similarity in erosional processes

    Science.gov (United States)

    Scheidegger, A.E.

    1963-01-01

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

  17. Compressive Sequential Learning for Action Similarity Labeling.

    Science.gov (United States)

    Qin, Jie; Liu, Li; Zhang, Zhaoxiang; Wang, Yunhong; Shao, Ling

    2016-02-01

    Human action recognition in videos has been extensively studied in recent years due to its wide range of applications. Instead of classifying video sequences into a number of action categories, in this paper, we focus on a particular problem of action similarity labeling (ASLAN), which aims at verifying whether a pair of videos contain the same type of action or not. To address this challenge, a novel approach called compressive sequential learning (CSL) is proposed by leveraging the compressive sensing theory and sequential learning. We first project data points to a low-dimensional space by effectively exploring an important property in compressive sensing: the restricted isometry property. In particular, a very sparse measurement matrix is adopted to reduce the dimensionality efficiently. We then learn an ensemble classifier for measuring similarities between pairwise videos by iteratively minimizing its empirical risk with the AdaBoost strategy on the training set. Unlike conventional AdaBoost, the weak learner for each iteration is not explicitly defined and its parameters are learned through greedy optimization. Furthermore, an alternative of CSL named compressive sequential encoding is developed as an encoding technique and followed by a linear classifier to address the similarity-labeling problem. Our method has been systematically evaluated on four action data sets: ASLAN, KTH, HMDB51, and Hollywood2, and the results show the effectiveness and superiority of our method for ASLAN.

  18. Similarly shaped letters evoke similar colors in grapheme-color synesthesia.

    Science.gov (United States)

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

    2011-04-01

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

  19. Similarity of samples and trimming

    CERN Document Server

    Álvarez-Esteban, Pedro C; Cuesta-Albertos, Juan A; Matrán, Carlos; 10.3150/11-BEJ351

    2012-01-01

    We say that two probabilities are similar at level $\\alpha$ if they are contaminated versions (up to an $\\alpha$ fraction) of the same common probability. We show how this model is related to minimal distances between sets of trimmed probabilities. Empirical versions turn out to present an overfitting effect in the sense that trimming beyond the similarity level results in trimmed samples that are closer than expected to each other. We show how this can be combined with a bootstrap approach to assess similarity from two data samples.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  1. Self-similar aftershock rates

    CERN Document Server

    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.

  2. Self-similar aftershock rates

    Science.gov (United States)

    Davidsen, Jörn; Baiesi, Marco

    2016-08-01

    In many important systems exhibiting crackling noise—an intermittent avalanchelike 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 particularly 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 particularly clear evidence for a unified description of aftershocks and foreshocks. This may offer an improved framework for time-dependent seismic hazard assessment and earthquake forecasting.

  3. Contextual Bandits with Similarity Information

    CERN Document Server

    Slivkins, Aleksandrs

    2009-01-01

    In a multi-armed bandit (MAB) problem, an online algorithm makes a sequence of choices. In each round it chooses from a time-invariant set of alternatives and receives the payoff associated with this alternative. While the case of small strategy sets is by now well-understood, a lot of recent work has focused on MAB problems with exponentially or infinitely large strategy sets, where one needs to assume extra structure in order to make the problem tractable. In particular, recent literature considered information on similarity between arms. We consider similarity information in the setting of "contextual bandits", a natural extension of the basic MAB problem where before each round an algorithm is given the "context" -- a hint about the payoffs in this round. Contextual bandits are directly motivated by placing advertisements on webpages, one of the crucial problems in sponsored search. A particularly simple way to represent similarity information in the contextual bandit setting is via a "similarity distance...

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

    Science.gov (United States)

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

    2014-08-01

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

  5. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    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...... a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single...

  6. Embedded systems for controlling LED matrix displays

    Science.gov (United States)

    Marghescu, Cristina; Drumea, Andrei

    2016-12-01

    LED matrix displays are a common presence in everyday life - they can be found in trains, buses, tramways, office information tables or outdoor media. The structure of the display unit is similar for all these devices, a matrix of light emitting diodes coupled between row and column lines, but there are many options for the display controller that switches these lines. Present paper analyzes different types of embedded systems that can control the LED matrix, based on single board computers, on microcontrollers with different peripheral devices or with programmable logic devices like field programmable gate arrays with implemented soft processor cores. Scalability, easiness of implementation and costs are analyzed for all proposed solutions.

  7. Similarity of atoms in molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cioslowski, J.; Nanayakkara, A. (Florida State Univ., Tallahassee, FL (United States))

    1993-12-01

    Similarity of atoms in molecules is quantitatively assessed with a measure that employs electron densities within respective atomic basins. This atomic similarity measure does not rely on arbitrary assumptions concerning basis functions or 'atomic orbitals', is relatively inexpensive to compute, and has straightforward interpretation. Inspection of similarities between pairs of carbon, hydrogen, and fluorine atoms in the CH[sub 4], CH[sub 3]F, CH[sub 2]F[sub 2], CHF[sub 3], CF[sub 4], C[sub 2]H[sub 2], C[sub 2]H[sub 4], and C[sub 2]H[sub 6] molecules, calculated at the MP2/6-311G[sup **] level of theory, reveals that the atomic similarity is greatly reduced by a change in the number or the character of ligands (i.e. the atoms with nuclei linked through bond paths to the nucleus of the atom in question). On the other hand, atoms with formally identical (i.e. having the same nuclei and numbers of ligands) ligands resemble each other to a large degree, with the similarity indices greater than 0.95 for hydrogens and 0.99 for non-hydrogens. 19 refs., 6 tabs.

  8. Parallelism in matrix computations

    CERN Document Server

    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...

  9. Phosphine in various matrixes

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Matrix-bound phosphine was determined in the Jiaozhou Bay coastal sediment, in prawn-pond bottom soil, in the eutrophic lake Wulongtan, in the sewage sludge and in paddy soil as well. Results showed that matrix-bound phosphine levels in freshwater and coastal sediment, as well as in sewage sludge, are significantly higher than that in paddy soil. The correlation between matrix bound phosphine concentrations and organic phosphorus contents in sediment samples is discussed.

  10. Similarity measures for face recognition

    CERN Document Server

    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.

  11. Novel entries in a fungal biofilm matrix encyclopedia.

    Science.gov (United States)

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

    2014-08-05

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

  12. Mixed matrix membrane development.

    Science.gov (United States)

    Kulprathipanja, Santi

    2003-03-01

    Two types of mixed matrix membranes were developed by UOP in the late 1980s. The first type includes adsorbent polymers, such as silicalite-cellulose acetate (CA), NaX-CA, and AgX-CA mixed matrix membranes. The silicalite-CA has a CO(2)/H(2) selectivity of 5.15 +/- 2.2. In contrast, the CA membrane has a CO(2)/H(2) selectivity of 0.77 +/- 0.06. The second type of mixed matrix membrane is PEG-silicone rubber. The PEG-silicone rubber mixed matrix membrane has high selectivity for polar gases, such as SO(2), NH(3), and H(2)S.

  13. Distance learning for similarity estimation

    NARCIS (Netherlands)

    Yu, J.; Amores, J.; Sebe, N.; Radeva, P.; Tian, Q.

    2008-01-01

    In this paper, we present a general guideline to find a better distance measure for similarity estimation based on statistical analysis of distribution models and distance functions. A new set of distance measures are derived from the harmonic distance, the geometric distance, and their generalized

  14. Distance learning for similarity estimation.

    Science.gov (United States)

    Yu, Jie; Amores, Jaume; Sebe, Nicu; Radeva, Petia; Tian, Qi

    2008-03-01

    In this paper, we present a general guideline to find a better distance measure for similarity estimation based on statistical analysis of distribution models and distance functions. A new set of distance measures are derived from the harmonic distance, the geometric distance, and their generalized variants according to the Maximum Likelihood theory. These measures can provide a more accurate feature model than the classical Euclidean and Manhattan distances. We also find that the feature elements are often from heterogeneous sources that may have different influence on similarity estimation. Therefore, the assumption of single isotropic distribution model is often inappropriate. To alleviate this problem, we use a boosted distance measure framework that finds multiple distance measures which fit the distribution of selected feature elements best for accurate similarity estimation. The new distance measures for similarity estimation are tested on two applications: stereo matching and motion tracking in video sequences. The performance of boosted distance measure is further evaluated on several benchmark data sets from the UCI repository and two image retrieval applications. In all the experiments, robust results are obtained based on the proposed methods.

  15. Comparison of hydrological similarity measures

    Science.gov (United States)

    Rianna, Maura; Ridolfi, Elena; Manciola, Piergiorgio; Napolitano, Francesco; Russo, Fabio

    2016-04-01

    The use of a traditional at site approach for the statistical characterization and simulation of spatio-temporal precipitation fields has a major recognized drawback. Indeed, the weakness of the methodology is related to the estimation of rare events and it involves the uncertainty of the at-site sample statistical inference, because of the limited length of records. In order to overcome the lack of at-site observations, regional frequency approach uses the idea of substituting space for time to estimate design floods. The conventional regional frequency analysis estimates quantile values at a specific site from multi-site analysis. The main idea is that homogeneous sites, once pooled together, have similar probability distribution curves of extremes, except for a scaling factor. The method for pooling groups of sites can be based on geographical or climatological considerations. In this work the region of influence (ROI) pooling method is compared with an entropy-based one. The ROI is a flexible pooling group approach which defines for each site its own "region" formed by a unique set of similar stations. The similarity is found through the Euclidean distance metric in the attribute space. Here an alternative approach based on entropy is introduced to cluster homogeneous sites. The core idea is that homogeneous sites share a redundant (i.e. similar) amount of information. Homogeneous sites are pooled through a hierarchical selection based on the mutual information index (i.e. a measure of redundancy). The method is tested on precipitation data in Central Italy area.

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

    Energy Technology Data Exchange (ETDEWEB)

    Murakami, Kazumasa; Sato, Asami; Hashimoto, Kenro; Fujino, Tatsuya, E-mail: fujino@tmu.ac.jp

    2013-06-20

    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]{sup +} in the electronic ground state.

  17. HOW DISSIMILARLY SIMILAR ARE BIOSIMILARS?

    Directory of Open Access Journals (Sweden)

    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.

  18. [Modern polymers in matrix tablets technology].

    Science.gov (United States)

    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.

  19. Involvement of extracellular matrix constituents in breast cancer

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Patience of matrix games

    DEFF Research Database (Denmark)

    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...

  1. Protein structure similarity from principle component correlation analysis

    Directory of Open Access Journals (Sweden)

    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

  2. Detailed protein sequence alignment based on Spectral Similarity Score (SSS

    Directory of Open Access Journals (Sweden)

    Thomas Dina

    2005-04-01

    Full Text Available Abstract Background The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. Results Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. Conclusion An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral

  3. Sparse Similarity-Based Fisherfaces

    DEFF Research Database (Denmark)

    Fagertun, Jens; Gomez, David Delgado; Hansen, Mads Fogtmann;

    2011-01-01

    In this work, the effect of introducing Sparse Principal Component Analysis within the Similarity-based Fisherfaces algorithm is examined. The technique aims at mimicking the human ability to discriminate faces by projecting the faces in a highly discriminative and easy interpretative way. Pixel...... obtain the same recognition results as the technique in a dense version using only a fraction of the input data. Furthermore, the presented results suggest that using SPCA in the technique offers robustness to occlusions....

  4. Active browsing using similarity pyramids

    Science.gov (United States)

    Chen, Jau-Yuen; Bouman, Charles A.; Dalton, John C.

    1998-12-01

    In this paper, we describe a new approach to managing large image databases, which we call active browsing. Active browsing integrates relevance feedback into the browsing environment, so that users can modify the database's organization to suit the desired task. Our method is based on a similarity pyramid data structure, which hierarchically organizes the database, so that it can be efficiently browsed. At coarse levels, the similarity pyramid allows users to view the database as large clusters of similar images. Alternatively, users can 'zoom into' finer levels to view individual images. We discuss relevance feedback for the browsing process, and argue that it is fundamentally different from relevance feedback for more traditional search-by-query tasks. We propose two fundamental operations for active browsing: pruning and reorganization. Both of these operations depend on a user-defined relevance set, which represents the image or set of images desired by the user. We present statistical methods for accurately pruning the database, and we propose a new 'worm hole' distance metric for reorganizing the database, so that members of the relevance set are grouped together.

  5. Self-Similar Collisionless Shocks

    CERN Document Server

    Katz, B; Waxman, E; Katz, Boaz; Keshet, Uri; Waxman, Eli

    2006-01-01

    Observations of gamma-ray burst afterglows suggest that the correlation length of magnetic field fluctuations downstream of relativistic non-magnetized collisionless shocks grows with distance from the shock to scales much larger than the plasma skin depth. We argue that this indicates that the plasma properties are described by a self-similar solution, and derive constraints on the scaling properties of the solution. For example, we find that the scaling of the characteristic magnetic field amplitude with distance from the shock is B \\propto D^{s_B} with -1 \\propto x^{2s_B} (for x>>D). We show that the plasma may be approximated as a combination of two self-similar components: a kinetic component of energetic particles and an MHD-like component representing "thermal" particles. We argue that the latter may be considered as infinitely conducting, in which case s_B=0 and the scalings are completely determined (e.g. dn/dE \\propto E^{-2} and B \\propto D^0). Similar claims apply to non- relativistic shocks such a...

  6. Roget's Thesaurus and Semantic Similarity

    CERN Document Server

    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 ...

  7. Differential Effects of Domoic Acid and E. coli Lipopolysaccharide on Tumor Necrosis Factor-α, Transforming Growth Factor-β1 and Matrix Metalloproteinase-9 Release by Rat Neonatal Microglia: Evaluation of the Direct Activation Hypothesis

    Directory of Open Access Journals (Sweden)

    Sarath P. Gunasekera

    2007-09-01

    Full Text Available The excitatory amino acid domoic acid is the causative agent of amnesic shellfish poisoning in humans. The in vitro effects of domoic acid on rat neonatal brain microglia were compared with E. coli lipopolysaccharide (LPS, a known activator of microglia mediator release over a 4 to 24 hour observation period. LPS [3 ng/mL] but not domoic acid [1mM] stimulated a statistically significant increase in TNF-α mRNA and protein generation. Furthermore, both LPS and domoic acid did not significantly affect TGF- β1 gene expression and protein release. Finally, an in vitro exposure of microglia to LPS resulted in statistically significant MMP-9 expression and release, thus extending and confirming our previous observations. However, in contrast, no statistically significant increase in MMP-9 expression and release was observed after domoic acid treatment. Taken together our observations do not support the hypothesis that a short term (4 to 24 hours in vitro exposure to domoic acid, at a concentration toxic to neuronal cells, activates rat neonatal microglia and the concomitant release of the pro-inflammatory mediators tumor necrosis factor-α (TNF-α and matrix metalloproteinases-9 (MMP-9, as well as the anti- inflammatory cytokine transforming growth factor β1 (TGF-β1.

  8. Assessing protein kinase target similarity

    DEFF Research Database (Denmark)

    Gani, Osman A; Thakkar, Balmukund; Narayanan, Dilip

    2015-01-01

    : focussed chemical libraries, drug repurposing, polypharmacological design, to name a few. Protein kinase target similarity is easily quantified by sequence, and its relevance to ligand design includes broad classification by key binding sites, evaluation of resistance mutations, and the use of surrogate......" of sequence and crystal structure information, with statistical methods able to identify key correlates to activity but also here, "the devil is in the details." Examples from specific repurposing and polypharmacology applications illustrate these points. This article is part of a Special Issue entitled...

  9. Measurement of Similarity for Spatial Directions Between Areal Objects

    Institute of Scientific and Technical Information of China (English)

    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.

  10. Improved Matrix Uncertainty Selector

    CERN Document Server

    Rosenbaum, Mathieu

    2011-01-01

    We consider the regression model with observation error in the design: y=X\\theta* + e, Z=X+N. Here the random vector y in R^n and the random n*p matrix Z are observed, the n*p matrix X is unknown, N is an n*p random noise matrix, e in R^n is a random noise vector, and \\theta* is a vector of unknown parameters to be estimated. We consider the setting where the dimension p can be much larger than the sample size n and \\theta* is sparse. Because of the presence of the noise matrix N, the commonly used Lasso and Dantzig selector are unstable. An alternative procedure called the Matrix Uncertainty (MU) selector has been proposed in Rosenbaum and Tsybakov (2010) in order to account for the noise. The properties of the MU selector have been studied in Rosenbaum and Tsybakov (2010) for sparse \\theta* under the assumption that the noise matrix N is deterministic and its values are small. In this paper, we propose a modification of the MU selector when N is a random matrix with zero-mean entries having the variances th...

  11. Mechanisms for similarity based cooperation

    Science.gov (United States)

    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.

  12. Elementary matrix theory

    CERN Document Server

    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

  13. Rheocasting Al matrix composites

    Energy Technology Data Exchange (ETDEWEB)

    Girot, F.A.; Albingre, L.; Quenisset, J.M.; Naslain, R.

    1987-11-01

    A development status account is given for the rheocasting method of Al-alloy matrix/SiC-whisker composites, which involves the incorporation and homogeneous distribution of 8-15 vol pct of whiskers through the stirring of the semisolid matrix melt while retaining sufficient fluidity for casting. Both 1-, 3-, and 6-mm fibers of Nicalon SiC and and SiC whisker reinforcements have been experimentally investigated, with attention to the characterization of the resulting microstructures and the effects of fiber-matrix interactions. A thin silica layer is found at the whisker surface. 7 references.

  14. Interneurons targeting similar layers receive synaptic inputs with similar kinetics.

    Science.gov (United States)

    Cossart, Rosa; Petanjek, Zdravko; Dumitriu, Dani; Hirsch, June C; Ben-Ari, Yehezkel; Esclapez, Monique; Bernard, Christophe

    2006-01-01

    GABAergic interneurons play diverse and important roles in controlling neuronal network dynamics. They are characterized by an extreme heterogeneity morphologically, neurochemically, and physiologically, but a functionally relevant classification is still lacking. Present taxonomy is essentially based on their postsynaptic targets, but a physiological counterpart to this classification has not yet been determined. Using a quantitative analysis based on multidimensional clustering of morphological and physiological variables, we now demonstrate a strong correlation between the kinetics of glutamate and GABA miniature synaptic currents received by CA1 hippocampal interneurons and the laminar distribution of their axons: neurons that project to the same layer(s) receive synaptic inputs with similar kinetics distributions. In contrast, the kinetics distributions of GABAergic and glutamatergic synaptic events received by a given interneuron do not depend upon its somatic location or dendritic arborization. Although the mechanisms responsible for this unexpected observation are still unclear, our results suggest that interneurons may be programmed to receive synaptic currents with specific temporal dynamics depending on their targets and the local networks in which they operate.

  15. Algorithm Research of Individualized Travelling Route Recommendation Based on Similarity

    Directory of Open Access Journals (Sweden)

    Xue Shan

    2015-01-01

    Full Text Available Although commercial recommendation system has made certain achievement in travelling route development, the recommendation system is facing a series of challenges because of people’s increasing interest in travelling. It is obvious that the core content of the recommendation system is recommendation algorithm. The advantages of recommendation algorithm can bring great effect to the recommendation system. Based on this, this paper applies traditional collaborative filtering algorithm for analysis. Besides, illustrating the deficiencies of the algorithm, such as the rating unicity and rating matrix sparsity, this paper proposes an improved algorithm combing the multi-similarity algorithm based on user and the element similarity algorithm based on user, so as to compensate for the deficiencies that traditional algorithm has within a controllable range. Experimental results have shown that the improved algorithm has obvious advantages in comparison with the traditional one. The improved algorithm has obvious effect on remedying the rating matrix sparsity and rating unicity.

  16. Performance Indexes: Similarities and Differences

    Directory of Open Access Journals (Sweden)

    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.

  17. Semantically enabled image similarity search

    Science.gov (United States)

    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.

  18. SIMILARITIES AND DIFFERENCES BETWEEN COMPANIES

    Directory of Open Access Journals (Sweden)

    NAGY CRISTINA MIHAELA

    2015-05-01

    Full Text Available act: Similarities between the accounting of companies and territorial administrative units accounting are the following: organizing double entry accounting; accounting method both in terms of fundamental theoretical principles and specific practical tools. The differences between the accounting of companies and of territorial administrative units refer to: the accounting of territorial administrative units includes besides general accounting (financial also budgetary accounting, and the accounts system of the budgetary accounting is completely different from that of companies; financial statements of territorial administrative units to which leaders are not main authorizing officers are submitted to the hierarchically superior body (not at MPF; the accounts of territorial administrative units are opened at treasury and financial institutions, accounts at commercial banks being prohibited; equity accounts in territorial administrative units are structured into groups of funds; long term debts have a specific structure in territorial administrative units (internal local public debt and external local public debt.

  19. Features Based Text Similarity Detection

    CERN Document Server

    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...

  20. Physiology and pathophysiology of matrix metalloproteases

    NARCIS (Netherlands)

    Klein, T.; Bischoff, R.

    2011-01-01

    Matrix metalloproteases (MMPs) comprise a family of enzymes that cleave protein substrates based on a conserved mechanism involving activation of an active site-bound water molecule by a Zn(2+) ion. Although the catalytic domain of MMPs is structurally highly similar, there are many differences with

  1. Pesticide-Exposure Matrix

    Science.gov (United States)

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

  2. Matrix comparison, Part 2

    DEFF Research Database (Denmark)

    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...... important. Alternatively, or as a supplement, Procrustes analysis compares the actual ordination results without investigating the underlying proximity measures, by matching two configurations of the same objects in a multidimensional space. An advantage of the Procrustes analysis though, is the graphical...

  3. The Matrix Organization Revisited

    DEFF Research Database (Denmark)

    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)....

  4. Matrix fractional systems

    Science.gov (United States)

    Tenreiro Machado, J. A.

    2015-08-01

    This paper addresses the matrix representation of dynamical systems in the perspective of fractional calculus. Fractional elements and fractional systems are interpreted under the light of the classical Cole-Cole, Davidson-Cole, and Havriliak-Negami heuristic models. Numerical simulations for an electrical circuit enlighten the results for matrix based models and high fractional orders. The conclusions clarify the distinction between fractional elements and fractional systems.

  5. HYALURONIC ACID IN DERMAL REJUVENATION: AN IN VITRO STUDY.

    Science.gov (United States)

    Avantaggiato, A; Pascali, M; Lauritano, D; Cura, F; Pezzetti, F; Palmieri, A

    2015-01-01

    The purpose of this paper is to evaluate the role of hyaluronic acid in bio-revitalization by testing several extracellular matrix biological parameters in cultured dermal fibroblasts. To this aim, fibroblastic expressed genes after exposition to three hyaluronic acid medical devices were evaluated. Cells were seeded on a layer of three different medical devices containing 6.2, 10 and 20 mg/ml of hyaluronic acid for 24 h. Real Time Polymerase Chain Reaction was performed to investigate gene expressions. Genes encoding hyaluronic acid synthesis and degradation, Metalloproteinases 2 and 3 and Desmoplakin production as well as GDF6, and IGF1 were activated by hyaluronic acid products. The in vitro study showed similar effects on tested genes despite a different concentration of hyaluronic acid contained in the medical devices and the simultaneous presence of other additives. Based on the reported data, gene activations are an aspect of metabolic modulation of signalling pathways rather than the proportional production of a specific connective tissue molecule. Indeed different hyaluronic acid concentration and the presence of other additives did not change the overall effect on the studied genes. We believe that the optimization of extracellular matrix micro-environment, obtained by enhanced structural support with hyaluronic acid, leads to functional and metabolic improvement.

  6. Effects of extracts of Dragon's blood on fibroblast proliferation and extracellular matrix hyaluronic acid%血竭提取物对成纤维细胞增殖及合成透明质酸的影响

    Institute of Scientific and Technical Information of China (English)

    李丹; 惠瑞; 胡咏武; 韩岩; 郭树忠

    2015-01-01

    Objective To investigate the effects of Dragon' s blood extract on proliferation and secret extracellular matrix function of fibroblasts in vitro.Methods Dragon ' s blood was extracted by chloroform,acetoacetic ester,alcohol.Human fibroblast were cultured in vitro in media containing gradient dilutions of Dragon's blood extracts (0.002,0.02,0.2,2,20 mg/ml),which was followed by cell proliferation assessed with MTT assay on 0,12,24,36,48,60,72 h.Under the optimal concentration,the cell growth curves were drawn and the flow cytometry (FCM) was used to determine the changes of cell cycle.On 0,12,24,36,48,60,72 h,the concentration of hyaluronic acid in the supernatant of fibroblast culture was measured by radioimmunoassay.Results 0.2-2 mg/ml Dragon' s blood extracts enhanced the proliferation of fibroblasts in a dose-dependent manner.2 mg/ml was the optimal dilution of Dragon' s blood extract,and it increased the ratio of S cells in cell cycle[(25.80 ± 3.10) %] than control group[(7.50 ± 0.70)%,P < 0.01].From 12 h to 72 h,in 2 mg/ml Dragon's blood group,concentration of Hyaluronic acid secreted by fibroblasts gradually increased,but were less than control(P < 0.01).Conclusions Dragon ' s blood acetoacetic ester extract improved the proliferation of cultured human fibroblasts in vitro,might be beneficial to promote wound healing.%目的 研究血竭提取物对成纤维细胞生物学作用的影响.方法 将血竭经过氯仿、乙酸乙酯、乙醇依次回流提取分别得到3种血竭提取液,培养液稀释后行成纤维细胞培养.噻唑蓝法MTT检测浓度分别为0.002、0.02、0.2、2、20 mg/ml的血竭提取物,在0、12、24、36、48、60、72h7个检测点对体外培养成纤维细胞增殖的影响,并绘制最适浓度下细胞生长曲线.流式细胞术FCM分析最适浓度培养下成纤维细胞的细胞周期变化.应用放射免疫分析法检测0、12、24、36、48、60、72 h细胞培养上清液中透明质酸(hyaluronic acid

  7. Structure and assembly of a paramyxovirus matrix protein.

    Science.gov (United States)

    Battisti, Anthony J; Meng, Geng; Winkler, Dennis C; McGinnes, Lori W; Plevka, Pavel; Steven, Alasdair C; Morrison, Trudy G; Rossmann, Michael G

    2012-08-28

    Many pleomorphic, lipid-enveloped viruses encode matrix proteins that direct their assembly and budding, but the mechanism of this process is unclear. We have combined X-ray crystallography and cryoelectron tomography to show that the matrix protein of Newcastle disease virus, a paramyxovirus and relative of measles virus, forms dimers that assemble into pseudotetrameric arrays that generate the membrane curvature necessary for virus budding. We show that the glycoproteins are anchored in the gaps between the matrix proteins and that the helical nucleocapsids are associated in register with the matrix arrays. About 90% of virions lack matrix arrays, suggesting that, in agreement with previous biological observations, the matrix protein needs to dissociate from the viral membrane during maturation, as is required for fusion and release of the nucleocapsid into the host's cytoplasm. Structure and sequence conservation imply that other paramyxovirus matrix proteins function similarly.

  8. 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.

    Directory of Open Access Journals (Sweden)

    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

  9. 聚乳酸/骨基质明胶多孔复合材料的生物相容性研究%BIOCOMPATIBILITY OF POROUS POLY LACTIC ACID/BONE MATRIX GELATIN COMPOSITE BIOMATERIALS FOR BONE REPAIR

    Institute of Scientific and Technical Information of China (English)

    张育敏; 李晶; 牛晓军; 刘建春; 王珏; 高岚

    2016-01-01

    目的 探讨超临界CO2法制备的聚乳酸(poly lactic acid,PLA)/骨基质明胶(bone matrix gelatin, BMG)多孔复合材料的生物相容性,为其下一步骨缺损修复奠定基础.方法 取小鼠成骨前体细胞MCT3T-E1细胞,分别与PLA/BMG多孔复合材料和PLA材料的浸提液培养7d,每天采用MTT法测定细胞增殖率并进行细胞毒性分级.将PLA/BMG多孔复合材料与MC3T3-E1细胞复合培养,1、3、5d于倒置相差显微镜下观察细胞生长及与材料贴附情况,5d时取材行扫描电镜观察细胞贴附情况.将PLA材料(PLA组)及PLA/BMG多孔复合材料(PLA/BMG组)分别植于15只Wistar大鼠背部两侧皮下,术后大体观察大鼠一般情况,2、4、8周取材行组织学观察,测量包膜厚度、炎性细胞数及血管面积.结果 体外细胞毒性检测示,培养1 ~7 d PLA/BMG组细胞增殖率均达100%以上,细胞毒性均为0级;而PLA组除1、3、5、6d细胞毒性为0级外,2、4、7d细胞增殖率均低于100%,细胞毒性级为1级.PLA/BMG多孔复合材料与细胞复合培养,可见随时间延长细胞逐渐长入材料孔隙内,细胞形态良好.材料皮下植入后,大鼠均存活至实验完成,切口愈合良好;PLA组材料被纤维结缔组织所包裹,周围组织及材料内含有较多炎性细胞,结缔组织向材料内部生长缓慢;PLA/BMG组纤维组织包裹不明显,结缔组织易于向材料中心长入且其中炎性细胞少见.两组各时间点包膜厚度差异无统计学意义(P>0.05).PLA/BMG组2、4、8周炎性细胞数均显著低于PLA组(P<0.05),8周血管面积高于PLA组(P<0.05).结论 超临界CO2法制备的PLA/BMG多孔复合材料具有良好的细胞和组织相容性.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  12. Processing of continuous fiber composites using thermoplastic polyimide matrix resins

    Energy Technology Data Exchange (ETDEWEB)

    Kranjc, M.D.

    1993-01-01

    Composites have been produced which contain a solvent resistant polyimide matrix with favorable physical properties. The polyimide matrix resin has been designated as P12. The prepegs used to produce the composite contain a low molecular weight resin which is the polyamic acid precursor to P12. Polymerization and imidization of the precursor resin occurs in-situ during processing. Similar commercial systems are often processed in an autoclave and pressure is used at high temperatures to obtain consolidation between prepreg laminates. Pressure is generally applied after polymerization and imidization are complete and at temperatures above the melting point of the polymer. In this research a significant decrease in composite void content was obtained by applying pressure earlier in the cure. Obtaining composites with low void content with these types of systems can be difficult. This is due in part to the generation of low molecular weight reaction by products, water and methanol. High void content results in a decrease in the physical properties of the composite structure. This is especially true for fracture properties. An empirical equation was used to describe the rate of resin removal from the composite to the bleeder cloth during processing. This equation is based on Springer-Loos resin flow model. The conditions in which this model does not apply were also determined. Determining resin removal rates is helpful in producing composites with consistent fiber/resin ratios. In addition, conditions which favor void growth can be prevented.

  13. Similarities between decapod and insect neuropeptidomes

    Science.gov (United States)

    2016-01-01

    Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives, and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases, the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified: elongated PDH (pigment dispersing hormone), a variation on PDH that has a two-amino-acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species, and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for decapod neuropeptides

  14. Similarities between decapod and insect neuropeptidomes

    Directory of Open Access Journals (Sweden)

    Jan A. Veenstra

    2016-05-01

    Full Text Available Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives, and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases, the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified: elongated PDH (pigment dispersing hormone, a variation on PDH that has a two-amino-acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species, and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for

  15. Similarities between decapod and insect neuropeptidomes.

    Science.gov (United States)

    Veenstra, Jan A

    2016-01-01

    Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives, and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases, the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified: elongated PDH (pigment dispersing hormone), a variation on PDH that has a two-amino-acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species, and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for decapod neuropeptides

  16. 2matrix: A Utility for Indel Coding and Phylogenetic Matrix Concatenation

    Directory of Open Access Journals (Sweden)

    Nelson R. Salinas

    2014-01-01

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

  17. A Novel MALDI Matrix for Analyzing Peptides and Proteins: Paraffin Wax Immobilized Matrix

    Institute of Scientific and Technical Information of China (English)

    WEI Yuanlong; MEI Yuan; XU Zhe; WANG Cuihong; GUO Yinlong; DU Yiping; ZHANG Weibing

    2009-01-01

    A new kind of MALDI matrix, termed paraffin wax immobilized matrix, was used to study peptide mixtures and proteins. During the preparation process, the paraffin wax was heated and coated on the stainless-steel target plate, and then 2,5-dihydrobenzoic acid (DHB) was deposited on the paraffin layer and stainless-steel target plate to obtain different kinds of matrix spots. The morphology of matrices on different supports and peptide-matrix co-crystallization were observed by a high resolution digital-video microscopy system. Peptide mixtures and bovine serum albumin (BSA) digests were used to investigate the performance of the immobilized matrices on the paraffin target. The MALDI-FTMS analysis results also showed that the detection sensitivity of matrices immobilized in the paraffin sample support was better than that on other sample supports.

  18. Matrix Information Geometry

    CERN Document Server

    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.  

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

    Institute of Scientific and Technical Information of China (English)

    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.

  20. Extracellular matrix structure.

    Science.gov (United States)

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

    2016-02-01

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

  1. Ceramic Matrix Composites .

    Directory of Open Access Journals (Sweden)

    J. Mukerji

    1993-10-01

    Full Text Available The present state of the knowledge of ceramic-matrix composites have been reviewed. The fracture toughness of present structural ceramics are not enough to permit design of high performance machines with ceramic parts. They also fail by catastrophic brittle fracture. It is generally believed that further improvement of fracture toughness is only possible by making composites of ceramics with ceramic fibre, particulate or platelets. Only ceramic-matrix composites capable of working above 1000 degree centigrade has been dealt with keeping reinforced plastics and metal-reinforced ceramics outside the purview. The author has discussed the basic mechanisms of toughening and fabrication of composites and the difficulties involved. Properties of available fibres and whiskers have been given. The best results obtained so far have been indicated. The limitations of improvement in properties of ceramic-matrix composites have been discussed.

  2. Matrix interdiction problem

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Finite Temperature Matrix Theory

    CERN Document Server

    Meana, M L; Peñalba, J P; Meana, Marco Laucelli; Peñalba, Jesús Puente

    1998-01-01

    We present the way the Lorentz invariant canonical partition function for Matrix Theory as a light-cone formulation of M-theory can be computed. We explicitly show how when the eleventh dimension is decompactified, the N=1 eleven dimensional SUGRA partition function appears. From this particular analysis we also clarify the question about the discernibility problem when making statistics with supergravitons (the N! problem) in Matrix black hole configurations. We also provide a high temperature expansion which captures some structure of the canonical partition function when interactions amongst D-particles are on. The connection with the semi-classical computations thermalizing the open superstrings attached to a D-particle is also clarified through a Born-Oppenheimer approximation. Some ideas about how Matrix Theory would describe the complementary degrees of freedom of the massless content of eleven dimensional SUGRA are also discussed.

  4. Matrixed business support comparison study.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  5. Reduced Google matrix

    CERN Document Server

    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.

  6. IIB Matrix Model

    CERN Document Server

    Aoki, H; Kawai, H; Kitazawa, Y; Tada, T; Tsuchiya, A

    1999-01-01

    We review our proposal for a constructive definition of superstring, type IIB matrix model. The IIB matrix model is a manifestly covariant model for space-time and matter which possesses N=2 supersymmetry in ten dimensions. We refine our arguments to reproduce string perturbation theory based on the loop equations. We emphasize that the space-time is dynamically determined from the eigenvalue distributions of the matrices. We also explain how matter, gauge fields and gravitation appear as fluctuations around dynamically determined space-time.

  7. Little IIB Matrix Model

    CERN Document Server

    Kitazawa, Y; Saito, O; Kitazawa, Yoshihisa; Mizoguchi, Shun'ya; Saito, Osamu

    2006-01-01

    We study the zero-dimensional reduced model of D=6 pure super Yang-Mills theory and argue that the large N limit describes the (2,0) Little String Theory. The one-loop effective action shows that the force exerted between two diagonal blocks of matrices behaves as 1/r^4, implying a six-dimensional spacetime. We also observe that it is due to non-gravitational interactions. We construct wave functions and vertex operators which realize the D=6, (2,0) tensor representation. We also comment on other "little" analogues of the IIB matrix model and Matrix Theory with less supercharges.

  8. Density matrix perturbation theory.

    Science.gov (United States)

    Niklasson, Anders M N; Challacombe, Matt

    2004-05-14

    An orbital-free quantum perturbation theory is proposed. It gives the response of the density matrix upon variation of the Hamiltonian by quadratically convergent recursions based on perturbed projections. The technique allows treatment of embedded quantum subsystems with a computational cost scaling linearly with the size of the perturbed region, O(N(pert.)), and as O(1) with the total system size. The method allows efficient high order perturbation expansions, as demonstrated with an example involving a 10th order expansion. Density matrix analogs of Wigner's 2n+1 rule are also presented.

  9. Rheocasting Al Matrix Composites

    Science.gov (United States)

    Girot, F. A.; Albingre, L.; Quenisset, J. M.; Naslain, R.

    1987-11-01

    Aluminum alloy matrix composites reinforced by SiC short fibers (or whiskers) can be prepared by rheocasting, a process which consists of the incorporation and homogeneous distribution of the reinforcement by stirring within a semi-solid alloy. Using this technique, composites containing fiber volume fractions in the range of 8-15%, have been obtained for various fibers lengths (i.e., 1 mm, 3 mm and 6 mm for SiC fibers). This paper attempts to delineate the best compocasting conditions for aluminum matrix composites reinforced by short SiC (e.g Nicalon) or SiC whiskers (e.g., Tokamax) and characterize the resulting microstructures.

  10. Elementary matrix algebra

    CERN Document Server

    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

  11. Proteins from the organic matrix of core-top and fossil planktonic foraminifera

    Science.gov (United States)

    Robbins, L. L.; Brew, K.

    1990-08-01

    Organic constituents isolated from the tests (shells) of six species of core-top planktonic foraminifera, ranging in age between 2 and 4 Ka BP, consist of a heterogeneous mixture of proteins and polypeptides. At least seven discrete polypeptides are present as indicated by reverse phase HPLC and by gel electrophoresis. High percentages of aspartic acid and glutamic acid characterize one class of protein, while glycine, serine, and alanine-rich proteins dominate in a second class. Similar HPLC Chromatographie elution profiles are observed for all species analyzed, varying only in intensity of the peaks and in amino acid composition from species to species. The approximate molecular weights of two major fossil proteins ranged between 50,000 and 70,000 daltons. A comparison of 2-4 and 300 Ka Bp samples shows that while most of the polypeptides are present in both samples, some acidic polypeptides are not present in the older sample. These data suggest that some of the acidic polypeptides may be more soluble than other fractions and are lost more quickly from the test. The remaining hydrophobic, possibly more insoluble, polypeptides may be preserved in much older specimens and may be useful in tracing phylogeny of the planktonic foraminifera. Amino acid analyses of total test extracts before and after dialysis demonstrate that some acidic amino acids, particularly aspartic acid, and possibly peptides less than 6000-8000 daltons are lost during dialysis. Although a large percentage of these components are undoubtedly from the original organic matrix, at this point adsorbed components cannot be ruled out. These data caution against the use of total amino acid compositions in biogeochemical studies.

  12. Inequalities Involving Upper Bounds for Certain Matrix Operators

    Indian Academy of Sciences (India)

    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].

  13. Dynamic Matrix Rank

    DEFF Research Database (Denmark)

    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) entri...... 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.......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...

  14. Matrix Embedded Organic Synthesis

    Science.gov (United States)

    Kamakolanu, U. G.; Freund, F. T.

    2016-05-01

    In the matrix of minerals such as olivine, a redox reaction of the low-z elements occurs. Oxygen is oxidized to the peroxy state while the low-Z-elements become chemically reduced. We assign them a formula [CxHyOzNiSj]n- and call them proto-organics.

  15. Generalized Framework for Similarity Measure of Time Series

    Directory of Open Access Journals (Sweden)

    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.

  16. Evaluation of dried blood spots as sample matrix for gas chromatography/mass spectrometry based metabolomic profiling.

    Science.gov (United States)

    Kong, Sing Teang; Lin, Hai-Shu; Ching, Jianhong; Ho, Paul C

    2011-06-01

    We propose using dried blood spots (DBS) as sample matrix for gas chromatography/mass spectrometry (GC/MS) based metabolomic profiling for the benefits of higher sample stability, more convenient sample acquisition with DBS, higher analyte separation power, and more readily biomarker identification with GC/MS. To establish this proposition, the metabolomic profiles generated from DBS were compared with that obtained from the conventional whole blood and plasma matrixes and also with dried plasma spots (DPS) as another covariate control. Our findings indicated that whole blood produced the most number of detectable markers (866), whereas DPS yielded the least number (614). DBS and plasma matrix, on the other hand, produced the most similar numbers of detectable (695 vs 749) and identifiable markers (137 vs 147, matching with Fiehn library). From the analysis of the DBS and plasma metabolomic profiles, it was concluded that when l-lysine 2, iminodiacetic acid 2, dl-threo-beta-hydroxyaspartic acid, citric acid, or adenosine-5-monophosphate 2 are not involved as markers, DBS could be a suitable substitute for plasma for metabolomic profiling.

  17. Redesigning Triangular Dense Matrix Computations on GPUs

    KAUST Repository

    Charara, Ali

    2016-08-09

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

  18. Inequalities between similarities for numerical data

    NARCIS (Netherlands)

    Warrens, Matthijs J.

    2016-01-01

    Similarity measures are entities that can be used to quantify the similarity between two vectors with real numbers. We present inequalities between seven well known similarities. The inequalities are valid if the vectors contain non-negative real numbers.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  20. Molecular cloning and characterization of lustrin A, a matrix protein from shell and pearl nacre of Haliotis rufescens.

    Science.gov (United States)

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

    1997-12-19

    A specialized extracellular matrix of proteins and polysaccharides controls the morphology and packing of calcium carbonate crystals and becomes occluded within the mineralized composite during formation of the molluscan shell and pearl. We have cloned and characterized the cDNA coding for Lustrin A, a newly described matrix protein from the nacreous layer of the shell and pearl produced by the abalone, Haliotis rufescens, a marine gastropod mollusc. The full-length cDNA is 4,439 base pairs (bp) long and contains an open reading frame coding for 1,428 amino acids. The deduced amino acid sequence reveals a highly modular structure with a high proportion of Ser (16%), Pro (14%), Gly (13%), and Cys (9%). The protein contains ten highly conserved cysteine-rich domains interspersed by eight proline-rich domains; a glycine- and serine-rich domain lies between the two cysteine-rich domains nearest the C terminus, and these are followed by a basic domain and a C-terminal domain that is highly similar to known protease inhibitors. The glycine- and serine-rich domain and at least one of the proline-rich domains show sequence similarity to proteins of two extracellular matrix superfamilies (one of which also is involved in the mineralized matrixes of bone, dentin, and avian eggshell). The arrangement of alternating cysteine-rich domains and proline-rich domains is strikingly similar to that found in frustulins, the proteins that are integral to the silicified cell wall of diatoms. Its modular structure suggests that Lustrin A is a multifunctional protein, whereas the occurrence of related sequences suggest it is a member of a multiprotein family.

  1. 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

    Institute of Scientific and Technical Information of China (English)

    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

  2. Matrix string theory

    Science.gov (United States)

    Dijkgraaf, Robbert; Verlinde, Erik; Verlinde, Herman

    1997-02-01

    Via compactification on a circle, the matrix mode] of M-theory proposed by Banks et a]. suggests a concrete identification between the large N limit of two-dimensional N = 8 supersymmetric Yang-Mills theory and type IIA string theory. In this paper we collect evidence that supports this identification. We explicitly identify the perturbative string states and their interactions, and describe the appearance of D-particle and D-membrane states.

  3. Matrix string theory

    Energy Technology Data Exchange (ETDEWEB)

    Dijkgraaf, R. [Amsterdam Univ. (Netherlands). Dept. of Mathematics; Verlinde, E. [TH-Division, CERN, CH-1211 Geneva 23 (Switzerland)]|[Institute for Theoretical Physics, Universtity of Utrecht, 3508 TA Utrecht (Netherlands); Verlinde, H. [Institute for Theoretical Physics, University of Amsterdam, 1018 XE Amsterdam (Netherlands)

    1997-09-01

    Via compactification on a circle, the matrix model of M-theory proposed by Banks et al. suggests a concrete identification between the large N limit of two-dimensional N=8 supersymmetric Yang-Mills theory and type IIA string theory. In this paper we collect evidence that supports this identification. We explicitly identify the perturbative string states and their interactions, and describe the appearance of D-particle and D-membrane states. (orig.).

  4. Matrix String Theory

    CERN Document Server

    Dijkgraaf, R; Verlinde, Herman L

    1997-01-01

    Via compactification on a circle, the matrix model of M-theory proposed by Banks et al suggests a concrete identification between the large N limit of two-dimensional N=8 supersymmetric Yang-Mills theory and type IIA string theory. In this paper we collect evidence that supports this identification. We explicitly identify the perturbative string states and their interactions, and describe the appearance of D-particle and D-membrane states.

  5. Holomorphic matrix integrals

    CERN Document Server

    Felder, G; Felder, Giovanni; Riser, Roman

    2004-01-01

    We study a class of holomorphic matrix models. The integrals are taken over middle dimensional cycles in the space of complex square matrices. As the size of the matrices tends to infinity, the distribution of eigenvalues is given by a measure with support on a collection of arcs in the complex planes. We show that the arcs are level sets of the imaginary part of a hyperelliptic integral connecting branch points.

  6. NMR structure of the myristylated feline immunodeficiency virus matrix protein.

    Science.gov (United States)

    Brown, Lola A; Cox, Cassiah; Baptiste, Janae; Summers, Holly; Button, Ryan; Bahlow, Kennedy; Spurrier, Vaughn; Kyser, Jenna; Luttge, Benjamin G; Kuo, Lillian; Freed, Eric O; Summers, Michael F

    2015-04-30

    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(4,5)P2]. 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(4,5)P2 from the plasma membrane of FIV-infected CRFK cells inhibited production of FIV particles, indicating that, like HIV, FIV hijacks the PI(4,5)P2 cellular signaling system to direct intracellular Gag trafficking during virus assembly.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Metal matrix Composites

    Directory of Open Access Journals (Sweden)

    Pradeep K. Rohatgi

    1993-10-01

    Full Text Available This paper reviews the world wide upsurge in metal matrix composite research and development activities with particular emphasis on cast metal-matrix particulate composites. Extensive applications of cast aluminium alloy MMCs in day-to-day use in transportation as well as durable good industries are expected to advance rapidly in the next decade. The potential for extensive application of cast composites is very large in India, especially in the areas of transportation, energy and electromechanical machinery; the extensive use of composites can lead to large savings in materials and energy, and in several instances, reduce environmental pollution. It is important that engineering education and short-term courses be organized to bring MMCs to the attention of students and engineering industry leaders. India already has excellent infrastructure for development of composites, and has a long track record of world class research in cast metal matrix particulate composites. It is now necessary to catalyze prototype and regular production of selected composite components, and get them used in different sectors, especially railways, cars, trucks, buses, scooters and other electromechanical machinery. This will require suitable policies backed up by funding to bring together the first rate talent in cast composites which already exists in India, to form viable development groups followed by setting up of production plants involving the process engineering capability already available within the country. On the longer term, cast composites should be developed for use in energy generation equipment, electronic packaging aerospace systems, and smart structures.

  9. Risk evaluation with enhaced covariance matrix

    CERN Document Server

    Urbanowicz, K; Richmond, P; Holyst, Janusz A.; Richmond, Peter; Urbanowicz, Krzysztof

    2006-01-01

    We propose a route for the evaluation of risk based on a transformation of the covariance matrix. The approach uses a `potential' or `objective' function. This allows us to rescale data from diferent assets (or sources) such that each set then has similar statistical properties in terms of their probability distributions. The method is tested using historical data from both the New York and Warsaw Stock Exchanges.

  10. Matrix-addressable electrochromic display cell

    Science.gov (United States)

    Beni, G.; Schiavone, L. M.

    1981-04-01

    We report an electrochromic display cell with intrinsic matrix addressability. The cell, based on a sputtered iridium oxide film (SIROF) and a tantalum-oxide hysteretic counterelectrode, has electrochromic parameters (i.e., response times, operating voltages, and contrast) similar to those of other SIROF display devices, but in addition, has short-circuit memory and voltage threshold. Memory and threshold are sufficiently large to allow, in principle, multiplexing of electrochromic display panels of large-screen TV pixel size.

  11. Chromatographic fingerprint similarity analysis for pollutant source identification.

    Science.gov (United States)

    Xie, Juan-Ping; Ni, Hong-Gang

    2015-12-01

    In the present study, a similarity analysis method was proposed to evaluate the source-sink relationships among environmental media for polybrominated diphenyl ethers (PBDEs), which were taken as the representative contaminants. Chromatographic fingerprint analysis has been widely used in the fields of natural products chemistry and forensic chemistry, but its application to environmental science has been limited. We established a library of various sources of media containing contaminants (e.g., plastics), recognizing that the establishment of a more comprehensive library allows for a better understanding of the sources of contamination. We then compared an environmental complex mixture (e.g., sediment, soil) with the profiles in the library. These comparisons could be used as the first step in source tracking. The cosine similarities between plastic and soil or sediment ranged from 0.53 to 0.68, suggesting that plastic in electronic waste is an important source of PBDEs in the environment, but it is not the only source. A similarity analysis between soil and sediment indicated that they have a source-sink relationship. Generally, the similarity analysis method can encompass more relevant information of complex mixtures in the environment than a profile-based approach that only focuses on target pollutants. There is an inherent advantage to creating a data matrix containing all peaks and their relative levels after matching the peaks based on retention times and peak areas. This data matrix can be used for source identification via a similarity analysis without quantitative or qualitative analysis of all chemicals in a sample.

  12. Matrix Theory of Small Oscillations

    Science.gov (United States)

    Chavda, L. K.

    1978-01-01

    A complete matrix formulation of the theory of small oscillations is presented. Simple analytic solutions involving matrix functions are found which clearly exhibit the transients, the damping factors, the Breit-Wigner form for resonances, etc. (BB)

  13. Boric acid and boronic acids inhibition of pigeonpea urease.

    Science.gov (United States)

    Reddy, K Ravi Charan; Kayastha, Arvind M

    2006-08-01

    Urease from the seeds of pigeonpea was competitively inhibited by boric acid, butylboronic acid, phenylboronic acid, and 4-bromophenylboronic acid; 4-bromophenylboronic acid being the strongest inhibitor, followed by boric acid > butylboronic acid > phenylboronic acid, respectively. Urease inhibition by boric acid is maximal at acidic pH (5.0) and minimal at alkaline pH (10.0), i.e., the trigonal planar B(OH)3 form is a more effective inhibitor than the tetrahedral B(OH)4 -anionic form. Similarly, the anionic form of phenylboronic acid was least inhibiting in nature.

  14. Matrix Completions and Chordal Graphs

    Institute of Scientific and Technical Information of China (English)

    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.

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

    DEFF Research Database (Denmark)

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

    1994-01-01

    , and analyzed directly by MALDI-MS. Based on the three mass spectrometric peptide maps, an error in the sequence deduced from cDNA, resulting in a mass difference of 28 Da, was located to a sequence stretch of 5 amino acid residues; furthermore, a dihexose substituent was identified on Thr410. Subsequent Edman...

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

    Directory of Open Access Journals (Sweden)

    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.

  17. THE GENERALIZED POLARIZATION SCATTERING MATRIX

    Science.gov (United States)

    the Least Square Best Estimate of the Generalized Polarization matrix from a set of measurements is then developed. It is shown that the Faraday...matrix data. It is then shown that the Least Square Best Estimate of the orientation angle of a symmetric target is also determinable from Faraday rotation contaminated short pulse monostatic polarization matrix data.

  18. Synthetic and Biopolymer Gels - Similarities and Difference.

    Science.gov (United States)

    Horkay, Ferenc

    2006-03-01

    Ion exchange plays a central role in a variety of physiological processes, such as nerve excitation, muscle contraction and cell locomotion. Hydrogels can be used as model systems for identifying fundamental chemical and physical interactions that govern structure formation, phase transition, etc. in biopolymer systems. Polyelectrolyte gels are particularly well-suited to study ion-polymer interactions because their structure and physical-chemical properties (charge density, crosslink density, etc) can be carefully controlled. They are sensitive to different external stimuli such as temperature, ionic composition and pH. Surprisingly few investigations have been made on polyelectrolyte gels in salt solutions containing both monovalent and multivalent cations. We have developed an experimental approach that combines small angle neutron scattering and osmotic swelling pressure measurements. The osmotic pressure exerted on a macroscopic scale is a consequence of changes occurring at a molecular level. The intensity of the neutron scattering signal, which provides structural information as a function of spatial resolution, is directly related to the osmotic pressure. We have found a striking similarity in the scattering and osmotic behavior of polyacrylic acid gels and DNA gels swollen in nearly physiological salt solutions. Addition of calcium ions to both systems causes a sudden volume change. This volume transition, which occurs when the majority of the sodium counterions are replaced by calcium ions, is reversible. Such reversibility implies that the calcium ions are not strongly bound by the polyanion, but are free to move along the polymer chain, which allows these ions to form temporary bridges between negative charges on adjacent chains. Mechanical measurements reveal that the elastic modulus is practically unchanged in the calcium-containing gels, i.e., ion bridging is qualitatively different from covalent crosslinks.

  19. Safety and efficacy findings from a non-interventional study of a new hyaluronic acid/sorbitol formulation (GO-ON® matrix) for intra-articular injection to relieve pain and disability in osteoarthritis patients.

    Science.gov (United States)

    Heisel, J; Kipshoven, C

    2013-09-01

    This non-interventional study was intended to examine the efficacy and tolerability of intra-articular injections with the GO-ON® matrix, a new viscosupplement product made of non-animal sodium hyaluronate combined with the oxygen free radical scavenger sorbitol, when used in routine clinical practice. A total of 1 147 patients (43.5% male, 53,5% female, 3% missing) aged on average 63.3 years with osteoarthritis were enrolled in 398 centers and treated with the product. The most commonly treated joint was the knee (92.9%) with a Kellgren-Lawrence classification of Grade I (6.7%), Grade II (31.4%), Grade III (48.0%), and Grade IV (13.9%).Most patients (58-66%, imputing for missing data) received 1 injection, 29-40% received 3 injections. Using a Likert scale to asses pain, the mean change in pain due to osteoarthritis was a reduction of 56.5% from baseline (2.61±0.80) to 6 months (1.07±0.86). At baseline, 56.2% of patients reported severe/very severe pain versus 5.9% after 6 months. Accordingly, 6.8% of patients reported no pain/mild pain at baseline vs. 67.1% after 6 months. At baseline, 28.9% reported no pain/mild pain vs. to 66.4% after 6 months. At baseline, 29.1% of patients reported severe/very severe functional impairment vs. 3.9% 6 months after the first injection. The 3 and 6 month results were comparable.Adverse reactions were rare and confined to musculoskeletal and connective tissue disorders. No infections were reported in any treated joints. The results confirm that the GO-ON matrix® treatment is effective and well tolerated in the treatment of symptoms due to osteoarthritis.

  20. Statistical meaning of the differential Mueller matrix of depolarizing homogeneous media.

    Science.gov (United States)

    Ossikovski, Razvigor; Arteaga, Oriol

    2014-08-01

    By applying the statistical definition of a depolarizing Mueller matrix we formally derive and physically interpret the differential matrix of a depolarizing homogeneous medium. The depolarization phenomenon being a direct consequence of the fluctuations of the six elementary polarization properties of the medium, the differential matrix contains the mean values and the variances of the properties, thus fully describing those from a statistical viewpoint. Similarly, the reduced coherency matrix associated with the G-symmetric component of the differential matrix has an immediate physical interpretation as being the covariance matrix of the three basic groups of polarization properties. The formal developments are illustrated on experimental examples.

  1. The cellulose resource matrix.

    Science.gov (United States)

    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

  2. Supported Molecular Matrix Electrophoresis.

    Science.gov (United States)

    Matsuno, Yu-Ki; Kameyama, Akihiko

    2015-01-01

    Mucins are difficult to separate using conventional gel electrophoresis methods such as SDS-PAGE and agarose gel electrophoresis, owing to their large size and heterogeneity. On the other hand, cellulose acetate membrane electrophoresis can separate these molecules, but is not compatible with glycan analysis. Here, we describe a novel membrane electrophoresis technique, termed "supported molecular matrix electrophoresis" (SMME), in which a porous polyvinylidene difluoride (PVDF) membrane filter is used to achieve separation. This description includes the separation, visualization, and glycan analysis of mucins with the SMME technique.

  3. Matrix vector analysis

    CERN Document Server

    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

  4. Matrix string partition function

    CERN Document Server

    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.

  5. Matrix algebra for linear models

    CERN Document Server

    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

  6. Reconstructing propagation networks with temporal similarity metrics

    CERN Document Server

    Liao, Hao

    2014-01-01

    Node similarity is a significant property driving the growth of real networks. In this paper, based on the observed spreading results we apply the node similarity metrics to reconstruct propagation networks. We find that the reconstruction accuracy of the similarity metrics is strongly influenced by the infection rate of the spreading process. Moreover, there is a range of infection rate in which the reconstruction accuracy of some similarity metrics drops to nearly zero. In order to improve the similarity-based reconstruction method, we finally propose a temporal similarity metric to take into account the time information of the spreading. The reconstruction results are remarkably improved with the new method.

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

    Directory of Open Access Journals (Sweden)

    Žel Jana

    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

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

    Institute of Scientific and Technical Information of China (English)

    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...

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Conditional Similarity Solutions of the Boussinesq Equation

    Institute of Scientific and Technical Information of China (English)

    TANG Xiao-Yan; LIN Ji; LOU Sen-Yue

    2001-01-01

    The direct method proposed by Clarkson and Kruskal is modified to obtain some conditional similarity solutions of a nonlinear physics model. Taking the (1+ 1 )-dimensional Boussinesq equation as a simple example, six types of conditional similarity reductions are obtained.

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

    CERN Document Server

    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".

  12. Shape Similarity Measures of Linear Entities

    Institute of Scientific and Technical Information of China (English)

    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.

  13. Optical Characterization of Chemically Etched Nanoporous Silicon Embedded in Sol-Gel Matrix

    Directory of Open Access Journals (Sweden)

    A. S. Al Dwayyan

    2012-01-01

    Full Text Available Nanoporous (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.

  14. Google matrix, dynamical attractors, and Ulam networks

    Science.gov (United States)

    Shepelyansky, D. L.; Zhirov, O. V.

    2010-03-01

    We study the properties of the Google matrix generated by a coarse-grained Perron-Frobenius operator of the Chirikov typical map with dissipation. The finite-size matrix approximant of this operator is constructed by the Ulam method. This method applied to the simple dynamical model generates directed Ulam networks with approximate scale-free scaling and characteristics being in certain features similar to those of the world wide web with approximate scale-free degree distributions as well as two characteristics similar to the web: a power-law decay in PageRank that mirrors the decay of PageRank on the world wide web and a sensitivity to the value α in PageRank. The simple dynamical attractors play here the role of popular websites with a strong concentration of PageRank. A variation in the Google parameter α or other parameters of the dynamical map can drive the PageRank of the Google matrix to a delocalized phase with a strange attractor where the Google search becomes inefficient.

  15. Light cone matrix product

    Energy Technology Data Exchange (ETDEWEB)

    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.

  16. Matrix Graph Grammars

    CERN Document Server

    Velasco, Pedro Pablo Perez

    2008-01-01

    This book objective is to develop an algebraization of graph grammars. Equivalently, we study graph dynamics. From the point of view of a computer scientist, graph grammars are a natural generalization of Chomsky grammars for which a purely algebraic approach does not exist up to now. A Chomsky (or string) grammar is, roughly speaking, a precise description of a formal language (which in essence is a set of strings). On a more discrete mathematical style, it can be said that graph grammars -- Matrix Graph Grammars in particular -- study dynamics of graphs. Ideally, this algebraization would enforce our understanding of grammars in general, providing new analysis techniques and generalizations of concepts, problems and results known so far.

  17. Matrix Quantization of Turbulence

    CERN Document Server

    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.

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

    Science.gov (United States)

    Liu, Xiaojun; Zeng, Shimei; Dong, Shaojian; Jin, Can; Li, Jiale

    2015-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Xiaojun Liu

    Full Text Available In this study, we clone and characterize a novel matrix protein, hic31, from the mantle of Hyriopsis cumingii. The amino acid composition of hic31 consists of a high proportion of Glycine residues (26.67%. Tissue expression detection by RT-PCR indicates that hic31 is expressed specifically at the mantle edge. In situ hybridization results reveals strong signals from the dorsal epithelial cells of the outer fold at the mantle edge, and weak signals from inner epithelial cells of the same fold, indicating that hic31 is a prismatic-layer matrix protein. Although BLASTP results identify no shared homology with other shell-matrix proteins or any other known proteins, the hic31 tertiary structure is similar to that of collagen I, alpha 1 and alpha 2. It has been well proved that collagen forms the basic organic frameworks in way of collagen fibrils and minerals present within or outside of these fibrils. Therefore, hic31 might be a framework-matrix protein involved in the prismatic-layer biomineralization. Besides, the gene expression of hic31 increase in the early stages of pearl sac development, indicating that hic31 may play important roles in biomineralization of the pearl prismatic layer.

  20. Aspartic acid

    Science.gov (United States)

    Aspartic acid is a nonessential amino acids . Amino acids are building blocks of proteins. "Nonessential" means that our ... this amino acid from the food we eat. Aspartic acid is also called asparaginic acid. Aspartic acid helps ...

  1. Algebraic matrix equations in two unknowns

    CERN Document Server

    Bourgeois, Gerald

    2011-01-01

    Let r1,r2,s1,s2 be integers such that gcd(r1,r2)=1 and gcd(s1,s2)=1. We solve the matrix equation A^{r1}B^{s1}A^{r2}B^{s2}=+-Identity where A,B are 2,2 complex matrices that have no common eigenvectors. Let p,q be coprime integers such that |p|+|q|>2. We study the matrix equation B^{-1}A^pB=A^q where A,B are n,n complex invertible matrices. We show that such matrices satisfy B^{-1}AB and A commute. We provide a necessary and sufficient condition for similarity of A^p and A^q. We explicitly solve this problem when A has n distinct eigenvalues and in other particular cases.

  2. Relativistic recursion relations for transition matrix elements

    CERN Document Server

    Martínez y Romero, R P; Salas-Brito, A L

    2004-01-01

    We review some recent results on recursion relations which help evaluating arbitrary non-diagonal, radial hydrogenic matrix elements of $r^\\lambda$ and of $\\beta r^\\lambda$ ($\\beta$ a Dirac matrix) derived in the context of Dirac relativistic quantum mechanics. Similar recursion relations were derived some years ago by Blanchard in the non relativistic limit. Our approach is based on a generalization of the second hypervirial method previously employed in the non-relativistic Schr\\"odinger case. An extension of the relations to the case of two potentials in the so-called unshifted case, but using an arbitrary radial function instead of a power one, is also given. Several important results are obtained as special instances of our recurrence relations, such as a generalization to the relativistic case of the Pasternack-Sternheimer rule. Our results are useful in any atomic or molecular calculation which take into account relativistic corrections.

  3. Association of Chromosomal Telomere DNA With Nuclear Matrix in HeLa Cell

    Institute of Scientific and Technical Information of China (English)

    汪国顺; 罗文捷; 潘惟钧; 丁明孝; 翟中和

    1994-01-01

    Using Electron Spectroscopic Imaging (ESI), we visualized the in situ binding of nucleic acids to nuclear matrix and 3H-thymidine incorporation which indicates that a small partial DNA bound to nuclear matrix tightly. Furthermore we found that chromosomal telomere DNA could bind to nuclear matrix specifically by the dot and Southern hybridization. The result of the Southwestern blot suggests that telomere DNA has high affinity to lamin B, vimentin and some nuclear matrix proteins. Therefore, the nuclear matrix and lamina of HeLa cell are possibly associated with spatial organization and action of chromosome.

  4. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji

    2016-07-14

    Self-similar processes have been widely used in modeling real-world phenomena occurring in environmetrics, network traffic, image processing, and stock pricing, to name but a few. The estimation of the degree of self-similarity has been studied extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi-self-similarity for a random field indexed in higher dimensions. If self-similarity is not rejected, our test provides a set of estimated self-similarity indexes. The key is to test stationarity of the inverse Lamperti transformations of the process. The inverse Lamperti transformation of a self-similar process is a strongly stationary process, revealing a theoretical connection between the two processes. To demonstrate the capability of our test, we test self-similarity of fractional Brownian motions and sheets, their time deformations and mixtures with Gaussian white noise, and the generalized Cauchy family. We also apply the self-similarity test to real data: annual minimum water levels of the Nile River, network traffic records, and surface heights of food wrappings. © 2016, International Biometric Society.

  5. Matrix elements of unstable states

    CERN Document Server

    Bernard, V; Meißner, U -G; Rusetsky, A

    2012-01-01

    Using the language of non-relativistic effective Lagrangians, we formulate a systematic framework for the calculation of resonance matrix elements in lattice QCD. The generalization of the L\\"uscher-Lellouch formula for these matrix elements is derived. We further discuss in detail the procedure of the analytic continuation of the resonance matrix elements into the complex energy plane and investigate the infinite-volume limit.

  6. Lectures on Matrix Field Theory

    Science.gov (United States)

    Ydri, Badis

    The subject of matrix field theory involves matrix models, noncommutative geometry, fuzzy physics and noncommutative field theory and their interplay. In these lectures, a lot of emphasis is placed on the matrix formulation of noncommutative and fuzzy spaces, and on the non-perturbative treatment of the corresponding field theories. In particular, the phase structure of noncommutative $\\phi^4$ theory is treated in great detail, and an introduction to noncommutative gauge theory is given.

  7. Enhancing an R-matrix

    CERN Document Server

    MacKaay, M A

    1996-01-01

    In order to construct a representation of the tangle category one needs an enhanced R-matrix. In this paper we define a sufficient and necessary condition for enhancement that can be checked easily for any R-matrix. If the R-matrix can be enhanced, we also show how to construct the additional data that define the enhancement. As a direct consequence we find a sufficient condition for the construction of a knot invariant.

  8. Genetically similar VHSV isolates are differentially virulent in olive flounder Paralichthys olivaceus.

    Science.gov (United States)

    Cho, Mi Young; Lee, Unn Hwa; Moon, Chang Hoon; Bang, Jong Deuk; Jee, Bo Young; Cha, Seung Ju; Kim, Jin Woo; Park, Myoung Ae; Do, Jeong Wan; Park, Jeong Woo

    2012-11-08

    Two viral hemorrhagic septicemia virus (VHSV) isolates, VHSV-KR-CJA and VHSV-KR-YGH, were isolated from viral hemorrhagic septicemia disease outbreaks in flounder farms in South Korea. The VHSV-KR-CJA isolate was isolated from a flounder farm with high mortality (80%), while the VHSV-KR-YGH isolate was isolated from a flounder farm with low mortality (15%), suggesting that these isolates differ in virulence. The virulence of these isolates was evaluated in juvenile flounder via intraperitoneal injection. Consistent with their virulence in the field, mortality data revealed that the VHSV-KR-CJA isolate was highly pathogenic (cumulative mortality of 80%), while the VHSV-KR-YGH isolate was less pathogenic in flounder (cumulative mortality of 20%). To characterize the genotypes of these viruses, the full open reading frames (ORFs) encoding nucleoprotein N, phosphoprotein P, matrix protein M, glycoprotein G, nonstructural viral protein NV, and polymerase L of these viruses were sequenced and analyzed. Sequence analysis revealed that both isolates are genetically very similar (identical amino acid sequences for P, M, NV, and L and >99.7 and 99.8% amino acid sequence identity for N and G, respectively). Phylogenetic analysis indicated that both of these viruses belong to the Genotype IVa group, suggesting that they originated from a common ancestral virus. The low pathogenicity VHSV strain may potentially evolve to become a more pathogenic strain through only a few nucleotide substitutions. Further functional analyses of mutations in VHSV genes are necessary to identify factors that determine VHSV pathogenicity in flounder.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. Matrix Models and Gravitational Corrections

    CERN Document Server

    Dijkgraaf, R; Temurhan, M; Dijkgraaf, Robbert; Sinkovics, Annamaria; Temurhan, Mine

    2002-01-01

    We provide evidence of the relation between supersymmetric gauge theories and matrix models beyond the planar limit. We compute gravitational R^2 couplings in gauge theories perturbatively, by summing genus one matrix model diagrams. These diagrams give the leading 1/N^2 corrections in the large N limit of the matrix model and can be related to twist field correlators in a collective conformal field theory. In the case of softly broken SU(N) N=2 super Yang-Mills theories, we find that these exact solutions of the matrix models agree with results obtained by topological field theory methods.

  12. A Matrix Model for WZW

    CERN Document Server

    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.

  13. Molecular quantum similarity using conceptual DFT descriptors

    Indian Academy of Sciences (India)

    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.

  14. Cholesterol and stigmasterol within a sunflower oil matrix: Thermal degradation and oxysterols formation.

    Science.gov (United States)

    Barriuso, Blanca; Ansorena, Diana; Poyato, Candelaria; Astiasarán, Iciar

    2015-07-01

    The characteristics of the lipid matrix surrounding sterols exert a great influence in their thermal oxidation process. The objective of this work was to assess the oxidation susceptibility of equal amounts of cholesterol and stigmasterol within a sunflower oil lipid matrix (ratio 1:1:200) during heating (180°C, 0-180min). Remaining percentage of sterols was determined and seven sterol oxidation products (SOPs) were analysed for each type of sterol along the heating treatment. Evolution of the fatty acid profile and vitamin E content of the oil was also studied. Overall oxidation status of the model system was assessed by means of Peroxides Value (PV) and TBARS. PV remained constant from 30min onwards and TBARS continued increasing along the whole heating treatment. Degradation of both cholesterol and stigmasterol fitted a first order curve (R(2)=0.937 and 0.883, respectively), with very similar degradation constants (0.004min(-1) and 0.005min(-1), respectively). However, higher concentrations of oxidation products were found from cholesterol (79μg/mg) than from stigmasterol (53μg/mg) at the end of the heating treatment. Profile of individual oxidation products was similar for both sterols, except for the fact that no 25-hydroxystigmasterol was detected. 7α-Hydroxy and 7-keto-derivatives were the most abundant SOPs at the end of the treatment. PUFA and vitamin E suffered a significant degradation along the process, which was correlated to sterols oxidation.

  15. Similarity effects in visual working memory.

    Science.gov (United States)

    Jiang, Yuhong V; Lee, Hyejin J; Asaad, Anthony; Remington, Roger

    2016-04-01

    Perceptual similarity is an important property of multiple stimuli. Its computation supports a wide range of cognitive functions, including reasoning, categorization, and memory recognition. It is important, therefore, to determine why previous research has found conflicting effects of inter-item similarity on visual working memory. Studies reporting a similarity advantage have used simple stimuli whose similarity varied along a featural continuum. Studies reporting a similarity disadvantage have used complex stimuli from either a single or multiple categories. To elucidate stimulus conditions for similarity effects in visual working memory, we tested memory for complex stimuli (faces) whose similarity varied along a morph continuum. Participants encoded 3 morphs generated from a single face identity in the similar condition, or 3 morphs generated from different face identities in the dissimilar condition. After a brief delay, a test face appeared at one of the encoding locations for participants to make a same/different judgment. Two experiments showed that similarity enhanced memory accuracy without changing the response criterion. These findings support previous computational models that incorporate featural variance as a component of working memory load. They delineate limitations of models that emphasize cortical resources or response decisions.

  16. Cluster Tree Based Hybrid Document Similarity Measure

    Directory of Open Access Journals (Sweden)

    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.

  17. Extended Matrix Variate Hypergeometric Functions and Matrix Variate Distributions

    Directory of Open Access Journals (Sweden)

    Daya K. Nagar

    2015-01-01

    Full Text Available 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.

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

    CERN Document Server

    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...

  19. Quantitative analysis of biopolymers by matrix-assisted laser desorption

    Energy Technology Data Exchange (ETDEWEB)

    Tang, K.; Allman, S.L.; Jones, R.B.; Chen, C.H. (Oak Ridge National Lab., TN (United States))

    1993-08-01

    During the past few years, major efforts have been made to use mass spectrometry to measure biopolymers because of the great potential benefit to biological and medical research. Although the theoretical details of laser desorption and ionization mechanisms of MALDI are not yet fully understood, several models have been presented to explain the production of large biopolymer ions. In brief, it is very difficult to obtain reliable measurements of the absolute quantity of analytes by MALDI. If MALDI is going to become a routine analytical tool, it is obvious that quantitative measurement capability must be pursued. Oligonucleotides and protein samples used in this work were purchased from commercial sources. Nicotinic acid was used as matrix for both types of biopolymers. From this experiment, it is seen that it is difficult to obtain absolute quantitative measurements of biopolymers using MALDI. However, internal calibration with molecules having similar chemical properties can be used to resolve these difficulties. Chemical reactions between biopolymers must be avoided to prevent the destruction of the analyte materials. 10 refs., 8 figs.

  20. Extracellular matrix proteins and the dynamics of dentin formation.

    Science.gov (United States)

    Butler, William T; Brunn, Jan C; Qin, Chunlin; McKee, Marc D

    2002-01-01

    Dentinogenesis involves controlled reactions that result in conversion of unmineralized predentin to dentin when apatite crystals are formed. This process is dynamic: Maturation events occur within predentin beginning at the proximal layer and progressing to the predentin-dentin (PD) border. One type of controlled reaction is the proteolytic processing of dentin sialophosphoprotein (DSPP) to dentin sialoprotein (DSP) and dentin phosphoprotein (DPP), by cleavage of at least three highly conserved peptide bonds. We postulate that this processing event represents an activation step, resulting in release of DPP, which is active in its effects on formation and growth of apatite crystals. Dentin matrix protein 1 (DPM1), present as a processed fragment (57-kD protein) in bone, is seen in dentin on sodium dodecyl sulfate polyacrylamide gel electrophoresis as one intact protein of 150-200 kD. Anti-57-kD antibodies elicit immunoreactivity in bone, dentin, and cellular cementum. In bone, the reactivity is associated with osteocytes and their cell processes. Similarly, dentin shows reactivity in odontoblasts, predentin, and the odontoblast processes. In summary, the processing of large sialic acid-rich proteins into smaller fragments may be an important part of the controlled conversion of predentin to dentin and osteoid to bone.

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

    Science.gov (United States)

    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.

  2. Skeletal growth after oral administration of demineralized bone matrix.

    Science.gov (United States)

    Martínez, J A; Elorriaga, M; Marquínez, M; Larralde, J

    1993-03-01

    Oral administration of bone extracts obtained from bovine demineralized bone matrix to rats has a direct effect on bone metabolism, affecting bone proportions and some markers of bone formation such as bone malate dehydrogenase, serum alkaline phosphatase and serum osteocalcin. Furthermore collagen deposition, bone protein synthesis and nucleic acids content were significantly increased by the treatment.

  3. Similarity Structure of Wave-Collapse

    DEFF Research Database (Denmark)

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

    1985-01-01

    Similarity transformations of the cubic Schrödinger equation (CSE) are investigated. The transformations are used to remove the explicit time variation in the CSE and reduce it to differential equations in the spatial variables only. Two different methods for similarity reduction are employed and...

  4. Perceived Similarity, Proactive Adjustment, and Organizational Socialization

    Science.gov (United States)

    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…

  5. Appropriate Similarity Measures for Author Cocitation Analysis

    NARCIS (Netherlands)

    N.J.P. van Eck (Nees Jan); L. 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 similar

  6. Outsourced Similarity Search on Metric Data Assets

    DEFF Research Database (Denmark)

    Yiu, Man Lung; Assent, Ira; Jensen, Christian S.

    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...

  7. Interleaving Helps Students Distinguish among Similar Concepts

    Science.gov (United States)

    Rohrer, Doug

    2012-01-01

    When students encounter a set of concepts (or terms or principles) that are similar in some way, they often confuse one with another. For instance, they might mistake one word for another word with a similar spelling (e.g., allusion instead of illusion) or choose the wrong strategy for a mathematics problem because it resembles a different kind of…

  8. Similar methodological analysis involving the user experience.

    Science.gov (United States)

    Almeida e Silva, Caio Márcio; Okimoto, Maria Lúcia R L; Tanure, Raffaela Leane Zenni

    2012-01-01

    This article deals with the use of a protocol for analysis of similar methodological analysis related to user experience. For both, were selected articles recounting experiments in the area. They were analyze based on the similar analysis protocol and finally, synthesized and associated.

  9. Similarity indices I: what do they measure.

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. The effect of extracellular pH on matrix turnover by cells of the bovine nucleus pulposus

    OpenAIRE

    Razaq, Sajjad; Wilkins, Robert J.; Urban, Jill P. G.

    2003-01-01

    It has long been known that very acidic conditions can be found in degenerate discs. The effect of these acid conditions on matrix turnover are, however, unknown. This study aimed to examine the effect of acidity on production of matrix components and on agents which break down the matrix in order to gain insight into the effect of pathological values of pH on matrix turnover. Cells were isolated from the nucleus of bovine discs and from bovine articular cartilage, embedded in alginate beads ...

  11. Starved epithelial cells uptake extracellular matrix for survival

    Science.gov (United States)

    Muranen, Taru; Iwanicki, Marcin P.; Curry, Natasha L.; Hwang, Julie; DuBois, Cory D.; Coloff, Jonathan L.; Hitchcock, Daniel S.; Clish, Clary B.; Brugge, Joan S.; Kalaany, Nada Y.

    2017-01-01

    Extracellular matrix adhesion is required for normal epithelial cell survival, nutrient uptake and metabolism. This requirement can be overcome by oncogene activation. Interestingly, inhibition of PI3K/mTOR leads to apoptosis of matrix-detached, but not matrix-attached cancer cells, suggesting that matrix-attached cells use alternate mechanisms to maintain nutrient supplies. Here we demonstrate that under conditions of dietary restriction or growth factor starvation, where PI3K/mTOR signalling is decreased, matrix-attached human mammary epithelial cells upregulate and internalize β4-integrin along with its matrix substrate, laminin. Endocytosed laminin localizes to lysosomes, results in increased intracellular levels of essential amino acids and enhanced mTORC1 signalling, preventing cell death. Moreover, we show that starved human fibroblasts secrete matrix proteins that maintain the growth of starved mammary epithelial cells contingent upon epithelial cell β4-integrin expression. Our study identifies a crosstalk between stromal fibroblasts and epithelial cells under starvation that could be exploited therapeutically to target tumours resistant to PI3K/mTOR inhibition. PMID:28071763

  12. Matrix-assisted laser desorption/ionization mass spectrometric analysis of aliphatic biodegradable photoluminescent polymers using new ionic liquid matrices.

    Science.gov (United States)

    Serrano, Carlos A; Zhang, Yi; Yang, Jian; Schug, Kevin A

    2011-05-15

    In this study, two novel ionic liquid matrices (ILMs), N,N-diisopropylethylammonium 3-oxocoumarate and N,N-diisopropylethylammonium dihydroxymonooxoacetophenoate, were tested for the structural elucidation of recently developed aliphatic biodegradable polymers by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The polymers, formed by a condensation reaction of three components, citric acid, octane diol, and an amino acid, are fluorescent, but the exact mechanism behind their luminescent properties has not been fully elucidated. In the original studies, which introduced the polymer class (J. Yang et al., Proc. Natl. Acad. Sci. USA 2009, 106, 10086-10091), a hyper-conjugated cyclic structure was proposed as the source for the photoluminescent behavior. With the use of the two new ILMs, we present evidence that supports the presence of the proposed cyclization product. In addition, the new ILMs, when compared with a previously established ILM, N,N-diisopropylethylammonium α-cyano-3-hydroxycinnimate, provided similar signal intensities and maintained similar spectral profiles. This research also established that the new ILMs provided good spot-to-spot reproducibility and high ionization efficiency compared with corresponding crystalline matrix preparations. Many polymer features revealed through the use of the ILMs could not be observed with crystalline matrices. Ultimately, the new ILMs highlighted the composition of the synthetic polymers, as well as the loss of water that was expected for the formation of the proposed cyclic structure on the polymer backbone.

  13. Measure of Node Similarity in Multilayer Networks

    CERN Document Server

    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...

  14. Myocardial matrix-polyethylene glycol hybrid hydrogels for tissue engineering

    Science.gov (United States)

    Grover, Gregory N.; Rao, Nikhil; Christman, Karen L.

    2014-01-01

    Similar to other protein-based hydrogels, extracellular matrix (ECM) based hydrogels, derived from decellularized tissues, have a narrow range of mechanical properties and are rapidly degraded. These hydrogels contain natural cellular adhesion sites, form nanofibrous networks similar to native ECM, and are biodegradable. In this study, we expand the properties of these types of materials by incorporating poly(ethylene glycol) (PEG) into the ECM network. We use decellularized myocardial matrix as an example of a tissue specific ECM derived hydrogel. Myocardial matrix-PEG hybrids were synthesized by two different methods, cross-linking the proteins with an amine-reactive PEG-star and photo-induced radical polymerization of two different multi-armed PEG-acrylates. We show that both methods allow for conjugation of PEG to the myocardial matrix by gel electrophoresis and infrared spectroscopy. Scanning electron microscopy demonstrated that the hybrid materials still contain a nanofibrous network similar to unmodified myocardial matrix and that the fiber diameter is changed by the method of PEG incorporation and PEG molecular weight. PEG conjugation also decreased the rate of enzymatic degradation in vitro, and increased material stiffness. Hybrids synthesized with amine-reactive PEG had gelation rates of 30 min, similar to the unmodified myocardial matrix, and incorporation of PEG did not prevent cell adhesion and migration through the hydrogels, thus offering the possibility to have an injectable ECM hydrogel that degrades more slowly in vivo. The photo-polymerized radical systems gelled in 4 min upon irradiation, allowing 3D encapsulation and culture of cells, unlike the soft unmodified myocardial matrix. This work demonstrates that PEG incorporation into ECM-based hydrogels can expand material properties, thereby opening up new possibilities for in vitro and in vivo applications.

  15. Performance Comparison of New Combinations of Acids with Mud Acid in Sandstone Acidizing

    Directory of Open Access Journals (Sweden)

    Mian Umer Shafiq

    2014-01-01

    Full Text Available The aim of this research is to find the best suitable acid to acidize undamaged low permeable sandstone formation Stimulation of sandstone formations is a challenging task, which involves several chemicals and physical interactions of the acid with the formation. Mud acid has been successfully used to stimulate sandstone reservoirs for a number of years. Matrix acidizing may also be used to increase formation permeability in undamaged wells. The change may be up to 50 to 100% with the mud acid. For any acidizing process, the selection of acid (Formulation and Concentration and the design (Pre-flush, Main Acid, After-flush is very important. Different researchers are using different combinations of acids with different concentrations to get the best results for acidization. Mainly the common practice is combination of Hydrochloric Acid- Hydrofluoric with Concentration (3% HF-12% HCl. This study presents the results of a laboratory investigation of Orthophosphoric acid instead of hydrochloric acid in one combination and the second combination is Fluoboric and formic acid and the third one is formic and hydrofluoric acid. The results are compared with the mud acid and the results analyzed are porosity, permeability, strength, color change and FESEM Analysis. All of these new combinations shows that these have the potential to be used as acidizing acids on sandstone formations.

  16. Structuring Chemical Space: Similarity-Based Characterization of the PubChem Database.

    Science.gov (United States)

    Cincilla, Giovanni; Thormann, Michael; Pons, Miquel

    2010-01-12

    The ensemble of conceivable molecules is referred to as the Chemical Space. In this article we describe a hierarchical version of the Affinity Propagation (AP) clustering algorithm and apply it to analyze the LINGO-based similarity matrix of a 500 000-molecule subset of the PubChem database, which contains more than 19 million compounds. The combination of two highly efficient methods, namely the AP clustering algorithm and LINGO-based molecular similarity calculations, allows the unbiased analysis of large databases. Hierarchical clustering generates a numerical diagonalization of the similarity matrix. The target-independent, intrinsic structure of the database , derived without any previous information on the physical or biological properties of the compounds, maps together molecules experimentally shown to bind the same biological target or to have similar physical properties.

  17. Defining a similarity threshold for a functional proteinsequence pattern: The signal peptide cleavage site

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; von Heijne, Gunnar

    1996-01-01

    prediction. We have developed a similar procedure based on pair-wise alignments for sequences with functional sites. We show how a correlation coefficient between sequence similarity and functional homology can be used to compare the efficiency of different similarity measures and choose a nonarbitrary...... threshold value for excluding redundant sequences. The impact of the choice of scoring matrix used in the alignments is examined. We demonstrate that the parameter determining the quality of the correlation is the relative entropy of the matrix, rather than the assumed(PAM or identity) substitution model....... Results are presented for the case of prediction of cleavage sites in signal peptides. By inspection of the false positives, several errors in the database were found. The procedure presented may be used as a general outline for finding a problem-specific similarity measure and threshold value...

  18. How to Study a Matrix

    Science.gov (United States)

    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…

  19. Cosmology and the S-matrix

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Matrix convolution operators on groups

    CERN Document Server

    Chu, Cho-Ho

    2008-01-01

    In the last decade, convolution operators of matrix functions have received unusual attention due to their diverse applications. This monograph presents some new developments in the spectral theory of these operators. The setting is the Lp spaces of matrix-valued functions on locally compact groups. The focus is on the spectra and eigenspaces of convolution operators on these spaces, defined by matrix-valued measures. Among various spectral results, the L2-spectrum of such an operator is completely determined and as an application, the spectrum of a discrete Laplacian on a homogeneous graph is computed using this result. The contractivity properties of matrix convolution semigroups are studied and applications to harmonic functions on Lie groups and Riemannian symmetric spaces are discussed. An interesting feature is the presence of Jordan algebraic structures in matrix-harmonic functions.

  1. Matrix Model Approach to Cosmology

    CERN Document Server

    Chaney, A; Stern, A

    2015-01-01

    We perform a systematic search for rotationally invariant cosmological solutions to matrix models, or more specifically the bosonic sector of Lorentzian IKKT-type matrix models, in dimensions $d$ less than ten, specifically $d=3$ and $d=5$. After taking a continuum (or commutative) limit they yield $d-1$ dimensional space-time surfaces, with an attached Poisson structure, which can be associated with closed, open or static cosmologies. For $d=3$, we obtain recursion relations from which it is possible to generate rotationally invariant matrix solutions which yield open universes in the continuum limit. Specific examples of matrix solutions have also been found which are associated with closed and static two-dimensional space-times in the continuum limit. The solutions provide for a matrix resolution of cosmological singularities. The commutative limit reveals other desirable features, such as a solution describing a smooth transition from an initial inflation to a noninflationary era. Many of the $d=3$ soluti...

  2. Multivariate Matrix-Exponential Distributions

    DEFF Research Database (Denmark)

    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...

  3. Machining of Metal Matrix Composites

    CERN Document Server

    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...

  4. On the employment of lambda carrageenan in a matrix system. III. Optimization of a lambda carrageenan-HPMC hydrophilic matrix

    NARCIS (Netherlands)

    Bonferoni, MC; Rossi, S; Ferrari, F; Bertoni, M; Bolhuis, GK; Caramella, C

    1998-01-01

    The lambda carrageenan/HPMC ratio in matrix tablets has been optimized in order to obtain pH-independent release profiles of chlorpheniramine maleate, a freely soluble drug. Release profiles in acidic (pH 1.2) and neutral (pH 6.8) media were fitted according to the Weibull and the power law models.

  5. GPU accelerated chemical similarity calculation for compound library comparison.

    Science.gov (United States)

    Ma, Chao; Wang, Lirong; Xie, Xiang-Qun

    2011-07-25

    Chemical similarity calculation plays an important role in compound library design, virtual screening, and "lead" optimization. In this manuscript, we present a novel GPU-accelerated algorithm for all-vs-all Tanimoto matrix calculation and nearest neighbor search. By taking advantage of multicore GPU architecture and CUDA parallel programming technology, the algorithm is up to 39 times superior to the existing commercial software that runs on CPUs. Because of the utilization of intrinsic GPU instructions, this approach is nearly 10 times faster than existing GPU-accelerated sparse vector algorithm, when Unity fingerprints are used for Tanimoto calculation. The GPU program that implements this new method takes about 20 min to complete the calculation of Tanimoto coefficients between 32 M PubChem compounds and 10K Active Probes compounds, i.e., 324G Tanimoto coefficients, on a 128-CUDA-core GPU.

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

    CERN Document Server

    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.

  7. Production and characterization of bacterial cellulose membranes with hyaluronic acid from chicken comb.

    Science.gov (United States)

    de Oliveira, Sabrina Alves; da Silva, Bruno Campos; Riegel-Vidotti, Izabel Cristina; Urbano, Alexandre; de Sousa Faria-Tischer, Paula Cristina; Tischer, Cesar Augusto

    2017-04-01

    The bacterial cellulose (BC), from Gluconacetobacter hansenii, is a biofilm with a high degree of crystallinity that can be used for therapeutic purposes and as a candidate for healing wounds. Hyaluronic acid (HA) is a constitutive polysaccharide found in the extracellular matrix and is a material used in tissue engineering and scaffolding for tissue regeneration. In this study, polymeric composites were produced in presence of hyaluronic acid isolated from chicken comb on different days of fermentation, specifically on the first (BCHA-SABT0) and third day (BCHA-SABT3) of fermentation. The structural characteristics, thermal stability and molar mass of hyaluronic acid from chicken comb were evaluated. Native membrane and polymeric composites were characterized with respect to their morphology and crystallinity. The optimized process of extraction and purification of hyaluronic acid resulted in low molar mass hyaluronic acid with structural characteristics similar to the standard commercial hyaluronic acid. The results demonstrate that the polymeric composites (BC/HA-SAB) can be produced in situ. The membranes produced on the third day presented better incorporation of HA-SAB between cellulose microfiber, resulting in membranes with higher thermal stability, higher roughness and lower crystallinity. The biocompatiblily of bacterial cellulose and the importance of hyaluronic acid as a component of extracellular matrix qualify the polymeric composites as promising biomaterials for tissue engineering.

  8. Notions of similarity for computational biology models

    KAUST Repository

    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.

  9. Mining Object Similarity for Predicting Next Locations

    Institute of Scientific and Technical Information of China (English)

    Meng Chen; Xiaohui Yu; Yang Liu

    2016-01-01

    Next location prediction is of great importance for many location-based applications. With the virtue of solid theoretical foundations, Markov-based approaches have gained success along this direction. In this paper, we seek to enhance the prediction performance by understanding the similarity between objects. In particular, we propose a novel method, called weighted Markov model (weighted-MM), which exploits both the sequence of just-passed locations and the object similarity in mining the mobility patterns. To this end, we first train a Markov model for each object with its own trajectory records, and then quantify the similarities between different objects from two aspects: spatial locality similarity and trajectory similarity. Finally, we incorporate the object similarity into the Markov model by considering the similarity as the weight of the probability of reaching each possible next location, and return the top-rankings as results. We have conducted extensive experiments on a real dataset, and the results demonstrate significant improvements in prediction accuracy over existing solutions.

  10. Measure of Node Similarity in Multilayer Networks.

    Directory of Open Access Journals (Sweden)

    Anders Mollgaard

    Full Text Available The weight of links in a network is often related to the similarity of the nodes. Here, we introduce a simple tunable measure for analysing the similarity of nodes across different link weights. In particular, we use the measure to analyze homophily in a group of 659 freshman students at a large university. Our analysis is based on data obtained using smartphones equipped with custom data collection software, complemented by questionnaire-based data. The network of social contacts is represented as a weighted multilayer network constructed from different channels of telecommunication as well as data on face-to-face contacts. We find that even strongly connected individuals are not more similar with respect to basic personality traits than randomly chosen pairs of individuals. In contrast, several socio-demographics variables have a significant degree of similarity. We further observe that similarity might be present in one layer of the multilayer network and simultaneously be absent in the other layers. For a variable such as gender, our measure reveals a transition from similarity between nodes connected with links of relatively low weight to dis-similarity for the nodes connected by the strongest links. We finally analyze the overlap between layers in the network for different levels of acquaintanceships.

  11. Efficient Privacy Preserving Protocols for Similarity Join

    Directory of Open Access Journals (Sweden)

    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.

  12. Measure of Node Similarity in Multilayer Networks

    Science.gov (United States)

    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

  13. Similarity-based pattern analysis and recognition

    CERN Document Server

    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

  14. Notes on Mayer expansions and matrix models

    Energy Technology Data Exchange (ETDEWEB)

    Bourgine, Jean-Emile, E-mail: jebourgine@apctp.org

    2014-03-15

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  16. Distances and similarities in intuitionistic fuzzy sets

    CERN Document Server

    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.

  17. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Parrado-Hernandez, Emilio; Meng, Anders;

    Automatic methods for music navigation and music recommendation exploit the structure in the music to carry out a meaningful exploration of the “song space”. To get a satisfactory performance from such systems, one should incorporate as much information about songs similarity as possible; however...... semantics”, in such a way that all observed similarities can be satisfactorily explained using the latent semantics. Therefore, one can think of these semantics as the real structure in music, in the sense that they can explain the observed similarities among songs. The suitability of the PLSA model...... for representing music structure is studied in a simplified scenario consisting of 4412 songs and two similarity measures among them. The results suggest that the PLSA model is a useful framework to combine different sources of information, and provides a reasonable space for song representation....

  18. Similarity Theory of Withdrawn Water Temperature Experiment

    Directory of Open Access Journals (Sweden)

    Yunpeng Han

    2015-01-01

    Full Text Available 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 theoretically based on the modification of governing equations, the Boussinesq approximation, and some simplifications. The similarity conditions between the model and the prototype were suggested. The conversion of withdrawn water temperature between the model and the prototype was proposed. Meanwhile, the fundamental theory of temperature distribution conversion was firstly proposed, which could significantly improve the experiment efficiency when the basic temperature of the model was different from the prototype. Based on the similarity theory, an experiment was performed on the withdrawn water temperature which was verified by numerical method.

  19. Outsourced similarity search on metric data assets

    KAUST Repository

    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.

  20. Bilateral Trade Flows and Income Distribution Similarity.

    Science.gov (United States)

    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.

  1. Interpersonal Congruency, Attitude Similarity, and Interpersonal Attraction

    Science.gov (United States)

    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)

  2. Correlation between social proximity and mobility similarity

    CERN Document Server

    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...

  3. Integrated Semantic Similarity Model Based on Ontology

    Institute of Scientific and Technical Information of China (English)

    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.

  4. Exploiting Data Similarity to Reduce Memory Footprints

    Science.gov (United States)

    2011-01-01

    leslie3d Fortran Computational Fluid Dynamics (CFD) application 122. tachyon C Parallel Ray Tracing application 128.GAPgeofem C and Fortran Simulates...benefits most from SBLLmalloc; LAMMPS, which shows moderate similarity from primarily zero pages; and 122. tachyon , a parallel ray- tracing application...similarity across MPI tasks. They primarily are zero- pages although a small fraction (≈10%) are non-zero pages. 122. tachyon is an image rendering

  5. Some more similarities between Peirce and Skinner

    OpenAIRE

    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...

  6. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    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.

  7. Interlinguistic similarity and language death dynamics

    CERN Document Server

    Mira, J

    2005-01-01

    We analyze the time evolution of a system of two coexisting languages (Castillian Spanish and Galician, both spoken in northwest Spain) in the framework of a model given by Abrams and Strogatz [Nature 424, 900 (2003)]. It is shown that, contrary to the model's initial prediction, a stable bilingual situation is possible if the languages in competition are similar enough. Similarity is described with a simple parameter, whose value can be estimated from fits of the data.

  8. On distributional assumptions and whitened cosine similarities

    DEFF Research Database (Denmark)

    Loog, Marco

    2008-01-01

    Recently, an interpretation of the whitened cosine similarity measure as a Bayes decision rule was proposed (C. Liu, "The Bayes Decision Rule Induced Similarity Measures,'' IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 29, no. 6, pp. 1086-1090, June 2007. This communication makes th...... the observation that some of the distributional assumptions made to derive this measure are very restrictive and, considered simultaneously, even inconsistent....

  9. Similarity search processing. Paralelization and indexing technologies.

    Directory of Open Access Journals (Sweden)

    Eder Dos Santos

    2015-08-01

    The next Scientific-Technical Report addresses the similarity search and the implementation of metric structures on parallel environments. It also presents the state of the art related to similarity search on metric structures and parallelism technologies. Comparative analysis are also proposed, seeking to identify the behavior of a set of metric spaces and metric structures over processing platforms multicore-based and GPU-based.

  10. High-accuracy determination of iron in seawater by isotope dilution multiple collector inductively coupled plasma mass spectrometry (ID-MC-ICP-MS) using nitrilotriacetic acid chelating resin for pre-concentration and matrix separation

    Energy Technology Data Exchange (ETDEWEB)

    Jong, Jeroen de [Universite Libre de Bruxelles (ULB), Departement des Sciences de la Terre et de l' Environnement (DSTE), Unite Isotopes: Petrologie et Environnement - IPE CP 160/02, Avenue F.D. Roosevelt 50, B-1050 Brussels (Belgium)], E-mail: jdejong@ulb.ac.be; Schoemann, Veronique [Universite Libre de Bruxelles (ULB), Ecologie des Systemes Aquatiques (ESA) CP 221, Avenue F.D. Roosevelt 50, B-1050 Brussels (Belgium); Lannuzel, Delphine [Universite Libre de Bruxelles (ULB), Departement des Sciences de la Terre et de l' Environnement (DSTE), Laboratoire d' Oceanographie Chimique et Geochimie des Eaux - LOCGE CP 208, Avenue F.D. Roosevelt 50, B-1050 Brussels (Belgium); Tison, Jean-Louis [Universite Libre de Bruxelles (ULB), Departement des Sciences de la Terre et de l' Environnement (DSTE), Laboratoire de Glaciologie - GLACIOL CP 160/03, Avenue F.D. Roosevelt 50, B-1050 Brussels (Belgium); Mattielli, Nadine [Universite Libre de Bruxelles (ULB), Departement des Sciences de la Terre et de l' Environnement (DSTE), Unite Isotopes: Petrologie et Environnement - IPE CP 160/02, Avenue F.D. Roosevelt 50, B-1050 Brussels (Belgium)

    2008-08-15

    In the present paper we describe a robust and simple method to measure dissolved iron (DFe) concentrations in seawater down to <0.1 nmol L{sup -1} level, by isotope dilution multiple collector inductively coupled plasma mass spectrometry (ID-MC-ICP-MS) using a {sup 54}Fe spike and measuring the {sup 57}Fe/{sup 54}Fe ratio. The method provides for a pre-concentration step (100:1) by micro-columns filled with the resin NTA Superflow of 50 mL seawater samples acidified to pH 1.9. NTA Superflow is demonstrated to quantitatively extract Fe from acidified seawater samples at this pH. Blanks are kept low (grand mean 0.045 {+-} 0.020 nmol L{sup -1}, n = 21, 3x S.D. limit of detection per session 0.020-0.069 nmol L{sup -1} range), as no buffer is required to adjust the sample pH for optimal extraction, and no other reagents are needed than ultrapure nitric acid, 12 mM H{sub 2}O{sub 2}, and acidified (pH 1.9) ultra-high purity (UHP) water. We measured SAFe (sampling and analysis of Fe) reference seawater samples Surface-1 (0.097 {+-} 0.043 nmol L{sup -1}) and Deep-2 (0.91 {+-} 0.17 nmol L{sup -1}) and obtained results that were in excellent agreement with their DFe consensus values: 0.118 {+-} 0.028 nmol L{sup -1} (n = 7) for Surface-1 and 0.932 {+-} 0.059 nmol L{sup -1} (n = 9) for Deep-2. We also present a vertical DFe profile from the western Weddell Sea collected during the Ice Station Polarstern (ISPOL) ice drift experiment (ANT XXII-2, RV Polarstern) in November 2004-January 2005. The profile shows near-surface DFe concentrations of {approx}0.6 nmol L{sup -1} and bottom water enrichment up to 23 nmol L{sup -1} DFe.

  11. A metal ion charged mixed matrix membrane for selective adsorption of hemoglobin

    NARCIS (Netherlands)

    Tetala, K.K.R.; Skrzypek, K.; Levisson, M.; Stamatialis, D.F.

    2013-01-01

    In this work, we developed a mixed matrix membrane by incorporating 20–40 µm size iminodiacetic acid modified immobeads within porous Ethylene vinyl alcohol (EVAL) polymer matrix. The MMM were charged with copper ions for selective adsorption of bovine hemoglobin in presence of bovine serum albumin.

  12. Mechanisms for similarity matching in disparity measurement

    Directory of Open Access Journals (Sweden)

    Ross eGoutcher

    2014-01-01

    Full Text Available Early neural mechanisms for the measurement of binocular disparity appear to operate in a manner consistent with cross-correlation-like processes. Consequently, cross-correlation, or cross-correlation-like procedures have been used in a range of models of disparity measurement. Using such procedures as the basis for disparity measurement creates a preference for correspondence solutions that maximise the similarity between local left and right eye image regions. Here, we examine how observers’ perception of depth in an ambiguous stereogram is affected by manipulations of luminance and orientation-based image similarity. Results show a strong effect of coarse-scale luminance similarity manipulations, but a relatively weak effect of finer-scale manipulations of orientation similarity. This is in contrast to the measurements of depth obtained from a standard cross-correlation model. This model shows strong effects of orientation similarity manipulations and weaker effects of luminance similarity. In order to account for these discrepancies, the standard cross-correlation approach may be modified to include an initial spatial frequency filtering stage. The performance of this adjusted model most closely matches human psychophysical data when spatial frequency filtering favours coarser scales. This is consistent with the operation of disparity measurement processes where spatial frequency and disparity tuning are correlated, or where disparity measurement operates in a coarse-to-fine manner.

  13. Similarity searching in large combinatorial chemistry spaces

    Science.gov (United States)

    Rarey, Matthias; Stahl, Martin

    2001-06-01

    We present a novel algorithm, called Ftrees-FS, for similarity searching in large chemistry spaces based on dynamic programming. Given a query compound, the algorithm generates sets of compounds from a given chemistry space that are similar to the query. The similarity search is based on the feature tree similarity measure representing molecules by tree structures. This descriptor allows handling combinatorial chemistry spaces as a whole instead of looking at subsets of enumerated compounds. Within few minutes of computing time, the algorithm is able to find the most similar compound in very large spaces as well as sets of compounds at an arbitrary similarity level. In addition, the diversity among the generated compounds can be controlled. A set of 17 000 fragments of known drugs, generated by the RECAP procedure from the World Drug Index, was used as the search chemistry space. These fragments can be combined to more than 1018 compounds of reasonable size. For validation, known antagonists/inhibitors of several targets including dopamine D4, histamine H1, and COX2 are used as queries. Comparison of the compounds created by Ftrees-FS to other known actives demonstrates the ability of the method to jump between structurally unrelated molecule classes.

  14. MATRIX EQUATION AXB = E WITH PX = sXP CONSTRAINT

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The matrix equation AXB = E with the constraint PX = sXP is considered, where P is a given Hermitian matrix satisfying P2 = I and s = ±1. By an eigenvalue decomposition of P, the constrained problem can be equivalently transformed to a well-known unconstrained problem of matrix equation whose coefficient matrices contain the corresponding eigenvector, and hence the constrained problem can be solved in terms of the eigenvectors of P. A simple and eigenvector-free formula of the general solutions to the constrained problem by generalized inverses of the coefficient matrices A and B is presented.Moreover, a similar problem of the matrix equation with generalized constraint is discussed.

  15. IMP: A Message-Passing Algorithmfor Matrix Completion

    CERN Document Server

    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. Bioreporter pseudomonas fluorescens HK44 immobilized in a silica matrix

    Directory of Open Access Journals (Sweden)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    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. Formation of Metal-Related Ions in Matrix-Assisted Laser Desorption Ionization

    Science.gov (United States)

    Lee, Chuping; Lu, I.-Chung; Hsu, Hsu Chen; Lin, Hou-Yu; Liang, Sheng-Ping; Lee, Yuan-Tseh; Ni, Chi-Kung

    2016-09-01

    In a study of the metal-related ion generation mechanism in matrix-assisted laser desorption ionization (MALDI), crystals of matrix used in MALDI were grown from matrix- and salt-containing solutions. The intensities of metal ion and metal adducts of the matrix ion obtained from unwashed crystals were higher than those from crystals washed with deionized water, indicating that metal ions and metal adducts of the matrix ions are mainly generated from the surface of crystals. The contributions of preformed metal ions and metal adducts of the matrix ions inside the matrix crystals were minor. Metal adducts of the matrix and analyte ion intensities generated from a mixture of dried matrix, salt, and analyte powders were similar to or higher than those generated from the powder of dried droplet crystals, indicating that the contributions of the preformed metal adducts of the matrix and analyte ions were insignificant. Correlation between metal-related ion intensity fluctuation and protonated ion intensity fluctuation was observed, indicating that the generation mechanism of the metal-related ions is similar to that of the protonated ions. Because the thermally induced proton transfer model effectively describes the generation of the protonated ions, we suggest that metal-related ions are mainly generated from the salt dissolution in the matrix melted by the laser.

  19. New pole placement algorithm - Polynomial matrix approach

    Science.gov (United States)

    Shafai, B.; Keel, L. H.

    1990-01-01

    A simple and direct pole-placement algorithm is introduced for dynamical systems having a block companion matrix A. The algorithm utilizes well-established properties of matrix polynomials. Pole placement is achieved by appropriately assigning coefficient matrices of the corresponding matrix polynomial. This involves only matrix additions and multiplications without requiring matrix inversion. A numerical example is given for the purpose of illustration.

  20. High temperature polymer matrix composites

    Science.gov (United States)

    Serafini, Tito T. (Editor)

    1987-01-01

    These are the proceedings of the High Temperature Polymer Matrix Composites Conference held at the NASA Lewis Research Center on March 16 to 18, 1983. The purpose of the conference is to provide scientists and engineers working in the field of high temperature polymer matrix composites an opportunity to review, exchange, and assess the latest developments in this rapidly expanding area of materials technology. Technical papers are presented in the following areas: (1) matrix development; (2) adhesive development; (3) Characterization; (4) environmental effects; and (5) applications.

  1. Scientific articles recommendation with topic regression and relational matrix factorization

    Institute of Scientific and Technical Information of China (English)

    Ming YANG; Ying-ming LI; Zhongfei(Mark)ZHANG

    2014-01-01

    In this paper we study the problem of recommending scientifi c articles to users in an online community with a new perspective of considering topic regression modeling and articles relational structure analysis simultane-ously. First, we present a novel topic regression model, the topic regression matrix factorization (tr-MF), to solve the problem. The main idea of tr-MF lies in extending the matrix factorization with a probabilistic topic modeling. In particular, tr-MF introduces a regression model to regularize user factors through probabilistic topic modeling under the basic hypothesis that users share similar preferences if they rate similar sets of items. Consequently, tr-MF provides interpretable latent factors for users and items, and makes accurate predictions for community users. To incorporate the relational structure into the framework of tr-MF, we introduce relational matrix factorization. Through combining tr-MF with the relational matrix factorization, we propose the topic regression collective matrix factorization (tr-CMF) model. In addition, we also present the collaborative topic regression model with relational matrix factorization (CTR-RMF) model, which combines the existing collaborative topic regression (CTR) model and relational matrix factorization (RMF). From this point of view, CTR-RMF can be considered as an appropriate baseline for tr-CMF. Further, we demonstrate the efficacy of the proposed models on a large subset of the data from CiteULike, a bibliography sharing service dataset. The proposed models outperform the state-of-the-art matrix factorization models with a signifi cant margin. Specifi cally, the proposed models are effective in making predictions for users with only few ratings or even no ratings, and support tasks that are specifi c to a certain fi eld, neither of which has been addressed in the existing literature.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  3. Identifying mechanistic similarities in drug responses

    KAUST Repository

    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.

  4. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

    In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

  5. Earthquake detection through computationally efficient similarity search

    Science.gov (United States)

    Yoon, Clara E.; O’Reilly, Ossian; Bergen, Karianne J.; Beroza, Gregory C.

    2015-01-01

    Seismology is experiencing rapid growth in the quantity of data, which has outpaced the development of processing algorithms. Earthquake detection—identification of seismic events in continuous data—is a fundamental operation for observational seismology. We developed an efficient method to detect earthquakes using waveform similarity that overcomes the disadvantages of existing detection methods. Our method, called Fingerprint And Similarity Thresholding (FAST), can analyze a week of continuous seismic waveform data in less than 2 hours, or 140 times faster than autocorrelation. FAST adapts a data mining algorithm, originally designed to identify similar audio clips within large databases; it first creates compact “fingerprints” of waveforms by extracting key discriminative features, then groups similar fingerprints together within a database to facilitate fast, scalable search for similar fingerprint pairs, and finally generates a list of earthquake detections. FAST detected most (21 of 24) cataloged earthquakes and 68 uncataloged earthquakes in 1 week of continuous data from a station located near the Calaveras Fault in central California, achieving detection performance comparable to that of autocorrelation, with some additional false detections. FAST is expected to realize its full potential when applied to extremely long duration data sets over a distributed network of seismic stations. The widespread application of FAST has the potential to aid in the discovery of unexpected seismic signals, improve seismic monitoring, and promote a greater understanding of a variety of earthquake processes. PMID:26665176

  6. Efficient Video Similarity Measurement and Search

    Energy Technology Data Exchange (ETDEWEB)

    Cheung, S-C S

    2002-12-19

    The amount of information on the world wide web has grown enormously since its creation in 1990. Duplication of content is inevitable because there is no central management on the web. Studies have shown that many similar versions of the same text documents can be found throughout the web. This redundancy problem is more severe for multimedia content such as web video sequences, as they are often stored in multiple locations and different formats to facilitate downloading and streaming. Similar versions of the same video can also be found, unknown to content creators, when web users modify and republish original content using video editing tools. Identifying similar content can benefit many web applications and content owners. For example, it will reduce the number of similar answers to a web search and identify inappropriate use of copyright content. In this dissertation, they present a system architecture and corresponding algorithms to efficiently measure, search, and organize similar video sequences found on any large database such as the web.

  7. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    Science.gov (United States)

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

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (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 parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  8. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    Science.gov (United States)

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

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (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 parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  9. Gas-phase Acidities of Aspartic Acid, Glutamic Acid, and their Amino Acid Amides.

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhong; Matus, Myrna H; Velazquez, Hector A; Dixon, David A; Cassady, Carolyn J

    2007-02-14

    Gas-phase acidities (GA or ΔGacid) for the two most acidic common amino acids, aspartic acid and glutamic acid, have been determined for the first time. Because of the amide linkage’s importance in peptides and as an aid in studying side chain versus main chain deprotonation, aspartic acid amide and glutamic acid amide were also studied. Experimental GA values were measured by proton transfer reactions in an electrospray ionization/Fourier transform ion cyclotron resonance mass spectrometer. Calculated GAs were obtained by density functional and molecular orbital theory approaches. The best agreement with experiment was found at the G3MP2 level; the MP2/CBS and B3LYP/aug-cc-pVDZ results are 3–4 kcal/mol more acidic than the G3MP2 results. Experiment shows that aspartic acid is more acidic than glutamic acid by ca. 3 kcal/mol whereas the G3MP2 results show a smaller acidity difference of 0.2 kcal/mol. Similarly, aspartic acid amide is experimentally observed to be ca. 2 kcal/mol more acidic than glutamic acid amide whereas the G3MP2 results show a correspondingly smaller energy difference of 0.7 kcal/mol. The computational results clearly show that the anions are all ring-like structures with strong hydrogen bonds between the OH or NH2 groups and the CO2- group from which the proton is removed. The two amino acids are main-chain deprotonated. In addition, use of the COSMO model for the prediction of the free energy differences in aqueous solution gave values in excellent agreement with the most recent experimental values for pKa. Glutamic acid is predicted to be more acidic than aspartic acid in aqueous solution due to differential solvation effects.

  10. Mixed-matrix membrane adsorbers for protein separation

    NARCIS (Netherlands)

    Avramescu, Maria-Elena; Borneman, Zandrie; Wessling, Matthias

    2003-01-01

    The separation of two similarly sized proteins, bovine serum albumin (BSA) and bovine hemoglobin (Hb) was carried out using a new type of ion-exchange mixed-matrix adsorber membranes. The adsorber membranes were prepared by incorporation of various types of Lewatit ion-exchange resins into an ethyle

  11. Universal self-similarity of propagating populations

    Science.gov (United States)

    Eliazar, Iddo; Klafter, Joseph

    2010-07-01

    This paper explores the universal self-similarity of propagating populations. The following general propagation model is considered: particles are randomly emitted from the origin of a d -dimensional Euclidean space and propagate randomly and independently of each other in space; all particles share a statistically common—yet arbitrary—motion pattern; each particle has its own random propagation parameters—emission epoch, motion frequency, and motion amplitude. The universally self-similar statistics of the particles’ displacements and first passage times (FPTs) are analyzed: statistics which are invariant with respect to the details of the displacement and FPT measurements and with respect to the particles’ underlying motion pattern. Analysis concludes that the universally self-similar statistics are governed by Poisson processes with power-law intensities and by the Fréchet and Weibull extreme-value laws.

  12. Electroconvective instability of self-similar equilibria

    CERN Document Server

    Demekhin, E; Shtemler, Yury

    2010-01-01

    Stability of electro-hydrodynamic processes between ion-exchange membranes is investigated. Solutions of the equilibrium problem which represents the balance between diffusion and electro-migration are commonly described in an one-dimensional (1D) steady-state approximation. In the present work a novel class of the 1D unsteady self-similar equilibrium solution is developed asymptotically in small Debye length, epsilon, and large distance between membranes (both made dimensionless with the diffusion-layer thickness). First, the 1D unsteady family of self-similar equilibrium solutions is developed. Then, a linear stability of the self-similar solutions slowly varied with time is investigated in the limit of small epsilonand the marginal stability curves are obtained. Method of matched asymptotics is applied provided that only the outer solution is considered, ignoring the inner solutions. The success of the analysis is provided by transforming the equations to the divergent type (nabla G=0) with the patching co...

  13. Statistical energy analysis of similarly coupled systems

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jian

    2002-01-01

    Based on the principle of Statistical Energy Analysis (SEA) for non-conservatively coupled dynamical systems under non-correlative or correlative excitations, energy relationship between two similar SEA systems is established in the paper. The energy relationship is verified theoretically and experimentally from two similar SEA systems i.e., the structure of a coupled panel-beam and that of a coupled panel-sideframe, in the cases of conservative coupling and non-conservative coupling respectively. As an application of the method, relationship between noise power radiated from two similar cutting systems is studied. Results show that there are good agreements between the theory and the experiments, and the method is valuable to analysis of dynamical problems associated with a complicated system from that with a simple one.

  14. Structural similarity and category-specificity

    DEFF Research Database (Denmark)

    Gerlach, Christian; Law, Ian; Paulson, Olaf B

    2004-01-01

    It has been suggested that category-specific recognition disorders for natural objects may reflect that natural objects are more structurally (visually) similar than artefacts and therefore more difficult to recognize following brain damage. On this account one might expect a positive relationship...... between blood flow and structural similarity in areas involved in visual object recognition. Contrary to this expectation we report a negative relationship in that identification of articles of clothing cause more extensive activation than identification of vegetables/fruit and animals even though items...... from the categories of animals and vegetables/fruit are rated as more structurally similar than items from the category of articles of clothing. Given that this pattern cannot be explained in terms of a tradeoff between activation and accuracy, we interpret these findings within a model where...

  15. Visual Similarity Based Document Layout Analysis

    Institute of Scientific and Technical Information of China (English)

    Di Wen; Xiao-Qing Ding

    2006-01-01

    In this paper, a visual similarity based document layout analysis (DLA) scheme is proposed, which by using clustering strategy can adaptively deal with documents in different languages, with different layout structures and skew angles. Aiming at a robust and adaptive DLA approach, the authors first manage to find a set of representative filters and statistics to characterize typical texture patterns in document images, which is through a visual similarity testing process.Texture features are then extracted from these filters and passed into a dynamic clustering procedure, which is called visual similarity clustering. Finally, text contents are located from the clustered results. Benefit from this scheme, the algorithm demonstrates strong robustness and adaptability in a wide variety of documents, which previous traditional DLA approaches do not possess.

  16. GoM Diet Matrix

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set was taken from CRD 08-18 at the NEFSC. Specifically, the Gulf of Maine diet matrix was developed for the EMAX exercise described in that center...

  17. Matrix Quantum Mechanics from Qubits

    CERN Document Server

    Hartnoll, Sean A; Mazenc, Edward A

    2016-01-01

    We introduce a transverse field Ising model with order N^2 spins interacting via a nonlocal quartic interaction. The model has an O(N,Z), hyperoctahedral, symmetry. We show that the large N partition function admits a saddle point in which the symmetry is enhanced to O(N). We further demonstrate that this `matrix saddle' correctly computes large N observables at weak and strong coupling. The matrix saddle undergoes a continuous quantum phase transition at intermediate couplings. At the transition the matrix eigenvalue distribution becomes disconnected. The critical excitations are described by large N matrix quantum mechanics. At the critical point, the low energy excitations are waves propagating in an emergent 1+1 dimensional spacetime.

  18. The R-matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Descouvemont, P; Baye, D [Physique Nucleaire Theorique et Physique Mathematique, C.P. 229, Universite Libre de Bruxelles (ULB), B 1050 Brussels (Belgium)], E-mail: pdesc@ulb.ac.be, E-mail: dbaye@ulb.ac.be

    2010-03-15

    The different facets of the R-matrix method are presented pedagogically in a general framework. Two variants have been developed over the years: (i) The 'calculable' R-matrix method is a calculational tool to derive scattering properties from the Schroedinger equation in a large variety of physical problems. It was developed rather independently in atomic and nuclear physics with too little mutual influence. (ii) The 'phenomenological' R-matrix method is a technique to parametrize various types of cross sections. It was mainly (or uniquely) used in nuclear physics. Both directions are explained by starting from the simple problem of scattering by a potential. They are illustrated by simple examples in nuclear and atomic physics. In addition to elastic scattering, the R-matrix formalism is applied to inelastic and radiative-capture reactions. We also present more recent and more ambitious applications of the theory in nuclear physics.

  19. Linear connections on matrix geometries

    CERN Document Server

    Madore, J; Mourad, J; Madore, John; Masson, Thierry; Mourad, Jihad

    1994-01-01

    A general definition of a linear connection in noncommutative geometry has been recently proposed. Two examples are given of linear connections in noncommutative geometries which are based on matrix algebras. They both possess a unique metric connection.

  20. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim

    2016-01-07

    Classification with indefinite similarities has attracted attention in the machine learning community. This is partly due to the fact that many similarity functions that arise in practice are not symmetric positive semidefinite, i.e. the Mercer condition is not satisfied, or the Mercer condition is difficult to verify. Examples of such indefinite similarities in machine learning applications are ample including, for instance, the BLAST similarity score between protein sequences, human-judged similarities between concepts and words, and the tangent distance or the shape matching distance in computer vision. Nevertheless, previous works on classification with indefinite similarities are not fully satisfactory. They have either introduced sources of inconsistency in handling past and future examples using kernel approximation, settled for local-minimum solutions using non-convex optimization, or produced non-sparse solutions by learning in Krein spaces. Despite the large volume of research devoted to this subject lately, we demonstrate in this paper how an old idea, namely the 1-norm support vector machine (SVM) proposed more than 15 years ago, has several advantages over more recent work. In particular, the 1-norm SVM method is conceptually simpler, which makes it easier to implement and maintain. It is competitive, if not superior to, all other methods in terms of predictive accuracy. Moreover, it produces solutions that are often sparser than more recent methods by several orders of magnitude. In addition, we provide various theoretical justifications by relating 1-norm SVM to well-established learning algorithms such as neural networks, SVM, and nearest neighbor classifiers. Finally, we conduct a thorough experimental evaluation, which reveals that the evidence in favor of 1-norm SVM is statistically significant.

  1. Inferring Trust Based on Similarity with TILLIT

    Science.gov (United States)

    Tavakolifard, Mozhgan; Herrmann, Peter; Knapskog, Svein J.

    A network of people having established trust relations and a model for propagation of related trust scores are fundamental building blocks in many of today’s most successful e-commerce and recommendation systems. However, the web of trust is often too sparse to predict trust values between non-familiar people with high accuracy. Trust inferences are transitive associations among users in the context of an underlying social network and may provide additional information to alleviate the consequences of the sparsity and possible cold-start problems. Such approaches are helpful, provided that a complete trust path exists between the two users. An alternative approach to the problem is advocated in this paper. Based on collaborative filtering one can exploit the like-mindedness resp. similarity of individuals to infer trust to yet unknown parties which increases the trust relations in the web. For instance, if one knows that with respect to a specific property, two parties are trusted alike by a large number of different trusters, one can assume that they are similar. Thus, if one has a certain degree of trust to the one party, one can safely assume a very similar trustworthiness of the other one. In an attempt to provide high quality recommendations and proper initial trust values even when no complete trust propagation path or user profile exists, we propose TILLIT — a model based on combination of trust inferences and user similarity. The similarity is derived from the structure of the trust graph and users’ trust behavior as opposed to other collaborative-filtering based approaches which use ratings of items or user’s profile. We describe an algorithm realizing the approach based on a combination of trust inferences and user similarity, and validate the algorithm using a real large-scale data-set.

  2. Molecular fingerprint similarity search in virtual screening.

    Science.gov (United States)

    Cereto-Massagué, Adrià; Ojeda, María José; Valls, Cristina; Mulero, Miquel; Garcia-Vallvé, Santiago; Pujadas, Gerard

    2015-01-01

    Molecular fingerprints have been used for a long time now in drug discovery and virtual screening. Their ease of use (requiring little to no configuration) and the speed at which substructure and similarity searches can be performed with them - paired with a virtual screening performance similar to other more complex methods - is the reason for their popularity. However, there are many types of fingerprints, each representing a different aspect of the molecule, which can greatly affect search performance. This review focuses on commonly used fingerprint algorithms, their usage in virtual screening, and the software packages and online tools that provide these algorithms.

  3. Matrix analysis of electrical machinery

    CERN Document Server

    Hancock, N N

    2013-01-01

    Matrix Analysis of Electrical Machinery, Second Edition is a 14-chapter edition that covers the systematic analysis of electrical machinery performance. This edition discusses the principles of various mathematical operations and their application to electrical machinery performance calculations. The introductory chapters deal with the matrix representation of algebraic equations and their application to static electrical networks. The following chapters describe the fundamentals of different transformers and rotating machines and present torque analysis in terms of the currents based on the p

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    examinations were performed, and stimulated saliva was collected and analyzed for concentrations of MMP-8, TIMP-1 and total protein, using an immunofluorometric assay, an enzyme-linked immunosorbent assay and the Bradford assay, respectively. Salivary numbers of mutans streptococci and lactobacilli were......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...

  5. RAPSearch: a fast protein similarity search tool for short reads

    Directory of Open Access Journals (Sweden)

    Choi Jeong-Hyeon

    2011-05-01

    Full Text Available Abstract Background Next Generation Sequencing (NGS is producing enormous corpuses of short DNA reads, affecting emerging fields like metagenomics. Protein similarity search--a key step to achieve annotation of protein-coding genes in these short reads, and identification of their biological functions--faces daunting challenges because of the very sizes of the short read datasets. Results We developed a fast protein similarity search tool RAPSearch that utilizes a reduced amino acid alphabet and suffix array to detect seeds of flexible length. For short reads (translated in 6 frames we tested, RAPSearch achieved ~20-90 times speedup as compared to BLASTX. RAPSearch missed only a small fraction (~1.3-3.2% of BLASTX similarity hits, but it also discovered additional homologous proteins (~0.3-2.1% that BLASTX missed. By contrast, BLAT, a tool that is even slightly faster than RAPSearch, had significant loss of sensitivity as compared to RAPSearch and BLAST. Conclusions RAPSearch is implemented as open-source software and is accessible at http://omics.informatics.indiana.edu/mg/RAPSearch. It enables faster protein similarity search. The application of RAPSearch in metageomics has also been demonstrated.

  6. Nuclear markers reveal that inter-lake cichlids' similar morphologies do not reflect similar genealogy.

    Science.gov (United States)

    Kassam, Daud; Seki, Shingo; Horic, Michio; Yamaoka, Kosaku

    2006-08-01

    The apparent inter-lake morphological similarity among East African Great Lakes' cichlid species/genera has left evolutionary biologists asking whether such similarity is due to sharing of common ancestor or mere convergent evolution. In order to answer such question, we first used Geometric Morphometrics, GM, to quantify morphological similarity and then subsequently used Amplified Fragment Length Polymorphism, AFLP, to determine if similar morphologies imply shared ancestry or convergent evolution. GM revealed that not all presumed morphological similar pairs were indeed similar, and the dendrogram generated from AFLP data indicated distinct clusters corresponding to each lake and not inter-lake morphological similar pairs. Such results imply that the morphological similarity is due to convergent evolution and not shared ancestry. The congruency of GM and AFLP generated dendrograms imply that GM is capable of picking up phylogenetic signal, and thus GM can be potential tool in phylogenetic systematics.

  7. A new similarity computing method based on concept similarity in Chinese text processing

    Institute of Scientific and Technical Information of China (English)

    PENG Jing; YANG DongQing; TANG ShiWei; WANG TengJiao; GAO Jun

    2008-01-01

    The paper proposes a new text similarity computing method based on concept similarity in Chinese text processing. The new method converts text to words vec-tor space modet al first, and then splits words into a set of concepts. Through computing the inner products between concepts, it obtains the similarity between words. The new method computes the similarity of text based on the similarity of words at last. The contributions of the paper include: 1) propose a new computing formula between words; 2) propose a new text similarity computing method based on words similarity; 3) successfully use the method in the application of similarity computing of WEB news; and 4) prove the validity of the method through extensive experiments.

  8. Rapid detection of B2-ST131 clonal group of extended-spectrum β-lactamase-producing Escherichia coli by matrix-assisted laser desorption ionization-time-of-flight mass spectrometry: discovery of a peculiar amino acid substitution in B2-ST131 clonal group.

    Science.gov (United States)

    Nakamura, Akihiro; Komatsu, Masaru; Kondo, Akira; Ohno, Yuki; Kohno, Hisashi; Nakamura, Fumihiko; Matsuo, Shuji; Ohnuma, Kenichiro; Hatano, Naoya; Kawano, Seiji

    2015-11-01

    One reason for the spread of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli worldwide is the global pandemic of the B2-ST131 clonal group. We searched for the specific biomarker peaks to distinguish between the B2-ST131 clonal group and other sequence type (ST) clonal groups isolated from clinical specimens obtained in our hospital. Biomarker peaks at m/z 7650 in the B2-ST131 group (sensitivity of 100% and specificity of 89.7%) and m/z 7707 in the other ST clonal groups showed the highest discrimination abilities. We further verified reproducibility against other Japanese clinical isolates obtained in another area of Japan. Differences between the molecular mass at the 7650m/z and 7707m/z peaks indicated an E34A amino acid substitution by proteomic and genomic analysis. Matrix-assisted laser desorption ionization-time-of-flight mass spectrometry rapidly and simply identified the B2-ST131 clonal group in routine examinations and will allow for adequate empirical therapy and the possibility to control both hospital infections and the global pandemic.

  9. Value of urinary bladder cancer antigen,nuclear matrix protein 22 and hyaluronic acid in the diagnosis of bladder cancer%尿膀胱癌抗原、核基质蛋白22和透明质酸诊断膀胱癌的临床价值

    Institute of Scientific and Technical Information of China (English)

    张绍谨; 刘红耀

    2011-01-01

    Objective To assess the diagnostic value of testing of urinary bladder cancer antigen (UBC) ,nuclear matrix protein 22 (NMP22) and hyaluronic acid (HA) in the detection of bladder cancer. Methods This study included 70 bladder cancer patients and 23 urinary benign disease patients. UBC and NMP22 were detected by ELISA, and HA by radioimmunology assay. After that, urine cytology were performed. Results The sensitivities of UBC [ 84. 3% ( 59/70 ) ], NMP22 [ 81. 4% ( 57/70 ) ] and HA [ 88. 6 % (62/70 ) ] were significantly higher than that of urine cytology 95.7 % ( 22/23 ) ( P 0.05).HA检测值G2、G3组均明显高于G1 组(P0.05);各分期之间比较差异无统计学意义(P>0.05).尿细胞学检查,肿瘤分级越高,敏感性越高(P0.05).结论 尿UBC、NMP22、HA检测均有较高的诊断膀胱癌的敏感性,是诊断膀胱肿瘤较好的无创性诊断措施.

  10. SVD row or column symmetric matrix

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A new architecture for row or column symmetric matrix called extended matrix is defined, and a precise correspondence of the singular values and singular vectors between the extended matrix and its original (namely, the mother matrix) is derived. As an illustration of potential, we show that, for a class of extended matrices, the singular value decomposition using the mother matrix rather than the extended matrix per se can save the CPU time and memory without loss of numerical precision.

  11. Unveiling Music Structure Via PLSA Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Meng, Anders; Petersen, Kaare Brandt

    2007-01-01

    observed similarities can be satisfactorily explained using the latent semantics. Additionally, this approach significantly simplifies the song retrieval phase, leading to a more practical system implementation. The suitability of the PLSA model for representing music structure is studied in a simplified...

  12. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2016-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds enorm

  13. Efficient Similarity Retrieval in Music Databases

    DEFF Research Database (Denmark)

    Ruxanda, Maria Magdalena; Jensen, Christian Søndergaard

    2006-01-01

    object is modeled as a time sequence of high-dimensional feature vectors, and dynamic time warping (DTW) is used as the similarity measure. To accomplish this, the paper extends techniques for time-series-length reduction and lower bounding of DTW distance to the multi-dimensional case. Further...

  14. Mental Institutions and Similar Phenomena Called Schools

    Science.gov (United States)

    Fischer, Ronald W.

    1971-01-01

    Mental institutions and public schools appear to have many similarities, and they often operate in ways that would seem contradictory to their philosophy. This article explores certain atrocities to the self" that result from programs that are intended to be beneficial but, in reality, often result in dehumanization. (Author)

  15. Music Retrieval based on Melodic Similarity

    NARCIS (Netherlands)

    Typke, R.

    2007-01-01

    This thesis introduces a method for measuring melodic similarity for notated music such as MIDI files. This music search algorithm views music as sets of notes that are represented as weighted points in the two-dimensional space of time and pitch. Two point sets can be compared by calculating how mu

  16. Measure of Node Similarity in Multilayer Networks

    DEFF Research Database (Denmark)

    Møllgaard, Anders; Zettler, Ingo; Dammeyer, Jesper;

    2016-01-01

    The weight of links in a network is often related to the similarity of thenodes. Here, we introduce a simple tunable measure for analysing the similarityof nodes across different link weights. In particular, we use the measure toanalyze homophily in a group of 659 freshman students at a large...

  17. Cultural Similarities and Differences on Idiom Translation

    Institute of Scientific and Technical Information of China (English)

    黄频频; 陈于全

    2010-01-01

    Both English and Chinese are abound with idioms. Idioms are an important part of the hnguage and culture of a society. English and Chinese idioms carved with cultural characteristics account for a great part in the tramlation. This paper studies the translation of idioms concerning their cultural similarities, cultural differences and transhtion principles.

  18. Partial order similarity based on mutual information

    CERN Document Server

    Tibély, Gergely; Palla, Gergely

    2016-01-01

    Comparing the ranking of candidates by different voters is an important topic in social and information science with a high relevance from the point of view of practical applications. In general, ties and pairs of incomparable candidates may occur, thus, the alternative rankings are described by partial orders. Various distance measures between partial orders have already been introduced, where zero distance is corresponding to a perfect match between a pair of partial orders, and larger values signal greater differences. Here we take a different approach and propose a similarity measure based on adjusted mutual information. In general, the similarity value of unity is corresponding to exactly matching partial orders, while a low similarity is associated to a pair of independent partial orders. The time complexity of the computation of this similarity measure is $\\mathcal{O}(\\left|{\\mathcal C}\\right|^3)$ in the worst case, and $\\mathcal{O}(\\left|{\\mathcal C}\\right|^2\\ln \\left|{\\mathcal C}\\right|)$ in the typi...

  19. Some Similarity between Contractions and Kannan Mappings

    Directory of Open Access Journals (Sweden)

    Tomonari Suzuki

    2008-03-01

    Full Text Available Contractions are always continuous and Kannan mappings are not necessarily continuous. This is a very big difference between both mappings. However, we know that relaxed both mappings are quite similar. In this paper, we discuss both mappings from a new point of view.

  20. Recognizing Similarities between Fraction Word Problems.

    Science.gov (United States)

    Hardiman, Pamela Thibodeau

    Deciding how to approach a word problem for solution is a critical stage of problem solving, and is the stage which frequently presents considerable difficulty for novices. Do novices use the same information that experts do in deciding that two problems would be solved similarly? This set of four studies indicates that novices rely more on…