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Sample records for structure polymorphism detection

  1. Effect of secondary structure on single nucleotide polymorphism detection with a porous microarray matrix; implications for probe selection

    NARCIS (Netherlands)

    Anthony, R. M.; Schuitema, A. R. J.; Chan, A. B.; Boender, P. J.; Klatser, P. R.; Oskam, L.

    2003-01-01

    Oligonucleotide arrays capable of detecting single nucleotide polymorphisms (SNPs) from amplified nucleic acid have many applications. The expected SNP is usually placed approximately in the center of the probe to ensure the maximum shift in Tm between complementary and SNP sequences. Unfortunately,

  2. Natural single amino acid polymorphism (F19Y) in human galectin-8: detection of structural alterations and increased growth-regulatory activity on tumor cells.

    Science.gov (United States)

    Ruiz, Federico M; Scholz, Barbara A; Buzamet, Eliza; Kopitz, Jürgen; André, Sabine; Menéndez, Margarita; Romero, Antonio; Solís, Dolores; Gabius, Hans-Joachim

    2014-03-01

    Natural amino acid substitution by single-site nucleotide polymorphism can become a valuable tool for structure-activity correlations, especially if evidence for association to disease parameters exists. Focusing on the F19Y change in human galectin-8, connected clinically to rheumatoid arthritis, we here initiate the study of consequences of a single-site substitution in the carbohydrate recognition domain of this family of cellular effectors. We apply a strategically combined set of structural and cell biological techniques for comparing properties of the wild-type and variant proteins. The overall hydrodynamic behavior of the full-length protein and of the separate N-domain is not noticeably altered, but displacements in the F0 β-strand of the β-sandwich fold in the N-domain are induced, as evidenced by protein crystallography. Analysis of thermal stability by circular dichroism spectroscopy revealed perceptible differences for the full-length proteins, pointing to an impact of the substitution beyond the N-domain. In addition, small differences in thermodynamic parameters of carbohydrate binding are detected. On the level of two types of tumor cells, characteristics of binding appeared rather similar. In further comparison of the influence on proliferation, the variant proved to be more active as growth regulator in the six tested lines of neuroblastoma, erythroleukemia and colon adenocarcinoma. The seemingly subtle structural change identified here thus has functional implications in vitro, encouraging further analysis in autoimmune regulation and, in a broad context, in work with other natural single-site variants, using the documented combined strategy. The atomic coordinates and structure factors (codes 4BMB, 4BME) have been deposited in the Protein Data Bank. © 2014 FEBS.

  3. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis

    International Nuclear Information System (INIS)

    Goldman, D.; Merril, C.R.

    1983-01-01

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of 14 C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses

  4. Similarity-based Polymorphic Shellcode Detection

    Directory of Open Access Journals (Sweden)

    Denis Yurievich Gamayunov

    2013-02-01

    Full Text Available In the work the method for polymorphic shellcode dedection based on the set of known shellcodes is proposed. The method’s main idea is in sequential applying of deobfuscating transformations to a data analyzed and then recognizing similarity with malware samples. The method has been tested on the sets of shellcodes generated using Metasploit Framework v.4.1.0 and PELock Obfuscator and shows 87 % precision with zero false positives rate.

  5. Thermal, spectroscopic, and ab initio structural characterization of carprofen polymorphs.

    Science.gov (United States)

    Bruni, Giovanna; Gozzo, Fabia; Capsoni, Doretta; Bini, Marcella; Macchi, Piero; Simoncic, Petra; Berbenni, Vittorio; Milanese, Chiara; Girella, Alessandro; Ferrari, Stefania; Marini, Amedeo

    2011-06-01

    Commercial and recrystallized polycrystalline samples of carprofen, a nonsteroidal anti-inflammatory drug, were studied by thermal, spectroscopic, and structural techniques. Our investigations demonstrated that recrystallized sample, stable at room temperature (RT), is a single polymorphic form of carprofen (polymorph I) that undergoes an isostructural polymorphic transformation by heating (polymorph II). Polymorph II remains then metastable at ambient conditions. Commercial sample is instead a mixture of polymorphs I and II. The thermodynamic relationships between the two polymorphs were determined through the construction of an energy/temperature diagram. The ab initio structural determination performed on synchrotron X-Ray powder diffraction patterns recorded at RT on both polymorphs allowed us to elucidate, for the first time, their crystal structure. Both crystallize in the monoclinic space group type P2(1) /c, and the unit cell similarity index and the volumetric isostructurality index indicate that the temperature-induced polymorphic transformation I → II is isostructural. Polymorphs I and II are conformational polymorphs, sharing a very similar hydrogen bond network, but with different conformation of the propanoic skeleton, which produces two different packing. The small conformational change agrees with the low value of transition enthalpy obtained by differential scanning calorimetry measurements and the small internal energy computed with density functional methods. Copyright © 2011 Wiley-Liss, Inc.

  6. Detection of somaclonal variation by random amplified polymorphic ...

    African Journals Online (AJOL)

    Detection of somaclonal variation by random amplified polymorphic DNA analysis during micropropagation of Phalaenopsis bellina (Rchb.f.) Christenson. ... Among the primers used, P 16 produced the highest number of bands (29), while primer OPU 10 produced the lowest number (15). The range of similarity coefficient ...

  7. Detection of DNA polymorphisms in Dendrobium Sonia White mutant lines

    International Nuclear Information System (INIS)

    Affrida Abu Hassan; Putri Noor Faizah Megat Mohd Tahir; Zaiton Ahmad; Mohd Nazir Basiran

    2006-01-01

    Dendrobium Sonia white mutant lines were obtained through gamma ray induced mutation of purple flower Dendrobium Sonia at dosage 35 Gy. Amplified Fragment Length Polymorphism (AFLP) technique was used to compare genomic variations in these mutant lines with the control. Our objectives were to detect polymorphic fragments from these mutants to provide useful information on genes involving in flower colour expression. AFLP is a PCR based DNA fingerprinting technique. It involves digestion of DNA with restriction enzymes, ligation of adapter and selective amplification using primer with one (pre-amplification) and three (selective amplification) arbitrary nucleotides. A total number of 20 primer combinations have been tested and 7 produced clear fingerprint patterns. Of these, 13 polymorphic bands have been successfully isolate and cloned. (Author)

  8. Polymorphism in phenobarbital: discovery of a new polymorph and crystal structure of elusive form V.

    Science.gov (United States)

    Roy, Saikat; Goud, N Rajesh; Matzger, Adam J

    2016-03-21

    This report highlights the discovery of a new polymorph of the anticonvulsant drug phenobarbital (PB) using polymer-induced heteronucleation (PIHn) and unravelling the crystal structure of the elusive form V. Both forms are characterized by structural, thermal and VT-Raman spectroscopy methods to elucidate phase transformation behavior and shed light on stability relationships.

  9. Polymorphism in 'L' shaped lipids: structure of N-, O-diacylethanolamines with mixed acyl chains.

    Science.gov (United States)

    Tarafdar, Pradip K; Swamy, Musti J

    2009-11-01

    Although solid state polymorphism in lipids has been established by spectroscopic and calorimetric studies long ago, only in a few cases crystal structures of different polymorphs of the same compound have been reported, possibly due to difficulties in obtaining high quality single crystals of individual polymorphs. Recent studies show that N-, O-diacylethanolamines (DAEs) can be derived by the O-acylation of the stress-related lipids, the N-acylethanolamines under physiological conditions. In this study, two DAEs with mixed acyl chains, namely N-palmitoyl, O-octanoylethanolamine and N-palmitoyl, O-decanoylethanolamine have been synthesized and their three-dimensional structures were determined. Both the compounds were found to adopt 'L' shaped structures and exist in two polymorphic forms, alpha and beta. In the alpha form a mixed-type chain packing has been observed whereas in the beta form the chain packing is symmetric. Similar polymorphic forms are likely to exist in other 'L' shaped lipids such as 1,3-diacylglycerols and ceramides, where polymorphism has been detected earlier, but three-dimensional structures - which can give precise information about the packing at atomic resolution - have not been reported.

  10. Rapid detection of dihydropteroate polymorphism in AIDS-related Pneumocystis carinii pneumonia by restriction fragment length polymorphism

    DEFF Research Database (Denmark)

    Helweg-Larsen, J; Eugen-Olsen, Jesper; Lundgren, B

    2000-01-01

    are associated with failure of sulpha prophylaxis and increased mortality in HIV-1 positive patients with PCP, suggesting that DHPS mutations may cause sulpha resistance. To facilitate detection of DHPS mutations we developed a restriction fragment length polymorphism (RFLP) assay, detecting mutations at codon...

  11. Redetermined structure of gossypol (P3 polymorph

    Directory of Open Access Journals (Sweden)

    Muhabbat Honkeldieva

    2015-07-01

    Full Text Available An improved crystal structure of the title compound, C30H30O8 (systematic name: 1,1′,6,6′,7,7′-hexahydroxy-5,5′-diisopropyl-3,3′-dimethyl[2,2′-binaphthalene]-8,8′-dicarbaldehyde, was determined based on modern CCD data. Compared to the previous structure [Talipov et al. (1985. Khim. Prirod. Soedin. (Chem. Nat. Prod., 6, 20–24], geometrical precision has been improved (typical C—C bond-distance s.u. = 0.002 Å in the present structure compared to 0.005 Å in the previous structure and the locations of several H atoms have been corrected. The gossypol molecules are in the aldehyde tautomeric form and the dihedral angle between the naphthyl fragments is 80.42 (4°. Four intramolecular O—H...O hydrogen bonds are formed. In the crystal, inversion dimers with graph-set motif R22(20 are formed by pairs of O—H...O hydrogen bonds; another pair of O—H...O hydrogen bonds with the same graph-set motif links the dimers into [001] chains. The packing of such chains in the crystal leads to the formation of channels (diameter = 5–8 Å propagating in the [101] direction. The channels presumably contain highly disordered solvent molecules; their contribution to the scattering was removed with the SQUEEZE [Spek (2015. Acta Cryst. C71, 9–18] routine in PLATON and the stated molecular mass, density etc., do not take them into account.

  12. Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP).

    Science.gov (United States)

    Peraza-Echeverria, S; Herrera-Valencia, V A.; Kay, A -J.

    2001-07-01

    The extent of DNA methylation polymorphisms was evaluated in micropropagated banana (Musa AAA cv. 'Grand Naine') derived from either the vegetative apex of the sucker or the floral apex of the male inflorescence using the methylation-sensitive amplification polymorphism (MSAP) technique. In all, 465 fragments, each representing a recognition site cleaved by either or both of the isoschizomers were amplified using eight combinations of primers. A total of 107 sites (23%) were found to be methylated at cytosine in the genome of micropropagated banana plants. In plants micropropagated from the male inflorescence explant 14 (3%) DNA methylation events were polymorphic, while plants micropropagated from the sucker explant produced 8 (1.7%) polymorphisms. No DNA methylation polymorphisms were detected in conventionally propagated banana plants. These results demonstrated the usefulness of MSAP to detect DNA methylation events in micropropagated banana plants and indicate that DNA methylation polymorphisms are associated with micropropagation.

  13. Structures and energetics of Ga2O3 polymorphs

    International Nuclear Information System (INIS)

    Yoshioka, S; Hayashi, H; Kuwabara, A; Oba, F; Matsunaga, K; Tanaka, I

    2007-01-01

    First-principles calculations are made for five Ga 2 O 3 polymorphs. The structure of ε-Ga 2 O 3 with the space group Pna 2 1 (No. 33, orthorhombic), which is sometimes called κ-Ga 2 O 3 in the literature, is consistent with experimental reports. The structure of γ-Ga 2 O 3 is optimized within 14 inequivalent configurations of defective spinel structures. Phonon dispersion curves of four polymorphs are obtained. The volume expansivity, bulk modulus, and specific heat at constant volume are computed as a function of temperature within the quasi-harmonic approximation. The Helmholtz free energies of the polymorphs are thus compared. The expansivity shows a relationship of β<ε<α<δ, while β<ε<δ<α for the bulk modulus. The formation free energies have the tendency β<ε<α<δ<γ at low temperatures. With the increase of temperature, the difference in free energy between the β-phase and the ε-phase becomes smaller. Eventually the ε phase becomes more stable at above 1600 K

  14. Population structure of Salmonella investigated by amplified fragment length polymorphism

    DEFF Research Database (Denmark)

    Torpdahl, M.; Ahrens, Peter

    2004-01-01

    Aims: This study was undertaken to investigate the usefulness of amplified fragment length polymorphism (AFLP) in determining the population structure of Salmonella. Methods and Results: A total of 89 strains were subjected to AFLP analysis using the enzymes BglII and BspDI, a combination...... that is novel in Salmonella. Both species S. bongori and S. enterica and all subsp. of S. enterica were represented with emphasis on S. enterica subsp. enterica using a local strain collection and strains from the Salmonella Reference Collection B (SARB). The amplified fragments were used in a band...

  15. Boron doping compensation of hydrogenated amorphous and polymorphous germanium thin films for infrared detection applications

    International Nuclear Information System (INIS)

    Moreno, M.; Delgadillo, N.; Torres, A.; Ambrosio, R.; Rosales, P.; Kosarev, A.; Reyes-Betanzo, C.; Hidalga-Wade, J. de la; Zuniga, C.; Calleja, W.

    2013-01-01

    In this work we have studied boron doping of hydrogenated amorphous germanium a-Ge:H and polymorphous germanium (pm-Ge:H) in low regimes, in order to compensate the material from n-type (due to oxygen contamination that commonly occurs during plasma deposition) to intrinsic, and in this manner improve the properties that are important for infrared (IR) detection, as activation energy (E a ) and temperature coefficient of resistance (TCR). Electrical, structural and optical characterization was performed on the films produced. Measurements of the temperature dependence of conductivity, room temperature conductivity (σ RT ), E a and current–voltage characteristics under IR radiation were performed in the compensated a-Ge:H and pm-Ge:H films. Our results demonstrate that, effectively, the values of E a , TCR and IR detection are improved on the a-Ge:H/pm-Ge:H films, using boron doping in low regimes, which results of interest for infrared detectors. - Highlights: • We reported boron doping compensation of amorphous and polymorphous germanium. • The films were deposited by plasma enhanced chemical vapor deposition. • The aim is to use the films as thermo-sensing elements in un-cooled microbolometers. • Those films have advantages over boron doped a-Si:H used in commercial detectors

  16. Boron doping compensation of hydrogenated amorphous and polymorphous germanium thin films for infrared detection applications

    Energy Technology Data Exchange (ETDEWEB)

    Moreno, M., E-mail: mmoreno@inaoep.mx [National Institute of Astrophysics, Optics and Electronics, INAOE, P.O. Box 51 and 216, Puebla, Z. P. 72840 Puebla (Mexico); Delgadillo, N. [Universidad Autónoma de Tlaxcala, Av. Universidad No. 1, Z. P. 90006 Tlaxcala (Mexico); Torres, A. [National Institute of Astrophysics, Optics and Electronics, INAOE, P.O. Box 51 and 216, Puebla, Z. P. 72840 Puebla (Mexico); Ambrosio, R. [Technology and Engineering Institute, Ciudad Juarez University UACJ, Av. Del Charro 450N, Z. P. 32310 Chihuahua (Mexico); Rosales, P.; Kosarev, A.; Reyes-Betanzo, C.; Hidalga-Wade, J. de la; Zuniga, C.; Calleja, W. [National Institute of Astrophysics, Optics and Electronics, INAOE, P.O. Box 51 and 216, Puebla, Z. P. 72840 Puebla (Mexico)

    2013-12-02

    In this work we have studied boron doping of hydrogenated amorphous germanium a-Ge:H and polymorphous germanium (pm-Ge:H) in low regimes, in order to compensate the material from n-type (due to oxygen contamination that commonly occurs during plasma deposition) to intrinsic, and in this manner improve the properties that are important for infrared (IR) detection, as activation energy (E{sub a}) and temperature coefficient of resistance (TCR). Electrical, structural and optical characterization was performed on the films produced. Measurements of the temperature dependence of conductivity, room temperature conductivity (σ{sub RT}), E{sub a} and current–voltage characteristics under IR radiation were performed in the compensated a-Ge:H and pm-Ge:H films. Our results demonstrate that, effectively, the values of E{sub a}, TCR and IR detection are improved on the a-Ge:H/pm-Ge:H films, using boron doping in low regimes, which results of interest for infrared detectors. - Highlights: • We reported boron doping compensation of amorphous and polymorphous germanium. • The films were deposited by plasma enhanced chemical vapor deposition. • The aim is to use the films as thermo-sensing elements in un-cooled microbolometers. • Those films have advantages over boron doped a-Si:H used in commercial detectors.

  17. Investigation of the Sensitivity of Transmission Raman Spectroscopy for Polymorph Detection in Pharmaceutical Tablets.

    Science.gov (United States)

    Feng, Hanzhou; Bondi, Robert W; Anderson, Carl A; Drennen, James K; Igne, Benoît

    2017-08-01

    Polymorph detection is critical for ensuring pharmaceutical product quality in drug substances exhibiting polymorphism. Conventional analytical techniques such as X-ray powder diffraction and solid-state nuclear magnetic resonance are utilized primarily for characterizing the presence and identity of specific polymorphs in a sample. These techniques have encountered challenges in analyzing the constitution of polymorphs in the presence of other components commonly found in pharmaceutical dosage forms. Laborious sample preparation procedures are usually required to achieve satisfactory data interpretability. There is a need for alternative techniques capable of probing pharmaceutical dosage forms rapidly and nondestructively, which is dictated by the practical requirements of applications such as quality monitoring on production lines or when quantifying product shelf lifetime. The sensitivity of transmission Raman spectroscopy for detecting polymorphs in final tablet cores was investigated in this work. Carbamazepine was chosen as a model drug, polymorph form III is the commercial form, whereas form I is an undesired polymorph that requires effective detection. The concentration of form I in a direct compression tablet formulation containing 20% w/w of carbamazepine, 74.00% w/w of fillers (mannitol and microcrystalline cellulose), and 6% w/w of croscarmellose sodium, silicon dioxide, and magnesium stearate was estimated using transmission Raman spectroscopy. Quantitative models were generated and optimized using multivariate regression and data preprocessing. Prediction uncertainty was estimated for each validation sample by accounting for all the main variables contributing to the prediction. Multivariate detection limits were calculated based on statistical hypothesis testing. The transmission Raman spectroscopic model had an absolute prediction error of 0.241% w/w for the independent validation set. The method detection limit was estimated at 1.31% w/w. The

  18. Species-specific markers for the differential diagnosis of Trypanosoma cruzi and Trypanosoma rangeli and polymorphisms detection in Trypanosoma rangeli.

    Science.gov (United States)

    Ferreira, Keila Adriana Magalhães; Fajardo, Emanuella Francisco; Baptista, Rodrigo P; Macedo, Andrea Mara; Lages-Silva, Eliane; Ramírez, Luis Eduardo; Pedrosa, André Luiz

    2014-06-01

    Trypanosoma cruzi and Trypanosoma rangeli are kinetoplastid parasites which are able to infect humans in Central and South America. Misdiagnosis between these trypanosomes can be avoided by targeting barcoding sequences or genes of each organism. This work aims to analyze the feasibility of using species-specific markers for identification of intraspecific polymorphisms and as target for diagnostic methods by PCR. Accordingly, primers which are able to specifically detect T. cruzi or T. rangeli genomic DNA were characterized. The use of intergenic regions, generally divergent in the trypanosomatids, and the serine carboxypeptidase gene were successful. Using T. rangeli genomic sequences for the identification of group-specific polymorphisms and a polymorphic AT(n) dinucleotide repeat permitted the classification of the strains into two groups, which are entirely coincident with T. rangeli main lineages, KP1 (+) and KP1 (-), previously determined by kinetoplast DNA (kDNA) characterization. The sequences analyzed totalize 622 bp (382 bp represent a hypothetical protein sequence, and 240 bp represent an anonymous sequence), and of these, 581 (93.3%) are conserved sites and 41 bp (6.7%) are polymorphic, with 9 transitions (21.9%), 2 transversions (4.9%), and 30 (73.2%) insertion/deletion events. Taken together, the species-specific markers analyzed may be useful for the development of new strategies for the accurate diagnosis of infections. Furthermore, the identification of T. rangeli polymorphisms has a direct impact in the understanding of the population structure of this parasite.

  19. Detection of new single nucleotide polymorphisms by means of real ...

    Indian Academy of Sciences (India)

    Unknown

    amplified millions to billions of times by means of a PCR before the PCR product ... Keywords. Single nucleotide polymorphism; real time PCR; DNA melting curve analysis. ... VAL158MET SNP and alcoholism and to test for interac- tions between the .... indicate a heterozygote sample (VAL/MET genotype). The curve with ...

  20. Canine olfactory receptor gene polymorphism and its relation to odor detection performance by sniffer dogs.

    Science.gov (United States)

    Lesniak, Anna; Walczak, Marta; Jezierski, Tadeusz; Sacharczuk, Mariusz; Gawkowski, Maciej; Jaszczak, Kazimierz

    2008-01-01

    The outstanding sensitivity of the canine olfactory system has been acknowledged by using sniffer dogs in military and civilian service for detection of a variety of odors. It is hypothesized that the canine olfactory ability is determined by polymorphisms in olfactory receptor (OR) genes. We investigated 5 OR genes for polymorphic sites which might affect the olfactory ability of service dogs in different fields of specific substance detection. All investigated OR DNA sequences proved to have allelic variants, the majority of which lead to protein sequence alteration. Homozygous individuals at 2 gene loci significantly differed in their detection skills from other genotypes. This suggests a role of specific alleles in odor detection and a linkage between single-nucleotide polymorphism and odor recognition efficiency.

  1. A lateral flow biosensor for detection of single nucleotide polymorphism by circular strand displacement reaction.

    Science.gov (United States)

    Xiao, Zhuo; Lie, Puchang; Fang, Zhiyuan; Yu, Luxin; Chen, Junhua; Liu, Jie; Ge, Chenchen; Zhou, Xuemeng; Zeng, Lingwen

    2012-09-04

    A lateral flow biosensor for detection of single nucleotide polymorphism based on circular strand displacement reaction (CSDPR) has been developed. Taking advantage of high fidelity of T4 DNA ligase, signal amplification by CSDPR, and the optical properties of gold nanoparticles, this assay has reached a detection limit of 0.01 fM.

  2. Electronic structure and insulating gap in epitaxial VO2 polymorphs

    Directory of Open Access Journals (Sweden)

    Shinbuhm Lee

    2015-12-01

    Full Text Available Determining the origin of the insulating gap in the monoclinic V O2(M1 is a long-standing issue. The difficulty of this study arises from the simultaneous occurrence of structural and electronic transitions upon thermal cycling. Here, we compare the electronic structure of the M1 phase with that of single crystalline insulating V O2(A and V O2(B thin films to better understand the insulating phase of VO2. As these A and B phases do not undergo a structural transition upon thermal cycling, we comparatively study the origin of the gap opening in the insulating VO2 phases. By x-ray absorption and optical spectroscopy, we find that the shift of unoccupied t2g orbitals away from the Fermi level is a common feature, which plays an important role for the insulating behavior in VO2 polymorphs. The distinct splitting of the half-filled t2g orbital is observed only in the M1 phase, widening the bandgap up to ∼0.6 eV. Our approach of comparing all three insulating VO2 phases provides insight into a better understanding of the electronic structure and the origin of the insulating gap in VO2.

  3. Single nucleotide polymorphism (SNP) detection on a magnetoresistive sensor

    DEFF Research Database (Denmark)

    Rizzi, Giovanni; Østerberg, Frederik Westergaard; Dufva, Martin

    2013-01-01

    We present a magnetoresistive sensor platform for hybridization assays and demonstrate its applicability on single nucleotide polymorphism (SNP) genotyping. The sensor relies on anisotropic magnetoresistance in a new geometry with a local negative reference and uses the magnetic field from...... the sensor bias current to magnetize magnetic beads in the vicinity of the sensor. The method allows for real-time measurements of the specific bead binding to the sensor surface during DNA hybridization and washing. Compared to other magnetic biosensing platforms, our approach eliminates the need...... for external electromagnets and thus allows for miniaturization of the sensor platform....

  4. Lead(ii) soaps: crystal structures, polymorphism, and solid and liquid mesophases.

    Science.gov (United States)

    Martínez-Casado, F J; Ramos-Riesco, M; Rodríguez-Cheda, J A; Redondo-Yélamos, M I; Garrido, L; Fernández-Martínez, A; García-Barriocanal, J; da Silva, I; Durán-Olivencia, M; Poulain, A

    2017-07-05

    The long-chain members of the lead(ii) alkanoate series or soaps, from octanoate to octadecanoate, have been thoroughly characterized by means of XRD, PDF analysis, DSC, FTIR, ssNMR and other techniques, in all their phases and mesophases. The crystal structures at room temperature of all of the members of the series are now solved, showing the existence of two polymorphic forms in the room temperature crystal phase, different to short and long-chain members. Only nonanoate and decanoate present both forms, and this polymorphism is proven to be monotropic. At higher temperature, these compounds present a solid mesophase, defined as rotator, a liquid crystal phase and a liquid phase, all of which have a similar local arrangement. Since some lead(ii) soaps appear as degradation compounds in oil paintings, the solved crystal structures of lead(ii) soaps can now be used as fingerprints for their detection using X-ray diffraction. Pair distribution function analysis on these compounds is very similar in the same phases and mesophases for the different members, showing the same short range order. This observation suggests that this technique could also be used in the detection of these compounds in disordered phases or in the initial stages of formation in paintings.

  5. Synthesis, structure and electronic structure of a new polymorph of CaGe2

    International Nuclear Information System (INIS)

    Tobash, Paul H.; Bobev, Svilen

    2007-01-01

    Reported are the flux synthesis, the crystal structure determination, the properties and the band structure calculations of a new polymorph of CaGe 2 , which crystallizes with the hexagonal space group P6 3 mc (no. 186) with cell parameters of a=3.9966(9) and c=10.211(4)A (Z=2; Pearson's code hP6). The structure can be viewed as puckered layers of three-bonded germanium atoms, ∼ 2 [Ge 2 ] 2- , which are stacked along the direction of the c-axis in an ABAB-fashion. The germanium polyanionic layers are separated by the Ca cations. As such, this structure is closely related to the structure of the other CaGe 2 polymorph, which crystallizes with the rhombohedral CaSi 2 type in the R3-bar m space group (No. 166), where the ∼ 2 [Ge 2 ] 2- layers are arranged in an AA'BB'CC'-fashion, and are also interspaced by Ca 2+ cations. LMTO calculations suggest that in spite of the formal closed-shell configuration for all atoms and the apparent adherence to the Zintl rules for electron counting, i.e., Ca 2+ [3b-Ge 1- ] 2 ), the phase will be a poor metal due to a small Ca-3d-Ge-4p band overlap. Magnetic susceptibility measurements as a function of the temperature indicate that the new CaGe 2 polymorph exhibits weak, temperature independent, Pauli-paramagnetism

  6. A novel polymorphism of human complement component C3 detected by means of a monoclonal antibody

    DEFF Research Database (Denmark)

    Koch, C; Behrendt, N

    1986-01-01

    A mouse monoclonal antibody, HAV 4-1, obtained after immunization of a BALB/c mouse with purified C3F, detected a novel genetic polymorphism of human complement component C3 in a simple immunoblotting system. The frequency of HAV 4-1-positive genes was 20.1%. Reactivity of HAV 4-1 was closely...... related to C3F, but certain individuals with the C3F allele did not react with HAV 4-1. Conversely, certain C3S homozygous individuals did react with HAV 4-1. The polymorphism detected by this monoclonal antibody is therefore different from the previously described polymorphism based on charge differences....

  7. Detecting Hierarchical Structure in Networks

    DEFF Research Database (Denmark)

    Herlau, Tue; Mørup, Morten; Schmidt, Mikkel Nørgaard

    2012-01-01

    Many real-world networks exhibit hierarchical organization. Previous models of hierarchies within relational data has focused on binary trees; however, for many networks it is unknown whether there is hierarchical structure, and if there is, a binary tree might not account well for it. We propose...... a generative Bayesian model that is able to infer whether hierarchies are present or not from a hypothesis space encompassing all types of hierarchical tree structures. For efficient inference we propose a collapsed Gibbs sampling procedure that jointly infers a partition and its hierarchical structure....... On synthetic and real data we demonstrate that our model can detect hierarchical structure leading to better link-prediction than competing models. Our model can be used to detect if a network exhibits hierarchical structure, thereby leading to a better comprehension and statistical account the network....

  8. Direct detection of single-nucleotide polymorphisms in bacterial DNA by SNPtrap

    DEFF Research Database (Denmark)

    Grønlund, Hugo Ahlm; Moen, Birgitte; Hoorfar, Jeffrey

    2011-01-01

    A major challenge with single-nucleotide polymorphism (SNP) fingerprinting of bacteria and higher organisms is the combination of genome-wide screenings with the potential of multiplexing and accurate SNP detection. Single-nucleotide extension by the minisequencing principle represents a technolo...

  9. Genetic structure of Balearic honeybee populations based on microsatellite polymorphism

    Directory of Open Access Journals (Sweden)

    Moritz Robin FA

    2003-05-01

    Full Text Available Abstract The genetic variation of honeybee colonies collected in 22 localities on the Balearic Islands (Spain was analysed using eight polymorphic microsatellite loci. Previous studies have demonstrated that these colonies belong either to the African or west European evolutionary lineages. These populations display low variability estimated from both the number of alleles and heterozygosity values, as expected for the honeybee island populations. Although genetic differentiation within the islands is low, significant heterozygote deficiency is present, indicating a subpopulation genetic structure. According to the genetic differentiation test, the honeybee populations of the Balearic Islands cluster into two groups: Gimnesias (Mallorca and Menorca and Pitiusas (Ibiza and Formentera, which agrees with the biogeography postulated for this archipelago. The phylogenetic analysis suggests an Iberian origin of the Balearic honeybees, thus confirming the postulated evolutionary scenario for Apis mellifera in the Mediterranean basin. The microsatellite data from Formentera, Ibiza and Menorca show that ancestral populations are threatened by queen importations, indicating that adequate conservation measures should be developed for protecting Balearic bees.

  10. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms.

    Science.gov (United States)

    Guo, Qingsheng; Bai, Zhixiong; Liu, Yuqian; Sun, Qingjiang

    2016-03-15

    In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. An unusual haplotype structure on human chromosome 8p23 derived from the inversion polymorphism.

    Science.gov (United States)

    Deng, Libin; Zhang, Yuezheng; Kang, Jian; Liu, Tao; Zhao, Hongbin; Gao, Yang; Li, Chaohua; Pan, Hao; Tang, Xiaoli; Wang, Dunmei; Niu, Tianhua; Yang, Huanming; Zeng, Changqing

    2008-10-01

    Chromosomal inversion is an important type of genomic variations involved in both evolution and disease pathogenesis. Here, we describe the refined genetic structure of a 3.8-Mb inversion polymorphism at chromosome 8p23. Using HapMap data of 1,073 SNPs generated from 209 unrelated samples from CEPH-Utah residents with ancestry from northern and western Europe (CEU); Yoruba in Ibadan, Nigeria (YRI); and Asian (ASN) samples, which were comprised of Han Chinese from Beijing, China (CHB) and Japanese from Tokyo, Japan (JPT)-we successfully deduced the inversion orientations of all their 418 haplotypes. In particular, distinct haplotype subgroups were identified based on principal component analysis (PCA). Such genetic substructures were consistent with clustering patterns based on neighbor-joining tree reconstruction, which revealed a total of four haplotype clades across all samples. Metaphase fluorescence in situ hybridization (FISH) in a subset of 10 HapMap samples verified their inversion orientations predicted by PCA or phylogenetic tree reconstruction. Positioning of the outgroup haplotype within one of YRI clades suggested that Human NCBI Build 36-inverted order is most likely the ancestral orientation. Furthermore, the population differentiation test and the relative extended haplotype homozygosity (REHH) analysis in this region discovered multiple selection signals, also in a population-specific manner. A positive selection signal was detected at XKR6 in the ASN population. These results revealed the correlation of inversion polymorphisms to population-specific genetic structures, and various selection patterns as possible mechanisms for the maintenance of a large chromosomal rearrangement at 8p23 region during evolution. In addition, our study also showed that haplotype-based clustering methods, such as PCA, can be applied in scanning for cryptic inversion polymorphisms at a genome-wide scale.

  12. CdWO4 polymorphs: Selective preparation, electronic structures, and photocatalytic activities

    International Nuclear Information System (INIS)

    Yan, Tingjiang; Li, Liping; Tong, Wenming; Zheng, Jing; Wang, Yunjian; Li, Guangshe

    2011-01-01

    This work explored the selective synthesis of polymorphs of CdWO 4 in either tetragonal or monoclinic phase by optimizing the experimental parameters. Systematic characterization indicated that both polymorphs possessed similar spherical morphologies but different structural building blocks. Electronic structures calculations for both polymorphs demonstrated the same constructions of conduction band or valence band, while the conduction band widths of both polymorphs were quite different. Both CdWO 4 polymorphs exhibited good photocatalytic activity for degradation of methyl orange under UV light irradiation. When comparing to some other well-known tungstate oxide materials, the photocatalytic activity was found to follow such a consequence, monoclinic CdWO 4 ∼monoclinic ZnWO 4 >tetragonal CdWO 4 >tetragonal CaWO 4 . The specific photocatalytic activity of monoclinic CdWO 4 was even higher than that of commercial TiO 2 photocatalyst (Degussa P25). The increased activity from the tetragonal CdWO 4 to the monoclinic was consistent with the trend of the decreased symmetry, and this could be explained in terms of the geometric structures and electronic structures for both polymorphs. -- Graphical abstract: Monoclinic CdWO 4 exhibited a much higher photocatalytic activity than the tetragonal form owing to the lower symmetry, more distorted geometric structure, and the dispersive band configuration. Display Omitted Research highlights: → Polymorphs of CdWO 4 in either tetragonal or monoclinic phase were selectively synthesized. → Both polymorphs possessed similar spherical morphologies, while the relevant structural building blocks were different. → Photocatalytic activities of CdWO 4 polymorphs depended strongly on the symmetry, geometric structure, as well as band configuration.

  13. [Detection of UGT1A1*28 Polymorphism Using Fragment Analysis].

    Science.gov (United States)

    Huang, Ying; Su, Jian; Huang, Xiaosui; Lu, Danxia; Xie, Zhi; Yang, Suqing; Guo, Weibang; Lv, Zhiyi; Wu, Hongsui; Zhang, Xuchao

    2017-12-20

    Uridine-diphosphoglucuronosyl transferase 1A1 (UGT1A1), UGT1A1*28 polymorphism can reduce UGT1A1 enzymatic activity, which may lead to severe toxicities in patients who receive irinotecan. This study tries to build a fragment analysis method to detect UGT1A1*28 polymorphism. A total of 286 blood specimens from the lung cancer patients who were hospitalized in Guangdong General Hospital between April 2014 to May 2015 were detected UGT1A1*28 polymorphism by fragment analysis method. Comparing with Sanger sequencing, precision and accuracy of the fragment analysis method were 100%. Of the 286 patients, 236 (82.5% harbored TA6/6 genotype, 48 (16.8%) TA 6/7 genotype and 2 (0.7%) TA7/7 genotype. Our data suggest hat the fragment analysis method is robust for detecting UGT1A1*28 polymorphism in clinical practice. It's simple, time-saving, and easy-to-carry.

  14. Isoschizomers and amplified fragment length polymorphism for the detection of specific cytosine methylation changes.

    Science.gov (United States)

    Ruiz-García, Leonor; Cabezas, Jose Antonio; de María, Nuria; Cervera, María-Teresa

    2010-01-01

    Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is a modification of the Amplified Fragment Length Polymorphism (AFLP) technique that has been used to study methylation of anonymous CCGG sequences in different fungi, plant and animal species. The main variation of this technique is based on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent cutter restriction enzyme. For each sample, AFLP analysis is performed using both EcoRI/HpaII and EcoRI/MspI digested samples. Comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) "Methylation-insensitive polymorphisms" that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples; and (2) "Methylation-sensitive polymorphisms" that are associated with amplified fragments differing in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses modifications that can be applied to adjust the technology to different species of interest.

  15. Pinched flow fractionation devices for detection of single nucleotide polymorphisms

    DEFF Research Database (Denmark)

    Larsen, Asger Vig; Poulsen, Lena; Birgens, Henrik

    2008-01-01

    and 5.6 mu m were functionalized with biotin-labeled oligonucleotides for the detection of a mutant (Mt) or wild-type (Wt) DNA sequence in the HBB gene, respectively. Hybridization to functionalized beads was performed with fluorescent targets comprising synthetic DNA oligonucleotides or amplified RNA...

  16. Detection of polymorphism in booroola gene and growth ...

    African Journals Online (AJOL)

    [12] and Davis et al [17], forced PCR–RFLP DNA test was used to detect the mutations of FecB and GDF9 in Lori breed sheep. The primer sequences used for the FecB AvaII site and. GDF9 HhaI site are presented in Table 1. Polymerase chain reactions were performed in a. 25 μL reaction mixture containing approximately.

  17. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique

    International Nuclear Information System (INIS)

    Noll, W.W.; Collins, M.

    1987-01-01

    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. The authors have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and the reaction mixture is electrophoresed on a denaturing gradient gel. Only the genomic DNA probe hybrids migrate into the gel. Differences in hybrid mobility on the gel indicate base pair changes in the genomic DNA. They have used this technique to identify two polymorphic sites within a 1.2-kilobase region of human chromosome 20. This approach should greatly facilitate the identification of DNA polymorphisms useful for gene linkage studies and the diagnosis of genetic diseases

  18. A Lateral Flow Biosensor for the Detection of Single Nucleotide Polymorphisms.

    Science.gov (United States)

    Zeng, Lingwen; Xiao, Zhuo

    2017-01-01

    A lateral flow biosensor (LFB) is introduced for the detection of single nucleotide polymorphisms (SNPs). The assay is composed of two steps: circular strand displacement reaction and lateral flow biosensor detection. In step 1, the nucleotide at SNP site is recognized by T4 DNA ligase and the signal is amplified by strand displacement DNA polymerase, which can be accomplished at a constant temperature. In step 2, the reaction product of step 1 is detected by a lateral flow biosensor, which is a rapid and cost effective tool for nuclei acid detection. Comparing with conventional methods, it requires no complicated machines. It is suitable for the use of point of care diagnostics. Therefore, this simple, cost effective, robust, and promising LFB detection method of SNP has great potential for the detection of genetic diseases, personalized medicine, cancer related mutations, and drug-resistant mutations of infectious agents.

  19. Alu polymorphic insertions reveal genetic structure of north Indian populations.

    Science.gov (United States)

    Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

    2008-10-01

    The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

  20. A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    2015-01-01

    Full Text Available Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1 C3435T/A from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature.

  1. A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays

    Directory of Open Access Journals (Sweden)

    Fujisawa Hironori

    2010-05-01

    Full Text Available Abstract Background High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: Results We compared the single feature polymorphism (SFP detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip® Rice Genome Array, using the rice cultivars with full genome sequence, japonica cultivar Nipponbare and indica cultivar 93-11. Both genomes were surveyed for all probe target sequences. Only completely matched 25-mer single copy probes of the Nipponbare genome were extracted, and SFPs between them and 93-11 sequences were predicted. We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets. Several statistical methods of SFP detection by whole-genome hybridization were compared under the optimized conditions. Causes of false positives and negatives in SFP detection in both types of hybridization were investigated. Conclusions The optimizations allowed a more than 20% increase in true SFP detection in whole-genome hybridization and a large improvement of SFP detection performance in transcript hybridization. Significance analysis of the microarray for log-transformed raw intensities of PM probes gave the best performance in whole genome hybridization, and 22,936 true SFPs were detected with 23.58% false positives by whole genome hybridization. For transcript hybridization, stable SFP detection was achieved for highly expressed genes, and about 3,500 SFPs were detected at a high sensitivity (> 50% in both shoot and young panicle transcripts. High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa can be

  2. Intra-strain polymorphisms are detected but no genomic alteration is found in cloned mice

    International Nuclear Information System (INIS)

    Gotoh, Koshichi; Inoue, Kimiko; Ogura, Atsuo; Oishi, Michio

    2006-01-01

    In-gel competitive reassociation (IGCR) is a method for differential subtraction of polymorphic (RFLP) DNA fragments between two DNA samples of interest without probes or specific sequence information. Here, we applied the IGCR procedure to two cloned mice derived from an F1 hybrid of the C57BL/6Cr and DBA/2 strains, in order to investigate the possibility of genomic alteration in the cloned mouse genomes. Each of the five of the genomic alterations we detected between the two cloned mice corresponded to the 'intra-strain' polymorphisms in the C57BL/6Cr and DBA/2 mouse strains. Our result suggests that no severe aberration of genome sequences occurs due to somatic cell nuclear transfer

  3. Human population structure detection via multilocus genotype clustering

    Directory of Open Access Journals (Sweden)

    Starmer Joshua

    2007-06-01

    Full Text Available Abstract Background We describe a hierarchical clustering algorithm for using Single Nucleotide Polymorphism (SNP genetic data to assign individuals to populations. The method does not assume Hardy-Weinberg equilibrium and linkage equilibrium among loci in sample population individuals. Results We show that the algorithm can assign sample individuals highly accurately to their corresponding ethnic groups in our tests using HapMap SNP data and it is also robust to admixed populations when tested with Perlegen SNP data. Moreover, it can detect fine-scale population structure as subtle as that between Chinese and Japanese by using genome-wide high-diversity SNP loci. Conclusion The algorithm provides an alternative approach to the popular STRUCTURE program, especially for fine-scale population structure detection in genome-wide association studies. This is the first successful separation of Chinese and Japanese samples using random SNP loci with high statistical support.

  4. Crystalline structure of the marketed form of Rifampicin: a case of conformational and charge transfer polymorphism

    Science.gov (United States)

    de Pinho Pessoa Nogueira, Luciana; de Oliveira, Yara S.; de C. Fonseca, Jéssica; Costa, Wendell S.; Raffin, Fernanda N.; Ellena, Javier; Ayala, Alejandro Pedro

    2018-03-01

    Rifampicin is a semi-synthetic drug derived from rifamycin B, and currently integrates the fixed dose combination tablet formulations used in the treatment of tuberculosis. It is also used in the leprosy polychemotherapy and prophylaxis, which are diseases classified as neglected according to the World Health Organization. Rifampicin is a polymorphic drug and its desirable polymorphic form is labeled as II, being the main goal of this study the elucidation of its crystalline structure. Polymorph II is characterized by two molecules with different conformations in the asymmetric unit and the following lattice parameters: a = 14.0760 (10) Å, b = 17.5450 (10) Å, c = 17.5270 (10) Å, β = 92.15°. Differently to the previously reported structures, a charge transference from the hydroxyl group of the naphthoquinone of one conformer to the nitrogen of the piperazine group of the second conformer was observed. The relevance of the knowledge of this crystalline structure, which is the preferred polymorph for pharmaceutical formulations, was evidenced by analyzing raw materials with polymorphic mixtures. Thus, the results presented in this contribution close an old information gap allowing the complete solid-state characterization of rifampicin.

  5. Polymorphism in Elemental Silicon: Probabilistic Interpretation of the Realizability of Metastable Structures

    Energy Technology Data Exchange (ETDEWEB)

    Stevanovic, Vladan [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Jones, Eric [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2017-11-03

    With few systems of technological interest having been studied as extensively as elemental silicon, there currently exists a wide disparity between the number of predicted low-energy silicon polymorphs and those that have been experimentally realized as metastable at ambient conditions. We put forward an explanation for this disparity wherein the likelihood of formation of a given polymorph under near-equilibrium conditions can be estimated on the basis of mean-field isothermal-isobaric (N,p,T) ensemble statistics. The probability that a polymorph will be experimentally realized is shown to depend upon both the hypervolume of that structure's potential energy basin of attraction and a Boltzmann factor weight containing the polymorph's potential enthalpy per particle. Both attributes are calculated using density functional theory relaxations of randomly generated initial structures. We find that the metastable polymorphism displayed by silicon can be accounted for using this framework to the exclusion of a very large number of other low-energy structures.

  6. Powder X-ray diffraction studies of structural and kinetic aspects of polymorphism

    International Nuclear Information System (INIS)

    Chan, F.C.

    1999-01-01

    Polymorphism is a poorly understood phenomenon that is of considerable technological interest to the pharmaceutical industry. The polymorph selected can influence the bioavailability, processing and stability of the pharmaceutical dosage form. In this study structural, kinetic and thermodynamics aspects of polymorphism and polymorphic phase transformations have been examined using powder X-ray diffraction (PXRD). The compound sulphathiazole is a well-studied model in the investigation of polymorphism and crystal growth. There are five known polymorphic forms and the structure of form V was unknown until this study. The difficulty has been that it has not been possibly to prepare crystals of appropriate size and quality for single crystal diffraction. Furthermore, structure solution from powder data for organic molecules is almost impossible. Despite the challenge the structure of sulphathiazole form V have been solved ab initio from powder data using direct methods. With 16 non-hydrogen atoms in the molecule and two molecules in the asymmetric unit, this structure represents a significant advance in terms of the complexity of an organic structure solved from PXRD data. The structural data should be invaluable for rationalizing experimental observations and the development of theoretical ideas regarding polymorphism and crystal growth. The second part of the study, has examined kinetics of polymorphic phase transformations as a function of pressure combined with temperature using real-time synchrotron PXRD. The significance of pressure arises from the fact that phase transitions can be induced in pharmaceuticals during tabletting. The phase transformation behaviour of rubidium iodide (chosen as a simple test model) has been investigated as a function of isobaric pressure at ambient and elevated temperatures. The kinetics have been characterized by using the Johnson-Melil-Avrami equation. The effect of successive cycling across the transition pressure was also

  7. The BDNF Val66Met Polymorphism Affects the Vulnerability of the Brain Structural Network

    Directory of Open Access Journals (Sweden)

    Chang-hyun Park

    2017-08-01

    Full Text Available Val66Met, a naturally occurring polymorphism in the human brain-derived neurotrophic factor (BDNF gene resulting in a valine (Val to methionine (Met substitution at codon 66, plays an important role in neuroplasticity. While the effect of the BDNF Val66Met polymorphism on local brain structures has previously been examined, its impact on the configuration of the graph-based white matter structural networks is yet to be investigated. In the current study, we assessed the effect of the BDNF polymorphism on the network properties and robustness of the graph-based white matter structural networks. Graph theory was employed to investigate the structural connectivity derived from white matter tractography in two groups, Val homozygotes (n = 18 and Met-allele carriers (n = 55. Although there were no differences in the global network measures including global efficiency, local efficiency, and modularity between the two genotype groups, we found the effect of the BDNF Val66Met polymorphism on the robustness properties of the white matter structural networks. Specifically, the white matter structural networks of the Met-allele carrier group showed higher vulnerability to targeted removal of central nodes as compared with those of the Val homozygote group. These findings suggest that the central role of the BDNF Val66Met polymorphism in regards to neuroplasticity may be associated with inherent differences in the robustness of the white matter structural network according to the genetic variants. Furthermore, greater susceptibility to brain disorders in Met-allele carriers may be understood as being due to their limited stability in white matter structural connectivity.

  8. Polymorphism of fibrillar structures depending on the size of assembled Aβ17-42 peptides

    Science.gov (United States)

    Cheon, Mookyung; Kang, Mooseok; Chang, Iksoo

    2016-01-01

    The size of assembled Aβ17-42 peptides can determine polymorphism during oligomerization and fibrillization, but the mechanism of this effect is unknown. Starting from separate random monomers, various fibrillar oligomers with distinct structural characteristics were identified using discontinuous molecular dynamics simulations based on a coarse-grained protein model. From the structures observed in the simulations, two characteristic oligomer sizes emerged, trimer and paranuclei, which generated distinct structural patterns during fibrillization. A majority of the simulations for trimers and tetramers formed non-fibrillar oligomers, which primarily progress to off-pathway oligomers. Pentamers and hexamers were significantly converted into U-shape fibrillar structures, meaning that these oligomers, called paranuclei, might be potent on-pathway intermediates in fibril formation. Fibrillar oligomers larger than hexamers generated substantial polymorphism in which hybrid structures were readily formed and homogeneous fibrillar structures appeared infrequently. PMID:27901087

  9. Application of virtual phase-shifting speckle-interferometry for detection of polymorphism in the Chlamydia trachomatis omp1 gene

    Science.gov (United States)

    Feodorova, Valentina A.; Saltykov, Yury V.; Zaytsev, Sergey S.; Ulyanov, Sergey S.; Ulianova, Onega V.

    2018-04-01

    Method of phase-shifting speckle-interferometry has been used as a new tool with high potency for modern bioinformatics. Virtual phase-shifting speckle-interferometry has been applied for detection of polymorphism in the of Chlamydia trachomatis omp1 gene. It has been shown, that suggested method is very sensitive to natural genetic mutations as single nucleotide polymorphism (SNP). Effectiveness of proposed method has been compared with effectiveness of the newest bioinformatic tools, based on nucleotide sequence alignment.

  10. A gold nanoparticles-based colorimetric test to detect single nucleotide polymorphisms for improvement of personalized therapy of psoriasis

    Science.gov (United States)

    Marsella, Alessandra; Valentini, Paola; Tarantino, Paolo; Congedo, Maurizio; Pompa, Pier Paolo

    2016-04-01

    We report a simple, rapid and low-cost test, based on gold nanoparticles, for the naked-eye colorimetric detection of a signature of single nucleotide polymorphisms (SNPs) relevant for the personalized medicine of psoriasis patients. We validated the colorimetric assay on real-world DNA samples from a cohort of 30 psoriasis patients and we compared the results, in double-blind, with those obtained with two state-of-the-art instrumental techniques, namely reverse dot blotting and direct sequencing, finding 100% agreement. We demonstrated high accuracy, sensitivity and specificity of the colorimetric test that can be easily adapted for the genotypization of different SNPs, important for the pharmacogenomics of various diseases, and in other fields, such as food traceability and population structure analysis.

  11. Genetic polymorphism and population structure of Echinococcus ortleppi.

    Science.gov (United States)

    Addy, F; Wassermann, M; Banda, F; Mbaya, H; Aschenborn, J; Aschenborn, O; Koskei, P; Umhang, G; DE LA Rue, M; Elmahdi, I E; Mackenstedt, U; Kern, P; Romig, T

    2017-04-01

    The zoonotic cestode Echinococcus ortleppi (Lopez-Neyra and Soler Planas, 1943) is mainly transmitted between dogs and cattle. It occurs worldwide but is only found sporadically in most regions, with the notable exception of parts of southern Africa and South America. Its epidemiology is little understood and the extent of intraspecific variability is unknown. We have analysed in the present study the genetic diversity among 178 E. ortleppi isolates from sub-Saharan Africa, Europe and South America using the complete mitochondrial cox1 (1608 bp) and nad1 (894 bp) DNA sequences. Genetic polymorphism within the loci revealed 15 cox1 and six nad1 haplotypes, respectively, and 20 haplotypes of the concatenated genes. Presence of most haplotypes was correlated to geographical regions, and only one haplotype had a wider spread in both eastern and southern Africa. Intraspecific microvariance was low in comparison with Echinococcus granulosus sensu stricto, despite the wide geographic range of examined isolates. In addition, the various sub-populations showed only subtle deviation from neutrality and were mostly genetically differentiated. This is the first insight into the population genetics of the enigmatic cattle adapted Echinococcus ortleppi. It, therefore, provides baseline data for biogeographical comparison among E. ortleppi endemic regions and for tracing its translocation paths.

  12. Val66Met polymorphism of BDNF alters prodomain structure to induce neuronal growth cone retraction.

    Science.gov (United States)

    Anastasia, Agustin; Deinhardt, Katrin; Chao, Moses V; Will, Nathan E; Irmady, Krithi; Lee, Francis S; Hempstead, Barbara L; Bracken, Clay

    2013-01-01

    A common single-nucleotide polymorphism (SNP) in the human brain-derived neurotrophic factor (BDNF) gene results in a Val66Met substitution in the BDNF prodomain region. This SNP is associated with alterations in memory and with enhanced risk to develop depression and anxiety disorders in humans. Here we show that the isolated BDNF prodomain is detected in the hippocampus and that it can be secreted from neurons in an activity-dependent manner. Using nuclear magnetic resonance spectroscopy and circular dichroism, we find that the prodomain is intrinsically disordered, and the Val66Met substitution induces structural changes. Surprisingly, application of Met66 (but not Val66) BDNF prodomain induces acute growth cone retraction and a decrease in Rac activity in hippocampal neurons. Expression of p75(NTR) and differential engagement of the Met66 prodomain to the SorCS2 receptor are required for this effect. These results identify the Met66 prodomain as a new active ligand, which modulates neuronal morphology.

  13. Chemical and structural properties of polymorphous silicon thin films grown from dichlorosilane

    Energy Technology Data Exchange (ETDEWEB)

    Álvarez-Macías, C.; Monroy, B.M.; Huerta, L.; Canseco-Martínez, M.A. [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, A.P. 70-360, Coyoacán, C.P. 04510 México, D.F. (Mexico); Picquart, M. [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, A.P. 55-534, 09340 México, D.F. (Mexico); Santoyo-Salazar, J. [Departamento de Física, CINVESTAV-IPN, A.P. 14-740, C.P. 07000 México, D.F. (Mexico); Sánchez, M.F. García [Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, Av. I.P.N. 2580, Gustavo A. Madero, 07340 México .D.F. (Mexico); Santana, G., E-mail: gsantana@iim.unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, A.P. 70-360, Coyoacán, C.P. 04510 México, D.F. (Mexico)

    2013-11-15

    We have examined the effects of hydrogen dilution (R{sub H}) and deposition pressure on the morphological, structural and chemical properties of polymorphous silicon thin films (pm-Si:H), using dichlorosilane as silicon precursor in the plasma enhanced chemical vapor deposition (PECVD) process. The use of silicon chlorinated precursors enhances the crystallization process in as grown pm-Si:H samples, obtaining crystalline fractions from Raman spectra in the range of 65–95%. Atomic Force Microscopy results show the morphological differences obtained when the chlorine chemistry dominates the growth process and when the plasma–surface interactions become more prominent. Augmenting R{sub H} causes a considerable reduction in both roughness and topography, demonstrating an enhancement of ion bombardment and attack of the growing surface. X-ray Photoelectron Spectroscopy results show that, after ambient exposure, there is low concentration of oxygen inside the films grown at low R{sub H}, present in the form of Si-O, which can be considered as structural defects. Instead, oxidation increases with deposition pressure and dilution, along with film porosity, generating a secondary SiO{sub x} phase. For higher pressure and dilution, the amount of chlorine incorporated to the film decreases congruently with HCl chlorine extraction processes involving atomic hydrogen interactions with the surface. In all cases, weak silicon hydride (Si-H) bonds were not detected by infrared spectroscopy, while bonding configurations associated to the silicon nanocrystal surface were clearly observed. Since these films are generally used in photovoltaic devices, analyzing their chemical and structural properties such as oxygen incorporation to the films, along with chlorine and hydrogen, is fundamental in order to understand and optimize their electrical and optical properties.

  14. Single Nucleotide Polymorphism Detection Using Au-Decorated Single-Walled Carbon Nanotube Field Effect Transistors

    Directory of Open Access Journals (Sweden)

    Keum-Ju Lee

    2011-01-01

    Full Text Available We demonstrate that Au-cluster-decorated single-walled carbon nanotubes (SWNTs may be used to discriminate single nucleotide polymorphism (SNP. Nanoscale Au clusters were formed on the side walls of carbon nanotubes in a transistor geometry using electrochemical deposition. The effect of Au cluster decoration appeared as hole doping when electrical transport characteristics were examined. Thiolated single-stranded probe peptide nucleic acid (PNA was successfully immobilized on Au clusters decorating single-walled carbon nanotube field-effect transistors (SWNT-FETs, resulting in a conductance decrease that could be explained by a decrease in Au work function upon adsorption of thiolated PNA. Although a target single-stranded DNA (ssDNA with a single mismatch did not cause any change in electrical conductance, a clear decrease in conductance was observed with matched ssDNA, thereby showing the possibility of SNP (single nucleotide polymorphism detection using Au-cluster-decorated SWNT-FETs. However, a power to discriminate SNP target is lost in high ionic environment. We can conclude that observed SNP discrimination in low ionic environment is due to the hampered binding of SNP target on nanoscale surfaces in low ionic conditions.

  15. Evaluation of a reverse-hybridization StripAssay for the detection of genetic polymorphisms leading to acenocoumarol sensitivity.

    Science.gov (United States)

    Gialeraki, Argyri; Markatos, Christos; Grouzi, Elisabeth; Merkouri, Efrosyni; Travlou, Anthi; Politou, Marianna

    2010-04-01

    Acenocoumarol is mainly catabolized by CYP2C9 isoform of cytochrome P450 (CYP) liver complex and exerts its anticoagulant effect through the inhibition of Vitamin K Epoxide Reductase (VKOR). The most important genetic polymorphisms which lead to an impaired enzymatic activity and therefore predispose to acenocoumarol sensitivity, are considered to be CYP2C9*2 (Arg144Cys), CYP2C9*3 (Ile359Leu) and VKORC1-1639G>A, respectively. In this study we compared the results of the PGXThrombo StripAssay kit (ViennaLab Diagnostics,Vienna, Austria) with direct DNA sequencing and in house Restriction Fragment Length Polymorphisms (RFLP) for the detection of the aforementioned Single Nucleotide Polymorphisms (SNPs). The reverse hybridization StripAssay was found to be equally effective with RFLP and direct DNA sequencing for the detection of CYP2C9*2 and CYP2C9*3 polymorphisms, respectively. The comparison of the RFLP reference method with the reverse hybridization StripAssay for the detection of VKORC1-1639 G>A polymorphism showed that the reverse hybridization StripAsssay might misclassify some A/A homozygotes as heterozygotes. Optimization of the hybridization procedures may eliminate the extra low signal band observed in some samples at the reverse hybridization StripAssay and improve its diagnostic value.

  16. Amyloid structure exhibits polymorphism on multiple length scales in human brain tissue

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jiliang; Costantino, Isabel; Venugopalan, Nagarajan; Fischetti, Robert F.; Hyman, Bradley; Frosch, Matthew; Gomez-Isla, Teresa; Makowski, Lee

    2016-09-15

    Although aggregation of Aβ amyloid fibrils into plaques in the brain is a hallmark of Alzheimer's Disease (AD), the correlation between amyloid burden and severity of symptoms is weak. One possible reason is that amyloid fibrils are structurally polymorphic and different polymorphs may contribute differentially to disease. However, the occurrence and distribution of amyloid polymorphisms in human brain is poorly documented. Here we seek to fill this knowledge gap by using X-ray microdiffraction of histological sections of human tissue to map the abundance, orientation and structural heterogeneities of amyloid within individual plaques; among proximal plaques and in subjects with distinct clinical histories. A 5 µ x-ray beam was used to generate diffraction data with each pattern arising from a scattering volume of only ~ 450 µ3 , making possible collection of dozens to hundreds of diffraction patterns from a single amyloid plaque. X-ray scattering from these samples exhibited all the properties expected for scattering from amyloid. Amyloid distribution was mapped using the intensity of its signature 4.7 Å reflection which also provided information on the orientation of amyloid fibrils across plaques. Margins of plaques exhibited a greater degree of orientation than cores and orientation around blood vessels frequently appeared tangential. Variation in the structure of Aβ fibrils is reflected in the shape of the 4.7 Å peak which usually appears as a doublet. Variations in this peak correspond to differences between the structure of amyloid within cores of plaques and at their periphery. Examination of tissue from a mismatch case - an individual with high plaque burden but no overt signs of dementia at time of death - revealed a diversity of structure and spatial distribution of amyloid that is distinct from typical AD cases. We demonstrate the existence of structural polymorphisms among amyloid within and among plaques of a single individual and suggest

  17. The Detection of Hostile Structures

    National Research Council Canada - National Science Library

    Colton, David; Monk, Peter B

    2004-01-01

    This grant was concerned with the development of the linear sampling method to determine the location and shape of hostile structures hidden in a known background medium from measured electromagnetic scattering data...

  18. Detection of Helicobacter pylori virulence factors and interleukin-1 polymorphisms in patients with abdominal complaint

    International Nuclear Information System (INIS)

    Anarkhuu, B.; Munguntsetseg, B.; Khosbayar, T.; Enkh-Amar, A.; Bayasgalan, P.; Yadamjav, Ch.; Oyuntsetseg, K.; Bira, N.; Choi, P.W.

    2007-01-01

    Full text: Gastric Cancer is the second leading cause of cancer related death in Mongolia (National Cancer Center, report-2006). Chronic infection with Helicobacter pylori affects approximately half the world and results in malignancy in a small subset of this population. There was sufficient evidence that the Working Group of the International Agency for Research on Cancer (IARC-1994) classified it as a class I carcinogen, the only bacterial agent on this list. The aim of the study is to detect and define the role of H.pylori virulence factors and host IL-1 polymorphisms to prevent further gastric cancer. In the future, this combined bacterial/host genotyping may provide an important opportunity to identify patients who are at high risk for the development of gastric carcinoma long before malignancy occurs. Patients and biopsy specimens. Two biopsy specimens and 5ml of blood samples were collected from each of 59 patients who had abdominal complaint, after informed consent was obtained. All patients lived in Ulaanbaatar, Mongolia, 100% were of Mongolian nationality. Their mean age was 40.33 years (range, 1575 years). One biopsy specimen was used to test urease, and another was stored for molecular testing. DNA isolation from blood and tissue sample was performed with ''Promega'' kit, according to the manufacturer's instruction. Tissue samples were homogenized treated with proteinase K prior to DNA extraction. H. pylori detection and genotyping. For H.pylori, detection was by UreC primer. For virulence gene typing of H.pylori cagA and vacA, gene specific primer were used. Genotyping of IL-1 polymorphisms. IL-1B polymorphisms were distinguished by 2 methods, 5-nuclease PCR assay and restriction fragment length polymorphism analysis (RFLP). Result. Strain characteristics of H. pylori were investigated in all 59 patients. 66,7% (40/59) and 76,3% (29/36) of the patients were infected with H. pylori by UreC PCR and by urea test, respectively. The vacAs1 genotype was

  19. HLA-DQBl*0402 alleles polymorphisms detected in Javanese HIV patients with positive anti-Toxoplasma gondii IgM

    Science.gov (United States)

    Sari, Yulia; Haryati, Sri; Prasetyo, Afiono Agung; Hartono, Adnan, Zainal Arifin

    2017-02-01

    The human leukocyte antigen (HLA)-DQB1 gene polymorphisms may associated with the infection risk of Toxoplasma gondii in HIV patients. The HLA-DQB1*0402 in HIV-1-positive patients could be considered risk factors for developing neurological opportunistic infections, mainly Toxoplasma encephalitis. However, the HLA-DQB1*0402 gene polymorphisms status in the Javanese HIV patients is unknown. This study evaluated the prevalence of HLA-DQB*0402 alleles polymorphisms in Javanese HIV patients with positive anti-Toxoplasma gondii IgM status. Since 2009 our research group performing a molecular epidemiology of blood borne viruses in Central Java Indonesia, by collecting the epidemiological and clinical data from the high risk communities. All blood samples were screened for blood borne pathogens by serological and molecular assays including for HIV and Toxoplasma gondii. The genomic DNA was isolated from the whole blood samples. Genetic polymorphisms of HLA-DQB1*0402 alleles were detected with polymerase chain reaction-sequence-specific primers (PCR-SSPs) technique. The genotypes were defined according to generated fragment patterns in the agarose gel electrophoresis analysis of PCR products. All of the samples were tested at least in duplicate. HLA-DQB1*0402 alleles were detected in 20.8% (16/77) patients and not detected in all HIV positive samples with negative anti-Toxoplasma gondii IgM status (n= 200). The HLA-DQB1*0402 alleles polymorphisms were detected in Javanese HIV patients with positive anti-Toxoplasma gondii IgM. The polymorphisms found may have association with the infection risk of Toxoplasma gondii in HIV patients.

  20. Structural study of piracetam polymorphs and cocrystals: crystallography redetermination and quantum mechanics calculations.

    Science.gov (United States)

    Tilborg, Anaëlle; Jacquemin, Denis; Norberg, Bernadette; Perpète, Eric; Michaux, Catherine; Wouters, Johan

    2011-12-01

    Pharmaceutical compounds are mostly developed as solid dosage forms containing a single-crystal form. It means that the selection of a particular crystal state for a given molecule is an important step for further clinical outlooks. In this context, piracetam, a pharmaceutical molecule known since the sixties for its nootropic properties, is considered in the present work. This molecule is analyzed using several experimental and theoretical approaches. First, the conformational space of the molecule has been systematically explored by performing a quantum mechanics scan of the two most relevant dihedral angles of the lateral chain. The predicted stable conformations have been compared to all the reported experimental geometries retrieved from the Cambridge Structural Database (CSD) covering polymorphs and cocrystals structures. In parallel, different batches of powders have been recrystallized. Under specific conditions, single crystals of polymorph (III) of piracetam have been obtained, an outcome confirmed by crystallographic analysis. © 2011 International Union of Crystallography. Printed in Singapore – all rights reserved.

  1. DNA polymorphism sensitive impedimetric detection on gold-nanoislands modified electrodes.

    Science.gov (United States)

    Bonanni, Alessandra; Pividori, Maria Isabel; del Valle, Manel

    2015-05-01

    Nanocomposite materials are being increasingly used in biosensing applications as they can significantly improve biosensor performance. Here we report the use of a novel impedimetric genosensor based on gold nanoparticles graphite-epoxy nanocomposite (nanoAu-GEC) for the detection of triple base mutation deletion in a cystic-fibrosis (CF) related human DNA sequence. The developed platform consists of chemisorbing gold nano-islands surrounded by rigid, non-chemisorbing, and conducting graphite-epoxy composite. The ratio of the gold nanoparticles in the composite was carefully optimized by electrochemical and microscopy studies. Such platform allows the very fast and stable thiol immobilization of DNA probes on the gold islands, thus minimizing the steric and electrostatic repulsion among the DNA probes and improving the detection of DNA polymorphism down to 2.25fmol by using electrochemical impedance spectroscopy. These findings are very important in order to develop new and renewable platforms to be used in point-of-care devices for the detection of biomolecules. Copyright © 2015 Elsevier B.V. All rights reserved.

  2. Single-strand conformation polymorphism analysis of ribosomal DNA for detection of Phytophthora ramorum directly from plant tissues

    Science.gov (United States)

    Ping Kong; Patricia A. Richardson; Chuanxue Hong; Thomas L. Kubisiak

    2006-01-01

    At the first Sudden Oak Death Science Symposium, we reported on the use of a single strand conformation polymorphism (SSCP) analysis for rapid identification of Phytophthora ramorum in culture. We have since assessed and improved the fingerprinting technique for detecting this pathogen directly from plant tissues. The improved SSCP protocol uses a...

  3. Damage Detection and Deteriorating Structural Systems

    DEFF Research Database (Denmark)

    Long, Lijia; Thöns, Sebastian; Döhler, Michael

    2017-01-01

    This paper addresses the quantification of the value of damage detection system and algorithm information on the basis of Value of Information (VoI) analysis to enhance the benefit of damage detection information by providing the basis for its optimization before it is performed and implemented....... The approach of the quantification the value of damage detection information builds upon the Bayesian decision theory facilitating the utilization of damage detection performance models, which describe the information and its precision on structural system level, facilitating actions to ensure the structural...... detection information is determined utilizing Bayesian updating. The damage detection performance is described with the probability of indication for different component and system damage states taking into account type 1 and type 2 errors. The value of damage detection information is then calculated...

  4. First principles study of structural, electronic and optical properties of polymorphic forms of Rb 2Te

    Science.gov (United States)

    Alay-e-Abbas, S. M.; Shaukat, A.

    2011-05-01

    First-principles density functional theory calculations have been performed for structural, electronic and optical properties of three polymorphic forms of rubidium telluride. Our calculations show that the sequence of pressure induced phase transitions for Rb 2Te is Fm3¯m → Pnma → P6 3/mmc which is governed by the coordination numbers of the anions. From our calculated low transition pressure value for the Fm3¯m phase to the Pnma phase transition of Rb 2Te, the experimentally observed meta-stability of Fm3¯m phase at ambient conditions seems reasonable. The electronic band structure has been calculated for all the three phases and the change in the energy band gap is discussed for the transitioning phases. The energy band gaps obtained for the three phases of Rb 2Te decrease on going from the meta-stable phase to the high-pressure phases. Total and partial density of states for the polymorphs of Rb 2Te has been computed to elucidate the contribution of various atomic states on the electronic band structure. Furthermore, optical properties for all the polymorphic forms have been presented in form of the complex dielectric function.

  5. Serotonin transporter gene-linked polymorphism affects detection of facial expressions.

    Directory of Open Access Journals (Sweden)

    Ai Koizumi

    Full Text Available Previous studies have demonstrated that the serotonin transporter gene-linked polymorphic region (5-HTTLPR affects the recognition of facial expressions and attention to them. However, the relationship between 5-HTTLPR and the perceptual detection of others' facial expressions, the process which takes place prior to emotional labeling (i.e., recognition, is not clear. To examine whether the perceptual detection of emotional facial expressions is influenced by the allelic variation (short/long of 5-HTTLPR, happy and sad facial expressions were presented at weak and mid intensities (25% and 50%. Ninety-eight participants, genotyped for 5-HTTLPR, judged whether emotion in images of faces was present. Participants with short alleles showed higher sensitivity (d' to happy than to sad expressions, while participants with long allele(s showed no such positivity advantage. This effect of 5-HTTLPR was found at different facial expression intensities among males and females. The results suggest that at the perceptual stage, a short allele enhances the processing of positive facial expressions rather than that of negative facial expressions.

  6. Mitochondrial and nuclear sequence polymorphisms reveal geographic structuring in Amazonian populations of Echinococcus vogeli (Cestoda: Taeniidae).

    Science.gov (United States)

    Santos, Guilherme B; Soares, Manoel do C P; de F Brito, Elisabete M; Rodrigues, André L; Siqueira, Nilton G; Gomes-Gouvêa, Michele S; Alves, Max M; Carneiro, Liliane A; Malheiros, Andreza P; Póvoa, Marinete M; Zaha, Arnaldo; Haag, Karen L

    2012-12-01

    To date, nothing is known about the genetic diversity of the Echinococcus neotropical species, Echinococcus vogeli and Echinococcus oligarthrus. Here we used mitochondrial and nuclear DNA sequence polymorphisms to uncover the genetic structure, transmission and history of E. vogeli in the Brazilian Amazon, based on a sample of 38 isolates obtained from human and wild animal hosts. We confirm that the parasite is partially synanthropic and show that its populations are diverse. Furthermore, significant geographical structuring is found, with western and eastern populations being genetically divergent. Copyright © 2012 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  7. Genetic polymorphisms and protein structures in growth hormone, growth hormone receptor, ghrelin, insulin-like growth factor 1 and leptin in Mehraban sheep.

    Science.gov (United States)

    Bahrami, A; Behzadi, Sh; Miraei-Ashtiani, S R; Roh, S-G; Katoh, K

    2013-09-15

    The somatotropic axis, the control system for growth hormone (GH) secretion and its endogenous factors involved in the regulation of metabolism and energy partitioning, has promising potentials for producing economically valuable traits in farm animals. Here we investigated single nucleotide polymorphisms (SNPs) of the genes of factors involved in the somatotropic axis for growth hormone (GH1), growth hormone receptor (GHR), ghrelin (GHRL), insulin-like growth factor 1 (IGF-I) and leptin (LEP), using polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and DNA sequencing methods in 452 individual Mehraban sheep. A nonradioactive method to allow SSCP detection was used for genomic DNA and PCR amplification of six fragments: exons 4 and 5 of GH1; exon 10 of GH receptor (GHR); exon 1 of ghrelin (GHRL); exon 1 of insulin-like growth factor-I (IGF-I), and exon 3 of leptin (LEP). Polymorphisms were detected in five of the six PCR products. Two electrophoretic patterns were detected for GH1 exon 4. Five conformational patterns were detected for GH1 exon 5 and LEP exon 3, and three for IGF-I exon 1. Only GHR and GHRL were monomorphic. Changes in protein structures due to variable SNPs were also analyzed. The results suggest that Mehraban sheep, a major breed that is important for the animal industry in Middle East countries, has high genetic variability, opening interesting prospects for future selection programs and preservation strategies. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Damage Detection in an Offshore Structure

    DEFF Research Database (Denmark)

    Brincker, Rune; Kirkegaard, Poul Henning; Andersen, P.

    The structural integrity of a multi-pile offshore platform is investigated by using a vibration based damage detection scheme. Changes in structural integrity are assumed to be reflected in the modal parameters estimated from only output data using an Auto-Regressive Moving Average (ARMA) model....... By use of the estimates of the modal parameters and their corresponding variances a probability based damage indicator is formulated. This approach indicates, that since the construction of the platform, minor structural changes have taken place....

  9. Damage Detection in an Offshore Structure

    DEFF Research Database (Denmark)

    Brincker, Rune; Kirkegaard, Poul Henning; Andersen, Palle

    1995-01-01

    The structural integrity of a multi-pile offshore platform is investigated by using a vibration based damage detection scheme. Changes in structural integrity are assumed to be reflected in the modal parameters estimated from only output data using an Auto-Regressive Moving Average (ARMA) model....... By use of the estimates of the modal parameters and their corresponding variances a probability based damage indicator is formulated. This approach indicates, that since the construction of the platform, minor structural changes have taken place....

  10. Crystal structure of a second triclinic polymorph of 2-methylpyridinium picrate

    Directory of Open Access Journals (Sweden)

    Jeganathan Gomathi

    2015-11-01

    Full Text Available The title molecular salt, C6H8N+·C6H2N3O7− (systematic name: 2-methylpyridinium 2,4,6-trinitrophenolate, crystallizes with two cations and two anions in the asymmetric unit. In the crystal, the cations are linked to the anions via bifurcated N—H...(O,O hydrogen bonds, generating R12(6 graph-set motifs. Numerous C—H...O hydrogen bonds are observed between these cation–anion pairs, which result in a three-dimensional network. In addition, weak aromatic π–π stacking between the 2-methylpyridinium rings [inter-centroid distance = 3.8334 (19 Å] and very weak stacking [inter-centroid distance = 4.0281 (16 Å] between inversion-related pairs of picrate anions is observed. The title salt is a second triclinic polymorph of the structure (also with Z′ = 2 reported earlier [Anita et al. (2006. Acta Cryst. C62, o567–o570; Chan et al. (2014. CrystEngComm, 16, 4508–4538]. In the title compound, the cations and anions display a chequerboard arrangement when viewed down [100], whereas in the first polymorph, (010 layers of alternating cations and anions are apparent in a [100] view. It is interesting that the unit-cell lengths are almost identical for the two polymorphs, although the inter-axial angles are quite different.

  11. DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism

    Science.gov (United States)

    Aguiar, Derek; Halldórsson, Bjarni V.; Morrow, Eric M.; Istrail, Sorin

    2012-01-01

    Motivation: The understanding of the genetic determinants of complex disease is undergoing a paradigm shift. Genetic heterogeneity of rare mutations with deleterious effects is more commonly being viewed as a major component of disease. Autism is an excellent example where research is active in identifying matches between the phenotypic and genomic heterogeneities. A considerable portion of autism appears to be correlated with copy number variation, which is not directly probed by single nucleotide polymorphism (SNP) array or sequencing technologies. Identifying the genetic heterogeneity of small deletions remains a major unresolved computational problem partly due to the inability of algorithms to detect them. Results: In this article, we present an algorithmic framework, which we term DELISHUS, that implements three exact algorithms for inferring regions of hemizygosity containing genomic deletions of all sizes and frequencies in SNP genotype data. We implement an efficient backtracking algorithm—that processes a 1 billion entry genome-wide association study SNP matrix in a few minutes—to compute all inherited deletions in a dataset. We further extend our model to give an efficient algorithm for detecting de novo deletions. Finally, given a set of called deletions, we also give a polynomial time algorithm for computing the critical regions of recurrent deletions. DELISHUS achieves significantly lower false-positive rates and higher power than previously published algorithms partly because it considers all individuals in the sample simultaneously. DELISHUS may be applied to SNP array or sequencing data to identify the deletion spectrum for family-based association studies. Availability: DELISHUS is available at http://www.brown.edu/Research/Istrail_Lab/. Contact: Eric_Morrow@brown.edu and Sorin_Istrail@brown.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22689755

  12. Real time hybridization studies by resonant waveguide gratings using nanopattern imaging for Single Nucleotide Polymorphism detection

    KAUST Repository

    Bougot-Robin, Kristelle

    2013-12-20

    2D imaging of biochips is particularly interesting for multiplex biosensing. Resonant properties allow label-free detection using the change of refractive index at the chip surface. We demonstrate a new principle of Scanning Of Resonance on Chip by Imaging (SORCI) based on spatial profiles of nanopatterns of resonant waveguide gratings (RWGs) and its embodiment in a fluidic chip for real-time biological studies. This scheme allows multiplexing of the resonance itself by providing nanopattern sensing areas in a bioarray format. Through several chip designs we discuss resonance spatial profiles, dispersion and electric field distribution for optimal light-matter interaction with biological species of different sizes. Fluidic integration is carried out with a black anodized aluminum chamber, advantageous in term of mechanical stability, multiple uses of the chip, temperature control and low optical background. Real-time hybridization experiments are illustrated by SNP (Single Nucleotide Polymorphism) detection in gyrase A of E. coli K12, observed in evolution studies of resistance to the antibiotic ciprofloxacin. We choose a 100 base pairs (bp) DNA target (∼30 kDa) including the codon of interest and demonstrate the high specificity of our technique for probes and targets with close affinity constants. This work validates the safe applicability of our unique combination of RWGs and simple instrumentation for real-time biosensing with sensitivity in buffer solution of ∼10 pg/mm2. Paralleling the success of RWGs sensing for cells sensing, our work opens new avenues for a large number of biological studies. © 2013 Springer Science+Business Media.

  13. Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Behavior in Sapsaree Dog (

    Directory of Open Access Journals (Sweden)

    J. H. Ha

    2015-07-01

    Full Text Available The purpose of this study was to characterize genetic architecture of behavior patterns in Sapsaree dogs. The breed population (n = 8,256 has been constructed since 1990 over 12 generations and managed at the Sapsaree Breeding Research Institute, Gyeongsan, Korea. Seven behavioral traits were investigated for 882 individuals. The traits were classified as a quantitative or a categorical group, and heritabilities (h2 and variance components were estimated under the Animal model using ASREML 2.0 software program. In general, the h2 estimates of the traits ranged between 0.00 and 0.16. Strong genetic (rG and phenotypic (rP correlations were observed between nerve stability, affability and adaptability, i.e. 0.9 to 0.94 and 0.46 to 0.68, respectively. To detect significant single nucleotide polymorphism (SNP for the behavioral traits, a total of 134 and 60 samples were genotyped using the Illumina 22K CanineSNP20 and 170K CanineHD bead chips, respectively. Two datasets comprising 60 (Sap60 and 183 (Sap183 samples were analyzed, respectively, of which the latter was based on the SNPs that were embedded on both the 22K and 170K chips. To perform genome-wide association analysis, each SNP was considered with the residuals of each phenotype that were adjusted for sex and year of birth as fixed effects. A least squares based single marker regression analysis was followed by a stepwise regression procedure for the significant SNPs (p<0.01, to determine a best set of SNPs for each trait. A total of 41 SNPs were detected with the Sap183 samples for the behavior traits. The significant SNPs need to be verified using other samples, so as to be utilized to improve behavior traits via marker-assisted selection in the Sapsaree population.

  14. Non-invasive prenatal detection of trisomy 21 using tandem single nucleotide polymorphisms.

    Directory of Open Access Journals (Sweden)

    Sujana Ghanta

    Full Text Available BACKGROUND: Screening tests for Trisomy 21 (T21, also known as Down syndrome, are routinely performed for the majority of pregnant women. However, current tests rely on either evaluating non-specific markers, which lead to false negative and false positive results, or on invasive tests, which while highly accurate, are expensive and carry a risk of fetal loss. We outline a novel, rapid, highly sensitive, and targeted approach to non-invasively detect fetal T21 using maternal plasma DNA. METHODS AND FINDINGS: Highly heterozygous tandem Single Nucleotide Polymorphism (SNP sequences on chromosome 21 were analyzed using High-Fidelity PCR and Cycling Temperature Capillary Electrophoresis (CTCE. This approach was used to blindly analyze plasma DNA obtained from peripheral blood from 40 high risk pregnant women, in adherence to a Medical College of Wisconsin Institutional Review Board approved protocol. Tandem SNP sequences were informative when the mother was heterozygous and a third paternal haplotype was present, permitting a quantitative comparison between the maternally inherited haplotype and the paternally inherited haplotype to infer fetal chromosomal dosage by calculating a Haplotype Ratio (HR. 27 subjects were assessable; 13 subjects were not informative due to either low DNA yield or were not informative at the tandem SNP sequences examined. All results were confirmed by a procedure (amniocentesis/CVS or at postnatal follow-up. Twenty subjects were identified as carrying a disomy 21 fetus (with two copies of chromosome 21 and seven subjects were identified as carrying a T21 fetus. The sensitivity and the specificity of the assay was 100% when HR values lying between 3/5 and 5/3 were used as a threshold for normal subjects. CONCLUSIONS: In summary, a targeted approach, based on calculation of Haplotype Ratios from tandem SNP sequences combined with a sensitive and quantitative DNA measurement technology can be used to accurately detect fetal

  15. Outlier Detection in Structural Time Series Models

    DEFF Research Database (Denmark)

    Marczak, Martyna; Proietti, Tommaso

    investigate via Monte Carlo simulations how this approach performs for detecting additive outliers and level shifts in the analysis of nonstationary seasonal time series. The reference model is the basic structural model, featuring a local linear trend, possibly integrated of order two, stochastic seasonality......Structural change affects the estimation of economic signals, like the underlying growth rate or the seasonally adjusted series. An important issue, which has attracted a great deal of attention also in the seasonal adjustment literature, is its detection by an expert procedure. The general......–to–specific approach to the detection of structural change, currently implemented in Autometrics via indicator saturation, has proven to be both practical and effective in the context of stationary dynamic regression models and unit–root autoregressions. By focusing on impulse– and step–indicator saturation, we...

  16. A rapid detection method for PAI-1 promoter insertion/deletion polymorphism (4G/5G

    Directory of Open Access Journals (Sweden)

    Annichino-Bizzacchi Joyce M.

    1998-01-01

    Full Text Available Plasminogen activator inhibitor-1 (PAI-1 is an important inhibitor of fibrinolysis, and increased levels of PAI-1 are associated with atheroma and myocardial infarction. A common 4G/5G insertion/deletion polymorphism located in the promoter region of PAI-1 gene has been described associated with PAI-1 activity in plasma levels. Genotyping of this polymorphism is commonly conducted with an allele-specific oligonucleotide melting technique. In the present study, we describe a quick, easy method for genotyping 4G/5G polymorphism in the promoter region of the PAI-1 gene.

  17. Manifold structure preservative for hyperspectral target detection

    Science.gov (United States)

    Imani, Maryam

    2018-05-01

    A nonparametric method termed as manifold structure preservative (MSP) is proposed in this paper for hyperspectral target detection. MSP transforms the feature space of data to maximize the separation between target and background signals. Moreover, it minimizes the reconstruction error of targets and preserves the topological structure of data in the projected feature space. MSP does not need to consider any distribution for target and background data. So, it can achieve accurate results in real scenarios due to avoiding unreliable assumptions. The proposed MSP detector is compared to several popular detectors and the experiments on a synthetic data and two real hyperspectral images indicate the superior ability of it in target detection.

  18. Genetic diversity and structure analysis based on hordein protein polymorphism in barley landrace populations from jordan

    International Nuclear Information System (INIS)

    Baloch, A.W.; Ali, M.; Baloch, A.M.; Mangan, B.U.N.; Song, W

    2014-01-01

    Jordan is unanimously considered to be one of the centers of genetic diversity for barley, where wild and landraces of barley has been grown under different climatic conditions. The genetic diversity and genetic structure based on hordein polymorphism was assessed in 90 different accessions collected from four different sites of Jordan. A-PAGE was used to reveal hordein polymorphism among the genotypes. A total of 29 distinct bands were identified, out of them 9 bands were distinguished for D, 11 for C, and 9 for the B hordein regions. The observed genetic similarity was an exceptionally high between the populations than expected, which is probably due to high gene flow estimated between them. The genetic diversity parameters were not differ largely among the populations, indicating that local selection of a particular site did not play a key role in shaping genetic diversity. Analysis of molecular variance (AMOVA) revealed significant population structure when accessions were structured according to population site. There was 94% of hordein variation resided within the populations and only 8% present among the populations. Both Bayesian and Principale Coordinate Analysis (PCoA) concordantly demonstrated admixture genotypes of the landraces barley populations. Consequently, none of the population found to be clustered separately according to its population site. It is concluded that this approach can be useful to explore the germplasm for genetic diversity but perhaps is not suitable for determining phylogenic relations in barley. (author)

  19. Detecting structure of haplotypes and local ancestry

    Science.gov (United States)

    We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local an...

  20. Molecular polymorphism of a cell surface proteoglycan: distinct structures on simple and stratified epithelia.

    Science.gov (United States)

    Sanderson, R D; Bernfield, M

    1988-12-01

    Epithelial cells are organized into either a single layer (simple epithelia) or multiple layers (stratified epithelia). Maintenance of these cellular organizations requires distinct adhesive mechanisms involving many cell surface molecules. One such molecule is a cell surface proteoglycan, named syndecan, that contains both heparan sulfate and chondroitin sulfate chains. This proteoglycan binds cells to fibrillar collagens and fibronectin and thus acts as a receptor for interstitial matrix. The proteoglycan is restricted to the basolateral surface of simple epithelial cells, but is located over the entire surface of stratified epithelial cells, even those surfaces not contacting matrix. We now show that the distinct localization in simple and stratified epithelia correlates with a distinct proteoglycan structure. The proteoglycan from simple epithelia (modal molecular size, 160 kDa) is larger than that from stratified epithelia (modal molecular size, 92 kDa), but their core proteins are identical in size and immunoreactivity. The proteoglycan from simple epithelia has more and larger heparan sulfate and chondroitin sulfate chains than the proteoglycan from stratified epithelia. Thus, the cell surface proteoglycan shows a tissue-specific structural polymorphism due to distinct posttranslational modifications. This polymorphism likely reflects distinct proteoglycan functions in simple and stratified epithelia, potentially meeting the different adhesive requirements of the cells in these different organizations.

  1. Detection of structural heterogeneity of glass melts

    DEFF Research Database (Denmark)

    Yue, Yuanzheng

    2004-01-01

    The structural heterogeneity of both supercooled liquid and molten states of silicate has been studied using calorimetric method. The objects of this study are basaltic glasses and liquids. Two experimental approaches are taken to detect the structural heterogeneity of the liquids. One is the hyp......The structural heterogeneity of both supercooled liquid and molten states of silicate has been studied using calorimetric method. The objects of this study are basaltic glasses and liquids. Two experimental approaches are taken to detect the structural heterogeneity of the liquids. One...... is the hyperquench-anneal-calorimetric scan approach, by which the structural information of a basaltic supercooled liquid and three binary silicate liquids is acquired. Another is the calorimetrically repeated up- and downscanning approach, by which the structural heterogeneity, the intermediate range order...... is discussed. The ordered structure of glass melts above the liquidus temperature is indirectly characterized by use of X-ray diffraction method. The new approaches are of importance for monitoring the glass melting and forming process and for improving the physical properties of glasses and glass fibers....

  2. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

    Science.gov (United States)

    Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

    2013-01-01

    The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

  3. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

    Directory of Open Access Journals (Sweden)

    Theresa A Hill

    Full Text Available The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs. Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP. Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and

  4. Detection in a Japanese population of a length polymorphism in the 5' flanking region of the human β-globin gene with denaturing gradient gel electrophoresis

    International Nuclear Information System (INIS)

    Takahashi, Noria; Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko

    1992-10-01

    An analysis of the ATTTT repeat polymorphism located approximately 1,400 base pairs upstream from the β-globin structural gene was carried out by denaturing gradient gel electrophoresis (DGGE) of RNA:DNA duplexes. Genomic or cloned DNAs were digested with restriction enzymes and hybridized with 32 P-labeled RNA probes, and resulting RNA:DNA duplexes were examined by DGGE. A difference in the number of repeat units was recognized by differences in duplex mobility on the DGGE gel. In this study of 81 unrelated Japanese from Hiroshima, a sequence heteromorphism was observed at this site. Alleles with 5 and 6 repeats of the ATTTT unit, which had already been reported, were found in polymorphic proportions. In addition, two unreported alleles, one having 7 repeats and the other having an A-to-G nucleotide substitution in the 5th repeat, were detected. Family study data showed that the segregation of these four types of variants is consistent with an autosomal codominant mode of inheritance. This study also demonstrated that DGGE of RNA:DNA duplexes is a sensitive tool for detecting variations in DNA. (author)

  5. Salient Object Detection via Structured Matrix Decomposition.

    Science.gov (United States)

    Peng, Houwen; Li, Bing; Ling, Haibin; Hu, Weiming; Xiong, Weihua; Maybank, Stephen J

    2016-05-04

    Low-rank recovery models have shown potential for salient object detection, where a matrix is decomposed into a low-rank matrix representing image background and a sparse matrix identifying salient objects. Two deficiencies, however, still exist. First, previous work typically assumes the elements in the sparse matrix are mutually independent, ignoring the spatial and pattern relations of image regions. Second, when the low-rank and sparse matrices are relatively coherent, e.g., when there are similarities between the salient objects and background or when the background is complicated, it is difficult for previous models to disentangle them. To address these problems, we propose a novel structured matrix decomposition model with two structural regularizations: (1) a tree-structured sparsity-inducing regularization that captures the image structure and enforces patches from the same object to have similar saliency values, and (2) a Laplacian regularization that enlarges the gaps between salient objects and the background in feature space. Furthermore, high-level priors are integrated to guide the matrix decomposition and boost the detection. We evaluate our model for salient object detection on five challenging datasets including single object, multiple objects and complex scene images, and show competitive results as compared with 24 state-of-the-art methods in terms of seven performance metrics.

  6. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    DEFF Research Database (Denmark)

    Neumann, M A; van de Streek, J; Fabbiani, F P A

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination...

  7. The 3.2 Angstrom Resolution Structure of the Polymorphic Cowpea Chlorotic Mottle Virus Ribonucleoprotein Particle

    Science.gov (United States)

    Speir, Jeffrey Alan

    Structural studies of the polymorphic cowpea chlorotic mottle virus have resulted in high resolution structures for two distinct icosahedral ribonucleoprotein particle conformations dependent upon whether acidic or basic pH conditions prevail. CCMV is stable below pH 6.5, however metal-free particles maintain a 10% increase in hydrodynamic volume at pH >=q 7.5. Identification of this swollen' form of CCMV, which can easily be disrupted with 1M NaCl, led to the first reassembly of an icosahedral virus in vitro from purified viral protein and RNA to form infectious particles, and its assembly has been the subject of biochemical and biophysical investigations for over twenty-five years. Under well defined conditions of pH, ionic strength and divalent metal ion concentration, CCMV capsid protein or capsid protein and RNA will reassemble to form icosahedral particles of various sizes, sheets, tubes, rosettes, and a variety of laminar structures which resemble virion structures from non-related virus families. Analysis of native particles at 3.2A resolution and swollen particles at 28A resolution has suggested that the chemical basis for the formation of polymorphic icosahedral and anisometric structures is: (i) hexamers formed of beta-barrel subunits stabilized by an unusual hexameric parallel beta structure made up of their N-termini, (ii) the location of protein-RNA interactions, (iii) divalent metal cation binding sites that regulate quasi-symmetrical subunit associations, (iv) charge repulsion across the same interfaces when lacking divalent metal ions at basic pH, which induces the formation of sixty 20A diameter portals for RNA release, and (v) a novel, C-terminal-based, subunit dimer assembly unit. The use of C- and N-terminal arms in CCMV has not been observed in other icosahedral RNA virus structures determined at near atomic resolution, however, their detailed interactions and roles in stabilizing the quaternary organization of CCMV are related to that found

  8. DCDC2 polymorphism is associated with left temporoparietal gray and white matter structures during development.

    Science.gov (United States)

    Darki, Fahimeh; Peyrard-Janvid, Myriam; Matsson, Hans; Kere, Juha; Klingberg, Torkel

    2014-10-22

    Three genes, DYX1C1, DCDC2, and KIAA0319, have been previously associated with dyslexia, neuronal migration, and ciliary function. Three polymorphisms within these genes, rs3743204 (DYX1C1), rs793842 (DCDC2), and rs6935076 (KIAA0319) have also been linked to normal variability of left temporoparietal white matter volume connecting the middle temporal cortex to the angular and supramarginal gyri. Here, we assessed whether these polymorphisms are also related to the cortical thickness of the associated regions during childhood development using a longitudinal dataset of 76 randomly selected children and young adults who were scanned up to three times each, 2 years apart. rs793842 in DCDC2 was significantly associated with the thickness of left angular and supramarginal gyri as well as the left lateral occipital cortex. The cortex was significantly thicker for T-allele carriers, who also had lower white matter volume and lower reading comprehension scores. There was a negative correlation between white matter volume and cortical thickness, but only white matter volume predicted reading comprehension 2 years after scanning. These results show how normal variability in reading comprehension is related to gene, white matter volume, and cortical thickness in the inferior parietal lobe. Possibly, the variability of gray and white matter structures could both be related to the role of DCDC2 in ciliary function, which affects both neuronal migration and axonal outgrowth. Copyright © 2014 the authors 0270-6474/14/3414455-08$15.00/0.

  9. Leak detection using structure-borne noise

    Science.gov (United States)

    Holland, Stephen D. (Inventor); Chimenti, Dale E. (Inventor); Roberts, Ronald A. (Inventor)

    2010-01-01

    A method for detection and location of air leaks in a pressure vessel, such as a spacecraft, includes sensing structure-borne ultrasound waveforms associated with turbulence caused by a leak from a plurality of sensors and cross correlating the waveforms to determine existence and location of the leak. Different configurations of sensors and corresponding methods can be used. An apparatus for performing the methods is also provided.

  10. No evidence of association between structural polymorphism at the dopamine D3 receptor locus and alcoholism in the Japanese

    Energy Technology Data Exchange (ETDEWEB)

    Higuchi, Susumu; Muramatsu, Taro; Matsushita, Sachio [National Institute on Alcoholism, Kanagawa (Japan); Murayama, Masanobu [Akagi Kougen Hospital, Gunma (Japan)

    1996-07-26

    Dopaminergic systems mediate reward mechanisms and are involved in reinforcing self-administration of dependence-forming substances, including alcohol. Studies have reported that polymorphisms of the dopamine D2 receptor, whose structure and function are similar to those of the dopamine D3 receptor, increase the susceptibility to alcoholism. The observations led to the examination of the possible association between a structural polymorphism of the D3 receptor gene and alcoholism. Genotyping results, employing a PCR-RFLP method, showed no difference in allele and genotype frequencies of the D3 BalI polymorphism (Ser{sup 9}/Gly{sup 9}) between Japanese alcoholics and controls. Moreover, these frequencies were not altered in alcoholics with inactive aldehyde dehydrogenase-2 (ALDH2), a well-defined negative risk factor for alcoholism. These results strongly suggest that the dopamine D3 receptor is not associated with alcoholism. 19 refs., 1 fig., 1 tab.

  11. Structural impact on the eigenenergy renormalization for carbon and silicon allotropes and boron nitride polymorphs

    Science.gov (United States)

    Tutchton, Roxanne; Marchbanks, Christopher; Wu, Zhigang

    2018-05-01

    The phonon-induced renormalization of electronic band structures is investigated through first-principles calculations based on the density functional perturbation theory for nine materials with various crystal symmetries. Our results demonstrate that the magnitude of the zero-point renormalization (ZPR) of the electronic band structure is dependent on both crystal structure and material composition. We have performed analysis of the electron-phonon-coupling-induced renormalization for two silicon (Si) allotropes, three carbon (C) allotropes, and four boron nitride (BN) polymorphs. Phonon dispersions of each material were computed, and our analysis indicates that materials with optical phonons at higher maximum frequencies, such as graphite and hexagonal BN, have larger absolute ZPRs, with the exception of graphene, which has a considerably smaller ZPR despite having phonon frequencies in the same range as graphite. Depending on the structure and material, renormalizations can be comparable to the GW many-body corrections to Kohn-Sham eigenenergies and, thus, need to be considered in electronic structure calculations. The temperature dependence of the renormalizations is also considered, and in all materials, the eigenenergy renormalization at the band gap and around the Fermi level increases with increasing temperature.

  12. Anisotropic crystal structure distortion of the monoclinic polymorph of acetaminophen at high hydrostatic pressures.

    Science.gov (United States)

    Boldyreva, E V; Shakhtshneider, T P; Vasilchenko, M A; Ahsbahs, H; Uchtmann, H

    2000-04-01

    The anisotropy of structural distortion of the monoclinic polymorph of acetaminophen induced by hydrostatic pressure up to 4.0 GPa was studied by single-crystal X-ray diffraction in a Merrill-Bassett diamond anvil cell (DAC). The space group (P2(1)/n) and the general structural pattern remained unchanged with pressure. Despite the overall decrease in the molar volume with pressure, the structure expanded in particular crystallographic directions. One of the linear cell parameters (c) passed through a minimum as the pressure increased. The intramolecular bond lengths changed only slightly with pressure, but the changes in the dihedral and torsion angles were very large. The compressibility of the intermolecular hydrogen bonds NH...O and OH...O was measured. NH...O bonds were shown to be slightly more compressible than OH...O bonds. The anisotropy of structural distortion was analysed in detail in relation to the pressure-induced changes in the molecular conformations, to the compression of the hydrogen-bond network, and to the changes in the orientation of molecules with respect to each other in the pleated sheets in the structure. Dirichlet domains were calculated in order to analyse the relative shifts of the centroids of the hydrogen-bonded cycles and of the centroids of the benzene rings with pressure.

  13. Genomic variations of Mycoplasma capricolum subsp capripneumoniae detected by amplified fragment length polymorphism (AFLP) analysis

    DEFF Research Database (Denmark)

    Kokotovic, Branko; Bolske, G.; Ahrens, Peter

    2000-01-01

    The genetic diversity of Mycoplasma capricolum subsp. capripneumoniae strains based on determination of amplified fragment length polymorphisms (AFLP) is described. AFLP fingerprints of 38 strains derived from different countries in Africa and the Middle East consisted of over 100 bands in the size...

  14. Detection of polymorphism of the insulin-like growth factor-I (IGF-I ...

    African Journals Online (AJOL)

    Molecular genetic selection on individual genes is a promising method to genetically improve economically important traits in chickens. The insulin-like growth factor-I (IGF-I) gene may play important roles in growth of multiple tissues, including muscle cells, cartilage and bone. In the present study, polymorphism of the ...

  15. Detection of Ribosomal DNA Sequence Polymorphisms in the Protist Plasmodiophora brassicae for the Identification of Geographical Isolates

    Directory of Open Access Journals (Sweden)

    Rawnak Laila

    2017-01-01

    Full Text Available Clubroot is a soil-borne disease caused by the protist Plasmodiophora brassicae (P. brassicae. It is one of the most economically important diseases of Brassica rapa and other cruciferous crops as it can cause remarkable yield reductions. Understanding P. brassicae genetics, and developing efficient molecular markers, is essential for effective detection of harmful races of this pathogen. Samples from 11 Korean field populations of P. brassicae (geographic isolates, collected from nine different locations in South Korea, were used in this study. Genomic DNA was extracted from the clubroot-infected samples to sequence the ribosomal DNA. Primers and probes for P. brassicae were designed using a ribosomal DNA gene sequence from a Japanese strain available in GenBank (accession number AB526843; isolate NGY. The nuclear ribosomal DNA (rDNA sequence of P. brassicae, comprising 6932 base pairs (bp, was cloned and sequenced and found to include the small subunits (SSUs and a large subunit (LSU, internal transcribed spacers (ITS1 and ITS2, and a 5.8s. Sequence variation was observed in both the SSU and LSU. Four markers showed useful differences in high-resolution melting analysis to identify nucleotide polymorphisms including single- nucleotide polymorphisms (SNPs, oligonucleotide polymorphisms, and insertions/deletions (InDels. A combination of three markers was able to distinguish the geographical isolates into two groups.

  16. Crystal structure of the tetragonal polymorph of bis(1-ethyl-3-methylimidazolium tetrabromidocadmate

    Directory of Open Access Journals (Sweden)

    Tamara Đorđević

    2016-07-01

    Full Text Available Both unique Cd atoms in the tetragonal polymorph of bis(1-ethyl-3-methylimidazolium tetrabromidocadmate, (C6H11N22[CdBr4], occupy special positions (site symmetry -4. The crystal structure consists of isolated tetrahedral [CdBr4]2− anions which are surrounded by 1-ethyl-3-methylimidazolium cations. The methyl and ethyl side chains of the cations show positional disorder in a 0.590 (11:0.410 (11 ratio. In the crystal, (C6H11N2+ cations display three weak C—H...Br hydrogen-bond interactions through the imidazolium ring H atoms with the Br− ligands of the surrounding complex anions. The alkyl groups of the side chains are not involved in hydrogen bonding.

  17. Intelligent-based Structural Damage Detection Model

    International Nuclear Information System (INIS)

    Lee, Eric Wai Ming; Yu, K.F.

    2010-01-01

    This paper presents the application of a novel Artificial Neural Network (ANN) model for the diagnosis of structural damage. The ANN model, denoted as the GRNNFA, is a hybrid model combining the General Regression Neural Network Model (GRNN) and the Fuzzy ART (FA) model. It not only retains the important features of the GRNN and FA models (i.e. fast and stable network training and incremental growth of network structure) but also facilitates the removal of the noise embedded in the training samples. Structural damage alters the stiffness distribution of the structure and so as to change the natural frequencies and mode shapes of the system. The measured modal parameter changes due to a particular damage are treated as patterns for that damage. The proposed GRNNFA model was trained to learn those patterns in order to detect the possible damage location of the structure. Simulated data is employed to verify and illustrate the procedures of the proposed ANN-based damage diagnosis methodology. The results of this study have demonstrated the feasibility of applying the GRNNFA model to structural damage diagnosis even when the training samples were noise contaminated.

  18. Intelligent-based Structural Damage Detection Model

    Science.gov (United States)

    Lee, Eric Wai Ming; Yu, Kin Fung

    2010-05-01

    This paper presents the application of a novel Artificial Neural Network (ANN) model for the diagnosis of structural damage. The ANN model, denoted as the GRNNFA, is a hybrid model combining the General Regression Neural Network Model (GRNN) and the Fuzzy ART (FA) model. It not only retains the important features of the GRNN and FA models (i.e. fast and stable network training and incremental growth of network structure) but also facilitates the removal of the noise embedded in the training samples. Structural damage alters the stiffness distribution of the structure and so as to change the natural frequencies and mode shapes of the system. The measured modal parameter changes due to a particular damage are treated as patterns for that damage. The proposed GRNNFA model was trained to learn those patterns in order to detect the possible damage location of the structure. Simulated data is employed to verify and illustrate the procedures of the proposed ANN-based damage diagnosis methodology. The results of this study have demonstrated the feasibility of applying the GRNNFA model to structural damage diagnosis even when the training samples were noise contaminated.

  19. Direct detection of the AR-E211 G > A gene polymorphism from blood and tissue samples without DNA isolation.

    Science.gov (United States)

    Reptova, Silvie; Trtkova, Katerina Smesny; Kolar, Zdenek

    2014-04-01

    The pathogenesis of prostate cancer (CaP) involves alterations in a gene structure of the androgen receptor (AR). The single nucleotide polymorphism AR-E211 G > A localized in exon 1 of the AR gene (G1733A) was detected using direct polymerase chain reaction and restriction digestion (PCR-RFLP) method on blood and tissue samples without prior DNA isolation. We used blood samples of patients with a diagnosis of benign prostatic hyperplasia (BPH) or CaP. From monitored group of CaP patients were selected specimen in formalin-fixed paraffin-embedded tissue blocks with morphology of BPH and CaP. The main objective of our study was to develop a method based the direct PCR-RFLP analysis from blood and tissue without prior DNA isolation for faster genotyping analysis of a large number of samples. We found no statistically significant differences in allelic % of the AR-E211 G > A polymorphism between BPH and CaP patients (p ≤ 0.8462). Genotyping of the AR-E211 G > A variant in blood was not identical with tumor tissue genotyping analysis. Significant agreement between blood and tissue AR-E211 G > A polymorphism only in non-tumor tissue focus was confirmed. Although we analyzed a limited number of the tissue samples, we suppose that a presence of the minor allele A may be associated with cancer transformation-induced changes of the modified AR gene.

  20. Detection experiments with humans implicate visual predation as a driver of colour polymorphism dynamics in pygmy grasshoppers

    Science.gov (United States)

    2013-01-01

    Background Animal colour patterns offer good model systems for studies of biodiversity and evolution of local adaptations. An increasingly popular approach to study the role of selection for camouflage for evolutionary trajectories of animal colour patterns is to present images of prey on paper or computer screens to human ‘predators’. Yet, few attempts have been made to confirm that rates of detection by humans can predict patterns of selection and evolutionary modifications of prey colour patterns in nature. In this study, we first analyzed encounters between human ‘predators’ and images of natural black, grey and striped colour morphs of the polymorphic Tetrix subulata pygmy grasshoppers presented on background images of unburnt, intermediate or completely burnt natural habitats. Next, we compared detection rates with estimates of capture probabilities and survival of free-ranging grasshoppers, and with estimates of relative morph frequencies in natural populations. Results The proportion of grasshoppers that were detected and time to detection depended on both the colour pattern of the prey and on the type of visual background. Grasshoppers were detected more often and faster on unburnt backgrounds than on 50% and 100% burnt backgrounds. Striped prey were detected less often than grey or black prey on unburnt backgrounds; grey prey were detected more often than black or striped prey on 50% burnt backgrounds; and black prey were detected less often than grey prey on 100% burnt backgrounds. Rates of detection mirrored previously reported rates of capture by humans of free-ranging grasshoppers, as well as morph specific survival in the wild. Rates of detection were also correlated with frequencies of striped, black and grey morphs in samples of T. subulata from natural populations that occupied the three habitat types used for the detection experiment. Conclusions Our findings demonstrate that crypsis is background-dependent, and implicate visual predation

  1. Outlying plasmasphere structure detected by whistlers

    International Nuclear Information System (INIS)

    Ho, D.; Carpenter, D.L.

    1976-01-01

    Whistlers recorded at Eights (L approximately equal to 4) and Byrd (L approximately equal to 7), Antarctica have been used to study large-scale structure in equatorial plasma density at geocentric distances approximately equal to 3 to 6 Rsub(E). The observations were made during conditions of magnetic quieting following moderate disturbance. The structures were detected by a 'scanning' process involving relative motion, at about one tenth of the Earth's angular velocity or greater, between the observed density features and the observing whistler station or stations. Three case studies are described, from 26 March 1965, 11 May 1965 and 29 August 1966. The cases support satellite results by showing outlying high density regions at approximately equal to 4 to 6 Rsub(E) that are separated from the main plasmasphere by trough-like depressions ranging in width from 0.2 to 1 Rsub(E). The structures evidently endured for periods of 12 hr or more. In the cases of deepest quieting their slow east-west motions with respect to the Earth are probably of dynamo origin. The cases observed during deep quieting (11 May 1965 and 29 August 1966) suggest the approximate rotation with the Earth of structure formed during previous moderate disturbance activity in the dusk sector. The third case, from 26 March 1965, may represent a structure formed near local midnight. The reported structures appear to be closely related to the bulge phenomenon. The present work supports other experimental and theoretical evidence that the dusk sector is one of major importance in the generation of outlying density structure. (author)

  2. Solid state characterization and crystal structure from X-ray powder diffraction of two polymorphic forms of ranitidine base.

    Science.gov (United States)

    de Armas, Héctor Novoa; Peeters, Oswald M; Blaton, Norbert; Van Gyseghem, Elke; Martens, Johan; Van Haele, Gerrit; Van Den Mooter, Guy

    2009-01-01

    Ranitidine hydrochloride (RAN-HCl), a known anti-ulcer drug, is the product of reaction between HCl and ranitidine base (RAN-B). RAN-HCl has been extensively studied; however this is not the case of the RAN-B. The solid state characterization of RAN-B polymorphs has been carried out using different analytical techniques (microscopy, thermal analysis, Fourier transform infrared spectrometry in the attenuated total reflection mode, (13)C-CPMAS-NMR spectroscopy and X-ray powder diffraction). The crystal structures of RAN-B form I and form II have been determined using conventional X-ray powder diffraction in combination with simulated annealing and whole profile pattern matching, and refined using rigid-body Rietveld refinement. RAN-B form I is a monoclinic polymorph with cell parameters: a = 7.317(2), b = 9.021(2), c = 25.098(6) A, beta = 95.690(1) degrees and space group P2(1)/c. The form II is orthorhombic: a = 31.252(4), b = 13.052(2), c = 8.0892(11) A with space group Pbca. In RAN-B polymorphs, the nitro group is involved in a strong intramolecular hydrogen bond responsible for the existence of a Z configuration in the enamine portion of the molecules. A tail to tail packing motif can be denoted via intermolecular hydrogen bonds. The crystal structures of RAN-B forms are compared to those of RAN-HCl polymorphs. RAN-B polymorphs are monotropic polymorphic pairs. (c) 2008 Wiley-Liss, Inc. and the American Pharmacists Association

  3. Using Random Amplified Polymorphic DNA to Assess Genetic Diversity and Structure of Natural Calophyllum brasiliense (Clusiaceae Populations in Riparian Forests

    Directory of Open Access Journals (Sweden)

    Evânia Galvão Mendonça

    2014-01-01

    Full Text Available The objective of this study was to assess the genetic variability in two natural populations of Calophyllum brasiliense located along two different rivers in the state of Minas Gerais, Brazil, using RAPD molecular markers. Eighty-two polymorphic fragments were amplified using 27 primers. The values obtained for Shannon index (I were 0.513 and 0.530 for the populations located on the margins of the Rio Grande and Rio das Mortes, respectively, demonstrating the high genetic diversity in the studied populations. Nei’s genetic diversity (He was 0.341 for the Rio Grande population and 0.357 for the Rio das Mortes population. These results were not significantly different between populations and suggest a large proportion of heterozygote individuals within both populations. AMOVA showed that 70.42% of the genetic variability is found within populations and 29.58% is found among populations (ФST=0.2958. The analysis of kinship coefficients detected the existence of family structures in both populations. Average kinship coefficients between neighboring individuals were 0.053 (P<0.001 in Rio das Mortes and 0.040 (P<0.001 in Rio Grande. This could be due to restricted pollen and seed dispersal and the history of anthropogenic disturbance in the area. These factors are likely to contribute to the relatedness observed among these genotypes.

  4. Cosmic Ray Hit Detection with Homogenous Structures

    Science.gov (United States)

    Smirnov, O. M.

    Cosmic ray (CR) hits can affect a significant number of pixels both on long-exposure ground-based CCD observations and on the Space Telescope frames. Thus, methods of identifying the damaged pixels are an important part of the data preprocessing for practically any application. The paper presents an implementation of a CR hit detection algorithm based on a homogenous structure (also called cellular automata ), a concept originating in artificial intelligence and dicrete mathematics. Each pixel of the image is represented by a small automaton, which interacts with its neighbors and assumes a distinct state if it ``decides'' that a CR hit is present. On test data, the algorithm has shown a high detection rate (~0.7 ) and a low false alarm rate (frame. A homogenous structure is extremely trainable, which can be very important for processing large batches of data obtained under similar conditions. Training and optimizing issues are discussed, as well as possible other applications of this concept to image processing.

  5. Host species and developmental stage, but not host social structure, affects bacterial community structure in socially polymorphic bees.

    Science.gov (United States)

    McFrederick, Quinn S; Wcislo, William T; Hout, Michael C; Mueller, Ulrich G

    2014-05-01

    Social transmission and host developmental stage are thought to profoundly affect the structure of bacterial communities associated with honey bees and bumble bees, but these ideas have not been explored in other bee species. The halictid bees Megalopta centralis and M. genalis exhibit intrapopulation social polymorphism, which we exploit to test whether bacterial communities differ by host social structure, developmental stage, or host species. We collected social and solitary Megalopta nests and sampled bees and nest contents from all stages of host development. To survey these bacterial communities, we used 16S rRNA gene 454 pyrosequencing. We found no effect of social structure, but found differences by host species and developmental stage. Wolbachia prevalence differed between the two host species. Bacterial communities associated with different developmental stages appeared to be driven by environmentally acquired bacteria. A Lactobacillus kunkeei clade bacterium that is consistently associated with other bee species was dominant in pollen provisions and larval samples, but less abundant in mature larvae and pupae. Foraging adults appeared to often reacquire L. kunkeei clade bacteria, likely while foraging at flowers. Environmental transmission appears to be more important than social transmission for Megalopta bees at the cusp between social and solitary behavior. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  6. Detection of Egg Production of Tegal Duck by Blood Protein Polymorphism

    Directory of Open Access Journals (Sweden)

    Ismoyowati Ismoyowati

    2008-05-01

    Full Text Available The aim of this research was to study the effect of transfferine, albumine, and haemoglobine loci to egg production characteristic of Tegal duck.  100 lying of Tegal ducks keeping by batteray-pen were used in this study.  Individual egg production was recorded until period of 120 days. Blood protein polymorphism analysed by electrophoresis method, and blood sample taken from each ducks.. Egg production and transfferine albumine, and haemoglobine phenotipe on electrophoresis gel were observed in this study.  Genotipe and gene frequencies and genetic variant were applied in data analysis. The result showed that (1 in the transferine locus were identified 3 aleles forming 4 genotipes (TfAA,TfAB, TfBB, and TfBC, (2 in albumine were identified 3 aleles forming 5 genotipes (AlbAA, AlbAB, AlbAC, AlbBB and AlbBC and (3 haemoglobine locus were identified 6 aleles forming 4 genotipes ((HbAA, HbAB, HbAC, HbBB, HbBC dan HbCC.  This study demostrated that B gene frequenci in transfferine, albumine and haemoglonine loci was highest than A and C gene frequency.  Tegal Duck with AA genotipe on all loci had higher egg production than BB and CC homozigote.  This research revealed that the most efective of selection method by haemoglobine protein polymorphism. (Animal Production 10(2: 122-128 (2008   Key Words: Tegal duck, egg production, selection, blood protein polymorphism

  7. Development of a set of SSR markers for genetic polymorphism detection and interspecific hybrid jute breeding

    Directory of Open Access Journals (Sweden)

    Dipnarayan Saha

    2017-10-01

    Full Text Available Corchorus capsularis (white jute and C. olitorius (dark jute are the two principal cultivated species of jute that produce natural bast fiber of commercial importance. We have identified 4509 simple sequence repeat (SSR loci from 34,163 unigene sequences of C. capsularis to develop a non-redundant set of 2079 flanking primer pairs. Among the SSRs, trinucleotide repeats were most frequent (60% followed by dinucleotide repeats (37.6%. Annotation of the SSR-containing unigenes revealed their putative functions in various biological and molecular processes, including responses to biotic and abiotic signals. Eighteen expressed gene-derived SSR (eSSR markers were successfully mapped to the existing single-nucleotide polymorphism (SNP linkage map of jute, providing additional anchor points. Amplification of 72% of the 74 randomly selected primer pairs was successful in a panel of 24 jute accessions, comprising five and twelve accessions of C. capsularis and C. olitorius, respectively, and seven wild jute species. Forty-three primer pairs produced an average of 2.7 alleles and 58.1% polymorphism in a panel of 24 jute accessions. The mean PIC value was 0.34 but some markers showed PIC values higher than 0.5, suggesting that these markers can efficiently measure genetic diversity and serve for mapping of quantitative trait loci (QTLs in jute. A primer polymorphism survey with parents of a wide-hybridized population between a cultivated jute and its wild relative revealed their efficacy for interspecific hybrid identification. For ready accessibility of jute eSSR primers, we compiled all information in a user-friendly web database, JuteMarkerdb (http://jutemarkerdb.icar.gov.in/ for the first time in jute. This eSSR resource in jute is expected to be of use in characterization of germplasm, interspecific hybrid and variety identification, and marker-assisted breeding of superior-quality jute.

  8. LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E

    DEFF Research Database (Denmark)

    Jacobsen, Nana; Bentzen, Joan; Meldgaard, Michael

    2002-01-01

    Genotyping of single nucleotide polymorphisms (SNPs) in large populations presents a great challenge, especially if the SNPs are embedded in GC-rich regions, such as the codon 112 SNP in the human apolipoprotein E (apoE). In the present study, we have used immobilized locked nucleic acid (LNA...... was applied to a panel of patient samples with simultaneous genotyping of the patients by DNA sequencing. The apoE genotyping assays for the codons 112 and 158 SNPs resulted in unambiguous results for all patient samples, concurring with those obtained by DNA sequencing....

  9. Detection and characterization of polymorphisms in XRCC DNA repair genes in human population

    International Nuclear Information System (INIS)

    Staynova, A.; Hadjidekova, V.; Savov, A.

    2004-01-01

    Human population is continuously exposed to low levels of ionizing radiation. The main contribution gives the exposure due to medical applications. Nevertheless, most of the damage induced is repaired shortly after exposure by cellular repair systems. The review is focused on the development and application of methods to estimate the character of polymorphisms in repair genes (XRCC1, APE1), involved in single strand breaks repair which is corresponding mainly to the repair of X-ray induced DNA damage. Since, DSB are major factor for chromosomal aberrations formation, the assays described in this review might be useful for the assessment of the radiation risk for human population. (authors)

  10. Semantic-less Breach Detection of Polymorphic Malware in Federated Cloud

    Directory of Open Access Journals (Sweden)

    Yahav Biran

    2017-06-01

    Full Text Available Cloud computing is one of the largest emerging utility services that is expected to grow enormously over the next decade. Many organizations are moving into hybrid cloud/hosted computing models. Single cloud service provider introduces cost and environmental challenges. Also, multi-cloud solution implemented by the Cloud tenant is suboptimal as it requires expensive adaptation costs. Cloud Federation is a useful structure for aggregating cloud based services under a single umbrella to share resources and responsibilities for the benefit of the member cloud service providers. An efficient security model is crucial for successful cloud business. However, with the advent of large scale and multi-tenant environments, the traditional perimeter boundaries along with traditional security practices are changing. Defining and securing asset and enclave boundaries is more challenging, and system perimeter boundaries are more susceptible to breach. This paper to describe security best practices for Cloud Federation. The paper also describes a tool and technique for detecting anomalous behavior in resource usage across the federation participants. This is a particularly serious issue because of the possibility of an attacker potentially gaining access to more than one CSP federation member. Specifically, this technique is developed for Cloud Federations since they have to deal with heterogeneous multi-platform environments with a diverse mixture of data and security log schema, and it has to do this in real time. A Semantic-less Breach detection system that implements a self-learning system was prototyped and resulted in up to 87% True-Positive rate with 93% True-Negative.

  11. Single Nucleotide Polymorphisms in Common Bean: Their Discovery and Genotyping Using a Multiplex Detection System

    Directory of Open Access Journals (Sweden)

    E. Gaitán-Solís

    2008-11-01

    Full Text Available Single nucleotide polymorphism (SNP markers are by far the most common form of DNA polymorphism in a genome. The objectives of this study were to discover SNPs in common bean ( L. by comparing sequences from coding and noncoding regions obtained from the GenBank and genomic DNA and to compare sequencing results with those obtained using single base extension (SBE assays on the Luminex-100 system for use in high-throughput germplasm evaluation. We assessed the frequency of SNPs in 47 fragments of common bean DNA, using SBE as the evaluation methodology. We conducted a sequence analysis of 10 genotypes of cultivated and wild beans belonging to the Mesoamerican and Andean genetic pools of . For the 10 genotypes evaluated, a total of 20,964 bp of sequence were analyzed in each genotype and compared, resulting in the discovery of 239 SNPs and 133 InDels, giving an average SNP frequency of one per 88 bp and an InDel frequency of one per 157 bp. This is the equivalent of a nucleotide diversity (θ of 6.27 × 10. Comparisons with the SNP genotypes previously obtained by direct sequencing showed that the SBE assays on the Luminex-100 were accurate, with 2.5% being miscalled and 1% showing no signal. These results indicate that the Luminex-100 provides a high-throughput system that can be used to analyze SNPs in large samples of genotypes both for purposes of assessing diversity and also for mapping studies.

  12. Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp using a soybean genome array

    Directory of Open Access Journals (Sweden)

    Wanamaker Steve

    2008-02-01

    Full Text Available Abstract Background Cowpea (Vigna unguiculata L. Walp is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP is a microarray-based marker which can be used for high throughput genotyping and high density mapping. Results Here we report detection and validation of SFPs in cowpea using a readily available soybean (Glycine max genome array. Robustified projection pursuit (RPP was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL population segregating for several important traits including drought tolerance, Fusarium and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%. Conclusion We conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources.

  13. Lagrangian based methods for coherent structure detection

    Energy Technology Data Exchange (ETDEWEB)

    Allshouse, Michael R., E-mail: mallshouse@chaos.utexas.edu [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States); Peacock, Thomas, E-mail: tomp@mit.edu [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2015-09-15

    There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows.

  14. Crystal structure of a new monoclinic polymorph of N-(4-methylphenyl-3-nitropyridin-2-amine

    Directory of Open Access Journals (Sweden)

    Aina Mardia Akhmad Aznan

    2014-08-01

    Full Text Available The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, with Z′ = 4 of the previously reported monoclinic (P21/c, with Z′ = 2 form [Akhmad Aznan et al. (2010. Acta Cryst. E66, o2400]. Four independent molecules comprise the asymmetric unit, which have the common features of a syn disposition of the pyridine N atom and the toluene ring, and an intramolecular amine–nitro N—H...O hydrogen bond. The differences between molecules relate to the dihedral angles between the rings which range from 2.92 (19 to 26.24 (19°. The geometry-optimized structure [B3LYP level of theory and 6–311 g+(d,p basis set] has the same features except that the entire molecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C—H...O, C—H...π, nitro-N—O...π and π–π interactions [inter-centroid distances = 3.649 (2–3.916 (2 Å].

  15. The relationship between CA repeat polymorphism of the IGF-1 gene and the structure of motor skills in young athletes.

    Science.gov (United States)

    Karpowicz, Krzysztof; Krych, Katarzyna; Karpowicz, Małgorzata; Nowak, Witold; Gronek, Piotr

    2018-01-01

    The map of candidate genes that can potentially affect physical fitness becomes larger every year, and they are associated with such aspects as respiratory and cardiovascular stability; body build and composition - especially muscle mass and strength; carbohydrate and lipid metabolism; response to training; and exercise intolerance.The aim of this study was to analyze the relationship between the CA repeat polymorphism of the P1 promoter of the IGF1 gene and the structure of motor skills in the two groups of Polish young athletes in 2007-2009. In this study, 350 young sportsmen representing different sports disciplines were examined (age = 15.5 ± 0.5 years), by genotyping the IGF1 gene and determining the structure of motor skills using the International Physical Fitness Test (IPFT) battery. The multiple stepwise regression was used to determine the impact of the investigated motor skills on the indicator of the overall physical fitness, measured by the total score of the International Physical Fitness Test (IPFT). The analysis showed some regularity related to the character of the IGF1 gene polymorphism. It can be concluded that the two groups of young boys athletes practicing various sports disciplines (kinds of physical exercise) displayed similar associations between CA repeat polymorphism of the P1 promoter of the IGF1 gene and the level of motor effects. Our results suggest that this polymorphism may be a genetic marker of the physical performance phenotype. We demonstrated that CA repeat polymorphism of the P1 promoter of the IGF1 gene was associated with strength predispositions in the homozygous and non-carriers groups. In the group who were heterozygous it was speed-strength aptitudes.

  16. First-principles study of structural, elastic and electronic properties of thorium dicarbide (ThC2) polymorphs

    International Nuclear Information System (INIS)

    Shein, I.R.; Ivanovskii, A.L.

    2009-01-01

    The comparative study of the structural, elastic, cohesive and electronic properties of three polymorphs (α-monoclinic, β-tetragonal and γ-cubic) of thorium dicarbide ThC 2 is performed within the density-functional theory. The optimized atomic coordinates, lattice parameters, theoretical density (ρ), bulk moduli (B), compressibility (β), as well as electronic densities of states, electronic heat capacity (γ) and molar Pauli paramagnetic susceptibility (χ) for all ThC 2 polymorphs are obtained and analyzed in comparison with available experimental data. The peculiarities of inter-atomic bonding for thorium dicarbide are discussed. Besides, we have evaluated the formation energies (E f ) of ThC 2 polymorphs for different possible preparation routes (namely for the reactions with the participation of simple substances (metallic Th and graphite) or thorium monocarbide ThC and graphite). The results show that the synthesis of the ThC 2 polymorphs from simple substances is more favorable - in comparison with the reactions with participation of Th monocarbide.

  17. Randomly amplified polymorphic-DNA analysis for detecting genotoxic effects of Boron on maize (Zea mays L.).

    Science.gov (United States)

    Sakcali, M Serdal; Kekec, Guzin; Uzonur, Irem; Alpsoy, Lokman; Tombuloglu, Huseyin

    2015-08-01

    This study was carried out to investigate the genotoxic effect of boron (B) on maize using randomly amplified polymorphic DNA (RAPD) method. Experimental design was conducted under 0, 5, 10, 25, 50, 100, 125, and 150 ppm B exposures, and physiological changes have revealed a sharp decrease in root growth rates from 28% to 85%, starting from 25 ppm to 150 ppm, respectively. RAPD-polymerase chain reaction (PCR) analysis shows that DNA alterations are clearly observed from beginning to 100 ppm. B-induced inhibition in root growth had a positive correlation with DNA alterations. Total soluble protein, root and stem lengths, and B content analysis in root and leaves encourage these results as a consequence. These preliminary findings reveal that B causes chromosomal aberration and genotoxic effects on maize. Meanwhile, usage of RAPD-PCR technique is a suitable biomarker to detect genotoxic effect of B on maize and other crops for the future. © The Author(s) 2013.

  18. DNA polymorphisms in cuban varieties of avocado (persea americana mill.) as detected by inverse sequence tagged repeat (ISTR) analysis

    Energy Technology Data Exchange (ETDEWEB)

    Ramirez, M; Fuentes, J L [Centro de Estudios Aplicados al Desarrollo Nuclear, La Habana (Cuba); Rodriguez, N N; Cueto, J [Max Planck Institut fur Zuchtungsforschung (MPIZ), Koln (Germany); Becker, D; Rohde, W [Instituto de Investigaciones en Fruticultura Tropical (IIFT). C. Habana (Cuba)

    2001-07-01

    A survey of the genetic diversity among commercial Cuban avocado varieties was initiated using ISTR analysis. ISTR markers were efficient in detecting polymorphisms among the genotypes. The obtained dissimilarities values ranged from 0.24 between var. Suardia and Hass to 1.00 between Lula and Los Moros or CHI-3 with an average dissimilarity of 0.78. A cluster analysis was performed based on dissimilarity using UPGMA as the clustering method. The efficiency of UPGMA in estimating genetic relationships between varieties was corroborated by the cophenetic correlation coefficients, which indicated that the distortion degree in the relationship of the estimated dissimilarities was minimal. Ecological groups were not adequately represented in the dendrogram. Thus, West Indians, Guatemalan and Mexican genotypes were positioned across the dendrogram. The utility of ISTR for genotype identification and assessment of genetic diversity in commercial avocado varieties is discussed.

  19. DNA polymorphisms in cuban varieties of avocado (persea americana mill.) as detected by inverse sequence tagged repeat (ISTR) analysis

    International Nuclear Information System (INIS)

    Ramirez, M; Fuentes, J. L.; Rodriguez, N.N.; Cueto, J.; Becker, D.; Rohde, W.

    2001-01-01

    A survey of the genetic diversity among commercial Cuban avocado varieties was initiated using ISTR analysis. ISTR markers were efficient in detecting polymorphisms among the genotypes. The obtained dissimilarities values ranged from 0.24 between var. Suardia and Hass to 1.00 between Lula and Los Moros or CHI-3 with an average dissimilarity of 0.78. A cluster analysis was performed based on dissimilarity using UPGMA as the clustering method. The efficiency of UPGMA in estimating genetic relationships between varieties was corroborated by the cophenetic correlation coefficients, which indicated that the distortion degree in the relationship of the estimated dissimilarities was minimal. Ecological groups were not adequately represented in the dendrogram. Thus, West Indians, Guatemalan and Mexican genotypes were positioned across the dendrogram. The utility of ISTR for genotype identification and assessment of genetic diversity in commercial avocado varieties is discussed

  20. Real time hybridization studies by resonant waveguide gratings using nanopattern imaging for Single Nucleotide Polymorphism detection

    KAUST Repository

    Bougot-Robin, Kristelle; Kodzius, Rimantas; Yue, Weisheng; Chen, Longqing; Li, Shunbo; Zhang, Xixiang; Bé nisty, Henri; Wen, Weijia

    2013-01-01

    2D imaging of biochips is particularly interesting for multiplex biosensing. Resonant properties allow label-free detection using the change of refractive index at the chip surface. We demonstrate a new principle of Scanning Of Resonance on Chip

  1. Detection of human DNA polymorphisms with a simplified denaturing gradient gel electrophoresis technique.

    OpenAIRE

    Noll, W W; Collins, M

    1987-01-01

    Single base pair differences between otherwise identical DNA molecules can result in altered melting behavior detectable by denaturing gradient gel electrophoresis. We have developed a simplified procedure for using denaturing gradient gel electrophoresis to detect base pair changes in genomic DNA. Genomic DNA is digested with restriction enzymes and hybridized in solution to labeled single-stranded probe DNA. The excess probe is then hybridized to complementary phage M13 template DNA, and th...

  2. Genetic and epigenetic diversity and structure of Phragmites australis from local habitats of the Songnen Prairie using amplified fragment length polymorphism markers.

    Science.gov (United States)

    Qiu, T; Jiang, L L; Yang, Y F

    2016-08-19

    The genetic and epigenetic diversity and structure of naturally occurring Phragmites australis populations occupying two different habitats on a small spatial scale in the Songnen Prairie in northeastern China were investigated by assessing amplified fragment length polymorphisms (AFLPs) and methylation-sensitive amplified polymorphisms (MSAPs) through fluorescent capillary detection. The two groups of P. australis were located in a seasonal waterlogged low-lying and alkalized meadow with a pH of 8-8.5 and in an alkaline patch without accumulated rainwater and with a pH greater than 10. These groups showed high levels of genetic diversity at the habitat level based on the percentage of polymorphic bands (90.32, 82.56%), Nei's gene diversity index (0.262, 0.248), and the Shannon diversity index (0.407, 0.383). Although little is known about the between-habitat genetic differentiation of P. australis on a small spatial scale, our results implied significant genetic differentiation between habitats. Extensive epigenetic diversity within habitats, along with clear differentiation, was found. Specifically, the former habitat (Habitat 1, designated H1) harbored higher levels of genetic and epigenetic diversity than the latter (Habitat 2, designated H2), and population-level diversity was also high. This study represents one of few attempts to predict habitat-based genetic differentiation of reeds on a small scale. These assessments of genetic and epigenetic variation are integral aspects of molecular ecological studies on P. australis. Possible causes for within- and between-habitat genetic and epigenetic variations are discussed.

  3. Spatial and temporal distribution of the neutral polymorphisms in the last ZFX intron: analysis of the haplotype structure and genealogy.

    Science.gov (United States)

    Jaruzelska, J; Zietkiewicz, E; Batzer, M; Cole, D E; Moisan, J P; Scozzari, R; Tavaré, S; Labuda, D

    1999-07-01

    With 10 segregating sites (simple nucleotide polymorphisms) in the last intron (1089 bp) of the ZFX gene we have observed 11 haplotypes in 336 chromosomes representing a worldwide array of 15 human populations. Two haplotypes representing 77% of all chromosomes were distributed almost evenly among four continents. Five of the remaining haplotypes were detected in Africa and 4 others were restricted to Eurasia and the Americas. Using the information about the ancestral state of the segregating positions (inferred from human-great ape comparisons), we applied coalescent analysis to estimate the age of the polymorphisms and the resulting haplotypes. The oldest haplotype, with the ancestral alleles at all the sites, was observed at low frequency only in two groups of African origin. Its estimated age of 740 to 1100 kyr corresponded to the time to the most recent common ancestor. The two most frequent worldwide distributed haplotypes were estimated at 550 to 840 and 260 to 400 kyr, respectively, while the age of the continentally restricted polymorphisms was 120 to 180 kyr and smaller. Comparison of spatial and temporal distribution of the ZFX haplotypes suggests that modern humans diverged from the common ancestral stock in the Middle Paleolithic era. Subsequent range expansion prevented substantial gene flow among continents, separating African groups from populations that colonized Eurasia and the New World.

  4. Detecting high-order interactions of single nucleotide polymorphisms using genetic programming.

    Science.gov (United States)

    Nunkesser, Robin; Bernholt, Thorsten; Schwender, Holger; Ickstadt, Katja; Wegener, Ingo

    2007-12-15

    Not individual single nucleotide polymorphisms (SNPs), but high-order interactions of SNPs are assumed to be responsible for complex diseases such as cancer. Therefore, one of the major goals of genetic association studies concerned with such genotype data is the identification of these high-order interactions. This search is additionally impeded by the fact that these interactions often are only explanatory for a relatively small subgroup of patients. Most of the feature selection methods proposed in the literature, unfortunately, fail at this task, since they can either only identify individual variables or interactions of a low order, or try to find rules that are explanatory for a high percentage of the observations. In this article, we present a procedure based on genetic programming and multi-valued logic that enables the identification of high-order interactions of categorical variables such as SNPs. This method called GPAS cannot only be used for feature selection, but can also be employed for discrimination. In an application to the genotype data from the GENICA study, an association study concerned with sporadic breast cancer, GPAS is able to identify high-order interactions of SNPs leading to a considerably increased breast cancer risk for different subsets of patients that are not found by other feature selection methods. As an application to a subset of the HapMap data shows, GPAS is not restricted to association studies comprising several 10 SNPs, but can also be employed to analyze whole-genome data. Software can be downloaded from http://ls2-www.cs.uni-dortmund.de/~nunkesser/#Software

  5. DroidEnsemble: Detecting Android Malicious Applications with Ensemble of String and Structural Static Features

    KAUST Repository

    Wang, Wei

    2018-05-11

    Android platform has dominated the Operating System of mobile devices. However, the dramatic increase of Android malicious applications (malapps) has caused serious software failures to Android system and posed a great threat to users. The effective detection of Android malapps has thus become an emerging yet crucial issue. Characterizing the behaviors of Android applications (apps) is essential to detecting malapps. Most existing work on detecting Android malapps was mainly based on string static features such as permissions and API usage extracted from apps. There also exists work on the detection of Android malapps with structural features, such as Control Flow Graph (CFG) and Data Flow Graph (DFG). As Android malapps have become increasingly polymorphic and sophisticated, using only one type of static features may result in false negatives. In this work, we propose DroidEnsemble that takes advantages of both string features and structural features to systematically and comprehensively characterize the static behaviors of Android apps and thus build a more accurate detection model for the detection of Android malapps. We extract each app’s string features, including permissions, hardware features, filter intents, restricted API calls, used permissions, code patterns, as well as structural features like function call graph. We then use three machine learning algorithms, namely, Support Vector Machine (SVM), k-Nearest Neighbor (kNN) and Random Forest (RF), to evaluate the performance of these two types of features and of their ensemble. In the experiments, We evaluate our methods and models with 1386 benign apps and 1296 malapps. Extensive experimental results demonstrate the effectiveness of DroidEnsemble. It achieves the detection accuracy as 95.8% with only string features and as 90.68% with only structural features. DroidEnsemble reaches the detection accuracy as 98.4% with the ensemble of both types of features, reducing 9 false positives and 12 false

  6. The changing face of glucagon fibrillation: Structural polymorphism and conformational imprinting

    DEFF Research Database (Denmark)

    Pedersen, J.S.; Dikov, D.; Flink, J.L.

    2006-01-01

    is not the result of the global energy minimization, but rather kinetically controlled by solvent conditions and seed-imprinting. Fibrillar polymorphism, which is being reported for an increasing number of proteins, probably reflects that fibrils have not been under evolutionary constraints to retain a single...

  7. Porcine perilipin (PLIN) gene: Structure, polymorphism and association study in Large White Pigs

    Czech Academy of Sciences Publication Activity Database

    Vykoukalová, Z.; Knoll, Aleš; Čepica, Stanislav

    2009-01-01

    Roč. 54, č. 8 (2009), s. 359-364 ISSN 1212-1819 Institutional research plan: CEZ:AV0Z50450515 Keywords : pigs * perilipin * polymorphism Subject RIV: GI - Animal Husbandry ; Breeding Impact factor: 1.008, year: 2009

  8. Barcode DNA length polymorphisms vs fatty acid profiling for adulteration detection in olive oil.

    Science.gov (United States)

    Uncu, Ali Tevfik; Uncu, Ayse Ozgur; Frary, Anne; Doganlar, Sami

    2017-04-15

    The aim of this study was to compare the performance of a DNA-barcode assay with fatty acid profile analysis to authenticate the botanical origin of olive oil. To achieve this aim, we performed a PCR-capillary electrophoresis (PCR-CE) approach on olive oil: seed oil blends using the plastid trnL (UAA) intron barcode. In parallel to genomic analysis, we subjected the samples to gas chromatography analysis of fatty acid composition. While the PCR-CE assay proved equally efficient as gas chromatography analysis in detecting adulteration with soybean, palm, rapeseed, sunflower, sesame, cottonseed and peanut oils, it was superior to the widely utilized analytical chemistry approach in revealing the adulterant species and detecting small quantities of corn and safflower oils in olive oil. Moreover, the DNA-based test correctly identified all tested olive oil: hazelnut oil blends whereas it was not feasible to detect hazelnut oil adulteration through fatty acid profile analysis. Thus, the present research has shown the feasibility of a PCR-CE barcode assay to detect adulteration in olive oil. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Detection of Sequence Polymorphism in Rubus Occidentalis L. Monomorphic Microsatellite Markers by High Resolution Melting

    Science.gov (United States)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. Development of microsatellite primers through the identification of appropriate repeate...

  10. High resolution melting detects sequence polymorphism in rubus occidentalis L. monomorphic microsatellite markers

    Science.gov (United States)

    Microsatellite, or simple sequence repeat (SSR) markers, are valuable as co-dominant genetic markers with a variety of applications such as DNA fingerprinting, linkage mapping, and population structure analysis. However, primer pairs designed from the regions that flank SSRs often generate fragment...

  11. [Polymorphism and structure of the population of Proteocephalus longicollis Zeder, 1800 (Cestoda: Proteocephalidae) in the vendace Coregonus albula L].

    Science.gov (United States)

    Anikieva, L V; Kharin, V N; Spektor, E N

    2004-01-01

    Polymorphism and phenotypic diversity of a hostal ecoform of Proteocephalus longicollis from its typical host, the vendace, Coregonus albula L., were studied. A complex phenotypic structure of the parasite population and presence of morphologically different groupings were revealed. We distinguished four groupings based on the external characters and three groupings based on the feed and reproduction features; among latter groupings one has very specific variations of features. We conclude that P. longicollis has high intraspecific and intrapopulation heterogeneity, and the host plays a stabilising role in the parasite species formation.

  12. High-pressure polymorphism of As2S3 and new AsS2 modification with layered structure

    Science.gov (United States)

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Katayama, Y.; Kulikova, L. F.; Lityagina, L. V.; Nikolaev, N. A.

    2014-01-01

    At normal pressure, the As2S3 compound is the most stable equilibrium modification with unique layered structure. The possibility of high-pressure polymorphism of this substance remains questionable. Our research showed that the As2S3 substance was metastable under pressures P > 6 GPa decomposing into two high-pressure phases: As2S3 → AsS2 + AsS. New AsS2 phase can be conserved in the single crystalline form in metastable state at room pressure up to its melting temperature (470 K). This modification has the layered structure with P1211 monoclinic symmetry group; the unit-cell values are a = 7.916(2) Å, b = 9.937(2) Å, c = 7.118(1) Å, β = 106.41° ( Z = 8, density 3.44 g/cm3). Along with the recently studied AsS high-pressure modification, the new AsS2 phase suggests that high pressure polymorphism is a very powerful tool to create new layered-structure phases with "wrong" stoichiometry.

  13. Evidence for charge-trapping inducing polymorphic structural-phase transition in pentacene.

    Science.gov (United States)

    Ando, Masahiko; Kehoe, Tom B; Yoneya, Makoto; Ishii, Hiroyuki; Kawasaki, Masahiro; Duffy, Claudia M; Minakata, Takashi; Phillips, Richard T; Sirringhaus, Henning

    2015-01-07

    Trapped-charge-induced transformation of pentacene polymorphs is observed by using in situ Raman spectroscopy and molecular dynamics simulations reveal that the charge should be localized in pentacene molecules at the interface with static intermolecular disorder along the long axis. Quantum chemical calculations of the intermolecular transfer integrals suggest the disorder to be large enough to induce Anderson-type localization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Semantic-less Breach Detection of Polymorphic Malware in Federated Cloud

    OpenAIRE

    Yahav Biran; George Collins; Borky John M; Joel Dubow

    2017-01-01

    Cloud computing is one of the largest emerging utility services that is expected to grow enormously over the next decade. Many organizations are moving into hybrid cloud/hosted computing models. Single cloud service provider introduces cost and environmental challenges. Also, multi-cloud solution implemented by the Cloud tenant is suboptimal as it requires expensive adaptation costs. Cloud Federation is a useful structure for aggregating cloud based services under a single umbrella to share r...

  15. Structure family and polymorphous phase transition in the compounds with soft sublattice: Cu{sub 2}Se as an example

    Energy Technology Data Exchange (ETDEWEB)

    Qiu, Wujie [Department of Physics, East China Normal University, Shanghai 200241 (China); State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Lu, Ping; Yuan, Xun; Liu, Huili; Shi, Xun; Chen, Lidong [State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); CAS Key Laboratory of Energy conversion Materials, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Xu, Fangfang; Wu, Lihua [State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Ke, Xuezhi, E-mail: wqzhang@mail.sic.ac.cn, E-mail: xzke@phy.ecnu.edu.cn, E-mail: jihuiy@uw.edu [Department of Physics, East China Normal University, Shanghai 200241 (China); Yang, Jiong [Materials Genome Institute, Shanghai University, Shanghai 200444 (China); Yang, Jihui, E-mail: wqzhang@mail.sic.ac.cn, E-mail: xzke@phy.ecnu.edu.cn, E-mail: jihuiy@uw.edu [Materials Science and Engineering Department, University of Washington, Seattle, Washington 98195 (United States); Zhang, Wenqing, E-mail: wqzhang@mail.sic.ac.cn, E-mail: xzke@phy.ecnu.edu.cn, E-mail: jihuiy@uw.edu [State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050 (China); Materials Genome Institute, Shanghai University, Shanghai 200444 (China)

    2016-05-21

    Quite a few interesting but controversial phenomena, such as simple chemical composition but complex structures, well-defined high-temperature cubic structure but intriguing phase transition, coexist in Cu{sub 2}Se, originating from the relatively rigid Se framework and “soft” Cu sublattice. However, the electrical transport properties are almost uninfluenced by such complex substructures, which make Cu{sub 2}Se a promising high-performance thermoelectric compound with extremely low thermal conductivity and good power factor. Our work reveals that the crystal structure of Cu{sub 2}Se at the temperature below the phase-transition point (∼400 K) should have a group of candidate structures that all contain a Se-dominated face-centered-cubic-like layered framework but nearly random site occupancy of atoms from the “soft” Cu sublattice. The energy differences among those structures are very low, implying the coexistence of various structures and thus an intrinsic structure complexity with a Se-based framework. Detailed analyses indicate that observed structures should be a random stacking of those representative structure units. The transition energy barriers between each two of those structures are estimated to be zero, leading to a polymorphous phase transition of Cu{sub 2}Se at increasing temperature. Those are all consistent with experimental observations.

  16. Genetic polymorphism in Gymnodinium galatheanum chloroplast DNA sequences and development of a molecular detection assay.

    Science.gov (United States)

    Tengs, T; Bowers, H A; Ziman, A P; Stoecker, D K; Oldach, D W

    2001-02-01

    Nuclear and chloroplast-encoded small subunit ribosomal DNA sequences were obtained from several strains of the toxic dinoflagellate Gymnodinium galatheanum. Phylogenetic analyses and comparison of sequences indicate that the chloroplast sequences show a higher degree of sequence divergence than the nuclear homologue. The chloroplast sequences were chosen as targets for the development of a 5'--3' exonuclease assay for detection of the organism. The assay has a very high degree of specificity and has been used to screen environmental water samples from a fish farm where the presence of this dinoflagellate species has previously been associated with fish kills. Various hypotheses for the derived nature of the chloroplast sequences are discussed, as well as what is known about the toxicity of the species.

  17. Expanding the structural landscape of niclosamide: a high Z ' polymorph, two new solvates and monohydrate HA

    DEFF Research Database (Denmark)

    Sovago, Ioana; Bond, Andrew D.

    2015-01-01

    to be twinned by twofold rotation around that axis. The acetonitrile molecules occupy channels in the structure. A complete structure is provided for niclosamide monohydrate, C13H8Cl2N2O4·H2O, polymorph HA, obtained by Rietveld refinement against laboratory powder X-ray diffraction data. It has been suggested...... that this compound is related to the methanol solvate of niclosamide [Harriss, Wilson & Radosevljevic Evans (2014). Acta Cryst. C70, 758-763], but it is found that the two are not fully isostructural: they contain isostructural two-dimensional layers, but the layers are arranged differently in the two structures....... This suggests that HA may have the potential for polytypism, and features in the Rietveld difference curve indicate that a polytype fully isostructural with the methanol solvate might be present....

  18. Linkage disequilibria among (CA){sub n} polymorphisms in the human dystrophin gene and their implications in carrier detection and prenatal diagnosis in Duchenne and Becker musclar dystrophies

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, R.; Zhong, Y.; Andrade, M. de [Univ. of Texas Graduate School of Biomedical Sciences, Houston, TX (United States)] [and others

    1994-06-01

    Four short tandem repeat loci, characterized by length polymorphisms of (CA){sub n} repeats, have been detected within introns 44, 45, 49, and 50 of the human dystrophin gene. The predicted heterozygosites for these loci range from 72 to 93%, and observed allele numbers range from 6 to 19 in 57 normal chromosomes, revealing their high degree of polymorphism. Evidence for significant disequilibria between the loci within introns 49 and 50 is found. These data appear to be consistent with observations of recombination frequencies between these markers and the length of the intron 44 in relation to the entire region. In addition, these four loci are collectively found to be 100% informative in carrier detection/prenatal diagnosis of Becker and Duchenne muscular dystrophies (B/DMD), whereas scoring the (CA){sub n} markers within introns 45 and 49 alone gives a 99.6% success rate. 13 refs., 4 tabs.

  19. Diversity of equine major histocompatiblity complex class II DRA locus in Posavina and Croatian Coldblood horse: a new polymorphism detected

    Directory of Open Access Journals (Sweden)

    Ino Curik

    2010-01-01

    Full Text Available Domestic equidae display polymorphism within ELA-DRA locus which is not characteristic for other species. We characterised sequence polymorphism present at ELADRA locus exon 2 and estimated allele frequencies in two autochthonous breeds, Posavina and Croatian Coldblood. In 88 horses, four different alleles were found, one of them not reported before in horses. The new allele shows non-synonymous mutation at position 65 (T→A causing amino acid change (Phe→Tyr in antigen binding site and synonymous mutation at position 105 (C→T. Our findings emphasize the importance of DRA polymorphism among equids and some specific DRA frequency pattern potentially specific in draught horses.

  20. Renal fine structures detected by NMR imaging

    International Nuclear Information System (INIS)

    Zilch, H.G.

    1986-01-01

    A significantly improved image quality is achieved by the technique described, as compared to the magnetic resonance data obtained so far. The detailed analysis of the kidney goes as deep as into anatomic fine structures, and there is reason to hope for far better diagnostic details. (orig.) [de

  1. Identification and Damage Detection on Structural Systems

    DEFF Research Database (Denmark)

    Brincker, Rune; Kirkegaard, Poul Henning; Andersen, Palle

    1994-01-01

    A short introduction is given to system identification and damage assessment in civil engineering structures. The most commonly used FFT-based techniques for system identification are mentioned, and the Random decrement technique and parametric methods based on ARMA models are introduced. Speed...

  2. Statistics on gene-based laser speckles with a small number of scatterers: implications for the detection of polymorphism in the Chlamydia trachomatis omp1 gene

    Science.gov (United States)

    Ulyanov, Sergey S.; Ulianova, Onega V.; Zaytsev, Sergey S.; Saltykov, Yury V.; Feodorova, Valentina A.

    2018-04-01

    The transformation mechanism for a nucleotide sequence of the Chlamydia trachomatis gene into a speckle pattern has been considered. The first and second-order statistics of gene-based speckles have been analyzed. It has been demonstrated that gene-based speckles do not obey Gaussian statistics and belong to the class of speckles with a small number of scatterers. It has been shown that gene polymorphism can be easily detected through analysis of the statistical characteristics of gene-based speckles.

  3. Effects of single nucleotide polymorphisms on human N-acetyltransferase 2 structure and dynamics by molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    M Rajasekaran

    Full Text Available BACKGROUND: Arylamine N-acetyltransferase 2 (NAT2 is an important catalytic enzyme that metabolizes the carcinogenic arylamines, hydrazine drugs and chemicals. This enzyme is highly polymorphic in different human populations. Several polymorphisms of NAT2, including the single amino acid substitutions R64Q, I114T, D122N, L137F, Q145P, R197Q, and G286E, are classified as slow acetylators, whereas the wild-type NAT2 is classified as a fast acetylator. The slow acetylators are often associated with drug toxicity and efficacy as well as cancer susceptibility. The biological functions of these 7 mutations have previously been characterized, but the structural basis behind the reduced catalytic activity and reduced protein level is not clear. METHODOLOGY/PRINCIPAL FINDINGS: We performed multiple molecular dynamics simulations of these mutants as well as NAT2 to investigate the structural and dynamical effects throughout the protein structure, specifically the catalytic triad, cofactor binding site, and the substrate binding pocket. None of these mutations induced unfolding; instead, their effects were confined to the inter-domain, domain 3 and 17-residue insert region, where the flexibility was significantly reduced relative to the wild-type. Structural effects of these mutations propagate through space and cause a change in catalytic triad conformation, cofactor binding site, substrate binding pocket size/shape and electrostatic potential. CONCLUSIONS/SIGNIFICANCE: Our results showed that the dynamical properties of all the mutant structures, especially in inter-domain, domain 3 and 17-residue insert region were affected in the same manner. Similarly, the electrostatic potential of all the mutants were altered and also the functionally important regions such as catalytic triad, cofactor binding site, and substrate binding pocket adopted different orientation and/or conformation relative to the wild-type that may affect the functions of the mutants

  4. Comprehensive analysis of Salmonella sequence polymorphisms and development of a LDR-UA assay for the detection and characterization of selected serotypes.

    Science.gov (United States)

    Lauri, Andrea; Castiglioni, Bianca; Mariani, Paola

    2011-07-01

    Salmonella is a major cause of food-borne disease, and Salmonella enterica subspecies I includes the most clinically relevant serotypes. Salmonella serotype determination is important for the disease etiology assessment and contamination source tracking. This task will be facilitated by the disclosure of Salmonella serotype sequence polymorphisms, here annotated in seven genes (sefA, safA, safC, bigA, invA, fimA, and phsB) from 139 S. enterica strains, of which 109 belonging to 44 serotypes of subsp. I. One hundred nineteen polymorphic sites were scored and associated to single serotypes or to serotype groups belonging to S. enterica subsp. I. A diagnostic tool was constructed based on the Ligation Detection Reaction-Universal Array (LDR-UA) for the detection of polymorphic sites uniquely associated to serotypes of primary interest (Salmonella Hadar, Salmonella Infantis, Salmonella Enteritidis, Salmonella Typhimurium, Salmonella Gallinarum, Salmonella Virchow, and Salmonella Paratyphi B). The implementation of promiscuous probes allowed the diagnosis of ten further serotypes that could be associated to a unique hybridization pattern. Finally, the sensitivity and applicability of the tool was tested on target DNA dilutions and with controlled meat contamination, allowing the detection of one Salmonella CFU in 25 g of meat.

  5. Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

    Directory of Open Access Journals (Sweden)

    Tammy M K Cheng

    Full Text Available Recent analyses of human genome sequences have given rise to impressive advances in identifying non-synonymous single nucleotide polymorphisms (nsSNPs. By contrast, the annotation of nsSNPs and their links to diseases are progressing at a much slower pace. Many of the current approaches to analysing disease-associated nsSNPs use primarily sequence and evolutionary information, while structural information is relatively less exploited. In order to explore the potential of such information, we developed a structure-based approach, Bongo (Bonds ON Graph, to predict structural effects of nsSNPs. Bongo considers protein structures as residue-residue interaction networks and applies graph theoretical measures to identify the residues that are critical for maintaining structural stability by assessing the consequences on the interaction network of single point mutations. Our results show that Bongo is able to identify mutations that cause both local and global structural effects, with a remarkably low false positive rate. Application of the Bongo method to the prediction of 506 disease-associated nsSNPs resulted in a performance (positive predictive value, PPV, 78.5% similar to that of PolyPhen (PPV, 77.2% and PANTHER (PPV, 72.2%. As the Bongo method is solely structure-based, our results indicate that the structural changes resulting from nsSNPs are closely associated to their pathological consequences.

  6. Interactions of early adversity with stress-related gene polymorphisms impact regional brain structure in females.

    Science.gov (United States)

    Gupta, Arpana; Labus, Jennifer; Kilpatrick, Lisa A; Bonyadi, Mariam; Ashe-McNalley, Cody; Heendeniya, Nuwanthi; Bradesi, Sylvie; Chang, Lin; Mayer, Emeran A

    2016-04-01

    Early adverse life events (EALs) have been associated with regional thinning of the subgenual cingulate cortex (sgACC), a brain region implicated in the development of disorders of mood and affect, and often comorbid functional pain disorders, such as irritable bowel syndrome (IBS). Regional neuroinflammation related to chronic stress system activation has been suggested as a possible mechanism underlying these neuroplastic changes. However, the interaction of genetic and environmental factors in these changes is poorly understood. The current study aimed to evaluate the interactions of EALs and candidate gene polymorphisms in influencing thickness of the sgACC. 210 female subjects (137 healthy controls; 73 IBS) were genotyped for stress and inflammation-related gene polymorphisms. Genetic variation with EALs, and diagnosis on sgACC thickness was examined, while controlling for race, age, and total brain volume. Compared to HCs, IBS had significantly reduced sgACC thickness (p = 0.03). Regardless of disease group (IBS vs. HC), thinning of the left sgACC was associated with a significant gene-gene environment interaction between the IL-1β genotype, the NR3C1 haplotype, and a history of EALs (p = 0.05). Reduced sgACC thickness in women with the minor IL-1β allele, was associated with EAL total scores regardless of NR3C1 haplotype status (p = 0.02). In subjects homozygous for the major IL-1β allele, reduced sgACC with increasing levels of EALs was seen only with the less common NR3C1 haplotype (p = 0.02). These findings support an interaction between polymorphisms related to stress and inflammation and early adverse life events in modulating a key region of the emotion arousal circuit.

  7. Analysis of the population structure of Uruguayan Creole cattle as inferred from milk major gene polymorphisms

    Directory of Open Access Journals (Sweden)

    Gonzalo Rincón

    2006-01-01

    Full Text Available The ancestors of Uruguayan Creole cattle were introduced by the Spanish conquerors in the XVII century, following which the population grew extensively and became semi-feral before the introduction of selected breeds. Today the Uruguayan Creole cattle genetic reserve consists of 575 animals. We used the tetra primer amplification refractory mutation system polymerase chain reaction (ARMS-PCR to analyze the kappa-casein, beta-casein, alphaS1-casein and alpha-lactoalbumin gene polymorphisms and restriction fragment length polymorphism PCR (RFLP-PCR for the beta-lactoglobulin and the acylCoA:diacyl glycerol acyltransferase 1 (DGAT1 genes. The kappa-casein and beta-lactoglobulin genes presented very similar A and B allele frequencies, while the alphas1-casein and alpha-lactoalbumin gene B alleles showed much higher frequencies than the corresponding A alleles. The beta-casein B allele was not found in the population sampled. There was a very high frequency of the DGAT1 gene A allele which is associated with low milk fat content and high milk yield. All loci were in Hardy-Weinberg equilibrium and the level of heterozygosity agreed with the high genetic diversity observed in a previous analysis of this population. Preservation of the allelic richness observed in the Uruguayan Creole cattle should be considered for future dairy management and livestock genetic improvement. The results also emphasize the value of the tetra primers ARMS-PCR technique as a rapid, easy and economical way of genotyping cattle breeds for milk gene single nucleotide polymorphisms.

  8. On multiple crack detection in beam structures

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Shapour; Kargozarfard, Mohammad [Shahid Chamran University, Ahvaz (Iran, Islamic Republic of)

    2013-01-15

    This study presents an inverse procedure to identify multiple cracks in beams using an evolutionary algorithm. By considering the crack detection procedure as an optimization problem, an objective function can be constructed based on the change of the eigenfrequencies and some strain energy parameters. Each crack is modeled by a rotational spring. The changes in natural frequencies due to the presence of the cracks are related to a damage index vector. Then, the bees algorithm, a swarm-based evolutionary optimization technique, is used to optimize the objective function and find the damage index vector, whose positive components show the number and position of the cracks. A second objective function is also optimized to find the crack depths. Several experimental studies on cracked cantilever beams are conducted to ensure the integrity of the proposed method. The results show that the number of cracks as well as their sizes and locations can be predicted well through this method.

  9. Detecting Structural Breaks using Hidden Markov Models

    DEFF Research Database (Denmark)

    Ntantamis, Christos

    Testing for structural breaks and identifying their location is essential for econometric modeling. In this paper, a Hidden Markov Model (HMM) approach is used in order to perform these tasks. Breaks are defined as the data points where the underlying Markov Chain switches from one state to another....... The estimation of the HMM is conducted using a variant of the Iterative Conditional Expectation-Generalized Mixture (ICE-GEMI) algorithm proposed by Delignon et al. (1997), that permits analysis of the conditional distributions of economic data and allows for different functional forms across regimes...

  10. Nondestructive damage detection and evaluation technique for seismically damaged structures

    Science.gov (United States)

    Adachi, Yukio; Unjoh, Shigeki; Kondoh, Masuo; Ohsumi, Michio

    1999-02-01

    The development of quantitative damage detection and evaluation technique, and damage detection technique for invisible damages of structures are required according to the lessons from the 1995 Hyogo-ken Nanbu earthquake. In this study, two quantitative damage sensing techniques for highway bridge structures are proposed. One method is to measure the change of vibration characteristics of the bridge structure. According to the damage detection test for damaged bridge column by shaking table test, this method can successfully detect the vibration characteristic change caused by damage progress due to increment excitations. The other method is to use self-diagnosis intelligent materials. According to the reinforced concrete beam specimen test, the second method can detect the damage by rupture of intelligent sensors, such as optical fiber or carbon fiber reinforced plastic rod.

  11. Enhancing community detection by using local structural information

    International Nuclear Information System (INIS)

    Xiang, Ju; Bao, Mei-Hua; Tang, Liang; Li, Jian-Ming; Hu, Ke; Chen, Benyan; Hu, Jing-Bo; Zhang, Yan; Tang, Yan-Ni; Gao, Yuan-Yuan

    2016-01-01

    Many real-world networks, such as gene networks, protein–protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods. (paper: interdisciplinary statistical mechanics)

  12. Multi-Dimensional Damage Detection for Surfaces and Structures

    Science.gov (United States)

    Williams, Martha; Lewis, Mark; Roberson, Luke; Medelius, Pedro; Gibson, Tracy; Parks, Steen; Snyder, Sarah

    2013-01-01

    Current designs for inflatable or semi-rigidized structures for habitats and space applications use a multiple-layer construction, alternating thin layers with thicker, stronger layers, which produces a layered composite structure that is much better at resisting damage. Even though such composite structures or layered systems are robust, they can still be susceptible to penetration damage. The ability to detect damage to surfaces of inflatable or semi-rigid habitat structures is of great interest to NASA. Damage caused by impacts of foreign objects such as micrometeorites can rupture the shell of these structures, causing loss of critical hardware and/or the life of the crew. While not all impacts will have a catastrophic result, it will be very important to identify and locate areas of the exterior shell that have been damaged by impacts so that repairs (or other provisions) can be made to reduce the probability of shell wall rupture. This disclosure describes a system that will provide real-time data regarding the health of the inflatable shell or rigidized structures, and information related to the location and depth of impact damage. The innovation described here is a method of determining the size, location, and direction of damage in a multilayered structure. In the multi-dimensional damage detection system, layers of two-dimensional thin film detection layers are used to form a layered composite, with non-detection layers separating the detection layers. The non-detection layers may be either thicker or thinner than the detection layers. The thin-film damage detection layers are thin films of materials with a conductive grid or striped pattern. The conductive pattern may be applied by several methods, including printing, plating, sputtering, photolithography, and etching, and can include as many detection layers that are necessary for the structure construction or to afford the detection detail level required. The damage is detected using a detector or

  13. Structure and population genetics of the breakpoints of a polymorphic inversion in Drosophila subobscura.

    Science.gov (United States)

    Papaceit, Montserrat; Segarra, Carmen; Aguadé, Montserrat

    2013-01-01

    Drosophila subobscura is a paleartic species of the obscura group with a rich chromosomal polymorphism. To further our understanding on the origin of inversions and on how they regain variation, we have identified and sequenced the two breakpoints of a polymorphic inversion of D. subobscura--inversion 3 of the O chromosome--in a population sample. The breakpoints could be identified as two rather short fragments (∼300 bp and 60 bp long) with no similarity to any known transposable element family or repetitive sequence. The presence of the ∼300-bp fragment at the two breakpoints of inverted chromosomes implies its duplication, an indication of the inversion origin via staggered double-strand breaks. Present results and previous findings support that the mode of origin of inversions is neither related to the inversion age nor species-group specific. The breakpoint regions do not consistently exhibit the lower level of variation within and stronger genetic differentiation between arrangements than more internal regions that would be expected, even in moderately small inversions, if gene conversion were greatly restricted at inversion breakpoints. Comparison of the proximal breakpoint region in species of the obscura group shows that this breakpoint lies in a small high-turnover fragment within a long collinear region (∼300 kb). © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  14. Synthesis and structural, spectroscopic and magnetic studies of two new polymorphs of Mn(SeO3).H2O

    International Nuclear Information System (INIS)

    Larranaga, Aitor; Mesa, Jose L.; Pizarro, Jose L.; Pena, A.; Olazcuaga, Roger; Arriortua, Maria I.; Rojo, Teofilo

    2005-01-01

    Two new manganese(II) selenite polymorphs with formula Mn(SeO 3 ).H 2 O have been synthesized by slow evaporation from an aqueous solution. The crystal structure of both compounds (1) and (2) have been solved from X-ray diffraction data. The structure of (1) was determined from single-crystal X-ray diffraction techniques. The compound crystallizes in the Ama2 space group, with a=5.817(1), b=13.449(3), c=4.8765(9)A and Z=4. The structure of (2) has been solved from X-ray powder diffraction data. This phase crystallizes in the P2 1 /n space group with unit-cell parameters of a=4.921(3), b=13.121(7), c=5.816(1)A, β=90.03(2) o and Z=4. Both polymorphs exhibit a layered structure formed by isolated sheets of MnO 6 octahedra and (SeO 3 ) 2- trigonal pyramids in the (010) plane. These layers, which contain one manganese and selenium atom crystallographically independent, are formed by octahedra linked between them through the selenite oxoanions. The difference of both compounds consists in the stacking of the layers along the b-axis. The IR spectra show the characteristic bands of the selenite anion. Studies of luminescence performed at 6K and diffuse reflectance spectroscopy have been carried out for both phases. The Dq and Racah (B and C) parameters, from luminescence and diffuse reflectance spectroscopy, are Dq=705, B=750, C=3325cm -1 for (1) and Dq=720, B=745, C=3350cm -1 for (2). The ESR spectra of both compounds are isotropic with g-values of 1.99(1). Magnetic measurements indicate the presence of antiferromagnetic couplings in both phases. The J-exchange parameters have been estimated by fitting the experimental magnetic data to a model for square-planar lattice. The values obtained are J/k=-0.83, -0.91K and J ' /k=-0.97, -1.20K, for polymorphs (1) and (2), respectively

  15. Structural Acoustic UXO Detection and Identification in Marine Environments

    Science.gov (United States)

    2016-05-01

    a thick steel wall, is cylindrical, and has an aspect ratio of about 5:1. Further, the interior water can support acoustic waves as does the epoxy...FINAL REPORT Structural Acoustic UXO Detection and Identification in Marine Environments SERDP Project MR-2103 MAY 2016 B. H...NUMBER Structural Acoustic UXO Detection and Identification in Marine Environments- Final report for Follow-on Work- MR-2103 Sb. GRANT NUMBER Sc

  16. Leveraging disjoint communities for detecting overlapping community structure

    International Nuclear Information System (INIS)

    Chakraborty, Tanmoy

    2015-01-01

    Network communities represent mesoscopic structure for understanding the organization of real-world networks, where nodes often belong to multiple communities and form overlapping community structure in the network. Due to non-triviality in finding the exact boundary of such overlapping communities, this problem has become challenging, and therefore huge effort has been devoted to detect overlapping communities from the network.In this paper, we present PVOC (Permanence based Vertex-replication algorithm for Overlapping Community detection), a two-stage framework to detect overlapping community structure. We build on a novel observation that non-overlapping community structure detected by a standard disjoint community detection algorithm from a network has high resemblance with its actual overlapping community structure, except the overlapping part. Based on this observation, we posit that there is perhaps no need of building yet another overlapping community finding algorithm; but one can efficiently manipulate the output of any existing disjoint community finding algorithm to obtain the required overlapping structure. We propose a new post-processing technique that by combining with any existing disjoint community detection algorithm, can suitably process each vertex using a new vertex-based metric, called permanence, and thereby finds out overlapping candidates with their community memberships. Experimental results on both synthetic and large real-world networks show that PVOC significantly outperforms six state-of-the-art overlapping community detection algorithms in terms of high similarity of the output with the ground-truth structure. Thus our framework not only finds meaningful overlapping communities from the network, but also allows us to put an end to the constant effort of building yet another overlapping community detection algorithm. (paper)

  17. Single nucleotide polymorphism analysis of the enterocin P structural gene of Enterococcus faecium strains isolated from nonfermented animal foods.

    Science.gov (United States)

    Arlindo, Samuel; Calo, Pilar; Franco, Carlos; Prado, Marta; Cepeda, Alberto; Barros-Velázquez, Jorge

    2006-12-01

    The bacteriocins produced by two lactic acid bacteria isolated from nonfermented fresh meat and fish, respectively, and exhibiting a remarkable antilisterial activity, were characterized. Bacteriocinogenic strains were identified as Enterococcus faecium and the maximum bacteriocin production by both strains was detected in the stationary phase of growth. The activity against Listeria monocytogenes was maintained in pH range of 3-7 and was stable in both strains after heating at 100 or 121 degrees C. The genes coding for enterocin P were detected, isolated, and sequenced in both E. faecium strains. They exhibited DNA/DNA homology in the 87.1-97.2% range with respect to the other four enterocin P genes reported so far. Three single nucleotide polymorphism events, silent at the amino acid level, were detected at nucleotide positions 45 (G/A), 75 (A/G), and 90 (T/C) in E. faecium LHICA 28-4 and may explain the differences reported for those loci in other enterocin P-producing E. faecium strains. This work provides the first description of enterocin P-producing E. faecium strains in nonfermented foodstuffs and, in the case of E. faecium LHICA 51, the first report of an enterocin P-producing strain isolated from fish so far.

  18. Musical Tone Law Method for the Structural Damage Detection

    Directory of Open Access Journals (Sweden)

    Weisong Yang

    2017-01-01

    Full Text Available Damage detection tests of inclined cables, steel pipes, spherical shells, and an actual cable-stayed bridge were conducted based on the proposed musical tone law method. The results show that the musical tone law method could be used in the damage detection of isotropic material structures with simple shape, like cables, pipes, plates, and shells. Having distinct spectral lines like a comb with a certain interval distribution rule is the main characteristic of the music tone law. Damage detection baseline could be established by quantizing the fitting relationship between modal orders and the corresponding frequency values. The main advantage of this method is that it could be used in the structural damage detection without vibration information of an intact structure as a reference.

  19. Edge detection based on computational ghost imaging with structured illuminations

    Science.gov (United States)

    Yuan, Sheng; Xiang, Dong; Liu, Xuemei; Zhou, Xin; Bing, Pibin

    2018-03-01

    Edge detection is one of the most important tools to recognize the features of an object. In this paper, we propose an optical edge detection method based on computational ghost imaging (CGI) with structured illuminations which are generated by an interference system. The structured intensity patterns are designed to make the edge of an object be directly imaged from detected data in CGI. This edge detection method can extract the boundaries for both binary and grayscale objects in any direction at one time. We also numerically test the influence of distance deviations in the interference system on edge extraction, i.e., the tolerance of the optical edge detection system to distance deviation. Hopefully, it may provide a guideline for scholars to build an experimental system.

  20. Allelic variation of the inducible costimulator (ICOS) gene: detection of polymorphisms, analysis of the promoter region, and extended haplotype estimation

    DEFF Research Database (Denmark)

    Andersen, A.D.H.; Lange, Marianne; Lillevang, S.T.

    2003-01-01

    The human chromosome region 2q33 including the three costimulatory molecules CD28, CTLA-4 and ICOS, has been subject to much attention due to its linkage to a number of autoimmune diseases. The search for the causal relationship of this linkage has revealed several polymorphisms, but no variations...... in the amino acid sequences except for one polymorphism in, the leader sequence of CTLA-4. In the present study, we examined the ICOS gene of an unrelated group of healthy donors from the Danish population. We were able to report 16 intronic SNP, one intronic G-insert and two repeat regions in intron 4......, consistent with the [T](n) and the [GT](n) regions reported in a Japanese study. Putative haplotypes for the established SNP and repeat polymorphisms have been estimated by computational analysis. Sequencing of similar to3500 by of the upstream region of ICOS revealed an additional eight SNP of which two...

  1. Multi-scale structural similarity index for motion detection

    Directory of Open Access Journals (Sweden)

    M. Abdel-Salam Nasr

    2017-07-01

    Full Text Available The most recent approach for measuring the image quality is the structural similarity index (SSI. This paper presents a novel algorithm based on the multi-scale structural similarity index for motion detection (MS-SSIM in videos. The MS-SSIM approach is based on modeling of image luminance, contrast and structure at multiple scales. The MS-SSIM has resulted in much better performance than the single scale SSI approach but at the cost of relatively lower processing speed. The major advantages of the presented algorithm are both: the higher detection accuracy and the quasi real-time processing speed.

  2. Calcium Carbonate Polymorphs Growing in the Presence of Sericin: A New Composite Mimicking the Hierarchic Structure of Nacre

    Directory of Open Access Journals (Sweden)

    Linda Pastero

    2018-06-01

    Full Text Available Bioinspired self-assembled composite materials are appealing both for their industrial applications and importance in natural sciences, and represent a stimulating topic in the area of materials science, biology, and medicine. The function of the organic matrix has been studied from the biological, chemical, crystallographic, and engineering point of view. Little attention has been paid to the effect of one of the two main components of the organic matrix, the sericin fraction, on the growth morphology of calcium carbonate polymorphs. In the present work, we address this issue experimentally, emphasizing the morphological effects of sericin on calcite and aragonite crystals, and on the formation of a sericin-aragonite-calcite self-assembled composite with a hierarchic structure comparable to that of natural nacre.

  3. Genetic structuring and fixed polymorphisms in the gene period among natural populations of Lutzomyia longipalpis in Brazil.

    Science.gov (United States)

    Lima Costa, César Raimundo; Freitas, Moises Thiago de Souza; Santiago Figueirêdo, Carlos Alberto; Aragão, Nádia Consuelo; da Silva, Lidiane Gomes; Marcondes, Carlos Brisola; Dias, Raimundo Vieira; Leal-Balbino, Tereza Cristina; Souza, Manuela Barbosa Rodrigues; Ramalho-Ortigão, Marcelo; Balbino, Valdir de Queiroz

    2015-04-01

    Even one hundred years after being originally identified, aspects of the taxonomy of the sand fly Lutzomyia longipalpis, the principal vector of Leishmania infantum in the Americas, remain unresolved for Brazilian populations of this vector. The diversity of morphological, behavioral, biochemical, and ethological characters, as well as the genetic variability detected by molecular markers are indicative of the presence of a complex of species. In this study, a 525 bp fragment of the period gene was used to evaluate sympatric populations of L. longipalpis. A combination of probabilistic methods such as maximum likelihood and genetic assignment approach to investigate sympatric species of L. longipalpis were applied in three populations of Northeast Brazil. Fixed polymorphisms in geographically isolated populations of L. longipalpis from two localities in the state of Ceará and one in the state of Pernambuco, Brazil, was identified in a 525 bp fragment of the gene period (per). Our results suggest a direct relationship between the number of spots found in males' tergites and the genetic variation in cryptic species of L. longipalpis. The fragment used in this study revealed the nature of the ancestral morphotype 1S. New polymorphisms were identified in the gene per which can be used as a genetic barcode to sympatric taxonomy of L. longipalpis. The per gene fragment confirmed the presence of two siblings species of L. longipalpis in Sobral and showed that these same species are present in two other localities, representing an expansion within the L. longipalpis species complex with regards to the states of Ceará and Pernambuco.

  4. Population structure of pigs determined by single nucleotide polymorphisms observed in assembled expressed sequence tags.

    Science.gov (United States)

    Matsumoto, Toshimi; Okumura, Naohiko; Uenishi, Hirohide; Hayashi, Takeshi; Hamasima, Noriyuki; Awata, Takashi

    2012-01-01

    We have collected more than 190000 porcine expressed sequence tags (ESTs) from full-length complementary DNA (cDNA) libraries and identified more than 2800 single nucleotide polymorphisms (SNPs). In this study, we tentatively chose 222 SNPs observed in assembled ESTs to study pigs of different breeds; 104 were selected by comparing the cDNA sequences of a Meishan pig and samples of three-way cross pigs (Landrace, Large White, and Duroc: LWD), and 118 were selected from LWD samples. To evaluate the genetic variation between the chosen SNPs from pig breeds, we determined the genotypes for 192 pig samples (11 pig groups) from our DNA reference panel with matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Of the 222 reference SNPs, 186 were successfully genotyped. A neighbor-joining tree showed that the pig groups were classified into two large clusters, namely, Euro-American and East Asian pig populations. F-statistics and the analysis of molecular variance of Euro-American pig groups revealed that approximately 25% of the genetic variations occurred because of intergroup differences. As the F(IS) values were less than the F(ST) values(,) the clustering, based on the Bayesian inference, implied that there was strong genetic differentiation among pig groups and less divergence within the groups in our samples. © 2011 The Authors. Animal Science Journal © 2011 Japanese Society of Animal Science.

  5. Binuclear Copper(I Borohydride Complex Containing Bridging Bis(diphenylphosphino Methane Ligands: Polymorphic Structures of [(µ2-dppm2Cu2(η2-BH42] Dichloromethane Solvate

    Directory of Open Access Journals (Sweden)

    Natalia V. Belkova

    2017-10-01

    Full Text Available Bis(diphenylphosphinomethane copper(I tetrahydroborate was synthesized by ligands exchange in bis(triphenylphosphine copper(I tetrahydroborate, and characterized by XRD, FTIR, NMR spectroscopy. According to XRD the title compound has dimeric structure, [(μ2-dppm2Cu2(η2-BH42], and crystallizes as CH2Cl2 solvate in two polymorphic forms (orthorhombic, 1, and monoclinic, 2 The details of molecular geometry and the crystal-packing pattern in polymorphs were studied. The rare Twisted Boat-Boat conformation of the core Cu2P4C2 cycle in 1 is found being more stable than Boat-Boat conformation in 2.

  6. Ribo HRM--detection of inter- and intra-species polymorphisms within ribosomal DNA by high resolution melting analysis supported by application of artificial allelic standards.

    Science.gov (United States)

    Masny, Aleksander; Jagiełło, Agata; Płucienniczak, Grażyna; Golab, Elzbieta

    2012-09-01

    Ribo HRM, a single-tube PCR and high resolution melting (HRM) assay for detection of polymorphisms in the large subunit ribosomal DNA expansion segment V, was developed on a Trichinella model. Four Trichinella species: T. spiralis (isolates ISS3 and ISS160), T. nativa (isolates ISS10 and ISS70), T. britovi (isolates ISS2 and ISS392) and T. pseudospiralis (isolates ISS13 and ISS1348) were genotyped. Cloned allelic variants of the expansion segment V were used as standards to prepare reference HRM curves characteristic for single sequences and mixtures of several cloned sequences imitating allelic composition detected in Trichinella isolates. Using the primer pair Tsr1 and Trich1bi, it was possible to amplify a fragment of the ESV and detect PCR products obtained from the genomic DNA of pools of larvae belonging to the four investigated species: T. pseudospiralis, T. spiralis, T. britovi and T. nativa, in a single tube Real-Time PCR reaction. Differences in the shape of the HRM curves of Trichinella isolates suggested the presence of differences between examined isolates of T. nativa, T. britovi and T. pseudospiralis species. No differences were observed between T. spiralis isolates. The presence of polymorphisms within the amplified ESV sequence fragment of T. nativa T. britovi and T. pseudospiralis was confirmed by sequencing of the cloned PCR products. Novel sequences were discovered and deposited in GenBank (GenBank IDs: JN971020-JN971027, JN120902.1, JN120903.1, JN120904.1, JN120906.1, JN120905.1). Screening the ESV region of Trichinella for polymorphism is possible using the genotyping assay Ribo HRM at the current state of its development. The Ribo HRM assay could be useful in phylogenetic studies of the Trichinella genus. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Polymorphs and polymorphic cocrystals of temozolomide.

    Science.gov (United States)

    Babu, N Jagadeesh; Reddy, L Sreenivas; Aitipamula, Srinivasulu; Nangia, Ashwini

    2008-07-07

    Crystal polymorphism in the antitumor drug temozolomide (TMZ), cocrystals of TMZ with 4,4'-bipyridine-N,N'-dioxide (BPNO), and solid-state stability were studied. Apart from a known X-ray crystal structure of TMZ (form 1), two new crystalline modifications, forms 2 and 3, were obtained during attempted cocrystallization with carbamazepine and 3-hydroxypyridine-N-oxide. Conformers A and B of the drug molecule are stabilized by intramolecular amide N--HN(imidazole) and N--HN(tetrazine) interactions. The stable conformer A is present in forms 1 and 2, whereas both conformers crystallized in form 3. Preparation of polymorphic cocrystals I and II (TMZBPNO 1:0.5 and 2:1) were optimized by using solution crystallization and grinding methods. The metastable nature of polymorph 2 and cocrystal II is ascribed to unused hydrogen-bond donors/acceptors in the crystal structure. The intramolecularly bonded amide N-H donor in the less stable structure makes additional intermolecular bonds with the tetrazine C==O group and the imidazole N atom in stable polymorph 1 and cocrystal I, respectively. All available hydrogen-bond donors and acceptors are used to make intermolecular hydrogen bonds in the stable crystalline form. Synthon polymorphism and crystal stability are discussed in terms of hydrogen-bond reorganization.

  8. Isolation and characterization of DNA probes from a flow-sorted human chromosome 8 library that detect restriction fragment length polymorphism (RFLP).

    Science.gov (United States)

    Wood, S; Starr, T V; Shukin, R J

    1986-01-01

    We have used a recombinant DNA library constructed from flow-sorted human chromosome 8 as a source of single-copy human probes. These probes have been screened for restriction fragment length polymorphism (RFLP) by hybridization to Southern transfers of genomic DNA from five unrelated individuals. We have detected six RFLPs distributed among four probes after screening 741 base pairs for restriction site variation. These RFLPs all behave as codominant Mendelian alleles. Two of the probes detect rare variants, while the other two detect RFLPs with PIC values of .36 and .16. Informative probes will be useful for the construction of a linkage map for chromosome 8 and for the localization of mutant alleles to this chromosome. Images Fig. 1 PMID:2879441

  9. Recent divergence, intercontinental dispersal and shared polymorphism are shaping the genetic structure of amphi-Atlantic peatmoss populations.

    Science.gov (United States)

    Szövényi, P; Terracciano, S; Ricca, M; Giordano, S; Shaw, A J

    2008-12-01

    Several lines of evidence suggest that recent long-distance dispersal may have been important in the evolution of intercontinental distribution ranges of bryophytes. However, the absolute rate of intercontinental migration and its relative role in the development of certain distribution ranges is still poorly understood. To this end, the genetic structure of intercontinental populations of six peatmoss species showing an amphi-Atlantic distribution was investigated using microsatellite markers. Methods relying on the coalescent were applied (IM and MIGRATE) to understand the evolution of this distribution pattern in peatmosses. Intercontinental populations of the six peatmoss species were weakly albeit significantly differentiated (average F(ST) = 0.104). This suggests that the North Atlantic Ocean is acting as a barrier to gene flow even in bryophytes adapted to long-range dispersal. The im analysis suggested a relatively recent split of intercontinental populations dating back to the last two glacial periods (9000-289,000 years ago). In contrast to previous hypotheses, analyses indicated that both ongoing migration and ancestral polymorphism are important in explaining the intercontinental genetic similarity of peatmoss populations, but their relative contribution varies with species. Migration rates were significantly asymmetric towards America suggesting differential extinction of genotypes on the two continents or invasion of the American continent by European lineages. These results indicate that low genetic divergence of amphi-Atlantic populations is a general pattern across numerous flowering plants and bryophytes. However, in bryophytes, ongoing intercontinental gene flow and retained shared ancestral polymorphism must both be considered to explain the genetic similarity of intercontinental populations.

  10. Study of the effect of the deposition parameters on the structural, electric and optical characteristics of polymorphous silicon films prepared by low frequency PECVD

    Energy Technology Data Exchange (ETDEWEB)

    Moreno, M., E-mail: mmoreno@inaoep.mx [Instituto Nacional de Astrofisica, Optica y Electronica, INAOE, Puebla (Mexico); Torres, A. [Instituto Nacional de Astrofisica, Optica y Electronica, INAOE, Puebla (Mexico); Ambrosio, R. [Universidad Autonoma de Ciudad Juarez, Electrical Deparment, Chihuahua (Mexico); Zuniga, C.; Torres-Rios, A.; Monfil, K.; Rosales, P.; Itzmoyotl, A. [Instituto Nacional de Astrofisica, Optica y Electronica, INAOE, Puebla (Mexico)

    2011-10-25

    In this work we present our results on the deposition and characterization of polymorphous silicon (pm-Si:H) films prepared by low frequency plasma enhanced chemical vapor deposition (LF-PECVD). We have studied the effect of the plasma deposition parameters (as the chamber pressure and gas flow rates of SiH{sub 4} and H{sub 2}) on the structural, electric, and optical characteristics of the films. The temperature dependence of conductivity ({sigma}(T)), activation energy (E{sub a}), optical band gap (E{sub g}) and deposition rate (V{sub d}) were extracted for pm-Si:H films deposited at different pressure values and different gas flow rates. We observed that the chamber pressure is an important parameter that has a significant effect on the electric characteristics, and as well on the morphology of the pm-Si:H films (deduced from atomic force microscopy). It was found an optimal pressure range, in order to produce pm-Si:H films with high E{sub a} and room temperature conductivity, {sigma}{sub RT}, which are key parameters for thermal detection applications.

  11. Study of the effect of the deposition parameters on the structural, electric and optical characteristics of polymorphous silicon films prepared by low frequency PECVD

    International Nuclear Information System (INIS)

    Moreno, M.; Torres, A.; Ambrosio, R.; Zuniga, C.; Torres-Rios, A.; Monfil, K.; Rosales, P.; Itzmoyotl, A.

    2011-01-01

    In this work we present our results on the deposition and characterization of polymorphous silicon (pm-Si:H) films prepared by low frequency plasma enhanced chemical vapor deposition (LF-PECVD). We have studied the effect of the plasma deposition parameters (as the chamber pressure and gas flow rates of SiH 4 and H 2 ) on the structural, electric, and optical characteristics of the films. The temperature dependence of conductivity (σ(T)), activation energy (E a ), optical band gap (E g ) and deposition rate (V d ) were extracted for pm-Si:H films deposited at different pressure values and different gas flow rates. We observed that the chamber pressure is an important parameter that has a significant effect on the electric characteristics, and as well on the morphology of the pm-Si:H films (deduced from atomic force microscopy). It was found an optimal pressure range, in order to produce pm-Si:H films with high E a and room temperature conductivity, σ RT , which are key parameters for thermal detection applications.

  12. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata

    Directory of Open Access Journals (Sweden)

    Meghann K. Devlin-Durante

    2017-11-01

    Full Text Available The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata, to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  13. Genome-wide survey of single-nucleotide polymorphisms reveals fine-scale population structure and signs of selection in the threatened Caribbean elkhorn coral, Acropora palmata.

    Science.gov (United States)

    Devlin-Durante, Meghann K; Baums, Iliana B

    2017-01-01

    The advent of next-generation sequencing tools has made it possible to conduct fine-scale surveys of population differentiation and genome-wide scans for signatures of selection in non-model organisms. Such surveys are of particular importance in sharply declining coral species, since knowledge of population boundaries and signs of local adaptation can inform restoration and conservation efforts. Here, we use genome-wide surveys of single-nucleotide polymorphisms in the threatened Caribbean elkhorn coral, Acropora palmata , to reveal fine-scale population structure and infer the major barrier to gene flow that separates the eastern and western Caribbean populations between the Bahamas and Puerto Rico. The exact location of this break had been subject to discussion because two previous studies based on microsatellite data had come to differing conclusions. We investigate this contradiction by analyzing an extended set of 11 microsatellite markers including the five previously employed and discovered that one of the original microsatellite loci is apparently under selection. Exclusion of this locus reconciles the results from the SNP and the microsatellite datasets. Scans for outlier loci in the SNP data detected 13 candidate loci under positive selection, however there was no correlation between available environmental parameters and genetic distance. Together, these results suggest that reef restoration efforts should use local sources and utilize existing functional variation among geographic regions in ex situ crossing experiments to improve stress resistance of this species.

  14. Structural impact detection with vibro-haptic interfaces

    Science.gov (United States)

    Jung, Hwee-Kwon; Park, Gyuhae; Todd, Michael D.

    2016-07-01

    This paper presents a new sensing paradigm for structural impact detection using vibro-haptic interfaces. The goal of this study is to allow humans to ‘feel’ structural responses (impact, shape changes, and damage) and eventually determine health conditions of a structure. The target applications for this study are aerospace structures, in particular, airplane wings. Both hardware and software components are developed to realize the vibro-haptic-based impact detection system. First, L-shape piezoelectric sensor arrays are deployed to measure the acoustic emission data generated by impacts on a wing. Unique haptic signals are then generated by processing the measured acoustic emission data. These haptic signals are wirelessly transmitted to human arms, and with vibro-haptic interface, human pilots could identify impact location, intensity and possibility of subsequent damage initiation. With the haptic interface, the experimental results demonstrate that human could correctly identify such events, while reducing false indications on structural conditions by capitalizing on human’s classification capability. Several important aspects of this study, including development of haptic interfaces, design of optimal human training strategies, and extension of the haptic capability into structural impact detection are summarized in this paper.

  15. Laser-based structural sensing and surface damage detection

    Science.gov (United States)

    Guldur, Burcu

    Damage due to age or accumulated damage from hazards on existing structures poses a worldwide problem. In order to evaluate the current status of aging, deteriorating and damaged structures, it is vital to accurately assess the present conditions. It is possible to capture the in situ condition of structures by using laser scanners that create dense three-dimensional point clouds. This research investigates the use of high resolution three-dimensional terrestrial laser scanners with image capturing abilities as tools to capture geometric range data of complex scenes for structural engineering applications. Laser scanning technology is continuously improving, with commonly available scanners now capturing over 1,000,000 texture-mapped points per second with an accuracy of ~2 mm. However, automatically extracting meaningful information from point clouds remains a challenge, and the current state-of-the-art requires significant user interaction. The first objective of this research is to use widely accepted point cloud processing steps such as registration, feature extraction, segmentation, surface fitting and object detection to divide laser scanner data into meaningful object clusters and then apply several damage detection methods to these clusters. This required establishing a process for extracting important information from raw laser-scanned data sets such as the location, orientation and size of objects in a scanned region, and location of damaged regions on a structure. For this purpose, first a methodology for processing range data to identify objects in a scene is presented and then, once the objects from model library are correctly detected and fitted into the captured point cloud, these fitted objects are compared with the as-is point cloud of the investigated object to locate defects on the structure. The algorithms are demonstrated on synthetic scenes and validated on range data collected from test specimens and test-bed bridges. The second objective of

  16. Nonlinear structural damage detection using support vector machines

    Science.gov (United States)

    Xiao, Li; Qu, Wenzhong

    2012-04-01

    An actual structure including connections and interfaces may exist nonlinear. Because of many complicated problems about nonlinear structural health monitoring (SHM), relatively little progress have been made in this aspect. Statistical pattern recognition techniques have been demonstrated to be competitive with other methods when applied to real engineering datasets. When a structure existing 'breathing' cracks that open and close under operational loading may cause a linear structural system to respond to its operational and environmental loads in a nonlinear manner nonlinear. In this paper, a vibration-based structural health monitoring when the structure exists cracks is investigated with autoregressive support vector machine (AR-SVM). Vibration experiments are carried out with a model frame. Time-series data in different cases such as: initial linear structure; linear structure with mass changed; nonlinear structure; nonlinear structure with mass changed are acquired.AR model of acceleration time-series is established, and different kernel function types and corresponding parameters are chosen and compared, which can more accurate, more effectively locate the damage. Different cases damaged states and different damage positions have been recognized successfully. AR-SVM method for the insufficient training samples is proved to be practical and efficient on structure nonlinear damage detection.

  17. Nonlinear damage detection in composite structures using bispectral analysis

    Science.gov (United States)

    Ciampa, Francesco; Pickering, Simon; Scarselli, Gennaro; Meo, Michele

    2014-03-01

    Literature offers a quantitative number of diagnostic methods that can continuously provide detailed information of the material defects and damages in aerospace and civil engineering applications. Indeed, low velocity impact damages can considerably degrade the integrity of structural components and, if not detected, they can result in catastrophic failure conditions. This paper presents a nonlinear Structural Health Monitoring (SHM) method, based on ultrasonic guided waves (GW), for the detection of the nonlinear signature in a damaged composite structure. The proposed technique, based on a bispectral analysis of ultrasonic input waveforms, allows for the evaluation of the nonlinear response due to the presence of cracks and delaminations. Indeed, such a methodology was used to characterize the nonlinear behaviour of the structure, by exploiting the frequency mixing of the original waveform acquired from a sparse array of sensors. The robustness of bispectral analysis was experimentally demonstrated on a damaged carbon fibre reinforce plastic (CFRP) composite panel, and the nonlinear source was retrieved with a high level of accuracy. Unlike other linear and nonlinear ultrasonic methods for damage detection, this methodology does not require any baseline with the undamaged structure for the evaluation of the nonlinear source, nor a priori knowledge of the mechanical properties of the specimen. Moreover, bispectral analysis can be considered as a nonlinear elastic wave spectroscopy (NEWS) technique for materials showing either classical or non-classical nonlinear behaviour.

  18. a Probabilistic Embedding Clustering Method for Urban Structure Detection

    Science.gov (United States)

    Lin, X.; Li, H.; Zhang, Y.; Gao, L.; Zhao, L.; Deng, M.

    2017-09-01

    Urban structure detection is a basic task in urban geography. Clustering is a core technology to detect the patterns of urban spatial structure, urban functional region, and so on. In big data era, diverse urban sensing datasets recording information like human behaviour and human social activity, suffer from complexity in high dimension and high noise. And unfortunately, the state-of-the-art clustering methods does not handle the problem with high dimension and high noise issues concurrently. In this paper, a probabilistic embedding clustering method is proposed. Firstly, we come up with a Probabilistic Embedding Model (PEM) to find latent features from high dimensional urban sensing data by "learning" via probabilistic model. By latent features, we could catch essential features hidden in high dimensional data known as patterns; with the probabilistic model, we can also reduce uncertainty caused by high noise. Secondly, through tuning the parameters, our model could discover two kinds of urban structure, the homophily and structural equivalence, which means communities with intensive interaction or in the same roles in urban structure. We evaluated the performance of our model by conducting experiments on real-world data and experiments with real data in Shanghai (China) proved that our method could discover two kinds of urban structure, the homophily and structural equivalence, which means clustering community with intensive interaction or under the same roles in urban space.

  19. A PROBABILISTIC EMBEDDING CLUSTERING METHOD FOR URBAN STRUCTURE DETECTION

    Directory of Open Access Journals (Sweden)

    X. Lin

    2017-09-01

    Full Text Available Urban structure detection is a basic task in urban geography. Clustering is a core technology to detect the patterns of urban spatial structure, urban functional region, and so on. In big data era, diverse urban sensing datasets recording information like human behaviour and human social activity, suffer from complexity in high dimension and high noise. And unfortunately, the state-of-the-art clustering methods does not handle the problem with high dimension and high noise issues concurrently. In this paper, a probabilistic embedding clustering method is proposed. Firstly, we come up with a Probabilistic Embedding Model (PEM to find latent features from high dimensional urban sensing data by “learning” via probabilistic model. By latent features, we could catch essential features hidden in high dimensional data known as patterns; with the probabilistic model, we can also reduce uncertainty caused by high noise. Secondly, through tuning the parameters, our model could discover two kinds of urban structure, the homophily and structural equivalence, which means communities with intensive interaction or in the same roles in urban structure. We evaluated the performance of our model by conducting experiments on real-world data and experiments with real data in Shanghai (China proved that our method could discover two kinds of urban structure, the homophily and structural equivalence, which means clustering community with intensive interaction or under the same roles in urban space.

  20. Family Polymorphism

    DEFF Research Database (Denmark)

    Ernst, Erik

    2001-01-01

    safety and flexibility at the level of multi-object systems. We are granted the flexibility of using different families of kinds of objects, and we are guaranteed the safety of the combination. This paper highlights the inability of traditional polymorphism to handle multiple objects, and presents family...... polymorphism as a way to overcome this problem. Family polymorphism has been implemented in the programming language gbeta, a generalized version of Beta, and the source code of this implementation is available under GPL....

  1. Investigation on the thermographic detection of corrosion in RC structures

    Science.gov (United States)

    Tantele, Elia A.; Votsis, Renos A.; Kyriakides, Nicholas; Georgiou, Panagiota G.; Ioannou, Fotia G.

    2017-09-01

    Corrosion of the steel reinforcement is the main problem of reinforced concrete (RC) structures. Over the past decades, several methods have been developed aiming to detect the corrosion process early in order to minimise the structural damage and consequently the repairing costs. Emphasis was given in developing methods and techniques of non-destructive nature providing fast on-the-spot detection and covering large areas rather that concentrating on single locations. This study, investigates a non-destructive corrosion detection technique for reinforced concrete, which is based on infrared thermography and the difference in thermal characteristics of corroded and non-corroded steel rebars. The technique is based on the principle that corrosion products have poor heat conductivity, and they inhibit the diffusion of heat that is generated in the reinforcing bar due to heating. For the investigation RC specimens, have been constructed in the laboratory using embedded steel bars of different corrosion states. Afterward, one surface of the specimens was heated using an electric device while thermal images were captured at predefined time instants on the opposite surface with an IR camera. The test results showed a clear difference between the thermal characteristics of the corroded and the non-corroded samples, which demonstrates the potential of using thermography in corrosion detection in RC structures.

  2. Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique.

    Science.gov (United States)

    Xiong, L Z; Xu, C G; Saghai Maroof, M A; Zhang, Q

    1999-04-01

    DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. In this study, we assessed the extent and pattern of cytosine methylation in the rice genome, using the technique of methylation-sensitive amplified polymorphism (MSAP), which is a modification of the amplified fragment length polymorphism (AFLP) method that makes use of the differential sensitivity of a pair of isoschizomers to cytosine methylation. The tissues assayed included seedlings and flag leaves of an elite rice hybrid, Shanyou 63, and the parental lines Zhenshan 97 and Minghui 63. In all, 1076 fragments, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified using 16 pairs of selective primers. A total of 195 sites were found to be methylated at cytosines in one or both parents, and the two parents showed approximately the same overall degree of methylation (16.3%), as revealed by the incidence of differential digestion by the isoschizomers. Four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrid; increased methylation was detected in the hybrid compared to the parents at some of the recognition sites, while decreased methylation in the hybrid was detected at other sites. A small proportion of the sites was found to be differentially methylated in seedlings and flag leaves; DNA from young seedlings was methylated to a greater extent than that from flag leaves. Almost all of the methylation patterns detected by MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrate that the MSAP technique is highly efficient for large-scale detection of cytosine methylation in the rice genome. We believe that the technique can be adapted for use in other plant species.

  3. The changing face of glucagon fibrillation: Structural polymorphism and conformational imprinting

    DEFF Research Database (Denmark)

    Pedersen, J.S.; Dikov, D.; Flink, J.L.

    2006-01-01

    concentration) appear less thermostable than those formed under more challenging conditions (high temperatures, low glucagon or low salt concentrations). Properties of preformed fibrils used for seeding are inherited in a prion-like manner. Thus, we conclude that the structure of fibrils formed by glucagon...

  4. Metabolic Polymorphisms and Clinical Findings Related to Benzene Poisoning Detected in Exposed Brazilian Gas-Station Workers

    Directory of Open Access Journals (Sweden)

    Simone Mitri

    2015-07-01

    Full Text Available Benzene is a ubiquitous environmental pollutant and an important industrial chemical present in both gasoline and motor vehicle emissions. Occupational human exposure to benzene occurs in the petrochemical and petroleum refining industries as well as in gas-station workers, where it can lead to benzene poisoning (BP, but the mechanisms of BP are not completely understood. In Brazil, a significant number of gas-station service workers are employed. The aim of the present study was to evaluate alterations related to BP and metabolic polymorphisms in gas-station service workers exposed to benzene in the city of Rio de Janeiro, Brazil. Occupational exposure was based on clinical findings related to BP, and metabolic polymorphisms in 114 Brazilian gas-station attendants. These workers were divided into No Clinical Findings (NCF and Clinical Findings (CF groups. Neutrophil and Mean Corpuscular Volume (MCV showed a significant difference between the two study groups, and neutrophil has the greatest impact on the alterations suggestive of BP. The clinical findings revealed higher frequencies of symptoms in the CF group, although not all members presented statistical significance. The frequencies of alleles related to risk were higher in the CF group for GSTM1, GSTT1, CYP2E1 7632T > A, but lower for NQO1 and CYP2E1 1053C > T genotypes. Moreover, an association was found between GSTM1 null and alterations related to BP, but we did not observe any effects of other polymorphisms. Variations in benzene metabolizing genes may modify benzene toxicity and should be taken into consideration during risk assessment evaluations.

  5. Fast Detection of Material Deformation through Structural Dissimilarity

    Energy Technology Data Exchange (ETDEWEB)

    Ushizima, Daniela; Perciano, Talita; Parkinson, Dilworth

    2015-10-29

    Designing materials that are resistant to extreme temperatures and brittleness relies on assessing structural dynamics of samples. Algorithms are critically important to characterize material deformation under stress conditions. Here, we report on our design of coarse-grain parallel algorithms for image quality assessment based on structural information and on crack detection of gigabyte-scale experimental datasets. We show how key steps can be decomposed into distinct processing flows, one based on structural similarity (SSIM) quality measure, and another on spectral content. These algorithms act upon image blocks that fit into memory, and can execute independently. We discuss the scientific relevance of the problem, key developments, and decomposition of complementary tasks into separate executions. We show how to apply SSIM to detect material degradation, and illustrate how this metric can be allied to spectral analysis for structure probing, while using tiled multi-resolution pyramids stored in HDF5 chunked multi-dimensional arrays. Results show that the proposed experimental data representation supports an average compression rate of 10X, and data compression scales linearly with the data size. We also illustrate how to correlate SSIM to crack formation, and how to use our numerical schemes to enable fast detection of deformation from 3D datasets evolving in time.

  6. [Structure of the gene pool of ethnic groups from the Altai-Sayan region from data on mitochondrial polymorphism].

    Science.gov (United States)

    Derenko, M V; Denisova, G A; Maliarchuk, B A; Dambueva, I K; Luzina, F A; Lotosh, E A; Dorzhu, Ch M; Karamchakova, O N; Solovenchuk, L L; Zakharov, I A

    2001-10-01

    Using the data on mitochondrial DNA (mtDNA) polymorphism, genetic structures of the four Turkic-speaking ethnic groups of Altai-Sayan highlands, Southern Altaians (Altai-Kizhi), Khakassians, Shorians, and Sojots, were described. Mitochondrial gene pools of the populations examined were characterized by different ratios between Mongoloid (M*, C, D, E, G, A, B, and F) and Caucasoid (H, U, T, J, and K) mtDNA lineages. All the populations studied had a strongly pronounced Mongoloid component, the frequency of which was 88.2% in Sojots, 75.9% in Khakassians, 67.4% in Altaians, and 64.3% in Shorians. Maximum frequency of the Caucasoid component (35.7%) was observed in Shorians. Phylogenetic and statistical analyses of the mtDNA group frequency distribution patterns in the gene pools of the ethnic populations of Altai-Sayan highlands and the adjacent territories showed that the populations of the region fell into three groups. The first group included Khakassians, Tuvinians and Altaians, the second group consisted of Sojots, Buryats, and Mongols, while the third group was composed of Uigurs, Kazakhs, and Kyrgyzes. The isolated position of Shorians among the populations examined can be explained by their different anthropological composition and their presumptive relatedness to Finno-Ugric populations of Siberia.

  7. Crystal structure of a new monoclinic polymorph of N-(4-methyl-phen-yl)-3-nitro-pyridin-2-amine.

    Science.gov (United States)

    Aznan, Aina Mardia Akhmad; Abdullah, Zanariah; Lee, Vannajan Sanghiran; Tiekink, Edward R T

    2014-08-01

    The title compound, C12H11N3O2, is a second monoclinic polymorph (P21, with Z' = 4) of the previously reported monoclinic (P21/c, with Z' = 2) form [Akhmad Aznan et al. (2010 ▶). Acta Cryst. E66, o2400]. Four independent mol-ecules comprise the asymmetric unit, which have the common features of a syn disposition of the pyridine N atom and the toluene ring, and an intra-molecular amine-nitro N-H⋯O hydrogen bond. The differences between mol-ecules relate to the dihedral angles between the rings which range from 2.92 (19) to 26.24 (19)°. The geometry-optimized structure [B3LYP level of theory and 6-311 g+(d,p) basis set] has the same features except that the entire mol-ecule is planar. In the crystal, the three-dimensional architecture is consolidated by a combination of C-H⋯O, C-H⋯π, nitro-N-O⋯π and π-π inter-actions [inter-centroid distances = 3.649 (2)-3.916 (2) Å].

  8. Polymorphism in Self-Assembled Structures of 9-Anthracene Carboxylic Acid on Ag(111

    Directory of Open Access Journals (Sweden)

    Bo Xu

    2012-06-01

    Full Text Available Surface self-assembly process of 9-anthracene carboxylic acid (AnCA on Ag(111 was investigated using STM. Depending on the molecular surface density, four spontaneously formed and one annealed AnCA ordered phases were observed, namely a straight belt phase, a zigzag double-belt phase, two simpler dimer phases, and a kagome phase. The two high-density belt phases possess large unit cells on the scale length of 10 nm, which are seldom observed in molecular self-assembled structures. This structural diversity stems from a complicated competition of different interactions of AnCA molecules on metal surface, including intermolecular and molecular-substrate interactions, as well as the steric demand from high molecular surface density.

  9. Electromigration and Deposition of Micro-Scale Calcium Carbonate Structures with Controlled Morphology and Polymorphism

    Science.gov (United States)

    2013-04-01

    precipitation of calcium carbonate in structured templates including microporous polycarbonate membranes and polyethylene foams. Para- meters...polyethylene foam). Microporous polycarbonate membranes and Medium-Density PolyEthylene (MDPE) foam specimens were used as the porous organic...voids in hardened concrete. DOI:10.1520/C624-06. West Conshohocken, PA: ASTM International . www.astm.org. Bersa, L., and M. Liu. 2007. A review on

  10. Structural Polymorphism in a Self-Assembled Tri-Aromatic Peptide System.

    Science.gov (United States)

    Brown, Noam; Lei, Jiangtao; Zhan, Chendi; Shimon, Linda J W; Adler-Abramovich, Lihi; Wei, Guanghong; Gazit, Ehud

    2018-04-24

    Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.

  11. In Situ Polymorphic Alteration of Filler Structures for Biomimetic Mechanically Adaptive Elastomer Nanocomposites.

    Science.gov (United States)

    Natarajan, Tamil Selvan; Okamoto, Shigeru; Stöckelhuber, Klaus Werner; Wießner, Sven; Reuter, Uta; Fischer, Dieter; Ghosh, Anik Kumar; Heinrich, Gert; Das, Amit

    2018-04-30

    A mechanically adaptable elastomer composite is prepared with reversible soft-stiff properties that can be easily controlled. By the exploitation of different morphological structures of calcium sulfate, which acts as the active filler in a soft elastomer matrix, the magnitude of filler reinforcement can be reversibly altered, which will be reflected in changes of the final stiffness of the material. The higher stiffness, in other words, the higher modulus of the composites, is realized by the in situ development of fine nanostructured calcium sulfate dihydrate crystals, which are formed during exposure to water and, further, these highly reinforcing crystals can be transformed to a nonreinforcing hemihydrate mesocrystalline structure by simply heating the system in a controlled way. The Young's modulus of the developed material can be reversibly altered from ∼6 to ∼17 MPa, and the dynamic stiffness (storage modulus at room temperature and 10 Hz frequency) alters its value in the order of 1000%. As the transformation is related to the presence of water molecules in the crystallites, a hydrophilic elastomer matrix was selected, which is a blend of two hydrophilic polymers, namely, epichlorohydrin-ethylene oxide-allyl glycidyl ether terpolymer and a terpolymer of ethylene oxide-propylene oxide-allyl glycidyl ether. For the first time, this method also provides a route to regulate the morphology and structure of calcium sulfate nanocrystals in a confined ambient of cross-linked polymer chains.

  12. Agglomerative concentric hypersphere clustering applied to structural damage detection

    Science.gov (United States)

    Silva, Moisés; Santos, Adam; Santos, Reginaldo; Figueiredo, Eloi; Sales, Claudomiro; Costa, João C. W. A.

    2017-08-01

    The present paper proposes a novel cluster-based method, named as agglomerative concentric hypersphere (ACH), to detect structural damage in engineering structures. Continuous structural monitoring systems often require unsupervised approaches to automatically infer the health condition of a structure. However, when a structure is under linear and nonlinear effects caused by environmental and operational variability, data normalization procedures are also required to overcome these effects. The proposed approach aims, through a straightforward clustering procedure, to discover automatically the optimal number of clusters, representing the main state conditions of a structural system. Three initialization procedures are introduced to evaluate the impact of deterministic and stochastic initializations on the performance of this approach. The ACH is compared to state-of-the-art approaches, based on Gaussian mixture models and Mahalanobis squared distance, on standard data sets from a post-tensioned bridge located in Switzerland: the Z-24 Bridge. The proposed approach demonstrates more efficiency in modeling the normal condition of the structure and its corresponding main clusters. Furthermore, it reveals a better classification performance than the alternative ones in terms of false-positive and false-negative indications of damage, demonstrating a promising applicability in real-world structural health monitoring scenarios.

  13. Apparatus and method for detecting tampering in flexible structures

    Science.gov (United States)

    Maxey, Lonnie C [Knoxville, TN; Haynes, Howard D [Knoxville, TN

    2011-02-01

    A system for monitoring or detecting tampering in a flexible structure includes taking electrical measurements on a sensing cable coupled to the structure, performing spectral analysis on the measured data, and comparing the spectral characteristics of the event to those of known benign and/or known suspicious events. A threshold or trigger value may used to identify an event of interest and initiate data collection. Alternatively, the system may be triggered at preset intervals, triggered manually, or triggered by a signal from another sensing device such as a motion detector. The system may be used to monitor electrical cables and conduits, hoses and flexible ducts, fences and other perimeter control devices, structural cables, flexible fabrics, and other flexible structures.

  14. Network structure detection and analysis of Shanghai stock market

    Directory of Open Access Journals (Sweden)

    Sen Wu

    2015-04-01

    Full Text Available Purpose: In order to investigate community structure of the component stocks of SSE (Shanghai Stock Exchange 180-index, a stock correlation network is built to find the intra-community and inter-community relationship. Design/methodology/approach: The stock correlation network is built taking the vertices as stocks and edges as correlation coefficients of logarithm returns of stock price. It is built as undirected weighted at first. GN algorithm is selected to detect community structure after transferring the network into un-weighted with different thresholds. Findings: The result of the network community structure analysis shows that the stock market has obvious industrial characteristics. Most of the stocks in the same industry or in the same supply chain are assigned to the same community. The correlation of the internal stock prices’ fluctuation is closer than in different communities. The result of community structure detection also reflects correlations among different industries. Originality/value: Based on the analysis of the community structure in Shanghai stock market, the result reflects some industrial characteristics, which has reference value to relationship among industries or sub-sectors of listed companies.

  15. Detection of electromagnetic radiation using micromechanical multiple quantum wells structures

    Science.gov (United States)

    Datskos, Panagiotis G [Knoxville, TN; Rajic, Slobodan [Knoxville, TN; Datskou, Irene [Knoxville, TN

    2007-07-17

    An apparatus and method for detecting electromagnetic radiation employs a deflectable micromechanical apparatus incorporating multiple quantum wells structures. When photons strike the quantum-well structure, physical stresses are created within the sensor, similar to a "bimetallic effect." The stresses cause the sensor to bend. The extent of deflection of the sensor can be measured through any of a variety of conventional means to provide a measurement of the photons striking the sensor. A large number of such sensors can be arranged in a two-dimensional array to provide imaging capability.

  16. Evaluation of feature detection algorithms for structure from motion

    CSIR Research Space (South Africa)

    Govender, N

    2009-11-01

    Full Text Available technique with an application to stereo vision,” in International Joint Conference on Artificial Intelligence, April 1981. [17] C.Tomasi and T.Kanade, “Detection and tracking of point fetaures,” Carnegie Mellon, Tech. Rep., April 1991. [18] P. Torr... Algorithms for Structure from Motion Natasha Govender Mobile Intelligent Autonomous Systems CSIR Pretoria Email: ngovender@csir.co.za Abstract—Structure from motion is a widely-used technique in computer vision to perform 3D reconstruction. The 3D...

  17. Printed strain sensors for early damage detection in engineering structures

    Science.gov (United States)

    Zymelka, Daniel; Yamashita, Takahiro; Takamatsu, Seiichi; Itoh, Toshihiro; Kobayashi, Takeshi

    2018-05-01

    In this paper, we demonstrate the analysis of strain measurements recorded using a screen-printed sensors array bonded to a metal plate and subjected to high strains. The analysis was intended to evaluate the capabilities of the printed strain sensors to detect abnormal strain distribution before actual defects (cracks) in the analyzed structures appear. The results demonstrate that the developed device can accurately localize the enhanced strains at the very early stage of crack formation. The promising performance and low fabrication cost confirm the potential suitability of the printed strain sensors for applications within the framework of structural health monitoring (SHM).

  18. Graph-based structural change detection for rotating machinery monitoring

    Science.gov (United States)

    Lu, Guoliang; Liu, Jie; Yan, Peng

    2018-01-01

    Detection of structural changes is critically important in operational monitoring of a rotating machine. This paper presents a novel framework for this purpose, where a graph model for data modeling is adopted to represent/capture statistical dynamics in machine operations. Meanwhile we develop a numerical method for computing temporal anomalies in the constructed graphs. The martingale-test method is employed for the change detection when making decisions on possible structural changes, where excellent performance is demonstrated outperforming exciting results such as the autoregressive-integrated-moving average (ARIMA) model. Comprehensive experimental results indicate good potentials of the proposed algorithm in various engineering applications. This work is an extension of a recent result (Lu et al., 2017).

  19. How does structured sparsity work in abnormal event detection?

    DEFF Research Database (Denmark)

    Ren, Huamin; Pan, Hong; Olsen, Søren Ingvor

    the training, which is the due to the fact that abnormal videos are limited or even unavailable in advance in most video surveillance applications. As a result, there could be only one label in the training data which hampers supervised learning; 2) Even though there are multiple types of normal behaviors, how...... many normal patterns lie in the whole surveillance data is still unknown. This is because there is huge amount of video surveillance data and only a small proportion is used in algorithm learning, consequently, the normal patterns in the training data could be incomplete. As a result, any sparse...... structure learned from the training data could have a high bias and ruin the precision of abnormal event detection. Therefore, we in the paper propose an algorithm to solve the abnormality detection problem by sparse representation, in which local structured sparsity is preserved in coefficients. To better...

  20. Detecting structural breaks in time series via genetic algorithms

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Fischer, Paul; Hilbert, Astrid

    2016-01-01

    of the time series under consideration is available. Therefore, a black-box optimization approach is our method of choice for detecting structural breaks. We describe a genetic algorithm framework which easily adapts to a large number of statistical settings. To evaluate the usefulness of different crossover...... and mutation operations for this problem, we conduct extensive experiments to determine good choices for the parameters and operators of the genetic algorithm. One surprising observation is that use of uniform and one-point crossover together gave significantly better results than using either crossover...... operator alone. Moreover, we present a specific fitness function which exploits the sparse structure of the break points and which can be evaluated particularly efficiently. The experiments on artificial and real-world time series show that the resulting algorithm detects break points with high precision...

  1. Role of sequence and structural polymorphism on the mechanical properties of amyloid fibrils.

    Directory of Open Access Journals (Sweden)

    Gwonchan Yoon

    Full Text Available Amyloid fibrils playing a critical role in disease expression, have recently been found to exhibit the excellent mechanical properties such as elastic modulus in the order of 10 GPa, which is comparable to that of other mechanical proteins such as microtubule, actin filament, and spider silk. These remarkable mechanical properties of amyloid fibrils are correlated with their functional role in disease expression. This suggests the importance in understanding how these excellent mechanical properties are originated through self-assembly process that may depend on the amino acid sequence. However, the sequence-structure-property relationship of amyloid fibrils has not been fully understood yet. In this work, we characterize the mechanical properties of human islet amyloid polypeptide (hIAPP fibrils with respect to their molecular structures as well as their amino acid sequence by using all-atom explicit water molecular dynamics (MD simulation. The simulation result suggests that the remarkable bending rigidity of amyloid fibrils can be achieved through a specific self-aggregation pattern such as antiparallel stacking of β strands (peptide chain. Moreover, we have shown that a single point mutation of hIAPP chain constituting a hIAPP fibril significantly affects the thermodynamic stability of hIAPP fibril formed by parallel stacking of peptide chain, and that a single point mutation results in a significant change in the bending rigidity of hIAPP fibrils formed by antiparallel stacking of β strands. This clearly elucidates the role of amino acid sequence on not only the equilibrium conformations of amyloid fibrils but also their mechanical properties. Our study sheds light on sequence-structure-property relationships of amyloid fibrils, which suggests that the mechanical properties of amyloid fibrils are encoded in their sequence-dependent molecular architecture.

  2. Detecting highly overlapping community structure by greedy clique expansion

    OpenAIRE

    Lee, Conrad; Reid, Fergal; McDaid, Aaron; Hurley, Neil

    2010-01-01

    In complex networks it is common for each node to belong to several communities, implying a highly overlapping community structure. Recent advances in benchmarking indicate that existing community assignment algorithms that are capable of detecting overlapping communities perform well only when the extent of community overlap is kept to modest levels. To overcome this limitation, we introduce a new community assignment algorithm called Greedy Clique Expansion (GCE). The algorithm identifies d...

  3. Convolution neural-network-based detection of lung structures

    Science.gov (United States)

    Hasegawa, Akira; Lo, Shih-Chung B.; Freedman, Matthew T.; Mun, Seong K.

    1994-05-01

    Chest radiography is one of the most primary and widely used techniques in diagnostic imaging. Nowadays with the advent of digital radiology, the digital medical image processing techniques for digital chest radiographs have attracted considerable attention, and several studies on the computer-aided diagnosis (CADx) as well as on the conventional image processing techniques for chest radiographs have been reported. In the automatic diagnostic process for chest radiographs, it is important to outline the areas of the lungs, the heart, and the diaphragm. This is because the original chest radiograph is composed of important anatomic structures and, without knowing exact positions of the organs, the automatic diagnosis may result in unexpected detections. The automatic extraction of an anatomical structure from digital chest radiographs can be a useful tool for (1) the evaluation of heart size, (2) automatic detection of interstitial lung diseases, (3) automatic detection of lung nodules, and (4) data compression, etc. Based on the clearly defined boundaries of heart area, rib spaces, rib positions, and rib cage extracted, one should be able to use this information to facilitate the tasks of the CADx on chest radiographs. In this paper, we present an automatic scheme for the detection of lung field from chest radiographs by using a shift-invariant convolution neural network. A novel algorithm for smoothing boundaries of lungs is also presented.

  4. Oxytocin receptor polymorphism and childhood social experiences shape adult personality, brain structure and neural correlates of mentalizing.

    Science.gov (United States)

    Schneider-Hassloff, H; Straube, B; Jansen, A; Nuscheler, B; Wemken, G; Witt, S H; Rietschel, M; Kircher, T

    2016-07-01

    The oxytocin system is involved in human social behavior and social cognition such as attachment, emotion recognition and mentalizing (i.e. the ability to represent mental states of oneself and others). It is shaped by social experiences in early life, especially by parent-infant interactions. The single nucleotid polymorphism rs53576 in the oxytocin receptor (OXTR) gene has been linked to social behavioral phenotypes. In 195 adult healthy subjects we investigated the interaction of OXTR rs53576 and childhood attachment security (CAS) on the personality traits "adult attachment style" and "alexithymia" (i.e. emotional self-awareness), on brain structure (voxel-based morphometry) and neural activation (fMRI) during an interactive mentalizing paradigm (prisoner's dilemma game; subgroup: n=163). We found that in GG-homozygotes, but not in A-allele carriers, insecure childhood attachment is - in adulthood - associated with a) higher attachment-related anxiety and alexithymia, b) higher brain gray matter volume of left amygdala and lower volumes in right superior parietal lobule (SPL), left temporal pole (TP), and bilateral frontal regions, and c) higher mentalizing-related neural activity in bilateral TP and precunei, and right middle and superior frontal gyri. Interaction effects of genotype and CAS on brain volume and/or function were associated with individual differences in alexithymia and attachment-related anxiety. Interactive effects were in part sexually dimorphic. The interaction of OXTR genotype and CAS modulates adult personality as well as brain structure and function of areas implicated in salience processing and mentalizing. Rs53576 GG-homozygotes are partially more susceptible to childhood attachment experiences than A-allele carriers. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Damage detection in concrete structures with smart piezoceramic transducers

    Science.gov (United States)

    Naidu, Akshay S. K.; Bhalla, Suresh

    2003-10-01

    Detection of damages and progressive deterioration in structures is a critical issue. Visual inspections are tedious and unreliable. Incipient damages are often not discernible by low frequency dynamic response and other NDE techniques. Smart piezoelectric ceramic (PZT) transducers are emerging as an effective alternative in health monitoring of structures. The electro-mechanical impedance method employs the self-actuating and sensing characteristics of the PZT, without having to use actuators and sensors separately. When excited by an ac source, the PZT transducers bonded to the host structure activates the higher modes of vibration locally. Changes in the admittance response of the transducer serves as an indicator of damage around the transducer. In this paper, the effectiveness of PZT transducers for characterizing damages in concrete, in terms of the damage extent and location, is experimentally examined. The root mean square deviation (RMSD) index, adopted to quantify the changes in the admittance signatures, correlates with the damage extent. The damages on the surface that is not mounted by the PZT are also discernible. An array of transducers proves effective in detecting the damaged zone. The progressive incipient crack can be detected much before it actually becomes visible to the naked eye.

  6. Development and validation of cross-transferable and polymorphic DNA markers for detecting alien genome introgression in Oryza sativa from Oryza brachyantha.

    Science.gov (United States)

    Ray, Soham; Bose, Lotan K; Ray, Joshitha; Ngangkham, Umakanta; Katara, Jawahar L; Samantaray, Sanghamitra; Behera, Lambodar; Anumalla, Mahender; Singh, Onkar N; Chen, Meingsheng; Wing, Rod A; Mohapatra, Trilochan

    2016-08-01

    African wild rice Oryza brachyantha (FF), a distant relative of cultivated rice Oryza sativa (AA), carries genes for pests and disease resistance. Molecular marker assisted alien gene introgression from this wild species to its domesticated counterpart is largely impeded due to the scarce availability of cross-transferable and polymorphic molecular markers that can clearly distinguish these two species. Availability of the whole genome sequence (WGS) of both the species provides a unique opportunity to develop markers, which are cross-transferable. We observed poor cross-transferability (~0.75 %) of O. sativa specific sequence tagged microsatellite (STMS) markers to O. brachyantha. By utilizing the genome sequence information, we developed a set of 45 low cost PCR based co-dominant polymorphic markers (STS and CAPS). These markers were found cross-transferrable (84.78 %) between the two species and could distinguish them from each other and thus allowed tracing alien genome introgression. Finally, we validated a Monosomic Alien Addition Line (MAAL) carrying chromosome 1 of O. brachyantha in O. sativa background using these markers, as a proof of concept. Hence, in this study, we have identified a set molecular marker (comprising of STMS, STS and CAPS) that are capable of detecting alien genome introgression from O. brachyantha to O. sativa.

  7. Structural Insight Into the Role of Mutual Polymorphism and Conservatism in the Contact Zone of the NFR5-K1 Heterodimer With the Nod Factor.

    Science.gov (United States)

    Igolkina, A A; Porozov, Yu B; Chizhevskaya, E P; Andronov, E E

    2018-01-01

    Sandwich-like docking configurations of the heterodimeric complex of NFR5 and K1 Vicia sativa receptor-like kinases together with the putative ligand, Nod factor (NF) of Rhizobium leguminosarum bv. viciae , were modeled and two of the most probable configurations were assessed through the analysis of the mutual polymorphisms and conservatism. We carried out this analysis based on the hypothesis that in a contact zone of two docked components (proteins or ligands) the population polymorphism or conservatism is mutual, i.e., the variation in one component has a reflected variation in the other component. The population material of 30 wild-growing V. sativa (leaf pieces) was collected from a large field (uncultivated for the past 25-years) and pooled; form this pool, 100 randomly selected cloned fragments of NFR5 gene and 100 of K1 gene were sequenced by the Sanger method. Congruence between population trees of NFR5 and K1 haplotypes allowed us to select two respective haplotypes, build their 3D structures, and perform protein-protein docking. In a separate simulation, the protein-ligand docking between NFR5 and NF was carried out. We merged the results of the two docking experiments and extracted NFR5-NF-K1 complexes, in which NF was located within the cavity between two receptors. Molecular dynamics simulations indicated two out of six complexes as stable. Regions of mutual polymorphism in the contact zone of one complex overlapped with known NF structural variations produced by R. leguminosarum bv. viciae . A total of 74% of the contact zone of another complex contained mutually polymorphic and conservative areas. Common traits of the obtained two stable structures allowed us to hypothesize the functional role of three-domain structure of plant LysM-RLKs in their heteromers.

  8. Structural Insight Into the Role of Mutual Polymorphism and Conservatism in the Contact Zone of the NFR5–K1 Heterodimer With the Nod Factor

    Directory of Open Access Journals (Sweden)

    A. A. Igolkina

    2018-04-01

    Full Text Available Sandwich-like docking configurations of the heterodimeric complex of NFR5 and K1 Vicia sativa receptor-like kinases together with the putative ligand, Nod factor (NF of Rhizobium leguminosarum bv. viciae, were modeled and two of the most probable configurations were assessed through the analysis of the mutual polymorphisms and conservatism. We carried out this analysis based on the hypothesis that in a contact zone of two docked components (proteins or ligands the population polymorphism or conservatism is mutual, i.e., the variation in one component has a reflected variation in the other component. The population material of 30 wild-growing V. sativa (leaf pieces was collected from a large field (uncultivated for the past 25-years and pooled; form this pool, 100 randomly selected cloned fragments of NFR5 gene and 100 of K1 gene were sequenced by the Sanger method. Congruence between population trees of NFR5 and K1 haplotypes allowed us to select two respective haplotypes, build their 3D structures, and perform protein–protein docking. In a separate simulation, the protein-ligand docking between NFR5 and NF was carried out. We merged the results of the two docking experiments and extracted NFR5–NF–K1 complexes, in which NF was located within the cavity between two receptors. Molecular dynamics simulations indicated two out of six complexes as stable. Regions of mutual polymorphism in the contact zone of one complex overlapped with known NF structural variations produced by R. leguminosarum bv. viciae. A total of 74% of the contact zone of another complex contained mutually polymorphic and conservative areas. Common traits of the obtained two stable structures allowed us to hypothesize the functional role of three-domain structure of plant LysM-RLKs in their heteromers.

  9. Covariance of dynamic strain responses for structural damage detection

    Science.gov (United States)

    Li, X. Y.; Wang, L. X.; Law, S. S.; Nie, Z. H.

    2017-10-01

    A new approach to address the practical problems with condition evaluation/damage detection of structures is proposed based on the distinct features of a new damage index. The covariance of strain response function (CoS) is a function of modal parameters of the structure. A local stiffness reduction in structure would cause monotonous increase in the CoS. Its sensitivity matrix with respect to local damages of structure is negative and narrow-banded. The damage extent can be estimated with an approximation to the sensitivity matrix to decouple the identification equations. The CoS sensitivity can be calibrated in practice from two previous states of measurements to estimate approximately the damage extent of a structure. A seven-storey plane frame structure is numerically studied to illustrate the features of the CoS index and the proposed method. A steel circular arch in the laboratory is tested. Natural frequencies changed due to damage in the arch and the damage occurrence can be judged. However, the proposed CoS method can identify not only damage happening but also location, even damage extent without need of an analytical model. It is promising for structural condition evaluation of selected components.

  10. Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems

    Science.gov (United States)

    2011-01-01

    successfully used for gene identification, polymorphism detection and transcript profiling in alfalfa, a non-model, allogamous, autotetraploid species. The alfalfa gene index assembled in this study, and the SNPs, SSRs and candidate genes identified can be used to improve alfalfa as a forage crop and cellulosic feedstock. PMID:21504589

  11. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.

    Science.gov (United States)

    Bromberg, Yana; Yachdav, Guy; Ofran, Yanay; Schneider, Reinhard; Rost, Burkhard

    2009-05-01

    The rapidly increasing quantity of protein sequence data continues to widen the gap between available sequences and annotations. Comparative modeling suggests some aspects of the 3D structures of approximately half of all known proteins; homology- and network-based inferences annotate some aspect of function for a similar fraction of the proteome. For most known protein sequences, however, there is detailed knowledge about neither their function nor their structure. Comprehensive efforts towards the expert curation of sequence annotations have failed to meet the demand of the rapidly increasing number of available sequences. Only the automated prediction of protein function in the absence of homology can close the gap between available sequences and annotations in the foreseeable future. This review focuses on two novel methods for automated annotation, and briefly presents an outlook on how modern web software may revolutionize the field of protein sequence annotation. First, predictions of protein binding sites and functional hotspots, and the evolution of these into the most successful type of prediction of protein function from sequence will be discussed. Second, a new tool, comprehensive in silico mutagenesis, which contributes important novel predictions of function and at the same time prepares for the onset of the next sequencing revolution, will be described. While these two new sub-fields of protein prediction represent the breakthroughs that have been achieved methodologically, it will then be argued that a different development might further change the way biomedical researchers benefit from annotations: modern web software can connect the worldwide web in any browser with the 'Deep Web' (ie, proprietary data resources). The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation.

  12. Automated detection of repeated structures in building facades

    Directory of Open Access Journals (Sweden)

    M. Previtali

    2013-10-01

    Full Text Available Automatic identification of high-level repeated structures in 3D point clouds of building façades is crucial for applications like digitalization and building modelling. Indeed, in many architectural styles building façades are governed by arrangements of objects into repeated patterns. In particular, façades are generally designed as the repetition of some few basic objects organized into interlaced and\\or concatenated grid structures. Starting from this key observation, this paper presents an algorithm for Repeated Structure Detection (RSD in 3D point clouds of building façades. The presented methodology consists of three main phases. First, in the point cloud segmentation stage (i the building façade is decomposed into planar patches which are classified by means of some weak prior knowledge of urban buildings formulated in a classification tree. Secondly (ii, in the element clustering phase detected patches are grouped together by means of a similarity function and pairwise transformations between patches are computed. Eventually (iii, in the structure regularity estimation step the parameters of repeated grid patterns are calculated by using a Least- Squares optimization. Workability of the presented approach is tested using some real data from urban scenes.

  13. Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction.

    Science.gov (United States)

    Wang, Dingzhong; Tang, Wei; Wu, Xiaojie; Wang, Xinyi; Chen, Gengjia; Chen, Qiang; Li, Na; Liu, Feng

    2012-08-21

    Toehold-mediated strand displacement reaction (SDR) is first introduced to develop a simple quartz crystal microbalance (QCM) biosensor without an enzyme or label at normal temperature for highly selective and sensitive detection of single-nucleotide polymorphism (SNP) in the p53 tumor suppressor gene. A hairpin capture probe with an external toehold is designed and immobilized on the gold electrode surface of QCM. A successive SDR is initiated by the target sequence hybridization with the toehold domain and ends with the unfolding of the capture probe. Finally, the open-loop capture probe hybridizes with the streptavidin-coupled reporter probe as an efficient mass amplifier to enhance the QCM signal. The proposed biosensor displays remarkable specificity to target the p53 gene fragment against single-base mutant sequences (e.g., the largest discrimination factor is 63 to C-C mismatch) and high sensitivity with the detection limit of 0.3 nM at 20 °C. As the crucial component of the fabricated biosensor for providing the high discrimination capability, the design rationale of the capture probe is further verified by fluorescence sensing and atomic force microscopy imaging. Additionally, a recovery of 84.1% is obtained when detecting the target sequence in spiked HeLa cells lysate, demonstrating the feasibility of employing this biosensor in detecting SNPs in biological samples.

  14. A supramolecular structure insight for conversion property of cellulose in hot compressed water: Polymorphs and hydrogen bonds changes.

    Science.gov (United States)

    Wang, Yan; Lian, Jie; Wan, Jinquan; Ma, Yongwen; Zhang, Yingshi

    2015-11-20

    Waste paper samples with different cellulose supramolecular structure were treated in hot compressed water (HCW) at 375°C and 22.5MPa within 200s to evaluate the specific effect mechanism of cellulose supramolecular structure on the conversion of waste paper to reusable resource. Although the distribution of liquid products and the oligosaccharides were related to reaction time, depolymerization and decrystallization of the cellulose, the characteristics absorption peak of cellulose from FTIR analysis and crystal structure of the cellulose detected in the residues with hydrolysis rate up 96.5% indicated crystal structure was the dominant factor that affect conversion behavior of waste paper. The conversion of cellulose Iβ to cellulose Iα or cellulose I(α+β) in HCW demonstrated that the recrystallization occurred during the decrystallization of cellulose through the rearrangement of hydrogen bonds. Copyright © 2015 Elsevier Ltd. All rights reserved.

  15. Genetic structure of Mount Huang honey bee (Apis cerana) populations: evidence from microsatellite polymorphism.

    Science.gov (United States)

    Liu, Fang; Shi, Tengfei; Huang, Sisi; Yu, Linsheng; Bi, Shoudong

    2016-01-01

    The Mount Huang eastern honey bees ( Apis cerana ) are an endemic population, which is well adapted to the local agricultural and ecological environment. In this study, the genetic structure of seven eastern honey bees ( A. cerana ) populations from Mount Huang in China were analyzed by SSR (simple sequence repeat) markers. The results revealed that 16 pairs of primers used amplified a total of 143 alleles. The number of alleles per locus ranged from 6 to 13, with a mean value of 8.94 alleles per locus. Observed and expected heterozygosities showed mean values of 0.446 and 0.831 respectively. UPGMA cluster analysis grouped seven eastern honey bees in three groups. The results obtained show a high genetic diversity in the honey bee populations studied in Mount Huang, and high differentiation among all the populations, suggesting that scarce exchange of honey bee species happened in Mount Huang. Our study demonstrated that the Mount Huang honey bee populations still have a natural genome worth being protected for conservation.

  16. Diabetes Drug Discovery: hIAPP1–37 Polymorphic Amyloid Structures as Novel Therapeutic Targets

    Directory of Open Access Journals (Sweden)

    Isaac Fernández-Gómez

    2018-03-01

    Full Text Available Human islet amyloid peptide (hIAPP1–37 aggregation is an early step in Diabetes Mellitus. We aimed to evaluate a family of pharmaco-chaperones to act as modulators that provide dynamic interventions and the multi-target capacity (native state, cytotoxic oligomers, protofilaments and fibrils of hIAPP1–37 required to meet the treatment challenges of diabetes. We used a cross-functional approach that combines in silico and in vitro biochemical and biophysical methods to study the hIAPP1–37 aggregation-oligomerization process as to reveal novel potential anti-diabetic drugs. The family of pharmaco-chaperones are modulators of the oligomerization and fibre formation of hIAPP1–37. When they interact with the amino acid in the amyloid-like steric zipper zone, they inhibit and/or delay the aggregation-oligomerization pathway by binding and stabilizing several amyloid structures of hIAPP1–37. Moreover, they can protect cerebellar granule cells (CGC from the cytotoxicity produced by the hIAPP1–37 oligomers. The modulation of proteostasis by the family of pharmaco-chaperones A–F is a promising potential approach to limit the onset and progression of diabetes and its comorbidities.

  17. Diabetes Drug Discovery: hIAPP1-37 Polymorphic Amyloid Structures as Novel Therapeutic Targets.

    Science.gov (United States)

    Fernández-Gómez, Isaac; Sablón-Carrazana, Marquiza; Bencomo-Martínez, Alberto; Domínguez, Guadalupe; Lara-Martínez, Reyna; Altamirano-Bustamante, Nelly F; Jiménez-García, Luis Felipe; Pasten-Hidalgo, Karina; Castillo-Rodríguez, Rosa Angélica; Altamirano, Perla; Marrero, Suchitil Rivera; Revilla-Monsalve, Cristina; Valdés-Sosa, Peter; Salamanca-Gómez, Fabio; Garrido-Magaña, Eulalia; Rodríguez-Tanty, Chryslaine; Altamirano-Bustamante, Myriam M

    2018-03-19

    Human islet amyloid peptide (hIAPP 1-37 ) aggregation is an early step in Diabetes Mellitus. We aimed to evaluate a family of pharmaco-chaperones to act as modulators that provide dynamic interventions and the multi-target capacity (native state, cytotoxic oligomers, protofilaments and fibrils of hIAPP 1-37 ) required to meet the treatment challenges of diabetes. We used a cross-functional approach that combines in silico and in vitro biochemical and biophysical methods to study the hIAPP 1-37 aggregation-oligomerization process as to reveal novel potential anti-diabetic drugs. The family of pharmaco-chaperones are modulators of the oligomerization and fibre formation of hIAPP 1-37 . When they interact with the amino acid in the amyloid-like steric zipper zone, they inhibit and/or delay the aggregation-oligomerization pathway by binding and stabilizing several amyloid structures of hIAPP 1-37 . Moreover, they can protect cerebellar granule cells (CGC) from the cytotoxicity produced by the hIAPP 1-37 oligomers. The modulation of proteostasis by the family of pharmaco-chaperones A - F is a promising potential approach to limit the onset and progression of diabetes and its comorbidities.

  18. Identification of BDNF sensitive electrophysiological markers of synaptic activity and their structural correlates in healthy subjects using a genetic approach utilizing the functional BDNF Val66Met polymorphism.

    Directory of Open Access Journals (Sweden)

    Fruzsina Soltész

    Full Text Available Increasing evidence suggests that synaptic dysfunction is a core pathophysiological hallmark of neurodegenerative disorders. Brain-derived neurotropic factor (BDNF is key synaptogenic molecule and targeting synaptic repair through modulation of BDNF signalling has been suggested as a potential drug discovery strategy. The development of such "synaptogenic" therapies depend on the availability of BDNF sensitive markers of synaptic function that could be utilized as biomarkers for examining target engagement or drug efficacy in humans. Here we have utilized the BDNF Val66Met genetic polymorphism to examine the effect of the polymorphism and genetic load (i.e. Met allele load on electrophysiological (EEG markers of synaptic activity and their structural (MRI correlates. Sixty healthy adults were prospectively recruited into the three genetic groups (Val/Val, Val/Met, Met/Met. Subjects also underwent fMRI, tDCS/TMS, and cognitive assessments as part of a larger study. Overall, some of the EEG markers of synaptic activity and brain structure measured with MRI were the most sensitive markers of the polymorphism. Met carriers showed decreased oscillatory activity and synchrony in the neural network subserving error-processing, as measured during a flanker task (ERN; and showed increased slow-wave activity during resting. There was no evidence for a Met load effect on the EEG measures and the polymorphism had no effects on MMN and P300. Met carriers also showed reduced grey matter volume in the anterior cingulate and in the (left prefrontal cortex. Furthermore, anterior cingulate grey matter volume, and oscillatory EEG power during the flanker task predicted subsequent behavioural adaptation, indicating a BDNF dependent link between brain structure, function and behaviour associated with error processing and monitoring. These findings suggest that EEG markers such as ERN and resting EEG could be used as BDNF sensitive functional markers in early

  19. Molecular diagnosis of Prader-Willi syndrome: Parent-of-origin dependent methylation sites and non-isotopic detection of (CA){sub n} dinucleotide repeat polymorphisms

    Energy Technology Data Exchange (ETDEWEB)

    Lerer, I.; Meiner, V.; Pashut-Lavon, I.; Abeliovich, D.

    1994-08-01

    We describe our experience in the molecular diagnosis of 22 patients suspected of Prader-Willi syndrome (PWS) using a DNA probe PW71 (D15S63) which detects a parent-of-origin specific methylated site in the PWS critical region. The cause of the syndrome was determined as deletion or uniparental disomy according to the segregation of (CA){sub n} dinucleotide repeat polymorphisms of the PWS/AS region and more distal markers of chromosome 15. In 10 patients the clinical diagnosis was confirmed by the segregation of (CA){sub n}, probably due to paternal microdeletion in the PWs critical region which did not include the loci D15S97, D15S113, GABRB3, and GABRA5. This case demonstrates the advantage of the DNA probe PW71 in the diagnosis of PWS. 31 refs., 2 figs., 3 tabs.

  20. Object tracking by occlusion detection via structured sparse learning

    KAUST Repository

    Zhang, Tianzhu

    2013-06-01

    Sparse representation based methods have recently drawn much attention in visual tracking due to good performance against illumination variation and occlusion. They assume the errors caused by image variations can be modeled as pixel-wise sparse. However, in many practical scenarios these errors are not truly pixel-wise sparse but rather sparsely distributed in a structured way. In fact, pixels in error constitute contiguous regions within the object\\'s track. This is the case when significant occlusion occurs. To accommodate for non-sparse occlusion in a given frame, we assume that occlusion detected in previous frames can be propagated to the current one. This propagated information determines which pixels will contribute to the sparse representation of the current track. In other words, pixels that were detected as part of an occlusion in the previous frame will be removed from the target representation process. As such, this paper proposes a novel tracking algorithm that models and detects occlusion through structured sparse learning. We test our tracker on challenging benchmark sequences, such as sports videos, which involve heavy occlusion, drastic illumination changes, and large pose variations. Experimental results show that our tracker consistently outperforms the state-of-the-art. © 2013 IEEE.

  1. Occlusion detection via structured sparse learning for robust object tracking

    KAUST Repository

    Zhang, Tianzhu

    2014-01-01

    Sparse representation based methods have recently drawn much attention in visual tracking due to good performance against illumination variation and occlusion. They assume the errors caused by image variations can be modeled as pixel-wise sparse. However, in many practical scenarios, these errors are not truly pixel-wise sparse but rather sparsely distributed in a structured way. In fact, pixels in error constitute contiguous regions within the object’s track. This is the case when significant occlusion occurs. To accommodate for nonsparse occlusion in a given frame, we assume that occlusion detected in previous frames can be propagated to the current one. This propagated information determines which pixels will contribute to the sparse representation of the current track. In other words, pixels that were detected as part of an occlusion in the previous frame will be removed from the target representation process. As such, this paper proposes a novel tracking algorithm that models and detects occlusion through structured sparse learning. We test our tracker on challenging benchmark sequences, such as sports videos, which involve heavy occlusion, drastic illumination changes, and large pose variations. Extensive experimental results show that our proposed tracker consistently outperforms the state-of-the-art trackers.

  2. Detection of genetic variability in Basmati and non-Basmati rice varieties and their radiation induced mutants through random amplified polymorphic DNA (RAPD)

    Energy Technology Data Exchange (ETDEWEB)

    Farooq, S; Iqbal, N; Arif, M [Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad (Pakistan)

    1998-03-01

    Random Amplified Polymorphic DNA (RAPDs) markers were utilized to detect polymorphism between pure lines and commercially available Basmati rice varieties to assess variation which may be helpful in quality control and varietal identification (Basmati-370 and derived radiation induced mutants), differentiation of mutants and parents, and identification of RAPD markers co-segregating with important agronomic traits including plant height, days to flower and grain quality. Basmati varieties were distinguished from non-Basmati varieties with the help of five diagnostic markers which will be useful for detecting mixing of non-Basmati and Basmati rices, currently a serious marketing problem. Different Basmati cultivars were identified with the help of diagnostic RAPD markers which can be used in quality control as well as for ``fingerprinting`` of cultivars. Different radiation induced mutants were also successfully distinguished from the parents on the basis of variety specific and mutant specific markers which will be useful for varietal identification. In addition to this, other markers were also identified which can differentiate mutants from each other and are being, used for the fingerprinting of different mutants, particularly the dwarf mutants having similar appearance but different parentage. For identification of RAPD markers co-segregating with plant height and days to flower, 50 F{sub 2} plants and four F{sub 3} families were studied from a reciprocal cross made between Kashmir Basmati (tall and early) and Basmati-198 (dwarf and late). Segregating bands were observed within these populations, and indicating the possible use of RAPD markers for tagging gene(s) of agronomic importance in rice. (author). 38 refs, 6 figs, 3 tabs.

  3. Detection of genetic variability in Basmati and non-Basmati rice varieties and their radiation induced mutants through random amplified polymorphic DNA (RAPD)

    International Nuclear Information System (INIS)

    Farooq, S.; Iqbal, N.; Arif, M.

    1998-01-01

    Random Amplified Polymorphic DNA (RAPDs) markers were utilized to detect polymorphism between pure lines and commercially available Basmati rice varieties to assess variation which may be helpful in quality control and varietal identification (Basmati-370 and derived radiation induced mutants), differentiation of mutants and parents, and identification of RAPD markers co-segregating with important agronomic traits including plant height, days to flower and grain quality. Basmati varieties were distinguished from non-Basmati varieties with the help of five diagnostic markers which will be useful for detecting mixing of non-Basmati and Basmati rices, currently a serious marketing problem. Different Basmati cultivars were identified with the help of diagnostic RAPD markers which can be used in quality control as well as for ''fingerprinting'' of cultivars. Different radiation induced mutants were also successfully distinguished from the parents on the basis of variety specific and mutant specific markers which will be useful for varietal identification. In addition to this, other markers were also identified which can differentiate mutants from each other and are being, used for the fingerprinting of different mutants, particularly the dwarf mutants having similar appearance but different parentage. For identification of RAPD markers co-segregating with plant height and days to flower, 50 F 2 plants and four F 3 families were studied from a reciprocal cross made between Kashmir Basmati (tall and early) and Basmati-198 (dwarf and late). Segregating bands were observed within these populations, and indicating the possible use of RAPD markers for tagging gene(s) of agronomic importance in rice. (author)

  4. Detection of rifampin resistance patterns in Mycobacterium tuberculosis strains isolated in Iran by polymerase chain reaction-single-strand conformation polymorphism and direct sequencing methods

    Directory of Open Access Journals (Sweden)

    Bahram Nasr Isfahani

    2006-09-01

    Full Text Available Mutations in the rpoB locus confer conformational changes leading to defective binding of rifampin (RIF to rpoB and consequently resistance in Mycobacterium tuberculosis. Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP was established as a rapid screening test for the detection of mutations in the rpoB gene, and direct sequencing has been unambiguously applied to characterize mutations. A total of 37 of Iranian isolates of M. tuberculosis, 16 sensitive and 21 resistant to RIF, were used in this study. A 193-bp region of the rpoB gene was amplified and PCR-SSCP patterns were determined by electrophoresis in 10% acrylamide gel and silver staining. Also, 21 samples of 193-bp rpoB amplicons with different PCR-SSCP patterns from RIFr and 10 from RIFs were sequenced. Seven distinguishable PCR-SSCP patterns were recognized in the 21 Iranian RIFr strains, while 15 out of 16 RIFs isolates demonstrated PCR-SSCP banding patterns similar to that of sensitive standard strain H37Rv. However one of the sensitive isolates demonstrated a different pattern. There were seen six different mutations in the amplified region of rpoB gene: codon 516(GAC/GTC, 523(GGG/GGT, 526(CAC/TAC, 531(TCG/TTG, 511(CTG/TTG, and 512(AGC/TCG. This study demonstrated the high specificity (93.8% and sensitivity (95.2% of PCR-SSCP method for detection of mutation in rpoB gene; 85.7% of RIFr strains showed a single mutation and 14.3% had no mutations. Three strains showed mutations caused polymorphism. Our data support the common notion that rifampin resistance genotypes are generally present mutations in codons 531 and 526, most frequently found in M. tuberculosis populations regardless of geographic origin.

  5. FRF-based structural damage detection of controlled buildings with podium structures: Experimental investigation

    Science.gov (United States)

    Xu, Y. L.; Huang, Q.; Zhan, S.; Su, Z. Q.; Liu, H. J.

    2014-06-01

    How to use control devices to enhance system identification and damage detection in relation to a structure that requires both vibration control and structural health monitoring is an interesting yet practical topic. In this study, the possibility of using the added stiffness provided by control devices and frequency response functions (FRFs) to detect damage in a building complex was explored experimentally. Scale models of a 12-storey main building and a 3-storey podium structure were built to represent a building complex. Given that the connection between the main building and the podium structure is most susceptible to damage, damage to the building complex was experimentally simulated by changing the connection stiffness. To simulate the added stiffness provided by a semi-active friction damper, a steel circular ring was designed and used to add the related stiffness to the building complex. By varying the connection stiffness using an eccentric wheel excitation system and by adding or not adding the circular ring, eight cases were investigated and eight sets of FRFs were measured. The experimental results were used to detect damage (changes in connection stiffness) using a recently proposed FRF-based damage detection method. The experimental results showed that the FRF-based damage detection method could satisfactorily locate and quantify damage.

  6. A structural framework for anomalous change detection and characterization

    Energy Technology Data Exchange (ETDEWEB)

    Prasad, Lakshman [Los Alamos National Laboratory; Theiler, James P [Los Alamos National Laboratory

    2009-01-01

    We present a spatially adaptive scheme for automatically searching a pair of images of a scene for unusual and interesting changes. Our motivation is to bring into play structural aspects of image features alongside the spectral attributes used for anomalous change detection (ACD). We leverage a small but informative subset of pixels, namely edge pixels of the images, as anchor points of a Delaunay triangulation to jointly decompose the images into a set of triangular regions, called trixels, which are spectrally uniform. Such decomposition helps in image regularization by simple-function approximation on a feature-adaptive grid. Applying ACD to this trixel grid instead of pixels offers several advantages. It allows: (1) edge-preserving smoothing of images, (2) speed-up of spatial computations by significantly reducing the representation of the images, and (3) the easy recovery of structure of the detected anomalous changes by associating anomalous trixels with polygonal image features. The latter facility further enables the application of shape-theoretic criteria and algorithms to characterize the changes and recognize them as interesting or not. This incorporation of spatial information has the potential to filter out some spurious changes, such as due to parallax, shadows, and misregistration, by identifying and filtering out those that are structurally similar and spatially pervasive. Our framework supports the joint spatial and spectral analysis of images, potentially enabling the design of more robust ACD algorithms.

  7. Guided wave crack detection and size estimation in stiffened structures

    Science.gov (United States)

    Bhuiyan, Md Yeasin; Faisal Haider, Mohammad; Poddar, Banibrata; Giurgiutiu, Victor

    2018-03-01

    Structural health monitoring (SHM) and nondestructive evaluation (NDE) deals with the nondestructive inspection of defects, corrosion, leaks in engineering structures by using ultrasonic guided waves. In the past, simplistic structures were often considered for analyzing the guided wave interaction with the defects. In this study, we focused on more realistic and relatively complicated structure for detecting any defect by using a non-contact sensing approach. A plate with a stiffener was considered for analyzing the guided wave interactions. Piezoelectric wafer active transducers were used to produce excitation in the structures. The excitation generated the multimodal guided waves (aka Lamb waves) that propagate in the plate with stiffener. The presence of stiffener in the plate generated scattered waves. The direct wave and the additional scattered waves from the stiffener were experimentally recorded and studied. These waves were considered as a pristine case in this research. A fine horizontal semi-circular crack was manufactured by using electric discharge machining in the same stiffener. The presence of crack in the stiffener produces additional scattered waves as well as trapped waves. These scattered waves and trapped wave modes from the cracked stiffener were experimentally measured by using a scanning laser Doppler vibrometer (SLDV). These waves were analyzed and compared with that from the pristine case. The analyses suggested that both size and shape of the horizontal crack may be predicted from the pattern of the scattered waves. Different features (reflection, transmission, and mode-conversion) of the scattered wave signals are analyzed. We found direct transmission feature for incident A0 wave mode and modeconversion feature for incident S0 mode are most suitable for detecting the crack in the stiffener. The reflection feature may give a better idea of sizing the crack.

  8. Detection of damage in welded structure using experimental modal data

    Energy Technology Data Exchange (ETDEWEB)

    Abu Husain, N [Transportation Research Alliance, Universiti Teknologi Malaysia, 81310 UTM Johor Bahru, Johor (Malaysia); Ouyang, H, E-mail: nurul@fkm.utm.my, E-mail: h.ouyang@liv.ac.uk [Department of Engineering, Harrison-Hughes Building, University of Liverpool, Brownlow Hill, Liverpool L69 3GH (United Kingdom)

    2011-07-19

    A typical automotive structure could contain thousands of spot weld joints that contribute significantly to the vehicle's structural stiffness and dynamic characteristics. However, some of these joints may be imperfect or even absent during the manufacturing process and they are also highly susceptible to damage due to operational and environmental conditions during the vehicle lifetime. Therefore, early detection and estimation of damage are important so necessary actions can be taken to avoid further problems. Changes in physical parameters due to existence of damage in a structure often leads to alteration of vibration modes; thus demonstrating the dependency between the vibration characteristics and the physical properties of structures. A sensitivity-based model updating method, performed using a combination of MATLAB and NASTRAN, has been selected for the purpose of this work. The updating procedure is regarded as parameter identification which aims to bring the numerical prediction to be as closely as possible to the measured natural frequencies and mode shapes data of the damaged structure in order to identify the damage parameters (characterised by the reductions in the Young's modulus of the weld patches to indicate the loss of material/stiffness at the damage region).

  9. A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Blood Components (Immunity in a Cross between Korean Native Pig and Yorkshire

    Directory of Open Access Journals (Sweden)

    Y.-M. Lee

    2012-12-01

    Full Text Available The purpose of this study was to detect significant SNPs for blood components that were related to immunity using high single nucleotide polymorphism (SNP density panels in a Korean native pig (KNP×Yorkshire (YK cross population. A reciprocal design of KNP×YK produced 249 F2 individuals that were genotyped for a total of 46,865 available SNPs in the Illumina porcine 60K beadchip. To perform whole genome association analysis (WGA, phenotypes were regressed on each SNP under a simple linear regression model after adjustment for sex and slaughter age. To set up a significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were determined using a stepwise regression procedure with the rates of inclusion and exclusion of each SNP out of the model at 0.001 level. A total of 54 SNPs were detected; 10, 6, 4, 4, 5, 4, 5, 10, and 6 SNPs for neutrophil, lymphocyte, monocyte, eosinophil, basophil, atypical lymph, immunoglobulin, insulin, and insulin-like growth factor-I, respectively. Each set of significant SNPs per trait explained 24 to 42% of phenotypic variance. Several pleiotropic SNPs were detected on SSCs 4, 13, 14 and 15.

  10. Detecting 3D Vegetation Structure with the Galileo Space Probe: Can a Distant Probe Detect Vegetation Structure on Earth?

    Science.gov (United States)

    Doughty, Christopher E; Wolf, Adam

    2016-01-01

    Sagan et al. (1993) used the Galileo space probe data and first principles to find evidence of life on Earth. Here we ask whether Sagan et al. (1993) could also have detected whether life on Earth had three-dimensional structure, based on the Galileo space probe data. We reanalyse the data from this probe to see if structured vegetation could have been detected in regions with abundant photosynthetic pigments through the anisotropy of reflected shortwave radiation. We compare changing brightness of the Amazon forest (a region where Sagan et al. (1993) noted a red edge in the reflectance spectrum, indicative of photosynthesis) as the planet rotates to a common model of reflectance anisotropy and found measured increase of surface reflectance of 0.019 ± 0.003 versus a 0.007 predicted from only anisotropic effects. We hypothesize the difference was due to minor cloud contamination. However, the Galileo dataset had only a small change in phase angle (sun-satellite position) which reduced the observed anisotropy signal and we demonstrate that theoretically if the probe had a variable phase angle between 0-20°, there would have been a much larger predicted change in surface reflectance of 0.1 and under such a scenario three-dimensional vegetation structure on Earth could possibly have been detected. These results suggest that anisotropic effects may be useful to help determine whether exoplanets have three-dimensional vegetation structure in the future, but that further comparisons between empirical and theoretical results are first necessary.

  11. Detecting 3D Vegetation Structure with the Galileo Space Probe: Can a Distant Probe Detect Vegetation Structure on Earth?

    Directory of Open Access Journals (Sweden)

    Christopher E Doughty

    Full Text Available Sagan et al. (1993 used the Galileo space probe data and first principles to find evidence of life on Earth. Here we ask whether Sagan et al. (1993 could also have detected whether life on Earth had three-dimensional structure, based on the Galileo space probe data. We reanalyse the data from this probe to see if structured vegetation could have been detected in regions with abundant photosynthetic pigments through the anisotropy of reflected shortwave radiation. We compare changing brightness of the Amazon forest (a region where Sagan et al. (1993 noted a red edge in the reflectance spectrum, indicative of photosynthesis as the planet rotates to a common model of reflectance anisotropy and found measured increase of surface reflectance of 0.019 ± 0.003 versus a 0.007 predicted from only anisotropic effects. We hypothesize the difference was due to minor cloud contamination. However, the Galileo dataset had only a small change in phase angle (sun-satellite position which reduced the observed anisotropy signal and we demonstrate that theoretically if the probe had a variable phase angle between 0-20°, there would have been a much larger predicted change in surface reflectance of 0.1 and under such a scenario three-dimensional vegetation structure on Earth could possibly have been detected. These results suggest that anisotropic effects may be useful to help determine whether exoplanets have three-dimensional vegetation structure in the future, but that further comparisons between empirical and theoretical results are first necessary.

  12. Detection and Location of Structural Degradation in Mechanical Systems

    International Nuclear Information System (INIS)

    Blakeman, E.D.; Damiano, B.; Phillips, L.D.

    1999-01-01

    The investigation of a diagnostic method for detecting and locating the source of structural degradation in a mechanical system is described in this paper. The diagnostic method uses a mathematical model of the mechanical system to determine relationships between system parameters and measurable spectral features. These relationships are incorporated into a neural network, which associates measured spectral features with system parameters. Condition diagnosis is performed by presenting the neural network with measured spectral features and comparing the system parameters estimated by the neural network to previously estimated values. Changes in the estimated system parameters indicate the location and severity of degradation in the mechanical system

  13. Different mutation patterns of atovaquone resistance to Plasmodium falciparum in vitro and in vivo: rapid detection of codon 268 polymorphisms in the cytochrome b as potential in vivo resistance marker

    DEFF Research Database (Denmark)

    Schwöbel, Babett; Alifrangis, Michael; Salanti, Ali

    2003-01-01

    , we developed a detection method for the diagnostic of codon 268 polymorphisms as a potential atovaquone/proguanil resistance marker. A nested PCR with 3 different pairs of primers for the second round was designed. Each product was digested with restriction enzymes, capable to distinguish the wild...

  14. Vitamin K 3 family members - Part II: Single crystal X-ray structures, temperature-induced packing polymorphism, magneto-structural correlations and probable anti-oncogenic candidature

    Science.gov (United States)

    Rane, Sandhya; Ahmed, Khursheed; Salunke-Gawali, Sunita; Zaware, Santosh B.; Srinivas, D.; Gonnade, Rajesh; Bhadbhade, Mohan

    2008-12-01

    Temperature-induced packing polymorphism is observed for vitamin K 3 (menadione, 3-methyl-1,4-naphthoquinone, 1). Form 1a crystallizes at 300 K and 1b at 277 K both in the same space group P2 1/ c. Form 1b contains one molecule per asymmetric unit, performing anisotropy in g-factor viz. g z = 2.0082, g y = 2.0055 and g x = 2.0025, whereas form 1a contains two molecules in its asymmetric unit. Vitamin K 3 family members 2, [2-hydroxy vitamin K 3] and 3, [2-hydroxy-1-oximino vitamin K 3] also perform intrinsic neutral active naphthosemiquinone valence tautomers even in dark having spin concentrations due to hydrogen bonding and aromatic stacking interactions which are compared to vitamin K 3. The significant lateral C-H⋯O and O-H⋯π bifurcated or π-π ∗ interactions are discussed for molecular associations and radical formations. X-ray structure of 3 revealed π-π ∗ stack dimers as radicals signatured in EPR as triplet with five hyperfine splits [ Ā( 14N) = 11.9 G]. The centrosymmetric biradicals in 3 show diamagnetism at high temperature but below 10 K it shows paramagnetism with μeff as 0.19 B.M. Vitamin K 3 and its family members inhibit biological activities of acid phosphatase ( APase), which are proportional to their spin concentrations. This may relate to their probable anti-oncogenic candidature in future.

  15. Structural damage detection using deep learning of ultrasonic guided waves

    Science.gov (United States)

    Melville, Joseph; Alguri, K. Supreet; Deemer, Chris; Harley, Joel B.

    2018-04-01

    Structural health monitoring using ultrasonic guided waves relies on accurate interpretation of guided wave propagation to distinguish damage state indicators. However, traditional physics based models do not provide an accurate representation, and classic data driven techniques, such as a support vector machine, are too simplistic to capture the complex nature of ultrasonic guide waves. To address this challenge, this paper uses a deep learning interpretation of ultrasonic guided waves to achieve fast, accurate, and automated structural damaged detection. To achieve this, full wavefield scans of thin metal plates are used, half from the undamaged state and half from the damaged state. This data is used to train our deep network to predict the damage state of a plate with 99.98% accuracy given signals from just 10 spatial locations on the plate, as compared to that of a support vector machine (SVM), which achieved a 62% accuracy.

  16. Community structures and role detection in music networks

    Science.gov (United States)

    Teitelbaum, T.; Balenzuela, P.; Cano, P.; Buldú, Javier M.

    2008-12-01

    We analyze the existence of community structures in two different social networks using data obtained from similarity and collaborative features between musical artists. Our analysis reveals some characteristic organizational patterns and provides information about the driving forces behind the growth of the networks. In the similarity network, we find a strong correlation between clusters of artists and musical genres. On the other hand, the collaboration network shows two different kinds of communities: rather small structures related to music bands and geographic zones, and much bigger communities built upon collaborative clusters with a high number of participants related through the period the artists were active. Finally, we detect the leading artists inside their corresponding communities and analyze their roles in the network by looking at a few topological properties of the nodes.

  17. DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress.

    Science.gov (United States)

    Wang, Wensheng; Zhao, Xiuqin; Pan, Yajiao; Zhu, Linghua; Fu, Binying; Li, Zhikang

    2011-09-20

    DNA methylation, one of the most important epigenetic phenomena, plays a vital role in tuning gene expression during plant development as well as in response to environmental stimuli. In the present study, a methylation-sensitive amplified polymorphism (MSAP) analysis was performed to profile DNA methylation changes in two contrasting rice genotypes under salt stress. Consistent with visibly different phenotypes in response to salt stress, epigenetic markers classified as stable inter-cultivar DNA methylation differences were determined between salt-tolerant FL478 and salt-sensitive IR29. In addition, most tissue-specific DNA methylation loci were conserved, while many of the growth stage-dependent DNA methylation loci were dynamic between the two genotypes. Strikingly, salt stress induced a decrease in DNA methylation specifically in roots at the seedling stage that was more profound in IR29 than in the FL478. This result may indicate that demethylation of genes is an active epigenetic response to salt stress in roots at the seedling stage, and helps to further elucidate the implications of DNA methylation in crop growth and development. Copyright © 2011. Published by Elsevier Ltd.

  18. Cloning and characterization of transferrin cDNA and rapid detection of transferrin gene polymorphism in rainbow trout (Oncorhynchus mykiss).

    Science.gov (United States)

    Tange, N; Jong-Young, L; Mikawa, N; Hirono, I; Aoki, T

    1997-12-01

    A cDNA clone of rainbow trout (Oncorhynchus mykiss) transferrin was obtained from a liver cDNA library. The 2537-bp cDNA sequence contained an open reading frame encoding 691 amino acids and the 5' and 3' noncoding regions. The amino acid sequences at the iron-binding sites and the two N-linked glycosylation sites, and the cysteine residues were consistent with known, conserved vertebrate transferrin cDNA sequences. Single N-linked glycosylation sites existed on the N- and C-lobe. The deduced amino acid sequence of the rainbow trout transferrin cDNA had 92.9% identities with transferrin of coho salmon (Oncorhynchus kisutch); 85%, Atlantic salmon (Salmo salar); 67.3%, medaka (Oryzias latipes); 61.3% Atlantic cod (Gadus morhua); and 59.7%, Japanese flounder (Paralichthys olivaceus). The long and accurate polymerase chain reaction (LA-PCR) was used to amplify approximately 6.5 kb of the transferrin gene from rainbow trout genomic DNA. Restriction fragment length polymorphisms (RFLPs) of the LA-PCR products revealed three digestion patterns in 22 samples.

  19. Detection of individual radiosensitivity by radiation–induced micronuclei in human peripheral blood lymphocytes and polymorphisms in DNA repair genes

    Energy Technology Data Exchange (ETDEWEB)

    Staynova, A.; Hadjidekova, V.; Popova, L.; Hristova, R. [Radiation Genetics Laboratory, National Centre of Radiobology and Radiation Protection, Sofia (Bulgaria); Savov, A. [National Genetic Laboratory, University Hospital of Obstetrics and Gynecology, Sofia (Bulgaria)

    2013-07-01

    Aim: To investigate the association of two polymorphisms – in XRCC1 gene (Arg399Gln) and in APE1 gene (Asp148Glu) and the radiation induced frequency of micronuclei in human peripheral blood lymphocytes. Material and methods: Genomic DNA from 34 cancer patients and 52 controls were genotyped using PCR–RFLP technique. Micronucleus test (MNT) was performed on 15 cancer patients and 15 controls, before and after in vitro irradiation with 2Gy gamma rays. Results: The data showed that cancer patients had a significantly higher spontaneous frequency of cells with micronuclei than controls (P=0.009). No statistical difference was registered when comparing the mean frequency of cells with micronuclei after in vitro irradiation between these groups. Four subjects were selected as radiosensitive after applying cut–off of the mean frequency of radiation induced micronuclei. Three of them are carriers of the XRCC1 399Gln allele and two of them are carriers of the APE1 148Glu allele. (author)

  20. On polymorphism of dysprosium trichloride

    Energy Technology Data Exchange (ETDEWEB)

    Zakiryanova, Irina D.; Khokhlov, Vladimir A.; Salyulev, Alexander B.; Korzun, Iraida V. [RAS Ural Branch, Ekaterinburg (Russian Federation). Institute of High-Temperature Electrochemistry

    2015-07-01

    For the first time, the structure of crystalline DyCl{sub 3} over a wide temperature range from room temperature to melting point was studied by Raman spectroscopy. The phonon modes (cm{sup -1}) of dysprosium trichloride (monoclinic crystal lattice of AlCl{sub 3} type, Z = 4, CN = 6) at room temperature are 257 (A{sub 1g}), 201 (E{sub g}), 112 (E{sub g}), 88 (A{sub 1g}), and 63 (E{sub g}). The monoclinic structure of the crystalline DyCl{sub 3} C{sub 2h}{sup 3} symmetry was found to remain constant over the studied temperature range. No polymorphic transformation in the solid state was detected. Gravimetry, calorimetry, and mass spectrometry have been used in addition to support the conclusions made on the basis of Raman spectroscopic data.

  1. On polymorphism of dysprosium trichloride

    International Nuclear Information System (INIS)

    Zakiryanova, Irina D.; Khokhlov, Vladimir A.; Salyulev, Alexander B.; Korzun, Iraida V.

    2015-01-01

    For the first time, the structure of crystalline DyCl 3 over a wide temperature range from room temperature to melting point was studied by Raman spectroscopy. The phonon modes (cm -1 ) of dysprosium trichloride (monoclinic crystal lattice of AlCl 3 type, Z = 4, CN = 6) at room temperature are 257 (A 1g ), 201 (E g ), 112 (E g ), 88 (A 1g ), and 63 (E g ). The monoclinic structure of the crystalline DyCl 3 C 2h 3 symmetry was found to remain constant over the studied temperature range. No polymorphic transformation in the solid state was detected. Gravimetry, calorimetry, and mass spectrometry have been used in addition to support the conclusions made on the basis of Raman spectroscopic data.

  2. QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species

    Directory of Open Access Journals (Sweden)

    Voorrips Roeland E

    2006-10-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. Results We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans. Conclusion QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at

  3. A Study of the Surface Structure of Polymorphic Graphene and Other Two-Dimensional Materials for Use in Novel Electronics and Organic Photovoltaics

    Science.gov (United States)

    Grady, Maxwell

    For some time there has been interest in the fundamental physical properties of low- dimensional material systems. The discovery of graphene as a stable two-dimensional form of solid carbon lead to an exponential increase in research in two-dimensional and other re- duced dimensional systems. It is now known that there is a wide range of materials which are stable in two-dimensional form. These materials span a large configuration space of struc- tural, mechanical, and electronic properties, which results in the potential to create novel electronic devices from nano-scale heterostructures with exactly tailored device properties. Understanding the material properties at the nanoscale level requires specialized tools to probe materials with atomic precision. Here I present the growth and analysis of a novel graphene-ruthenium system which exhibits unique polymorphism in its surface structure, hereby referred to as polymorphic graphene. Scanning Tunneling Microscopy (STM) investigations of the polymorphic graphene surface reveal a periodically rippled structure with a vast array of domains, each exhibiting xvia unique moire period. The majority of moire domains found in this polymorphic graphene system are previously unreported in past studies of the structure of graphene on ruthenium. To better understand many of the structural properties of this system, characterization methods beyond those available at the UNH surface science lab are employed. Further investigation using Low Energy Electron Microscopy (LEEM) has been carried out at Sandia National Laboratory's Center for Integrated Nanotechnology and the Brookhaven National Laboratory Center for Functional Nanomaterials. To aid in analysis of the LEEM data, I have developed an open source software package to automate extraction of electron reflectivity curves from real space and reciprocal space data sets. This software has been used in the study of numerous other two-dimensional materials beyond graphene. When

  4. Coplanar capacitance sensors for detecting water intrusion in composite structures

    International Nuclear Information System (INIS)

    Nassr, Amr A; El-Dakhakhni, Wael W; Ahmed, Wael H

    2008-01-01

    Composite materials are becoming more affordable and widely used for retrofitting, rehabilitating and repairing reinforced concrete structures designed and constructed under older specifications. However, the mechanical properties and long-term durability of composite materials may degrade severely in the presence of water intrusion. This study presents a new non-destructive evaluation (NDE) technique for detecting the water intrusion in composite structures by evaluating the dielectric properties of different composite system constituent materials. The variation in the dielectric signatures was employed to design a coplanar capacitance sensor with high sensitivity to detect such defects. An analytical model was used to study the effect of the sensor geometry on the output signal and to optimize sensor design. A finite element model was developed to validate analytical results and to evaluate other sensor design-related parameters. Experimental testing of a concrete specimen wrapped with composite laminate and containing a series of pre-induced water intrusion defects was conducted in order to validate the concept of the new technique. Experimental data showed excellent agreement with the finite element model predictions and confirmed sensor performance

  5. Structural damage detection robust against time synchronization errors

    International Nuclear Information System (INIS)

    Yan, Guirong; Dyke, Shirley J

    2010-01-01

    Structural damage detection based on wireless sensor networks can be affected significantly by time synchronization errors among sensors. Precise time synchronization of sensor nodes has been viewed as crucial for addressing this issue. However, precise time synchronization over a long period of time is often impractical in large wireless sensor networks due to two inherent challenges. First, time synchronization needs to be performed periodically, requiring frequent wireless communication among sensors at significant energy cost. Second, significant time synchronization errors may result from node failures which are likely to occur during long-term deployment over civil infrastructures. In this paper, a damage detection approach is proposed that is robust against time synchronization errors in wireless sensor networks. The paper first examines the ways in which time synchronization errors distort identified mode shapes, and then proposes a strategy for reducing distortion in the identified mode shapes. Modified values for these identified mode shapes are then used in conjunction with flexibility-based damage detection methods to localize damage. This alternative approach relaxes the need for frequent sensor synchronization and can tolerate significant time synchronization errors caused by node failures. The proposed approach is successfully demonstrated through numerical simulations and experimental tests in a lab

  6. Efficient and robust cell detection: A structured regression approach.

    Science.gov (United States)

    Xie, Yuanpu; Xing, Fuyong; Shi, Xiaoshuang; Kong, Xiangfei; Su, Hai; Yang, Lin

    2018-02-01

    Efficient and robust cell detection serves as a critical prerequisite for many subsequent biomedical image analysis methods and computer-aided diagnosis (CAD). It remains a challenging task due to touching cells, inhomogeneous background noise, and large variations in cell sizes and shapes. In addition, the ever-increasing amount of available datasets and the high resolution of whole-slice scanned images pose a further demand for efficient processing algorithms. In this paper, we present a novel structured regression model based on a proposed fully residual convolutional neural network for efficient cell detection. For each testing image, our model learns to produce a dense proximity map that exhibits higher responses at locations near cell centers. Our method only requires a few training images with weak annotations (just one dot indicating the cell centroids). We have extensively evaluated our method using four different datasets, covering different microscopy staining methods (e.g., H & E or Ki-67 staining) or image acquisition techniques (e.g., bright-filed image or phase contrast). Experimental results demonstrate the superiority of our method over existing state of the art methods in terms of both detection accuracy and running time. Copyright © 2017. Published by Elsevier B.V.

  7. High-resolution melting analysis for detection of a single-nucleotide polymorphism and the genotype of the myostatin gene in warmblood horses.

    Science.gov (United States)

    Serpa, Priscila B S; Garbade, Petra; Natalini, Cláudio C; Pires, Ananda R; Tisotti, Tainor M

    2017-01-01

    OBJECTIVE To develop a high-resolution melting (HRM) assay to detect the g.66493737C>T polymorphism in the myostatin gene (MSTN) and determine the frequency of 3 previously defined g.66493737 genotypes (T/T, T/C, and C/C) in warmblood horses. SAMPLES Blood samples from 23 horses. PROCEDURES From each blood sample, DNA was extracted and analyzed by standard PCR methods and an HRM assay to determine the MSTN genotype. Three protocols (standard protocol, protocol in which a high-salt solution was added to the reaction mixture before the first melting cycle, and protocol in which an unlabeled probe was added to the reaction mixture before analysis) for the HRM assay were designed and compared. Genotype results determined by the HRM protocol that generated the most consistent melting curves were compared with those determined by sequencing. RESULTS The HRM protocol in which an unlabeled probe was added to the reaction mixture generated the most consistent melting curves. The genotypes of the g.66493737C>T polymorphism were determined for 22 horses (16 by HRM analysis and 20 by sequencing); 14, 7, and 1 had the T/T, T/C, and C/C genotypes, respectively. The genotype determined by HRM analysis agreed with that determined by sequencing for 14 of 16 horses. The frequency of alleles T and C was 79.5% and 20.5%, respectively. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that HRM analysis may be a faster and more economical alternative than PCR methods for genotyping. Genotyping results might be useful as predictors of athletic performance for horses.

  8. Automatic Detection and Quantification of WBCs and RBCs Using Iterative Structured Circle Detection Algorithm

    Directory of Open Access Journals (Sweden)

    Yazan M. Alomari

    2014-01-01

    Full Text Available Segmentation and counting of blood cells are considered as an important step that helps to extract features to diagnose some specific diseases like malaria or leukemia. The manual counting of white blood cells (WBCs and red blood cells (RBCs in microscopic images is an extremely tedious, time consuming, and inaccurate process. Automatic analysis will allow hematologist experts to perform faster and more accurately. The proposed method uses an iterative structured circle detection algorithm for the segmentation and counting of WBCs and RBCs. The separation of WBCs from RBCs was achieved by thresholding, and specific preprocessing steps were developed for each cell type. Counting was performed for each image using the proposed method based on modified circle detection, which automatically counted the cells. Several modifications were made to the basic (RCD algorithm to solve the initialization problem, detecting irregular circles (cells, selecting the optimal circle from the candidate circles, determining the number of iterations in a fully dynamic way to enhance algorithm detection, and running time. The validation method used to determine segmentation accuracy was a quantitative analysis that included Precision, Recall, and F-measurement tests. The average accuracy of the proposed method was 95.3% for RBCs and 98.4% for WBCs.

  9. Genetic effect of interleukin-1 beta (C-511T) polymorphism on the structural covariance network and white matter integrity in Alzheimer's disease.

    Science.gov (United States)

    Huang, Chi-Wei; Hsu, Shih-Wei; Tsai, Shih-Jen; Chen, Nai-Ching; Liu, Mu-En; Lee, Chen-Chang; Huang, Shu-Hua; Chang, Weng-Neng; Chang, Ya-Ting; Tsai, Wan-Chen; Chang, Chiung-Chih

    2017-01-18

    Inflammatory processes play a pivotal role in the degenerative process of Alzheimer's disease. In humans, a biallelic (C/T) polymorphism in the promoter region (position-511) (rs16944) of the interleukin-1 beta gene has been significantly associated with differences in the secretory capacity of interleukin-1 beta. In this study, we investigated whether this functional polymorphism mediates the brain networks in patients with Alzheimer's disease. We enrolled a total of 135 patients with Alzheimer's disease (65 males, 70 females), and investigated their gray matter structural covariance networks using 3D T1 magnetic resonance imaging and their white matter macro-structural integrities using fractional anisotropy. The patients were classified into two genotype groups: C-carriers (n = 108) and TT-carriers (n = 27), and the structural covariance networks were constructed using seed-based analysis focusing on the default mode network medial temporal or dorsal medial subsystem, salience network and executive control network. Neurobehavioral scores were used as the major outcome factors for clinical correlations. There were no differences between the two genotype groups in the cognitive test scores, seed, or peak cluster volumes and white matter fractional anisotropy. The covariance strength showing C-carriers > TT-carriers was the entorhinal-cingulum axis. There were two peak clusters (Brodmann 6 and 10) in the salience network and four peak clusters (superior prefrontal, precentral, fusiform, and temporal) in the executive control network that showed C-carriers covariance strength. The salience network and executive control network peak clusters in the TT group and the default mode network peak clusters in the C-carriers strongly predicted the cognitive test scores. Interleukin-1 beta C-511 T polymorphism modulates the structural covariance strength on the anterior brain network and entorhinal-interconnected network which were independent of the white

  10. Analysis of polymorphisms and haplotype structure of the human thymidylate synthase genetic region: a tool for pharmacogenetic studies.

    Directory of Open Access Journals (Sweden)

    Soma Ghosh

    Full Text Available 5-Fluorouracil (5FU, a widely used chemotherapeutic drug, inhibits the DNA replicative enzyme, thymidylate synthase (Tyms. Prior studies implicated a VNTR (variable numbers of tandem repeats polymorphism in the 5'-untranslated region (5'-UTR of the TYMS gene as a determinant of Tyms expression in tumors and normal tissues and proposed that these VNTR genotypes could help decide fluoropyrimidine dosing. Clinical associations between 5FU-related toxicity and the TYMS VNTR were reported, however, results were inconsistent, suggesting that additional genetic variation in the TYMS gene might influence Tyms expression. We thus conducted a detailed genetic analysis of this region, defining new polymorphisms in this gene including mononucleotide (poly A:T repeats and novel single nucleotide polymorphisms (SNPs flanking the VNTR in the TYMS genetic region. Our haplotype analysis of this region used data from both established and novel genetic variants and found nine SNP haplotypes accounting for more than 90% of the studied population. We observed non-exclusive relationships between the VNTR and adjacent SNP haplotypes, such that each type of VNTR commonly occurred on several haplotype backgrounds. Our results confirmed the expectation that the VNTR alleles exhibit homoplasy and lack the common ancestry required for a reliable marker of a linked adjacent locus that might govern toxicity. We propose that it may be necessary in a clinical trial to assay multiple types of genetic polymorphisms in the TYMS region to meaningfully model linkage of genetic markers to 5FU-related toxicity. The presence of multiple long (up to 26 nt, polymorphic monothymidine repeats in the promoter region of the sole human thymidylate synthetic enzyme is intriguing.

  11. Extended Structures of Planetary Nebulae Detected in H2 Emission

    Science.gov (United States)

    Fang, Xuan; Zhang, Yong; Kwok, Sun; Hsia, Chih-Hao; Chau, Wayne; Ramos-Larios, Gerardo; Guerrero, Martín A.

    2018-06-01

    We present narrowband near-infrared images of a sample of 11 Galactic planetary nebulae (PNe) obtained in the H2 2.122 μm and Brγ 2.166 μm emission lines and the K c 2.218 μm continuum. These images were collected with the Wide-field Infrared Camera on the 3.6 m Canada–France–Hawaii Telescope (CFHT); their unprecedented depth and wide field of view allow us to find extended nebular structures in H2 emission in several PNe, some of these being the first detection. The nebular morphologies in H2 emission are studied in analogy with the optical images, and indication of stellar wind interactions is discussed. In particular, the complete structure of the highly asymmetric halo in NGC 6772 is witnessed in H2, which strongly suggests interaction with the interstellar medium. Our sample confirms the general correlation between H2 emission and the bipolarity of PNe. The knotty or filamentary fine structures of the H2 gas are resolved in the inner regions of several ring-like PNe, also confirming the previous argument that H2 emission mostly comes from knots or clumps embedded within fully ionized material at the equatorial regions. Moreover, the H2 image of the butterfly-shaped Sh 1-89, after removal of field stars, clearly reveals a tilted ring structure at the waist. These high-quality CFHT images justify follow-up detailed morphokinematic studies that are desired in order to deduce the true physical structures of a few PNe in the sample. Based on observations obtained with WIRCam, a joint project of CFHT, Taiwan, Korea, Canada, and France, at the Canada–France–Hawaii Telescope (CFHT), which is operated by the National Research Council (NRC) of Canada, the Institut National des Sciences de l’Univers of the Centre National de la Recherche Scientifique of France, and the University of Hawaii.

  12. Local pulmonary structure classification for computer-aided nodule detection

    Science.gov (United States)

    Bahlmann, Claus; Li, Xianlin; Okada, Kazunori

    2006-03-01

    We propose a new method of classifying the local structure types, such as nodules, vessels, and junctions, in thoracic CT scans. This classification is important in the context of computer aided detection (CAD) of lung nodules. The proposed method can be used as a post-process component of any lung CAD system. In such a scenario, the classification results provide an effective means of removing false positives caused by vessels and junctions thus improving overall performance. As main advantage, the proposed solution transforms the complex problem of classifying various 3D topological structures into much simpler 2D data clustering problem, to which more generic and flexible solutions are available in literature, and which is better suited for visualization. Given a nodule candidate, first, our solution robustly fits an anisotropic Gaussian to the data. The resulting Gaussian center and spread parameters are used to affine-normalize the data domain so as to warp the fitted anisotropic ellipsoid into a fixed-size isotropic sphere. We propose an automatic method to extract a 3D spherical manifold, containing the appropriate bounding surface of the target structure. Scale selection is performed by a data driven entropy minimization approach. The manifold is analyzed for high intensity clusters, corresponding to protruding structures. Techniques involve EMclustering with automatic mode number estimation, directional statistics, and hierarchical clustering with a modified Bhattacharyya distance. The estimated number of high intensity clusters explicitly determines the type of pulmonary structures: nodule (0), attached nodule (1), vessel (2), junction (>3). We show accurate classification results for selected examples in thoracic CT scans. This local procedure is more flexible and efficient than current state of the art and will help to improve the accuracy of general lung CAD systems.

  13. 单核苷酸多态性检测技术的研究%Research on single nucleotide polymorphism detecting technologies

    Institute of Scientific and Technical Information of China (English)

    龙波; 陈仕国; 马显光; 邓玲; 廖新华

    2011-01-01

    This article represent our research and thinking about single nueleotide polymorphism detecting technologies, which probably be applied to normal hospital. It will be true that there are some economic and high - output SNP detecting technique.%单核苷酸多态性(sNP)的研究已成为人类后基因组时代的主要内容之一。SNP作为第三代遗传标记具有数量多、分布广泛的特点,且比第一、二代遗传标记更适合于对复杂性疾病遗传解析以及基于群体基因识别等方面的研究,因此在临床检验工作中,建立高度自动化和高通量的SNP检测分析技术十分重要。本文就最新发展的几种SNP检测技术进行分析,并对可能应用于医院临床检验具有经济意义的SNP检测技术进行展望。

  14. Development of a TaqMan Allelic Discrimination Assay for detection of Single Nucleotides Polymorphisms associated with anti-malarial drug resistance

    Directory of Open Access Journals (Sweden)

    Kamau Edwin

    2012-01-01

    Full Text Available Abstract Background Anti-malarial drug resistance poses a threat to current global efforts towards control and elimination of malaria. Several methods are used in monitoring anti-malarial drug resistance. Molecular markers such as single nucleotide polymorphism (SNP for example are increasingly being used to identify genetic mutations related to anti-malarial drug resistance. Several methods are currently being used in analysis of SNP associated with anti-malarial drug resistance and although each one of these methods has unique strengths and shortcoming, there is still need to improve and/or develop new methods that will close the gap found in the current methods. Methods TaqMan Allelic Discrimination assays for detection of SNPs associated with anti-malarial drug resistance were designed for analysis on Applied Biosystems PCR platform. These assays were designed by submitting SNP sequences associated with anti-malarial drug resistance to Applied Biosystems website. Eleven SNPs associated with resistance to anti-malarial drugs were selected and tested. The performance of each SNP assay was tested by creating plasmid DNAs carrying codons of interests and analysing them for analysis. To test the sensitivity and specificity of each SNP assay, 12 clinical samples were sequenced at codons of interest and used in the analysis. Plasmid DNAs were used to establish the Limit of Detection (LoD for each assay. Results Data from genetic profiles of the Plasmodium falciparum laboratory strains and sequence data from 12 clinical samples was used as the reference method with which the performance of the SNP assays were compared to. The sensitivity and specificity of each SNP assay was establish at 100%. LoD for each assay was established at 2 GE, equivalent to less than 1 parasite/μL. SNP assays performed well in detecting mixed infection and analysis of clinical samples. Conclusion TaqMan Allelic Discrimination assay provides a good alternative tool in

  15. Synthesis, structure, and polymorphism of A{sub 3}LnSi{sub 2}O{sub 7} (A=Na, K; Ln=Sm, Ho, Yb)

    Energy Technology Data Exchange (ETDEWEB)

    Latshaw, Allison M.; Yeon, Jeongho; Smith, Mark D.; Loye, Hans-Conrad zur, E-mail: zurloye@mailbox.sc.edu

    2016-03-15

    Four new members of the A{sub 3}LnSi{sub 2}O{sub 7} family, K{sub 3}SmSi{sub 2}O{sub 7}, Na{sub 3}HoSi{sub 2}O{sub 7}, and two polymorphs of Na{sub 3}YbSi{sub 2}O{sub 7}, are reported. K{sub 3}SmSi{sub 2}O{sub 7} crystallizes in the hexagonal space group P6{sub 3}/mcm, Na{sub 3}HoSi{sub 2}O{sub 7} and Na{sub 3}YbSi{sub 2}O{sub 7} crystallize in the hexagonal space group P6{sub 3}/m, and Na{sub 3}YbSi{sub 2}O{sub 7} crystallizes in the trigonal space group P31c. The Na{sub 3}YbSi{sub 2}O{sub 7} composition that crystallizes in P31c is a new structure type. The magnetic properties for the Ho and Yb analogs are reported. - Graphical abstract: The different structure types and polymorphs of the A{sub 3}LnSi{sub 2}O{sub 7} family reported. - Highlights: • Four new members of the A{sub 3}LnSi{sub 2}O{sub 7} family are presented. • Na{sub 3}YbSi{sub 2}O{sub 7} is reported as two polymorphs, one is a new structure type. • Crystals synthesized out of molten fluoride fluxes.

  16. DNA barcode detects high genetic structure within neotropical bird species.

    Directory of Open Access Journals (Sweden)

    Erika Sendra Tavares

    Full Text Available BACKGROUND: Towards lower latitudes the number of recognized species is not only higher, but also phylogeographic subdivision within species is more pronounced. Moreover, new genetically isolated populations are often described in recent phylogenies of Neotropical birds suggesting that the number of species in the region is underestimated. Previous COI barcoding of Argentinean bird species showed more complex patterns of regional divergence in the Neotropical than in the North American avifauna. METHODS AND FINDINGS: Here we analyzed 1,431 samples from 561 different species to extend the Neotropical bird barcode survey to lower latitudes, and detected even higher geographic structure within species than reported previously. About 93% (520 of the species were identified correctly from their DNA barcodes. The remaining 41 species were not monophyletic in their COI sequences because they shared barcode sequences with closely related species (N = 21 or contained very divergent clusters suggestive of putative new species embedded within the gene tree (N = 20. Deep intraspecific divergences overlapping with among-species differences were detected in 48 species, often with samples from large geographic areas and several including multiple subspecies. This strong population genetic structure often coincided with breaks between different ecoregions or areas of endemism. CONCLUSIONS: The taxonomic uncertainty associated with the high incidence of non-monophyletic species and discovery of putative species obscures studies of historical patterns of species diversification in the Neotropical region. We showed that COI barcodes are a valuable tool to indicate which taxa would benefit from more extensive taxonomic revisions with multilocus approaches. Moreover, our results support hypotheses that the megadiversity of birds in the region is associated with multiple geographic processes starting well before the Quaternary and extending to more recent

  17. Dark matter direct detection with non-Maxwellian velocity structure

    International Nuclear Information System (INIS)

    Kuhlen, Michael; Weiner, Neal; Diemand, Jürg; Moore, Ben; Potter, Doug; Stadel, Joachim; Madau, Piero; Zemp, Marcel

    2010-01-01

    The velocity distribution function of dark matter particles is expected to show significant departures from a Maxwell-Boltzmann distribution. This can have profound effects on the predicted dark matter - nucleon scattering rates in direct detection experiments, especially for dark matter models in which the scattering is sensitive to the high velocity tail of the distribution, such as inelastic dark matter (iDM) or light (few GeV) dark matter (LDM), and for experiments that require high energy recoil events, such as many directionally sensitive experiments. Here we determine the velocity distribution functions from two of the highest resolution numerical simulations of Galactic dark matter structure (Via Lactea II and GHALO), and study the effects for these scenarios. For directional detection, we find that the observed departures from Maxwell-Boltzmann increase the contrast of the signal and change the typical direction of incoming DM particles. For iDM, the expected signals at direct detection experiments are changed dramatically: the annual modulation can be enhanced by more than a factor two, and the relative rates of DAMA compared to CDMS can change by an order of magnitude, while those compared to CRESST can change by a factor of two. The spectrum of the signal can also change dramatically, with many features arising due to substructure. For LDM the spectral effects are smaller, but changes do arise that improve the compatibility with existing experiments. We find that the phase of the modulation can depend upon energy, which would help discriminate against background should it be found

  18. Predictive modeling of neuroanatomic structures for brain atrophy detection

    Science.gov (United States)

    Hu, Xintao; Guo, Lei; Nie, Jingxin; Li, Kaiming; Liu, Tianming

    2010-03-01

    In this paper, we present an approach of predictive modeling of neuroanatomic structures for the detection of brain atrophy based on cross-sectional MRI image. The underlying premise of applying predictive modeling for atrophy detection is that brain atrophy is defined as significant deviation of part of the anatomy from what the remaining normal anatomy predicts for that part. The steps of predictive modeling are as follows. The central cortical surface under consideration is reconstructed from brain tissue map and Regions of Interests (ROI) on it are predicted from other reliable anatomies. The vertex pair-wise distance between the predicted vertex and the true one within the abnormal region is expected to be larger than that of the vertex in normal brain region. Change of white matter/gray matter ratio within a spherical region is used to identify the direction of vertex displacement. In this way, the severity of brain atrophy can be defined quantitatively by the displacements of those vertices. The proposed predictive modeling method has been evaluated by using both simulated atrophies and MRI images of Alzheimer's disease.

  19. Structure-dependent vibrational dynamics of Mg(BH 4 ) 2 polymorphs probed with neutron vibrational spectroscopy and first-principles calculations

    Energy Technology Data Exchange (ETDEWEB)

    Dimitrievska, Mirjana; White, James L.; Zhou, Wei; Stavila, Vitalie; Klebanoff, Leonard E.; Udovic, Terrence J.

    2016-01-01

    The structure-dependent vibrational properties of different Mg(BH4)2 polymorphs (..alpha.., ..beta.., ..gamma.., and ..delta.. phases) were investigated with a combination of neutron vibrational spectroscopy (NVS) measurements and density functional theory (DFT) calculations, with emphasis placed on the effects of the local structure and orientation of the BH4- anions. DFT simulations closely match the neutron vibrational spectra. The main bands in the low-energy region (20-80 meV) are associated with the BH4- librational modes. The features in the intermediate energy region (80-120 meV) are attributed to overtones and combination bands arising from the lower-energy modes. The features in the high-energy region (120-200 meV) correspond to the BH4- symmetric and asymmetric bending vibrations, of which four peaks located at 140, 142, 160, and 172 meV are especially intense. There are noticeable intensity distribution variations in the vibrational bands for different polymorphs. This is explained by the differences in the spatial distribution of BH4- anions within various structures. An example of the possible identification of products after the hydrogenation of MgB2, using NVS measurements, is presented. These results provide fundamental insights of benefit to researchers currently studying these promising hydrogen-storage materials.

  20. Genetic effect of MTHFR C677T polymorphism on the structural covariance network and white-matter integrity in Alzheimer's disease.

    Science.gov (United States)

    Chang, Yu-Tzu; Hsu, Shih-Wei; Tsai, Shih-Jen; Chang, Ya-Ting; Huang, Chi-Wei; Liu, Mu-En; Chen, Nai-Ching; Chang, Wen-Neng; Hsu, Jung-Lung; Lee, Chen-Chang; Chang, Chiung-Chih

    2017-06-01

    The 677 C to T transition in the MTHFR gene is a genetic determinant for hyperhomocysteinemia. We investigated whether this polymorphism modulates gray matter (GM) structural covariance networks independently of white-matter integrity in patients with Alzheimer's disease (AD). GM structural covariance networks were constructed by 3D T1-magnetic resonance imaging and seed-based analysis. The patients were divided into two genotype groups: C homozygotes (n = 73) and T carriers (n = 62). Using diffusion tensor imaging and white-matter parcellation, 11 fiber bundle integrities were compared between the two genotype groups. Cognitive test scores were the major outcome factors. The T carriers had higher homocysteine levels, lower posterior cingulate cortex GM volume, and more clusters in the dorsal medial lobe subsystem showing stronger covariance strength. Both posterior cingulate cortex seed and interconnected peak cluster volumes predicted cognitive test scores, especially in the T carriers. There were no between-group differences in fiber tract diffusion parameters. The MTHFR 677T polymorphism modulates posterior cingulate cortex-anchored structural covariance strength independently of white matter integrities. Hum Brain Mapp 38:3039-3051, 2017. © 2017 The Authors Human Brain Mapping Published Wiley by Periodicals, Inc. © 2017 The Authors Human Brain Mapping Published Wiley by Periodicals, Inc.

  1. A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

    Directory of Open Access Journals (Sweden)

    Yi Li

    2017-01-01

    Full Text Available Objective A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results A total of 18 (0, 15 (3, 12 (8, 15 (18, 11 (7, and 21 (1 SNPs were detected at the 5% chromosome (genome - wise level for weaning weight (WWT, yearling weight (YWT, carcass weight (CWT, backfat thickness (BFT, longissimus dorsi muscle area (LMA and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29 were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA. Conclusion The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.

  2. Detection and Resolution of Cryptosporidium Species and Species Mixtures by Genus-Specific Nested PCR-Restriction Fragment Length Polymorphism Analysis, Direct Sequencing, and Cloning ▿

    Science.gov (United States)

    Ruecker, Norma J.; Hoffman, Rebecca M.; Chalmers, Rachel M.; Neumann, Norman F.

    2011-01-01

    Molecular methods incorporating nested PCR-restriction fragment length polymorphism (RFLP) analysis of the 18S rRNA gene of Cryptosporidium species were validated to assess performance based on limit of detection (LoD) and for detecting and resolving mixtures of species and genotypes within a single sample. The 95% LoD was determined for seven species (Cryptosporidium hominis, C. parvum, C. felis, C. meleagridis, C. ubiquitum, C. muris, and C. andersoni) and ranged from 7 to 11 plasmid template copies with overlapping 95% confidence limits. The LoD values for genomic DNA from oocysts on microscope slides were 7 and 10 template copies for C. andersoni and C. parvum, respectively. The repetitive nested PCR-RFLP slide protocol had an LoD of 4 oocysts per slide. When templates of two species were mixed in equal ratios in the nested PCR-RFLP reaction mixture, there was no amplification bias toward one species over another. At high ratios of template mixtures (>1:10), there was a reduction or loss of detection of the less abundant species by RFLP analysis, most likely due to heteroduplex formation in the later cycles of the PCR. Replicate nested PCR was successful at resolving many mixtures of Cryptosporidium at template concentrations near or below the LoD. The cloning of nested PCR products resulted in 17% of the cloned sequences being recombinants of the two original templates. Limiting-dilution nested PCR followed by the sequencing of PCR products resulted in no sequence anomalies, suggesting that this method is an effective and accurate way to study the species diversity of Cryptosporidium, particularly for environmental water samples, in which mixtures of parasites are common. PMID:21498746

  3. High-pressure polymorphism as a step towards high density structures of LiAlH{sub 4}

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Xiaoli; Duan, Defang; Li, Xin; Li, Fangfei; Huang, Yanping; Wu, Gang; Liu, Yunxian; Zhou, Qiang; Liu, Bingbing; Cui, Tian, E-mail: cuitian@jlu.edu.cn [State Key Laboratory of Superhard Materials, College of Physics, Jilin University, Changchun 130012 (China)

    2015-07-27

    Two high density structures β- and γ-LiAlH{sub 4} are detected in LiAlH{sub 4}, a promising hydrogen storage compound, upon compression in diamond anvil cells, investigated with synchrotron X-ray diffraction and first-principle calculations. The joint of the experimental and theoretical results has confirmed the sequence of the pressure-induced structural phase transitions from α-LiAlH{sub 4} (space group P2{sub 1}/c) to β-LiAlH{sub 4} (P2{sub 1}/c-6C symmetry), and then to γ-LiAlH{sub 4} (space group Pnc2), which are not reported in previous literatures. At the α to β transition point for LiAlH{sub 4}, the estimated difference in cell volume is about 20%, while the transformation from β to γ phase is with a volume drop smaller than 1%. The α to β phase transition is accompanied by the local structure change from a AlH{sub 4} tetrahedron into a AlH{sub 6} octahedron, which contributes to a large volume collapse.

  4. DETECTING PRESENCE OF C/T POLYMORPHISM AT POSITION 34 SECOND INTRON OF THE MYOSTATIN GENE IN RABBITS

    Directory of Open Access Journals (Sweden)

    Agnieszka MARKOWSKA

    2011-01-01

    Full Text Available Myostatin gene is a negative regulator of skeletal muscles growth. It is responsible for normal development of skeletal muscles. The objective of the research was to detect variation of C/T at position 34 of the second intron of the MNST gene in rabbits. The research included 114 rabbits: 54 of them Polish Rabbits, and 60 of them White Flemish Giants, examined by means of the PCR-RFLP method using AluI restriction enzyme. We found allele C with a frequency of 0.6184 of the examined rabbit population, and allele T with a frequency of 0.3816 of the examined rabbits.

  5. Heat-transfer resistance at solid-liquid interfaces: a tool for the detection of single-nucleotide polymorphisms in DNA.

    Science.gov (United States)

    van Grinsven, Bart; Vanden Bon, Natalie; Strauven, Hannelore; Grieten, Lars; Murib, Mohammed; Monroy, Kathia L Jiménez; Janssens, Stoffel D; Haenen, Ken; Schöning, Michael J; Vermeeren, Veronique; Ameloot, Marcel; Michiels, Luc; Thoelen, Ronald; De Ceuninck, Ward; Wagner, Patrick

    2012-03-27

    In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA. © 2012 American Chemical Society

  6. Combination of Complement-Dependent Cytotoxicity and Relative Fluorescent Quantification of HLA Length Polymorphisms Facilitates the Detection of a Loss of Heterozygosity

    Directory of Open Access Journals (Sweden)

    Klaus Witter

    2014-01-01

    Full Text Available Loss of heterozygosity (LOH is a common event in malignant cells. In this work we introduce a new approach to identify patients with loss of heterozygosity in the HLA region either at first diagnosis or after HLA mismatched allogeneic HSCT. Diagnosis of LOH requires a high purity of recipient target cells. FACS is time consuming and also frequently prevented by rather nonspecific or unknown immune phenotype. The approach for recipient cell enrichment is based on HLA targeted complement-dependent cytotoxicity (CDC. Relative fluorescent quantification (RFQ analysis of HLA intron length polymorphisms then allows analysis of HLA heterozygosity. The approach is exemplified in recent clinical cases illustrating the detection of an acquired allele loss. As illustrated in one case with DPB1, distinct HLA loci in donor and patient were sufficient for both proof of donor cell removal and evaluation of allele loss in the patient's leukemic cells. Results were confirmed using HLA-B RFQ analysis and leukemia-associated aberrant immunophenotype (LAIP based cell sort. Both results confirmed suspected loss of HLA heterozygosity. Our approach complements or substitutes for FACS-based cell enrichment; hence it may be further developed as novel routine diagnostic tool. This allows rapid recipient cell purification and testing for loss of HLA heterozygosity before and after allogeneic HSCT in easily accessible peripheral blood samples.

  7. Structural health monitoring and probability of detection estimation

    Science.gov (United States)

    Forsyth, David S.

    2016-02-01

    Structural health monitoring (SHM) methods are often based on nondestructive testing (NDT) sensors and are often proposed as replacements for NDT to lower cost and/or improve reliability. In order to take advantage of SHM for life cycle management, it is necessary to determine the Probability of Detection (POD) of the SHM system just as for traditional NDT to ensure that the required level of safety is maintained. Many different possibilities exist for SHM systems, but one of the attractive features of SHM versus NDT is the ability to take measurements very simply after the SHM system is installed. Using a simple statistical model of POD, some authors have proposed that very high rates of SHM system data sampling can result in high effective POD even in situations where an individual test has low POD. In this paper, we discuss the theoretical basis for determining the effect of repeated inspections, and examine data from SHM experiments against this framework to show how the effective POD from multiple tests can be estimated.

  8. Damage Detection Using Lamb Waves for Structural Health Monitoring

    National Research Council Canada - National Science Library

    Crider II, Jeffrey S

    2007-01-01

    .... This study evaluates Lamb wave approaches used to detect simulated cracks in laboratory experiments on thin plates to detect more realistic damage in a test article representing the complex geometry...

  9. Quail FMO3 gene cloning, tissue expression profiling, polymorphism detection and association analysis with fishy taint in eggs.

    Directory of Open Access Journals (Sweden)

    Fengtao Mo

    Full Text Available Quail eggs comprise a significant and favourable part of table eggs in certain countries. Some quail eggs, however, present fishy off-flavor which directly influences their quality. It is reported that flavin-containing monooxygenase 3 (FMO3 is associated with fish-odour trait in human and animal products. FMO3 is responsible for the degradation of trimethylamine (TMA in vivo. Loss-of-function mutations in FMO3 gene can result in defective TMA N-oxygenation, giving rise to disorder known as "fish-odour syndrome" in human, as well as the fishy off-flavor in cow milk and chicken eggs. In order to reveal the genetic factor of fishy taint in quail eggs, we cloned the cDNA sequence of quail FMO3 gene, investigated FMO3 mRNA expression level in various tissues, detected SNPs in the coding region of the gene and conducted association analysis between a mutation and the TMA content in quail egg yolks. The 1888 bp cDNA sequence of quail FMO3 gene encoding 532 amino acids was obtained and characterized. The phylogenetic analysis revealed quail FMO3 had a closer relationship with chicken FMO3. The FMO3 mRNA was highly expressed in liver and kidney of quail. Nine SNPs were detected in the coding sequence of quail FMO3 gene, including a nonsense mutation (Q319X which was significantly associated with the elevated TMA content in quail egg yolks. Genotype TT at Q319X mutation loci was sensitive to choline. With addition of choline in the feed, the quails with homozygote TT at the Q319X mutation loci laid fish-odour eggs, indicating an interaction between genotype and diet. The results indicated that Q319X mutation was associated with the fishy off-flavor in quail eggs. Identification of the unfavorable allele T of quail FMO3 gene can be applied in future quail breeding to eliminate fishy off-flavor trait in quail eggs.

  10. Polymorphic Contracts

    Science.gov (United States)

    Belo, João Filipe; Greenberg, Michael; Igarashi, Atsushi; Pierce, Benjamin C.

    Manifest contracts track precise properties by refining types with predicates - e.g., {x : Int |x > 0 } denotes the positive integers. Contracts and polymorphism make a natural combination: programmers can give strong contracts to abstract types, precisely stating pre- and post-conditions while hiding implementation details - for example, an abstract type of stacks might specify that the pop operation has input type {x :α Stack |not ( empty x )} . We formalize this combination by defining FH, a polymorphic calculus with manifest contracts, and establishing fundamental properties including type soundness and relational parametricity. Our development relies on a significant technical improvement over earlier presentations of contracts: instead of introducing a denotational model to break a problematic circularity between typing, subtyping, and evaluation, we develop the metatheory of contracts in a completely syntactic fashion, omitting subtyping from the core system and recovering it post facto as a derived property.

  11. Detection of a periodic structure hidden in random background: the role of signal amplitude in the matched filter detection method

    International Nuclear Information System (INIS)

    Vani, V C; Chatterjee, S

    2010-01-01

    The matched filter method for detecting a periodic structure on a surface hidden behind randomness is known to detect up to (r 0 /Λ)≥0.11, where r 0 is the coherence length of light on scattering from the rough part and Λ is the wavelength of the periodic part of the surface-the above limit being much lower than what is allowed by conventional detection methods. The primary goal of this technique is the detection and characterization of the periodic structure hidden behind randomness without the use of any complicated experimental or computational procedures. This paper examines this detection procedure for various values of the amplitude a of the periodic part beginning from a=0 to small finite values of a. We thus address the importance of the following quantities: '(a/λ)', which scales the amplitude of the periodic part with the wavelength of light, and (r 0 /Λ), in determining the detectability of the intensity peaks.

  12. Detection of the Single Nucleotide Polymorphism at Position rs2735940 in the Human Telomerase Reverse Transcriptase Gene by the Introduction of a New Restriction Enzyme Site for the PCR-RFLP Assay.

    Science.gov (United States)

    Wang, Sihua; Ding, Mingcui; Duan, Xiaoran; Wang, Tuanwei; Feng, Xiaolei; Wang, Pengpeng; Yao, Wu; Wu, Yongjun; Yan, Zhen; Feng, Feifei; Yu, Songcheng; Wang, Wei

    2017-09-01

    It has been shown that the single nucleotide polymorphism (SNP) of the rs2735940 site in the human telomerase reverse transcriptase ( hTERT ) gene is associated with increased cancer risk. The traditional method to detect SNP genotypes is polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). However, there is a limitation to utilizing PCR-RFLP due to a lack of proper restriction enzyme sites at many polymorphic loci. This study used an improved PCR-RFLP method with a mismatched base for detection of the SNP rs2735940. A new restriction enzyme cutting site was created by created restriction site PCR (CRS-PCR), and in addition, the restriction enzyme Msp I for CRS-PCR was cheaper than other enzymes. We used this novel assay to determine the allele frequencies in 552 healthy Chinese Han individuals, and found the allele frequencies to be 63% for allele C and 37% for allele T In summary, the modified PCR-RFLP can be used to detect the SNP of rs2735940 with low cost and high efficiency. © 2017 by the Association of Clinical Scientists, Inc.

  13. A monoclinic polymorph of theophylline

    Directory of Open Access Journals (Sweden)

    Shuo Zhang

    2011-12-01

    Full Text Available A monoclinic polymorph of theophylline, C7H8N4O2, has been obtained from a chloroform/methanol mixture by evaporation under ambient conditions. The new polymorph crystallizes with two molecules in the asymmetric unit. The structure features intermolecular N—H...O hydrogen bonds, resulting in the formation of dimers between two crystallographically different molecules; each molecule acts as both donor and acceptor.

  14. Detection of a 4-bp Insertion/deletion Polymorphism within the Promoter of EGLN2 Using Mismatch PCR-RFLP and Its Association with Susceptibility to Breast Cancer

    Science.gov (United States)

    Hashemi, Mohammad; Danesh, Hiva; Bizhani, Fatemeh; Sattarifard, Hedieh; Hashemi, Seyed Mehdi; Bahari, Gholamreza

    2018-04-25

    It has been shown that a 4-bp insertion/deletion (ins/del) polymorphism of EGLN2 influences the risk of several cancers. However, to date, no study has inspected the impact of the 4-bp ins/del polymorphism on breast cancer (BC) risk. A case-control study, including 134 breast cancer patients and 154 healthy women, was here conducted to examine the possible association between EGLN2 4-bp ins/del polymorphism and BC risk in a southeast Iranian population. A mismatched polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was designed for genotyping of the variant. Our findings did not support any association between the 4-bp ins/del polymorphism and the risk of BC in the codominant, dominant, recessive and allele inheritance models tested. When links between the EGLN2 4-bp ins/del polymorphism and clinicopathological characteristics of the patients were evaluate the variant was only associated with HER2 status. More studies with larger sample sizes and diverse ethnicities are warranted to verify our finding. Creative Commons Attribution License

  15. Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group

    Science.gov (United States)

    Kong, Tingting; Chen, Yahao; Guo, Yuxin; Wei, Yuanyuan; Jin, Xiaoye; Xie, Tong; Mu, Yuling; Dong, Qian; Wen, Shaoqing; Zhou, Boyan; Zhang, Li; Shen, Chunmei; Zhu, Bofeng

    2017-01-01

    In the present study, we assessed the genetic diversities of the Chinese Kazak ethnic group on the basis of 30 well-chosen autosomal insertion and deletion loci and explored the genetic relationships between Kazak and 23 reference groups. We detected the level of the expected heterozygosity ranging from 0.3605 at HLD39 locus to 0.5000 at HLD136 locus and the observed heterozygosity ranging from 0.3548 at HLD39 locus to 0.5283 at HLD136 locus. The combined power of discrimination and the combined power of exclusion for all 30 loci in the studied Kazak group were 0.999999999999128 and 0.9945, respectively. The dataset generated in this study indicated the panel of 30 InDels was highly efficient in forensic individual identifcation but may not have enough power in paternity cases. The results of the interpopulation differentiations, PCA plots, phylogenetic trees and STRUCTURE analyses showed a close genetic affiliation between the Kazak and Uigur group. PMID:28915619

  16. Identification, detection, and validation of vibrating structures: a signal processing approach

    International Nuclear Information System (INIS)

    Candy, J.V.; Lager, D.L.

    1979-01-01

    This report discusses the application of modern signal processing techniques to characterize parameters governing the vibrational response of a structure. Simulated response data is used to explore the feasibility of applying these techniques to various structural problems. On-line estimator/indentifiers are used to estimate structural parameters, validate designed structures, and detect structural failure when used with a detector

  17. Detection of Hereditary 1,25-Hydroxyvitamin D-Resistant Rickets Caused by Uniparental Disomy of Chromosome 12 Using Genome-Wide Single Nucleotide Polymorphism Array.

    Directory of Open Access Journals (Sweden)

    Mayuko Tamura

    Full Text Available Hereditary 1,25-dihydroxyvitamin D-resistant rickets (HVDRR is an autosomal recessive disease caused by biallelic mutations in the vitamin D receptor (VDR gene. No patients have been reported with uniparental disomy (UPD.Using genome-wide single nucleotide polymorphism (SNP array to confirm whether HVDRR was caused by UPD of chromosome 12.A 2-year-old girl with alopecia and short stature and without any family history of consanguinity was diagnosed with HVDRR by typical laboratory data findings and clinical features of rickets. Sequence analysis of VDR was performed, and the origin of the homozygous mutation was investigated by target SNP sequencing, short tandem repeat analysis, and genome-wide SNP array.The patient had a homozygous p.Arg73Ter nonsense mutation. Her mother was heterozygous for the mutation, but her father was negative. We excluded gross deletion of the father's allele or paternal discordance. Genome-wide SNP array of the family (the patient and her parents showed complete maternal isodisomy of chromosome 12. She was successfully treated with high-dose oral calcium.This is the first report of HVDRR caused by UPD, and the third case of complete UPD of chromosome 12, in the published literature. Genome-wide SNP array was useful for detecting isodisomy and the parental origin of the allele. Comprehensive examination of the homozygous state is essential for accurate genetic counseling of recurrence risk and appropriate monitoring for other chromosome 12 related disorders. Furthermore, oral calcium therapy was effective as an initial treatment for rickets in this instance.

  18. A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.

    LENUS (Irish Health Repository)

    Song, Yajun

    2010-08-01

    OBJECTIVES: Decreased susceptibility to fluoroquinolones has become a major problem for the successful therapy of human infections caused by Salmonella enterica, especially the life-threatening typhoid and paratyphoid fevers. METHODS: By using Luminex xTAG beads, we developed a rapid, reliable and cost-effective multiplexed genotyping assay for simultaneously detecting 11 mutations in gyrA, gyrB and parE of S. enterica serovars Typhi and Paratyphi A that result in nalidixic acid resistance (Nal(R)) and\\/or decreased susceptibility to fluoroquinolones. RESULTS: This assay yielded unambiguous single nucleotide polymorphism calls on extracted DNA from 292 isolates of Salmonella Typhi (Nal(R) = 223 and Nal(S) = 69) and 106 isolates of Salmonella Paratyphi A (Nal(R) = 24 and Nal(S) = 82). All of the 247 Nal(R) Salmonella Typhi and Salmonella Paratyphi A isolates were found to harbour at least one of the target mutations, with GyrA Phe-83 as the most common one (143\\/223 for Salmonella Typhi and 18\\/24 for Salmonella Paratyphi A). We also identified three GyrB mutations in eight Nal(S) Salmonella Typhi isolates (six for GyrB Phe-464, one for GyrB Leu-465 and one for GyrB Asp-466), and mutations GyrB Phe-464 and GyrB Asp-466 seem to be related to the decreased ciprofloxacin susceptibility phenotype in Salmonella Typhi. This assay can also be used directly on boiled single colonies. CONCLUSIONS: The assay presented here would be useful for clinical and reference laboratories to rapidly screen quinolone-resistant isolates of Salmonella Typhi and Salmonella Paratyphi A, and decipher the underlying genetic changes for epidemiological purposes.

  19. Statistical methods for damage detection applied to civil structures

    DEFF Research Database (Denmark)

    Gres, Szymon; Ulriksen, Martin Dalgaard; Döhler, Michael

    2017-01-01

    Damage detection consists of monitoring the deviations of a current system from its reference state, characterized by some nominal property repeatable for every healthy state. Preferably, the damage detection is performed directly on vibration data, hereby avoiding modal identification of the str...

  20. Statistical Damage Detection of Civil Engineering Structures using ARMAV Models

    DEFF Research Database (Denmark)

    Andersen, P.; Kirkegaard, Poul Henning

    In this paper a statistically based damage detection of a lattice steel mast is performed. By estimation of the modal parameters and their uncertainties it is possible to detect whether some of the modal parameters have changed with a statistical significance. The estimation of the uncertainties ...

  1. Impact of the canine double-deletion β1 adrenoreceptor polymorphisms on protein structure and heart rate response to atenolol, a β1-selective β-blocker.

    Science.gov (United States)

    Meurs, Kathryn M; Stern, Josh A; Reina-Doreste, Yamir; Maran, Brian A; Chdid, Lhoucine; Lahmers, Sunshine; Keene, Bruce W; Mealey, Katrina L

    2015-09-01

    β-Adrenergic receptor antagonists are widely utilized for the management of cardiac diseases in dogs. We have recently identified two deletion polymorphisms in the canine adrenoreceptor 1 (ADRB1) gene.We hypothesized that canine ADRB1 deletions would alter the structure of the protein, as well as the heart rate response to the β-adrenergic receptor antagonist, atenolol. The objectives of this study were to predict the impact of these deletions on the predicted structure of the protein and on the heart rate response to atenolol in a population of healthy adult dogs. Eighteen apparently healthy, mature dogs with (11) and without (seven) ADRB1 deletions were evaluated. The heart rate of the dogs was evaluated with a baseline ambulatory ECG before and 14-21 days after atenolol therapy (1 mg/kg orally q12 h). Minimum, average, and maximum heart rates were compared between groups of dogs (deletions, controls) using an unpaired t-test and within each group of dogs using a paired t-test. The protein structure of ADRB1 was predicted by computer modeling. Deletions were predicted to alter the structure of the ADRB1 protein. The heart rates of the dogs with deletions were lower than those of the control dogs (the average heart rates were significantly lower). ADRB1 deletions appear to have structural and functional consequences. Individual genome-based treatment recommendations could impact the management of dogs with heart disease.

  2. CaCO3-III and CaCO3-VI, high-pressure polymorphs of calcite: Possible host structures for carbon in the Earth's mantle

    Science.gov (United States)

    Merlini, M.; Hanfland, M.; Crichton, W. A.

    2012-06-01

    Calcite, CaCO3, undergoes several high pressure phase transitions. We report here the crystal structure determination of the CaCO3-III and CaCO3-VI high-pressure polymorphs obtained by single-crystal synchrotron X-ray diffraction. This new technical development at synchrotron beamlines currently affords the possibility of collecting single-crystal data suitable for structure determination in-situ at non-ambient conditions, even after multiphase transitions. CaCO3-III, observed in the pressure range 2.5-15 GPa, is triclinic, and it presents two closely related structural modifications, one, CaCO3-III, with 50 atoms in the unit cell [a=6.281(1) Å, b=7.507(2) Å, c=12.516(3) Å, α=93.76(2)°, β=98.95(2)°, γ=106.49(2)°, V=555.26(20) Å3 at 2.8 GPa], the second, CaCO3-IIIb, with 20 atoms [a=6.144(3) Å, b=6.3715(14) Å, c=6.3759(15) Å, α= 93.84(2)°, β=107.34(3)°, γ=107.16(3)°, V=224.33(13) Å3 at 3.1 GPa]. Different pressure-time experimental paths can stabilise one or the other polymorph. Both structures are characterised by the presence of non-coplanar CO3 groups. The densities of CaCO3-III (2.99 g/cm3 at 2.8 GPa) and CaCO3-IIIb (2.96 g/cm3 at 3.1 GPa) are lower than aragonite, in agreement with the currently accepted view of aragonite as the thermodynamically stable Ca-carbonate phase at these pressures. The presence of different cation sites, with variable volume and coordination number (7-9), suggests however that these structures have the potential to accommodate cations with different sizes without introducing major structural strain. Indeed, this structure can be adopted by natural Ca-rich carbonates, which often exhibit compositions deviating from pure calcite. Mg-calcites are found both in nature (Frezzotti et al., 2011) and in experimental syntheses at conditions corresponding to deep subduction environments (Poli et al., 2009). At these conditions, the low pressure rhombohedral calcite structure is most unlikely to be stable, and, at the same

  3. How to detect and visualize extinction thresholds for structured PVA models

    NARCIS (Netherlands)

    Hildenbrandt, H.; Grimm, V.

    2006-01-01

    An extinction threshold is a population size below which extinction risk increases to beyond critical values. However, detecting extinction thresholds for structured population models is not straightforward because many different population structures may correspond to the same population size.

  4. Salient man-made structure detection in infrared images

    Science.gov (United States)

    Li, Dong-jie; Zhou, Fu-gen; Jin, Ting

    2013-09-01

    Target detection, segmentation and recognition is a hot research topic in the field of image processing and pattern recognition nowadays, among which salient area or object detection is one of core technologies of precision guided weapon. Many theories have been raised in this paper; we detect salient objects in a series of input infrared images by using the classical feature integration theory and Itti's visual attention system. In order to find the salient object in an image accurately, we present a new method to solve the edge blur problem by calculating and using the edge mask. We also greatly improve the computing speed by improving the center-surround differences method. Unlike the traditional algorithm, we calculate the center-surround differences through rows and columns separately. Experimental results show that our method is effective in detecting salient object accurately and rapidly.

  5. Analyses Of Techniques On Structural Fatigue Failure Detection ...

    African Journals Online (AJOL)

    Machines and structures are subjected to variable loading conditions where the stress cycle does not remain the same during the operation of the machine. Fatigue is undoubtedly one of the most serious of all causes of breakdowns of machines and structures which results in sudden failures. The use of the time domain ...

  6. Combined Data with Particle Swarm Optimization for Structural Damage Detection

    Directory of Open Access Journals (Sweden)

    Fei Kang

    2013-01-01

    Full Text Available This paper proposes a damage detection method based on combined data of static and modal tests using particle swarm optimization (PSO. To improve the performance of PSO, some immune properties such as selection, receptor editing, and vaccination are introduced into the basic PSO and an improved PSO algorithm is formed. Simulations on three benchmark functions show that the new algorithm performs better than PSO. The efficiency of the proposed damage detection method is tested on a clamped beam, and the results demonstrate that it is more efficient than PSO, differential evolution, and an adaptive real-parameter simulated annealing genetic algorithm.

  7. A comparison of damage detection methods applied to civil engineering structures

    DEFF Research Database (Denmark)

    Gres, Szymon; Andersen, Palle; Johansen, Rasmus Johan

    2018-01-01

    Facilitating detection of early-stage damage is crucial for in-time repairs and cost-optimized maintenance plans of civil engineering structures. Preferably, the damage detection is performed by use of output vibration data, hereby avoiding modal identification of the structure. Most of the work...

  8. A comparison of damage detection methods applied to civil engineering structures

    DEFF Research Database (Denmark)

    Gres, Szymon; Andersen, Palle; Johansen, Rasmus Johan

    2017-01-01

    Facilitating detection of early-stage damage is crucial for in-time repairs and cost-optimized maintenance plans of civil engineering structures. Preferably, the damage detection is performed by use of output vibration data, hereby avoiding modal identification of the structure. Most of the work...

  9. Structural and abinitio studies on the polymorphism of iminophosphorane (CH3C6H4)3Pdbnd NP[(dbnd O)(OPh)2

    Science.gov (United States)

    Petric, Mihaela F.; Crisan, Manuela E.; Chumakov, Yurii M.; Varga, Richard A.; Micle, Andreea; Neda, Ion; Ilia, Gheorghe

    2015-03-01

    Two polymorphic forms of a new iminophosphorane have been investigated by infrared, nuclear magnetic resonance and mass spectroscopy, X-ray crystallography and studied through ab initio quantum chemical calculations. The monoclinic polymorph α contains two independent molecules (αI and αII) in the asymmetric unit, while the orthorhombic polymorph ß has one molecule in the asymmetric unit. The molecules in polymorphs α and β adopt different conformations. Hirshfeld surfaces and fingerprint plots were generated in order to compare the two independent molecules αI and αII in the asymmetric unit and also for a comparison of ß molecule, in the orthorhombic crystal system, with the previously reported monoclinic polymorph. The results show that the packing motifs in polymorphs α and β differ mainly due to the redistribution of Csbnd H⋯O and Csbnd H⋯π hydrogen-bond interactions rather than their percentage Hirshfeld surface area contributions. The dipole-dipole interactions significantly influence the intermolecular interactions in polymorphs α and β. The calculated lattice energies indicate that polymorph α is slightly more stable than polymorph α.

  10. A cost-effective melting temperature assay for the detection of single-nucleotide polymorphism in the MBL2 gene of HIV-1-infected children

    Directory of Open Access Journals (Sweden)

    Arraes L.C.

    2006-01-01

    Full Text Available We report a fast (less than 3 h and cost-effective melting temperature assay method for the detection of single-nucleotide polymorphisms in the MBL2 gene. The protocol, which is based on the Corbett Rotor Gene real time PCR platform and SYBR Green I chemistry, yielded, in the cohorts studied, sensitive (100% and specific (100% PCR amplification without the use of costly fluorophore-labeled probes or post-PCR manipulation. At the end of the PCR, the dissociation protocol included a slow heating from 60º to 95ºC in 0.2ºC steps, with an 8-s interval between steps. Melting curve profiles were obtained using the dissociation software of the Rotor Gene-3000 apparatus. Samples were analyzed in duplicate and in different PCR runs to test the reproducibility of this technique. No supplementary data handling is required to determine the MBL2 genotype. MBL2 genotyping performed on a cohort of 164 HIV-1-positive Brazilian children and 150 healthy controls, matched for age and sex and ethnic origin, yielded reproducible results confirmed by direct sequencing of the amplicon performed in blind. The three MBL2 variants (Arg52Cys, Gly54Asp, Gly57Glu were grouped together and called allele 0, while the combination of three wild-type alleles was called allele A. The frequency of the A/A homozygotes was significantly higher among healthy controls (0.68 than in HIV-infected children (0.55; P = 0.0234 and the frequency of MBL2 0/0 homozygotes was higher among HIV-1-infected children than healthy controls (P = 0.0296. The 0 allele was significantly more frequent among the 164 HIV-1-infected children (0.29 than among the 150 healthy controls (0.18; P = 0.0032. Our data confirm the association between the presence of the mutated MBL2 allele (allele 0 and HIV-1 infection in perinatally exposed children. Our results are in agreement with the literature data which indicate that the presence of the allele 0 confers a relative risk of 1.37 for HIV-1 infection through

  11. Effect of PECVD deposition parameters on structural and optoelectronics properties of hydrogenated polymorphous silicon thin films deposited by dichlorosilane for implementation in solar cells

    International Nuclear Information System (INIS)

    Álvarez-Macías, C.; Hernández González, Oscar Daniel; Barrera Calva, Enrique; Gómez González, L.; Santana, G.

    2015-01-01

    Hydrogenated polymorphous silicon (pm-Si: H) thin films were deposited at room temperature by plasma enhanced chemical vapor deposition (PECVD) using SiH2Cl2 as precursor gas. We examine the effect of deposition pressure (250 y 500 mTorr) and H2 dilution (flow rates 25, 50, 75 y 100 sccm) on the structural and optoelectronics properties. The nano-structural properties was confirmed by Raman spectroscopy studies in terms of the changes in crystallite sizes and their volume fractions. On the other hand, by FTIR analysis we notice bond configurations associated to photostability of the nanostructures, which was confirmed by Light soaking experiments during 250h. We found a tunable band gap and important behaviors on the electronic transport properties measurements for samples with high and low incorporation of oxygen whose compositions were determined by XPS measurements. Understanding structural and chemical properties of pm- Si: H thin films is key towards optimizing their electrical and optical properties for applications in solar cells. (full text)

  12. Detection of a periodic structure embedded in surface roughness, for ...

    Indian Academy of Sciences (India)

    sary to distinguish between the two cases, i.e. a = 0 and a = amatched (value of a obtained by matched ..... This procedure has the following advantages: .... is fair. The fact that for smaller values of y, detection becomes difficult, results from the.

  13. cDNA cloning, structural analysis, SNP detection and tissue ...

    Indian Academy of Sciences (India)

    THOMAS NAICY

    detection and tissue expression profile of the IGF1 gene in Malabari and Attappady Black goats of India. J. Genet. ... Keywords. gene cloning; gene expression; goat; insulin-like growth factor 1; mRNA; single-nucleotide ..... cle tenderness (Koohmaraie et al. .... growth factor (IGF) system in the bovine oviduct at oestrus and.

  14. Detecting the temporal structure of sound sequences in newborn infants

    NARCIS (Netherlands)

    Háden, G.P.; Honing, H.; Török, M.; Winkler, I.

    2015-01-01

    Most high-level auditory functions require one to detect the onset and offset of sound sequences as well as registering the rate at which sounds are presented within the sound trains. By recording event-related brain potentials to onsets and offsets of tone trains as well as to changes in the

  15. Classification of projection images of proteins with structural polymorphism by manifold: A simulation study for x-ray free-electron laser diffraction imaging

    Science.gov (United States)

    Yoshidome, Takashi; Oroguchi, Tomotaka; Nakasako, Masayoshi; Ikeguchi, Mitsunori

    2015-09-01

    Coherent x-ray diffraction imaging (CXDI) enables us to visualize noncrystalline sample particles with micrometer to submicrometer dimensions. Using x-ray free-electron laser (XFEL) sources, two-dimensional diffraction patterns are collected from fresh samples supplied to the irradiation area in the "diffraction-before-destruction" scheme. A recent significant increase in the intensity of the XFEL pulse is promising and will allow us to visualize the three-dimensional structures of proteins using XFEL-CXDI in the future. For the protocol proposed for molecular structure determination using future XFEL-CXDI [T. Oroguchi and M. Nakasako, Phys. Rev. E 87, 022712 (2013), 10.1103/PhysRevE.87.022712], we require an algorithm that can classify the data in accordance with the structural polymorphism of proteins arising from their conformational dynamics. However, most of the algorithms proposed primarily require the numbers of conformational classes, and then the results are biased by the numbers. To improve this point, here we examine whether a method based on the manifold concept can classify simulated XFEL-CXDI data with respect to the structural polymorphism of a protein that predominantly adopts two states. After random sampling of the conformations of the two states and in-between states from the trajectories of molecular dynamics simulations, a diffraction pattern is calculated from each conformation. Classification was performed by using our custom-made program suite named enma, in which the diffusion map (DM) method developed based on the manifold concept was implemented. We successfully classify most of the projection electron density maps phase retrieved from diffraction patterns into each of the two states and in-between conformations without the knowledge of the number of conformational classes. We also examined the classification of the projection electron density maps of each of the three states with respect to the Euler angle. The present results suggest

  16. Advanced photonic structures for biological and chemical detection

    CERN Document Server

    Fan, Xudong

    2009-01-01

    One of a series of books on Integrated Microanalytical Systems, this text discusses the latest applications of photonic technologies in bio/chemical sensing. The book is divided into four sections, each one being based on photonic structures.

  17. Occlusion detection via structured sparse learning for robust object tracking

    KAUST Repository

    Zhang, Tianzhu; Ghanem, Bernard; Xu, Changsheng; Ahuja, Narendra

    2014-01-01

    occlusion through structured sparse learning. We test our tracker on challenging benchmark sequences, such as sports videos, which involve heavy occlusion, drastic illumination changes, and large pose variations. Extensive experimental results show that our

  18. Object tracking by occlusion detection via structured sparse learning

    KAUST Repository

    Zhang, Tianzhu; Ghanem, Bernard; Xu, Changsheng; Ahuja, Narendra

    2013-01-01

    occlusion through structured sparse learning. We test our tracker on challenging benchmark sequences, such as sports videos, which involve heavy occlusion, drastic illumination changes, and large pose variations. Experimental results show that our tracker

  19. Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii.

    Science.gov (United States)

    McAllister, Christine A; Miller, Allison J

    2016-07-01

    Autopolyploidy, genome duplication within a single lineage, can result in multiple cytotypes within a species. Geographic distributions of cytotypes may reflect the evolutionary history of autopolyploid formation and subsequent population dynamics including stochastic (drift) and deterministic (differential selection among cytotypes) processes. Here, we used a population genomic approach to investigate whether autopolyploidy occurred once or multiple times in Andropogon gerardii, a widespread, North American grass with two predominant cytotypes. Genotyping by sequencing was used to identify single nucleotide polymorphisms (SNPs) in individuals collected from across the geographic range of A. gerardii. Two independent approaches to SNP calling were used: the reference-free UNEAK pipeline and a reference-guided approach based on the sequenced Sorghum bicolor genome. SNPs generated using these pipelines were analyzed independently with genetic distance and clustering. Analyses of the two SNP data sets showed very similar patterns of population-level clustering of A. gerardii individuals: a cluster of A. gerardii individuals from the southern Plains, a northern Plains cluster, and a western cluster. Groupings of individuals corresponded to geographic localities regardless of cytotype: 6x and 9x individuals from the same geographic area clustered together. SNPs generated using reference-guided and reference-free pipelines in A. gerardii yielded unique subsets of genomic data. Both data sets suggest that the 9x cytotype in A. gerardii likely evolved multiple times from 6x progenitors across the range of the species. Genomic approaches like GBS and diverse bioinformatics pipelines used here facilitate evolutionary analyses of complex systems with multiple ploidy levels. © 2016 Botanical Society of America.

  20. The rs1527483, but not rs3212018, CD36 polymorphism associates with linoleic acid detection and obesity in Czech young adults

    Czech Academy of Sciences Publication Activity Database

    Plesník, J.; Šerý, Omar; Khan, A. S.; Bielik, P.; Khan, N. A.

    2018-01-01

    Roč. 119, č. 4 (2018), s. 472-478 ISSN 0007-1145 R&D Projects: GA MZd(CZ) NV16-29900A Institutional support: RVO:67985904 Keywords : CD36 * fat taste * genetic polymorphism * rs1527483 Subject RIV: ED - Physiology OBOR OECD: Physiology (including cytology) Impact factor: 3.706, year: 2016

  1. Orosensory detection of bitter in fat-taster healthy and obese participants: Genetic polymorphism of CD36 and TAS2R38

    Czech Academy of Sciences Publication Activity Database

    Karmous, I.; Plesník, J.; Khan, A. S.; Šerý, Omar; Abid, A.; Mankai, A.; Aouidet, A.; Khan, N. A.

    2018-01-01

    Roč. 37, č. 1 (2018), s. 313-320 ISSN 0261-5614 Institutional support: RVO:67985904 Keywords : obesity * fat taste * bitter taste * genetic polymorphism Subject RIV: ED - Physiology OBOR OECD: Physiology (including cytology) Impact factor: 4.548, year: 2016

  2. A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

    Science.gov (United States)

    Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

    2012-09-01

    Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

  3. Structural material anomaly detection system using water chemistry data

    International Nuclear Information System (INIS)

    Asakura, Yamato; Nagase, Makoto; Uchida, Shunsuke; Ohsumi, Katsumi.

    1992-01-01

    The concept of an advanced water chemistry diagnosis system for detection of anomalies and preventive maintenance of system components is proposed and put into a concrete form. Using the analogy to a medical inspection system, analyses of water chemistry change will make it possible to detect symptoms of anomalies in system components. Then, correlations between water chemistry change and anomaly occurrence in the components of the BWR primary cooling system are analyzed theoretically. These fragmentary correlations are organized and reduced to an algorithm for the on-line diagnosis system using on-line monitoring data, pH and conductivity. By using actual plant data, the on-line diagnosis model system is verified to be applicable for early and automatic finding of the anomaly cause and for timely supply of much diagnostic information to plant operators. (author)

  4. Structural material anomaly detection system using water chemistry data, (7)

    International Nuclear Information System (INIS)

    Nagase, Makoto; Uchida, Shunsuke; Asakura, Yamato; Ohsumi, Katsumi.

    1993-01-01

    A method to detect small changes in water quality and diagnose their causes by analyzing on-line conductivity and pH data was proposed. Laboratory tests showed that effective noise reduction of measured on-line data could be got by using median filter to detect small changes of conductivity ; a relative change of 0.001 μS/cm was distinguishable. By simulating the changes of pH and conductivity in the reactor water against a small concentration change of sodium ion or sulfate ion in the feedwater, it was found that an adequate elapsed time for the diagnosis was 4 h from the start of the concentration change. A conductivity difference of 0.001 μS/cm in the reactor water made it theoretically possible to distinguish between a sodium ion concentration change of 4.6 ppt and a sulfate ion concentration change of 9.6 ppt in the feedwater. (author)

  5. New polymorphic mtDNA restriction site in the 12S rRNA gene detected in Tunisian patients with non-syndromic hearing loss

    International Nuclear Information System (INIS)

    Mkaouar-Rebai, Emna; Tlili, Abdelaziz; Masmoudi, Saber; Charfeddine, Ilhem; Fakhfakh, Faiza

    2008-01-01

    The 12S rRNA gene was shown to be a hot spot for aminoglycoside-induced and non-syndromic hearing loss since several deafness-associated mtDNA mutations were identified in this gene. Among them, we distinguished the A1555G, the C1494T and the T1095C mutations and C-insertion or deletion at position 961. One hundred Tunisian patients with non-syndromic hearing loss and 100 hearing individuals were analysed in this study. A PCR-RFLP analysis with HaeIII restriction enzyme showed the presence of the A1555G mutation in the 12S rRNA gene in only one out of the 100 patients. In addition, PCR-RFLP and radioactive PCR revealed the presence of a new HaeIII polymorphic restriction site in the same gene of 12S rRNA site in 4 patients with non-syndromic hearing loss. UVIDOC-008-XD analyses showed the presence of this new polymorphic restriction site with a variable heteroplasmic rates at position +1517 of the human mitochondrial genome. On the other hand, direct sequencing of the entire mitochondrial 12S rRNA gene in the 100 patients and in 100 hearing individuals revealed the presence of the A750G and A1438G polymorphisms and the absence of the C1494T, T1095C and 961insC mutations in all the tested individuals. Sequencing of the whole mitochondrial genome in the 4 patients showing the new HaeIII polymorphic restriction site revealed only the presence of the A8860G transition in the MT-ATP6 gene and the A4769G polymorphism in the ND2 gene

  6. A soft kinetic data structure for lesion border detection.

    Science.gov (United States)

    Kockara, Sinan; Mete, Mutlu; Yip, Vincent; Lee, Brendan; Aydin, Kemal

    2010-06-15

    The medical imaging and image processing techniques, ranging from microscopic to macroscopic, has become one of the main components of diagnostic procedures to assist dermatologists in their medical decision-making processes. Computer-aided segmentation and border detection on dermoscopic images is one of the core components of diagnostic procedures and therapeutic interventions for skin cancer. Automated assessment tools for dermoscopic images have become an important research field mainly because of inter- and intra-observer variations in human interpretations. In this study, a novel approach-graph spanner-for automatic border detection in dermoscopic images is proposed. In this approach, a proximity graph representation of dermoscopic images in order to detect regions and borders in skin lesion is presented. Graph spanner approach is examined on a set of 100 dermoscopic images whose manually drawn borders by a dermatologist are used as the ground truth. Error rates, false positives and false negatives along with true positives and true negatives are quantified by digitally comparing results with manually determined borders from a dermatologist. The results show that the highest precision and recall rates obtained to determine lesion boundaries are 100%. However, accuracy of assessment averages out at 97.72% and borders errors' mean is 2.28% for whole dataset.

  7. Detection of Anatomic Structures in Human Retinal Imagery

    Energy Technology Data Exchange (ETDEWEB)

    Tobin Jr, Kenneth William [ORNL; Chaum, Edward [ORNL; Muthusamy Govindasamy, Vijaya Priya [ORNL; Karnowski, Thomas Paul [ORNL

    2007-01-01

    The widespread availability of electronic imaging devices throughout the medical community is leading to a growing body of research on image processing and analysis to diagnose retinal disease such as diabetic retinopathy (DR). Productive computer-based screening of large, at-risk populations at low cost requires robust, automated image analysis. In this paper we present results for the automatic detection of the optic nerve and localization of the macula using digital red-free fundus photography. Our method relies on the accurate segmentation of the vasculature of the retina followed by the determination of spatial features describing the density,average thickness, and average orientation of the vasculature in relation to the position of the optic nerve. Localization of the macula follows using knowledge of the optic nerve location to detect the horizontal raphe of the retina using a geometric model of the vasculature. We report 90.4% detection performance for the optic nerve and 92.5% localization performance for the macula for red-free fundus images representing a population of 345 images corresponding to 269 patients with 18 different pathologies associated with DR and other common retinal diseases such as age-related macular degeneration.

  8. Marginal space learning for medical image analysis efficient detection and segmentation of anatomical structures

    CERN Document Server

    Zheng, Yefeng

    2014-01-01

    Presents an award winning image analysis technology (Thomas Edison Patent Award, MICCAI Young Investigator Award) that achieves object detection and segmentation with state-of-the-art accuracy and efficiency Flexible, machine learning-based framework, applicable across multiple anatomical structures and imaging modalities Thirty five clinical applications on detecting and segmenting anatomical structures such as heart chambers and valves, blood vessels, liver, kidney, prostate, lymph nodes, and sub-cortical brain structures, in CT, MRI, X-Ray and Ultrasound.

  9. Experimental validation of a structural damage detection method based on marginal Hilbert spectrum

    Science.gov (United States)

    Banerji, Srishti; Roy, Timir B.; Sabamehr, Ardalan; Bagchi, Ashutosh

    2017-04-01

    Structural Health Monitoring (SHM) using dynamic characteristics of structures is crucial for early damage detection. Damage detection can be performed by capturing and assessing structural responses. Instrumented structures are monitored by analyzing the responses recorded by deployed sensors in the form of signals. Signal processing is an important tool for the processing of the collected data to diagnose anomalies in structural behavior. The vibration signature of the structure varies with damage. In order to attain effective damage detection, preservation of non-linear and non-stationary features of real structural responses is important. Decomposition of the signals into Intrinsic Mode Functions (IMF) by Empirical Mode Decomposition (EMD) and application of Hilbert-Huang Transform (HHT) addresses the time-varying instantaneous properties of the structural response. The energy distribution among different vibration modes of the intact and damaged structure depicted by Marginal Hilbert Spectrum (MHS) detects location and severity of the damage. The present work investigates damage detection analytically and experimentally by employing MHS. The testing of this methodology for different damage scenarios of a frame structure resulted in its accurate damage identification. The sensitivity of Hilbert Spectral Analysis (HSA) is assessed with varying frequencies and damage locations by means of calculating Damage Indices (DI) from the Hilbert spectrum curves of the undamaged and damaged structures.

  10. Structural insight of dopamine β-hydroxylase, a drug target for complex traits, and functional significance of exonic single nucleotide polymorphisms.

    Directory of Open Access Journals (Sweden)

    Abhijeet Kapoor

    Full Text Available Human dopamine β-hydroxylase (DBH is an important therapeutic target for complex traits. Several single nucleotide polymorphisms (SNPs have also been identified in DBH with potential adverse physiological effect. However, difficulty in obtaining diffractable crystals and lack of a suitable template for modeling the protein has ensured that neither crystallographic three-dimensional structure nor computational model for the enzyme is available to aid rational drug design, prediction of functional significance of SNPs or analytical protein engineering.Adequate biochemical information regarding human DBH, structural coordinates for peptidylglycine alpha-hydroxylating monooxygenase and computational data from a partial model of rat DBH were used along with logical manual intervention in a novel way to build an in silico model of human DBH. The model provides structural insight into the active site, metal coordination, subunit interface, substrate recognition and inhibitor binding. It reveals that DOMON domain potentially promotes tetramerization, while substrate dopamine and a potential therapeutic inhibitor nepicastat are stabilized in the active site through multiple hydrogen bonding. Functional significance of several exonic SNPs could be described from a structural analysis of the model. The model confirms that SNP resulting in Ala318Ser or Leu317Pro mutation may not influence enzyme activity, while Gly482Arg might actually do so being in the proximity of the active site. Arg549Cys may cause abnormal oligomerization through non-native disulfide bond formation. Other SNPs like Glu181, Glu250, Lys239 and Asp290 could potentially inhibit tetramerization thus affecting function.The first three-dimensional model of full-length human DBH protein was obtained in a novel manner with a set of experimental data as guideline for consistency of in silico prediction. Preliminary physicochemical tests validated the model. The model confirms, rationalizes and

  11. Structural insight of dopamine β-hydroxylase, a drug target for complex traits, and functional significance of exonic single nucleotide polymorphisms.

    Science.gov (United States)

    Kapoor, Abhijeet; Shandilya, Manish; Kundu, Suman

    2011-01-01

    Human dopamine β-hydroxylase (DBH) is an important therapeutic target for complex traits. Several single nucleotide polymorphisms (SNPs) have also been identified in DBH with potential adverse physiological effect. However, difficulty in obtaining diffractable crystals and lack of a suitable template for modeling the protein has ensured that neither crystallographic three-dimensional structure nor computational model for the enzyme is available to aid rational drug design, prediction of functional significance of SNPs or analytical protein engineering. Adequate biochemical information regarding human DBH, structural coordinates for peptidylglycine alpha-hydroxylating monooxygenase and computational data from a partial model of rat DBH were used along with logical manual intervention in a novel way to build an in silico model of human DBH. The model provides structural insight into the active site, metal coordination, subunit interface, substrate recognition and inhibitor binding. It reveals that DOMON domain potentially promotes tetramerization, while substrate dopamine and a potential therapeutic inhibitor nepicastat are stabilized in the active site through multiple hydrogen bonding. Functional significance of several exonic SNPs could be described from a structural analysis of the model. The model confirms that SNP resulting in Ala318Ser or Leu317Pro mutation may not influence enzyme activity, while Gly482Arg might actually do so being in the proximity of the active site. Arg549Cys may cause abnormal oligomerization through non-native disulfide bond formation. Other SNPs like Glu181, Glu250, Lys239 and Asp290 could potentially inhibit tetramerization thus affecting function. The first three-dimensional model of full-length human DBH protein was obtained in a novel manner with a set of experimental data as guideline for consistency of in silico prediction. Preliminary physicochemical tests validated the model. The model confirms, rationalizes and provides

  12. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum

    Science.gov (United States)

    Pei, Haisheng; Chen, Zhou; Tan, Xiaoyan; Hu, Jing; Yang, Bin; Sun, Junshe

    2017-01-01

    Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS) sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1–3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP) site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality control in the

  13. Intraspecific Variation and Phylogenetic Relationships Are Revealed by ITS1 Secondary Structure Analysis and Single-Nucleotide Polymorphism in Ganoderma lucidum.

    Directory of Open Access Journals (Sweden)

    Xiuqing Zhang

    Full Text Available Ganoderma lucidum is a typical polypore fungus used for traditional Chinese medical purposes. The taxonomic delimitation of Ganoderma lucidum is still debated. In this study, we sequenced seven internal transcribed spacer (ITS sequences of Ganoderma lucidum strains and annotated the ITS1 and ITS2 regions. Phylogenetic analysis of ITS1 differentiated the strains into three geographic groups. Groups 1-3 were originated from Europe, tropical Asia, and eastern Asia, respectively. While ITS2 could only differentiate the strains into two groups in which Group 2 originated from tropical Asia gathered with Groups 1 and 3 originated from Europe and eastern Asia. By determining the secondary structures of the ITS1 sequences, these three groups exhibited similar structures with a conserved central core and differed helices. While compared to Group 2, Groups 1 and 3 of ITS2 sequences shared similar structures with the difference in helix 4. Large-scale evaluation of ITS1 and ITS2 both exhibited that the majority of subgroups in the same group shared the similar structures. Further Weblogo analysis of ITS1 sequences revealed two main variable regions located in helix 2 in which C/T or A/G substitutions frequently occurred and ITS1 exhibited more nucleotide variances compared to ITS2. ITS1 multi-alignment of seven spawn strains and culture tests indicated that a single-nucleotide polymorphism (SNP site at position 180 correlated with strain antagonism. The HZ, TK and 203 fusion strains of Ganoderma lucidum had a T at position 180, whereas other strains exhibiting antagonism, including DB, RB, JQ, and YS, had a C. Taken together, compared to ITS2 region, ITS1 region could differentiated Ganoderma lucidum into three geographic originations based on phylogenetic analysis and secondary structure prediction. Besides, a SNP in ITS 1 could delineate Ganoderma lucidum strains at the intraspecific level. These findings will be implemented to improve species quality

  14. New high-pressure polymorph of In{sub 2}S{sub 3} with defect Th{sub 3}P{sub 4}-type structure

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Xiaojing; Zhu, Feng; Wu, Ye; Huang, Rong [Key Laboratory of Orogenic Belts and Crustal Evolution, MOE, Peking University, Beijing 100871 (China); School of Earth and Space Sciences, Peking University, Beijing 100871 (China); Wu, Xiang, E-mail: xiang.wu@pku.edu.cn [Key Laboratory of Orogenic Belts and Crustal Evolution, MOE, Peking University, Beijing 100871 (China); School of Earth and Space Sciences, Peking University, Beijing 100871 (China); Zhang, Qian [Key Laboratory of Orogenic Belts and Crustal Evolution, MOE, Peking University, Beijing 100871 (China); School of Earth and Space Sciences, Peking University, Beijing 100871 (China); Yang, Ke [Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201204 (China); Qin, Shan, E-mail: sqin@pku.edu.cn [Key Laboratory of Orogenic Belts and Crustal Evolution, MOE, Peking University, Beijing 100871 (China); School of Earth and Space Sciences, Peking University, Beijing 100871 (China)

    2014-02-15

    The high pressure behavior of β-In{sub 2}S{sub 3} (I4{sub 1}/amd and Z=16) has been studied by in situ synchrotron radiation X-ray diffraction combined with diamond anvil cell up to 71.7 GPa. Three pressure-induced phase transitions are evidenced at ∼6.6 GPa, ∼11.1 GPa at room temperature and 35.6 GPa after the high-temperature annealing using a portable laser heating system. The new polymorph of In{sub 2}S{sub 3} at 35.6 GPa is assigned to the denser cubic defect Th{sub 3}P{sub 4} structure (I4¯3d and Z=5.333), whose unit-cell parameters are a=7.557(1) Å and V=431.6(2) Å{sup 3}. The Th{sub 3}P{sub 4}-type phase can be stable at least up to 71.7 GPa and cannot be preserved at ambient pressure. The pressure–volume relationship is well described by the second-order Birch–Murnaghan Equation of State, which yields B{sub 0}=63(3) GPa and B{sub 0}′=4 (fixed) for the β-In{sub 2}S{sub 3} phase and B{sub 0}=87(3) GPa and B{sub 0}′=4 (fixed) for the defect Th{sub 3}P{sub 4}-type phase respectively. - Graphical abstract: The structure and Rietveld refinement of new polymorph the defect Th{sub 3}P{sub 4}-type In{sub 2}S{sub 3}. This structure was observed at 35.6 GPa after laser heating by X-ray diffraction. Display Omitted - Highlights: Three pressure-induced phase transitions of β-In{sub 2}S{sub 3} were observed. β-In{sub 2}S{sub 3} was stable up to 6.6 GPa. The defect Th{sub 3}P{sub 4}-type In{sub 2}S{sub 3} was identified at 35.6 GPa after laser heating and was stable up to 71.7 GPa. Elastic properties of β-In{sub 2}S{sub 3} and Th{sub 3}P{sub 4}-type In{sub 2}S{sub 3} are well presented by Birch–Murnaghan EoS.

  15. Detecting the overlapping and hierarchical community structure in complex networks

    International Nuclear Information System (INIS)

    Lancichinetti, Andrea; Fortunato, Santo; Kertesz, Janos

    2009-01-01

    Many networks in nature, society and technology are characterized by a mesoscopic level of organization, with groups of nodes forming tightly connected units, called communities or modules, that are only weakly linked to each other. Uncovering this community structure is one of the most important problems in the field of complex networks. Networks often show a hierarchical organization, with communities embedded within other communities; moreover, nodes can be shared between different communities. Here, we present the first algorithm that finds both overlapping communities and the hierarchical structure. The method is based on the local optimization of a fitness function. Community structure is revealed by peaks in the fitness histogram. The resolution can be tuned by a parameter enabling different hierarchical levels of organization to be investigated. Tests on real and artificial networks give excellent results.

  16. A simple, high-throughput method to detect Plasmodium falciparum single nucleotide polymorphisms in the dihydrofolate reductase, dihydropteroate synthase, and P. falciparum chloroquine resistance transporter genes using polymerase chain reaction- and enzyme-linked immunosorbent

    DEFF Research Database (Denmark)

    Alifrangis, Michael; Enosse, Sonia; Pearce, Richard

    2005-01-01

    Single nucleotide polymorphisms (SNPs) in the Plasmodium falciparum dihydrofolate reductase (dhfr), and dihydropteroate synthetase (dhps), and chloroquine resistance transporter (Pfcrt) genes are used as molecular markers of P. falciparum resistance to sulfadoxine/pyrimethamine and chloroquine....... However, to be a practical tool in the surveillance of drug resistance, simpler methods for high-throughput haplotyping are warranted. Here we describe a quick and simple technique that detects dhfr, dhps, and Pfcrt SNPs using polymerase chain reaction (PCR)- and enzyme-linked immunosorbent assay (ELISA...

  17. Automated Structure Detection in HRTEM Images: An Example with Graphene

    DEFF Research Database (Denmark)

    Kling, Jens; Vestergaard, Jacob Schack; Dahl, Anders Bjorholm

    Graphene, as the forefather of 2D-materials, attracts much attention due to its extraordinary properties like transparency, flexibility and outstanding high conductivity, together with a thickness of only one atom. The properties seem to be dependent on the atomic structure of graphene and theref...

  18. Damage Detection with Streamlined Structural Health Monitoring Data

    Directory of Open Access Journals (Sweden)

    Jian Li

    2015-04-01

    Full Text Available The huge amounts of sensor data generated by large scale sensor networks in on-line structural health monitoring (SHM systems often overwhelms the systems’ capacity for data transmission and analysis. This paper presents a new concept for an integrated SHM system in which a streamlined data flow is used as a unifying thread to integrate the individual components of on-line SHM systems. Such an integrated SHM system has a few desirable functionalities including embedded sensor data compression, interactive sensor data retrieval, and structural knowledge discovery, which aim to enhance the reliability, efficiency, and robustness of on-line SHM systems. Adoption of this new concept will enable the design of an on-line SHM system with more uniform data generation and data handling capacity for its subsystems. To examine this concept in the context of vibration-based SHM systems, real sensor data from an on-line SHM system comprising a scaled steel bridge structure and an on-line data acquisition system with remote data access was used in this study. Vibration test results clearly demonstrated the prominent performance characteristics of the proposed integrated SHM system including rapid data access, interactive data retrieval and knowledge discovery of structural conditions on a global level.

  19. Damage detection with streamlined structural health monitoring data.

    Science.gov (United States)

    Li, Jian; Deng, Jun; Xie, Weizhi

    2015-04-15

    The huge amounts of sensor data generated by large scale sensor networks in on-line structural health monitoring (SHM) systems often overwhelms the systems' capacity for data transmission and analysis. This paper presents a new concept for an integrated SHM system in which a streamlined data flow is used as a unifying thread to integrate the individual components of on-line SHM systems. Such an integrated SHM system has a few desirable functionalities including embedded sensor data compression, interactive sensor data retrieval, and structural knowledge discovery, which aim to enhance the reliability, efficiency, and robustness of on-line SHM systems. Adoption of this new concept will enable the design of an on-line SHM system with more uniform data generation and data handling capacity for its subsystems. To examine this concept in the context of vibration-based SHM systems, real sensor data from an on-line SHM system comprising a scaled steel bridge structure and an on-line data acquisition system with remote data access was used in this study. Vibration test results clearly demonstrated the prominent performance characteristics of the proposed integrated SHM system including rapid data access, interactive data retrieval and knowledge discovery of structural conditions on a global level.

  20. DETECTING UNSPECIFIED STRUCTURE IN LOW-COUNT IMAGES

    International Nuclear Information System (INIS)

    Stein, Nathan M.; Dyk, David A. van; Kashyap, Vinay L.; Siemiginowska, Aneta

    2015-01-01

    Unexpected structure in images of astronomical sources often presents itself upon visual inspection of the image, but such apparent structure may either correspond to true features in the source or be due to noise in the data. This paper presents a method for testing whether inferred structure in an image with Poisson noise represents a significant departure from a baseline (null) model of the image. To infer image structure, we conduct a Bayesian analysis of a full model that uses a multiscale component to allow flexible departures from the posited null model. As a test statistic, we use a tail probability of the posterior distribution under the full model. This choice of test statistic allows us to estimate a computationally efficient upper bound on a p-value that enables us to draw strong conclusions even when there are limited computational resources that can be devoted to simulations under the null model. We demonstrate the statistical performance of our method on simulated images. Applying our method to an X-ray image of the quasar 0730+257, we find significant evidence against the null model of a single point source and uniform background, lending support to the claim of an X-ray jet

  1. Structural cause of dysphagia detected during videofluoroscopic swallow study

    OpenAIRE

    Toh Yoon, Ezekiel Wong; Kabuto, Syu

    2017-01-01

    Key Clinical Message Dysphagia can be caused by many different underlying conditions. The assessment and management of dysphagia depend on each individual patient, often requiring a multidisciplinary approach. Structural cause of dysphagia can be dealt with using endoscopic interventions before the patient's general status deteriorates.

  2. A new approach for structural health monitoring by applying anomaly detection on strain sensor data

    Science.gov (United States)

    Trichias, Konstantinos; Pijpers, Richard; Meeuwissen, Erik

    2014-03-01

    Structural Health Monitoring (SHM) systems help to monitor critical infrastructures (bridges, tunnels, etc.) remotely and provide up-to-date information about their physical condition. In addition, it helps to predict the structure's life and required maintenance in a cost-efficient way. Typically, inspection data gives insight in the structural health. The global structural behavior, and predominantly the structural loading, is generally measured with vibration and strain sensors. Acoustic emission sensors are more and more used for measuring global crack activity near critical locations. In this paper, we present a procedure for local structural health monitoring by applying Anomaly Detection (AD) on strain sensor data for sensors that are applied in expected crack path. Sensor data is analyzed by automatic anomaly detection in order to find crack activity at an early stage. This approach targets the monitoring of critical structural locations, such as welds, near which strain sensors can be applied during construction and/or locations with limited inspection possibilities during structural operation. We investigate several anomaly detection techniques to detect changes in statistical properties, indicating structural degradation. The most effective one is a novel polynomial fitting technique, which tracks slow changes in sensor data. Our approach has been tested on a representative test structure (bridge deck) in a lab environment, under constant and variable amplitude fatigue loading. In both cases, the evolving cracks at the monitored locations were successfully detected, autonomously, by our AD monitoring tool.

  3. Multi-stage identification scheme for detecting damage in structures under ambient excitations

    International Nuclear Information System (INIS)

    Bao, Chunxiao; Li, Zhong-Xian; Hao, Hong

    2013-01-01

    Structural damage identification methods are critical to the successful application of structural health monitoring (SHM) systems to civil engineering structures. The dynamic response of civil engineering structures is usually characterized by high nonlinearity and non-stationarity. Accordingly, an improved Hilbert–Huang transform (HHT) method which is adaptive, output-only and applicable to system identification of in-service structures under ambient excitations is developed in this study. Based on this method, a multi-stage damage detection scheme including the detection of damage occurrence, damage existence, damage location and the estimation of damage severity is developed. In this scheme, the improved HHT method is used to analyse the structural acceleration response, the obtained instantaneous frequency detects the instant of damage occurrence, the instantaneous phase is sensitive to minor damage and provides reliable damage indication, and the damage indicator developed based on statistical analysis of the Hilbert marginal spectrum detects damage locations. Finally, the response sampled at the detected damage location is continuously analysed to estimate the damage severity. Numerical and experimental studies of frame structures under ambient excitations are performed. The results demonstrate that this scheme accomplishes the above damage detection functions within one flow. It is robust, time efficient, simply implemented and applicable to the real-time SHM of in-service structures. (paper)

  4. Track structure theory in radiobiology and in radiation detection

    International Nuclear Information System (INIS)

    Katz, R.

    1978-01-01

    The response of biological cells, and many physical radiation and track detectors to ionizing radiations and to energetic heavily ionizing particles, results from the secondary and higher generation electrons ejected from the atoms and molecules of the detector by the incident primary radiation. The theory uses a calculation of the radial distribution of local dose deposited by secondary electrons (delta-rays) from an energetic heavy ion as a transfer function, relating the dose-response relation measured (or postulated) for a particular detector in a uniform radiation field (gamma-rays) to obtain the radial distribution in response about the ion's path, and thus the structure of the track of a particle. Subsequent calculations yield the response of the detector to radiation fields of arbitrary quality. The models which have been used for detector response arise from target theory, and are of the form of statistical models called multi-hit or multi-target detectors, in which it is assumed that there are sensitive elements (emulsion grains, or biological cell nuclei) which may require many hits (emulsion grains) or single hits in different targets (say, cellular chromosomes) in order to produce the observed end-point. Recent work has demonstrated that many-hit physical detectors do exist. From both emulsion sensitometry and from the structure of tracks of heavy ions, it can be shown that emulsion-developer combinations exist which yield many-hit response. There is also some evidence that the supralinearity in thermoluminescent dosimeters arises from a mixture of 1-hit and 2-hit response, perhaps of different trap structures within the same TLD crystal. These detectors can be expected to mimic the response of biological cells to radiations of different quality. Their patterns of response may help us to understand better the structure of particle tracks in SSNTD's. (author)

  5. Damage Detection with Streamlined Structural Health Monitoring Data

    OpenAIRE

    Li, Jian; Deng, Jun; Xie, Weizhi

    2015-01-01

    The huge amounts of sensor data generated by large scale sensor networks in on-line structural health monitoring (SHM) systems often overwhelms the systems’ capacity for data transmission and analysis. This paper presents a new concept for an integrated SHM system in which a streamlined data flow is used as a unifying thread to integrate the individual components of on-line SHM systems. Such an integrated SHM system has a few desirable functionalities including embedded sensor data compressio...

  6. Fast detection of the main anatomical structures in digital retinal images based on intra- and inter-structure relational knowledge.

    Science.gov (United States)

    Molina-Casado, José M; Carmona, Enrique J; García-Feijoó, Julián

    2017-10-01

    The anatomical structure detection in retinal images is an open problem. However, most of the works in the related literature are oriented to the detection of each structure individually or assume the previous detection of a structure which is used as a reference. The objective of this paper is to obtain simultaneous detection of the main retinal structures (optic disc, macula, network of vessels and vascular bundle) in a fast and robust way. We propose a new methodology oriented to accomplish the mentioned objective. It consists of two stages. In an initial stage, a set of operators is applied to the retinal image. Each operator uses intra-structure relational knowledge in order to produce a set of candidate blobs that belongs to the desired structure. In a second stage, a set of tuples is created, each of which contains a different combination of the candidate blobs. Next, filtering operators, using inter-structure relational knowledge, are used in order to find the winner tuple. A method using template matching and mathematical morphology is implemented following the proposed methodology. A success is achieved if the distance between the automatically detected blob center and the actual structure center is less than or equal to one optic disc radius. The success rates obtained in the different public databases analyzed were: MESSIDOR (99.33%, 98.58%, 97.92%), DIARETDB1 (96.63%, 100%, 97.75%), DRIONS (100%, n/a, 100%) and ONHSD (100%, 98.85%, 97.70%) for optic disc (OD), macula (M) and vascular bundle (VB), respectively. Finally, the overall success rate obtained in this study for each structure was: 99.26% (OD), 98.69% (M) and 98.95% (VB). The average time of processing per image was 4.16 ± 0.72 s. The main advantage of the use of inter-structure relational knowledge was the reduction of the number of false positives in the detection process. The implemented method is able to simultaneously detect four structures. It is fast, robust and its detection

  7. Flux-mediated syntheses, structural characterization and low-temperature polymorphism of the p-type semiconductor Cu2Ta4O11

    Science.gov (United States)

    King, Nacole; Sullivan, Ian; Watkins-Curry, Pilanda; Chan, Julia Y.; Maggard, Paul A.

    2016-04-01

    A new low-temperature polymorph of the copper(I)-tantalate, α-Cu2Ta4O11, has been synthesized in a molten CuCl-flux reaction at 665 °C for 1 h and characterized by powder X-ray diffraction Rietveld refinements (space group Cc (#9), a=10.734(1) Å, b = 6.2506(3) Å, c=12.887(1) Å, β = 106.070(4)°). The α-Cu2Ta4O11 phase is a lower-symmetry monoclinic polymorph of the rhombohedral Cu2Ta4O11 structure (i.e., β-Cu2Ta4O11 space group R 3 ̅ c (#167), a = 6.2190(2) Å, c=37.107(1) Å), and related crystallographically by ahex=amono/√3, bhex=bmono, and chex=3cmonosinβmono. Its structure is similar to the rhombohedral β-Cu2Ta4O11 and is composed of single layers of highly-distorted and edge-shared TaO7 and TaO6 polyhedra alternating with layers of nearly linearly-coordinated Cu(I) cations and isolated TaO6 octahedra. Temperature dependent powder X-ray diffraction data show the α-Cu2Ta4O11 phase is relatively stable under vacuum at 223 K and 298 K, but reversibly transforms to β-Cu2Ta4O11 by at least 523 K and higher temperatures. The symmetry-lowering distortions from β-Cu2Ta4O11 to α-Cu2Ta4O11 arise from the out-of-center displacements of the Ta 5d0 cations in the TaO7 pentagonal bipyramids. The UV-vis diffuse reflectance spectrum of the monoclinic α-Cu2Ta4O11 shows an indirect bandgap transition of ∼2.6 eV, with the higher-energy direct transitions starting at ∼2.7 eV. Photoelectrochemical measurements on polycrystalline films of α-Cu2Ta4O11 show strong cathodic photocurrents of ∼1.5 mA/cm2 under AM 1.5 G solar irradiation.

  8. The retinal fascin gene 2 (FSCN2) - partial structural analysis and polymorphisms detection in dogs with progressive retinal atrophy (PRA)

    Czech Academy of Sciences Publication Activity Database

    Horák, Pavel; Knoll, Aleš; Dvořák, J.

    2006-01-01

    Roč. 47, č. 4 (2006), s. 361-364 ISSN 1234-1983 R&D Projects: GA AV ČR 1QS500450578 Institutional research plan: CEZ:AV0Z50450515 Keywords : canis familiaris * FSCN2 gene * PCR-RFLP Subject RIV: EB - Genetics ; Molecular Biology

  9. Different DNA methylation patterns detected by the Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) technique among various cell types of bulls

    OpenAIRE

    Phutikanit, Nawapen; Suwimonteerabutr, Junpen; Harrison, Dion; D'Occhio, Michael; Carroll, Bernie; Techakumphu, Mongkol

    2010-01-01

    Abstract Background The purpose of this study was to apply an arbitrarily primed methylation sensitive polymerase chain reaction (PCR) assay called Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR) to investigate the methylation profiles of somatic and germ cells obtained from Holstein bulls. Methods Genomic DNA was extracted from sperm, leukocytes and fibroblasts obtained from three bulls and digested with a methylation sensitive endonuclease (HpaII). The native genomic ...

  10. Real-time vibration-based structural damage detection using one-dimensional convolutional neural networks

    Science.gov (United States)

    Abdeljaber, Osama; Avci, Onur; Kiranyaz, Serkan; Gabbouj, Moncef; Inman, Daniel J.

    2017-02-01

    Structural health monitoring (SHM) and vibration-based structural damage detection have been a continuous interest for civil, mechanical and aerospace engineers over the decades. Early and meticulous damage detection has always been one of the principal objectives of SHM applications. The performance of a classical damage detection system predominantly depends on the choice of the features and the classifier. While the fixed and hand-crafted features may either be a sub-optimal choice for a particular structure or fail to achieve the same level of performance on another structure, they usually require a large computation power which may hinder their usage for real-time structural damage detection. This paper presents a novel, fast and accurate structural damage detection system using 1D Convolutional Neural Networks (CNNs) that has an inherent adaptive design to fuse both feature extraction and classification blocks into a single and compact learning body. The proposed method performs vibration-based damage detection and localization of the damage in real-time. The advantage of this approach is its ability to extract optimal damage-sensitive features automatically from the raw acceleration signals. Large-scale experiments conducted on a grandstand simulator revealed an outstanding performance and verified the computational efficiency of the proposed real-time damage detection method.

  11. Track structure theory in radiobiology and in radiation detection

    International Nuclear Information System (INIS)

    Katz, R.

    1976-01-01

    The response of biological cells, and many physical radiation and track detectors to ionizing radiations, and to energetic heavily ionizing particles results from the secondary and higher generation electrons ejected from the atoms and molecules of the detector by the incident primary radiation. The models which have been used for detector response arise from target theory, and are of the form of statistical models called multi-hit or multi-target detectors, in which it is assumed that there are sensitive elements (emulsion grains, or biological cell nuclei) which may require many hits (emulsion grains) or single hits in different targets (say, cellular chromosomes) in order to produce the observed endpoint. Physically, a hit is interpreted as a 'registered event' caused by an electron passing through the sensitive site, with an efficiency which depends on the electron's speed. Some knowledge of size of the sensitive volume and of the sensitive target is required to make the transition from gamma-ray response to heavy ion response. Recent work has demonstrated that many-hit physical detectors do exist. From both emulsion sensitometry and from the structure of tracks of heavy ions, we are able to show that emulsion-developer combinations exist which yield many-hit response. There is also some evidence that the supralinearity in thermoluminescent dosimeters arises from a trap structures within the same TLD crystal. These detectors can be expected to mimic the response of biological cells to radiations of different quality. Their patterns of response may help us to understand better the structure of particle tracks in SSNTD's. (orig./ORU) [de

  12. New geometric data structures for collision detection and haptics

    CERN Document Server

    Weller, René

    2013-01-01

    Starting with novel algorithms for optimally updating bounding volume hierarchies of objects undergoing arbitrary deformations, the author presents a new data structure that allows, for the first time, the computation of the penetration volume. The penetration volume is related to the water displacement of the overlapping region, and thus corresponds to a physically motivated and continuous force. The practicability of the approaches used is shown by realizing new applications in the field of robotics and haptics, including a user study that evaluates the influence of the degrees of freedom in

  13. Detection for flatness of large surface based on structured light

    Science.gov (United States)

    He, Wenyan; Cao, Xuedong; Long, Kuang; Peng, Zhang

    2016-09-01

    In order to get flatness of a large plane, this paper set up a measurement system, composed by Line Structured Light, imaging system, CCD, etc. Line Structured Light transmits parallel fringes at a proper angle onto the plane which is measured; the imaging system and CCD locate above the plane to catch the fringes. When the plane is perfect, CCD will catch straight fringes; however, the real plane is not perfect; according to the theory of projection, the fringes caught by CCD will be distorted by convex and concave. Extract the center of line fringes to obtain the distortion of the fringe, according to the functional relationship between the distortion of fringes and the height which is measured, then we will get flatness of the entire surface. Data from experiment approached the analysis of theory. In the simulation, the vertical resolution is 0.0075 mm per pixel when measuring a plane of 400mm×400mm, choosing the size of CCD 4096×4096, at the angle 85°. Helped by sub-pixel, the precision will get the level of submicron. There are two obvious advantages: method of surface sampling can increase the efficiency for auto-repairing of machines; considering the center of fringe is required mainly in this system, as a consequence, there is no serious demand for back light.

  14. Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry

    NARCIS (Netherlands)

    O. Lao Grueso (Oscar); K. van Duijn (Kate); P. Kersbergen (Paula); P. de Knijff (Peter); M.H. Kayser (Manfred)

    2006-01-01

    textabstractThe identification of geographic population structure and genetic ancestry on the basis of a minimal set of genetic markers is desirable for a wide range of applications in medical and forensic sciences. However, the absence of sharp discontinuities in the neutral genetic diversity among

  15. Proportioning whole-genome single-nucleotide-polymorphism diversity for the identification of geographic population structure and genetic ancestry

    NARCIS (Netherlands)

    O. Lao Grueso (Oscar); K. van Duijn (Kate); P. Kersbergen; P. de Knijff (Peter); M.H. Kayser (Manfred)

    2006-01-01

    textabstractThe identification of geographic population structure and genetic ancestry on the basis of a minimal set of genetic markers is desirable for a wide range of applications in medical and forensic sciences. However, the absence of sharp discontinuities in the neutral

  16. In silico Analysis of the Functional and Structural Impacts of Non-synonymous Single Nucleotide Polymorphisms in the Human Paraxonase 1 Gene

    Directory of Open Access Journals (Sweden)

    Sudip Paul

    2015-09-01

    Full Text Available Computational approaches could help in identifying deleterious non-synonymous single nucleotide polymorphisms (nsSNPs in a disease related gene which is a difficult and laborious task through laboratory experiments. In the present study, we analyzed the impacts of nsSNPs on structure and function of Paraxonase 1 (PON1 using different bioinformatics tools. The human PON1 protein sequence and its corresponding gene's SNP information were collected from UniProt and dbSNP databases, respectively. We utilized SIFT, Polyphen, I-Mutant 2.0, MutPred, SNP and GO, PhD-SNP and PANTHER tools in order to examine the total 39 nsSNPs occurring in the PON1 coding region. We filtered the most pathological mutations by combining the scores of the aforementioned servers and found 8 SNPs (G344C, S302L, W281C, D279Y, H134R, F120S, L90P, C42R as deleterious and disease causing. The PDB structure of PON1 protein was obtained from RCSB Protein Data Bank (PDB ID: 1V04. The deleterious SNPs in native PON1 were introduced using Swiss-PDB Viewer package and changes in free energy were observed for six out of eight mutant structures. Two SNPs, S302L (substitution of serine to leucine at 302 position in amino acid sequence and L90P (substitution of leucine to proline at 90 position in amino acid sequence caused the highest energy increase amongst all. The findings implicate that these nsSNPs would be analyzed further in detail to enumerate their possible association with the protein deteriorating and disease causal potentialities.

  17. Automated detection of structural alerts (chemical fragments in (ecotoxicology

    Directory of Open Access Journals (Sweden)

    Ronan Bureau

    2013-02-01

    Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

  18. AUTOMATED DETECTION OF STRUCTURAL ALERTS (CHEMICAL FRAGMENTS IN (ECOTOXICOLOGY

    Directory of Open Access Journals (Sweden)

    Alban Lepailleur

    2013-02-01

    Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

  19. Detecting the long-distance structure of the X(3872)

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Feng-Kun [Universitaet Bonn, Helmholtz-Institut fuer Strahlen- und Kernphysik and Bethe Center for Theoretical Physics, Bonn (Germany); Hidalgo-Duque, Carlos; Nieves, Juan [Centro Mixto CSIC-Universidad de Valencia, Institutos de Investigacion de Paterna, Instituto de Fisica Corpuscular (IFIC), Valencia (Spain); Ozpineci, Altug [Middle East Technical University, Department of Physics, Ankara (Turkey); Valderrama, Manuel Pavon [Universite Paris-Sud, IN2P3/CNRS, Institut de Physique Nucleaire, Orsay Cedex (France)

    2014-05-15

    We study the X(3872) → D{sup 0} anti D{sup 0}π{sup 0} decay within a D anti D* molecular picture for the X(3872) state. This decay mode is more sensitive to the long-distance structure of the X(3872) resonance than its J/ψππ and J/ψ3π decays, which are mainly controlled by the details of the X(3872) wave function at short distances. We show that the D{sup 0} anti D{sup 0} final state interaction can be important, and that a precise measurement of this partial decay width can provide valuable information on the interaction strength between the D{sup (*)} anti D{sup (*)} charm mesons. (orig.)

  20. Community detection for networks with unipartite and bipartite structure

    Science.gov (United States)

    Chang, Chang; Tang, Chao

    2014-09-01

    Finding community structures in networks is important in network science, technology, and applications. To date, most algorithms that aim to find community structures only focus either on unipartite or bipartite networks. A unipartite network consists of one set of nodes and a bipartite network consists of two nonoverlapping sets of nodes with only links joining the nodes in different sets. However, a third type of network exists, defined here as the mixture network. Just like a bipartite network, a mixture network also consists of two sets of nodes, but some nodes may simultaneously belong to two sets, which breaks the nonoverlapping restriction of a bipartite network. The mixture network can be considered as a general case, with unipartite and bipartite networks viewed as its limiting cases. A mixture network can represent not only all the unipartite and bipartite networks, but also a wide range of real-world networks that cannot be properly represented as either unipartite or bipartite networks in fields such as biology and social science. Based on this observation, we first propose a probabilistic model that can find modules in unipartite, bipartite, and mixture networks in a unified framework based on the link community model for a unipartite undirected network [B Ball et al (2011 Phys. Rev. E 84 036103)]. We test our algorithm on synthetic networks (both overlapping and nonoverlapping communities) and apply it to two real-world networks: a southern women bipartite network and a human transcriptional regulatory mixture network. The results suggest that our model performs well for all three types of networks, is competitive with other algorithms for unipartite or bipartite networks, and is applicable to real-world networks.

  1. Structural Damage Detection Using Changes in Natural Frequencies: Theory and Applications

    Science.gov (United States)

    He, K.; Zhu, W. D.

    2011-07-01

    A vibration-based method that uses changes in natural frequencies of a structure to detect damage has advantages over conventional nondestructive tests in detecting various types of damage, including loosening of bolted joints, using minimum measurement data. Two major challenges associated with applications of the vibration-based damage detection method to engineering structures are addressed: accurate modeling of structures and the development of a robust inverse algorithm to detect damage, which are defined as the forward and inverse problems, respectively. To resolve the forward problem, new physics-based finite element modeling techniques are developed for fillets in thin-walled beams and for bolted joints, so that complex structures can be accurately modeled with a reasonable model size. To resolve the inverse problem, a logistical function transformation is introduced to convert the constrained optimization problem to an unconstrained one, and a robust iterative algorithm using a trust-region method, called the Levenberg-Marquardt method, is developed to accurately detect the locations and extent of damage. The new methodology can ensure global convergence of the iterative algorithm in solving under-determined system equations and deal with damage detection problems with relatively large modeling error and measurement noise. The vibration-based damage detection method is applied to various structures including lightning masts, a space frame structure and one of its components, and a pipeline. The exact locations and extent of damage can be detected in the numerical simulation where there is no modeling error and measurement noise. The locations and extent of damage can be successfully detected in experimental damage detection.

  2. Structural Damage Detection Using Changes in Natural Frequencies: Theory and Applications

    International Nuclear Information System (INIS)

    He, K; Zhu, W D

    2011-01-01

    A vibration-based method that uses changes in natural frequencies of a structure to detect damage has advantages over conventional nondestructive tests in detecting various types of damage, including loosening of bolted joints, using minimum measurement data. Two major challenges associated with applications of the vibration-based damage detection method to engineering structures are addressed: accurate modeling of structures and the development of a robust inverse algorithm to detect damage, which are defined as the forward and inverse problems, respectively. To resolve the forward problem, new physics-based finite element modeling techniques are developed for fillets in thin-walled beams and for bolted joints, so that complex structures can be accurately modeled with a reasonable model size. To resolve the inverse problem, a logistical function transformation is introduced to convert the constrained optimization problem to an unconstrained one, and a robust iterative algorithm using a trust-region method, called the Levenberg-Marquardt method, is developed to accurately detect the locations and extent of damage. The new methodology can ensure global convergence of the iterative algorithm in solving under-determined system equations and deal with damage detection problems with relatively large modeling error and measurement noise. The vibration-based damage detection method is applied to various structures including lightning masts, a space frame structure and one of its components, and a pipeline. The exact locations and extent of damage can be detected in the numerical simulation where there is no modeling error and measurement noise. The locations and extent of damage can be successfully detected in experimental damage detection.

  3. Damage detection strategies for aircraft shell-like structures based on propagation guided elastic waves

    International Nuclear Information System (INIS)

    Zak, A; Ostachowicz, W; Krawczuk, M

    2011-01-01

    Damage of aircraft structural elements in any form always present high risks. Failures of these elements can be caused by various reasons including material fatigue or impact leading to damage initiation and growth. Detection of these failures at their earliest stage of development, estimation of their size and location, are one of the most crucial factors for each damage detection method. Structural health monitoring strategies based on propagation of guided elastic waves in structures and wave interaction with damage related discontinuities are very promising tools that offer not only damage detection capabilities, but are also meant to provide precise information about the state of the structures and their remaining lifetime. Because of that various techniques are employed to simulate and mimic the wave-discontinuity interactions. The use of various types of sensors, their networks together with sophisticated contactless measuring techniques are investigated both numerically and experimentally. Certain results of numerical simulations obtained by the use of the spectral finite element method are presented by the authors and related with propagation of guided elastic waves in shell-type aircraft structures. Two types of structures are considered: flat 2D panels with or without stiffeners and 3D shell structures. The applicability of two different damage detection approaches is evaluated in order to detect and localise damage in these structures. Selected results related with the use of laser scanning vibrometry are also presented and discussed by the authors.

  4. Population structure of a lodgepole pine (Pinus contorta) and jack pine (P. banksiana) complex as revealed by random amplified polymorphic DNA.

    Science.gov (United States)

    Ye, Terrance Z; Yang, Rong-Cai; Yeh, Francis C

    2002-06-01

    We studied the population structure of a lodgepole (Pinus contorta Dougl.) and jack pine (Pinus banksiana Lamb.) complex in west central Alberta and neighboring areas by assessing random amplified polymorphic DNA (RAPD) variability in 23 lodgepole pine, 9 jack pine, and 8 putative hybrid populations. Of 200 random primers screened, 10 that amplified 39 sharp and reproducible RAPDs were chosen for the study. None of the 39 RAPDs were unique to the parental species. RAPD diversity ranged from 0.085 to 0.190 among populations and averaged 0.143 for lodgepole pine, 0.156 for jack pine, 0.152 for hybrids, and 0.148 for all 40 populations. The estimated population differentiation based on G(ST) was 0.168 for hybrids, 0.162 for lodgepole pine, 0.155 for jack pine, and 0.247 across all 40 populations. Cluster analysis of genetic distances generally separated jack pine from lodgepole pine and hybrids, but no division could be identified that further separated lodgepole pine from hybrids. The observed weak to mild trend of "introgression by distance" in the complex and neighbouring areas was consistent with the view that introgressive hybridization between lodgepole and jack pines within and outside the hybrid zone may have been through secondary contact and primary intergradation, respectively.

  5. Genetic structure in contemporary south Tyrolean isolated populations revealed by analysis of Y-chromosome, mtDNA, and Alu polymorphisms.

    Science.gov (United States)

    Pichler, Irene; Mueller, Jakob C; Stefanov, Stefan A; De Grandi, Alessandro; Volpato, Claudia Beu; Pinggera, Gerd K; Mayr, Agnes; Ogriseg, Martin; Ploner, Franz; Meitinger, Thomas; Pramstaller, Peter P

    2006-08-01

    Most of the inhabitants of South Tyrol in the eastern Italian Alps can be considered isolated populations because of their physical separation by mountain barriers and their sociocultural heritage. We analyzed the genetic structure of South Tyrolean populations using three types of genetic markers: Y-chromosome, mitochondrial DNA (mtDNA), and autosomal Alu markers. Using random samples taken from the populations of Val Venosta, Val Pusteria, Val Isarco, Val Badia, and Val Gardena, we calculated genetic diversity within and among the populations. Microsatellite diversity and unique event polymorphism diversity (on the Y chromosome) were substantially lower in the Ladin-speaking population of Val Badia compared to the neighboring German-speaking populations. In contrast, the genetic diversity of mtDNA haplotypes was lowest for the upper Val Venosta and Val Pusteria. These data suggest a low effective population size, or little admixture, for the gene pool of the Ladin-speaking population from Val Badia. Interestingly, this is more pronounced for Ladin males than for Ladin females. For the pattern of genetic Alu variation, both Ladin samples (Val Gardena and Val Badia) are among the samples with the lowest diversity. An admixture analysis of one German-speaking valley (Val Venosta) indicates a relatively high genetic contribution of Ladin origin. The reduced genetic diversity and a high genetic differentiation in the Rhaetoroman- and German-speaking South Tyrolean populations may constitute an important basis for future medical genetic research and gene mapping studies in South Tyrol.

  6. X-ray structural studies and physicochemical characterization of (E)-6-(3,4-dimethoxyphenyl)-1-ethyl-4-mesitylimino-3-methyl- 3,4-dihydro-2(1H)-pyrimidinone polymorphs.

    Science.gov (United States)

    Miyamae, A; Kitamura, S; Tada, T; Koda, S; Yasuda, T

    1991-10-01

    The polymorphism of (E)-6-(3,4-dimethoxyphenyl)-1-ethyl-4-mesitylimino-3-methyl-3,4-di hydro- 2(1 H)-pyrimidinone (FK664; 1) was characterized by using X-ray powder diffractometry, differential scanning calorimetry (DSC), and IR spectroscopy. Structures of two polymorphs (Forms A and B) were determined by X-ray crystallographic analysis. Form A crystallized in the monoclinic space group P2(1)/c, with a = 13.504(2), b = 6.733(1), c = 24.910(8) A, beta = 96.55(4) degrees, z = 4, and dcal = 1.203 g/cm3, while Form B crystallized in the same space group, with a = 8.067(2), b = 15.128(4), c = 18.657(4) A, beta = 102.34(3) degrees, z = 4, and dcal = 1.216 g/cm3. The conformational features of 1 were very similar between the two polymorphs. Compound 1, in both crystal forms, took an energetically reasonable conformation in three rigid planes, such as 2-pyrimidone, trimethylphenyl, and dimethoxyphenyl rings, but the molecules were packed in different ways between the two polymorphs. In the Form B crystal, a short contact was possible, to form pi-pi interactions between two dimethoxyphenyl groups related with the inversion center in the crystal lattice; this interaction seems to contribute to stabilizing the crystal structure of Form B. Both Forms A and B showed only one endothermic peak due to fusion at 115 and 140 degrees C, respectively, on the DSC thermograms; therefore, it is suggested that there are no transition points between the two polymorphs. The heats of fusion obtained from the DSC thermograms were 33.2(2) kJ/mol for Form A and 36.8(1) kJ/mol for Form B.(ABSTRACT TRUNCATED AT 250 WORDS)

  7. Converting structures to optimize the Synchrotron X radiation detection by CCD systems

    International Nuclear Information System (INIS)

    Zanella, G.; Zannoni, R.

    1987-01-01

    It is pointed out how the quantum efficiency of X ray detection for CCD detecting system can be improved enlarging their sensivity range by means of heavy element converting structures. So the problem of fabricating CCD with a deep emptying layer is avoided

  8. H-/H∞ structural damage detection filter design using an iterative linear matrix inequality approach

    International Nuclear Information System (INIS)

    Chen, B; Nagarajaiah, S

    2008-01-01

    The existence of damage in different members of a structure can be posed as a fault detection problem. It is also necessary to isolate structural members in which damage exists, which can be posed as a fault isolation problem. It is also important to detect the time instants of occurrence of the faults/damage. The structural damage detection filter developed in this paper is a model-based fault detection and isolation (FDI) observer suitable for detecting and isolating structural damage. In systems, possible faults, disturbances and noise are coupled together. When system disturbances and sensor noise cannot be decoupled from faults/damage, the detection filter needs to be designed to be robust to disturbances as well as sensitive to faults/damage. In this paper, a new H - /H ∞ and iterative linear matrix inequality (LMI) technique is developed and a new stabilizing FDI filter is proposed, which bounds the H ∞ norm of the transfer function from disturbances to the output residual and simultaneously does not degrade the component of the output residual due to damage. The reduced-order error dynamic system is adopted to form bilinear matrix inequalities (BMIs), then an iterative LMI algorithm is developed to solve the BMIs. The numerical example and experimental verification demonstrate that the proposed algorithm can successfully detect and isolate structural damage in the presence of measurement noise

  9. A novel reduced-complexity group detection structure in MIMO frequency selective fading channels

    KAUST Repository

    Qaraqe, Khalid A.; Ahimian, Nariman R.; Alouini, Mohamed-Slim

    2010-01-01

    In this paper a novel reduced complexity detection method named modified symbol flipping method is introduced and its advantages on reducing the burden of the calculations at the receiver compared to the optimum maximum likelihood detection method on multiple input- multiple output frequency selective fading channels are explained. The initial concept of the symbol flipping method is derived from a preliminary detection scheme named bit flipping which was introduced in [1]. The detection structure employed in this paper is ing, detection, and cancellation. On the detection stage, the proposed method is employed and the results are compared to the group maximum likelihood detection scheme proposed in [2]. Simulation results show that a 6 dB performance gain can be achieved at the expense of a slight increase in complexity in comparison with the conventional symbol flipping scheme. © 2010 Crown.

  10. A novel reduced-complexity group detection structure in MIMO frequency selective fading channels

    KAUST Repository

    Qaraqe, Khalid A.

    2010-09-01

    In this paper a novel reduced complexity detection method named modified symbol flipping method is introduced and its advantages on reducing the burden of the calculations at the receiver compared to the optimum maximum likelihood detection method on multiple input- multiple output frequency selective fading channels are explained. The initial concept of the symbol flipping method is derived from a preliminary detection scheme named bit flipping which was introduced in [1]. The detection structure employed in this paper is ing, detection, and cancellation. On the detection stage, the proposed method is employed and the results are compared to the group maximum likelihood detection scheme proposed in [2]. Simulation results show that a 6 dB performance gain can be achieved at the expense of a slight increase in complexity in comparison with the conventional symbol flipping scheme. © 2010 Crown.

  11. Polymorphism of nickel sulfate hexahydrate

    International Nuclear Information System (INIS)

    Angel, R.J.; Finger, L.W.

    1988-01-01

    NiSO 4 .6H 2 O, M r =262.85; data collections with Mo Kα radiation, λ=0.7093 A, room temperature. Monoclinic polymorph: C2/c, a=9.880(3), b=7.228(2), c=24.130(3) A, β=98.38(2) 0 , V=1704.7(6) A 3 , Z=8, D x =2.05 g cm -3 , μ=25.54 cm -1 , F(000)=1088, R=0.031 (wR=0.038) for 2176 observed reflections. Tetragonal polymorph: P4 1 2 1 2, a=6.780 (1), c=18.285 (2) A, V=840.5 (3) A 3 , Z=4, D x =2.07 g cm -3 , μ=25.81 cm -1 , F(000)=544, R=0.045 (wR=0.050) for 2102 observed reflections. The structure of the tetragonal polymorph originally determined (without H positions) by Beevers and Lipson and refined by O'Connor and Dale and Stadnicka, Glazer and Koralewski, is confirmed by refinement of X-ray diffraction data. The structure of the monoclinic polymorph is confirmed as being isostructural with NiSO 4 .6D 2 O, and a number of other hexahydrate sulfates, e.g. MgSO 4 .6H 2 O. Both structures contain isolated [Ni(H 2 O 6 ] octahedra and [SO 4 ] tetrahedra linked by hydrogen bonding. (orig.)

  12. You Can't Unscramble an Egg: Population Genetic Structure of Oncorhynchus mykiss in the California Central Valley Inferred from Combined Microsatellite and Single Nucleotide Polymorphism Data

    Directory of Open Access Journals (Sweden)

    Devon E. Pearse

    2015-12-01

    Full Text Available doi: http://dx.doi.org/10.15447/sfews.2015v13iss4art3Steelhead/rainbow trout (Oncorhynchus mykiss are found in all of the major tributaries of the Sacramento and San Joaquin rivers, which flow through California’s Central Valley and enter the ocean through San Francisco Bay and the Golden Gate. This river system is heavily affected by water development, agriculture, and invasive species, and salmon and trout hatchery propagation has been occurring for over 100 years. We collected genotype data for 18 highly variable microsatellite loci and 95 single nucleotide polymorphisms (SNPs from more than 1,900 fish from Central Valley drainages to analyze genetic diversity, population structure, differentiation between populations above and below dams, and the relationship of Central Valley O. mykiss populations to coastal California steelhead. In addition, we evaluate introgression by both hatchery rainbow trout strains, which have primarily native Central Valley ancestry, and imported coastal steelhead stocks. In contrast to patterns typical of coastal steelhead, Central Valley O. mykiss above and below dams within the same tributary were not found to be each others’ closest relatives, and we found no relationship between genetic and geographic distance among below-barrier populations. While introgression by hatchery rainbow trout strains does not appear to be widespread among above-barrier populations, steelhead in the American River and some neighboring tributaries have been introgressed by coastal steelhead. Together, these results demonstrate that the ancestral population genetic structure that existed among Central Valley tributaries has been significantly altered in contemporary populations. Future conservation, restoration, and mitigation efforts should take this into account when working to meet recovery planning goals.

  13. Drug Development in Conformational Diseases: A Novel Family of Chemical Chaperones that Bind and Stabilise Several Polymorphic Amyloid Structures.

    Directory of Open Access Journals (Sweden)

    Marquiza Sablón-Carrazana

    Full Text Available The increasing prevalence of conformational diseases, including Alzheimer's disease, type 2 Diabetes Mellitus and Cancer, poses a global challenge at many different levels. It has devastating effects on the sufferers as well as a tremendous economic impact on families and the health system. In this work, we apply a cross-functional approach that combines ideas, concepts and technologies from several disciplines in order to study, in silico and in vitro, the role of a novel chemical chaperones family (NCHCHF in processes of protein aggregation in conformational diseases. Given that Serum Albumin (SA is the most abundant protein in the blood of mammals, and Bovine Serum Albumin (BSA is an off-the-shelf protein available in most labs around the world, we compared the ligandability of BSA:NCHCHF with the interaction sites in the Human Islet Amyloid Polypeptide (hIAPP:NCHCHF, and in the amyloid pharmacophore fragments (Aβ17-42 and Aβ16-21:NCHCHF. We posit that the merging of this interaction sites is a meta-structure of pharmacophore which allows the development of chaperones that can prevent protein aggregation at various states from: stabilizing the native state to destabilizing oligomeric state and protofilament. Furthermore to stabilize fibrillar structures, thus decreasing the amount of toxic oligomers in solution, as is the case with the NCHCHF. The paper demonstrates how a set of NCHCHF can be used for studying and potentially treating the various physiopathological stages of a conformational disease. For instance, when dealing with an acute phase of cytotoxicity, what is needed is the recruitment of cytotoxic oligomers, thus chaperone F, which accelerates fiber formation, would be very useful; whereas in a chronic stage it is better to have chaperones A, B, C, and D, which stabilize the native and fibril structures halting self-catalysis and the creation of cytotoxic oligomers as a consequence of fiber formation. Furthermore, all the

  14. Evolutionary Algorithms for the Detection of Structural Breaks in Time Series

    DEFF Research Database (Denmark)

    Doerr, Benjamin; Fischer, Paul; Hilbert, Astrid

    2013-01-01

    Detecting structural breaks is an essential task for the statistical analysis of time series, for example, for fitting parametric models to it. In short, structural breaks are points in time at which the behavior of the time series changes. Typically, no solid background knowledge of the time...

  15. Similarity between community structures of different online social networks and its impact on underlying community detection

    Science.gov (United States)

    Fan, W.; Yeung, K. H.

    2015-03-01

    As social networking services are popular, many people may register in more than one online social network. In this paper we study a set of users who have accounts of three online social networks: namely Foursquare, Facebook and Twitter. Community structure of this set of users may be reflected in these three online social networks. Therefore, high correlation between these reflections and the underlying community structure may be observed. In this work, community structures are detected in all three online social networks. Also, we investigate the similarity level of community structures across different networks. It is found that they show strong correlation with each other. The similarity between different networks may be helpful to find a community structure close to the underlying one. To verify this, we propose a method to increase the weights of some connections in networks. With this method, new networks are generated to assist community detection. By doing this, value of modularity can be improved and the new community structure match network's natural structure better. In this paper we also show that the detected community structures of online social networks are correlated with users' locations which are identified on Foursquare. This information may also be useful for underlying community detection.

  16. Ab initio localized basis set study of structural parameters and elastic properties of HfO2 polymorphs

    International Nuclear Information System (INIS)

    Caravaca, M A; Casali, R A

    2005-01-01

    The SIESTA approach based on pseudopotentials and a localized basis set is used to calculate the electronic, elastic and equilibrium properties of P 2 1 /c, Pbca, Pnma, Fm3m, P4 2 nmc and Pa3 phases of HfO 2 . Using separable Troullier-Martins norm-conserving pseudopotentials which include partial core corrections for Hf, we tested important physical properties as a function of the basis set size, grid size and cut-off ratio of the pseudo-atomic orbitals (PAOs). We found that calculations in this oxide with the LDA approach and using a minimal basis set (simple zeta, SZ) improve calculated phase transition pressures with respect to the double-zeta basis set and LDA (DZ-LDA), and show similar accuracy to that determined with the PPPW and GGA approach. Still, the equilibrium volumes and structural properties calculated with SZ-LDA compare better with experiments than the GGA approach. The bandgaps and elastic and structural properties calculated with DZ-LDA are accurate in agreement with previous state of the art ab initio calculations and experimental evidence and cannot be improved with a polarized basis set. These calculated properties show low sensitivity to the PAO localization parameter range between 40 and 100 meV. However, this is not true for the relative energy, which improves upon decrease of the mentioned parameter. We found a non-linear behaviour in the lattice parameters with pressure in the P 2 1 /c phase, showing a discontinuity of the derivative of the a lattice parameter with respect to external pressure, as found in experiments. The common enthalpy values calculated with the minimal basis set give pressure transitions of 3.3 and 10.8?GPa for P2 1 /c → Pbca and Pbca → Pnma, respectively, in accordance with different high pressure experimental values

  17. Ab initio localized basis set study of structural parameters and elastic properties of HfO{sub 2} polymorphs

    Energy Technology Data Exchange (ETDEWEB)

    Caravaca, M A [Facultad de Ingenieria, Universidad Nacional del Nordeste, Avenida Las Heras 727, 3500-Resistencia (Argentina); Casali, R A [Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad, 5600-Corrientes (Argentina)

    2005-09-21

    The SIESTA approach based on pseudopotentials and a localized basis set is used to calculate the electronic, elastic and equilibrium properties of P 2{sub 1}/c, Pbca, Pnma, Fm3m, P4{sub 2}nmc and Pa3 phases of HfO{sub 2}. Using separable Troullier-Martins norm-conserving pseudopotentials which include partial core corrections for Hf, we tested important physical properties as a function of the basis set size, grid size and cut-off ratio of the pseudo-atomic orbitals (PAOs). We found that calculations in this oxide with the LDA approach and using a minimal basis set (simple zeta, SZ) improve calculated phase transition pressures with respect to the double-zeta basis set and LDA (DZ-LDA), and show similar accuracy to that determined with the PPPW and GGA approach. Still, the equilibrium volumes and structural properties calculated with SZ-LDA compare better with experiments than the GGA approach. The bandgaps and elastic and structural properties calculated with DZ-LDA are accurate in agreement with previous state of the art ab initio calculations and experimental evidence and cannot be improved with a polarized basis set. These calculated properties show low sensitivity to the PAO localization parameter range between 40 and 100 meV. However, this is not true for the relative energy, which improves upon decrease of the mentioned parameter. We found a non-linear behaviour in the lattice parameters with pressure in the P 2{sub 1}/c phase, showing a discontinuity of the derivative of the a lattice parameter with respect to external pressure, as found in experiments. The common enthalpy values calculated with the minimal basis set give pressure transitions of 3.3 and 10.8?GPa for P2{sub 1}/c {yields} Pbca and Pbca {yields} Pnma, respectively, in accordance with different high pressure experimental values.

  18. Fine structure of excitons and electron-hole exchange energy in polymorphic CsPbBr3 single nanocrystals.

    Science.gov (United States)

    Ramade, Julien; Andriambariarijaona, Léon Marcel; Steinmetz, Violette; Goubet, Nicolas; Legrand, Laurent; Barisien, Thierry; Bernardot, Frédérick; Testelin, Christophe; Lhuillier, Emmanuel; Bramati, Alberto; Chamarro, Maria

    2018-04-05

    All inorganic CsPbX3 (X = Cl, Br, I) nanocrystals (NCs) belong to the novel class of confined metal-halide perovskites which are currently arousing enthusiasm and stimulating huge activity across several fields of optoelectronics due to outstanding properties. A deep knowledge of the band-edge excitonic properties of these materials is thus crucial to further optimize their performances. Here, high-resolution photoluminescence (PL) spectroscopy of single bromide-based NCs reveals the exciton fine structure in the form of sharp peaks that are linearly polarized and grouped in doublets or triplets, which directly mirror the adopted crystalline structure, tetragonal (D4h symmetry) or orthorhombic (D2h symmetry). Intelligible equations are found that show how the fundamental parameters (spin-orbit coupling, ΔSO, crystal field term, T, and electron-hole exchange energy, J) rule the energy spacings in doublets and triplets. From experimental data, fine estimations of each parameter are obtained. The analysis of the absorption spectra of an ensemble of NCs with a "quasi-bulk" behavior leads to ΔSO = 1.20 ± 0.06 eV and T = -0.34 ± 0.05 eV in CsPbBr3. The study of individual luminescence responses of NCs having sizes comparable to the exciton Bohr diameter, 7 nm, allows us to estimate the value of J to be around ≈3 meV in both tetragonal and orthorhombic phases. This value is already enhanced by confinement.

  19. Application of Ultrasonic Phased Array Technology to the Detection of Defect in Composite Stiffened-structures

    Science.gov (United States)

    Zhou, Yuan-Qi; Zhan, Li-Hua

    2016-05-01

    Composite stiffened-structure consists of the skin and stringer has been widely used in aircraft fuselage and wings. The main purpose of the article is to detect the composite material reinforced structure accurately and explore the relationship between defect formation and structural elements or curing process. Based on ultrasonic phased array inspection technology, the regularity of defects in the manufacture of composite materials are obtained, the correlation model between actual defects and nondestructive testing are established. The article find that the forming quality of deltoid area in T-stiffened structure is obviously improved by pre-curing, the defects of hat-stiffened structure are affected by the mandrel. The results show that the ultrasonic phased array inspection technology can be an effectively way for the detection of composite stiffened-structures, which become an important means to control the defects of composite and improve the quality of the product.

  20. Polymorphic Embedding of DSLs

    DEFF Research Database (Denmark)

    Hofer, Christian; Ostermann, Klaus; Rendel, Tillmann

    2008-01-01

    propose polymorphic embedding of DSLs, where many different interpretations of a DSL can be provided as reusable components, and show how polymorphic embedding can be realized in the programming language Scala. With polymorphic embedding, the static type-safety, modularity, composability and rapid...

  1. Detecting deletions, insertions, and single nucleotide substitutions in cloned β-globin genes and new polymorphic nucleotide substitutions in β-globin genes in a Japanese population using ribonuclease cleavage at mismatches in RNA: DNA duplexes

    International Nuclear Information System (INIS)

    Hiyama, Keiko; Kodaira, Mieko; Satoh, Chiyoko.

    1990-08-01

    The applicability of ribonuclease (RNase) cleavage at mismatches in RNA:DNA duplexes (the RNase cleavage method) for determining nucleotide variant rates was examined in a Japanese population. DNA segments of various lengths obtained from four different regions of one normal and three thalassemic cloned human β-globin genes were inserted into transcription vectors. Sense and antisense RNA probes uniformly labeled with 32 P were prepared. When RNA probes of 771 nucleotides (nt) or less were hybridized with cloned DNAs and the resulting duplexes were treated with a mixture of RNases A and T1, the length of products agreed with theoretical values. Twelve possible mismatches were examined. Since both sense and antisense probes were used, uncleavable mismatches such as G:T and G:G which were made from one combination of RNA and DNA strands could be converted to the cleavable C:A and C:C mismatches, respectively, by using the opposite combination. Deletions and insertions of one (G), four(TTCT), five (ATTTT), and 10 (ATTTTATTTT) nt were easily detected. A polymorphic substitution of T to C at position 666 of the second intervening sequence (IVS2-666) of the β-globin gene was detected using genomic DNAs from cell lines established from the peripheral B lymphocytes of 59 unrelated Japanese from Hiroshima or those amplified by polymerase chain reaction (PCR). The frequency of the gene with C at the IVS2-666 (allele C) was 0.48 and that of the gene with T (allene T) was 0.52. Two new polymorphic substitutions of C to A and A to T were detected at nucleotide positions 1789 and 1945 from the capping site, respectively, using genomic DNAs amplified by PCR. We conclude that it would be feasible to use the RNase cleavage method combined with PCR for large-scale screening of variation in chromosomal DNA. (J.P.N.)

  2. Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions.

    Science.gov (United States)

    Miyoshi, Daisuke; Nakamura, Kaori; Tateishi-Karimata, Hisae; Ohmichi, Tatsuo; Sugimoto, Naoki

    2009-03-18

    It has been revealed recently that molecular crowding, which is one of the largest differences between in vivo and in vitro conditions, is a critical factor determining the structure, stability, and function of nucleic acids. However, the effects of molecular crowding on Watson-Crick and Hoogsteen base pairs remain unclear. In order to investigate directly and quantitatively the molecular crowding effects on base pair types in nucleic acids, we designed intramolecular parallel- and antiparallel-stranded DNA duplexes consisting of Hoogsteen and Watson-Crick base pairs, respectively, as well as an intramolecular parallel-stranded triplex containing both types of base pairs. Thermodynamic analyses demonstrated that the values of free energy change at 25 degrees C for Hoogsteen base-pair formations decreased from +1.45 +/- 0.15 to +1.09 +/- 0.13 kcal mol(-1), and from -1.89 +/- 0.13 to -2.71 +/- 0.11 kcal mol(-1) in the intramolecular duplex and triplex, respectively, when the concentration of PEG 200 (polyethylene glycol with average molecular weight 200) increased from 0 to 20 wt %. However, corresponding values for Watson-Crick formation in the duplex and triplex increased from -10.2 +/- 0.2 to -8.7 +/- 0.1 kcal mol(-1), and from -10.8 +/- 0.2 to -9.2 +/- 0.2 kcal mol(-1), respectively. Furthermore, it was revealed that the opposing effects of molecular crowding on the Hoogsteen and Watson-Crick base pairs were due to different behaviors of water molecules binding to the DNA strands.

  3. Fast and objective detection and analysis of structures in downhole images

    Science.gov (United States)

    Wedge, Daniel; Holden, Eun-Jung; Dentith, Mike; Spadaccini, Nick

    2017-09-01

    Downhole acoustic and optical televiewer images, and formation microimager (FMI) logs are important datasets for structural and geotechnical analyses for the mineral and petroleum industries. Within these data, dipping planar structures appear as sinusoids, often in incomplete form and in abundance. Their detection is a labour intensive and hence expensive task and as such is a significant bottleneck in data processing as companies may have hundreds of kilometres of logs to process each year. We present an image analysis system that harnesses the power of automated image analysis and provides an interactive user interface to support the analysis of televiewer images by users with different objectives. Our algorithm rapidly produces repeatable, objective results. We have embedded it in an interactive workflow to complement geologists' intuition and experience in interpreting data to improve efficiency and assist, rather than replace the geologist. The main contributions include a new image quality assessment technique for highlighting image areas most suited to automated structure detection and for detecting boundaries of geological zones, and a novel sinusoid detection algorithm for detecting and selecting sinusoids with given confidence levels. Further tools are provided to perform rapid analysis of and further detection of structures e.g. as limited to specific orientations.

  4. Complex relationships between occupation, environment, DNA adducts, genetic polymorphisms and bladder cancer in a case-control study using a structural equation modeling.

    Directory of Open Access Journals (Sweden)

    Stefano Porru

    Full Text Available DNA adducts are considered an integrate measure of carcinogen exposure and the initial step of carcinogenesis. Their levels in more accessible peripheral blood lymphocytes (PBLs mirror that in the bladder tissue. In this study we explore whether the formation of PBL DNA adducts may be associated with bladder cancer (BC risk, and how this relationship is modulated by genetic polymorphisms, environmental and occupational risk factors for BC. These complex interrelationships, including direct and indirect effects of each variable, were appraised using the structural equation modeling (SEM analysis. Within the framework of a hospital-based case/control study, study population included 199 BC cases and 213 non-cancer controls, all Caucasian males. Data were collected on lifetime smoking, coffee drinking, dietary habits and lifetime occupation, with particular reference to exposure to aromatic amines (AAs and polycyclic aromatic hydrocarbons (PAHs. No indirect paths were found, disproving hypothesis on association between PBL DNA adducts and BC risk. DNA adducts were instead positively associated with occupational cumulative exposure to AAs (p = 0.028, whereas XRCC1 Arg 399 (p<0.006 was related with a decreased adduct levels, but with no impact on BC risk. Previous findings on increased BC risk by packyears (p<0.001, coffee (p<0.001, cumulative AAs exposure (p = 0.041 and MnSOD (p = 0.009 and a decreased risk by MPO (p<0.008 were also confirmed by SEM analysis. Our results for the first time make evident an association between occupational cumulative exposure to AAs with DNA adducts and BC risk, strengthening the central role of AAs in bladder carcinogenesis. However the lack of an association between PBL DNA adducts and BC risk advises that these snapshot measurements are not representative of relevant exposures. This would envisage new scenarios for biomarker discovery and new challenges such as repeated measurements at different

  5. Shear and Rapeseed Oil Addition Affect the Crystal Polymorphic Behavior of Milk Fat

    DEFF Research Database (Denmark)

    Kaufmann, Niels; Kirkensgaard, Jacob Judas Kain; Andersen, Ulf

    2013-01-01

    The effect of shear on the crystallization kinetics of anhydrous milk fat (AMF) and blends with 20 and 30 % w/w added rapeseed oil (RO) was studied. Pulse 1H NMR was used to follow the a to b0 polymorphic transition. The NMR method was confirmed and supported by SAXS/WAXS experiments. Samples were...... faster in the presence of RO allowing more room for the conformational changes to occur. Final SFC decreased with increasing RO content. Shear applied in 20 and 30 % blends caused the destruction of b0-related 3L structure leaving only 2L packing. In AMF and statically crystallized samples, both 3L and 2......L packing existed. Shear did not affect the amount of b crystals formed. The study shows that both shear and RO affect the polymorphic behavior of milk fat, and that 1H NMR is able to detect polymorphic transition in blends with up to 30 % w/w RO....

  6. Structural damage detection for in-service highway bridge under operational and environmental variability

    Science.gov (United States)

    Jin, Chenhao; Li, Jingcheng; Jang, Shinae; Sun, Xiaorong; Christenson, Richard

    2015-03-01

    Structural health monitoring has drawn significant attention in the past decades with numerous methodologies and applications for civil structural systems. Although many researchers have developed analytical and experimental damage detection algorithms through vibration-based methods, these methods are not widely accepted for practical structural systems because of their sensitivity to uncertain environmental and operational conditions. The primary environmental factor that influences the structural modal properties is temperature. The goal of this article is to analyze the natural frequency-temperature relationships and detect structural damage in the presence of operational and environmental variations using modal-based method. For this purpose, correlations between natural frequency and temperature are analyzed to select proper independent variables and inputs for the multiple linear regression model and neural network model. In order to capture the changes of natural frequency, confidence intervals to detect the damages for both models are generated. A long-term structural health monitoring system was installed on an in-service highway bridge located in Meriden, Connecticut to obtain vibration and environmental data. Experimental testing results show that the variability of measured natural frequencies due to temperature is captured, and the temperature-induced changes in natural frequencies have been considered prior to the establishment of the threshold in the damage warning system. This novel approach is applicable for structural health monitoring system and helpful to assess the performance of the structure for bridge management and maintenance.

  7. The uses of AFLP for detecting DNA polymorphism, genotype identification and genetic diversity between yeasts isolated from Mexican agave-distilled beverages and from grape musts.

    Science.gov (United States)

    Flores Berrios, E P; Alba González, J F; Arrizon Gaviño, J P; Romano, P; Capece, A; Gschaedler Mathis, A

    2005-01-01

    The objectives were to determine the variability and to compare the genetic diversity obtained using amplified fragment length polymorphism (AFLP) markers in analyses of wine, tequila, mezcal, sotol and raicilla yeasts. A molecular characterization of yeasts isolated from Mexican agave musts, has been performed by AFLP marker analysis, using reference wine strains from Italian and South African regions. A direct co-relation between genetic profile, origin and fermentation process of strains was found especially in strains isolated from agave must. In addition, unique molecular markers were obtained for all the strains using six combination primers, confirming the discriminatory power of AFLP markers. This is the first report of molecular characterization between yeasts isolated from different Mexican traditional agave-distilled beverages, which shows high genetic differences with respect to wine strains.

  8. Monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism.

    Science.gov (United States)

    Jernberg, Cecilia; Sullivan, Asa; Edlund, Charlotta; Jansson, Janet K

    2005-01-01

    Terminal restriction fragment length polymorphism (T-RFLP) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. Fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. During treatment, four subjects were given a probiotic, and four subjects were given a placebo. Changes in the microbial intestinal community composition and relative abundance of specific microbial populations in each subject were monitored by using viable counts and T-RFLP fingerprints. T-RFLP was also used to monitor specific bacterial populations that were either positively or negatively affected by clindamycin. Some dominant bacterial groups, such as Eubacterium spp., were easily monitored by T-RFLP, while they were hard to recover by cultivation. Furthermore, the two probiotic Lactobacillus strains were easily tracked by T-RFLP and were shown to be the dominant Lactobacillus community members in the intestinal microflora of subjects who received the probiotic.

  9. Hidden corrosion detection in aircraft aluminum structures using laser ultrasonics and wavelet transform signal analysis.

    Science.gov (United States)

    Silva, M Z; Gouyon, R; Lepoutre, F

    2003-06-01

    Preliminary results of hidden corrosion detection in aircraft aluminum structures using a noncontact laser based ultrasonic technique are presented. A short laser pulse focused to a line spot is used as a broadband source of ultrasonic guided waves in an aluminum 2024 sample cut from an aircraft structure and prepared with artificially corroded circular areas on its back surface. The out of plane surface displacements produced by the propagating ultrasonic waves were detected with a heterodyne Mach-Zehnder interferometer. Time-frequency analysis of the signals using a continuous wavelet transform allowed the identification of the generated Lamb modes by comparison with the calculated dispersion curves. The presence of back surface corrosion was detected by noting the loss of the S(1) mode near its cutoff frequency. This method is applicable to fast scanning inspection techniques and it is particularly suited for early corrosion detection.

  10. Different DNA methylation patterns detected by the Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR technique among various cell types of bulls

    Directory of Open Access Journals (Sweden)

    Carroll Bernie

    2010-03-01

    Full Text Available Abstract Background The purpose of this study was to apply an arbitrarily primed methylation sensitive polymerase chain reaction (PCR assay called Amplified Methylation Polymorphism Polymerase Chain Reaction (AMP PCR to investigate the methylation profiles of somatic and germ cells obtained from Holstein bulls. Methods Genomic DNA was extracted from sperm, leukocytes and fibroblasts obtained from three bulls and digested with a methylation sensitive endonuclease (HpaII. The native genomic and enzyme treated DNA samples were used as templates in an arbitrarily primed-PCR assay with 30 sets of single short oligonucleotide primer. The PCR products were separated on silver stained denaturing polyacrylamide gels. Three types of PCR markers; digestion resistant-, digestion sensitive-, and digestion dependent markers, were analyzed based on the presence/absence polymorphism of the markers between the two templates. Results Approximately 1,000 PCR markers per sample were produced from 27 sets of primer and most of them (>90% were digestion resistant markers. The highest percentage of digestion resistant markers was found in leukocytic DNA (94.8% and the lowest in fibroblastic DNA (92.3%, P ≤ 0.05. Spermatozoa contained a higher number of digestion sensitive markers when compared with the others (3.6% vs. 2.2% and 2.6% in leukocytes and fibroblasts respectively, P ≤ 0.05. Conclusions The powerfulness of the AMP PCR assay was the generation of methylation-associated markers without any prior knowledge of the genomic sequence. The data obtained from different primers provided an overview of genome wide DNA methylation content in different cell types. By using this technique, we found that DNA methylation profile is tissue-specific. Male germ cells were hypomethylated at the HpaII locations when compared with somatic cells, while the chromatin of the well-characterized somatic cells was heavily methylated when compared with that of the versatile somatic

  11. Automated crack detection in conductive smart-concrete structures using a resistor mesh model

    Science.gov (United States)

    Downey, Austin; D'Alessandro, Antonella; Ubertini, Filippo; Laflamme, Simon

    2018-03-01

    Various nondestructive evaluation techniques are currently used to automatically detect and monitor cracks in concrete infrastructure. However, these methods often lack the scalability and cost-effectiveness over large geometries. A solution is the use of self-sensing carbon-doped cementitious materials. These self-sensing materials are capable of providing a measurable change in electrical output that can be related to their damage state. Previous work by the authors showed that a resistor mesh model could be used to track damage in structural components fabricated from electrically conductive concrete, where damage was located through the identification of high resistance value resistors in a resistor mesh model. In this work, an automated damage detection strategy that works through placing high value resistors into the previously developed resistor mesh model using a sequential Monte Carlo method is introduced. Here, high value resistors are used to mimic the internal condition of damaged cementitious specimens. The proposed automated damage detection method is experimentally validated using a 500 × 500 × 50 mm3 reinforced cement paste plate doped with multi-walled carbon nanotubes exposed to 100 identical impact tests. Results demonstrate that the proposed Monte Carlo method is capable of detecting and localizing the most prominent damage in a structure, demonstrating that automated damage detection in smart-concrete structures is a promising strategy for real-time structural health monitoring of civil infrastructure.

  12. Polymorphic Evolutionary Games.

    Science.gov (United States)

    Fishman, Michael A

    2016-06-07

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Action detection by double hierarchical multi-structure space-time statistical matching model

    Science.gov (United States)

    Han, Jing; Zhu, Junwei; Cui, Yiyin; Bai, Lianfa; Yue, Jiang

    2018-03-01

    Aimed at the complex information in videos and low detection efficiency, an actions detection model based on neighboring Gaussian structure and 3D LARK features is put forward. We exploit a double hierarchical multi-structure space-time statistical matching model (DMSM) in temporal action localization. First, a neighboring Gaussian structure is presented to describe the multi-scale structural relationship. Then, a space-time statistical matching method is proposed to achieve two similarity matrices on both large and small scales, which combines double hierarchical structural constraints in model by both the neighboring Gaussian structure and the 3D LARK local structure. Finally, the double hierarchical similarity is fused and analyzed to detect actions. Besides, the multi-scale composite template extends the model application into multi-view. Experimental results of DMSM on the complex visual tracker benchmark data sets and THUMOS 2014 data sets show the promising performance. Compared with other state-of-the-art algorithm, DMSM achieves superior performances.

  14. SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes.

    Science.gov (United States)

    Antaki, Danny; Brandler, William M; Sebat, Jonathan

    2018-05-15

    Structural variation (SV) detection from short-read whole genome sequencing is error prone, presenting significant challenges for population or family-based studies of disease. Here, we describe SV2, a machine-learning algorithm for genotyping deletions and duplications from paired-end sequencing data. SV2 can rapidly integrate variant calls from multiple structural variant discovery algorithms into a unified call set with high genotyping accuracy and capability to detect de novo mutations. SV2 is freely available on GitHub (https://github.com/dantaki/SV2). jsebat@ucsd.edu. Supplementary data are available at Bioinformatics online.

  15. An experimental study on damage detection of structures using a timber beam

    International Nuclear Information System (INIS)

    Choi, Fook Choon; Li, Jianchun; Samali, Bijan; Crews, Keith

    2007-01-01

    Using vibration methods for the damage detection and structural health monitoring in bridge structures is rapidly developing. However, very little work has so far been reported on timber bridges. This paper intends to address such shortcomings by experimental investigation on a timber beam using a vibration based method to detect damage. A promising damage detection algorithm based on modal strain energy was adopted and modified to locate/evaluate damage. A laboratory investigation was conducted on a timber beam inflicted with various damage scenarios using modal tests. The modal parameters obtained from the undamaged and damaged state of the test beam were used in the computation of damage index, were then applied using a damage detection algorithm utilising modal strain energy and a statistical approach to detect location of damage. A mode shape reconstruction technique was used to enhance the capability of the damage detection algorithm with limited number of sensors. The test results and analysis show that location of damage can be accurately identified with limited sensors. The modified method is less dependent on the number of modes selected and can detect damage with a higher degree of confidence

  16. Detection of image structures using the Fisher information and the Rao metric.

    Science.gov (United States)

    Maybank, Stephen J

    2004-12-01

    In many detection problems, the structures to be detected are parameterized by the points of a parameter space. If the conditional probability density function for the measurements is known, then detection can be achieved by sampling the parameter space at a finite number of points and checking each point to see if the corresponding structure is supported by the data. The number of samples and the distances between neighboring samples are calculated using the Rao metric on the parameter space. The Rao metric is obtained from the Fisher information which is, in turn, obtained from the conditional probability density function. An upper bound is obtained for the probability of a false detection. The calculations are simplified in the low noise case by making an asymptotic approximation to the Fisher information. An application to line detection is described. Expressions are obtained for the asymptotic approximation to the Fisher information, the volume of the parameter space, and the number of samples. The time complexity for line detection is estimated. An experimental comparison is made with a Hough transform-based method for detecting lines.

  17. An automated procedure for covariation-based detection of RNA structure

    International Nuclear Information System (INIS)

    Winker, S.; Overbeek, R.; Woese, C.R.; Olsen, G.J.; Pfluger, N.

    1989-12-01

    This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential bondings of secondary and tertiary structure, but also provides the covariation evidence that supports the proposed bondings, and any counter-evidence that can be detected in the known sequences. A small number of previously unknown bondings have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. Currently, we are systematically studying mitochondrial rRNA. Our goal is to detect tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosome structure. Our colleagues in biology have begun experiments to test certain hypotheses suggested by an examination of our program's output. These experiments involve sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. The hope is that the 23S ribosomal RNA of these species will exhibit corresponding complementary variation or generalized covariation. 24 refs

  18. Deep Neural Network for Structural Prediction and Lane Detection in Traffic Scene.

    Science.gov (United States)

    Li, Jun; Mei, Xue; Prokhorov, Danil; Tao, Dacheng

    2017-03-01

    Hierarchical neural networks have been shown to be effective in learning representative image features and recognizing object classes. However, most existing networks combine the low/middle level cues for classification without accounting for any spatial structures. For applications such as understanding a scene, how the visual cues are spatially distributed in an image becomes essential for successful analysis. This paper extends the framework of deep neural networks by accounting for the structural cues in the visual signals. In particular, two kinds of neural networks have been proposed. First, we develop a multitask deep convolutional network, which simultaneously detects the presence of the target and the geometric attributes (location and orientation) of the target with respect to the region of interest. Second, a recurrent neuron layer is adopted for structured visual detection. The recurrent neurons can deal with the spatial distribution of visible cues belonging to an object whose shape or structure is difficult to explicitly define. Both the networks are demonstrated by the practical task of detecting lane boundaries in traffic scenes. The multitask convolutional neural network provides auxiliary geometric information to help the subsequent modeling of the given lane structures. The recurrent neural network automatically detects lane boundaries, including those areas containing no marks, without any explicit prior knowledge or secondary modeling.

  19. An automated procedure for covariation-based detection of RNA structure

    Energy Technology Data Exchange (ETDEWEB)

    Winker, S.; Overbeek, R.; Woese, C.R.; Olsen, G.J.; Pfluger, N.

    1989-12-01

    This paper summarizes our investigations into the computational detection of secondary and tertiary structure of ribosomal RNA. We have developed a new automated procedure that not only identifies potential bondings of secondary and tertiary structure, but also provides the covariation evidence that supports the proposed bondings, and any counter-evidence that can be detected in the known sequences. A small number of previously unknown bondings have been detected in individual RNA molecules (16S rRNA and 7S RNA) through the use of our automated procedure. Currently, we are systematically studying mitochondrial rRNA. Our goal is to detect tertiary structure within 16S rRNA and quaternary structure between 16S and 23S rRNA. Our ultimate hope is that automated covariation analysis will contribute significantly to a refined picture of ribosome structure. Our colleagues in biology have begun experiments to test certain hypotheses suggested by an examination of our program's output. These experiments involve sequencing key portions of the 23S ribosomal RNA for species in which the known 16S ribosomal RNA exhibits variation (from the dominant pattern) at the site of a proposed bonding. The hope is that the 23S ribosomal RNA of these species will exhibit corresponding complementary variation or generalized covariation. 24 refs.

  20. Comparison between Radioisotopic and Non-radioisotopic Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) Procedures in the Detection of Mutations at the rpoB Gene Associated with Rifampicin Resistance in Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Lee, H.; Bang, H.E.; Johnson, R.; Jordaan, A.M.; Victor, T.C. . E-mail : tv@sun.ac.za; Dar, L.; Khan, B.K.; Cho, S.N. . E-mail : raycho@yonsei.ac.kr

    2006-01-01

    Rapid and sensitive detection of mutations at the rpoB gene of Mycobacterium tuberculosis would be of great importance for proper management of tuberculosis (TB) patients and control of multi-drug resistant TB. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) using both radioisotopic and non-radioisotopic methods have been widely used for detecting such mutations. However, the silver staining method, which is the most frequently employed in PCR-SSCP, has been reported to be producing results of varying sensitivity. Radioisotope-based methods have shown greater sensitivity in detecting the rpoB mutations than the silver staining method. The primary objective of this study was therefore to compare the radioisotopic method with the silver staining method detection of mutations of rpoB gene by PCR-SSCP in the same laboratory. Purified DNAs from M. tuberculosis H37Rv were serially diluted and used for PCR amplification with and without radionuclides. The PCR products were then detected by silver staining and autoradiography methods. In addition, clinical isolates were analyzed by PCR-SSCP. The radioisotopic method showed about four-fold increase in the detection of PCR products over ethidium bromide staining in agarose gel. When compared with silver staining, the radioisotopic method gave a sensitivity of more than 10-fold in detecting PCR products and about 8-fold in PCR-SSCP. Radioisotope-based detection methods provided a clearer resolution in PCR-SSCP than the silver staining method when applied to clinical isolates of M. tuberculosis. Radioisotope-based detection method was shown to be more sensitive than non-isotope-based method in detecting PCR products and mutations at the rpoB gene of M. tuberculosis by PCR-SSCP. It may be noted that mutations in the rpoB gene as a marker have significant clinical importance because of the increasing number of MDR-TB cases in the world. It is especially relevant to MDR and Extreme Drug Resistance TB

  1. Scenario based approach to structural damage detection and its value in a risk and reliability perspective

    DEFF Research Database (Denmark)

    Hovgaard, Mads Knude; Hansen, Jannick Balleby; Brincker, Rune

    2013-01-01

    A scenario- and vibration based structural damage detection method is demonstrated though simulation. The method is Finite Element (FE) based. The value of the monitoring is calculated using structural reliability theory. A high cycle fatigue crack propagation model is assumed as the damage mecha......- and without monitoring. Monte Carlo Sampling (MCS) is used to estimate the probabilities and the tower of an onshore NREL 5MW wind turbine is given as a calculation case......A scenario- and vibration based structural damage detection method is demonstrated though simulation. The method is Finite Element (FE) based. The value of the monitoring is calculated using structural reliability theory. A high cycle fatigue crack propagation model is assumed as the damage...

  2. Quantitative structure carcinogenicity relationship for detecting structural alerts in nitroso-compounds

    International Nuclear Information System (INIS)

    Helguera, Aliuska Morales; Cordeiro, M. Natalia D.S.; Perez, Miguel Angel Cabrera; Combes, Robert D.; Gonzalez, Maykel Perez

    2008-01-01

    In this work, Quantitative Structure-Activity Relationship (QSAR) modelling was used as a tool for predicting the carcinogenic potency of a set of 39 nitroso-compounds, which have been bioassayed in male rats by using the oral route of administration. The optimum QSAR model provided evidence of good fit and performance of predicitivity from training set. It was able to account for about 84% of the variance in the experimental activity and exhibited high values of the determination coefficients of cross validations, leave one out and bootstrapping (q 2 LOO = 78.53 and q 2 Boot = 74.97). Such a model was based on spectral moments weighted with Gasteiger-Marsilli atomic charges, polarizability and hydrophobicity, as well as with Abraham indexes, specifically the summation solute hydrogen bond basicity and the combined dipolarity/polarizability. This is the first study to have explored the possibility of combining Abraham solute descriptors with spectral moments. A reasonable interpretation of these molecular descriptors from a toxicological point of view was achieved by means of taking into account bond contributions. The set of relationships so derived revealed the importance of the length of the alkyl chains for determining carcinogenic potential of the chemicals analysed, and were able to explain the difference between mono-substituted and di-substituted nitrosoureas as well as to discriminate between isomeric structures with hydroxyl-alkyl and alkyl substituents in different positions. Moreover, they allowed the recognition of structural alerts in classical structures of two potent nitrosamines, consistent with their biotransformation. These results indicate that this new approach has the potential for improving carcinogenicity predictions based on the identification of structural alerts

  3. Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms : VISCERAL Anatomy Benchmarks

    OpenAIRE

    Jimenez-del-Toro, Oscar; Muller, Henning; Krenn, Markus; Gruenberg, Katharina; Taha, Abdel Aziz; Winterstein, Marianne; Eggel, Ivan; Foncubierta-Rodriguez, Antonio; Goksel, Orcun; Jakab, Andres; Kontokotsios, Georgios; Langs, Georg; Menze, Bjoern H.; Fernandez, Tomas Salas; Schaer, Roger

    2016-01-01

    Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the ...

  4. Fault Detection Algorithm based on Null-Space Analysis for On-Line Structural Health Monitoring

    OpenAIRE

    Yan, Ai-Min; Golinval, Jean-Claude; Marin, Frédéric

    2005-01-01

    Early diagnosis of structural damages or machinery malfunctions allows to reduce the maintenance cost of systems and to increase their reliability and safety. This paper addresses the damage detection problem by statistical analysis on output-only measurements of structures. The developed method is based on subspace analysis of the Hankel matrices constructed by vibration measurement data. The column active subspace of the Hankel matrix defined by the first principal components is orthonormal...

  5. A framework for data compression and damage detection in structural health monitoring applied on a laboratory three-story structure

    Directory of Open Access Journals (Sweden)

    Manoel Afonso Pereira de Lima

    2016-09-01

    Full Text Available Structural Health Monitoring (SHM is an important technique used to preserve many types of structures in the short and long run, using sensor networks to continuously gather the desired data. However, this causes a strong impact in the data size to be stored and processed. A common solution to this is using compression algorithms, where the level of data compression should be adequate enough to allow the correct damage identification. In this work, we use the data sets from a laboratory three-story structure to evaluate the performance of common compression algorithms which, then, are combined with damage detection algorithms used in SHM. We also analyze how the use of Independent Component Analysis, a common technique to reduce noise in raw data, can assist the detection performance. The results showed that Piecewise Linear Histogram combined with Nonlinear PCA have the best trade-off between compression and detection for small error thresholds while Adaptive PCA with Principal Component Analysis perform better with higher values.

  6. Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis.

    Science.gov (United States)

    Glavac, Damjan; Potocnik, Uros; Podpecnik, Darja; Zizek, Teofil; Smerkolj, Sava; Ravnik-Glavac, Metka

    2002-04-01

    We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct insight into the mechanism of CE-SSCP and showed that MFOLD prediction could be helpful in making decisions about the running temperatures and in prediction of CE-SSCP data patterns, especially for shorter (50-100 bp) DNA fragments. Copyright 2002 Wiley-Liss, Inc.

  7. Detection of single-nucleotide polymorphisms using an ON-OFF switching of regenerated biosensor based on a locked nucleic acid-integrated and toehold-mediated strand displacement reaction.

    Science.gov (United States)

    Gao, Zhong Feng; Ling, Yu; Lu, Lu; Chen, Ning Yu; Luo, Hong Qun; Li, Nian Bing

    2014-03-04

    Although various strategies have been reported for single-nucleotide polymorphisms (SNPs) detection, development of a time-saving, specific, and regenerated electrochemical sensing platform still remains a realistic goal. In this study, an ON-OFF switching of a regenerated biosensor based on a locked nucleic acid (LNA)-integrated and toehold-mediated strand displacement reaction technique is constructed for detection of SNPs. The LNA-integrated and methylene blue-labeled capture probe with an external toehold is designed to switch on the sensing system. The mutant-type DNA probe completes complementary with the capture probe to trigger the strand displacement reaction, which switches off the sensing system. However, when the single-base mismatched wild-type DNA probe is presented, the strand displacement reaction cannot be achieved; therefore, the sensing system still keeps the ON state. This DNA sensor is stable over five reuses. We further testify that the LNA-integrated sequence has better recognition ability for SNPs detection compared to the DNA-integrated sequence. Moreover, this DNA senor exhibits a remarkable discrimination capability of SNPs among abundant wild-type targets and 6000-fold (m/m) excess of genomic DNA. In addition, it is selective enough in complex and contaminant-ridden samples, such as human urine, soil, saliva, and beer. Overall, these results demonstrate that this reliable DNA sensor is easy to be fabricated, simple to operate, and stable enough to be readily regenerated.

  8. Vibration-based damage detection of structural joints in presence of uncertainty

    Directory of Open Access Journals (Sweden)

    Al-Bugharbee Hussein

    2018-01-01

    Full Text Available Early damage detection of structure’s joints is essential in order to ensure the integrity of structures. Vibration-based methods are the most popular way of diagnosing damage in machinery joints. Any technique that is used for such a purpose requires dealing with the variability inherent to the system due to manufacturing tolerances, environmental conditions or aging. The level of variability in vibrational response can be very high for mass-produced complex structures that possess a large number of components. In this study, a simple and efficient time frequency method is proposed for detection of damage in connecting joints. The method suggests using singular spectrum analysis for building a reference space from the signals measured on a healthy structure and then compares all other signals to that reference space in order to detect the presence of faults. A model of two plates connected by a series of mounts is used to examine the effectiveness of the method where the uncertainty in the mount properties is taken into account to model the variability in the built-up structure. The motivation behind the simplified model is to identify the faulty mounts in trim-structure joints of an automotive vehicle where a large number of simple plastic clips are used to connect the trims to the vehicle structure.

  9. Development of an ultrasonic nondestructive inspection method for impact damage detection in composite aircraft structures

    Science.gov (United States)

    Capriotti, M.; Kim, H. E.; Lanza di Scalea, F.; Kim, H.

    2017-04-01

    High Energy Wide Area Blunt Impact (HEWABI) due to ground service equipment can often occur in aircraft structures causing major damages. These Wide Area Impact Damages (WAID) can affect the internal components of the structure, hence are usually not visible nor detectable by typical one-sided NDE techniques and can easily compromise the structural safety of the aircraft. In this study, the development of an NDI method is presented together with its application to impacted aircraft frames. The HEWABI from a typical ground service scenario has been previously tested and the desired type of damages have been generated, so that the aircraft panels could become representative study cases. The need of the aircraft industry for a rapid, ramp-friendly system to detect such WAID is here approached with guided ultrasonic waves (GUW) and a scanning tool that accesses the whole structure from the exterior side only. The wide coverage of the specimen provided by GUW has been coupled to a differential detection approach and is aided by an outlier statistical analysis to be able to inspect and detect faults in the challenging composite material and complex structure. The results will be presented and discussed with respect to the detection capability of the system and its response to the different damage types. Receiving Operating Characteristics curves (ROC) are also produced to quantify and assess the performance of the proposed method. Ongoing work is currently aimed at the penetration of the inner components of the structure, such as shear ties and C-frames, exploiting different frequency ranges and signal processing techniques. From the hardware and tool development side, different transducers and coupling methods, such as air-coupled transducers, are under investigation together with the design of a more suitable scanning technique.

  10. TRANSAT-- method for detecting the conserved helices of functional RNA structures, including transient, pseudo-knotted and alternative structures.

    Science.gov (United States)

    Wiebe, Nicholas J P; Meyer, Irmtraud M

    2010-06-24

    The prediction of functional RNA structures has attracted increased interest, as it allows us to study the potential functional roles of many genes. RNA structure prediction methods, however, assume that there is a unique functional RNA structure and also do not predict functional features required for in vivo folding. In order to understand how functional RNA structures form in vivo, we require sophisticated experiments or reliable prediction methods. So far, there exist only a few, experimentally validated transient RNA structures. On the computational side, there exist several computer programs which aim to predict the co-transcriptional folding pathway in vivo, but these make a range of simplifying assumptions and do not capture all features known to influence RNA folding in vivo. We want to investigate if evolutionarily related RNA genes fold in a similar way in vivo. To this end, we have developed a new computational method, Transat, which detects conserved helices of high statistical significance. We introduce the method, present a comprehensive performance evaluation and show that Transat is able to predict the structural features of known reference structures including pseudo-knotted ones as well as those of known alternative structural configurations. Transat can also identify unstructured sub-sequences bound by other molecules and provides evidence for new helices which may define folding pathways, supporting the notion that homologous RNA sequence not only assume a similar reference RNA structure, but also fold similarly. Finally, we show that the structural features predicted by Transat differ from those assuming thermodynamic equilibrium. Unlike the existing methods for predicting folding pathways, our method works in a comparative way. This has the disadvantage of not being able to predict features as function of time, but has the considerable advantage of highlighting conserved features and of not requiring a detailed knowledge of the cellular

  11. Three-dimensional glue detection and evaluation based on linear structured light

    Science.gov (United States)

    Xiao, Zhitao; Yang, Ruipeng; Geng, Lei; Liu, Yanbei

    2018-01-01

    During the online glue detection of body in white (BIW), the purpose of traditional glue detection based on machine vision is the localization and segmentation of glue, which is dissatisfactory for estimating the uniformity of glue with complex shape. A three-dimensional glue detection method based on the linear structured light and the movement parameters of robot is proposed. Firstly, the linear structured light and epipolar constraint algorithm are used for sign matching of binocular vision. Then, hand-eye relationship between robot and binocular camera is utilized to unified coordinate system. Finally, a structured light stripe extraction method is proposed to extract the sub-pixel coordinates of the light strip center. Experiments results demonstrate that the propose method can estimate the shape of glue accurately. For three kinds of glue with complex shape and uneven illumination, our method can detect the positions of blemishes. The absolute error of measurement is less than 1.04mm and the relative error is less than 10% respectively, which is suitable for online glue detection in BIW.

  12. Detection of Answer Copying Based on the Structure of a High-Stakes Test

    Science.gov (United States)

    Belov, Dmitry I.

    2011-01-01

    This article presents the Variable Match Index (VM-Index), a new statistic for detecting answer copying. The power of the VM-Index relies on two-dimensional conditioning as well as the structure of the test. The asymptotic distribution of the VM-Index is analyzed by reduction to Poisson trials. A computational study comparing the VM-Index with the…

  13. Structural damage detection-oriented multi-type sensor placement with multi-objective optimization

    Science.gov (United States)

    Lin, Jian-Fu; Xu, You-Lin; Law, Siu-Seong

    2018-05-01

    A structural damage detection-oriented multi-type sensor placement method with multi-objective optimization is developed in this study. The multi-type response covariance sensitivity-based damage detection method is first introduced. Two objective functions for optimal sensor placement are then introduced in terms of the response covariance sensitivity and the response independence. The multi-objective optimization problem is formed by using the two objective functions, and the non-dominated sorting genetic algorithm (NSGA)-II is adopted to find the solution for the optimal multi-type sensor placement to achieve the best structural damage detection. The proposed method is finally applied to a nine-bay three-dimensional frame structure. Numerical results show that the optimal multi-type sensor placement determined by the proposed method can avoid redundant sensors and provide satisfactory results for structural damage detection. The restriction on the number of each type of sensors in the optimization can reduce the searching space in the optimization to make the proposed method more effective. Moreover, how to select a most optimal sensor placement from the Pareto solutions via the utility function and the knee point method is demonstrated in the case study.

  14. Structure and dynamics of paramagnetic transients by pulsed EPR and NMR detection of nuclear resonance

    International Nuclear Information System (INIS)

    Trifunac, A.D.

    1981-01-01

    Structure and dynamics of transient radicals in pulse radiolysis can be studied by time resolved EPR and NMR techniques. EPR study of kinetics and relaxation is illustrated. The NMR detection of nuclear resonance in transient radicals is a new method which allows the study of hyperfine coupling, population dynamics, radical kinetics, and reaction mechanism. 9 figures

  15. [Polymorphisms of mitochondrial DNA hypervariable regions HVR I and HVR II in Changdu Tibetan in China].

    Science.gov (United States)

    Zhao, Jianmin; Kang, Longli; Bian, Liqiang; La, Zong

    2008-10-01

    To analyze the sequence polymorphisms of mitochondrial DNA HVR I and HVR II in Tibetan population in Changdu area of Tibet. mtDNAs obtained from 97 unrelated individuals were amplified and directly sequenced. One hundred and eleven variable sites were identified, including nucleotide transitions, transversions, insertions and deletions. In HVR I region (nt16024-nt16365), sixty-eight polymorphic sites and 92 haplotypes were observed, and the genetic diversity was 0.9985. In HVR II region (nt73-nt340), forty-three polymorphic sites and 91 haplotypes were detected, and the genetic diversity was 0.9882. The random match probability of HVR I and HVR II regions were 0.0120 and 0.0118, respectively. When the sequence analysis of HVR I and HVR II regions were combined, ninety-seven different haplotypes were found. The combined match probability of two unrelated persons having the same sequence was 0.0103. There are some unique polymorphic loci in the Changdu Tibetan population. The results suggest that there are significant difference in the genetic structure in the mitochondrial DNA D-loop region between Changdu Tibetans and other Asian populations and Caucasians. Sequence polymorphism in mitochondrial DNA HVR I and HVR II can be used as a genetic marker for forensic individual identification and genetic analysis.

  16. A game theoretic algorithm to detect overlapping community structure in networks

    Science.gov (United States)

    Zhou, Xu; Zhao, Xiaohui; Liu, Yanheng; Sun, Geng

    2018-04-01

    Community detection can be used as an important technique for product and personalized service recommendation. A game theory based approach to detect overlapping community structure is introduced in this paper. The process of the community formation is converted into a game, when all agents (nodes) cannot improve their own utility, the game process will be terminated. The utility function is composed of a gain and a loss function and we present a new gain function in this paper. In addition, different from choosing action randomly among join, quit and switch for each agent to get new label, two new strategies for each agent to update its label are designed during the game, and the strategies are also evaluated and compared for each agent in order to find its best result. The overlapping community structure is naturally presented when the stop criterion is satisfied. The experimental results demonstrate that the proposed algorithm outperforms other similar algorithms for detecting overlapping communities in networks.

  17. Structural damage detection using higher-order finite elements and a scanning laser vibrometer

    Science.gov (United States)

    Jin, Si

    In contrast to conventional non-destructive evaluation methods, dynamics-based damage detection methods are capable of rapid integrity evaluation of large structures and have received considerable attention from aerospace, mechanical, and civil engineering communities in recent years. However, the identifiable damage size using dynamics-based methods is determined by the number of sensors used, level of measurement noise, accuracy of structural models, and signal processing techniques. In this thesis we study dynamics of structures with damage and then derive and experimentally verify new model-independent structural damage detection methods that can locate small damage to structures. To find sensitive damage detection parameters we develop a higher-order beam element that enforces the continuity of displacements, slopes, bending moments, and shear forces at all nodes, and a higher-order rectangular plate element that enforces the continuity of displacements, slopes, and bending and twisting moments at all nodes. These two elements are used to study the dynamics of beams and plates. Results show that high-order spatial derivatives of high-frequency modes are important sensitive parameters that can locate small structural damage. Unfortunately the most powerful and popular structural modeling technique, the finite element method, is not accurate in predicting high-frequency responses. Hence, a model-independent method using dynamic responses obtained from high density measurements is concluded to be the best approach. To increase measurement density and reduce noise a Polytec PI PSV-200 scanning laser vibrometer is used to provide non-contact, dense, and accurate measurements of structural vibration velocities. To avoid the use of structural models and to extract sensitive detection parameters from experimental data, a brand-new structural damage detection method named BED (Boundary-Effect Detection) is developed for pinpointing damage locations using Operational

  18. A spectral method to detect community structure based on distance modularity matrix

    Science.gov (United States)

    Yang, Jin-Xuan; Zhang, Xiao-Dong

    2017-08-01

    There are many community organizations in social and biological networks. How to identify these community structure in complex networks has become a hot issue. In this paper, an algorithm to detect community structure of networks is proposed by using spectra of distance modularity matrix. The proposed algorithm focuses on the distance of vertices within communities, rather than the most weakly connected vertex pairs or number of edges between communities. The experimental results show that our method achieves better effectiveness to identify community structure for a variety of real-world networks and computer generated networks with a little more time-consumption.

  19. Polymorphous computing fabric

    Science.gov (United States)

    Wolinski, Christophe Czeslaw [Los Alamos, NM; Gokhale, Maya B [Los Alamos, NM; McCabe, Kevin Peter [Los Alamos, NM

    2011-01-18

    Fabric-based computing systems and methods are disclosed. A fabric-based computing system can include a polymorphous computing fabric that can be customized on a per application basis and a host processor in communication with said polymorphous computing fabric. The polymorphous computing fabric includes a cellular architecture that can be highly parameterized to enable a customized synthesis of fabric instances for a variety of enhanced application performances thereof. A global memory concept can also be included that provides the host processor random access to all variables and instructions associated with the polymorphous computing fabric.

  20. An enhanced structure tensor method for sea ice ridge detection from GF-3 SAR imagery

    Science.gov (United States)

    Zhu, T.; Li, F.; Zhang, Y.; Zhang, S.; Spreen, G.; Dierking, W.; Heygster, G.

    2017-12-01

    In SAR imagery, ridges or leads are shown as the curvilinear features. The proposed ridge detection method is facilitated by their curvilinear shapes. The bright curvilinear features are recognized as the ridges while the dark curvilinear features are classified as the leads. In dual-polarization HH or HV channel of C-band SAR imagery, the bright curvilinear feature may be false alarm because the frost flowers of young leads may show as bright pixels associated with changes in the surface salinity under calm surface conditions. Wind roughened leads also trigger the backscatter increasing that can be misclassified as ridges [1]. Thus the width limitation is considered in this proposed structure tensor method [2], since only shape feature based method is not enough for detecting ridges. The ridge detection algorithm is based on the hypothesis that the bright pixels are ridges with curvilinear shapes and the ridge width is less 30 meters. Benefited from GF-3 with high spatial resolution of 3 meters, we provide an enhanced structure tensor method for detecting the significant ridge. The preprocessing procedures including the calibration and incidence angle normalization are also investigated. The bright pixels will have strong response to the bandpass filtering. The ridge training samples are delineated from the SAR imagery in the Log-Gabor filters to construct structure tensor. From the tensor, the dominant orientation of the pixel representing the ridge is determined by the dominant eigenvector. For the post-processing of structure tensor, the elongated kernel is desired to enhance the ridge curvilinear shape. Since ridge presents along a certain direction, the ratio of the dominant eigenvector will be used to measure the intensity of local anisotropy. The convolution filter has been utilized in the constructed structure tensor is used to model spatial contextual information. Ridge detection results from GF-3 show the proposed method performs better compared to the

  1. Novel Damage Detection Techniques for Structural Health Monitoring Using a Hybrid Sensor

    Directory of Open Access Journals (Sweden)

    Dengjiang Wang

    2016-01-01

    Full Text Available This study presents a technique for detecting fatigue cracks based on a hybrid sensor monitoring system consisting of a combination of intelligent coating monitoring (ICM and piezoelectric transducer (PZT sensors. An experimental procedure using this hybrid sensor system was designed to monitor the cracks generated by fatigue testing in plate structures. A probability of detection (POD model that quantifies the reliability of damage detection for a specific sensor or the nondestructive testing (NDT method was used to evaluate the weight factor for the ICM and PZT sensors. To estimate the uncertainty of model parameters in this study, the Bayesian method was employed. Realistic data from fatigue testing was used to validate the overall method, and the results show that the novel damage detection technique using a hybrid sensor can quantify fatigue cracks more accurately than results obtained by conventional sensor methods.

  2. Enhanced Detectability of Community Structure in Multilayer Networks through Layer Aggregation.

    Science.gov (United States)

    Taylor, Dane; Shai, Saray; Stanley, Natalie; Mucha, Peter J

    2016-06-03

    Many systems are naturally represented by a multilayer network in which edges exist in multiple layers that encode different, but potentially related, types of interactions, and it is important to understand limitations on the detectability of community structure in these networks. Using random matrix theory, we analyze detectability limitations for multilayer (specifically, multiplex) stochastic block models (SBMs) in which L layers are derived from a common SBM. We study the effect of layer aggregation on detectability for several aggregation methods, including summation of the layers' adjacency matrices for which we show the detectability limit vanishes as O(L^{-1/2}) with increasing number of layers, L. Importantly, we find a similar scaling behavior when the summation is thresholded at an optimal value, providing insight into the common-but not well understood-practice of thresholding pairwise-interaction data to obtain sparse network representations.

  3. Structural damage detection based on stochastic subspace identification and statistical pattern recognition: I. Theory

    Science.gov (United States)

    Ren, W. X.; Lin, Y. Q.; Fang, S. E.

    2011-11-01

    One of the key issues in vibration-based structural health monitoring is to extract the damage-sensitive but environment-insensitive features from sampled dynamic response measurements and to carry out the statistical analysis of these features for structural damage detection. A new damage feature is proposed in this paper by using the system matrices of the forward innovation model based on the covariance-driven stochastic subspace identification of a vibrating system. To overcome the variations of the system matrices, a non-singularity transposition matrix is introduced so that the system matrices are normalized to their standard forms. For reducing the effects of modeling errors, noise and environmental variations on measured structural responses, a statistical pattern recognition paradigm is incorporated into the proposed method. The Mahalanobis and Euclidean distance decision functions of the damage feature vector are adopted by defining a statistics-based damage index. The proposed structural damage detection method is verified against one numerical signal and two numerical beams. It is demonstrated that the proposed statistics-based damage index is sensitive to damage and shows some robustness to the noise and false estimation of the system ranks. The method is capable of locating damage of the beam structures under different types of excitations. The robustness of the proposed damage detection method to the variations in environmental temperature is further validated in a companion paper by a reinforced concrete beam tested in the laboratory and a full-scale arch bridge tested in the field.

  4. Polymorphic microsatellite loci for the sand pocket mouse Chaetodipus arenarius, an endemic from the Baja California Peninsula

    Science.gov (United States)

    Munguia-Vega, A.; Rodriguez-Estrella, R.; Nachman, M.; Culver, M.

    2009-01-01

    Fifteen polymorphic microsatellite loci were isolated from an enriched genomic library of the sand pocket mouse Chaetodipus arenarius. The mean number of alleles per locus was 11.53 (range five to 19) and the average observed heterozygosity was 0.764 (range 0.121 to 1.0). The markers will be used for detecting the impact of human-induced habitat fragmentation on patterns of gene flow, genetic structure, and extinction risk. In addition, these markers will be useful across the genus because most of the loci cross-amplified and were polymorphic in three other species of Chaetodipus. ?? 2008 The Authors.

  5. Foundations of computer vision computational geometry, visual image structures and object shape detection

    CERN Document Server

    Peters, James F

    2017-01-01

    This book introduces the fundamentals of computer vision (CV), with a focus on extracting useful information from digital images and videos. Including a wealth of methods used in detecting and classifying image objects and their shapes, it is the first book to apply a trio of tools (computational geometry, topology and algorithms) in solving CV problems, shape tracking in image object recognition and detecting the repetition of shapes in single images and video frames. Computational geometry provides a visualization of topological structures such as neighborhoods of points embedded in images, while image topology supplies us with structures useful in the analysis and classification of image regions. Algorithms provide a practical, step-by-step means of viewing image structures. The implementations of CV methods in Matlab and Mathematica, classification of chapter problems with the symbols (easily solved) and (challenging) and its extensive glossary of key words, examples and connections with the fabric of C...

  6. Flood protection structure detection with Lidar: examples on French Mediterranean rivers and coastal areas

    Directory of Open Access Journals (Sweden)

    Trmal Céline

    2016-01-01

    Full Text Available This paper aims at presenting different topographic analysis conducted with GIS software in order to detect flood protection structures, natural or artificial, in river floodplains but also in coastal zones. Those computations are relevant because of the availability of high-resolution lidar digital terrain model (DTM. An automatic detection permits to map the footprint of those structures. Then detailed mapping of structure crest is achieved by implementing a least cost path analysis on DTM but also on other terrain aspects such as the curvature. On coastal zones, the analysis is going further by identifying flood protected areas and the level of protection regarding sea level. This article is illustrated by examples on French Mediterranean rivers and coastal areas.

  7. Polymorphism of nickel sulfate hexahydrate

    Energy Technology Data Exchange (ETDEWEB)

    Angel, R.J.; Finger, L.W.

    1988-11-15

    NiSO/sub 4/.6H/sub 2/O, M/sub r/=262.85; data collections with Mo K..cap alpha.. radiation, lambda=0.7093 A, room temperature. Monoclinic polymorph: C2/c, a=9.880(3), b=7.228(2), c=24.130(3) A, ..beta..=98.38(2)/sup 0/, V=1704.7(6) A/sup 3/, Z=8, D/sub x/=2.05 g cm/sup -3/, ..mu..=25.54 cm/sup -1/, F(000)=1088, R=0.031 (wR=0.038) for 2176 observed reflections. Tetragonal polymorph: P4/sub 1/2/sub 1/2, a=6.780 (1), c=18.285 (2) A, V=840.5 (3) A/sup 3/, Z=4, D/sub x/=2.07 g cm/sup -3/, ..mu..=25.81 cm/sup -1/, F(000)=544, R=0.045 (wR=0.050) for 2102 observed reflections. The structure of the tetragonal polymorph originally determined (without H positions) by Beevers and Lipson and refined by O'Connor and Dale and Stadnicka, Glazer and Koralewski, is confirmed by refinement of X-ray diffraction data. The structure of the monoclinic polymorph is confirmed as being isostructural with NiSO/sub 4/.6D/sub 2/O, and a number of other hexahydrate sulfates, e.g. MgSO/sub 4/.6H/sub 2/O. Both structures contain isolated (Ni(H/sub 2/O/sub 6/) octahedra and (SO/sub 4/) tetrahedra linked by hydrogen bonding.

  8. Design of a piezoelectric-based structural health monitoring system for damage detection in composite materials

    Science.gov (United States)

    Kessler, Seth S.; Spearing, S. Mark

    2002-07-01

    Cost-effective and reliable damage detection is critical for the utilization of composite materials. This paper presents the conclusions of an experimental and analytical survey of candidate methods for in-situ damage detection in composite structures. Experimental results are presented for the application of modal analysis and Lamb wave techniques to quasi-isotropic graphite/epoxy test specimens containing representative damage. Piezoelectric patches were used as actuators and sensors for both sets of experiments. Modal analysis methods were reliable for detecting small amounts of global damage in a simple composite structure. By comparison, Lamb wave methods were sensitive to all types of local damage present between the sensor and actuator, provided useful information about damage presence and severity, and present the possibility of estimating damage type and location. Analogous experiments were also performed for more complex built-up structures. These techniques are suitable for structural health monitoring applications since they can be applied with low power conformable sensors and can provide useful information about the state of a structure during operation. Piezoelectric patches could also be used as multipurpose sensors to detect damage by a variety of methods such as modal analysis, Lamb wave, acoustic emission and strain based methods simultaneously, by altering driving frequencies and sampling rates. This paper present guidelines and recommendations drawn from this research to assist in the design of a structural health monitoring system for a vehicle. These systems will be an important component in future designs of air and spacecraft to increase the feasibility of their missions.

  9. DNA Characterization and Polymorphism of KISS1 Gene in Egyptian ...

    African Journals Online (AJOL)

    The objective of this study was the detection of the restriction fragment length polymorphism (RFLP) and single nucleotide polymorphisms (SNPs) of KISS1 gene in six major Egyptian small ruminant breeds. The primers used in this study flanked a 377 bp fragment from intron 1 of KISS1 gene in sheep and goat. These PCR ...

  10. A Time-Domain Structural Damage Detection Method Based on Improved Multiparticle Swarm Coevolution Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    Shao-Fei Jiang

    2014-01-01

    Full Text Available Optimization techniques have been applied to structural health monitoring and damage detection of civil infrastructures for two decades. The standard particle swarm optimization (PSO is easy to fall into the local optimum and such deficiency also exists in the multiparticle swarm coevolution optimization (MPSCO. This paper presents an improved MPSCO algorithm (IMPSCO firstly and then integrates it with Newmark’s algorithm to localize and quantify the structural damage by using the damage threshold proposed. To validate the proposed method, a numerical simulation and an experimental study of a seven-story steel frame were employed finally, and a comparison was made between the proposed method and the genetic algorithm (GA. The results show threefold: (1 the proposed method not only is capable of localization and quantification of damage, but also has good noise-tolerance; (2 the damage location can be accurately detected using the damage threshold proposed in this paper; and (3 compared with the GA, the IMPSCO algorithm is more efficient and accurate for damage detection problems in general. This implies that the proposed method is applicable and effective in the community of damage detection and structural health monitoring.

  11. STRUCTURE LINE DETECTION FROM LIDAR POINT CLOUDS USING TOPOLOGICAL ELEVATION ANALYSIS

    Directory of Open Access Journals (Sweden)

    C. Y. Lo

    2012-07-01

    Full Text Available Airborne LIDAR point clouds, which have considerable points on object surfaces, are essential to building modeling. In the last two decades, studies have developed different approaches to identify structure lines using two main approaches, data-driven and modeldriven. These studies have shown that automatic modeling processes depend on certain considerations, such as used thresholds, initial value, designed formulas, and predefined cues. Following the development of laser scanning systems, scanning rates have increased and can provide point clouds with higher point density. Therefore, this study proposes using topological elevation analysis (TEA to detect structure lines instead of threshold-dependent concepts and predefined constraints. This analysis contains two parts: data pre-processing and structure line detection. To preserve the original elevation information, a pseudo-grid for generating digital surface models is produced during the first part. The highest point in each grid is set as the elevation value, and its original threedimensional position is preserved. In the second part, using TEA, the structure lines are identified based on the topology of local elevation changes in two directions. Because structure lines can contain certain geometric properties, their locations have small relieves in the radial direction and steep elevation changes in the circular direction. Following the proposed approach, TEA can be used to determine 3D line information without selecting thresholds. For validation, the TEA results are compared with those of the region growing approach. The results indicate that the proposed method can produce structure lines using dense point clouds.

  12. Electrostatic control of phospholipid polymorphism.

    Science.gov (United States)

    Tarahovsky, Y S; Arsenault, A L; MacDonald, R C; McIntosh, T J; Epand, R M

    2000-12-01

    A regular progression of polymorphic phase behavior was observed for mixtures of the anionic phospholipid, cardiolipin, and the cationic phospholipid derivative, 1, 2-dioleoyl-sn-glycero-3-ethylphosphocholine. As revealed by freeze-fracture electron microscopy and small-angle x-ray diffraction, whereas the two lipids separately assume only lamellar phases, their mixtures exhibit a symmetrical (depending on charge ratio and not polarity) sequence of nonlamellar phases. The inverted hexagonal phase, H(II,) formed from equimolar mixtures of the two lipids, i.e., at net charge neutrality (charge ratio (CR((+/-))) = 1:1). When one type of lipid was in significant excess (CR((+/-)) = 2:1 or CR((+/-)) = 1:2), a bicontinuous cubic structure was observed. These cubic phases were very similar to those sometimes present in cellular organelles that contain cardiolipin. Increasing the excess of cationic or anionic charge to CR((+/-)) = 4:1 or CR((+/-)) = 1:4 led to the appearance of membrane bilayers with numerous interlamellar contacts, i.e., sponge structures. It is evident that interactions between cationic and anionic moieties can influence the packing of polar heads and hence control polymorphic phase transitions. The facile isothermal, polymorphic interconversion of these lipids may have important biological and technical implications.

  13. Improving Anomaly Detection for Text-Based Protocols by Exploiting Message Structures

    Directory of Open Access Journals (Sweden)

    Christian M. Mueller

    2010-12-01

    Full Text Available Service platforms using text-based protocols need to be protected against attacks. Machine-learning algorithms with pattern matching can be used to detect even previously unknown attacks. In this paper, we present an extension to known Support Vector Machine (SVM based anomaly detection algorithms for the Session Initiation Protocol (SIP. Our contribution is to extend the amount of different features used for classification (feature space by exploiting the structure of SIP messages, which reduces the false positive rate. Additionally, we show how combining our approach with attribute reduction significantly improves throughput.

  14. Algorithms and data structures for automated change detection and classification of sidescan sonar imagery

    Science.gov (United States)

    Gendron, Marlin Lee

    During Mine Warfare (MIW) operations, MIW analysts perform change detection by visually comparing historical sidescan sonar imagery (SSI) collected by a sidescan sonar with recently collected SSI in an attempt to identify objects (which might be explosive mines) placed at sea since the last time the area was surveyed. This dissertation presents a data structure and three algorithms, developed by the author, that are part of an automated change detection and classification (ACDC) system. MIW analysts at the Naval Oceanographic Office, to reduce the amount of time to perform change detection, are currently using ACDC. The dissertation introductory chapter gives background information on change detection, ACDC, and describes how SSI is produced from raw sonar data. Chapter 2 presents the author's Geospatial Bitmap (GB) data structure, which is capable of storing information geographically and is utilized by the three algorithms. This chapter shows that a GB data structure used in a polygon-smoothing algorithm ran between 1.3--48.4x faster than a sparse matrix data structure. Chapter 3 describes the GB clustering algorithm, which is the author's repeatable, order-independent method for clustering. Results from tests performed in this chapter show that the time to cluster a set of points is not affected by the distribution or the order of the points. In Chapter 4, the author presents his real-time computer-aided detection (CAD) algorithm that automatically detects mine-like objects on the seafloor in SSI. The author ran his GB-based CAD algorithm on real SSI data, and results of these tests indicate that his real-time CAD algorithm performs comparably to or better than other non-real-time CAD algorithms. The author presents his computer-aided search (CAS) algorithm in Chapter 5. CAS helps MIW analysts locate mine-like features that are geospatially close to previously detected features. A comparison between the CAS and a great circle distance algorithm shows that the

  15. Spectral methods for the detection of network community structure: a comparative analysis

    International Nuclear Information System (INIS)

    Shen, Hua-Wei; Cheng, Xue-Qi

    2010-01-01

    Spectral analysis has been successfully applied to the detection of community structure of networks, respectively being based on the adjacency matrix, the standard Laplacian matrix, the normalized Laplacian matrix, the modularity matrix, the correlation matrix and several other variants of these matrices. However, the comparison between these spectral methods is less reported. More importantly, it is still unclear which matrix is more appropriate for the detection of community structure. This paper answers the question by evaluating the effectiveness of these five matrices against benchmark networks with heterogeneous distributions of node degree and community size. Test results demonstrate that the normalized Laplacian matrix and the correlation matrix significantly outperform the other three matrices at identifying the community structure of networks. This indicates that it is crucial to take into account the heterogeneous distribution of node degree when using spectral analysis for the detection of community structure. In addition, to our surprise, the modularity matrix exhibits very similar performance to the adjacency matrix, which indicates that the modularity matrix does not gain benefits from using the configuration model as a reference network with the consideration of the node degree heterogeneity

  16. Damage Detection in Bridge Structure Using Vibration Data under Random Travelling Vehicle Loads

    International Nuclear Information System (INIS)

    Loh, C H; Hung, T Y; Chen, S F; Hsu, W T

    2015-01-01

    Due to the random nature of the road excitation and the inherent uncertainties in bridge-vehicle system, damage identification of bridge structure through continuous monitoring under operating situation become a challenge problem. Methods for system identification and damage detection of a continuous two-span concrete bridge structure in time domain is presented using interaction forces from random moving vehicles as excitation. The signals recorded in different locations of the instrumented bridge are mixed with signals from different internal and external (road roughness) vibration sources. The damage structure is also modelled as the stiffness reduction in one of the beam element. For the purpose of system identification and damage detection three different output-only modal analysis techniques are proposed: The covariance-driven stochastic subspace identification (SSI-COV), the blind source separation algorithms (called Second Order Blind Identification) and the multivariate AR model. The advantages and disadvantages of the three algorithms are discussed. Finally, the null-space damage index, subspace damage indices and mode shape slope change are used to detect and locate the damage. The proposed approaches has been tested in simulation and proved to be effective for structural health monitoring. (paper)

  17. Methods of the Detection and Identification of Structural Defects in Saturated Metallic Composite Castings

    Directory of Open Access Journals (Sweden)

    Gawdzińska K.

    2017-09-01

    Full Text Available Diagnostics of composite castings, due to their complex structure, requires that their characteristics are tested by an appropriate description method. Any deviation from the specific characteristic will be regarded as a material defect. The detection of defects in composite castings sometimes is not sufficient and the defects have to be identified. This study classifies defects found in the structures of saturated metallic composite castings and indicates those stages of the process where such defects are likely to be formed. Not only does the author determine the causes of structural defects, describe methods of their detection and identification, but also proposes a schematic procedure to be followed during detection and identification of structural defects of castings made from saturated reinforcement metallic composites. Alloys examination was conducted after technological process, while using destructive (macroscopic tests, light and scanning electron microscopy and non-destructive (ultrasonic and X-ray defectoscopy, tomography, gravimetric method methods. Research presented in this article are part of author’s work on castings quality.

  18. Deep Defect Detection within Thick Multilayer Aircraft Structures Containing Steel Fasteners Using a Giant-Magneto Resistive (GMR) Sensor (Preprint)

    National Research Council Canada - National Science Library

    Ko, Ray T; Steffes, Gary J

    2007-01-01

    Defect detection within thick multilayer structures containing steel fasteners is a challenging task in eddy current testing due to the magnetic permeability of the fasteners and overall thickness of the structure...

  19. Extended Polymorphism of Two-Dimensional Material

    NARCIS (Netherlands)

    Yoshida, Masaro; Ye, Jianting; Zhang, Yijin; Imai, Yasuhiko; Kimura, Shigeru; Fujiwara, Akihiko; Nishizaki, Terukazu; Kobayashi, Norio; Nakano, Masaki; Iwasa, Yoshihiro

    When controlling electronic properties of bulk materials, we usually assume that the basic crystal structure is fixed. However, in two-dimensional (2D) materials, atomic structure or to functionalize their properties. Various polymorphs can exist in transition metal dichalcogenides (TMDCs) from

  20. Significant population genetic structure detected in the rock bream Oplegnathus fasciatus (Temminck & Schlegel, 1844) inferred from fluorescent-AFLP analysis

    Science.gov (United States)

    Xiao, Yongshuang; Ma, Daoyuan; Xu, Shihong; Liu, Qinghua; Wang, Yanfeng; Xiao, Zhizhong; Li, Jun

    2016-05-01

    Oplegnathus fasciatus (rock bream) is a commercial rocky reef fish species in East Asia that has been considered for aquaculture. We estimated the population genetic diversity and population structure of the species along the coastal waters of China using fluorescent-amplified fragment length polymorphisms technology. Using 53 individuals from three populations and four pairs of selective primers, we amplified 1 264 bands, 98.73% of which were polymorphic. The Zhoushan population showed the highest Nei's genetic diversity and Shannon genetic diversity. The results of analysis of molecular variance (AMOVA) showed that 59.55% of genetic variation existed among populations and 40.45% occurred within populations, which indicated that a significant population genetic structure existed in the species. The pairwise fixation index F st ranged from 0.20 to 0.63 and were significant after sequential Bonferroni correction. The topology of an unweighted pair group method with arithmetic mean tree showed two significant genealogical branches corresponding to the sampling locations of North and South China. The AMOVA and STRUCTURE analyses suggested that the O. fasciatus populations examined should comprise two stocks.

  1. Artificial immune pattern recognition for damage detection in structural health monitoring sensor networks

    Science.gov (United States)

    Chen, Bo; Zang, Chuanzhi

    2009-03-01

    This paper presents an artificial immune pattern recognition (AIPR) approach for the damage detection and classification in structures. An AIPR-based Structure Damage Classifier (AIPR-SDC) has been developed by mimicking immune recognition and learning mechanisms. The structure damage patterns are represented by feature vectors that are extracted from the structure's dynamic response measurements. The training process is designed based on the clonal selection principle in the immune system. The selective and adaptive features of the clonal selection algorithm allow the classifier to generate recognition feature vectors that are able to match the training data. In addition, the immune learning algorithm can learn and remember various data patterns by generating a set of memory cells that contains representative feature vectors for each class (pattern). The performance of the presented structure damage classifier has been validated using a benchmark structure proposed by the IASC-ASCE (International Association for Structural Control - American Society of Civil Engineers) Structural Health Monitoring Task Group. The validation results show a better classification success rate comparing to some of other classification algorithms.

  2. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    KAUST Repository

    Cui, Xuefeng

    2016-06-15

    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find transitive paths in the protein structure space demonstrate the importance of incorporating network information of the structure space. Yet, current methods merge the sequence space and the structure space into a single space, and thus introduce inconsistency in combining different sources of information. Method: We present a novel network-based protein homology detection method, CMsearch, based on cross-modal learning. Instead of exploring a single network built from the mixture of sequence and structure space information, CMsearch builds two separate networks to represent the sequence space and the structure space. It then learns sequence–structure correlation by simultaneously taking sequence information, structure information, sequence space information and structure space information into consideration. Results: We tested CMsearch on two challenging tasks, protein homology detection and protein structure prediction, by querying all 8332 PDB40 proteins. Our results demonstrate that CMsearch is insensitive to the similarity metrics used to define the sequence and the structure spaces. By using HMM–HMM alignment as the sequence similarity metric, CMsearch clearly outperforms state-of-the-art homology detection methods and the CASP-winning template-based protein structure prediction methods.

  3. Item bias detection in the Hospital Anxiety and Depression Scale using structural equation modeling: comparison with other item bias detection methods

    NARCIS (Netherlands)

    Verdam, M.G.E.; Oort, F.J.; Sprangers, M.A.G.

    Purpose Comparison of patient-reported outcomes may be invalidated by the occurrence of item bias, also known as differential item functioning. We show two ways of using structural equation modeling (SEM) to detect item bias: (1) multigroup SEM, which enables the detection of both uniform and

  4. Use of Time- and Frequency-Domain Approaches for Damage Detection in Civil Engineering Structures

    Directory of Open Access Journals (Sweden)

    V. H. Nguyen

    2014-01-01

    Full Text Available The aim of this paper is to apply both time- and frequency-domain-based approaches on real-life civil engineering structures and to assess their capability for damage detection. The methodology is based on Principal Component Analysis of the Hankel matrix built from output-only measurements and of Frequency Response Functions. Damage detection is performed using the concept of subspace angles between a current (possibly damaged state and a reference (undamaged state. The first structure is the Champangshiehl Bridge located in Luxembourg. Several damage levels were intentionally created by cutting a growing number of prestressed tendons and vibration data were acquired by the University of Luxembourg for each damaged state. The second example consists in reinforced and prestressed concrete panels. Successive damages were introduced in the panels by loading heavy weights and by cutting steel wires. The illustrations show different consequences in damage identification by the considered techniques.

  5. Characterization of TBP containing polysiloxane membrane/insulator/semiconductor structures for hexavalent chromium detection

    Energy Technology Data Exchange (ETDEWEB)

    Zazoua, A. [Universite de Jijel, BP 98, Ouled Aissa, 18000 Jijel (Algeria); Universite de Annaba, BP 12, El-Hadjar, Annaba (Algeria); Kherrat, R.; Samar, M.H. [Universite de Annaba, BP 12, El-Hadjar, Annaba (Algeria); Errachid, A. [Laboratori de Nanobioenginyeria-IBEC, CIBER, Parc Cientific de Barcelona (PCB)-Departament d' Electronica. Universitat de Barcelona, C/Marti i Franques 1, 08028 Barcelona (Spain); Jaffrezic-Renault, N. [LSA - UMR 5180 CNRS - Universite Claude Bernard Lyon 1, 69622 Villeurbanne cedex (France)], E-mail: nicole.jaffrezic@univ-lyon1.fr; Bessueille, F.; Leonard, D. [LSA - UMR 5180 CNRS - Universite Claude Bernard Lyon 1, 69622 Villeurbanne cedex (France)

    2008-07-01

    A hexavalent chromium-sensitive EMIS sensor (electrolyte membrane insulator semiconductor sensor) is prepared by deposition of a tributylphosphate (TBP) ionophore-containing siloprene membrane on a Si/SiO{sub 2}/Si{sub 3}N{sub 4} structure. The developed EMIS sensor was studied by means of impedance spectroscopy, capacitance-voltage, X-ray photoelectron spectrometry and FT-IR spectroscopy. From the flat-band shift of the EMIS structure, the nersntian response to the anionic species Cr{sub 2}O{sub 7}{sup -} was demonstrated. The linear range of detection is 10{sup -4} M to 10{sup -1} M and the detection limit is 10{sup -5} M. Sulfate and chloride anions are shown not to be interfering whereas carbonate ions present a pK{sup pot} equal to 0.19.

  6. Influence on ultrasonic incident angle and defect detection sensitivity by cast stainless steel structure

    International Nuclear Information System (INIS)

    Kurozumi, Y.

    2004-01-01

    It is well known that ultrasonic waves are affected strongly by macro-structures in cast stainless steel, as in the primary pipe or other components in pressurized water reactors (PWRs). In this work, ultrasonic refractive angles and defect detection sensitivities are investigated at different incident angles to cast stainless steel. The aims of the investigation are to clarify the transmission of ultrasonic waves in cast stainless steel and to contribute to the transducer design. The results are that ultrasonic refractive angles in cast stainless steel shift towards the 45-degree direction with respect to the direction of dendritic structures by 11.8 degrees at the maximum and that the sensitivity of transducer for inner surface breaking cracks increases with decreasing incident angle. However, in an ultrasonic inspection of actual welds at smaller incident angles, a trade-off occurs between increased defect detection sensitivity and decreased defect discrimination capability due to intense false signals produced by non-defective features. (orig.)

  7. Damage Detection on Thin-walled Structures Utilizing Laser Scanning and Standing Waves

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Se Hyeok; Jeon, Jun Young; Kim, Du Hwan; Park, Gyuhae [Chonnam Nat’l Univ., Gwangju (Korea, Republic of); Kang, To; Han, Soon Woo [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2017-05-15

    This paper describes wavenumber filtering for damage detection using single-frequency standing wave excitation and laser scanning sensing. An embedded piezoelectric sensor generates ultrasonic standing waves, and the responses are measured using a laser Doppler vibrometer and mirror tilting device. After scanning, newly developed damage detection techniques based on wavenumber filtering are applied to the full standing wave field. To demonstrate the performance of the proposed techniques, several experiments were performed on composite plates with delamination and aluminum plates with corrosion damage. The results demonstrated that the developed techniques could be applied to various structures to localize the damage, with the potential to improve the damage detection capability at a high interrogation speed.

  8. Test of a detection structure for a high-resolution vertex chamber

    International Nuclear Information System (INIS)

    Gruenewald, M.W.

    1988-01-01

    For the LEP experiment L3 a self-supporting detection structure in the TEC principle for the central vertex chamber was tested both with particles and with laser beams. The main topic of this thesis lied thereby on the determination of the coordinate of the particle passage along the signal-wire axis. Two different methods for the determination of this coordinate along the signal wire were studied. (orig./HSI) [de

  9. Ensembles of novelty detection classifiers for structural health monitoring using guided waves

    Science.gov (United States)

    Dib, Gerges; Karpenko, Oleksii; Koricho, Ermias; Khomenko, Anton; Haq, Mahmoodul; Udpa, Lalita

    2018-01-01

    Guided wave structural health monitoring uses sparse sensor networks embedded in sophisticated structures for defect detection and characterization. The biggest challenge of those sensor networks is developing robust techniques for reliable damage detection under changing environmental and operating conditions (EOC). To address this challenge, we develop a novelty classifier for damage detection based on one class support vector machines. We identify appropriate features for damage detection and introduce a feature aggregation method which quadratically increases the number of available training observations. We adopt a two-level voting scheme by using an ensemble of classifiers and predictions. Each classifier is trained on a different segment of the guided wave signal, and each classifier makes an ensemble of predictions based on a single observation. Using this approach, the classifier can be trained using a small number of baseline signals. We study the performance using Monte-Carlo simulations of an analytical model and data from impact damage experiments on a glass fiber composite plate. We also demonstrate the classifier performance using two types of baseline signals: fixed and rolling baseline training set. The former requires prior knowledge of baseline signals from all EOC, while the latter does not and leverages the fact that EOC vary slowly over time and can be modeled as a Gaussian process.

  10. Detecting Difference between Process Models Based on the Refined Process Structure Tree

    Directory of Open Access Journals (Sweden)

    Jing Fan

    2017-01-01

    Full Text Available The development of mobile workflow management systems (mWfMS leads to large number of business process models. In the meantime, the location restriction embedded in mWfMS may result in different process models for a single business process. In order to help users quickly locate the difference and rebuild the process model, detecting the difference between different process models is needed. Existing detection methods either provide a dissimilarity value to represent the difference or use predefined difference template to generate the result, which cannot reflect the entire composition of the difference. Hence, in this paper, we present a new approach to solve this problem. Firstly, we parse the process models to their corresponding refined process structure trees (PSTs, that is, decomposing a process model into a hierarchy of subprocess models. Then we design a method to convert the PST to its corresponding task based process structure tree (TPST. As a consequence, the problem of detecting difference between two process models is transformed to detect difference between their corresponding TPSTs. Finally, we obtain the difference between two TPSTs based on the divide and conquer strategy, where the difference is described by an edit script and we make the cost of the edit script close to minimum. The extensive experimental evaluation shows that our method can meet the real requirements in terms of precision and efficiency.

  11. Wireless and embedded carbon nanotube networks for damage detection in concrete structures

    International Nuclear Information System (INIS)

    Saafi, Mohamed

    2009-01-01

    Concrete structures undergo an uncontrollable damage process manifesting in the form of cracks due to the coupling of fatigue loading and environmental effects. In order to achieve long-term durability and performance, continuous health monitoring systems are needed to make critical decisions regarding operation, maintenance and repairs. Recent advances in nanostructured materials such as carbon nanotubes have opened the door for new smart and advanced sensing materials that could effectively be used in health monitoring of structures where wireless and real time sensing could provide information on damage development. In this paper, carbon nanotube networks were embedded into a cement matrix to develop an in situ wireless and embedded sensor for damage detection in concrete structures. By wirelessly measuring the change in the electrical resistance of the carbon nanotube networks, the progress of damage can be detected and monitored. As a proof of concept, wireless cement-carbon nanotube sensors were embedded into concrete beams and subjected to monotonic and cyclic loading to evaluate the effect of damage on their response. Experimental results showed that the wireless response of the embedded nanotube sensors changes due to the formation of cracks during loading. In addition, the nanotube sensors were able to detect the initiation of damage at an early stage of loading.

  12. Wireless and embedded carbon nanotube networks for damage detection in concrete structures

    Science.gov (United States)

    Saafi, Mohamed

    2009-09-01

    Concrete structures undergo an uncontrollable damage process manifesting in the form of cracks due to the coupling of fatigue loading and environmental effects. In order to achieve long-term durability and performance, continuous health monitoring systems are needed to make critical decisions regarding operation, maintenance and repairs. Recent advances in nanostructured materials such as carbon nanotubes have opened the door for new smart and advanced sensing materials that could effectively be used in health monitoring of structures where wireless and real time sensing could provide information on damage development. In this paper, carbon nanotube networks were embedded into a cement matrix to develop an in situ wireless and embedded sensor for damage detection in concrete structures. By wirelessly measuring the change in the electrical resistance of the carbon nanotube networks, the progress of damage can be detected and monitored. As a proof of concept, wireless cement-carbon nanotube sensors were embedded into concrete beams and subjected to monotonic and cyclic loading to evaluate the effect of damage on their response. Experimental results showed that the wireless response of the embedded nanotube sensors changes due to the formation of cracks during loading. In addition, the nanotube sensors were able to detect the initiation of damage at an early stage of loading.

  13. Evaluation of polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis for the detection of the rpoB mutations associated with resistance to rifampicin in Mycobacterium tuberculosis

    International Nuclear Information System (INIS)

    Lee, H.; Cho, S.-N.; Bang, H.-E.; Kim, S.-C.; Victor, T.C.; Jordaan, A.; Suffys, P.N.; Gomes, H.M.; Singh, U.; Suresh, V.N.; Khan, B.K.

    2003-01-01

    Resistance of Mycobacterium tuberculosis to rifampicin (RIF) has been associated with mutations of the rpoB gene, which encodes for the RNA polymerase B subunit. Based on this information, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) has been suggested as a sensitive and rapid screening test for the detection of RIF-resistant M. tuberculosis from clinical isolates. PCR-SSCP analyses with radioisotopes and without radioisotopes were employed to detect mutations of the rpoB gene associated with resistance to RIF in four laboratories, and results were compared with those of sequence analysis and the conventional proportion method of drug susceptibility test between laboratories. Radioisotopic PCR-SSCP showed an excellent correlation with sequence analysis of the 157 bp region of the rpoB gene by identifying correctly all 32 isolates analyzed in this study, with a high resolution of the banding patterns obtained. In a separate study, non-radioisotopic PCR-SSCP also gave a good correlation with sequence analysis in 22 isolates, but two (9.1%) isolates were classified as resistant by PCR-SSCP despite wild type sequences. When PCR-SSCP was compared with the results obtained using the proportion method, sensitivity of 44% to 85% were obtained in the 4 laboratories that participated in this study. Possible reasons for discordant results are discussed. It has been concluded that despite discordant results, which were sometimes observed, depending on the experimental conditions, PCR-SSCP appears to be an effective and promising method for the rapid detection of RIF-resistant M. tuberculosis, a marker of multidrug resistant tuberculosis. (author)

  14. The war of tools: how can NMR spectroscopists detect errors in their structures?

    Energy Technology Data Exchange (ETDEWEB)

    Saccenti, Edoardo; Rosato, Antonio [University of Florence, Magnetic Resonance Center (Italy)], E-mail: rosato@cerm.unifi.it

    2008-04-15

    Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we examined various tools for the assessment of structural quality to ascertain the extent to which these tools could be applied to detect flaws in NMR structures. In particular, we investigated the variation in the scores assigned by these programs as a function of the deviation of the structures induced by errors in assignments or in the upper distance limits used. These perturbations did not distort radically the protein fold, but resulted in backbone RMS deviations up to 3 A, which is in line with errors highlighted in the available literature. We found that it is quite difficult to discriminate the structures perturbed because of misassignments from the original ones, also because the spread in score over the conformers of the original bundle is relatively large. {phi}-{psi} distributions and normality scores related to the backbone conformation and to the distribution of side-chain dihedral angles are the most sensitive indicators of flaws.

  15. Damage Detection of Structures for Ambient Loading Based on Cross Correlation Function Amplitude and SVM

    Directory of Open Access Journals (Sweden)

    Lin-sheng Huo

    2016-01-01

    Full Text Available An effective method for the damage detection of skeletal structures which combines the cross correlation function amplitude (CCFA with the support vector machine (SVM is presented in this paper. The proposed method consists of two stages. Firstly, the data features are extracted from the CCFA, which, calculated from dynamic responses and as a representation of the modal shapes of the structure, changes when damage occurs on the structure. The data features are then input into the SVM with the one-against-one (OAO algorithm to classify the damage status of the structure. The simulation data of IASC-ASCE benchmark model and a vibration experiment of truss structure are adopted to verify the feasibility of proposed method. The results show that the proposed method is suitable for the damage identification of skeletal structures with the limited sensors subjected to ambient excitation. As the CCFA based data features are sensitive to damage, the proposed method demonstrates its reliability in the diagnosis of structures with damage, especially for those with minor damage. In addition, the proposed method shows better noise robustness and is more suitable for noisy environments.

  16. Toward Smart Aerospace Structures: Design of a Piezoelectric Sensor and Its Analog Interface for Flaw Detection

    Science.gov (United States)

    Boukabache, Hamza; Escriba, Christophe; Fourniols, Jean-Yves

    2014-01-01

    Structural health monitoring using noninvasive methods is one of the major challenges that aerospace manufacturers face in this decade. Our work in this field focuses on the development and the system integration of millimetric piezoelectric sensors/ actuators to generate and measure specific guided waves. The aim of the application is to detect mechanical flaws on complex composite and alloy structures to quantify efficiently the global structures' reliability. The study begins by a physical and analytical analysis of a piezoelectric patch. To preserve the structure's integrity, the transducers are directly pasted onto the surface which leads to a critical issue concerning the interfacing layer. In order to improve the reliability and mitigate the influence of the interfacing layer, the global equations of piezoelectricity are coupled with a load transfer model. Thus we can determine precisely the shear strain developed on the surface of the structure. To exploit the generated signal, a high precision analog charge amplifier coupled to a double T notch filter were designed and scaled. Finally, a novel joined time-frequency analysis based on a wavelet decomposition algorithm is used to extract relevant structures signatures. Finally, this paper provides examples of application on aircraft structure specimens and the feasibility of the system is thus demonstrated. PMID:25365457

  17. Experimental Studies on Damage Detection in Frame Structures Using Vibration Measurements

    Directory of Open Access Journals (Sweden)

    Giancarlo Fraraccio

    2010-01-01

    Full Text Available This paper presents an experimental study of frequency and time domain identification algorithms and discusses their effectiveness in structural health monitoring of frame structures using acceleration input and response data. Three algorithms were considered: 1 a frequency domain decomposition algorithm (FDD, 2 a time domain Observer Kalman IDentification algorithm (OKID, and 3 a subsequent physical parameter identification algorithm (MLK. Through experimental testing of a four-story steel frame model on a uniaxial shake table, the inherent complications of physical instrumentation and testing are explored. Primarily, this study aims to provide a dependable first-order and second-order identification of said test structure in a fully instrumented state. Once the characteristics (i.e. the stiffness matrix for a benchmark structure have been determined, structural damage can be detected by a change in the identified structural stiffness matrix. This work also analyzes the stability of the identified structural stiffness matrix with respect to fluctuations of input excitation magnitude and frequency content in an experimental setting.

  18. Toward smart aerospace structures: design of a piezoelectric sensor and its analog interface for flaw detection.

    Science.gov (United States)

    Boukabache, Hamza; Escriba, Christophe; Fourniols, Jean-Yves

    2014-10-31

    Structural health monitoring using noninvasive methods is one of the major challenges that aerospace manufacturers face in this decade. Our work in this field focuses on the development and the system integration of millimetric piezoelectric sensors/ actuators to generate and measure specific guided waves. The aim of the application is to detect mechanical flaws on complex composite and alloy structures to quantify efficiently the global structures' reliability. The study begins by a physical and analytical analysis of a piezoelectric patch. To preserve the structure's integrity, the transducers are directly pasted onto the surface which leads to a critical issue concerning the interfacing layer. In order to improve the reliability and mitigate the influence of the interfacing layer, the global equations of piezoelectricity are coupled with a load transfer model. Thus we can determine precisely the shear strain developed on the surface of the structure. To exploit the generated signal, a high precision analog charge amplifier coupled to a double T notch filter were designed and scaled. Finally, a novel joined time-frequency analysis based on a wavelet decomposition algorithm is used to extract relevant structures signatures. Finally, this paper provides examples of application on aircraft structure specimens and the feasibility of the system is thus demonstrated.

  19. Association between the polymorphisms of angiotensin converting ...

    African Journals Online (AJOL)

    Detailed history taking was done with stress on age, family history, menstrual, obstetric, medical and drug history. Physical examination including body mass index calculation was done. Histopathological examination was done for tumor grading and staging. Detection of ACE gene (I/D) polymorphism by PCR and AT1R ...

  20. Structural damage detection in wind turbine blades based on time series representations of dynamic responses

    Science.gov (United States)

    Hoell, Simon; Omenzetter, Piotr

    2015-03-01

    The development of large wind turbines that enable to harvest energy more efficiently is a consequence of the increasing demand for renewables in the world. To optimize the potential energy output, light and flexible wind turbine blades (WTBs) are designed. However, the higher flexibilities and lower buckling capacities adversely affect the long-term safety and reliability of WTBs, and thus the increased operation and maintenance costs reduce the expected revenue. Effective structural health monitoring techniques can help to counteract this by limiting inspection efforts and avoiding unplanned maintenance actions. Vibration-based methods deserve high attention due to the moderate instrumentation efforts and the applicability for in-service measurements. The present paper proposes the use of cross-correlations (CCs) of acceleration responses between sensors at different locations for structural damage detection in WTBs. CCs were in the past successfully applied for damage detection in numerical and experimental beam structures while utilizing only single lags between the signals. The present approach uses vectors of CC coefficients for multiple lags between measurements of two selected sensors taken from multiple possible combinations of sensors. To reduce the dimensionality of the damage sensitive feature (DSF) vectors, principal component analysis is performed. The optimal number of principal components (PCs) is chosen with respect to a statistical threshold. Finally, the detection phase uses the selected PCs of the healthy structure to calculate scores from a current DSF vector, where statistical hypothesis testing is performed for making a decision about the current structural state. The method is applied to laboratory experiments conducted on a small WTB with non-destructive damage scenarios.

  1. Machine learning approach to detect intruders in database based on hexplet data structure

    Directory of Open Access Journals (Sweden)

    Saad M. Darwish

    2016-09-01

    Full Text Available Most of valuable information resources for any organization are stored in the database; it is a serious subject to protect this information against intruders. However, conventional security mechanisms are not designed to detect anomalous actions of database users. An intrusion detection system (IDS, delivers an extra layer of security that cannot be guaranteed by built-in security tools, is the ideal solution to defend databases from intruders. This paper suggests an anomaly detection approach that summarizes the raw transactional SQL queries into a compact data structure called hexplet, which can model normal database access behavior (abstract the user's profile and recognize impostors specifically tailored for role-based access control (RBAC database system. This hexplet lets us to preserve the correlation among SQL statements in the same transaction by exploiting the information in the transaction-log entry with the aim to improve detection accuracy specially those inside the organization and behave strange behavior. The model utilizes naive Bayes classifier (NBC as the simplest supervised learning technique for creating profiles and evaluating the legitimacy of a transaction. Experimental results show the performance of the proposed model in the term of detection rate.

  2. Au-Pt-Au nanoraspberry structures used for mercury ion detection

    Science.gov (United States)

    Huang, Jiang-Hao; Huang, Shuai; Wen, Xiaoyan; Li, Min; Lu, Haifei

    2017-12-01

    Detection of Hg2+ with high sensitivity is of great significance in the biochemical sensing field. Quantitative of Hg2+ was realized based on the influence of Hg2+ on the UV-vis absorption performance of Au-Pt-Au core-shell nanoraspberry (APA)-rhodamine-6G (R6G) structure. First, APA sol was added into R6G indicator solution and the UV-vis absorption signal intensity of R6G was evidently promoted. The signal intensity monotonously increased as more APA sol was added. However, when HgCl2 solution was introduced, the signal intensity declined. A linear relationship between Hg2+ concentration and signal intensity at 527 nm was revealed, based on which quantitative determination of Hg2+ could be realized. Hg2+ detection sensitivity was measured to be 0.031 a.u./M with a limit of detection of 10-7 M and the response time was 20 s. A high Hg2+ detection selectivity over Cu2+, Na+, Li+, and K+ was demonstrated. Due to its simplicity and high sensitivity, the proposed method could find an extensive application prospect in the Hg2+ detection field.

  3. Allelic polymorphism of Makoei sheep leptin gene identified by ...

    African Journals Online (AJOL)

    use

    2011-12-05

    Dec 5, 2011 ... Lord et al., 1998) have shed light on the influence of leptin on both the .... A weak correlation between leptin serum levels and cow body condition ... Detection of polymorphisms in the ovine leptin (LEP) gene: .... Signals that.

  4. Prion protein gene polymorphisms in Turkish native goat breeds

    Indian Academy of Sciences (India)

    HASAN MEYDAN

    3The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of ... Eighteen single-nucleotide polymorphisms were detected in the caprine PRNP .... Sampling localities, sample size (n) and sex of Turkish native goat breeds.

  5. A damage detection method for instrumented civil structures using prerecorded Green’s functions and cross-correlation

    OpenAIRE

    Heckman, Vanessa; Kohler, Monica; Heaton, Thomas

    2011-01-01

    Automated damage detection methods have application to instrumented structures that are susceptible to types of damage that are difficult or costly to detect. The presented method has application to the detection of brittle fracture of welded beam-column connections in steel moment-resisting frames (MRFs), where locations of potential structural damage are known a priori. The method makes use of a prerecorded catalog of Green’s function templates and a cross-correlation method ...

  6. Advances in molecular modeling of human cytochrome P450 polymorphism.

    Science.gov (United States)

    Martiny, Virginie Y; Miteva, Maria A

    2013-11-01

    Cytochrome P450 (CYP) is a supergene family of metabolizing enzymes involved in the phase I metabolism of drugs and endogenous compounds. CYP oxidation often leads to inactive drug metabolites or to highly toxic or carcinogenic metabolites involved in adverse drug reactions (ADR). During the last decade, the impact of CYP polymorphism in various drug responses and ADR has been demonstrated. Of the drugs involved in ADR, 56% are metabolized by polymorphic phase I metabolizing enzymes, 86% among them being CYP. Here, we review the major CYP polymorphic forms, their impact for drug response and current advances in molecular modeling of CYP polymorphism. We focus on recent studies exploring CYP polymorphism performed by the use of sequence-based and/or protein-structure-based computational approaches. The importance of understanding the molecular mechanisms related to CYP polymorphism and drug response at the atomic level is outlined. © 2013.

  7. Low-Cost Impact Detection and Location for Automated Inspections of 3D Metallic Based Structures

    Directory of Open Access Journals (Sweden)

    Carlos Morón

    2015-05-01

    Full Text Available This paper describes a new low-cost means to detect and locate mechanical impacts (collisions on a 3D metal-based structure. We employ the simple and reasonably hypothesis that the use of a homogeneous material will allow certain details of the impact to be automatically determined by measuring the time delays of acoustic wave propagation throughout the 3D structure. The location of strategic piezoelectric sensors on the structure and an electronic-computerized system has allowed us to determine the instant and position at which the impact is produced. The proposed automatic system allows us to fully integrate impact point detection and the task of inspecting the point or zone at which this impact occurs. What is more, the proposed method can be easily integrated into a robot-based inspection system capable of moving over 3D metallic structures, thus avoiding (or minimizing the need for direct human intervention. Experimental results are provided to show the effectiveness of the proposed approach.

  8. Sensitivity of PZT Impedance Sensors for Damage Detection of Concrete Structures.

    Science.gov (United States)

    Yang, Yaowen; Hu, Yuhang; Lu, Yong

    2008-01-21

    Piezoelectric ceramic Lead Zirconate Titanate (PZT) based electro-mechanicalimpedance (EMI) technique for structural health monitoring (SHM) has been successfullyapplied to various engineering systems. However, fundamental research work on thesensitivity of the PZT impedance sensors for damage detection is still in need. In thetraditional EMI method, the PZT electro-mechanical (EM) admittance (inverse of theimpedance) is used as damage indicator, which is difficult to specify the effect of damage onstructural properties. This paper uses the structural mechanical impedance (SMI) extractedfrom the PZT EM admittance signature as the damage indicator. A comparison study on thesensitivity of the EM admittance and the structural mechanical impedance to the damages ina concrete structure is conducted. Results show that the SMI is more sensitive to the damagethan the EM admittance thus a better indicator for damage detection. Furthermore, this paperproposes a dynamic system consisting of a number of single-degree-of-freedom elementswith mass, spring and damper components to model the SMI. A genetic algorithm isemployed to search for the optimal value of the unknown parameters in the dynamic system.An experiment is carried out on a two-storey concrete frame subjected to base vibrations thatsimulate earthquake. A number of PZT sensors are regularly arrayed and bonded to the framestructure to acquire PZT EM admittance signatures. The relationship between the damageindex and the distance of the PZT sensor from the damage is studied. Consequently, thesensitivity of the PZT sensors is discussed and their sensing region in concrete is derived.

  9. New method for early detection of two random amplified polymorphic DNA (RAPD groups of Staphylococcus aureus causing bovine mastitis infection in Paraná State, Brazil

    Directory of Open Access Journals (Sweden)

    Dicezar Gonçalves

    2010-04-01

    Full Text Available The aim of this work was to develop a fast and accurate molecular approach to allow early detection of two RAPD groups of S. aureus causing bovine mastitis. Seventy five S. aureus isolates from infected animals were characterized by RAPD. Genomic fragments isolated from the unique bands present in either group were cloned and sequenced. Based on the DNA sequences, specific primers were designed to allow for the simultaneous detection of either group by multiplex PCR of S. aureus DNA isolated from clinical and subclinical bovine mastitis. Results showed that these proposed primers set could be used to detect various clinical and subclinical S. aureus isolates as well as the detection of the microorganism in bulk milk. Their use as a specific method for effective and early diagnostic tool for S. aureus infection in dairy herds is suggested.Esta pesquisa objetivou o desenvolvimento de técnica rápida e eficiente para diagnosticar precocemente diferentes linhagens de S. aureus causadoras de mastite bovina. Como resultados da metodologia empregada, foram isoladas duas linhagens destas bactérias que causam diferentes tipos de mastite bovina. Os fragmentos de DNA genômico caracterizando ambas as linhagens, por meio de RAPD foram inseridos em vetor plasmidial pGEM e clonados por meio de clones T10 F1 de Escherichia coli. As seqüências obtidas permitiram desenhar iniciadores específicos para o reconhecimento de ambas as linhagens, os quais foram testados com amostras de S. aureus e com outras linhagens próximas. O diagnóstico por meios moleculares, pode ser realizado diretamente de amostras coletadas de rebanhos leiteiros assim como dos equipamentos de ordenha. A significância deste estudo consiste em um rápido e acurado método para localizar animais infectados, representando importante ferramenta no manejo do rebanho, na redução de custos com tratamentos e, rápida recuperação de rebanhos infectados.

  10. An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data.

    Science.gov (United States)

    Wang, Yejun; MacKenzie, Keith D; White, Aaron P

    2015-05-07

    As sequencing costs are being lowered continuously, RNA-seq has gradually been adopted as the first choice for comparative transcriptome studies with bacteria. Unlike microarrays, RNA-seq can directly detect cDNA derived from mRNA transcripts at a single nucleotide resolution. Not only does this allow researchers to determine the absolute expression level of genes, but it also conveys information about transcript structure. Few automatic software tools have yet been established to investigate large-scale RNA-seq data for bacterial transcript structure analysis. In this study, 54 directional RNA-seq libraries from Salmonella serovar Typhimurium (S. Typhimurium) 14028s were examined for potential relationships between read mapping patterns and transcript structure. We developed an empirical method, combined with statistical tests, to automatically detect key transcript features, including transcriptional start sites (TSSs), transcriptional termination sites (TTSs) and operon organization. Using our method, we obtained 2,764 TSSs and 1,467 TTSs for 1331 and 844 different genes, respectively. Identification of TSSs facilitated further discrimination of 215 putative sigma 38 regulons and 863 potential sigma 70 regulons. Combining the TSSs and TTSs with intergenic distance and co-expression information, we comprehensively annotated the operon organization in S. Typhimurium 14028s. Our results show that directional RNA-seq can be used to detect transcriptional borders at an acceptable resolution of ±10-20 nucleotides. Technical limitations of the RNA-seq procedure may prevent single nucleotide resolution. The automatic transcript border detection methods, statistical models and operon organization pipeline that we have described could be widely applied to RNA-seq studies in other bacteria. Furthermore, the TSSs, TTSs, operons, promoters and unstranslated regions that we have defined for S. Typhimurium 14028s may constitute valuable resources that can be used for

  11. Quantitative detection of glucose level based on radiofrequency patch biosensor combined with volume-fixed structures.

    Science.gov (United States)

    Qiang, Tian; Wang, Cong; Kim, Nam-Young

    2017-12-15

    A concept for characterizing a radiofrequency (RF) patch biosensor combined with volume-fixed structures is presented for timely monitoring of an individual's glucose levels based on frequency variation. Two types of patch biosensors-separately integrated with a backside slot (0.53μL) and a front-side tank (0.70μL) structure-were developed to achieve precise and efficient detection while excluding the effects of interference due to the liquidity, shape, and thickness of the tested glucose sample. A glucose test analyte at different concentrations (50-600mg/dL) was dropped into the volume-fixed structures. It fully interacted with the RF patch electromagnetic field, effectively and sensitively changing the resonance frequency and magnitude of the reflection coefficient. Measurement results based on the resonance frequency showed high sensitivity up to 1.13MHz and 1.97MHz per mg/dL, and low detection limits of 26.54mg/dL and 15.22mg/dL, for the two types of patch biosensors, respectively, as well as a short response time of less than 1s. Excellent reusability of the proposed biosensors was verified through three sets of measurements for each individual glucose sample. Regression analysis revealed a good linear correlation between glucose concentrations and the resonance frequency shift. Moreover, to facilitate a multi-parameter-sensitive detection of glucose, the magnitude of the reflection coefficient was also tested, and it showed a good linear correlation with the glucose concentration. Thus, the proposed approach can be adopted for distinguishing glucose solution levels, and it is a potential candidate for early-stage detection of glucose levels in diabetes patients. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. A Methodological Review of Piezoelectric Based Acoustic Wave Generation and Detection Techniques for Structural Health Monitoring

    Directory of Open Access Journals (Sweden)

    Zhigang Sun

    2013-01-01

    Full Text Available Piezoelectric transducers have a long history of applications in nondestructive evaluation of material and structure integrity owing to their ability of transforming mechanical energy to electrical energy and vice versa. As condition based maintenance has emerged as a valuable approach to enhancing continued aircraft airworthiness while reducing the life cycle cost, its enabling structural health monitoring (SHM technologies capable of providing on-demand diagnosis of the structure without interrupting the aircraft operation are attracting increasing R&D efforts. Piezoelectric transducers play an essential role in these endeavors. This paper is set forth to review a variety of ingenious ways in which piezoelectric transducers are used in today’s SHM technologies as a means of generation and/or detection of diagnostic acoustic waves.

  13. Improved detection rate of structural abnormalities in the first trimester using an extended examination protocol.

    Science.gov (United States)

    Iliescu, D; Tudorache, S; Comanescu, A; Antsaklis, P; Cotarcea, S; Novac, L; Cernea, N; Antsaklis, A

    2013-09-01

    To assess the potential of first-trimester sonography in the detection of fetal abnormalities using an extended protocol that is achievable with reasonable resources of time, personnel and ultrasound equipment. This was a prospective two-center 2-year study of 5472 consecutive unselected pregnant women examined at 12 to 13 + 6 gestational weeks. Women were examined using an extended morphogenetic ultrasound protocol that, in addition to the basic evaluation, involved a color Doppler cardiac sweep and identification of early contingent markers for major abnormalities. The prevalence of lethal and severe malformations was 1.39%. The first-trimester scan identified 40.6% of the cases detected overall and 76.3% of major structural defects. The first-trimester detection rate (DR) for major congenital heart disease (either isolated or associated with extracardiac abnormalities) was 90% and that for major central nervous system anomalies was 69.5%. In fetuses with increased nuchal translucency (NT), the first-trimester DR for major anomalies was 96%, and in fetuses with normal NT it was 66.7%. Most (67.1%) cases with major abnormalities presented with normal NT. A detailed first-trimester anomaly scan using an extended protocol is an efficient screening method to detect major fetal structural abnormalities in low-risk pregnancies. It is feasible at 12 to 13 + 6 weeks with ultrasound equipment and personnel already used for routine first-trimester screening. Rate of detection of severe malformations is greater in early- than in mid-pregnancy and on postnatal evaluation. Early heart investigation could be improved by an extended protocol involving use of color Doppler. Copyright © 2013 ISUOG. Published by John Wiley & Sons Ltd.

  14. Development of dual PZT transducers for reference-free crack detection in thin plate structures.

    Science.gov (United States)

    Sohn, Hoon; Kim, Seuno Bum

    2010-01-01

    A new Lamb-wave-based nondestructive testing (NDT) technique, which does not rely on previously stored baseline data, is developed for crack monitoring in plate structures. Commonly, the presence of damage is identified by comparing "current data" measured from a potentially damaged stage of a structure with "baseline data" previously obtained at the intact condition of the structure. In practice, structural defects typically take place long after collection of the baseline data, and the baseline data can be also affected by external loading, temperature variations, and changing boundary conditions. To eliminate the dependence on the baseline data comparison, the authors previously developed a reference-free NDT technique using 2 pairs of collocated lead zirconate titanate (PZT) transducers placed on both sides of a plate. This reference-free technique is further advanced in the present study by the necessity of attaching transducers only on a single surface of a structure for certain applications such as aircraft. To achieve this goal, a new design of PZT transducers called dual PZT transducers is proposed. Crack formation creates Lamb wave mode conversion due to a sudden thickness change of the structure. This crack appearance is instantly detected from the measured Lamb wave signals using the dual PZT transducers. This study also suggests a reference-free statistical approach that enables damage classification using only the currently measured data set. Numerical simulations and experiments were conducted using an aluminum plate with uniform thickness and fundamental Lamb waves modes to demonstrate the applicability of the proposed technique to reference-free crack detection.

  15. Evaluation of the use of amplified 16S rRNA gene-restriction fragment length polymorphism analysis to detect enterobacter cloacae and bacillus licheniformis for microbial enhanced oil recovery field pilot

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, Kazuhiro; Tanaka, Shinji; Otsuka, Makiko; Ichimura, Naoya [Lansai Research Institute, Kyoto (Japan); Yonebayashi, Hideharu [Japan National Oil Corp., Chiba (Japan); Hong, Chengxie; Enomoto, Heiji [Tohoku University, Miyagi (Japan)

    1999-09-01

    Evaluation of effectiveness of restriction fragment length polymorphism (RFLP) analysis of the 16S rRNA gene of microorganisms injected into an oil reservoir, for monitoring their levels over time, was conducted. Two microorganisms, enterobacter cloacae TRC-322 and Bacillus licheniformis TRC-18-2-a, were focused in this paper among the microorganisms selected for injection, and gene fragments of the 16S rRNA gene of these microorganisms were amplified by polymerase chain reaction (PCP), using one set of universal primers. Samples of the reservoir brine and reservoir rock were obtained; the microorganisms inhabiting in the reservoir were isolated from these samples, and the 16S rRNA gene of these microorganisms was amplified, condition remaining the same. RFLP analysis was performed on the 16S rRNA gene of each of these microorganisms, using restriction endonucleases HhaI, MspI, AluI and TaqI as necessary. Comparison of the resultant rRNA gene fragments, demonstrated that closely-related species displaying RFLP profile similar to that of E. cloacae TRC-322 or B. licheniformis TRC-18-2-a were not among the microorganisms isolated from the reservoir. PCR-RFLP analysis of the 16S rRNA gene, using the protocol; presented in this paper, is effective to detect the presence appropriate injecting microorganisms. This method was also effective for studying microorganisms isolated from the reservoir, which have the ability to grow on a molasses. (author)

  16. Improving model construction of profile HMMs for remote homology detection through structural alignment

    Directory of Open Access Journals (Sweden)

    Zaverucha Gerson

    2007-11-01

    Full Text Available Abstract Background Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. Results We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. Conclusion We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  17. Improving model construction of profile HMMs for remote homology detection through structural alignment.

    Science.gov (United States)

    Bernardes, Juliana S; Dávila, Alberto M R; Costa, Vítor S; Zaverucha, Gerson

    2007-11-09

    Remote homology detection is a challenging problem in Bioinformatics. Arguably, profile Hidden Markov Models (pHMMs) are one of the most successful approaches in addressing this important problem. pHMM packages present a relatively small computational cost, and perform particularly well at recognizing remote homologies. This raises the question of whether structural alignments could impact the performance of pHMMs trained from proteins in the Twilight Zone, as structural alignments are often more accurate than sequence alignments at identifying motifs and functional residues. Next, we assess the impact of using structural alignments in pHMM performance. We used the SCOP database to perform our experiments. Structural alignments were obtained using the 3DCOFFEE and MAMMOTH-mult tools; sequence alignments were obtained using CLUSTALW, TCOFFEE, MAFFT and PROBCONS. We performed leave-one-family-out cross-validation over super-families. Performance was evaluated through ROC curves and paired two tailed t-test. We observed that pHMMs derived from structural alignments performed significantly better than pHMMs derived from sequence alignment in low-identity regions, mainly below 20%. We believe this is because structural alignment tools are better at focusing on the important patterns that are more often conserved through evolution, resulting in higher quality pHMMs. On the other hand, sensitivity of these tools is still quite low for these low-identity regions. Our results suggest a number of possible directions for improvements in this area.

  18. Automated laser-based barely visible impact damage detection in honeycomb sandwich composite structures

    International Nuclear Information System (INIS)

    Girolamo, D.; Yuan, F. G.; Girolamo, L.

    2015-01-01

    Nondestructive evaluation (NDE) for detection and quantification of damage in composite materials is fundamental in the assessment of the overall structural integrity of modern aerospace systems. Conventional NDE systems have been extensively used to detect the location and size of damages by propagating ultrasonic waves normal to the surface. However they usually require physical contact with the structure and are time consuming and labor intensive. An automated, contactless laser ultrasonic imaging system for barely visible impact damage (BVID) detection in advanced composite structures has been developed to overcome these limitations. Lamb waves are generated by a Q-switched Nd:YAG laser, raster scanned by a set of galvano-mirrors over the damaged area. The out-of-plane vibrations are measured through a laser Doppler Vibrometer (LDV) that is stationary at a point on the corner of the grid. The ultrasonic wave field of the scanned area is reconstructed in polar coordinates and analyzed for high resolution characterization of impact damage in the composite honeycomb panel. Two methodologies are used for ultrasonic wave-field analysis: scattered wave field analysis (SWA) and standing wave energy analysis (SWEA) in the frequency domain. The SWA is employed for processing the wave field and estimate spatially dependent wavenumber values, related to discontinuities in the structural domain. The SWEA algorithm extracts standing waves trapped within damaged areas and, by studying the spectrum of the standing wave field, returns high fidelity damage imaging. While the SWA can be used to locate the impact damage in the honeycomb panel, the SWEA produces damage images in good agreement with X-ray computed tomographic (X-ray CT) scans. The results obtained prove that the laser-based nondestructive system is an effective alternative to overcome limitations of conventional NDI technologies

  19. Wireless and real-time structural damage detection: A novel decentralized method for wireless sensor networks

    Science.gov (United States)

    Avci, Onur; Abdeljaber, Osama; Kiranyaz, Serkan; Hussein, Mohammed; Inman, Daniel J.

    2018-06-01

    Being an alternative to conventional wired sensors, wireless sensor networks (WSNs) are extensively used in Structural Health Monitoring (SHM) applications. Most of the Structural Damage Detection (SDD) approaches available in the SHM literature are centralized as they require transferring data from all sensors within the network to a single processing unit to evaluate the structural condition. These methods are found predominantly feasible for wired SHM systems; however, transmission and synchronization of huge data sets in WSNs has been found to be arduous. As such, the application of centralized methods with WSNs has been a challenge for engineers. In this paper, the authors are presenting a novel application of 1D Convolutional Neural Networks (1D CNNs) on WSNs for SDD purposes. The SDD is successfully performed completely wireless and real-time under ambient conditions. As a result of this, a decentralized damage detection method suitable for wireless SHM systems is proposed. The proposed method is based on 1D CNNs and it involves training an individual 1D CNN for each wireless sensor in the network in a format where each CNN is assigned to process the locally-available data only, eliminating the need for data transmission and synchronization. The proposed damage detection method operates directly on the raw ambient vibration condition signals without any filtering or preprocessing. Moreover, the proposed approach requires minimal computational time and power since 1D CNNs merge both feature extraction and classification tasks into a single learning block. This ability is prevailingly cost-effective and evidently practical in WSNs considering the hardware systems have been occasionally reported to suffer from limited power supply in these networks. To display the capability and verify the success of the proposed method, large-scale experiments conducted on a laboratory structure equipped with a state-of-the-art WSN are reported.

  20. Theoretical reflections on the structural polymorphism of the oxygen-evolving complex in the S2 state and the correlations to substrate water exchange and water oxidation mechanism in photosynthesis.

    Science.gov (United States)

    Guo, Yu; Li, Hui; He, Lan-Lan; Zhao, Dong-Xia; Gong, Li-Dong; Yang, Zhong-Zhi

    2017-10-01

    The structural polymorphism of the oxygen-evolving complex is of great significance to photosynthetic water oxidation. Employing density functional theory calculations, we have made further advisement on the interconversion mechanism of O5 transfer in the S 2 state, mainly focusing on the potentiality of multi-state reactivity and spin transitions. Then, O5 protonation is proven impossible in S 2 for irreversibility of the interconversion, which serves as an auxiliary judgment for the protonation state of O5 in S 1 . Besides, the structural polymorphism could also be archived by alternative mechanisms involving Mn3 ligand exchange, one of which with Mn3(III) makes sense to substrate water exchange in S 2 , although being irresponsible for the derivations of the observed EPR signals. During the water exchange, high-spin states would prevail to facilitate electron transfer between the ferromagnetically coupled Mn centers. In addition, water exchange in S 1 could account for the closed-cubane structure as the initial form entering S 2 at cryogenic temperatures. With regard to water oxidation, the structural flexibility and variability in both S 2 and S 3 guarantee smooth W2-O5 coupling in S 4 , according to the substrate assignments from water exchange kinetics. Within this theoretical framework, the new XFEL findings on S 1 -S 3 can be readily rationalized. Finally, an alternative mechanistic scenario for OO bond formation with ·OH radical near O4 is presented, followed by water binding to the pivot Mn4(III) from O4 side during S 4 -S 0 . This may diversify the substrate sources combined with the Ca channel in water delivery for the forthcoming S-cycle. Copyright © 2017. Published by Elsevier B.V.

  1. Stochastic output error vibration-based damage detection and assessment in structures under earthquake excitation

    Science.gov (United States)

    Sakellariou, J. S.; Fassois, S. D.

    2006-11-01

    A stochastic output error (OE) vibration-based methodology for damage detection and assessment (localization and quantification) in structures under earthquake excitation is introduced. The methodology is intended for assessing the state of a structure following potential damage occurrence by exploiting vibration signal measurements produced by low-level earthquake excitations. It is based upon (a) stochastic OE model identification, (b) statistical hypothesis testing procedures for damage detection, and (c) a geometric method (GM) for damage assessment. The methodology's advantages include the effective use of the non-stationary and limited duration earthquake excitation, the handling of stochastic uncertainties, the tackling of the damage localization and quantification subproblems, the use of "small" size, simple and partial (in both the spatial and frequency bandwidth senses) identified OE-type models, and the use of a minimal number of measured vibration signals. Its feasibility and effectiveness are assessed via Monte Carlo experiments employing a simple simulation model of a 6 storey building. It is demonstrated that damage levels of 5% and 20% reduction in a storey's stiffness characteristics may be properly detected and assessed using noise-corrupted vibration signals.

  2. DETECTING FLARING STRUCTURES IN SAGITTARIUS A* WITH HIGH-FREQUENCY VLBI

    International Nuclear Information System (INIS)

    Doeleman, Sheperd S.; Fish, Vincent L.; Rogers, Alan E. E.; Broderick, Avery E.; Loeb, Abraham

    2009-01-01

    The super-massive black hole candidate, Sagittarius A*, exhibits variability from radio to X-ray wavelengths on timescales that correspond to <10 Schwarzschild radii. We survey the potential of millimeter wavelength very long baseline interferometry (VLBI) to detect and constrain time-variable structures that could give rise to such variations, focusing on a model in which an orbiting hot spot is embedded in an accretion disk. Nonimaging algorithms are developed that use interferometric closure quantities to test for periodicity, and applied to an ensemble of hot spot models that sample a range of parameter space. We find that structural periodicity in a wide range of cases can be detected on most potential VLBI arrays using modern VLBI instrumentation. Future enhancements of millimeter/submillimeter VLBI arrays including phased-array processors to aggregate VLBI station collecting area, increased bandwidth recording, and addition of new VLBI sites all significantly aid periodicity detection. The methods described herein can be applied to other models of Sagittarius A*, including jet outflows and magnetohydrodynamic accretion simulations.

  3. Low Genetic Diversity Among Garlic (Allium sativum L. Accessions Detected Using Random Amplified Polymorphic DNA (RAPD Escasa Diversidad Genética entre Accesiones de Ajo (Allium sativum L. Detectada Mediante ADN Polimórfico Amplificado al Azar (RAPD

    Directory of Open Access Journals (Sweden)

    Mario Paredes C

    2008-03-01

    Full Text Available Garlic (Allium sativum L. is a species of vegetative propagation, showing high morphological diversity. Besides, its clones have specific adaptations to different agroclimatic regions. The objective of this study was to determine the genetic diversity of 65 garlic clones collected in Chile and introduced from different countries, by using RAPD (Random Amplified Polymorphic DNA. Fourty random primers of 10 mers generated a total of 398 bands with an 87% of polymorphism. Each primer amplified between two and 20 bands. The size of the fragments obtained fluctuated between 3200 and 369 bp. The results showed that the clones analyzed had a genetic similarity rate of 94%. In addition, 70% of them were clustered in one major group. However, in spite of that situation several clones have different agronomic characteristicsEl ajo (Allium sativum L. es una especie de propagación vegetativa, que presenta una amplia variabilidad morfológica. Los clones de esta especie tienen una adaptación específica a diferentes regiones agroclimáticas. El objetivo de este estudio fue determinar la diversidad genética existente en 65 clones de ajos colectados en Chile e introducidos desde diferentes países, utilizando RAPD (ADN Polimórfico Amplificado al Azar. Para esta evaluación se utilizaron 40 partidores de 10-mers. Los partidores generaron entre dos y 20 bandas, observándose un alto número de patrones con bandas múltiples. Los fragmentos generados difieren en su tamaño entre 3.200 y 369 pb. Los partidores generaron 398 bandas, de las cuales un 87% fueron polimórficas. El análisis estadístico realizado detectó una similitud genética alta, de un 94% entre las accesiones evaluadas, donde aproximadamente un 70% de los clones formaron un grupo homogéneo. Sin embargo, este grupo incluye clones que presentan diferentes características agronómicas

  4. Simple, Low-Cost Detection of Candida parapsilosis Complex Isolates and Molecular Fingerprinting of Candida orthopsilosis Strains in Kuwait by ITS Region Sequencing and Amplified Fragment Length Polymorphism Analysis.

    Science.gov (United States)

    Asadzadeh, Mohammad; Ahmad, Suhail; Hagen, Ferry; Meis, Jacques F; Al-Sweih, Noura; Khan, Ziauddin

    2015-01-01

    Candida parapsilosis has now emerged as the second or third most important cause of healthcare-associated Candida infections. Molecular studies have shown that phenotypically identified C. parapsilosis isolates represent a complex of three species, namely, C. parapsilosis, C. orthopsilosis and C. metapsilosis. Lodderomyces elongisporus is another species phenotypically closely related to the C. parapsilosis-complex. The aim of this study was to develop a simple, low cost multiplex (m) PCR assay for species-specific identification of C. parapsilosis complex isolates and to study genetic relatedness of C. orthopsilosis isolates in Kuwait. Species-specific amplicons from C. parapsilosis (171 bp), C. orthopsilosis (109 bp), C. metapsilosis (217 bp) and L. elongisporus (258 bp) were obtained in mPCR. Clinical isolates identified as C. parapsilosis (n = 380) by Vitek2 in Kuwait and an international collection of 27 C. parapsilosis complex and L. elongisporus isolates previously characterized by rDNA sequencing were analyzed to evaluate mPCR. Species-specific PCR and DNA sequencing of internal transcribed spacer (ITS) region of rDNA were performed to validate the results of mPCR. Fingerprinting of 19 clinical C. orthopsilosis isolates (including 4 isolates from a previous study) was performed by amplified fragment length polymorphism (AFLP) analysis. Phenotypically identified C. parapsilosis isolates (n = 380) were identified as C. parapsilosis sensu stricto (n = 361), C. orthopsilosis (n = 15), C. metapsilosis (n = 1) and L. elongisporus (n = 3) by mPCR. The mPCR also accurately detected all epidemiologically unrelated C. parapsilosis complex and L. elongisporus isolates. The 19 C. orthopsilosis isolates obtained from 16 patients were divided into 3 haplotypes based on ITS region sequence data. Seven distinct genotypes were identified among the 19 C. orthopsilosis isolates by AFLP including a dominant genotype (AFLP1) comprising 11 isolates recovered from 10 patients. A

  5. Designing lymphocyte functional structure for optimal signal detection: voilà, T cells.

    Science.gov (United States)

    Noest, A J

    2000-11-21

    One basic task of immune systems is to detect signals from unknown "intruders" amidst a noisy background of harmless signals. To clarify the functional importance of many observed lymphocyte properties, I ask: What properties would a cell have if one designed it according to the theory of optimal detection, with minimal regard for biological constraints? Sparse and reasonable assumptions about the statistics of available signals prove sufficient for deriving many features of the optimal functional structure, in an incremental and modular design. The use of one common formalism guarantees that all parts of the design collaborate to solve the detection task. Detection performance is computed at several stages of the design. Comparison between design variants reveals e.g. the importance of controlling the signal integration time. This predicts that an appropriate control mechanism should exist. Comparing the design to reality, I find a striking similarity with many features of T cells. For example, the formalism dictates clonal specificity, serial receptor triggering, (grades of) anergy, negative and positive selection, co-stimulation, high-zone tolerance, and clonal production of cytokines. Serious mismatches should be found if T cells were hindered by mechanistic constraints or vestiges of their (co-)evolutionary history, but I have not found clear examples. By contrast, fundamental mismatches abound when comparing the design to immune systems of e.g. invertebrates. The wide-ranging differences seem to hinge on the (in)ability to generate a large diversity of receptors. Copyright 2000 Academic Press.

  6. Multi-branched gold nanostars with fractal structure for SERS detection of the pesticide thiram

    Science.gov (United States)

    Zhu, Jian; Liu, Mei-Jin; Li, Jian-Jun; Li, Xin; Zhao, Jun-Wu

    2018-01-01

    The surface-enhanced Raman scattering (SERS) activity of multi-branched gold nanostars with fractal structure has been investigated for trace detection of pesticide thiram. Raman spectrum results show that the gold nanostars substrate can produce about 102 fold stronger signal than the thiram alone with the thiram concentration increase of 103 times and 1.4 fold stronger signal than the gold nanostars without fractal feature. In the detection procedure, the most prominent SERS peak at 1376 cm- 1 has been chosen to characterize and quantify the concentration of thiram. Experimental results indicate this Raman substrate based on fractal gold nanostars exhibits excellent selective probing performance for thiram with a detection limit as low as 10- 10 M in solution and 0.24 ng/cm2 in apple peels. Interference experiment results show that the effects from the interfering pesticides could be neglected in the detection procedure. Therefore, the gold nanostars as a SERS substrate have excellent sensitivity and selectivity.

  7. The electronic band structures of gadolinium chalcogenides: a first-principles prediction for neutron detecting.

    Science.gov (United States)

    Li, Kexue; Liu, Lei; Yu, Peter Y; Chen, Xiaobo; Shen, D Z

    2016-05-11

    By converting the energy of nuclear radiation to excited electrons and holes, semiconductor detectors have provided a highly efficient way for detecting them, such as photons or charged particles. However, for detecting the radiated neutrons, those conventional semiconductors hardly behave well, as few of them possess enough capability for capturing these neutral particles. While the element Gd has the highest nuclear cross section, here for searching proper neutron-detecting semiconductors, we investigate theoretically the Gd chalcogenides whose electronic band structures have never been characterized clearly. Among them, we identify that γ-phase Gd2Se3 should be the best candidate for neutron detecting since it possesses not only the right bandgap of 1.76 eV for devices working under room temperature but also the desired indirect gap nature for charge carriers surviving longer. We propose further that semiconductor neutron detectors with single-neutron sensitivity can be realized with such a Gd-chalcogenide on the condition that their crystals can be grown with good quality.

  8. Facilitating adverse drug event detection in pharmacovigilance databases using molecular structure similarity: application to rhabdomyolysis

    Science.gov (United States)

    Vilar, Santiago; Harpaz, Rave; Chase, Herbert S; Costanzi, Stefano; Rabadan, Raul

    2011-01-01

    Background Adverse drug events (ADE) cause considerable harm to patients, and consequently their detection is critical for patient safety. The US Food and Drug Administration maintains an adverse event reporting system (AERS) to facilitate the detection of ADE in drugs. Various data mining approaches have been developed that use AERS to detect signals identifying associations between drugs and ADE. The signals must then be monitored further by domain experts, which is a time-consuming task. Objective To develop a new methodology that combines existing data mining algorithms with chemical information by analysis of molecular fingerprints to enhance initial ADE signals generated from AERS, and to provide a decision support mechanism to facilitate the identification of novel adverse events. Results The method achieved a significant improvement in precision in identifying known ADE, and a more than twofold signal enhancement when applied to the ADE rhabdomyolysis. The simplicity of the method assists in highlighting the etiology of the ADE by identifying structurally similar drugs. A set of drugs with strong evidence from both AERS and molecular fingerprint-based modeling is constructed for further analysis. Conclusion The results demonstrate that the proposed methodology could be used as a pharmacovigilance decision support tool to facilitate ADE detection. PMID:21946238

  9. Structural health monitoring strategy for detection of interlaminar delamination in composite plates

    International Nuclear Information System (INIS)

    Quaegebeur, N; Micheau, P; Masson, P; Maslouhi, A

    2010-01-01

    In this paper, a structural health monitoring strategy for detecting interlaminar delamination in a carbon fiber reinforced polymer structure using Lamb waves is proposed. The delamination is simulated by inserting a Teflon tape between two transverse plies and the Lamb wave generation and measurement is enabled by using piezoceramic elements. The Lamb wave theoretical propagation and through thickness strain distribution are studied, in order to determine the optimal configuration of the final system in terms of mode and frequency selection, and piezoceramic sizing and spacing, for detection of cross-sectional delamination. Pitch and catch measurements are performed by comparing wave propagations for different frequencies and along damaged and undamaged paths of the structure, and the analysis of results is performed using the reassigned short time Fourier transform. It appears that in the low frequency range (below 300 kHz), the A0 mode is sensitive to the damage, while in the high frequency range, S1 and A1 modes are both very sensitive to the damage while the propagation of the S0 mode is not affected very much

  10. Intermolecular G-quadruplex structure-based fluorescent DNA detection system.

    Science.gov (United States)

    Zhou, Hui; Wu, Zai-Sheng; Shen, Guo-Li; Yu, Ru-Qin

    2013-03-15

    Adopting multi-donors to pair with one acceptor could improve the performance of fluorogenic detection probes. However, common dyes (e.g., fluorescein) in close proximity to each other would self-quench the fluorescence, and the fluorescence is difficult to restore. In this contribution, we constructed a novel "multi-donors-to-one acceptor" fluorescent DNA detection system by means of the intermolecular G-quadruplex (IGQ) structure-based fluorescence signal enhancement combined with the hairpin oligonucleotide. The novel IGQ-hairpin system was characterized using the p53 gene as the model target DNA. The proposed system showed an improved assay performance due to the introduction of IGQ-structure into fluorescent signaling probes, which could inhibit the background fluorescence and increase fluorescence restoration amplitude of fluoresceins upon target DNA hybridization. The proof-of-concept scheme is expected to provide new insight into the potential of G-quadruplex structure and promote the application of fluorescent oligonucleotide probes in fundamental research, diagnosis, and treatment of genetic diseases. Copyright © 2012 Elsevier B.V. All rights reserved.

  11. A fiber optic Doppler sensor and its application in debonding detection for composite structures.

    Science.gov (United States)

    Li, Fucai; Murayama, Hideaki; Kageyama, Kazuro; Meng, Guang; Ohsawa, Isamu; Shirai, Takehiro

    2010-01-01

    Debonding is one of the most important damage forms in fiber-reinforced composite structures. This work was devoted to the debonding damage detection of lap splice joints in carbon fiber reinforced plastic (CFRP) structures, which is based on guided ultrasonic wave signals captured by using fiber optic Doppler (FOD) sensor with spiral shape. Interferometers based on two types of laser sources, namely the He-Ne laser and the infrared semiconductor laser, are proposed and compared in this study for the purpose of measuring Doppler frequency shift of the FOD sensor. Locations of the FOD sensors are optimized based on mechanical characteristics of lap splice joint. The FOD sensors are subsequently used to detect the guided ultrasonic waves propagating in the CFRP structures. By taking advantage of signal processing approaches, features of the guided wave signals can be revealed. The results demonstrate that debonding in the lap splice joint results in arrival time delay of the first package in the guided wave signals, which can be the characteristic for debonding damage inspection and damage extent estimation.

  12. Line grouping using perceptual saliency and structure prediction for car detection in traffic scenes

    Science.gov (United States)

    Denasi, Sandra; Quaglia, Giorgio

    1993-08-01

    Autonomous and guide assisted vehicles make a heavy use of computer vision techniques to perceive the environment where they move. In this context, the European PROMETHEUS program is carrying on activities in order to develop autonomous vehicle monitoring that assists people to achieve safer driving. Car detection is one of the topics that are faced by the program. Our contribution proposes the development of this task in two stages: the localization of areas of interest and the formulation of object hypotheses. In particular, the present paper proposes a new approach that builds structural descriptions of objects from edge segmentations by using geometrical organization. This approach has been applied to the detection of cars in traffic scenes. We have analyzed images taken from a moving vehicle in order to formulate obstacle hypotheses: preliminary results confirm the efficiency of the method.

  13. Complex networks from experimental horizontal oil–water flows: Community structure detection versus flow pattern discrimination

    International Nuclear Information System (INIS)

    Gao, Zhong-Ke; Fang, Peng-Cheng; Ding, Mei-Shuang; Yang, Dan; Jin, Ning-De

    2015-01-01

    We propose a complex network-based method to distinguish complex patterns arising from experimental horizontal oil–water two-phase flow. We first use the adaptive optimal kernel time–frequency representation (AOK TFR) to characterize flow pattern behaviors from the energy and frequency point of view. Then, we infer two-phase flow complex networks from experimental measurements and detect the community structures associated with flow patterns. The results suggest that the community detection in two-phase flow complex network allows objectively discriminating complex horizontal oil–water flow patterns, especially for the segregated and dispersed flow patterns, a task that existing method based on AOK TFR fails to work. - Highlights: • We combine time–frequency analysis and complex network to identify flow patterns. • We explore the transitional flow behaviors in terms of betweenness centrality. • Our analysis provides a novel way for recognizing complex flow patterns. • Broader applicability of our method is demonstrated and articulated

  14. Mueller matrix ellipsometric detection of profile asymmetry in nanoimprinted grating structures

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xiuguo; Ma, Zhichao; Xu, Zhimou [Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074 (China); Zhang, Chuanwei; Jiang, Hao [State Key Laboratory of Digital Manufacturing Equipment and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China); Liu, Shiyuan, E-mail: shyliu@mail.hust.edu.cn [Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074 (China); State Key Laboratory of Digital Manufacturing Equipment and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2014-11-21

    Mueller matrix ellipsometry (MME) is applied to detect foot-like asymmetry encountered in nanoimprint lithography (NIL) processes. We present both theoretical and experimental results which show that MME has good sensitivity to both the magnitude and direction of asymmetric profiles. The physics behind the use of MME for asymmetry detection is the breaking of electromagnetic reciprocity theorem for the zeroth-order diffraction of asymmetric gratings. We demonstrate that accurate characterization of asymmetric nanoimprinted gratings can be achieved by performing MME measurements in a conical mounting with the plane of incidence parallel to grating lines and meanwhile incorporating depolarization effects into the optical model. The comparison of MME-extracted asymmetric profile with the measurement by cross-sectional scanning electron microscopy also reveals the strong potential of this technique for in-line monitoring NIL processes, where symmetric structures are desired.

  15. Isolation and Characterization of Polymorphic Microsatellite Loci from Metapenaeopsis barbata Using PCR-Based Isolation of Microsatellite Arrays (PIMA)

    Science.gov (United States)

    Chiang, Tzen-Yuh; Tzeng, Tzong-Der; Lin, Hung-Du; Cho, Ching-Ju; Lin, Feng-Jiau

    2012-01-01

    The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species. PMID:22489123

  16. DEEP LEARNING AND IMAGE PROCESSING FOR AUTOMATED CRACK DETECTION AND DEFECT MEASUREMENT IN UNDERGROUND STRUCTURES

    Directory of Open Access Journals (Sweden)

    F. Panella

    2018-05-01

    Full Text Available This work presents the combination of Deep-Learning (DL and image processing to produce an automated cracks recognition and defect measurement tool for civil structures. The authors focus on tunnel civil structures and survey and have developed an end to end tool for asset management of underground structures. In order to maintain the serviceability of tunnels, regular inspection is needed to assess their structural status. The traditional method of carrying out the survey is the visual inspection: simple, but slow and relatively expensive and the quality of the output depends on the ability and experience of the engineer as well as on the total workload (stress and tiredness may influence the ability to observe and record information. As a result of these issues, in the last decade there is the desire to automate the monitoring using new methods of inspection. The present paper has the goal of combining DL with traditional image processing to create a tool able to detect, locate and measure the structural defect.

  17. Ligand Binding Site Detection by Local Structure Alignment and Its Performance Complementarity

    Science.gov (United States)

    Lee, Hui Sun; Im, Wonpil

    2013-01-01

    Accurate determination of potential ligand binding sites (BS) is a key step for protein function characterization and structure-based drug design. Despite promising results of template-based BS prediction methods using global structure alignment (GSA), there is a room to improve the performance by properly incorporating local structure alignment (LSA) because BS are local structures and often similar for proteins with dissimilar global folds. We present a template-based ligand BS prediction method using G-LoSA, our LSA tool. A large benchmark set validation shows that G-LoSA predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, a GSA-based method, while the overall success rate of TM-align is better. G-LoSA is particularly efficient for accurate detection of local structures conserved across proteins with diverse global topologies. Recognizing the performance complementarity of G-LoSA to TM-align and a non-template geometry-based method, fpocket, a robust consensus scoring method, CMCS-BSP (Complementary Methods and Consensus Scoring for ligand Binding Site Prediction), is developed and shows improvement on prediction accuracy. The G-LoSA source code is freely available at http://im.bioinformatics.ku.edu/GLoSA. PMID:23957286

  18. Detection of secondary structure elements in proteins by hydrophobic cluster analysis.

    Science.gov (United States)

    Woodcock, S; Mornon, J P; Henrissat, B

    1992-10-01

    Hydrophobic cluster analysis (HCA) is a protein sequence comparison method based on alpha-helical representations of the sequences where the size, shape and orientation of the clusters of hydrophobic residues are primarily compared. The effectiveness of HCA has been suggested to originate from its potential ability to focus on the residues forming the hydrophobic core of globular proteins. We have addressed the robustness of the bidimensional representation used for HCA in its ability to detect the regular secondary structure elements of proteins. Various parameters have been studied such as those governing cluster size and limits, the hydrophobic residues constituting the clusters as well as the potential shift of the cluster positions with respect to the position of the regular secondary structure elements. The following results have been found to support the alpha-helical bidimensional representation used in HCA: (i) there is a positive correlation (clearly above background noise) between the hydrophobic clusters and the regular secondary structure elements in proteins; (ii) the hydrophobic clusters are centred on the regular secondary structure elements; (iii) the pitch of the helical representation which gives the best correspondence is that of an alpha-helix. The correspondence between hydrophobic clusters and regular secondary structure elements suggests a way to implement variable gap penalties during the automatic alignment of protein sequences.

  19. Toward Smart Aerospace Structures: Design of a Piezoelectric Sensor and Its Analog Interface for Flaw Detection

    Directory of Open Access Journals (Sweden)

    Hamza Boukabache

    2014-10-01

    Full Text Available Structural health monitoring using noninvasive methods is one of the major challenges that aerospace manufacturers face in this decade. Our work in this field focuses on the development and the system integration of millimetric piezoelectric sensors/ actuators to generate and measure specific guided waves. The aim of the application is to detect mechanical flaws on complex composite and alloy structures to quantify efficiently the global structures’ reliability. The study begins by a physical and analytical analysis of a piezoelectric patch. To preserve the structure’s integrity, the transducers are directly pasted onto the surface which leads to a critical issue concerning the interfacing layer. In order to improve the reliability and mitigate the influence of the interfacing layer, the global equations of piezoelectricity are coupled with a load transfer model. Thus we can determine precisely the shear strain developed on the surface of the structure. To exploit the generated signal, a high precision analog charge amplifier coupled to a double T notch filter were designed and scaled. Finally, a novel joined time-frequency analysis based on a wavelet decomposition algorithm is used to extract relevant structures signatures. Finally, this paper provides examples of application on aircraft structure specimens and the feasibility of the system is thus demonstrated.

  20. Smart bricks for strain sensing and crack detection in masonry structures

    Science.gov (United States)

    Downey, Austin; D'Alessandro, Antonella; Laflamme, Simon; Ubertini, Filippo

    2018-01-01

    The paper proposes the novel concept of smart bricks as a durable sensing solution for structural health monitoring of masonry structures. The term smart bricks denotes piezoresistive clay bricks with suitable electronics capable of outputting measurable changes in their electrical properties under changes in their state of strain. This feature can be exploited to evaluate stress at critical locations inside a masonry wall and to detect changes in loading paths associated with structural damage, for instance following an earthquake. Results from an experimental campaign show that normal clay bricks, fabricated in the laboratory with embedded electrodes made of a special steel for resisting the high baking temperature, exhibit a quite linear and repeatable piezoresistive behavior. That is a change in electrical resistance proportional to a change in axial strain. In order to be able to exploit this feature for strain sensing, high-resolution electronics are used with a biphasic DC measurement approach to eliminate any resistance drift due to material polarization. Then, an enhanced nanocomposite smart brick is proposed, where titania is mixed with clay before baking, in order to enhance the brick’s mechanical properties, improve its noise rejection, and increase its electrical conductivity. Titania was selected among other possible conductive nanofillers due to its resistance to high temperatures and its ability to improve the durability of construction materials while maintaining the aesthetic appearance of clay bricks. An application of smart bricks for crack detection in masonry walls is demonstrated by laboratory testing of a small-scale wall specimen under different loading conditions and controlled damage. Overall, it is demonstrated that a few strategically placed smart bricks enable monitoring of the state of strain within the wall and provide information that is capable of crack detection.

  1. Highly parallel and short-acting amplification with locus-specific primers to detect single nucleotide polymorphisms by the DigiTag2 assay.

    Directory of Open Access Journals (Sweden)

    Nao Nishida

    Full Text Available The DigiTag2 assay enables analysis of a set of 96 SNPs using Kapa 2GFast HotStart DNA polymerase with a new protocol that has a total running time of about 7 hours, which is 6 hours shorter than the previous protocol. Quality parameters (conversion rate, call rate, reproducibility and concordance were at the same levels as when genotype calls were acquired using the previous protocol. Multiplex PCR with 192 pairs of locus-specific primers was available for target preparation in the DigiTag2 assay without the optimization of reaction conditions, and quality parameters had the same levels as those acquired with 96-plex PCR. The locus-specific primers were able to achieve sufficient (concentration of target amplicon ≥5 nM and specific (concentration of unexpected amplicons <2 nM amplification within 2 hours, were also able to achieve detectable amplifications even when working in a 96-plex or 192-plex form. The improved DigiTag2 assay will be an efficient platform for screening an intermediate number of SNPs (tens to hundreds of sites in the replication analysis after genome-wide association study. Moreover, highly parallel and short-acting amplification with locus-specific primers may thus facilitate widespread application to other PCR-based assays.

  2. CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

    KAUST Repository

    Cui, Xuefeng; Lu, Zhiwu; Wang, Sheng; Jing-Yan Wang, Jim; Gao, Xin

    2016-01-01

    Motivation: Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment

  3. Detecting Multi-scale Structures in Chandra Images of Centaurus A

    Science.gov (United States)

    Karovska, M.; Fabbiano, G.; Elvis, M. S.; Evans, I. N.; Kim, D. W.; Prestwich, A. H.; Schwartz, D. A.; Murray, S. S.; Forman, W.; Jones, C.; Kraft, R. P.; Isobe, T.; Cui, W.; Schreier, E. J.

    1999-12-01

    Centaurus A (NGC 5128) is a giant early-type galaxy with a merger history, containing the nearest radio-bright AGN. Recent Chandra High Resolution Camera (HRC) observations of Cen A reveal X-ray multi-scale structures in this object with unprecedented detail and clarity. We show the results of an analysis of the Chandra data with smoothing and edge enhancement techniques that allow us to enhance and quantify the multi-scale structures present in the HRC images. These techniques include an adaptive smoothing algorithm (Ebeling et al 1999), and a multi-directional gradient detection algorithm (Karovska et al 1994). The Ebeling et al adaptive smoothing algorithm, which is incorporated in the CXC analysis s/w package, is a powerful tool for smoothing images containing complex structures at various spatial scales. The adaptively smoothed images of Centaurus A show simultaneously the high-angular resolution bright structures at scales as small as an arcsecond and the extended faint structures as large as several arc minutes. The large scale structures suggest complex symmetry, including a component possibly associated with the inner radio lobes (as suggested by the ROSAT HRI data, Dobereiner et al 1996), and a separate component with an orthogonal symmetry that may be associated with the galaxy as a whole. The dust lane and the x-ray ridges are very clearly visible. The adaptively smoothed images and the edge-enhanced images also suggest several filamentary features including a large filament-like structure extending as far as about 5 arcminutes to North-West.

  4. Alpha- and gamma-detection by the avalanche detectors with metal-resistor-semiconductor structure

    International Nuclear Information System (INIS)

    Vetokhin, S.S.; Evtushenko, V.P.; Zalesskij, V.B.; Malyshev, S.A.; Chudakov, V.A.; Shunevich, S.A.

    1992-01-01

    Possibility to use silicon avalanche photodetectors with metal-resistor-semiconductor structure with 0.12 cm 2 photosensitive area as detectors of α-particles, as well as, photodetector of γ-quanta scintillation detector is shown. When detection of α-particles the energy resolution reaches 10%. R energy resolution for avalanche photodetector-CsI(Tl) scintillator system cooled up to - 60 deg C at 59 keV ( 241 Am) and 662 keV ( 137 Cs) energy of γ-quanta constitutes 60% and 80%, respectively. R minimal value in the conducted experiments is determined by the degree of irregularity of avalanche amplification along the photodetector area

  5. Application of AMT in detecting deep geological structures in Lejia district of Xiangshan uranium ore field

    International Nuclear Information System (INIS)

    Duan Shuxin; Liu Hu

    2014-01-01

    In recent years, exploration in Xiangshan uranium ore field shows that the intersection of faults and the interface of different rock formation and the basement is an important sign of deep ore- prospecting. In order to evaluate deep uranium resource in Lejia district, audio magnetotelluric method (AMT) was undertaken to carry out profile investigation. With that method, we discerned the interface of different rock formation and the basement successfully, and faults in the deep, which provides a good basis for the prediction of deep uranium resource. Drilling results show that AMT method has an obvious advantage in detecting deep geological structures in Xiangshan. (authors)

  6. Surface extended x-ray absorption fine structure of low-Z absorbates using fluorescence detection

    International Nuclear Information System (INIS)

    Stoehr, J.; Kollin, E.B.; Fischer, D.A.; Hastings, J.B.; Zaera, F.; Sette, F.

    1985-05-01

    Comparison of x-ray fluorescence yield (FY) and electron yield surface extended x-ray absorption fine structure spectra above the S K-edge for c(2 x 2) S on Ni(100) reveals an order of magnitude higher sensitivity of the FY technique. Using FY detection, thiophene (C 4 H 4 S) chemisorption on Ni(100) is studied with S coverages down to 0.08 monolayer. The molecule dissociates at temperatures as low as 100K by interaction with fourfold hollow Ni sites. Blocking of these sites by oxygen leaves the molecule intact

  7. Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

    Science.gov (United States)

    Fu, Qianqian; Zhu, Biting; Ge, Jianping

    2017-02-16

    A SiO 2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO 2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

  8. Development and characterization of polymorphic microsatellite markers in Dysosma pleiantha (Berberidaceae).

    Science.gov (United States)

    Guan, Bi-Cai; Gong, Xi; Zhou, Shi-Liang

    2011-08-01

    The development of compound microsatellite markers was conducted in Dysosma pleiantha to investigate genetic diversity and population genetic structure of this threatened medicinal plant. Using the compound microsatellite marker technique, 14 microsatellite markers that were successfully amplified showed polymorphism when tested on 38 individuals from three populations in eastern China. Overall, the number of alleles per locus ranged from 2 to 14, with an average of 7.71 alleles per locus. These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure and genetic diversity in Dysosma pleiantha.

  9. Solid state transformations in consequence of electrospraying--a novel polymorphic form of piroxicam.

    Science.gov (United States)

    Nyström, Maija; Roine, Jorma; Murtomaa, Matti; Mohan Sankaran, R; Santos, Hélder A; Salonen, Jarno

    2015-01-01

    The aim of the research was to verify that electrospraying of piroxicam yielded a new polymorphic form of this drug. In the experiments, piroxicam was dissolved in chloroform and the solution was atomised electrostatically. Subsequently, the charged droplets were neutralised and dried. The solid drug particles were collected and analysed by scanning electron microscopy, X-ray diffraction, differential scanning calorimetry, high performance liquid chromatography, and infrared and Raman spectroscopy. The X-ray diffractogram measured for the electrosprayed piroxicam particles did not match with any of the known piroxicam crystal structures (Cambridge Crystallographic Data Centre). The variable temperature X-ray diffraction showed that the structure recrystallised completely into piroxicam polymorphic formI during heating. No degradation products or solvate removal was detected by high performance liquid chromatography and thermal analysis. The infrared and Raman spectra of the electrosprayed piroxicam were compared to those of formI, and some notable differences in the peak positions, shapes and intensities were detected. The results indicate that electrospraying leads to piroxicam crystallisation in a currently unknown polymorphic form. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Assessment of Genetic Diversity in Faba Bean Based on Single Nucleotide Polymorphism

    Directory of Open Access Journals (Sweden)

    Sukhjiwan Kaur

    2014-01-01

    Full Text Available Detection of genetic diversity is important for characterisation of crop plant collections in order to detect the presence of valuable trait variation for use in breeding programs. A collection of faba bean (Vicia faba L. genotypes was evaluated for intra- and inter-population diversity using a set of 768 genome-wide distributed single nucleotide polymorphism (SNP markers, of which 657 obtained successful amplification and detected polymorphisms. Gene diversity and polymorphism information content (PIC values varied between 0.022–0.500 and 0.023–1.00, with averages of 0.363 and 0.287, respectively. The genetic structure of the germplasm collection was analysed and a neighbour-joining (NJ dendrogram was constructed. The faba bean accessions grouped into two major groups, with several additional smaller sub-groups, predominantly on the basis of geographical origin. These results were further supported by principal co-ordinate analysis (PCoA, deriving two major groupings which were differentiated on the basis of site of origin and pedigree relationships. In general, high levels of heterozygosity were observed, presumably due to the partially allogamous nature of the species. The results will facilitate targeted crossing strategies in future faba bean breeding programs in order to achieve genetic gain.

  11. High-Pressure Polymorphism in Orthoamphiboles

    Science.gov (United States)

    Finkelstein, G. J.; Zhang, D.; Shelton, H.; Dera, P.

    2017-12-01

    Amphiboles are double-chain silicate minerals that are the structurally hydrated counterpart to single-chain, anhydrous pyroxenes. They may play an important role in the earth as a carrier for volatiles in subduction zones, as well as a generator for seismic anisotropy in the upper mantle. Recent work has described previously unrecognized high-pressure polymorphism at low temperatures in a variety of pyroxene minerals, which may be relevant for the structure and dynamics of thick, cold, subducted slabs. However, high-pressure polymorphism in amphiboles above a few GPa in pressure has not been well explored, and if similar polymorphism to pyroxenes exists in this mineral family, it may affect the extent and depth of volatile transport in amphiboles, as well as their rheological properties. At low temperatures and high pressures, orthopyroxenes undergo crystal structure transitions at lower pressures than clinopyroxenes (10-30 GPa vs. > 50 GPa), so for this study we have investigated polymorphism in the anthophyllite-gedrite (Al-free and Al rich) orthoamphibole solid solution series. Using neon gas-loaded diamond anvil cells, we compressed both phases to a maximum pressure of 31 GPa, and observed transitions to new monoclinic structures in both endmembers. In this presentation, we will discuss the details of these transitions and implications for the earth's interior.

  12. Fatigue crack detection on structural steel members by using ultrasound excited thermography

    International Nuclear Information System (INIS)

    Plum, Robin Marc

    2015-01-01

    In the field of non-destructive testing (NDT), ultrasound excited thermography has been recognised as a promising technique that was successfully applied to metals, fibre composites and many more engineering materials in order to detect cracks, delaminations and other types of internal flaws. Dating back to the late 1970s, the idea of high-frequency vibration excitation of structural members combined with monitoring the surface temperature by means of infrared thermography aims at the localised energy dissipation at defect regions and its thermal detection. The purpose of this thesis is to investigate the potential use of ultrasound excited thermography for detecting surface breaking fatigue cracks in thick-walled components relevant to steel construction. The presented research is motivated by a lack of fast and imaging crack detection methods in the field and the growing acceptance and technological progress of active thermography techniques. After introducing the concept of ultrasound excited thermography or vibrothermography, its current state of the art is described by means of a comprehensive literature review focusing on research activities towards crack detection on metals. Owing to the interdisciplinarity of the test method, all relevant technical subdisciplines from the excitation of plate vibrations via potential heat generation mechanisms and heat transfer to infrared thermography are outlined. The experimental work starts with the manufacture and fatigue loading of suitable plate specimens made from low-carbon steel S355, mostly in the high cycle fatigue regime, to generate throughthickness cracks with specified depths. Using a modified high-power ultrasonic welding generator, basic dependencies of the defect heating on frequency, coupling location and excitation duration are clarified at first. Besides of an estimation of realistic detection limits depending on the plate thickness, main issues such as the relation between vibration intensity and

  13. Fatigue crack detection on structural steel members by using ultrasound excited thermography

    Energy Technology Data Exchange (ETDEWEB)

    Plum, Robin Marc

    2015-07-01

    In the field of non-destructive testing (NDT), ultrasound excited thermography has been recognised as a promising technique that was successfully applied to metals, fibre composites and many more engineering materials in order to detect cracks, delaminations and other types of internal flaws. Dating back to the late 1970s, the idea of high-frequency vibration excitation of structural members combined with monitoring the surface temperature by means of infrared thermography aims at the localised energy dissipation at defect regions and its thermal detection. The purpose of this thesis is to investigate the potential use of ultrasound excited thermography for detecting surface breaking fatigue cracks in thick-walled components relevant to steel construction. The presented research is motivated by a lack of fast and imaging crack detection metho