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Sample records for oxidation domain similar

  1. Domain similarity based orthology detection.

    Science.gov (United States)

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

    2015-05-13

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

  2. Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach.

    Science.gov (United States)

    Dhir, Somdutta; Pacurar, Mircea; Franklin, Dino; Gáspári, Zoltán; Kertész-Farkas, Attila; Kocsor, András; Eisenhaber, Frank; Pongor, Sándor

    2010-11-01

    SBASE is a project initiated to detect known domain types and predicting domain architectures using sequence similarity searching (Simon et al., Protein Seq Data Anal, 5: 39-42, 1992, Pongor et al, Nucl. Acids. Res. 21:3111-3115, 1992). The current approach uses a curated collection of domain sequences - the SBASE domain library - and standard similarity search algorithms, followed by postprocessing which is based on a simple statistics of the domain similarity network (http://hydra.icgeb.trieste.it/sbase/). It is especially useful in detecting rare, atypical examples of known domain types which are sometimes missed even by more sophisticated methodologies. This approach does not require multiple alignment or machine learning techniques, and can be a useful complement to other domain detection methodologies. This article gives an overview of the project history as well as of the concepts and principles developed within this the project.

  3. Semantic similarity measure in biomedical domain leverage web search engine.

    Science.gov (United States)

    Chen, Chi-Huang; Hsieh, Sheau-Ling; Weng, Yung-Ching; Chang, Wen-Yung; Lai, Feipei

    2010-01-01

    Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

  4. Between-domain relations of students' academic emotions and their judgments of school domain similarity

    Science.gov (United States)

    Goetz, Thomas; Haag, Ludwig; Lipnevich, Anastasiya A.; Keller, Melanie M.; Frenzel, Anne C.; Collier, Antonie P. M.

    2014-01-01

    With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual) emotions reflected students' judgments of domain similarities, whereas between-domain relations of state (i.e., momentary) emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals' beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders) was to gather salient characteristics of academic domains from students' perspective. In Study 2 (N = 1709; 8th and 11th graders) the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English) using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders) by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed. PMID:25374547

  5. Between-Domain Relations of Students’ Academic Emotions and Their Judgments of School Domain Similarity

    Directory of Open Access Journals (Sweden)

    Thomas eGoetz

    2014-10-01

    Full Text Available With the aim to deepen our understanding of the between-domain relations of academic emotions, a series of three studies was conducted. We theorized that between-domain relations of trait (i.e., habitual emotions reflected students’ judgments of domain similarities, whereas between-domain relations of state (i.e., momentary emotions did not. This supposition was based on the accessibility model of emotional self-report, according to which individuals’ beliefs tend to strongly impact trait, but not state emotions. The aim of Study 1 (interviews; N = 40; 8th and 11th graders was to gather salient characteristics of academic domains from students’ perspective. In Study 2 (N=1709; 8th and 11th graders the 13 characteristics identified in Study 1 were assessed along with academic emotions in four different domains (mathematics, physics, German, and English using a questionnaire-based trait assessment. With respect to the same domains, state emotions were assessed in Study 3 (N = 121; 8th and 11th graders by employing an experience sampling approach. In line with our initial assumptions, between-domain relations of trait but not state academic emotions reflected between-domain relations of domain characteristics. Implications for research and practice are discussed.

  6. Textual and chemical information processing: different domains but similar algorithms

    Directory of Open Access Journals (Sweden)

    Peter Willett

    2000-01-01

    Full Text Available This paper discusses the extent to which algorithms developed for the processing of textual databases are also applicable to the processing of chemical structure databases, and vice versa. Applications discussed include: an algorithm for distribution sorting that has been applied to the design of screening systems for rapid chemical substructure searching; the use of measures of inter-molecular structural similarity for the analysis of hypertext graphs; a genetic algorithm for calculating term weights for relevance feedback searching for determining whether a molecule is likely to exhibit biological activity; and the use of data fusion to combine the results of different chemical similarity searches.

  7. A review of similarities between domain-specific determinants of four health behaviors among adolescents

    NARCIS (Netherlands)

    Peters, L.W.H.; Wiefferink, C.H.; Hoekstra, F.; Buijs, G.J.; Ten Dam, G.T.M.; Paulussen, T.G.W.M.

    2009-01-01

    Schools are overloaded with health promotion programs that, altogether, focus on a broad array of behavioral domains, including substance abuse, sexuality and nutrition. Although the specific content of programs varies according to the domain focus, programs usually address similar concepts:

  8. Conduction at domain walls in oxide multiferroics

    Science.gov (United States)

    Seidel, J.; Martin, L. W.; He, Q.; Zhan, Q.; Chu, Y.-H.; Rother, A.; Hawkridge, M. E.; Maksymovych, P.; Yu, P.; Gajek, M.; Balke, N.; Kalinin, S. V.; Gemming, S.; Wang, F.; Catalan, G.; Scott, J. F.; Spaldin, N. A.; Orenstein, J.; Ramesh, R.

    2009-03-01

    Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO3. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

  9. Domain Wall Evolution in Phase Transforming Oxides

    Science.gov (United States)

    2015-01-14

    Chemically Derived PZT Thin Films on Pt Substrates, Journal of the American Ceramic Society, (09 2014): 2973. doi: 10.1111/jace.13007 Jacob L. Jones...Mari-Ann Einarsrud, D. Johnson. Piezoelectric K0.5Na0.5NbO3 ceramics textured using needle-like K0.5Na0.5NbO3 templates, Journal of the American...Jones. Quantitative comparison between the degree of domain orientation and nonlinear properties of a PZT ceramic during electrical and mechanical

  10. Inference-Based Similarity Search in Randomized Montgomery Domains for Privacy-Preserving Biometric Identification.

    Science.gov (United States)

    Wang, Yi; Wan, Jianwu; Guo, Jun; Cheung, Yiu-Ming; C Yuen, Pong

    2017-07-14

    Similarity search is essential to many important applications and often involves searching at scale on high-dimensional data based on their similarity to a query. In biometric applications, recent vulnerability studies have shown that adversarial machine learning can compromise biometric recognition systems by exploiting the biometric similarity information. Existing methods for biometric privacy protection are in general based on pairwise matching of secured biometric templates and have inherent limitations in search efficiency and scalability. In this paper, we propose an inference-based framework for privacy-preserving similarity search in Hamming space. Our approach builds on an obfuscated distance measure that can conceal Hamming distance in a dynamic interval. Such a mechanism enables us to systematically design statistically reliable methods for retrieving most likely candidates without knowing the exact distance values. We further propose to apply Montgomery multiplication for generating search indexes that can withstand adversarial similarity analysis, and show that information leakage in randomized Montgomery domains can be made negligibly small. Our experiments on public biometric datasets demonstrate that the inference-based approach can achieve a search accuracy close to the best performance possible with secure computation methods, but the associated cost is reduced by orders of magnitude compared to cryptographic primitives.

  11. Improvement of training set structure in fusion data cleaning using Time-Domain Global Similarity method

    International Nuclear Information System (INIS)

    Liu, J.; Lan, T.; Qin, H.

    2017-01-01

    Traditional data cleaning identifies dirty data by classifying original data sequences, which is a class-imbalanced problem since the proportion of incorrect data is much less than the proportion of correct ones for most diagnostic systems in Magnetic Confinement Fusion (MCF) devices. When using machine learning algorithms to classify diagnostic data based on class-imbalanced training set, most classifiers are biased towards the major class and show very poor classification rates on the minor class. By transforming the direct classification problem about original data sequences into a classification problem about the physical similarity between data sequences, the class-balanced effect of Time-Domain Global Similarity (TDGS) method on training set structure is investigated in this paper. Meanwhile, the impact of improved training set structure on data cleaning performance of TDGS method is demonstrated with an application example in EAST POlarimetry-INTerferometry (POINT) system.

  12. Different methods of membrane domains isolation result in similar 2-D distribution patterns of membrane domain proteins

    Czech Academy of Sciences Publication Activity Database

    Matoušek, Petr; Hodný, Zdeněk; Švandová, I.; Svoboda, Petr

    2003-01-01

    Roč. 81, č. 6 (2003), s. 365-372 ISSN 0829-8211 R&D Projects: GA MŠk LN00A026 Grant - others:Wellcome Trust(GB) xx Institutional research plan: CEZ:AV0Z5011922; CEZ:MSM 113100003; CEZ:AV0Z5039906 Keywords : membrane domain * G protein * two-dimensional electrophoresis * GPI-ancored proteins Subject RIV: CE - Biochemistry Impact factor: 2.456, year: 2003

  13. Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses.

    Science.gov (United States)

    Evgen'ev, M B; Corces, V G; Lankenau, D H

    1992-06-05

    We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.

  14. Heparan sulfate chains from glypican and syndecans bind the Hep II domain of fibronectin similarly despite minor structural differences

    DEFF Research Database (Denmark)

    Tumova, S; Woods, A; Couchman, J R

    2000-01-01

    syndecan-4. Despite distinct molecular masses of glypican and syndecan glycosaminoglycans and minor differences in disaccharide composition and sulfation pattern, the overall proportion and distribution of sulfated regions and the affinity for the Hep II domain were similar. Therefore, adhesion regulation...

  15. Semantic similarity measures in the biomedical domain by leveraging a web search engine.

    Science.gov (United States)

    Hsieh, Sheau-Ling; Chang, Wen-Yung; Chen, Chi-Huang; Weng, Yung-Ching

    2013-07-01

    Various researches in web related semantic similarity measures have been deployed. However, measuring semantic similarity between two terms remains a challenging task. The traditional ontology-based methodologies have a limitation that both concepts must be resided in the same ontology tree(s). Unfortunately, in practice, the assumption is not always applicable. On the other hand, if the corpus is sufficiently adequate, the corpus-based methodologies can overcome the limitation. Now, the web is a continuous and enormous growth corpus. Therefore, a method of estimating semantic similarity is proposed via exploiting the page counts of two biomedical concepts returned by Google AJAX web search engine. The features are extracted as the co-occurrence patterns of two given terms P and Q, by querying P, Q, as well as P AND Q, and the web search hit counts of the defined lexico-syntactic patterns. These similarity scores of different patterns are evaluated, by adapting support vector machines for classification, to leverage the robustness of semantic similarity measures. Experimental results validating against two datasets: dataset 1 provided by A. Hliaoutakis; dataset 2 provided by T. Pedersen, are presented and discussed. In dataset 1, the proposed approach achieves the best correlation coefficient (0.802) under SNOMED-CT. In dataset 2, the proposed method obtains the best correlation coefficient (SNOMED-CT: 0.705; MeSH: 0.723) with physician scores comparing with measures of other methods. However, the correlation coefficients (SNOMED-CT: 0.496; MeSH: 0.539) with coder scores received opposite outcomes. In conclusion, the semantic similarity findings of the proposed method are close to those of physicians' ratings. Furthermore, the study provides a cornerstone investigation for extracting fully relevant information from digitizing, free-text medical records in the National Taiwan University Hospital database.

  16. Computational design of selective peptides to discriminate between similar PDZ domains in an oncogenic pathway.

    Science.gov (United States)

    Zheng, Fan; Jewell, Heather; Fitzpatrick, Jeremy; Zhang, Jian; Mierke, Dale F; Grigoryan, Gevorg

    2015-01-30

    Reagents that target protein-protein interactions to rewire signaling are of great relevance in biological research. Computational protein design may offer a means of creating such reagents on demand, but methods for encoding targeting selectivity are sorely needed. This is especially challenging when targeting interactions with ubiquitous recognition modules--for example, PDZ domains, which bind C-terminal sequences of partner proteins. Here we consider the problem of designing selective PDZ inhibitor peptides in the context of an oncogenic signaling pathway, in which two PDZ domains (NHERF-2 PDZ2-N2P2 and MAGI-3 PDZ6-M3P6) compete for a receptor C-terminus to differentially modulate oncogenic activities. Because N2P2 has been shown to increase tumorigenicity and M3P6 to decreases it, we sought to design peptides that inhibit N2P2 without affecting M3P6. We developed a structure-based computational design framework that models peptide flexibility in binding yet is efficient enough to rapidly analyze tradeoffs between affinity and selectivity. Designed peptides showed low-micromolar inhibition constants for N2P2 and no detectable M3P6 binding. Peptides designed for reverse discrimination bound M3P6 tighter than N2P2, further testing our technology. Experimental and computational analysis of selectivity determinants revealed significant indirect energetic coupling in the binding site. Successful discrimination between N2P2 and M3P6, despite their overlapping binding preferences, is highly encouraging for computational approaches to selective PDZ targeting, especially because design relied on a homology model of M3P6. Still, we demonstrate specific deficiencies of structural modeling that must be addressed to enable truly robust design. The presented framework is general and can be applied in many scenarios to engineer selective targeting. Copyright © 2014 Elsevier Ltd. All rights reserved.

  17. OS2: Oblivious similarity based searching for encrypted data outsourced to an untrusted domain

    Science.gov (United States)

    Pervez, Zeeshan; Ahmad, Mahmood; Khattak, Asad Masood; Ramzan, Naeem

    2017-01-01

    Public cloud storage services are becoming prevalent and myriad data sharing, archiving and collaborative services have emerged which harness the pay-as-you-go business model of public cloud. To ensure privacy and confidentiality often encrypted data is outsourced to such services, which further complicates the process of accessing relevant data by using search queries. Search over encrypted data schemes solve this problem by exploiting cryptographic primitives and secure indexing to identify outsourced data that satisfy the search criteria. Almost all of these schemes rely on exact matching between the encrypted data and search criteria. A few schemes which extend the notion of exact matching to similarity based search, lack realism as those schemes rely on trusted third parties or due to increase storage and computational complexity. In this paper we propose Oblivious Similarity based Search (OS2) for encrypted data. It enables authorized users to model their own encrypted search queries which are resilient to typographical errors. Unlike conventional methodologies, OS2 ranks the search results by using similarity measure offering a better search experience than exact matching. It utilizes encrypted bloom filter and probabilistic homomorphic encryption to enable authorized users to access relevant data without revealing results of search query evaluation process to the untrusted cloud service provider. Encrypted bloom filter based search enables OS2 to reduce search space to potentially relevant encrypted data avoiding unnecessary computation on public cloud. The efficacy of OS2 is evaluated on Google App Engine for various bloom filter lengths on different cloud configurations. PMID:28692697

  18. The C-Terminal RpoN Domain of sigma54 Forms an unpredictedHelix-Turn-Helix Motif Similar to domains of sigma70

    Energy Technology Data Exchange (ETDEWEB)

    Doucleff, Michaeleen; Malak, Lawrence T.; Pelton, Jeffrey G.; Wemmer, David E.

    2005-11-01

    The ''{delta}'' subunit of prokaryotic RNA-polymerase allows gene-specific transcription initiation. Two {sigma} families have been identified, {sigma}{sup 70} and {sigma}{sup 54}, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the {sigma}{sup 70}-type factors have been well characterized structurally by x-ray crystallography, no high-resolution structural information is available for the {sigma}{sup 54}-type factors. Here we present the NMR derived structure of the C-terminal domain of {sigma}{sup 54} from Aquifex aeolicus. This domain (Thr323 to Gly389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the {sigma}{sup 70}-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. This structure's homology with other DNA binding proteins, combined with previous biochemical data, suggest how the C-terminal domain of {sigma}{sup 54} binds to DNA.

  19. [Formula: see text]: Oblivious similarity based searching for encrypted data outsourced to an untrusted domain.

    Science.gov (United States)

    Pervez, Zeeshan; Ahmad, Mahmood; Khattak, Asad Masood; Ramzan, Naeem; Khan, Wajahat Ali

    2017-01-01

    Public cloud storage services are becoming prevalent and myriad data sharing, archiving and collaborative services have emerged which harness the pay-as-you-go business model of public cloud. To ensure privacy and confidentiality often encrypted data is outsourced to such services, which further complicates the process of accessing relevant data by using search queries. Search over encrypted data schemes solve this problem by exploiting cryptographic primitives and secure indexing to identify outsourced data that satisfy the search criteria. Almost all of these schemes rely on exact matching between the encrypted data and search criteria. A few schemes which extend the notion of exact matching to similarity based search, lack realism as those schemes rely on trusted third parties or due to increase storage and computational complexity. In this paper we propose Oblivious Similarity based Search ([Formula: see text]) for encrypted data. It enables authorized users to model their own encrypted search queries which are resilient to typographical errors. Unlike conventional methodologies, [Formula: see text] ranks the search results by using similarity measure offering a better search experience than exact matching. It utilizes encrypted bloom filter and probabilistic homomorphic encryption to enable authorized users to access relevant data without revealing results of search query evaluation process to the untrusted cloud service provider. Encrypted bloom filter based search enables [Formula: see text] to reduce search space to potentially relevant encrypted data avoiding unnecessary computation on public cloud. The efficacy of [Formula: see text] is evaluated on Google App Engine for various bloom filter lengths on different cloud configurations.

  20. Oxidative stress reduces levels of dysbindin-1A via its PEST domain.

    Science.gov (United States)

    Yap, Mei-Yi Alicia; Lo, Yew-Long; Talbot, Konrad; Ong, Wei-Yi

    2014-12-01

    Oxidative stress resulting from the generation of reactive oxygen species has been proposed as an etiological factor in schizophrenia. The present study tests the hypothesis that oxidative stress can affect levels of dysbindin-1A, encoded by Dtnbp1, a genetic risk factor for schizophrenia, via its PEST domain. In vitro studies on SH-SY5Y cells indicate that oxidative stress triggers proteasomal degradation of dysbindin-1A, and that this requires interactions with its PEST domain, which may be a TRIM32 target. We specifically found (a) that oxidative stress induced in SH-SY5Y cells by 500 µM hydrogen peroxide reduced levels of full-length dysbindin-1, but did not reduce levels of that protein lacking its PEST domain and (b) that levels of full-length dysbindin-1, but not dysbindin-1 lacking its PEST domain, were higher in cells treated with the proteasome inhibitor MG132. Oxidative stress thus emerges as the first known cellular factor regulating dysbindin-1 isoforms with PEST domains. These findings are consistent with the previously noted fact that phosphorylation of PEST domains often marks proteins for proteasomal degradation, and raises the possibility that treatments reducing oxidative stress in the brain, especially during development, may lower schizophrenia risk. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria.

    Science.gov (United States)

    Vandieken, Verona; Pester, Michael; Finke, Niko; Hyun, Jung-Ho; Friedrich, Michael W; Loy, Alexander; Thamdrup, Bo

    2012-11-01

    Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetate-utilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 10(6) acetate-utilizing manganese-reducing cells cm(-3) in Gullmar Fjord sediment. A 16S rRNA gene clone library that was established from the highest MPN dilutions was dominated by sequences of Colwellia and Arcobacter species and members of the Oceanospirillaceae, supporting the obtained RNA-SIP results. In conclusion, these findings strongly suggest that (i) acetate-dependent manganese reduction in manganese oxide-rich sediments is catalyzed by members of taxa (Arcobacter, Colwellia and Oceanospirillaceae) previously not known to possess this physiological function, (ii) similar acetate-utilizing manganese reducers thrive in geographically distinct regions and (iii) the identified manganese reducers differ greatly from the extensively explored iron reducers in marine sediments.

  2. Comparison of Ductile-to-Brittle Transition Behavior in Two Similar Ferritic Oxide Dispersion Strengthened Alloys

    Science.gov (United States)

    Chao, Jesus; Rementeria, Rosalia; Aranda, Maria; Capdevila, Carlos; Gonzalez-Carrasco, Jose Luis

    2016-01-01

    The ductile-to-brittle transition (DBT) behavior of two similar Fe-Cr-Al oxide dispersion strengthened (ODS) stainless steels was analyzed following the Cottrell–Petch model. Both alloys were manufactured by mechanical alloying (MA) but by different forming routes. One was manufactured as hot rolled tube, and the other in the form of hot extruded bar. The two hot forming routes considered do not significantly influence the microstructure, but cause differences in the texture and the distribution of oxide particles. These have little influence on tensile properties; however, the DBT temperature and the upper shelf energy (USE) are significantly affected because of delamination orientation with regard to the notch plane. Whereas in hot rolled material the delaminations are parallel to the rolling surface, in the hot extruded material, they are randomly oriented because the material is transversally isotropic. PMID:28773764

  3. Comparison of Ductile-to-Brittle Transition Behavior in Two Similar Ferritic Oxide Dispersion Strengthened Alloys.

    Science.gov (United States)

    Chao, Jesus; Rementeria, Rosalia; Aranda, Maria; Capdevila, Carlos; Gonzalez-Carrasco, Jose Luis

    2016-07-29

    The ductile-to-brittle transition (DBT) behavior of two similar Fe-Cr-Al oxide dispersion strengthened (ODS) stainless steels was analyzed following the Cottrell-Petch model. Both alloys were manufactured by mechanical alloying (MA) but by different forming routes. One was manufactured as hot rolled tube, and the other in the form of hot extruded bar. The two hot forming routes considered do not significantly influence the microstructure, but cause differences in the texture and the distribution of oxide particles. These have little influence on tensile properties; however, the DBT temperature and the upper shelf energy (USE) are significantly affected because of delamination orientation with regard to the notch plane. Whereas in hot rolled material the delaminations are parallel to the rolling surface, in the hot extruded material, they are randomly oriented because the material is transversally isotropic.

  4. Fingerprinting of near-homogeneous DNA ligase I and II from human cells. Similarity of their AMP-binding domains.

    Science.gov (United States)

    Yang, S W; Becker, F F; Chan, J Y

    1990-10-25

    DNA ligases play obligatory roles during replication, repair, and recombination. Multiple forms of DNA ligase have been reported in mammalian cells including DNA ligase I, the high molecular mass species which functions during replication, and DNA ligase II, the low molecular mass species which is associated with repair. In addition, alterations in DNA ligase activities have been reported in acute lymphocytic leukemia cells, Bloom's syndrome cells, and cells undergoing differentiation and development. To better distinguish the biochemical and molecular properties of the various DNA ligases from human cells, we have developed a method of purifying multiple species of DNA ligase from HeLa cells by chromatography through DEAE-Bio-Gel, CM-Bio-Gel, hydroxylapatite, Sephacryl S-300, Mono P, and DNA-cellulose. DNA-cellulose chromatography of the partially purified enzymes resolved multiple species of DNA ligase after labeling the enzyme with [alpha-32P]ATP to form the ligase-[32P]AMP adduct. The early eluting enzyme activity (0.25 M NaCl) contained a major 67-kDa-labeled protein, while the late eluting activity (0.48 M NaCl) contained two major labeled proteins of 90 and 78 kDa. Neutralization experiments with antiligase I antibodies indicated that the early and late eluting activity peaks were DNA ligase II and I, respectively. The three major ligase-[32P]AMP polypeptides (90, 78, and 67 kDa) were subsequently purified to near homogeneity by elution from preparative sodium dodecyl sulfate-polyacrylamide gels. All three polypeptides retained DNA ligase activities after gel elution and renaturation. To further reveal the relationship between these enzymes, partial digestion by V8-protease was performed. All three purified polypeptides gave rise to a common 22-kDa-labeled fragment for their AMP-binding domains, indicating that the catalytic sites of ligase I and II are quite similar, if not identical. Similar findings were obtained from the two-dimensional gel

  5. Radiation-induced oxidative damage to the DNA-binding domain of the lactose repressor

    Czech Academy of Sciences Publication Activity Database

    Gillard, N.; Goffinont, S.; Buré, C.; Davídková, Marie; Maurizot, J. C.; Cadene, M.; Spotheim-Maurizot, M.

    2007-01-01

    Roč. 403, part 3 (2007), s. 463-472 ISSN 0264-6021 R&D Projects: GA MŠk 1P05OC085 Institutional research plan: CEZ:AV0Z10480505 Keywords : ionizing radiation * oxidative damage * DNA binding domain * lac repressor Subject RIV: CE - Biochemistry Impact factor: 4.009, year: 2007

  6. Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria

    OpenAIRE

    Vandieken, Verona; Pester, Michael; Finke, Niko; Hyun, Jung-Ho; Friedrich, Michael W; Loy, Alexander; Thamdrup, Bo

    2012-01-01

    Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the p...

  7. An effective framework for finding similar cases of dengue from audio and text data using domain thesaurus and case base reasoning

    Science.gov (United States)

    Sandhu, Rajinder; Kaur, Jaspreet; Thapar, Vivek

    2018-02-01

    Dengue, also known as break-bone fever, is a tropical disease transmitted by mosquitoes. If the similarity between dengue infected users can be identified, it can help government's health agencies to manage the outbreak more effectively. To find similarity between cases affected by Dengue, user's personal and health information are the two fundamental requirements. Identification of similar symptoms, causes, effects, predictions and treatment procedures, is important. In this paper, an effective framework is proposed which finds similar patients suffering from dengue using keyword aware domain thesaurus and case base reasoning method. This paper focuses on the use of ontology dependent domain thesaurus technique to extract relevant keywords and then build cases with the help of case base reasoning method. Similar cases can be shared with users, nearby hospitals and health organizations to manage the problem more adequately. Two million case bases were generated to test the proposed similarity method. Experimental evaluations of proposed framework resulted in high accuracy and low error rate for finding similar cases of dengue as compared to UPCC and IPCC algorithms. The framework developed in this paper is for dengue but can easily be extended to other domains also.

  8. Fluorescent fusion proteins of soluble guanylyl cyclase indicate proximity of the heme nitric oxide domain and catalytic domain.

    Directory of Open Access Journals (Sweden)

    Tobias Haase

    Full Text Available BACKGROUND: To examine the structural organisation of heterodimeric soluble guanylyl cyclase (sGC Förster resonance energy transfer (FRET was measured between fluorescent proteins fused to the amino- and carboxy-terminal ends of the sGC beta1 and alpha subunits. METHODOLOGY/PRINCIPAL FINDINGS: Cyan fluorescent protein (CFP was used as FRET donor and yellow fluorescent protein (YFP as FRET acceptor. After generation of recombinant baculovirus, fluorescent-tagged sGC subunits were co-expressed in Sf9 cells. Fluorescent variants of sGC were analyzed in vitro in cytosolic fractions by sensitized emission FRET. Co-expression of the amino-terminally tagged alpha subunits with the carboxy-terminally tagged beta1 subunit resulted in an enzyme complex that showed a FRET efficiency of 10% similar to fluorescent proteins separated by a helix of only 48 amino acids. Because these findings indicated that the amino-terminus of the alpha subunits is close to the carboxy-terminus of the beta1 subunit we constructed fusion proteins where both subunits are connected by a fluorescent protein. The resulting constructs were not only fluorescent, they also showed preserved enzyme activity and regulation by NO. CONCLUSIONS/SIGNIFICANCE: Based on the ability of an amino-terminal fragment of the beta1 subunit to inhibit activity of an heterodimer consisting only of the catalytic domains (alphacatbetacat, Winger and Marletta (Biochemistry 2005, 44:4083-90 have proposed a direct interaction of the amino-terminal region of beta1 with the catalytic domains. In support of such a concept of "trans" regulation of sGC activity by the H-NOX domains our results indicate that the domains within sGC are organized in a way that allows for direct interaction of the amino-terminal regulatory domains with the carboxy-terminal catalytic region. In addition, we constructed "fluorescent-conjoined" sGC's by fusion of the alpha amino-terminus to the beta1 carboxy-terminus leading to a

  9. A similar local immune and oxidative stress phenotype in vitiligo and halo nevus.

    Science.gov (United States)

    Yang, Yuqi; Li, Shuli; Zhu, Guannan; Zhang, Qian; Wang, Gang; Gao, Tianwen; Li, Chunying; Wang, Lin; Jian, Zhe

    2017-07-01

    Vitiligo and halo nevus are two common T-cell-mediated skin disorders. Although autoimmunity has been suggested to be involved in both diseases, the relationship between vitiligo and halo nevus is not fully understood. The aim of the current study was to investigate whether vitiligo and halo nevus share the same immunological and oxidative stress response. Infiltrations of T cells, and expressions of chemokine receptors (CXCR3, CCR4, CCR5) and cytotoxic markers (Granzyme B, Perforin) in the lesions of vitiligo and halo nevus were examined by immunohistochemistry. Enzyme-linked immunosorbent assay was performed to analyze the expressions of chemokines in the serum samples and cytotoxic markers secreted by CD8 + T cells which were sorted from the peripheral blood mononuclear cells in healthy donors, vitiligo and halo nevus patients. Tissue levels of chemokine receptors and CXCR3 ligands in healthy controls, vitiligo patients and halo nevus patients were determined by qRT-PCR analysis. The percentages of CXCR3 + CD4 + T and CXCR3 + CD8 + T cells from the peripheral blood samples were examined by flow cytometry. Tissue and serum hydrogen peroxide (H 2 O 2 ) concentrations were measured using H 2 O 2 assay kit. Immunohistochemistry revealed a significant T-cell response, with pronounced dermal infiltrates of CD8 + T cells in vitiligo and halo nevus. The inflammatory cytotoxic markers such as Granzyme B and Perforin were also elevated in vitiligo and halo nevus, suggesting inflammatory responses in situ. By qRT-PCR and ELISA assay, we found significantly increased expressions of the chemokine receptor CXCR3 and its ligands, especially the accumulated CXCL10 in the skin lesions of vitiligo and halo nevus. Moreover, the level of H 2 O 2 , a key player involved in regulation of the immune response was significantly upregulated in the skin lesions of vitiligo and halo nevus. In addition, the increased H 2 O 2 concentration correlated positively with CXCL10 level in skin

  10. A protein-tyrosine phosphatase with sequence similarity to the SH2 domain of the protein-tyrosine kinases.

    Science.gov (United States)

    Shen, S H; Bastien, L; Posner, B I; Chrétien, P

    1991-08-22

    The phosphorylation of proteins at tyrosine residues is critical in cellular signal transduction, neoplastic transformation and control of the mitotic cycle. These mechanisms are regulated by the activities of both protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPases). As in the PTKs, there are two classes of PTPases: membrane associated, receptor-like enzymes and soluble proteins. Here we report the isolation of a complementary DNA clone encoding a new form of soluble PTPase, PTP1C. The enzyme possesses a large noncatalytic region at the N terminus which unexpectedly contains two adjacent copies of the Src homology region 2 (the SH2 domain) found in various nonreceptor PTKs and other cytoplasmic signalling proteins. As with other SH2 sequences, the SH2 domains of PTP1C formed high-affinity complexes with the activated epidermal growth factor receptor and other phosphotyrosine-containing proteins. These results suggest that the SH2 regions in PTP1C may interact with other cellular components to modulate its own phosphatase activity against interacting substrates. PTPase activity may thus directly link growth factor receptors and other signalling proteins through protein-tyrosine phosphorylation.

  11. Similarity of recombinant human perlecan domain 1 by alternative expression systems bioactive heterogenous recombinant human perlecan D1

    DEFF Research Database (Denmark)

    Ellis, April L; Pan, Wensheng; Yang, Guang

    2010-01-01

    BACKGROUND: Heparan sulfate glycosaminoglycans are diverse components of certain proteoglycans and are known to interact with growth factors as a co-receptor necessary to induce signalling and growth factor activity. In this report we characterize heterogeneously glycosylated recombinant human...... perlecan domain 1 (HSPG2 abbreviated as rhPln.D1) synthesized in either HEK 293 cells or HUVECs by transient gene delivery using either adenoviral or expression plasmid technology. RESULTS: By SDS-PAGE analysis following anion exchange chromatography, the recombinant proteoglycans appeared to possess...... glycosaminoglycan chains ranging, in total, from 6 kDa to >90 kDa per recombinant. Immunoblot analysis of enzyme-digested high Mr rhPln.D1 demonstrated that the rhPln.D1 was synthesized as either a chondroitin sulfate or heparan sulfate proteoglycan, in an approximately 2:1 ratio, with negligible hybrids. Secondary...

  12. Evolutionary genomics of plant genes encoding N-terminal-TM-C2 domain proteins and the similar FAM62 genes and synaptotagmin genes of metazoans

    Directory of Open Access Journals (Sweden)

    Craxton Molly

    2007-07-01

    Full Text Available Abstract Background Synaptotagmin genes are found in animal genomes and are known to function in the nervous system. Genes with a similar domain architecture as well as sequence similarity to synaptotagmin C2 domains have also been found in plant genomes. The plant genes share an additional region of sequence similarity with a group of animal genes named FAM62. FAM62 genes also have a similar domain architecture. Little is known about the functions of the plant genes and animal FAM62 genes. Indeed, many members of the large and diverse Syt gene family await functional characterization. Understanding the evolutionary relationships among these genes will help to realize the full implications of functional studies and lead to improved genome annotation. Results I collected and compared plant Syt-like sequences from the primary nucleotide sequence databases at NCBI. The collection comprises six groups of plant genes conserved in embryophytes: NTMC2Type1 to NTMC2Type6. I collected and compared metazoan FAM62 sequences and identified some similar sequences from other eukaryotic lineages. I found evidence of RNA editing and alternative splicing. I compared the intron patterns of Syt genes. I also compared Rabphilin and Doc2 genes. Conclusion Genes encoding proteins with N-terminal-transmembrane-C2 domain architectures resembling synaptotagmins, are widespread in eukaryotes. A collection of these genes is presented here. The collection provides a resource for studies of intron evolution. I have classified the collection into homologous gene families according to distinctive patterns of sequence conservation and intron position. The evolutionary histories of these gene families are traceable through the appearance of family members in different eukaryotic lineages. Assuming an intron-rich eukaryotic ancestor, the conserved intron patterns distinctive of individual gene families, indicate independent origins of Syt, FAM62 and NTMC2 genes. Resemblances

  13. Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

    International Nuclear Information System (INIS)

    He, Yuan; Roth, Christian; Turkenburg, Johan P.; Davies, Gideon J.

    2013-01-01

    The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily. The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP-05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain

  14. Three-dimensional structure of a Streptomyces sviceus GNAT acetyltransferase with similarity to the C-terminal domain of the human GH84 O-GlcNAcase

    Energy Technology Data Exchange (ETDEWEB)

    He, Yuan [Northwest University, Xi’an 710069 (China); The University of York, York YO10 5DD (United Kingdom); Roth, Christian; Turkenburg, Johan P.; Davies, Gideon J., E-mail: gideon.davies@york.ac.uk [The University of York, York YO10 5DD (United Kingdom); Northwest University, Xi’an 710069 (China)

    2014-01-01

    The crystal structure of a bacterial acetyltransferase with 27% sequence identity to the C-terminal domain of human O-GlcNAcase has been solved at 1.5 Å resolution. This S. sviceus protein is compared with known GCN5-related acetyltransferases, adding to the diversity observed in this superfamily. The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP-05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain.

  15. Mutations in the FMN domain modulate MCD spectra of the heme site in the oxygenase domain of inducible nitric oxide synthase.

    Science.gov (United States)

    Sempombe, Joseph; Elmore, Bradley O; Sun, Xi; Dupont, Andrea; Ghosh, Dipak K; Guillemette, J Guy; Kirk, Martin L; Feng, Changjian

    2009-05-27

    The nitric oxide synthase (NOS) output state for NO production is a complex of the flavin mononucleotide (FMN)-binding domain and the heme domain, and thereby it facilitates the interdomain electron transfer from the FMN to the catalytic heme site. Emerging evidence suggests that interdomain FMN-heme interactions are important in the formation of the output state because they guide the docking of the FMN domain to the heme domain. In this study, notable effects of mutations in the adjacent FMN domain on the heme structure in a human iNOS bidomain oxygenase/FMN construct have been observed by using low-temperature magnetic circular dichroism (MCD) spectroscopy. The comparative MCD study of wild-type and mutant proteins clearly indicates that a properly docked FMN domain contributes to the observed L-Arg perturbation of the heme MCD spectrum in the wild-type protein and that the conserved surface residues in the FMN domain (E546 and E603) play key roles in facilitating a productive alignment of the FMN and heme domains in iNOS.

  16. Terrestrial Fe-oxide Concretions and Mars Blueberries: Comparisons of Similar Advective and Diffusive Chemical Infiltration Reaction Mechanisms

    Science.gov (United States)

    Park, A. J.; Chan, M. A.

    2006-12-01

    Abundant iron oxide concretions occurring in Navajo Sandstone of southern Utah and those discovered at Meridiani Planum, Mars share many common observable physical traits such as their spheriodal shapes, occurrence, and distribution patterns in sediments. Terrestrial concretions are products of interaction between oxygen-rich aquifer water and basin-derived reducing (iron-rich) water. Water-rock interaction simulations show that diffusion of oxygen and iron supplied by slow-moving water is a reasonable mechanism for producing observed concretion patterns. In short, southern Utah iron oxide concretions are results of Liesegang-type diffusive infiltration reactions in sediments. We propose that the formation of blueberry hematite concretions in Mars sediments followed a similar diagenetic mechanism where iron was derived from the alteration of volcanic substrate and oxygen was provided by the early Martian atmosphere. Although the terrestrial analog differs in the original host rock composition, both the terrestrial and Mars iron-oxide precipitation mechanisms utilize iron and oxygen interactions in sedimentary host rock with diffusive infiltration of solutes from two opposite sources. For the terrestrial model, slow advection of iron-rich water is an important factor that allowed pervasive and in places massive precipitation of iron-oxide concretions. In Mars, evaporative flux of water at the top of the sediment column may have produced a slow advective mass-transfer mechanism that provided a steady source and the right quantity of iron. The similarities of the terrestrial and Martian systems are demonstrated using a water-rock interaction simulator Sym.8, initially in one-dimensional systems. Boundary conditions such as oxygen content of water, partial pressure of oxygen, and supply rate of iron were varied. The results demonstrate the importance of slow advection of water and diffusive processes for producing diagenetic iron oxide concretions.

  17. Adaptor proteins intersectin 1 and 2 bind similar proline-rich ligands but are differentially recognized by SH2 domain-containing proteins.

    Directory of Open Access Journals (Sweden)

    Olga Novokhatska

    Full Text Available BACKGROUND: Scaffolding proteins of the intersectin (ITSN family, ITSN1 and ITSN2, are crucial for the initiation stage of clathrin-mediated endocytosis. These proteins are closely related but have implications in distinct pathologies. To determine how these proteins could be separated in certain cell pathways we performed a comparative study of ITSNs. METHODOLOGY/PRINCIPAL FINDINGS: We have shown that endogenous ITSN1 and ITSN2 colocalize and form a complex in cells. A structural comparison of five SH3 domains, which mediated most ITSNs protein-protein interactions, demonstrated a similarity of their ligand-binding sites. We showed that the SH3 domains of ITSN2 bound well-established interactors of ITSN1 as well as newly identified ITSNs protein partners. A search for a novel interacting interface revealed multiple tyrosines that could be phosphorylated in ITSN2. Phosphorylation of ITSN2 isoforms but not ITSN1 short isoform was observed in various cell lines. EGF stimulation of HeLa cells enhanced tyrosine phosphorylation of ITSN2 isoforms and enabled their recognition by the SH2 domains of the Fyn, Fgr and Abl1 kinases, the regulatory subunit of PI3K, the adaptor proteins Grb2 and Crk, and phospholipase C gamma. The SH2 domains mentioned were unable to bind ITSN1 short isoform. CONCLUSIONS/SIGNIFICANCE: Our results indicate that during evolution of vertebrates ITSN2 acquired a novel protein-interaction interface that allows its specific recognition by the SH2 domains of signaling proteins. We propose that these data could be important to understand the functional diversity of paralogous ITSN proteins.

  18. Activation of Endothelial Nitric Oxide (eNOS Occurs through Different Membrane Domains in Endothelial Cells.

    Directory of Open Access Journals (Sweden)

    Jason Tran

    Full Text Available Endothelial cells respond to a large range of stimuli including circulating lipoproteins, growth factors and changes in haemodynamic mechanical forces to regulate the activity of endothelial nitric oxide synthase (eNOS and maintain blood pressure. While many signalling pathways have been mapped, the identities of membrane domains through which these signals are transmitted are less well characterized. Here, we manipulated bovine aortic endothelial cells (BAEC with cholesterol and the oxysterol 7-ketocholesterol (7KC. Using a range of microscopy techniques including confocal, 2-photon, super-resolution and electron microscopy, we found that sterol enrichment had differential effects on eNOS and caveolin-1 (Cav1 colocalisation, membrane order of the plasma membrane, caveolae numbers and Cav1 clustering. We found a correlation between cholesterol-induced condensation of the plasma membrane and enhanced high density lipoprotein (HDL-induced eNOS activity and phosphorylation suggesting that cholesterol domains, but not individual caveolae, mediate HDL stimulation of eNOS. Vascular endothelial growth factor (VEGF-induced and shear stress-induced eNOS activity was relatively independent of membrane order and may be predominantly controlled by the number of caveolae on the cell surface. Taken together, our data suggest that signals that activate and phosphorylate eNOS are transmitted through distinct membrane domains in endothelial cells.

  19. Similarity in the superconducting properties of chalcogenides, cuprate oxides and fullerides

    International Nuclear Information System (INIS)

    Tsendin, K.D.; Popov, B.P.; Denisov, D.V.

    2004-01-01

    The idea of Anderson pairs has been put forward for explanation of many extraordinary properties of chalcogenides glassy semiconductors. Recent decades made obvious that these pairs localized on the centers with negative effective correlation energy (negative-U centers) really exist in chalcogenides. If the concentration of negative-U centers is enough to create the pair band states, this can lead to superconductivity because Anderson pairs are Bose particles. In the present paper we show that several puzzling superconductivity properties of chalcogenides, high-temperature cuprate superconductors and fullerides are similar for these three groups of materials and can be naturally explained in the frame of negative-U centers model of superconductivity

  20. Weight of Polyethylene Wear Particles is Similar in TKAs with Oxidized Zirconium and Cobalt-chrome Prostheses

    Science.gov (United States)

    Kim, Jun-Shik; Huh, Wansoo; Lee, Kwang-Hoon

    2009-01-01

    Background The greater lubricity and resistance to scratching of oxidized zirconium femoral components are expected to result in less polyethylene wear than cobalt-chrome femoral components. Questions/purposes We examined polyethylene wear particles in synovial fluid and compared the weight, size (equivalent circle diameter), and shape (aspect ratio) of polyethylene wear particles in knees with an oxidized zirconium femoral component with those in knees with a cobalt-chrome femoral component. Patients and Methods One hundred patients received an oxidized zirconium femoral component in one knee and a cobalt-chrome femoral component in the other. There were 73 women and 27 men with a mean age of 55.6 years (range, 44–60 years). The minimum followup was 5 years (mean, 5.5 years; range, 5–6 years). Polyethylene wear particles were analyzed using thermogravimetric methods and scanning electron microscopy. Results The weight of polyethylene wear particles produced at the bearing surface was 0.0223 ± 0.0054 g in 1 g synovial fluid in patients with an oxidized zirconium femoral component and 0.0228 ± 0.0062 g in patients with a cobalt-chrome femoral component. Size and shape of polyethylene wear particles were 0.59 ± 0.05 μm and 1.21 ± 0.24, respectively, in the patients with an oxidized zirconium femoral component and 0.52 ± 0.03 μm and 1.27 ± 0.31, respectively, in the patients with a cobalt-chrome femoral component. Knee Society knee and function scores, radiographic results, and complication rate were similar between the knees with an oxidized zirconium and cobalt-chrome femoral component. Conclusions The weight, size, and shape of polyethylene wear particles were similar in the knees with an oxidized zirconium and a cobalt-chrome femoral component. We found the theoretical advantages of this surface did not provide the actual advantage. Level of Evidence Level I, therapeutic study. See the guidelines for Authors for a complete

  1. RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins

    International Nuclear Information System (INIS)

    Hoffman, D.W.; Query, C.C.; Golden, B.L.; White, S.W.; Keene, J.D.

    1991-01-01

    An RNA recognition motif (RRM) of ∼80 amino acids constitutes the core of RNA-binding domains found in a large family of proteins involved in RNA processing. The U1 RNA-binding domain of the A protein component of the human U1 small nuclear ribonucleoprotein (RNP), which encompasses the RRM sequence, was analyzed by using NMR spectroscopy. The domain of the A protein is a highly stable monomer in solution consisting of four antiparallel β-strands and two α-helices. The highly conserved RNP1 and RNP2 consensus sequences, containing residues previously suggested to be involved in nucleic acid binding, are juxtaposed in adjacent β-strands. Conserved aromatic side chains that are critical for RNA binding are clustered on the surface to the molecule adjacent to a variable loop that influences recognition of specific RNA sequences. The secondary structure and topology of the RRM are similar to those of ribosomal proteins L12 and L30, suggesting a distant evolutionary relationship between these two types of RNA-associated proteins

  2. Domain similarity based orthology detection

    OpenAIRE

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

    2015-01-01

    Background Orthologous protein detection software mostly uses pairwise comparisons of amino-acid sequences to assert whether two proteins are orthologous or not. Accordingly, when the number of sequences for comparison increases, the number of comparisons to compute grows in a quadratic order. A current challenge of bioinformatic research, especially when taking into account the increasing number of sequenced organisms available, is to make this ever-growing number of comparisons computationa...

  3. Oxidation of the N-terminal domain of the wheat metallothionein Ec -1 leads to the formation of three distinct disulfide bridges.

    Science.gov (United States)

    Tarasava, Katsiaryna; Chesnov, Serge; Freisinger, Eva

    2016-05-01

    Metallothioneins (MTs) are low molecular weight proteins, characterized by a high cysteine content and the ability to coordinate large amounts of d(10) metal ions, for example, Zn(II), Cd(II), and Cu(I), in form of metal-thiolate clusters. Depending on intracellular conditions such as redox potential or metal ion concentrations, MTs can occur in various states ranging from the fully metal-loaded holo- to the metal-free apo-form. The Cys thiolate groups in the apo-form can be either reduced or be involved in disulfide bridges. Although oxidation-mediated Zn(II) release might be a possible mechanism for the regulation of Zn(II) availability by MTs, no concise information regarding the associated pathways and the structure of oxidized apo-MT forms is available. Using the well-studied Zn2 γ-Ec -1 domain of the wheat Zn6 Ec -1 MT we attempt here to answer several question regarding the structure and biophysical properties of oxidized MT forms, such as: (1) does disulfide bond formation increase the stability against proteolysis, (2) is the overall peptide backbone fold similar for the holo- and the oxidized apo-MT form, and (3) are disulfide bridges specifically or randomly formed? Our investigations show that oxidation leads to three distinct disulfide bridges independently of the applied oxidation conditions and of the initial species used for oxidation, that is, the apo- or the holo-form. In addition, the oxidized apo-form is as stable against proteolysis as Zn2 γ-Ec -1, rendering the currently assumed degradation of oxidized MTs unlikely and suggesting a role of the oxidation process for the extension of protein lifetime in absence of sufficient amounts of metal ions. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 295-308, 2016. © 2016 Wiley Periodicals, Inc.

  4. Spin Hall driven domain wall motion in magnetic bilayers coupled by a magnetic oxide interlayer

    Science.gov (United States)

    Liu, Yang; Furuta, Masaki; Zhu, Jian-Gang Jimmy

    2018-05-01

    mCell, previously proposed by our group, is a four-terminal magnetoresistive device with isolated write- and read-paths for all-spin logic and memory applications. A mCell requires an electric-insulating magnetic layer to couple the spin Hall driven write-path to the magnetic free layer of the read-path. Both paths are magnetic layers with perpendicular anisotropy and their perpendicularly oriented magnetization needs to be maintained with this insertion layer. We have developed a magnetic oxide (FeOx) insertion layer to serve for these purposes. We show that the FeOx insertion layer provides sufficient magnetic coupling between adjacent perpendicular magnetic layers. Resistance measurement shows that this magnetic oxide layer can act as an electric-insulating layer. In addition, spin Hall driven domain wall motion in magnetic bi-layers coupled by the FeOx insertion layer is significantly enhanced compared to that in magnetic single layer; it also requires low voltage threshold that poses possibility for power-efficient device applications.

  5. Crystallization of the NADH-oxidizing domain of the Na+-translocating NADH:ubiquinone oxidoreductase from Vibrio cholerae

    International Nuclear Information System (INIS)

    Tao, Minli; Türk, Karin; Diez, Joachim; Grütter, Markus G.; Fritz, Günter; Steuber, Julia

    2006-01-01

    The FAD domain of the NqrF subunit from the Na + -translocating NADH dehydrogenase from V. cholerae has been purified and crystallized. A complete data set was recorded at 3.1 Å. The Na + -translocating NADH:quinone oxidoreductase (Na + -NQR) from pathogenic and marine bacteria is a respiratory complex that couples the exergonic oxidation of NADH by quinone to the transport of Na + across the membrane. The NqrF subunit oxidizes NADH and transfers the electrons to other redox cofactors in the enzyme. The FAD-containing domain of NqrF has been expressed, purified and crystallized. The purified NqrF FAD domain exhibited high rates of NADH oxidation and contained stoichiometric amounts of the FAD cofactor. Initial crystallization of the flavin domain was achieved by the sitting-drop technique using a Cartesian MicroSys4000 robot. Optimization of the crystallization conditions yielded yellow hexagonal crystals with dimensions of 30 × 30 × 70 µm. The protein mainly crystallizes in long hexagonal needles with a diameter of up to 30 µm. Crystals diffract to 2.8 Å and belong to space group P622, with unit-cell parameters a = b = 145.3, c = 90.2 Å, α = β = 90, γ = 120°

  6. Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

    Directory of Open Access Journals (Sweden)

    R. E. Schwartz

    2010-06-01

    Full Text Available Submicron particles collected at Whistler, British Columbia, at 1020 m a.s.l. during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR and X-ray fluorescence (XRF techniques for organic functional groups (OFG and elemental composition. Organic mass (OM concentrations ranged from less than 0.5 to 3.1 μg m−3, with a project mean and standard deviation of 1.3±1.0 μg m−3 and 0.21±0.16 μg m−3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and <1% of the average organic aerosol composition, respectively. Measurements of volatile organic compounds (VOC, including isoprene and monoterpenes from biogenic VOC (BVOC emissions and their oxidation products (methyl-vinylketone / methacrolein, MVK/MACR, were made using co-located proton transfer reaction mass spectrometry (PTR-MS. We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 21% organic hydroxyl, 16% ketone, and 6% amine groups was similar to that of secondary organic aerosol (SOA reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional

  7. Biogenic oxidized organic functional groups in aerosol particles from a mountain forest site and their similarities to laboratory chamber products

    Science.gov (United States)

    Schwartz, R. E.; Russell, L. M.; Sjostedt, S. J.; Vlasenko, A.; Slowik, J. G.; Abbatt, J. P. D.; MacDonald, A. M.; Li, S. M.; Liggio, J.; Toom-Sauntry, D.; Leaitch, W. R.

    2010-06-01

    Submicron particles collected at Whistler, British Columbia, at 1020 m a.s.l. during May and June 2008 on Teflon filters were analyzed by Fourier transform infrared (FTIR) and X-ray fluorescence (XRF) techniques for organic functional groups (OFG) and elemental composition. Organic mass (OM) concentrations ranged from less than 0.5 to 3.1 μg m-3, with a project mean and standard deviation of 1.3±1.0 μg m-3 and 0.21±0.16 μg m-3 for OM and sulfate, respectively. On average, organic hydroxyl, alkane, and carboxylic acid groups represented 34%, 33%, and 23% of OM, respectively. Ketone, amine and organosulfate groups constituted 6%, 5%, and volatile organic compounds (VOC), including isoprene and monoterpenes from biogenic VOC (BVOC) emissions and their oxidation products (methyl-vinylketone / methacrolein, MVK/MACR), were made using co-located proton transfer reaction mass spectrometry (PTR-MS). We present chemically-specific evidence of OFG associated with BVOC emissions. Positive matrix factorization (PMF) analysis attributed 65% of the campaign OM to biogenic sources, based on the correlations of one factor to monoterpenes and MVK/MACR. The remaining fraction was attributed to anthropogenic sources based on a correlation to sulfate. The functional group composition of the biogenic factor (consisting of 32% alkane, 25% carboxylic acid, 21% organic hydroxyl, 16% ketone, and 6% amine groups) was similar to that of secondary organic aerosol (SOA) reported from the oxidation of BVOCs in laboratory chamber studies, providing evidence that the magnitude and chemical composition of biogenic SOA simulated in the laboratory is similar to that found in actual atmospheric conditions. The biogenic factor OM is also correlated to dust elements, indicating that dust may act as a non-acidic SOA sink. This role is supported by the organic functional group composition and morphology of single particles, which were analyzed by scanning transmission X-ray microscopy near edge X

  8. Refolding and characterization of the functional ligand-binding domain of human lectin-like oxidized LDL receptor.

    Science.gov (United States)

    Xie, Qiuhong; Matsunaga, Shigeru; Shi, Xiaohua; Ogawa, Setsuko; Niimi, Setsuko; Wen, Zhesheng; Tokuyasu, Ken; Machida, Sachiko

    2003-11-01

    Lectin-like oxidized low-density lipoprotein receptor (LOX-1), a type II membrane protein that can recognize a variety of structurally unrelated macromolecules, plays an important role in host defense and is implicated in atherogenesis. To understand the interaction between human LOX-1 and its ligands, in this study the functional C-type lectin-like domain (CTLD) of LOX-1 was reconstituted at high efficiency from inactive aggregates in Escherichia coli using a refolding technique based on an artificial chaperone. The CD spectra of the purified domain suggested that the domain has alpha-helical structure and the blue shift of Trp residues was observed on refolding of the domain. Like wild-type hLOX-1, the refolded CTLD domain was able to bind modified LDL. Thus, even though CTLD contains six Cys residues that form disulfide bonds, it recovered its specific binding ability on refolding. This suggests that the correct disulfide bonds in CTLD were formed by the artificial chaperone technique. Although the domain lacked N-glycosylation, it showed high affinity for its ligand in surface plasmon resonance experiments. Thus, unglycosylated CTLD is sufficient for binding modified LDL.

  9. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

    Directory of Open Access Journals (Sweden)

    Katarzyna Marta Bocian-Ostrzycka

    2015-10-01

    Full Text Available Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595 with a -propeller structure. The aim of presented work was to assess relations between HP0231 structure and function.We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobacter cysteine-rich protein C, a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in E. coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (Escherichia coli DsbA protein were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity.

  10. Visualized effect of oxidation on magnetic recording fidelity in pseudo-single-domain magnetite particles

    DEFF Research Database (Denmark)

    Almeida, Trevor P.; Kasama, Takeshi; Muxworthy, Adrian R.

    2014-01-01

    fidelity of Fe3O4 particles is greatly diminished over time by progressive oxidation to less magnetic iron oxides, such as maghemite (γ-Fe2O3), with consequent alteration of remanent magnetization potentially having important geological significance. Here we use the complementary techniques...... of environmental transmission electron microscopy and off-axis electron holography to induce and visualize the effects of oxidation on the magnetization of individual nanoscale Fe3O4 particles as they transform towards γ-Fe2O3. Magnetic induction maps demonstrate a change in both strength and direction of remanent...... magnetization within Fe3O4 particles in the size range dominant in rocks, confirming that oxidation can modify the original stored magnetic information....

  11. Formation and effect of orientation domains in layered oxide cathodes of lithium-ion batteries

    International Nuclear Information System (INIS)

    Jarvis, Karalee A.; Wang, Chih-Chieh; Knight, James C.; Rabenberg, Lew; Manthiram, Arumugam; Ferreira, Paulo J.

    2016-01-01

    We show that in layered oxides that are employed as cathodes in lithium-ion batteries, the cation layers can order on different {111} NaCl planes within a single particle, which makes the lithium layer discontinuous across a particle. The findings challenge previous assertions that lithium undergoes 2-D diffusion in layered oxides and the data provide new insights into the decrease in rate capabilities for some layered oxides. Therefore, it is critically important to understand how these discontinuities form and how the loss of 2-D diffusion impacts the overall performance of the layered oxide cathode materials. Employing X-ray diffraction (XRD) and aberration-corrected scanning transmission electron microscopy (STEM), we find that as the material transitions from a disordered to an ordered state, it forms four orientation variants corresponding to the four {111} NaCl planes. This transition is not intrinsic to all layered oxides and appears to be more strongly affected by nickel. Furthermore, with energy dispersive spectroscopy (EDS), we show that there is an increase in the nickel concentration at the interface between each orientation variant. This reduces the rate of lithium diffusion, negatively affects the rate capability, and could be contributing to the overall capacity fade.

  12. CO oxidation on PtSn nanoparticle catalysts occurs at the interface of Pt and Sn oxide domains formed under reaction conditions

    KAUST Repository

    Michalak, William D.

    2014-04-01

    The barrier to CO oxidation on Pt catalysts is the strongly bound adsorbed CO, which inhibits O2 adsorption and hinders CO2 formation. Using reaction studies and in situ X-ray spectroscopy with colloidally prepared, monodisperse ∼2 nm Pt and PtSn nanoparticle catalysts, we show that the addition of Sn to Pt provides distinctly different reaction sites and a more efficient reaction mechanism for CO oxidation compared to pure Pt catalysts. To probe the influence of Sn, we intentionally poisoned the Pt component of the nanoparticle catalysts using a CO-rich atmosphere. With a reaction environment comprised of 100 Torr CO and 40 Torr O2 and a temperature range between 200 and 300 C, Pt and PtSn catalysts exhibited activation barriers for CO2 formation of 133 kJ/mol and 35 kJ/mol, respectively. While pure Sn is readily oxidized and is not active for CO oxidation, the addition of Sn to Pt provides an active site for O2 adsorption that is important when Pt is covered with CO. Sn oxide was identified as the active Sn species under reaction conditions by in situ ambient pressure X-ray photoelectron spectroscopy measurements. While chemical signatures of Pt and Sn indicated intermixed metallic components under reducing conditions, Pt and Sn were found to reversibly separate into isolated domains of Pt and oxidic Sn on the nanoparticle surface under reaction conditions of 100 mTorr CO and 40 mTorr O2 between temperatures of 200-275 C. Under these conditions, PtSn catalysts exhibited apparent reaction orders in O2 for CO 2 production that were 0.5 and lower with increasing partial pressures. These reaction orders contrast the first-order dependence in O 2 known for pure Pt. The differences in activation barriers, non-first-order dependence in O2, and the presence of a partially oxidized Sn indicate that the enhanced activity is due to a reaction mechanism that occurs at a Pt/Sn oxide interface present at the nanoparticle surface. © 2014 Published by Elsevier Inc.

  13. Differences in inflammation and acute phase response but similar genotoxicity in mice following pulmonary exposure to graphene oxide and reduced graphene oxide

    DEFF Research Database (Denmark)

    Bengtson, Stefan; Knudsen, Kristina Bram; Kyjovska, Zdenka O.

    2017-01-01

    assessed exposure levels of particulate matter emitted during production of graphene in a clean room and in a normal industrial environment using chemical vapour deposition. Toxicity was evaluated at day 1, 3, 28 and 90 days (18, 54 and 162 μg/mouse), except for GO exposed mice at day 28 and 90 where only......We investigated toxicity of 2-3 layered >1 μm sized graphene oxide (GO) and reduced graphene oxide (rGO) in mice following single intratracheal exposure with respect to pulmonary inflammation, acute phase response (biomarker for risk of cardiovascular disease) and genotoxicity. In addition, we...

  14. Local Symmetry and Domain Patterns: Ordering Phenomena in Transition-Metal Oxides

    OpenAIRE

    Buchholz, Marcel

    2013-01-01

    Transition-metal oxides (TMOs) show rich phase diagrams with various magnetic and electronic phases that arise from the complex interplay between spin, charge, orbital, and lattice degrees of freedom. The most prominent class of materials, which has attracted a lot of attention in the last decades, are probably high-temperature superconductors (HTS), in which the resitivity drops to zero below a critical temperature. Further examples are different kind of complex ordering phenomena, for examp...

  15. Glutaredoxins Grx4 and Grx3 of Saccharomyces cerevisiae play a role in actin dynamics through their Trx domains, which contributes to oxidative stress resistance.

    Science.gov (United States)

    Pujol-Carrion, Nuria; de la Torre-Ruiz, Maria Angeles

    2010-12-01

    Grx3 and Grx4 are two monothiol glutaredoxins of Saccharomyces cerevisiae that have previously been characterized as regulators of Aft1 localization and therefore of iron homeostasis. In this study, we present data showing that both Grx3 and Grx4 have new roles in actin cytoskeleton remodeling and in cellular defenses against oxidative stress caused by reactive oxygen species (ROS) accumulation. The Grx4 protein plays a unique role in the maintenance of actin cable integrity, which is independent of its role in the transcriptional regulation of Aft1. Grx3 plays an additive and redundant role, in combination with Grx4, in the organization of the actin cytoskeleton, both under normal conditions and in response to external oxidative stress. Each Grx3 and Grx4 protein contains a thioredoxin domain sequence (Trx), followed by a glutaredoxin domain (Grx). We performed functional analyses of each of the two domains and characterized different functions for them. Each of the two Grx domains plays a role in ROS detoxification and cell viability. However, the Trx domain of each Grx4 and Grx3 protein acts independently of its respective Grx domain in a novel function that involves the polarization of the actin cytoskeleton, which also determines cell resistance against oxidative conditions. Finally, we present experimental evidence demonstrating that Grx4 behaves as an antioxidant protein increasing cell survival under conditions of oxidative stress.

  16. Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors.

    Science.gov (United States)

    Kumar, Sivakumar Prasanth; Jasrai, Yogesh T; Mehta, Vijay P; Pandya, Himanshu A

    2015-01-01

    Quantitative pharmacophore hypothesis combines the 3D spatial arrangement of pharmacophore features with biological activities of the ligand data-set and predicts the activities of geometrically and/or pharmacophoric similar ligands. Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands. Towards this focus, we describe a ligand-based computational procedure to introduce flexibility in aligning the small molecules and generating a pharmacophore hypothesis without geometrical constraints to define pharmacophore space, enriched with chemical features necessary to elucidate common pharmacophore hypotheses (CPHs). Maximal common substructure (MCS)-based alignment method was adopted to guide the alignment of carbon molecules, deciphered the MCS atom connectivity to cluster molecules in bins and subsequently, calculated the pharmacophore similarity matrix with the bin-specific reference molecules. After alignment, the carbon molecules were enriched with original atoms in their respective positions and conventional pharmacophore features were perceived. Distance-based pharmacophoric descriptors were enumerated by computing the interdistance between perceived features and MCS-aligned 'centroid' position. The descriptor set and biological activities were used to develop support vector machine models to predict the activities of the external test set. Finally, fitness score was estimated based on pharmacophore similarity with its bin-specific reference molecules to recognize the best and poor alignments and, also with each reference molecule to predict outliers of the quantitative hypothesis model. We applied this procedure to a diverse data-set of 40 HIV-1 integrase inhibitors and discussed its effectiveness with the reported CPH model.

  17. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    OpenAIRE

    Bolton, Michael J; Garry, Robert F

    2011-01-01

    Abstract Background The surface glycoprotein (SU, gp120) of the human immunodeficiency virus (HIV) must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP) to bind the Duffy Antigen Receptor for Chemokines (DARC) and invade reticulocytes. Results Variable loop 3 (V3) of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, ...

  18. Architecture of the nitric-oxide synthase holoenzyme reveals large conformational changes and a calmodulin-driven release of the FMN domain.

    Science.gov (United States)

    Yokom, Adam L; Morishima, Yoshihiro; Lau, Miranda; Su, Min; Glukhova, Alisa; Osawa, Yoichi; Southworth, Daniel R

    2014-06-13

    Nitric-oxide synthase (NOS) is required in mammals to generate NO for regulating blood pressure, synaptic response, and immune defense. NOS is a large homodimer with well characterized reductase and oxygenase domains that coordinate a multistep, interdomain electron transfer mechanism to oxidize l-arginine and generate NO. Ca(2+)-calmodulin (CaM) binds between the reductase and oxygenase domains to activate NO synthesis. Although NOS has long been proposed to adopt distinct conformations that alternate between interflavin and FMN-heme electron transfer steps, structures of the holoenzyme have remained elusive and the CaM-bound arrangement is unknown. Here we have applied single particle electron microscopy (EM) methods to characterize the full-length of the neuronal isoform (nNOS) complex and determine the structural mechanism of CaM activation. We have identified that nNOS adopts an ensemble of open and closed conformational states and that CaM binding induces a dramatic rearrangement of the reductase domain. Our three-dimensional reconstruction of the intact nNOS-CaM complex reveals a closed conformation and a cross-monomer arrangement with the FMN domain rotated away from the NADPH-FAD center, toward the oxygenase dimer. This work captures, for the first time, the reductase-oxygenase structural arrangement and the CaM-dependent release of the FMN domain that coordinates to drive electron transfer across the domains during catalysis. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Terahertz time domain spectroscopy of amorphous and crystalline aluminum oxide nanostructures synthesized by thermal decomposition of AACH

    Energy Technology Data Exchange (ETDEWEB)

    Mehboob, Shoaib, E-mail: smehboob@pieas.edu.pk [National Center for Nanotechnology, Department of Metallurgy and Materials Engineering, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore 45650, Islamabad (Pakistan); Mehmood, Mazhar [National Center for Nanotechnology, Department of Metallurgy and Materials Engineering, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore 45650, Islamabad (Pakistan); Ahmed, Mushtaq [National Institute of Lasers and Optronics (NILOP), Nilore 45650, Islamabad (Pakistan); Ahmad, Jamil; Tanvir, Muhammad Tauseef [National Center for Nanotechnology, Department of Metallurgy and Materials Engineering, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore 45650, Islamabad (Pakistan); Ahmad, Izhar [National Institute of Lasers and Optronics (NILOP), Nilore 45650, Islamabad (Pakistan); Hassan, Syed Mujtaba ul [National Center for Nanotechnology, Department of Metallurgy and Materials Engineering, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore 45650, Islamabad (Pakistan)

    2017-04-15

    The objective of this work is to study the changes in optical and dielectric properties with the transformation of aluminum ammonium carbonate hydroxide (AACH) to α-alumina, using terahertz time domain spectroscopy (THz-TDS). The nanostructured AACH was synthesized by hydrothermal treatment of the raw chemicals at 140 °C for 12 h. This AACH was then calcined at different temperatures. The AACH was decomposed to amorphous phase at 400 °C and transformed to δ* + α-alumina at 1000 °C. Finally, the crystalline α-alumina was achieved at 1200 °C. X-ray diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy were employed to identify the phases formed after calcination. The morphology of samples was studied using scanning electron microscopy (SEM), which revealed that the AACH sample had rod-like morphology which was retained in the calcined samples. THz-TDS measurements showed that AACH had lowest refractive index in the frequency range of measurements. The refractive index at 0.1 THZ increased from 2.41 for AACH to 2.58 for the amorphous phase and to 2.87 for the crystalline α-alumina. The real part of complex permittivity increased with the calcination temperature. Further, the absorption coefficient was highest for AACH, which reduced with calcination temperature. The amorphous phase had higher absorption coefficient than the crystalline alumina. - Highlights: • Aluminum oxide nanostructures were obtained by thermal decomposition of AACH. • Crystalline phases of aluminum oxide have higher refractive index than that of amorphous phase. • The removal of heavier ionic species led to the lower absorption of THz radiations.

  20. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    OpenAIRE

    Bolton, Michael J; Garry, Robert F

    2011-01-01

    Abstract Background The HIV surface glycoprotein gp120 (SU, gp120) and the Plasmodium vivax Duffy binding protein (PvDBP) bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM). Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infectio...

  1. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    Directory of Open Access Journals (Sweden)

    Garry Robert F

    2011-01-01

    Full Text Available Abstract Background The surface glycoprotein (SU, gp120 of the human immunodeficiency virus (HIV must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP to bind the Duffy Antigen Receptor for Chemokines (DARC and invade reticulocytes. Results Variable loop 3 (V3 of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, for DARC binding and contained a consensus heparin binding site essential for DARC binding. Both HIV-1 and P. vivax can be blocked from binding to their chemokine receptors by the chemokine, RANTES and its analog AOP-RANTES. Site directed mutagenesis of the heparin binding motif in members of the DBP family, the P. knowlesi alpha, beta and gamma proteins abrogated their binding to erythrocytes. Positively charged residues within domain 1 are required for binding of P. vivax and P. knowlesi erythrocyte binding proteins. Conclusion A heparin binding site motif in members of the DBP family may form part of a conserved erythrocyte receptor binding pocket.

  2. Distinctive functions of Syk N-terminal and C-terminal SH2 domains in the signaling cascade elicited by oxidative stress in B cells.

    Science.gov (United States)

    Ding, J; Takano, T; Hermann, P; Gao, S; Han, W; Noda, C; Yanagi, S; Yamamura, H

    2000-05-01

    Syk plays a crucial role in the transduction of oxidative stress signaling. In this paper, we investigated the roles of Src homology 2 (SH2) domains of Syk in oxidative stress signaling, using Syk-negative DT40 cells expressing the N- or C-terminal SH2 domain mutant [mSH2(N) or mSH2(C)] of Syk. Tyrosine phosphorylation of Syk in cells expressing mSH2(N) Syk after H(2)O(2) treatment was higher than that in cells expressing wild-type Syk or mSH2(C) Syk. The tyrosine phosphorylation of wild-type Syk and mSH2(C) Syk, but not that of mSH2(N), was sensitive to PP2, a specific inhibitor of Src-family protein-tyrosine kinase. In oxidative stress, the C-terminal SH2 domain of Syk was demonstrated to be required for induction of tyrosine phosphorylation of cellular proteins, phospholipase C (PLC)-gamma2 phosphorylation, inositol 1,4, 5-triphosphate (IP(3)) generation, Ca(2)(+) release from intracellular stores, and c-Jun N-terminal kinase activation. In contrast, in mSH2(N) Syk-expressing cells, tyrosine phosphorylation of intracellular proteins including PLC-gamma2 was markedly induced in oxidative stress. The enhanced phosphorylation of mSH2(N) Syk and PLC-gamma2, however, did not link to Ca(2)(+) mobilization from intracellular pools and IP(3) generation. Thus, the N- and C-terminal SH2 domains of Syk possess distinctive functions in oxidative stress signaling.

  3. Doping profile measurements in silicon using terahertz time domain spectroscopy (THz-TDS) via electrochemical anodic oxidation

    Science.gov (United States)

    Tulsyan, Gaurav

    Doping profiles are engineered to manipulate device properties and to determine electrical performances of microelectronic devices frequently. To support engineering studies afterward, essential information is usually required from physically characterized doping profiles. Secondary Ion Mass Spectrometry (SIMS), Spreading Resistance Profiling (SRP) and Electrochemical Capacitance Voltage (ECV) profiling are standard techniques for now to map profile. SIMS yields a chemical doping profile via ion sputtering process and owns a better resolution, whereas ECV and SRP produce an electrical doping profile detecting free carriers in microelectronic devices. The major difference between electrical and chemical doping profiles is at heavily doped regions greater than 1020 atoms/cm3. At the profile region over the solubility limit, inactive dopants induce a flat plateau and detected by electrical measurements only. Destructive techniques are usually designed as stand-alone systems to study impurities. For an in-situ process control purpose, non-contact methods, such as ellipsometry and non-contact capacitance voltage (CV) techniques are current under development. In this theses work, terahertz time domain spectroscopy (THz-TDS) is utilized to achieve electrical doping profile in both destructive and non-contact manners. In recent years the Terahertz group at Rochester Institute Technology developed several techniques that use terahertz pulses to non-destructively map doping profiles. In this thesis, we study a destructive but potentially higher resolution version of the terahertz based approach to map the profile of activated dopants and augment the non-destructive approaches already developed. The basic idea of the profile mapping approach developed in this MS thesis is to anodize, and thus oxidize to silicon dioxide, thin layers (down to below 10 nm) of the wafer with the doping profile to be mapped. Since the dopants atoms and any free carriers in the silicon oxide thin

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

    Science.gov (United States)

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

    1995-04-01

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

  5. CLA isomer t10,c12 induce oxidation and apoptosis in 3t3 adipocyte cells in a similar effect as omega-3 linolenic acid and DHA.

    Directory of Open Access Journals (Sweden)

    Jon Meadus

    2017-02-01

    Full Text Available Background: Commercial conjugated linoleic acid (CLA dietary supplements contain an equal mixture of the C18:2 isomers, cis-9trans-11 and trans-10cis-12. Predominantly, CLA-c9t11 occurs naturally in meat and dairy products at ~ 0.5% of total fat , whereas CLA-t10c12 occurs at >0.1%. Recent studies show that CLA-c9t11 generally promotes lipid accumulation but CLA-t10c12 may inhibit lipid accumulation and may also promote inflammation. The omega-3 fatty acids α-linolenic acid (C18:3n-3 and docosahexaenoic acid (DHA have also been observed to inhibit lipid accumulation and effect inflammation; therefore we examined the effects of the two main isomersof CLA and omega -3 fatty acids C18:3n-3 and DHA at the molecular levelto determine if they are causing similar oxidative stresses.Methods:Purified CLA-c9t11 and CLA-t10c12 were added to 3T3 cells induced into mature adipocyte cultures at 100uM concentrations and compared with 100uM C18:3n-3(α-linolenic acid and 50uM docosahexaenoic acid (DHA to observe their effect on growth, gene transcription and general oxidation. The results of multiple separate trials were averaged and compared for significance at levels of P< 0.05, using one way ANOVA and Student’s t-test.Results:C18:3n-3, DHA and CLA-t10c12inhibited 3T3 adipose cell growth and caused a significant increase in lipid hydro peroxide activity. CLA-t10c12 and c9t11 increased AFABP, FAS and ACOX1 mRNA gene expression but DHA and C18:3n-3decreased the same mRNAs. CLA-c9t11 but not the t10c12 stimulated adipoQ expression even though; CLA-c9t11 had only a slightly greater affinity for PPARγ than CLA-t10c12, according to TR-FRET assays. The expression of the xenobiotic metabolism genes, aldo-keto reduct as 1c1 (akr1c1, superoxide dismutase (SODand inflammation chemokine secretions of eotaxin (CCL11, Rantes (CCL5, MIG (CCL9 and MCP-1 were increased by DHA, C18:3n-3and CLA-t10c12 but not CLA-c9t11. This correlated with an increase in apoptosis factors

  6. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    Directory of Open Access Journals (Sweden)

    Bolton Michael J

    2011-11-01

    Full Text Available Abstract Background The HIV surface glycoprotein gp120 (SU, gp120 and the Plasmodium vivax Duffy binding protein (PvDBP bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM. Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infection of erythrocytes and DBP binding to the Duffy Antigen Receptor for Chemokines (DARC. A peptide including the HBM of PvDBP had similar affinity for heparin as RANTES and V3 loop peptides, and could be specifically inhibited from heparin binding by the same polyanions that inhibit DBP binding to DARC. However, some V3 peptides can competitively inhibit RANTES binding to heparin, but not the PvDBP HBM peptide. Three other members of the DBP family have an HBM sequence that is necessary for erythrocyte binding, however only the protein which binds to DARC, the P. knowlesi alpha protein, is inhibited by heparin from binding to erythrocytes. Heparitinase digestion does not affect the binding of DBP to erythrocytes. Conclusion The HBMs of DBPs that bind to DARC have similar heparin binding affinities as some V3 loop peptides and chemokines, are responsible for specific sulfated polysaccharide inhibition of parasite binding and invasion of red blood cells, and are more likely to bind to negative charges on the receptor than cell surface glycosaminoglycans.

  7. Kinetics and mechanisms of the oxide film growth on the surface of α-Fe in transitional domains

    International Nuclear Information System (INIS)

    Mukhambetov, D.G.; Berber, N.N.; Kargin, D.B.; Chalaya, O.V.

    2003-01-01

    The object of this work was to study the kinetics of the α-Fe surface oxidation with prevailing cubic texture at temperatures of 450-500 deg. C. The basic conformity to natural laws and mechanisms of the two-phase thin oxide films grows are determined. (author)

  8. Examining the similarities and differences of OMERACT core sets using the ICF: first step towards an improved domain specification and development of an item pool to measure functioning and health.

    Science.gov (United States)

    Escorpizo, Reuben; Boers, Maarten; Stucki, Gerold; Boonen, Annelies

    2011-08-01

    To contribute to the discussion on a common approach for domain selection in the Outcomes in Rheumatology Clinical Trials (OMERACT) process. First, this article reports on the consistency in the selection and names of the domains of the current OMERACT core set, and next on the comparability of the specifications of concepts that are relevant within the domains. For this purpose, a convenience sample of 4 OMERACT core sets was used: rheumatoid arthritis (RA), psoriatic arthritis (PsA), longitudinal observational studies (LOS) in rheumatology, and ankylosing spondylitis (AS). Domains from the different core sets were compared directly. To be able to compare the specific content of the domains, the concepts contained in the questionnaires that were considered or proposed to measure the domains were identified and linked to the category of the International Classification of Functioning, Disability, and Health (ICF) that best fit that construct. Large differences in the domains, and lack of domain definitions, were noted among the 4 OMERACT core sets. When comparing the concepts in the questionnaires that represent the domains, core sets differed also in the number and type of constructs that were addressed within each of the domains. Especially for the specification of the concepts within the domains Discomfort and Disability, the ICF proved to be useful as external reference to classify the different constructs. Our exercise suggests that the OMERACT process could benefit from a standardized approach to select, define, and specify domains, and demonstrated that the ICF is useful for further classification of the more specific concepts of "what to measure" within the domains. A clear definition and classification of domains and their specification can be useful as a starting point to build a pool of items that could then be used to develop new instruments to assess functioning and health for rheumatological conditions.

  9. Domains and domain loss

    DEFF Research Database (Denmark)

    Haberland, Hartmut

    2005-01-01

    politicians and in the media, especially in the discussion whether some languages undergo ‘domain loss’ vis-à-vis powerful international languages like English. An objection that has been raised here is that domains, as originally conceived, are parameters of language choice and not properties of languages...

  10. The semantic similarity ensemble

    Directory of Open Access Journals (Sweden)

    Andrea Ballatore

    2013-12-01

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

  11. CO oxidation on PtSn nanoparticle catalysts occurs at the interface of Pt and Sn oxide domains formed under reaction conditions

    KAUST Repository

    Michalak, William D.; Krier, James M.; Alayoglu, Selim; Shin, Jae-Yoon; An, Kwangjin; Komvopoulos, Kyriakos; Liu, Zhi; Somorjai, Gabor A.

    2014-01-01

    The barrier to CO oxidation on Pt catalysts is the strongly bound adsorbed CO, which inhibits O2 adsorption and hinders CO2 formation. Using reaction studies and in situ X-ray spectroscopy with colloidally prepared, monodisperse ∼2 nm Pt and PtSn

  12. Oxidative Unfolding of the Rubredoxin Domain and the Natively Disordered N-terminal Region Regulate the Catalytic Activity of Mycobacterium tuberculosis Protein Kinase G.

    Science.gov (United States)

    Wittwer, Matthias; Luo, Qi; Kaila, Ville R I; Dames, Sonja A

    2016-12-30

    Mycobacterium tuberculosis escapes killing in human macrophages by secreting protein kinase G (PknG). PknG intercepts host signaling to prevent fusion of the phagosome engulfing the mycobacteria with the lysosome and, thus, their degradation. The N-terminal NORS (no regulatory secondary structure) region of PknG (approximately residues 1-75) has been shown to play a role in PknG regulation by (auto)phosphorylation, whereas the following rubredoxin-like metal-binding motif (RD, residues ∼74-147) has been shown to interact tightly with the subsequent catalytic domain (approximately residues 148-420) to mediate its redox regulation. Deletions or mutations in NORS or the redox-sensitive RD significantly decrease PknG survival function. Based on combined NMR spectroscopy, in vitro kinase assay, and molecular dynamics simulation data, we provide novel insights into the regulatory roles of the N-terminal regions. The NORS region is indeed natively disordered and rather dynamic. Consistent with most earlier data, autophosphorylation occurs in our assays only when the NORS region is present and, thus, in the NORS region. Phosphorylation of it results only in local conformational changes and does not induce interactions with the subsequent RD. Although the reduced, metal-bound RD makes tight interactions with the following catalytic domain in the published crystal structures, it can also fold in its absence. Our data further suggest that oxidation-induced unfolding of the RD regulates substrate access to the catalytic domain and, thereby, PknG function under different redox conditions, e.g. when exposed to increased levels of reactive oxidative species in host macrophages. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  13. Recombinant epidermal growth factor-like domain-1 from coagulation factor VII functionalized iron oxide nanoparticles for targeted glioma magnetic resonance imaging.

    Science.gov (United States)

    Liu, Heng; Chen, Xiao; Xue, Wei; Chu, Chengchao; Liu, Yu; Tong, Haipeng; Du, Xuesong; Xie, Tian; Liu, Gang; Zhang, Weiguo

    The highly infiltrative and invasive nature of glioma cells often leads to blurred tumor margins, resulting in incomplete tumor resection and tumor recurrence. Accurate detection and precise delineation of glioma help in preoperative delineation, surgical planning and survival prediction. In this study, recombinant epidermal growth factor-like domain-1, derived from human coagulation factor VII, was conjugated to iron oxide nanoparticles (IONPs) for targeted glioma magnetic resonance (MR) imaging. The synthesized EGF1-EGFP-IONPs exhibited excellent targeting ability toward tissue factor (TF)-positive U87MG cells and human umbilical vein endothelial cells in vitro, and demonstrated persistent and efficient MR contrast enhancement up to 12 h for preclinical glioma models with high targeting specificity in vivo. They hold great potential for clinical translation and developing targeted theranostics against brain glioma.

  14. (1)H, (13)C, (15)N backbone and side-chain resonance assignment of Nostoc sp. C139A variant of the heme-nitric oxide/oxygen binding (H-NOX) domain.

    Science.gov (United States)

    Alexandropoulos, Ioannis I; Argyriou, Aikaterini I; Marousis, Kostas D; Topouzis, Stavros; Papapetropoulos, Andreas; Spyroulias, Georgios A

    2016-10-01

    The H-NOX (Heme-nitric oxide/oxygen binding) domain is conserved across eukaryotes and bacteria. In human soluble guanylyl cyclase (sGC) the H-NOX domain functions as a sensor for the gaseous signaling agent nitric oxide (NO). sGC contains the heme-binding H-NOX domain at its N-terminus, which regulates the catalytic site contained within the C-terminal end of the enzyme catalyzing the conversion of GTP (guanosine 5'-triphosphate) to GMP (guanylyl monophosphate). Here, we present the backbone and side-chain assignments of the (1)H, (13)C and (15)N resonances of the 183-residue H-NOX domain from Nostoc sp. through solution NMR.

  15. Vitamin K3 and vitamin C alone or in combination induced apoptosis in leukemia cells by a similar oxidative stress signalling mechanism.

    Science.gov (United States)

    Bonilla-Porras, Angelica R; Jimenez-Del-Rio, Marlene; Velez-Pardo, Carlos

    2011-06-10

    Secondary therapy-related acute lymphoblastic leukemia might emerge following chemotherapy and/or radiotherapy for primary malignancies. Therefore, other alternatives should be pursued to treat leukemia. It is shown that vitamin K3- or vitamin C- induced apoptosis in leukemia cells by oxidative stress mechanism involving superoxide anion radical and hydrogen peroxide generation, activation of NF-κB, p53, c-Jun, protease caspase-3 activation and mitochondria depolarization leading to nuclei fragmentation. Cell death was more prominent when Jurkat and K562 cells are exposed to VC and VK3 in a ratio 1000:1 (10 mM: 10 μM) or 100:1 (300 μM: 3 μM), respectively. We provide for the first time in vitro evidence supporting a causative role for oxidative stress in VK3- and VC-induced apoptosis in Jurkat and K562 cells in a domino-like mechanism. Altogether these data suggest that VK3 and VC should be useful in the treatment of leukemia.

  16. Vitamin K3 and vitamin C alone or in combination induced apoptosis in leukemia cells by a similar oxidative stress signalling mechanism

    Directory of Open Access Journals (Sweden)

    Velez-Pardo Carlos

    2011-06-01

    Full Text Available Abstract Background Secondary therapy-related acute lymphoblastic leukemia might emerge following chemotherapy and/or radiotherapy for primary malignancies. Therefore, other alternatives should be pursued to treat leukemia. Results It is shown that vitamin K3- or vitamin C- induced apoptosis in leukemia cells by oxidative stress mechanism involving superoxide anion radical and hydrogen peroxide generation, activation of NF-κB, p53, c-Jun, protease caspase-3 activation and mitochondria depolarization leading to nuclei fragmentation. Cell death was more prominent when Jurkat and K562 cells are exposed to VC and VK3 in a ratio 1000:1 (10 mM: 10 μM or 100:1 (300 μM: 3 μM, respectively. Conclusion We provide for the first time in vitro evidence supporting a causative role for oxidative stress in VK3- and VC-induced apoptosis in Jurkat and K562 cells in a domino-like mechanism. Altogether these data suggest that VK3 and VC should be useful in the treatment of leukemia.

  17. Engineering metal (hydr)oxide sorbents for removal of arsenate and similar weak-acid oxyanion contaminants: A critical review with emphasis on factors governing sorption processes.

    Science.gov (United States)

    Hristovski, Kiril D; Markovski, Jasmina

    2017-11-15

    To create an integrative foundation for engineering of the next generation inexpensive sorbent systems, this critical review addresses the existing knowledge gap in factor/performance relationships between weak-acid oxyanion contaminants and metal (hydr)oxide sorbents. In-depth understanding of fundamental thermodynamics and kinetics mechanisms, material fabrication, and analytical and characterization techniques, is necessary to engineer sorbent that exhibit high capacity, selectivity, stability, durability and mass transport of contaminants under a wide range of operating and water matrix conditions requirements. From the perspective of thermodynamics and kinetics, this critical review examines the factors affecting sorbent performances and analyzes the existing research to elucidate future directions aimed at developing novel sorbents for removal of weak-acid oxyanion contaminants from water. Only sorbents that allow construction of simple and inexpensive water treatment systems adapted to overcome fiscal and technological barriers burdening small communities could pave the road for providing inexpensive potable water to millions of people. Novel sorbents, which exhibit (1) poor performances in realistic operating and water matrix conditions and/or (2) do not comply with the purely driven economics factors of production scalability or cost expectations, are predestined to never be commercialized. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Cerebellar oxidative DNA damage and altered DNA methylation in the BTBR T+tf/J mouse model of autism and similarities with human post mortem cerebellum.

    Directory of Open Access Journals (Sweden)

    Svitlana Shpyleva

    Full Text Available The molecular pathogenesis of autism is complex and involves numerous genomic, epigenomic, proteomic, metabolic, and physiological alterations. Elucidating and understanding the molecular processes underlying the pathogenesis of autism is critical for effective clinical management and prevention of this disorder. The goal of this study is to investigate key molecular alterations postulated to play a role in autism and their role in the pathophysiology of autism. In this study we demonstrate that DNA isolated from the cerebellum of BTBR T+tf/J mice, a relevant mouse model of autism, and from human post-mortem cerebellum of individuals with autism, are both characterized by an increased levels of 8-oxo-7-hydrodeoxyguanosine (8-oxodG, 5-methylcytosine (5mC, and 5-hydroxymethylcytosine (5hmC. The increase in 8-oxodG and 5mC content was associated with a markedly reduced expression of the 8-oxoguanine DNA-glycosylase 1 (Ogg1 and increased expression of de novo DNA methyltransferases 3a and 3b (Dnmt3a and Dnmt3b. Interestingly, a rise in the level of 5hmC occurred without changes in the expression of ten-eleven translocation expression 1 (Tet1 and Tet2 genes, but significantly correlated with the presence of 8-oxodG in DNA. This finding and similar elevation in 8-oxodG in cerebellum of individuals with autism and in the BTBR T+tf/J mouse model warrant future large-scale studies to specifically address the role of OGG1 alterations in pathogenesis of autism.

  19. Domain analysis

    DEFF Research Database (Denmark)

    Hjørland, Birger

    2017-01-01

    The domain-analytic approach to knowledge organization (KO) (and to the broader field of library and information science, LIS) is outlined. The article reviews the discussions and proposals on the definition of domains, and provides an example of a domain-analytic study in the field of art studies....... Varieties of domain analysis as well as criticism and controversies are presented and discussed....

  20. Concrete domains

    OpenAIRE

    Kahn, G.; Plotkin, G.D.

    1993-01-01

    This paper introduces the theory of a particular kind of computation domains called concrete domains. The purpose of this theory is to find a satisfactory framework for the notions of coroutine computation and sequentiality of evaluation.

  1. Domain Engineering

    Science.gov (United States)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  2. Similarities and discrepancies in homozygous factor VII defects due to mutations in the region of residues Met298 to Cys310 (exon 8) in the catalytic domain of factor VII.

    Science.gov (United States)

    Girolami, A; Berti de Marinis, G; Bonamigo, E; Vettore, S

    2011-06-01

    Patients with the Arg304Gln mutation in factor VII Padua (FVII Padua) show discrepant activity levels that depend on the thromboplastin used in the assay system. This report investigates the possibility that residues close to Arg304 (exon 8) show the same discrepant behavior. All available homozygous patients with a mutation in a 13-residue region (preceding and following Arg304) have been evaluated. Only the Arg304Trp mutation showed a discrepancy similar to that shown by the Arg304Gln mutation. Other homozygotes failed to show differences, despite their all being positive for cross-reacting material. Another FVII amino acid residue involved in tissue factor binding and activation is Arg79 (exon 4). No comparison could be carried out because no homozygotes for deficiency in this region have ever been described. The relationship between these 2 residues involved in tissue factor binding and activation has not yet been completely clarified; however, Arg residues 79 and 304 are the only 2 residues definitely shown thus far to be involved in this important function.

  3. Towards Personalized Medicine: Leveraging Patient Similarity and Drug Similarity Analytics

    Science.gov (United States)

    Zhang, Ping; Wang, Fei; Hu, Jianying; Sorrentino, Robert

    2014-01-01

    The rapid adoption of electronic health records (EHR) provides a comprehensive source for exploratory and predictive analytic to support clinical decision-making. In this paper, we investigate how to utilize EHR to tailor treatments to individual patients based on their likelihood to respond to a therapy. We construct a heterogeneous graph which includes two domains (patients and drugs) and encodes three relationships (patient similarity, drug similarity, and patient-drug prior associations). We describe a novel approach for performing a label propagation procedure to spread the label information representing the effectiveness of different drugs for different patients over this heterogeneous graph. The proposed method has been applied on a real-world EHR dataset to help identify personalized treatments for hypercholesterolemia. The experimental results demonstrate the effectiveness of the approach and suggest that the combination of appropriate patient similarity and drug similarity analytics could lead to actionable insights for personalized medicine. Particularly, by leveraging drug similarity in combination with patient similarity, our method could perform well even on new or rarely used drugs for which there are few records of known past performance. PMID:25717413

  4. Domain architecture of protein-disulfide isomerase facilitates its dual role as an oxidase and an isomerase in Ero1p-mediated disulfide formation

    DEFF Research Database (Denmark)

    Kulp, M. S.; Frickel, E. M.; Ellgaard, Lars

    2006-01-01

    reduction/rearrangement of non-native disulfides is poorly understood. We analyzed the role of individual PDI domains in disulfide bond formation in a reaction driven by their natural oxidant, Ero1p. We found that Ero1p oxidizes the isolated PDI catalytic thioredoxin domains, A and A' at the same rate......Native disulfide bond formation in eukaryotes is dependent on protein-disulfide isomerase (PDI) and its homologs, which contain varying combinations of catalytically active and inactive thioredoxin domains. However, the specific contribution of PDI to the formation of new disulfides versus...... catalytic (A) domain. The specific order of thioredoxin domains in PDI is important in establishing the asymmetry in the rate of oxidation of the two active sites thus allowing A and A', two thioredoxin domains that are similar in sequence and structure, to serve opposing functional roles as a disulfide...

  5. New Similarity Functions

    DEFF Research Database (Denmark)

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

    2016-01-01

    spaces, in addition to their similarity in the vector space. Prioritized Weighted Feature Distance (PWFD) works similarly as WFD, but provides the ability to give priorities to desirable features. The accuracy of the proposed functions are compared with other similarity functions on several data sets....... Our results show that the proposed functions work better than other methods proposed in the literature....

  6. Phoneme Similarity and Confusability

    Science.gov (United States)

    Bailey, T.M.; Hahn, U.

    2005-01-01

    Similarity between component speech sounds influences language processing in numerous ways. Explanation and detailed prediction of linguistic performance consequently requires an understanding of these basic similarities. The research reported in this paper contrasts two broad classes of approach to the issue of phoneme similarity-theoretically…

  7. Modification by covalent reaction or oxidation of cysteine residues in the tandem-SH2 domains of ZAP-70 and Syk can block phosphopeptide binding.

    Science.gov (United States)

    Visperas, Patrick R; Winger, Jonathan A; Horton, Timothy M; Shah, Neel H; Aum, Diane J; Tao, Alyssa; Barros, Tiago; Yan, Qingrong; Wilson, Christopher G; Arkin, Michelle R; Weiss, Arthur; Kuriyan, John

    2015-01-01

    Zeta-chain associated protein of 70 kDa (ZAP-70) and spleen tyrosine kinase (Syk) are non-receptor tyrosine kinases that are essential for T-cell and B-cell antigen receptor signalling respectively. They are recruited, via their tandem-SH2 (Src-homology domain 2) domains, to doubly phosphorylated immunoreceptor tyrosine-based activation motifs (ITAMs) on invariant chains of immune antigen receptors. Because of their critical roles in immune signalling, ZAP-70 and Syk are targets for the development of drugs for autoimmune diseases. We show that three thiol-reactive small molecules can prevent the tandem-SH2 domains of ZAP-70 and Syk from binding to phosphorylated ITAMs. We identify a specific cysteine residue in the phosphotyrosine-binding pocket of each protein (Cys39 in ZAP-70, Cys206 in Syk) that is necessary for inhibition by two of these compounds. We also find that ITAM binding to ZAP-70 and Syk is sensitive to the presence of H2O2 and these two cysteine residues are also necessary for inhibition by H2O2. Our findings suggest a mechanism by which the reactive oxygen species generated during responses to antigen could attenuate signalling through these kinases and may also inform the development of ZAP-70 and Syk inhibitors that bind covalently to their SH2 domains.

  8. Domain architecture conservation in orthologs

    Science.gov (United States)

    2011-01-01

    Background As orthologous proteins are expected to retain function more often than other homologs, they are often used for functional annotation transfer between species. However, ortholog identification methods do not take into account changes in domain architecture, which are likely to modify a protein's function. By domain architecture we refer to the sequential arrangement of domains along a protein sequence. To assess the level of domain architecture conservation among orthologs, we carried out a large-scale study of such events between human and 40 other species spanning the entire evolutionary range. We designed a score to measure domain architecture similarity and used it to analyze differences in domain architecture conservation between orthologs and paralogs relative to the conservation of primary sequence. We also statistically characterized the extents of different types of domain swapping events across pairs of orthologs and paralogs. Results The analysis shows that orthologs exhibit greater domain architecture conservation than paralogous homologs, even when differences in average sequence divergence are compensated for, for homologs that have diverged beyond a certain threshold. We interpret this as an indication of a stronger selective pressure on orthologs than paralogs to retain the domain architecture required for the proteins to perform a specific function. In general, orthologs as well as the closest paralogous homologs have very similar domain architectures, even at large evolutionary separation. The most common domain architecture changes observed in both ortholog and paralog pairs involved insertion/deletion of new domains, while domain shuffling and segment duplication/deletion were very infrequent. Conclusions On the whole, our results support the hypothesis that function conservation between orthologs demands higher domain architecture conservation than other types of homologs, relative to primary sequence conservation. This supports the

  9. Molecular similarity measures.

    Science.gov (United States)

    Maggiora, Gerald M; Shanmugasundaram, Veerabahu

    2011-01-01

    Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

  10. 15N and 31P solid-state NMR study of transmembrane domain alignment of M2 protein of influenza A virus in hydrated cylindrical lipid bilayers confined to anodic aluminum oxide nanopores.

    Science.gov (United States)

    Chekmenev, Eduard Y; Hu, Jun; Gor'kov, Peter L; Brey, William W; Cross, Timothy A; Ruuge, Andres; Smirnov, Alex I

    2005-04-01

    This communication reports the first example of a high resolution solid-state 15N 2D PISEMA NMR spectrum of a transmembrane peptide aligned using hydrated cylindrical lipid bilayers formed inside nanoporous anodic aluminum oxide (AAO) substrates. The transmembrane domain SSDPLVVA(A-15N)SIIGILHLILWILDRL of M2 protein from influenza A virus was reconstituted in hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine bilayers that were macroscopically aligned by a conventional micro slide glass support or by the AAO nanoporous substrate. 15N and 31P NMR spectra demonstrate that both the phospholipids and the protein transmembrane domain are uniformly aligned in the nanopores. Importantly, nanoporous AAO substrates may offer several advantages for membrane protein alignment in solid-state NMR studies compared to conventional methods. Specifically, higher thermal conductivity of aluminum oxide is expected to suppress thermal gradients associated with inhomogeneous radio frequency heating. Another important advantage of the nanoporous AAO substrate is its excellent accessibility to the bilayer surface for exposure to solute molecules. Such high accessibility achieved through the substrate nanochannel network could facilitate a wide range of structure-function studies of membrane proteins by solid-state NMR.

  11. Similarity Measure of Graphs

    Directory of Open Access Journals (Sweden)

    Amine Labriji

    2017-07-01

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

  12. Processes of Similarity Judgment

    Science.gov (United States)

    Larkey, Levi B.; Markman, Arthur B.

    2005-01-01

    Similarity underlies fundamental cognitive capabilities such as memory, categorization, decision making, problem solving, and reasoning. Although recent approaches to similarity appreciate the structure of mental representations, they differ in the processes posited to operate over these representations. We present an experiment that…

  13. Judgments of brand similarity

    NARCIS (Netherlands)

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

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

  14. Domain crossing

    DEFF Research Database (Denmark)

    Schraefel, M. C.; Rouncefield, Mark; Kellogg, Wendy

    2012-01-01

    In CSCW, how much do we need to know about another domain/culture before we observe, intersect and intervene with designs. What optimally would that other culture need to know about us? Is this a “how long is a piece of string” question, or an inquiry where we can consider a variety of contexts a...

  15. Gender similarities and differences.

    Science.gov (United States)

    Hyde, Janet Shibley

    2014-01-01

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

  16. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    remote access via IP-based devices such as smartphones. The Trusted Domain platform fits existing legacy technologies by managing their interoperability and access controls, and it seeks to avoid the security issues of relying on third-party servers outside the home. It is a distributed system...... of wireless standards, limited resources of embedded systems, etc. Taking these challenges into account, we present a Trusted Domain home automation platform, which dynamically and securely connects heterogeneous networks of Short-Range Wireless devices via simple non-expert user. interactions, and allows......In the digital age of home automation and with the proliferation of mobile Internet access, the intelligent home and its devices should be accessible at any time from anywhere. There are many challenges such as security, privacy, ease of configuration, incompatible legacy devices, a wealth...

  17. Expansion of protein domain repeats.

    Directory of Open Access Journals (Sweden)

    Asa K Björklund

    2006-08-01

    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  18. Similarity or difference?

    DEFF Research Database (Denmark)

    Villadsen, Anders Ryom

    2013-01-01

    While the organizational structures and strategies of public organizations have attracted substantial research attention among public management scholars, little research has explored how these organizational core dimensions are interconnected and influenced by pressures for similarity....... In this paper I address this topic by exploring the relation between expenditure strategy isomorphism and structure isomorphism in Danish municipalities. Different literatures suggest that organizations exist in concurrent pressures for being similar to and different from other organizations in their field......-shaped relation exists between expenditure strategy isomorphism and structure isomorphism in a longitudinal quantitative study of Danish municipalities....

  19. Comparing Harmonic Similarity Measures

    NARCIS (Netherlands)

    de Haas, W.B.; Robine, M.; Hanna, P.; Veltkamp, R.C.; Wiering, F.

    2010-01-01

    We present an overview of the most recent developments in polyphonic music retrieval and an experiment in which we compare two harmonic similarity measures. In contrast to earlier work, in this paper we specifically focus on the symbolic chord description as the primary musical representation and

  20. A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity.

    Science.gov (United States)

    Mills, Jamie E; Whitford, Paul C; Shaffer, Jennifer; Onuchic, Jose N; Adams, Joseph A; Jennings, Patricia A

    2007-02-02

    The SH2 domain of the C-terminal Src kinase [Csk] contains a unique disulfide bond that is not present in other known SH2 domains. To investigate whether this unusual disulfide bond serves a novel function, the effects of disulfide bond formation on catalytic activity of the full-length protein and on the structure of the SH2 domain were investigated. The kinase activity of full-length Csk decreases by an order of magnitude upon formation of the disulfide bond in the distal SH2 domain. NMR spectra of the fully oxidized and fully reduced SH2 domains exhibit similar chemical shift patterns and are indicative of similar, well-defined tertiary structures. The solvent-accessible disulfide bond in the isolated SH2 domain is highly stable and far from the small lobe of the kinase domain. However, reduction of this bond results in chemical shift changes of resonances that map to a cluster of residues that extend from the disulfide bond across the molecule to a surface that is in direct contact with the small lobe of the kinase domain in the intact molecule. Normal mode analyses and molecular dynamics calculations suggest that disulfide bond formation has large effects on residues within the kinase domain, most notably within the active-site cleft. Overall, the data indicate that reversible cross-linking of two cysteine residues in the SH2 domain greatly impacts catalytic function and interdomain communication in Csk.

  1. Topological domain walls in helimagnets

    Science.gov (United States)

    Schoenherr, P.; Müller, J.; Köhler, L.; Rosch, A.; Kanazawa, N.; Tokura, Y.; Garst, M.; Meier, D.

    2018-05-01

    Domain walls naturally arise whenever a symmetry is spontaneously broken. They interconnect regions with different realizations of the broken symmetry, promoting structure formation from cosmological length scales to the atomic level1,2. In ferroelectric and ferromagnetic materials, domain walls with unique functionalities emerge, holding great promise for nanoelectronics and spintronics applications3-5. These walls are usually of Ising, Bloch or Néel type and separate homogeneously ordered domains. Here we demonstrate that a wide variety of new domain walls occurs in the presence of spatially modulated domain states. Using magnetic force microscopy and micromagnetic simulations, we show three fundamental classes of domain walls to arise in the near-room-temperature helimagnet iron germanium. In contrast to conventional ferroics, the domain walls exhibit a well-defined inner structure, which—analogous to cholesteric liquid crystals—consists of topological disclination and dislocation defects. Similar to the magnetic skyrmions that form in the same material6,7, the domain walls can carry a finite topological charge, permitting an efficient coupling to spin currents and contributions to a topological Hall effect. Our study establishes a new family of magnetic nano-objects with non-trivial topology, opening the door to innovative device concepts based on helimagnetic domain walls.

  2. AarF Domain Containing Kinase 3 (ADCK3 Mutant Cells Display Signs of Oxidative Stress, Defects in Mitochondrial Homeostasis and Lysosomal Accumulation.

    Directory of Open Access Journals (Sweden)

    Jason K Cullen

    Full Text Available Autosomal recessive ataxias are a clinically diverse group of syndromes that in some cases are caused by mutations in genes with roles in the DNA damage response, transcriptional regulation or mitochondrial function. One of these ataxias, known as Autosomal Recessive Cerebellar Ataxia Type-2 (ARCA-2, also known as SCAR9/COQ10D4; OMIM: #612016, arises due to mutations in the ADCK3 gene. The product of this gene (ADCK3 is an atypical kinase that is thought to play a regulatory role in coenzyme Q10 (CoQ10 biosynthesis. Although much work has been performed on the S. cerevisiae orthologue of ADCK3, the cellular and biochemical role of its mammalian counterpart, and why mutations in this gene lead to human disease is poorly understood. Here, we demonstrate that ADCK3 localises to mitochondrial cristae and is targeted to this organelle via the presence of an N-terminal localisation signal. Consistent with a role in CoQ10 biosynthesis, ADCK3 deficiency decreased cellular CoQ10 content. In addition, endogenous ADCK3 was found to associate in vitro with recombinant Coq3, Coq5, Coq7 and Coq9, components of the CoQ10 biosynthetic machinery. Furthermore, cell lines derived from ARCA-2 patients display signs of oxidative stress, defects in mitochondrial homeostasis and increases in lysosomal content. Together, these data shed light on the possible molecular role of ADCK3 and provide insight into the cellular pathways affected in ARCA-2 patients.

  3. Similar or different?

    DEFF Research Database (Denmark)

    Cornér, Solveig; Pyhältö, Kirsi; Peltonen, Jouni

    2018-01-01

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

  4. .Gov Domains API

    Data.gov (United States)

    General Services Administration — This dataset offers the list of all .gov domains, including state, local, and tribal .gov domains. It does not include .mil domains, or other federal domains outside...

  5. Plant injury due to air pollution - similar symptoms. Part I

    Energy Technology Data Exchange (ETDEWEB)

    Matsuoka, Y

    1976-01-01

    Many plant diseases cause injuries to leaves which mimic the damage inflicted by air pollution. The relationship between air pollution injuries and those caused by meteorological conditions are discussed. Rice plants often contract akagare which causes reddish-brown spots on leaves similar to the symptoms caused by photochemical oxidants. Spider mites produce leaf damage in kidney beans which mimics the spotting caused by photochemical oxidants. Lace bugs produce minute white spots on azaleas similar to those caused by photochemical oxidants.

  6. Similar Task Features Shape Judgment and Categorization Processes

    Science.gov (United States)

    Hoffmann, Janina A.; von Helversen, Bettina; Rieskamp, Jörg

    2016-01-01

    The distinction between similarity-based and rule-based strategies has instigated a large body of research in categorization and judgment. Within both domains, the task characteristics guiding strategy shifts are increasingly well documented. Across domains, past research has observed shifts from rule-based strategies in judgment to…

  7. Evaluating gender similarities and differences using metasynthesis.

    Science.gov (United States)

    Zell, Ethan; Krizan, Zlatan; Teeter, Sabrina R

    2015-01-01

    Despite the common lay assumption that males and females are profoundly different, Hyde (2005) used data from 46 meta-analyses to demonstrate that males and females are highly similar. Nonetheless, the gender similarities hypothesis has remained controversial. Since Hyde's provocative report, there has been an explosion of meta-analytic interest in psychological gender differences. We utilized this enormous collection of 106 meta-analyses and 386 individual meta-analytic effects to reevaluate the gender similarities hypothesis. Furthermore, we employed a novel data-analytic approach called metasynthesis (Zell & Krizan, 2014) to estimate the average difference between males and females and to explore moderators of gender differences. The average, absolute difference between males and females across domains was relatively small (d = 0.21, SD = 0.14), with the majority of effects being either small (46%) or very small (39%). Magnitude of differences fluctuated somewhat as a function of the psychological domain (e.g., cognitive variables, social and personality variables, well-being), but remained largely constant across age, culture, and generations. These findings provide compelling support for the gender similarities hypothesis, but also underscore conditions under which gender differences are most pronounced. PsycINFO Database Record (c) 2015 APA, all rights reserved.

  8. Improving the efficiency of copper indium gallium (Di-)selenide (CIGS) solar cells through integration of a moth-eye textured resist with a refractive index similar to aluminum doped zinc oxide

    Energy Technology Data Exchange (ETDEWEB)

    Burghoorn, M.; Kniknie, B.; Deelen, J. van; Ee, R. van [The Netherlands Organisation for Applied Scientific Research (TNO), De Rondom 1, 5612 AP, Eindhoven (Netherlands); Xu, M. [The Netherlands Organisation for Applied Scientific Research (TNO), De Rondom 1, 5612 AP, Eindhoven (Netherlands); Delft University of Technology, Optics Group, Van der Waalsweg 8, 2628 CH, Delft (Netherlands); Vroon, Z. [The Netherlands Organisation for Applied Scientific Research (TNO), De Rondom 1, 5612 AP, Eindhoven (Netherlands); Zuyd Hogeschool, Nieuw Eyckholt 300, 6419 DJ, Heerlen (Netherlands); Belt, R. van de [Kriya Materials BV, Urmonderbaan 22, 6167 RD, Geleen (Netherlands); Buskens, P., E-mail: pascal.buskens@tno.nl, E-mail: buskens@dwi.rwth-aachen.de [The Netherlands Organisation for Applied Scientific Research (TNO), De Rondom 1, 5612 AP, Eindhoven (Netherlands); DWI – Leibniz Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen (Germany)

    2014-12-15

    Textured transparent conductors are widely used in thin-film silicon solar cells. They lower the reflectivity at interfaces between different layers in the cell and/or cause an increase in the path length of photons in the Si absorber layer, which both result in an increase in the number of absorbed photons and, consequently, an increase in short-circuit current density (J{sub sc}) and cell efficiency. Through optical simulations, we recently obtained strong indications that texturing of the transparent conductor in copper indium gallium (di-)selenide (CIGS) solar cells is also optically advantageous. Here, we experimentally demonstrate that the J{sub sc} and efficiency of CIGS solar cells with an absorber layer thickness (d{sub CIGS}) of 0.85 μm, 1.00 μm and 2.00 μm increase through application of a moth-eye textured resist with a refractive index that is sufficiently similar to AZO (n{sub resist} = 1.792 vs. n{sub AZO} = 1.913 at 633 nm) to avoid large optical losses at the resist-AZO interface. On average, J{sub sc} increases by 7.2%, which matches the average reduction in reflection of 7.0%. The average relative increase in efficiency is slightly lower (6.0%). No trend towards a larger relative increase in J{sub sc} with decreasing d{sub CIGS} was observed. Ergo, the increase in J{sub sc} can be fully explained by the reduction in reflection, and we did not observe any increase in J{sub sc} based on an increased photon path length.

  9. Improving the efficiency of copper indium gallium (Di-selenide (CIGS solar cells through integration of a moth-eye textured resist with a refractive index similar to aluminum doped zinc oxide

    Directory of Open Access Journals (Sweden)

    M. Burghoorn

    2014-12-01

    Full Text Available Textured transparent conductors are widely used in thin-film silicon solar cells. They lower the reflectivity at interfaces between different layers in the cell and/or cause an increase in the path length of photons in the Si absorber layer, which both result in an increase in the number of absorbed photons and, consequently, an increase in short-circuit current density (Jsc and cell efficiency. Through optical simulations, we recently obtained strong indications that texturing of the transparent conductor in copper indium gallium (di-selenide (CIGS solar cells is also optically advantageous. Here, we experimentally demonstrate that the Jsc and efficiency of CIGS solar cells with an absorber layer thickness (dCIGS of 0.85 μm, 1.00 μm and 2.00 μm increase through application of a moth-eye textured resist with a refractive index that is sufficiently similar to AZO (nresist = 1.792 vs. nAZO = 1.913 at 633 nm to avoid large optical losses at the resist-AZO interface. On average, Jsc increases by 7.2%, which matches the average reduction in reflection of 7.0%. The average relative increase in efficiency is slightly lower (6.0%. No trend towards a larger relative increase in Jsc with decreasing dCIGS was observed. Ergo, the increase in Jsc can be fully explained by the reduction in reflection, and we did not observe any increase in Jsc based on an increased photon path length.

  10. Removal of binary dyes mixtures with opposite and similar charges by adsorption, coagulation/flocculation and catalytic oxidation in the presence of CeO2/H2O2 Fenton-like system.

    Science.gov (United States)

    Issa Hamoud, Houeida; Finqueneisel, Gisèle; Azambre, Bruno

    2017-06-15

    In this study, the removal of binary mixtures of dyes with similar (Orange II/Acid Green 25) or opposite charges (Orange II/Malachite Green) was investigated either by simple adsorption on ceria or by the heterogeneous Fenton reaction in presence of H 2 O 2 . First, the CeO 2 nanocatalyst with high specific surface area (269 m 2 /g) and small crystal size (5 nm) was characterized using XRD, Raman spectroscopy and N 2 physisorption at 77 K. The adsorption of single dyes was studied either from thermodynamic and kinetic viewpoints. It is shown that the adsorption of dyes on ceria surface is highly pH-dependent and followed a pseudo-second order kinetic model. Adsorption isotherms fit well the Langmuir model with a complete monolayer coverage and higher affinity towards Orange II at pH 3, compared to other dyes. For the (Orange II/Acid Green 25) mixture, both the amounts of dyes adsorbed on ceria surface and discoloration rates measured from Fenton experiments were decreased by comparison with single dyes. This is due to the adsorption competition existing onto the same surface Ce x+ sites and the reaction competition with hydroxyl radicals, respectively. The behavior of the (Orange II/Malachite Green) mixture is markedly different. Dyes with opposite charges undergo paired adsorption on ceria as well as homogeneous and heterogeneous coagulation/flocculation processes, but can also be removed by heterogeneous Fenton process. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Similarity is not enough: Tipping points of Ebola Zaire mortalities

    Science.gov (United States)

    Phillips, J. C.

    2015-06-01

    In early 2014 an outbreak of a slightly mutated Zaire Ebola subtype appeared in West Africa which is less virulent than 1976 and 1994 strains. The numbers of cases per year appear to be ∼1000 times larger than the earlier strains, suggesting a greatly enhanced transmissibility. Although the fraction of the 2014 spike glycoprotein mutations is very small (∼3%), the mortality is significantly reduced, while the transmission appears to have increased strongly. Bioinformatic scaling had previously shown similar inversely correlated trends in virulence and transmission in N1 (H1N1) and N2 (H3N2) influenza spike glycoprotein mutations. These trends appear to be related to various external factors (migration, availability of pure water, and vaccination programs). The molecular mechanisms for Ebola's mutational response involve mainly changes in the disordered mucin-like domain (MLD) of its spike glycoprotein amino acids. The MLD has been observed to form the tip of an oligomeric amphiphilic wedge that selectively pries apart cell-cell interfaces via an oxidative mechanism.

  12. Visual reconciliation of alternative similarity spaces in climate modeling

    Science.gov (United States)

    J Poco; A Dasgupta; Y Wei; William Hargrove; C.R. Schwalm; D.N. Huntzinger; R Cook; E Bertini; C.T. Silva

    2015-01-01

    Visual data analysis often requires grouping of data objects based on their similarity. In many application domains researchers use algorithms and techniques like clustering and multidimensional scaling to extract groupings from data. While extracting these groups using a single similarity criteria is relatively straightforward, comparing alternative criteria poses...

  13. Solution structure of GSP13 from Bacillus subtilis exhibits an S1 domain related to cold shock proteins

    International Nuclear Information System (INIS)

    Yu Wenyu; Hu Jicheng; Yu Bingke; Xia Wei; Jin Changwen; Xia Bin

    2009-01-01

    GSP13 encoded by gene yugI is a σ B -dependent general stress protein in Bacillus subtilis, which can be induced by heat shock, salt stress, ethanol stress, glucose starvation, oxidative stress and cold shock. Here we report the solution structure of GSP13 and it is the first structure of S1 domain containing protein in Bacillus subtilis. The structure of GSP13 mainly consists of a typical S1 domain along with a C-terminal 50-residue flexible tail, different from the other known S1 domain containing proteins. Comparison with other S1 domain structures reveals that GSP13 has a conserved RNA binding surface, and it may function similarly to cold shock proteins in response to cold stress

  14. Domain-to-domain coupling in voltage-sensing phosphatase.

    Science.gov (United States)

    Sakata, Souhei; Matsuda, Makoto; Kawanabe, Akira; Okamura, Yasushi

    2017-01-01

    Voltage-sensing phosphatase (VSP) consists of a transmembrane voltage sensor and a cytoplasmic enzyme region. The enzyme region contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization. Although the detailed molecular characteristics of the voltage sensor domain and the enzyme region have been revealed, little is known how these two regions are coupled. In addition, it is important to know whether mechanism for coupling between the voltage sensor domain and downstream effector function is shared among other voltage sensor domain-containing proteins. Recent studies in which specific amino acid sites were genetically labeled using a fluorescent unnatural amino acid have enabled detection of the local structural changes in the cytoplasmic region of Ciona intestinalis VSP that occur with a change in membrane potential. The results of those studies provide novel insight into how the enzyme activity of the cytoplasmic region of VSP is regulated by the voltage sensor domain.

  15. Phonological similarity effect in complex span task.

    Science.gov (United States)

    Camos, Valérie; Mora, Gérôme; Barrouillet, Pierre

    2013-01-01

    The aim of our study was to test the hypothesis that two systems are involved in verbal working memory; one is specifically dedicated to the maintenance of phonological representations through verbal rehearsal while the other would maintain multimodal representations through attentional refreshing. This theoretical framework predicts that phonologically related phenomena such as the phonological similarity effect (PSE) should occur when the domain-specific system is involved in maintenance, but should disappear when concurrent articulation hinders its use. Impeding maintenance in the domain-general system by a concurrent attentional demand should impair recall performance without affecting PSE. In three experiments, we manipulated the concurrent articulation and the attentional demand induced by the processing component of complex span tasks in which participants had to maintain lists of either similar or dissimilar words. Confirming our predictions, PSE affected recall performance in complex span tasks. Although both the attentional demand and the articulatory requirement of the concurrent task impaired recall, only the induction of an articulatory suppression during maintenance made the PSE disappear. These results suggest a duality in the systems devoted to verbal maintenance in the short term, constraining models of working memory.

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

    Directory of Open Access Journals (Sweden)

    Q. X. Xu

    2012-08-01

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

  17. Renewing the Respect for Similarity

    Directory of Open Access Journals (Sweden)

    Shimon eEdelman

    2012-07-01

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

  18. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan

    2012-11-19

    Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

  19. Multiple graph regularized protein domain ranking

    KAUST Repository

    Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

    2012-01-01

    Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.

  20. Multiple graph regularized protein domain ranking.

    Science.gov (United States)

    Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin

    2012-11-19

    Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

  1. Multiple graph regularized protein domain ranking

    Directory of Open Access Journals (Sweden)

    Wang Jim

    2012-11-01

    Full Text Available Abstract Background Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods. Results To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods. Conclusion The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.

  2. Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens

    Energy Technology Data Exchange (ETDEWEB)

    Bianchetti, Christopher M.; Bingman, Craig A.; Phillips, Jr., George N. (UW)

    2012-03-15

    functionally characterized. On the basis of prior work, we predicted that cTHAP4 is composed of a heme-binding nitrobindin domain, making THAP4 the only human THAP protein predicted to bind a cofactor. Nitrobindin, a recently characterized protein from Arabidopsis thaliana, is structurally similar and exhibits nitric oxide (NO)-binding properties that resemble the heme-binding nitrophorins. Nitrophorins use a heme moiety to store, transport, and release NO in a pH-specific manner. Although the exact function of nitrobindin is not fully known, the similarities between the well-characterized nitrophorins imply a role in NO transport, sensing, or metabolism. To better elucidate the possible function of THAP4, we solved the hemebound structure of cTHAP4 to a resolution of 1.79 {angstrom}.

  3. Escalation of the Space Domain

    Science.gov (United States)

    2015-04-01

    vision of Arnold and other Air Force pioneers. Manned flight becomes the domain of NASA , and the United States shelves the idea of an aircraft-like...are similar in nature and application to those seen in science fiction moves or on television (i.e., Star Trek ) that can provide direct kinetic...Space, Infobase Publishing, New York: NY, 2011, pg. 12. 45 Ibid., pg. 12. 46 “Whom Gods Destroy.” Star Trek (original television series), Season 3

  4. Self-similar cosmological models

    Energy Technology Data Exchange (ETDEWEB)

    Chao, W Z [Cambridge Univ. (UK). Dept. of Applied Mathematics and Theoretical Physics

    1981-07-01

    The kinematics and dynamics of self-similar cosmological models are discussed. The degrees of freedom of the solutions of Einstein's equations for different types of models are listed. The relation between kinematic quantities and the classifications of the self-similarity group is examined. All dust local rotational symmetry models have been found.

  5. Self-similar factor approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.; Sornette, D.

    2003-01-01

    The problem of reconstructing functions from their asymptotic expansions in powers of a small variable is addressed by deriving an improved type of approximants. The derivation is based on the self-similar approximation theory, which presents the passage from one approximant to another as the motion realized by a dynamical system with the property of group self-similarity. The derived approximants, because of their form, are called self-similar factor approximants. These complement the obtained earlier self-similar exponential approximants and self-similar root approximants. The specific feature of self-similar factor approximants is that their control functions, providing convergence of the computational algorithm, are completely defined from the accuracy-through-order conditions. These approximants contain the Pade approximants as a particular case, and in some limit they can be reduced to the self-similar exponential approximants previously introduced by two of us. It is proved that the self-similar factor approximants are able to reproduce exactly a wide class of functions, which include a variety of nonalgebraic functions. For other functions, not pertaining to this exactly reproducible class, the factor approximants provide very accurate approximations, whose accuracy surpasses significantly that of the most accurate Pade approximants. This is illustrated by a number of examples showing the generality and accuracy of the factor approximants even when conventional techniques meet serious difficulties

  6. Dynamic similarity in erosional processes

    Science.gov (United States)

    Scheidegger, A.E.

    1963-01-01

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

  7. Personalized recommendation with corrected similarity

    International Nuclear Information System (INIS)

    Zhu, Xuzhen; Tian, Hui; Cai, Shimin

    2014-01-01

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

  8. Similarity measures for face recognition

    CERN Document Server

    Vezzetti, Enrico

    2015-01-01

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

  9. Revisiting Inter-Genre Similarity

    DEFF Research Database (Denmark)

    Sturm, Bob L.; Gouyon, Fabien

    2013-01-01

    We revisit the idea of ``inter-genre similarity'' (IGS) for machine learning in general, and music genre recognition in particular. We show analytically that the probability of error for IGS is higher than naive Bayes classification with zero-one loss (NB). We show empirically that IGS does...... not perform well, even for data that satisfies all its assumptions....

  10. Fast business process similarity search

    NARCIS (Netherlands)

    Yan, Z.; Dijkman, R.M.; Grefen, P.W.P.J.

    2012-01-01

    Nowadays, it is common for organizations to maintain collections of hundreds or even thousands of business processes. Techniques exist to search through such a collection, for business process models that are similar to a given query model. However, those techniques compare the query model to each

  11. Glove boxes and similar containments

    International Nuclear Information System (INIS)

    Anon.

    1975-01-01

    According to the present invention a glove box or similar containment is provided with an exhaust system including a vortex amplifier venting into the system, the vortex amplifier also having its main inlet in fluid flow connection with the containment and a control inlet in fluid flow connection with the atmosphere outside the containment. (U.S.)

  12. System Identification A Frequency Domain Approach

    CERN Document Server

    Pintelon, Rik

    2012-01-01

    System identification is a general term used to describe mathematical tools and algorithms that build dynamical models from measured data. Used for prediction, control, physical interpretation, and the designing of any electrical systems, they are vital in the fields of electrical, mechanical, civil, and chemical engineering. Focusing mainly on frequency domain techniques, System Identification: A Frequency Domain Approach, Second Edition also studies in detail the similarities and differences with the classical time domain approach. It high??lights many of the important steps in the identi

  13. Multi-domain comparison of safety standards

    International Nuclear Information System (INIS)

    Baufreton, Ph.; Derrien, J.C.; Ricque, B.; Blanquart, J.P.; Boulanger, J.L.; Delseny, H.; Gassino, J.; Ladier, G.; Ledinot, E.; Leeman, M.; Quere, Ph.

    2011-01-01

    This paper presents an analysis of safety standards and their implementation in certification strategies from different domains such as aeronautics, automation, automotive, nuclear, railway and space. This work, performed in the context of the CG2E ('Club des Grandes Entreprises de l'Embarque'), aims at identifying the main similarities and dissimilarities, for potential cross-domain harmonization. We strive to find the most comprehensive 'trans-sectorial' approach, within a large number of industrial domains. Exhibiting the 'true goals' of their numerous applicable standards, related to the safety of system and software, is a first important step towards harmonization, sharing common approaches, methods and tools whenever possible. (authors)

  14. An Alfven eigenmode similarity experiment

    International Nuclear Information System (INIS)

    Heidbrink, W W; Fredrickson, E; Gorelenkov, N N; Hyatt, A W; Kramer, G; Luo, Y

    2003-01-01

    The major radius dependence of Alfven mode stability is studied by creating plasmas with similar minor radius, shape, magnetic field (0.5 T), density (n e ≅3x10 19 m -3 ), electron temperature (1.0 keV) and beam ion population (near-tangential 80 keV deuterium injection) on both NSTX and DIII-D. The major radius of NSTX is half the major radius of DIII-D. The super-Alfvenic beam ions that drive the modes have overlapping values of v f /v A in the two devices. Observed beam-driven instabilities include toroidicity-induced Alfven eigenmodes (TAE). The stability threshold for the TAE is similar in the two devices. As expected theoretically, the most unstable toroidal mode number n is larger in DIII-D

  15. Compressional Alfven Eigenmode Similarity Study

    Science.gov (United States)

    Heidbrink, W. W.; Fredrickson, E. D.; Gorelenkov, N. N.; Rhodes, T. L.

    2004-11-01

    NSTX and DIII-D are nearly ideal for Alfven eigenmode (AE) similarity experiments, having similar neutral beams, fast-ion to Alfven speed v_f/v_A, fast-ion pressure, and shape of the plasma, but with a factor of 2 difference in the major radius. Toroidicity-induced AE with ˜100 kHz frequencies were compared in an earlier study [1]; this paper focuses on higher frequency AE with f ˜ 1 MHz. Compressional AE (CAE) on NSTX have a polarization, dependence on the fast-ion distribution function, frequency scaling, and low-frequency limit that are qualitatively consistent with CAE theory [2]. Global AE (GAE) are also observed. On DIII-D, coherent modes in this frequency range are observed during low-field (0.6 T) similarity experiments. Experiments will compare the CAE stability limits on DIII-D with the NSTX stability limits, with the aim of determining if CAE will be excited by alphas in a reactor. Predicted differences in the frequency splitting Δ f between excited modes will also be used. \\vspace0.25em [1] W.W. Heidbrink, et al., Plasmas Phys. Control. Fusion 45, 983 (2003). [2] E.D. Fredrickson, et al., Princeton Plasma Physics Laboratory Report PPPL-3955 (2004).

  16. Supersymmetric domain walls

    NARCIS (Netherlands)

    Bergshoeff, Eric A.; Kleinschmidt, Axel; Riccioni, Fabio

    2012-01-01

    We classify the half-supersymmetric "domain walls," i.e., branes of codimension one, in toroidally compactified IIA/IIB string theory and show to which gauged supergravity theory each of these domain walls belong. We use as input the requirement of supersymmetric Wess-Zumino terms, the properties of

  17. Narcissists of a Feather Flock Together: Narcissism and the Similarity of Friends.

    Science.gov (United States)

    Maaß, Ulrike; Lämmle, Lena; Bensch, Doreen; Ziegler, Matthias

    2016-03-01

    Who is willing to expose himself or herself to narcissists on a long-term basis? Studies that address the interactions of narcissists focus mainly on their interactions with strangers. Hence, the aim of the present study was to investigate the extent to which two best friends' similarity in narcissism would influence their similarities in other personality profiles. A total of 290 best friends' dyads filled out measurements of the whole Dark Triad as well as the Big Five. For each personality domain, profile similarity and its dependence on the similarity in the Dark Triad were determined. Results showed that the friends' similarity in narcissism significantly predicted similarity in all Big Five domains. For the general Big Five similarity as well as extraversion, the effect of narcissism similarity was stronger for male than female or mixed friends. Similarity in psychopathy and Machiavellianism significantly predicted all domains except for openness and extraversion, respectively. © 2016 by the Society for Personality and Social Psychology, Inc.

  18. Enhancing Media Personalization by Extracting Similarity Knowledge from Metadata

    DEFF Research Database (Denmark)

    Butkus, Andrius

    be seen as a cognitive foundation for modeling concepts. Conceptual Spaces is applied in this thesis to analyze media in terms of its dimensions and knowledge domains, which in return defines properties and concepts. One of the most important domains in terms of describing media is the emotional one...... only “more of the same” type of content which does not necessarily lead to the meaningful personalization. Another way to approach similarity is to find a similar underlying meaning in the content. Aspects of meaning in media can be represented using Gardenfors Conceptual Spaces theory, which can......) using Latent Semantic Analysis (one of the unsupervised machine learning techniques). It presents three separate cases to illustrate the similarity knowledge extraction from the metadata, where the emotional components in each case represents different abstraction levels – genres, synopsis and lyrics...

  19. Similarity analysis between quantum images

    Science.gov (United States)

    Zhou, Ri-Gui; Liu, XingAo; Zhu, Changming; Wei, Lai; Zhang, Xiafen; Ian, Hou

    2018-06-01

    Similarity analyses between quantum images are so essential in quantum image processing that it provides fundamental research for the other fields, such as quantum image matching, quantum pattern recognition. In this paper, a quantum scheme based on a novel quantum image representation and quantum amplitude amplification algorithm is proposed. At the end of the paper, three examples and simulation experiments show that the measurement result must be 0 when two images are same, and the measurement result has high probability of being 1 when two images are different.

  20. Similarity flows in relativistic hydrodynamics

    International Nuclear Information System (INIS)

    Blaizot, J.P.; Ollitrault, J.Y.

    1986-01-01

    In ultra-relativistic heavy ion collisions, one expects in particular to observe a deconfinement transition leading to a formation of quark gluon plasma. In the framework of the hydrodynamic model, experimental signatures of such a plasma may be looked for as observable consequences of a first order transition on the evolution of the system. In most of the possible scenario, the phase transition is accompanied with discontinuities in the hydrodynamic flow, such as shock waves. The method presented in this paper has been developed to treat without too much numerical effort such discontinuous flow. It relies heavily on the use of similarity solutions of the hydrodynamic equations

  1. Diffusionless phase transitions and related structures in oxides

    International Nuclear Information System (INIS)

    Boulesteix, C.

    1992-01-01

    The relative importance of oxides in the field of materials science has been spectacularly increasing during the last twenty years. First the study of ferroelectrics kept the attention of scientists. Nevertheless this domain is far from being worked out and a lot of new results and of new fields of interest were recently discovered. Other ferroic oxides, especially ferroelastics, have also been the subject of a very great number of new results. In these cases the properties of oxides are at room temperature very tightly related to the phase transition that is generally occurring a few hundred of degrees above this room temperature. In many other cases also properties of oxides can be related to the existence of a phase transition or to a rather similar phenomenon. This book has been specially devoted to the study of the properties of oxides which are in some way related to the existence of a phase transition. The first chapters are focussed on general considerations: the first one is devoted to a general study of phase transitions, the second one to the twinning phenomenon which is of special interest for many oxides. Chapters 3 and 4 are focussed on ferroelectric and ferroelastic materials. These four chapters consitute the first part of the book. Chapters 5 to 8 are devoted to the study of oxides of special interest which have some of their properties related to a phase transition or to a rather similar phenomenon: rare earth oxides, oxides with a diffuse phase transition, zirconia and alumina systems, tungsten oxides and their relatives. These four chapters constitute the second part of the book. (orig.)

  2. Self-similar gravitational clustering

    International Nuclear Information System (INIS)

    Efstathiou, G.; Fall, S.M.; Hogan, C.

    1979-01-01

    The evolution of gravitational clustering is considered and several new scaling relations are derived for the multiplicity function. These include generalizations of the Press-Schechter theory to different densities and cosmological parameters. The theory is then tested against multiplicity function and correlation function estimates for a series of 1000-body experiments. The results are consistent with the theory and show some dependence on initial conditions and cosmological density parameter. The statistical significance of the results, however, is fairly low because of several small number effects in the experiments. There is no evidence for a non-linear bootstrap effect or a dependence of the multiplicity function on the internal dynamics of condensed groups. Empirical estimates of the multiplicity function by Gott and Turner have a feature near the characteristic luminosity predicted by the theory. The scaling relations allow the inference from estimates of the galaxy luminosity function that galaxies must have suffered considerable dissipation if they originally formed from a self-similar hierarchy. A method is also developed for relating the multiplicity function to similar measures of clustering, such as those of Bhavsar, for the distribution of galaxies on the sky. These are shown to depend on the luminosity function in a complicated way. (author)

  3. Compiling Dictionaries Using Semantic Domains*

    Directory of Open Access Journals (Sweden)

    Ronald Moe

    2011-10-01

    Full Text Available

    Abstract: The task of providing dictionaries for all the world's languages is prodigious, re-quiring efficient techniques. The text corpus method cannot be used for minority languages lacking texts. To meet the need, the author has constructed a list of 1 600 semantic domains, which he has successfully used to collect words. In a workshop setting, a group of speakers can collect as many as 17 000 words in ten days. This method results in a classified word list that can be efficiently expanded into a full dictionary. The method works because the mental lexicon is a giant web or-ganized around key concepts. A semantic domain can be defined as an important concept together with the words directly related to it by lexical relations. A person can utilize the mental web to quickly jump from word to word within a domain. The author is developing a template for each domain to aid in collecting words and in de-scribing their semantics. Investigating semantics within the context of a domain yields many in-sights. The method permits the production of both alphabetically and semantically organized dic-tionaries. The list of domains is intended to be universal in scope and applicability. Perhaps due to universals of human experience and universals of linguistic competence, there are striking simi-larities in various lists of semantic domains developed for languages around the world. Using a standardized list of domains to classify multiple dictionaries opens up possibilities for cross-lin-guistic research into semantic and lexical universals.

    Keywords: SEMANTIC DOMAINS, SEMANTIC FIELDS, SEMANTIC CATEGORIES, LEX-ICAL RELATIONS, SEMANTIC PRIMITIVES, DOMAIN TEMPLATES, MENTAL LEXICON, SEMANTIC UNIVERSALS, MINORITY LANGUAGES, LEXICOGRAPHY

    Opsomming: Samestelling van woordeboeke deur gebruikmaking van se-mantiese domeine. Die taak van die voorsiening van woordeboeke aan al die tale van die wêreld is geweldig en vereis doeltreffende tegnieke. Die

  4. Seniority bosons from similarity transformations

    International Nuclear Information System (INIS)

    Geyer, H.B.

    1986-01-01

    The requirement of associating in the boson space seniority with twice the number of non-s bosons defines a similarity transformation which re-expresses the Dyson pair boson images in terms of seniority bosons. In particular the fermion S-pair creation operator is mapped onto an operator which, unlike the pair boson image, does not change the number of non-s bosons. The original results of Otsuka, Arima and Iachello are recovered by this procedure while at the same time they are generalized to include g-bosons or even bosons with J>4 as well as any higher order boson terms. Furthermore the seniority boson images are valid for an arbitrary number of d- or g-bosons - a result which is not readily obtainable within the framework of the usual Marumori- or OAI-method

  5. Conserved Domain Database (CDD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins.

  6. Alaska, Gulf spills share similarities

    International Nuclear Information System (INIS)

    Usher, D.

    1991-01-01

    The accidental Exxon Valdez oil spill in Alaska and the deliberate dumping of crude oil into the Persian Gulf as a tactic of war contain both glaring differences and surprising similarities. Public reaction and public response was much greater to the Exxon Valdez spill in pristine Prince William Sound than to the war-related tragedy in the Persian Gulf. More than 12,000 workers helped in the Alaskan cleanup; only 350 have been involved in Kuwait. But in both instances, environmental damages appear to be less than anticipated. Natures highly effective self-cleansing action is primarily responsible for minimizing the damages. One positive action growing out of the two incidents is increased international cooperation and participation in oil-spill clean-up efforts. In 1990, in the aftermath of the Exxon Valdez spill, 94 nations signed an international accord on cooperation in future spills. The spills can be historic environmental landmarks leading to creation of more sophisticated response systems worldwide

  7. Exploring similarities among many species distributions

    Science.gov (United States)

    Simmerman, Scott; Wang, Jingyuan; Osborne, James; Shook, Kimberly; Huang, Jian; Godsoe, William; Simons, Theodore R.

    2012-01-01

    Collecting species presence data and then building models to predict species distribution has been long practiced in the field of ecology for the purpose of improving our understanding of species relationships with each other and with the environment. Due to limitations of computing power as well as limited means of using modeling software on HPC facilities, past species distribution studies have been unable to fully explore diverse data sets. We build a system that can, for the first time to our knowledge, leverage HPC to support effective exploration of species similarities in distribution as well as their dependencies on common environmental conditions. Our system can also compute and reveal uncertainties in the modeling results enabling domain experts to make informed judgments about the data. Our work was motivated by and centered around data collection efforts within the Great Smoky Mountains National Park that date back to the 1940s. Our findings present new research opportunities in ecology and produce actionable field-work items for biodiversity management personnel to include in their planning of daily management activities.

  8. Calibration of TAMA300 in time domain

    International Nuclear Information System (INIS)

    Telada, Souichi; Tatsumi, Daisuke; Akutsu, Tomomi; Ando, Masaki; Kanda, Nobuyuki

    2005-01-01

    We could reconstruct the strain of gravitational wave signals from acquired data in the time domain by using the infinite impulse response filter technique in TAMA300. We would like to analyse the waveform in the time domain for burst-like signal, merger phase waveform of binary neutron stars, and so on. We established the way to make a continuous time-series gravitational wave strain signal. We compared the time-domain reconstruction with the Fourier-space reconstruction. Both coincided within 3% in the observation range. We could also produce the voltage signal which would be recorded by the data-acquisition system from a simulated gravitational wave. This is useful for some analyses of simulations and signal injections. We could extract the waveform of the hardware injection signal in an observational run in the time domain. The extracted waveform was similar to the injection signal

  9. Structural and Histone Binding Ability Characterizations of Human PWWP Domains

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Hong; Zeng, Hong; Lam, Robert; Tempel, Wolfram; Amaya, Maria F.; Xu, Chao; Dombrovski, Ludmila; Qiu, Wei; Wang, Yanming; Min, Jinrong (Toronto); (Penn)

    2013-09-25

    The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently. The PWWP domain has been shown to be a DNA binding domain, but sequence analysis and previous structural studies show that the PWWP domain exhibits significant similarity to other 'Royal Family' members, implying that the PWWP domain has the potential to bind histones. In order to further explore the function of the PWWP domain, we used the protein family approach to determine the crystal structures of the PWWP domains from seven different human proteins. Our fluorescence polarization binding studies show that PWWP domains have weak histone binding ability, which is also confirmed by our NMR titration experiments. Furthermore, we determined the crystal structures of the BRPF1 PWWP domain in complex with H3K36me3, and HDGF2 PWWP domain in complex with H3K79me3 and H4K20me3. PWWP proteins constitute a new family of methyl lysine histone binders. The PWWP domain consists of three motifs: a canonical {beta}-barrel core, an insertion motif between the second and third {beta}-strands and a C-terminal {alpha}-helix bundle. Both the canonical {beta}-barrel core and the insertion motif are directly involved in histone binding. The PWWP domain has been previously shown to be a DNA binding domain. Therefore, the PWWP domain exhibits dual functions: binding both DNA and methyllysine histones.

  10. Compactified webs and domain wall partition functions

    Energy Technology Data Exchange (ETDEWEB)

    Shabbir, Khurram [Government College University, Department of Mathematics, Lahore (Pakistan)

    2017-04-15

    In this paper we use the topological vertex formalism to calculate a generalization of the ''domain wall'' partition function of M-strings. This generalization allows calculation of partition function of certain compactified webs using a simple gluing algorithm similar to M-strings case. (orig.)

  11. Similarity Decay of Enstrophy in an Electron Fluid

    International Nuclear Information System (INIS)

    Rodgers, D. J.; Matthaeus, W. H.; Mitchell, T. B.; Montgomery, D. C.

    2010-01-01

    A similarity decay law is proposed for enstrophy of a one-signed-vorticity fluid in a circular free-slip domain. It excludes the metastable equilibrium enstrophy which cannot drive turbulence, and approaches Batchelor's t -2 law for strong turbulence. Measurements of the decay of a turbulent electron fluid agree well with the predictions of the decay law for a variety of initial conditions.

  12. Evolutionary dynamics of protein domain architecture in plants

    Directory of Open Access Journals (Sweden)

    Zhang Xue-Cheng

    2012-01-01

    Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

  13. Biochemical characterization of an exonuclease from Arabidopsis thaliana reveals similarities to the DNA exonuclease of the human Werner syndrome protein.

    Science.gov (United States)

    Plchova, Helena; Hartung, Frank; Puchta, Holger

    2003-11-07

    The human Werner syndrome protein (hWRN-p) possessing DNA helicase and exonuclease activities is essential for genome stability. Plants have no homologue of this bifunctional protein, but surprisingly the Arabidopsis genome contains a small open reading frame (ORF) (AtWRNexo) with homology to the exonuclease domain of hWRN-p. Expression of this ORF in Escherichia coli revealed an exonuclease activity for AtWRN-exo-p with similarities but also some significant differences to hWRN-p. The protein digests recessed strands of DNA duplexes in the 3' --> 5' direction but hardly single-stranded DNA or blunt-ended duplexes. In contrast to the Werner exonuclease, AtWRNexo-p is also able to digest 3'-protruding strands. DNA with recessed 3'-PO4 and 3'-OH termini is degraded to a similar extent. AtWRNexo-p hydrolyzes the 3'-recessed strand termini of duplexes containing mismatched bases. AtWRNexo-p needs the divalent cation Mg2+ for activity, which can be replaced by Mn2+. Apurinic sites, cholesterol adducts, and oxidative DNA damage (such as 8-oxoadenine and 8-oxoguanine) inhibit or block the enzyme. Other DNA modifications, including uracil, hypoxanthine and ethenoadenine, did not inhibit AtWRNexo-p. A mutation of a conserved residue within the exonuclease domain (E135A) completely abolished the exonucleolytic activity. Our results indicate that a type of WRN-like exonuclease activity seems to be a common feature of the DNA metabolism of animals and plants.

  14. Oxidative stress

    Directory of Open Access Journals (Sweden)

    Stevanović Jelka

    2012-01-01

    Full Text Available The unceasing need for oxygen is in contradiction to the fact that it is in fact toxic to mammals. Namely, its monovalent reduction can have as a consequence the production of short-living, chemically very active free radicals and certain non-radical agents (nitrogen-oxide, superoxide-anion-radicals, hydroxyl radicals, peroxyl radicals, singlet oxygen, peroxynitrite, hydrogen peroxide, hypochlorous acid, and others. There is no doubt that they have numerous positive roles, but when their production is stepped up to such an extent that the organism cannot eliminate them with its antioxidants (superoxide-dismutase, glutathione-peroxidase, catalase, transferrin, ceruloplasmin, reduced glutathion, and others, a series of disorders is developed that are jointly called „oxidative stress.“ The reactive oxygen species which characterize oxidative stress are capable of attacking all main classes of biological macromolecules, actually proteins, DNA and RNA molecules, and in particular lipids. The free radicals influence lipid peroxidation in cellular membranes, oxidative damage to DNA and RNA molecules, the development of genetic mutations, fragmentation, and the altered function of various protein molecules. All of this results in the following consequences: disrupted permeability of cellular membranes, disrupted cellular signalization and ion homeostasis, reduced or loss of function of damaged proteins, and similar. That is why the free radicals that are released during oxidative stress are considered pathogenic agents of numerous diseases and ageing. The type of damage that will occur, and when it will take place, depends on the nature of the free radicals, their site of action and their source. [Projekat Ministarstva nauke Republike Srbije, br. 173034, br. 175061 i br. 31085

  15. Domain: Labour market

    NARCIS (Netherlands)

    Oude Mulders, J.; Wadensjö, E.; Hasselhorn, H.M.; Apt, W.

    This domain chapter is dedicated to summarize research on the effects of labour market contextual factors on labour market participation of older workers (aged 50+) and identify research gaps. While employment participation and the timing of (early) retirement is often modelled as an individual

  16. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  17. Domain-Specific Multimodeling

    DEFF Research Database (Denmark)

    Hessellund, Anders

    the overall level of abstraction. It does, however, also introduce a new problem of coordinating multiple different languages in a single system. We call this problem the coordination problem. In this thesis, we present the coordination method for domain-specific multimodeling that explicitly targets...

  18. GlycoDomainViewer

    DEFF Research Database (Denmark)

    Joshi, Hiren J; Jørgensen, Anja; Schjoldager, Katrine T

    2018-01-01

    features, which enhances visibility and accessibility of the wealth of glycoproteomic data being generated. The GlycoDomainViewer enables visual exploration of glycoproteomic data, incorporating information from recent N- and O-glycoproteome studies on human and animal cell lines and some organs and body...

  19. One Health Core Competency Domains

    Directory of Open Access Journals (Sweden)

    Rebekah Frankson

    2016-09-01

    Full Text Available The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting ‘One Health’ approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education as they describe the knowledge, skills and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  20. One Health Core Competency Domains.

    Science.gov (United States)

    Frankson, Rebekah; Hueston, William; Christian, Kira; Olson, Debra; Lee, Mary; Valeri, Linda; Hyatt, Raymond; Annelli, Joseph; Rubin, Carol

    2016-01-01

    The emergence of complex global challenges at the convergence of human, animal, and environmental health has catalyzed a movement supporting "One Health" approaches. Despite recognition of the importance of One Health approaches to address these complex challenges, little effort has been directed at identifying the seminal knowledge, skills, and attitudes necessary for individuals to successfully contribute to One Health efforts. Between 2008 and 2011, three groups independently embarked on separate initiatives to identify core competencies for professionals involved with One Health approaches. Core competencies were considered critically important for guiding curriculum development and continuing professional education, as they describe the knowledge, skills, and attitudes required to be effective. A workshop was convened in 2012 to synthesize the various strands of work on One Health competencies. Despite having different mandates, participants, and approaches, all of these initiatives identified similar core competency domains: management; communication and informatics; values and ethics; leadership; teams and collaboration; roles and responsibilities; and systems thinking. These core competency domains have been used to develop new continuing professional education programs for One Health professionals and help university curricula prepare new graduates to be able to contribute more effectively to One Health approaches.

  1. The framing of scientific domains

    DEFF Research Database (Denmark)

    Dam Christensen, Hans

    2014-01-01

    domains, and UNISIST helps understanding this navigation. Design/methodology/approach The UNISIST models are tentatively applied to the domain of art history at three stages, respectively two modern, partially overlapping domains, as well as an outline of an art historical domain anno c1820...

  2. Graphene oxide powders with different oxidation degree, prepared by synthesis variations of the Hummers method

    International Nuclear Information System (INIS)

    Guerrero-Contreras, Jesus; Caballero-Briones, F.

    2015-01-01

    Graphene oxide (GO) powders with different oxidation degree estimated through the relative intensity of the infrared absorption bands related to oxygen containing groups were prepared through variations of the Hummers method. The GO powders were analyzed by Transmission Electron Microscopy, Energy dispersive spectroscopy, X-ray Photoelectron Spectroscopy, Fourier Transform Infrared Spectroscopy, Raman spectroscopy, X-ray Diffraction, UV–VIS spectroscopy and Electrical Resistance measurements. Several square micron GO sheets with low wrinkling were obtained. Oxygen to carbon ratio is around 0.2 in all the samples although a strong variance in the relative intensity of the oxygen related infrared bands is evident. Thus, the oxidation degree was estimated from the FTIR measurements using the quotient between the C–O related bands area to the total area under the spectra. FTIR shows presence of hydroxyl (–OH), epoxy (C–O–C), carboxyl (–COOH) and carbonyl (C=O) moieties and evidence of intermolecular interactions between adjacent groups. These interactions influence the exfoliation degree, the absorbance of the GO suspensions, as well as the electrical resistance, while the crystalline domain sizes, estimated from XRD and Raman do not show a noticeable behavior related with the composition and molecular structure. The results indicate that the electrical resistance is influenced mainly by the surface chemistry of the GO powders and not only by the O/C ratio. The control of the surface chemistry of GO powders would allow their use as additives in organic bulk heterojunction solar cells with enhanced photoconversion efficiency. - Highlights: • Powders of graphene oxide with different oxidation degree were prepared through variations of the Hummers method. • Raman spectroscopy and XRD demonstrated similar crystallite domain size in the samples. • Electrical resistance, exfoliation degree and optical absorption depend on the molecular structure.

  3. Graphene oxide powders with different oxidation degree, prepared by synthesis variations of the Hummers method

    Energy Technology Data Exchange (ETDEWEB)

    Guerrero-Contreras, Jesus; Caballero-Briones, F., E-mail: fcaballero@ipn.mx

    2015-03-01

    Graphene oxide (GO) powders with different oxidation degree estimated through the relative intensity of the infrared absorption bands related to oxygen containing groups were prepared through variations of the Hummers method. The GO powders were analyzed by Transmission Electron Microscopy, Energy dispersive spectroscopy, X-ray Photoelectron Spectroscopy, Fourier Transform Infrared Spectroscopy, Raman spectroscopy, X-ray Diffraction, UV–VIS spectroscopy and Electrical Resistance measurements. Several square micron GO sheets with low wrinkling were obtained. Oxygen to carbon ratio is around 0.2 in all the samples although a strong variance in the relative intensity of the oxygen related infrared bands is evident. Thus, the oxidation degree was estimated from the FTIR measurements using the quotient between the C–O related bands area to the total area under the spectra. FTIR shows presence of hydroxyl (–OH), epoxy (C–O–C), carboxyl (–COOH) and carbonyl (C=O) moieties and evidence of intermolecular interactions between adjacent groups. These interactions influence the exfoliation degree, the absorbance of the GO suspensions, as well as the electrical resistance, while the crystalline domain sizes, estimated from XRD and Raman do not show a noticeable behavior related with the composition and molecular structure. The results indicate that the electrical resistance is influenced mainly by the surface chemistry of the GO powders and not only by the O/C ratio. The control of the surface chemistry of GO powders would allow their use as additives in organic bulk heterojunction solar cells with enhanced photoconversion efficiency. - Highlights: • Powders of graphene oxide with different oxidation degree were prepared through variations of the Hummers method. • Raman spectroscopy and XRD demonstrated similar crystallite domain size in the samples. • Electrical resistance, exfoliation degree and optical absorption depend on the molecular structure.

  4. On Automatic Modeling and Use of Domain-specific Ontologies

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

    In this paper, we firstly introduce an approach to the modeling of a domain-specific ontology for use in connection with a given document collection. Secondly, we present a methodology for deriving conceptual similarity from the domain-specific ontology. Adopted for ontology representation is a s...

  5. Development of similarity theory for control systems

    Science.gov (United States)

    Myshlyaev, L. P.; Evtushenko, V. F.; Ivushkin, K. A.; Makarov, G. V.

    2018-05-01

    The area of effective application of the traditional similarity theory and the need necessity of its development for systems are discussed. The main statements underlying the similarity theory of control systems are given. The conditions for the similarity of control systems and the need for similarity control control are formulated. Methods and algorithms for estimating and similarity control of control systems and the results of research of control systems based on their similarity are presented. The similarity control of systems includes the current evaluation of the degree of similarity of control systems and the development of actions controlling similarity, and the corresponding targeted change in the state of any element of control systems.

  6. The Enzymatic Oxidation of Graphene Oxide

    Science.gov (United States)

    Kotchey, Gregg P.; Allen, Brett L.; Vedala, Harindra; Yanamala, Naveena; Kapralov, Alexander A.; Tyurina, Yulia Y.; Klein-Seetharaman, Judith; Kagan, Valerian E.; Star, Alexander

    2011-01-01

    Two-dimensional graphitic carbon is a new material with many emerging applications, and studying its chemical properties is an important goal. Here, we reported a new phenomenon – the enzymatic oxidation of a single layer of graphitic carbon by horseradish peroxidase (HRP). In the presence of low concentrations of hydrogen peroxide (~40 µM), HRP catalyzed the oxidation of graphene oxide, which resulted in the formation of holes on its basal plane. During the same period of analysis, HRP failed to oxidize chemically reduced graphene oxide (RGO). The enzymatic oxidation was characterized by Raman, UV-Vis, EPR and FT-IR spectroscopy, TEM, AFM, SDS-PAGE, and GC-MS. Computational docking studies indicated that HRP was preferentially bound to the basal plane rather than the edge for both graphene oxide and RGO. Due to the more dynamic nature of HRP on graphene oxide, the heme active site of HRP was in closer proximity to graphene oxide compared to RGO, thereby facilitating the oxidation of the basal plane of graphene oxide. We also studied the electronic properties of the reduced intermediate product, holey reduced graphene oxide (hRGO), using field-effect transistor (FET) measurements. While RGO exhibited a V-shaped transfer characteristic similar to a single layer of graphene that was attributed to its zero band gap, hRGO demonstrated a p-type semiconducting behavior with a positive shift in the Dirac points. This p-type behavior rendered hRGO, which can be conceptualized as interconnected graphene nanoribbons, as a potentially attractive material for FET sensors. PMID:21344859

  7. Self-similarity in incompressible Navier-Stokes equations.

    Science.gov (United States)

    Ercan, Ali; Kavvas, M Levent

    2015-12-01

    The self-similarity conditions of the 3-dimensional (3D) incompressible Navier-Stokes equations are obtained by utilizing one-parameter Lie group of point scaling transformations. It is found that the scaling exponents of length dimensions in i = 1, 2, 3 coordinates in 3-dimensions are not arbitrary but equal for the self-similarity of 3D incompressible Navier-Stokes equations. It is also shown that the self-similarity in this particular flow process can be achieved in different time and space scales when the viscosity of the fluid is also scaled in addition to other flow variables. In other words, the self-similarity of Navier-Stokes equations is achievable under different fluid environments in the same or different gravity conditions. Self-similarity criteria due to initial and boundary conditions are also presented. Utilizing the proposed self-similarity conditions of the 3D hydrodynamic flow process, the value of a flow variable at a specified time and space can be scaled to a corresponding value in a self-similar domain at the corresponding time and space.

  8. Marriage Matters: Spousal Similarity in Life Satisfaction

    OpenAIRE

    Ulrich Schimmack; Richard Lucas

    2006-01-01

    Examined the concurrent and cross-lagged spousal similarity in life satisfaction over a 21-year period. Analyses were based on married couples (N = 847) in the German Socio-Economic Panel (SOEP). Concurrent spousal similarity was considerably higher than one-year retest similarity, revealing spousal similarity in the variable component of life satisfac-tion. Spousal similarity systematically decreased with length of retest interval, revealing simi-larity in the changing component of life sati...

  9. TENCompetence Domain Model

    NARCIS (Netherlands)

    2006-01-01

    This is the version 1.1 of the TENCompetence Domain Model (version 1.0 released at 19-6-2006; version 1.1 at 9-11-2008). It contains several files: a) a pdf with the model description, b) three jpg files with class models (also in the pdf), c) a MagicDraw zip file with the model itself, d) a release

  10. SH2 Domain Histochemistry.

    Science.gov (United States)

    Buhs, Sophia; Nollau, Peter

    2017-01-01

    Among posttranslational modifications, the phosphorylation of tyrosine residues is a key modification in cell signaling. Because of its biological importance, characterization of the cellular state of tyrosine phosphorylation is of great interest. Based on the unique properties of endogenously expressed SH2 domains recognizing tyrosine phosphorylated signaling proteins with high specificity we have developed an alternative approach, coined SH2 profiling, enabling us to decipher complex patterns of tyrosine phosphorylation in various normal and cancerous tissues. So far, SH2 profiling has largely been applied for the analysis of protein extracts with the limitation that information on spatial distribution and intensity of tyrosine phosphorylation within a tissue is lost. Here, we describe a novel SH2 domain based strategy for differential characterization of the state of tyrosine phosphorylation in formaldehyde-fixed and paraffin-embedded tissues. This approach demonstrates that SH2 domains may serve as very valuable tools for the analysis of the differential state of tyrosine phosphorylation in primary tissues fixed and processed under conditions frequently applied by routine pathology laboratories.

  11. Crystal shapes on striped surface domains

    International Nuclear Information System (INIS)

    Valencia, Antoni

    2004-01-01

    The equilibrium shapes of a simple cubic crystal in contact with a planar chemically patterned substrate are studied theoretically using an effective interface model. The substrate is primarily made of lyophobic material and is patterned with a lyophilic (easily wettable) stripe domain. Three regimes can be distinguished for the equilibrium shapes of the crystal. The transitions between these regimes as the volume of the crystal is changed are continuous or discontinuous depending on the strength of the couplings between the crystal and the lyophilic and lyophobic surface domains. If the crystal grows through a series of states close to equilibrium, the discontinuous transitions correspond to growth instabilities. These transitions are compared with similar results that have been obtained for a volume of liquid wetting a lyophilic stripe domain

  12. Work-domain knowledge in usability evaluation

    DEFF Research Database (Denmark)

    Følstad, Asbjørn; Hornbæk, Kasper

    2010-01-01

    Usability evaluation helps to determine whether interactive systems support users in their work tasks. However, knowledge about those tasks and, more generally, about the work-domain is difficult to bring to bear on the processes and outcome of usability evaluation. One way to include such work......-domain knowledge might be Cooperative Usability Testing, an evaluation method that consists of (a) interaction phases, similar to classic usability testing, and (b) interpretation phases, where the test participant and the moderator discuss incidents and experiences from the interaction phases. We have studied...... whether such interpretation phases improve the relevance of usability evaluations in the development of work-domain specific systems. The study included two development cases. We conclude that the interpretation phases generate additional insight and redesign suggestions related to observed usability...

  13. Concept similarity in publications precedes cross-disciplinary collaboration.

    Science.gov (United States)

    Post, Andrew R; Harrison, James H

    2008-11-06

    Innovative science frequently occurs as a result of cross-disciplinary collaboration, the importance of which is reflected by recent NIH funding initiatives that promote communication and collaboration. If shared research interests between collaborators are important for the formation of collaborations,methods for identifying these shared interests across scientific domains could potentially reveal new and useful collaboration opportunities. MEDLINE represents a comprehensive database of collaborations and research interests, as reflected by article co-authors and concept content. We analyzed six years of citations using information retrieval based methods to compute articles conceptual similarity, and found that articles by basic and clinical scientists who later collaborated had significantly higher average similarity than articles by similar scientists who did not collaborate.Refinement of these methods and characterization of found conceptual overlaps could allow automated discovery of collaboration opportunities that are currently missed.

  14. Oxidizer Scoping Studies

    Energy Technology Data Exchange (ETDEWEB)

    Chancellor, Christopher John [Los Alamos National Laboratory

    2016-11-07

    The purpose of this report is to present the results of the acceptable knowledge (AK) review of oxidizers present in active waste streams, provide a technical analysis of the oxidizers, and report the results of the scoping study testing. This report will determine the fastest burning oxidizer to be used in the development of a Test Plan for Preparation and Testing of Sorbents Mixed with Oxidizer found in Transuranic Waste (DWT-TP-001). The companion report, DWT-RPT-002, Sorbent Scoping Studies, contains similar information for sorbents identified during the AK review of TRU waste streams. The results of the oxidizer and sorbent scoping studies will be used to inform the QL1 test plan. The QL1 test results will support the development of a basis of knowledge document that will evaluate oxidizing chemicals and sorbents in TRU waste and provide guidance for treatment.

  15. Rating knowledge sharing in cross-domain collaborative filtering.

    Science.gov (United States)

    Li, Bin; Zhu, Xingquan; Li, Ruijiang; Zhang, Chengqi

    2015-05-01

    Cross-domain collaborative filtering (CF) aims to share common rating knowledge across multiple related CF domains to boost the CF performance. In this paper, we view CF domains as a 2-D site-time coordinate system, on which multiple related domains, such as similar recommender sites or successive time-slices, can share group-level rating patterns. We propose a unified framework for cross-domain CF over the site-time coordinate system by sharing group-level rating patterns and imposing user/item dependence across domains. A generative model, say ratings over site-time (ROST), which can generate and predict ratings for multiple related CF domains, is developed as the basic model for the framework. We further introduce cross-domain user/item dependence into ROST and extend it to two real-world cross-domain CF scenarios: 1) ROST (sites) for alleviating rating sparsity in the target domain, where multiple similar sites are viewed as related CF domains and some items in the target domain depend on their correspondences in the related ones; and 2) ROST (time) for modeling user-interest drift over time, where a series of time-slices are viewed as related CF domains and a user at current time-slice depends on herself in the previous time-slice. All these ROST models are instances of the proposed unified framework. The experimental results show that ROST (sites) can effectively alleviate the sparsity problem to improve rating prediction performance and ROST (time) can clearly track and visualize user-interest drift over time.

  16. Domain decomposition method for solving elliptic problems in unbounded domains

    International Nuclear Information System (INIS)

    Khoromskij, B.N.; Mazurkevich, G.E.; Zhidkov, E.P.

    1991-01-01

    Computational aspects of the box domain decomposition (DD) method for solving boundary value problems in an unbounded domain are discussed. A new variant of the DD-method for elliptic problems in unbounded domains is suggested. It is based on the partitioning of an unbounded domain adapted to the given asymptotic decay of an unknown function at infinity. The comparison of computational expenditures is given for boundary integral method and the suggested DD-algorithm. 29 refs.; 2 figs.; 2 tabs

  17. On different forms of self similarity

    International Nuclear Information System (INIS)

    Aswathy, R.K.; Mathew, Sunil

    2016-01-01

    Fractal geometry is mainly based on the idea of self-similar forms. To be self-similar, a shape must able to be divided into parts that are smaller copies, which are more or less similar to the whole. There are different forms of self similarity in nature and mathematics. In this paper, some of the topological properties of super self similar sets are discussed. It is proved that in a complete metric space with two or more elements, the set of all non super self similar sets are dense in the set of all non-empty compact sub sets. It is also proved that the product of self similar sets are super self similar in product metric spaces and that the super self similarity is preserved under isometry. A characterization of super self similar sets using contracting sub self similarity is also presented. Some relevant counterexamples are provided. The concepts of exact super and sub self similarity are introduced and a necessary and sufficient condition for a set to be exact super self similar in terms of condensation iterated function systems (Condensation IFS’s) is obtained. A method to generate exact sub self similar sets using condensation IFS’s and the denseness of exact super self similar sets are also discussed.

  18. Learning Faster by Discovering and Exploiting Object Similarities

    Directory of Open Access Journals (Sweden)

    Tadej Janež

    2013-03-01

    Full Text Available In this paper we explore the question: “Is it possible to speed up the learning process of an autonomous agent by performing experiments in a more complex environment (i.e., an environment with a greater number of different objects?” To this end, we use a simple robotic domain, where the robot has to learn a qualitative model predicting the change in the robot's distance to an object. To quantify the environment's complexity, we defined cardinal complexity as the number of objects in the robot's world, and behavioural complexity as the number of objects' distinct behaviours. We propose Error reduction merging (ERM, a new learning method that automatically discovers similarities in the structure of the agent's environment. ERM identifies different types of objects solely from the data measured and merges the observations of objects that behave in the same or similar way in order to speed up the agent's learning. We performed a series of experiments in worlds of increasing complexity. The results in our simple domain indicate that ERM was capable of discovering structural similarities in the data which indeed made the learning faster, clearly superior to conventional learning. This observed trend occurred with various machine learning algorithms used inside the ERM method.

  19. Functional Domain Driven Design

    OpenAIRE

    Herrera Guzmán, Sergio

    2016-01-01

    Las tecnologías están en constante expansión y evolución, diseñando nuevas técnicas para cumplir con su fin. En el desarrollo de software, las herramientas y pautas para la elaboración de productos software constituyen una pieza en constante evolución, necesarias para la toma de decisiones sobre los proyectos a realizar. Uno de los arquetipos para el desarrollo de software es el denominado Domain Driven Design, donde es importante conocer ampliamente el negocio que se desea modelar en form...

  20. Feature-level domain adaptation

    DEFF Research Database (Denmark)

    Kouw, Wouter M.; Van Der Maaten, Laurens J P; Krijthe, Jesse H.

    2016-01-01

    -level domain adaptation (flda), that models the dependence between the two domains by means of a feature-level transfer model that is trained to describe the transfer from source to target domain. Subsequently, we train a domain-adapted classifier by minimizing the expected loss under the resulting transfer...... modeled via a dropout distribution, which allows the classiffier to adapt to differences in the marginal probability of features in the source and the target domain. Our experiments on several real-world problems show that flda performs on par with state-of-the-art domainadaptation techniques.......Domain adaptation is the supervised learning setting in which the training and test data are sampled from different distributions: training data is sampled from a source domain, whilst test data is sampled from a target domain. This paper proposes and studies an approach, called feature...

  1. Compensating for Incomplete Domain Knowledge

    National Research Council Canada - National Science Library

    Scott, Lynn M; Drezner, Steve; Rue, Rachel; Reyes, Jesse

    2007-01-01

    .... First, many senior leader positions require experience in more than one functional or operational domain, but it is difficult to develop a corps of senior leaders with all the required combinations of domain knowledge...

  2. Hidden Supersymmetry of Domain Walls and Cosmologies

    International Nuclear Information System (INIS)

    Skenderis, Kostas; Townsend, Paul K.

    2006-01-01

    We show that all domain-wall solutions of gravity coupled to scalar fields for which the world-volume geometry is Minkowski or anti-de Sitter admit Killing spinors, and satisfy corresponding first-order equations involving a superpotential determined by the solution. By analytic continuation, all flat or closed Friedmann-Lemaitre-Robertson-Walker cosmologies are shown to satisfy similar first-order equations arising from the existence of 'pseudo Killing' spinors

  3. Ligand binding by PDZ domains

    DEFF Research Database (Denmark)

    Chi, Celestine N.; Bach, Anders; Strømgaard, Kristian

    2012-01-01

    , for example, are particularly rich in these domains. The general function of PDZ domains is to bring proteins together within the appropriate cellular compartment, thereby facilitating scaffolding, signaling, and trafficking events. The many functions of PDZ domains under normal physiological as well...... as pathological conditions have been reviewed recently. In this review, we focus on the molecular details of how PDZ domains bind their protein ligands and their potential as drug targets in this context....

  4. Summarization by domain ontology navigation

    DEFF Research Database (Denmark)

    Andreasen, Troels; Bulskov, Henrik

    2013-01-01

    of the subject. In between these two extremes, conceptual summaries encompass selected concepts derived using background knowledge. We address in this paper an approach where conceptual summaries are provided through a conceptualization as given by an ontology. The ontology guiding the summarization can...... be a simple taxonomy or a generative domain ontology. A domain ontology can be provided by a preanalysis of a domain corpus and can be used to condense improved summaries that better reflects the conceptualization of a given domain....

  5. Personality Similarity between Teachers and Their Students Influences Teacher Judgement of Student Achievement

    Science.gov (United States)

    Rausch, Tobias; Karing, Constance; Dörfler, Tobias; Artelt, Cordula

    2016-01-01

    This study examined personality similarity between teachers and their students and its impact on teacher judgement of student achievement in the domains of reading comprehension and mathematics. Personality similarity was quantified through intraclass correlations between personality characteristics of 409 dyads of German teachers and their…

  6. Solution structure of leptospiral LigA4 Big domain

    Energy Technology Data Exchange (ETDEWEB)

    Mei, Song; Zhang, Jiahai [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China); Zhang, Xuecheng [School of Life Sciences, Anhui University, Hefei, Anhui 230039 (China); Tu, Xiaoming, E-mail: xmtu@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2015-11-13

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca{sup 2+} binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca{sup 2+}-binding site was identified by strains-all and NMR chemical shift perturbation.

  7. Solution structure of leptospiral LigA4 Big domain

    International Nuclear Information System (INIS)

    Mei, Song; Zhang, Jiahai; Zhang, Xuecheng; Tu, Xiaoming

    2015-01-01

    Pathogenic Leptospiraspecies express immunoglobulin-like proteins which serve as adhesins to bind to the extracellular matrices of host cells. Leptospiral immunoglobulin-like protein A (LigA), a surface exposed protein containing tandem repeats of bacterial immunoglobulin-like (Big) domains, has been proved to be involved in the interaction of pathogenic Leptospira with mammalian host. In this study, the solution structure of the fourth Big domain of LigA (LigA4 Big domain) from Leptospira interrogans was solved by nuclear magnetic resonance (NMR). The structure of LigA4 Big domain displays a similar bacterial immunoglobulin-like fold compared with other Big domains, implying some common structural aspects of Big domain family. On the other hand, it displays some structural characteristics significantly different from classic Ig-like domain. Furthermore, Stains-all assay and NMR chemical shift perturbation revealed the Ca"2"+ binding property of LigA4 Big domain. - Highlights: • Determining the solution structure of a bacterial immunoglobulin-like domain from a surface protein of Leptospira. • The solution structure shows some structural characteristics significantly different from the classic Ig-like domains. • A potential Ca"2"+-binding site was identified by strains-all and NMR chemical shift perturbation.

  8. Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species

    Directory of Open Access Journals (Sweden)

    Chandra Sekhar Reddy Chilamakuri

    2011-01-01

    Full Text Available Accurate functional annotation of protein sequences is hampered by important factors such as the failure of sequence search methods to identify relationships and the inherent diversity in function of proteins related at low sequence similarities. Earlier, we had employed intermediate sequence search approach to establish new domain relationships in the unassigned regions of gene products at the whole genome level by taking Mycoplasma gallisepticum as a specific example and established new domain relationships. In this paper, we report a detailed comparison of the conservation status of the domain and domain architectures of the gene products that bear our newly predicted domains amongst 14 other Mycoplasma genomes and reported the probable implications for the organisms. Some of the domain associations, observed in Mycoplasma that afflict humans and other non-human primates, are involved in regulation of solute transport and DNA binding suggesting specific modes of host-pathogen interactions.

  9. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim; Cisse, Moustapha; Gao, Xin; Zhang, Xiangliang

    2016-01-01

    Classification with indefinite similarities has attracted attention in the machine learning community. This is partly due to the fact that many similarity functions that arise in practice are not symmetric positive semidefinite, i.e. the Mercer

  10. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji; Genton, Marc G.; Jun, Mikyoung

    2016-01-01

    extensively, while statistical tests for self-similarity are scarce and limited to processes indexed in one dimension. This paper proposes a statistical hypothesis test procedure for self-similarity of a stochastic process indexed in one dimension and multi

  11. Personality similarity and life satisfaction in couples

    OpenAIRE

    Furler Katrin; Gomez Veronica; Grob Alexander

    2013-01-01

    The present study examined the association between personality similarity and life satisfaction in a large nationally representative sample of 1608 romantic couples. Similarity effects were computed for the Big Five personality traits as well as for personality profiles with global and differentiated indices of similarity. Results showed substantial actor and partner effects indicating that both partners' personality traits were related to both partners' life satisfaction. Personality similar...

  12. BLAST and FASTA similarity searching for multiple sequence alignment.

    Science.gov (United States)

    Pearson, William R

    2014-01-01

    BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancestry-homology. The most effective similarity searches compare protein sequences, rather than DNA sequences, for sequences that encode proteins, and use expectation values, rather than percent identity, to infer homology. The BLAST and FASTA packages of sequence comparison programs provide programs for comparing protein and DNA sequences to protein databases (the most sensitive searches). Protein and translated-DNA comparisons to protein databases routinely allow evolutionary look back times from 1 to 2 billion years; DNA:DNA searches are 5-10-fold less sensitive. BLAST and FASTA can be run on popular web sites, but can also be downloaded and installed on local computers. With local installation, target databases can be customized for the sequence data being characterized. With today's very large protein databases, search sensitivity can also be improved by searching smaller comprehensive databases, for example, a complete protein set from an evolutionarily neighboring model organism. By default, BLAST and FASTA use scoring strategies target for distant evolutionary relationships; for comparisons involving short domains or queries, or searches that seek relatively close homologs (e.g. mouse-human), shallower scoring matrices will be more effective. Both BLAST and FASTA provide very accurate statistical estimates, which can be used to reliably identify protein sequences that diverged more than 2 billion years ago.

  13. Time Domain Induced Polarization

    DEFF Research Database (Denmark)

    Fiandaca, Gianluca; Auken, Esben; Christiansen, Anders Vest

    2012-01-01

    Time-domain-induced polarization has significantly broadened its field of reference during the last decade, from mineral exploration to environmental geophysics, e.g., for clay and peat identification and landfill characterization. Though, insufficient modeling tools have hitherto limited the use...... of time-domaininduced polarization for wider purposes. For these reasons, a new forward code and inversion algorithm have been developed using the full-time decay of the induced polarization response, together with an accurate description of the transmitter waveform and of the receiver transfer function......, to reconstruct the distribution of the Cole-Cole parameters of the earth. The accurate modeling of the transmitter waveform had a strong influence on the forward response, and we showed that the difference between a solution using a step response and a solution using the accurate modeling often is above 100...

  14. Ontology Matching Across Domains

    Science.gov (United States)

    2010-05-01

    matching include GMO [1], Anchor-Prompt [2], and Similarity Flooding [3]. GMO is an iterative structural matcher, which uses RDF bipartite graphs to...AFRL under contract# FA8750-09-C-0058. References [1] Hu, W., Jian, N., Qu, Y., Wang, Y., “ GMO : a graph matching for ontologies”, in: Proceedings of

  15. Dimers in Piecewise Temperleyan Domains

    Science.gov (United States)

    Russkikh, Marianna

    2018-03-01

    We study the large-scale behavior of the height function in the dimer model on the square lattice. Richard Kenyon has shown that the fluctuations of the height function on Temperleyan discretizations of a planar domain converge in the scaling limit (as the mesh size tends to zero) to the Gaussian Free Field with Dirichlet boundary conditions. We extend Kenyon's result to a more general class of discretizations. Moreover, we introduce a new factorization of the coupling function of the double-dimer model into two discrete holomorphic functions, which are similar to discrete fermions defined in Smirnov (Proceedings of the international congress of mathematicians (ICM), Madrid, Spain, 2006; Ann Math (2) 172:1435-1467, 2010). For Temperleyan discretizations with appropriate boundary modifications, the results of Kenyon imply that the expectation of the double-dimer height function converges to a harmonic function in the scaling limit. We use the above factorization to extend this result to the class of all polygonal discretizations, that are not necessarily Temperleyan. Furthermore, we show that, quite surprisingly, the expectation of the double-dimer height function in the Temperleyan case is exactly discrete harmonic (for an appropriate choice of Laplacian) even before taking the scaling limit.

  16. Protein domain organisation: adding order

    Directory of Open Access Journals (Sweden)

    Kummerfeld Sarah K

    2009-01-01

    Full Text Available Abstract Background Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. Results We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. Conclusion Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected

  17. Protein domain organisation: adding order.

    Science.gov (United States)

    Kummerfeld, Sarah K; Teichmann, Sarah A

    2009-01-29

    Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected degree of clustering and more domain pairs in forward and

  18. Prediction Reweighting for Domain Adaptation.

    Science.gov (United States)

    Shuang Li; Shiji Song; Gao Huang

    2017-07-01

    There are plenty of classification methods that perform well when training and testing data are drawn from the same distribution. However, in real applications, this condition may be violated, which causes degradation of classification accuracy. Domain adaptation is an effective approach to address this problem. In this paper, we propose a general domain adaptation framework from the perspective of prediction reweighting, from which a novel approach is derived. Different from the major domain adaptation methods, our idea is to reweight predictions of the training classifier on testing data according to their signed distance to the domain separator, which is a classifier that distinguishes training data (from source domain) and testing data (from target domain). We then propagate the labels of target instances with larger weights to ones with smaller weights by introducing a manifold regularization method. It can be proved that our reweighting scheme effectively brings the source and target domains closer to each other in an appropriate sense, such that classification in target domain becomes easier. The proposed method can be implemented efficiently by a simple two-stage algorithm, and the target classifier has a closed-form solution. The effectiveness of our approach is verified by the experiments on artificial datasets and two standard benchmarks, a visual object recognition task and a cross-domain sentiment analysis of text. Experimental results demonstrate that our method is competitive with the state-of-the-art domain adaptation algorithms.

  19. Testing Self-Similarity Through Lamperti Transformations

    KAUST Repository

    Lee, Myoungji

    2016-07-14

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

  20. Similarity increases altruistic punishment in humans.

    Science.gov (United States)

    Mussweiler, Thomas; Ockenfels, Axel

    2013-11-26

    Humans are attracted to similar others. As a consequence, social networks are homogeneous in sociodemographic, intrapersonal, and other characteristics--a principle called homophily. Despite abundant evidence showing the importance of interpersonal similarity and homophily for human relationships, their behavioral correlates and cognitive foundations are poorly understood. Here, we show that perceived similarity substantially increases altruistic punishment, a key mechanism underlying human cooperation. We induced (dis)similarity perception by manipulating basic cognitive mechanisms in an economic cooperation game that included a punishment phase. We found that similarity-focused participants were more willing to punish others' uncooperative behavior. This influence of similarity is not explained by group identity, which has the opposite effect on altruistic punishment. Our findings demonstrate that pure similarity promotes reciprocity in ways known to encourage cooperation. At the same time, the increased willingness to punish norm violations among similarity-focused participants provides a rationale for why similar people are more likely to build stable social relationships. Finally, our findings show that altruistic punishment is differentially involved in encouraging cooperation under pure similarity vs. in-group conditions.

  1. Self-assembled domain structures: From micro- to nanoscale

    Directory of Open Access Journals (Sweden)

    Vladimir Shur

    2015-06-01

    Full Text Available The recent achievements in studying the self-assembled evolution of micro- and nanoscale domain structures in uniaxial single crystalline ferroelectrics lithium niobate and lithium tantalate have been reviewed. The results obtained by visualization of static domain patterns and kinetics of the domain structure by different methods from common optical microscopy to more sophisticated scanning probe microscopy, scanning electron microscopy and confocal Raman microscopy, have been discussed. The kinetic approach based on various nucleation processes similar to the first-order phase transition was used for explanation of the domain structure evolution scenarios. The main mechanisms of self-assembling for nonequilibrium switching conditions caused by screening ineffectiveness including correlated nucleation, domain growth anisotropy, and domain–domain interaction have been considered. The formation of variety of self-assembled domain patterns such as fractal-type, finger and web structures, broad domain boundaries, and dendrites have been revealed at each of all five stages of domain structure evolution during polarization reversal. The possible applications of self-assembling for micro- and nanodomain engineering were reviewed briefly. The review covers mostly the results published by our research group.

  2. Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jun; Wu, Ruiying; Adkins, Joshua N.; Joachimiak, Andrzej; Glover, Mark

    2014-09-16

    In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity in the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.

  3. Multifunctionalities driven by ferroic domains

    Science.gov (United States)

    Yang, J. C.; Huang, Y. L.; He, Q.; Chu, Y. H.

    2014-08-01

    Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

  4. Notions of similarity for systems biology models.

    Science.gov (United States)

    Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knüpfer, Christian; Liebermeister, Wolfram; Waltemath, Dagmar

    2018-01-01

    Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here we survey existing methods for the comparison of models, introduce quantitative measures for model similarity, and discuss potential applications of combined similarity measures. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on a combination of different model aspects. The six aspects that we define as potentially relevant for similarity are underlying encoding, references to biological entities, quantitative behaviour, qualitative behaviour, mathematical equations and parameters and network structure. We argue that future similarity measures will benefit from combining these model aspects in flexible, problem-specific ways to mimic users' intuition about model similarity, and to support complex model searches in databases. © The Author 2016. Published by Oxford University Press.

  5. Similar speaker recognition using nonlinear analysis

    International Nuclear Information System (INIS)

    Seo, J.P.; Kim, M.S.; Baek, I.C.; Kwon, Y.H.; Lee, K.S.; Chang, S.W.; Yang, S.I.

    2004-01-01

    Speech features of the conventional speaker identification system, are usually obtained by linear methods in spectral space. However, these methods have the drawback that speakers with similar voices cannot be distinguished, because the characteristics of their voices are also similar in spectral space. To overcome the difficulty in linear methods, we propose to use the correlation exponent in the nonlinear space as a new feature vector for speaker identification among persons with similar voices. We show that our proposed method surprisingly reduces the error rate of speaker identification system to speakers with similar voices

  6. Mapping the Moral Domain

    Science.gov (United States)

    Graham, Jesse; Nosek, Brian A.; Haidt, Jonathan; Iyer, Ravi; Koleva, Spassena; Ditto, Peter H.

    2010-01-01

    The moral domain is broader than the empathy and justice concerns assessed by existing measures of moral competence, and it is not just a subset of the values assessed by value inventories. To fill the need for reliable and theoretically-grounded measurement of the full range of moral concerns, we developed the Moral Foundations Questionnaire (MFQ) based on a theoretical model of five universally available (but variably developed) sets of moral intuitions: Harm/care, Fairness/reciprocity, Ingroup/loyalty, Authority/respect, and Purity/sanctity. We present evidence for the internal and external validity of the scale and the model, and in doing so present new findings about morality: 1. Comparative model fitting of confirmatory factor analyses provides empirical justification for a five-factor structure of moral concerns. 2. Convergent/discriminant validity evidence suggests that moral concerns predict personality features and social group attitudes not previously considered morally relevant. 3. We establish pragmatic validity of the measure in providing new knowledge and research opportunities concerning demographic and cultural differences in moral intuitions. These analyses provide evidence for the usefulness of Moral Foundations Theory in simultaneously increasing the scope and sharpening the resolution of psychological views of morality. PMID:21244182

  7. Nanostructure of propylammonium nitrate in the presence of poly(ethylene oxide) and halide salts

    Science.gov (United States)

    Stefanovic, Ryan; Webber, Grant B.; Page, Alister J.

    2018-05-01

    Nanoscale structure of protic ionic liquids is critical to their utility as molecular electrochemical solvents since it determines the capacity to dissolve salts and polymers such as poly(ethylene oxide) (PEO). Here we use quantum chemical molecular dynamics simulations to investigate the impact of dissolved halide anions on the nanostructure of an archetypal nanostructured protic ionic liquid, propylammonium nitrate (PAN), and how this impacts the solvation of a model PEO polymer. At the molecular level, PAN is nanostructured, consisting of charged/polar and uncharged/nonpolar domains. The charged domain consists of the cation/anion charge groups, and is formed by their electrostatic interaction. This domain solvophobically excludes the propyl chains on the cation, which form a distinct, self-assembled nonpolar domain within the liquid. Our simulations demonstrate that the addition of Cl- and Br- anions to PAN disrupts the structure within the PAN charged domain due to competition between nitrate and halide anions for the ammonium charge centre. This disruption increases with halide concentration (up to 10 mol. %). However, at these concentrations, halide addition has little effect on the structure of the PAN nonpolar domain. Addition of PEO to pure PAN also disrupts the structure within the charged domain of the liquid due to hydrogen bonding between the charge groups and the terminal PEO hydroxyl groups. There is little other association between the PEO structure and the surrounding ionic liquid solvent, with strong PEO self-interaction yielding a compact, coiled polymer morphology. Halide addition results in greater association between the ionic liquid charge centres and the ethylene oxide components of the PEO structure, resulting in reduced conformational flexibility, compared to that observed in pure PAN. Similarly, PEO self-interactions increase in the presence of Cl- and Br- anions, compared to PAN, indicating that the addition of halide salts to PAN

  8. Domain wall networks on solitons

    International Nuclear Information System (INIS)

    Sutcliffe, Paul

    2003-01-01

    Domain wall networks on the surface of a soliton are studied in a simple theory. It consists of two complex scalar fields, in 3+1 dimensions, with a global U(1)xZ n symmetry, where n>2. Solutions are computed numerically in which one of the fields forms a Q ball and the other field forms a network of domain walls localized on the surface of the Q ball. Examples are presented in which the domain walls lie along the edges of a spherical polyhedron, forming junctions at its vertices. It is explained why only a small restricted class of polyhedra can arise as domain wall networks

  9. Catalytic oxidation using nitrous oxide

    Directory of Open Access Journals (Sweden)

    Juan Carlos Beltran-Prieto

    2017-01-01

    Full Text Available Nitrous oxide is a very inert gas used generally as oxidant as it offers some advantage compared with other oxidants such as O2 but a considerably higher temperature (> 526 °C is often required. For particular cases such as the oxidation of sugar alcohols, especially for the oxidation of primary alcohols to aldehydes, N2O has the advantage over O2 of a higher reaction selectivity. In the present paper we present the modelling of oxidation reaction of sugar alcohols using an oxidizing agent in low concentrations, which is important to suppress subsequent oxidation reactions due to the very low residual concentrations of the oxidizing agent. For orientation experiments we chose nitrous oxide generated by thermal decomposition of ammonium nitrate. Kinetic modeling of the reaction was performed after determination of the differential equations that describe the system under study.

  10. Self-similarity in the inertial region of wall turbulence.

    Science.gov (United States)

    Klewicki, J; Philip, J; Marusic, I; Chauhan, K; Morrill-Winter, C

    2014-12-01

    The inverse of the von Kármán constant κ is the leading coefficient in the equation describing the logarithmic mean velocity profile in wall bounded turbulent flows. Klewicki [J. Fluid Mech. 718, 596 (2013)] connects the asymptotic value of κ with an emerging condition of dynamic self-similarity on an interior inertial domain that contains a geometrically self-similar hierarchy of scaling layers. A number of properties associated with the asymptotic value of κ are revealed. This is accomplished using a framework that retains connection to invariance properties admitted by the mean statement of dynamics. The development leads toward, but terminates short of, analytically determining a value for κ. It is shown that if adjacent layers on the hierarchy (or their adjacent positions) adhere to the same self-similarity that is analytically shown to exist between any given layer and its position, then κ≡Φ(-2)=0.381966..., where Φ=(1+√5)/2 is the golden ratio. A number of measures, derived specifically from an analysis of the mean momentum equation, are subsequently used to empirically explore the veracity and implications of κ=Φ(-2). Consistent with the differential transformations underlying an invariant form admitted by the governing mean equation, it is demonstrated that the value of κ arises from two geometric features associated with the inertial turbulent motions responsible for momentum transport. One nominally pertains to the shape of the relevant motions as quantified by their area coverage in any given wall-parallel plane, and the other pertains to the changing size of these motions in the wall-normal direction. In accord with self-similar mean dynamics, these two features remain invariant across the inertial domain. Data from direct numerical simulations and higher Reynolds number experiments are presented and discussed relative to the self-similar geometric structure indicated by the analysis, and in particular the special form of self-similarity

  11. Nanocarbons as catalyst for selective oxidation of acrolein to acrylic acid

    Energy Technology Data Exchange (ETDEWEB)

    Frank, B.; Blume, R.; Rinaldi, A.; Trunschke, A.; Schloegl, R. [Fritz Haber Institute of the Max Planck Society, Berlin (Germany). Dept. of Inorganic Chemistry

    2011-07-01

    Selective oxidations are key steps of industrial oil and gas processing for the synthesis of high-value chemicals. Mixed metal oxides based on redox active V or Mo are frequently used for oxidative C-H bond activation. However, multiple processes require precious metals or suffer from low product selectivity demanding an ongoing search for cost-effective alternatives. Recently, the nanostructured carbon was reported to catalyze the metal-free selective alkane activation by oxidative dehydrogenation (ODH). Electron-rich surface carbonyls coordinate this reaction and mimic the active oxygen species in metal oxide catalysts. Here we show that the graphitic carbon, beyond ODH, has the potential to selectively mediate the insertion of an oxygen atom into an organic molecule, i.e., acrolein. Multi-step atom rearrangements considerably exceed the mechanistic complexity of hydrogen abstraction and were so far believed to be the exclusive domain of metal (oxide) catalysis. In the carbon catalyzed process, the nucleophilic oxygen atoms terminating the graphite (0001) surface abstract the formyl hydrogen and the activated aldehyde gets oxidized by epoxide-type mobile oxygen, thus the sp{sup 2} carbon acts as a bifunctional catalyst. Substantial similarities between the metal oxide- and carbon-catalyzed reactions could be identified. Our results shed light on a rarely known facet of applications of nanostructured carbon materials being decorated with diverse oxygen functionalities to coordinate complex catalytic processes. We could successfully transfer the results obtained from the graphite model to carbon nanotubes (CNTs) providing a higher surface area, defect density, and intrinsic activity, to substantially increase the reactivity per catalyst volume. Indeed, low dimensional nanostructured carbon is a highly flexible and robust material which can be modified in a multiple manner to optimize its properties with respect to the intended application. The exploration of

  12. The BRCT domain is a phospho-protein binding domain.

    Science.gov (United States)

    Yu, Xiaochun; Chini, Claudia Christiano Silva; He, Miao; Mer, Georges; Chen, Junjie

    2003-10-24

    The carboxyl-terminal domain (BRCT) of the Breast Cancer Gene 1 (BRCA1) protein is an evolutionarily conserved module that exists in a large number of proteins from prokaryotes to eukaryotes. Although most BRCT domain-containing proteins participate in DNA-damage checkpoint or DNA-repair pathways, or both, the function of the BRCT domain is not fully understood. We show that the BRCA1 BRCT domain directly interacts with phosphorylated BRCA1-Associated Carboxyl-terminal Helicase (BACH1). This specific interaction between BRCA1 and phosphorylated BACH1 is cell cycle regulated and is required for DNA damage-induced checkpoint control during the transition from G2 to M phase of the cell cycle. Further, we show that two other BRCT domains interact with their respective physiological partners in a phosphorylation-dependent manner. Thirteen additional BRCT domains also preferentially bind phospho-peptides rather than nonphosphorylated control peptides. These data imply that the BRCT domain is a phospho-protein binding domain involved in cell cycle control.

  13. On self-similar Tolman models

    International Nuclear Information System (INIS)

    Maharaj, S.D.

    1988-01-01

    The self-similar spherically symmetric solutions of the Einstein field equation for the case of dust are identified. These form a subclass of the Tolman models. These self-similar models contain the solution recently presented by Chi [J. Math. Phys. 28, 1539 (1987)], thereby refuting the claim of having found a new solution to the Einstein field equations

  14. Mining Diagnostic Assessment Data for Concept Similarity

    Science.gov (United States)

    Madhyastha, Tara; Hunt, Earl

    2009-01-01

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

  15. Similarity indices I: what do they measure

    International Nuclear Information System (INIS)

    Johnston, J.W.

    1976-11-01

    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities

  16. Measuring transferring similarity via local information

    Science.gov (United States)

    Yin, Likang; Deng, Yong

    2018-05-01

    Recommender systems have developed along with the web science, and how to measure the similarity between users is crucial for processing collaborative filtering recommendation. Many efficient models have been proposed (i.g., the Pearson coefficient) to measure the direct correlation. However, the direct correlation measures are greatly affected by the sparsity of dataset. In other words, the direct correlation measures would present an inauthentic similarity if two users have a very few commonly selected objects. Transferring similarity overcomes this drawback by considering their common neighbors (i.e., the intermediates). Yet, the transferring similarity also has its drawback since it can only provide the interval of similarity. To break the limitations, we propose the Belief Transferring Similarity (BTS) model. The contributions of BTS model are: (1) BTS model addresses the issue of the sparsity of dataset by considering the high-order similarity. (2) BTS model transforms uncertain interval to a certain state based on fuzzy systems theory. (3) BTS model is able to combine the transferring similarity of different intermediates using information fusion method. Finally, we compare BTS models with nine different link prediction methods in nine different networks, and we also illustrate the convergence property and efficiency of the BTS model.

  17. On distributional assumptions and whitened cosine similarities

    DEFF Research Database (Denmark)

    Loog, Marco

    2008-01-01

    Recently, an interpretation of the whitened cosine similarity measure as a Bayes decision rule was proposed (C. Liu, "The Bayes Decision Rule Induced Similarity Measures,'' IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 29, no. 6, pp. 1086-1090, June 2007. This communication makes th...

  18. Self-Similar Traffic In Wireless Networks

    OpenAIRE

    Jerjomins, R.; Petersons, E.

    2005-01-01

    Many studies have shown that traffic in Ethernet and other wired networks is self-similar. This paper reveals that wireless network traffic is also self-similar and long-range dependant by analyzing big amount of data captured from the wireless router.

  19. Similarity Structure of Wave-Collapse

    DEFF Research Database (Denmark)

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

    1985-01-01

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

  20. Similarity indices I: what do they measure.

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, J.W.

    1976-11-01

    A method for estimating the effects of environmental effusions on ecosystems is described. The characteristics of 25 similarity indices used in studies of ecological communities were investigated. The type of data structure, to which these indices are frequently applied, was described as consisting of vectors of measurements on attributes (species) observed in a set of samples. A general similarity index was characterized as the result of a two-step process defined on a pair of vectors. In the first step an attribute similarity score is obtained for each attribute by comparing the attribute values observed in the pair of vectors. The result is a vector of attribute similarity scores. These are combined in the second step to arrive at the similarity index. The operation in the first step was characterized as a function, g, defined on pairs of attribute values. The second operation was characterized as a function, F, defined on the vector of attribute similarity scores from the first step. Usually, F was a simple sum or weighted sum of the attribute similarity scores. It is concluded that similarity indices should not be used as the test statistic to discriminate between two ecological communities.

  1. Information filtering based on transferring similarity.

    Science.gov (United States)

    Sun, Duo; Zhou, Tao; Liu, Jian-Guo; Liu, Run-Ran; Jia, Chun-Xiao; Wang, Bing-Hong

    2009-07-01

    In this Brief Report, we propose an index of user similarity, namely, the transferring similarity, which involves all high-order similarities between users. Accordingly, we design a modified collaborative filtering algorithm, which provides remarkably higher accurate predictions than the standard collaborative filtering. More interestingly, we find that the algorithmic performance will approach its optimal value when the parameter, contained in the definition of transferring similarity, gets close to its critical value, before which the series expansion of transferring similarity is convergent and after which it is divergent. Our study is complementary to the one reported in [E. A. Leicht, P. Holme, and M. E. J. Newman, Phys. Rev. E 73, 026120 (2006)], and is relevant to the missing link prediction problem.

  2. Self-similar continued root approximants

    International Nuclear Information System (INIS)

    Gluzman, S.; Yukalov, V.I.

    2012-01-01

    A novel method of summing asymptotic series is advanced. Such series repeatedly arise when employing perturbation theory in powers of a small parameter for complicated problems of condensed matter physics, statistical physics, and various applied problems. The method is based on the self-similar approximation theory involving self-similar root approximants. The constructed self-similar continued roots extrapolate asymptotic series to finite values of the expansion parameter. The self-similar continued roots contain, as a particular case, continued fractions and Padé approximants. A theorem on the convergence of the self-similar continued roots is proved. The method is illustrated by several examples from condensed-matter physics.

  3. Correlation between social proximity and mobility similarity.

    Science.gov (United States)

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

    2017-09-20

    Human behaviors exhibit ubiquitous correlations in many aspects, such as individual and collective levels, temporal and spatial dimensions, content, social and geographical layers. With rich Internet data of online behaviors becoming available, it attracts academic interests to explore human mobility similarity from the perspective of social network proximity. Existent analysis shows a strong correlation between online social proximity and offline mobility similarity, namely, mobile records between friends are significantly more similar than between strangers, and those between friends with common neighbors are even more similar. We argue the importance of the number and diversity of common friends, with a counter intuitive finding that the number of common friends has no positive impact on mobility similarity while the diversity plays a key role, disagreeing with previous studies. Our analysis provides a novel view for better understanding the coupling between human online and offline behaviors, and will help model and predict human behaviors based on social proximity.

  4. Scalar Similarity for Relaxed Eddy Accumulation Methods

    Science.gov (United States)

    Ruppert, Johannes; Thomas, Christoph; Foken, Thomas

    2006-07-01

    The relaxed eddy accumulation (REA) method allows the measurement of trace gas fluxes when no fast sensors are available for eddy covariance measurements. The flux parameterisation used in REA is based on the assumption of scalar similarity, i.e., similarity of the turbulent exchange of two scalar quantities. In this study changes in scalar similarity between carbon dioxide, sonic temperature and water vapour were assessed using scalar correlation coefficients and spectral analysis. The influence on REA measurements was assessed by simulation. The evaluation is based on observations over grassland, irrigated cotton plantation and spruce forest. Scalar similarity between carbon dioxide, sonic temperature and water vapour showed a distinct diurnal pattern and change within the day. Poor scalar similarity was found to be linked to dissimilarities in the energy contained in the low frequency part of the turbulent spectra ( definition.

  5. Surf similarity and solitary wave runup

    DEFF Research Database (Denmark)

    Fuhrman, David R.; Madsen, Per A.

    2008-01-01

    The notion of surf similarity in the runup of solitary waves is revisited. We show that the surf similarity parameter for solitary waves may be effectively reduced to the beach slope divided by the offshore wave height to depth ratio. This clarifies its physical interpretation relative to a previ...... functional dependence on their respective surf similarity parameters. Important equivalencies in the runup of sinusoidal and solitary waves are thus revealed.......The notion of surf similarity in the runup of solitary waves is revisited. We show that the surf similarity parameter for solitary waves may be effectively reduced to the beach slope divided by the offshore wave height to depth ratio. This clarifies its physical interpretation relative...... to a previous parameterization, which was not given in an explicit form. Good coherency with experimental (breaking) runup data is preserved with this simpler parameter. A recasting of analytical (nonbreaking) runup expressions for sinusoidal and solitary waves additionally shows that they contain identical...

  6. Similarity in Bilateral Isolated Internal Orbital Fractures.

    Science.gov (United States)

    Chen, Hung-Chang; Cox, Jacob T; Sanyal, Abanti; Mahoney, Nicholas R

    2018-04-13

    In evaluating patients sustaining bilateral isolated internal orbital fractures, the authors have observed both similar fracture locations and also similar expansion of orbital volumes. In this study, we aim to investigate if there is a propensity for the 2 orbits to fracture in symmetrically similar patterns when sustaining similar trauma. A retrospective chart review was performed studying all cases at our institution of bilateral isolated internal orbital fractures involving the medial wall and/or the floor at the time of presentation. The similarity of the bilateral fracture locations was evaluated using the Fisher's exact test. The bilateral expanded orbital volumes were analyzed using the Wilcoxon signed-rank test to assess for orbital volume similarity. Twenty-four patients with bilateral internal orbital fractures were analyzed for fracture location similarity. Seventeen patients (70.8%) had 100% concordance in the orbital subregion fractured, and the association between the right and the left orbital fracture subregion locations was statistically significant (P < 0.0001). Fifteen patients were analyzed for orbital volume similarity. The average orbital cavity volume was 31.2 ± 3.8 cm on the right and 32.0 ± 3.7 cm on the left. There was a statistically significant difference between right and left orbital cavity volumes (P = 0.0026). The data from this study suggest that an individual who suffers isolated bilateral internal orbital fractures has a statistically significant similarity in the location of their orbital fractures. However, there does not appear to be statistically significant similarity in the expansion of the orbital volumes in these patients.

  7. Resource Unavailability (RU) Per Domain Behavior

    NARCIS (Netherlands)

    Karagiannis, Georgios; Westberg, L.; Bader, A.; Tschofenig, Hannes; Tschofenig, H.

    2006-01-01

    This draft specifies a Per Domain Behavior that provides the ability to Diffserv nodes located outside Diffserv domain(s), e.g., receiver or other Diffserv enabled router to detect when the resources provided by the Diffserv domain(s) are not available. The unavailability of resources in the domain

  8. Measure of Node Similarity in Multilayer Networks.

    Directory of Open Access Journals (Sweden)

    Anders Mollgaard

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

  9. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar

    2016-03-21

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users\\' intuition about model similarity, and to support complex model searches in databases.

  10. Trajectory similarity join in spatial networks

    KAUST Repository

    Shang, Shuo

    2017-09-07

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider the case of trajectory similarity join (TS-Join), where the objects are trajectories of vehicles moving in road networks. Thus, given two sets of trajectories and a threshold θ, the TS-Join returns all pairs of trajectories from the two sets with similarity above θ. This join targets applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm\\'s per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

  11. The baryonic self similarity of dark matter

    International Nuclear Information System (INIS)

    Alard, C.

    2014-01-01

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

  12. Notions of similarity for computational biology models

    KAUST Repository

    Waltemath, Dagmar; Henkel, Ron; Hoehndorf, Robert; Kacprowski, Tim; Knuepfer, Christian; Liebermeister, Wolfram

    2016-01-01

    Computational models used in biology are rapidly increasing in complexity, size, and numbers. To build such large models, researchers need to rely on software tools for model retrieval, model combination, and version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of similarity may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing. Here, we introduce a general notion of quantitative model similarities, survey the use of existing model comparison methods in model building and management, and discuss potential applications of model comparison. To frame model comparison as a general problem, we describe a theoretical approach to defining and computing similarities based on different model aspects. Potentially relevant aspects of a model comprise its references to biological entities, network structure, mathematical equations and parameters, and dynamic behaviour. Future similarity measures could combine these model aspects in flexible, problem-specific ways in order to mimic users' intuition about model similarity, and to support complex model searches in databases.

  13. PENGATURAN PASSING OFF DALAM PENGGUNAAN DOMAIN NAME TERKAIT DENGAN MEREK

    Directory of Open Access Journals (Sweden)

    Herti Yunita Putri

    2016-09-01

    Full Text Available In cyber world we often hear about domain name’s term. Domain name is a unique name to identify the server computer’s name like a web server or email server on a computer network or Internet. Passing off also make causes confusion in using merk from a famous brand or merk on the goods and services. Selected domain name in the internet media often creates the similar domain name with the other parties. This similar domain name are often used by people who are not responsible to take advantages of the domain name for themself. This can be caused by the presence of competition from Internet media business. This things called passing off. This research is a normative juridical research with a qualitative analysis. The legal materials include primary legal, secondary law and tertiary legal materials. Collection technique applied is literary study. Legal materials were analyzed to see the argument implementation of the definition of merk, the definition of domain name, definition of passing off, passing off in use related by merk and domain name and the rules of law in Indonesia related by merk, domain name and passing off. Big wishes in the future it can assist as a basic reference and legal considerations which are useful in Indonesian law practice. There are two passing off related to the merk and domain name, called Crybersquatting and Tiposquatting. Domain name rules are not regulated clearly in merk regulation named Act No. 15 of 2001. It regulated in PP 24 Year 1993 about The Class List of Goods or Services In Merk, Telecommunications are included in the goods or services in merk. Domain name are regulated in UDRP (Uniform Dispute Resolution Policy with competent institutions called ICANN (Internet Corporation for Assigned Names and Numbers. Dalam dunia maya (cyber world, kita sering mendengar istilah domain name. Domain name adalah nama unik yang diberikan untuk mengidentifikasi nama server komputer seperti web server atau email server di

  14. Taxonomies of Educational Objective Domain

    OpenAIRE

    Eman Ghanem Nayef; Nik Rosila Nik Yaacob; Hairul Nizam Ismail

    2013-01-01

    This paper highlights an effort to study the educational objective domain taxonomies including Bloom’s taxonomy, Lorin Anderson’s taxonomy, and Wilson’s taxonomy. In this study a comparison among these three taxonomies have been done. Results show that Bloom’s taxonomy is more suitable as an analysis tool to Educational Objective domain.

  15. A Similarity Search Using Molecular Topological Graphs

    Directory of Open Access Journals (Sweden)

    Yoshifumi Fukunishi

    2009-01-01

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

  16. Similarity-based pattern analysis and recognition

    CERN Document Server

    Pelillo, Marcello

    2013-01-01

    This accessible text/reference presents a coherent overview of the emerging field of non-Euclidean similarity learning. The book presents a broad range of perspectives on similarity-based pattern analysis and recognition methods, from purely theoretical challenges to practical, real-world applications. The coverage includes both supervised and unsupervised learning paradigms, as well as generative and discriminative models. Topics and features: explores the origination and causes of non-Euclidean (dis)similarity measures, and how they influence the performance of traditional classification alg

  17. Texture of lipid bilayer domains

    DEFF Research Database (Denmark)

    Jensen, Uffe Bernchou; Brewer, Jonathan R.; Midtiby, Henrik Skov

    2009-01-01

    We investigate the texture of gel (g) domains in binary lipid membranes composed of the phospholipids DPPC and DOPC. Lateral organization of lipid bilayer membranes is a topic of fundamental and biological importance. Whereas questions related to size and composition of fluid membrane domain...... are well studied, the possibility of texture in gel domains has so far not been examined. When using polarized light for two-photon excitation of the fluorescent lipid probe Laurdan, the emission intensity is highly sensitive to the angle between the polarization and the tilt orientation of lipid acyl...... chains. By imaging the intensity variations as a function of the polarization angle, we map the lateral variations of the lipid tilt within domains. Results reveal that gel domains are composed of subdomains with different lipid tilt directions. We have applied a Fourier decomposition method...

  18. Polar and chemical domain structures of lead scandium tantalate (PST)

    International Nuclear Information System (INIS)

    Peng, J.L.; Bursill, L.A.

    1993-01-01

    The local structure of chemical and polar domains and domain walls is determined directly by atomic resolution high-resolution electron microscopy. Thus the Pb, Ta and Sc atomic positions may be located in the images of very thin crystals. Furthermore the Pb cation displacements away from the ideal perovskite A-site have been measured directly for the first time. Local variations in polarization direction may be mapped directly off the images, provided certain electron optical conditions are met. The results are relevant to recent theories of polar-glass behaviour in relaxor-type complex oxide functional ceramics. 17 refs., 9 figs

  19. Polar Domain Discovery with Sparkler

    Science.gov (United States)

    Duerr, R.; Khalsa, S. J. S.; Mattmann, C. A.; Ottilingam, N. K.; Singh, K.; Lopez, L. A.

    2017-12-01

    The scientific web is vast and ever growing. It encompasses millions of textual, scientific and multimedia documents describing research in a multitude of scientific streams. Most of these documents are hidden behind forms which require user action to retrieve and thus can't be directly accessed by content crawlers. These documents are hosted on web servers across the world, most often on outdated hardware and network infrastructure. Hence it is difficult and time-consuming to aggregate documents from the scientific web, especially those relevant to a specific domain. Thus generating meaningful domain-specific insights is currently difficult. We present an automated discovery system (Figure 1) using Sparkler, an open-source, extensible, horizontally scalable crawler which facilitates high throughput and focused crawling of documents pertinent to a particular domain such as information about polar regions. With this set of highly domain relevant documents, we show that it is possible to answer analytical questions about that domain. Our domain discovery algorithm leverages prior domain knowledge to reach out to commercial/scientific search engines to generate seed URLs. Subject matter experts then annotate these seed URLs manually on a scale from highly relevant to irrelevant. We leverage this annotated dataset to train a machine learning model which predicts the `domain relevance' of a given document. We extend Sparkler with this model to focus crawling on documents relevant to that domain. Sparkler avoids disruption of service by 1) partitioning URLs by hostname such that every node gets a different host to crawl and by 2) inserting delays between subsequent requests. With an NSF-funded supercomputer Wrangler, we scaled our domain discovery pipeline to crawl about 200k polar specific documents from the scientific web, within a day.

  20. Fungal mediator tail subunits contain classical transcriptional activation domains.

    Science.gov (United States)

    Liu, Zhongle; Myers, Lawrence C

    2015-04-01

    Classical activation domains within DNA-bound eukaryotic transcription factors make weak interactions with coactivator complexes, such as Mediator, to stimulate transcription. How these interactions stimulate transcription, however, is unknown. The activation of reporter genes by artificial fusion of Mediator subunits to DNA binding domains that bind to their promoters has been cited as evidence that the primary role of activators is simply to recruit Mediator. We have identified potent classical transcriptional activation domains in the C termini of several tail module subunits of Saccharomyces cerevisiae, Candida albicans, and Candida dubliniensis Mediator, while their N-terminal domains are necessary and sufficient for their incorporation into Mediator but do not possess the ability to activate transcription when fused to a DNA binding domain. This suggests that Mediator fusion proteins actually are functioning in a manner similar to that of a classical DNA-bound activator rather than just recruiting Mediator. Our finding that deletion of the activation domains of S. cerevisiae Med2 and Med3, as well as C. dubliniensis Tlo1 (a Med2 ortholog), impairs the induction of certain genes shows these domains function at native promoters. Activation domains within coactivators are likely an important feature of these complexes and one that may have been uniquely leveraged by a common fungal pathogen. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  1. HYPOTHESIS TESTING WITH THE SIMILARITY INDEX

    Science.gov (United States)

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

  2. On self-similarity of crack layer

    Science.gov (United States)

    Botsis, J.; Kunin, B.

    1987-01-01

    The crack layer (CL) theory of Chudnovsky (1986), based on principles of thermodynamics of irreversible processes, employs a crucial hypothesis of self-similarity. The self-similarity hypothesis states that the value of the damage density at a point x of the active zone at a time t coincides with that at the corresponding point in the initial (t = 0) configuration of the active zone, the correspondence being given by a time-dependent affine transformation of the space variables. In this paper, the implications of the self-similarity hypothesis for qusi-static CL propagation is investigated using polystyrene as a model material and examining the evolution of damage distribution along the trailing edge which is approximated by a straight segment perpendicular to the crack path. The results support the self-similarity hypothesis adopted by the CL theory.

  3. Bilateral Trade Flows and Income Distribution Similarity

    Science.gov (United States)

    2016-01-01

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

  4. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

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

  5. Abundance estimation of spectrally similar minerals

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2009-07-01

    Full Text Available This paper evaluates a spectral unmixing method for estimating the partial abundance of spectrally similar minerals in complex mixtures. The method requires formulation of a linear function of individual spectra of individual minerals. The first...

  6. Lagrangian-similarity diffusion-deposition model

    International Nuclear Information System (INIS)

    Horst, T.W.

    1979-01-01

    A Lagrangian-similarity diffusion model has been incorporated into the surface-depletion deposition model. This model predicts vertical concentration profiles far downwind of the source that agree with those of a one-dimensional gradient-transfer model

  7. Discovering Music Structure via Similarity Fusion

    DEFF Research Database (Denmark)

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

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

  8. Outsourced similarity search on metric data assets

    KAUST Repository

    Yiu, Man Lung

    2012-02-01

    This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying it to the service provider for similarity queries on the transformed data. Our techniques provide interesting trade-offs between query cost and accuracy. They are then further extended to offer an intuitive privacy guarantee. Empirical studies with real data demonstrate that the techniques are capable of offering privacy while enabling efficient and accurate processing of similarity queries.

  9. The Effect of Script Similarity on Executive Control in Bilinguals

    Directory of Open Access Journals (Sweden)

    Emily L Coderre

    2014-09-01

    Full Text Available The need for executive control (EC during bilingual language processing is thought to enhance these abilities, conferring a ‘bilingual advantage’ on EC tasks. Recently, the reliability and robustness of the bilingual advantage has been questioned, with many variables reportedly affecting the size and presence of the bilingual advantage. This study investigates one further variable that may affect bilingual EC abilities: the similarity of a bilingual’s two languages. We hypothesize that bilinguals whose two languages have a larger degree of orthographic overlap will require greater EC to manage their languages compared to bilinguals who use two languages with less overlap. We tested three groups of bilinguals with language pairs ranging from high- to low-similarity (German-English (GE, Polish-English (PE, and Arabic-English (AE, respectively and a group of English monolinguals on a Stroop and Simon task. Two components of the bilingual advantage were investigated: an interference advantage, such that bilinguals have smaller interference effects than monolinguals; and a global RT advantage, such that bilinguals are faster overall than monolinguals. Between bilingual groups, these effects were expected to be modulated by script similarity. AE bilinguals showed the smallest Stroop interference effects, but the longest overall RTs in both tasks. These seemingly contradictory results are explained by the presence of cross-linguistic interference in the Stroop task. We conclude that similar-script bilinguals demonstrated more effective domain-general EC than different-script bilinguals, since high orthographic overlap creates more cross-linguistic activation and increases the daily demands on cognitive control. The role of individual variation is also discussed. These results suggest that script similarity is an important variable to consider in investigations of bilingual executive control abilities.

  10. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  11. Similarity search processing. Paralelization and indexing technologies.

    Directory of Open Access Journals (Sweden)

    Eder Dos Santos

    2015-08-01

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

  12. Parallel trajectory similarity joins in spatial networks

    KAUST Repository

    Shang, Shuo

    2018-04-04

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

  13. Parallel trajectory similarity joins in spatial networks

    KAUST Repository

    Shang, Shuo; Chen, Lisi; Wei, Zhewei; Jensen, Christian S.; Zheng, Kai; Kalnis, Panos

    2018-01-01

    The matching of similar pairs of objects, called similarity join, is fundamental functionality in data management. We consider two cases of trajectory similarity joins (TS-Joins), including a threshold-based join (Tb-TS-Join) and a top-k TS-Join (k-TS-Join), where the objects are trajectories of vehicles moving in road networks. Given two sets of trajectories and a threshold θ, the Tb-TS-Join returns all pairs of trajectories from the two sets with similarity above θ. In contrast, the k-TS-Join does not take a threshold as a parameter, and it returns the top-k most similar trajectory pairs from the two sets. The TS-Joins target diverse applications such as trajectory near-duplicate detection, data cleaning, ridesharing recommendation, and traffic congestion prediction. With these applications in mind, we provide purposeful definitions of similarity. To enable efficient processing of the TS-Joins on large sets of trajectories, we develop search space pruning techniques and enable use of the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer search framework that lays the foundation for the algorithms for the Tb-TS-Join and the k-TS-Join that rely on different pruning techniques to achieve efficiency. For each trajectory, the algorithms first find similar trajectories. Then they merge the results to obtain the final result. The algorithms for the two joins exploit different upper and lower bounds on the spatiotemporal trajectory similarity and different heuristic scheduling strategies for search space pruning. Their per-trajectory searches are independent of each other and can be performed in parallel, and the mergings have constant cost. An empirical study with real data offers insight in the performance of the algorithms and demonstrates that they are capable of outperforming well-designed baseline algorithms by an order of magnitude.

  14. Are calanco landforms similar to river basins?

    Science.gov (United States)

    Caraballo-Arias, N A; Ferro, V

    2017-12-15

    In the past badlands have been often considered as ideal field laboratories for studying landscape evolution because of their geometrical similarity to larger fluvial systems. For a given hydrological process, no scientific proof exists that badlands can be considered a model of river basin prototypes. In this paper the measurements carried out on 45 Sicilian calanchi, a type of badlands that appears as a small-scale hydrographic unit, are used to establish their morphological similarity with river systems whose data are available in the literature. At first the geomorphological similarity is studied by identifying the dimensionless groups, which can assume the same value or a scaled one in a fixed ratio, representing drainage basin shape, stream network and relief properties. Then, for each property, the dimensionless groups are calculated for the investigated calanchi and the river basins and their corresponding scale ratio is evaluated. The applicability of Hack's, Horton's and Melton's laws for establishing similarity criteria is also tested. The developed analysis allows to conclude that a quantitative morphological similarity between calanco landforms and river basins can be established using commonly applied dimensionless groups. In particular, the analysis showed that i) calanchi and river basins have a geometrically similar shape respect to the parameters Rf and Re with a scale factor close to 1, ii) calanchi and river basins are similar respect to the bifurcation and length ratios (λ=1), iii) for the investigated calanchi the Melton number assumes values less than that (0.694) corresponding to the river case and a scale ratio ranging from 0.52 and 0.78 can be used, iv) calanchi and river basins have similar mean relief ratio values (λ=1.13) and v) calanchi present active geomorphic processes and therefore fall in a more juvenile stage with respect to river basins. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Domain shape instabilities and dendrite domain growth in uniaxial ferroelectrics

    Science.gov (United States)

    Shur, Vladimir Ya.; Akhmatkhanov, Andrey R.

    2018-01-01

    The effects of domain wall shape instabilities and the formation of nanodomains in front of moving walls obtained in various uniaxial ferroelectrics are discussed. Special attention is paid to the formation of self-assembled nanoscale and dendrite domain structures under highly non-equilibrium switching conditions. All obtained results are considered in the framework of the unified kinetic approach to domain structure evolution based on the analogy with first-order phase transformation. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

  16. Separated matter and antimatter domains with vanishing domain walls

    Energy Technology Data Exchange (ETDEWEB)

    Dolgov, A.D.; Godunov, S.I.; Rudenko, A.S.; Tkachev, I.I., E-mail: dolgov@fe.infn.it, E-mail: sgodunov@itep.ru, E-mail: a.s.rudenko@inp.nsk.su, E-mail: tkachev@ms2.inr.ac.ru [Physics Department and Laboratory of Cosmology and Elementary Particle Physics, Novosibirsk State University, Pirogova st. 2, Novosibirsk, 630090 (Russian Federation)

    2015-10-01

    We present a model of spontaneous (or dynamical) C and CP violation where it is possible to generate domains of matter and antimatter separated by cosmologically large distances. Such C(CP) violation existed only in the early universe and later it disappeared with the only trace of generated baryonic and/or antibaryonic domains. So the problem of domain walls in this model does not exist. These features are achieved through a postulated form of interaction between inflaton and a new scalar field, realizing short time C(CP) violation.

  17. Multicriteria Similarity-Based Anomaly Detection Using Pareto Depth Analysis.

    Science.gov (United States)

    Hsiao, Ko-Jen; Xu, Kevin S; Calder, Jeff; Hero, Alfred O

    2016-06-01

    We consider the problem of identifying patterns in a data set that exhibits anomalous behavior, often referred to as anomaly detection. Similarity-based anomaly detection algorithms detect abnormally large amounts of similarity or dissimilarity, e.g., as measured by the nearest neighbor Euclidean distances between a test sample and the training samples. In many application domains, there may not exist a single dissimilarity measure that captures all possible anomalous patterns. In such cases, multiple dissimilarity measures can be defined, including nonmetric measures, and one can test for anomalies by scalarizing using a nonnegative linear combination of them. If the relative importance of the different dissimilarity measures are not known in advance, as in many anomaly detection applications, the anomaly detection algorithm may need to be executed multiple times with different choices of weights in the linear combination. In this paper, we propose a method for similarity-based anomaly detection using a novel multicriteria dissimilarity measure, the Pareto depth. The proposed Pareto depth analysis (PDA) anomaly detection algorithm uses the concept of Pareto optimality to detect anomalies under multiple criteria without having to run an algorithm multiple times with different choices of weights. The proposed PDA approach is provably better than using linear combinations of the criteria, and shows superior performance on experiments with synthetic and real data sets.

  18. Lattice gas simulations of replicating domains

    International Nuclear Information System (INIS)

    Dawson, S.P.; Hasslacher, B.; Pearson, J.E.

    1993-01-01

    We use the lattice gas cellular automation (LGCA) developed to simulate a process of pattern-formation recently observed in reaction-diffusion systems. We study the reaction mechanism, which is an extension of the Selkov model for glycolytic oscillations. We are able to reproduce the self-replicating domains observed in this work. We use the LGCA simulation to estimate the smallest length-scale on which this process can occur under conditions encountered in the cell. These estimates are similar to those obtained for Turing patterns in the same setting

  19. Lattice gas simulations of replicating domains

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, S.P.; Hasslacher, B.; Pearson, J.E.

    1993-12-31

    We use the lattice gas cellular automation (LGCA) developed to simulate a process of pattern-formation recently observed in reaction-diffusion systems. We study the reaction mechanism, which is an extension of the Selkov model for glycolytic oscillations. We are able to reproduce the self-replicating domains observed in this work. We use the LGCA simulation to estimate the smallest length-scale on which this process can occur under conditions encountered in the cell. These estimates are similar to those obtained for Turing patterns in the same setting.

  20. Corium Oxidation at Temperatures Above 2000 K

    International Nuclear Information System (INIS)

    Hagrman, Donald L.; Rempe, Joy L.

    2001-01-01

    A mechanistic model, based on a quasi-equilibrium analysis of oxidation reactions, is proposed for predicting high-temperature corium oxidation. The analysis suggests that oxide forming on the surface of corium containing uranium, zirconium, and iron is similar to the oxides formed on zirconium and uranium as long as there is a small percentage of unoxidized zirconium or uranium in the metallic phase. This is because of the higher affinity of zirconium and uranium for oxygen. Hence, oxidation rates and heat production rates are similar to (U,Zr) compounds until nearly all the uranium and zirconium in the corium oxidizes. Oxidation rates after this point are predicted to be similar to those implied by the oxide thickness present when the forming oxide ceases to be protective, and heat generation rates should be similar to those implied by iron oxidation, i.e., ∼4% of the zirconium oxidation heating rate.The maximum atomic ratio of unoxidized iron to unoxidized liquid zirconium plus uranium for the formation of a solid protective oxide below 2800 K is estimated for a temperature, T (in Kelvin), as follows:(unoxidized iron)/(unoxidized zirconium + turanium) = (1/28){5.7/exp[-(147 061 + 12.08T log(T) - 61.03T - 0.000555T 2 /1.986T)]} 1/2 .As long as this limit is not exceeded, either zirconium or uranium metal oxidation rates and heating describe the corium oxidation rate. If this limit is exceeded, diffusion of steam to the corium surface will limit the oxidation rate, and linear time-dependent growth of a nonprotective, mostly FeO, layer will occur below the protective (Zr,U) O 2 scale. When this happens, the oxidation should be at the constant rate given by the thickness of the protective layer. Heat generation should be similar to that of iron oxidation

  1. Corium Oxidation at Temperatures Above 2000 K

    Energy Technology Data Exchange (ETDEWEB)

    Hagrman, Donald Lee; Rempe, Joy Lynn

    2001-02-01

    A mechanistic model, based on a quasi-equilibrium analysis of oxidation reactions, is proposed for predicting high-temperature corium oxidation. The analysis suggests that oxide forming on the surface of corium containing uranium, zirconium, and iron is similar to the oxides formed on zirconium and uranium as long as there is a small percentage of unoxidized zirconium or uranium in the metallic phase. This is because of the higher affinity of zirconium and uranium for oxygen. Hence, oxidation rates and heat production rates are similar to (U,Zr) compounds until nearly all the uranium and zirconium in the corium oxidizes. Oxidation rates after this point are predicted to be similar to those implied by the oxide thickness present when the forming oxide ceases to be protective, and heat generation rates should be similar to those implied by iron oxidation, i.e., ~4% of the zirconium oxidation heating rate. The maximum atomic ratio of unoxidized iron to unoxidized liquid zirconium plus uranium for the formation of a solid protective oxide below 2800 K is estimated for a temperature, T (in Kelvin), as follows: (unoxidized iron)/(unoxidized zirconium + turanium) = (1/28){5.7/exp[-(147 061 + 12.08T log(T) - 61.03T - 0.000555T2/1.986T)]}1/2. As long as this limit is not exceeded, either zirconium or uranium metal oxidation rates and heating describe the corium oxidation rate. If this limit is exceeded, diffusion of steam to the corium surface will limit the oxidation rate, and linear time-dependent growth of a nonprotective, mostly FeO, layer will occur below the protective (Zr,U) O2 scale. When this happens, the oxidation should be at the constant rate given by the thickness of the protective layer. Heat generation should be similar to that of iron oxidation.

  2. Oxidation of uraninite

    International Nuclear Information System (INIS)

    Janeczek, J.; Ewing, R.C.

    1993-06-01

    Samples of uraninite and pitchblende annealed at 1200 degrees C in H 2 , and untreated pitchblende were sequentially oxidized in air at 180-190 degrees C, 230 degrees C, and 300 degrees C. Uraninite and untreated pitchblende oxidized to the U 4 O 9 -type oxide, and their x-ray symmetry remained isometric up to 300 degrees C. Reduced pitchblende, after oxidation to UO 2+x and U 4 O 9 -type oxides, transformed into α-U 3 O 8 at 300 degrees C. Two major mechanisms control uraninite and untreated pitchblende stability during oxidation: 1. Th and/or lanthanide elements maintain charge balance and block oxygen interstitials near impurity cations; 2. the uraninite structure saturates with respect to excess and radiation-induced oxygen interstitials. Untreated pitchblende during oxidation behaved similarly to irradiated UO 2 in spent nuclear fuel; whereas, reduced pitchblende resembled non-irradiated UO 2 . An analysis of the data in the literature, as well as our own efforts (XRD, EMPA, SEM, AEM) to identify U 3 O 7 in samples form Cigar Lake, Canada, failed to provide conclusive evidence of the natural occurrence of tetragonal αU 3 O 7 . Most probably, reported occurrences of U 3 O 7 are mixtures of isometric uraninites of slightly different compositions, 45 refs

  3. Identifying mechanistic similarities in drug responses

    KAUST Repository

    Zhao, C.

    2012-05-15

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

  4. Semantic similarity between ontologies at different scales

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

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

  5. Ferroelectric negative capacitance domain dynamics

    Science.gov (United States)

    Hoffmann, Michael; Khan, Asif Islam; Serrao, Claudy; Lu, Zhongyuan; Salahuddin, Sayeef; Pešić, Milan; Slesazeck, Stefan; Schroeder, Uwe; Mikolajick, Thomas

    2018-05-01

    Transient negative capacitance effects in epitaxial ferroelectric Pb(Zr0.2Ti0.8)O3 capacitors are investigated with a focus on the dynamical switching behavior governed by domain nucleation and growth. Voltage pulses are applied to a series connection of the ferroelectric capacitor and a resistor to directly measure the ferroelectric negative capacitance during switching. A time-dependent Ginzburg-Landau approach is used to investigate the underlying domain dynamics. The transient negative capacitance is shown to originate from reverse domain nucleation and unrestricted domain growth. However, with the onset of domain coalescence, the capacitance becomes positive again. The persistence of the negative capacitance state is therefore limited by the speed of domain wall motion. By changing the applied electric field, capacitor area or external resistance, this domain wall velocity can be varied predictably over several orders of magnitude. Additionally, detailed insights into the intrinsic material properties of the ferroelectric are obtainable through these measurements. A new method for reliable extraction of the average negative capacitance of the ferroelectric is presented. Furthermore, a simple analytical model is developed, which accurately describes the negative capacitance transient time as a function of the material properties and the experimental boundary conditions.

  6. Effect of domain size and interface characteristics on the impact resistance of selected polymer composites

    Science.gov (United States)

    Viratyaporn, Wantinee

    Nanocomposite technology has advanced considerably in recent years and excellent engineering properties have been achieved in numerous systems. In multiphase materials the enhancement of properties relies heavily on the nature at the interphase region between polymer domains and nanoparticle reinforcements. Strong adhesion between the phases provides excellent load-transfer and good mechanical elastic modulus and strength, whereas weak interaction contributes to crack deflection mechanisms and toughness. Polymer molecules are large and the presence of comparably sized filler particles affects chain gyration, which in turn influences the conformation of the polymer and the properties of the composite. Nanoparticles were incorporated into a poly(methyl methacrylate) matrix by means of in situ free radical (bulk) polymerization. Aluminum oxide and zinc oxide nanoparticles were added to study the effects of particle chemistry and shape on selected mechanical properties such as impact resistance, which showed significant improvement at a certain loading of zinc oxide. The elongated shape of zinc oxide particles appears to promote crack deflection processes and to introduce a pull-out mechanism similar to that observed in fiber composite systems. Moreover, the thermal stability of PMMA was improved with the addition of nanoparticles, apparently by steric hindrance of polymer chain motion and a second mechanism related to the dipole inducing effect of the oxide particles. The sensitivity of infrared spectroscopy to changes in molecular dipoles was used to study the nature of the polymer/particle interface. The results revealed some interesting aspects of the secondary bonds between polymers and oxides. Raman spectroscopy was used to investigate the extent of polymerization and changes in polymer conformation. A degree of polymerization of 93% was achieved in neat PMMA, and even when 5.0 v/o of PGMEA was introduced into the system no monomer was detected. However, when

  7. Oxide ceramics

    International Nuclear Information System (INIS)

    Ryshkewitch, E.; Richerson, D.W.

    1985-01-01

    The book explores single-phase ceramic oxide systems from the standpoint of physical chemistry and technology. This second edition also focuses on advances in technology since publication of the original edition. These include improvements in raw materials and forming and sintering techniques, and the major role that oxide ceramics have had in development of advanced products and processes. The text is divided into five major sections: general fundamentals of oxide ceramics, advances in aluminum oxide technology, advances in zirconia technology, and advances in beryllium oxide technology

  8. Evaluating, Comparing, and Interpreting Protein Domain Hierarchies

    Science.gov (United States)

    2014-01-01

    Abstract Arranging protein domain sequences hierarchically into evolutionarily divergent subgroups is important for investigating evolutionary history, for speeding up web-based similarity searches, for identifying sequence determinants of protein function, and for genome annotation. However, whether or not a particular hierarchy is optimal is often unclear, and independently constructed hierarchies for the same domain can often differ significantly. This article describes methods for statistically evaluating specific aspects of a hierarchy, for probing the criteria underlying its construction and for direct comparisons between hierarchies. Information theoretical notions are used to quantify the contributions of specific hierarchical features to the underlying statistical model. Such features include subhierarchies, sequence subgroups, individual sequences, and subgroup-associated signature patterns. Underlying properties are graphically displayed in plots of each specific feature's contributions, in heat maps of pattern residue conservation, in “contrast alignments,” and through cross-mapping of subgroups between hierarchies. Together, these approaches provide a deeper understanding of protein domain functional divergence, reveal uncertainties caused by inconsistent patterns of sequence conservation, and help resolve conflicts between competing hierarchies. PMID:24559108

  9. Wavefield extrapolation in pseudodepth domain

    KAUST Repository

    Ma, Xuxin

    2013-02-01

    Wavefields are commonly computed in the Cartesian coordinate frame. Its efficiency is inherently limited due to spatial oversampling in deep layers, where the velocity is high and wavelengths are long. To alleviate this computational waste due to uneven wavelength sampling, we convert the vertical axis of the conventional domain from depth to vertical time or pseudodepth. This creates a nonorthognal Riemannian coordinate system. Isotropic and anisotropic wavefields can be extrapolated in the new coordinate frame with improved efficiency and good consistency with Cartesian domain extrapolation results. Prestack depth migrations are also evaluated based on the wavefield extrapolation in the pseudodepth domain.© 2013 Society of Exploration Geophysicists. All rights reserved.

  10. MEASURING THE PERFORMANCE OF SIMILARITY PROPAGATION IN AN SEMANTIC SEARCH ENGINE

    Directory of Open Access Journals (Sweden)

    S. K. Jayanthi

    2013-10-01

    Full Text Available In the current scenario, web page result personalization is playing a vital role. Nearly 80 % of the users expect the best results in the first page itself without having any persistence to browse longer in URL mode. This research work focuses on two main themes: Semantic web search through online and Domain based search through offline. The first part is to find an effective method which allows grouping similar results together using BookShelf Data Structure and organizing the various clusters. The second one is focused on the academic domain based search through offline. This paper focuses on finding documents which are similar and how Vector space can be used to solve it. So more weightage is given for the principles and working methodology of similarity propagation. Cosine similarity measure is used for finding the relevancy among the documents.

  11. Measure of Node Similarity in Multilayer Networks

    DEFF Research Database (Denmark)

    Møllgaard, Anders; Zettler, Ingo; Dammeyer, Jesper

    2016-01-01

    The weight of links in a network is often related to the similarity of thenodes. Here, we introduce a simple tunable measure for analysing the similarityof nodes across different link weights. In particular, we use the measure toanalyze homophily in a group of 659 freshman students at a large...... university.Our analysis is based on data obtained using smartphones equipped with customdata collection software, complemented by questionnaire-based data. The networkof social contacts is represented as a weighted multilayer network constructedfrom different channels of telecommunication as well as data...... might bepresent in one layer of the multilayer network and simultaneously be absent inthe other layers. For a variable such as gender, our measure reveals atransition from similarity between nodes connected with links of relatively lowweight to dis-similarity for the nodes connected by the strongest...

  12. A Novel Hybrid Similarity Calculation Model

    Directory of Open Access Journals (Sweden)

    Xiaoping Fan

    2017-01-01

    Full Text Available This paper addresses the problems of similarity calculation in the traditional recommendation algorithms of nearest neighbor collaborative filtering, especially the failure in describing dynamic user preference. Proceeding from the perspective of solving the problem of user interest drift, a new hybrid similarity calculation model is proposed in this paper. This model consists of two parts, on the one hand the model uses the function fitting to describe users’ rating behaviors and their rating preferences, and on the other hand it employs the Random Forest algorithm to take user attribute features into account. Furthermore, the paper combines the two parts to build a new hybrid similarity calculation model for user recommendation. Experimental results show that, for data sets of different size, the model’s prediction precision is higher than the traditional recommendation algorithms.

  13. Universal self-similarity of propagating populations.

    Science.gov (United States)

    Eliazar, Iddo; Klafter, Joseph

    2010-07-01

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

  14. Universal self-similarity of propagating populations

    Science.gov (United States)

    Eliazar, Iddo; Klafter, Joseph

    2010-07-01

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

  15. Trajectory similarity join in spatial networks

    KAUST Repository

    Shang, Shuo; Chen, Lisi; Wei, Zhewei; Jensen, Christian S.; Zheng, Kai; Kalnis, Panos

    2017-01-01

    With these applications in mind, we provide a purposeful definition of similarity. To enable efficient TS-Join processing on large sets of trajectories, we develop search space pruning techniques and take into account the parallel processing capabilities of modern processors. Specifically, we present a two-phase divide-and-conquer algorithm. For each trajectory, the algorithm first finds similar trajectories. Then it merges the results to achieve a final result. The algorithm exploits an upper bound on the spatiotemporal similarity and a heuristic scheduling strategy for search space pruning. The algorithm's per-trajectory searches are independent of each other and can be performed in parallel, and the merging has constant cost. An empirical study with real data offers insight in the performance of the algorithm and demonstrates that is capable of outperforming a well-designed baseline algorithm by an order of magnitude.

  16. Phonological similarity in working memory span tasks.

    Science.gov (United States)

    Chow, Michael; Macnamara, Brooke N; Conway, Andrew R A

    2016-08-01

    In a series of four experiments, we explored what conditions are sufficient to produce a phonological similarity facilitation effect in working memory span tasks. By using the same set of memoranda, but differing the secondary-task requirements across experiments, we showed that a phonological similarity facilitation effect is dependent upon the semantic relationship between the memoranda and the secondary-task stimuli, and is robust to changes in the representation, ordering, and pool size of the secondary-task stimuli. These findings are consistent with interference accounts of memory (Brown, Neath, & Chater, Psychological Review, 114, 539-576, 2007; Oberauer, Lewandowsky, Farrell, Jarrold, & Greaves, Psychonomic Bulletin & Review, 19, 779-819, 2012), whereby rhyming stimuli provide a form of categorical similarity that allows distractors to be excluded from retrieval at recall.

  17. Unveiling Music Structure Via PLSA Similarity Fusion

    DEFF Research Database (Denmark)

    Arenas-García, Jerónimo; Meng, Anders; Petersen, Kaare Brandt

    2007-01-01

    Nowadays there is an increasing interest in developing methods for building music recommendation systems. In order to get a satisfactory performance from such a system, one needs to incorporate as much information about songs similarity as possible; however, how to do so is not obvious. In this p......Nowadays there is an increasing interest in developing methods for building music recommendation systems. In order to get a satisfactory performance from such a system, one needs to incorporate as much information about songs similarity as possible; however, how to do so is not obvious...... observed similarities can be satisfactorily explained using the latent semantics. Additionally, this approach significantly simplifies the song retrieval phase, leading to a more practical system implementation. The suitability of the PLSA model for representing music structure is studied in a simplified...

  18. The Control of Anisotropic Transport in Manganites by Stripy Domains

    Science.gov (United States)

    Ju, Changcheng; Lu, Xiaomei; Chu, Yinghao

    2014-03-01

    Epitaxial thin film acts as a significant tool to investigate novel phenomena of complex oxide systems. Extrinsic constraint1 of uniform or certain designed buffer layer strain could be easily implanted to these materials. However, the strain distribution might be quite complicated by involving micro- or nano-lattice distortions which could partially relax the strain and determine the complex phase diagrams of thin film, meanwhile introducing structural and physical inhomogeneities. In this work , we report 71° striped ferroelectric domains created in BFO can also epitaxially lock the perovskite manganites leading to the emerge of ordered structural domain. LSMO/BFO hetero-epitaxial samples are deposited by PLD. The 71° periodic striped domains and coherent growth are demonstrated by PFM and X-ray analysis. Plan-view TEM and X-ray RSM have been used to confirm the epitaxial relationships of the functional layers and IP lattice constant. Both the simulation and structural analysis demonstrate we can create a periodic ordered stripe structural domain in LSMO. And this will leave an anisotropic distribution of structural domain walls which makes it possible to capture the anisotropic tunneling for strong electron-lattice coupling in manganites. Temperature-dependent resistivity measurements reveal a substantial anisotropic resistivities and a remarkable shift of the MI transition between the perpendicular and parallel to the stripe domain directions.

  19. Hepatitis C virus NS4B carboxy terminal domain is a membrane binding domain

    Directory of Open Access Journals (Sweden)

    Spaan Willy JM

    2009-05-01

    Full Text Available Abstract Background Hepatitis C virus (HCV induces membrane rearrangements during replication. All HCV proteins are associated to membranes, pointing out the importance of membranes for HCV. Non structural protein 4B (NS4B has been reported to induce cellular membrane alterations like the membranous web. Four transmembrane segments in the middle of the protein anchor NS4B to membranes. An amphipatic helix at the amino-terminus attaches to membranes as well. The carboxy-terminal domain (CTD of NS4B is highly conserved in Hepaciviruses, though its function remains unknown. Results A cytosolic localization is predicted for the NS4B-CTD. However, using membrane floatation assays and immunofluorescence, we now show targeting of the NS4B-CTD to membranes. Furthermore, a profile-profile search, with an HCV NS4B-CTD multiple sequence alignment, indicates sequence similarity to the membrane binding domain of prokaryotic D-lactate dehydrogenase (d-LDH. The crystal structure of E. coli d-LDH suggests that the region similar to NS4B-CTD is located in the membrane binding domain (MBD of d-LDH, implying analogy in membrane association. Targeting of d-LDH to membranes occurs via electrostatic interactions of positive residues on the outside of the protein with negative head groups of lipids. To verify that anchorage of d-LDH MBD and NS4B-CTD is analogous, NS4B-CTD mutants were designed to disrupt these electrostatic interactions. Membrane association was confirmed by swopping the membrane contacting helix of d-LDH with the corresponding domain of the 4B-CTD. Furthermore, the functionality of these residues was tested in the HCV replicon system. Conclusion Together these data show that NS4B-CTD is associated to membranes, similar to the prokaryotic d-LDH MBD, and is important for replication.

  20. Large margin classification with indefinite similarities

    KAUST Repository

    Alabdulmohsin, Ibrahim

    2016-01-07

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

  1. Inhibitory effect of organotin compounds on rat neuronal nitric oxide synthase through interaction with calmodulin

    International Nuclear Information System (INIS)

    Ohashi, Koji; Kominami, Shiro; Yamazaki, Takeshi; Ohta, Shigeru; Kitamura, Shigeyuki

    2004-01-01

    Organotin compounds, triphenyltin (TPT), tributyltin, dibutyltin, and monobutyltin (MBT), showed potent inhibitory effects on both L-arginine oxidation to nitric oxide and L-citrulline, and cytochrome c reduction catalyzed by recombinant rat neuronal nitric oxide synthase (nNOS). The two inhibitory effects were almost parallel. MBT and TPT showed the highest inhibitory effects, followed by tributyltin and dibutyltin; TPT and MBT showed inhibition constant (IC 50 ) values of around 10 μM. Cytochrome c reduction activity was markedly decreased by removal of calmodulin (CaM) from the complete mixture, and the decrease was similar to the extent of inhibition by TPT and MBT. The inhibitory effect of MBT on the cytochrome c reducing activity was rapidly attenuated upon dilution of the inhibitor, and addition of a high concentration of CaM reactivated the cytochrome c reduction activity inhibited by MBT. However, other cofactors such as FAD, FMN or tetrahydrobiopterin had no such ability. The inhibitory effect of organotin compounds (100 μM) on L-arginine oxidation of nNOS almost vanished when the amount of CaM was sufficiently increased (150-300 μM). It was confirmed by CaM-agarose column chromatography that the dissociation of nNOS-CaM complex was induced by organotin compounds. These results indicate that organotin compounds disturb the interaction between CaM and nNOS, thereby inhibiting electron transfer from the reductase domain to cytochrome c and the oxygenase domain

  2. Similarity joins in relational database systems

    CERN Document Server

    Augsten, Nikolaus

    2013-01-01

    State-of-the-art database systems manage and process a variety of complex objects, including strings and trees. For such objects equality comparisons are often not meaningful and must be replaced by similarity comparisons. This book describes the concepts and techniques to incorporate similarity into database systems. We start out by discussing the properties of strings and trees, and identify the edit distance as the de facto standard for comparing complex objects. Since the edit distance is computationally expensive, token-based distances have been introduced to speed up edit distance comput

  3. Outsourced Similarity Search on Metric Data Assets

    DEFF Research Database (Denmark)

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

    2012-01-01

    . Outsourcing offers the data owner scalability and a low initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise confidential. Given this setting, the paper presents techniques that transform the data prior to supplying......This paper considers a cloud computing setting in which similarity querying of metric data is outsourced to a service provider. The data is to be revealed only to trusted users, not to the service provider or anyone else. Users query the server for the most similar data objects to a query example...

  4. Measure of Node Similarity in Multilayer Networks

    DEFF Research Database (Denmark)

    Møllgaard, Anders; Zettler, Ingo; Dammeyer, Jesper

    2016-01-01

    university.Our analysis is based on data obtained using smartphones equipped with customdata collection software, complemented by questionnaire-based data. The networkof social contacts is represented as a weighted multilayer network constructedfrom different channels of telecommunication as well as data...... might bepresent in one layer of the multilayer network and simultaneously be absent inthe other layers. For a variable such as gender, our measure reveals atransition from similarity between nodes connected with links of relatively lowweight to dis-similarity for the nodes connected by the strongest...

  5. Cultural similarity and adjustment of expatriate academics

    DEFF Research Database (Denmark)

    Selmer, Jan; Lauring, Jakob

    2009-01-01

    The findings of a number of recent empirical studies of business expatriates, using different samples and methodologies, seem to support the counter-intuitive proposition that cultural similarity may be as difficult to adjust to as cultural dissimilarity. However, it is not obvious...... and non-EU countries. Results showed that although the perceived cultural similarity between host and home country for the two groups of investigated respondents was different, there was neither any difference in their adjustment nor in the time it took for them to become proficient. Implications...

  6. Topology Based Domain Search (TBDS)

    National Research Council Canada - National Science Library

    Manning, William

    2002-01-01

    This effort will explore radical changes in the way Domain Name System (DNS) is used by endpoints in a network to improve the resilience of the endpoint and its applications in the face of dynamically changing infrastructure topology...

  7. Domain Discretization and Circle Packings

    DEFF Research Database (Denmark)

    Dias, Kealey

    A circle packing is a configuration of circles which are tangent with one another in a prescribed pattern determined by a combinatorial triangulation, where the configuration fills a planar domain or a two-dimensional surface. The vertices in the triangulation correspond to centers of circles...... to domain discretization problems such as triangulation and unstructured mesh generation techniques. We wish to ask ourselves the question: given a cloud of points in the plane (we restrict ourselves to planar domains), is it possible to construct a circle packing preserving the positions of the vertices...... and constrained meshes having predefined vertices as constraints. A standard method of two-dimensional mesh generation involves conformal mapping of the surface or domain to standardized shapes, such as a disk. Since circle packing is a new technique for constructing discrete conformal mappings, it is possible...

  8. Heliborne time domain electromagnetic system

    International Nuclear Information System (INIS)

    Bhattacharya, S.

    2009-01-01

    Atomic Minerals Directorate (AMD), are using heliborne and ground time domain electromagnetic (TDEM) system for the exploration of deep seated unconformity type uranium deposits. Uranium has been explored in various parts of the world like Athabasca basin using time domain electromagnetic system. AMD has identified some areas in India where such deposits are available. Apart from uranium exploration, the TDEM systems are used for the exploration of deep seated minerals like diamonds. Bhabha Atomic Research Centre (BARC) is involved in the indigenous design of the heliborne time domain system since this system is useful for DAE and also it has a scope of wide application. In this paper we discuss about the principle of time domain electromagnetic systems, their capabilities and the development and problems of such system for various other mineral exploration. (author)

  9. Anisotropy of domain wall resistance

    Science.gov (United States)

    Viret; Samson; Warin; Marty; Ott; Sondergard; Klein; Fermon

    2000-10-30

    The resistive effect of domain walls in FePd films with perpendicular anisotropy was studied experimentally as a function of field and temperature. The films were grown directly on MgO substrates, which induces an unusual virgin magnetic configuration composed of 60 nm wide parallel stripe domains. This allowed us to carry out the first measurements of the anisotropy of domain wall resistivity in the two configurations of current perpendicular and parallel to the walls. At 18 K, we find 8.2% and 1.3% for the domain wall magnetoresistance normalized to the wall width (8 nm) in these two respective configurations. These values are consistent with the predictions of Levy and Zhang.

  10. Metrology for terahertz time-domain spectrometers

    Science.gov (United States)

    Molloy, John F.; Naftaly, Mira

    2015-12-01

    In recent years the terahertz time-domain spectrometer (THz TDS) [1] has emerged as a key measurement device for spectroscopic investigations in the frequency range of 0.1-5 THz. To date, almost every type of material has been studied using THz TDS, including semiconductors, ceramics, polymers, metal films, liquid crystals, glasses, pharmaceuticals, DNA molecules, proteins, gases, composites, foams, oils, and many others. Measurements with a TDS are made in the time domain; conversion from the time domain data to a frequency spectrum is achieved by applying the Fourier Transform, calculated numerically using the Fast Fourier Transform (FFT) algorithm. As in many other types of spectrometer, THz TDS requires that the sample data be referenced to similarly acquired data with no sample present. Unlike frequency-domain spectrometers which detect light intensity and measure absorption spectra, a TDS records both amplitude and phase information, and therefore yields both the absorption coefficient and the refractive index of the sample material. The analysis of the data from THz TDS relies on the assumptions that: a) the frequency scale is accurate; b) the measurement of THz field amplitude is linear; and c) that the presence of the sample does not affect the performance characteristics of the instrument. The frequency scale of a THz TDS is derived from the displacement of the delay line; via FFT, positioning errors may give rise to frequency errors that are difficult to quantify. The measurement of the field amplitude in a THz TDS is required to be linear with a dynamic range of the order of 10 000. And attention must be given to the sample positioning and handling in order to avoid sample-related errors.

  11. Structure of an isolated unglycosylated antibody CH2 domain

    International Nuclear Information System (INIS)

    Prabakaran, Ponraj; Vu, Bang K.; Gan, Jianhua; Feng, Yang; Dimitrov, Dimiter S.; Ji, Xinhua

    2008-01-01

    The crystal structure of an isolated unglycosylated antibody C H 2 domain has been determined at 1.7 Å resolution. The C H 2 (C H 3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein–protein interactions with another C H 2 domain solely through sugar moieties. The N-linked glycosylation at Asn297 is conserved in mammalian IgGs as well as in homologous regions of other antibody isotypes. To examine the structural details of the C H 2 domain in the absence of glycosylation and other antibody domains, the crystal structure of an isolated unglycosylated antibody γ1 C H 2 domain was determined at 1.7 Å resolution and compared with corresponding C H 2 structures from intact Fc, IgG and Fc receptor complexes. Furthermore, the oligomeric state of the protein in solution was studied using size-exclusion chromatography. The results suggested that the unglycosylated human antibody C H 2 domain is a monomer and that its structure is similar to that found in the intact Fc, IgG and Fc receptor complex structures. However, certain structural variations were observed in the Fc receptor-binding sites. Owing to its small size, stability and non-immunogenic Ig template, the C H 2-domain structure could be useful for the development by protein design of antibody domains exerting effector functions and/or antigen specificity and as a robust scaffold in protein-engineering applications

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

    Science.gov (United States)

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

    2006-08-01

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

  13. Maneuver from the Air Domain

    Science.gov (United States)

    2016-05-26

    Overload From the previous discussion, cognitive maneuver seeks to degrade the enemy’s capacity for...in all domains, the ability to maneuver from the air domain in the cognitive sense, comes primarily from air power’s unique ability to overload the... cognitive maneuver mechanisms developed in the 1980s as part of broader maneuver warfare theory. The result is a proposed definition of maneuver from

  14. Ferroelectric Negative Capacitance Domain Dynamics

    OpenAIRE

    Hoffmann, Michael; Khan, Asif Islam; Serrao, Claudy; Lu, Zhongyuan; Salahuddin, Sayeef; Pešić, Milan; Slesazeck, Stefan; Schroeder, Uwe; Mikolajick, Thomas

    2017-01-01

    Transient negative capacitance effects in epitaxial ferroelectric Pb(Zr$_{0.2}$Ti$_{0.8}$)O$_3$ capacitors are investigated with a focus on the dynamical switching behavior governed by domain nucleation and growth. Voltage pulses are applied to a series connection of the ferroelectric capacitor and a resistor to directly measure the ferroelectric negative capacitance during switching. A time-dependent Ginzburg-Landau approach is used to investigate the underlying domain dynamics. The transien...

  15. Gravity and domain wall problem

    International Nuclear Information System (INIS)

    Rai, B.; Senjanovic, G.

    1992-11-01

    It is well known that the spontaneous breaking of discrete symmetries may lead to conflict with big-bang cosmology. This is due to formation of domain walls which give unacceptable contribution to the energy density of the universe. On the other hand, it is expected that gravity breaks global symmetries explicitly. In this work we propose that this could provide a natural solution to the domain-wall problem. (author). 17 refs

  16. Incompleteness in the finite domain

    Czech Academy of Sciences Publication Activity Database

    Pudlák, Pavel

    2017-01-01

    Roč. 23, č. 4 (2017), s. 405-441 ISSN 1079-8986 EU Projects: European Commission(XE) 339691 - FEALORA Institutional support: RVO:67985840 Keywords : finite domain Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics Impact factor: 0.742, year: 2016 https://www.cambridge.org/core/journals/bulletin-of-symbolic-logic/article/incompleteness-in-the-finite-domain/D239B1761A73DCA534A4805A76D81C76

  17. Clustering biomolecular complexes by residue contacts similarity

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, João; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J; Garcia Lopes Maia Rodrigues, João

    Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions.

  18. Similarity principles for equipment qualification by experience

    International Nuclear Information System (INIS)

    Kana, D.D.; Pomerening, D.J.

    1988-07-01

    A methodology is developed for seismic qualification of nuclear plant equipment by applying similarity principles to existing experience data. Experience data are available from previous qualifications by analysis or testing, or from actual earthquake events. Similarity principles are defined in terms of excitation, equipment physical characteristics, and equipment response. Physical similarity is further defined in terms of a critical transfer function for response at a location on a primary structure, whose response can be assumed directly related to ultimate fragility of the item under elevated levels of excitation. Procedures are developed for combining experience data into composite specifications for qualification of equipment that can be shown to be physically similar to the reference equipment. Other procedures are developed for extending qualifications beyond the original specifications under certain conditions. Some examples for application of the procedures and verification of them are given for certain cases that can be approximated by a two degree of freedom simple primary/secondary system. Other examples are based on use of actual test data available from previous qualifications. Relationships of the developments with other previously-published methods are discussed. The developments are intended to elaborate on the rather broad revised guidelines developed by the IEEE 344 Standards Committee for equipment qualification in new nuclear plants. However, the results also contribute to filling a gap that exists between the IEEE 344 methodology and that previously developed by the Seismic Qualification Utilities Group. The relationship of the results to safety margin methodology is also discussed. (author)

  19. 7 CFR 51.1997 - Similar type.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Similar type. 51.1997 Section 51.1997 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946...

  20. Efficient Similarity Retrieval in Music Databases

    DEFF Research Database (Denmark)

    Ruxanda, Maria Magdalena; Jensen, Christian Søndergaard

    2006-01-01

    Audio music is increasingly becoming available in digital form, and the digital music collections of individuals continue to grow. Addressing the need for effective means of retrieving music from such collections, this paper proposes new techniques for content-based similarity search. Each music...

  1. Similarity search of business process models

    NARCIS (Netherlands)

    Dumas, M.; García-Bañuelos, L.; Dijkman, R.M.

    2009-01-01

    Similarity search is a general class of problems in which a given object, called a query object, is compared against a collection of objects in order to retrieve those that most closely resemble the query object. This paper reviews recent work on an instance of this class of problems, where the

  2. Cross-kingdom similarities in microbiome functions

    NARCIS (Netherlands)

    Mendes, R.; Raaijmakers, J.M.

    2015-01-01

    Recent advances in medical research have revealed how humans rely on their microbiome for diverse traits and functions. Similarly, microbiomes of other higher organisms play key roles in disease, health, growth and development of their host. Exploring microbiome functions across kingdoms holds

  3. Measuring structural similarity in large online networks.

    Science.gov (United States)

    Shi, Yongren; Macy, Michael

    2016-09-01

    Structural similarity based on bipartite graphs can be used to detect meaningful communities, but the networks have been tiny compared to massive online networks. Scalability is important in applications involving tens of millions of individuals with highly skewed degree distributions. Simulation analysis holding underlying similarity constant shows that two widely used measures - Jaccard index and cosine similarity - are biased by the distribution of out-degree in web-scale networks. However, an alternative measure, the Standardized Co-incident Ratio (SCR), is unbiased. We apply SCR to members of Congress, musical artists, and professional sports teams to show how massive co-following on Twitter can be used to map meaningful affiliations among cultural entities, even in the absence of direct connections to one another. Our results show how structural similarity can be used to map cultural alignments and demonstrate the potential usefulness of social media data in the study of culture, politics, and organizations across the social and behavioral sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

  4. Phonological Similarity in American Sign Language.

    Science.gov (United States)

    Hildebrandt, Ursula; Corina, David

    2002-01-01

    Investigates deaf and hearing subjects' ratings of American Sign Language (ASL) signs to assess whether linguistic experience shapes judgments of sign similarity. Findings are consistent with linguistic theories that posit movement and location as core structural elements of syllable structure in ASL. (Author/VWL)

  5. Structural similarity and category-specificity

    DEFF Research Database (Denmark)

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

    2004-01-01

    It has been suggested that category-specific recognition disorders for natural objects may reflect that natural objects are more structurally (visually) similar than artefacts and therefore more difficult to recognize following brain damage. On this account one might expect a positive relationshi...

  6. Music Retrieval based on Melodic Similarity

    NARCIS (Netherlands)

    Typke, R.

    2007-01-01

    This thesis introduces a method for measuring melodic similarity for notated music such as MIDI files. This music search algorithm views music as sets of notes that are represented as weighted points in the two-dimensional space of time and pitch. Two point sets can be compared by calculating how

  7. Measurement of Similarity in Academic Contexts

    Directory of Open Access Journals (Sweden)

    Omid Mahian

    2017-06-01

    Full Text Available We propose some reflections, comments and suggestions about the measurement of similar and matched content in scientific papers and documents, and the need to develop appropriate tools and standards for an ethically fair and equitable treatment of authors.

  8. Appropriate Similarity Measures for Author Cocitation Analysis

    NARCIS (Netherlands)

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

    2007-01-01

    textabstractWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of

  9. Similarity of Experience and Empathy in Preschoolers.

    Science.gov (United States)

    Barnett, Mark A.

    The present study examined the role of similarity of experience in young children's affective reactions to others. Some preschoolers played one of two games (Puzzle Board or Buckets) and were informed that they had either failed or succeeded; others merely observed the games being played and were given no evaluative feedback. Subsequently, each…

  10. Cultural Similarities and Differences on Idiom Translation

    Institute of Scientific and Technical Information of China (English)

    黄频频; 陈于全

    2010-01-01

    Both English and Chinese are abound with idioms. Idioms are an important part of the hnguage and culture of a society. English and Chinese idioms carved with cultural characteristics account for a great part in the tramlation. This paper studies the translation of idioms concerning their cultural similarities, cultural differences and transhtion principles.

  11. Learning by similarity in coordination problems

    Czech Academy of Sciences Publication Activity Database

    Steiner, Jakub; Stewart, C.

    -, č. 324 (2007), s. 1-40 ISSN 1211-3298 R&D Projects: GA MŠk LC542 Institutional research plan: CEZ:AV0Z70850503 Keywords : similarity * learning * case-based reasoning Subject RIV: AH - Economics http://www.cerge-ei.cz/pdf/wp/Wp324.pdf

  12. Outsourced similarity search on metric data assets

    KAUST Repository

    Yiu, Man Lung; Assent, Ira; Jensen, Christian Sø ndergaard; Kalnis, Panos

    2012-01-01

    for the most similar data objects to a query example. Outsourcing offers the data owner scalability and a low-initial investment. The need for privacy may be due to the data being sensitive (e.g., in medicine), valuable (e.g., in astronomy), or otherwise

  13. EH domain of EHD1

    Energy Technology Data Exchange (ETDEWEB)

    Kieken, Fabien; Jovic, Marko; Naslavsky, Naava; Caplan, Steve, E-mail: scaplan@unmc.edu; Sorgen, Paul L. [University of Nebraska Medical Center, Department of Biochemistry and Molecular Biology and Eppley Cancer Center (United States)], E-mail: psorgen@unmc.edu

    2007-12-15

    EHD1 is a member of the mammalian C-terminal Eps15 homology domain (EH) containing protein family, and regulates the recycling of various receptors from the endocytic recycling compartment to the plasma membrane. The EH domain of EHD1 binds to proteins containing either an Asn-Pro-Phe or Asp-Pro-Phe motif, and plays an important role in the subcellular localization and function of EHD1. Thus far, the structures of five N-terminal EH domains from other proteins have been solved, but to date, the structure of the EH domains from the four C-terminal EHD family paralogs remains unknown. In this study, we have assigned the 133 C-terminal residues of EHD1, which includes the EH domain, and solved its solution structure. While the overall structure resembles that of the second of the three N-terminal Eps15 EH domains, potentially significant differences in surface charge and the structure of the tripeptide-binding pocket are discussed.

  14. EH domain of EHD1

    International Nuclear Information System (INIS)

    Kieken, Fabien; Jovic, Marko; Naslavsky, Naava; Caplan, Steve; Sorgen, Paul L.

    2007-01-01

    EHD1 is a member of the mammalian C-terminal Eps15 homology domain (EH) containing protein family, and regulates the recycling of various receptors from the endocytic recycling compartment to the plasma membrane. The EH domain of EHD1 binds to proteins containing either an Asn-Pro-Phe or Asp-Pro-Phe motif, and plays an important role in the subcellular localization and function of EHD1. Thus far, the structures of five N-terminal EH domains from other proteins have been solved, but to date, the structure of the EH domains from the four C-terminal EHD family paralogs remains unknown. In this study, we have assigned the 133 C-terminal residues of EHD1, which includes the EH domain, and solved its solution structure. While the overall structure resembles that of the second of the three N-terminal Eps15 EH domains, potentially significant differences in surface charge and the structure of the tripeptide-binding pocket are discussed

  15. Extending the Similarity-Attraction Effect : The effects of When-Similarity in mediated communication

    NARCIS (Netherlands)

    Kaptein, M.C.; Castaneda, D.; Fernandez, N.; Nass, C.

    2014-01-01

    The feeling of connectedness experienced in computer-mediated relationships can be explained by the similarity-attraction effect (SAE). Though SAE is well established in psychology, the effects of some types of similarity have not yet been explored. In 2 studies, we demonstrate similarity-attraction

  16. Investigating Correlation between Protein Sequence Similarity and Semantic Similarity Using Gene Ontology Annotations.

    Science.gov (United States)

    Ikram, Najmul; Qadir, Muhammad Abdul; Afzal, Muhammad Tanvir

    2018-01-01

    Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic similarity methods, and in protein function prediction. In this research, we investigate the relationship between the two similarity methods. The results suggest absence of a strong correlation between sequence and semantic similarities. There is a large number of proteins with low sequence similarity and high semantic similarity. We observe that Pearson's correlation coefficient is not sufficient to explain the nature of this relationship. Interestingly, the term semantic similarity values above 0 and below 1 do not seem to play a role in improving the correlation. That is, the correlation coefficient depends only on the number of common GO terms in proteins under comparison, and the semantic similarity measurement method does not influence it. Semantic similarity and sequence similarity have a distinct behavior. These findings are of significant effect for future works on protein comparison, and will help understand the semantic similarity between proteins in a better way.

  17. Creativity as Action: Findings from Five Creative Domains

    Directory of Open Access Journals (Sweden)

    Vlad eGlaveanu

    2013-04-01

    Full Text Available The present paper outlines an action theory of creativity and substantiates this approach by investigating creative expression in five different domains. We propose an action framework for the analysis of creative acts built on the assumption that creativity is a relational, inter-subjective phenomenon. This framework, drawing extensively from the work of Dewey (1934 on art as experience, is used to derive a coding frame for the analysis of interview material. The article reports findings from the analysis of 60 interviews with recognised French creators in five creative domains: art, design, science, scriptwriting, and music. Results point to complex models of action and inter-action specific for each domain and also to interesting patterns of similarity and differences between domains. These findings highlight the fact that creative action takes place not ‘inside’ individual creators but ‘in between’ actors and their environment. Implications for the field of educational psychology are discussed.

  18. The TIR domain of TIR-NB-LRR resistance proteins is a signaling domain involved in cell death induction.

    Science.gov (United States)

    Swiderski, Michal R; Birker, Doris; Jones, Jonathan D G

    2009-02-01

    In plants, the TIR (toll interleukin 1 receptor) domain is found almost exclusively in nucleotide-binding (NB) leucine-rich repeat resistance proteins and their truncated homologs, and has been proposed to play a signaling role during resistance responses mediated by TIR containing R proteins. Transient expression in Nicotiana benthamiana leaves of "TIR + 80", the RPS4 truncation without the NB-ARC domain, leads to EDS1-, SGT1-, and HSP90-dependent cell death. Transgenic Arabidopsis plants expressing the RPS4 TIR+80 from either dexamethasone or estradiol-inducible promoters display inducer-dependent cell death. Cell death is also elicited by transient expression of similarly truncated constructs from two other R proteins, RPP1A and At4g19530, but is not elicited by similar constructs representing RPP2A and RPP2B proteins. Site-directed mutagenesis of the RPS4 TIR domain identified many loss-of-function mutations but also revealed several gain-of function substitutions. Lack of cell death induction by the E160A substitution suggests that amino acids outside of the TIR domain contribute to cell death signaling in addition to the TIR domain itself. This is consistent with previous observations that the TIR domain itself is insufficient to induce cell death upon transient expression.

  19. Similarity Analysis for Reactor Flow Distribution Test and Its Validation

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Soon Joon; Ha, Jung Hui [Heungdeok IT Valley, Yongin (Korea, Republic of); Lee, Taehoo; Han, Ji Woong [KAERI, Daejeon (Korea, Republic of)

    2015-05-15

    The newly derived dimensionless groups are slightly different from Hetsroni's. Reynolds number, relative wall roughness, and Euler don't appear, instead, friction factor appears newly. In order to conserve friction factor Reynolds number and relative wall roughness should be conserved. Since the effect of Reynolds number in high range is small, and since the scaled model is far smaller than prototype the conservation of friction factor is easily obtained by making the model wall just smooth. It is much easier to implement the test design than Hetsroni's because the Reynolds number and relative wall roughness do not appear explicitly. In case that there is no free surface within the interested domain of the reactor, the gravity is of second importance, and in this case the pressure drops should be compensated for in order to compare them between prototype and model. The gravity head compensated pressure drop is directly same to the measured value by a differential pressure transmitter. In order to conserve the gravity effect Froude number should be conserved. In pool type SFR (Sodium Cooled Fast Reactor) there exists liquid level difference, and if the level difference is desired to be conserved, the Froude number should be conserved. Euler number, which represents pressure terms in momentum equation, should be well conserved according to Hetsroni's approach. It is not a wrong statement, but it should be noted that Euler number is NOT an independent variable BUT a dependent variable according to Hong et al. It means that if all the geometrical similarity and the dimensionless numbers are conserved, Euler number is automatically conserved. So Euler number need not be considered in case that the perfect geometrical similarity is kept. However, even in case that the geometrical similarity is not conserved, it possible to conserved the velocity field similarity by just conserve Euler number. It gives tolerance to the engineer who designs the test

  20. GIS: a comprehensive source for protein structure similarities.

    Science.gov (United States)

    Guerler, Aysam; Knapp, Ernst-Walter

    2010-07-01

    A web service for analysis of protein structures that are sequentially or non-sequentially similar was generated. Recently, the non-sequential structure alignment algorithm GANGSTA+ was introduced. GANGSTA+ can detect non-sequential structural analogs for proteins stated to possess novel folds. Since GANGSTA+ ignores the polypeptide chain connectivity of secondary structure elements (i.e. alpha-helices and beta-strands), it is able to detect structural similarities also between proteins whose sequences were reshuffled during evolution. GANGSTA+ was applied in an all-against-all comparison on the ASTRAL40 database (SCOP version 1.75), which consists of >10,000 protein domains yielding about 55 x 10(6) possible protein structure alignments. Here, we provide the resulting protein structure alignments as a public web-based service, named GANGSTA+ Internet Services (GIS). We also allow to browse the ASTRAL40 database of protein structures with GANGSTA+ relative to an externally given protein structure using different constraints to select specific results. GIS allows us to analyze protein structure families according to the SCOP classification scheme. Additionally, users can upload their own protein structures for pairwise protein structure comparison, alignment against all protein structures of the ASTRAL40 database (SCOP version 1.75) or symmetry analysis. GIS is publicly available at http://agknapp.chemie.fu-berlin.de/gplus.

  1. On fuzzy semantic similarity measure for DNA coding.

    Science.gov (United States)

    Ahmad, Muneer; Jung, Low Tang; Bhuiyan, Md Al-Amin

    2016-02-01

    A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemical attributes of nucleotides have been proposed in recent decades. Such coding measure schemes lack the biologically meaningful aspects of nucleotide data and hence do not significantly discriminate coding regions from non-coding regions. This paper presents a novel fuzzy semantic similarity measure (FSSM) coding scheme centering on FSSM codons׳ clustering and genetic code context of nucleotides. Certain natural characteristics of nucleotides i.e. appearance as a unique combination of triplets, preserving special structure and occurrence, and ability to own and share density distributions in codons have been exploited in FSSM. The nucleotides׳ fuzzy behaviors, semantic similarities and defuzzification based on the center of gravity of nucleotides revealed a strong correlation between nucleotides in codons. The proposed FSSM coding scheme attains a significant enhancement in coding regions identification i.e. 36-133% as compared to other existing coding measure schemes tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. Copyright © 2015 Elsevier Ltd. All rights reserved.

  2. Popularity versus similarity in growing networks

    Science.gov (United States)

    Krioukov, Dmitri; Papadopoulos, Fragkiskos; Kitsak, Maksim; Serrano, Mariangeles; Boguna, Marian

    2012-02-01

    Preferential attachment is a powerful mechanism explaining the emergence of scaling in growing networks. If new connections are established preferentially to more popular nodes in a network, then the network is scale-free. Here we show that not only popularity but also similarity is a strong force shaping the network structure and dynamics. We develop a framework where new connections, instead of preferring popular nodes, optimize certain trade-offs between popularity and similarity. The framework admits a geometric interpretation, in which preferential attachment emerges from local optimization processes. As opposed to preferential attachment, the optimization framework accurately describes large-scale evolution of technological (Internet), social (web of trust), and biological (E.coli metabolic) networks, predicting the probability of new links in them with a remarkable precision. The developed framework can thus be used for predicting new links in evolving networks, and provides a different perspective on preferential attachment as an emergent phenomenon.

  3. Similarity, trust in institutions, affect, and populism

    DEFF Research Database (Denmark)

    Scholderer, Joachim; Finucane, Melissa L.

    -based evaluations are fundamental to human information processing, they can contribute significantly to other judgments (such as the risk, cost-effectiveness, trustworthiness) of the same stimulus object. Although deliberation and analysis are certainly important in some decision-making circumstances, reliance...... on affect is a quicker, easier, and a more efficient way of navigating in a complex and uncertain world. Hence, many theorists give affect a direct and primary role in motivating behavior. Taken together, the results provide uncannily strong support for the value-similarity hypothesis, strengthening...... types of information about gene technology. The materials were attributed to different institutions. The results indicated that participants' trust in an institution was a function of the similarity between the position advocated in the materials and participants' own attitudes towards gene technology...

  4. Contingency and similarity in response selection.

    Science.gov (United States)

    Prinz, Wolfgang

    2018-05-09

    This paper explores issues of task representation in choice reaction time tasks. How is it possible, and what does it take, to represent such a task in a way that enables a performer to do the task in line with the prescriptions entailed in the instructions? First, a framework for task representation is outlined which combines the implementation of task sets and their use for performance with different kinds of representational operations (pertaining to feature compounds for event codes and code assemblies for task sets, respectively). Then, in a second step, the framework is itself embedded in the bigger picture of the classical debate on the roles of contingency and similarity for the formation of associations. The final conclusion is that both principles are needed and that the operation of similarity at the level of task sets requires and presupposes the operation of contingency at the level of event codes. Copyright © 2018 The Author. Published by Elsevier Inc. All rights reserved.

  5. Similarity and Modeling in Science and Engineering

    CERN Document Server

    Kuneš, Josef

    2012-01-01

    The present text sets itself in relief to other titles on the subject in that it addresses the means and methodologies versus a narrow specific-task oriented approach. Concepts and their developments which evolved to meet the changing needs of applications are addressed. This approach provides the reader with a general tool-box to apply to their specific needs. Two important tools are presented: dimensional analysis and the similarity analysis methods. The fundamental point of view, enabling one to sort all models, is that of information flux between a model and an original expressed by the similarity and abstraction. Each chapter includes original examples and ap-plications. In this respect, the models can be divided into several groups. The following models are dealt with separately by chapter; mathematical and physical models, physical analogues, deterministic, stochastic, and cybernetic computer models. The mathematical models are divided into asymptotic and phenomenological models. The phenomenological m...

  6. Similarity solutions for phase-change problems

    Science.gov (United States)

    Canright, D.; Davis, S. H.

    1989-01-01

    A modification of Ivantsov's (1947) similarity solutions is proposed which can describe phase-change processes which are limited by diffusion. The method has application to systems that have n-components and possess cross-diffusion and Soret and Dufour effects, along with convection driven by density discontinuities at the two-phase interface. Local thermal equilibrium is assumed at the interface. It is shown that analytic solutions are possible when the material properties are constant.

  7. Stochastic self-similar and fractal universe

    International Nuclear Information System (INIS)

    Iovane, G.; Laserra, E.; Tortoriello, F.S.

    2004-01-01

    The structures formation of the Universe appears as if it were a classically self-similar random process at all astrophysical scales. An agreement is demonstrated for the present hypotheses of segregation with a size of astrophysical structures by using a comparison between quantum quantities and astrophysical ones. We present the observed segregated Universe as the result of a fundamental self-similar law, which generalizes the Compton wavelength relation. It appears that the Universe has a memory of its quantum origin as suggested by R. Penrose with respect to quasi-crystal. A more accurate analysis shows that the present theory can be extended from the astrophysical to the nuclear scale by using generalized (stochastically) self-similar random process. This transition is connected to the relevant presence of the electromagnetic and nuclear interactions inside the matter. In this sense, the presented rule is correct from a subatomic scale to an astrophysical one. We discuss the near full agreement at organic cell scale and human scale too. Consequently the Universe, with its structures at all scales (atomic nucleus, organic cell, human, planet, solar system, galaxy, clusters of galaxy, super clusters of galaxy), could have a fundamental quantum reason. In conclusion, we analyze the spatial dimensions of the objects in the Universe as well as space-time dimensions. The result is that it seems we live in an El Naschie's E-infinity Cantorian space-time; so we must seriously start considering fractal geometry as the geometry of nature, a type of arena where the laws of physics appear at each scale in a self-similar way as advocated long ago by the Swedish school of astrophysics

  8. 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.

  9. Quasi-Similarity Model of Synthetic Jets

    Czech Academy of Sciences Publication Activity Database

    Tesař, Václav; Kordík, Jozef

    2009-01-01

    Roč. 149, č. 2 (2009), s. 255-265 ISSN 0924-4247 R&D Projects: GA AV ČR IAA200760705; GA ČR GA101/07/1499 Institutional research plan: CEZ:AV0Z20760514 Keywords : jets * synthetic jets * similarity solution Subject RIV: BK - Fluid Dynamics Impact factor: 1.674, year: 2009 http://www.sciencedirect.com

  10. Multidimensional Scaling Visualization using Parametric Similarity Indices

    OpenAIRE

    Machado, J. A. Tenreiro; Lopes, António M.; Galhano, A.M.

    2015-01-01

    In this paper, we apply multidimensional scaling (MDS) and parametric similarity indices (PSI) in the analysis of complex systems (CS). Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, an...

  11. The fluid similarity of the boiling crisis

    International Nuclear Information System (INIS)

    Katsaounis, A.

    1986-01-01

    Most of the measurements related to the boiling crisis have, until now, been undertaken for a wide parameter variation in the water, and were mainly related to the water-cooled reactor. This article investigates, whether or how the measuring results can be transferred to other fluids. Derived dimensionless similarity figures and those taken from literature are verified by measurements from complex geometries in water and freon 12. (orig.) [de

  12. The fluid similarity of the boiling crisis

    International Nuclear Information System (INIS)

    Katsaounis, A.

    1987-01-01

    Most of the measurements related to the boiling crisis have, until now, been undertaken for a wide parameter variation in the water, and were mainly related to the water-cooled reactor. This article investigates, whether or how the measuring results can be transferred to other fluids. Derived dimensionless similarity figures and those taken from literature are verified by measurements from complex geometries in water and freon 12. (orig./GL) [de

  13. Domain Decomposition Solvers for Frequency-Domain Finite Element Equations

    KAUST Repository

    Copeland, Dylan; Kolmbauer, Michael; Langer, Ulrich

    2010-01-01

    The paper is devoted to fast iterative solvers for frequency-domain finite element equations approximating linear and nonlinear parabolic initial boundary value problems with time-harmonic excitations. Switching from the time domain to the frequency domain allows us to replace the expensive time-integration procedure by the solution of a simple linear elliptic system for the amplitudes belonging to the sine- and to the cosine-excitation or a large nonlinear elliptic system for the Fourier coefficients in the linear and nonlinear case, respectively. The fast solution of the corresponding linear and nonlinear system of finite element equations is crucial for the competitiveness of this method. © 2011 Springer-Verlag Berlin Heidelberg.

  14. Domain Decomposition Solvers for Frequency-Domain Finite Element Equations

    KAUST Repository

    Copeland, Dylan

    2010-10-05

    The paper is devoted to fast iterative solvers for frequency-domain finite element equations approximating linear and nonlinear parabolic initial boundary value problems with time-harmonic excitations. Switching from the time domain to the frequency domain allows us to replace the expensive time-integration procedure by the solution of a simple linear elliptic system for the amplitudes belonging to the sine- and to the cosine-excitation or a large nonlinear elliptic system for the Fourier coefficients in the linear and nonlinear case, respectively. The fast solution of the corresponding linear and nonlinear system of finite element equations is crucial for the competitiveness of this method. © 2011 Springer-Verlag Berlin Heidelberg.

  15. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-06-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  16. Semantic Similarity between Web Documents Using Ontology

    Science.gov (United States)

    Chahal, Poonam; Singh Tomer, Manjeet; Kumar, Suresh

    2018-03-01

    The World Wide Web is the source of information available in the structure of interlinked web pages. However, the procedure of extracting significant information with the assistance of search engine is incredibly critical. This is for the reason that web information is written mainly by using natural language, and further available to individual human. Several efforts have been made in semantic similarity computation between documents using words, concepts and concepts relationship but still the outcome available are not as per the user requirements. This paper proposes a novel technique for computation of semantic similarity between documents that not only takes concepts available in documents but also relationships that are available between the concepts. In our approach documents are being processed by making ontology of the documents using base ontology and a dictionary containing concepts records. Each such record is made up of the probable words which represents a given concept. Finally, document ontology's are compared to find their semantic similarity by taking the relationships among concepts. Relevant concepts and relations between the concepts have been explored by capturing author and user intention. The proposed semantic analysis technique provides improved results as compared to the existing techniques.

  17. Comparison of structure, function and regulation of plant cold shock domain proteins to bacterial and animal cold shock domain proteins.

    Science.gov (United States)

    Chaikam, Vijay; Karlson, Dale T

    2010-01-01

    The cold shock domain (CSD) is among the most ancient and well conserved nucleic acid binding domains from bacteria to higher animals and plants. The CSD facilitates binding to RNA, ssDNA and dsDNA and most functions attributed to cold shock domain proteins are mediated by this nucleic acid binding activity. In prokaryotes, cold shock domain proteins only contain a single CSD and are termed cold shock proteins (Csps). In animal model systems, various auxiliary domains are present in addition to the CSD and are commonly named Y-box proteins. Similar to animal CSPs, plant CSPs contain auxiliary C-terminal domains in addition to their N-terminal CSD. Cold shock domain proteins have been shown to play important roles in development and stress adaptation in wide variety of organisms. In this review, the structure, function and regulation of plant CSPs are compared and contrasted to the characteristics of bacterial and animal CSPs. [BMB reports 2010; 43(1): 1-8].

  18. The Importance of Domain-Specific Expertise in Creativity

    Science.gov (United States)

    Baer, John

    2015-01-01

    Although creativity and expertise are related, they are nonetheless very different things. Expertise does not usually require creativity, but creativity generally does require a certain level of expertise. There are similarities in the relationships of both expertise and creativity to domains, however. Research has shown that just as expertise in…

  19. Domain III function of Mu transposase analysed by directed ...

    Indian Academy of Sciences (India)

    Unknown

    factor, the MuB protein (Harshey and Cuneo 1986; Leung and Harshey 1991; Wu and ... the opposite R end, while the DDE+ subunit at R1 carries out similar chemistry at .... complex formed in figure 3B, lane 4 (absence of product band in lane L). ... grey subunit = R146V variant; apple-sized 'bite' = domain IIIα–. Arrowhead ...

  20. Mechanisms of wet oxidation by hydrogen peroxide

    International Nuclear Information System (INIS)

    Baxter, R.A.

    1987-08-01

    A research programme is currently under way at BNL and MEL to investigate the possible use of Hydrogen Peroxide with metal ion catalysts as a wet oxidation treatment system for CEGB organic radioactive wastes. The published literature relating to the kinetics and mechanism of oxidation and decomposition reactions of hydrogen peroxide is reviewed and the links with practical waste management by wet oxidation are examined. Alternative wet oxidation systems are described and the similarities to the CEGB research effort are noted. (author)

  1. Sequence Similarity Presenter: a tool for the graphic display of similarities of long sequences for use in presentations.

    Science.gov (United States)

    Fröhlich, K U

    1994-04-01

    A new method for the presentation of alignments of long sequences is described. The degree of identity for the aligned sequences is averaged for sections of a fixed number of residues. The resulting values are converted to shades of gray, with white corresponding to lack of identity and black corresponding to perfect identity. A sequence alignment is represented as a bar filled with varying shades of gray. The display is compact and allows for a fast and intuitive recognition of the distribution of regions with a high similarity. It is well suited for the presentation of alignments of long sequences, e.g. of protein superfamilies, in plenary lectures. The method is implemented as a HyperCard stack for Apple Macintosh computers. Several options for the modification of the output are available (e.g. background reduction, size of the summation window, consideration of amino acid similarity, inclusion of graphic markers to indicate specific domains). The output is a PostScript file which can be printed, imported as EPS or processed further with Adobe Illustrator.

  2. Is Domain Highlighting Actually Helpful in Identifying Phishing Web Pages?

    Science.gov (United States)

    Xiong, Aiping; Proctor, Robert W; Yang, Weining; Li, Ninghui

    2017-06-01

    To evaluate the effectiveness of domain highlighting in helping users identify whether Web pages are legitimate or spurious. As a component of the URL, a domain name can be overlooked. Consequently, browsers highlight the domain name to help users identify which Web site they are visiting. Nevertheless, few studies have assessed the effectiveness of domain highlighting, and the only formal study confounded highlighting with instructions to look at the address bar. We conducted two phishing detection experiments. Experiment 1 was run online: Participants judged the legitimacy of Web pages in two phases. In Phase 1, participants were to judge the legitimacy based on any information on the Web page, whereas in Phase 2, they were to focus on the address bar. Whether the domain was highlighted was also varied. Experiment 2 was conducted similarly but with participants in a laboratory setting, which allowed tracking of fixations. Participants differentiated the legitimate and fraudulent Web pages better than chance. There was some benefit of attending to the address bar, but domain highlighting did not provide effective protection against phishing attacks. Analysis of eye-gaze fixation measures was in agreement with the task performance, but heat-map results revealed that participants' visual attention was attracted by the highlighted domains. Failure to detect many fraudulent Web pages even when the domain was highlighted implies that users lacked knowledge of Web page security cues or how to use those cues. Potential applications include development of phishing prevention training incorporating domain highlighting with other methods to help users identify phishing Web pages.

  3. Thermomagnetic Stability in Pseudo Single Domain Grains

    Science.gov (United States)

    Nagy, Lesleis; Williams, Wyn; Muxworthy, Adrian; Fabian, Karl; Conbhuí, Pádraig Ó.

    2016-04-01

    The reliability of paleomagnetic remanences are well understood for fine grains of magnetite that are single-domain (SD, uniformly magnetized). In particular Néel's theory [1] outlined the thermal energies required to block and unblock magnetic remanences. This lead to determination of thermal stability for magnetization in fine grains as outlined in Pullaiah et. al. [2] and a comprehensive understanding of SD paleomagnetic recordings. It has been known for some time that single domain magnetite is possible only in the grain size range 30 - 80nm, which may only account for a small fraction of the grain size distribution in any rock sample. Indeed rocks are often dominated by grains in the pseudo single domain (PSD) size range, at approximately 80 - 1000nm. Toward the top end of this range multi-domain features begin to dominate. In order to determine thermomagnetic stability in PSD grains we need to identify the energy barriers between all possible pairs of local energy minima (LEM) domain states as a function of both temperature and grain size. We have attempted to do this using the nudged elastic band (NEB) method [3] which searches for minimum energy paths between any given pair of LEM states. Using this technique we have determined, for the first time, complete thermomagnetic stability curves for PSD magnetite. The work presented is at a preliminary stage. However it can be shown that PSD grains of magnetite with simple geometries (e.g. cubes or cuboctahedra) have very few low energy transition paths and the stability is likely to be similar to that observed for SD grains (as expected form experimental observations). The results will provide a basis for a much more rigorous understanding of the fidelity of paleomagnetic signals in assemblages of PSD grains and their ability to retain ancient recordings of the geomagnetic field. References: [1] Néel, Louis. "Théorie du traînage magnétique des ferromagnétiques en grains fins avec applications aux terres

  4. Emergent self-similarity of cluster coagulation

    Science.gov (United States)

    Pushkin, Dmtiri O.

    A wide variety of nonequilibrium processes, such as coagulation of colloidal particles, aggregation of bacteria into colonies, coalescence of rain drops, bond formation between polymerization sites, and formation of planetesimals, fall under the rubric of cluster coagulation. We predict emergence of self-similar behavior in such systems when they are 'forced' by an external source of the smallest particles. The corresponding self-similar coagulation spectra prove to be power laws. Starting from the classical Smoluchowski coagulation equation, we identify the conditions required for emergence of self-similarity and show that the power-law exponent value for a particular coagulation mechanism depends on the homogeneity index of the corresponding coagulation kernel only. Next, we consider the current wave of mergers of large American banks as an 'unorthodox' application of coagulation theory. We predict that the bank size distribution has propensity to become a power law, and verify our prediction in a statistical study of the available economical data. We conclude this chapter by discussing economically significant phenomenon of capital condensation and predicting emergence of power-law distributions in other economical and social data. Finally, we turn to apparent semblance between cluster coagulation and turbulence and conclude that it is not accidental: both of these processes are instances of nonlinear cascades. This class of processes also includes river network formation models, certain force-chain models in granular mechanics, fragmentation due to collisional cascades, percolation, and growing random networks. We characterize a particular cascade by three indicies and show that the resulting power-law spectrum exponent depends on the indicies values only. The ensuing algebraic formula is remarkable for its simplicity.

  5. FRESCO: Referential compression of highly similar sequences.

    Science.gov (United States)

    Wandelt, Sebastian; Leser, Ulf

    2013-01-01

    In many applications, sets of similar texts or sequences are of high importance. Prominent examples are revision histories of documents or genomic sequences. Modern high-throughput sequencing technologies are able to generate DNA sequences at an ever-increasing rate. In parallel to the decreasing experimental time and cost necessary to produce DNA sequences, computational requirements for analysis and storage of the sequences are steeply increasing. Compression is a key technology to deal with this challenge. Recently, referential compression schemes, storing only the differences between a to-be-compressed input and a known reference sequence, gained a lot of interest in this field. In this paper, we propose a general open-source framework to compress large amounts of biological sequence data called Framework for REferential Sequence COmpression (FRESCO). Our basic compression algorithm is shown to be one to two orders of magnitudes faster than comparable related work, while achieving similar compression ratios. We also propose several techniques to further increase compression ratios, while still retaining the advantage in speed: 1) selecting a good reference sequence; and 2) rewriting a reference sequence to allow for better compression. In addition,we propose a new way of further boosting the compression ratios by applying referential compression to already referentially compressed files (second-order compression). This technique allows for compression ratios way beyond state of the art, for instance,4,000:1 and higher for human genomes. We evaluate our algorithms on a large data set from three different species (more than 1,000 genomes, more than 3 TB) and on a collection of versions of Wikipedia pages. Our results show that real-time compression of highly similar sequences at high compression ratios is possible on modern hardware.

  6. Spherically symmetric self-similar universe

    Energy Technology Data Exchange (ETDEWEB)

    Dyer, C C [Toronto Univ., Ontario (Canada)

    1979-10-01

    A spherically symmetric self-similar dust-filled universe is considered as a simple model of a hierarchical universe. Observable differences between the model in parabolic expansion and the corresponding homogeneous Einstein-de Sitter model are considered in detail. It is found that an observer at the centre of the distribution has a maximum observable redshift and can in principle see arbitrarily large blueshifts. It is found to yield an observed density-distance law different from that suggested by the observations of de Vaucouleurs. The use of these solutions as central objects for Swiss-cheese vacuoles is discussed.

  7. Image magnification based on similarity analogy

    International Nuclear Information System (INIS)

    Chen Zuoping; Ye Zhenglin; Wang Shuxun; Peng Guohua

    2009-01-01

    Aiming at the high time complexity of the decoding phase in the traditional image enlargement methods based on fractal coding, a novel image magnification algorithm is proposed in this paper, which has the advantage of iteration-free decoding, by using the similarity analogy between an image and its zoom-out and zoom-in. A new pixel selection technique is also presented to further improve the performance of the proposed method. Furthermore, by combining some existing fractal zooming techniques, an efficient image magnification algorithm is obtained, which can provides the image quality as good as the state of the art while greatly decrease the time complexity of the decoding phase.

  8. Modeling Timbre Similarity of Short Music Clips.

    Science.gov (United States)

    Siedenburg, Kai; Müllensiefen, Daniel

    2017-01-01

    There is evidence from a number of recent studies that most listeners are able to extract information related to song identity, emotion, or genre from music excerpts with durations in the range of tenths of seconds. Because of these very short durations, timbre as a multifaceted auditory attribute appears as a plausible candidate for the type of features that listeners make use of when processing short music excerpts. However, the importance of timbre in listening tasks that involve short excerpts has not yet been demonstrated empirically. Hence, the goal of this study was to develop a method that allows to explore to what degree similarity judgments of short music clips can be modeled with low-level acoustic features related to timbre. We utilized the similarity data from two large samples of participants: Sample I was obtained via an online survey, used 16 clips of 400 ms length, and contained responses of 137,339 participants. Sample II was collected in a lab environment, used 16 clips of 800 ms length, and contained responses from 648 participants. Our model used two sets of audio features which included commonly used timbre descriptors and the well-known Mel-frequency cepstral coefficients as well as their temporal derivates. In order to predict pairwise similarities, the resulting distances between clips in terms of their audio features were used as predictor variables with partial least-squares regression. We found that a sparse selection of three to seven features from both descriptor sets-mainly encoding the coarse shape of the spectrum as well as spectrotemporal variability-best predicted similarities across the two sets of sounds. Notably, the inclusion of non-acoustic predictors of musical genre and record release date allowed much better generalization performance and explained up to 50% of shared variance ( R 2 ) between observations and model predictions. Overall, the results of this study empirically demonstrate that both acoustic features related

  9. Similar on the Inside (pre-grinding)

    Science.gov (United States)

    2004-01-01

    This approximate true-color image taken by the panoramic camera on the Mars Exploration Rover Opportunity show the rock called 'Pilbara' located in the small crater dubbed 'Fram.' The rock appears to be dotted with the same 'blueberries,' or spherules, found at 'Eagle Crater.' Spirit drilled into this rock with its rock abrasion tool. After analyzing the hole with the rover's scientific instruments, scientists concluded that Pilbara has a similar chemical make-up, and thus watery past, to rocks studied at Eagle Crater. This image was taken with the panoramic camera's 480-, 530- and 600-nanometer filters.

  10. Similar on the Inside (post-grinding)

    Science.gov (United States)

    2004-01-01

    This approximate true-color image taken by the panoramic camera on the Mars Exploration Rover Opportunity show the hole drilled into the rock called 'Pilbara,' which is located in the small crater dubbed 'Fram.' Spirit drilled into this rock with its rock abrasion tool. The rock appears to be dotted with the same 'blueberries,' or spherules, found at 'Eagle Crater.' After analyzing the hole with the rover's scientific instruments, scientists concluded that Pilbara has a similar chemical make-up, and thus watery past, to rocks studied at Eagle Crater. This image was taken with the panoramic camera's 480-, 530- and 600-nanometer filters.

  11. Self-similar magnetohydrodynamic boundary layers

    Energy Technology Data Exchange (ETDEWEB)

    Nunez, Manuel; Lastra, Alberto, E-mail: mnjmhd@am.uva.e [Departamento de Analisis Matematico, Universidad de Valladolid, 47005 Valladolid (Spain)

    2010-10-15

    The boundary layer created by parallel flow in a magnetized fluid of high conductivity is considered in this paper. Under appropriate boundary conditions, self-similar solutions analogous to the ones studied by Blasius for the hydrodynamic problem may be found. It is proved that for these to be stable, the size of the Alfven velocity at the outer flow must be smaller than the flow velocity, a fact that has a ready physical explanation. The process by which the transverse velocity and the thickness of the layer grow with the size of the Alfven velocity is detailed.

  12. Self-similar magnetohydrodynamic boundary layers

    International Nuclear Information System (INIS)

    Nunez, Manuel; Lastra, Alberto

    2010-01-01

    The boundary layer created by parallel flow in a magnetized fluid of high conductivity is considered in this paper. Under appropriate boundary conditions, self-similar solutions analogous to the ones studied by Blasius for the hydrodynamic problem may be found. It is proved that for these to be stable, the size of the Alfven velocity at the outer flow must be smaller than the flow velocity, a fact that has a ready physical explanation. The process by which the transverse velocity and the thickness of the layer grow with the size of the Alfven velocity is detailed.

  13. Domain walls at finite temperature

    International Nuclear Information System (INIS)

    Carvalho, C.A. de; Marques, G.C.; Silva, A.J. da; Ventura, I.

    1983-08-01

    It is suggested that the phase transition of lambda phi 4 theory as a function of temperature coincides with the spontaneous appearance of domain walls. Based on one-loop calculations, T sub(c) = 4M/√ lambda is estimated as the temperature for these domains to because energetically favored, to be compared with T sub(c) = 4.9M/√ lambda from effective potential calculations (which are performed directly in the broken phase). Domain walls, as well as other Types of fluctuations, disorder the system above T sub(c), leading to =0. The critical exponent for the specific heat above T sub(c) is computed; and α=2/3 + 0 (√ lambda) is obtained. (Author) [pt

  14. [Similarity system theory to evaluate similarity of chromatographic fingerprints of traditional Chinese medicine].

    Science.gov (United States)

    Liu, Yongsuo; Meng, Qinghua; Jiang, Shumin; Hu, Yuzhu

    2005-03-01

    The similarity evaluation of the fingerprints is one of the most important problems in the quality control of the traditional Chinese medicine (TCM). Similarity measures used to evaluate the similarity of the common peaks in the chromatogram of TCM have been discussed. Comparative studies were carried out among correlation coefficient, cosine of the angle and an improved extent similarity method using simulated data and experimental data. Correlation coefficient and cosine of the angle are not sensitive to the differences of the data set. They are still not sensitive to the differences of the data even after normalization. According to the similarity system theory, an improved extent similarity method was proposed. The improved extent similarity is more sensitive to the differences of the data sets than correlation coefficient and cosine of the angle. And the character of the data sets needs not to be changed compared with log-transformation. The improved extent similarity can be used to evaluate the similarity of the chromatographic fingerprints of TCM.

  15. Selective oxidation

    International Nuclear Information System (INIS)

    Cortes Henao, Luis F.; Castro F, Carlos A.

    2000-01-01

    It is presented a revision and discussion about the characteristics and factors that relate activity and selectivity in the catalytic and not catalytic partial oxidation of methane and the effect of variables as the temperature, pressure and others in the methane conversion to methanol. It thinks about the zeolites use modified for the catalytic oxidation of natural gas

  16. A Fast, Efficient Domain Adaptation Technique for Cross-Domain Electroencephalography(EEG-Based Emotion Recognition

    Directory of Open Access Journals (Sweden)

    Xin Chai

    2017-05-01

    Full Text Available Electroencephalography (EEG-based emotion recognition is an important element in psychiatric health diagnosis for patients. However, the underlying EEG sensor signals are always non-stationary if they are sampled from different experimental sessions or subjects. This results in the deterioration of the classification performance. Domain adaptation methods offer an effective way to reduce the discrepancy of marginal distribution. However, for EEG sensor signals, both marginal and conditional distributions may be mismatched. In addition, the existing domain adaptation strategies always require a high level of additional computation. To address this problem, a novel strategy named adaptive subspace feature matching (ASFM is proposed in this paper in order to integrate both the marginal and conditional distributions within a unified framework (without any labeled samples from target subjects. Specifically, we develop a linear transformation function which matches the marginal distributions of the source and target subspaces without a regularization term. This significantly decreases the time complexity of our domain adaptation procedure. As a result, both marginal and conditional distribution discrepancies between the source domain and unlabeled target domain can be reduced, and logistic regression (LR can be applied to the new source domain in order to train a classifier for use in the target domain, since the aligned source domain follows a distribution which is similar to that of the target domain. We compare our ASFM method with six typical approaches using a public EEG dataset with three affective states: positive, neutral, and negative. Both offline and online evaluations were performed. The subject-to-subject offline experimental results demonstrate that our component achieves a mean accuracy and standard deviation of 80.46% and 6.84%, respectively, as compared with a state-of-the-art method, the subspace alignment auto-encoder (SAAE, which

  17. The Distributed-SDF Domain

    DEFF Research Database (Denmark)

    Cuadrado, Daniel Lázaro; Ravn, Anders Peter; Koch, Peter

    2005-01-01

    The purpose of the Distributed-SDF domain for Ptolemy II is to allow distributed simulation of SDF models. It builds on top of the existing SDF domain by extending it. From the user’s point of view, using the Distributed-SDF director is sufficient to run the distributed version. It provides optio...... distributed nature. First of all, known memory bounds of the JVM can be overcome. Second, it yields smaller simulation times, mainly for models with high degree of parallelism and granularity....

  18. Gait Recognition Using Image Self-Similarity

    Directory of Open Access Journals (Sweden)

    Chiraz BenAbdelkader

    2004-04-01

    Full Text Available Gait is one of the few biometrics that can be measured at a distance, and is hence useful for passive surveillance as well as biometric applications. Gait recognition research is still at its infancy, however, and we have yet to solve the fundamental issue of finding gait features which at once have sufficient discrimination power and can be extracted robustly and accurately from low-resolution video. This paper describes a novel gait recognition technique based on the image self-similarity of a walking person. We contend that the similarity plot encodes a projection of gait dynamics. It is also correspondence-free, robust to segmentation noise, and works well with low-resolution video. The method is tested on multiple data sets of varying sizes and degrees of difficulty. Performance is best for fronto-parallel viewpoints, whereby a recognition rate of 98% is achieved for a data set of 6 people, and 70% for a data set of 54 people.

  19. Self-similarity in applied superconductivity

    International Nuclear Information System (INIS)

    Dresner, Lawrence

    1981-09-01

    Self-similarity is a descriptive term applying to a family of curves. It means that the family is invariant to a one-parameter group of affine (stretching) transformations. The property of self-similarity has been exploited in a wide variety of problems in applied superconductivity, namely, (i) transient distribution of the current among the filaments of a superconductor during charge-up, (ii) steady distribution of current among the filaments of a superconductor near the current leads, (iii) transient heat transfer in superfluid helium, (iv) transient diffusion in cylindrical geometry (important in studying the growth rate of the reacted layer in A15 materials), (v) thermal expulsion of helium from quenching cable-in-conduit conductors, (vi) eddy current heating of irregular plates by slow, ramped fields, and (vii) the specific heat of type-II superconductors. Most, but not all, of the applications involve differential equations, both ordinary and partial. The novel methods explained in this report should prove of great value in other fields, just as they already have done in applied superconductivity. (author)

  20. Popularity versus similarity in growing networks.

    Science.gov (United States)

    Papadopoulos, Fragkiskos; Kitsak, Maksim; Serrano, M Ángeles; Boguñá, Marián; Krioukov, Dmitri

    2012-09-27

    The principle that 'popularity is attractive' underlies preferential attachment, which is a common explanation for the emergence of scaling in growing networks. If new connections are made preferentially to more popular nodes, then the resulting distribution of the number of connections possessed by nodes follows power laws, as observed in many real networks. Preferential attachment has been directly validated for some real networks (including the Internet), and can be a consequence of different underlying processes based on node fitness, ranking, optimization, random walks or duplication. Here we show that popularity is just one dimension of attractiveness; another dimension is similarity. We develop a framework in which new connections optimize certain trade-offs between popularity and similarity, instead of simply preferring popular nodes. The framework has a geometric interpretation in which popularity preference emerges from local optimization. As opposed to preferential attachment, our optimization framework accurately describes the large-scale evolution of technological (the Internet), social (trust relationships between people) and biological (Escherichia coli metabolic) networks, predicting the probability of new links with high precision. The framework that we have developed can thus be used for predicting new links in evolving networks, and provides a different perspective on preferential attachment as an emergent phenomenon.

  1. Predicting the performance of fingerprint similarity searching.

    Science.gov (United States)

    Vogt, Martin; Bajorath, Jürgen

    2011-01-01

    Fingerprints are bit string representations of molecular structure that typically encode structural fragments, topological features, or pharmacophore patterns. Various fingerprint designs are utilized in virtual screening and their search performance essentially depends on three parameters: the nature of the fingerprint, the active compounds serving as reference molecules, and the composition of the screening database. It is of considerable interest and practical relevance to predict the performance of fingerprint similarity searching. A quantitative assessment of the potential that a fingerprint search might successfully retrieve active compounds, if available in the screening database, would substantially help to select the type of fingerprint most suitable for a given search problem. The method presented herein utilizes concepts from information theory to relate the fingerprint feature distributions of reference compounds to screening libraries. If these feature distributions do not sufficiently differ, active database compounds that are similar to reference molecules cannot be retrieved because they disappear in the "background." By quantifying the difference in feature distribution using the Kullback-Leibler divergence and relating the divergence to compound recovery rates obtained for different benchmark classes, fingerprint search performance can be quantitatively predicted.

  2. Big domains are novel Ca²+-binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig proteins.

    Directory of Open Access Journals (Sweden)

    Rajeev Raman

    Full Text Available BACKGROUND: Many bacterial surface exposed proteins mediate the host-pathogen interaction more effectively in the presence of Ca²+. Leptospiral immunoglobulin-like (Lig proteins, LigA and LigB, are surface exposed proteins containing Bacterial immunoglobulin like (Big domains. The function of proteins which contain Big fold is not known. Based on the possible similarities of immunoglobulin and βγ-crystallin folds, we here explore the important question whether Ca²+ binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. PRINCIPAL FINDINGS: We selected six individual Big domains for this study (three from the conserved part of LigA and LigB, denoted as Lig A3, Lig A4, and LigBCon5; two from the variable region of LigA, i.e., 9(th (Lig A9 and 10(th repeats (Lig A10; and one from the variable region of LigB, i.e., LigBCen2. We have also studied the conserved region covering the three and six repeats (LigBCon1-3 and LigCon. All these proteins bind the calcium-mimic dye Stains-all. All the selected four domains bind Ca²+ with dissociation constants of 2-4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm, probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. CONCLUSIONS: We demonstrate that the Lig are Ca²+-binding proteins, with Big domains harbouring the binding motif. We conclude that despite differences in sequence, a Big motif binds Ca²+. This work thus sets up a strong possibility for classifying the proteins containing Big domains as a novel family of Ca²+-binding proteins. Since Big domain is a part of many proteins in bacterial kingdom, we suggest a possible function these proteins via Ca²+ binding.

  3. Big domains are novel Ca²+-binding modules: evidences from big domains of Leptospira immunoglobulin-like (Lig) proteins.

    Science.gov (United States)

    Raman, Rajeev; Rajanikanth, V; Palaniappan, Raghavan U M; Lin, Yi-Pin; He, Hongxuan; McDonough, Sean P; Sharma, Yogendra; Chang, Yung-Fu

    2010-12-29

    Many bacterial surface exposed proteins mediate the host-pathogen interaction more effectively in the presence of Ca²+. Leptospiral immunoglobulin-like (Lig) proteins, LigA and LigB, are surface exposed proteins containing Bacterial immunoglobulin like (Big) domains. The function of proteins which contain Big fold is not known. Based on the possible similarities of immunoglobulin and βγ-crystallin folds, we here explore the important question whether Ca²+ binds to a Big domains, which would provide a novel functional role of the proteins containing Big fold. We selected six individual Big domains for this study (three from the conserved part of LigA and LigB, denoted as Lig A3, Lig A4, and LigBCon5; two from the variable region of LigA, i.e., 9(th) (Lig A9) and 10(th) repeats (Lig A10); and one from the variable region of LigB, i.e., LigBCen2. We have also studied the conserved region covering the three and six repeats (LigBCon1-3 and LigCon). All these proteins bind the calcium-mimic dye Stains-all. All the selected four domains bind Ca²+ with dissociation constants of 2-4 µM. Lig A9 and Lig A10 domains fold well with moderate thermal stability, have β-sheet conformation and form homodimers. Fluorescence spectra of Big domains show a specific doublet (at 317 and 330 nm), probably due to Trp interaction with a Phe residue. Equilibrium unfolding of selected Big domains is similar and follows a two-state model, suggesting the similarity in their fold. We demonstrate that the Lig are Ca²+-binding proteins, with Big domains harbouring the binding motif. We conclude that despite differences in sequence, a Big motif binds Ca²+. This work thus sets up a strong possibility for classifying the proteins containing Big domains as a novel family of Ca²+-binding proteins. Since Big domain is a part of many proteins in bacterial kingdom, we suggest a possible function these proteins via Ca²+ binding.

  4. Improving the performance of DomainDiscovery of protein domain boundary assignment using inter-domain linker index

    Directory of Open Access Journals (Sweden)

    Zomaya Albert Y

    2006-12-01

    Full Text Available Abstract Background Knowledge of protein domain boundaries is critical for the characterisation and understanding of protein function. The ability to identify domains without the knowledge of the structure – by using sequence information only – is an essential step in many types of protein analyses. In this present study, we demonstrate that the performance of DomainDiscovery is improved significantly by including the inter-domain linker index value for domain identification from sequence-based information. Improved DomainDiscovery uses a Support Vector Machine (SVM approach and a unique training dataset built on the principle of consensus among experts in defining domains in protein structure. The SVM was trained using a PSSM (Position Specific Scoring Matrix, secondary structure, solvent accessibility information and inter-domain linker index to detect possible domain boundaries for a target sequence. Results Improved DomainDiscovery is compared with other methods by benchmarking against a structurally non-redundant dataset and also CASP5 targets. Improved DomainDiscovery achieves 70% accuracy for domain boundary identification in multi-domains proteins. Conclusion Improved DomainDiscovery compares favourably to the performance of other methods and excels in the identification of domain boundaries for multi-domain proteins as a result of introducing support vector machine with benchmark_2 dataset.

  5. Similar or different?: the importance of similarities and differences for support between siblings

    NARCIS (Netherlands)

    Voorpostel, M.; van der Lippe, T.; Dykstra, P.A.; Flap, H.

    2007-01-01

    Using a large-scale Dutch national sample (N = 7,126), the authors examine the importance of similarities and differences in the sibling dyad for the provision of support. Similarities are assumed to enhance attraction and empathy; differences are assumed to be related to different possibilities for

  6. Similar or Different? The Importance of Similarities and Differences for Support Between Siblings

    NARCIS (Netherlands)

    Voorpostel, Marieke; Lippe, Tanja van der; Dykstra, Pearl A.; Flap, Henk

    2007-01-01

    Using a large-scale Dutch national sample (N = 7,126), the authors examine the importance of similarities and differences in the sibling dyad for the provision of support. Similarities are assumed to enhance attraction and empathy; differences are assumed to be related to different possibilities for

  7. Similarity problems and completely bounded maps

    CERN Document Server

    Pisier, Gilles

    2001-01-01

    These notes revolve around three similarity problems, appearing in three different contexts, but all dealing with the space B(H) of all bounded operators on a complex Hilbert space H. The first one deals with group representations, the second one with C* -algebras and the third one with the disc algebra. We describe them in detail in the introduction which follows. This volume is devoted to the background necessary to understand these three problems, to the solutions that are known in some special cases and to numerous related concepts, results, counterexamples or extensions which their investigation has generated. While the three problems seem different, it is possible to place them in a common framework using the key concept of "complete boundedness", which we present in detail. Using this notion, the three problems can all be formulated as asking whether "boundedness" implies "complete boundedness" for linear maps satisfying certain additional algebraic identities. Two chapters have been added on the HALMO...

  8. Social values as arguments: similar is convincing

    Science.gov (United States)

    Maio, Gregory R.; Hahn, Ulrike; Frost, John-Mark; Kuppens, Toon; Rehman, Nadia; Kamble, Shanmukh

    2014-01-01

    Politicians, philosophers, and rhetors engage in co-value argumentation: appealing to one value in order to support another value (e.g., “equality leads to freedom”). Across four experiments in the United Kingdom and India, we found that the psychological relatedness of values affects the persuasiveness of the arguments that bind them. Experiment 1 found that participants were more persuaded by arguments citing values that fulfilled similar motives than by arguments citing opposing values. Experiments 2 and 3 replicated this result using a wider variety of values, while finding that the effect is stronger among people higher in need for cognition and that the effect is mediated by the greater plausibility of co-value arguments that link motivationally compatible values. Experiment 4 extended the effect to real-world arguments taken from political propaganda and replicated the mediating effect of argument plausibility. The findings highlight the importance of value relatedness in argument persuasiveness. PMID:25147529

  9. Image Steganalysis with Binary Similarity Measures

    Directory of Open Access Journals (Sweden)

    Kharrazi Mehdi

    2005-01-01

    Full Text Available We present a novel technique for steganalysis of images that have been subjected to embedding by steganographic algorithms. The seventh and eighth bit planes in an image are used for the computation of several binary similarity measures. The basic idea is that the correlation between the bit planes as well as the binary texture characteristics within the bit planes will differ between a stego image and a cover image. These telltale marks are used to construct a classifier that can distinguish between stego and cover images. We also provide experimental results using some of the latest steganographic algorithms. The proposed scheme is found to have complementary performance vis-à-vis Farid's scheme in that they outperform each other in alternate embedding techniques.

  10. A Lithium Vapor Box Divertor Similarity Experiment

    Science.gov (United States)

    Cohen, Robert A.; Emdee, Eric D.; Goldston, Robert J.; Jaworski, Michael A.; Schwartz, Jacob A.

    2017-10-01

    A lithium vapor box divertor offers an alternate means of managing the extreme power density of divertor plasmas by leveraging gaseous lithium to volumetrically extract power. The vapor box divertor is a baffled slot with liquid lithium coated walls held at temperatures which increase toward the divertor floor. The resulting vapor pressure differential drives gaseous lithium from hotter chambers into cooler ones, where the lithium condenses and returns. A similarity experiment was devised to investigate the advantages offered by a vapor box divertor design. We discuss the design, construction, and early findings of the vapor box divertor experiment including vapor can construction, power transfer calculations, joint integrity tests, and thermocouple data logging. Heat redistribution of an incident plasma-based heat flux from a typical linear plasma device is also presented. This work supported by DOE Contract No. DE-AC02-09CH11466 and The Princeton Environmental Institute.

  11. Correct Bayesian and frequentist intervals are similar

    International Nuclear Information System (INIS)

    Atwood, C.L.

    1986-01-01

    This paper argues that Bayesians and frequentists will normally reach numerically similar conclusions, when dealing with vague data or sparse data. It is shown that both statistical methodologies can deal reasonably with vague data. With sparse data, in many important practical cases Bayesian interval estimates and frequentist confidence intervals are approximately equal, although with discrete data the frequentist intervals are somewhat longer. This is not to say that the two methodologies are equally easy to use: The construction of a frequentist confidence interval may require new theoretical development. Bayesians methods typically require numerical integration, perhaps over many variables. Also, Bayesian can easily fall into the trap of over-optimism about their amount of prior knowledge. But in cases where both intervals are found correctly, the two intervals are usually not very different. (orig.)

  12. Soldier motivation – different or similar?

    DEFF Research Database (Denmark)

    Brænder, Morten; Andersen, Lotte Bøgh

    Recent research in military sociology has shown that in addition to their strong peer motivation modern soldiers are oriented toward contributing to society. It has not, however, been tested how soldier motivation differs from the motivation of other citizens in this respect. In this paper......, by means of public service motivation, a concept developed within the public administration literature, we compare soldier and civilian motivation. The contribution of this paper is an analysis of whether and how Danish combat soldiers differs from other Danes in regard to public service motivation? Using...... surveys with similar questions, we find that soldiers are more normatively motivated to contribute to society than other citizens (higher commitment to the public interest), while their affectively based motivation is lower (lower compassion). This points towards a potential problem in regard...

  13. Social Values as Arguments: Similar is Convincing

    Directory of Open Access Journals (Sweden)

    Gregory R Maio

    2014-08-01

    Full Text Available Politicians, philosophers, and rhetors engage in co-value argumentation: appealing to one value in order to support another value (e.g., equality leads to freedom. Across four experiments in the United Kingdom and India, we found that the psychological relatedness of values affects the persuasiveness of the arguments that bind them. Experiment 1 found that participants were more persuaded by arguments citing values that fulfilled similar motives than by arguments citing opposing values. Experiments 2 and 3 replicated this result using a wider variety of values, while finding that the effect is stronger among people higher in need for cognition and that the effect is mediated by the greater plausibility of co-value arguments that link motivationally compatible values. Experiment 4 extended the effect to real-world arguments taken from political propaganda and replicated the mediating effect of argument plausibility. The findings highlight the importance of value relatedness in argument persuasiveness.

  14. Formulation of similarity porous media systems

    International Nuclear Information System (INIS)

    Anderson, R.M.; Ford, W.T.; Ruttan, A.; Strauss, M.J.

    1982-01-01

    The mathematical formulation of the Porous Media System (PMS) describing two-phase, immiscible, compressible fluid flow in linear, homogeneous porous media is reviewed and expanded. It is shown that families of common vertex, coaxial parabolas and families of parallel lines are the only families of curves on which solutions of the PMS may be constant. A coordinate transformation is used to change the partial differential equations of the PMS to a system of ordinary differential equations, referred to as a similarity Porous Media System (SPMS), in which the independent variable denotes movement from curve to curve in a selected family of curves. Properties of solutions of the first boundary value problem are developed for the SPMS

  15. Contextual Factors for Finding Similar Experts

    DEFF Research Database (Denmark)

    Hofmann, Katja; Balog, Krisztian; Bogers, Toine

    2010-01-01

    -seeking models, are rarely taken into account. In this article, we extend content-based expert-finding approaches with contextual factors that have been found to influence human expert finding. We focus on a task of science communicators in a knowledge-intensive environment, the task of finding similar experts......, given an example expert. Our approach combines expertise-seeking and retrieval research. First, we conduct a user study to identify contextual factors that may play a role in the studied task and environment. Then, we design expert retrieval models to capture these factors. We combine these with content......-based retrieval models and evaluate them in a retrieval experiment. Our main finding is that while content-based features are the most important, human participants also take contextual factors into account, such as media experience and organizational structure. We develop two principled ways of modeling...

  16. Optimal neighborhood indexing for protein similarity search.

    Science.gov (United States)

    Peterlongo, Pierre; Noé, Laurent; Lavenier, Dominique; Nguyen, Van Hoa; Kucherov, Gregory; Giraud, Mathieu

    2008-12-16

    Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  17. Optimal neighborhood indexing for protein similarity search

    Directory of Open Access Journals (Sweden)

    Nguyen Van

    2008-12-01

    Full Text Available Abstract Background Similarity inference, one of the main bioinformatics tasks, has to face an exponential growth of the biological data. A classical approach used to cope with this data flow involves heuristics with large seed indexes. In order to speed up this technique, the index can be enhanced by storing additional information to limit the number of random memory accesses. However, this improvement leads to a larger index that may become a bottleneck. In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. Results The paper presents two main contributions. First, we show that an optimal neighborhood indexing combining an alphabet reduction and a longer neighborhood leads to a reduction of 35% of memory involved into the process, without sacrificing the quality of results nor the computational time. Second, our approach led us to develop a new kind of substitution score matrices and their associated e-value parameters. In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. We describe the method used for computing those matrices and we provide some typical examples that can be used in such comparisons. Supplementary data can be found on the website http://bioinfo.lifl.fr/reblosum. Conclusion We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. Such an index can be used in any study involving large protein data. Moreover, rectangular substitution score matrices and their associated statistical parameters can have applications in any study involving an alphabet reduction.

  18. Characterizing Functional Domains for TIM-Mediated Enveloped Virus Entry

    Science.gov (United States)

    Moller-Tank, Sven; Albritton, Lorraine M.; Rennert, Paul D.

    2014-01-01

    membrane. While it is known that the PtdSer binding is essential for the PVEER function of TIM-1, TIM-3 shares this binding activity but does not enhance virus entry. No comprehensive studies have been done to characterize the other domains of TIM-1. In this study, using a variety of chimeric proteins and deletion mutants, we define the features necessary for a functional PVEER. With these features in mind, we generated a TIM-1 mimic using functionally similar domains from other proteins. This mimic, like TIM-1, effectively enhanced transduction. These studies provide insight into the key features necessary for PVEERs and will allow for more effective identification of unknown PVEERs. PMID:24696470

  19. Learning processes across knowledge domains

    DEFF Research Database (Denmark)

    Hall-Andersen, Lene Bjerg; Broberg, Ole

    2014-01-01

    Purpose - The purpose of this paper is to shed light on the problematics of learning across knowledge boundaries in organizational settings. The paper specifically explores learning processes that emerge, when a new knowledge domain is introduced into an existing organizational practice with the ...

  20. Ubiquitin domain proteins in disease

    DEFF Research Database (Denmark)

    Klausen, Louise Kjær; Schulze, Andrea; Seeger, Michael

    2007-01-01

    The human genome encodes several ubiquitin-like (UBL) domain proteins (UDPs). Members of this protein family are involved in a variety of cellular functions and many are connected to the ubiquitin proteasome system, an essential pathway for protein degradation in eukaryotic cells. Despite...... and cancer. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com)....

  1. Cellulose binding domain fusion proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  2. Gradability in the nominal domain

    NARCIS (Netherlands)

    Constantinescu, Camelia

    2011-01-01

    This dissertation investigates whether and how gradability is manifested in the nominal domain, as well as the implications this could have for theories of the representation of gradability. It is shown that the various gradability diagnostics proposed in the literature not only yield different

  3. The theory of syntactic domains

    NARCIS (Netherlands)

    Kracht, M.

    In this essay we develop a mathematical theory of syntactic domains with special attention to the theory of government and binding. Starting from an intrinsic characterization of command relations as defined in [Ba 90] we determine the structure of the distributive lattice of command relations.

  4. Impedance models in time domain

    NARCIS (Netherlands)

    Rienstra, S.W.

    2005-01-01

    Necessary conditions for an impedance function are derived. Methods available in the literature are discussed. A format with recipe is proposed for an exact impedance condition in time domain on a time grid, based on the Helmholtz resonator model. An explicit solution is given of a pulse reflecting

  5. Domains of psychosocial disability and mental disorders.

    Science.gov (United States)

    Ro, Eunyoe; Watson, David; Clark, Lee Anna

    2018-06-07

    This study examined relations between comprehensive domains of psychosocial disability and mental disorders to determine (1) whether differential patterns of associations exist between psychosocial disability dimensions and commonly diagnosed mental disorders and (2) whether these relations differ between self-reported and interviewer-rated psychosocial disability domains. Self-reported and interviewer-rated psychosocial functioning measures and an interviewer-rated diagnostic assessment tool were administered to 181 psychiatric outpatients. Internalizing disorders showed the strongest and most pervasive associations with psychosocial impairment across both self-reported and interviewer-rated measures, followed by thought disorder; externalizing showed the weakest associations. More specifically, logistic regression analyses indicated that lower well-being factor score significantly increased the odds of distress-disorder diagnoses, and poor basic functioning increased the odds of PTSD. Results clearly showed differences in the magnitude of associations between three dimensions of psychosocial-disability and commonly diagnosed disorders, and that these differences were similar regardless of rater type. © 2018 Wiley Periodicals, Inc.

  6. A Bayesian Sampler for Optimization of Protein Domain Hierarchies

    Science.gov (United States)

    2014-01-01

    Abstract The process of identifying and modeling functionally divergent subgroups for a specific protein domain class and arranging these subgroups hierarchically has, thus far, largely been done via manual curation. How to accomplish this automatically and optimally is an unsolved statistical and algorithmic problem that is addressed here via Markov chain Monte Carlo sampling. Taking as input a (typically very large) multiple-sequence alignment, the sampler creates and optimizes a hierarchy by adding and deleting leaf nodes, by moving nodes and subtrees up and down the hierarchy, by inserting or deleting internal nodes, and by redefining the sequences and conserved patterns associated with each node. All such operations are based on a probability distribution that models the conserved and divergent patterns defining each subgroup. When we view these patterns as sequence determinants of protein function, each node or subtree in such a hierarchy corresponds to a subgroup of sequences with similar biological properties. The sampler can be applied either de novo or to an existing hierarchy. When applied to 60 protein domains from multiple starting points in this way, it converged on similar solutions with nearly identical log-likelihood ratio scores, suggesting that it typically finds the optimal peak in the posterior probability distribution. Similarities and differences between independently generated, nearly optimal hierarchies for a given domain help distinguish robust from statistically uncertain features. Thus, a future application of the sampler is to provide confidence measures for various features of a domain hierarchy. PMID:24494927

  7. Anodic oxidation

    CERN Document Server

    Ross, Sidney D; Rudd, Eric J; Blomquist, Alfred T; Wasserman, Harry H

    2013-01-01

    Anodic Oxidation covers the application of the concept, principles, and methods of electrochemistry to organic reactions. This book is composed of two parts encompassing 12 chapters that consider the mechanism of anodic oxidation. Part I surveys the theory and methods of electrochemistry as applied to organic reactions. These parts also present the mathematical equations to describe the kinetics of electrode reactions using both polarographic and steady-state conditions. Part II examines the anodic oxidation of organic substrates by the functional group initially attacked. This part particular

  8. An ontological approach to domain engineering

    NARCIS (Netherlands)

    Falbo, R.A.; Guizzardi, G.; Duarte, K.

    2002-01-01

    Domain engineering aims to support systematic reuse, focusing on modeling common knowledge in a problem domain. Ontologies have also been pointed as holding great promise for software reuse. In this paper, we present ODE (Ontology-based Domain Engineering), an ontological approach for domain

  9. Inferring domain-domain interactions from protein-protein interactions with formal concept analysis.

    Directory of Open Access Journals (Sweden)

    Susan Khor

    Full Text Available Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains.

  10. Inferring Domain-Domain Interactions from Protein-Protein Interactions with Formal Concept Analysis

    Science.gov (United States)

    Khor, Susan

    2014-01-01

    Identifying reliable domain-domain interactions will increase our ability to predict novel protein-protein interactions, to unravel interactions in protein complexes, and thus gain more information about the function and behavior of genes. One of the challenges of identifying reliable domain-domain interactions is domain promiscuity. Promiscuous domains are domains that can occur in many domain architectures and are therefore found in many proteins. This becomes a problem for a method where the score of a domain-pair is the ratio between observed and expected frequencies because the protein-protein interaction network is sparse. As such, many protein-pairs will be non-interacting and domain-pairs with promiscuous domains will be penalized. This domain promiscuity challenge to the problem of inferring reliable domain-domain interactions from protein-protein interactions has been recognized, and a number of work-arounds have been proposed. This paper reports on an application of Formal Concept Analysis to this problem. It is found that the relationship between formal concepts provides a natural way for rare domains to elevate the rank of promiscuous domain-pairs and enrich highly ranked domain-pairs with reliable domain-domain interactions. This piggybacking of promiscuous domain-pairs onto less promiscuous domain-pairs is possible only with concept lattices whose attribute-labels are not reduced and is enhanced by the presence of proteins that comprise both promiscuous and rare domains. PMID:24586450

  11. Music genre classification using temporal domain features

    Science.gov (United States)

    Shiu, Yu; Kuo, C.-C. Jay

    2004-10-01

    Music genre provides an efficient way to index songs in the music database, and can be used as an effective means to retrieval music of a similar type, i.e. content-based music retrieval. In addition to other features, the temporal domain features of a music signal are exploited so as to increase the classification rate in this research. Three temporal techniques are examined in depth. First, the hidden Markov model (HMM) is used to emulate the time-varying properties of music signals. Second, to further increase the classification rate, we propose another feature set that focuses on the residual part of music signals. Third, the overall classification rate is enhanced by classifying smaller segments from a test material individually and making decision via majority voting. Experimental results are given to demonstrate the performance of the proposed techniques.

  12. PUBLIC DOMAIN PROTECTION. USES AND REUSES OF PUBLIC DOMAIN WORKS

    Directory of Open Access Journals (Sweden)

    Monica Adriana LUPAȘCU

    2015-07-01

    Full Text Available This study tries to highlight the necessity of an awareness of the right of access to the public domain, particularly using the example of works whose protection period has expired, as well as the ones which the law considers to be excluded from protection. Such works are used not only by large libraries from around the world, but also by rights holders, via different means of use, including incorporations into original works or adaptations. However, the reuse that follows these uses often only remains at the level of concept, as the notion of the public’s right of access to public domain works is not substantiated, nor is the notion of the correct or legal use of such works.

  13. Is it about "pink" or about "girls"? The inherence heuristic across social and nonsocial domains.

    Science.gov (United States)

    Kinzler, Katherine D; Sullivan, Kathleen R

    2014-10-01

    The inherence heuristic provides an intriguing and novel explanation for early thought in a variety of domains. Exploring similarities and differences in inherent reasoning across social and nonsocial domains can help us understand the role that inherent thinking plays in the development of human reasoning and the process by which more elaborate essentialist reasoning develops.

  14. BOUNDARY VALUE PROBLEM FOR A LOADED EQUATION ELLIPTIC-HYPERBOLIC TYPE IN A DOUBLY CONNECTED DOMAIN

    Directory of Open Access Journals (Sweden)

    O.Kh. Abdullaev

    2014-06-01

    Full Text Available We study the existence and uniqueness of the solution of one boundary value problem for the loaded elliptic-hyperbolic equation of the second order with two lines of change of type in double-connected domain. Similar results have been received by D.M.Kuryhazov, when investigated domain is one-connected.

  15. Neurobiological correlates of internet gaming disorder: Similarities to pathological gambling.

    Science.gov (United States)

    Fauth-Bühler, M; Mann, K

    2017-01-01

    The number of massively multiplayer online games (MMOs) is on the rise worldwide along with the fascination that they inspire. Problems occur when the use of MMOs becomes excessive at the expense of other life domains. Although not yet formally included as disorder in common diagnostic systems, internet gaming disorder (IGD) is considered a "condition for further study" in section III of the DSM-5. The current review aims to provide an overview of cognitive and neurobiological data currently available on IGD, with a particular focus on impulsivity, compulsivity, and sensitivity to reward and punishment. Additionally, we also compare these findings on IGD with data from studies on pathological gambling (PG)-so far the only condition officially classified as a behavioral addiction in the DSM-5. Multiple similarities have been observed in the neurobiology of IGD and PG, as measured by alterations in brain function and behavior. Both patients with IGD and those with PG exhibited decreased loss sensitivity; enhanced reactivity to gaming and gambling cues, respectively; enhanced impulsive choice behavior; aberrant reward-based learning; and no changes in cognitive flexibility. In conclusion, the evidence base on the neurobiology of gaming and gambling disorders is beginning to illuminate the similarities between the two. However, as only a few studies have addressed the neurobiological basis of IGD, and some of these studies suffer from significant limitations, more research is required before IGD's inclusion as a second behavioral addiction in the next versions of the ICD and DSM can be justified. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Domain-Specific Partitioning of Uterine Artery Endothelial Connexin43 and Caveolin-1.

    Science.gov (United States)

    Ampey, Bryan C; Morschauser, Timothy J; Ramadoss, Jayanth; Magness, Ronald R

    2016-10-01

    Uterine vascular adaptations facilitate rises in uterine blood flow during pregnancy, which are associated with gap junction connexin (Cx) proteins and endothelial nitric oxide synthase. In uterine artery endothelial cells (UAECs), ATP activates endothelial nitric oxide synthase in a pregnancy (P)-specific manner that is dependent on Cx43 function. Caveolar subcellular domain partitioning plays key roles in ATP-induced endothelial nitric oxide synthase activation and nitric oxide production. Little is known regarding the partitioning of Cx proteins to caveolar domains or their dynamics with ATP treatment. We observed that Cx43-mediated gap junction function with ATP stimulation is associated with Cx43 repartitioning between the noncaveolar and caveolar domains. Compared with UAECs from nonpregnant (NP) ewes, levels of ATP, PGI2, cAMP, NOx, and cGMP were 2-fold higher (PLucifer yellow dye transfer, a response abrogated by Gap27, but not Gap 26, indicating involvement of Cx43, but not Cx37. Confocal microscopy revealed domain partitioning of Cx43 and caveolin-1. In pregnant UAECs, LC/MS/MS analysis revealed only Cx43 in the caveolar domain. In contrast, Cx37 was located only in the noncaveolar pool. Western analysis revealed that ATP increased Cx43 distribution (1.7-fold; P=0.013) to the caveolar domain, but had no effect on Cx37. These data demonstrate rapid ATP-stimulated repartitioning of Cx43 to the caveolae, where endothelial nitric oxide synthase resides and plays an important role in nitric oxide-mediated increasing uterine blood flow during pregnancy. © 2016 American Heart Association, Inc.

  17. Magnesium Oxide

    Science.gov (United States)

    Magnesium is an element your body needs to function normally. Magnesium oxide may be used for different reasons. Some people use it as ... one to four times daily depending on which brand is used and what condition you have. Follow ...

  18. Similarity queries for temporal toxicogenomic expression profiles.

    Directory of Open Access Journals (Sweden)

    Adam A Smith

    2008-07-01

    Full Text Available We present an approach for answering similarity queries about gene expression time series that is motivated by the task of characterizing the potential toxicity of various chemicals. Our approach involves two key aspects. First, our method employs a novel alignment algorithm based on time warping. Our time warping algorithm has several advantages over previous approaches. It allows the user to impose fairly strong biases on the form that the alignments can take, and it permits a type of local alignment in which the entirety of only one series has to be aligned. Second, our method employs a relaxed spline interpolation to predict expression responses for unmeasured time points, such that the spline does not necessarily exactly fit every observed point. We evaluate our approach using expression time series from the Edge toxicology database. Our experiments show the value of using spline representations for sparse time series. More significantly, they show that our time warping method provides more accurate alignments and classifications than previous standard alignment methods for time series.

  19. Humans and mice express similar olfactory preferences.

    Directory of Open Access Journals (Sweden)

    Nathalie Mandairon

    Full Text Available In humans, the pleasantness of odors is a major contributor to social relationships and food intake. Smells evoke attraction and repulsion responses, reflecting the hedonic value of the odorant. While olfactory preferences are known to be strongly modulated by experience and learning, it has been recently suggested that, in humans, the pleasantness of odors may be partly explained by the physicochemical properties of the odorant molecules themselves. If odor hedonic value is indeed predetermined by odorant structure, then it could be hypothesized that other species will show similar odor preferences to humans. Combining behavioral and psychophysical approaches, we here show that odorants rated as pleasant by humans were also those which, behaviorally, mice investigated longer and human subjects sniffed longer, thereby revealing for the first time a component of olfactory hedonic perception conserved across species. Consistent with this, we further show that odor pleasantness rating in humans and investigation time in mice were both correlated with the physicochemical properties of the molecules, suggesting that olfactory preferences are indeed partly engraved in the physicochemical structure of the odorant. That odor preferences are shared between mammal species and are guided by physicochemical features of odorant stimuli strengthens the view that odor preference is partially predetermined. These findings open up new perspectives for the study of the neural mechanisms of hedonic perception.

  20. Different-but-Similar Judgments by Bumblebees

    Directory of Open Access Journals (Sweden)

    Vicki Xu

    2016-08-01

    Full Text Available This study examines picture perception in an invertebrate. Two questions regarding possible picture-object correspondence are addressed for bumblebees (Bombus impatiens: (1 Do bees perceive the difference between an object and its corresponding picture even when they have not been trained to do so? (2 Do they also perceive the similarity? Twenty bees from each of four colonies underwent discrimination training of stimuli placed in a radial maze. Bees were trained to discriminate between two objects (artificial flowers in one group and between photos of those objects in another. Subsequent testing on unrewarding stimuli revealed, for both groups, a significant discrimination between the object and its photo: discrimination training was not necessary for bees to detect a difference between corresponding objects and pictures. We obtained not only object-to-picture transfer, as in previous research, but also the reverse: picture-to-object transfer. In the absence of the rewarding object, its photo, though never seen before by the bees, was accepted as a substitute. The reverse was also true. Bumblebees treated pictures as “different-but-similar” without having been trained to do so, which is in turn useful in floral categorization.

  1. Block generators for the similarity renormalization group

    Energy Technology Data Exchange (ETDEWEB)

    Huether, Thomas; Roth, Robert [TU Darmstadt (Germany)

    2016-07-01

    The Similarity Renormalization Group (SRG) is a powerful tool to improve convergence behavior of many-body calculations using NN and 3N interactions from chiral effective field theory. The SRG method decouples high and low-energy physics, through a continuous unitary transformation implemented via a flow equation approach. The flow is determined by a generator of choice. This generator governs the decoupling pattern and, thus, the improvement of convergence, but it also induces many-body interactions. Through the design of the generator we can optimize the balance between convergence and induced forces. We explore a new class of block generators that restrict the decoupling to the high-energy sector and leave the diagonalization in the low-energy sector to the many-body method. In this way one expects a suppression of induced forces. We analyze the induced many-body forces and the convergence behavior in light and medium-mass nuclei in No-Core Shell Model and In-Medium SRG calculations.

  2. State and Mafia, Differences and Similarities

    Directory of Open Access Journals (Sweden)

    Alfano Vincenzo

    2015-02-01

    Full Text Available The purpose of this article is to investigate about the differences and, if any, the similarities among the modern State and the mafia criminal organizations. In particular, starting from their definitions, I will try to find the differences between State and mafia, to then focus on the operational aspects of the functioning of these two organizations, with specific reference to the effect/impact that both these human constructs have on citizens’ existences, and especially on citizen’s economic lives. All this in order to understand whether it is possible to identify an objective difference – beside morals – between taxation by the modern State and extortion by criminal organizations. With this of course I do not want to argue that the mafia is in any way justifiable or absolvable, nor that it is better than the State. However, I want to investigate whether there is a real, logical reason why the State should be considered by the citizens more desirable than the criminal organizations oppressing Southern Italy, from a strictly logical point of view and not from the point of view of ethics and morality.

  3. Similarity of eigenstates in generalized labyrinth tilings

    International Nuclear Information System (INIS)

    Thiem, Stefanie; Schreiber, Michael

    2010-01-01

    The eigenstates of d-dimensional quasicrystalline models with a separable Hamiltonian are studied within the tight-binding model. The approach is based on mathematical sequences, constructed by an inflation rule P = {w → s,s → sws b-1 } describing the weak/strong couplings of atoms in a quasiperiodic chain. Higher-dimensional quasiperiodic tilings are constructed as a direct product of these chains and their eigenstates can be directly calculated by multiplying the energies E or wave functions ψ of the chain, respectively. Applying this construction rule, the grid in d dimensions splits into 2 d-1 different tilings, for which we investigated the characteristics of the wave functions. For the standard two-dimensional labyrinth tiling constructed from the octonacci sequence (b = 2) the lattice breaks up into two identical lattices, which consequently yield the same eigenstates. While this is not the case for b ≠ 2, our numerical results show that the wave functions of the different grids become increasingly similar for large system sizes. This can be explained by the fact that the structure of the 2 d-1 grids mainly differs at the boundaries and thus for large systems the eigenstates approach each other. This property allows us to analytically derive properties of the higher-dimensional generalized labyrinth tilings from the one-dimensional results. In particular participation numbers and corresponding scaling exponents have been determined.

  4. Genetic and 'cultural' similarity in wild chimpanzees.

    Science.gov (United States)

    Langergraber, Kevin E; Boesch, Christophe; Inoue, Eiji; Inoue-Murayama, Miho; Mitani, John C; Nishida, Toshisada; Pusey, Anne; Reynolds, Vernon; Schubert, Grit; Wrangham, Richard W; Wroblewski, Emily; Vigilant, Linda

    2011-02-07

    The question of whether animals possess 'cultures' or 'traditions' continues to generate widespread theoretical and empirical interest. Studies of wild chimpanzees have featured prominently in this discussion, as the dominant approach used to identify culture in wild animals was first applied to them. This procedure, the 'method of exclusion,' begins by documenting behavioural differences between groups and then infers the existence of culture by eliminating ecological explanations for their occurrence. The validity of this approach has been questioned because genetic differences between groups have not explicitly been ruled out as a factor contributing to between-group differences in behaviour. Here we investigate this issue directly by analysing genetic and behavioural data from nine groups of wild chimpanzees. We find that the overall levels of genetic and behavioural dissimilarity between groups are highly and statistically significantly correlated. Additional analyses show that only a very small number of behaviours vary between genetically similar groups, and that there is no obvious pattern as to which classes of behaviours (e.g. tool-use versus communicative) have a distribution that matches patterns of between-group genetic dissimilarity. These results indicate that genetic dissimilarity cannot be eliminated as playing a major role in generating group differences in chimpanzee behaviour.

  5. Multidimensional Scaling Visualization Using Parametric Similarity Indices

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2015-03-01

    Full Text Available In this paper, we apply multidimensional scaling (MDS and parametric similarity indices (PSI in the analysis of complex systems (CS. Each CS is viewed as a dynamical system, exhibiting an output time-series to be interpreted as a manifestation of its behavior. We start by adopting a sliding window to sample the original data into several consecutive time periods. Second, we define a given PSI for tracking pieces of data. We then compare the windows for different values of the parameter, and we generate the corresponding MDS maps of ‘points’. Third, we use Procrustes analysis to linearly transform the MDS charts for maximum superposition and to build a globalMDS map of “shapes”. This final plot captures the time evolution of the phenomena and is sensitive to the PSI adopted. The generalized correlation, theMinkowski distance and four entropy-based indices are tested. The proposed approach is applied to the Dow Jones Industrial Average stock market index and the Europe Brent Spot Price FOB time-series.

  6. Similarities and differences in vapor explosion criteria

    International Nuclear Information System (INIS)

    Cronenberg, A.W.

    1978-01-01

    An overview of recent ideas pertaining to vapor explosion criteria indicates that in general sense, a consensus of opinion is emerging on the conditions applicable to explosive vaporization. Experimental and theoretical work has lead a number of investigators to the formulation of such conditions which are quite similar in many respects, although the quantitative details of the model formulation of such conditions are somewhat different. All model concepts are consistent in that an initial period of stable film boiling, separating molten fuel from coolant, is considered necessary (at least for large-scale interactions and efficient intermixing), with subsequent breakdown of film boiling due to pressure and/or thermal effects, followed by intimate fuel-coolant contact and a rapid vaporization process which is sufficient to cause shock pressurization. Although differences arise as to the conditions for and the energetics associated with film boiling destabilization and the mode and energetics of fragmentation and intermixing. However, the principal area of difference seems to be the question of what constitutes the requisite condition(s) for rapid vapor production to cause shock pressurization

  7. Multiscale Hybrid Nonlocal Means Filtering Using Modified Similarity Measure

    Directory of Open Access Journals (Sweden)

    Zahid Hussain Shamsi

    2015-01-01

    Full Text Available A new multiscale implementation of nonlocal means filtering (MHNLM for image denoising is proposed. The proposed algorithm also introduces a modification of the similarity measure for patch comparison. Assuming the patch as an oriented surface, the notion of a normal vectors patch is introduced. The inner product of these normal vectors patches is defined and then used in the weighted Euclidean distance of intensity patches as the weight factor. The algorithm involves two steps: the first step is a multiscale implementation of an accelerated nonlocal means filtering in the discrete stationary wavelet domain to obtain a refined version of the noisy patches for later comparison. The next step is to apply the proposed modification of standard nonlocal means filtering to the noisy image using the reference patches obtained in the first step. These refined patches contain less noise, and consequently the computation of normal vectors and partial derivatives is more precise. Experimental results show equivalent or better performance of the proposed algorithm compared to various state-of-the-art algorithms.

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

    Science.gov (United States)

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

    2011-04-01

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

  9. Asteroid clusters similar to asteroid pairs

    Science.gov (United States)

    Pravec, P.; Fatka, P.; Vokrouhlický, D.; Scheeres, D. J.; Kušnirák, P.; Hornoch, K.; Galád, A.; Vraštil, J.; Pray, D. P.; Krugly, Yu. N.; Gaftonyuk, N. M.; Inasaridze, R. Ya.; Ayvazian, V. R.; Kvaratskhelia, O. I.; Zhuzhunadze, V. T.; Husárik, M.; Cooney, W. R.; Gross, J.; Terrell, D.; Világi, J.; Kornoš, L.; Gajdoš, Š.; Burkhonov, O.; Ehgamberdiev, Sh. A.; Donchev, Z.; Borisov, G.; Bonev, T.; Rumyantsev, V. V.; Molotov, I. E.

    2018-04-01

    We studied the membership, size ratio and rotational properties of 13 asteroid clusters consisting of between 3 and 19 known members that are on similar heliocentric orbits. By backward integrations of their orbits, we confirmed their cluster membership and estimated times elapsed since separation of the secondaries (the smaller cluster members) from the primary (i.e., cluster age) that are between 105 and a few 106 years. We ran photometric observations for all the cluster primaries and a sample of secondaries and we derived their accurate absolute magnitudes and rotation periods. We found that 11 of the 13 clusters follow the same trend of primary rotation period vs mass ratio as asteroid pairs that was revealed by Pravec et al. (2010). We generalized the model of the post-fission system for asteroid pairs by Pravec et al. (2010) to a system of N components formed by rotational fission and we found excellent agreement between the data for the 11 asteroid clusters and the prediction from the theory of their formation by rotational fission. The two exceptions are the high-mass ratio (q > 0.7) clusters of (18777) Hobson and (22280) Mandragora for which a different formation mechanism is needed. Two candidate mechanisms for formation of more than one secondary by rotational fission were published: the secondary fission process proposed by Jacobson and Scheeres (2011) and a cratering collision event onto a nearly critically rotating primary proposed by Vokrouhlický et al. (2017). It will have to be revealed from future studies which of the clusters were formed by one or the other process. To that point, we found certain further interesting properties and features of the asteroid clusters that place constraints on the theories of their formation, among them the most intriguing being the possibility of a cascade disruption for some of the clusters.

  10. Expanding the boundaries of local similarity analysis.

    Science.gov (United States)

    Durno, W Evan; Hanson, Niels W; Konwar, Kishori M; Hallam, Steven J

    2013-01-01

    Pairwise comparison of time series data for both local and time-lagged relationships is a computationally challenging problem relevant to many fields of inquiry. The Local Similarity Analysis (LSA) statistic identifies the existence of local and lagged relationships, but determining significance through a p-value has been algorithmically cumbersome due to an intensive permutation test, shuffling rows and columns and repeatedly calculating the statistic. Furthermore, this p-value is calculated with the assumption of normality -- a statistical luxury dissociated from most real world datasets. To improve the performance of LSA on big datasets, an asymptotic upper bound on the p-value calculation was derived without the assumption of normality. This change in the bound calculation markedly improved computational speed from O(pm²n) to O(m²n), where p is the number of permutations in a permutation test, m is the number of time series, and n is the length of each time series. The bounding process is implemented as a computationally efficient software package, FASTLSA, written in C and optimized for threading on multi-core computers, improving its practical computation time. We computationally compare our approach to previous implementations of LSA, demonstrate broad applicability by analyzing time series data from public health, microbial ecology, and social media, and visualize resulting networks using the Cytoscape software. The FASTLSA software package expands the boundaries of LSA allowing analysis on datasets with millions of co-varying time series. Mapping metadata onto force-directed graphs derived from FASTLSA allows investigators to view correlated cliques and explore previously unrecognized network relationships. The software is freely available for download at: http://www.cmde.science.ubc.ca/hallam/fastLSA/.

  11. UNSOLVED AND LATENT CRIME: DIFFERENCES AND SIMILARITIES

    Directory of Open Access Journals (Sweden)

    Mikhail Kleymenov

    2017-01-01

    Full Text Available УДК 343Purpose of the article is to study the specific legal and informational nature of the unsolved crime in comparison with the phenomenon of delinquency, special study and analysis to improve the efficiency of law enforcement.Methods of research are abstract-logical, systematic, statistical, study of documents. The main results of research. Unsolved crime has specific legal, statistical and informational na-ture as the crime phenomenon, which is expressed in cumulative statistical population of unsolved crimes. An array of unsolved crimes is the sum of the number of acts, things of which is suspended and not terminated. The fault of the perpetrator in these cases is not proven, they are not considered by the court, it is not a conviction. Unsolved crime must be registered. Latent crime has a different informational nature. The main symptom of latent crimes is the uncertainty for the subjects of law enforcement, which delegated functions of identification, registration and accounting. Latent crime is not recorded. At the same time, there is a "border" area between the latent and unsolved crimes, which includes covered from the account of the crime. In modern Russia the majority of crimes covered from accounting by passing the decision about refusal in excitation of criminal case. Unsolved crime on their criminogenic consequences represents a significant danger to the public is higher compared to latent crime.It is conducted in the article a special analysis of the differences and similarities in the unsolved latent crime for the first time in criminological literature.The analysis proves the need for radical changes in the current Russian assessment of the state of crime and law enforcement to solve crimes. The article argues that an unsolved crime is a separate and, in contrast to latent crime, poorly understood phenomenon. However unsolved latent crime and have common features and areas of interaction.

  12. Investigation of Ferroelectric Domain Walls by Raman Spectroscopy

    Science.gov (United States)

    Stone, Gregory A.

    Ferroelectric materials are characterized by an intrinsic spontaneous electric dipole moment that can be manipulated by the application of an electric field. Regions inside the crystal, known as domains, can have the spontaneous dipole moments oriented in a different direction than the surrounding crystal. Due to favorable piezoelectric, pyroelectric, electro-optic, and nonlinear optical properties, ferroelectric materials are attractive for commercial applications. Many devices, such as nonlinear frequency converters, require precisely engineered domain patterns. The properties of domains and their boundaries, known as domain walls, are vital to the performance and limitations of these devices. As a result, ferroelectric domains and the domain walls have been the focus of many scientific studies. Despite all this work, questions remain regarding their properties. This work is aimed at developing a better understanding of the properties of the domain wall using confocal Raman spectroscopy. Raman spectra taken from domain walls in Lithium Niobate and Lithium Tantalate reveal two distinct changes in the Raman spectra: (1) Shifts in frequency of the bulk Raman modes, which persists over a range of 0.2-0.5 mu m from the domain wall. The absence of this effect in defect free stoichiometric Lithium Tantalate indicates that the shifts are related to defects inside the crystal. (2) The presence of Raman modes corresponding to phonons propagating orthogonal to the laser beam axis, which are not collected in the bulk crystal. The phonons also preferential propagate normal to the domain wall. These modes are detected up to 0.35 mum from the domain wall. The observation and separation of these effects was made possible by the optimized spatial resolution (0.23 mum) of a home-built scanning confocal microscope and the fact that degeneracy of the transverse and longitudinal phonon polarization is lifted by polar phonons in Lithium Niobate and Lithium Tantalate. Raman

  13. Self-similar pattern formation and continuous mechanics of self-similar systems

    Directory of Open Access Journals (Sweden)

    A. V. Dyskin

    2007-01-01

    Full Text Available In many cases, the critical state of systems that reached the threshold is characterised by self-similar pattern formation. We produce an example of pattern formation of this kind – formation of self-similar distribution of interacting fractures. Their formation starts with the crack growth due to the action of stress fluctuations. It is shown that even when the fluctuations have zero average the cracks generated by them could grow far beyond the scale of stress fluctuations. Further development of the fracture system is controlled by crack interaction leading to the emergence of self-similar crack distributions. As a result, the medium with fractures becomes discontinuous at any scale. We develop a continuum fractal mechanics to model its physical behaviour. We introduce a continuous sequence of continua of increasing scales covering this range of scales. The continuum of each scale is specified by the representative averaging volume elements of the corresponding size. These elements determine the resolution of the continuum. Each continuum hides the cracks of scales smaller than the volume element size while larger fractures are modelled explicitly. Using the developed formalism we investigate the stability of self-similar crack distributions with respect to crack growth and show that while the self-similar distribution of isotropically oriented cracks is stable, the distribution of parallel cracks is not. For the isotropically oriented cracks scaling of permeability is determined. For permeable materials (rocks with self-similar crack distributions permeability scales as cube of crack radius. This property could be used for detecting this specific mechanism of formation of self-similar crack distributions.

  14. Domains of bosonic functional integrals

    International Nuclear Information System (INIS)

    Botelho, Luiz C.L.; Para Univ., Belem, PA

    1998-07-01

    We propose a mathematical framework for bosonic Euclidean quantum field functional integrals based on the theory of integration on the dual algebraic vector space of classical field sources. We present a generalization of the Minlos-Dao Xing theorem and apply it to determine exactly the domain of integration associated to the functional integral representation of the two-dimensional quantum electrodynamics Schwinger generating functional. (author)

  15. Categorization in the Affective Domain

    DEFF Research Database (Denmark)

    Sauciuc, Gabriela-Alina

    2011-01-01

    Data collected in Romance and Scandinavian languages (N=474) in a superordinate category name production task indicate that a multiple-strategy approach would be more suitable for accounting of categorization in the affective domain instead of a prototype approach as suggested by previous studies....... This paper will highlight performance aspects which appear to be consistent with such an interpretation, as well as an important layman- expert knowledge asymmetry in affective categorization....

  16. Superconductivity in domains with corners

    DEFF Research Database (Denmark)

    Bonnaillie-Noel, Virginie; Fournais, Søren

    2007-01-01

    We study the two-dimensional Ginzburg-Landau functional in a domain with corners for exterior magnetic field strengths near the critical field where the transition from the superconducting to the normal state occurs. We discuss and clarify the definition of this field and obtain a complete...... asymptotic expansion for it in the large $\\kappa$ regime. Furthermore, we discuss nucleation of superconductivity at the boundary....

  17. Flexible time domain averaging technique

    Science.gov (United States)

    Zhao, Ming; Lin, Jing; Lei, Yaguo; Wang, Xiufeng

    2013-09-01

    Time domain averaging(TDA) is essentially a comb filter, it cannot extract the specified harmonics which may be caused by some faults, such as gear eccentric. Meanwhile, TDA always suffers from period cutting error(PCE) to different extent. Several improved TDA methods have been proposed, however they cannot completely eliminate the waveform reconstruction error caused by PCE. In order to overcome the shortcomings of conventional methods, a flexible time domain averaging(FTDA) technique is established, which adapts to the analyzed signal through adjusting each harmonic of the comb filter. In this technique, the explicit form of FTDA is first constructed by frequency domain sampling. Subsequently, chirp Z-transform(CZT) is employed in the algorithm of FTDA, which can improve the calculating efficiency significantly. Since the signal is reconstructed in the continuous time domain, there is no PCE in the FTDA. To validate the effectiveness of FTDA in the signal de-noising, interpolation and harmonic reconstruction, a simulated multi-components periodic signal that corrupted by noise is processed by FTDA. The simulation results show that the FTDA is capable of recovering the periodic components from the background noise effectively. Moreover, it can improve the signal-to-noise ratio by 7.9 dB compared with conventional ones. Experiments are also carried out on gearbox test rigs with chipped tooth and eccentricity gear, respectively. It is shown that the FTDA can identify the direction and severity of the eccentricity gear, and further enhances the amplitudes of impulses by 35%. The proposed technique not only solves the problem of PCE, but also provides a useful tool for the fault symptom extraction of rotating machinery.

  18. Dressed Domain Walls and holography

    International Nuclear Information System (INIS)

    Grisa, Luca; Pujolas, Oriol

    2008-01-01

    The cutoff version of the AdS/CFT correspondence states that the Randall Sundrum scenario is dual to a Conformal Field Theory (CFT) coupled to gravity in four dimensions. The gravitational field produced by relativistic Domain Walls can be exactly solved in both sides of the correspondence, and thus provides one further check of it. We show in the two sides that for the most symmetric case, the wall motion does not lead to particle production of the CFT fields. Still, there are nontrivial effects. Due to the trace anomaly, the CFT effectively renormalizes the Domain Wall tension. On the five dimensional side, the wall is a codimension 2 brane localized on the Randall-Sundrum brane, which pulls the wall in a uniform acceleration. This is perceived from the brane as a Domain Wall with a tension slightly larger than its bare value. In both cases, the deviation from General Relativity appears at nonlinear level in the source, and the leading corrections match to the numerical factors.

  19. Alternative to domain wall fermions

    International Nuclear Information System (INIS)

    Neuberger, H.

    2002-01-01

    An alternative to commonly used domain wall fermions is presented. Some rigorous bounds on the condition number of the associated linear problem are derived. On the basis of these bounds and some experimentation it is argued that domain wall fermions will in general be associated with a condition number that is of the same order of magnitude as the product of the condition number of the linear problem in the physical dimensions by the inverse bare quark mass. Thus, the computational cost of implementing true domain wall fermions using a single conjugate gradient algorithm is of the same order of magnitude as that of implementing the overlap Dirac operator directly using two nested conjugate gradient algorithms. At a cost of about a factor of two in operation count it is possible to make the memory usage of direct implementations of the overlap Dirac operator independent of the accuracy of the approximation to the sign function and of the same order as that of standard Wilson fermions

  20. Solution structure of the isolated Pelle death domain.

    Science.gov (United States)

    Moncrieffe, Martin C; Stott, Katherine M; Gay, Nicholas J

    2005-07-18

    The interaction between the death domains (DDs) of Tube and the protein kinase Pelle is an important component of the Toll pathway. Published crystallographic data suggests that the Pelle-Tube DD interface is plastic and implies that in addition to the two predominant Pelle-Tube interfaces, a third interaction is possible. We present the NMR solution structure of the isolated death domain of Pelle and a study of the interaction between the DDs of Pelle and Tube. Our data suggests the solution structure of the isolated Pelle DD is similar to that of Pelle DD in complex with Tube. Additionally, they suggest that the plasticity observed in the crystal structure may not be relevant in the functioning death domain complex.

  1. Oxidative stress

    Directory of Open Access Journals (Sweden)

    Osredkar Joško

    2012-05-01

    Full Text Available The human organism is exposed to the influence of various forms of stress, either physical, psychological or chemical, which all have in common that they may adversely affect our body. A certain amount of stress is always present and somehow directs, promotes or inhibits the functioning of the human body. Unfortunately, we are now too many and too often exposed to excessive stress, which certainly has adverse consequences. This is especially true for a particular type of stress, called oxidative stress. All aerobic organisms are exposed to this type of stress because they produce energy by using oxygen. For this type of stress you could say that it is rather imperceptibly involved in our lives, as it becomes apparent only at the outbreak of certain diseases. Today we are well aware of the adverse impact of radicals, whose surplus is the main cause of oxidative stress. However, the key problem remains the detection of oxidative stress, which would allow us to undertake timely action and prevent outbreak of many diseases of our time. There are many factors that promote oxidative stress, among them are certainly a fast lifestyle and environmental pollution. The increase in oxidative stress can also trigger intense physical activity that is directly associated with an increased oxygen consumption and the resulting formation of free radicals. Considering generally positive attitude to physical activity, this fact may seem at first glance contradictory, but the finding has been confimed by several studies in active athletes. Training of a top athlete daily demands great physical effort, which is also reflected in the oxidative state of the organism. However, it should be noted that the top athletes in comparison with normal individuals have a different defense system, which can counteract the negative effects of oxidative stress. Quite the opposite is true for irregular or excessive physical activity to which the body is not adapted.

  2. KEJAHATAN NAMA DOMAIN BERKAITAN DENGAN MEREK

    Directory of Open Access Journals (Sweden)

    Muhammad Nizar

    2018-02-01

    Full Text Available Indonesia already has an ITE Law governing domain names in general terms and on certain provisions in chapter VI, but the regulation of domain name crimes is not regulated in the ITE Law as mandated in the academic draft of the ITE Bill. The absence of regulation of domain name norm in the ITE Law creates problems with registrant of domain name (registrant which deliberately register the domain name is bad faith. The characteristic of a crime in a domain name relating to the mark is that the registered domain name has an equation in essence with another party’s well-known brand, the act of doing so by exploiting a reputation for well-known or previously commercially valuable names as domain names for addresses for sites (websites it manages. The Prosecutor may include articles of the KUHP in filing his indictment before the Court during the absence of special regulatory provisions concerning domain name crime.

  3. DIMA 3.0: Domain Interaction Map.

    Science.gov (United States)

    Luo, Qibin; Pagel, Philipp; Vilne, Baiba; Frishman, Dmitrij

    2011-01-01

    Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

  4. A micromagnetic study of domain structure modeling

    International Nuclear Information System (INIS)

    Matsuo, Tetsuji; Mimuro, Naoki; Shimasaki, Masaaki

    2008-01-01

    To develop a mesoscopic model for magnetic-domain behavior, a domain structure model (DSM) was examined and compared with a micromagnetic simulation. The domain structure of this model is given by several domains with uniform magnetization vectors and domain walls. The directions of magnetization vectors and the locations of domain walls are determined so as to minimize the magnetic total energy of the magnetic material. The DSM was modified to improve its representation capability for domain behavior. The domain wall energy is multiplied by a vanishing factor to represent the disappearance of magnetic domain. The sequential quadratic programming procedure is divided into two steps to improve an energy minimization process. A comparison with micromagnetic simulation shows that the modified DSM improves the representation accuracy of the magnetization process

  5. Ferromagnetic and twin domains in LCMO manganites

    International Nuclear Information System (INIS)

    Jung, G.; Markovich, V.; Mogilyanski, D.; Beek, C. van der; Mukovskii, Y.M.

    2005-01-01

    Ferromagnetic and twin domains in lightly Ca-doped La 1-x Ca x MnO 3 single crystals have been visualized and investigated by means of the magneto-optical technique. Both types of domains became visible below the Curie temperature. The dominant structures seen in applied magnetic field are associated with magneto-crystalline anisotropy and twin domains. In a marked difference to the twin domains which appear only in applied magnetic field, ferromagnetic domains show up in zero applied field and are characterized by oppositely oriented spontaneous magnetization in adjacent domains. Ferromagnetic domains take form of almost periodic, corrugated strip-like structures. The corrugation of the ferromagnetic domain pattern is enforced by the underlying twin domains

  6. Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus

    Energy Technology Data Exchange (ETDEWEB)

    Asojo, Oluwatoyin A., E-mail: oasojo@unmc.edu [Pathology and Microbiology Department, 986495 Nebraska Medical Center, Omaha, NE 68198-6495 (United States)

    2011-05-01

    The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite N. americanus refined to a resolution limit of 2.2 Å is presented. Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structure was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linked by an extended loop. Overall, the carboxyl-terminal CAP domain is more similar to Na-ASP-2 than to the amino-terminal CAP domain. A large central cavity extends from the amino-terminal CAP domain to the carboxyl-terminal CAP domain, encompassing the putative CAP-binding cavity. The putative CAP-binding cavity is a characteristic cavity in the carboxyl-terminal CAP domain that contains a His and Glu pair. These residues are conserved in all single-CAP-domain proteins, but are absent in the amino-terminal CAP domain. The conserved His residues are oriented such that they appear to be capable of directly coordinating a zinc ion as observed for CAP proteins from reptile venoms. This first structure of a two-CAP-domain ASP can serve as a template for homology modeling of other two-CAP-domain proteins.

  7. Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus

    International Nuclear Information System (INIS)

    Asojo, Oluwatoyin A.

    2011-01-01

    The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite N. americanus refined to a resolution limit of 2.2 Å is presented. Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structure was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linked by an extended loop. Overall, the carboxyl-terminal CAP domain is more similar to Na-ASP-2 than to the amino-terminal CAP domain. A large central cavity extends from the amino-terminal CAP domain to the carboxyl-terminal CAP domain, encompassing the putative CAP-binding cavity. The putative CAP-binding cavity is a characteristic cavity in the carboxyl-terminal CAP domain that contains a His and Glu pair. These residues are conserved in all single-CAP-domain proteins, but are absent in the amino-terminal CAP domain. The conserved His residues are oriented such that they appear to be capable of directly coordinating a zinc ion as observed for CAP proteins from reptile venoms. This first structure of a two-CAP-domain ASP can serve as a template for homology modeling of other two-CAP-domain proteins

  8. Similarities and differences in ablative and non-ablative iron oxide nanoparticle hyperthermia cancer treatment

    Science.gov (United States)

    Petryk, Alicia A.; Misra, Adwiteeya; Kastner, Elliot J.; Mazur, Courtney M.; Petryk, James D.; Hoopes, P. Jack

    2015-03-01

    The use of hyperthermia to treat cancer is well studied and has utilized numerous delivery techniques, including microwaves, radio frequency, focused ultrasound, induction heating, infrared radiation, warmed perfusion liquids (combined with chemotherapy), and recently, metallic nanoparticles (NP) activated by near infrared radiation (NIR) and alternating magnetic field (AMF) based platforms. It has been demonstrated by many research groups that ablative temperatures and cytotoxicity can be produced with locally NP-based hyperthermia. Such ablative NP techniques have demonstrated the potential for success. Much attention has also been given to the fact that NP may be administered systemically, resulting in a broader cancer therapy approach, a lower level of tumor NP content and a different type of NP cancer therapy (most likely in the adjuvant setting). To use NP based hyperthermia successfully as a cancer treatment, the technique and its goal must be understood and utilized in the appropriate clinical context. The parameters include, but are not limited to, NP access to the tumor (large vs. small quantity), cancer cell-specific targeting, drug carrying capacity, potential as an ionizing radiation sensitizer, and the material properties (magnetic characteristics, size and charge). In addition to their potential for cytotoxicity, the material properties of the NP must also be optimized for imaging, detection and direction. In this paper we will discuss the differences between, and potential applications for, ablative and non-ablative magnetic nanoparticle hyperthermia.

  9. Similar Symmetries: The Role of Wallpaper Groups in Perceptual Texture Similarity

    Directory of Open Access Journals (Sweden)

    Fraser Halley

    2011-05-01

    Full Text Available Periodic patterns and symmetries are striking visual properties that have been used decoratively around the world throughout human history. Periodic patterns can be mathematically classified into one of 17 different Wallpaper groups, and while computational models have been developed which can extract an image's symmetry group, very little work has been done on how humans perceive these patterns. This study presents the results from a grouping experiment using stimuli from the different wallpaper groups. We find that while different images from the same wallpaper group are perceived as similar to one another, not all groups have the same degree of self-similarity. The similarity relationships between wallpaper groups appear to be dominated by rotations.

  10. Fashionista: A Fashion-aware Graphical System for Exploring Visually Similar Items

    OpenAIRE

    He, Ruining; Lin, Chunbin; McAuley, Julian

    2016-01-01

    To build a fashion recommendation system, we need to help users retrieve fashionable items that are visually similar to a particular query, for reasons ranging from searching alternatives (i.e., substitutes), to generating stylish outfits that are visually consistent, among other applications. In domains like clothing and accessories, such considerations are particularly paramount as the visual appearance of items is a critical feature that guides users' decisions. However, existing systems l...

  11. IMPLICATIONS OF CROSS DOMAIN FIRES IN MULTI-DOMAIN BATTLE

    Science.gov (United States)

    2017-04-06

    meeting the threats or defeating the challenges posed by today’s enemy. As such, in a rapidly changing and demanding environment, I would contend...Joint Power.”10 As such, the Army, Marine Corps, Air Force and Navy are developing a new joint concept in order to adequately meet the challenges of...TRADOC Pamphlet 525-3-1, AOC, p. 13. 5 TRADOC Pamphlet 525-3-1, AOC, p. 13. 6 Kris Osborn, “Cross-Domain Fires: US Military’s Master Plan to Win the

  12. Similarity and self-similarity in high energy density physics: application to laboratory astrophysics

    International Nuclear Information System (INIS)

    Falize, E.

    2008-10-01

    The spectacular recent development of powerful facilities allows the astrophysical community to explore, in laboratory, astrophysical phenomena where radiation and matter are strongly coupled. The titles of the nine chapters of the thesis are: from high energy density physics to laboratory astrophysics; Lie groups, invariance and self-similarity; scaling laws and similarity properties in High-Energy-Density physics; the Burgan-Feix-Munier transformation; dynamics of polytropic gases; stationary radiating shocks and the POLAR project; structure, dynamics and stability of optically thin fluids; from young star jets to laboratory jets; modelling and experiences for laboratory jets

  13. Elemental composition and oxidation of chamber organic aerosol

    Directory of Open Access Journals (Sweden)

    P. S. Chhabra

    2011-09-01

    Full Text Available Recently, graphical representations of aerosol mass spectrometer (AMS spectra and elemental composition have been developed to explain the oxidative and aging processes of secondary organic aerosol (SOA. It has been shown previously that oxygenated organic aerosol (OOA components from ambient and laboratory data fall within a triangular region in the f44 vs. f43 space, where f44 and f43 are the ratios of the organic signal at m/z 44 and 43 to the total organic signal in AMS spectra, respectively; we refer to this graphical representation as the "triangle plot." Alternatively, the Van Krevelen diagram has been used to describe the evolution of functional groups in SOA. In this study we investigate the variability of SOA formed in chamber experiments from twelve different precursors in both "triangle plot" and Van Krevelen domains. Spectral and elemental data from the high-resolution Aerodyne aerosol mass spectrometer are compared to offline species identification analysis and FTIR filter analysis to better understand the changes in functional and elemental composition inherent in SOA formation and aging. We find that SOA formed under high- and low-NOx conditions occupy similar areas in the "triangle plot" and Van Krevelen diagram and that SOA generated from already oxidized precursors allows for the exploration of areas higher on the "triangle plot" not easily accessible with non-oxidized precursors. As SOA ages, it migrates toward the top of the triangle along a path largely dependent on the precursor identity, which suggests increasing organic acid content and decreasing mass spectral variability. The most oxidized SOA come from the photooxidation of methoxyphenol precursors which yielded SOA O/C ratios near unity. α-pinene ozonolysis and naphthalene photooxidation SOA systems have had the highest degree of mass closure in previous chemical characterization studies and also show the

  14. Multi-domain comparison of safety standards; Comparaison de normes de securite-innocuite de plusieurs domaines industriels

    Energy Technology Data Exchange (ETDEWEB)

    Baufreton, Ph.; Derrien, J.C.; Ricque, B. [Sagem Defense Securite, 75 - Paris (France); Blanquart, J.P. [Astrium Satellites, France (France); Boulanger, J.L. [CERTIFER, 75 - Paris (France); Delseny, H. [Airbus, 31 - Toulouse (France); Gassino, J. [Institut de Radioprotection et de Surete Nucleaire, IRSN, 92 - Fontenay aux Roses (France); Ladier, G. [Airbus / Aerospace Valley, 31 - Toulouse (France); Ledinot, E. [Dassault Aviation, 92 - Saint Cloud (France); Leeman, M. [Valeo, 75 - Paris (France); Quere, Ph. [Renault, 75 - Paris (France)

    2011-07-01

    This paper presents an analysis of safety standards and their implementation in certification strategies from different domains such as aeronautics, automation, automotive, nuclear, railway and space. This work, performed in the context of the CG2E ('Club des Grandes Entreprises de l'Embarque'), aims at identifying the main similarities and dissimilarities, for potential cross-domain harmonization. We strive to find the most comprehensive 'trans-sectorial' approach, within a large number of industrial domains. Exhibiting the 'true goals' of their numerous applicable standards, related to the safety of system and software, is a first important step towards harmonization, sharing common approaches, methods and tools whenever possible. (authors)

  15. ASH structure alignment package: Sensitivity and selectivity in domain classification

    Directory of Open Access Journals (Sweden)

    Toh Hiroyuki

    2007-04-01

    Full Text Available Abstract Background Structure alignment methods offer the possibility of measuring distant evolutionary relationships between proteins that are not visible by sequence-based analysis. However, the question of how structural differences and similarities ought to be quantified in this regard remains open. In this study we construct a training set of sequence-unique CATH and SCOP domains, from which we develop a scoring function that can reliably identify domains with the same CATH topology and SCOP fold classification. The score is implemented in the ASH structure alignment package, for which the source code and a web service are freely available from the PDBj website http://www.pdbj.org/ASH/. Results The new ASH score shows increased selectivity and sensitivity compared with values reported for several popular programs using the same test set of 4,298,905 structure pairs, yielding an area of .96 under the receiver operating characteristic (ROC curve. In addition, weak sequence homologies between similar domains are revealed that could not be detected by BLAST sequence alignment. Also, a subset of domain pairs is identified that exhibit high similarity, even though their CATH and SCOP classification differs. Finally, we show that the ranking of alignment programs based solely on geometric measures depends on the choice of the quality measure. Conclusion ASH shows high selectivity and sensitivity with regard to domain classification, an important step in defining distantly related protein sequence families. Moreover, the CPU cost per alignment is competitive with the fastest programs, making ASH a practical option for large-scale structure classification studies.

  16. Iron oxides as a cause of GPR reflections

    NARCIS (Netherlands)

    van Dam, R.L.; Schlager, W.; Dekkers, M.; Huisman, J.A.

    2002-01-01

    Iron oxides frequently occur as secondary precipitates in both modern and ancient sediments and may form bands or irregular patterns. We show from time-domain reflectometry (TDR) field studies that goethite iron-oxide precipitates significantly lower the electromagnetic wave velocity of sediments.

  17. Influence of water on the anodic oxidation mechanism of ...

    African Journals Online (AJOL)

    Diethylenetriamine was oxidised in different electrolytes on platinum electrode. In non-aqueous electrolyte, an irreversible oxidation peak characteristic of DETA oxidation appears on the voltammogram followed by a constant current until the higher limit of the sweeping potential domain is attained. The following successive ...

  18. Ferroelectric Polarization Switching Dynamics and Domain Growth of Triglycine Sulfate and Imidazolium Perchlorate

    KAUST Repository

    Ma, He

    2016-04-10

    The weak bond energy and large anisotropic domain wall energy induce many special characteristics of the domain nucleation, growth, and polarization switch in triglycine sulfate (TGS) and imidazolium perchlorate (IM), two typical molecular ferroelectrics. Their domain nucleation and polarization switch are rather slower than those of conventional oxide ferroelectrics, which may be due to the weaker bond energy of hydrogen bond or van der Waals bond than that of ionic bond. These chemical bonds dominate the elastic energy, with the latter being an important component of domain wall energy and playing an important role in domain nucleation and domain growth. The ratio of anisotropic domain wall energy to Gibbs free energy is large in TGS and IM, which allows a favorable domain shape and a special domain evolution under a certain electric field. Therefore, this study not only sheds light on the physical nature but also indicates the application direction for molecular ferroelectrics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

  19. Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

    Directory of Open Access Journals (Sweden)

    Lyngsø Rune

    2010-04-01

    Full Text Available Abstract Background The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs to compare the dynamic motions of different proteins. Comparing the dynamics of distinct proteins may also provide insight into how protein motions are modified by variations in sequence and, consequently, by structure. The optimal way of comparing complex molecular motions is, however, far from trivial. The majority of comparative molecular dynamics studies performed to date relied upon prior sequence or structural alignment to define which residues were equivalent in 3-dimensional space. Results Here we discuss an alternative methodology for comparative molecular dynamics that does not require any prior alignment information. We show it is possible to align proteins based solely on their dynamics and that we can use these dynamics-based alignments to quantify the dynamic similarity of proteins. Our method was tested on 10 representative members of the PDZ domain family. Conclusions As a result of creating pair-wise dynamics-based alignments of PDZ domains, we have found evolutionarily conserved patterns in their backbone dynamics. The dynamic similarity of PDZ domains is highly correlated with their structural similarity as calculated with Dali. However, significant differences in their dynamics can be detected indicating that sequence has a more refined role to play in protein dynamics than just dictating the overall fold. We suggest that the method should be generally applicable.

  20. UV and ionizing radiations induced DNA damage, differences and similarities

    Science.gov (United States)

    Ravanat, Jean-Luc; Douki, Thierry

    2016-11-01

    Both UV and ionizing radiations damage DNA. Two main mechanisms, so-called direct and indirect pathways, are involved in the degradation of DNA induced by ionizing radiations. The direct effect of radiation corresponds to direct ionization of DNA (one electron ejection) whereas indirect effects are produced by reactive oxygen species generated through water radiolysis, including the highly reactive hydroxyl radicals, which damage DNA. UV (and visible) light damages DNA by again two distinct mechanisms. UVC and to a lesser extend UVB photons are directly absorbed by DNA bases, generating their excited states that are at the origin of the formation of pyrimidine dimers. UVA (and visible) light by interaction with endogenous or exogenous photosensitizers induce the formation of DNA damage through photosensitization reactions. The excited photosensitizer is able to induce either a one-electron oxidation of DNA (type I) or to produce singlet oxygen (type II) that reacts with DNA. In addition, through an energy transfer from the excited photosensitizer to DNA bases (sometime called type III mechanism) formation of pyrimidine dimers could be produced. Interestingly it has been shown recently that pyrimidine dimers are also produced by direct absorption of UVA light by DNA, even if absorption of DNA bases at these wavelengths is very low. It should be stressed that some excited photosensitizers (such as psoralens) could add directly to DNA bases to generate adducts. The review will described the differences and similarities in terms of damage formation (structure and mechanisms) between these two physical genotoxic agents.

  1. Comparative analysis of glutaredoxin domains from bacterial opportunistic pathogens

    International Nuclear Information System (INIS)

    Leeper, Thomas; Zhang, Suxin; Van Voorhis, Wesley C.; Myler, Peter J.; Varani, Gabriele

    2011-01-01

    NMR structures of the glutaredoxin (GLXR) domains from Br. melitensis and Ba. henselae have been determined as part of the SSGCID initiative. Comparison of the domains with known structures reveals overall structural similarity between these proteins and previously determined E. coli GLXR structures, with minor changes associated with the position of helix 1 and with regions that diverge from similar structures found in the closest related human homolog. Glutaredoxin proteins (GLXRs) are essential components of the glutathione system that reductively detoxify substances such as arsenic and peroxides and are important in the synthesis of DNA via ribonucleotide reductases. NMR solution structures of glutaredoxin domains from two Gram-negative opportunistic pathogens, Brucella melitensis and Bartonella henselae, are presented. These domains lack the N-terminal helix that is frequently present in eukaryotic GLXRs. The conserved active-site cysteines adopt canonical proline/tyrosine-stabilized geometries. A difference in the angle of α-helix 2 relative to the β-sheet surface and the presence of an extended loop in the human sequence suggests potential regulatory regions and/or protein–protein interaction motifs. This observation is consistent with mutations in this region that suppress defects in GLXR–ribonucleotide reductase interactions. These differences between the human and bacterial forms are adjacent to the dithiol active site and may permit species-selective drug design

  2. Different Principles of ADP-Ribose-Mediated Activation and Opposite Roles of the NUDT9 Homology Domain in the TRPM2 Orthologs of Man and Sea Anemone

    Directory of Open Access Journals (Sweden)

    Frank Kühn

    2017-10-01

    Full Text Available A decisive element in the human cation channel TRPM2 is a region in its cytosolic C-terminus named NUDT9H because of its homology to the NUDT9 enzyme, a pyrophosphatase degrading ADP-ribose (ADPR. In hTRPM2, however, the NUDT9H domain has lost its enzymatic activity but serves as a binding domain for ADPR. As consequence of binding, gating of the channel is initiated. Since ADPR is produced after oxidative DNA damage, hTRPM2 mediates Ca2+ influx in response to oxidative stress which may lead to cell death. In the genome of the sea anemone Nematostella vectensis (nv, a preferred model organism for the evolution of key bilaterian features, a TRPM2 ortholog has been identified that contains a NUDT9H domain as well. Heterologous expression of nvTRPM2 in HEK-293 cells reveals a cation channel with many close similarities to the human counterpart. Most notably, nvTRPM2 is activated by ADPR, and Ca2+ is a co-agonist. However, the intramolecular mechanisms of ADPR gating as well as the role of NUDT9H are strikingly different in the two species. Whereas already subtle changes of NUDT9H abolish ADPR gating in hTRPM2, the region can be completely removed from nvTRPM2 without loss of responses to ADPR. An alternative ADPR binding site seems to be present but has not yet been characterized. The ADP-ribose pyrophosphatase (ADPRase function of nvNUDT9H has been preserved but can be abolished by numerous genetic manipulations. All these manipulations create channels that are sensitive to hydrogen peroxide which fails to induce channel activity in wild-type nvTRPM2. Therefore, the function of NUDT9H in nvTRPM2 is the degradation of ADPR, thereby reducing agonist concentration in the presence of oxidative stress. Thus, the two TRPM2 orthologs have evolved divergently but nevertheless gained analogous functional properties, i.e., gating by ADPR with Ca2+ as co-factor. Opposite roles are played by the respective NUDT9H domains, either binding of ADPR and mediating

  3. Hydrogen oxidation in Azospirillum brasilense

    Energy Technology Data Exchange (ETDEWEB)

    Tibelius, K.

    1984-01-01

    Hydrogen oxidation by Azospirillum brasilense Sp7 was studied in N/sub 2/-fixing and NH/sub 4//sup +/-grown batch cultures. The K/sub m/ for H/sub 2/ of O/sub 2/-dependent H/sup 3/H oxidation in whole cells was 9 uM. The rates of H/sup 3/H and H/sub 2/ oxidation were very similar, indicating that the initial H/sub 2/ activation step in the overall H/sub 2/ oxidation reaction was not rate-limiting and that H/sup 3/H oxidation was a valid measure of H/sub 2/-oxidation activity. Hydrogen-oxidation activity was inhibited irreversibly by air. In N-free cultures the O/sub 2/ optima for O/sub 2/-dependent H/sub 2/ oxidation, ranging from 0.5-1.25% O/sub 2/ depending on the phase of growth, were significantly higher than those of C/sub 2/H/sub 2/ reduction, 0.15-0.35%, suggesting that the H/sub 2/-oxidation system may have a limited ability to aid in the protection of nitrogenase against inactivation by O/sub 2/. Oxygen-dependent H/sub 2/ oxidation was inhibited by NO/sub 2//sup +/, NO, CO, and C/sub 2/H/sub 2/ with apparent K/sub 1/ values of 20, 0.4, 28, and 88 uM, respectively. Hydrogen-oxidation activity was 50 to 100 times higher in denitrifying cultures when the terminal electron acceptor for growth was N/sub 2/O rather than NO/sub 3//sup -/, possibly due to the irreversible inhibition of hydrogenase by NO/sub 2//sup -/ and NO in NO/sub 3//sup -/-grown cultures.

  4. Improved cosine similarity measures of simplified neutrosophic setsfor medical diagnoses

    OpenAIRE

    Jun Ye

    2014-01-01

    In pattern recognition and medical diagnosis, similarity measure is an important mathematicaltool. To overcome some disadvantages of existing cosine similarity measures of simplified neutrosophicsets (SNSs) in vector space, this paper proposed improved cosine similarity measures of SNSs based oncosine function, including single valued neutrosophic cosine similarity measures and interval neutro-sophic cosine similarity measures. Then, weighted cosine similarity measures of SNSs were introduced...

  5. Drug-domain interaction networks in myocardial infarction.

    Science.gov (United States)

    Wang, Haiying; Zheng, Huiru; Azuaje, Francisco; Zhao, Xing-Ming

    2013-09-01

    It has been well recognized that the pace of the development of new drugs and therapeutic interventions lags far behind biological knowledge discovery. Network-based approaches have emerged as a promising alternative to accelerate the discovery of new safe and effective drugs. Based on the integration of several biological resources including two recently published datasets i.e., Drug-target interactions in myocardial infarction (My-DTome) and drug-domain interaction network, this paper reports the association between drugs and protein domains in the context of myocardial infarction (MI). A MI drug-domain interaction network, My-DDome, was firstly constructed, followed by topological analysis and functional characterization of the network. The results show that My-DDome has a very clear modular structure, where drugs interacting with the same domain(s) within each module tend to have similar therapeutic effects. Moreover it has been found that drugs acting on blood and blood forming organs (ATC code B) and sensory organs (ATC code S) are significantly enriched in My-DDome (p drugs, their known targets, and seemingly unrelated proteins can be revealed.

  6. Domain organizations of modular extracellular matrix proteins and their evolution.

    Science.gov (United States)

    Engel, J

    1996-11-01

    Multidomain proteins which are composed of modular units are a rather recent invention of evolution. Domains are defined as autonomously folding regions of a protein, and many of them are similar in sequence and structure, indicating common ancestry. Their modular nature is emphasized by frequent repetitions in identical or in different proteins and by a large number of different combinations with other domains. The extracellular matrix is perhaps the largest biological system composed of modular mosaic proteins, and its astonishing complexity and diversity are based on them. A cluster of minireviews on modular proteins is being published in Matrix Biology. These deal with the evolution of modular proteins, the three-dimensional structure of domains and the ways in which these interact in a multidomain protein. They discuss structure-function relationships in calcium binding domains, collagen helices, alpha-helical coiled-coil domains and C-lectins. The present minireview is focused on some general aspects and serves as an introduction to the cluster.

  7. Hilar cholangiocarcinoma is pathologically similar to pancreatic duct adenocarcinoma: suggestions of similar background and development.

    Science.gov (United States)

    Nakanuma, Yasuni; Sato, Yasunori

    2014-07-01

    Routine experiences suggest that cholangiocarcinomas (CCAs) show different clinicopathological behaviors along the biliary tree, and hilar CCA apparently resembles pancreatic duct adenocarcinoma (PDAC). Herein, the backgrounds for these similarities were reviewed. While all cases of PDAC, hilar CCA, intrahepatic CCA (ICCA) and CCA components of combined hepatocellular-cholangiocarcinoma (cHC-CCA) were adenocarcinomas, micropapillary patterns and columnar carcinoma cells were common in PDAC and hilar CCA, and trabecular components and cuboidal carcinoma cells were common in ICCA and CCA components of cHC-CCA. Anterior gradient protein-2 and S100P were frequently expressed in perihilar CCA and PDAC, while neural cell adhesion molecule and luminal epithelial membrane antigen were common in CCA components of c-HC-CCA. Pdx1 and Hes1 were frequently and markedly expressed aberrantly in PDAC and perihilar CCA, although their expression was rare and mild in CCA components in cHC-CCA and ICCA. Hilar CCA showed a similar postoperative prognosis to PDAC but differed from ICCA and cHC-CCA. Taken together, hilar CCA may differ from ICCA and CCA components of cHC-CCA but have a similar development to PDAC. These similarities may be explained by the unique anatomical, embryological and reactive nature of the pancreatobiliary tract. Further studies of these intractable malignancies are warranted. © 2014 Japanese Society of Hepato-Biliary-Pancreatic Surgery.

  8. When high similarity copycats lose and moderate similarity copycats gain: The impact of comparative evaluation

    NARCIS (Netherlands)

    Van Horen, F.; Pieters, R.

    2012-01-01

    Copycats imitate features of leading brands to free ride on their equity. The prevailing belief is that the more similar copycats are to the leader brand, the more positive their evaluation is, and thus the more they free ride. Three studies demonstrate when the reverse holds true:

  9. When high similarity copycats lose and moderate similarity copycats gain : The impact of comparative evaluation

    NARCIS (Netherlands)

    van Horen, F.; Pieters, R.

    2012-01-01

    Copycats imitate features of leading brands to free ride on their equity. The prevailing belief is that the more similar copycats are to the leader brand, the more positive their evaluation is, and thus the more they free ride. Three studies demonstrate when the reverse holds true:

  10. The Ambiguous Role of Constraints in Creativity: A Cross-Domain Exploration

    DEFF Research Database (Denmark)

    Biskjaer, Michael Mose; Onarheim, Balder; Wiltschnig, Stefan

    2011-01-01

    The relationship between creativity and constraints is often described in the literature either in rather imprecise, general concepts or in relation to very specific domains. Cross-domain and cross-disciplinary takes on how the handling of constraints influences creative activities are rare...... studies of Danish cutting-edge proponents of creative expertise thus exemplifying each domain, this preliminary exploration mainly focuses on similarities in how such successful professionals work with constraints to frame their creative process and ensure its progression toward the final outcome. Our...... main observations suggest that despite vast differences between the two domains, significant patterns and strategies reoccur. From a list of nine such similarities identified, four patterns are analyzed across the two domains in more detail as a contribution to encourage further advancement of cross-disciplinary...

  11. Different Binding Properties and Function of CXXC Zinc Finger Domains in Dnmt1 and Tet1

    Science.gov (United States)

    Meilinger, Daniela; Bultmann, Sebastian; Fellinger, Karin; Hasenöder, Stefan; Wang, Mengxi; Qin, Weihua; Söding, Johannes; Spada, Fabio; Leonhardt, Heinrich

    2011-01-01

    Several mammalian proteins involved in chromatin and DNA modification contain CXXC zinc finger domains. We compared the structure and function of the CXXC domains in the DNA methyltransferase Dnmt1 and the methylcytosine dioxygenase Tet1. Sequence alignment showed that both CXXC domains have a very similar framework but differ in the central tip region. Based on the known structure of a similar MLL1 domain we developed homology models and designed expression constructs for the isolated CXXC domains of Dnmt1 and Tet1 accordingly. We show that the CXXC domain of Tet1 has no DNA binding activity and is dispensable for catalytic activity in vivo. In contrast, the CXXC domain of Dnmt1 selectively binds DNA substrates containing unmethylated CpG sites. Surprisingly, a Dnmt1 mutant construct lacking the CXXC domain formed covalent complexes with cytosine bases both in vitro and in vivo and rescued DNA methylation patterns in dnmt1−/− embryonic stem cells (ESCs) just as efficiently as wild type Dnmt1. Interestingly, neither wild type nor ΔCXXC Dnmt1 re-methylated imprinted CpG sites of the H19a promoter in dnmt1−/− ESCs, arguing against a role of the CXXC domain in restraining Dnmt1 methyltransferase activity on unmethylated CpG sites. PMID:21311766

  12. Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1.

    Directory of Open Access Journals (Sweden)

    Carina Frauer

    2011-02-01

    Full Text Available Several mammalian proteins involved in chromatin and DNA modification contain CXXC zinc finger domains. We compared the structure and function of the CXXC domains in the DNA methyltransferase Dnmt1 and the methylcytosine dioxygenase Tet1. Sequence alignment showed that both CXXC domains have a very similar framework but differ in the central tip region. Based on the known structure of a similar MLL1 domain we developed homology models and designed expression constructs for the isolated CXXC domains of Dnmt1 and Tet1 accordingly. We show that the CXXC domain of Tet1 has no DNA binding activity and is dispensable for catalytic activity in vivo. In contrast, the CXXC domain of Dnmt1 selectively binds DNA substrates containing unmethylated CpG sites. Surprisingly, a Dnmt1 mutant construct lacking the CXXC domain formed covalent complexes with cytosine bases both in vitro and in vivo and rescued DNA methylation patterns in dnmt1⁻/⁻ embryonic stem cells (ESCs just as efficiently as wild type Dnmt1. Interestingly, neither wild type nor ΔCXXC Dnmt1 re-methylated imprinted CpG sites of the H19a promoter in dnmt1⁻/⁻ ESCs, arguing against a role of the CXXC domain in restraining Dnmt1 methyltransferase activity on unmethylated CpG sites.

  13. Sherlock: A Semi-automatic Framework for Quiz Generation Using a Hybrid Semantic Similarity Measure.

    Science.gov (United States)

    Lin, Chenghua; Liu, Dong; Pang, Wei; Wang, Zhe

    In this paper, we present a semi-automatic system (Sherlock) for quiz generation using linked data and textual descriptions of RDF resources. Sherlock is distinguished from existing quiz generation systems in its generic framework for domain-independent quiz generation as well as in the ability of controlling the difficulty level of the generated quizzes. Difficulty scaling is non-trivial, and it is fundamentally related to cognitive science. We approach the problem with a new angle by perceiving the level of knowledge difficulty as a similarity measure problem and propose a novel hybrid semantic similarity measure using linked data. Extensive experiments show that the proposed semantic similarity measure outperforms four strong baselines with more than 47 % gain in clustering accuracy. In addition, we discovered in the human quiz test that the model accuracy indeed shows a strong correlation with the pairwise quiz similarity.

  14. Visual similarity in short-term recall for where and when.

    Science.gov (United States)

    Jalbert, Annie; Saint-Aubin, Jean; Tremblay, Sébastien

    2008-03-01

    Two experiments examined the effects of visual similarity on short-term recall for where and when in the visual spatial domain. A series of squares of similar or dissimilar colours were serially presented at various locations on the screen. At recall, all coloured squares were simultaneously presented in a random order at the bottom of the screen, and the locations used for presentation were indicated by white squares. Participants were asked to place the colours at their appropriate location in their presentation order. Performance for location (where) and order (when) was assessed separately. Results revealed that similarity severely hinders both memory for what was where and memory for what was when, under quiet and articulatory suppression conditions. These results provide further evidence that similarity has a major impact on processing relational information in memory.

  15. Oxidation catalyst

    Science.gov (United States)

    Ceyer, Sylvia T.; Lahr, David L.

    2010-11-09

    The present invention generally relates to catalyst systems and methods for oxidation of carbon monoxide. The invention involves catalyst compositions which may be advantageously altered by, for example, modification of the catalyst surface to enhance catalyst performance. Catalyst systems of the present invention may be capable of performing the oxidation of carbon monoxide at relatively lower temperatures (e.g., 200 K and below) and at relatively higher reaction rates than known catalysts. Additionally, catalyst systems disclosed herein may be substantially lower in cost than current commercial catalysts. Such catalyst systems may be useful in, for example, catalytic converters, fuel cells, sensors, and the like.

  16. Sex differences and sex similarities in disgust sensitivity

    NARCIS (Netherlands)

    Tybur, J.M.; Bryan, A.D.; Lieberman, D.L.; Caldwell Hooper, A.E.; Merriman, L.A.

    2011-01-01

    Across two studies, we test for sex differences in the factor structure, factor loadings, concurrent validity, and means of the Three Domain Disgust Scale. In Study 1, we find that the Three Domain Disgust Scale has indistinguishable factor structure and factor loadings for men and women. In Study

  17. The YARHG domain: an extracellular domain in search of a function.

    Directory of Open Access Journals (Sweden)

    Penny Coggill

    Full Text Available We have identified a new bacterial protein domain that we hypothesise binds to peptidoglycan. This domain is called the YARHG domain after the most highly conserved sequence-segment. The domain is found in the extracellular space and is likely to be composed of four alpha-helices. The domain is found associated with protein kinase domains, suggesting it is associated with signalling in some bacteria. The domain is also found associated with three different families of peptidases. The large number of different domains that are found associated with YARHG suggests that it is a useful functional module that nature has recombined multiple times.

  18. Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan; Gao, Xin

    2014-01-01

    Traditional cross-domain learning methods transfer learning from a source domain to a target domain. In this paper, we propose the multiple-domain learning problem for several equally treated domains. The multiple-domain learning problem assumes that samples from different domains have different distributions, but share the same feature and class label spaces. Each domain could be a target domain, while also be a source domain for other domains. A novel multiple-domain representation method is proposed for the multiple-domain learning problem. This method is based on nonnegative matrix factorization (NMF), and tries to learn a basis matrix and coding vectors for samples, so that the domain distribution mismatch among different domains will be reduced under an extended variation of the maximum mean discrepancy (MMD) criterion. The novel algorithm - multiple-domain NMF (MDNMF) - was evaluated on two challenging multiple-domain learning problems - multiple user spam email detection and multiple-domain glioma diagnosis. The effectiveness of the proposed algorithm is experimentally verified. © 2013 Elsevier Ltd. All rights reserved.

  19. Beyond cross-domain learning: Multiple-domain nonnegative matrix factorization

    KAUST Repository

    Wang, Jim Jing-Yan

    2014-02-01

    Traditional cross-domain learning methods transfer learning from a source domain to a target domain. In this paper, we propose the multiple-domain learning problem for several equally treated domains. The multiple-domain learning problem assumes that samples from different domains have different distributions, but share the same feature and class label spaces. Each domain could be a target domain, while also be a source domain for other domains. A novel multiple-domain representation method is proposed for the multiple-domain learning problem. This method is based on nonnegative matrix factorization (NMF), and tries to learn a basis matrix and coding vectors for samples, so that the domain distribution mismatch among different domains will be reduced under an extended variation of the maximum mean discrepancy (MMD) criterion. The novel algorithm - multiple-domain NMF (MDNMF) - was evaluated on two challenging multiple-domain learning problems - multiple user spam email detection and multiple-domain glioma diagnosis. The effectiveness of the proposed algorithm is experimentally verified. © 2013 Elsevier Ltd. All rights reserved.

  20. Domain specific MT in use

    DEFF Research Database (Denmark)

    Offersgaard, Lene; Povlsen, Claus; Almsten, Lisbeth Kjeldgaard

    2008-01-01

    point scale evaluate the sentence from the point of view of the post-editor. The post-editor profile defined by the LSP is based on the experiences of introducing MT in the LSP workflow. The relation between the Translation Edit Rate (TER) scores and “Usability” scores is tested. We find TER a candidate......The paper focuses on domain specific use of MT with a special focus on SMT in the workflow of a Language Service Provider (LSP). We report on the feedback of post-editors using fluency/adequacy evaluation and the evaluation metric ’Usability’, understood in this context as where users on a three...

  1. Meta-domains for Automated System Identification

    National Research Council Canada - National Science Library

    Easley, Matthew; Bradley, Elizabeth

    2000-01-01

    .... In particular we introduce a new structure for automated model building known as a meta-domain which, when instantiated with domain-specific components tailors the space of candidate models to the system at hand...

  2. An Analysis of Perturbed Quantization Steganography in the Spatial Domain

    Science.gov (United States)

    2005-03-01

    Transform Domain While LSB steganography hides data in the least significant areas of image pixels, this data is not robust against lossy digital...introduced a technique for detecting least significant bit ( LSB ) steganography in digital images called RS Steganalysis. RS Steganalysis produces a...the function has the effect of additive noise similar to that introduced by pixel based LSB steganography . In clean cover images , the flipping

  3. Single amino acids in the carboxyl terminal domain of aquaporin-1 contribute to cGMP-dependent ion channel activation

    Directory of Open Access Journals (Sweden)

    Yool Andrea J

    2003-10-01

    Full Text Available Abstract Background Aquaporin-1 (AQP1 functions as an osmotic water channel and a gated cation channel. Activation of the AQP1 ion conductance by intracellular cGMP was hypothesized to involve the carboxyl (C- terminus, based on amino acid sequence alignments with cyclic-nucleotide-gated channels and cGMP-selective phosphodiesterases. Results Voltage clamp analyses of human AQP1 channels expressed in Xenopus oocytes demonstrated that the nitric oxide donor, sodium nitroprusside (SNP; 3–14 mM activated the ionic conductance response in a dose-dependent manner. Block of soluble guanylate cyclase prevented the response. Enzyme immunoassays confirmed a linear dose-dependent relationship between SNP and the resulting intracellular cGMP levels (up to 1700 fmol cGMP /oocyte at 14 mM SNP. Results here are the first to show that the efficacy of ion channel activation is decreased by mutations of AQP1 at conserved residues in the C-terminal domain (aspartate D237 and lysine K243. Conclusions These data support the idea that the limited amino acid sequence similarities found between three diverse classes of cGMP-binding proteins are significant to the function of AQP1 as a cGMP-gated ion channel, and provide direct evidence for the involvement of the AQP1 C-terminal domain in cGMP-mediated ion channel activation.

  4. Generic domain models in software engineering

    Science.gov (United States)

    Maiden, Neil

    1992-01-01

    This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

  5. Diagrammatic Representations in Domain-Specific Languages

    OpenAIRE

    Tourlas, Konstantinos

    2002-01-01

    One emerging approach to reducing the labour and costs of software development favours the specialisation of techniques to particular application domains. The rationale is that programs within a given domain often share enough common features and assumptions to enable the incorporation of substantial support mechanisms into domain-specific programming languages and associated tools. Instead of being machine-oriented, algorithmic implementations, programs in many domain-speci...

  6. Oxidative stress at high altitude: genotype–phenotype correlations

    Directory of Open Access Journals (Sweden)

    Pandey P

    2014-05-01

    Full Text Available Priyanka Pandey,1,2 MA Qadar Pasha1,2 1CSIR-Institute of Genomics and Integrative Biology, Delhi, India; 2Department of Biotechnology, University of Pune, Ganeshkhind, Pune, India Abstract: It has been well-documented that the hypobaric hypoxic environment at high altitude (HA causes stress to both the permanent residents of HA and the sojourners. This oxidative stress primarily disturbs the oxygen-sensing and vascular homeostasis pathways, thereby upsetting normal human physiology, especially in sojourners. These environmental challenges have caused dynamic evolutionary changes within natives of HA, allowing them to develop adaptive plasticity. This review focuses on the genomic and biochemical features of the molecules involved in the oxygen-sensing and vascular homeostasis pathways with respect to HA pulmonary edema (HAPE and adaptation. We review the role of genetic markers such as HIF-prolyl hydroxylase 2, endothelial PAS domain-containing protein 1, endothelial nitric oxide synthase, endothelin 1, cytochrome b-245 alpha polypeptide, and glutathione S-transferase pi 1, as well as three circulatory biomarkers (nitric oxide, endothelin 1, and 8-iso-prostaglandin F2α, by highlighting approaches such as candidate gene and genome-wide, adopted in deciphering the pathways. A disagreement between the two approaches has also been highlighted. In addition, we discuss that an overrepresentation of wild-type alleles in HA natives and mutant alleles of same polymorphisms in HAPE patients implies that the allelic variants at the same locus are involved in adaptation and HAPE, respectively. Moreover, healthy sojourners present a number of genomic features similar to HA natives, further strengthening the concept of genetic predisposition. A trend in correlation between protective and risk alleles and altered levels of circulatory markers clearly documents the phenomenon of genotype–phenotype correlations. We conclude that the genetic and biochemical

  7. Templating Routes to Supported Oxide Catalysts by Design

    Energy Technology Data Exchange (ETDEWEB)

    Notestein, Justin M. [Northwestern Univ., Evanston, IL (United States)

    2016-09-08

    The rational design and understanding of supported oxide catalysts requires at least three advancements, in order of increasing complexity: the ability to quantify the number and nature of active sites in a catalytic material, the ability to place external controls on the number and structure of these active sites, and the ability to assemble these active sites so as to carry out more complex functions in tandem. As part of an individual investigator research program that is integrated with the Northwestern University Institute for Catalysis in Energy Processes (ICEP) as of 2015, significant advances were achieved in these three areas. First, phosphonic acids were utilized in the quantitative assessment of the number of active and geometrically-available sites in MOx-SiO2 catalysts, including nanocrystalline composites, co-condensed materials, and grafted structures, for M=Ti, Zr, Hf, Nb, and Ta. That work built off progress in understanding supported Fe, Cu, and Co oxide catalysts from chelating and/or multinuclear precursors to maximize surface reactivity. Secondly, significant progress was made in the new area of using thin oxide overcoats containing ‘nanocavities’ from organic templates as a method to control the dispersion and thermal stability of subsequently deposited metal nanoparticles or other catalytic domains. Similar methods were used to control surface reactivity in SiO2-Al2O3 acid catalysts and to control reactant selectivity in Al2O3-TiO2 photocatalysts. Finally, knowledge gained from the first two areas has been combined to synthesize a tandem catalyst for hydrotreating reactions and an orthogonal tandem catalyst system where two subsequent reactions in a reaction network are independently controlled by light and heat. Overall, work carried out under this project significantly advanced the knowledge of synthesis-structure-function relationships in supported

  8. RNA oxidation

    DEFF Research Database (Denmark)

    Kjaer, L. K.; Cejvanovic, V.; Henriken, T.

    2015-01-01

    .9 significant hazard ratio for death compared with the quartile with the lowest 8oxoGuo excretion when adjusted for age, sex, BMI, smoker status, s-HbA1c, urine protein excretion and s-cholesterol. We conclude that it is now established that RNA oxidation is an independent risk factor for death in type 2...

  9. Radiolytic oxidation

    International Nuclear Information System (INIS)

    Burns, W.G.; Ewart, F.T.; Hobley, J.; Smith, A.J.; Walters, W.S.; Williams, S.J.

    1991-01-01

    Work under the Radiolytic Oxidation Contract from 1986 until April 1989 is reported. The effects of alpha- and gamma-irradiation on the chemistries of plutonium, neptunium and technetium, under conditions representative of the near fields of intermediate and high level waste repositories, were investigated. Gamma-radiolysis of Np (IV) results in oxidation in solutions below pH 12. Solutions of Tc (VII) are reduced to Tc (IV) by gamma-irradiation in contact with blast furnace slag/ordinary Portland cement under an inert atmosphere but not when in contact with pulverized fuel ash/ordinary Portland cement. Tc (IV) is shown to be susceptible to oxidation by the products of the alpha-radiolysis of water. The results of 'overall effects' experiments, which combined representative components of typical ILW or HLW near fields, supported these observations and also showed enhanced plutonium concentrations in alpha-irradiated, HLW simulations. Mathematical models of the behaviour of plutonium and neptunium during gamma-radiolysis have been developed and indicate that oxidation to Pu (VI) is possible at dose rates typical of those expected for HLW. Simulations at ILW dose rates have indicated some effect upon the speciation of neptunium. Laboratory studies of the gamma-irradiation of Np (IV) in bentonite-equilibrated water have also been modelled. Computer code used: PHREEQE, 8 Figs.; 48 Tabs.; 38 refs

  10. Engaging narratives evoke similar neural activity and lead to similar time perception.

    Science.gov (United States)

    Cohen, Samantha S; Henin, Simon; Parra, Lucas C

    2017-07-04

    It is said that we lose track of time - that "time flies" - when we are engrossed in a story. How does engagement with the story cause this distorted perception of time, and what are its neural correlates? People commit both time and attentional resources to an engaging stimulus. For narrative videos, attentional engagement can be represented as the level of similarity between the electroencephalographic responses of different viewers. Here we show that this measure of neural engagement predicted the duration of time that viewers were willing to commit to narrative videos. Contrary to popular wisdom, engagement did not distort the average perception of time duration. Rather, more similar brain responses resulted in a more uniform perception of time across viewers. These findings suggest that by capturing the attention of an audience, narrative videos bring both neural processing and the subjective perception of time into synchrony.

  11. Spatial representations are specific to different domains of knowledge.

    Directory of Open Access Journals (Sweden)

    Rowena Beecham

    Full Text Available There is evidence that many abstract concepts are represented cognitively in a spatial format. However, it is unknown whether similar spatial processes are employed in different knowledge domains, or whether individuals exhibit similar spatial profiles within and across domains. This research investigated similarities in spatial representation in two knowledge domains--mathematics and music. Sixty-one adults completed analogous number magnitude and pitch discrimination tasks: the Spatial-Numerical Association of Response Codes and Spatial-Musical Association of Response Codes tasks. Subgroups of individuals with different response patterns were identified through cluster analyses. For both the mathematical and musical tasks, approximately half of the participants showed the expected spatial judgment effect when explicitly cued to focus on the spatial properties of the stimuli. Despite this, performances on the two tasks were largely independent. Consistent with previous research, the study provides evidence for the spatial representation of number and pitch in the majority of individuals. However, there was little evidence to support the claim that the same spatial representation processes underpin mathematical and musical judgments.

  12. A Domain Standard for Land Administration

    NARCIS (Netherlands)

    Lemmen, C.; Van Oosterom, P.; Van der Molen, P.

    2013-01-01

    This paper presents the design of a Domain Model for Land Administration (LA). As a result a formal International Standard is available: ISO 19152 Geographic Information – Land Administration Domain Model (LADM) (ISO, 2012). Domain specific standardisation is needed to capture the semantics of the

  13. Latent domain models for statistical machine translation

    NARCIS (Netherlands)

    Hoàng, C.

    2017-01-01

    A data-driven approach to model translation suffers from the data mismatch problem and demands domain adaptation techniques. Given parallel training data originating from a specific domain, training an MT system on the data would result in a rather suboptimal translation for other domains. But does

  14. Domain-specific languages in perspective

    NARCIS (Netherlands)

    J. Heering (Jan); M. Mernik (Marjan)

    2007-01-01

    textabstractDomain-specific languages (DSLs) are languages tailored to a specific application domain. They offer substantial gains in expressiveness and ease of use compared with general-purpose languages in their domain of application. Although the use of DSLs is by no means new, it is receiving

  15. Classification of domains of closed operators

    International Nuclear Information System (INIS)

    Lassner, G.; Timmermann, W.

    1975-01-01

    The structure of domains of determining closed operators in the Hilbert space by means of sequence spaces is investigated. The final classification provides three classes of these domains. Necessary and sufficient conditions of equivalence of these domains are obtained in the form of equivalency of corresponding sequences of natural numbers. Connection with the perturbation theory is mentioned [ru

  16. The Private Legal Governance of Domain Names

    DEFF Research Database (Denmark)

    Schovsbo, Jens Hemmingsen

    2015-01-01

    . the UDRP (WIPO) and the Danish Complaints Board for Internet Domain Names (the Board) to discuss how and to what extent the domain name system balances interests between trademark owners and other users of domain names and secures the rule of law (legal certainty and predictability) with a special focus...

  17. Faraday instability in deformable domains

    International Nuclear Information System (INIS)

    Pucci, G.

    2013-01-01

    Hydrodynamical instabilities are usually studied either in bounded regions or free to grow in space. In this article we review the experimental results of an intermediate situation, in which an instability develops in deformable domains. The Faraday instability, which consists in the formation of surface waves on a liquid experiencing a vertical forcing, is triggered in floating liquid lenses playing the role of deformable domains. Faraday waves deform the lenses from the initial circular shape and the mutual adaptation of instability patterns with the lens boundary is observed. Two archetypes of behaviour have been found. In the first archetype a stable elongated shape is reached, the wave vector being parallel to the direction of elongation. In the second archetype the waves exceed the response of the lens border and no equilibrium shape is reached. The lens stretches and eventually breaks into fragments that have a complex dynamics. The difference between the two archetypes is explained by the competition between the radiation pressure the waves exert on the lens border and its response due to surface tension.

  18. A Similarity Analysis of Audio Signal to Develop a Human Activity Recognition Using Similarity Networks

    Directory of Open Access Journals (Sweden)

    Alejandra García-Hernández

    2017-11-01

    Full Text Available Human Activity Recognition (HAR is one of the main subjects of study in the areas of computer vision and machine learning due to the great benefits that can be achieved. Examples of the study areas are: health prevention, security and surveillance, automotive research, and many others. The proposed approaches are carried out using machine learning techniques and present good results. However, it is difficult to observe how the descriptors of human activities are grouped. In order to obtain a better understanding of the the behavior of descriptors, it is important to improve the abilities to recognize the human activities. This paper proposes a novel approach for the HAR based on acoustic data and similarity networks. In this approach, we were able to characterize the sound of the activities and identify those activities looking for similarity in the sound pattern. We evaluated the similarity of the sounds considering mainly two features: the sound location and the materials that were used. As a result, the materials are a good reference classifying the human activities compared with the location.

  19. Phonological similarity and orthographic similarity affect probed serial recall of Chinese characters.

    Science.gov (United States)

    Lin, Yi-Chen; Chen, Hsiang-Yu; Lai, Yvonne C; Wu, Denise H

    2015-04-01

    The previous literature on working memory (WM) has indicated that verbal materials are dominantly retained in phonological representations, whereas other linguistic information (e.g., orthography, semantics) only contributes to verbal WM minimally, if not negligibly. Although accumulating evidence has suggested that multiple linguistic components jointly support verbal WM, the visual/orthographic contribution has rarely been addressed in alphabetic languages, possibly due to the difficulty of dissociating the effects of word forms from the effects of their pronunciations in relatively shallow orthography. In the present study, we examined whether the orthographic representations of Chinese characters support the retention of verbal materials in this language of deep orthography. In Experiments 1a and 2, we independently manipulated the phonological and orthographic similarity of horizontal and vertical characters, respectively, and found that participants' accuracy of probed serial recall was reduced by both similar pronunciations and shared phonetic radicals in the to-be-remembered stimuli. Moreover, Experiment 1b showed that only the effect of phonological, but not that of orthographic, similarity was affected by concurrent articulatory suppression. Taken together, the present results indicate the indispensable contribution of orthographic representations to verbal WM of Chinese characters, and suggest that the linguistic characteristics of a specific language not only determine long-term linguistic-processing mechanisms, but also delineate the organization of verbal WM for that language.

  20. Similar or different? The role of the ventrolateral prefrontal cortex in similarity detection.

    Directory of Open Access Journals (Sweden)

    Béatrice Garcin

    Full Text Available Patients with frontal lobe syndrome can exhibit two types of abnormal behaviour when asked to place a banana and an orange in a single category: some patients categorize them at a concrete level (e.g., "both have peel", while others continue to look for differences between these objects (e.g., "one is yellow, the other is orange". These observations raise the question of whether abstraction and similarity detection are distinct processes involved in abstract categorization, and that depend on separate areas of the prefrontal cortex (PFC. We designed an original experimental paradigm for a functional magnetic resonance imaging (fMRI study involving healthy subjects, confirming the existence of two distinct processes relying on different prefrontal areas, and thus explaining the behavioural dissociation in frontal lesion patients. We showed that: 1 Similarity detection involves the anterior ventrolateral PFC bilaterally with a right-left asymmetry: the right anterior ventrolateral PFC is only engaged in detecting physical similarities; 2 Abstraction per se activates the left dorsolateral PFC.

  1. [-25]A Similarity Analysis of Audio Signal to Develop a Human Activity Recognition Using Similarity Networks.

    Science.gov (United States)

    García-Hernández, Alejandra; Galván-Tejada, Carlos E; Galván-Tejada, Jorge I; Celaya-Padilla, José M; Gamboa-Rosales, Hamurabi; Velasco-Elizondo, Perla; Cárdenas-Vargas, Rogelio

    2017-11-21

    Human Activity Recognition (HAR) is one of the main subjects of study in the areas of computer vision and machine learning due to the great benefits that can be achieved. Examples of the study areas are: health prevention, security and surveillance, automotive research, and many others. The proposed approaches are carried out using machine learning techniques and present good results. However, it is difficult to observe how the descriptors of human activities are grouped. In order to obtain a better understanding of the the behavior of descriptors, it is important to improve the abilities to recognize the human activities. This paper proposes a novel approach for the HAR based on acoustic data and similarity networks. In this approach, we were able to characterize the sound of the activities and identify those activities looking for similarity in the sound pattern. We evaluated the similarity of the sounds considering mainly two features: the sound location and the materials that were used. As a result, the materials are a good reference classifying the human activities compared with the location.

  2. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains.

    Science.gov (United States)

    Keren, Ido; Klipcan, Liron; Bezawork-Geleta, Ayenachew; Kolton, Max; Shaya, Felix; Ostersetzer-Biran, Oren

    2008-08-22

    CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.

  3. A residue-specific shift in stability and amyloidogenicity of antibody variable domains.

    Science.gov (United States)

    Nokwe, Cardine N; Zacharias, Martin; Yagi, Hisashi; Hora, Manuel; Reif, Bernd; Goto, Yuji; Buchner, Johannes

    2014-09-26

    Variable (V) domains of antibodies are essential for antigen recognition by our adaptive immune system. However, some variants of the light chain V domains (VL) form pathogenic amyloid fibrils in patients. It is so far unclear which residues play a key role in governing these processes. Here, we show that the conserved residue 2 of VL domains is crucial for controlling its thermodynamic stability and fibril formation. Hydrophobic side chains at position 2 stabilize the domain, whereas charged residues destabilize and lead to amyloid fibril formation. NMR experiments identified several segments within the core of the VL domain to be affected by changes in residue 2. Furthermore, molecular dynamic simulations showed that hydrophobic side chains at position 2 remain buried in a hydrophobic pocket, and charged side chains show a high flexibility. This results in a predicted difference in the dissociation free energy of ∼10 kJ mol(-1), which is in excellent agreement with our experimental values. Interestingly, this switch point is found only in VL domains of the κ family and not in VLλ or in VH domains, despite a highly similar domain architecture. Our results reveal novel insight into the architecture of variable domains and the prerequisites for formation of amyloid fibrils. This might also contribute to the rational design of stable variable antibody domains. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. The Abl SH2-kinase linker naturally adopts a conformation competent for SH3 domain binding.

    Science.gov (United States)

    Chen, Shugui; Brier, Sébastien; Smithgall, Thomas E; Engen, John R

    2007-04-01

    The core of the Abelson tyrosine kinase (c-Abl) is structurally similar to Src-family kinases where SH3 and SH2 domains pack against the backside of the kinase domain in the down-regulated conformation. Both kinase families depend upon intramolecular association of SH3 with the linker joining the SH2 and kinase domains for suppression of kinase activity. Hydrogen deuterium exchange (HX) and mass spectrometry (MS) were used to probe intramolecular interaction of the c-Abl SH3 domain with the linker in recombinant constructs lacking the kinase domain. Under physiological conditions, the c-Abl SH3 domain undergoes partial unfolding, which is stabilized by ligand binding, providing a unique assay for SH3:linker interaction in solution. Using this approach, we observed dynamic association of the SH3 domain with the linker in the absence of the kinase domain. Truncation of the linker before W254 completely prevented cis-interaction with SH3, while constructs containing amino acids past this point showed SH3:linker interactions. The observation that the Abl linker sequence exhibits SH3-binding activity in the absence of the kinase domain is unique to Abl and was not observed with Src-family kinases. These results suggest that SH3:linker interactions may have a more prominent role in Abl regulation than in Src kinases, where the down-regulated conformation is further stabilized by a second intramolecular interaction between the C-terminal tail and the SH2 domain.

  5. Combining biophysical methods to analyze the disulfide bond in SH2 domain of C-terminal Src kinase.

    Science.gov (United States)

    Liu, Dongsheng; Cowburn, David

    2016-01-01

    The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk function, little is known about the relationship between the disulfide bond and binding of the ligand. In this study, we combined X-ray crystallography, solution NMR, and other biophysical methods to reveal the interaction network in Csk. Denaturation studies have shown that disulfide bond contributes significantly to the stability of SH2 domain, and crystal structures of the oxidized and C122S mutant showed minor conformational changes. We further investigated the binding of SH2 domain to a phosphorylated peptide from Csk-binding protein upon reduction and oxidation using both NMR and fluorescence approaches. This work employed NMR, X-ray cryptography, and other biophysical methods to study a disulfide bond in Csk SH2 domain. In addition, this work provides in-depth understanding of the structural dynamics of Csk SH2 domain.

  6. Word Domain Disambiguation via Word Sense Disambiguation

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.

    2006-06-04

    Word subject domains have been widely used to improve the perform-ance of word sense disambiguation al-gorithms. However, comparatively little effort has been devoted so far to the disambiguation of word subject do-mains. The few existing approaches have focused on the development of al-gorithms specific to word domain dis-ambiguation. In this paper we explore an alternative approach where word domain disambiguation is achieved via word sense disambiguation. Our study shows that this approach yields very strong results, suggesting that word domain disambiguation can be ad-dressed in terms of word sense disam-biguation with no need for special purpose algorithms.

  7. On the structure of order domains

    DEFF Research Database (Denmark)

    Geil, Olav; Pellikaan, Ruud

    2002-01-01

    The notion of an order domain is generalized. The behaviour of an order domain by taking a subalgebra, the extension of scalars, and the tensor product is studied. The relation of an order domain with valuation theory, Gröbner algebras, and graded structures is given. The theory of Gröbner bases...... for order domains is developed and used to show that the factor ring theorem and its converse, the presentation theorem, hold. The dimension of an order domain is related to the rank of its value semigroup....

  8. Measurement of semantic similarity for land use and land cover classification systems

    Science.gov (United States)

    Deng, Dongpo

    2008-12-01

    Land use and land cover (LULC) data is essential to environmental and ecological research. However, semantic heterogeneous of land use and land cover classification are often resulted from different data resources, different cultural contexts, and different utilities. Therefore, there is need to develop a method to measure, compare and integrate between land cover categories. To understand the meaning and the use of terminology from different domains, the common ontology approach is used to acquire information regarding the meaning of terms, and to compare two terms to determine how they might be related. Ontology is a formal specification of a shared conceptualization of a domain of interest. LULC classification system is a ontology. The semantic similarity method is used to compare to entities of three LULC classification systems: CORINE (European Environmental Agency), Oregon State, USA), and Taiwan. The semantic properties and relations firstly have been extracted from their definitions of LULC classification systems. Then semantic properties and relations of categories in three LULC classification systems are mutually compared. The visualization of semantic proximity is finally presented to explore the similarity or dissimilarity of data. This study shows the semantic similarity method efficiently detect semantic distance in three LULC classification systems and find out the semantic similar objects.

  9. Global Neural Pattern Similarity as a Common Basis for Categorization and Recognition Memory

    Science.gov (United States)

    Xue, Gui; Love, Bradley C.; Preston, Alison R.; Poldrack, Russell A.

    2014-01-01

    Familiarity, or memory strength, is a central construct in models of cognition. In previous categorization and long-term memory research, correlations have been found between psychological measures of memory strength and activation in the medial temporal lobes (MTLs), which suggests a common neural locus for memory strength. However, activation alone is insufficient for determining whether the same mechanisms underlie neural function across domains. Guided by mathematical models of categorization and long-term memory, we develop a theory and a method to test whether memory strength arises from the global similarity among neural representations. In human subjects, we find significant correlations between global similarity among activation patterns in the MTLs and both subsequent memory confidence in a recognition memory task and model-based measures of memory strength in a category learning task. Our work bridges formal cognitive theories and neuroscientific models by illustrating that the same global similarity computations underlie processing in multiple cognitive domains. Moreover, by establishing a link between neural similarity and psychological memory strength, our findings suggest that there may be an isomorphism between psychological and neural representational spaces that can be exploited to test cognitive theories at both the neural and behavioral levels. PMID:24872552

  10. Similar verbal memory impairments in schizophrenia and healthy aging. Implications for understanding of neural mechanisms.

    Science.gov (United States)

    Silver, Henry; Bilker, Warren B

    2015-03-30

    Memory is impaired in schizophrenia patients but it is not clear whether this is specific to the illness and whether different types of memory (verbal and nonverbal) or memories in different cognitive domains (executive, object recognition) are similarly affected. To study relationships between memory impairments and schizophrenia we compared memory functions in 77 schizophrenia patients, 58 elderly healthy individuals and 41 young healthy individuals. Tests included verbal associative and logical memory and memory in executive and object recognition domains. We compared relationships of memory functions to each other and to other cognitive functions including psychomotor speed and verbal and spatial working memory. Compared to the young healthy group, schizophrenia patients and elderly healthy individuals showed similar severe impairment in logical memory and in the ability to learn new associations (NAL), and similar but less severe impairment in spatial working memory and executive and object memory. Verbal working memory was significantly more impaired in schizophrenia patients than in the healthy elderly. Verbal episodic memory impairment in schizophrenia may share common mechanisms with similar impairment in healthy aging. Impairment in verbal working memory in contrast may reflect mechanisms specific to schizophrenia. Study of verbal explicit memory impairment tapped by the NAL index may advance understanding of abnormal hippocampus dependent mechanisms common to schizophrenia and aging. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  11. Blocking-resistant communication through domain fronting

    Directory of Open Access Journals (Sweden)

    Fifield David

    2015-06-01

    Full Text Available We describe “domain fronting,” a versatile censorship circumvention technique that hides the remote endpoint of a communication. Domain fronting works at the application layer, using HTTPS, to communicate with a forbidden host while appearing to communicate with some other host, permitted by the censor. The key idea is the use of different domain names at different layers of communication. One domain appears on the “outside” of an HTTPS request—in the DNS request and TLS Server Name Indication—while another domain appears on the “inside”—in the HTTP Host header, invisible to the censor under HTTPS encryption. A censor, unable to distinguish fronted and nonfronted traffic to a domain, must choose between allowing circumvention traffic and blocking the domain entirely, which results in expensive collateral damage. Domain fronting is easy to deploy and use and does not require special cooperation by network intermediaries. We identify a number of hard-to-block web services, such as content delivery networks, that support domain-fronted connections and are useful for censorship circumvention. Domain fronting, in various forms, is now a circumvention workhorse. We describe several months of deployment experience in the Tor, Lantern, and Psiphon circumvention systems, whose domain-fronting transports now connect thousands of users daily and transfer many terabytes per month.

  12. Phylogeny of the TRAF/MATH domain.

    Science.gov (United States)

    Zapata, Juan M; Martínez-García, Vanesa; Lefebvre, Sophie

    2007-01-01

    The TNF-receptor associated factor (TRAF) domain (TD), also known as the meprin and TRAF-C homology (MATH) domain is a fold of seven anti-parallel p-helices that participates in protein-protein interactions. This fold is broadly represented among eukaryotes, where it is found associated with a discrete set of protein-domains. Virtually all protein families encompassing a TRAF/MATH domain seem to be involved in the regulation of protein processing and ubiquitination, strongly suggesting a parallel evolution of the TRAF/MATH domain and certain proteolysis pathways in eukaryotes. The restricted number of living organisms for which we have information of their genetic and protein make-up limits the scope and analysis of the MATH domain in evolution. However, the available information allows us to get a glimpse on the origins, distribution and evolution of the TRAF/MATH domain, which will be overviewed in this chapter.

  13. Ferroelectric domain continuity over grain boundaries

    DEFF Research Database (Denmark)

    Mantri, Sukriti; Oddershede, Jette; Damjanovic, Dragan

    2017-01-01

    Formation and mobility of domain walls in ferroelectric materials is responsible for many of their electrical and mechanical properties. Domain wall continuity across grain boundaries has been observed since the 1950's and is speculated to affect the grain boundary-domain interactions, thereby...... impacting macroscopic ferroelectric properties in polycrystalline systems. However detailed studies of such correlated domain structures across grain boundaries are limited. In this work, we have developed the mathematical requirements for domain wall plane matching at grain boundaries of any given...... orientation. We have also incorporated the effect of grain boundary ferroelectric polarization charge created when any two domains meet at the grain boundary plane. The probability of domain wall continuity for three specific grain misorientations is studied. Use of this knowledge to optimize processing...

  14. Interoperable domain models : The ISO land administration domain model LADM and its external classes

    NARCIS (Netherlands)

    Lemmen, C.H.J.; Van Oosterom, P.J.M.; Uitermark, H.T.; Zevenbergen, J.A.; Cooper, A.K.

    2011-01-01

    This paper provides a brief overview of one of the first spatial domain standards: a standard for the domain of Land Administration (LA). This standard is in the draft stage of development now (May 2011). The development of domain standards is a logical follow up after domain-independent standards,

  15. High-Throughput, Protein-Targeted Biomolecular Detection Using Frequency-Domain Faraday Rotation Spectroscopy.

    Science.gov (United States)

    Murdock, Richard J; Putnam, Shawn A; Das, Soumen; Gupta, Ankur; Chase, Elyse D Z; Seal, Sudipta

    2017-03-01

    A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL -1 and broad detection range of 10 pg mL -1 ≲ c BSA ≲ 100 µg mL -1 are observed. Combining this technique with predictive analyte binding models quantifies (within an order of magnitude) the number of active binding sites on functionalized MNPs. Comparative enzyme-linked immunosorbent assay (ELISA) studies are conducted, reproducing the manufacturer advertised BSA ELISA detection limits from 1 ng mL -1 ≲ c BSA ≲ 500 ng mL -1 . In addition to the increased sensitivity, broader detection range, and similar specificity, fd-FRS can be conducted in less than ≈30 min, compared to ≈4 h with ELISA. Thus, fd-FRS is shown to be a sensitive optical technique with potential to become an efficient diagnostic in the chemical and biomolecular sciences. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Penerapan Microskills dalam Domain Multicultural

    Directory of Open Access Journals (Sweden)

    Happy Karlina Marjo

    2013-03-01

    Full Text Available Konselor multikultural menggunakan microskills yang bertujuan untuk memodifikasi interaksi konselor dalam membuat perbedaan yang signifikan pada kehidupan konseli dengan: (1 mengidentifikasi faktor-faktor dari respon nonverbal untuk diri konselor sendiri dan konseli, (2 memahami dasar intervieu microskills dalam proses menerima (attending, mendengarkan (listening, dan mempengaruhi (influencing, serta dampak potensial pada konseli untuk berubah, (3 mencatat fokus microskills, dan perhatian secara selektif yang merupakan dasar untuk masalah keluarga dan konseling multikultural, (4 mengetahui bagaimana dan kapan menggunakan konfrontasi microskill, dan (5 mengetahui keterampilan intervieu sebagai acuan frame multikultural. Sedangkan domain kompetensi konseling multikultural untuk pendidikan dan praktek, antara lain: (1 Counselor Awareness of Own Cultural Values and Biases, (2 Counselor Awareness of Client’ Worldview, dan (3 Culturally Appropriate Intervention Strategies.

  17. Time domain electromagnetic metal detectors

    International Nuclear Information System (INIS)

    Hoekstra, P.

    1996-01-01

    This presentation focuses on illustrating by case histories the range of applications and limitations of time domain electromagnetic (TDEM) systems for buried metal detection. Advantages claimed for TDEM metal detectors are: independent of instrument response (Geonics EM61) to surrounding soil and rock type; simple anomaly shape; mitigation of interference by ambient electromagnetic noise; and responsive to both ferrous and non-ferrous metallic targets. The data in all case histories to be presented were acquired with the Geonics EM61 TDEM system. Case histories are a test bed site on Molokai, Hawaii; Fort Monroe, Virginia; and USDOE, Rocky Flats Plant. The present limitations of this technology are: discrimination capabilities in terms of type of ordnance, and depth of burial is limited, and ability of resolving targets with small metallic ambient needs to be improved

  18. Pythoscape: A framework for generation of large protein similarity networks

    OpenAIRE

    Babbitt, Patricia; Barber, AE; Babbitt, PC

    2012-01-01

    Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among pr

  19. Crystal Structure of the FERM Domain of Focal Adhesion Kinase

    International Nuclear Information System (INIS)

    Ceccarelli, D.; Song, H.; Poy, F.; Schaller, M.; Eck, M.

    2006-01-01

    Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. Through phosphorylation of proteins assembled at the cytoplasmic tails of integrins, FAK promotes signaling events that modulate cellular growth, survival, and migration. The amino-terminal region of FAK contains a region of sequence homology with band 4.1 and ezrin/radixin/moesin (ERM) proteins termed a FERM domain. FERM domains are found in a variety of signaling and cytoskeletal proteins and are thought to mediate intermolecular interactions with partner proteins and phospholipids at the plasma membrane and intramolecular regulatory interactions. Here we report two crystal structures of an NH2-terminal fragment of avian FAK containing the FERM domain and a portion of the regulatory linker that connects the FERM and kinase domains. The tertiary folds of the three subdomains (F1, F2, and F3) are similar to those of known FERM structures despite low sequence conservation. Differences in the sequence and relative orientation of the F3 subdomain alters the nature of the interdomain interface, and the phosphoinositide binding site found in ERM family FERM domains is not present in FAK. A putative protein interaction site on the F3 lobe is masked by the proximal region of the linker. Additionally, in one structure the adjacent Src SH3 and SH2 binding sites in the linker associate with the surfaces of the F3 and F1 lobes, respectively. These structural features suggest the possibility that protein interactions of the FAK FERM domain can be regulated by binding of Src kinases to the linker segment

  20. Using concept similarity in cross ontology for adaptive e-Learning systems

    Directory of Open Access Journals (Sweden)

    B. Saleena

    2015-01-01

    Full Text Available e-Learning is one of the most preferred media of learning by the learners. The learners search the web to gather knowledge about a particular topic from the information in the repositories. Retrieval of relevant materials from a domain can be easily implemented if the information is organized and related in some way. Ontologies are a key concept that helps us to relate information for providing the more relevant lessons to the learner. This paper proposes an adaptive e-Learning system, which generates a user specific e-Learning content by comparing the concepts with more than one system using similarity measures. A cross ontology measure is defined, which consists of fuzzy domain ontology as the primary ontology and the domain expert’s ontology as the secondary ontology, for the comparison process. A personalized document is provided to the user with a user profile, which includes the data obtained from the processing of the proposed method under a User score, which is obtained through the user evaluation. The results of the proposed e-Learning system under the designed cross ontology similarity measure show a significant increase in performance and accuracy under different conditions. The assessment of the comparative analysis, showed the difference in performance of our proposed method over other methods. Based on the assessment results it is proved that the proposed approach is effective over other methods.