WorldWideScience

Sample records for gag-pol transframe domain

  1. Orthoretroviral-like prototype foamy virus gag-pol expression is compatible with viral replication

    Directory of Open Access Journals (Sweden)

    Reh Juliane

    2011-08-01

    Full Text Available Abstract Background Foamy viruses (FVs unlike orthoretroviruses express Pol as a separate precursor protein and not as a Gag-Pol fusion protein. A unique packaging strategy, involving recognition of briding viral RNA by both Pol precursor and Gag as well as potential Gag-Pol protein interactions, ensures Pol particle encapsidation. Results Several Prototype FV (PFV Gag-Pol fusion protein constructs were generated to examine whether PFV replication is compatible with an orthoretroviral-like Pol expression. During their analysis, non-particle-associated secreted Pol precursor protein was discovered in extracellular wild type PFV particle preparations of different origin, copurifying in simple virion enrichment protocols. Different analysis methods suggest that extracellular wild type PFV particles contain predominantly mature p85PR-RT and p40IN Pol subunits. Characterization of various PFV Gag-Pol fusion constructs revealed that PFV Pol expression in an orthoretroviral manner is compatible with PFV replication as long as a proteolytic processing between Gag and Pol proteins is possible. PFV Gag-Pol translation by a HIV-1 like ribosomal frameshift signal resulted in production of replication-competent virions, although cell- and particle-associated Pol levels were reduced in comparison to wild type. In-frame fusion of PFV Gag and Pol ORFs led to increased cellular Pol levels, but particle incorporation was only marginally elevated. Unlike that reported for similar orthoretroviral constructs, a full-length in-frame PFV Gag-Pol fusion construct showed wildtype-like particle release and infectivity characteristics. In contrast, in-frame PFV Gag-Pol fusion with C-terminal Gag ORF truncations or non-removable Gag peptide addition to Pol displayed wildtype particle release, but reduced particle infectivity. PFV Gag-Pol precursor fusion proteins with inactivated protease were highly deficient in regular particle release, although coexpression of p71Gag

  2. Control of gag-pol gene expression in the Candida albicans retrotransposon Tca2

    Directory of Open Access Journals (Sweden)

    Gibson Joanne

    2007-10-01

    Full Text Available Abstract Background In the C. albicans retrotransposon Tca2, the gag and pol ORFs are separated by a UGA stop codon, 3' of which is a potential RNA pseudoknot. It is unclear how the Tca2 gag UGA codon is bypassed to allow pol expression. However, in other retroelements, translational readthrough of the gag stop codon can be directed by its flanking sequence, including a 3' pseudoknot. Results The hypothesis was tested that in Tca2, gag stop codon flanking sequences direct translational readthrough and synthesis of a gag-pol fusion protein. Sequence from the Tca2 gag-UGA-pol junction (300 nt was inserted between fused lacZ and luciferase (luc genes in a Saccharomyces cerevisiae dual reporter construct. Although downstream of UGA, luc was expressed, but its expression was unaffected by inserting additional stop codons at the 3' end of lacZ. Luc expression was instead being driven by a previously unknown minor promoter activity within the gag-pol junction region. Evidence together indicated that junction sequence alone cannot direct UGA readthrough. Using reporter genes in C. albicans, the activities of this gag-pol junction promoter and the Tca2 long terminal repeat (LTR promoter were compared. Of the two promoters, only the LTR promoter was induced by heat-shock, which also triggers retrotransposition. Tca2 pol protein, epitope-tagged in C. albicans to allow detection, was also heat-shock induced, indicating that pol proteins were expressed from a gag-UGA-pol RNA. Conclusion This is the first demonstration that the LTR promoter directs Tca2 pol protein expression, and that pol proteins are translated from a gag-pol RNA, which thus requires a mechanism for stop codon bypass. However, in contrast to most other retroelement and viral readthrough signals, immediate gag UGA-flanking sequences were insufficient to direct stop readthrough in S. cerevisiae, indicating non-canonical mechanisms direct gag UGA bypass in Tca2.

  3. Gag-Pol processing during HIV-1 virion maturation: a systems biology approach.

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    Balázs Könnyű

    Full Text Available Proteolytic processing of Gag and Gag-Pol polyproteins by the viral protease (PR is crucial for the production of infectious HIV-1, and inhibitors of the viral PR are an integral part of current antiretroviral therapy. The process has several layers of complexity (multiple cleavage sites and substrates; multiple enzyme forms; PR auto-processing, which calls for a systems level approach to identify key vulnerabilities and optimal treatment strategies. Here we present the first full reaction kinetics model of proteolytic processing by HIV-1 PR, taking into account all canonical cleavage sites within Gag and Gag-Pol, intermediate products and enzyme forms, enzyme dimerization, the initial auto-cleavage of full-length Gag-Pol as well as self-cleavage of PR. The model allows us to identify the rate limiting step of virion maturation and the parameters with the strongest effect on maturation kinetics. Using the modelling framework, we predict interactions and compensatory potential between individual cleavage rates and drugs, characterize the time course of the process, explain the steep dose response curves associated with PR inhibitors and gain new insights into drug action. While the results of the model are subject to limitations arising from the simplifying assumptions used and from the uncertainties in the parameter estimates, the developed framework provides an extendable open-access platform to incorporate new data and hypotheses in the future.

  4. Association of human mitochondrial lysyl-tRNA synthetase with HIV-1 GagPol does not require other viral proteins

    Directory of Open Access Journals (Sweden)

    Lydia Kobbi

    2016-06-01

    Full Text Available In human, the cytoplasmic (cLysRS and mitochondrial (mLysRS species of lysyl-tRNA synthetase are encoded by a single gene. Following HIV-1 infection, mLysRS is selectively taken up into viral particles along with the three tRNALys isoacceptors. The GagPol polyprotein precursor is involved in this process. With the aim to reconstitute in vitro the HIV-1 tRNA3Lys packaging complex, we first searched for the putative involvement of another viral protein in the selective viral hijacking of mLysRS only. After screening all the viral proteins, we observed that Vpr and Rev have the potential to interact with mLysRS, but that this association does not take place at the level of the assembly of mLysRS into the packaging complex. We also show that tRNA3Lys can form a ternary complex with the two purified proteins mLysRS and the Pol domain of GagPol, which mimicks its packaging complex.

  5. Deciphering the role of the Gag-Pol ribosomal frameshift signal in HIV-1 RNA genome packaging.

    Science.gov (United States)

    Nikolaitchik, Olga A; Hu, Wei-Shau

    2014-04-01

    A key step of retroviral replication is packaging of the viral RNA genome during virus assembly. Specific packaging is mediated by interactions between the viral protein Gag and elements in the viral RNA genome. In HIV-1, similar to most retroviruses, the packaging signal is located within the 5' untranslated region and extends into the gag-coding region. A recent study reported that a region including the Gag-Pol ribosomal frameshift signal plays an important role in HIV-1 RNA packaging; deletions or mutations that affect the RNA structure of this signal lead to drastic decreases (10- to 50-fold) in viral RNA packaging and virus titer. We examined here the role of the ribosomal frameshift signal in HIV-1 RNA packaging by studying the RNA packaging and virus titer in the context of proviruses. Three mutants with altered ribosomal frameshift signal, either through direct deletion of the signal, mutation of the 6U slippery sequence, or alterations of the secondary structure were examined. We found that RNAs from all three mutants were packaged efficiently, and they generate titers similar to that of a virus containing the wild-type ribosomal frameshift signal. We conclude that although the ribosomal frameshift signal plays an important role in regulating the replication cycle, this RNA element is not directly involved in regulating RNA encapsidation. To generate infectious viruses, HIV-1 must package viral RNA genome during virus assembly. The specific HIV-1 genome packaging is mediated by interactions between the structural protein Gag and elements near the 5' end of the viral RNA known as packaging signal. In this study, we examined whether the Gag-Pol ribosomal frameshift signal is important for HIV-1 RNA packaging as recently reported. Our results demonstrated that when Gag/Gag-Pol is supplied in trans, none of the tested ribosomal frameshift signal mutants has defects in RNA packaging or virus titer. These studies provide important information on how HIV-1

  6. Predictors of HVTN 503 MRK-AD5 HIV-1 gag/pol/nef vaccine induced immune responses.

    Directory of Open Access Journals (Sweden)

    Kathryn L Hopkins

    Full Text Available Phambili, the Merck (MRK-Adenovirus Type 5 (Ad5 HIV-1 gag/pol/nef subtype B vaccine study, conducted in South Africa, suspended enrollment and vaccination when companion study, Step, was found non-efficacious. Although the vaccine did not prevent HIV-1 infection or lower viral-load setpoint, immune responses recognized clades B and C HIV-1 subtypes. We investigated predictors of the vaccine-induced antigen-specific immune responses.Vaccine-induced immunogenicity was ascertained by interferon-γ ELISpot assays on the first 186 enrolled participants receiving two vaccinations. Analyses, stratified by study arm/sex, were performed on baseline demographics [sex, age, Body Mass Index (BMI, site, Adenovirus Type-5 (Ad5 titer, Herpes Simplex Virus Type-2 (HSV2 status, heavy drinking]. Multivariate logistic regression determined predictors.Of the 186 participants, 53.7% (n = 100 were female, median BMI was 22.5 [IQR: 20.4-27.0], 85.5% (n = 159 were Ad5 seropositive, and 18.8% (n = 35 drank heavily. All vaccine recipients responded to both clade B (n = 87; 47% and/or C (n = 74; 40%, p = 0.17. In multivariate analysis, female sex [Adjusted Odds Ratio (AOR: 6.478; p = 0.0159], overweight/obese BMI (AOR: 0.186; p = 0.0452, and heavy drinking (AOR: 0.270; p = 0.048 significantly predicted immune response to clade C for any antigens. A marginally significant predictor of clade C-pol antigen was female sex (AOR: 3.182; p = 0.0500.Sex, BMI, and heavy drinking affected vaccine-induced HIV-1 specific immune responses to clade C antigens. The role of female sex and overweight/obese BMI boosting and suppressing vaccine-induced HIV-1 specific immune responses, respectively, requires elucidation, including any effect on HIV vaccine efficacy, especially in the era of colliding epidemics (HIV and obesity.

  7. Time-measured phylogenies of gag, pol and env sequence data reveal the direction and time interval of HIV-1 transmission.

    Science.gov (United States)

    Rachinger, Andrea; Groeneveld, Paul H P; van Assen, Sander; Lemey, Philippe; Schuitemaker, Hanneke

    2011-05-15

    To investigate whether time-measured phylogenetic analysis of longitudinal viral sequences can establish the direction and timing of HIV-1 transmission in an epidemiologically linked transmission cluster of three homosexual men. An HIV-1-infected homosexual man (patient 1) and his long-term HIV-negative partner (patient 2) engaged in a triangular relationship with an additional partner (patient 3). On the basis of phylogenetic analysis of gag sequences, patient 3 was previously identified as the source for superinfection of patient 1 but the source of HIV-1 infection of patient 2, who seroconverted during the triangular relationship, remained unclear. Here, we set out to analyze newly obtained gag, pol and env sequences from all three patients to fully elucidate the transmission history in this epidemiologically linked cluster. Bayesian Markov Chain Monte Carlo (MCMC) phylogenetic analyses incorporating a relaxed clock model and a flexible Bayesian skyride tree prior were applied to the longitudinally obtained gag, pol and env sequences from all three patients. Our time-measured evolutionary reconstructions convincingly supported transmission of HIV-1 from the new partner patient 3 to both patients 1 and 2. In addition, estimates of viral divergence times assisted in narrowing down the transmission intervals delineated by seroconversion estimates. Our analysis implies that Bayesian MCMC phylogenetic reconstruction incorporating temporal information can indeed reveal the direction of multiple HIV-1 transmission events in an epidemiologically linked cluster and provide more detail on the timing of transmission.

  8. Highly conserved RNA pseudoknots at the gag-pol junction of HIV-1 suggest a novel mechanism of −1 ribosomal frameshifting

    Science.gov (United States)

    Huang, Xiaolan; Yang, Yang; Wang, Guan; Cheng, Qiang; Du, Zhihua

    2014-01-01

    −1 programmed ribosomal frameshifting (PRF) is utilized by many viruses to synthesize their enzymatic (Pol) and structural (Gag) proteins at a defined ratio. For efficient −1 PRF, two cis-acting elements are required: a heptanucleotide frameshift site and a downstream stimulator such as a pseudoknot. We have analyzed the gag-pol junction sequences from 4254 HIV-1 strains. Approximately ninety-five percent of the sequences can form four pseudoknots PK1–PK4 (∼97% contain PK1, PK3, and PK4), covering ∼72 nt including the frameshift site. Some pseudoknots are mutually excluded due to sequence overlap. PK1 and PK3 arrange tandemly. Their stems form a quasi-continuous helix of ∼22 bp. We propose a novel mechanism for possible roles of these pseudoknots. Multiple alternative structures may exist at the gag-pol junction. In most strains, the PK1–PK3 tandem pseudoknots may dominate the structurally heterogeneous pool of RNA due to their greater overall stability. The tandem pseudoknots may function as a breaking system to slow down the ribosome. The ribosome unwinds PK1 and stem 1 of PK3 before it can reach the frameshift site. Then, PK4 can form rapidly because the intact stem 2 of PK3 makes up a large part of the stem 1 of PK4. The newly formed PK4 jams the entrance of the mRNA tunnel. The process then proceeds as in a typical case of −1 PRF. This mechanism incorporates several exquisite new features while still being consistent with the current paradigm of pseudoknot-dependent −1 PRF. PMID:24671765

  9. Clustered epitopes within the Gag-Pol fusion protein DNA vaccine enhance immune responses and protection against challenge with recombinant vaccinia viruses expressing HIV-1 Gag and Pol antigens

    International Nuclear Information System (INIS)

    Bolesta, Elizabeth; Gzyl, Jaroslaw; Wierzbicki, Andrzej; Kmieciak, Dariusz; Kowalczyk, Aleksandra; Kaneko, Yutaro; Srinivasan, Alagarsamy; Kozbor, Danuta

    2005-01-01

    We have generated a codon-optimized hGagp17p24-Polp51 plasmid DNA expressing the human immunodeficiency virus type 1 (HIV-1) Gag-Pol fusion protein that consists of clusters of highly conserved cytotoxic T lymphocyte (CTL) epitopes presented by multiple MHC class I alleles. In the hGagp17p24-Polp51 construct, the ribosomal frameshift site had been deleted together with the potentially immunosuppressive Gag nucleocapsid (p15) as well as Pol protease (p10) and integrase (p31). Analyses of the magnitude and breadth of cellular responses demonstrated that immunization of HLA-A2/K b transgenic mice with the hGagp17p24-Polp51 construct induced 2- to 5-fold higher CD8 + T-cell responses to Gag p17-, p24-, and Pol reverse transcriptase (RT)-specific CTL epitopes than the full-length hGag-PolΔFsΔPr counterpart. The increases were correlated with higher protection against challenge with recombinant vaccinia viruses (rVVs) expressing gag and pol gene products. Consistent with the profile of Gag- and Pol-specific CD8 + T cell responses, an elevated level of type 1 cytokine production was noted in p24- and RT-stimulated splenocyte cultures established from hGagp17p24-Polp51-immunized mice compared to responses induced with the hGag-PolΔFsΔPr vaccine. Sera of mice immunized with the hGagp17p24-Polp51 vaccine also exhibited an increased titer of p24- and RT-specific IgG2 antibody responses. The results from our studies provide insights into approaches for boosting the breadth of Gag- and Pol-specific immune responses

  10. The connection domain in reverse transcriptase facilitates the in vivo annealing of tRNALys3 to HIV-1 genomic RNA

    Directory of Open Access Journals (Sweden)

    Niu Meijuan

    2004-10-01

    Full Text Available Abstract The primer tRNA for reverse transcription in HIV-1, tRNALys3, is selectively packaged into the virus during its assembly, and annealed to the viral genomic RNA. The ribonucleoprotein complex that is involved in the packaging and annealing of tRNALys into HIV-1 consists of Gag, GagPol, tRNALys, lysyl-tRNA synthetase (LysRS, and viral genomic RNA. Gag targets tRNALys for viral packaging through Gag's interaction with LysRS, a tRNALys-binding protein, while reverse transcriptase (RT sequences within GagPol (the thumb domain bind to tRNALys. The further annealing of tRNALys3 to viral RNA requires nucleocapsid (NC sequences in Gag, but not the NC sequences GagPol. In this report, we further show that while the RT connection domain in GagPol is not required for tRNALys3 packaging into the virus, it is required for tRNALys3 annealing to the viral RNA genome.

  11. The Nucleocapsid Domain Is Responsible for the Ability of Spleen Necrosis Virus (SNV) Gag Polyprotein To Package both SNV and Murine Leukemia Virus RNA

    OpenAIRE

    Certo, Jeanine L.; Kabdulov, Timur O.; Paulson, Michelle L.; Anderson, Jeffrey A.; Hu, Wei-Shau

    1999-01-01

    Murine leukemia virus (MLV)-based vector RNA can be packaged and propagated by the proteins of spleen necrosis virus (SNV). We recently demonstrated that MLV proteins cannot support the replication of an SNV-based vector; RNA analysis revealed that MLV proteins cannot efficiently package SNV-based vector RNA. The domain in Gag responsible for the specificity of RNA packaging was identified using chimeric gag-pol expression constructs. A competitive packaging system was established by generati...

  12. Recombinant adenovirus type 5 HIV gag/pol/nef vaccine in South Africa: unblinded, long-term follow-up of the phase 2b HVTN 503/Phambili study.

    Science.gov (United States)

    Gray, Glenda E; Moodie, Zoe; Metch, Barbara; Gilbert, Peter B; Bekker, Linda-Gail; Churchyard, Gavin; Nchabeleng, Maphoshane; Mlisana, Koleka; Laher, Fatima; Roux, Surita; Mngadi, Kathryn; Innes, Craig; Mathebula, Matsontso; Allen, Mary; McElrath, M Julie; Robertson, Michael; Kublin, James; Corey, Lawrence

    2014-05-01

    The HVTN 503/Phambili study, which assessed the efficacy of the Merck Ad5 gag/pol/nef subtype B HIV-1 preventive vaccine in South Africa, was stopped when futility criteria in the Step study (assessing the same vaccine in the Americas, Caribbean, and Australia) were met. Here we report long-term follow-up data. HVTN 503/Phambili was a double-blind, placebo-controlled, randomised trial that recruited HIV-1 uninfected, sexually active adults aged 18-35 years from five sites in South Africa. Eligible participants were randomly assigned (1:1) by computer-generated random numbers to either vaccine or placebo, stratified by site and sex. Cox proportional hazards models were used to estimate HIV-1 infection in the modified intention-to-treat cohort, all of whom were unmasked early in follow-up. The trial is registered with ClinicalTrials.gov, number NCT00413725 and the South African National Health Research Database, number DOH-27-0207-1539. Between Jan 24, 2007, and Sept 19, 2007, 801 participants (26·7%) of a planned 3000 were randomly assigned (400 to vaccine, 401 to placebo); 216 (27%) received only one injection, 529 (66%) received only two injections, and 56 (7%) received three injections. At a median follow-up of 42 months (IQR 31-42), 63 vaccine recipients (16%) had HIV-1 infection compared with 37 placebo recipients (9%; adjusted HR 1·70, 95% CI 1·13-2·55; p=0·01). Risk for HIV-1 infection did not differ according to the number of vaccinations received, sex, circumcision, or adenovirus type 5 (Ad5) serostatus. Differences in risk behaviour at baseline or during the study, or annualised dropout rate (7·7% [95% CI 6·2-9·5] for vaccine recipients vs 8·8% [7·1-10·7] for placebo recipients; p=0·40) are unlikely explanations for the increased rate of HIV-1 infections seen in vaccine recipients. The increased risk of HIV-1 acquisition in vaccine recipients, irrespective of number of doses received, warrants further investigation to understand the biological

  13. The nucleocapsid domain is responsible for the ability of spleen necrosis virus (SNV) Gag polyprotein to package both SNV and murine leukemia virus RNA.

    Science.gov (United States)

    Certo, J L; Kabdulov, T O; Paulson, M L; Anderson, J A; Hu, W S

    1999-11-01

    Murine leukemia virus (MLV)-based vector RNA can be packaged and propagated by the proteins of spleen necrosis virus (SNV). We recently demonstrated that MLV proteins cannot support the replication of an SNV-based vector; RNA analysis revealed that MLV proteins cannot efficiently package SNV-based vector RNA. The domain in Gag responsible for the specificity of RNA packaging was identified using chimeric gag-pol expression constructs. A competitive packaging system was established by generating a cell line that expresses one viral vector RNA containing the MLV packaging signal (Psi) and another viral vector RNA containing the SNV packaging signal (E). The chimeric gag-pol expression constructs were introduced into the cells, and vector titers as well as the efficiency of RNA packaging were examined. Our data confirm that Gag is solely responsible for the selection of viral RNAs. Furthermore, the nucleocapsid (NC) domain in the SNV Gag is responsible for its ability to interact with both SNV E and MLV Psi. Replacement of the SNV NC with the MLV NC generated a chimeric Gag that could not package SNV RNA but retained its ability to package MLV RNA. A construct expressing SNV gag-MLV pol supported the replication of both MLV and SNV vectors, indicating that the gag and pol gene products from two different viruses can functionally cooperate to perform one cycle of retroviral replication. Viral titer data indicated that SNV cis-acting elements are not ideal substrates for MLV pol gene products since infectious viruses were generated at a lower efficiency. These results indicate that the nonreciprocal recognition between SNV and MLV extends beyond the Gag-RNA interaction and also includes interactions between Pol and other cis-acting elements.

  14. Proline residues in the HIV-1 NH2-terminal capsid domain: structure determinants for proper core assembly and subsequent steps of early replication.

    Science.gov (United States)

    Fitzon, T; Leschonsky, B; Bieler, K; Paulus, C; Schröder, J; Wolf, H; Wagner, R

    2000-03-15

    Recent analyses suggest that the p24 capsid (p24(CA)) domain of the HIV-1 group-specific antigen (Gag) may be divided into two structurally and functionally distinct moieties: (i) an amino-terminal portion, previously shown to bind the cellular chaperone cyclophilin A, and (ii) a carboxy-terminal domain, known to contribute to the interaction of the Gag and Gag-Pol precursors during the early assembly process. In order to gain deeper insight into the role of the amino-terminal domain of the p24(CA) protein during viral replication, eight highly conserved proline residues known to promote turns and to terminate alpha-helices within the p24 tertiary structure were replaced by a leucine residue (P-position-L). Following transfection of the proviral constructs in COS7 cells, the majority of the mutants resembled wild-type viruses with respect to the assembly and release of virions. However, although the released particles contained wild-type levels of genomic viral RNA, the mature products of the Gag and Gag-Pol polyproteins as well as the Env glycoproteins-all of them, except mutant P225L-were either noninfectious or severely affected in their replicative capacity. Entry assays monitoring the process of viral DNA synthesis led to the classification of selected provirus mutants into four different phenotypes: (i) mutant P225L was infectious and allowed complete reverse transcription including formation of 2-LTR circles; (ii) mutants P149L, P170L, and P217L failed to form 2-LTR circles; (iii) mutant P222L displayed a severe defect in binding and incorporating cyclophilin A into virions, was delayed with respect to DNA polymerization, and failed to form a 2-LTR replication intermediate; and (iv) mutant P133L was unable even to synthesize a first-strand cDNA product. All replication-defective mutants were characterized by severe alterations in the stability of virion cores, which were in two cases reflected by visible changes in the core morphology. These results suggest

  15. 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...... not described in terms of domains, and recent research e.g. about the multilingual communities in the Danish-German border area seems to confirm this....

  16. 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...

  17. Time-measured phylogenies of gag, pol and env sequence data reveal the direction and time interval of HIV-1 transmission

    NARCIS (Netherlands)

    Rachinger, Andrea; Groeneveld, Paul H. P.; van Assen, Sander; Lemey, Philippe; Schuitemaker, Hanneke

    2011-01-01

    Objective: To investigate whether time-measured phylogenetic analysis of longitudinal viral sequences can establish the direction and timing of HIV-1 transmission in an epidemiologically linked transmission cluster of three homosexual men. Design: An HIV-1-infected homosexual man (patient 1) and his

  18. A review on architecture of the gag-pol ribosomal frameshifting RNA in human immunodeficiency virus: a variability survey of virus genotypes.

    Science.gov (United States)

    Qiao, Qi; Yan, Yanhua; Guo, Jinmei; Du, Shuqiang; Zhang, Jiangtao; Jia, Ruyue; Ren, Haimin; Qiao, Yuanbiao; Li, Qingshan

    2017-06-01

    Programmed '-1' ribosomal frameshifting is necessary for expressing the pol gene overlapped from a gag of human immunodeficiency virus. A viral RNA structure that requires base pairing across the overlapping sequence region suggests a mechanism of regulating ribosome and helicase traffic during expression. To get precise roles of an element around the frameshift site, a review on architecture of the frameshifting RNA is performed in combination of reported information with augments of a representative set of 19 viral samples. In spite of a different length for the viral RNAs, a canonical comparison on the element sequence allocation is performed for viewing variability associations between virus genotypes. Additionally, recent and historical insights recognized in frameshifting regulation are looked back as for indel and single nucleotide polymorphism of RNA. As specially noted, structural changes at a frameshift site, the spacer sequence, and a three-helix junction element, as well as two Watson-Crick base pairs near a bulge and a C-G pair close a loop, are the most vital strategies for the virus frameshifting regulations. All of structural changes, which are dependent upon specific sequence variations, facilitate an elucidation about the RNA element conformation-dependent mechanism for frameshifting. These facts on disrupting base pair interactions also allow solving the problem of competition between ribosome and helicase on a same RNA template, common to single-stranded RNA viruses. In a broad perspective, each new insight of frameshifting regulation in the competition systems introduced by the RNA element construct changes will offer a compelling target for antiviral therapy.

  19. Trusted Domain

    DEFF Research Database (Denmark)

    Hjorth, Theis Solberg; Torbensen, Rune

    2012-01-01

    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...... 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...... 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...

  20. Magnetic Domains

    OpenAIRE

    Harland, Derek; Palmer, Sam; Saemann, Christian

    2012-01-01

    Recently a Nahm transform has been discovered for magnetic bags, which are conjectured to arise in the large n limit of magnetic monopoles with charge n. We interpret these ideas using string theory and present some partial proofs of this conjecture. We then extend the notion of bags and their Nahm transform to higher gauge theories and arbitrary domains. Bags in four dimensions conjecturally describe the large n limit of n self-dual strings. We show that the corresponding Basu-Harvey equatio...

  1. Cross Domain Analogies for Learning Domain Theories

    National Research Council Canada - National Science Library

    Klenk, Matthew; Forbus, Ken

    2007-01-01

    .... This work describes a method for learning new domain theories by analogy. We use analogies between pairs of problems and worked solutions to create a domain mapping between a familiar and a new domain...

  2. .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...

  3. Domain wall diffusion and domain wall softening

    International Nuclear Information System (INIS)

    Lee, W T; Salje, E K H; Bismayer, U

    2003-01-01

    A number of experimental and computational studies of materials have shown that transport rates in domain walls may significantly differ from those in the bulk. One possible explanation for enhanced transport in a domain wall is that the domain wall is elastically soft with respect to the bulk. We investigate the softening of a ferroelastic domain wall in a simple, generic model. We calculate saddle point energies of solute atoms in the bulk and domain wall, using a geometry such that variation in the saddle point energy cannot be attributed to the structural differences of the bulk and the wall, but must instead be attributed to softening of the wall. Our results show a reduction of the saddle point energy in the wall, thus indicating that, in this model at least, domain walls are elastically soft compared with the bulk. A simple analysis based on an Einstein model allows us to explain the observed softening of the wall

  4. Domain Theory for Concurrency

    DEFF Research Database (Denmark)

    Nygaard, Mikkel

    Concurrent computation can be given an abstract mathematical treatment very similar to that provided for sequential computation by domain theory and denotational semantics of Scott and Strachey. A simple domain theory for concurrency is presented. Based on a categorical model of linear logic and ...... towards more expressive languages than HOPLA and Affine HOPLA—in particular concerning extensions to cover independence models. The thesis concludes with a discussion of related work towards a fully fledged domain theory for concurrency....

  5. Learning and Domain Adaptation

    Science.gov (United States)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  6. 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

  7. Quantum Bounded Symmetric Domains

    OpenAIRE

    Vaksman, L. L.

    2008-01-01

    This is Leonid Vaksman's monograph "Quantum bounded symmetric domains" (in Russian), preceded with an English translation of the table of contents and (a part) of the introduction. Quantum bounded symmetric domains are interesting from several points of view. In particular, they provide interesting examples for noncommutative complex analysis (i.e., the theory of subalgebras of C^*-algebars) initiated by W. Arveson.

  8. Cholesterol Domains Enhance Transfection

    Science.gov (United States)

    Betker, Jamie L.; Kullberg, Max; Gomez, Joe; Anchordoquy, Thomas J.

    2014-01-01

    The formation of cholesterol domains in lipoplexes has been associated with enhanced serum stability and transfection rates both in cell culture and in vivo. This study utilizes the ability of saturated phosphatidylcholines to promote the formation of cholesterol domains at much lower cholesterol contents than have been utilized in previous work. The results show that lipoplexes with identical cholesterol and cationic lipid contents exhibit significantly improved transfection efficiencies when a domain is present, consistent with previous work. In addition, studies assessing transfection rates in the absence of serum demonstrate that the ability of domains to enhance transfection is not dependent on interactions with serum proteins. Consistent with this hypothesis, characterization of the adsorbed proteins composing the corona of these lipoplex formulations did not reveal a correlation between transfection and the adsorption of a specific protein. Finally, we show that the interaction with serum proteins can promote domain formation in some formulations, and thereby result in enhanced transfection only after serum exposure. PMID:23557286

  9. 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.

  10. Distant relationships amongst protein domains

    Indian Academy of Sciences (India)

    ncbs

    3. Small domains. The 'pleckstrin homology' (PH) domain is a domain of about 100 residues that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.

  11. Domain-Specific Multimodeling

    DEFF Research Database (Denmark)

    Hessellund, Anders

    Enterprise systems are complex artifacts. They are hard to build, manage, understand, and evolve. Existing software development paradigms fail to properly address challenges such as system size, domain complexity, and software evolution when development is scaled to enterprise systems. We propose...... domain-specific multimodeling as a development paradigm to tackle these challenges in a language-oriented manner. The different concerns of a system are conceptually separated and made explicit as independent domain-specific languages. This approach increases productivity and quality by raising...... this coordination problem. By systematically identifying language interactions, we can specify a coordination model for the system. Specifically, we explicitly identify name bindings and references across language boundaries. We argue that such a coordination model facilitates consistency, navigation, and guidance...

  12. Autoprocessing of human immunodeficiency virus type 1 protease miniprecursor fusions in mammalian cells

    Directory of Open Access Journals (Sweden)

    Chen Chaoping

    2010-07-01

    Full Text Available Abstract Background HIV protease (PR is a virus-encoded aspartic protease that is essential for viral replication and infectivity. The fully active and mature dimeric protease is released from the Gag-Pol polyprotein as a result of precursor autoprocessing. Results We here describe a simple model system to directly examine HIV protease autoprocessing in transfected mammalian cells. A fusion precursor was engineered encoding GST fused to a well-characterized miniprecursor, consisting of the mature protease along with its upstream transframe region (TFR, and small peptide epitopes to facilitate detection of the precursor substrate and autoprocessing products. In HEK 293T cells, the resulting chimeric precursor undergoes effective autoprocessing, producing mature protease that is rapidly degraded likely via autoproteolysis. The known protease inhibitors Darunavir and Indinavir suppressed both precursor autoprocessing and autoproteolysis in a dose-dependent manner. Protease mutations that inhibit Gag processing as characterized using proviruses also reduced autoprocessing efficiency when they were introduced to the fusion precursor. Interestingly, autoprocessing of the fusion precursor requires neither the full proteolytic activity nor the majority of the N-terminal TFR region. Conclusions We suggest that the fusion precursors provide a useful system to study protease autoprocessing in mammalian cells, and may be further developed for screening of new drugs targeting HIV protease autoprocessing.

  13. 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

  14. Normed Domains of Holomorphy

    Directory of Open Access Journals (Sweden)

    Steven G. Krantz

    2010-01-01

    Full Text Available We treat the classical concept of domain of holomorphy in ℂn when the holomorphic functions considered are restricted to lie in some Banach space. Positive and negative results are presented. A new view of the case n=1 is considered.

  15. Studi Literatur Perubahan Antara CISSP 10 Domain Dengan 8 Domain

    OpenAIRE

    Perkasa, Michael; Noertjahyana, Agustinus; Rostianingsih, Silvia

    2016-01-01

    Degree is one that is being achieved by most people in their work, in order to influence the potential possessed by an employee or the employee. So with the development of technology, people increasingly need a degree or certification in order to hone and enhance its capabilities.With the changes under discussion on the differences of the 10 CISSP domains domain into 8 domains in each domain has the characteristics of each and their respective utility functions. CISSP 8 domain is a new domain...

  16. Bifurcations of Baker domains

    Science.gov (United States)

    Lauber, Arnd

    2007-07-01

    We consider the family of transcendental entire functions given by \\{f_c:{\\mathbb C} \\rightarrow {\\mathbb C}:z-c+e^z, c \\in {\\mathbb C} \\} . If Re c > 0, then fc features a Baker domain as the only component of the Fatou set, while the functions fc show a different dynamical behaviour if c \\in \\rmi{\\mathbb R} . We describe the dynamical planes of these functions and show that the Julia sets converge in the limit process f_{c_1+\\rmi c_2} \\rightarrow f_{\\rmi c_2} with respect to the Hausdorff metric, where c_1 \\in {\\mathbb R}^+ and c_2 \\in {\\mathbb R} . We use this to show that Baker domains of any type (concerning a classification of König) are not necessarily stable under perturbation.

  17. 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......%. Furthermore, the presence of low-pass filters in time-domain-induced polarization instruments affects the early times of the acquired decays (typically up to 100 ms) and has to be modeled in the forward response to avoid significant loss of resolution. The developed forward code has been implemented in a 1D...

  18. 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

  19. Updating action domain descriptions.

    Science.gov (United States)

    Eiter, Thomas; Erdem, Esra; Fink, Michael; Senko, Ján

    2010-10-01

    Incorporating new information into a knowledge base is an important problem which has been widely investigated. In this paper, we study this problem in a formal framework for reasoning about actions and change. In this framework, action domains are described in an action language whose semantics is based on the notion of causality. Unlike the formalisms considered in the related work, this language allows straightforward representation of non-deterministic effects and indirect effects of (possibly concurrent) actions, as well as state constraints; therefore, the updates can be more general than elementary statements. The expressivity of this formalism allows us to study the update of an action domain description with a more general approach compared to related work. First of all, we consider the update of an action description with respect to further criteria, for instance, by ensuring that the updated description entails some observations, assertions, or general domain properties that constitute further constraints that are not expressible in an action description in general. Moreover, our framework allows us to discriminate amongst alternative updates of action domain descriptions and to single out a most preferable one, based on a given preference relation possibly dependent on the specified criteria. We study semantic and computational aspects of the update problem, and establish basic properties of updates as well as a decomposition theorem that gives rise to a divide and conquer approach to updating action descriptions under certain conditions. Furthermore, we study the computational complexity of decision problems around computing solutions, both for the generic setting and for two particular preference relations, viz. set-inclusion and weight-based preference. While deciding the existence of solutions and recognizing solutions are PSPACE-complete problems in general, the problems fall back into the polynomial hierarchy under restrictions on the additional

  20. 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...

  1. 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....

  2. XML for Domain Viewpoints

    CERN Document Server

    Van Lingen, F; Van der Stok, P D V; Willers, Ian Malcolm

    2001-01-01

    Within research institutions like CERN (European Organization for Nuclear Research) there are often disparate databases (different in format, type and structure) that users need to access in a domain-specific manner. Users may want to access a simple unit of information without having to understand detail of the underlying schema or they may want to access the same information from several different sources. It is neither desirable nor feasible to require users to have knowledge of these schemas. Instead it would be advantageous if a user could query these sources using his or her own domain models and abstractions of the data. This paper describes the basis of an XML (eXtended Markup Language) framework that provides this functionality and is currently being developed at CERN. The goal of the first prototype was to explore the possibilities of XML for data integration and model management. It shows how XML can be used to integrate data sources. The framework is not only applicable to CERN data sources but ot...

  3. On Probability Domains IV

    Science.gov (United States)

    Frič, Roman; Papčo, Martin

    2017-12-01

    Stressing a categorical approach, we continue our study of fuzzified domains of probability, in which classical random events are replaced by measurable fuzzy random events. In operational probability theory (S. Bugajski) classical random variables are replaced by statistical maps (generalized distribution maps induced by random variables) and in fuzzy probability theory (S. Gudder) the central role is played by observables (maps between probability domains). We show that to each of the two generalized probability theories there corresponds a suitable category and the two resulting categories are dually equivalent. Statistical maps and observables become morphisms. A statistical map can send a degenerated (pure) state to a non-degenerated one —a quantum phenomenon and, dually, an observable can map a crisp random event to a genuine fuzzy random event —a fuzzy phenomenon. The dual equivalence means that the operational probability theory and the fuzzy probability theory coincide and the resulting generalized probability theory has two dual aspects: quantum and fuzzy. We close with some notes on products and coproducts in the dual categories.

  4. Metaphors, domains and embodiment

    Directory of Open Access Journals (Sweden)

    M.E. Botha

    2005-07-01

    Full Text Available Investigations of metaphorical meaning constitution and meaning (in- variance have revealed the significance of semantic and semiotic domains and the contexts within which they function as basis for the grounding of metaphorical meaning. In this article some of the current views concerning the grounding of metaphorical meaning in experience and embodiment are explored. My provisional agreement with Lakoff, Johnson and others about the “conceptual” nature of metaphor rests on an important caveat, viz. that this bodily based conceptual structure which lies at the basis of linguistic articulations of metaphor, is grounded in a deeper ontic structure of the world and of human experience. It is the “metaphorical” (actually “analogical” ontological structure of this grounding that is of interest for the line of argumentation followed in this article. Because Johnson, Lakoff and other’s proposal to ground metaphorical meaning in embodiment and neural processes is open to being construed as subjectivist and materialist, I shall attempt to articulate the contours of an alternative theory of conceptual metaphor, meaning and embodiment which counteracts these possibilities. This theory grounds metaphorical meaning and meaning change in an ontological and anthropological framework which recognises the presence and conditioning functioning of radially ordered structures for reality. These categorisations in which humankind, human knowledge and reality participate, condition and constrain (ground analogical and metaphorical meaning transfer, cross-domain mappings, and blends in cognition and in language, provide the basis for the analogical concepts found in these disciplines.

  5. 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.

  6. Fuzzy Bases of Fuzzy Domains

    Directory of Open Access Journals (Sweden)

    Sanping Rao

    2013-01-01

    Full Text Available This paper is an attempt to develop quantitative domain theory over frames. Firstly, we propose the notion of a fuzzy basis, and several equivalent characterizations of fuzzy bases are obtained. Furthermore, the concept of a fuzzy algebraic domain is introduced, and a relationship between fuzzy algebraic domains and fuzzy domains is discussed from the viewpoint of fuzzy basis. We finally give an application of fuzzy bases, where the image of a fuzzy domain can be preserved under some special kinds of fuzzy Galois connections.

  7. The framing of scientific domains

    DEFF Research Database (Denmark)

    Dam Christensen, Hans

    2014-01-01

    Purpose: By using the UNISIST models this article argues for the necessity of domain analysis in order to qualify scientific information seeking. The models better understanding of communication processes in a scientific domain and embraces the point that domains are always both unstable over time...... and changeable according to the specific perspective. This understanding is even more important today as numerous digitally generated information tools as well as collaborative and interdisciplinary research are blurring the domain borders. Nevertheless, researchers navigate “intuitively” in “their” specific...... as according to the agents that are charting them. As such, power in a Foucauldian sense is unavoidable in outlining a domain. Originality/value 1. The UNISIST models are applied to the domain of art history; and 2. the article discusses the instability of a scientific domain as well as, at the same time...

  8. Feature-level domain adaptation

    DEFF Research Database (Denmark)

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

    2016-01-01

    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......-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...... model. For linear classifiers and a large family of loss functions and transfer models, this expected loss can be computed or approximated analytically, and minimized efficiently. Our empirical evaluation of flda focuses on problems comprising binary and count data in which the transfer can be naturally...

  9. 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

  10. 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

  11. The Garrison Domain: Civil Military Relations in the Cyberspace Domain

    Science.gov (United States)

    2015-04-01

    governance, commerce , communications, and entertainment. The reliance on cyberspace is so predominant it seems unacceptable to not be part of the domain...Almost every type of person and organization on this planet arguably touches the cyberspace domain, directly or indirectly. Because this domain is...Department of Justice (DOJ) has also begun using cyberspace to gather information intelligence. Flying small civilian aircraft with electronic boxes to

  12. 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.

  13. 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

  14. Ligand binding by PDZ domains

    DEFF Research Database (Denmark)

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

    2012-01-01

    The postsynaptic density protein-95/disks large/zonula occludens-1 (PDZ) protein domain family is one of the most common protein-protein interaction modules in mammalian cells, with paralogs present in several hundred human proteins. PDZ domains are found in most cell types, but neuronal proteins...... 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....

  15. 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.

  16. 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

  17. A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal.

    Science.gov (United States)

    Mueller, Nancy; Das, Atze T; Berkhout, Ben

    2016-07-21

    RNA splicing is a critical step in the human immunodeficiency virus type 1 (HIV-1) replication cycle because it controls the expression of the complex viral proteome. The major 5' splice site (5'ss) that is positioned in the untranslated leader of the HIV-1 RNA transcript is of particular interest because it is used for the production of the more than 40 differentially spliced subgenomic mRNAs. HIV-1 splicing needs to be balanced tightly to ensure the proper levels of all viral proteins, including the Gag-Pol proteins that are translated from the unspliced RNA. We previously presented evidence that the major 5'ss is regulated by a repressive local RNA structure, the splice donor (SD) hairpin, that masks the 11 nucleotides (nts) of the 5'ss signal for recognition by U1 small nuclear RNA (snRNA) of the spliceosome machinery. A strikingly different multiple-hairpin RNA conformation was recently proposed for this part of the HIV-1 leader RNA. We therefore inspected the sequence of natural HIV-1 isolates in search for support, in the form of base pair (bp) co-variations, for the different RNA conformations.

  18. Optimal Transport for Domain Adaptation.

    Science.gov (United States)

    Courty, Nicolas; Flamary, Remi; Tuia, Devis; Rakotomamonjy, Alain

    2017-09-01

    Domain adaptation is one of the most challenging tasks of modern data analytics. If the adaptation is done correctly, models built on a specific data representation become more robust when confronted to data depicting the same classes, but described by another observation system. Among the many strategies proposed, finding domain-invariant representations has shown excellent properties, in particular since it allows to train a unique classifier effective in all domains. In this paper, we propose a regularized unsupervised optimal transportation model to perform the alignment of the representations in the source and target domains. We learn a transportation plan matching both PDFs, which constrains labeled samples of the same class in the source domain to remain close during transport. This way, we exploit at the same time the labeled samples in the source and the distributions observed in both domains. Experiments on toy and challenging real visual adaptation examples show the interest of the method, that consistently outperforms state of the art approaches. In addition, numerical experiments show that our approach leads to better performances on domain invariant deep learning features and can be easily adapted to the semi-supervised case where few labeled samples are available in the target domain.

  19. 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...

  20. Parallel pseudospectral domain decomposition techniques

    Science.gov (United States)

    Gottlieb, David; Hirsch, Richard S.

    1989-01-01

    The influence of interface boundary conditions on the ability to parallelize pseudospectral multidomain algorithms is investigated. Using the properties of spectral expansions, a novel parallel two domain procedure is generalized to an arbitrary number of domains each of which can be solved on a separate processor. This interface boundary condition considerably simplifies influence matrix techniques.

  1. 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.

  2. 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'.

  3. Modeling software systems by domains

    Science.gov (United States)

    Dippolito, Richard; Lee, Kenneth

    1992-01-01

    The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

  4. Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines.

    Science.gov (United States)

    González, Alvaro J; Liao, Li

    2010-10-29

    Protein-protein interaction (PPI) plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI) is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. In this paper, we propose a computational method to predict DDI using support vector machines (SVMs), based on domains represented as interaction profile hidden Markov models (ipHMM) where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB). Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD). Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure), an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on the web at http

  5. Predicting domain-domain interaction based on domain profiles with feature selection and support vector machines

    Directory of Open Access Journals (Sweden)

    Liao Li

    2010-10-01

    Full Text Available Abstract Background Protein-protein interaction (PPI plays essential roles in cellular functions. The cost, time and other limitations associated with the current experimental methods have motivated the development of computational methods for predicting PPIs. As protein interactions generally occur via domains instead of the whole molecules, predicting domain-domain interaction (DDI is an important step toward PPI prediction. Computational methods developed so far have utilized information from various sources at different levels, from primary sequences, to molecular structures, to evolutionary profiles. Results In this paper, we propose a computational method to predict DDI using support vector machines (SVMs, based on domains represented as interaction profile hidden Markov models (ipHMM where interacting residues in domains are explicitly modeled according to the three dimensional structural information available at the Protein Data Bank (PDB. Features about the domains are extracted first as the Fisher scores derived from the ipHMM and then selected using singular value decomposition (SVD. Domain pairs are represented by concatenating their selected feature vectors, and classified by a support vector machine trained on these feature vectors. The method is tested by leave-one-out cross validation experiments with a set of interacting protein pairs adopted from the 3DID database. The prediction accuracy has shown significant improvement as compared to InterPreTS (Interaction Prediction through Tertiary Structure, an existing method for PPI prediction that also uses the sequences and complexes of known 3D structure. Conclusions We show that domain-domain interaction prediction can be significantly enhanced by exploiting information inherent in the domain profiles via feature selection based on Fisher scores, singular value decomposition and supervised learning based on support vector machines. Datasets and source code are freely available on

  6. 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.

  7. 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...

  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. 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...

  11. Fatou-Bieberbach domains in

    Science.gov (United States)

    Forstnerič, Franc; Wold, Erlend F.

    2015-10-01

    We construct Fatou-Bieberbach domains in for n>1 which contain a given compact set K and at the same time avoid a totally real affine subspace L of dimension < n, provided that K∪ L is polynomially convex. By using this result, we show that the domain for 1≤ k< n enjoys the basic Oka property with approximation for maps from any Stein manifold of dimension < n.

  12. 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

  13. Domain Walls with Strings Attached

    Energy Technology Data Exchange (ETDEWEB)

    Shmakova, Marina

    2001-08-20

    We have constructed a bulk and brane action of IIA theory which describes a pair of BPS domain walls on S{sub 1}/Z{sub 2}, with strings attached. The walls are given by two orientifold O8-planes with coincident D8-branes and F1-D0-strings are stretched between the walls. This static configuration satisfies all matching conditions for the string and domain wall sources and has 1/4 of unbroken supersymmetry.

  14. 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

  15. 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.

  16. 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...... for an automatic metric simulating the post-editors’ usability judgements. LSP tests show 67% saved time in post-editing for the tested domain. Finally, the use of weighted sub-domain phrase tables in a SMT system is shown to improve translation quality.......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...

  17. Application Scenarios and Deployment Domains

    NARCIS (Netherlands)

    Niamut, O.A.; Engström, A.; Kochale, A.; Macq, J.; Thomas, G.; Zorić, G.

    2014-01-01

    This chapter describes the impact of deploying the format-agnostic media approach, along the lines of three deployment domains and the end user perspective. The chapter elaborates on a series of potential application scenarios. These application scenarios describe features of a potential

  18. affective domain in developing environmental

    African Journals Online (AJOL)

    AN ETHIC FOR GEOGRAPHY: THE ROLE OF THE. AFFECTIVE DOMAIN IN DEVELOPING ENVIRONMENTAL. AWARENESS. Margaret E. Marker. Geography is a subject with integral ethical and moral components. However, because of the subject's traditionally close association with scientific rationality this factor has not ...

  19. 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...

  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. 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.

  2. 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.

  3. Certifying Domain-Specific Policies

    Science.gov (United States)

    Lowry, Michael; Pressburger, Thomas; Rosu, Grigore; Koga, Dennis (Technical Monitor)

    2001-01-01

    Proof-checking code for compliance to safety policies potentially enables a product-oriented approach to certain aspects of software certification. To date, previous research has focused on generic, low-level programming-language properties such as memory type safety. In this paper we consider proof-checking higher-level domain -specific properties for compliance to safety policies. The paper first describes a framework related to abstract interpretation in which compliance to a class of certification policies can be efficiently calculated Membership equational logic is shown to provide a rich logic for carrying out such calculations, including partiality, for certification. The architecture for a domain-specific certifier is described, followed by an implemented case study. The case study considers consistency of abstract variable attributes in code that performs geometric calculations in Aerospace systems.

  4. Frequency domain optical parametric amplification.

    Science.gov (United States)

    Schmidt, Bruno E; Thiré, Nicolas; Boivin, Maxime; Laramée, Antoine; Poitras, François; Lebrun, Guy; Ozaki, Tsuneyuki; Ibrahim, Heide; Légaré, François

    2014-05-07

    Today's ultrafast lasers operate at the physical limits of optical materials to reach extreme performances. Amplification of single-cycle laser pulses with their corresponding octave-spanning spectra still remains a formidable challenge since the universal dilemma of gain narrowing sets limits for both real level pumped amplifiers as well as parametric amplifiers. We demonstrate that employing parametric amplification in the frequency domain rather than in time domain opens up new design opportunities for ultrafast laser science, with the potential to generate single-cycle multi-terawatt pulses. Fundamental restrictions arising from phase mismatch and damage threshold of nonlinear laser crystals are not only circumvented but also exploited to produce a synergy between increased seed spectrum and increased pump energy. This concept was successfully demonstrated by generating carrier envelope phase stable, 1.43 mJ two-cycle pulses at 1.8 μm wavelength.

  5. Domain Specific Language Construction Technology

    Science.gov (United States)

    2000-03-28

    REPOSITORIES-89041-N, Software Produc- tivity Consortium Services Corporation, 2214 Rock Hill Road , Herndon, Virginia 22070, June 1989. [3] Grady...Consortium Services Corporation, 2214 Rock Hill Road , Herndon, Virginia 22070, 1990. [4] Charles Consel and Frangois Noel. A general approach for run...automation: Language design in the context of domain engenieering . In The 10th International Conference on Software Engineering & Knowl- edge Engineering (SEKE󈨦), pages 308-317, San Francisco Bay, California, June 1998.

  6. 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.

  7. Flexoelectricity in nematic domain walls.

    Science.gov (United States)

    Elston, Steve J

    2008-07-01

    Flexoelectric effects are studied in the domain walls of a nematic liquid crystal device showing the Freedericksz transition. Walls parallel to the alignment direction have a strong twist distortion and an electro-optic effect dominated by e1-e3 is seen. Walls perpendicular to the alignment direction have a strong splay-bend distortion and an electro-optic effect dominated by e1+e3 is seen. This allows the study of both flexoelectric coefficient combinations in a single device.

  8. 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....

  9. 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)

  10. 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.

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

    Science.gov (United States)

    2017-04-06

    academic research paper are those of the author and do not reflect the official policy or position of the US government, the Department of Defense, or...Wars of the Future,” The National Interest, July 19, 2016, p. 2, Retrieved on 2 December 2016, http://nationalinterest.org/ blog /the-buzz/cross-domain...www.nationaldefensemagazine.org/ blog /Lists/Posts/Post.aspx?ID=2319. 15 Sam LaGrone, “PACOM Commander Harris Wants the Army to Sink Ships, Expand

  12. Motion Compensation on DCT Domain

    Directory of Open Access Journals (Sweden)

    K. J. Ray Liu

    2001-10-01

    Full Text Available Alternative fully DCT-based video codec architectures have been proposed in the past to address the shortcomings of the conventional hybrid motion compensated DCT video codec structures traditionally chosen as the basis of implementation of standard-compliant codecs. However, no prior effort has been made to ensure interoperability of these two drastically different architectures so that fully DCT-based video codecs are fully compatible with the existing video coding standards. In this paper, we establish the criteria for matching conventional codecs with fully DCT-based codecs. We find that the key to this interoperability lies in the heart of the implementation of motion compensation modules performed in the spatial and transform domains at both the encoder and the decoder. Specifically, if the spatial-domain motion compensation is compatiable with the transform-domain motion compensation, then the states in both the coder and the decoder will keep track of each other even after a long series of P-frames. Otherwise, the states will diverge in proportion to the number of P-frames between two I-frames. This sets an important criterion for the development of any DCT-based motion compensation schemes. We also discuss and develop some DCT-based motion compensation schemes as important building blocks of fully DCT-based codecs. For the case of subpixel motion compensation, DCT-based approaches allow more accurate interpolation without any increase in computation. Furthermore, a scare number of DCT coefficients after quantization significantly decreases the number of calculations required for motion compensation. Coupled with the DCT-based motion estimation algorithms, it is possible to realize fully DCT-based codecs to overcome the disadvantages of conventional hybrid codecs.

  13. Domain Building or Risk Taking

    DEFF Research Database (Denmark)

    Hjort, Katrin; Abrahamsen, Marianne

    2012-01-01

    of the relations between gender, values and family obligation but reveals an interesting difference between two strategies for career development: Domain Building and Risk Taking. Both strategies are applied by both men and women. However, one of them seems to be the most effective with regard to achieve......The Nordic Countries are usually seen as the worlds must successful nations when it comes to gender equality, and the Scandinavian population in general appreciates values traditionally labeled feminine as caretaking and the quality of everyday life. However, the inequalities become obvious...

  14. Learning processes across knowledge domains

    DEFF Research Database (Denmark)

    Hall-Andersen, Lene Bjerg; Broberg, Ole

    2014-01-01

    with the aim of creating a new combined practice. Design/methodology/approach - A case study was carried out as a "natural experiment" in an engineering consultancy, where emerging initiatives to integrate the newly acquired competencies into the existing practice were explored. A theoretical framework......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...

  15. 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.

  16. Domain Tuning of Bilingual Lexicons for MT

    National Research Council Canada - National Science Library

    Ayan, Necip F; Dorr, Bonnie; Kolak, Okan

    2003-01-01

    ... (in this case, Chinese) to English. Using automatically induced domain-specific, comparable documents and language-independent clustering, we apply domain-tuning techniques to a bilingual lexicon for downstream translation of the input...

  17. Enhanced functional and structural domain assignments using ...

    Indian Academy of Sciences (India)

    Unknown

    ) by Seema Namboori, Natasha Mhatre, Sentivel Sujatha,. Narayanaswamy Srinivasan and Shashi Bhushan Pandit. The three-dimensional structure and subcellular localization of various domains and sub-domains of. Rv1318c, a putative ...

  18. 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...... techniques in manipulating the micro-structure and domain structure to result in desired interactions between neighbouring grains could prove to be beneficial for future polycrystalline ferroelectric materials....

  19. 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.

  20. 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.

  1. 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.

  2. Static domain wall in braneworld gravity

    Energy Technology Data Exchange (ETDEWEB)

    Abdalla, M.C.B.; Carlesso, P.F. [UNESP, Universidade Estadual Paulista, Instituto de Fisica Teiorica, Rua Dr. Bento Teobaldo Ferraz 271, Bloco II, Barra-Funda, Caixa Postal 70532-2, Sao Paulo, SP (Brazil); Hoff da Silva, J.M. [UNESP, Universidade Estadual Paulista, Departamento de Fisica e Quimica, Guaratingueta, SP (Brazil)

    2014-01-15

    In this paper we consider a static domain wall inside a 3-brane. Different from the standard achievement obtained in General Relativity, the analysis performed here gives a consistency condition for the existence of static domain walls in a braneworld gravitational scenario. Also the behavior of the domain wall's gravitational field in the newtonian limit is shown. (orig.)

  3. 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

  4. 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

  5. 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

  6. 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...

  7. Domain adaptation via transfer component analysis.

    Science.gov (United States)

    Pan, Sinno Jialin; Tsang, Ivor W; Kwok, James T; Yang, Qiang

    2011-02-01

    Domain adaptation allows knowledge from a source domain to be transferred to a different but related target domain. Intuitively, discovering a good feature representation across domains is crucial. In this paper, we first propose to find such a representation through a new learning method, transfer component analysis (TCA), for domain adaptation. TCA tries to learn some transfer components across domains in a reproducing kernel Hilbert space using maximum mean miscrepancy. In the subspace spanned by these transfer components, data properties are preserved and data distributions in different domains are close to each other. As a result, with the new representations in this subspace, we can apply standard machine learning methods to train classifiers or regression models in the source domain for use in the target domain. Furthermore, in order to uncover the knowledge hidden in the relations between the data labels from the source and target domains, we extend TCA in a semisupervised learning setting, which encodes label information into transfer components learning. We call this extension semisupervised TCA. The main contribution of our work is that we propose a novel dimensionality reduction framework for reducing the distance between domains in a latent space for domain adaptation. We propose both unsupervised and semisupervised feature extraction approaches, which can dramatically reduce the distance between domain distributions by projecting data onto the learned transfer components. Finally, our approach can handle large datasets and naturally lead to out-of-sample generalization. The effectiveness and efficiency of our approach are verified by experiments on five toy datasets and two real-world applications: cross-domain indoor WiFi localization and cross-domain text classification.

  8. Packaging the fly genome: domains and dynamics.

    Science.gov (United States)

    White, Rob

    2012-09-01

    Two independent genomic approaches have recently converged to provide insight into the domain organization of the Drosophila genome. Genome-wide mapping of chromosomal proteins and histone modifications has generated detailed maps of the Drosophila chromatin landscape and has led to the identification of a number of different chromatin states and their distribution in domains across the genome. A remarkably similar domain organization is derived from whole genome mapping of chromatin interactions that reveals the segmentation of the genome into structural domains. This review focuses on our current understanding of this domain architecture which provides a foundation for our understanding of the link between chromatin organization and the dynamic activity of the genome.

  9. 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.

  10. 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.

  11. Mechanical switching of ferroelectric domains beyond flexoelectricity

    Science.gov (United States)

    Chen, Weijin; Liu, Jianyi; Ma, Lele; Liu, Linjie; Jiang, G. L.; Zheng, Yue

    2018-02-01

    The resurgence of interest in flexoelectricity has prompted discussions on the feasibility of switching ferroelectric domains 'non-electrically'. In this work, we perform three-dimensional thermodynamic simulations in combination with ab initio calculations and effective Hamiltonian simulations to demonstrate the great effects of surface screening and surface bonding on ferroelectric domain switching triggered by local tip loading. A three-dimensional simulation scheme has been developed to capture the tip-induced domain switching behavior in ferroelectric thin films by adequately taking into account the surface screening effect and surface bonding effect of the ferroelectric film, as well as the finite elastic stiffness of the substrate and the electrode layers. The major findings are as follows. (i) Compared with flexoelectricity, surface effects can be overwhelming and lead to much more efficient mechanical switching caused by tip loading. (ii) The surface-assisted mechanical switching can be bi-directional without the necessity of reversing strain gradients. (iii) A mode transition from local to propagating domain switching occurs when the screening below a critical value. A ripple effect of domain switching appears with the formation of concentric loop domains. (iv) The ripple effect can lead to 'domain interference' and a deterministic writing of confined loop domain patterns by local excitations. Our study reveals the hidden switching mechanisms of ferroelectric domains and the possible roles of surface in mechanical switching. The ripple effect of domain switching, which is believed to be general in dipole systems, broadens our current knowledge of domain engineering.

  12. Domain Adaption Based on ELM Autoencoder

    Directory of Open Access Journals (Sweden)

    Wan-Yu Deng

    2017-01-01

    Full Text Available We propose a new ELM Autoencoder (ELM-AE based domain adaption algorithm which describes the subspaces of source and target domain by ELM-AE and then carries out subspace alignment to project different domains into a common new space. By leveraging nonlinear approximation ability and efficient one-pass learning ability of ELM-AE, the proposed domain adaption algorithm can efficiently seek a better cross-domain feature representation than linear feature representation approaches such as PCA to improve domain adaption performance. The widely experimental results on Office/Caltech-256 datasets show that the proposed algorithm can achieve better classification accuracy than PCA subspace alignment algorithm and other state-of-the-art domain adaption algorithms in most cases.

  13. 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......, and edges correspond to two circles (having centers corresponding to the endpoints of the edge) being tangent to each other. This circle packing creates a rigid structure having an underlying geometric triangulation, where the centers of circles again correspond to vertices in the triangulation......, and the edges are geodesic segments (Euclidean, hyperbolic, or spherical) connecting centers of circles that are tangent to each other. Three circles that are mutually tangent form a face of the triangulation. Since circle packing is closely related to triangulation, circle packing methods can be applied...

  14. Angular-domain scattering interferometry.

    Science.gov (United States)

    Shipp, Dustin W; Qian, Ruobing; Berger, Andrew J

    2013-11-15

    We present an angular-scattering optical method that is capable of measuring the mean size of scatterers in static ensembles within a field of view less than 20 μm in diameter. Using interferometry, the method overcomes the inability of intensity-based models to tolerate the large speckle grains associated with such small illumination areas. By first estimating each scatterer's location, the method can model between-scatterer interference as well as traditional single-particle Mie scattering. Direct angular-domain measurements provide finer angular resolution than digitally transformed image-plane recordings. This increases sensitivity to size-dependent scattering features, enabling more robust size estimates. The sensitivity of these angular-scattering measurements to various sizes of polystyrene beads is demonstrated. Interferometry also allows recovery of the full complex scattered field, including a size-dependent phase profile in the angular-scattering pattern.

  15. 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.

  16. 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

  17. Structure and Function of KH Domains

    Energy Technology Data Exchange (ETDEWEB)

    Valverde, R.; Regan, E

    2008-01-01

    The hnRNP K homology (KH) domain was first identified in the protein human heterogeneous nuclear ribonucleoprotein K (hnRNP K) 14 years ago. Since then, KH domains have been identified as nucleic acid recognition motifs in proteins that perform a wide range of cellular functions. KH domains bind RNA or ssDNA, and are found in proteins associated with transcriptional and translational regulation, along with other cellular processes. Several diseases, e.g. fragile X mental retardation syndrome and paraneoplastic disease, are associated with the loss of function of a particular KH domain. Here we discuss the progress made towards understanding both general and specific features of the molecular recognition of nucleic acids by KH domains. The typical binding surface of KH domains is a cleft that is versatile but that can typically accommodate only four unpaired bases. Van der Waals forces and hydrophobic interactions and, to a lesser extent, electrostatic interactions, contribute to the nucleic acid binding affinity. 'Augmented' KH domains or multiple copies of KH domains within a protein are two strategies that are used to achieve greater affinity and specificity of nucleic acid binding. Isolated KH domains have been seen to crystallize as monomers, dimers and tetramers, but no published data support the formation of noncovalent higher-order oligomers by KH domains in solution. Much attention has been given in the literature to a conserved hydrophobic residue (typically Ile or Leu) that is present in most KH domains. The interest derives from the observation that an individual with this Ile mutated to Asn, in the KH2 domain of fragile X mental retardation protein, exhibits a particularly severe form of the syndrome. The structural effects of this mutation in the fragile X mental retardation protein KH2 domain have recently been reported. We discuss the use of analogous point mutations at this position in other KH domains to dissect both structure and

  18. Reconstituting Protein Interaction Networks Using Parameter-Dependent Domain-Domain Interactions

    Science.gov (United States)

    2013-05-07

    that approximately 80% of eukaryotic proteins and 67% of prokaryotic proteins have multiple domains [13,14]. Most annotation databases characterize...domain annotations, Domain-domain interactions, Protein-protein interaction networks Background The living cell is a dynamic, interconnected system...detailed in Methods. Here, we illustrate its application on a well- annotated single- cell organism. We created a merged set of protein-domain annotations

  19. Domains in Ferroic Crystals and Thin Films

    CERN Document Server

    Tagantsev, Alexander K; Fousek, Jan

    2010-01-01

    Domains in Ferroic Crystals and Thin Films presents experimental findings and theoretical understanding of ferroic (non-magnetic) domains developed during the past 60 years. It addresses the situation by looking specifically at bulk crystals and thin films, with a particular focus on recently-developed microelectronic applications and methods for observation of domains with techniques such as scanning force microscopy, polarized light microscopy, scanning optical microscopy, electron microscopy, and surface decorating techniques. Domains in Ferroic Crystals and Thin Films covers a large area of material properties and effects connected with static and dynamic properties of domains, which are extremely relevant to materials referred to as ferroics. In most solid state physics books, one large group of ferroics is customarily covered: those in which magnetic properties play a dominant role. Numerous books are specifically devoted to magnetic ferroics and cover a wide spectrum of magnetic domain phenomena. In co...

  20. DENN Domain Proteins: Regulators of Rab GTPases*

    Science.gov (United States)

    Marat, Andrea L.; Dokainish, Hatem; McPherson, Peter S.

    2011-01-01

    The DENN domain is a common, evolutionarily ancient, and conserved protein module, yet it has gone largely unstudied; until recently, little was known regarding its functional roles. New studies reveal that various DENN domains interact directly with members of the Rab family of small GTPases and that DENN domains function enzymatically as Rab-specific guanine nucleotide exchange factors. Thus, DENN domain proteins appear to be generalized regulators of Rab function. Study of these proteins will provide new insights into Rab-mediated membrane trafficking pathways. PMID:21330364

  1. DENN domain proteins: regulators of Rab GTPases.

    Science.gov (United States)

    Marat, Andrea L; Dokainish, Hatem; McPherson, Peter S

    2011-04-22

    The DENN domain is a common, evolutionarily ancient, and conserved protein module, yet it has gone largely unstudied; until recently, little was known regarding its functional roles. New studies reveal that various DENN domains interact directly with members of the Rab family of small GTPases and that DENN domains function enzymatically as Rab-specific guanine nucleotide exchange factors. Thus, DENN domain proteins appear to be generalized regulators of Rab function. Study of these proteins will provide new insights into Rab-mediated membrane trafficking pathways.

  2. Building the DAML Electronic Commerce Domain

    National Research Council Canada - National Science Library

    Anyiwo, David

    2001-01-01

    The project captured additional functional and technical requirements for collaboration and exchange in the electronics industry's value chain, and refined the eCommerce domain ontology requirements...

  3. 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.

  4. Transform domain steganography with blind source separation

    Science.gov (United States)

    Jouny, Ismail

    2015-05-01

    This paper applies blind source separation or independent component analysis for images that may contain mixtures of text, audio, or other images for steganography purposes. The paper focuses on separating mixtures in the transform domain such as Fourier domain or the Wavelet domain. The study addresses the effectiveness of steganography when using linear mixtures of multimedia components and the ability of standard blind sources separation techniques to discern hidden multimedia messages. Mixing in the space, frequency, and wavelet (scale) domains is compared. Effectiveness is measured using mean square error rate between original and recovered images.

  5. Planar domain walls in black hole spacetimes

    Science.gov (United States)

    Ficek, Filip; Mach, Patryk

    2018-02-01

    We investigate the behavior of low-mass, planar domain walls in the so-called ϕ4 model of the scalar field on the Schwarzschild and Kerr backgrounds. We focus on a transit of a domain wall through a black hole and solve numerically the equations of motion for a range of parameters of the domain wall and the black hole. We observe a behavior resembling an occurrence of ringing modes. Perturbations of domain walls vanish during latter evolution, suggesting their stability against a passage through the black hole. The results obtained for Kerr and Reissner-Nordström black holes are also compared.

  6. Ferromagnetic stripe domains in ultrathin films

    Energy Technology Data Exchange (ETDEWEB)

    Kaplan, B. [Department of Secondary Science and Mathematics Education, University of Mersin, Yenisehir Campus, 33169 Mersin (Turkey)]. E-mail: bengukaplan@yahoo.com

    2005-03-01

    Using simple magnetostatic considerations, we discuss the domain structure and the domain-wall width, {omega}, in ultrathin magnetic films (of a few monolayer thickness) and in an atomic monolayer. The demagnetizing energy is calculated in a continuum theory which is valid provided that the domains are large compared with the lattice spacing. The calculated domain-wall width, {omega}, and the surface anisotropy constant, K{sub s}, are compared with the experimental data for thin epitaxial Co/Au (111) films and a good coincidence is obtained between both results.

  7. The All-DQ-Domain EMTP

    Directory of Open Access Journals (Sweden)

    Gibson H.M. Sianipar

    2011-04-01

    Full Text Available This paper presents an improvement to dq-domain method of calculating electromagnetic transients. The proposed methodology works on dq-domain model for all components of the power system and during all time iterations. This is a new direction distinct from the old one where the network is invariably modeled in phase-domain. By modeling the network in dq-domain there is no more problem of interfacing machine to network as usually met in the existing method as machine is modeled invariably in dq-domain. Besides eliminating the time consuming transformation procedure between dq-domain to phase-domain or visa versa the new method is able now to fully exploit the infinite stability region of the trapezoidal rule of integration. The prediction/correction procedure of the conventional dq-domain method, which is notoriously known limiting the stability region, is no longer required. Comparing simulations using the new method and ATP, one of the conventional dq-domain version, show perfect conformity for small time step. For long time step while ATP is failing, the new method still converges accurately up to Nyquist’s interval.

  8. Characterization of recombinantly expressed matrilin VWA domains.

    Science.gov (United States)

    Becker, Ann-Kathrin A; Mikolajek, Halina; Werner, Jörn M; Paulsson, Mats; Wagener, Raimund

    2015-03-01

    VWA domains are the predominant independent folding units within matrilins and mediate protein-protein interactions. Mutations in the matrilin-3 VWA domain cause various skeletal diseases. The analysis of the pathological mechanisms is hampered by the lack of detailed structural information on matrilin VWA domains. Attempts to resolve their structures were hindered by low solubility and a tendency to aggregation. We therefore took a comprehensive approach to improve the recombinant expression of functional matrilin VWA domains to enable X-ray crystallography and nuclear magnetic resonance (NMR) studies. The focus was on expression in Escherichia coli, as this allows incorporation of isotope-labeled amino acids, and on finding conditions that enhance solubility. Indeed, circular dichroism (CD) and NMR measurements indicated a proper folding of the bacterially expressed domains and, interestingly, expression of zebrafish matrilin VWA domains and addition of N-ethylmaleimide yielded the most stable proteins. However, such proteins did still not crystallize and allowed only partial peak assignment in NMR. Moreover, bacterially expressed matrilin VWA domains differ in their solubility and functional properties from the same domains expressed in eukaryotic cells. Structural studies of matrilin VWA domains will depend on the use of eukaryotic expression systems. Copyright © 2014. Published by Elsevier Inc.

  9. Maritime Domain Awareness Architecture Management Hub Strategy

    National Research Council Canada - National Science Library

    2008-01-01

    This document provides an initial high level strategy for carrying out the responsibilities of the national Maritime Domain Awareness Architecture Management Hub to deliver a standards based service...

  10. Trade name and trademark versus domain

    Directory of Open Access Journals (Sweden)

    Jarmila Pokorná

    2013-01-01

    Full Text Available Internet domains have become an integral part of our lives, so one can easily understand that during their use, conflicts can arise, whose participants will search for rules enabling resolution of conflicts. Since the domain name is a replacement of the computer IP address, in the technical sense of the word, this does not concern for domain names a commercial name or brand, because it primarily does not belong to a person in the legal sense of the word and does not serve for its individualization. The average user regularly affiliates domain names with a person offering goods or services on the relevant Website. Domain names used by entrepreneurs in their business activity are often chosen so that the second-level domain (SLD would use words that form the trade name of corporations formed of trading companies. This fact brings domain names close to such designations that serve the individualization of persons or products, especially the trademarks and the commercial name. Domains can come into conflict with the rights to designations, especially trademarks and commercial names. Court practice is resolving these conflicts using rules for unfair competition, or rules for protection of commercial names and trademarks, but it is not ruled out that in the future, special legal regulation of domain names could be established.

  11. On Domain Registries and Website Content

    DEFF Research Database (Denmark)

    Schwemer, Sebastian Felix

    2018-01-01

    such as Internet access service providers, hosting platforms, and websites that link to content. This article shows that in recent years, however, that the (secondary) liability of domain registries and registrars, and more specifically country code top-level domain registries (ccTLDs) for website content, has...... been tested in several EU Member States. The article investigates tendencies in the national lower-court jurisprudence and explores to what extent the liability exemption regime of the E-Commerce Directive applies to domain registries. The analysis concludes that whereas domain registries fall under...

  12. 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.

  13. 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.

  14. Superfast domain walls in KTP single crystals

    Science.gov (United States)

    Shur, V. Ya.; Esin, A. A.; Alam, M. A.; Akhmatkhanov, A. R.

    2017-10-01

    Potassium titanyl phosphate KTiOPO4 (KTP) crystals with periodical ferroelectric domain structures are one of the most promising materials for nonlinear optics, in which the main types of nonlinear optical interactions have been demonstrated. Despite the crucial importance of the in situ visualization of domain structure kinetics for creation of high quality periodical domain gratings, there are only a few works concerning KTP. We present the results of in situ visualization of domain kinetics in KTP with the time resolution down to 12.5 μs and simultaneous recording of the switching current data. The wide range of wall velocities with two orders of magnitude difference was observed for switching in a uniform electric field. The kinetic maps allowed analyzing the spatial distribution of wall motion velocities and classifying the walls by velocity ranges. The distinguished slow, fast, and superfast types of domain walls differed by their orientation. It was shown that the fast and slow domain walls provided the smooth input to the switching current, whereas the short-lived superfast walls resulted in short current peaks. The mobility and the threshold fields for all types of domain walls were estimated. The revealed increase in the wall velocity with deviation from low-index crystallographic planes for slow and fast walls was considered in terms of determined step generation and anisotropic kink motion. The obtained results are important for further development of domain engineering in KTP required for creation of high power, reliable, and effective coherent light sources.

  15. Multiple hypothesis tracking for the cyber domain

    Science.gov (United States)

    Schwoegler, Stefan; Blackman, Sam; Holsopple, Jared; Hirsch, Michael J.

    2011-09-01

    This paper discusses how methods used for conventional multiple hypothesis tracking (MHT) can be extended to domain-agnostic tracking of entities from non-kinematic constraints such as those imposed by cyber attacks in a potentially dense false alarm background. MHT is widely recognized as the premier method to avoid corrupting tracks with spurious data in the kinematic domain but it has not been extensively applied to other problem domains. The traditional approach is to tightly couple track maintenance (prediction, gating, filtering, probabilistic pruning, and target confirmation) with hypothesis management (clustering, incompatibility maintenance, hypothesis formation, and Nassociation pruning). However, by separating the domain specific track maintenance portion from the domain agnostic hypothesis management piece, we can begin to apply the wealth of knowledge gained from ground and air tracking solutions to the cyber (and other) domains. These realizations led to the creation of Raytheon's Multiple Hypothesis Extensible Tracking Architecture (MHETA). In this paper, we showcase MHETA for the cyber domain, plugging in a well established method, CUBRC's INFormation Engine for Real-time Decision making, (INFERD), for the association portion of the MHT. The result is a CyberMHT. We demonstrate the power of MHETA-INFERD using simulated data. Using metrics from both the tracking and cyber domains, we show that while no tracker is perfect, by applying MHETA-INFERD, advanced nonkinematic tracks can be captured in an automated way, perform better than non-MHT approaches, and decrease analyst response time to cyber threats.

  16. Domain 2: Sport Safety and Injury Prevention

    Science.gov (United States)

    Gurchiek, Larry; Mokha, Monique Butcher

    2004-01-01

    Most coaches recognize the importance of creating a safe environment and preventing injuries of their athletes. Domain 2 is dedicated to this important aspect of coaching, and outlines specific areas within safety and injury prevention that coaches should address. Domain 2 sets the standards for facility, equipment, and environmental safety…

  17. High energy transients: The millisecond domain

    Indian Academy of Sciences (India)

    A. R. RAO

    2018-02-09

    Feb 9, 2018 ... The search for high energy transients in the millisecond domain has come to the focus in recent ... ulation of transients in the high energy domain with .... The ATLAS col- laboration reported a object called ATLAS17aeu: a fading optical object from the same general direction as GW170104. This object was ...

  18. Identification of pseudomurein cell wall binding domains.

    Science.gov (United States)

    Steenbakkers, Peter J M; Geerts, Wim J; Ayman-Oz, Nilgün A; Keltjens, Jan T

    2006-12-01

    Methanothermobacter thermautotrophicus is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. Currently, no information is available on extracellular pseudomurein biology and so far only two prophage pseudomurein autolysins, PeiW and PeiP, have been reported. In this paper we show that PeiW and PeiP contain two different N-terminal pseudomurein cell wall binding domains. This finding was used to identify a novel domain, PB007923, on the M. thermautotrophicus genome present in 10 predicted open reading frames. Three homologues were identified in the Methanosphaera stadtmanae genome. Binding studies of fusion constructs of three separate PB007923 domains to green fluorescent protein revealed that it also constituted a cell wall binding domain. Both prophage domains and the PB007923 domain bound to the cell walls of Methanothermobacter species and fluorescence microscopy showed a preference for the septal region. Domain specificities were revealed by binding studies with other pseudomurein-containing archaea. Localized binding was observed for M. stadtmanae and Methanobrevibacter species, while others stained evenly. The identification of the first pseudomurein cell wall binding domains reveals the dynamics of the pseudomurein cell wall and provides marker proteins to study the extracellular pseudomurein biology of M. thermautotrophicus and of other pseudomurein-containing archaea.

  19. Structural principles governing domain motions in proteins

    NARCIS (Netherlands)

    Hayward, S

    1999-01-01

    With the use of a recently developed method, twenty-four proteins for which two or more X-ray conformers are known have been analyzed to reveal structural principles that govern domain motions in proteins. In all 24 cases, the domain motion is a rotation about a physical axis created through local

  20. Port-Based Modeling in Different Domains

    NARCIS (Netherlands)

    Batlle, C.; Couenne, F.; Doria-Cerezo, A.; Fossas, E.; Jallut, C.; Lefevre, L.; Le Gorrec, Y.; Maschke, B.M.; Ortega, R.; Schlacher, K.; Tayakout, M.; Duindam, V.; Macchelli, Alessandro; Stramigioli, Stefano; Bruyninckx, Herman

    2009-01-01

    In this Chapter we present some detailed examples of modelling in several domains using port and port-Hamiltonian concepts, as have been presented in the previous chapters. We start with the electromechanical domain in Sect. 3.1, while in Sect. 3.2 it is shown how port-Hamiltonian systems can be

  1. Genomewide analysis of LATERAL ORGAN BOUNDARIES Domain ...

    Indian Academy of Sciences (India)

    The investigation of transcription factor (TF) families is a major focus of postgenomic research. The plant-specific ASYMMETRIC LEAVES2-LIKE (ASL) / LATERAL ORGAN BOUNDARIES Domain (LBD) proteins constitute a major zincfinger-like-domain transcription factor family, and regulate diverse biological processes in ...

  2. Is the myonuclear domain size fixed?

    NARCIS (Netherlands)

    van der Meer, S.F.T.; Jaspers, R. T.; Degens, H.

    2011-01-01

    It has been suggested that the number of myonuclei in a muscle fibre changes in proportion to the change in fibre size, resulting in a constant myonuclear domain size, defined as the cytoplasmic volume per myonucleus. The myonuclear domain size varies, however, between fibre types and is inversely

  3. Frequency domain image filtering using cuda

    International Nuclear Information System (INIS)

    Rajput, M.A.; Khan, U.A.

    2014-01-01

    In this paper, we investigate the implementation of image filtering in frequency domain using NVIDIA's CUDA (Compute Unified Device Architecture). In contrast to signal and image filtering in spatial domain which uses convolution operations and hence is more compute-intensive for filters having larger spatial extent, the frequency domain filtering uses FFT (Fast Fourier Transform) which is much faster and significantly reduces the computational complexity of the filtering. We implement the frequency domain filtering on CPU and GPU respectively and analyze the speed-up obtained from the CUDA's parallel processing paradigm. In order to demonstrate the efficiency of frequency domain filtering on CUDA, we implement three frequency domain filters, i.e., Butter worth, low-pass and Gaussian for processing different sizes of images on CPU and GPU respectively and perform the GPU vs. CPU benchmarks. The results presented in this paper show that the frequency domain filtering with CUDA achieves significant speed-up over the CPU processing in frequency domain with the same level of (output) image quality on both the processing architectures. (author)

  4. Arrovian Social Choice Theory on Economic Domains

    OpenAIRE

    Le Breton, Michel; Weymark, John A.

    2002-01-01

    This article surveys the literature that investigates the consistency of Arrow's social choice axioms when his unrestricted domain assumptions are replaced by domain conditions that incorporate the restrictions on agendas and preferences encountered in economic environments. Both social welfare functions and social choice correspondences are considered.

  5. XML Based Markup Languages for Specific Domains

    Science.gov (United States)

    Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

    A challenging area in web based support systems is the study of human activities in connection with the web, especially with reference to certain domains. This includes capturing human reasoning in information retrieval, facilitating the exchange of domain-specific knowledge through a common platform and developing tools for the analysis of data on the web from a domain expert's angle. Among the techniques and standards related to such work, we have XML, the eXtensible Markup Language. This serves as a medium of communication for storing and publishing textual, numeric and other forms of data seamlessly. XML tag sets are such that they preserve semantics and simplify the understanding of stored information by users. Often domain-specific markup languages are designed using XML, with a user-centric perspective. Standardization bodies and research communities may extend these to include additional semantics of areas within and related to the domain. This chapter outlines the issues to be considered in developing domain-specific markup languages: the motivation for development, the semantic considerations, the syntactic constraints and other relevant aspects, especially taking into account human factors. Illustrating examples are provided from domains such as Medicine, Finance and Materials Science. Particular emphasis in these examples is on the Materials Markup Language MatML and the semantics of one of its areas, namely, the Heat Treating of Materials. The focus of this chapter, however, is not the design of one particular language but rather the generic issues concerning the development of domain-specific markup languages.

  6. Domain Theory, Its Models and Concepts

    DEFF Research Database (Denmark)

    Andreasen, Mogens Myrup; Howard, Thomas J.; Bruun, Hans Peter Lomholt

    2014-01-01

    Domain Theory is a systems approach for the analysis and synthesis of products. Its basic idea is to view a product as systems of activities, organs and parts and to define structure, elements, behaviour and function in these domains. The theory is a basis for a long line of research contribution...

  7. The different roles of aggrecan interaction domains

    DEFF Research Database (Denmark)

    Aspberg, Anders

    2012-01-01

    glycosaminoglycan chains, that provide the basis for the viscoelastic properties necessary for load distribution over the articular surface. This review is focused on the globular domains of aggrecan and their role in anchoring the proteoglycans to other extracellular matrix components. The N-terminal G1 domain...

  8. UBA domain containing proteins in fission yeast

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Semple, Colin A M; Ponting, Chris P

    2003-01-01

    characterised on both the functional and structural levels. One example of a widespread ubiquitin binding module is the ubiquitin associated (UBA) domain. Here, we discuss the approximately 15 UBA domain containing proteins encoded in the relatively small genome of the fission yeast Schizosaccharomyces pombe...

  9. Genomewide analysis of LATERAL ORGAN BOUNDARIES Domain ...

    Indian Academy of Sciences (India)

    2014-04-23

    Apr 23, 2014 ... finger-like-domain transcription factor family, and regulate diverse biological processes in plants. However, little is ... The expression profiles of the maize LBD genes under normal growth conditions were analysed by microarray data and. qRT-PCR. ... contain a distinct type of DNA-binding domain and tran-.

  10. implementation of spatial domain homomorphic filtering

    African Journals Online (AJOL)

    eobe

    theoretical approach and advantages for digital hardware implementation. The developed filters are implemented .... For the frequency domain transform of the image in the current domain is non-separable due to the multiplicative ... logarithmic transformation can be given in the mathematical form [9] as;. | ( )|. | ( ). ( )|. | ( )|.

  11. Frequency Domain Image Filtering Using CUDA

    Directory of Open Access Journals (Sweden)

    Muhammad Awais Rajput

    2014-10-01

    Full Text Available In this paper, we investigate the implementation of image filtering in frequency domain using NVIDIA?s CUDA (Compute Unified Device Architecture. In contrast to signal and image filtering in spatial domain which uses convolution operations and hence is more compute-intensive for filters having larger spatial extent, the frequency domain filtering uses FFT (Fast Fourier Transform which is much faster and significantly reduces the computational complexity of the filtering. We implement the frequency domain filtering on CPU and GPU respectively and analyze the speed-up obtained from the CUDA?s parallel processing paradigm. In order to demonstrate the efficiency of frequency domain filtering on CUDA, we implement three frequency domain filters, i.e., Butterworth, low-pass and Gaussian for processing different sizes of images on CPU and GPU respectively and perform the GPU vs. CPU benchmarks. The results presented in this paper show that the frequency domain filtering with CUDA achieves significant speed-up over the CPU processing in frequency domain with the same level of (output image quality on both the processing architectures

  12. Database Concepts in a Domain Ontology

    Directory of Open Access Journals (Sweden)

    Gorskis Henrihs

    2017-12-01

    Full Text Available There are multiple approaches for mapping from a domain ontology to a database in the task of ontology-based data access. For that purpose, external mapping documents are most commonly used. These documents describe how the data necessary for the description of ontology individuals and other values, are to be obtained from the database. The present paper investigates the use of special database concepts. These concepts are not separated from the domain ontology; they are mixed with domain concepts to form a combined application ontology. By creating natural relationships between database concepts and domain concepts, mapping can be implemented more easily and with a specific purpose. The paper also investigates how the use of such database concepts in addition to domain concepts impacts ontology building and data retrieval.

  13. Interoperable domain models: the ISO land administration domain model LADM and its external classes

    CSIR Research Space (South Africa)

    Lemmen, CHJ

    2011-09-01

    Full Text Available 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...

  14. Structural domain walls in polar hexagonal manganites

    Science.gov (United States)

    Kumagai, Yu

    2014-03-01

    The domain structure in the multiferroic hexagonal manganites is currently intensely investigated, motivated by the observation of intriguing sixfold topological defects at their meeting points [Choi, T. et al,. Nature Mater. 9, 253 (2010).] and nanoscale electrical conductivity at the domain walls [Wu, W. et al., Phys. Rev. Lett. 108, 077203 (2012).; Meier, D. et al., Nature Mater. 11, 284 (2012).], as well as reports of coupling between ferroelectricity, magnetism and structural antiphase domains [Geng, Y. et al., Nano Lett. 12, 6055 (2012).]. The detailed structure of the domain walls, as well as the origin of such couplings, however, was previously not fully understood. In the present study, we have used first-principles density functional theory to calculate the structure and properties of the low-energy structural domain walls in the hexagonal manganites [Kumagai, Y. and Spaldin, N. A., Nature Commun. 4, 1540 (2013).]. We find that the lowest energy domain walls are atomically sharp, with {210}orientation, explaining the orientation of recently observed stripe domains and suggesting their topological protection [Chae, S. C. et al., Phys. Rev. Lett. 108, 167603 (2012).]. We also explain why ferroelectric domain walls are always simultaneously antiphase walls, propose a mechanism for ferroelectric switching through domain-wall motion, and suggest an atomistic structure for the cores of the sixfold topological defects. This work was supported by ETH Zurich, the European Research Council FP7 Advanced Grants program me (grant number 291151), the JSPS Postdoctoral Fellowships for Research Abroad, and the MEXT Elements Strategy Initiative to Form Core Research Center TIES.

  15. MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain.

    Science.gov (United States)

    Iwaya, Naoko; Takasu, Hirotoshi; Goda, Natsuko; Shirakawa, Masahiro; Tanaka, Toshiki; Hamada, Daizo; Hiroaki, Hidekazu

    2013-05-01

    The microtubule interacting and trafficking (MIT) domain is a small protein module that is conserved in proteins of diverged function, such as Vps4, spastin and sorting nexin 15 (SNX15). The molecular function of the MIT domain is protein-protein interaction, in which the domain recognizes peptides containing MIT-interacting motifs. Recently, we identified an evolutionarily related domain, 'variant' MIT domain at the N-terminal region of the microtubule severing enzyme katanin p60. We found that the domain was responsible for binding to microtubules and Ca(2+). Here, we have examined whether the authentic MIT domains also bind Ca(2+). We found that the loop between the first and second α-helices of the MIT domain binds a Ca(2+) ion. Furthermore, the MIT domains derived from Vps4b and SNX15a showed phosphoinositide-binding activities in a Ca(2+)-dependent manner. We propose that the MIT domain is a novel membrane-associating domain involved in endosomal trafficking.

  16. Evolution of domain promiscuity in eukaryotic genomes—a perspective from the inferred ancestral domain architectures†

    Science.gov (United States)

    Cohen-Gihon, Inbar; Fong, Jessica H.; Sharan, Roded; Nussinov, Ruth

    2012-01-01

    Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution. PMID:21127809

  17. Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures.

    Science.gov (United States)

    Cohen-Gihon, Inbar; Fong, Jessica H; Sharan, Roded; Nussinov, Ruth; Przytycka, Teresa M; Panchenko, Anna R

    2011-03-01

    Most eukaryotic proteins are composed of two or more domains. These assemble in a modular manner to create new proteins usually by the acquisition of one or more domains to an existing protein. Promiscuous domains which are found embedded in a variety of proteins and co-exist with many other domains are of particular interest and were shown to have roles in signaling pathways and mediating network communication. The evolution of domain promiscuity is still an open problem, mostly due to the lack of sequenced ancestral genomes. Here we use inferred domain architectures of ancestral genomes to trace the evolution of domain promiscuity in eukaryotic genomes. We find an increase in average promiscuity along many branches of the eukaryotic tree. Moreover, domain promiscuity can proceed at almost a steady rate over long evolutionary time or exhibit lineage-specific acceleration. We also observe that many signaling and regulatory domains gained domain promiscuity around the Bilateria divergence. In addition we show that those domains that played a role in the creation of two body axes and existed before the divergence of the bilaterians from fungi/metazoan achieve a boost in their promiscuities during the bilaterian evolution.

  18. Insights into function of PSI domains from structure of the Met receptor PSI domain

    International Nuclear Information System (INIS)

    Kozlov, Guennadi; Perreault, Audrey; Schrag, Joseph D.; Park, Morag; Cygler, Miroslaw; Gehring, Kalle; Ekiel, Irena

    2004-01-01

    PSI domains are cysteine-rich modules found in extracellular fragments of hundreds of signaling proteins, including plexins, semaphorins, integrins, and attractins. Here, we report the solution structure of the PSI domain from the human Met receptor, a receptor tyrosine kinase critical for proliferation, motility, and differentiation. The structure represents a cysteine knot with short regions of secondary structure including a three-stranded antiparallel β-sheet and two α-helices. All eight cysteines are involved in disulfide bonds with the pattern consistent with that for the PSI domain from Sema4D. Comparison with the Sema4D structure identifies a structurally conserved core comprising the N-terminal half of the PSI domain. Interestingly, this part links adjacent SEMA and immunoglobulin domains in the Sema4D structure, suggesting that the PSI domain serves as a wedge between propeller and immunoglobulin domains and is responsible for the correct positioning of the ligand-binding site of the receptor

  19. The domain-specific and domain-general relationships of visuospatial working memory to reasoning ability.

    Science.gov (United States)

    Shipstead, Zach; Yonehiro, Jade

    2016-10-01

    The degree to which visuospatial working memory (VSWM) is separable from working memory in general is an open question. On one hand, the construct is often researched as a unitary, domain-specific system. On the other, there is evidence that VWSM shares a common processing component with verbal memory. One might interpret this shared component as domain-general attention. We used confirmatory factor analysis to demonstrate that VSWM shares a domain-general component with verbal memory tasks and has a domain-specific component that is independent of verbal memory. Furthermore, the domain-general component was found to correlate with reasoning ability in both the visuospatial and verbal domains. The domain-specific component only correlated with reasoning ability when the tests had a strong visuospatial component. We argue that theories of VSWM need to place greater emphasis on its multiply determined nature.

  20. Domain Specific Language Support for Exascale

    Energy Technology Data Exchange (ETDEWEB)

    Sadayappan, Ponnuswamy [The Ohio State Univ., Columbus, OH (United States)

    2017-02-24

    Domain-Specific Languages (DSLs) offer an attractive path to Exascale software since they provide expressive power through appropriate abstractions and enable domain-specific optimizations. But the advantages of a DSL compete with the difficulties of implementing a DSL, even for a narrowly defined domain. The DTEC project addresses how a variety of DSLs can be easily implemented to leverage existing compiler analysis and transformation capabilities within the ROSE open source compiler as part of a research program focusing on Exascale challenges. The OSU contributions to the DTEC project are in the area of code generation from high-level DSL descriptions, as well as verification of the automatically-generated code.

  1. 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

  2. Skyrmions from Instantons inside Domain Walls

    International Nuclear Information System (INIS)

    Eto, Minoru; Nitta, Muneto; Ohashi, Keisuke; Tong, David

    2005-01-01

    Some years ago, Atiyah and Manton described a method to construct approximate Skyrmion solutions from Yang-Mills instantons. Here we present a dynamical realization of this construction using domain walls in a five-dimensional gauge theory. The non-Abelian gauge symmetry is broken in each vacuum but restored in the core of the domain wall, allowing instantons to nestle inside the wall. We show that the world volume dynamics of the wall is given by the Skyrme model, including the four-derivative term, and the instantons appear as domain wall Skyrmions

  3. A Phase I Double Blind, Placebo-Controlled, Randomized Study of the Safety and Immunogenicity of an Adjuvanted HIV-1 Gag-Pol-Nef Fusion Protein and Adenovirus 35 Gag-RT-Int-Nef Vaccine in Healthy HIV-Uninfected African Adults.

    Directory of Open Access Journals (Sweden)

    Gloria Omosa-Manyonyi

    Full Text Available Sequential prime-boost or co-administration of HIV vaccine candidates based on an adjuvanted clade B p24, RT, Nef, p17 fusion protein (F4/AS01 plus a non-replicating adenovirus 35 expressing clade A Gag, RT, Int and Nef (Ad35-GRIN may lead to a unique immune profile, inducing both strong T-cell and antibody responses.In a phase 1, double-blind, placebo-controlled trial, 146 healthy adult volunteers were randomized to one of four regimens: heterologous prime-boost with two doses of F4/AS01E or F4/AS01B followed by Ad35-GRIN; Ad35-GRIN followed by two doses of F4/AS01B; or three co-administrations of Ad35-GRIN and F4/AS01B. T cell and antibody responses were measured.The vaccines were generally well-tolerated, and did not cause serious adverse events. The response rate, by IFN-γ ELISPOT, was greater when Ad35-GRIN was the priming vaccine and in the co-administration groups. F4/AS01 induced CD4+ T-cells expressing primarily CD40L and IL2 +/- TNF-α, while Ad35-GRIN induced predominantly CD8+ T-cells expressing IFN-γ +/- IL2 or TNF-α. Viral inhibition was induced after Ad35-GRIN vaccination, regardless of the regimen. Strong F4-specific antibody responses were induced. Immune responses persisted at least a year after the last vaccination. The complementary response profiles, characteristic of each vaccine, were both expressed after co-administration.Co-administration of an adjuvanted protein and an adenovirus vector showed an acceptable safety and reactogenicity profile and resulted in strong, multifunctional and complementary HIV-specific immune responses.ClinicalTrials.gov NCT01264445.

  4. Collaborative Networks for biodiversity domain organizations

    NARCIS (Netherlands)

    Ermilova, E.; Afsarmanesh, H.

    2010-01-01

    European scientific research and development organizations, operating in the domains of biology, ecology, and biodiversity, strongly need to cooperate/collaborate with other centers. Unavailability of interoperation infrastructure as well as the needed collaboration environment among research

  5. Meta-Domains for Automated Model Building

    National Research Council Canada - National Science Library

    Easley, Matthew; Bradley, Elizabeth

    1999-01-01

    .... In particular, we introduce a new structure for automated model building known as a meta-domain which, when instantiated with components, tailors the space of candidate models to the system at hand...

  6. Technique for designing a domain ontology

    OpenAIRE

    Palagin, A. V.; Petrenko, N. G.; Malakhov, K. S.

    2018-01-01

    The article describes the technique for designing a domain ontology, shows the flowchart of algorithm design and example of constructing a fragment of the ontology of the subject area of Computer Science is considered.

  7. Climiate Resilience Screening Index and Domain Scores

    Data.gov (United States)

    U.S. Environmental Protection Agency — CRSI and related-domain scores for all 50 states and 3135 counties in the U.S. This dataset is not publicly accessible because: They are already available within the...

  8. Domain walls and spacetime-filling branes

    NARCIS (Netherlands)

    Bergshoeff, E; Wess, J; Ivanov, EA

    1999-01-01

    We discuss branes with one transversal direction (domain walls) and no transversal direction (spacetime-filling branes). In particular, we briefly discuss a relationship between spacetime-filling branes and superstring theories with sixteen supercharges.

  9. Booted domain wall and charged Kaigorodov space

    International Nuclear Information System (INIS)

    Cai Ronggen

    2003-01-01

    The Kaigorodov space is a homogeneous Einstein space and it describes a pp-wave propagating in anti-de Sitter space. It is conjectured in the literature that M-theory or string theory on the Kaigorodov space times a compact manifold is dual to a conformal field theory in an infinitely-boosted frame with constant momentum density. In this Letter we present a charged generalization of the Kaigorodov space by boosting a non-extremal charged domain wall to the ultrarelativity limit where the boost velocity approaches the speed of light. The finite boost of the domain wall solution gives the charged generalization of the Carter-Novotny-Horsky metric. We study the thermodynamics associated with the charged Carter-Novotny-Horsky space and discuss its relation to that of the static black domain walls and its implications in the domain wall/QFT (quantum field theory) correspondence

  10. 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

  11. Behavioural domain knowledge transfer for autonomous agents

    CSIR Research Space (South Africa)

    Rosman, Benjamin S

    2014-11-01

    Full Text Available , and Behavior Transfer in Autonomous Robots, AAAI 2014 Fall Symposium Series, 13-15 November 2014 Behavioural Domain Knowledge Transfer for Autonomous Agents Benjamin Rosman Mobile Intelligent Autonomous Systems Modelling and Digital Science Council...

  12. Domain knowledge patterns in pedagogical diagnostics

    Science.gov (United States)

    Miarka, Rostislav

    2017-07-01

    This paper shows a proposal of representation of knowledge patterns in RDF(S) language. Knowledge patterns are used for reuse of knowledge. They can be divided into two groups - Top-level knowledge patterns and Domain knowledge patterns. Pedagogical diagnostics is aimed at testing of knowledge of students at primary and secondary school. An example of domain knowledge pattern from pedagogical diagnostics is part of this paper.

  13. Work-domain knowledge in usability evaluation

    DEFF Research Database (Denmark)

    Følstad, Asbjørn; Hornbæk, Kasper

    2010-01-01

    -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...... impact on the software development process. The benefits of the interpretation phases may be explained by the access these provide both to the test participants’ work-domain knowledge and to their experiences as users. ....

  14. A time domain technique for mechanism extraction

    Science.gov (United States)

    Dominek, Allen K.; Peters, Leon, Jr.; Burnside, Walter D.

    1987-01-01

    The properties of scattered fields from a structure can be better evaluated from the characteristics of the individual scatterers. Decomposition techniques can be classified either as a matrix or an integral formulation. With either formulation, aspect pattern of frequency information of a scattering center can be obtained. Emphasis is placed on an integral (time domain) isolation extraction technique to obtain the frequency characteristics of scattering mechanisms. This technique has its origins in the time domain interpretation of scattered fields.

  15. Applying Operational Art in the Space Domain

    Science.gov (United States)

    2010-11-01

    applicable in the space domain. The conclusion reviews the specific application of each attribute of operational art within the space domain and draws ...that are traceable throughout the history of land warfare. Within the last few decades, the concept of operational art has spread outside its...service doctrine manuals all contain definitions of the operational level of war and operational art . These definitions have underlying histories and

  16. Domain Specific Languages for Interactive Web Services

    DEFF Research Database (Denmark)

    Brabrand, Claus

    This dissertation shows how domain specific languages may be applied to the domain of interactive Web services to obtain flexible, safe, and efficient solutions. We show how each of four key aspects of interactive Web services involving sessions, dynamic creation of HTML/XML documents, form field......, , that supports virtually all aspects of the development of interactive Web services and provides flexible, safe, and efficient solutions....

  17. Imaging magnetic domains in Ni nanostructures

    International Nuclear Information System (INIS)

    Asenjo, A.; Jaafar, M.; Gonzalez, E.M.; Martin, J.I.; Vazquez, M.; Vicent, J.L.

    2007-01-01

    The study of nanomagnets is the subject of increasing scientific effort. The size, the thickness and the geometric shape of the elements determine the magnetic properties and then the domain configuration. In this work, we fabricated by electron-beam lithography the three different arrays of Ni nanostructures keeping the size, the thickness and also the distance constant between the elements but varying the geometry: square, triangular and circular. The domain structure of the nanomagnets is studied by magnetic force microscopy

  18. 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

  19. 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.

  20. Image-domain full waveform inversion

    KAUST Repository

    Zhang, Sanzong

    2013-08-20

    The main difficulty with the data-domain full waveform inversion (FWI) is that it tends to get stuck in the local minima associated with the waveform misfit function. This is because the waveform misfit function is highly nonlinear with respect to changes in velocity model. To reduce this nonlinearity, we define the image-domain objective function to minimize the difference of the suboffset-domain common image gathers (CIGs) obtained by migrating the observed data and the calculated data. The derivation shows that the gradient of this new objective function is the combination of the gradient of the conventional FWI and the image-domain differential semblance optimization (DSO). Compared to the conventional FWI, the imagedomain FWI is immune to cycle skipping problems by smearing the nonzero suboffset images along wavepath. It also can avoid the edge effects and the gradient artifacts that are inherent in DSO due to the falsely over-penalized focused images. This is achieved by subtracting the focused image associated with the calculated data from the unfocused image associated with the observed data in the image-domain misfit function. The numerical results of the Marmousi model show that image-domain FWI is less sensitive the initial model than the conventional FWI. © 2013 SEG.

  1. Structured hints : extracting and abstracting domain expertise.

    Energy Technology Data Exchange (ETDEWEB)

    Hereld, M.; Stevens, R.; Sterling, T.; Gao, G. R.; Mathematics and Computer Science; California Inst. of Tech.; Louisiana State Univ.; Univ. of Delaware

    2009-03-16

    We propose a new framework for providing information to help optimize domain-specific application codes. Its design addresses problems that derive from the widening gap between the domain problem statement by domain experts and the architectural details of new and future high-end computing systems. The design is particularly well suited to program execution models that incorporate dynamic adaptive methodologies for live tuning of program performance and resource utilization. This new framework, which we call 'structured hints', couples a vocabulary of annotations to a suite of performance metrics. The immediate target is development of a process by which a domain expert describes characteristics of objects and methods in the application code that would not be readily apparent to the compiler; the domain expert provides further information about what quantities might provide the best indications of desirable effect; and the interactive preprocessor identifies potential opportunities for the domain expert to evaluate. Our development of these ideas is progressing in stages from case study, through manual implementation, to automatic or semi-automatic implementation. In this paper we discuss results from our case study, an examination of a large simulation of a neural network modeled after the neocortex.

  2. Stable charged antiparallel domain walls in hyperferroelectrics

    Science.gov (United States)

    Liu, S.; Cohen, R. E.

    2017-06-01

    Charge-neutral 180° domain walls that separate domains of antiparallel polarization directions are common structural topological defects in ferroelectrics. In normal ferroelectrics, charged 180° domain walls running perpendicular to the polarization directions are highly energetically unfavorable because of the depolarization field and are difficult to stabilize. We explore both neutral and charged 180° domain walls in hyperferroelectrics, a class of proper ferroelectrics with persistent polarization in the presence of a depolarization field, using density functional theory. We obtain zero temperature equilibrium structures of head-to-head and tail-to-tail walls in recently discovered ABC-type hexagonal hyperferroelectrics. Charged domain walls can also be stabilized in canonical ferroelectrics represented by LiNbO3 without any dopants, defects or mechanical clamping. First-principles electronic structure calculations show that charged domain walls can reduce and even close the band gap of host materials and support quasi-two-dimensional electron(hole) gas with enhanced electrical conductivity.

  3. Separating Cognitive and Content Domains in Mathematical Competence

    Science.gov (United States)

    Harks, Birgit; Klieme, Eckhard; Hartig, Johannes; Leiss, Dominik

    2014-01-01

    The present study investigates the empirical separability of mathematical (a) content domains, (b) cognitive domains, and (c) content-specific cognitive domains. There were 122 items representing two content domains (linear equations vs. theorem of Pythagoras) combined with two cognitive domains (modeling competence vs. technical competence)…

  4. A Review of Domain Modelling and Domain Imaging Techniques in Ferroelectric Crystals.

    Science.gov (United States)

    Potnis, Prashant R; Tsou, Nien-Ti; Huber, John E

    2011-02-16

    The present paper reviews models of domain structure in ferroelectric crystals, thin films and bulk materials. Common crystal structures in ferroelectric materials are described and the theory of compatible domain patterns is introduced. Applications to multi-rank laminates are presented. Alternative models employing phase-field and related techniques are reviewed. The paper then presents methods of observing ferroelectric domain structure, including optical, polarized light, scanning electron microscopy, X-ray and neutron diffraction, atomic force microscopy and piezo-force microscopy. Use of more than one technique for unambiguous identification of the domain structure is also described.

  5. A Review of Domain Modelling and Domain Imaging Techniques in Ferroelectric Crystals

    Directory of Open Access Journals (Sweden)

    John E. Huber

    2011-02-01

    Full Text Available The present paper reviews models of domain structure in ferroelectric crystals, thin films and bulk materials. Common crystal structures in ferroelectric materials are described and the theory of compatible domain patterns is introduced. Applications to multi-rank laminates are presented. Alternative models employing phase-field and related techniques are reviewed. The paper then presents methods of observing ferroelectric domain structure, including optical, polarized light, scanning electron microscopy, X-ray and neutron diffraction, atomic force microscopy and piezo-force microscopy. Use of more than one technique for unambiguous identification of the domain structure is also described.

  6. Conversion of Dielectric Data from the Time Domain to the Frequency Domain

    Directory of Open Access Journals (Sweden)

    Vladimir Durman

    2005-01-01

    Full Text Available Polarisation and conduction processes in dielectric systems can be identified by the time domain or the frequency domain measurements. If the systems is a linear one, the results of the time domain measurements can be transformed into the frequency domain, and vice versa. Commonly, the time domain data of the absorption conductivity are transformed into the frequency domain data of the dielectric susceptibility. In practice, the relaxation are mainly evaluated by the frequency domain data. In the time domain, the absorption current measurement were prefered up to now. Recent methods are based on the recovery voltage measurements. In this paper a new method of the recovery data conversion from the time the frequency domain is proposed. The method is based on the analysis of the recovery voltage transient based on the Maxwell equation for the current density in a dielectric. Unlike the previous published solutions, the Laplace fransform was used to derive a formula suitable for practical purposes. the proposed procedure allows also calculating of the insulation resistance and separating the polarisation and conduction losses.

  7. Extracting meronomy relations from domain-specific, textual corporate databases

    NARCIS (Netherlands)

    Ittoo, R.A.; Bouma, G.; Maruster, L.; Wortmann, J.C.; Hopfe, C.J.; Rezgui, Y.; Métais, E.; Preece, A.; Li, H.

    2010-01-01

    Various techniques for learning meronymy relationships from open-domain corpora exist. However, extracting meronymy relationships from domain-specific, textual corporate databases has been overlooked, despite numerous application opportunities particularly in domains like product development and/or

  8. Human-computer interface incorporating personal and application domains

    Science.gov (United States)

    Anderson, Thomas G [Albuquerque, NM

    2011-03-29

    The present invention provides a human-computer interface. The interface includes provision of an application domain, for example corresponding to a three-dimensional application. The user is allowed to navigate and interact with the application domain. The interface also includes a personal domain, offering the user controls and interaction distinct from the application domain. The separation into two domains allows the most suitable interface methods in each: for example, three-dimensional navigation in the application domain, and two- or three-dimensional controls in the personal domain. Transitions between the application domain and the personal domain are under control of the user, and the transition method is substantially independent of the navigation in the application domain. For example, the user can fly through a three-dimensional application domain, and always move to the personal domain by moving a cursor near one extreme of the display.

  9. Wavefield Extrapolation in Pseudo-depth Domain

    KAUST Repository

    Ma, Xuxin

    2011-12-11

    Wave-equation based seismic migration and inversion tools are widely used by the energy industry to explore hydrocarbon and mineral resources. By design, most of these techniques simulate wave propagation in a space domain with the vertical axis being depth measured from the surface. Vertical depth is popular because it is a straightforward mapping of the subsurface space. It is, however, not computationally cost-effective because the wavelength changes with local elastic wave velocity, which in general increases with depth in the Earth. As a result, the sampling per wavelength also increases with depth. To avoid spatial aliasing in deep fast media, the seismic wave is oversampled in shallow slow media and therefore increase the total computation cost. This issue is effectively tackled by using the vertical time axis instead of vertical depth. This is because in a vertical time representation, the "wavelength" is essentially time period for vertical rays. This thesis extends the vertical time axis to the pseudo-depth axis, which features distance unit while preserving the properties of the vertical time representation. To explore the potentials of doing wave-equation based imaging in the pseudo-depth domain, a Partial Differential Equation (PDE) is derived to describe acoustic wave in this new domain. This new PDE is inherently anisotropic because the use of a constant vertical velocity to convert between depth and vertical time. Such anisotropy results in lower reflection coefficients compared with conventional space domain modeling results. This feature is helpful to suppress the low wavenumber artifacts in reverse-time migration images, which are caused by the widely used cross-correlation imaging condition. This thesis illustrates modeling acoustic waves in both conventional space domain and pseudo-depth domain. The numerical tool used to model acoustic waves is built based on the lowrank approximation of Fourier integral operators. To investigate the potential

  10. Changing domains in human capital measurement

    Directory of Open Access Journals (Sweden)

    Pharny D. Chrysler-Fox

    2014-09-01

    Research purpose: The aim of the study was to explore and describe changing domains within human capital management to be managed and measured. Motivation for the study: The motivation was to advance the understanding of changing measurement domains to aid practitioners to manage and measure the contribution of the human resource function and employees, in order to unlock and add value and ultimately contribute to the success of an organisation. Research design, approach and method: Unstructured, in-depth interview data of purposively selected cases from a selected panel of human resource practitioners specialising in human capital measurement was thematically analysed in this exploratory-descriptive investigation. Main findings: Findings suggested that seven domains should be managed and measured. These domains highlight new areas of impact and levels of management. In addition, crossdomain relationships in measurement allow for an understanding of the impact and potential value on which to capitalise. Practical/managerial implications: New domains to manage and measure focus the attention of practitioners beyond the transactional performance management paradigm to a transformational approach to influence the business strategy. Higher education institutions need to develop students’ cognitive skills to facilitate systems thinking. Contribution: This study suggests a new approach to managing and measuring the human capital function and the workforce.

  11. Full traveltime inversion in source domain

    KAUST Repository

    Liu, Lu

    2017-06-01

    This paper presents a new method of source-domain full traveltime inversion (FTI). The objective of this study is automatically building near-surface velocity using the early arrivals of seismic data. This method can generate the inverted velocity that can kinetically best match the reconstructed plane-wave source of early arrivals with true source in source domain. It does not require picking first arrivals for tomography, which is one of the most challenging aspects of ray-based tomographic inversion. Besides, this method does not need estimate the source wavelet, which is a necessity for receiver-domain wave-equation velocity inversion. Furthermore, we applied our method on one synthetic dataset; the results show our method could generate a reasonable background velocity even when shingling first arrivals exist and could provide a good initial velocity for the conventional full waveform inversion (FWI).

  12. Cross domains Arabic named entity recognition system

    KAUST Repository

    Al-Ahmari, S. Saad

    2016-07-11

    Named Entity Recognition (NER) plays an important role in many Natural Language Processing (NLP) applications such as; Information Extraction (IE), Question Answering (QA), Text Clustering, Text Summarization and Word Sense Disambiguation. This paper presents the development and implementation of domain independent system to recognize three types of Arabic named entities. The system works based on a set of domain independent grammar-rules along with Arabic part of speech tagger in addition to gazetteers and lists of trigger words. The experimental results shown, that the system performed as good as other systems with better results in some cases of cross-domains corpora. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.

  13. Anomalous feedback and negative domain wall resistance

    International Nuclear Information System (INIS)

    Cheng, Ran; Xiao, Di; Zhu, Jian-Gang

    2016-01-01

    Magnetic induction can be regarded as a negative feedback effect, where the motive-force opposes the change of magnetic flux that generates the motive-force. In artificial electromagnetics emerging from spintronics, however, this is not necessarily the case. By studying the current-induced domain wall dynamics in a cylindrical nanowire, we show that the spin motive-force exerting on electrons can either oppose or support the applied current that drives the domain wall. The switching into the anomalous feedback regime occurs when the strength of the dissipative torque β is about twice the value of the Gilbert damping constant α . The anomalous feedback manifests as a negative domain wall resistance, which has an analogy with the water turbine. (paper)

  14. Transactions in domain-specific information systems

    Science.gov (United States)

    Zacek, Jaroslav

    2017-07-01

    Substantial number of the current information system (IS) implementations is based on transaction approach. In addition, most of the implementations are domain-specific (e.g. accounting IS, resource planning IS). Therefore, we have to have a generic transaction model to build and verify domain-specific IS. The paper proposes a new transaction model for domain-specific ontologies. This model is based on value oriented business process modelling technique. The transaction model is formalized by the Petri Net theory. First part of the paper presents common business processes and analyses related to business process modeling. Second part defines the transactional model delimited by REA enterprise ontology paradigm and introduces states of the generic transaction model. The generic model proposal is defined and visualized by the Petri Net modelling tool. Third part shows application of the generic transaction model. Last part of the paper concludes results and discusses a practical usability of the generic transaction model.

  15. Domain switching of fatigued ferroelectric thin films

    International Nuclear Information System (INIS)

    Tak Lim, Yun; Yeog Son, Jong; Shin, Young-Han

    2014-01-01

    We investigate the domain wall speed of a ferroelectric PbZr 0.48 Ti 0.52 O 3 (PZT) thin film using an atomic force microscope incorporated with a mercury-probe system to control the degree of electrical fatigue. The depolarization field in the PZT thin film decreases with increasing the degree of electrical fatigue. We find that the wide-range activation field previously reported in ferroelectric domains result from the change of the depolarization field caused by the electrical fatigue. Domain wall speed exhibits universal behavior to the effective electric field (defined by an applied electric field minus the depolarization field), regardless of the degree of the electrical fatigue

  16. Multi-Domain Modeling Based on Modelica

    Directory of Open Access Journals (Sweden)

    Liu Jun

    2016-01-01

    Full Text Available With the application of simulation technology in large-scale and multi-field problems, multi-domain unified modeling become an effective way to solve these problems. This paper introduces several basic methods and advantages of the multidisciplinary model, and focuses on the simulation based on Modelica language. The Modelica/Mworks is a newly developed simulation software with features of an object-oriented and non-casual language for modeling of the large, multi-domain system, which makes the model easier to grasp, develop and maintain.It This article shows the single degree of freedom mechanical vibration system based on Modelica language special connection mechanism in Mworks. This method that multi-domain modeling has simple and feasible, high reusability. it closer to the physical system, and many other advantages.

  17. On thick domain walls in general relativity

    Science.gov (United States)

    Goetz, Guenter; Noetzold, Dirk

    1989-01-01

    Planar scalar field configurations in general relativity differ considerably from those in flat space. It is shown that static domain walls of finite thickness in curved space-time do not possess a reflection symmetry. At infinity, the space-time tends to the Taub vacuum on one side of the wall and to the Minkowski vacuum (Rindler space-time) on the other. Massive test particles are always accelerated towards the Minkowski side, i.e., domain walls are attractive on the Taub side, but repulsive on the Minkowski side (Taub-vacuum cleaner). It is also proved that the pressure in all directions is always negative. Finally, a brief comment is made concerning the possibility of infinite, i.e., bigger than horizon size, domain walls in our universe. All of the results are independent of the form of the potential V(phi) greater than or equal to 0 of the scalar field phi.

  18. 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

  19. Domain Specific Language Support for Exascale

    Energy Technology Data Exchange (ETDEWEB)

    Mellor-Crummey, John [Rice Univ., Houston, TX (United States)

    2017-10-20

    A multi-institutional project known as D-TEC (short for “Domain- specific Technology for Exascale Computing”) set out to explore technologies to support the construction of Domain Specific Languages (DSLs) to map application programs to exascale architectures. DSLs employ automated code transformation to shift the burden of delivering portable performance from application programmers to compilers. Two chief properties contribute: DSLs permit expression at a high level of abstraction so that a programmer’s intent is clear to a compiler and DSL implementations encapsulate human domain-specific optimization knowledge so that a compiler can be smart enough to achieve good results on specific hardware. Domain specificity is what makes these properties possible in a programming language. If leveraging domain specificity is the key to keep exascale software tractable, a corollary is that many different DSLs will be needed to encompass the full range of exascale computing applications; moreover, a single application may well need to use several different DSLs in conjunction. As a result, developing a general toolkit for building domain-specific languages was a key goal for the D-TEC project. Different aspects of the D-TEC research portfolio were the focus of work at each of the partner institutions in the multi-institutional project. D-TEC research and development work at Rice University focused on on three principal topics: understanding how to automate the tuning of code for complex architectures, research and development of the Rosebud DSL engine, and compiler technology to support complex execution platforms. This report provides a summary of the research and development work on the D-TEC project at Rice University.

  20. Domains within domains and walls within walls: Evidence for polar domains in cryogenic SrTiO.sub.3./sub..

    Czech Academy of Sciences Publication Activity Database

    Salje, E.K.H.; Aktas, O.; Carpenter, M.A.; Laguta, Valentyn; Scott, J.F.

    2013-01-01

    Roč. 111, č. 24 (2013), "247603-1"-"247603-5" ISSN 0031-9007 Institutional support: RVO:68378271 Keywords : ferroelectric domains * SrTiO 3 * phase transition Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 7.728, year: 2013

  1. PTEN-PDZ domain interactions: Binding of PTEN to PDZ domains of PTPN13.

    NARCIS (Netherlands)

    Sotelo, N.S.; Schepens, J.T.G.; Valiente, M.; Hendriks, W.J.A.J.; Pulido, R.

    2015-01-01

    Protein modular interactions mediated by PDZ domains are essential for the establishment of functional protein networks controlling diverse cellular functions. The tumor suppressor PTEN possesses a C-terminal PDZ-binding motif (PDZ-BM) that is recognized by a specific set of PDZ domains from

  2. Intellectual Growth in Children as a Function of Domain Specific and Domain General Working Memory Subgroups

    Science.gov (United States)

    Swanson, H. Lee

    2011-01-01

    This study examined whether children's growth on measures of fluid (Raven Colored Progressive Matrices) and crystallized (reading and math achievement) intelligence was attributable to domain-specific or domain-general functions of working memory (WM). A sample of 290 elementary school children was tested on measures of intelligence across three…

  3. Chemical shift assignments of the C-terminal Eps15 homology domain-3 EH domain.

    Science.gov (United States)

    Spagnol, Gaelle; Reiling, Calliste; Kieken, Fabien; Caplan, Steve; Sorgen, Paul L

    2014-10-01

    The C-terminal Eps15 homology (EH) domain 3 (EHD3) belongs to a eukaryotic family of endocytic regulatory proteins and is involved in the recycling of various receptors from the early endosome to the endocytic recycling compartment or in retrograde transport from the endosomes to the Golgi. EH domains are highly conserved in the EHD family and function as protein-protein interaction units that bind to Asn-Pro-Phe (NPF) motif-containing proteins. The EH domain of EHD1 was the first C-terminal EH domain from the EHD family to be solved by NMR. The differences observed between this domain and proteins with N-terminal EH domains helped describe a mechanism for the differential binding of NPF-containing proteins. Here, structural studies were expanded to include the EHD3 EH domain. While the EHD1 and EHD3 EH domains are highly homologous, they have different protein partners. A comparison of these structures will help determine the selectivity in protein binding between the EHD family members and lead to a better understanding of their unique roles in endocytic regulation.

  4. Matter antimatter domains: A possible solution to the CP domain wall problem in the early universe

    Science.gov (United States)

    Mohanty, A. K.; Stecker, F. W.

    1984-01-01

    An SU(5) grand unified theory model is used to show how the degeneracy between vacua with different spontaneously broken charge parity can be dynamically lifted by a condensate of heavy fermion pairs. This drives a phase transition to a unique vacuum state with definite charge parity. The transition eliminates the domain walls in a matter antimatter symmetric domain cosmology.

  5. Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains.

    Science.gov (United States)

    Starmer, Joshua; Magnuson, Terry

    2016-03-24

    Correctly identifying genomic regions enriched with histone modifications and transcription factors is key to understanding their regulatory and developmental roles. Conceptually, these regions are divided into two categories, narrow peaks and broad domains, and different algorithms are used to identify each one. Datasets that span these two categories are often analyzed with a single program for peak calling combined with an ad hoc method for domains. We developed hiddenDomains, which identifies both peaks and domains, and compare it to the leading algorithms using H3K27me3, H3K36me3, GABP, ESR1 and FOXA ChIP-seq datasets. The output from the programs was compared to qPCR-validated enriched and depleted sites, predicted transcription factor binding sites, and highly-transcribed gene bodies. With every method, hiddenDomains, performed as well as, if not better than algorithms dedicated to a specific type of analysis. hiddenDomains performs as well as the best domain and peak calling algorithms, making it ideal for analyzing ChIP-seq datasets, especially those that contain a mixture of peaks and domains.

  6. Magnetic domains the analysis of magnetic microstructures

    CERN Document Server

    Hubert, Alex

    1998-01-01

    The book gives a systematic and comprehensive survey of the complete area of magnetic microstructures. It reaches from micromagnetism of nanoparticles to complex structures of extended magnetic materials. The book starts with a comprehensive evaluation of traditional and modern experimental methods for the observation of magnetic domains and continues with the treatment of important methods for the theoretical analysis of magnetic microcstructures. A survey of the necessary techniques in materials characterization is given. The book offers an observation and analysis of magnetic domains in all

  7. Patient Centric Ontology for Telehealth Domain

    DEFF Research Database (Denmark)

    Jørgensen, Daniel Bjerring; Hallenborg, Kasper; Demazeau, Yves

    2015-01-01

    to the needs, habits, and personality of the patient through user modeling and context awareness. The ontology will be our foundation for user modeling of patients in the telehealth domain, and hence it is one of the initial steps toward our vision. Compared to other ontologies within the domain, ours has...... explicit focus on: 1) personality traits of the patient, which is vital for fulfillment of our vision in term of adaptability, and 2) use of international standards to describe diseases, func-tioning and physiological measurement – ICD, ICF and SNOMED respectively – to promote interoperability...

  8. Vector domain decomposition schemes for parabolic equations

    Science.gov (United States)

    Vabishchevich, P. N.

    2017-09-01

    A new class of domain decomposition schemes for finding approximate solutions of timedependent problems for partial differential equations is proposed and studied. A boundary value problem for a second-order parabolic equation is used as a model problem. The general approach to the construction of domain decomposition schemes is based on partition of unity. Specifically, a vector problem is set up for solving problems in individual subdomains. Stability conditions for vector regionally additive schemes of first- and second-order accuracy are obtained.

  9. Convergence Analysis of a Domain Decomposition Paradigm

    Energy Technology Data Exchange (ETDEWEB)

    Bank, R E; Vassilevski, P S

    2006-06-12

    We describe a domain decomposition algorithm for use in several variants of the parallel adaptive meshing paradigm of Bank and Holst. This algorithm has low communication, makes extensive use of existing sequential solvers, and exploits in several important ways data generated as part of the adaptive meshing paradigm. We show that for an idealized version of the algorithm, the rate of convergence is independent of both the global problem size N and the number of subdomains p used in the domain decomposition partition. Numerical examples illustrate the effectiveness of the procedure.

  10. Clojure for domain-specific languages

    CERN Document Server

    Kelker, Ryan D

    2013-01-01

    An example-oriented approach to develop custom domain-specific languages.If you've already developed a few Clojure applications and wish to expand your knowledge on Clojure or domain-specific languages in general, then this book is for you. If you're an absolute Clojure beginner, then you may only find the detailed examples of the core Clojure components of value. If you've developed DSLs in other languages, this Lisp and Java-based book might surprise you with the power of Clojure.

  11. Predicting detection performance with model observers: Fourier domain or spatial domain?

    Science.gov (United States)

    Chen, Baiyu; Yu, Lifeng; Leng, Shuai; Kofler, James; Favazza, Christopher; Vrieze, Thomas; McCollough, Cynthia

    2016-02-27

    The use of Fourier domain model observer is challenged by iterative reconstruction (IR), because IR algorithms are nonlinear and IR images have noise texture different from that of FBP. A modified Fourier domain model observer, which incorporates nonlinear noise and resolution properties, has been proposed for IR and needs to be validated with human detection performance. On the other hand, the spatial domain model observer is theoretically applicable to IR, but more computationally intensive than the Fourier domain method. The purpose of this study is to compare the modified Fourier domain model observer to the spatial domain model observer with both FBP and IR images, using human detection performance as the gold standard. A phantom with inserts of various low contrast levels and sizes was repeatedly scanned 100 times on a third-generation, dual-source CT scanner at 5 dose levels and reconstructed using FBP and IR algorithms. The human detection performance of the inserts was measured via a 2-alternative-forced-choice (2AFC) test. In addition, two model observer performances were calculated, including a Fourier domain non-prewhitening model observer and a spatial domain channelized Hotelling observer. The performance of these two mode observers was compared in terms of how well they correlated with human observer performance. Our results demonstrated that the spatial domain model observer correlated well with human observers across various dose levels, object contrast levels, and object sizes. The Fourier domain observer correlated well with human observers using FBP images, but overestimated the detection performance using IR images.

  12. Theory of topological edges and domain walls

    NARCIS (Netherlands)

    Bais, F.A.; Slingerland, J.K.; Haaker, S.M.

    2009-01-01

    We investigate domain walls between topologically ordered phases in two spatial dimensions. We present a method which allows for the determination of the superselection sectors of excitations of such walls and which leads to a unified description of the kinematics of a wall and the two phases to

  13. Entanglement versus negative domains of Wigner functions

    DEFF Research Database (Denmark)

    Dahl, Jens Peder; Mack, H.; Wolf, A.

    2006-01-01

    We show that s waves, that is wave functions that only depend on a hyperradius, are entangled if and only if the corresponding Wigner functions exhibit negative domains. We illustrate this feature using a special class of s waves which allows us to perform the calculations analytically. This clas...

  14. Domain walls in single-chain magnets

    Science.gov (United States)

    Pianet, Vivien; Urdampilleta, Matias; Colin, Thierry; Clérac, Rodolphe; Coulon, Claude

    2017-12-01

    The topology and creation energy of domain walls in different magnetic chains (called Single-Chain Magnets or SCMs) are discussed. As these domain walls, that can be seen as "defects", are known to control both static and dynamic properties of these one-dimensional systems, their study and understanding are necessary first steps before a deeper discussion of the SCM properties at finite temperature. The starting point of the paper is the simple regular ferromagnetic chain for which the characteristics of the domain walls are well known. Then two cases will be discussed (i) the "mixed chains" in which isotropic and anisotropic classical spins alternate, and (ii) the so-called "canted chains" where two different easy axis directions are present. In particular, we show that "strictly narrow" domain walls no longer exist in these more complex cases, while a cascade of phase transitions is found for canted chains as the canting angle approaches 45∘. The consequence for thermodynamic properties is briefly discussed in the last part of the paper.

  15. Time Domain Astronomy with Swift and Fermi

    African Journals Online (AJOL)

    J.D. Myers

    Time Domain Astronomy with Swift and Fermi. N. Gehrels1, J. K. Cannizzo23. 1NASA Goddard Space Flight Center, Mail Code 661, Greenbelt, MD 20771, USA. 2CRESST and Astroparticle Physics Laboratory, NASA/GSFC, Greenbelt, MD 20771, USA. 3Department of Physics, University of Maryland, Baltimore County, ...

  16. Towards Public Domain Management of Liberation Movement ...

    African Journals Online (AJOL)

    ... appropriate acquisition for long term public domain management of the liberation movement archives that are currently managed ineffectively by various private archives in the region. The study recommends that such archives, because of their national heritage importance, should be decommissioned from private custody ...

  17. 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.)

  18. Efficient integration method for fictitious domain approaches

    Science.gov (United States)

    Duczek, Sascha; Gabbert, Ulrich

    2015-10-01

    In the current article, we present an efficient and accurate numerical method for the integration of the system matrices in fictitious domain approaches such as the finite cell method (FCM). In the framework of the FCM, the physical domain is embedded in a geometrically larger domain of simple shape which is discretized using a regular Cartesian grid of cells. Therefore, a spacetree-based adaptive quadrature technique is normally deployed to resolve the geometry of the structure. Depending on the complexity of the structure under investigation this method accounts for most of the computational effort. To reduce the computational costs for computing the system matrices an efficient quadrature scheme based on the divergence theorem (Gauß-Ostrogradsky theorem) is proposed. Using this theorem the dimension of the integral is reduced by one, i.e. instead of solving the integral for the whole domain only its contour needs to be considered. In the current paper, we present the general principles of the integration method and its implementation. The results to several two-dimensional benchmark problems highlight its properties. The efficiency of the proposed method is compared to conventional spacetree-based integration techniques.

  19. Ecological Automation Design, Extending Work Domain Analysis

    NARCIS (Netherlands)

    Amelink, M.H.J.

    2010-01-01

    In high–risk domains like aviation, medicine and nuclear power plant control, automation has enabled new capabilities, increased the economy of operation and has greatly contributed to safety. However, automation increases the number of couplings in a system, which can inadvertently lead to more

  20. Ontological Engineering for the Cadastral Domain

    DEFF Research Database (Denmark)

    Stubkjær, Erik; Stuckenschmidt, Heiner

    2000-01-01

    that characterizes established academic disciplines, like geodesy. Many university courses address more application oriented fields, like cadastral law, and spatial planning, and they may benefit from the ontological engineering approach. The paper provides an introduction to the field of ontological engineering...... by means of examples from the cadastral domain....

  1. JavaScript domain-driven design

    CERN Document Server

    Fehre, Philipp

    2015-01-01

    If you are an experienced JavaScript developer who wants to improve the design of his or her applications, or find yourself in a situation to implement an application in an unfamiliar domain, this book is for you. Prior knowledge of JavaScript is required and prior experience with Node.js will also be helpful.

  2. An English language interface for constrained domains

    Science.gov (United States)

    Page, Brenda J.

    1989-01-01

    The Multi-Satellite Operations Control Center (MSOCC) Jargon Interpreter (MJI) demonstrates an English language interface for a constrained domain. A constrained domain is defined as one with a small and well delineated set of actions and objects. The set of actions chosen for the MJI is from the domain of MSOCC Applications Executive (MAE) Systems Test and Operations Language (STOL) directives and contains directives for signing a cathode ray tube (CRT) on or off, calling up or clearing a display page, starting or stopping a procedure, and controlling history recording. The set of objects chosen consists of CRTs, display pages, STOL procedures, and history files. Translation from English sentences to STOL directives is done in two phases. In the first phase, an augmented transition net (ATN) parser and dictionary are used for determining grammatically correct parsings of input sentences. In the second phase, grammatically typed sentences are submitted to a forward-chaining rule-based system for interpretation and translation into equivalent MAE STOL directives. Tests of the MJI show that it is able to translate individual clearly stated sentences into the subset of directives selected for the prototype. This approach to an English language interface may be used for similarly constrained situations by modifying the MJI's dictionary and rules to reflect the change of domain.

  3. Enhanced functional and structural domain assignments using ...

    Indian Academy of Sciences (India)

    The most populated families in MTB are involved in lipid metabolism, entry and survival of the bacillus in host. Interestingly, for 353 proteins, which we refer to as MTB-specific, no homologues have been identified. Numerous, previously unannotated, hypothetical proteins have been assigned domains and some of these ...

  4. Proteome compression via protein domain compositions.

    Science.gov (United States)

    Hayashida, Morihiro; Ruan, Peiying; Akutsu, Tatsuya

    2014-06-01

    In this paper, we study domain compositions of proteins via compression of whole proteins in an organism for the sake of obtaining the entropy that the individual contains. We suppose that a protein is a multiset of domains. Since gene duplication and fusion have occurred through evolutionary processes, the same domains and the same compositions of domains appear in multiple proteins, which enables us to compress a proteome by using references to proteins for duplicated and fused proteins. Such a network with references to at most two proteins is modeled as a directed hypergraph. We propose a heuristic approach by combining the Edmonds algorithm and an integer linear programming, and apply our procedure to 14 proteomes of Dictyostelium discoideum, Escherichia coli, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Oryza sativa, Danio rerio, Xenopus laevis, Gallus gallus, Mus musculus, Pan troglodytes, and Homo sapiens. The compressed size using both of duplication and fusion was smaller than that using only duplication, which suggests the importance of fusion events in evolution of a proteome. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Enhanced functional and structural domain assignments using ...

    Indian Academy of Sciences (India)

    Unknown

    Superfamily relationships between families of unknown and known structures have increased structural in- formation by ~ 11%. Remote similarity detection methods have enabled domain assignments for 1325 'hypo- thetical proteins'. The most populated families in MTB are involved in lipid metabolism, entry and survival of.

  6. Productivity? Domain Complexity vs. Tacit Knowledge

    DEFF Research Database (Denmark)

    Madsen, Erik Skov; Mikkelsen, Lars Lindegaard

    This paper discusses productivity in relation to tacit knowledge (which in the paper is regarded as skills, experiences, competences and attitudes) and domain complexity. The study is based on five very different case studies; three studies are conducted in Den¬mark, China, and the Czech Republic...

  7. Supporting Collaborative Learning in the Architectural Domain

    NARCIS (Netherlands)

    Wolpers, Martin; Memmel, Martin; Giretti, Alberto; Casals, Miquel; Niemann, Katja; Specht, Marcus

    2013-01-01

    Wolpers, M., Memmel, M., Giretti, A., Casals, M., Niemann, K., & Specht, M. (2012). Supporting Collaborative Learning in the Architectural Domain. In A. Okada, T. Connolly, & P. Scott (Eds.), Collaborative Learning 2.0: Open Educational Resources (pp. 328-356). Hershey, PA: Information Science

  8. Domain wall partition functions and KP

    International Nuclear Information System (INIS)

    Foda, O; Wheeler, M; Zuparic, M

    2009-01-01

    We observe that the partition function of the six-vertex model on a finite square lattice with domain wall boundary conditions is (a restriction of) a KP τ function and express it as an expectation value of charged free fermions (up to an overall normalization)

  9. Leptogenesis with left-right domain walls

    Indian Academy of Sciences (India)

    the scale of left-right symmetry breaking. Keywords. Leptogenesis; baryogenesis; domain walls; left-right symmetry. PACS Nos 12.10.Dm; 98.80.Cq; 98.80.Ft. Explaining the observed baryon asymmetry of the Universe within the framework of gauge theories and the standard Big Bang cosmology remains an open problem.

  10. Multi Domain Design: Integration and Reuse

    NARCIS (Netherlands)

    Woestenenk, Krijn; Alvarez Cabrera, Andres A.; Tragter, Hendrik; Tomiyama, Tetsuo; Bonnema, Gerrit Maarten; McAdams, D. Clarkson, J.

    2010-01-01

    Design of mechatronic systems is becoming increasingly complex. Companies must continuously reduce time-to-market while increasing the quality, diversity, and functionality of their products. As a result, more and more specialists from various domains are needed to develop such products. To reduce

  11. Learning domain abstractions for long lived robots

    CSIR Research Space (South Africa)

    Rosman, Benjamin S

    2014-06-01

    Full Text Available . This thesis aims to address the major question: what are the domain invariances which should be learnt by a long lived agent which encounters a range of different tasks? This question can be decomposed into three dimensions for learning invariances, based...

  12. Scalable Domain Decomposed Monte Carlo Particle Transport

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, Matthew Joseph [Univ. of California, Davis, CA (United States)

    2013-12-05

    In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation.

  13. On fictitious domain formulations for Maxwell's equations

    DEFF Research Database (Denmark)

    Dahmen, W.; Jensen, Torben Klint; Urban, K.

    2003-01-01

    We consider fictitious domain-Lagrange multiplier formulations for variational problems in the space H(curl: Omega) derived from Maxwell's equations. Boundary conditions and the divergence constraint are imposed weakly by using Lagrange multipliers. Both the time dependent and time harmonic...

  14. Promoting the Affective Domain within Online Education

    Science.gov (United States)

    Roche, Stephen H.

    2013-01-01

    In the past decade Higher Education Institutions have experienced tremendous growth in enrollments. To meet this demand, many higher education institutions have embraced online education and its requisite technologies. Online education has matured, and studies focusing on the cognitive domain indicate that distance education is as effective as the…

  15. Is It Kingdom or Domains? Confusion & Solutions

    Science.gov (United States)

    Blackwell, Will H.

    2004-01-01

    A confusion regarding the number of kingdoms that should be recognized and the inclusion of domains in the traditional kingdom-based classification found in the higher levels of classification of organisms is presented. Hence, it is important to keep in mind future modifications that may occur in the classification systems and to recognize…

  16. Biology as an Integrating Natural Science Domain

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 3. Biology as an Integrating Natural Science Domain: A Proposal for BSc (Hons) in Integrated Biology. Kambadur Muralidhar. Classroom Volume 13 Issue 3 March 2008 pp 272-276 ...

  17. Single Domain Antibodies as New Biomarker Detectors

    Science.gov (United States)

    Fischer, Katja; Leow, Chiuan Yee; Chuah, Candy; McCarthy, James

    2017-01-01

    Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition of biomarkers, and are widely deployed as analytical tools in clinical settings. For immunodiagnostics, antibodies are now exploited as binders for antigens of interest across a range of platforms. More recently, the discovery of antibody surface display and combinatorial chemistry techniques has allowed the exploration of new binders from a range of animals, for instance variable domains of new antigen receptors (VNAR) from shark and variable heavy chain domains (VHH) or nanobodies from camelids. These single domain antibodies (sdAbs) have some advantages over conventional murine immunoglobulin owing to the lack of a light chain, making them the smallest natural biomarker binders thus far identified. In this review, we will discuss several biomarkers used as a means to validate diseases progress. The potential functionality of modern singe domain antigen binders derived from phylogenetically early animals as new biomarker detectors for current diagnostic and research platforms development will be described. PMID:29039819

  18. Single Domain Antibodies as New Biomarker Detectors

    Directory of Open Access Journals (Sweden)

    Chiuan Herng Leow

    2017-10-01

    Full Text Available Biomarkers are defined as indicators of biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention. Biomarkers have been widely used for early detection, prediction of response after treatment, and for monitoring the progression of diseases. Antibodies represent promising tools for recognition of biomarkers, and are widely deployed as analytical tools in clinical settings. For immunodiagnostics, antibodies are now exploited as binders for antigens of interest across a range of platforms. More recently, the discovery of antibody surface display and combinatorial chemistry techniques has allowed the exploration of new binders from a range of animals, for instance variable domains of new antigen receptors (VNAR from shark and variable heavy chain domains (VHH or nanobodies from camelids. These single domain antibodies (sdAbs have some advantages over conventional murine immunoglobulin owing to the lack of a light chain, making them the smallest natural biomarker binders thus far identified. In this review, we will discuss several biomarkers used as a means to validate diseases progress. The potential functionality of modern singe domain antigen binders derived from phylogenetically early animals as new biomarker detectors for current diagnostic and research platforms development will be described.

  19. Overlapping domain decomposition methods for elliptic quasi ...

    Indian Academy of Sciences (India)

    [10] Lions P L, On the Schwarz alternating method ˙I˙I, Stochastic interpretation and order properties, Domain Decomposition Methods (Los Angeles, California, 1988) (SIAM,. Philadelphia) (1989) pp. 47–70. [11] Perthame B, Some remarks on quasi-variational inequalities and the associated impulsive control problem ...

  20. The Private Legal Governance of Domain Names

    DEFF Research Database (Denmark)

    Schovsbo, Jens Hemmingsen

    2015-01-01

    Abstract This article evaluates the performance of the special private tribunals or panels such as the UDRP which have been developed within complicated systems of self- and co-regulation such as ICANN to decide disputes over domain names. It uses two different dispute resolution models viz...

  1. The Private Legal Governance of Domain Names

    DEFF Research Database (Denmark)

    Schovsbo, Jens Hemmingsen

    2016-01-01

    This chapter evaluates the performance of the special private tribunals or panels such as the UDRP which have been developed within complicated systems of self- and co-regulation such as ICANN to decide disputes over domain names. It uses two different dispute resolution models viz. the UDRP (WIPO...

  2. Software Ecosystems for the Life Sciences Application Domains

    NARCIS (Netherlands)

    Tekinerdogan, B.; Scholten, H.

    2015-01-01

    Software ecosystems (SECOs) are gaining importance in and have been applied to different application domains. In this paper we focus on the needs for SECOs for the life science application domains. Similar to other domains the life science application domains also witnesses the emergence and

  3. Reflective measurement models, behavior domains, and common causes

    NARCIS (Netherlands)

    Markus, K.A.; Borsboom, D.

    Causal theories of measurement view test items as effects of a common cause. Behavior domain theories view test item responses as behaviors sampled from a common domain. A domain score is a composite score over this domain. The question arises whether latent variables can simultaneously constitute

  4. Domain Endurants: An Analysis and Description Process Model

    DEFF Research Database (Denmark)

    Bjørner, Dines

    2014-01-01

    We present a summary, Sect. 2, of a structure of domain analysis and description concepts: techniques and tools. And we link, in Sect. 3, these concepts, embodied in domain analysis prompts and domain description prompts, in a model of how a diligent domain analyser cum describer would use them. ...

  5. Domain adaptation of statistical machine translation with domain-focused web crawling.

    Science.gov (United States)

    Pecina, Pavel; Toral, Antonio; Papavassiliou, Vassilis; Prokopidis, Prokopis; Tamchyna, Aleš; Way, Andy; van Genabith, Josef

    In this paper, we tackle the problem of domain adaptation of statistical machine translation (SMT) by exploiting domain-specific data acquired by domain-focused crawling of text from the World Wide Web. We design and empirically evaluate a procedure for automatic acquisition of monolingual and parallel text and their exploitation for system training, tuning, and testing in a phrase-based SMT framework. We present a strategy for using such resources depending on their availability and quantity supported by results of a large-scale evaluation carried out for the domains of environment and labour legislation, two language pairs (English-French and English-Greek) and in both directions: into and from English. In general, machine translation systems trained and tuned on a general domain perform poorly on specific domains and we show that such systems can be adapted successfully by retuning model parameters using small amounts of parallel in-domain data, and may be further improved by using additional monolingual and parallel training data for adaptation of language and translation models. The average observed improvement in BLEU achieved is substantial at 15.30 points absolute.

  6. Simplicity and Specificity in Language: Domain general biases have domain specific effects

    Directory of Open Access Journals (Sweden)

    Jennifer eCulbertson

    2016-01-01

    Full Text Available The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be specific to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain­-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain­-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in a domain-­specific way.

  7. PTEN-PDZ domain interactions: binding of PTEN to PDZ domains of PTPN13.

    Science.gov (United States)

    Sotelo, Natalia S; Schepens, Jan T G; Valiente, Miguel; Hendriks, Wiljan J A J; Pulido, Rafael

    2015-05-01

    Protein modular interactions mediated by PDZ domains are essential for the establishment of functional protein networks controlling diverse cellular functions. The tumor suppressor PTEN possesses a C-terminal PDZ-binding motif (PDZ-BM) that is recognized by a specific set of PDZ domains from scaffolding and regulatory proteins. Here, we review the current knowledge on PTEN-PDZ domain interactions and tumor suppressor networks, describe methodology suitable to analyze these interactions, and report the binding of PTEN and the PDZ domain-containing protein tyrosine phosphatase PTPN13. Yeast two-hybrid and GST pull-down analyses showed that PTEN binds to PDZ2/PTPN13 domain in a manner that depends on the specific PTPN13 PDZ domain arrangement involving the interdomain region between PDZ1 and PDZ2. Furthermore, a specific binding profile of PTEN to PDZ2/PTPN13 domain was observed by mutational analysis of the PTEN PDZ-BM. Our results disclose a PDZ-mediated physical interaction of PTEN and PTPN13 with potential relevance in tumor suppression and cell homeostasis. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain.

    Science.gov (United States)

    Melcher, Rebecca L J; Neumann, Marten; Fuenzalida Werner, Juan Pablo; Gröhn, Franziska; Moerschbacher, Bruno M

    2017-03-22

    Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction-based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (Genebank TM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 10 5  M -1 ). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential.

  9. Individual globular domains and domain unfolding visualized in overstretched titin molecules with atomic force microscopy.

    Directory of Open Access Journals (Sweden)

    Zsolt Mártonfalvi

    Full Text Available Titin is a giant elastomeric protein responsible for the generation of passive muscle force. Mechanical force unfolds titin's globular domains, but the exact structure of the overstretched titin molecule is not known. Here we analyzed, by using high-resolution atomic force microscopy, the structure of titin molecules overstretched with receding meniscus. The axial contour of the molecules was interrupted by topographical gaps with a mean width of 27.7 nm that corresponds well to the length of an unfolded globular (immunoglobulin and fibronectin domain. The wide gap-width distribution suggests, however, that additional mechanisms such as partial domain unfolding and the unfolding of neighboring domain multimers may also be present. In the folded regions we resolved globules with an average spacing of 5.9 nm, which is consistent with a titin chain composed globular domains with extended interdomain linker regions. Topographical analysis allowed us to allocate the most distal unfolded titin region to the kinase domain, suggesting that this domain systematically unfolds when the molecule is exposed to overstretching forces. The observations support the prediction that upon the action of stretching forces the N-terminal ß-sheet of the titin kinase unfolds, thus exposing the enzyme's ATP-binding site and hence contributing to the molecule's mechanosensory function.

  10. Functional interchangeability of late domains, late domain cofactors and ubiquitin in viral budding.

    Directory of Open Access Journals (Sweden)

    Maria Zhadina

    2010-10-01

    Full Text Available The membrane scission event that separates nascent enveloped virions from host cell membranes often requires the ESCRT pathway, which can be engaged through the action of peptide motifs, termed late (L- domains, in viral proteins. Viral PTAP and YPDL-like L-domains bind directly to the ESCRT-I and ALIX components of the ESCRT pathway, while PPxY motifs bind Nedd4-like, HECT-domain containing, ubiquitin ligases (e.g. WWP1. It has been unclear precisely how ubiquitin ligase recruitment ultimately leads to particle release. Here, using a lysine-free viral Gag protein derived from the prototypic foamy virus (PFV, where attachment of ubiquitin to Gag can be controlled, we show that several different HECT domains can replace the WWP1 HECT domain in chimeric ubiquitin ligases and drive budding. Moreover, artificial recruitment of isolated HECT domains to Gag is sufficient to stimulate budding. Conversely, the HECT domain becomes dispensable if the other domains of WWP1 are directly fused to an ESCRT-1 protein. In each case where budding is driven by a HECT domain, its catalytic activity is essential, but Gag ubiquitination is dispensable, suggesting that ubiquitin ligation to trans-acting proteins drives budding. Paradoxically, however, we also demonstrate that direct fusion of a ubiquitin moiety to the C-terminus of PFV Gag can also promote budding, suggesting that ubiquitination of Gag can substitute for ubiquitination of trans-acting proteins. Depletion of Tsg101 and ALIX inhibits budding that is dependent on ubiquitin that is fused to Gag, or ligated to trans-acting proteins through the action of a PPxY motif. These studies underscore the flexibility in the ways that the ESCRT pathway can be engaged, and suggest a model in which the identity of the protein to which ubiquitin is attached is not critical for subsequent recruitment of ubiquitin-binding components of the ESCRT pathway and viral budding to proceed.

  11. Domain-General and Domain-Specific Patterns of Activity Supporting Metacognition in Human Prefrontal Cortex.

    Science.gov (United States)

    Morales, Jorge; Lau, Hakwan; Fleming, Stephen M

    2018-03-08

    Metacognition is the capacity to evaluate the success of one's own cognitive processes in various domains, e.g. memory and perception. It remains controversial whether metacognition relies on a domain-general resource that is applied to different tasks, or whether self-evaluative processes are domain-specific. Here we directly investigated this issue by examining the neural substrates engaged when metacognitive judgments were made by human participants of both sexes during perceptual and memory tasks matched for stimulus and performance characteristics. By comparing patterns of functional magnetic resonance imaging (fMRI) activity while subjects evaluated their performance, we revealed both domain-specific and domain-general metacognitive representations. Multi-voxel activity patterns in anterior prefrontal cortex predicted levels of confidence in a domain-specific fashion, whereas domain-general signals predicting confidence and accuracy were found in a widespread network in the frontal and posterior midline. The demonstration of domain-specific metacognitive representations suggests the presence of a content-rich mechanism available to introspection and cognitive control. Significance statement: We use human neuroimaging to investigate processes supporting memory and perceptual metacognition. It remains controversial whether metacognition relies on a global resource that is applied to different tasks, or whether self-evaluative processes are specific to particular tasks. Using multivariate decoding methods, we provide evidence that perceptual- and memory-specific metacognitive representations cortex co-exist with generic confidence signals. Our findings reconcile previously conflicting results on the domain-specificity/generality of metacognition, and lay the groundwork for a mechanistic understanding of metacognitive judgments. Copyright © 2018 Morales et al.

  12. Bglbrick strategy for the construction of single domain antibody fusions

    Directory of Open Access Journals (Sweden)

    Ellen R. Goldman

    2017-12-01

    Full Text Available Single domain antibodies, recombinantly expressed variable domains derived from camelid heavy chain antibodies, are often expressed as multimers for detection and therapeutic applications. Constructs in which several single domain antibodies are genetically fused serially, as well as those in which single domain antibodies are genetically linked with domains that naturally form multimers, yield improvement in apparent binding affinity due to avidity. Here, using a single domain antibody that binds envelope protein from the Dengue virus, we demonstrated the construction of single domain antibody dimers using the Bglbrick cloning strategy. Constructing single domain antibodies and multimerization domains as Bglbrick parts enables the easy mixing and matching of parts. The dimeric constructs provided enhanced fluorescent signal in assays for detection of Dengue virus like particles over the monomeric single domain antibody.

  13. A mixed finite element domain decomposition method for nearly elastic wave equations in the frequency domain

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Xiaobing [Univ. of Tennessee, Knoxville, TN (United States)

    1996-12-31

    A non-overlapping domain decomposition iterative method is proposed and analyzed for mixed finite element methods for a sequence of noncoercive elliptic systems with radiation boundary conditions. These differential systems describe the motion of a nearly elastic solid in the frequency domain. The convergence of the iterative procedure is demonstrated and the rate of convergence is derived for the case when the domain is decomposed into subdomains in which each subdomain consists of an individual element associated with the mixed finite elements. The hybridization of mixed finite element methods plays a important role in the construction of the discrete procedure.

  14. Protein subfamily assignment using the Conserved Domain Database

    Directory of Open Access Journals (Sweden)

    Marchler-Bauer Aron

    2008-11-01

    Full Text Available Abstract Background Domains, evolutionarily conserved units of proteins, are widely used to classify protein sequences and infer protein function. Often, two or more overlapping domain models match a region of a protein sequence. Therefore, procedures are required to choose appropriate domain annotations for the protein. Here, we propose a method for assigning NCBI-curated domains from the Curated Domain Database (CDD that takes into account the organization of the domains into hierarchies of homologous domain models. Findings Our analysis of alignment scores from NCBI-curated domain assignments suggests that identifying the correct model among closely related models is more difficult than choosing between non-overlapping domain models. We find that simple heuristics based on sorting scores and domain-specific thresholds are effective at reducing classification error. In fact, in our test set, the heuristics result in almost 90% of current misclassifications due to missing domain subfamilies being replaced by more generic domain assignments, thereby eliminating a significant amount of error within the database. Conclusion Our proposed domain subfamily assignment rule has been incorporated into the CD-Search software for assigning CDD domains to query protein sequences and has significantly improved pre-calculated domain annotations on protein sequences in NCBI's Entrez resource.

  15. Thermal Loss of High-Q Antennas in Time Domain vs. Frequency Domain Solver

    DEFF Research Database (Denmark)

    Bahramzy, Pevand; Pedersen, Gert Frølund

    2014-01-01

    High-Q structures pose great challenges to their loss simulations in Time Domain Solvers (TDS). Therefore, in this work the thermal loss of high-Q antennas is calculated both in TDS and Frequency Domain Solver (FDS), which are then compared with each other and with the actual measurements....... The thermal loss calculation in FDS is shown to be more accurate for high-Q antennas....

  16. Modeling Network Traffic in Wavelet Domain

    Directory of Open Access Journals (Sweden)

    Sheng Ma

    2004-12-01

    Full Text Available This work discovers that although network traffic has the complicated short- and long-range temporal dependence, the corresponding wavelet coefficients are no longer long-range dependent. Therefore, a "short-range" dependent process can be used to model network traffic in the wavelet domain. Both independent and Markov models are investigated. Theoretical analysis shows that the independent wavelet model is sufficiently accurate in terms of the buffer overflow probability for Fractional Gaussian Noise traffic. Any model, which captures additional correlations in the wavelet domain, only improves the performance marginally. The independent wavelet model is then used as a unified approach to model network traffic including VBR MPEG video and Ethernet data. The computational complexity is O(N for developing such wavelet models and generating synthesized traffic of length N, which is among the lowest attained.

  17. Estimation of Poisson noise in spatial domain

    Science.gov (United States)

    Švihlík, Jan; Fliegel, Karel; Vítek, Stanislav; Kukal, Jaromír.; Krbcová, Zuzana

    2017-09-01

    This paper deals with modeling of astronomical images in the spatial domain. We consider astronomical light images contaminated by the dark current which is modeled by Poisson random process. Dark frame image maps the thermally generated charge of the CCD sensor. In this paper, we solve the problem of an addition of two Poisson random variables. At first, the noise analysis of images obtained from the astronomical camera is performed. It allows estimating parameters of the Poisson probability mass functions in every pixel of the acquired dark frame. Then the resulting distributions of the light image can be found. If the distributions of the light image pixels are identified, then the denoising algorithm can be applied. The performance of the Bayesian approach in the spatial domain is compared with the direct approach based on the method of moments and the dark frame subtraction.

  18. Load Estimation by Frequency Domain Decomposition

    DEFF Research Database (Denmark)

    Pedersen, Ivar Chr. Bjerg; Hansen, Søren Mosegaard; Brincker, Rune

    2007-01-01

    by analysis of simulated responses of a 4 DOF system, for which the exact modal parameters are known. This estimation approach entails modal identification of the natural eigenfrequencies, mode shapes and damping ratios by the frequency domain decomposition technique. Scaled mode shapes are determined by use......When performing operational modal analysis the dynamic loading is unknown, however, once the modal properties of the structure have been estimated, the transfer matrix can be obtained, and the loading can be estimated by inverse filtering. In this paper loads in frequency domain are estimated...... of the mass change method. The problem of inverting the often singular or nearly singular transfer function matrix is solved by the singular value decomposition technique using a limited number of singular values. The dependence of the eigenfrequencies on the accuracy of the scaling factors is investigated...

  19. Damping Estimation by Frequency Domain Decomposition

    DEFF Research Database (Denmark)

    Brincker, Rune; Ventura, C. E.; Andersen, P.

    2001-01-01

    In this paper it is explained how the damping can be estimated using the Frequency Domain Decomposition technique for output-only modal identification, i.e. in the case where the modal parameters is to be estimated without knowing the forces exciting the system. Also it is explained how the natural...... back to time domain to identify damping and frequency. The technique is illustrated on a simple simulation case with 2 closely spaced modes. On this example it is illustrated how the identification is influenced by very closely spacing, by non-orthogonal modes, and by correlated input. The technique...... frequencies can be accurately estimated without being limited by the frequency resolution of the discrete Fourier transform. It is explained how the spectral density matrix is decomposed into a set of single degree of freedom systems, and how the individual SDOF auto spectral density functions are transformed...

  20. Temporal Annotation in the Clinical Domain

    Science.gov (United States)

    Styler, William F.; Bethard, Steven; Finan, Sean; Palmer, Martha; Pradhan, Sameer; de Groen, Piet C; Erickson, Brad; Miller, Timothy; Lin, Chen; Savova, Guergana; Pustejovsky, James

    2014-01-01

    This article discusses the requirements of a formal specification for the annotation of temporal information in clinical narratives. We discuss the implementation and extension of ISO-TimeML for annotating a corpus of clinical notes, known as the THYME corpus. To reflect the information task and the heavily inference-based reasoning demands in the domain, a new annotation guideline has been developed, “the THYME Guidelines to ISO-TimeML (THYME-TimeML)”. To clarify what relations merit annotation, we distinguish between linguistically-derived and inferentially-derived temporal orderings in the text. We also apply a top performing TempEval 2013 system against this new resource to measure the difficulty of adapting systems to the clinical domain. The corpus is available to the community and has been proposed for use in a SemEval 2015 task. PMID:29082229

  1. Role of domain in pattern formation.

    Science.gov (United States)

    Seirin-Lee, Sungrim

    2017-06-01

    Pattern formation during development is one of the elegant self-organized phenomena that allow cells to regulate their functions. At all levels, from DNA to a tissue or organ, many developmental processes include the determination of cellular functions through pattern formation. To elucidate the mechanism underlying pattern formation, numerous mathematical models have been developed and applied. However, model simplification has resulted in the role of domains not being seriously considered in pattern formation. Here, we introduce a novel application of the phase-field method for analysis of chromatin dynamics, and a mathematical approach that includes domain information into a biochemical model of pattern formation. Using this new modeling method, here, we consider the role of nuclear and cellular cell shapes on pattern formation. © 2017 Japanese Society of Developmental Biologists.

  2. Parametric time-frequency domain spatial audio

    CERN Document Server

    Delikaris-Manias, Symeon; Politis, Archontis

    2018-01-01

    This book provides readers with the principles and best practices in spatial audio signal processing. It describes how sound fields and their perceptual attributes are captured and analyzed within the time-frequency domain, how essential representation parameters are coded, and how such signals are efficiently reproduced for practical applications. The book is split into four parts starting with an overview of the fundamentals. It then goes on to explain the reproduction of spatial sound before offering an examination of signal-dependent spatial filtering. The book finishes with coverage of both current and future applications and the direction that spatial audio research is heading in. Parametric Time-frequency Domain Spatial Audio focuses on applications in entertainment audio, including music, home cinema, and gaming--covering the capturing and reproduction of spatial sound as well as its generation, transduction, representation, transmission, and perception. This book will teach readers the tools needed...

  3. Multiple Shooting and Time Domain Decomposition Methods

    CERN Document Server

    Geiger, Michael; Körkel, Stefan; Rannacher, Rolf

    2015-01-01

    This book offers a comprehensive collection of the most advanced numerical techniques for the efficient and effective solution of simulation and optimization problems governed by systems of time-dependent differential equations. The contributions present various approaches to time domain decomposition, focusing on multiple shooting and parareal algorithms.  The range of topics covers theoretical analysis of the methods, as well as their algorithmic formulation and guidelines for practical implementation. Selected examples show that the discussed approaches are mandatory for the solution of challenging practical problems. The practicability and efficiency of the presented methods is illustrated by several case studies from fluid dynamics, data compression, image processing and computational biology, giving rise to possible new research topics.  This volume, resulting from the workshop Multiple Shooting and Time Domain Decomposition Methods, held in Heidelberg in May 2013, will be of great interest to applied...

  4. Space Domain Awareness for Manned GEO Servicing

    Science.gov (United States)

    Blake, T.

    2010-09-01

    The Defense Advanced Research Projects Agency (DARPA) is embarking on a joint program to service spacecraft in Geosynchronous (GEO) Orbit. This ambitious program, known as R5 (Rendezvous, Refuel, Refurbish, Repair, and Reposition), will develop the technologies required to extend the life of billions of dollars of invested in building, launching and operating GEO spacecraft. Inherent in the R5 program, is the need for high quality awareness of the space domain at GEO. Servicing non-operational spacecraft in GEO will require enhanced debris detect/track and space weather monitoring for crew safety, as well as high resolution characterization of the spacecraft to understand the status of the spacecraft to manifest the repair mission. This paper will briefly describe the GEO space domain sensor and data processing requirements to support the R5 program and outline DARPA’s program plans to develop these capabilities. Distribution Statement A (Approved for Public Release, Distribution Unlimited). DISTAR case 15410.

  5. Light-Activated Gigahertz Ferroelectric Domain Dynamics

    Science.gov (United States)

    Akamatsu, Hirofumi; Yuan, Yakun; Stoica, Vladimir A.; Stone, Greg; Yang, Tiannan; Hong, Zijian; Lei, Shiming; Zhu, Yi; Haislmaier, Ryan C.; Freeland, John W.; Chen, Long-Qing; Wen, Haidan; Gopalan, Venkatraman

    2018-03-01

    Using time- and spatially resolved hard x-ray diffraction microscopy, the striking structural and electrical dynamics upon optical excitation of a single crystal of BaTiO3 are simultaneously captured on subnanoseconds and nanoscale within individual ferroelectric domains and across walls. A large emergent photoinduced electric field of up to 20 ×106 V /m is discovered in a surface layer of the crystal, which then drives polarization and lattice dynamics that are dramatically distinct in a surface layer versus bulk regions. A dynamical phase-field modeling method is developed that reveals the microscopic origin of these dynamics, leading to gigahertz polarization and elastic waves traveling in the crystal with sonic speeds and spatially varying frequencies. The advances in spatiotemporal imaging and dynamical modeling tools open up opportunities for disentangling ultrafast processes in complex mesoscale structures such as ferroelectric domains.

  6. Novel domain wall dynamics in synthetic antiferromagnets

    Science.gov (United States)

    Yang, See-Hun; Parkin, Stuart

    2017-08-01

    In this article, we review fascinating new mechanisms on recently observed remarkable current driven domain wall motion in nanowires formed from perpendicularly magnetized synthetic antiferromagnets interfaced with heavy metallic layers, sources of spin-orbit torques. All the associated torques such as volumetric adiabatic and non-adiabatic spin-transfer-torque, spin-orbit torques, shape anisotropy field torques, Dzyaloshinkii-Moriya interaction torques and most importantly a new powerful torque, exchange coupling torque, will be discussed based on an analytical model that provides an intuitive description of domain wall dynamics in synthetic ferromagnets as well as synthetic antiferromagnets. In addition, the current driven DW motion in the presence of in-plane fields will be investigated, thus deepening our knowledge about the role of the exchange coupling torque, which will be of potential use for application to various novel spintronic devices.

  7. Inviscid incompressible limits on expanding domains

    Czech Academy of Sciences Publication Activity Database

    Feireisl, Eduard; Nečasová, Šárka; Sun, Y.

    2014-01-01

    Roč. 27, č. 10 (2014), s. 2465-2477 ISSN 0951-7715 R&D Projects: GA ČR GA13-00522S Institutional support: RVO:67985840 Keywords : compressible Navier-Stokes system * large domain * inviscid limit * incompressible limit Subject RIV: BA - General Mathematics Impact factor: 1.208, year: 2014 http://iopscience.iop.org/0951-7715/27/10/2465/

  8. Strategic Leadership Development: An Operation Domain Application

    Science.gov (United States)

    1997-03-01

    effectiveness. The Stratified Systems Theory Model is used to identify skills and attributes for the three leadership domains of Direct, Operation, and...tools they need to help the organization achieve its goals. In discussing leadership , it is important to distinguish between management and leadership ...Peter Drucker and Warren Bennis, two noted authors on leadership , offered the following differentiation: “ Management is doing things right

  9. X-ray interference by nanocrystalline domains.

    Science.gov (United States)

    Gelisio, Luca; Scardi, Paolo

    2012-11-01

    Regular arrangement of nanocrystalline domains can introduce interference effects which alter considerably the powder diffraction pattern. Role of nanocrystal alignment (local texture) and mutual positioning are different, with the latter much more effective in controlling the interference effect. While it is demonstrated that these effects are unlikely to be observed on a conventional laboratory instrument, coherence conditions available at modern synchrotron radiation beamlines might support further investigations of interference in systems made of very fine nanocrystals.

  10. Domain decomposition multigrid for unstructured grids

    Energy Technology Data Exchange (ETDEWEB)

    Shapira, Yair

    1997-01-01

    A two-level preconditioning method for the solution of elliptic boundary value problems using finite element schemes on possibly unstructured meshes is introduced. It is based on a domain decomposition and a Galerkin scheme for the coarse level vertex unknowns. For both the implementation and the analysis, it is not required that the curves of discontinuity in the coefficients of the PDE match the interfaces between subdomains. Generalizations to nonmatching or overlapping grids are made.

  11. 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.

  12. 2015 Cross-Domain Deterrence Seminar Bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Juarez, Anthony [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-02-04

    In November 2015, the Center for Global Security Research, NSO, and Global Security program jointly sponsored a seminar investigating questions related to cross-domain deterrence at Lawrence Livermore National Laboratory. At the seminar, experts were asked to moderate discussion based on the four topics below. For each of these topics, we have compiled a short list of literature that will help analysts develop a baseline understanding of the issue.

  13. Optical Theory Improvements to Space Domain Awareness

    Science.gov (United States)

    2016-09-15

    ability to detect space objects and increase Space Domain Awareness (SDA) with space surveillance sensors through image processing and optical theory . SDA...are several ways to mitigate atmospheric effects. Adaptive Optics (AO) and image restoration are two popular methods. They can be used individually or...corrected for. To correct for remaining errors, additional methods such as image restoration can still be used. In [39, 40], the issue of image processing in

  14. Finite Temperature Qcd With Domain Wall Fermions

    CERN Document Server

    Fleming, G T

    2001-01-01

    Domain wall fermions are a new lattice fermion formulation which preserves the full chiral symmetry of the continuum at finite lattice spacing, up to terms exponentially small in an extra parameter. We discuss the main features of the formulation and its application to study of QCD with two light fermions of equal mass. We also present numerical studies of the two flavor QCD thermodynamics with aT = 1/4.

  15. Domain decomposition methods for hyperbolic problems

    Indian Academy of Sciences (India)

    Here K denotes a generic constant. Combining (2.6) and (2.7) we obtain the result. □. Let Oi be the domain as shown in figure 1, and wi be a continuously differentiable function defined on ¯Oi. Letw be the function defined on ×(0,τ)such that its restriction to. Oi is wi. Then w will, in general, be discontinuous across the lines li ...

  16. Domain decomposition methods for mortar finite elements

    Energy Technology Data Exchange (ETDEWEB)

    Widlund, O.

    1996-12-31

    In the last few years, domain decomposition methods, previously developed and tested for standard finite element methods and elliptic problems, have been extended and modified to work for mortar and other nonconforming finite element methods. A survey will be given of work carried out jointly with Yves Achdou, Mario Casarin, Maksymilian Dryja and Yvon Maday. Results on the p- and h-p-version finite elements will also be discussed.

  17. Broadband Beamspace DOA Estimation: Frequency-Domain and Time-Domain Processing Approaches

    Directory of Open Access Journals (Sweden)

    Yan Shefeng

    2007-01-01

    Full Text Available Frequency-domain and time-domain processing approaches to direction-of-arrival (DOA estimation for multiple broadband far field signals using beamspace preprocessing structures are proposed. The technique is based on constant mainlobe response beamforming. A set of frequency-domain and time-domain beamformers with constant (frequency independent mainlobe response and controlled sidelobes is designed to cover the spatial sector of interest using optimal array pattern synthesis technique and optimal FIR filters design technique. These techniques lead the resulting beampatterns higher mainlobe approximation accuracy and yet lower sidelobes. For the scenario of strong out-of-sector interfering sources, our approaches can form nulls or notches in the direction of them and yet guarantee that the mainlobe response of the beamformers is constant over the design band. Numerical results show that the proposed time-domain processing DOA estimator has comparable performance with the proposed frequency-domain processing method, and that both of them are able to resolve correlated source signals and provide better resolution at lower signal-to-noise ratio (SNR and lower root-mean-square error (RMSE of the DOA estimate compared with the existing method. Our beamspace DOA estimators maintain good DOA estimation and spatial resolution capability in the scenario of strong out-of-sector interfering sources.

  18. Evolution of a protein domain interaction network

    International Nuclear Information System (INIS)

    Li-Feng, Gao; Jian-Jun, Shi; Shan, Guan

    2010-01-01

    In this paper, we attempt to understand complex network evolution from the underlying evolutionary relationship between biological organisms. Firstly, we construct a Pfam domain interaction network for each of the 470 completely sequenced organisms, and therefore each organism is correlated with a specific Pfam domain interaction network; secondly, we infer the evolutionary relationship of these organisms with the nearest neighbour joining method; thirdly, we use the evolutionary relationship between organisms constructed in the second step as the evolutionary course of the Pfam domain interaction network constructed in the first step. This analysis of the evolutionary course shows: (i) there is a conserved sub-network structure in network evolution; in this sub-network, nodes with lower degree prefer to maintain their connectivity invariant, and hubs tend to maintain their role as a hub is attached preferentially to new added nodes; (ii) few nodes are conserved as hubs; most of the other nodes are conserved as one with very low degree; (iii) in the course of network evolution, new nodes are added to the network either individually in most cases or as clusters with relative high clustering coefficients in a very few cases. (general)

  19. Prion-Like Domains in Phagobiota

    Directory of Open Access Journals (Sweden)

    George Tetz

    2017-11-01

    Full Text Available Prions are molecules characterized by self-propagation, which can undergo a conformational switch leading to the creation of new prions. Prion proteins have originally been associated with the development of mammalian pathologies; however, recently they have been shown to contribute to the environmental adaptation in a variety of prokaryotic and eukaryotic organisms. Bacteriophages are widespread and represent the important regulators of microbiota homeostasis and have been shown to be diverse across various bacterial families. Here, we examined whether bacteriophages contain prion-like proteins and whether these prion-like protein domains are involved in the regulation of homeostasis. We used a computational algorithm, prion-like amino acid composition, to detect prion-like domains in 370,617 publicly available bacteriophage protein sequences, which resulted in the identification of 5040 putative prions. We analyzed a set of these prion-like proteins, and observed regularities in their distribution across different phage families, associated with their interactions with the bacterial host cells. We found that prion-like domains could be found across all phages of various groups of bacteria and archaea. The results obtained in this study indicate that bacteriophage prion-like proteins are predominantly involved in the interactions between bacteriophages and bacterial cell, such as those associated with the attachment and penetration of bacteriophage in the cell, and the release of the phage progeny. These data allow the identification of phage prion-like proteins as novel regulators of the interactions between bacteriophages and bacterial cells.

  20. Quality Issues with Public Domain Chemogenomics Data.

    Science.gov (United States)

    Kalliokoski, Tuomo; Kramer, Christian; Vulpetti, Anna

    2013-12-01

    The key concept in chemogenomics is the similarity principle that states that similar ligands should bind similar targets. Chemogenomic analysis requires large amounts of data and both powerful computational algorithms and computers. Data used for chemogenomics analysis can either be compiled from open sources, or they can be produced in-house as is often done in the pharmaceutical industry. The chemogenomic modeller often has to resort to mixing activity values from different laboratories and even assay types to facilitate chemogenomic analysis. The amount of chemogenomics data available in the public domain has dramatically increased in recent years, allowing fully traceable analysis on a continuously increasing scale. However, some warning flags about the data quality have been raised and because the primary data determine the accuracy of chemogenomic analysis, the quality of the data is one of the key questions in chemogenomics. This mini-review discusses some of the most common issues with public domain biological data related to chemogenomic analysis. The errors in data can originate from problems with the experiments themselves and their interpretation, or from more mundane issues such as data extraction and annotation. These issues are not unique for a certain database but are shared by all the public domain databases and can plague commercial and in-house bioactivity databases as well. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Bregmanized Domain Decomposition for Image Restoration

    KAUST Repository

    Langer, Andreas

    2012-05-22

    Computational problems of large-scale data are gaining attention recently due to better hardware and hence, higher dimensionality of images and data sets acquired in applications. In the last couple of years non-smooth minimization problems such as total variation minimization became increasingly important for the solution of these tasks. While being favorable due to the improved enhancement of images compared to smooth imaging approaches, non-smooth minimization problems typically scale badly with the dimension of the data. Hence, for large imaging problems solved by total variation minimization domain decomposition algorithms have been proposed, aiming to split one large problem into N > 1 smaller problems which can be solved on parallel CPUs. The N subproblems constitute constrained minimization problems, where the constraint enforces the support of the minimizer to be the respective subdomain. In this paper we discuss a fast computational algorithm to solve domain decomposition for total variation minimization. In particular, we accelerate the computation of the subproblems by nested Bregman iterations. We propose a Bregmanized Operator Splitting-Split Bregman (BOS-SB) algorithm, which enforces the restriction onto the respective subdomain by a Bregman iteration that is subsequently solved by a Split Bregman strategy. The computational performance of this new approach is discussed for its application to image inpainting and image deblurring. It turns out that the proposed new solution technique is up to three times faster than the iterative algorithm currently used in domain decomposition methods for total variation minimization. © Springer Science+Business Media, LLC 2012.

  2. Domain specific software design for decision aiding

    Science.gov (United States)

    Keller, Kirby; Stanley, Kevin

    1992-01-01

    McDonnell Aircraft Company (MCAIR) is involved in many large multi-discipline design and development efforts of tactical aircraft. These involve a number of design disciplines that must be coordinated to produce an integrated design and a successful product. Our interpretation of a domain specific software design (DSSD) is that of a representation or framework that is specialized to support a limited problem domain. A DSSD is an abstract software design that is shaped by the problem characteristics. This parallels the theme of object-oriented analysis and design of letting the problem model directly drive the design. The DSSD concept extends the notion of software reusability to include representations or frameworks. It supports the entire software life cycle and specifically leads to improved prototyping capability, supports system integration, and promotes reuse of software designs and supporting frameworks. The example presented in this paper is the task network architecture or design which was developed for the MCAIR Pilot's Associate program. The task network concept supported both module development and system integration within the domain of operator decision aiding. It is presented as an instance where a software design exhibited many of the attributes associated with DSSD concept.

  3. A segmental labeling strategy for unambiguous determination of domain–domain interactions of large multi-domain proteins

    International Nuclear Information System (INIS)

    Chen Jianglei; Wang Jianjun

    2011-01-01

    NMR structural determination of large multi-domain proteins is a challenging task due to significant spectral overlap with a particular difficulty in unambiguous identification of domain–domain interactions. Segmental labeling is a NMR strategy that allows for isotopically labeling one domain and leaves the other domain unlabeled. This significantly simplifies spectral overlaps and allows for quick identification of domain–domain interaction. Here, a novel segmental labeling strategy is presented for detection of inter-domain NOEs. To identify domain–domain interactions in human apolipoprotein E (apoE), a multi-domain, 299-residues α-helical protein, on-column expressed protein ligation was utilized to generate a segmental-labeled apoE samples in which the N-terminal (NT-) domain was 2 H(99%)/ 15 N-labeled whereas the C-terminal (CT-) domain was either 15 N- or 15 N/ 13 C-labeled. 3-D 15 N-edited NOESY spectra of these segmental-labeled apoE samples allow for direct observation of the inter-domain NOEs between the backbone amide protons of the NT-domain and the aliphatic protons of the CT-domain. This straightforward approach permits unambiguous identification of 78 inter-domain NOEs, enabling accurate definition of the relative positions of both the NT- and the CT-domains and determination of the NMR structure of apoE.

  4. Fast domain wall dynamics in amorphous and nanocrystalline magnetic microwires

    Energy Technology Data Exchange (ETDEWEB)

    Varga, R., E-mail: rvarga@upjs.sk [Institute of Physics, Faculty of Science, UPJS, Park Angelinum 9, 041 54, Kosice (Slovakia); Klein, P.; Richter, K. [Institute of Physics, Faculty of Science, UPJS, Park Angelinum 9, 041 54, Kosice (Slovakia); Zhukov, A. [Dept. Fisica de Materiales, Fac. Quimica, UPV/EHU, San Sebastian (Spain); Vazquez, M. [Instituto de Ciencia de Materiales de Madrid, CSIC, Sor Juana Ines de la Cruz 3, 28049 Cantoblanco, Madrid (Spain)

    2012-10-15

    We have studied the effect of thermal treatment on the domain wall dynamics of FeSiB and FeCoMoB microwires. It was shown that annealing in transversal magnetic field increases the domain wall mobility as well as the domain wall velocity. Annealing under the tensile stress hinders the appearance of the monodomain structure but application of tensile stress leads to the magnetic bistability having the domain wall mobility twice higher that in as-cast state. Further increase of the tensile stress reduces the domain wall mobility but the domain wall velocity increases as a result of the decrease of critical propagation field. Annealing of the FeCoMoB microwire by Joule heating leads to introduction of the circular anisotropy that favors the vortex domain wall. Such treatment increases the domain wall mobility as well as the maximum domain wall velocity.

  5. SH3 domain tyrosine phosphorylation--sites, role and evolution.

    Directory of Open Access Journals (Sweden)

    Zuzana Tatárová

    Full Text Available BACKGROUND: SH3 domains are eukaryotic protein domains that participate in a plethora of cellular processes including signal transduction, proliferation, and cellular movement. Several studies indicate that tyrosine phosphorylation could play a significant role in the regulation of SH3 domains. RESULTS: To explore the incidence of the tyrosine phosphorylation within SH3 domains we queried the PhosphoSite Plus database of phosphorylation sites. Over 100 tyrosine phosphorylations occurring on 20 different SH3 domain positions were identified. The tyrosine corresponding to c-Src Tyr-90 was by far the most frequently identified SH3 domain phosphorylation site. A comparison of sequences around this tyrosine led to delineation of a preferred sequence motif ALYD(Y/F. This motif is present in about 15% of human SH3 domains and is structurally well conserved. We further observed that tyrosine phosphorylation is more abundant than serine or threonine phosphorylation within SH3 domains and other adaptor domains, such as SH2 or WW domains. Tyrosine phosphorylation could represent an important regulatory mechanism of adaptor domains. CONCLUSIONS: While tyrosine phosphorylation typically promotes signaling protein interactions via SH2 or PTB domains, its role in SH3 domains is the opposite - it blocks or prevents interactions. The regulatory function of tyrosine phosphorylation is most likely achieved by the phosphate moiety and its charge interfering with binding of polyproline helices of SH3 domain interacting partners.

  6. Time Domain Diffraction by Composite Structures

    Science.gov (United States)

    Riccio, Giovanni; Frongillo, Marcello

    2017-04-01

    Time domain (TD) diffraction problems are receiving great attention because of the widespread use of ultra wide band (UWB) communication and radar systems. It is commonly accepted that, due to the large bandwidth of the UWB signals, the analysis of the wave propagation mechanisms in the TD framework is preferable to the frequency domain (FD) data processing. Furthermore, the analysis of transient scattering phenomena is also of importance for predicting the effects of electromagnetic pulses on civil structures. Diffraction in the TD framework represents a challenging problem and numerical discretization techniques can be used to support research and industry activities. Unfortunately, these methods become rapidly intractable when considering excitation pulses with high frequency content. This contribution deals with the TD diffraction phenomenon related to composite structures containing a dielectric wedge with arbitrary apex angle when illuminated by a plane wave. The approach is the same used in [1]-[3]. The transient diffracted field originated by an arbitrary function plane wave is evaluated via a convolution integral involving the TD diffraction coefficients, which are determined in closed form starting from the knowledge of the corresponding FD counterparts. In particular, the inverse Laplace transform is applied to the FD Uniform Asymptotic Physical Optics (FD-UAPO) diffraction coefficients available for the internal region of the structure and the surrounding space. For each observation domain, the FD-UAPO expressions are obtained by considering electric and magnetic equivalent PO surface currents located on the interfaces. The surface radiation integrals using these sources is assumed as starting point and manipulated for obtaining integrals able to be solved by means of the Steepest Descent Method and the Multiplicative Method. [1] G. Gennarelli and G. Riccio, "Time domain diffraction by a right-angled penetrable wedge," IEEE Trans. Antennas Propag., Vol

  7. 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.

  8. Non-local domain switching in ferroelectric nanostructures

    Science.gov (United States)

    Jeong, Seuri; Kim, Kwang-Eun; Yang, Chan-Ho

    Nanoscale ferroic materials have attracted considerable interest due to their novel properties including electronic, electromachanical and magnetoelectric properties. Until now, exotic ferroelectric structures have been described theoretically such as flux-closure domains, but experimental studies for ferroelectric multi-domains in nanostructures have been a lack of research due to their large domain wall energy. In this study, we realized the radial-quadrant domain structures using strain relaxation known as flexoelectricity. Moreover, we observed that local electric polarization switching can affect distant domain regions to minimize free energy. Our findings provide basic concepts to demonstrate and understand ferroelectric nano-scale multi-domain structures.

  9. Domain Walls and Matter-Antimatter Domains in the Early Universe

    Directory of Open Access Journals (Sweden)

    Dolgov A.D.

    2017-01-01

    Full Text Available We suggest a scenario of spontaneous (or dynamical C and CP violation according to which 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 matter and antimatter domains. So this scenario does not suffer from the problem of domain walls. According to this scenario the width of the domain wall should grow exponentially to prevent annihilation at the domain boundaries. Though there is a classical result obtained by Basu and Vilenkin that the width of the wall tends to the one of the stationary solution (constant physical width. That is why we considered thick domain walls in a de Sitter universe following paper by Basu and Vilenkin. However, we were interested not only in stationary solutions found therein, but also investigated the general case of domain wall evolution with time. When the wall thickness parameter, δ0 , is smaller than H−1/2 where H is the Hubble parameter in de Sitter space-time, then the stationary solutions exist, and initial field configurations tend with time to the stationary ones. However, there are no stationary solutions for δ0>H−1/2 We have calculated numerically the rate of the wall expansion in this case and have found that the width of the wall grows exponentially fast for δ0≫H−1 An explanation for the critical value δ0c=H−1/2 is also proposed.

  10. Domain-General Factors Influencing Numerical and Arithmetic Processing

    Directory of Open Access Journals (Sweden)

    André Knops

    2017-12-01

    Full Text Available This special issue contains 18 articles that address the question how numerical processes interact with domain-general factors. We start the editorial with a discussion of how to define domain-general versus domain-specific factors and then discuss the contributions to this special issue grouped into two core numerical domains that are subject to domain-general influences (see Figure 1. The first group of contributions addresses the question how numbers interact with spatial factors. The second group of contributions is concerned with factors that determine and predict arithmetic understanding, performance and development. This special issue shows that domain-general (Table 1a as well as domain-specific (Table 1b abilities influence numerical and arithmetic performance virtually at all levels and make it clear that for the field of numerical cognition a sole focus on one or several domain-specific factors like the approximate number system or spatial-numerical associations is not sufficient. Vice versa, in most studies that included domain-general and domain-specific variables, domain-specific numerical variables predicted arithmetic performance above and beyond domain-general variables. Therefore, a sole focus on domain-general aspects such as, for example, working memory, to explain, predict and foster arithmetic learning is also not sufficient. Based on the articles in this special issue we conclude that both domain-general and domain-specific factors contribute to numerical cognition. But the how, why and when of their contribution still needs to be better understood. We hope that this special issue may be helpful to readers in constraining future theory and model building about the interplay of domain-specific and domain-general factors.

  11. Compassion and professional care: exploring the domain.

    Science.gov (United States)

    van der Cingel, Margreet

    2009-04-01

    Compassion unites people during times of suffering and distress. Unfortunately, compassion cannot take away suffering. Why then, is compassion important for people who suffer? Nurses work in a domain where human suffering is evidently present. In order to give meaning to compassion in the domain of professional care, it is necessary to describe what compassion is. The purpose of this paper is to explore questions and contradictions in the debate on compassion related to nursing care. The paper reviews classical philosophers as well as contemporary scientists' main arguments on compassion. First, I will examine the relationship between compassion and suffering. Second, how does one recognize serious suffering? This issue raises questions about the role of imagination and the need for identification. Third, literature describes compassion as an emotion. Some philosophers consider emotions uncontrollable feelings; others see a clear rational dimension in emotions. In order to determine what compassion is, it is necessary to weigh these contradictional arguments. Fourth, I will discuss motives for compassion. Is compassion an act of altruism or egoism? In this debate Nietzsche and Schopenhauer are well-known opponents. Today, analysis of their arguments leads to some surprising conclusions. Fifth, there is the issue of fault and compassion. Can we only feel compassionate when people who suffer are not to blame for their own suffering? Such a condition faces professional caretakers with a dilemma which needs a thorough analysis if compassion is to be of use in the field of professional care. Finally, I will explore the moral meaning of compassion. Compassion, described as a concept with cognitive as well as affective dimensions, also has volitional and behavioural aspects. These aspects specifically are of importance to nursing care and further research of compassion in the nursing domain.

  12. Landauer's principle in the quantum domain

    Directory of Open Access Journals (Sweden)

    Eric Lutz

    2010-06-01

    Full Text Available Recent papers discussing thermodynamic processes in strongly coupled quantum systems claim a violation of Landauer's principle and imply a violation of the second law of thermodynamics. If true, this would have powerful consequences. Perpetuum mobiles could be build as long as the operating temperature is brought close to zero. It would also have serious consequences on thermodynamic derivations of information theoretic results, such as the Holevo bound. Here we argue why these claims are erroneous. Correlations occurring in the strongly coupled, quantum domain require a rethink of how entropy, heat and work are calculated. It is shown that a consistent treatment solves the paradox.

  13. Topological Luttinger liquids from decorated domain walls

    Science.gov (United States)

    Parker, Daniel E.; Scaffidi, Thomas; Vasseur, Romain

    2018-04-01

    We introduce a systematic construction of a gapless symmetry-protected topological phase in one dimension by "decorating" the domain walls of Luttinger liquids. The resulting strongly interacting phases provide a concrete example of a gapless symmetry-protected topological (gSPT) phase with robust symmetry-protected edge modes. Using boundary conformal field theory arguments, we show that while the bulks of such gSPT phases are identical to conventional Luttinger liquids, their boundary critical behavior is controlled by a different, strongly coupled renormalization group fixed point. Our results are checked against extensive density matrix renormalization group calculations.

  14. Fourier transforms in the complex domain

    CERN Document Server

    Wiener, N

    1934-01-01

    With the aid of Fourier-Mellin transforms as a tool in analysis, the authors were able to attack such diverse analytic questions as those of quasi-analytic functions, Mercer's theorem on summability, Milne's integral equation of radiative equilibrium, the theorems of Münz and Szász concerning the closure of sets of powers of an argument, Titchmarsh's theory of entire functions of semi-exponential type with real negative zeros, trigonometric interpolation and developments in polynomials of the form \\sum^N_1A_ne^{i\\lambda_nx}, lacunary series, generalized harmonic analysis in the complex domain,

  15. Neutron scattering from polarised proton domains

    CERN Document Server

    Van den Brandt, B; Kohbrecher, J; Konter, J A; Mango, S; Glattli, H; Leymarie, E; Grillo, I; May, R P; Jouve, H; Stuhrmann, H B; Stuhrmann, H B; Zimmer, O

    2002-01-01

    Time-dependent small-angle polarised neutron scattering from domains of polarised protons has been observed at the onset of dynamic nuclear polarisation in a frozen solution of 98% deuterated glycerol-water at 1 K containing a small concentration of paramagnetic centres (EHBA-Cr sup V). Simultaneous NMR measurements show that the observed scattering arises from protons around the Cr sup V -ions which are polarised to approx 10% in a few seconds, much faster than the protons in the bulk. (authors)

  16. 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

  17. Dental optical coherence domain reflectometry explorer

    Energy Technology Data Exchange (ETDEWEB)

    Everett, Matthew J. (Livermore, CA); Colston, Jr., Billy W. (Livermore, CA); Sathyam, Ujwal S. (Livermore, CA); Da Silva, Luiz B. (Pleasanton, CA)

    2001-01-01

    A hand-held, fiber optic based dental device with optical coherence domain reflectometry (OCDR) sensing capabilities provides a profile of optical scattering as a function of depth in the tissue at the point where the tip of the dental explorer touches the tissue. This system provides information on the internal structure of the dental tissue, which is then used to detect caries and periodontal disease. A series of profiles of optical scattering or tissue microstructure are generated by moving the explorer across the tooth or other tissue. The profiles are combined to form a cross-sectional, or optical coherence tomography (OCT), image.

  18. Designing Assistive Technologies for the ADHD Domain

    DEFF Research Database (Denmark)

    Sonne, Tobias; Grønbæk, Kaj

    (ADHD). In this paper, we identify a set of challenges that children with ADHD typically experience, which provides an empirical foundation for pervasive health researchers to address the ADHD domain. The work is grounded in extensive empirical studies and it is contextualized using literature on ADHD....... Based on these studies, we also present lessons learned that are relevant to consider when designing assistive technology to support children with ADHD. Finally, we provide an example (CASTT) of our own work to illustrate how the presented findings can frame research activities and be used to develop...... novel assistive technology to empower children with ADHD and improve their wellbeing....

  19. Quantum Image Filtering in the Spatial Domain

    Science.gov (United States)

    Yuan, Suzhen; Mao, Xuefeng; Zhou, Jing; Wang, Xiaofa

    2017-08-01

    Quantum image processing has developed rapidly in recent years. In this paper, we propose a framework of quantum image filtering in the spatial domain. We proved that a high quantum parallel method to correlate the image and the filter mask can be achieved, even though the quantum correlation of two sequences is physically impossible. In order to avoid this impossible, we use quantum addition operation instead of quantum multiplication. We provide the quantum circuit that can realize the filtering task and present several simulation results on grayscale images. The main advantage of the quantum version lies in the efficient correlation between the quantum image and the filter mask.

  20. Domain Wall Evolution in Phase Transforming Oxides

    Science.gov (United States)

    2015-01-14

    Domain wall motion and electric?field?induced strains in NBT ?xBT solid solutions from in situ neutron diffraction,” T.-M. Usher,* J. S. Forrester, E...Morphotropic Phase Boundary of NBT ?BT,” L. M. Denis,* J. Glaum, M. Hoffman, J. Forrester, and J. L. Jones, Electronic Materials and Applications 2013...titanate (PZT) and lead-free compositions Na0.5K0.5NbO3 (NKN) and Na0.5Bi0.5TiO3 ( NBT ). This past year, we reported results on piezoelectric compositions

  1. 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.

  2. Non-slipping domains of a pulled spool

    International Nuclear Information System (INIS)

    Wagner, Clemens; Vaterlaus, Andreas

    2014-01-01

    We have investigated the pulled spool by considering pulling angles up to 360 ∘ . Our focus was on downward pulling forces with pulling angles in the range of 180 ∘ to 360 ∘ . In this range we have found a domain of pulling angles where the spool never starts to slip independent of the strength of the pulling force. The size of the domain depends on the static friction coefficient and on the moment of inertia of the spool. The non-slipping domain is mainly formed around the critical angle where the static friction force becomes zero. For low static friction the non-slipping domain decays into two different domains. We have determined the limiting angles of the non-slipping domains and explored the transitions from a single domain to two separated domains in parameter space. (paper)

  3. Extending the Effective Ranging Depth of Spectral Domain Optical Coherence Tomography by Spatial Frequency Domain Multiplexing

    Directory of Open Access Journals (Sweden)

    Tong Wu

    2016-11-01

    Full Text Available We present a spatial frequency domain multiplexing method for extending the imaging depth range of a spectral domain optical coherence tomography (SDOCT system without any expensive device. This method uses two galvo scanners with different pivot-offset distances in two independent reference arms for spatial frequency modulation and multiplexing. The spatial frequency contents corresponding to different depth regions of the sample can be shifted to different frequency bands. The spatial frequency domain multiplexing SDOCT system provides an approximately 1.9-fold increase in the effective ranging depth compared with that of a conventional full-range SDOCT system. The reconstructed images of phantom and biological tissue demonstrate the expected increase in ranging depth. The parameters choice criterion for this method is discussed.

  4. Single-domain versus two-domain configuration in thin ferromagnetic prisms

    International Nuclear Information System (INIS)

    Pini, Maria Gloria; Politi, Paolo

    2007-01-01

    Thin ferromagnetic elements in the form of rectangular prisms are theoretically investigated in order to study the transition from single-domain to two-domain state, with changing the in-plane aspect ratio p. We address two main questions: first, how general is the transition; second, how the critical value p c depends on the physical parameters. We use two complementary methods: discrete-lattice calculations and a micromagnetic continuum approach. Ultrathin films do not appear to split in two domains. Instead, thicker films may undergo the above transition. We have used the continuum approach to analyze recent magnetic force microscopy observations in 30nm-thick patterned permalloy elements, finding a good agreement for p c

  5. [Characterization of the copy number of RIRE10 retrotransposon and transcriptional activity of its LTR in rice genome].

    Science.gov (United States)

    Wang, Rong; Hong, Guo-Fan; Han, Bin

    2003-08-01

    A full-length Ty3-like retrotransposon, named RIRE10, was identified on the long arm of chromosome 4 in rice genome. The internal region between two LTRs had another open reading frame in the region upstream of gag-pol sequence. The transcripts from LTR region were detected by Northern blot hybridization and RT-PCR. To assess the activity of RIRE10 in rice genome, the copy number of its internal region and long terminal repeat (LTR) domain were determined by dot blot analyses. Nearly 900 solo-LTR of the RIRE10 retrotransposon exist in rice genome, apart from those LTRs that flank 65 intact RIRE retrotransposons. Based on the experimental results, the retrotransposition of RIRE10 was speculated to be influenced by two factors: transcriptional activity of LTR region and homologous recombination resulting in solo-LTR.

  6. Effects of sub-domain structure on initial magnetization curve and domain size distribution of stacked media

    Energy Technology Data Exchange (ETDEWEB)

    Sato, S., E-mail: 231504@gmail.com; Kumagai, S.; Sugita, R.

    2015-03-01

    In this paper, in order to confirm the sub-domain structure in stacked media demagnetized with in-plane field, initial magnetization curves and magnetic domain size distribution were investigated. Both experimental and simulation results showed that an initial magnetization curve for the medium demagnetized with in-plane field (MDI) initially rose faster than that for the medium demagnetized with perpendicular field (MDP). It is inferred that this is because the MDI has a larger number of domain walls than the MDP due to the existence of the sub-domains, resulting in an increase in the probability of domain wall motion. Dispersion of domain size for the MDI was larger than that for the MDP. This is because sub-domains are formed not only inside the domain but also at the domain boundary region, and they change the position of the domain boundary to affect the domain size. - Highlights: • An initial magnetization curve for MDI initially rose faster than that for MDP. • Dispersion of domain size for the MDI was larger than that for the MDP. • Experimental and simulation results can be explained by existence of sub-domains.

  7. Cyberspace at the Operational Level: Warfighting In All Five Domains

    Science.gov (United States)

    2016-05-13

    5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER...connects all four of these domains to the people on our planet ? Cyberspace, the fifth domain of warfare, is now so ubiquitous and that any military...connects all four of these domains to the people on our planet ? Cyberspace, the fifth domain of warfare, is now so ubiquitous that any military commander

  8. Oscillatory domain wall velocity of current-induced domain wall motion

    International Nuclear Information System (INIS)

    Kim, W.J.; Seo, S.M.; Lee, T.D.; Lee, K.J.

    2007-01-01

    We studied the effect of Oersted field (H Oe ) on current-induced domain wall motion (CIDWM) in magnetic nanowires. We found that H Oe generates spin waves. Because of interaction between domain wall (DW) and spin wave, time-dependent wall velocity is oscillatory at the early stage of wall motion. The period of the oscillatory DW motion is in antiphase with the period of out-of-plane (OOP) magnetization oscillation inside the DW. The oscillatory wall velocity is suppressed as the thickness of nanowire decreases because of strong demagnetization field

  9. BAR domain proteins regulate Rho GTPase signaling.

    Science.gov (United States)

    Aspenström, Pontus

    2014-01-01

    BAR proteins comprise a heterogeneous group of multi-domain proteins with diverse biological functions. The common denominator is the Bin-Amphiphysin-Rvs (BAR) domain that not only confers targeting to lipid bilayers, but also provides scaffolding to mold lipid membranes into concave or convex surfaces. This function of BAR proteins is an important determinant in the dynamic reconstruction of membrane vesicles, as well as of the plasma membrane. Several BAR proteins function as linkers between cytoskeletal regulation and membrane dynamics. These links are provided by direct interactions between BAR proteins and actin-nucleation-promoting factors of the Wiskott-Aldrich syndrome protein family and the Diaphanous-related formins. The Rho GTPases are key factors for orchestration of this intricate interplay. This review describes how BAR proteins regulate the activity of Rho GTPases, as well as how Rho GTPases regulate the function of BAR proteins. This mutual collaboration is a central factor in the regulation of vital cellular processes, such as cell migration, cytokinesis, intracellular transport, endocytosis, and exocytosis.

  10. Face recognition in the thermal infrared domain

    Science.gov (United States)

    Kowalski, M.; Grudzień, A.; Palka, N.; Szustakowski, M.

    2017-10-01

    Biometrics refers to unique human characteristics. Each unique characteristic may be used to label and describe individuals and for automatic recognition of a person based on physiological or behavioural properties. One of the most natural and the most popular biometric trait is a face. The most common research methods on face recognition are based on visible light. State-of-the-art face recognition systems operating in the visible light spectrum achieve very high level of recognition accuracy under controlled environmental conditions. Thermal infrared imagery seems to be a promising alternative or complement to visible range imaging due to its relatively high resistance to illumination changes. A thermal infrared image of the human face presents its unique heat-signature and can be used for recognition. The characteristics of thermal images maintain advantages over visible light images, and can be used to improve algorithms of human face recognition in several aspects. Mid-wavelength or far-wavelength infrared also referred to as thermal infrared seems to be promising alternatives. We present the study on 1:1 recognition in thermal infrared domain. The two approaches we are considering are stand-off face verification of non-moving person as well as stop-less face verification on-the-move. The paper presents methodology of our studies and challenges for face recognition systems in the thermal infrared domain.

  11. Architectures for Time-domain Astronomy

    Science.gov (United States)

    Seaman, R.; Allan, A.; Pierfederici, F.; Williams, R.

    2009-09-01

    Wonder at the changing sky predates recorded history. Empirical studies of time-varying celestial phenomena date back to Galileo and Tycho. Telegrams conveying news of transient and recurrent events have been key astronomical infrastructure since the nineteenth century. Recent micro-lensing, supernova and gamma-ray burst studies have lead to a succession of exciting discoveries, but massive new time-domain surveys will soon overwhelm our nineteenth century transient response technologies. Meeting this challenge demands new autonomous architectures for astronomy. These Architectures should reach from proposing new research, through experimental design and the scheduling of telescope operations, to the archiving and pipeline-processing of data to discover new transients, to the publishing of these events, through automated follow-up via robotic and ToO assets, and to the display and analysis of observational results. All will lead to adaptive adjustment of time-domain investigations. The IVOA VOEvent protocol provides an engine for purpose-built astronomical architectures.

  12. Domain general constraints on statistical learning.

    Science.gov (United States)

    Thiessen, Erik D

    2011-01-01

    All theories of language development suggest that learning is constrained. However, theories differ on whether these constraints arise from language-specific processes or have domain-general origins such as the characteristics of human perception and information processing. The current experiments explored constraints on statistical learning of patterns, such as the phonotactic patterns of an infants' native language. Infants in these experiments were presented with a visual analog of a phonotactic learning task used by J. R. Saffran and E. D. Thiessen (2003). Saffran and Thiessen found that infants' phonotactic learning was constrained such that some patterns were learned more easily than other patterns. The current results indicate that infants' learning of visual patterns shows the same constraints as infants' learning of phonotactic patterns. This is consistent with theories suggesting that constraints arise from domain-general sources and, as such, should operate over many kinds of stimuli in addition to linguistic stimuli. © 2011 The Author. Child Development © 2011 Society for Research in Child Development, Inc.

  13. Domain learning naming game for color categorization.

    Science.gov (United States)

    Li, Doujie; Fan, Zhongyan; Tang, Wallace K S

    2017-01-01

    Naming game simulates the evolution of vocabulary in a population of agents. Through pairwise interactions in the games, agents acquire a set of vocabulary in their memory for object naming. The existing model confines to a one-to-one mapping between a name and an object. Focus is usually put onto name consensus in the population rather than knowledge learning in agents, and hence simple learning model is usually adopted. However, the cognition system of human being is much more complex and knowledge is usually presented in a complicated form. Therefore, in this work, we extend the agent learning model and design a new game to incorporate domain learning, which is essential for more complicated form of knowledge. In particular, we demonstrate the evolution of color categorization and naming in a population of agents. We incorporate the human perceptive model into the agents and introduce two new concepts, namely subjective perception and subliminal stimulation, in domain learning. Simulation results show that, even without any supervision or pre-requisition, a consensus of a color naming system can be reached in a population solely via the interactions. Our work confirms the importance of society interactions in color categorization, which is a long debate topic in human cognition. Moreover, our work also demonstrates the possibility of cognitive system development in autonomous intelligent agents.

  14. Magnetic domain formation in monolayer nanoparticle films

    Science.gov (United States)

    Maranville, Brian; Krycka, Kathryn; Borchers, Julie; Hogg, Charles; Majetich, Sara; Ijiri, Yumi

    2009-03-01

    Self-assembled magnetic nanoparticle films offer promise as data storage media, but an understanding of the interactions is missing. Modified Langmuir-Blodgett methods were used to prepare monolayer films of 7 and 11 nm diameter Fe3O4 nanoparticles with large structural domains. Small-angle neutron scattering (SANS) shows a peak at a wavevector Q corresponding to the particle size and spacing, and scattering at intermediate Q indicating possible long-range correlations. We extend to lower Q with off-specular neutron reflectivity, achieving high intensity by sacrificing resolution along one in-plane direction y while retaining high resolution in the other in-plane direction x and the normal direction z. We measure in saturation and zero field to extract magnetic scattering. In high fields, the specular scattering (Qx=0) is increased, consistent with aligned moments. Preliminary results show weak magnetic scattering for nonzero Qx . Since the maximal Qx roughly corresponds to the lowest Q in SANS, the combination of these techniques allows us to quantify field-dependent magnetic domain size.

  15. A Spatial Domain Quantum Watermarking Scheme

    International Nuclear Information System (INIS)

    Wei Zhan-Hong; Chen Xiu-Bo; Niu Xin-Xin; Yang Yi-Xian; Xu Shu-Jiang

    2016-01-01

    This paper presents a spatial domain quantum watermarking scheme. For a quantum watermarking scheme, a feasible quantum circuit is a key to achieve it. This paper gives a feasible quantum circuit for the presented scheme. In order to give the quantum circuit, a new quantum multi-control rotation gate, which can be achieved with quantum basic gates, is designed. With this quantum circuit, our scheme can arbitrarily control the embedding position of watermark images on carrier images with the aid of auxiliary qubits. Besides reversely acting the given quantum circuit, the paper gives another watermark extracting algorithm based on quantum measurements. Moreover, this paper also gives a new quantum image scrambling method and its quantum circuit. Differ from other quantum watermarking schemes, all given quantum circuits can be implemented with basic quantum gates. Moreover, the scheme is a spatial domain watermarking scheme, and is not based on any transform algorithm on quantum images. Meanwhile, it can make sure the watermark be secure even though the watermark has been found. With the given quantum circuit, this paper implements simulation experiments for the presented scheme. The experimental result shows that the scheme does well in the visual quality and the embedding capacity. (paper)

  16. Irregular Homogeneity Domains in Ternary Intermetallic Systems

    Directory of Open Access Journals (Sweden)

    Jean-Marc Joubert

    2015-12-01

    Full Text Available Ternary intermetallic A–B–C systems sometimes have unexpected behaviors. The present paper examines situations in which there is a tendency to simultaneously form the compounds ABx, ACx and BCx with the same crystal structure. This causes irregular shapes of the phase homogeneity domains and, from a structural point of view, a complete reversal of site occupancies for the B atom when crossing the homogeneity domain. This work reviews previous studies done in the systems Fe–Nb–Zr, Hf–Mo–Re, Hf–Re–W, Mo–Re–Zr, Re–W–Zr, Cr–Mn–Si, Cr–Mo–Re, and Mo–Ni–Re, and involving the topologically close-packed Laves, χ and σ phases. These systems have been studied using ternary isothermal section determination, DFT calculations, site occupancy measurement using joint X-ray, and neutron diffraction Rietveld refinement. Conclusions are drawn concerning this phenomenon. The paper also reports new experimental or calculated data on Co–Cr–Re and Fe–Nb–Zr systems.

  17. Natural Language Question Answering in Open Domains

    Directory of Open Access Journals (Sweden)

    Dan Tufis

    2011-10-01

    Full Text Available With the ever-growing volume of information on the web, the traditional search engines, returning hundreds or thousands of documents per query, become more and more demanding on the user patience in satisfying his/her information needs. Question Answering in Open Domains is a top research and development topic in current language technology. Unlike the standard search engines, based on the latest Information Retrieval (IR methods, open domain question-answering systems are expected to deliver not a list of documents that might be relevant for the user's query, but a sentence or a paragraph answering the question asked in natural language. This paper reports on the construction and testing of a Question Answering (QA system which builds on several web services developed at the Research Institute for Artificial Intelligence (ICIA/RACAI. The evaluation of the system has been independently done by the organizers of the ResPubliQA 2009 exercise and has been rated the best performing system with the highest improvement due to the natural language processing technology over a baseline state-of-the-art IR system. The system was trained on a specific corpus, but its functionality is independent on the linguistic register of the training data.

  18. Domain effects and financial risk attitudes.

    Science.gov (United States)

    Vlaev, Ivo; Kusev, Petko; Stewart, Neil; Aldrovandi, Silvio; Chater, Nick

    2010-09-01

    We investigated whether financial risk preferences are dependent on the financial domain (i.e., the context) in which the risky choice options are presented. Previous studies have demonstrated that risk attitudes change when gambles are framed as gains, losses, or as insurance. Our study explores this directly by offering choices between identical gambles, framed in terms of seven financial domains. Three factors were extracted, explaining 68.6% of the variance: Factor 1 (Positive)-opportunity to win, pension provision, and job salary change; Factor 2 (Positive-Complex)-investments and mortgage buying; Factor 3 (Negative)-possibility of loss and insurance. Inspection of the solution revealed context effects on risk perceptions across the seven scenarios. We also found that the commonly accepted assumption that women are more risk averse cannot be confirmed with the context structure suggested in this research; however, it is acknowledged that in the students' population the variance across genders might be considerably less. These results suggest that our financial risk attitude measures may be tapping into a stable aspect of "context dependence" of relevance to real-world decision making. © 2010 Society for Risk Analysis.

  19. Shape Statistics for Random Domains and Particles

    Science.gov (United States)

    Stoyan, Dietrich; Davtyan, Ashot; Turetayev, Daulet

    This paper surveys ideas of statistical analysis of planar images of particles such as powder particles or sand grains, domains such as monolayer domains on water or water droplets on planar surfaces and biological cells or vesicles. For a simple and fast discrimination between collectives of particles, shape ratios or indices such as `area:perimeter' ratio are powerful tools. A more detailed description is possible by means of various functions such as radius-vector function, tangent-angle function and erosion function. A deeper understanding of particle shape and size is possible by studying the relevant physical processes which generate them, such as fracture, abrasion and growth by aggregation. The second part of the paper discusses a particular stochastic model, called Gibbs pixel-particle. It produces two-dimensional connected lattice figures, often called lattice animals, the distribution of which depends on an energy function which is controled by particle area and boundary length and roughness. These pixel-particles vary in a broad spectrum of possible shapes and sizes.

  20. Bulk magnetic domain stability controls paleointensity fidelity

    Science.gov (United States)

    Paterson, Greig A.; Muxworthy, Adrian R.; Yamamoto, Yuhji; Pan, Yongxin

    2017-12-01

    Nonideal, nonsingle-domain magnetic grains are ubiquitous in rocks; however, they can have a detrimental impact on the fidelity of paleomagnetic records—in particular the determination of ancient magnetic field strength (paleointensity), a key means of understanding the evolution of the earliest geodynamo and the formation of the solar system. As a consequence, great effort has been expended to link rock magnetic behavior to paleointensity results, but with little quantitative success. Using the most comprehensive rock magnetic and paleointensity data compilations, we quantify a stability trend in hysteresis data that characterizes the bulk domain stability (BDS) of the magnetic carriers in a paleomagnetic specimen. This trend is evident in both geological and archeological materials that are typically used to obtain paleointensity data and is therefore pervasive throughout most paleomagnetic studies. Comparing this trend to paleointensity data from both laboratory and historical experiments reveals a quantitative relationship between BDS and paleointensity behavior. Specimens that have lower BDS values display higher curvature on the paleointensity analysis plot, which leads to more inaccurate results. In-field quantification of BDS therefore reflects low-field bulk remanence stability. Rapid hysteresis measurements can be used to provide a powerful quantitative method for preselecting paleointensity specimens and postanalyzing previous studies, further improving our ability to select high-fidelity recordings of ancient magnetic fields. BDS analyses will enhance our ability to understand the evolution of the geodynamo and can help in understanding many fundamental Earth and planetary science questions that remain shrouded in controversy.

  1. Selective targeting of epigenetic reader domains.

    Science.gov (United States)

    Greschik, Holger; Schüle, Roland; Günther, Thomas

    2017-05-01

    Epigenetic regulators including writers, erasers, and readers of chromatin marks have been implicated in numerous diseases and are therefore subject of intense academic and pharmaceutical research. While several small-molecule inhibitors targeting writers or erasers are either approved drugs or are currently being evaluated in clinical trials, the targeting of epigenetic readers has lagged behind. Proof-of-principle that epigenetic readers are also relevant drug targets was provided by landmark discoveries of selective inhibitors targeting the BET family of acetyl-lysine readers. More recently, high affinity chemical probes for non-BET acetyl- and methyl-lysine reader domains have also been developed. Areas covered: This article covers recent advances with the identification and validation of inhibitors and chemical probes targeting epigenetic reader domains. Issues related to epigenetic reader druggability, quality requirements for chemical probes, interpretation of cellular action, unexpected cross-talk, and future challenges are also discussed. Expert opinion: Chemical probes provide a powerful means to unravel biological functions of epigenetic readers and evaluate their potential as drug targets. To yield meaningful results, potency, selectivity, and cellular target engagement of chemical probes need to be stringently validated. Future chemical probes will probably need to fulfil additional criteria such as strict target specificity or the targeting of readers within protein complexes.

  2. Entropy based classifier for cross-domain opinion mining

    Directory of Open Access Journals (Sweden)

    Jyoti S. Deshmukh

    2018-01-01

    Full Text Available In recent years, the growth of social network has increased the interest of people in analyzing reviews and opinions for products before they buy them. Consequently, this has given rise to the domain adaptation as a prominent area of research in sentiment analysis. A classifier trained from one domain often gives poor results on data from another domain. Expression of sentiment is different in every domain. The labeling cost of each domain separately is very high as well as time consuming. Therefore, this study has proposed an approach that extracts and classifies opinion words from one domain called source domain and predicts opinion words of another domain called target domain using a semi-supervised approach, which combines modified maximum entropy and bipartite graph clustering. A comparison of opinion classification on reviews on four different product domains is presented. The results demonstrate that the proposed method performs relatively well in comparison to the other methods. Comparison of SentiWordNet of domain-specific and domain-independent words reveals that on an average 72.6% and 88.4% words, respectively, are correctly classified.

  3. Complementation between HIV integrase proteins mutated in different domains

    NARCIS (Netherlands)

    D.C. van Gent (Dik); C. Vink (Cornelis); A.A. Groeneger; R.H. Plassterk

    1993-01-01

    textabstractHIV integrase (IN) cleaves two nucleotides off the 3' end of viral DNA and integrates viral DNA into target DNA. Previously, three functional domains in the HIV IN protein have been identified: (i) the central catalytic domain, (ii) the C-terminal DNA binding domain,

  4. Conception of Learning Outcomes in the Bloom's Taxonomy Affective Domain

    Science.gov (United States)

    Savickiene, Izabela

    2010-01-01

    The article raises a problematic issue regarding an insufficient base of the conception of learning outcomes in the Bloom's taxonomy affective domain. The search for solutions introduces the conception of teaching and learning in the affective domain as well as presents validity criteria of learning outcomes in the affective domain. The…

  5. Identification of structural domains in proteins by a graph heuristic

    NARCIS (Netherlands)

    Wernisch, Lorenz; Hunting, M.M.G.; Wodak, Shoshana J.

    1999-01-01

    A novel automatic procedure for identifying domains from protein atomic coordinates is presented. The procedure, termed STRUDL (STRUctural Domain Limits), does not take into account information on secondary structures and handles any number of domains made up of contiguous or non-contiguous chain

  6. A global reference model of the domain name system

    NARCIS (Netherlands)

    Koc, Y.; Jamakovic, A.; Gijsen, B.M.M.

    2012-01-01

    The domain name system (DNS) is a crucial component of the Internet. At this time, the DNS is facing major changes such as the introduction of DNSSEC and Internationalized Domain Name extensions (IDNs), the adoption of IPv6 and the upcoming extension of new generic top-level domains. These changes

  7. Conserved C-terminal nascent peptide binding domain of HYPK ...

    Indian Academy of Sciences (India)

    2014-07-09

    Jul 9, 2014 ... viability and decreases caspase activities in Huntington's disease (HD) cell culture model. This domain is found to be required ... Huntington's disease (HD), this domain reduces cellular toxicity. We also find that ..... the adaptive functional value conferred by the NPAA domain of. HYPK is quite higher in case ...

  8. Recognition specificity of individual EH domains of mammals and yeast

    DEFF Research Database (Denmark)

    Paoluzi, S; Castagnoli, L; Lauro, I

    1998-01-01

    /SF) motif. Domains that have a low affinity for the majority of NPF peptides reveal some affinity for a third class of peptides that contains two consecutive amino acids with aromatic side chains (FW or WW). This is the case for the third EH domain of Eps15 and for the two N-terminal domains of YBL47c...

  9. Estimation for small domains in double sampling for stratification ...

    African Journals Online (AJOL)

    In this article, we investigate the effect of randomness of the size of a small domain on the precision of an estimator of mean for the domain under double sampling for stratification. The result shows that for a small domain that cuts across various strata with unknown weights, the sampling variance depends on the within ...

  10. Serine phosphorylation of syndecan-2 proteoglycan cytoplasmic domain

    DEFF Research Database (Denmark)

    Oh, E S; Couchman, J R; Woods, A

    1997-01-01

    sequence. We investigated phosphorylation of syndecan-2 cytoplasmic domain by PKC, using purified GST-syndecan-2 fusion proteins and synthetic peptides corresponding to regions of the cytoplasmic domain. A synthetic peptide encompassing the entire cytoplasmic domain of syndecan-2 was phosphorylated by PKC...

  11. Changing Your Domain Name in 25 Nail-Biting Steps

    Science.gov (United States)

    Hassler, Carol

    2012-01-01

    When staff at the Wisconsin State Law Library began compiling a wish list for a new website, the topic of a new domain name came up almost immediately. Their old website was located at http://wsll.state.wi.us. Spelling that relatively complex domain over the phone day after day provided the impetus to explore other options. Whatever domain name…

  12. The role of domain analysis in prediction instrument development

    NARCIS (Netherlands)

    van der Spoel, Sjoerd; Amrit, Chintan Amrit; van Hillegersberg, Jos

    2016-01-01

    In order to develop prediction instruments that have sufficient predictive power, it is essential to understand the specific domain the prediction instrument is developed for. This domain analysis is especially important for domains where human behavior, politics, or other soft factors play a role.

  13. Domain Specificity between Peer Support and Self-Concept

    Science.gov (United States)

    Leung, Kim Chau; Marsh, Herbert W.; Craven, Rhonda G.; Yeung, Alexander S.; Abduljabbar, Adel S.

    2013-01-01

    Peer support interventions have mostly neglected the domain specificity of intervention effects. In two studies, the present investigation examined the domain specificity of peer support interventions targeting specific domains of self-concept. In Study 1, participants ("n" = 50) who had received an academically oriented peer support…

  14. Segmental, Domain-Selective Perdeuteration and Small-Angle Neutron Scattering for Structural Analysis of Multi-Domain Proteins.

    Science.gov (United States)

    Sonntag, Miriam; Jagtap, Pravin Kumar Ankush; Simon, Bernd; Appavou, Marie-Sousai; Geerlof, Arie; Stehle, Ralf; Gabel, Frank; Hennig, Janosch; Sattler, Michael

    2017-08-01

    Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic rearrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi-domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA-1 using Sortase A mediated protein ligation. We show that domain-selective perdeuteration combined with contrast-matched small-angle neutron scattering (SANS), SAXS and computational modeling provides valuable information to precisely define relative domain arrangements. The approach is generally applicable to study conformational arrangements of individual domains in multi-domain proteins and changes induced by ligand binding. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. A Highly Accurate Regular Domain Collocation Method for Solving Potential Problems in the Irregular Doubly Connected Domains

    Directory of Open Access Journals (Sweden)

    Zhao-Qing Wang

    2014-01-01

    Full Text Available Embedding the irregular doubly connected domain into an annular regular region, the unknown functions can be approximated by the barycentric Lagrange interpolation in the regular region. A highly accurate regular domain collocation method is proposed for solving potential problems on the irregular doubly connected domain in polar coordinate system. The formulations of regular domain collocation method are constructed by using barycentric Lagrange interpolation collocation method on the regular domain in polar coordinate system. The boundary conditions are discretized by barycentric Lagrange interpolation within the regular domain. An additional method is used to impose the boundary conditions. The least square method can be used to solve the overconstrained equations. The function values of points in the irregular doubly connected domain can be calculated by barycentric Lagrange interpolation within the regular domain. Some numerical examples demonstrate the effectiveness and accuracy of the presented method.

  16. Applying Frequency-Domain Equalization to Code-Division Multiple Access and Transform-Domain Communications Systems

    Science.gov (United States)

    2008-03-01

    DMT Discrete Multitone . . . . . . . . . . . . . . . . . . . . . . 1 FEQ Frequency-Domain Equalizer . . . . . . . . . . . . . . . . 1 ADSL Asymmetric...asymmetric digital subscriber line ( ADSL ) equal- ization techniques in order to decrease the latency effects of equalization in the time- domain [20–22

  17. Crystal structure of the Ig1 domain of the neural cell adhesion molecule NCAM2 displays domain swapping

    DEFF Research Database (Denmark)

    Rasmussen, Kim Krighaar; Kulahin, Nikolaj; Kristensen, Ole

    2008-01-01

    The crystal structure of the first immunoglobulin (Ig1) domain of neural cell adhesion molecule 2 (NCAM2/OCAM/RNCAM) is presented at a resolution of 2.7 A. NCAM2 is a member of the immunoglobulin superfamily of cell adhesion molecules (IgCAMs). In the structure, two Ig domains interact by domain...

  18. Single-domain epitaxial silicene on diboride thin films

    Energy Technology Data Exchange (ETDEWEB)

    Fleurence, A., E-mail: antoine@jaist.ac.jp; Friedlein, R.; Aoyagi, K.; Yamada-Takamura, Y. [School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292 (Japan); Gill, T. G. [School of Materials Science, Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa 923-1292 (Japan); London Centre for Nanotechnology, University College London (UCL), London WC1H 0AH (United Kingdom); Department of Chemistry, UCL, London WC1H 0AJ (United Kingdom); Sadowski, J. T. [Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973 (United States); Copel, M.; Tromp, R. M. [IBM Research Division, Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Hirjibehedin, C. F. [London Centre for Nanotechnology, University College London (UCL), London WC1H 0AH (United Kingdom); Department of Chemistry, UCL, London WC1H 0AJ (United Kingdom); Department of Physics and Astronomy, UCL, London WC1E 6BT (United Kingdom)

    2016-04-11

    Epitaxial silicene, which forms spontaneously on ZrB{sub 2}(0001) thin films grown on Si(111) wafers, has a periodic stripe domain structure. By adsorbing additional Si atoms on this surface, we find that the domain boundaries vanish, and a single-domain silicene sheet can be prepared without altering its buckled honeycomb structure. The amount of Si required to induce this change suggests that the domain boundaries are made of a local distortion of the silicene honeycomb lattice. The realization of a single domain sheet with structural and electronic properties close to those of the original striped state demonstrates the high structural flexibility of silicene.

  19. Evolutionary cores of domain co-occurrence networks.

    Science.gov (United States)

    Wuchty, Stefan; Almaas, Eivind

    2005-03-23

    The modeling of complex systems, as disparate as the World Wide Web and the cellular metabolism, as networks has recently uncovered a set of generic organizing principles: Most of these systems are scale-free while at the same time modular, resulting in a hierarchical architecture. The structure of the protein domain network, where individual domains correspond to nodes and their co-occurrences in a protein are interpreted as links, also falls into this category, suggesting that domains involved in the maintenance of increasingly developed, multicellular organisms accumulate links. Here, we take the next step by studying link based properties of the protein domain co-occurrence networks of the eukaryotes S. cerevisiae, C. elegans, D. melanogaster, M. musculus and H. sapiens. We construct the protein domain co-occurrence networks from the PFAM database and analyze them by applying a k-core decomposition method that isolates the globally central (highly connected domains in the central cores) from the locally central (highly connected domains in the peripheral cores) protein domains through an iterative peeling process. Furthermore, we compare the subnetworks thus obtained to the physical domain interaction network of S. cerevisiae. We find that the innermost cores of the domain co-occurrence networks gradually grow with increasing degree of evolutionary development in going from single cellular to multicellular eukaryotes. The comparison of the cores across all the organisms under consideration uncovers patterns of domain combinations that are predominately involved in protein functions such as cell-cell contacts and signal transduction. Analyzing a weighted interaction network of PFAM domains of yeast, we find that domains having only a few partners frequently interact with these, while the converse is true for domains with a multitude of partners. Combining domain co-occurrence and interaction information, we observe that the co-occurrence of domains in the

  20. A Parametric Abstract Domain for Lattice-Valued Regular Expressions

    DEFF Research Database (Denmark)

    Midtgaard, Jan; Nielson, Flemming; Nielson, Hanne Riis

    2016-01-01

    We present a lattice-valued generalization of regular expressions as an abstract domain for static analysis. The parametric abstract domain rests on a generalization of Brzozowski derivatives and works for both finite and infinite lattices. We develop both a co-inductive, simulation algorithm...... for deciding ordering between two domain elements and a widening operator for the domain. Finally we illustrate the domain with a static analysis that analyses a communicating process against a lattice-valued regular expression expressing the environment’s network communication....

  1. Evolutionary cores of domain co-occurrence networks

    Directory of Open Access Journals (Sweden)

    Almaas Eivind

    2005-03-01

    Full Text Available Abstract Background The modeling of complex systems, as disparate as the World Wide Web and the cellular metabolism, as networks has recently uncovered a set of generic organizing principles: Most of these systems are scale-free while at the same time modular, resulting in a hierarchical architecture. The structure of the protein domain network, where individual domains correspond to nodes and their co-occurrences in a protein are interpreted as links, also falls into this category, suggesting that domains involved in the maintenance of increasingly developed, multicellular organisms accumulate links. Here, we take the next step by studying link based properties of the protein domain co-occurrence networks of the eukaryotes S. cerevisiae, C. elegans, D. melanogaster, M. musculus and H. sapiens. Results We construct the protein domain co-occurrence networks from the PFAM database and analyze them by applying a k-core decomposition method that isolates the globally central (highly connected domains in the central cores from the locally central (highly connected domains in the peripheral cores protein domains through an iterative peeling process. Furthermore, we compare the subnetworks thus obtained to the physical domain interaction network of S. cerevisiae. We find that the innermost cores of the domain co-occurrence networks gradually grow with increasing degree of evolutionary development in going from single cellular to multicellular eukaryotes. The comparison of the cores across all the organisms under consideration uncovers patterns of domain combinations that are predominately involved in protein functions such as cell-cell contacts and signal transduction. Analyzing a weighted interaction network of PFAM domains of Yeast, we find that domains having only a few partners frequently interact with these, while the converse is true for domains with a multitude of partners. Combining domain co-occurrence and interaction information, we observe

  2. Differences between time domain and Fourier domain optical coherence tomography in imaging tissues.

    Science.gov (United States)

    Gao, W; Wu, X

    2017-11-01

    It has been numerously demonstrated that both time domain and Fourier domain optical coherence tomography (OCT) can generate high-resolution depth-resolved images of living tissues and cells. In this work, we compare the common points and differences between two methods when the continuous and random properties of live tissue are taken into account. It is found that when relationships that exist between the scattered light and tissue structures are taken into account, spectral interference measurements in Fourier domain OCT (FDOCT) is more advantageous than interference fringe envelope measurements in time domain OCT (TDOCT) in the cases where continuous property of tissue is taken into account. It is also demonstrated that when random property of tissue is taken into account FDOCT measures the Fourier transform of the spatial correlation function of the refractive index and speckle phenomena will limit the effective limiting imaging resolution in both TDOCT and FDOCT. Finally, the effective limiting resolution of both TDOCT and FDOCT are given which can be used to estimate the effective limiting resolution in various practical applications. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

  3. Examining the Domain-Specificity of Metacognition Using Academic Domains and Task-Specific Individual Differences

    Science.gov (United States)

    Scott, Brianna M.; Berman, Ashleigh F.

    2013-01-01

    Metacognition refers to students' knowledge and regulation of cognition, as well as their accuracy in predicting their academic performance. This study addressed two major questions: 1) how do metacognitive knowledge, regulation and accuracy differ across domains?, and 2) how do students' individual differences relate to their reported…

  4. Application of modern tensor calculus to engineered domain structures. 2. Tensor distinction of domain states

    Czech Academy of Sciences Publication Activity Database

    Kopský, Vojtěch

    2006-01-01

    Roč. 62, - (2006), s. 65-76 ISSN 0108-7673 R&D Projects: GA ČR GA202/04/0992 Institutional research plan: CEZ:AV0Z10100520 Keywords : tensor ial covariants * domain states * stability spaces Subject RIV: BE - Theoretical Physics Impact factor: 1.676, year: 2006

  5. Structural and functional analysis of multi-interface domains.

    Directory of Open Access Journals (Sweden)

    Liang Zhao

    Full Text Available A multi-interface domain is a domain that can shape multiple and distinctive binding sites to contact with many other domains, forming a hub in domain-domain interaction networks. The functions played by the multiple interfaces are usually different, but there is no strict bijection between the functions and interfaces as some subsets of the interfaces play the same function. This work applies graph theory and algorithms to discover fingerprints for the multiple interfaces of a domain and to establish associations between the interfaces and functions, based on a huge set of multi-interface proteins from PDB. We found that about 40% of proteins have the multi-interface property, however the involved multi-interface domains account for only a tiny fraction (1.8% of the total number of domains. The interfaces of these domains are distinguishable in terms of their fingerprints, indicating the functional specificity of the multiple interfaces in a domain. Furthermore, we observed that both cooperative and distinctive structural patterns, which will be useful for protein engineering, exist in the multiple interfaces of a domain.

  6. Origin of stationary domain wall enhanced ferroelectric susceptibility

    Science.gov (United States)

    Liu, Shi; Cohen, R. E.

    2017-03-01

    Ferroelectrics usually adopt a multidomain state with domain walls separating domains with polarization axes oriented differently. It has long been recognized that domain walls can dramatically impact the properties of ferroelectric materials. The enhancement of low-field susceptibility/permittivity under subswitching conditions is usually attributed to reversible domain wall vibration. Recent experiments highlight the stationary domain wall contribution to the dielectric susceptibility irrespective of any lateral displacements or deformations of the wall. We study the effects of domain walls on the low-field permittivity of PbTiO3 with density functional theory and molecular dynamics simulations. The static dielectric constant is calculated as a function of increasing domain wall density and temperature. We find an increase of dielectric permittivity with increasing domain wall density, which is expected to occur at a low driving field where the lateral motion of domain walls is forbidden. Real-space decomposition of the dielectric response reveals that frustrated dipoles within the finite width of the domain walls are responsible for the enhanced low-field permittivity. We explain the 100 % enhancement of the dielectric susceptibility form domain walls, which arises from the softer potential wells within them.

  7. Membrane-sculpting BAR domains generate stable lipid microdomains

    DEFF Research Database (Denmark)

    Zhao, Hongxia; Michelot, Alphée; Koskela, Essi V.

    2013-01-01

    Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of many cellular processes involving membrane dynamics. BAR domains sculpt phosphoinositide-rich membranes to generate membrane protrusions or invaginations. Here, we report that, in addition to regulating membrane geometry, BAR...... domains can generate extremely stable lipid microdomains by "freezing" phosphoinositide dynamics. This is a general feature of BAR domains, because the yeast endocytic BAR and Fes/CIP4 homology BAR (F-BAR) domains, the inverse BAR domain of Pinkbar, and the eisosomal BAR protein Lsp1 induced...... phosphoinositide clustering and halted lipid diffusion, despite differences in mechanisms of membrane interactions. Lsp1 displays comparable low diffusion rates in vitro and in vivo, suggesting that BAR domain proteins also generate stable phosphoinositide microdomains in cells. These results uncover a conserved...

  8. Structural organization of the regulatory domain of human 5-lipoxygenase.

    Science.gov (United States)

    Allard, John B; Brock, Thomas G

    2005-04-01

    The enzyme 5-lipoxygenase (5-LO) initiates the synthesis of leukotrienes. For this reason, 5-LO activity is important for immune defense, whereas improper regulation contributes to pathogenesis, including chronic inflammation, asthma and atherosclerosis. Like all lipoxygenases, the 5-LO protein consists of two domains, a regulatory domain and a catalytic domain. Naturally, the regulatory domain determines catalytic activity and controls leukotriene synthesis. This domain shares features with classical C2 domains in that it has a beta-sandwich structure and binds calcium, nucleotides and phospholipids. However, important structural features place this domain in a distinct family, the PLATs (for Polycystin-1, Lipoxygenase, alpha-Toxin). In this review, we summarize our current understanding of the three dimensional organization of this important component of the 5-LO molecule. In addition, we point to findings from structural analyses of related proteins to suggest further details relating 5-LO structure to function.

  9. Efficient water table evolution discretization using domain transformation

    DEFF Research Database (Denmark)

    Boon, W. M.; Balbarini, Nicola; Binning, Philip John

    2017-01-01

    Domain transformation methods are useful techniques for solving problems on non-stationary domains. In this work, we consider the evolution of the water table in an unconfined aquifer. This nonlinear, time-dependent problem is greatly simplified by using a mapping from the physical domain to a re...... to a reference domain and is then further reduced to a single, (nonlinear) partial differential equation. We show well-posedness of the approach and propose a stable and convergent discretization scheme. Numerical results are presented supporting the theory.......Domain transformation methods are useful techniques for solving problems on non-stationary domains. In this work, we consider the evolution of the water table in an unconfined aquifer. This nonlinear, time-dependent problem is greatly simplified by using a mapping from the physical domain...

  10. Spin accumulation and magnetoresistance of ferromagnetic domain walls

    Science.gov (United States)

    Dzero, Maxim; Gor'kov, Lev; Zvezdin, Anatolii; Zvezdin, Konstantin

    2003-03-01

    Taking into account the difference in the density of states between the spin's majority and minority bands in a ferromagnet, we obtain a spatial behavior of the electrostatic potential at the domain wall boundaries. The value of discontinuity oscillates with the number of domains and contains information about system as a whole, such as the positions of the domain walls or collapse of the domain walls when an external magnetic field is applied. We explain experimentally observed values of magnetoresistance in terms of spin accumulation effects. For the latter we suggest that in nanowires made of itinerant ferromagnets a new type of domain walls is realized, in which system prefers to reduce the value of magnetization rather then rotating it going from one domain to another. We also discuss the questions related to conditions of stability of linear domain walls.

  11. The architectural design of networks of protein domain architectures.

    Science.gov (United States)

    Hsu, Chia-Hsin; Chen, Chien-Kuo; Hwang, Ming-Jing

    2013-08-23

    Protein domain architectures (PDAs), in which single domains are linked to form multiple-domain proteins, are a major molecular form used by evolution for the diversification of protein functions. However, the design principles of PDAs remain largely uninvestigated. In this study, we constructed networks to connect domain architectures that had grown out from the same single domain for every single domain in the Pfam-A database and found that there are three main distinctive types of these networks, which suggests that evolution can exploit PDAs in three different ways. Further analysis showed that these three different types of PDA networks are each adopted by different types of protein domains, although many networks exhibit the characteristics of more than one of the three types. Our results shed light on nature's blueprint for protein architecture and provide a framework for understanding architectural design from a network perspective.

  12. Effective Domain Partitioning for Multi-Clock Domain IP Core Wrapper Design under Power Constraints

    Science.gov (United States)

    Yu, Thomas Edison; Yoneda, Tomokazu; Zhao, Danella; Fujiwara, Hideo

    The rapid advancement of VLSI technology has made it possible for chip designers and manufacturers to embed the components of a whole system onto a single chip, called System-on-Chip or SoC. SoCs make use of pre-designed modules, called IP-cores, which provide faster design time and quicker time-to-market. Furthermore, SoCs that operate at multiple clock domains and very low power requirements are being utilized in the latest communications, networking and signal processing devices. As a result, the testing of SoCs and multi-clock domain embedded cores under power constraints has been rapidly gaining importance. In this research, a novel method for designing power-aware test wrappers for embedded cores with multiple clock domains is presented. By effectively partitioning the various clock domains, we are able to increase the solution space of possible test schedules for the core. Since previous methods were limited to concurrently testing all the clock domains, we effectively remove this limitation by making use of bandwidth conversion, multiple shift frequencies and properly gating the clock signals to control the shift activity of various core logic elements. The combination of the above techniques gains us greater flexibility when determining an optimal test schedule under very tight power constraints. Furthermore, since it is computationally intensive to search the entire expanded solution space for the possible test schedules, we propose a heuristic 3-D bin packing algorithm to determine the optimal wrapper architecture and test schedule while minimizing the test time under power and bandwidth constraints.

  13. Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives.

    Science.gov (United States)

    Jindal, Prateek; Roth, Dan

    2013-01-01

    This paper presents a coreference resolution system for clinical narratives. Coreference resolution aims at clustering all mentions in a single document to coherent entities. A knowledge-intensive approach for coreference resolution is employed. The domain knowledge used includes several domain-specific lists, a knowledge intensive mention parsing, and task informed discourse model. Mention parsing allows us to abstract over the surface form of the mention and represent each mention using a higher-level representation, which we call the mention's semantic representation (SR). SR reduces the mention to a standard form and hence provides better support for comparing and matching. Existing coreference resolution systems tend to ignore discourse aspects and rely heavily on lexical and structural cues in the text. The authors break from this tradition and present a discourse model for "person" type mentions in clinical narratives, which greatly simplifies the coreference resolution. This system was evaluated on four different datasets which were made available in the 2011 i2b2/VA coreference challenge. The unweighted average of F1 scores (over B-cubed, MUC and CEAF) varied from 84.2% to 88.1%. These experiments show that domain knowledge is effective for different mention types for all the datasets. Error analysis shows that most of the recall errors made by the system can be handled by further addition of domain knowledge. The precision errors, on the other hand, are more subtle and indicate the need to understand the relations in which mentions participate for building a robust coreference system. This paper presents an approach that makes an extensive use of domain knowledge to significantly improve coreference resolution. The authors state that their system and the knowledge sources developed will be made publicly available.

  14. Realization of Thermal Inertia in Frequency Domain

    Directory of Open Access Journals (Sweden)

    Boe-Shong Hong

    2014-02-01

    Full Text Available To realize the lagging behavior in heat conduction observed in these two decades, this paper firstly theoretically excludes the possibility that the underlying thermal inertia is a result of the time delay in heat diffusion. Instead, we verify in experiments the electro-thermal analogy, wherein the thermal inertial is parameterized by thermal inductance that formulates hyperbolic heat-conduction. The thermal hyperbolicity exhibits a special frequency response in Bode plot, wherein the amplitude ratios is kept flat after crossing some certain frequency, as opposed to Fourier heat-conduction. We apply this specialty to design an instrument that reliably identifies thermal inductances of some materials in frequency domain. The instrument is embedded with a DSP-based frequency synthesizer capable of modulating frequencies in utmost high-resolution. Thermal inertia implies a new possibility for energy storage in analogy to inductive energy storage in electricity or mechanics.

  15. Outlier Detection and Explanation for Domain Experts

    DEFF Research Database (Denmark)

    Micenková, Barbora

    In many data exploratory tasks, extraordinary and rarely occurring patterns called outliers are more interesting than the prevalent ones. For example, they could represent frauds in insurance, intrusions in network and system monitoring, or motion in video surveillance. Decades of research have...... in practice and we empirically evaluate them on synthetic and real world data sets. First, we tackle the problem that most algorithms leave the end user without any explanation of how or why the identified outliers deviate. Such knowledge is important for domain experts in order to be able to validate...... to a supervised classifier. The resulting method is robust to parameters and as such it can be easily applied to data by non-experts in data mining. We also consider the case where computational resources at test time are limited and introduce a feature selection technique that respects a computational budget...

  16. Nanoscale Membrane Domain Formation Driven by Cholesterol

    DEFF Research Database (Denmark)

    Javanainen, Matti; Martinez-Seara, Hector; Vattulainen, Ilpo

    2017-01-01

    Biological membranes generate specific functions through compartmentalized regions such as cholesterol-enriched membrane nanodomains that host selected proteins. Despite the biological significance of nanodomains, details on their structure remain elusive. They cannot be observed via microscopic...... dipalmitoylphosphatidylcholine and cholesterol - the "minimal standard" for nanodomain formation. The simulations reveal how cholesterol drives the formation of fluid cholesterol-rich nanodomains hosting hexagonally packed cholesterol-poor lipid nanoclusters, both of which show registration between the membrane leaflets....... The complex nanodomain substructure forms when cholesterol positions itself in the domain boundary region. Here cholesterol can also readily flip-flop across the membrane. Most importantly, replacing cholesterol with a sterol characterized by a less asymmetric ring region impairs the emergence of nanodomains...

  17. Cultural Heritage and the Public Domain

    Directory of Open Access Journals (Sweden)

    Bas Savenije

    2012-09-01

    by providing their resources on the Internet” (Berlin Declaration 2003. Therefore, in the spirit of the Berlin Declaration, the ARL encourages its members’ libraries to grant all non-commercial users “a free, irrevocable, worldwide, right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship”. And: “If fees are to be assessed for the use of digitised public domain works, those fees should only apply to commercial uses” (ARL Principles July 2010. In our view, cultural heritage institutions should make public domain material digitised with public funding as widely available as possible for access and reuse. The public sector has the primary responsibility to fund digitisation. The involvement of private partners, however, is encouraged by ARL as well as the Comité des Sages. Private funding for digitisation is a complement to the necessary public investment, especially in times of economic crisis, but should not be seen as a substitute for public funding. As we can see from these reports there are a number of arguments in favour of digitisation and also of providing maximum accessibility to the digitised cultural heritage. In this paper we will investigate the legal aspects of digitisation of cultural heritage, especially public domain material. On the basis of these we will make an inventory of policy considerations regarding reuse. Furthermore, we will describe the conclusions the National Library of the Netherlands (hereafter: KB has formulated and the arguments that support these. In this context we will review public-private partnerships and also the policy of the KB. We will conclude with recommendations for cultural heritage institutions concerning a reuse policy for digitised public domain material.

  18. 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.

  19. On the domain of string perturbation theory

    International Nuclear Information System (INIS)

    Davis, S.

    1989-06-01

    For a large class of effectively closed surfaces, it is shown that the only divergences in string scattering amplitudes at each order in perturbation theory are those associated with the coincidence of vertex operators and the boundary of moduli space. This class includes all closed surfaces of finite genus, and infinite-genus surfaces which can be uniformized by a group of Schottky type. While the computation is done explicitly for bosonic strings in their ground states, it can also be extended to excited states and to superstrings. The properties of these amplitudes lead to a definition of the domain of perturbation theory as the set of effectively closed surfaces. The implications of the restriction to effectively closed surfaces on the behavior of the perturbation series are discussed. (author). 20 refs, 6 figs

  20. Domain decomposition algorithms and computational fluid dynamics

    International Nuclear Information System (INIS)

    Chan, T.F.

    1988-01-01

    In the past several years, domain decomposition has been a very popular topic, partly because of the potential of parallelization. Although numerous theories and algorithms have been developed for model elliptic problems, they are only recently starting to be tested on realistic applications. This paper investigates the application of some of these methods to two model problems in computational fluid dynamics: two-dimensional convection-diffusion problems and the incompressible driven cavity flow problem. The authors approach is the construction and analysis of efficient preconditioners for the interface operator to be used in the iterative solution of the interface solution. For the convection-diffusion problems, they discuss the effect of the convection term and its discretization on the performance of some of the preconditioners. For the driven cavity problem, they discuss the effectiveness of a class of boundary probe preconditioners

  1. Counting nodal domains on surfaces of revolution

    International Nuclear Information System (INIS)

    Karageorge, Panos D; Smilansky, Uzy

    2008-01-01

    We consider eigenfunctions of the Laplace-Beltrami operator on special surfaces of revolution. For this separable system, the nodal domains of the (real) eigenfunctions form a checkerboard pattern, and their number ν n is proportional to the product of the angular and the 'surface' quantum numbers. Arranging the wavefunctions by increasing values of the Laplace-Beltrami spectrum, we obtain the nodal sequence, whose statistical properties we study. In particular, we investigate the distribution of the normalized counts ν n /n for sequences of eigenfunctions with K ≤ n ≤ K + ΔK, where K, ΔK element of N. We show that the distribution approaches a limit as K, ΔK → ∞ (the classical limit), and study the leading corrections in the semi-classical limit. With this information, we derive the central result of this work: the nodal sequence of a mirror-symmetric surface is sufficient to uniquely determine its shape (modulo scaling)

  2. Coherent combining pulse bursts in time domain

    Science.gov (United States)

    Galvanauskas, Almantas

    2018-01-09

    A beam combining and pulse stacking technique is provided that enhances laser pulse energy by coherent stacking pulse bursts (i.e. non-periodic pulsed signals) in time domain. This energy enhancement is achieved by using various configurations of Fabry-Perot, Gires-Tournois and other types of resonant cavities, so that a multiple-pulse burst incident at either a single input or multiple inputs of the system produces an output with a solitary pulse, which contains the summed energy of the incident multiple pulses from all beams. This disclosure provides a substantial improvement over conventional coherent-combining methods in that it achieves very high pulse energies using a relatively small number of combined laser systems, thus providing with orders of magnitude reduction in system size, complexity, and cost compared to current combining approaches.

  3. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2013-01-01

    Code clones (i.e., duplicate fragments of code) have been studied for long, and there is strong evidence that they are a major source of software faults. Anecdotal evidence suggests that this phenomenon occurs similarly in models, suggesting that model clones are as detrimental to model quality...... as they are to code quality. However, programming language code and visual models have significant differences that make it difficult to directly transfer notions and algorithms developed in the code clone arena to model clones. In this article, we develop and propose a definition of the notion of “model clone” based...... on the thorough analysis of practical scenarios. We propose a formal definition of model clones, specify a clone detection algorithm for UML domain models, and implement it prototypically. We investigate different similarity heuristics to be used in the algorithm, and report the performance of our approach. While...

  4. Towards Clone Detection in UML Domain Models

    DEFF Research Database (Denmark)

    Störrle, Harald

    2010-01-01

    Code clones - that is, duplicate fragments of code - have been studied for a long time. There is strong evidence that code clones are a major source of software faults. Anecdotal evidence suggests that this phenomenon is not restricted to code, but occurs in models in a very similar way. So...... it is likely that model clones are as detrimental to model quality as they are to code quality. However, programming language code and visual models also have significant differences so that notions and algorithms developed in the code clone arena cannot be transferred directly to model clones. In this article......, we discuss how model clones arise by analyzing several practical scenarios. We propose a formal definition of models and clones, that allows us to specify a generic clone detection algorithm. Through a thorough analysis of the detail structure of sample UML domain models, recommendations for clone...

  5. Gravitational Waves and Time Domain Astronomy

    Science.gov (United States)

    Centrella, Joan; Nissanke, Samaya; Williams, Roy

    2012-01-01

    The gravitational wave window onto the universe will open in roughly five years, when Advanced LIGO and Virgo achieve the first detections of high frequency gravitational waves, most likely coming from compact binary mergers. Electromagnetic follow-up of these triggers, using radio, optical, and high energy telescopes, promises exciting opportunities in multi-messenger time domain astronomy. In the decade, space-based observations of low frequency gravitational waves from massive black hole mergers, and their electromagnetic counterparts, will open up further vistas for discovery. This two-part workshop featured brief presentations and stimulating discussions on the challenges and opportunities presented by gravitational wave astronomy. Highlights from the workshop, with the emphasis on strategies for electromagnetic follow-up, are presented in this report.

  6. Wavefield extrapolation in pseudo-depth domain

    KAUST Repository

    Ma, Xuxin

    2012-01-01

    Extrapolating seismic waves in Cartesian coordinate is prone to uneven spatial sampling, because the seismic wavelength tends to grow with depth, as velocity increase. We transform the vertical depth axis to a pseudo one using a velocity weighted mapping, which can effectively mitigate this wavelength variation. We derive acoustic wave equations in this new domain based on the direct transformation of the Laplacian derivatives, which admits solutions that are more accurate and stable than those derived from the kinematic transformation. The anisotropic versions of these equations allow us to isolate the vertical velocity influence and reduce its impact on modeling and imaging. The major benefit of extrapolating wavefields in pseudo-depth space is its near uniform wavelength as opposed to the normally dramatic change of wavelength with the conventional approach. Time wavefield extrapolation on a complex velocity shows some of the features of this approach.

  7. Optimization Testbed Cometboards Extended into Stochastic Domain

    Science.gov (United States)

    Patnaik, Surya N.; Pai, Shantaram S.; Coroneos, Rula M.; Patnaik, Surya N.

    2010-01-01

    COMparative Evaluation Testbed of Optimization and Analysis Routines for the Design of Structures (CometBoards) is a multidisciplinary design optimization software. It was originally developed for deterministic calculation. It has now been extended into the stochastic domain for structural design problems. For deterministic problems, CometBoards is introduced through its subproblem solution strategy as well as the approximation concept in optimization. In the stochastic domain, a design is formulated as a function of the risk or reliability. Optimum solution including the weight of a structure, is also obtained as a function of reliability. Weight versus reliability traced out an inverted-S-shaped graph. The center of the graph corresponded to 50 percent probability of success, or one failure in two samples. A heavy design with weight approaching infinity could be produced for a near-zero rate of failure that corresponded to unity for reliability. Weight can be reduced to a small value for the most failure-prone design with a compromised reliability approaching zero. The stochastic design optimization (SDO) capability for an industrial problem was obtained by combining three codes: MSC/Nastran code was the deterministic analysis tool, fast probabilistic integrator, or the FPI module of the NESSUS software, was the probabilistic calculator, and CometBoards became the optimizer. The SDO capability requires a finite element structural model, a material model, a load model, and a design model. The stochastic optimization concept is illustrated considering an academic example and a real-life airframe component made of metallic and composite materials.

  8. Exploration of the Time Domain (Abstract)

    Science.gov (United States)

    Djorgovski, G.

    2017-06-01

    (Abstract only) Time-domain astronomy is one of the most active and growing areas of astronomical research today, thanks to the new generation of synoptic sky surveys, and leading to LSST. Catalina Real-Time Transient Survey (CRTS; http://crts.caltech.edu) is systematically exploring and characterizing the variable sky since 2008, with the archival data going back to 2005. The survey covers the total area of 33,000 deg2, down to 19±21 mag per exposure, with time baselines from 10 min to 10 years, and growing; there are now typically 200±400 exposures per pointing, and coadded images reach deeper than 23 magnitude. The survey has so far detected over 13,000 unique, high-amplitude transients, including 4,000 confirmed or likely supernovae, nearly 2,000 CVs (the great majority of them previously uncatalogued), about 4,000 blazars and other flaring AGN, and a broad variety of other types of objects. Many of these objects can benefit from a follow-up by the amateur community. CRTS is intended to be a data resource for the entire astronomical community. We have a completely open data policy: all discovered transient events are published in real time with no proprietary delay period, and all data are made public, in order to better serve the entire community, and maximize the scientific returns. This includes an archive of 500 million light curves, which are being updated continuously. This is an unprecedented data set for the exploration of the time domain, in terms of the area, depth, and temporal coverage. Numerous scientific projects have been enabled by this data stream, including: discoveries of ultraluminous and otherwise peculiar SNe; unusual CVs and dwarf novae; mapping of the structure in the Galactic halo using RR Lyrae; variability-based discovery of AGN and probes of their physics; and so on.

  9. Nuclear lipid droplets: a novel nuclear domain.

    Science.gov (United States)

    Layerenza, J P; González, P; García de Bravo, M M; Polo, M P; Sisti, M S; Ves-Losada, A

    2013-02-01

    We investigated nuclear neutral-lipid (NL) composition and organization, as NL may represent an alternative source for providing fatty acids and cholesterol (C) to membranes, signaling paths, and transcription factors in the nucleus. We show here that nuclear NL were organized into nonpolar domains in the form of nuclear-lipid droplets (nLD). By fluorescent confocal microscopy, representative nLD were observed in situ within the nuclei of rat hepatocytes in vivo and HepG2 cells, maintained under standard conditions in culture, and within nuclei isolated from rat liver. nLD were resistant to Triton X-100 and became stained with Sudan Red, OsO4, and BODIPY493/503. nLD and control cytosolic-lipid droplets (cLD) were isolated from rat-liver nuclei and from homogenates, respectively, by sucrose-gradient sedimentation. Lipids were extracted, separated by thin-layer chromatography, and quantified. nLD were composed of 37% lipids and 63% proteins. The nLD lipid composition was as follows: 19% triacylglycerols (TAG), 39% cholesteryl esters, 27% C, and 15% polar lipids; whereas the cLD composition contained different proportions of these same lipid classes, in particular 91% TAG. The TAG fatty acids from both lipid droplets were enriched in oleic, linoleic, and palmitic acids. The TAG from the nLD corresponded to a small pool, whereas the TAG from the cLD constituted the main cellular pool (at about 100% yield from the total homogenate). In conclusion, nLD are a domain within the nucleus where NL are stored and organized and may be involved in nuclear lipid homeostasis. Copyright © 2012 Elsevier B.V. All rights reserved.

  10. Digital Image Watermarking in Transform Domains

    International Nuclear Information System (INIS)

    EL-Shazly, E.H.M.

    2012-01-01

    Fast development of internet and availability of huge digital content make it easy to create, modify and copy digital media such as audio, video and images. This causes a problem for owners of that content and hence a need to copy right protection tool was essential. First, encryption was proposed but it ensures protection during transmission only and once decryption occurred any one can modify the data. at that point watermarking was introduced as a solution to such problem. Watermarking is a process of inserting a low energy signal in to a high energy one so that it doesn't affect the main signal features. A good digital image watermarking technique should satisfy four requirements: 1) Embedding of a watermark should not degrade the host image visual quality (imperceptibility). 2) The embedded watermark should stick to the host image so that it couldn’t be removed by common image processing operation and could be extracted from the attacked watermarked image (robustness). 3) Knowing the embedding and extraction procedures is sufficient but not enough to extract the watermark; extra keys should be needed (security). 4) The watermarking technique should allow embedding and extraction of more than one watermark each independent of the other (capacity). This thesis presents a watermarking scheme that full fill the mentioned four requirements by jointing transform domains with Fractional Fourier Transform Domain (FracFT). More work on cascaded Discrete Wavelet Transform DWT with FracFT was done to develop a joint transform simply called Fractional Wavelet Transform (FWT). The proposed schemes were tested with different image processing attacks to verify its robustness. Finally, the watermarked image is transmitted over simulated MC CDMA channel to prove robustness in real transmission conditions case.

  11. Navigation domain representation for interactive multiview imaging.

    Science.gov (United States)

    Maugey, Thomas; Daribo, Ismael; Cheung, Gene; Frossard, Pascal

    2013-09-01

    Enabling users to interactively navigate through different viewpoints of a static scene is a new interesting functionality in 3D streaming systems. While it opens exciting perspectives toward rich multimedia applications, it requires the design of novel representations and coding techniques to solve the new challenges imposed by the interactive navigation. In particular, the encoder must prepare a priori a compressed media stream that is flexible enough to enable the free selection of multiview navigation paths by different streaming media clients. Interactivity clearly brings new design constraints: the encoder is unaware of the exact decoding process, while the decoder has to reconstruct information from incomplete subsets of data since the server generally cannot transmit images for all possible viewpoints due to resource constrains. In this paper, we propose a novel multiview data representation that permits us to satisfy bandwidth and storage constraints in an interactive multiview streaming system. In particular, we partition the multiview navigation domain into segments, each of which is described by a reference image (color and depth data) and some auxiliary information. The auxiliary information enables the client to recreate any viewpoint in the navigation segment via view synthesis. The decoder is then able to navigate freely in the segment without further data request to the server; it requests additional data only when it moves to a different segment. We discuss the benefits of this novel representation in interactive navigation systems and further propose a method to optimize the partitioning of the navigation domain into independent segments, under bandwidth and storage constraints. Experimental results confirm the potential of the proposed representation; namely, our system leads to similar compression performance as classical inter-view coding, while it provides the high level of flexibility that is required for interactive streaming. Because of

  12. Domain enhanced lookup time accelerated BLAST

    Directory of Open Access Journals (Sweden)

    Boratyn Grzegorz M

    2012-04-01

    Full Text Available Abstract Background BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST iteratively searches a protein sequence database, using the matches in round i to construct a position-specific score matrix (PSSM for searching the database in round i + 1. Biegert and Söding developed Context-sensitive BLAST (CS-BLAST, which combines information from searching the sequence database with information derived from a library of short protein profiles to achieve better homology detection than PSI-BLAST, which builds its PSSMs from scratch. Results We describe a new method, called domain enhanced lookup time accelerated BLAST (DELTA-BLAST, which searches a database of pre-constructed PSSMs before searching a protein-sequence database, to yield better homology detection. For its PSSMs, DELTA-BLAST employs a subset of NCBI’s Conserved Domain Database (CDD. On a test set derived from ASTRAL, with one round of searching, DELTA-BLAST achieves a ROC5000 of 0.270 vs. 0.116 for CS-BLAST. The performance advantage diminishes in iterated searches, but DELTA-BLAST continues to achieve better ROC scores than CS-BLAST. Conclusions DELTA-BLAST is a useful program for the detection of remote protein homologs. It is available under the “Protein BLAST” link at http://blast.ncbi.nlm.nih.gov. Reviewers This article was reviewed by Arcady Mushegian, Nick V. Grishin, and Frank Eisenhaber.

  13. Conformational instability of the MARK3 UBA domain compromises ubiquitin recognition and promotes interaction with the adjacent kinase domain

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, James M.; Korzhnev, Dmitry M.; Ceccarelli, Derek F.; Briant, Douglas J.; Zarrine-Afsar, Arash; Sicheri, Frank; Kay, Lewis E.; Pawson, Tony (Mount Sinai Hospital); (Toronto)

    2012-10-23

    The Par-1/MARK protein kinases play a pivotal role in establishing cellular polarity. This family of kinases contains a unique domain architecture, in which a ubiquitin-associated (UBA) domain is located C-terminal to the kinase domain. We have used a combination of x-ray crystallography and NMR dynamics experiments to understand the interaction of the human (h) MARK3 UBA domain with the adjacent kinase domain as compared with ubiquitin. The x-ray crystal structure of the linked hMARK3 kinase and UBA domains establishes that the UBA domain forms a stable intramolecular interaction with the N-terminal lobe of the kinase domain. However, solution-state NMR studies of the isolated UBA domain indicate that it is highly dynamic, undergoing conformational transitions that can be explained by a folding-unfolding equilibrium. NMR titration experiments indicated that the hMARK3 UBA domain has a detectable but extremely weak affinity for mono ubiquitin, which suggests that conformational instability of the isolated hMARK3 UBA domain attenuates binding to ubiquitin despite the presence of residues typically involved in ubiquitin recognition. Our data identify a molecular mechanism through which the hMARK3 UBA domain has evolved to bind the kinase domain, in a fashion that stabilizes an open conformation of the N- and C-terminal lobes, at the expense of its capacity to engage ubiquitin. These results may be relevant more generally to the 30% of UBA domains that lack significant ubiquitin-binding activity, and they suggest a unique mechanism by which interaction domains may evolve new binding properties.

  14. Domain interplay in the urokinase receptor. Requirement for the third domain in high affinity ligand binding and demonstration of ligand contact sites in distinct receptor domains

    DEFF Research Database (Denmark)

    Behrendt, N; Ronne, E; Dano, K

    1996-01-01

    The urokinase plasminogen activator receptor (uPAR) is a membrane protein comprised of three extracellular domains. In order to study the importance of this domain organization in the ligand-binding process of the receptor we subjected a recombinant, soluble uPAR (suPAR) to specific proteolytic...

  15. Structural and histone binding ability characterizations of human PWWP domains.

    Directory of Open Access Journals (Sweden)

    Hong Wu

    Full Text Available 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 β-barrel core, an insertion motif between the second and third β-strands and a C-terminal α-helix bundle. Both the canonical β-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.This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the

  16. 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.

  17. 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.

  18. Multi-Domain Virtual Network Embedding with Coordinated Link Mapping

    Directory of Open Access Journals (Sweden)

    Shuopeng Li

    2017-06-01

    Full Text Available Network Virtualization, which allows the co-existence of various logical networks on shared physical infrastructure, has become popular in recent years. The optimal mapping of virtual resource to physical resource is a major issue in network virtualization. This problem, called virtual network embedding (VNE, has been well explored in the context of one physical domain, which is in practice operated by a single infrastructure provider (InP. However, the needs of virtual network (VN is rapidly growing, and quite a number of VNs have to be established across multi-domain. For multi-domain VNE, infrastructure providers can no longer just solve their own single domain VNE problem, but have to cooperate to build the whole VN. Therefore, new challenge arises for the multi-domain VNE, compared to traditional single domain VNE. The existing investigations on this problem mainly focus on decomposing a VN to sub VN for each domain, but little attention has been paid to the joint relation between intra-domain and inter-domain (peering links. In this paper, we propose a multi-domain link mapping method which combines the intra and peering link mapping so as to optimize the overall resource utilization. Our approach is easy to be deployed since it is based on current Internet architecture. Evaluation shows that our approach brings improvements related to existing methods.

  19. Evolution based on domain combinations: the case of glutaredoxins

    Directory of Open Access Journals (Sweden)

    Herrero Enrique

    2009-03-01

    Full Text Available Abstract Background Protein domains represent the basic units in the evolution of proteins. Domain duplication and shuffling by recombination and fusion, followed by divergence are the most common mechanisms in this process. Such domain fusion and recombination events are predicted to occur only once for a given multidomain architecture. However, other scenarios may be relevant in the evolution of specific proteins, such as convergent evolution of multidomain architectures. With this in mind, we study glutaredoxin (GRX domains, because these domains of approximately one hundred amino acids are widespread in archaea, bacteria and eukaryotes and participate in fusion proteins. GRXs are responsible for the reduction of protein disulfides or glutathione-protein mixed disulfides and are involved in cellular redox regulation, although their specific roles and targets are often unclear. Results In this work we analyze the distribution and evolution of GRX proteins in archaea, bacteria and eukaryotes. We study over one thousand GRX proteins, each containing at least one GRX domain, from hundreds of different organisms and trace the origin and evolution of the GRX domain within the tree of life. Conclusion Our results suggest that single domain GRX proteins of the CGFS and CPYC classes have, each, evolved through duplication and divergence from one initial gene that was present in the last common ancestor of all organisms. Remarkably, we identify a case of convergent evolution in domain architecture that involves the GRX domain. Two independent recombination events of a TRX domain to a GRX domain are likely to have occurred, which is an exception to the dominant mechanism of domain architecture evolution.

  20. 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.

  1. Institutionalizing the Human Domain: Achieving Cross Domain Synergy for Every Day Missions

    Science.gov (United States)

    2017-04-06

    The five elements of the Human Domain ( social , cultural , physical, informational, and psychological) are addressed in the subsequent section of this... social , cultural , physical, informational, and psychological) are critical to “shaping the behavior of actors in the environment” and occur as the first... Vietnam , where he participated in the Defense Department’s efforts to repatriate the remains of service members declared Missing in Action from the

  2. Improving the Effectiveness of Speaker Verification Domain Adaptation With Inadequate In-Domain Data

    Science.gov (United States)

    2017-08-20

    verification scores. One such scoring method is probabilistic linear discriminant analysis (PLDA) [2], which provides a sta- tistical tool for...error rate (EER) and minimum decision cost function (mindcf), and pooled across gender . For all adaptation methods, an adaptation coefficient of α=0.5...Elder, “Probabilistic linear discriminant analysis for inferences about identity,” in ICCV, 2007. [3] D. Garcia-Romero and A. McCree, “Supervised domain

  3. Particle Communication and Domain Neighbor Coupling: Scalable Domain Decomposed Algorithms for Monte Carlo Particle Transport

    Energy Technology Data Exchange (ETDEWEB)

    O' Brien, M. J.; Brantley, P. S.

    2015-01-20

    In order to run Monte Carlo particle transport calculations on new supercomputers with hundreds of thousands or millions of processors, care must be taken to implement scalable algorithms. This means that the algorithms must continue to perform well as the processor count increases. In this paper, we examine the scalability of:(1) globally resolving the particle locations on the correct processor, (2) deciding that particle streaming communication has finished, and (3) efficiently coupling neighbor domains together with different replication levels. We have run domain decomposed Monte Carlo particle transport on up to 221 = 2,097,152 MPI processes on the IBM BG/Q Sequoia supercomputer and observed scalable results that agree with our theoretical predictions. These calculations were carefully constructed to have the same amount of work on every processor, i.e. the calculation is already load balanced. We also examine load imbalanced calculations where each domain’s replication level is proportional to its particle workload. In this case we show how to efficiently couple together adjacent domains to maintain within workgroup load balance and minimize memory usage.

  4. On time-domain and frequency-domain MMSE-based TEQ design for DMT transmission

    CERN Document Server

    Vanbleu, K; Moonen, M; Ysebaert, G; 10.1109/TSP.2005.851161

    2005-01-01

    We reconsider the minimum mean square error (MMSE) time-domain equalizer (TEQ), bitrate maximizing TEQ (BM-TEQ), and per-tone equalizer design (PTEQ) for discrete multitone (DMT) transmission and cast them in a common least-squares (LS) based framework. The MMSE- TEQ design criterion can be formulated as a constrained linear least-squares (CLLS) criterion that minimizes a time-domain (TD) error energy. From this CLLS-based TD-MMSE-TEQ criterion, we derive two new least-squares (LS) based frequency-domain (FD) MMSE-TEQ design criteria: a CLLS-based FD-MMSE-TEQ criterion and a so-called separable nonlinear LS (SNLLS) based FD-MMSE-TEQ design. Finally, the original BM-TEQ design is shown to be equivalent to a so-called iteratively-reweighted (IR) version of the SNLLS-based FD-MMSE-TEQ design. This LS-based framework then results in the following contributions. The new, IR-SNLLS-based BM-TEQ design criterion gives rise to an elegant, iterative, fast converging, Gauss-Newton-based design algorithm that exploits th...

  5. Domain topology and domain switching kinetics in a hybrid improper ferroelectric

    Science.gov (United States)

    Huang, F.-T.; Xue, F.; Gao, B.; Wang, L. H.; Luo, X.; Cai, W.; Lu, X.-Z.; Rondinelli, J. M.; Chen, L. Q.; Cheong, S.-W.

    2016-05-01

    Charged polar interfaces such as charged ferroelectric walls or heterostructured interfaces of ZnO/(Zn,Mg)O and LaAlO3/SrTiO3, across which the normal component of electric polarization changes suddenly, can host large two-dimensional conduction. Charged ferroelectric walls, which are energetically unfavourable in general, were found to be mysteriously abundant in hybrid improper ferroelectric (Ca,Sr)3Ti2O7 crystals. From the exploration of antiphase boundaries in bilayer-perovskites, here we discover that each of four polarization-direction states is degenerate with two antiphase domains, and these eight structural variants form a Z4 × Z2 domain structure with Z3 vortices and five distinct types of domain walls, whose topology is directly relevant to the presence of abundant charged walls. We also discover a zipper-like nature of antiphase boundaries, which are the reversible creation/annihilation centres of pairs of two types of ferroelectric walls (and also Z3-vortex pairs) in 90° and 180° polarization switching. Our results demonstrate the unexpectedly rich nature of hybrid improper ferroelectricity.

  6. Transition from many domain to single domain martensite morphology in small-scale shape memory alloys

    International Nuclear Information System (INIS)

    Ueland, Stian M.; Schuh, Christopher A.

    2013-01-01

    The morphology of the martensitic transformation during a superelastic cycle is studied by in situ scanning electron microscopy deformation experiments in microwires of Cu–Zn–Al. The diameters of the wires studied (21–136 μm) span the range in which significant size effects upon transformation hysteresis have been observed. In larger wires the transformation is accommodated by the continual nucleation of many new martensite plates that grow and eventually coalesce with their neighbors. In small wires a single martensite plate nucleates at the start of transformation and then proceeds to grow in a monolithic fashion; the wire transforms by smooth axial propagation of a single interface. The transition from many domain to single domain transformation is gradual with wire diameter, and is based upon scaling of the domain density with sample size. We attribute it to a crossover from bulk to surface obstacle control of transformation front propagation. This observation also sheds light on reported size effects in energy dissipation in shape memory alloys

  7. Second-harmonic imaging of ferroelectric domain walls

    DEFF Research Database (Denmark)

    Bozhevolnyi, Sergey I.; Hvam, Jørn Märcher; Pedersen, Kjeld

    1998-01-01

    Domain walls in periodically poled ferroelectric KTiOPO4 and LiNbO3 crystals are observed by making use of second-harmonic (SH) generation enhancement in the transition regions between neighboring domains. SH images of domain walls obtained with various samples for different polarization...... configurations are presented. The SH generation enhancement is found especially pronounced for the polarization of the SH radiation being perpendicular to the domain walls. The origin and selection rules for the contrast in SH images of domain walls are discussed. The results obtained suggest that the domain...... walls produce a deteriorating effect on SH generation by quasiphase matching. (C) 1998 American Institute of Physics. [S0003-6951(98)02039-7]....

  8. Deriving ICD-11 personality disorder domains from dsm-5 traits

    DEFF Research Database (Denmark)

    Bach, B; Sellbom, M; Kongerslev, M

    2017-01-01

    OBJECTIVE: The personality disorder domains proposed for the ICD-11 comprise Negative Affectivity, Detachment, Dissociality, Disinhibition, and Anankastia, which are reasonably concordant with the higher-order trait domains in the Alternative DSM-5 Model for Personality Disorders. METHOD: We...... in the proposed ICD-11 five-domain structure as well as other recognizable higher-order models of personality and psychopathology. Model fits revealed that the five proposed ICD-11 personality disorder domains were satisfactorily resembled, and replicated in the independent US sample. CONCLUSION: The proposed ICD......-11 personality disorder domains can be accurately described using designated traits from the DSM-5 personality trait system. A scoring algorithm for the ICD-11 personality disorder domains is provided in appendix....

  9. The transcriptional repressor domain of Gli3 is intrinsically disordered.

    Directory of Open Access Journals (Sweden)

    Robert Tsanev

    Full Text Available The transcription factor Gli3 is acting mainly as a transcriptional repressor in the Sonic hedgehog signal transduction pathway. Gli3 contains a repressor domain in its N-terminus from residue G106 to E236. In this study we have characterized the intracellular structure of the Gli3 repressor domain using a combined bioinformatics and experimental approach. According to our findings the Gli3 repressor domain while being intrinsically disordered contains predicted anchor sites for partner interactions. The obvious interaction partners to test were Ski and DNA; however, with both of these the structure of Gli3 repressor domain remained disordered. To locate residues important for the repressor function we mutated several residues within the Gli3 repressor domain. Two of these, H141A and H157N, targeting predicted helical regions, significantly decreased transcriptional repression and thus identify important functional parts of the domain.

  10. Even-odd effects in magnetoresistance of ferromagnetic domain walls

    Science.gov (United States)

    Dzero, M.; Gor'kov, L. P.; Zvezdin, A. K.; Zvezdin, K. A.

    2003-03-01

    The difference in the density of states for the spin’s majority and minority bands in a ferromagnet changes the electrostatic potential along the domains, introducing discontinuities of the potential at domain boundaries. The value of the discontinuity oscillates with the number of domains. Discontinuity depends on the positions of domain walls, their motion, or the collapse of domain walls in applied magnetic field. Large values of the magnetoresistance are explained in terms of spin accumulation. We suggest a type of domain wall in nanowires made of itinerant ferromagnets, in which the magnetization vector changes without rotation. The absence of transverse magnetization components allows considerable spin accumulation, assuming the spin relaxation length LS is large enough.

  11. Domain Adaptation for Pedestrian Detection Based on Prediction Consistency

    Directory of Open Access Journals (Sweden)

    Yu Li-ping

    2014-01-01

    Full Text Available Pedestrian detection is an active area of research in computer vision. It remains a quite challenging problem in many applications where many factors cause a mismatch between source dataset used to train the pedestrian detector and samples in the target scene. In this paper, we propose a novel domain adaptation model for merging plentiful source domain samples with scared target domain samples to create a scene-specific pedestrian detector that performs as well as rich target domain simples are present. Our approach combines the boosting-based learning algorithm with an entropy-based transferability, which is derived from the prediction consistency with the source classifications, to selectively choose the samples showing positive transferability in source domains to the target domain. Experimental results show that our approach can improve the detection rate, especially with the insufficient labeled data in target scene.

  12. Updating the Psoriatic Arthritis (PsA) Core Domain Set

    DEFF Research Database (Denmark)

    Orbai, Ana-Maria; de Wit, Maarten; Mease, Philip J

    2017-01-01

    OBJECTIVE: To include the patient perspective in accordance with the Outcome Measures in Rheumatology (OMERACT) Filter 2.0 in the updated Psoriatic Arthritis (PsA) Core Domain Set for randomized controlled trials (RCT) and longitudinal observational studies (LOS). METHODS: At OMERACT 2016, research...... conducted to update the PsA Core Domain Set was presented and discussed in breakout groups. The updated PsA Core Domain Set was voted on and endorsed by OMERACT participants. RESULTS: We conducted a systematic literature review of domains measured in PsA RCT and LOS, and identified 24 domains. We conducted...... and breakout groups at OMERACT 2016 in which findings were presented and discussed. The updated PsA Core Domain Set endorsed with 90% agreement by OMERACT 2016 participants included musculoskeletal disease activity, skin disease activity, fatigue, pain, patient's global assessment, physical function, health...

  13. Towards Domain-specific Flow-based Languages

    DEFF Research Database (Denmark)

    Zarrin, Bahram; Baumeister, Hubert; Sarjoughian, Hessam S.

    2018-01-01

    describe their problems and solutions, instead of using general purpose programming languages. The goal of these languages is to improve the productivity and efficiency of the development and simulation of concurrent scientific models and systems. Moreover, they help to expose parallelism and to specify...... the concurrency within a component or across different independent components. In this paper, we introduce the concept of domain-specific flowbased languages which allows domain experts to use flow-based languages adapted to a particular problem domain. Flow-based programming is used to support concurrency, while......Due to the significant growth of the demand for data-intensive computing, in addition to the emergence of new parallel and distributed computing technologies, scientists and domain experts are leveraging languages specialized for their problem domain, i.e., domain-specific languages, to help them...

  14. Towards consolidating the plant trait data domain

    Science.gov (United States)

    Kattge, Jens

    2017-04-01

    In response to the basic concept of this session - 'the optimality principle proposes that organisms adjust to environmental variations so as to maximize measures that impinge on fitness, and are thereby subject to natural selection' - we propose that observable characteristics of individual plant organisms - plant traits - are the product of optimality principles and thus provide a first level to validate implementations of optimality principles in vegetation models. On the long term, the application of optimality principles may thus lead to a shift of paradigm in vegetation modeling, where plant traits were traditionally used for model parameterization, but in the future may provide the first step in a hierarchical cascade of model validation at multiple scales. However, so far the value of plant traits is obscured by two roadblocks: ecological research produces a tremendous amount of trait data, but the diversity in topics covered and the ways in which studies are carried out result in large numbers of small, idiosyncratic data sets using heterogeneous terminologies. Such heterogeneity can be attributed, in part, to a lack of standards for acquiring, organizing and describing data. We here present recent progress in consolidating the plant trait data domain by standardized terminology (TOP thesaurus of plant characteristics: top-thesaurus.org) and data integration (TRY database: try-db.org) - and we report current limits. Nevertheless, we suggest that consolidated trait data are a valuable tool for optimality driven vegetation model development and validation.

  15. New parallel SOR method by domain partitioning

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Dexuan [Courant Inst. of Mathematical Sciences New York Univ., NY (United States)

    1996-12-31

    In this paper, we propose and analyze a new parallel SOR method, the PSOR method, formulated by using domain partitioning together with an interprocessor data-communication technique. For the 5-point approximation to the Poisson equation on a square, we show that the ordering of the PSOR based on the strip partition leads to a consistently ordered matrix, and hence the PSOR and the SOR using the row-wise ordering have the same convergence rate. However, in general, the ordering used in PSOR may not be {open_quote}consistently ordered{close_quotes}. So, there is a need to analyze the convergence of PSOR directly. In this paper, we present a PSOR theory, and show that the PSOR method can have the same asymptotic rate of convergence as the corresponding sequential SOR method for a wide class of linear systems in which the matrix is {open_quotes}consistently ordered{close_quotes}. Finally, we demonstrate the parallel performance of the PSOR method on four different message passing multiprocessors (a KSR1, the Intel Delta, an Intel Paragon and an IBM SP2), along with a comparison with the point Red-Black and four-color SOR methods.

  16. Performance of scalable coding in depth domain

    Science.gov (United States)

    Sjöström, Mårten; Karlsson, Linda S.

    2010-02-01

    Common autostereoscopic 3D displays are based on multi-view projection. The diversity of resolutions and number of views of such displays implies a necessary flexibility of 3D content formats in order to make broadcasting efficient. Furthermore, distribution of content over a heterogeneous network should adapt to an available network capacity. Present scalable video coding provides the ability to adapt to network conditions; it allows for quality, temporal and spatial scaling of 2D video. Scalability for 3D data extends this list to the depth and the view domains. We have introduced scalability with respect to depth information. Our proposed scheme is based on the multi-view-plus-depth format where the center view data are preserved, and side views are extracted in enhancement layers depending on depth values. We investigate the performance of various layer assignment strategies: number of layers, and distribution of layers in depth, either based on equal number of pixels or histogram characteristics. We further consider the consequences to variable distortion due to encoder parameters. The results are evaluated considering their overall distortion verses bit rate, distortion per enhancement layer, as well as visual quality appearance. Scalability with respect to depth (and views) allows for an increased number of quality steps; the cost is a slight increase of required capacity for the whole sequence. The main advantage is, however, an improved quality for objects close to the viewer, even if overall quality is worse.

  17. Speech Enhancement in the STFT Domain

    CERN Document Server

    Benesty, Jacob; Habets, Emanuël A P

    2012-01-01

    This work addresses this problem in the short-time Fourier transform (STFT) domain. We divide the general problem into five basic categories depending on the number of microphones being used and whether the interframe or interband correlation is considered. The first category deals with the single-channel problem where STFT coefficients at different frames and frequency bands are assumed to be independent. In this case, the noise reduction filter in each frequency band is basically a real gain. Since a gain does not improve the signal-to-noise ratio (SNR) for any given subband and frame, the noise reduction is basically achieved by liftering the subbands and frames that are less noisy while weighing down on those that are more noisy. The second category also concerns the single-channel problem. The difference is that now the interframe correlation is taken into account and a filter is applied in each subband instead of just a gain. The advantage of using the interframe correlation is that we can improve not o...

  18. Domain-specific knowledge as playful interaction

    DEFF Research Database (Denmark)

    Valente, Andrea; Marchetti, Emanuela

    2015-01-01

    Starting from reflections on designing games for learning, aimed at providing a tangible grounding to abstract knowledge, we designed Prime Slaughter, a game to support learning of factorisation and prime numbers, targeted to primary and early secondary school children. This new study draws upon ...... on activity theory, aimed at facilitating the transposition of abstract knowledge into playful interactions, so to develop new learning games of this kind, also keeping into account children’s individual needs regarding play.......Starting from reflections on designing games for learning, aimed at providing a tangible grounding to abstract knowledge, we designed Prime Slaughter, a game to support learning of factorisation and prime numbers, targeted to primary and early secondary school children. This new study draws upon...... the design process of Prime Slaughter, to move further in developing a general approach in developing games, aimed at effectively conveying knowledge from a specific domain. Hence this paper will discuss the past design process, as a concrete case, and then formulate a theoretical framework, based...

  19. Domain wall QCD with physical quark masses

    CERN Document Server

    Blum, T.; Christ, N.H.; Frison, J.; Garron, N.; Hudspith, R.J.; Izubuchi, T.; Janowski, T.; Jung, C.; Jüttner, A.; Kelly, C.; Kenway, R.D.; Lehner, C.; Marinkovic, M.; Mawhinney, R.D.; McGlynn, G.; Murphy, D.J.; Ohta, S.; Portelli, A.; Sachrajda, C.T.; Soni, A.

    2016-01-01

    We present results for several light hadronic quantities ($f_\\pi$, $f_K$, $B_K$, $m_{ud}$, $m_s$, $t_0^{1/2}$, $w_0$) obtained from simulations of 2+1 flavor domain wall lattice QCD with large physical volumes and nearly-physical pion masses at two lattice spacings. We perform a short, O(3)%, extrapolation in pion mass to the physical values by combining our new data in a simultaneous chiral/continuum `global fit' with a number of other ensembles with heavier pion masses. We use the physical values of $m_\\pi$, $m_K$ and $m_\\Omega$ to determine the two quark masses and the scale - all other quantities are outputs from our simulations. We obtain results with sub-percent statistical errors and negligible chiral and finite-volume systematics for these light hadronic quantities, including: $f_\\pi$ = 130.2(9) MeV; $f_K$ = 155.5(8) MeV; the average up/down quark mass and strange quark mass in the $\\bar {\\rm MS}$ scheme at 3 GeV, 2.997(49) and 81.64(1.17) MeV respectively; and the neutral kaon mixing parameter, $B_K$...

  20. Chiral damping of magnetic domain walls

    KAUST Repository

    Jué, Emilie

    2015-12-21

    Structural symmetry breaking in magnetic materials is responsible for the existence of multiferroics1, current-induced spin–orbit torques2, 3, 4, 5, 6, 7 and some topological magnetic structures8, 9, 10, 11, 12. In this Letter we report that the structural inversion asymmetry (SIA) gives rise to a chiral damping mechanism, which is evidenced by measuring the field-driven domain-wall (DW) motion in perpendicularly magnetized asymmetric Pt/Co/Pt trilayers. The DW dynamics associated with the chiral damping and those with Dzyaloshinskii–Moriya interaction (DMI) exhibit identical spatial symmetry13, 14, 15, 16, 17, 18, 19. However, both scenarios are differentiated by their time reversal properties: whereas DMI is a conservative effect that can be modelled by an effective field, the chiral damping is purely dissipative and has no influence on the equilibrium magnetic texture. When the DW motion is modulated by an in-plane magnetic field, it reveals the structure of the internal fields experienced by the DWs, allowing one to distinguish the physical mechanism. The chiral damping enriches the spectrum of physical phenomena engendered by the SIA, and is essential for conceiving DW and skyrmion devices owing to its coexistence with DMI (ref. 20).

  1. Elasticity problems in domains with nonsmooth boundaries

    CERN Document Server

    Esparza, D

    2001-01-01

    In the present work we study the behaviour of elastic stress fields in domains with non-regular boundaries. We consider three-dimensional problems in elastic media with thin conical defects (inclusions or cavities) and analyse the stress singularity at their vertices. To construct asymptotic expansions for the stress and displacement fields in terms of a small parameter epsilon related to the 'thickness' of the defect, we employ a technique based on the work by Kondrat'ev, Maz'ya, Nazarov and Plamenevskii. We first study the stress distribution in an elastic body with a thin conical notch. We derive an asymptotic representation for the stress singularity exponent by reducing the original problem to a spectral problem for a 9x9 matrix. The elements of this matrix are found to depend upon the geometry of the cross-section of the notch and the elastic properties of the medium. We specify the sets of eigenvalues and the corresponding eigenvectors for a circular, elliptical, 'triangular' and 'square' cross-section...

  2. Refocusing your domain (until a better title)

    CERN Multimedia

    CERN. Geneva

    2017-01-01

    This forum's subject is from 'Zero to Production'. But what exactly goes on during the 'zero' phase? What are the questions that you and your team ask yourselves before starting to code, and which are the first decisions you make? 'Apache or Nginx? Flask or Django? PostreSQL or MongoDB? Containers or VMs?', are usual questions that are brought forward during the design phase. Albeit cool and exciting, these issues are the wrong things to consider ourselves with during the first stages of software development. What is the domain your application operates on? What are your core entities and how do they interract with each other on a logical level? Which are the business rules that would persist whether you would be creating a Web application, a Command Line Interface or simple drawings on a whiteboard? Not only should these issues be the first for a developer to consider but their importance should be clearly reflected in the application's code. In 2012, Robert C. Martin (Uncle Bob) proposed a layered soft...

  3. Domain Wall Mobility in Co-Based Amorphous Wire

    Directory of Open Access Journals (Sweden)

    Maria Kladivova

    2007-01-01

    Full Text Available Dynamics of the domain wall between opposite circularly magnetized domains in amorphous cylindrical sample with circular easy direction is theoretically studied. The wall is driven by DC current. Various mechanisms which influence the wall velocity were taken into account: current magnitude, deformation of the mowing wall, Hall effect, axially magnetized domain in the middle of the wire. Theoretical results obtained are in a good agreement with experiments on Cobased amorphous ferromagnetic wires.

  4. Multi-Domain SDN Survivability for Agricultural Wireless Sensor Networks

    OpenAIRE

    Huang, Tao; Yan, Siyu; Yang, Fan; Liu, Jiang

    2016-01-01

    Wireless sensor networks (WSNs) have been widely applied in agriculture field; meanwhile, the advent of multi-domain software-defined networks (SDNs) have improved the wireless resource utilization rate and strengthened network management. In recent times, multi-domain SDNs have been applied to agricultural sensor networks, namely multi-domain software-defined wireless sensor networks (SDWSNs). However, when the SDNs controlling agriculture networks suddenly become unavailable, whether intra-...

  5. Cyberspace at the Operational Level: Warfighting in All Five Domains

    Science.gov (United States)

    2016-05-13

    potential is not optimized. Great operational ideas of history have been innovative and bold. As mentioned before, due to the nature of cyberspace , no...FINAL 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE Cyberspace at the Operational Level: Warfighting In All Five Domains...connects all four of these domains to the people on our planet? Cyberspace , the fifth domain of warfare, is now so ubiquitous and that any military

  6. Stability estimates for hybrid coupled domain decomposition methods

    CERN Document Server

    Steinbach, Olaf

    2003-01-01

    Domain decomposition methods are a well established tool for an efficient numerical solution of partial differential equations, in particular for the coupling of different model equations and of different discretization methods. Based on the approximate solution of local boundary value problems either by finite or boundary element methods, the global problem is reduced to an operator equation on the skeleton of the domain decomposition. Different variational formulations then lead to hybrid domain decomposition methods.

  7. The Consequences of Chronic Stereotype Threat: Domain Disidentification and Abandonment

    OpenAIRE

    Woodcock, Anna; Hernandez, Paul R.; Estrada, Mica; Schultz, P. Wesley

    2012-01-01

    Stereotype threat impairs performance across many domains. Despite a wealth of research, the long-term consequences of chronic stereotype threat have received little empirical attention. Beyond the immediate impact on performance, the experience of chronic stereotype threat is hypothesized to lead to domain disidentification and eventual domain abandonment. Stereotype threat is 1 explanation why African Americans and Hispanic/Latino(a)s “leak” from each juncture of the academic scientific pip...

  8. Linked-data based domain-specific sentiment lexicons

    OpenAIRE

    Vulcu, Gabriela; Lario Monje, Raúl; Muñoz, Mario; Buitelaar, Paul; Iglesias Fernandez, Carlos Angel

    2014-01-01

    In this paper we present a dataset componsed of domain-specific sentiment lexicons in six languages for two domains. We used existing collections of reviews from Trip Advisor, Amazon, the Stanford Network Analysis Project and the OpinRank Review Dataset. We use an RDF model based on the lemon and Marl formats to represent the lexicons. We describe the methodology that we applied to generate the domain-specific lexicons and we provide access information to our datasets.

  9. Domain analysis and modeling to improve comparability of health statistics.

    Science.gov (United States)

    Okada, M; Hashimoto, H; Ohida, T

    2001-01-01

    Health statistics is an essential element to improve the ability of managers of health institutions, healthcare researchers, policy makers, and health professionals to formulate appropriate course of reactions and to make decisions based on evidence. To ensure adequate health statistics, standards are of critical importance. A study on healthcare statistics domain analysis is underway in an effort to improve usability and comparability of health statistics. The ongoing study focuses on structuring the domain knowledge and making the knowledge explicit with a data element dictionary being the core. Supplemental to the dictionary are a domain term list, a terminology dictionary, and a data model to help organize the concepts constituting the health statistics domain.

  10. Integral UBL domain proteins: a family of proteasome interacting proteins

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Gordon, Colin

    2004-01-01

    The family of ubiquitin-like (UBL) domain proteins (UDPs) comprises a conserved group of proteins involved in a multitude of different cellular activities. However, recent studies on UBL-domain proteins indicate that these proteins appear to share a common property in their ability to interact......-domain proteins catalyse the formation of ubiquitin-protein conjugates, whereas others appear to target ubiquitinated proteins for degradation and interact with chaperones. Hence, by binding to the 26S proteasome the UBL-domain proteins seem to tailor and direct the basic proteolytic functions of the particle...

  11. Friction anisotropy-driven domain imaging on exfoliated monolayer graphene.

    Science.gov (United States)

    Choi, Jin Sik; Kim, Jin-Soo; Byun, Ik-Su; Lee, Duk Hyun; Lee, Mi Jung; Park, Bae Ho; Lee, Changgu; Yoon, Duhee; Cheong, Hyeonsik; Lee, Ki Ho; Son, Young-Woo; Park, Jeong Young; Salmeron, Miquel

    2011-07-29

    Graphene produced by exfoliation has not been able to provide an ideal graphene with performance comparable to that predicted by theory, and structural and/or electronic defects have been proposed as one cause of reduced performance. We report the observation of domains on exfoliated monolayer graphene that differ by their friction characteristics, as measured by friction force microscopy. Angle-dependent scanning revealed friction anisotropy with a periodicity of 180° on each friction domain. The friction anisotropy decreased as the applied load increased. We propose that the domains arise from ripple distortions that give rise to anisotropic friction in each domain as a result of the anisotropic puckering of the graphene.

  12. Time-domain radio pulses from particle showers

    International Nuclear Information System (INIS)

    Alvarez-Muñiz, Jaime; Romero-Wolf, Andrés; Zas, Enrique

    2012-01-01

    The time-domain properties of the far-field coherent radio emission from electromagnetic showers are studied in depth. A purely time-domain technique for mapping the electromagnetic fields of charged tracks is developed. The method is applied to the ZHS shower code to produce electric fields. It is demonstrated that the technique is equivalent to the frequency domain methods used in the ZHS code and produces consistent results. In addition, a model for mapping the longitudinal charge profile of a shower to a time-domain electromagnetic field is developed. It is shown that the model is in good agreement to the results of shower simulation.

  13. Domain-wall trapping in a ferromagnetic nanowire network

    Science.gov (United States)

    Saitoh, E.; Tanaka, M.; Miyajima, H.; Yamaoka, T.

    2003-05-01

    The magnetic domain configuration in a submicron Ni81Fe19 wire network has been investigated by magnetic force microscopy. To improve the responsivity of the magnetic force microscope, an active quality factor autocontrol method was adopted. In the remanent state, domain walls were observed trapped firmly at the vertexes of the network. The magnetic domain configurations appear to minimize the exchange energy at the vertexes. These results indicate that the magnetic property of the ferromagnetic network can be described in terms of the uniform magnetic moments of the wires and interwire magnetic interactions at the vertexes. The observed structure of the domain walls is well reproduced by micromagnetic simulations.

  14. Stochastic single-molecule dynamics of synaptic membrane protein domains

    Science.gov (United States)

    Kahraman, Osman; Li, Yiwei; Haselwandter, Christoph A.

    2016-09-01

    Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the single-molecule trajectories observed for synaptic proteins, and spatially inhomogeneous protein lifetimes at the cell membrane. Our results suggest that central aspects of the single-molecule and collective dynamics observed for membrane protein domains can be understood in terms of stochastic reaction-diffusion processes at the cell membrane.

  15. Distributions of electric and elastic fields at domain boundaries

    International Nuclear Information System (INIS)

    Novak, Josef; Fousek, Jan; Maryska, Jiri; Marvan, Milan

    2005-01-01

    In this paper we describe the application of the finite element method (FEM) in modelling spatial distributions of electric and elastic fields in a ferroelectric crystals with two domains separated by a 90 deg. domain wall. The domain boundary is idealized as a two-dimensional defect in an electro-elastic continuum. It represents the source of inhomogenity and internal distortion in both elastic and electric fields. The main results are distributions of electric field, strain and mechanical force along the domain boundary

  16. Investigation of ferromagnetic domain structures by neutron small angle scattering

    International Nuclear Information System (INIS)

    Schild, L.

    1984-01-01

    The magnetic small angle scattering of thermal neutrons caused by magnetic refraction at domain walls of ferromagnetic materials without texture has been investigated. Experiments on Fe-Si alloys with a twin crystal diffractometer were carried out. It is shown that the mean extension of magnetic basic units (domains as well as parallel wall systems) can be determined. A comparison of grain sizes determined metallographically with domain sizes obtained by neutron small-angle scattering has shown that neither mean grain size nor domain size can be assessed by small-angle scattering experiments

  17. Preserving the positive functions of the public domain in science

    Directory of Open Access Journals (Sweden)

    Pamela Samuelson

    2003-11-01

    Full Text Available Science has advanced in part because data and scientific methodologies have traditionally not been subject to intellectual property protection. In recent years, intellectual property has played a greater role in scientific work. While intellectual property rights may have a positive role to play in some fields of science, so does the public domain. This paper will discuss some of the positive functions of the public domain and ways in which certain legal developments may negatively impact the public domain. It suggests some steps that scientists can take to preserve the positive functions of the public domain for science.

  18. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily

    Directory of Open Access Journals (Sweden)

    Marc Lenoir

    2015-10-01

    Full Text Available The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH and Tec homology (TH domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  19. Domain decomposition techniques for boundary elements application to fluid flow

    CERN Document Server

    Brebbia, C A; Skerget, L

    2007-01-01

    The sub-domain techniques in the BEM are nowadays finding its place in the toolbox of numerical modellers, especially when dealing with complex 3D problems. We see their main application in conjunction with the classical BEM approach, which is based on a single domain, when part of the domain needs to be solved using a single domain approach, the classical BEM, and part needs to be solved using a domain approach, BEM subdomain technique. This has usually been done in the past by coupling the BEM with the FEM, however, it is much more efficient to use a combination of the BEM and a BEM sub-domain technique. The advantage arises from the simplicity of coupling the single domain and multi-domain solutions, and from the fact that only one formulation needs to be developed, rather than two separate formulations based on different techniques. There are still possibilities for improving the BEM sub-domain techniques. However, considering the increased interest and research in this approach we believe that BEM sub-do...

  20. Patterns, principles, and practices of domain-driven design

    CERN Document Server

    Millett, Scott

    2015-01-01

    Methods for managing complex software construction following the practices, principles and patterns of Domain-Driven Design with code examples in C# This book presents the philosophy of Domain-Driven Design (DDD) in a down-to-earth and practical manner for experienced developers building applications for complex domains. A focus is placed on the principles and practices of decomposing a complex problem space as well as the implementation patterns and best practices for shaping a maintainable solution space. You will learn how to build effective domain models through the use of tactical pat

  1. Ratchet effect of the domain wall by asymmetric magnetostatic potentials

    Science.gov (United States)

    Piao, Hong-Guang; Choi, Hyeok-Cheol; Shim, Je-Ho; Kim, Dong-Hyun; You, Chun-Yeol

    2011-11-01

    We investigate a ratchet effect of magnetic domain wall motion in a ferromagnetic nanowire under AC magnetic fields using micromagnetic simulation. The ratchet effect for a transverse domain wall is achieved using an asymmetric magnetic potential generated by stray fields from non-contact trapezoidal ferromagnetic stubs near the straight nanowire. The ratchet phenomenon has been examined with various combinations of amplitude and frequency of the driving AC field. Interestingly, we find that the domain wall propagates along a preferential direction by the diode-like ratchet effect under AC field. The propagation of the domain wall strongly depends on the profile of the asymmetrical magnetic potentials and the driving AC field characteristics.

  2. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

    Science.gov (United States)

    Lenoir, Marc; Kufareva, Irina; Abagyan, Ruben; Overduin, Michael

    2015-10-23

    The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  3. 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.

  4. Response of biomembrane domains to external stimuli

    Science.gov (United States)

    Urbancic, Iztok

    To enrich our knowledge about membrane domains, new measurement techniques with extended spatial and temporal windows are being vigorously developed by combining various approaches. Following such efforts of the scientific community, we set up fluorescence microspectroscopy (FMS), bridging two well established methods: fluorescence microscopy, which enables imaging of the samples with spatial resolution down to 200 nm, and fluorescence spectroscopy that provides molecular information of the environment at nanometer and nanosecond scale. The combined method therefore allows us to localize this type of information with the precision suitable for studying various cellular structures. Faced with weak available fluorescence signals, we have put considerable efforts into optimization of measurement processes and analysis of the data. By introducing a novel acquisition scheme and by fitting the data with a mathematical model, we preserved the spectral resolution, characteristic for spectroscopic measurements of bulk samples, also at microscopic level. We have at the same time overcome the effects of photobleaching, which had previously considerably distorted the measured spectral lineshape of photosensitive dyes and consequently hindered the reliability of FMS. Our new approach has therefore greatly extended the range of applicable environmentally sensitive probes, which can now be designed to better accommodate the needs of each particular experiment. Moreover, photobleaching of fluorescence signal can now even be exploited to obtain new valuable information about molecular environment of the probes, as bleaching rates of certain probes also depend on physical and chemical properties of the local surroundings. In this manner we increased the number of available spatially localized spectral parameters, which becomes invaluable when investigating complex biological systems that can only be adequately characterized by several independent variables. Applying the developed

  5. 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

  6. Interaction Between the Biotin Carboxyl Carrier Domain and the Biotin Carboxylase Domain in Pyruvate Carboxylase from Rhizobium etli†

    Science.gov (United States)

    Lietzan, Adam D.; Menefee, Ann L.; Zeczycki, Tonya N.; Kumar, Sudhanshu; Attwood, Paul V.; Wallace, John C.; Cleland, W. Wallace; Maurice, Martin St.

    2011-01-01

    Pyruvate carboxylase (PC) catalyzes the ATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To effect catalysis, the tethered biotin of PC must gain access to active sites in both the biotin carboxylase domain and the carboxyl transferase domain. Previous studies have demonstrated that a mutation of threonine 882 to alanine in PC from Rhizobium etli renders the carboxyl transferase domain inactive and favors the positioning of biotin in the biotin carboxylase domain. We report the 2.4 Å resolution X-ray crystal structure of the Rhizobium etli PC T882A mutant which reveals the first high-resolution description of the domain interaction between the biotin carboxyl carrier protein domain and the biotin carboxylase domain. The overall quaternary arrangement of Rhizobium etli PC remains highly asymmetrical and is independent of the presence of allosteric activator. While biotin is observed in the biotin carboxylase domain, its access to the active site is precluded by the interaction between Arg353 and Glu248, revealing a mechanism for regulating carboxybiotin access to the BC domain active site. The binding location for the biotin carboxyl carrier protein domain demonstrates that tethered biotin cannot bind in the biotin carboxylase domain active site in the same orientation as free biotin, helping to explain the difference in catalysis observed between tethered biotin and free biotin substrates in biotin carboxylase enzymes. Electron density located in the biotin carboxylase domain active site is assigned to phosphonoacetate, offering a probable location for the putative carboxyphosphate intermediate formed during biotin carboxylation. The insights gained from the T882A Rhizobium etli PC crystal structure provide a new series of catalytic snapshots in PC and offer a revised perspective on catalysis in the biotin-dependent enzyme family. PMID:21958016

  7. RHOMBOID DOMAIN CONTAINING 2 (RHBDD2)

    Science.gov (United States)

    Abba, MC; Lacunza, E; Nunez, MI; Colussi, A; Isla-Larrain, M; Segal-Eiras, A; Croce, MV; Aldaz, CM

    2009-01-01

    In the course of breast cancer global gene expression studies, we identified an uncharacterized gene known as RHBDD2 (Rhomboid domain containing 2) to be markedly over-expressed in primary tumors from patients with recurrent disease. In this study, we identified RHBDD2 mRNA and protein expression significantly elevated in breast carcinomas compared with normal breast samples as analyzed by SAGE (n=46) and immunohistochemistry (n=213). Interestingly, specimens displaying RHBDD2 over-expression were predominantly advanced stage III breast carcinomas (p=0.001). Western-blot, RT-PCR and cDNA sequencing analyses allowed us to identify two RHBDD2 alternatively spliced mRNA isoforms expressed in breast cancer cell lines. We further investigated the occurrence and frequency of gene amplification and over-expression affecting RHBDD2 in 131 breast samples. RHBDD2 gene amplification was detected in 21% of 98 invasive breast carcinomas analyzed. However, no RHBDD2 amplification was detected in normal breast tissues (n=17) or breast benign lesions (n=16) (p=0.014). Interestingly, siRNA mediated silencing of RHBDD2 expression results in a decrease of MCF7 breast cancer cells proliferation compared with the corresponding controls (p=0.001). In addition, analysis of publicly available gene expression data showed a strong association between high RHBDD2 expression and decreased overall survival (p=0.0023), relapse-free survival (p= 0.0013), and metastasis-free interval (p=0.006) in patients with primary ER-negative breast carcinomas. In conclusion, our findings suggest that RHBDD2 over-expression behaves as an indicator of poor prognosis and may play a role facilitating breast cancer progression. PMID:19616622

  8. Parametric evaluation of an SMR design domain

    International Nuclear Information System (INIS)

    Al Rashdan, Ahmad; Tsvetkov, Pavel

    2015-01-01

    Highlights: • The design of nuclear reactors involves a large set of highly coupled variables. • The effects of 14 variables on 6 SMR performance characteristics was researched. • Screening and sensitivity analyses were applied to decouple the variables’ effects. • Significantly simpler system models were generated, enabling simple optimization. - Abstract: The complex and coupled behavior of the variables that affect the currently developing generation IV reactors and the increase of interest in Small Modular Reactors are major incentives to seek efficient design methods. Instead of the brute force design methodology, often applied to the analysis of nuclear reactors, other more economical and systematic methods should be applied. In a complex system with a high number of variables, it often is necessary to develop models to describe the behavior of each performance characteristic with respect to a set of variables and their interactions. If expensive experiments are needed to develop these models, the number of experiments should be minimized. This can be achieved by designing the experiments to be performed. Once the system’s models are developed, they can be used to decouple the variables’ effects on the performance characteristics and simplify the optimization process. In this article, three screening and sensitivity analysis methods are applied to decouple and understand the effects of fourteen variables on six performance characteristics of a Small Modular Reactor’s design, based on the Advanced Passive (AP-1000) reactor. The application of these methods facilitated the determination of the most important parameters of each performance characteristic, and resulted in several distinctive findings. These findings are applicable to any Light Water Small Modular Reactor that falls within the variables’ design domain

  9. An information theory framework for dynamic functional domain connectivity.

    Science.gov (United States)

    Vergara, Victor M; Miller, Robyn; Calhoun, Vince

    2017-06-01

    Dynamic functional network connectivity (dFNC) analyzes time evolution of coherent activity in the brain. In this technique dynamic changes are considered for the whole brain. This paper proposes an information theory framework to measure information flowing among subsets of functional networks call functional domains. Our method aims at estimating bits of information contained and shared among domains. The succession of dynamic functional states is estimated at the domain level. Information quantity is based on the probabilities of observing each dynamic state. Mutual information measurement is then obtained from probabilities across domains. Thus, we named this value the cross domain mutual information (CDMI). Strong CDMIs were observed in relation to the subcortical domain. Domains related to sensorial input, motor control and cerebellum form another CDMI cluster. Information flow among other domains was seldom found. Other methods of dynamic connectivity focus on whole brain dFNC matrices. In the current framework, information theory is applied to states estimated from pairs of multi-network functional domains. In this context, we apply information theory to measure information flow across functional domains. Identified CDMI clusters point to known information pathways in the basal ganglia and also among areas of sensorial input, patterns found in static functional connectivity. In contrast, CDMI across brain areas of higher level cognitive processing follow a different pattern that indicates scarce information sharing. These findings show that employing information theory to formally measured information flow through brain domains reveals additional features of functional connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Multi-Domain SDN Survivability for Agricultural Wireless Sensor Networks.

    Science.gov (United States)

    Huang, Tao; Yan, Siyu; Yang, Fan; Liu, Jiang

    2016-11-06

    Wireless sensor networks (WSNs) have been widely applied in agriculture field; meanwhile, the advent of multi-domain software-defined networks (SDNs) have improved the wireless resource utilization rate and strengthened network management. In recent times, multi-domain SDNs have been applied to agricultural sensor networks, namely multi-domain software-defined wireless sensor networks (SDWSNs). However, when the SDNs controlling agriculture networks suddenly become unavailable, whether intra-domain or inter-domain, sensor network communication is abnormal because of the loss of control. Moreover, there are controller and switch info-updating problems even if the controller becomes available again. To resolve these problems, this paper proposes a new approach based on an Open vSwitch extension for multi-domain SDWSNs, which can enhance agriculture network survivability and stability. We achieved this by designing a connection-state mechanism, a communication mechanism on both L2 and L3, and an info-updating mechanism based on Open vSwitch. The experimental results show that, whether it is agricultural inter-domain or intra-domain during the controller failure period, the sensor switches can enter failure recovery mode as soon as possible so that the sensor network keeps a stable throughput, a short failure recovery time below 300 ms, and low packet loss. Further, the domain can smoothly control the domain network again once the controller becomes available. This approach based on an Open vSwitch extension can enhance the survivability and stability of multi-domain SDWSNs in precision agriculture.

  11. Multi-Domain SDN Survivability for Agricultural Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Tao Huang

    2016-11-01

    Full Text Available Wireless sensor networks (WSNs have been widely applied in agriculture field; meanwhile, the advent of multi-domain software-defined networks (SDNs have improved the wireless resource utilization rate and strengthened network management. In recent times, multi-domain SDNs have been applied to agricultural sensor networks, namely multi-domain software-defined wireless sensor networks (SDWSNs. However, when the SDNs controlling agriculture networks suddenly become unavailable, whether intra-domain or inter-domain, sensor network communication is abnormal because of the loss of control. Moreover, there are controller and switch info-updating problems even if the controller becomes available again. To resolve these problems, this paper proposes a new approach based on an Open vSwitch extension for multi-domain SDWSNs, which can enhance agriculture network survivability and stability. We achieved this by designing a connection-state mechanism, a communication mechanism on both L2 and L3, and an info-updating mechanism based on Open vSwitch. The experimental results show that, whether it is agricultural inter-domain or intra-domain during the controller failure period, the sensor switches can enter failure recovery mode as soon as possible so that the sensor network keeps a stable throughput, a short failure recovery time below 300 ms, and low packet loss. Further, the domain can smoothly control the domain network again once the controller becomes available. This approach based on an Open vSwitch extension can enhance the survivability and stability of multi-domain SDWSNs in precision agriculture.

  12. On the Analysis Methods for the Time Domain and Frequency Domain Response of a Buried Objects*

    Science.gov (United States)

    Poljak, Dragan; Šesnić, Silvestar; Cvetković, Mario

    2014-05-01

    There has been a continuous interest in the analysis of ground-penetrating radar systems and related applications in civil engineering [1]. Consequently, a deeper insight of scattering phenomena occurring in a lossy half-space, as well as the development of sophisticated numerical methods based on Finite Difference Time Domain (FDTD) method, Finite Element Method (FEM), Boundary Element Method (BEM), Method of Moments (MoM) and various hybrid methods, is required, e.g. [2], [3]. The present paper deals with certain techniques for time and frequency domain analysis, respectively, of buried conducting and dielectric objects. Time domain analysis is related to the assessment of a transient response of a horizontal straight thin wire buried in a lossy half-space using a rigorous antenna theory (AT) approach. The AT approach is based on the space-time integral equation of the Pocklington type (time domain electric field integral equation for thin wires). The influence of the earth-air interface is taken into account via the simplified reflection coefficient arising from the Modified Image Theory (MIT). The obtained results for the transient current induced along the electrode due to the transmitted plane wave excitation are compared to the numerical results calculated via an approximate transmission line (TL) approach and the AT approach based on the space-frequency variant of the Pocklington integro-differential approach, respectively. It is worth noting that the space-frequency Pocklington equation is numerically solved via the Galerkin-Bubnov variant of the Indirect Boundary Element Method (GB-IBEM) and the corresponding transient response is obtained by the aid of inverse fast Fourier transform (IFFT). The results calculated by means of different approaches agree satisfactorily. Frequency domain analysis is related to the assessment of frequency domain response of dielectric sphere using the full wave model based on the set of coupled electric field integral

  13. Lantibiotic transporter requires cooperative functioning of the peptidase domain and the ATP binding domain.

    Science.gov (United States)

    Nishie, Mami; Sasaki, Makoto; Nagao, Jun-ichi; Zendo, Takeshi; Nakayama, Jiro; Sonomoto, Kenji

    2011-04-01

    Lantibiotics are ribosomally synthesized and post-translationally modified peptide antibiotics that contain unusual amino acids such as dehydro and lanthionine residues. Nukacin ISK-1 is a class II lantibiotic, whose precursor peptide (NukA) is modified by NukM to form modified NukA. ATP-binding cassette (ABC) transporter NukT is predicted to cleave off the N-terminal leader peptide of modified NukA and secrete the mature peptide. Multiple sequence alignments revealed that NukT has an N-terminal peptidase domain (PEP) and a C-terminal ATP binding domain (ABD). Previously, in vitro reconstitution of NukT has revealed that NukT peptidase activity depends on ATP hydrolysis. Here, we constructed a series of NukT mutants and investigated their transport activity in vivo and peptidase activity in vitro. Most of the mutations of the conserved residues of PEP or ABD resulted in failure of nukacin ISK-1 production and accumulation of modified NukA inside the cells. NukT(N106D) was found to be the only mutant capable of producing nukacin ISK-1. Asn(106) is conserved as Asp in other related ABC transporters. Additionally, an in vitro peptidase assay of NukT mutants demonstrated that PEP is on the cytosolic side and all of the ABD mutants as well as PEP (with the exception of NukT(N106D)) did not have peptidase activity in vitro. Taken together, these observations suggest that the leader peptide is cleaved off inside the cells before peptide secretion; both PEP and ABD are important for NukT peptidase activity, and cooperation between these two domains inside the cells is indispensable for proper functioning of NukT.

  14. Lantibiotic Transporter Requires Cooperative Functioning of the Peptidase Domain and the ATP Binding Domain*

    Science.gov (United States)

    Nishie, Mami; Sasaki, Makoto; Nagao, Jun-ichi; Zendo, Takeshi; Nakayama, Jiro; Sonomoto, Kenji

    2011-01-01

    Lantibiotics are ribosomally synthesized and post-translationally modified peptide antibiotics that contain unusual amino acids such as dehydro and lanthionine residues. Nukacin ISK-1 is a class II lantibiotic, whose precursor peptide (NukA) is modified by NukM to form modified NukA. ATP-binding cassette (ABC) transporter NukT is predicted to cleave off the N-terminal leader peptide of modified NukA and secrete the mature peptide. Multiple sequence alignments revealed that NukT has an N-terminal peptidase domain (PEP) and a C-terminal ATP binding domain (ABD). Previously, in vitro reconstitution of NukT has revealed that NukT peptidase activity depends on ATP hydrolysis. Here, we constructed a series of NukT mutants and investigated their transport activity in vivo and peptidase activity in vitro. Most of the mutations of the conserved residues of PEP or ABD resulted in failure of nukacin ISK-1 production and accumulation of modified NukA inside the cells. NukT(N106D) was found to be the only mutant capable of producing nukacin ISK-1. Asn106 is conserved as Asp in other related ABC transporters. Additionally, an in vitro peptidase assay of NukT mutants demonstrated that PEP is on the cytosolic side and all of the ABD mutants as well as PEP (with the exception of NukT(N106D)) did not have peptidase activity in vitro. Taken together, these observations suggest that the leader peptide is cleaved off inside the cells before peptide secretion; both PEP and ABD are important for NukT peptidase activity, and cooperation between these two domains inside the cells is indispensable for proper functioning of NukT. PMID:21303905

  15. A new method for constructing and reusing domain specific design patterns: Application to RT domain

    Directory of Open Access Journals (Sweden)

    Saoussen Rekhis

    2017-07-01

    Initially, we propose a pattern development process that guides pattern developers in the construction of patterns. The proposed process defines unification rules that apply a set of comparison criteria on various applications in the pattern domain. This process is illustrated through the design of the controller pattern. Moreover, we propose a process guiding the application designers in pattern instantiation based on model transformation. Finally, the proposed RT patterns and their development process are evaluated by calculating quality metrics and comparing the applications designed with our RT patterns and others developed by experts without the use of our patterns.

  16. Feasibility and Domain Validation of Rheumatoid Arthritis (RA) Flare Core Domain Set

    DEFF Research Database (Denmark)

    Bartlett, Susan J; Bykerk, Vivian P; Cooksey, Roxanne

    2015-01-01

    , and stiffness scores averaged ≥ 2 times higher (2 of 11 points) in flaring individuals. Correlations between flare domains and corresponding legacy instruments were obtained: r = 0.46 to 0.93. A combined definition (patient report of flare and 28-joint Disease Activity Score increase) was evaluated in 2 other...... provided input for stiffness, self-management, contextual factors, and measurement considerations. RESULTS: Flare data from 501 patients in an observational study indicated 39% were in flare, with mean (SD) severity of 6.0 (2.6) and 55% lasting > 14 days. Pain, physical function, fatigue, participation...

  17. An investigation into design of fair surfaces over irregular domains ...

    Indian Academy of Sciences (India)

    Design of fair surfaces over irregular domains is a fundamental problem in computer-aided geometric design (CAGD), and has applications in engineering sciences (in aircraft, automobile, ship science etc.). In the design of fair surfaces over irregular domains defined over scattered data, it was widely accepted till recently ...

  18. Two domains of RD3 antifreeze protein diffuse independently.

    Science.gov (United States)

    Holland, Nolan B; Nishimiya, Yoshiyuki; Tsuda, Sakae; Sönnichsen, Frank D

    2008-06-03

    Antifreeze proteins (AFPs) make up a class of structurally diverse proteins that help to protect many organisms from freezing temperatures by inhibiting ice crystal growth at temperatures below the colligative freezing point. AFPs are typically small proteins with a relatively flat, slightly hydrophobic binding region that matches the lattice structure of a specific ice crystal plane. The only known two-domain AFP is RD3 from the Antarctic eel pout. It consists of two nearly identical type III domains connected by a nine-residue linker. This protein exhibits higher activity than the single-domain protein at low concentrations. The initial solution structure of RD3 revealed that the domains were aligned so that the binding regions were nearly coplanar, effectively doubling the surface area for binding. A more recent report suggests that the domains may not be aligned in solution but rather diffuse independently. To resolve the issue, we have measured the NMR residual dipolar couplings using alignment media of stretched gels and filamentous phage to determine the relative orientation of the domains. We find that the two domains of RD3 are free to move relative to each other, within the constraint of the flexible nine-residue linker. Our data show that there is no strongly preferred alignment in solution. Furthermore, the flexibility and length of the linker are sufficient to allow the two domains to have their binding faces in the same orientation and coplanar for simultaneous binding to an ice crystal surface.

  19. Membrane-Sculpting BAR Domains Generate Stable Lipid Microdomains

    Science.gov (United States)

    Zhao, Hongxia; Michelot, Alphée; Koskela, Essi V.; Tkach, Vadym; Stamou, Dimitrios; Drubin, David G.; Lappalainen, Pekka

    2014-01-01

    SUMMARY Bin-Amphiphysin-Rvs (BAR) domain proteins are central regulators of many cellular processes involving membrane dynamics. BAR domains sculpt phosphoinositide-rich membranes to generate membrane protrusions or invaginations. Here, we report that, in addition to regulating membrane geometry, BAR domains can generate extremely stable lipid microdomains by “freezing” phosphoinositide dynamics. This is a general feature of BAR domains, because the yeast endocytic BAR and Fes/CIP4 homology BAR (F-BAR) domains, the inverse BAR domain of Pinkbar, and the eisosomal BAR protein Lsp1 induced phosphoinositide clustering and halted lipid diffusion, despite differences in mechanisms of membrane interactions. Lsp1 displays comparable low diffusion rates in vitro and in vivo, suggesting that BAR domain proteins also generate stable phosphoinositide microdomains in cells. These results uncover a conserved role for BAR superfamily proteins in regulating lipid dynamics within membranes. Stable microdomains induced by BAR domain scaffolds and specific lipids can generate phase boundaries and diffusion barriers, which may have profound impacts on diverse cellular processes. PMID:24055060

  20. Spin motive forces due to magnetic vortices and domain walls

    NARCIS (Netherlands)

    Lucassen, M.E.; Kruis, G.C.F.L.; Lavrijsen, R.; Swagten, H.J.M.; Koopmans, B.; Duine, R.A.

    2011-01-01

    We study spin motive forces, that is, spin-dependent forces and voltages induced by time-dependent magnetization textures, for moving magnetic vortices and domain walls. First, we consider the voltage generated by a one-dimensional field-driven domain wall. Next, we perform detailed calculations on

  1. One loop calculation of QCD with domain-wall quarks

    Energy Technology Data Exchange (ETDEWEB)

    Aoki, S.; Taniguchi, Y. [Tsukuba Univ., Sakura, Ibaraki (Japan). Inst. of Physics

    1998-04-01

    We calculate one loop corrections to the domain-wall quark propagator in QCD. We show how the wave function is renormalized in this theory. Especially we are interested in the behavior of the massless fermion mode, which exists near the domain wall at the tree level. We show that this massless mode is stable against the quantum correction. (orig.). 5 refs.

  2. Domain Approach: An Alternative Approach in Moral Education

    Science.gov (United States)

    Vengadasalam, Chander; Mamat, Wan Hasmah Wan; Mail, Fauziah; Sudramanian, Munimah

    2014-01-01

    This paper discusses the use of the domain approach in moral education in an upper secondary school in Malaysia. Moral Education needs a creative and an innovative approach. Therefore, a few forms of approaches are used in the teaching-learning of Moral Education. This research describes the use of domain approach which comprises the moral domain…

  3. Gravitational field of spherical domain wall in higher dimension

    Indian Academy of Sciences (India)

    An exact solution of Einstein's equations is found describing the gravitational field of a spherical domain wall with nonvanishing stress component in the direction perpendicular to the plane of the wall. Also we have studied the motion of test particle around the domain wall.

  4. Stripe domains and magnetoresistance in thermally deposited nickel films

    International Nuclear Information System (INIS)

    Sparks, P.D.; Stern, N.P.; Snowden, D.S.; Kappus, B.A.; Checkelsky, J.G.; Harberger, S.S.; Fusello, A.M.; Eckert, J.C.

    2004-01-01

    We report a study of the domain structure and magnetoresistance of thermally deposited nickel films. For films thicker than 17 nm, we observe striped domains with period varying with film thickness as a power law with exponent 0.21±0.02 up to 120 nm thickness. There is a negative magnetoresistance for fields out of the plane

  5. A fictitious domain method for particulate flows with heat transfer

    NARCIS (Netherlands)

    Yu, Z.; Yu, Zhaosheng; Shao, Xueming; Wachs, Anthony

    2006-01-01

    The distributed-Lagrange-multiplier/fictitious-domain (DLM/FD) method of Glowinski et al. [R. Glowinski, T.-W. Pan, T.I. Hesla, D.D. Joseph, A distributed Lagrange multiplier/fictitious domain method for particulate flows, Int. J. Multiphase Flow 25 (1999) 755–794] is extended to deal with heat

  6. Nucleation of domains under the influence of temperature in ...

    Indian Academy of Sciences (India)

    Abstract. It is found that the nucleation of domains can take place in Ba5Ti2O7Cl4 under the influence of temperature unlike in many other ferroelectrics. The nucleated domain can also be removed from the structure under the randomizing effect of tem- perature. These observations have been explained on the basis of a ...

  7. A Formal Approach to Domain-Oriented Software Design Environments

    Science.gov (United States)

    Lowry, Michael; Philpot, Andrew; Pressburger, Thomas; Underwood, Ian; Lum, Henry, Jr. (Technical Monitor)

    1994-01-01

    This paper describes a formal approach to domain-oriented software design environments, based on declarative domain theories, formal specifications, and deductive program synthesis. A declarative domain theory defines the semantics of a domain-oriented specification language and its relationship to implementation-level subroutines. Formal specification development and reuse is made accessible to end-users through an intuitive graphical interface that guides them in creating diagrams denoting formal specifications. The diagrams also serve to document the specifications. Deductive program synthesis ensures that end-user specifications are correctly implemented. AMPHION has been applied to the domain of solar system kinematics through the development of a declarative domain theory, which includes an axiomatization of JPL's SPICELIB subroutine library. Testing over six months with planetary scientists indicates that AMPHION's interactive specification acquisition paradigm enables users to develop, modify, and reuse specifications at least an order of magnitude more rapidly than manual program development. Furthermore, AMPHION synthesizes one to two page programs consisting of calls to SPICELIB subroutines from these specifications in just a few minutes. Test results obtained by metering AMPHION's deductive program synthesis component are examined. AMPHION has been installed at JPL and is currently undergoing further refinement in preparation for distribution to hundreds of SPICELIB users worldwide. Current work to support end-user customization of AMPHION's specification acquisition subsystem is briefly discussed, as well as future work to enable domain-expert creation of new AMPHION applications through development of suitable domain theories.

  8. Cholesterol Bilayer Domains in the Eye Lens Health: A Review.

    Science.gov (United States)

    Widomska, Justyna; Subczynski, Witold K; Mainali, Laxman; Raguz, Marija

    2017-12-01

    The most unique biochemical characteristic of the eye lens fiber cell plasma membrane is its extremely high cholesterol content, the need for which is still unclear. It is evident, however, that the disturbance of Chol homeostasis may result in damages associated with cataracts. Electron paramagnetic resonance methods allow discrimination of two types of lipid domains in model membranes overloaded with Chol, namely, phospholipid-cholesterol domains and pure Chol bilayer domains. These domains are also detected in human lens lipid membranes prepared from the total lipids extracted from lens cortices and nuclei of donors from different age groups. Independent of the age-related changes in phospholipid composition, the physical properties of phospholipid-Chol domains remain the same for all age groups and are practically identical for cortical and nuclear membranes. The presence of Chol bilayer domains in these membranes provides a buffering capacity for cholesterol concentration in the surrounding phospholipid-Chol domains, keeping it at a constant saturating level and thus keeping the physical properties of the membrane consistent with and independent of changes in phospholipid composition. It seems that the presence of Chol bilayer domains plays an integral role in the regulation of cholesterol-dependent processes in fiber cell plasm membranes and in the maintenance of fiber cell membrane homeostasis.

  9. RIZ Tumor and Breast Cancer: The PR Domain

    National Research Council Canada - National Science Library

    Aznar-Derunes, Celine

    2005-01-01

    .... RIZ is the founding member of the PR-domain family of zinc finger genes. Two protein products are produced from the RIZ gene which differ by the presence or the absence of the PR domain: RIZ1 and RIZ2...

  10. RIZ Tumor Suppressor and Breast Cancer: The PR Domain

    National Research Council Canada - National Science Library

    Aznar-Derunes, Celine

    2004-01-01

    .... RIZ is the founding member of the PR-domain family of zinc finger genes. Two protein products are produced from the RIZ gene which differ by the presence or the absence of the PR domain : RIZ1 and RIZ2...

  11. Estimated Frequency Domain Model Uncertainties used in Robust Controller Design

    DEFF Research Database (Denmark)

    Tøffner-Clausen, S.; Andersen, Palle; Stoustrup, Jakob

    1994-01-01

    This paper deals with the combination of system identification and robust controller design. Recent results on estimation of frequency domain model uncertainty are......This paper deals with the combination of system identification and robust controller design. Recent results on estimation of frequency domain model uncertainty are...

  12. Identification of Domains for Malaysian University Staff Happiness Index Development

    Science.gov (United States)

    Yassin, Sulaiman Md.

    2014-01-01

    Without any doubt happiness among staff in any organization is pertinent to ensure continued growth and development. However, not many studies were carried out to determine the domains that will be able to measure the level of happiness among staff in universities. Thus, the aim of this study is to elicit the domains that explain the overall…

  13. Impact of Virtual Work Environment on Traditional Team Domains.

    Science.gov (United States)

    Geroy, Gary D.; Olson, Joel; Hartman, Jackie

    2002-01-01

    Examines a virtual work team to determine the domains of the team and the effect the virtual work environment had on the domains. Discusses results of a literature review and a phenomenological heuristic case study, including the effects of post-modern philosophy and postindustrial society on changes in the marketplace. (Contains 79 references.)…

  14. Some asymptotic properties of functions holomorphic in tubular domains

    International Nuclear Information System (INIS)

    Zavialov, B.I.

    1988-10-01

    For the function holomorphic in curved tubular domain the connection between asymptotic behaviour of real part of its boundary value at a given point of base manifold and asymptotic behaviour of the whole function from the inside of this domain is studied. (author). 3 refs

  15. Teaching School Science within the Cognitive and Affective Domains

    Science.gov (United States)

    Tan, Kok Siang; Heng, Chong Yong; Tan, Shuhui

    2013-01-01

    In classrooms, science is usually taught within the cognitive domain while the psychomotor learning domain is achieved through performing science experiments in the laboratory. Although students attend civic and moral education and pastoral care classes where values and life skills are often taught directly, learning experiences in most school…

  16. Integral UBL domain proteins: a family of proteasome interacting proteins

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Gordon, Colin

    2004-01-01

    The family of ubiquitin-like (UBL) domain proteins (UDPs) comprises a conserved group of proteins involved in a multitude of different cellular activities. However, recent studies on UBL-domain proteins indicate that these proteins appear to share a common property in their ability to interact wi...

  17. Inter-domain linker prediction using amino acid compositional index.

    Science.gov (United States)

    Shatnawi, Maad; Zaki, Nazar

    2015-04-01

    Protein chains are generally long and consist of multiple domains. Domains are distinct structural units of a protein that can evolve and function independently. The accurate and reliable prediction of protein domain linkers and boundaries is often considered to be the initial step of protein tertiary structure and function predictions. In this paper, we introduce CISA as a method for predicting inter-domain linker regions solely from the amino acid sequence information. The method first computes the amino acid compositional index from the protein sequence dataset of domain-linker segments and the amino acid composition. A preference profile is then generated by calculating the average compositional index values along the amino acid sequence using a sliding window. Finally, the protein sequence is segmented into intervals and a simulated annealing algorithm is employed to enhance the prediction by finding the optimal threshold value for each segment that separates domains from inter-domain linkers. The method was tested on two standard protein datasets and showed considerable improvement over the state-of-the-art domain linker prediction methods. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Catalytic properties of ADAM12 and its domain deletion mutants

    DEFF Research Database (Denmark)

    Jacobsen, Jonas; Visse, Robert; Sørensen, Hans Peter

    2008-01-01

    of pro, catalytic, disintegrin, cysteine-rich, and EGF domains. Here we present a novel activity of recombinant ADAM12-S and its domain deletion mutants on S-carboxymethylated transferrin (Cm-Tf). Cleavage of Cm-Tf occurred at multiple sites, and N-terminal sequencing showed that the enzyme exhibits...

  19. Amino-acid composition after loop deletion drives domain swapping.

    Science.gov (United States)

    Nandwani, Neha; Surana, Parag; Udgaonkar, Jayant B; Das, Ranabir; Gosavi, Shachi

    2017-10-01

    Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain-swapped oligomer over the monomer. While it is known that the deletion of loops between β-strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop-deletion mutants of the non-domain-swapping protein monellin, frame-shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping. © 2017 The Protein Society.

  20. Alternating Direction Implicit Finite Difference Time Domain Acoustic ...

    African Journals Online (AJOL)

    A time domain numerical technique is presented for the modelling of acoustic wave phenomena. The technique is an adaptation of the alternating direction implicit finite difference time domain method. The stability condition for the algorithm is given. Simple illustrations of propagation in an infinite homogeneous medium are ...

  1. 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...

  2. Functional conservation study of polarity protein Crumbs intracellular domain.

    Science.gov (United States)

    Shi, Qi-ping; Cao, Hao-wei; Xu, Rui; Zhang, Dan-dan; Huang, Juan

    2017-01-20

    The transmembrane protein Crumbs (Crb) plays key roles in the establishing and maintaining cell apical-basal polarity in epithelial cells by determining the apical plasma membrane identity. Although its intracellular domain contains only 37 amino acids, it is absolutely essential for its function. In Drosophila, mutations in this intracellular domain result in severe defects in epithelial polarity and abnormal embryonic development. The intracellular domain of Crb shows high homology across species from Drosophila to Mus musculus and Homo sapiens. However, the intracellular domains of the two Crb proteins in C. elegans are rather divergent from those of Drosophila and mammals, raising the question on whether the function of the intracellular domain of the Crb protein is conserved in C. elegans. Using genomic engineering approach, we replaced the intracellular domain of the Drosophila Crb with that of C. elegans Crb2 (CeCrb2), which has extremely low homology with those from the Crb proteins of Drosophila and mammals. Surprisingly, substituting the intracellular domain of Drosophila Crb with that of CeCrb2 did not cause any abnormalities in development of the Drosophila embryo, in terms of expression and localization of Crb and other polarity proteins and apical-basal polarity in embryonic epithelial cells. Our results support the notion that despite their extensive sequence variations, all functionally critical amino acid residues and motifs of the intercellular domain of Crb proteins are fully conserved between Drosophila and C. elegans.

  3. Cognitive Development Includes Global and Domain-Specific Processes

    Science.gov (United States)

    Kail, Robert V.

    2004-01-01

    Global accounts of cognitive development, best illustrated by Piaget's theory, dominated the field until the 1970s and 1980s, when they were gradually superseded by domain-specific accounts. In this article I present evidence suggesting that both global and domain-specific processes make important contributions to cognitive development, and I…

  4. Structure function relations in PDZ-domain-containing proteins ...

    Indian Academy of Sciences (India)

    PDZ domains are subject toseveral means of regulations by virtue of their functional diversity. Additionally, the PDZ domains are refractive to theeffect of mutations and maintain their three-dimensional architecture under extreme mutational load. The biochemical andbiophysical basis for this selectivity as well as promiscuity ...

  5. Homogenization of a parabolic equation in perforated domain with ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Homogenization; perforated domain; two-scale convergence; correctors. 1. Introduction. Let be a bounded domain in R n ..... compact imbedding theorem to get the strong convergence of uε to u in some Lr( T ). However, we are able to achieve this by adapting a ..... of parabolic type, Am. Math. Soc. Transl. Mono.? 23, (1968).

  6. Membrane-Sculpting BAR Domains Generate Stable Lipid Microdomains

    Directory of Open Access Journals (Sweden)

    Hongxia Zhao

    2013-09-01

    Full Text Available Bin-Amphiphysin-Rvs (BAR domain proteins are central regulators of many cellular processes involving membrane dynamics. BAR domains sculpt phosphoinositide-rich membranes to generate membrane protrusions or invaginations. Here, we report that, in addition to regulating membrane geometry, BAR domains can generate extremely stable lipid microdomains by “freezing” phosphoinositide dynamics. This is a general feature of BAR domains, because the yeast endocytic BAR and Fes/CIP4 homology BAR (F-BAR domains, the inverse BAR domain of Pinkbar, and the eisosomal BAR protein Lsp1 induced phosphoinositide clustering and halted lipid diffusion, despite differences in mechanisms of membrane interactions. Lsp1 displays comparable low diffusion rates in vitro and in vivo, suggesting that BAR domain proteins also generate stable phosphoinositide microdomains in cells. These results uncover a conserved role for BAR superfamily proteins in regulating lipid dynamics within membranes. Stable microdomains induced by BAR domain scaffolds and specific lipids can generate phase boundaries and diffusion barriers, which may have profound impacts on diverse cellular processes.

  7. Stochastic response of nonlinear system in probability domain

    Indian Academy of Sciences (India)

    Stochastic average procedure; nonlinear single-DOF system; proba- bility density function. 1. Introduction. Stochastic response analysis of nonlinear systems has been extensively studied in the fre- quency, time and probability domains. In the frequency domain, the stochastic linearization technique is generally used for ...

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

    DEFF Research Database (Denmark)

    Andreasen, Troels; Knappe, Rasmus; Bulskov, Henrik

    2005-01-01

    collection the general ontology is restricted to a domain specific ontology encompassing concepts instantiated in the collection. The resulting domain specific ontology and similarity can be applied for surveying the collection through key concepts and conceptual relations and provides a means for topic...

  9. Reachback in crisis management: lessons learned from the military domain

    NARCIS (Netherlands)

    Rypkema, J.A.; Brake, G.M. te; Lee, M. van der

    2006-01-01

    Military and crisis management organizations show many similarities. Within the military domain, a study is being done on the use of reachback concepts for the Royal Netherlands Army (RNLA) brigade staff. This paper shows that the results are applicable to the crisis management domain. However,

  10. Library Research: A Domain Comparison of Two Library Journals

    Science.gov (United States)

    Davies, Karen; Thiele, Jennifer

    2013-01-01

    Research articles published by the "Community & Junior College Libraries" journal and the "College & Undergraduate Libraries" journal were analyzed to determine their domain. The discussion includes a comparison of past domain studies with the current research. The researchers found the majority of articles (52%) in the…

  11. Mesencephalic basolateral domain specification is dependent on Sonic Hedgehog

    Science.gov (United States)

    Martinez-Lopez, Jesus E.; Moreno-Bravo, Juan A.; Madrigal, M. Pilar; Martinez, Salvador; Puelles, Eduardo

    2015-01-01

    In the study of central nervous system morphogenesis, the identification of new molecular markers allows us to identify domains along the antero-posterior and dorso-ventral (DV) axes. In the past years, the alar and basal plates of the midbrain have been divided into different domains. The precise location of the alar-basal boundary is still under discussion. We have identified Barhl1, Nhlh1 and Six3 as appropriate molecular markers to the adjacent domains of this transition. The description of their expression patterns and the contribution to the different mesencephalic populations corroborated their role in the specification of these domains. We studied the influence of Sonic Hedgehog on these markers and therefore on the specification of these territories. The lack of this morphogen produced severe alterations in the expression pattern of Barhl1 and Nhlh1 with consequent misspecification of the basolateral (BL) domain. Six3 expression was apparently unaffected, however its distribution changed leading to altered basal domains. In this study we confirmed the localization of the alar-basal boundary dorsal to the BL domain and demonstrated that the development of the BL domain highly depends on Shh. PMID:25741244

  12. Semi-automatic ontology extension in the maritime domain

    NARCIS (Netherlands)

    de Vries, G.; Malaisé, V.; van Someren, M.; Adriaans, P.; Schreiber, G.

    2008-01-01

    One of the tasks of a maritime safety and security (MSS) system is to map incoming observations in the form of sensor data onto existing maritime domain knowledge. This domain knowledge is modeled in an ontology. The sensor data contains information on ship trajectories, labeled with ship types from

  13. Domain combination of the vertebrate-like TLR gene family ...

    Indian Academy of Sciences (India)

    Domain combination of the vertebrate-like TLR gene family: implications for their origin and evolution. Baojun Wu, Tianxiao Huan, Jing Gong, Pin Zhou and Zengliang Bai. J. Genet. 90, 401–408. Figure 1. Unrooted NJ phylogenetic tree of P-Toll proteins from selected phyla based on TIR domains. The putative V-TIR protein.

  14. Ligand Binding Domain Protein in Tetracycline-Inducible Expression

    African Journals Online (AJOL)

    Purpose: To investigate tetracycline-inducible expression system for producing clinically usable, highquality liver X receptor ligand-binding domain recombinant protein. Methods: In this study, we have expressed and purified the recombinant liver X receptor β-ligand binding domain proteins in E. coli using a tetracycline ...

  15. Functional genomic analysis of cassava proteins with TIR domains

    International Nuclear Information System (INIS)

    Roman Reyna, Veronica; Lopez, Camilo

    2012-01-01

    Proteins containing a TIR domain (toll interleukin receptor) are involved in plant and animal immunity. The aim of this work was to carry out an overall genomic analysis of cassava proteins with a TIR domain and discern their possible role in resistance to cassava bacterial blight. In total 46 proteins with a TIR domain were identified in the cassava proteome and were classed in four categories according the presence or absence of other domains: TIR (T), TIR -NB (TN), TIR - lRR (TL) and TIR - NB - lRR (TNL). 56.6 % of these 46 proteins have TIR, NB and lRR domains. Using multiple alignments it was possible to demonstrate that not all cassava TIR domains contain the AE region, involved in dimerization and activation of immune responses. Three of the four proteins categories (T, TNL and TN) presented a higher number of synonymous substitutions suggesting that they are not involved in recognition process. two TIR domains not presenting the ae region were analyzed by yeast two hybrid assays and by agro-infiltration, finding that both are able to form homo and heterodimers, but they do not trigger defense responses. With this study it was possible to conclude that TIR domains can function as adaptors in the signal transduction with other resistance proteins. In addition, it became clear that not always the AE region is important for TIR dimerization but it seems necessary to activate defense responses signals.

  16. On domain-wall/QFT dualities in various dimensions

    NARCIS (Netherlands)

    Behrndt, Klaus; Bergshoeff, Eric; Halbersma, Rein; Schaar, Jan Pieter van der

    1999-01-01

    We investigate domain-wall/quantum field-theory correspondences in various dimensions. Our general analysis covers not only the well studied cases in 10 and 11 dimensions, but also enables us to discuss new cases like a type I/heterotic 6-brane in 10 dimensions and domain-wall dualities in lower

  17. Development of Fourier domain optical coherence tomography

    Science.gov (United States)

    Wang, Rui

    Fourier domain optical coherence tomography (FD-OCT) is a high-speed, high-resolution, and noninvasive imaging technique that can obtain cross-sectional images of light scattering medium, such as biomedical tissues. In this thesis, I report three novel methods in FD-OCT technique including common-path endoscopic FD-OCT, streak-mode FD-OCT, and Doppler streak-mode FD-OCT. Finally, I apply the streak mode FD-OCT to ultrahigh-speed, noninvasive, live imaging of embryonic chick hearts. An extension of conventional FD-OCT technique is endoscopic FD-OCT, which can access internal organs by utilizing a miniaturized catheter design. However, its image signal suffers from the bending of the endoscopic catheter. To address this problem, a common-path endoscopic FD-OCT system was developed to avoid the polarization mismatch. Consequently, the OCT images were immune to the catheter bending. In addition, a Microelectromechanical system (MEMS) motor was integrated into the miniaturized probe to achieve circumferential scanning within lumen samples. In conventional FD-OCT, the imaging speed is limited by the slow line-scan rate of the camera. We developed the streak-mode FD-OCT technique, in which an area-scan camera is used instead of a line-scan camera to record the FD-OCT spectrum. Using this technique, high temporal resolution of 1000--2000 cross-sectional images of the sample were obtained in one second. Doppler FD-OCT is a functional extension of FD-OCT technique, which can measure the flow velocity within biomedical tissues. However, conventional techniques are not available to measure high speed flow due to slow imaging speed, phase wrapping, and fringe wash out issues. Based on the streak mode FD-OCT, a novel Doppler technique was developed that addressed these problems. It has been well established that cardiac dynamics play an important role in the early development of an embryonic heart. However, the mechanism by which cardiac dynamics affect the development of a

  18. Surgical data science: The new knowledge domain.

    Science.gov (United States)

    Vedula, S Swaroop; Hager, Gregory D

    2017-04-01

    -assisted active learning of surgical skill. However, the potential for transforming surgical care and training through SDS may only be realized through a cultural shift that not only institutionalizes technology to seamlessly capture data but also assimilates individuals with expertise in data science into clinical research teams. Furthermore, collaboration with industry partners from the inception of the discovery process promotes optimal design of data products as well as their efficient translation and commercialization. As surgery continues to evolve through advances in technology that enhance delivery of care, SDS represents a new knowledge domain to engineer surgical care of the future.

  19. Surgical data science: the new knowledge domain

    Directory of Open Access Journals (Sweden)

    Vedula S. Swaroop

    2017-04-01

    assessments, automated virtual coaching, and robot-assisted active learning of surgical skill. However, the potential for transforming surgical care and training through SDS may only be realized through a cultural shift that not only institutionalizes technology to seamlessly capture data but also assimilates individuals with expertise in data science into clinical research teams. Furthermore, collaboration with industry partners from the inception of the discovery process promotes optimal design of data products as well as their efficient translation and commercialization. As surgery continues to evolve through advances in technology that enhance delivery of care, SDS represents a new knowledge domain to engineer surgical care of the future.

  20. Domain Engineering - A Software Engineering discipline in Need of Research

    DEFF Research Database (Denmark)

    Bjørner, Dines

    2000-01-01

    , and these again seem more stable than software designs. Thus, almost like the universal laws of physics, it pays off to first develop theories of domains. But domain engineering, as in fact also requirements engineering, really is in need of thoroughly researched development principles, techniques and tools....... The aim of this paper is to advocate: that researchers study these development method components, and that universities focus their education on basing well-nigh any course on the use of formal techniques: Specification and verification, and that software engineers take heed: Start applying formal......Before software can be developed its requirements must be stated. Before requirements can be expressed the application domain must be understood. In this paper we outline some of the basic facets of domain engineering. Domains seem, it is our experience, far more stable than computing requirements...

  1. Contribution of domain wall networks to the CMB power spectrum

    Directory of Open Access Journals (Sweden)

    A. Lazanu

    2015-07-01

    Full Text Available We use three domain wall simulations from the radiation era to the late-time dark energy domination era based on the PRS algorithm to calculate the energy–momentum tensor components of domain wall networks in an expanding universe. Unequal time correlators in the radiation, matter and cosmological constant epochs are calculated using the scaling regime of each of the simulations. The CMB power spectrum of a network of domain walls is determined. The first ever quantitative constraint for the domain wall surface tension is obtained using a Markov chain Monte Carlo method; an energy scale of domain walls of 0.93 MeV, which is close but below the Zel'dovich bound, is determined.

  2. Domain Engineering, A Software Engineering Discipline in Need of Research

    DEFF Research Database (Denmark)

    Bjørner, Dines

    2000-01-01

    Before software can be developed its requirements must be stated. Before requirements can be expressed the application domain must be understood. In this paper we outline some of the basic facets of domain engineering. Domains seem, it is our experience, far more stable than computing requirements......, and these again seem more stable than software designs. Thus, almost like the universal laws of physics, it pays off to first develop theories of domains. But domain engineering, as in fact also requirements engineering, really is in need of thoroughly researched development principles, techniques and tools....... The aim of this paper is to advocate: that researchers study these development method components, and that universities focus their education on basing well-nigh any course on the use of formal techniques: Specification and verification, and that software engineers take heed: Start applying formal...

  3. Domain structure of a Reggeon field theory with three couplings

    International Nuclear Information System (INIS)

    Geer, K.A.; Pinsky, S.S.

    1974-01-01

    The high energy behavior of a Reggeon field theory with a three-Reggeon coupling and two four-Reggeon couplings is considered. Using the renormalization group equations which are calculated in lowest order for this model, one studies the way the couplings evolve to the fixed points in the high energy limit. It was found that there are three fixed points (plus a fourth at infinity) to which the couplings can evolve. The space of couplings divides into four domains, two of which are two-dimensional and two of which are three-dimensional. The couplings in one of the three-dimensional domains are found to evolve to infinity and the couplings in the other three domains are found to evolve to the fixed point couplings. The boundaries of these domains and some characteristic evolution curves are shown. The implications of the domain structure of the model are discussed. (U.S.)

  4. A role for chromatin topology in imprinted domain regulation.

    Science.gov (United States)

    MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

    2016-02-01

    Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

  5. Remote-sensing image encryption in hybrid domains

    Science.gov (United States)

    Zhang, Xiaoqiang; Zhu, Guiliang; Ma, Shilong

    2012-04-01

    Remote-sensing technology plays an important role in military and industrial fields. Remote-sensing image is the main means of acquiring information from satellites, which always contain some confidential information. To securely transmit and store remote-sensing images, we propose a new image encryption algorithm in hybrid domains. This algorithm makes full use of the advantages of image encryption in both spatial domain and transform domain. First, the low-pass subband coefficients of image DWT (discrete wavelet transform) decomposition are sorted by a PWLCM system in transform domain. Second, the image after IDWT (inverse discrete wavelet transform) reconstruction is diffused with 2D (two-dimensional) Logistic map and XOR operation in spatial domain. The experiment results and algorithm analyses show that the new algorithm possesses a large key space and can resist brute-force, statistical and differential attacks. Meanwhile, the proposed algorithm has the desirable encryption efficiency to satisfy requirements in practice.

  6. Frequency domain optoacoustic tomography using amplitude and phase

    Science.gov (United States)

    Mohajerani, Pouyan; Kellnberger, Stephan; Ntziachristos, Vasilis

    2014-01-01

    We introduce optoacoustic tomographic imaging using intensity modulated light sources and collecting amplitude and phase information in the frequency domain. Imaging is performed at multiple modulation frequencies. The forward modeling uses the Green's function solution to the pressure wave equation in frequency domain and the resulting inverse problem is solved using regularized least squares minimization. We study the effect of the number of frequencies and of the bandwidth employed on the image quality achieved. The possibility of employing an all-frequency domain optoacoustic imaging for experimental measurements is studied as a function of noise. We conclude that frequency domain optoacoustic tomography may evolve to a practical experimental method using light intensity modulated sources, with advantages over time-domain optoacoustics. PMID:25431755

  7. Information Worlds and Interpretive Practices: Toward an Integration of Domains

    Directory of Open Access Journals (Sweden)

    Burnett, Gary

    2015-09-01

    Full Text Available This article proposes an interwoven three-part framework for conceptualizing and analyzing the role of information in human activities, melding the cognitive and affective domain of the individual, the collective domain of the social, and the domain of signification and communication practices, focusing on the ways in which individual characteristics, social context and interaction, and signification and representation work together to form information behavior. The article presents an overview of each of these three domains and discusses the ways in which they are intertwined. It argues that considering the three domains in relation to each other offers a holistic framework within which to consider the ways in which information - needs, behavior, creation, and use - depends simultaneously on all three. It concludes by offering a brief discussion of the implications of the framework for information services, including (but not limited to libraries.

  8. Magnetic domains in Ni-Mn-Ga martensitic thin films

    International Nuclear Information System (INIS)

    Chernenko, V A; Anton, R Lopez; Kohl, M; Ohtsuka, M; Orue, I; Barandiaran, J M

    2005-01-01

    A series of martensitic Ni 52 Mn 24 Ga 24 thin films deposited on alumina ceramic substrates has been prepared by using RF(radio-frequency) magnetron sputtering. The film thickness, d, varies from 0.1 to 5.0m. Magnetic domain patterns have been imaged by the MFM (magnetic force microscopy) technique. A maze domain structure is found for all studied films. MFM shows a large out-of-plane magnetization component and a rather uniform domain width for each film thickness. The domain width, δ, depends on the film thickness as δ∝√d in the whole studied range of film thickness. This dependence is the expected one for magnetic anisotropy and magnetostatic contributions in a perpendicular magnetic domain configuration. The proportionality coefficient is also consistent with the values of saturation magnetization and magnetic anisotropy determined in the samples

  9. Stochastic lattice model of synaptic membrane protein domains

    Science.gov (United States)

    Li, Yiwei; Kahraman, Osman; Haselwandter, Christoph A.

    2017-05-01

    Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. We show that our stochastic lattice model yields quantitative agreement with mean-field models of nonlinear diffusion in crowded membranes. Through a combination of analytic and numerical solutions of the master equation governing the reaction dynamics at synaptic domains, together with kinetic Monte Carlo simulations, we find substantial discrepancies between mean-field and stochastic models for the reaction dynamics at synaptic domains. Based on the reaction and diffusion properties of synaptic receptors and scaffolds suggested by previous experiments and mean-field calculations, we show that the stochastic reaction-diffusion dynamics of synaptic receptors and scaffolds provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the observed single-molecule trajectories, and spatial heterogeneity in the effective rates at which receptors and scaffolds are recycled at the cell membrane. Our work sheds light on the physical mechanisms and principles linking the collective properties of membrane protein domains to the stochastic dynamics that rule their molecular components.

  10. Stochastic lattice model of synaptic membrane protein domains.

    Science.gov (United States)

    Li, Yiwei; Kahraman, Osman; Haselwandter, Christoph A

    2017-05-01

    Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments. We show that our stochastic lattice model yields quantitative agreement with mean-field models of nonlinear diffusion in crowded membranes. Through a combination of analytic and numerical solutions of the master equation governing the reaction dynamics at synaptic domains, together with kinetic Monte Carlo simulations, we find substantial discrepancies between mean-field and stochastic models for the reaction dynamics at synaptic domains. Based on the reaction and diffusion properties of synaptic receptors and scaffolds suggested by previous experiments and mean-field calculations, we show that the stochastic reaction-diffusion dynamics of synaptic receptors and scaffolds provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the observed single-molecule trajectories, and spatial heterogeneity in the effective rates at which receptors and scaffolds are recycled at the cell membrane. Our work sheds light on the physical mechanisms and principles linking the collective properties of membrane protein domains to the stochastic dynamics that rule their molecular components.

  11. Domains contributing to disability in activities of daily living.

    Science.gov (United States)

    den Ouden, Marjolein E M; Schuurmans, Marieke J; Mueller-Schotte, Sigrid; Brand, Judith S; van der Schouw, Yvonne T

    2013-01-01

    The WHO International Classification of Functioning, Disability, and Health (ICF)-model describes disability in activities of daily living (ADL) as a multifactorial concept. According to this model, ADL disability is influenced by health conditions, body function and structures, environmental and personal factors, and participation. Current research on ADL disability often focuses on one domain and the contribution of multiple domains is not taken into account. The aim was to investigate which domains contribute to ADL disability. Cross-sectional study. General community. A total of 537 middle-aged and older persons. Health conditions included number of chronic diseases. Body function comprised Mini-Mental State Examination (MMSE), processing speed, memory, grip strength, physical performance score (PPS), physical activity, sensory problems, body mass index (BMI), intra-abdominal fat, and cholesterol/HDL ratio. Body structure included atherosclerosis and bone mineral density. Environmental factors comprised the degree of urbanization. Personal factors included age, sex, education, smoking, self-management abilities, quality of life, anxiety/panic disorders, and depressive symptoms. Associations between candidate predictors and ADL disability, measured on the Katz ADL-scale, were examined by multivariable adjusted logistic regression analysis. Nagelkerke R(2)-statistic was calculated to investigate the contribution of each domain to ADL disability. Number of chronic diseases (domain health condition), MMSE, PPS, physical activity, BMI, intra-abdominal fat (domain body function), atherosclerosis (domain body structure) and sex, education, smoking, quality of life, and depressive symptoms (domain personal factors) were significant predictors of ADL disability. Fifty-seven percent of the variance in ADL disability was explained by the model. For each domain, the explained variance materially decreased after its exclusion, except for environmental factors. The present

  12. Domain-Specific and Domain-General Training to Improve Kindergarten Children’s Mathematics

    Directory of Open Access Journals (Sweden)

    Geetha B. Ramani

    2017-12-01

    Full Text Available Ensuring that kindergarten children have a solid foundation in early numerical knowledge is of critical importance for later mathematical achievement. In this study, we targeted improving the numerical knowledge of kindergarteners (n = 81 from primarily low-income backgrounds using two approaches: one targeting their conceptual knowledge, specifically, their understanding of numerical magnitudes; and the other targeting their underlying cognitive system, specifically, their working memory. Both interventions involved playing game-like activities on tablet computers over the course of several sessions. As predicted, both interventions improved children’s numerical magnitude knowledge as compared to a no-contact control group, suggesting that both domain-specific and domain-general interventions facilitate mathematical learning. Individual differences in effort during the working memory game, but not the number knowledge training game predicted children’s improvements in number line estimation. The results demonstrate the potential of using a rapidly growing technology in early childhood classrooms to promote young children’s numerical knowledge.

  13. Domain-Specific and Domain-General Precursors of Mathematical Achievement: A Longitudinal Study from Kindergarten to First Grade

    Science.gov (United States)

    Passolunghi, Maria Chiara; Lanfranchi, Silvia

    2012-01-01

    Background: Many contributing factors, both domain specific and domain general, influence children's performance in school achievement. Aims: This research aims to verify the importance of kindergarten measures of cognitive abilities and numerical competence in the role of predicting mathematical school achievement at the end of first grade.…

  14. CONCESSIONS ON THE MARITIME DOMAIN – THE RELATION OF THE CONCESSIONS ACT AND THE MARITIME DOMAIN AND SEAPORTS ACT

    Directory of Open Access Journals (Sweden)

    Frane Staničić

    2017-04-01

    Full Text Available In this paper, the authors analyse the legislative framework of concessions on maritime domain. The Maritime Domain and Seaports Act passed in 2003 prescribes concessions on maritime domain. In the meantime, two new general acts regarding concessions were passed in 2008, and in 2012 and the third general Concessions Act is in legislative procedure now. The authors will, by the methods of comparison and analysis, show that, unlike other laws governing concessions, the Maritime Domain and Seaports Act has never been aligned with the general law, which causes problems in practice and in its implementation. The frequent dilemmas regarding the question refer to the choice of norms to implement. The dilemma is whether the general act is applicable in procedures of granting concessions on maritime domain. The authors show in this paper that the Maritime Domain and Seaports Act is not aligned with the Concessions Act and point to the problems in practice due to obvious misalignment of these laws. The authors suggest solutions to the noticed problems. They also argue that it is necessary to align the Maritime Domain and Seaports Act with the general law and that the Concessions Act is applicable in the concessions granting procedures on maritime domain.

  15. Magnetic characteristics of synthetic pseudo-single-domain and multi-domain greigite (Fe3S4)

    Czech Academy of Sciences Publication Activity Database

    Chang, L.; Roberts, A. P.; Muxworthy, A. R.; Tang, Y.; Chen, Q.; Rowan, Ch. J.; Liu, Q.; Pruner, Petr

    2007-01-01

    Roč. 34, č. 24 (2007), L24304-L24304 ISSN 0094-8276 R&D Projects: GA AV ČR IAA3013406 Institutional research plan: CEZ:AV0Z30130516 Keywords : greigite * magnetic properties * grain size * pseudo-single-domain * multi-domain Subject RIV: DE - Earth Magnetism, Geodesy, Geography Impact factor: 2.744, year: 2007

  16. Crystal structure of the N-terminal domain of human SIRT7 reveals a three-helical domain architecture.

    Science.gov (United States)

    Priyanka, Anu; Solanki, Vipul; Parkesh, Raman; Thakur, Krishan Gopal

    2016-10-01

    Human SIRT7 is an NAD(+) dependent deacetylase, which belongs to sirtuin family of proteins. SIRT7, like other sirtuins has conserved catalytic domain and is flanked by N- and C-terminal domains reported to play vital functional roles. Here, we report the crystal structure of the N-terminal domain of human SIRT7 (SIRT7(NTD) ) at 2.3 Å resolution as MBP-SIRT7(NTD) fusion protein. SIRT7(NTD) adopts three-helical domain architecture and comparative structural analyses suggest similarities to some DNA binding motifs and transcription regulators. We also report here the importance of N- and C-terminal domains in soluble expression of SIRT7. Proteins 2016; 84:1558-1563. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Structural updates of alignment of protein domains and consequences on evolutionary models of domain superfamilies.

    Science.gov (United States)

    Mutt, Eshita; Rani, Sudha Sane; Sowdhamini, Ramanathan

    2013-11-15

    Influx of newly determined crystal structures into primary structural databases is increasing at a rapid pace. This leads to updation of primary and their dependent secondary databases which makes large scale analysis of structures even more challenging. Hence, it becomes essential to compare and appreciate replacement of data and inclusion of new data that is critical between two updates. PASS2 is a database that retains structure-based sequence alignments of protein domain superfamilies and relies on SCOP database for its hierarchy and definition of superfamily members. Since, accurate alignments of distantly related proteins are useful evolutionary models for depicting variations within protein superfamilies, this study aims to trace the changes in data in between PASS2 updates. In this study, differences in superfamily compositions, family constituents and length variations between different versions of PASS2 have been tracked. Studying length variations in protein domains, which have been introduced by indels (insertions/deletions), are important because theses indels act as evolutionary signatures in introducing variations in substrate specificity, domain interactions and sometimes even regulating protein stability. With this objective of classifying the nature and source of variations in the superfamilies during transitions (between the different versions of PASS2), increasing length-rigidity of the superfamilies in the recent version is observed. In order to study such length-variant superfamilies in detail, an improved classification approach is also presented, which divides the superfamilies into distinct groups based on their extent of length variation. An objective study in terms of transition between the database updates, detailed investigation of the new/old members and examination of their structural alignments is non-trivial and will help researchers in designing experiments on specific superfamilies, in various modelling studies, in linking

  18. Expression and Production of SH2 Domain Proteins.

    Science.gov (United States)

    Liu, Bernard A; Ogiue-Ikeda, Mari; Machida, Kazuya

    2017-01-01

    The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP). We describe stepwise protocols for expression and purification of SH2 domains using GST or poly His-tags, two widely adopted affinity tags. In addition, we address alternative approaches, challenges, and validation studies for assessing protein quality and provide general characteristics of purified human SH2 domains.

  19. SAW assisted domain wall motion in Co/Pt multilayers

    Science.gov (United States)

    Edrington, Westin; Singh, Uday; Dominguez, Maya Abo; Alexander, James Rehwaldt; Nepal, Rabindra; Adenwalla, S.

    2018-01-01

    The motion of domain walls in thin ferromagnetic films is of both fundamental and technological interest. In particular, the ability to use drivers other than magnetic fields to control the positions of domain walls could be exciting for memory applications. Here, we show that high frequency dynamic strain produced by surface acoustic waves is an efficient driver of magnetic domain walls in ferromagnetic films with perpendicular anisotropy. A standing surface acoustic wave of resonant frequency 96.6 MHz increases the domain wall velocities in thin films of [Co/Pt]n by an order of magnitude compared to magnetic fields alone. This effect is highly resonant, effectively ruling out thermal effects, and the velocity shows distinct variations in the domain wall velocity at the nodes and antinodes of the standing wave. The data indicate that standing strain waves can drive the domain wall motion from the creep to the flow regime as the amplitude increases. Hence, strain waves could provide an alternative route to rapid domain wall motion.

  20. Domain nesting for multi-scale large eddy simulation

    Science.gov (United States)

    Fuka, Vladimir; Xie, Zheng-Tong

    2016-04-01

    The need to simulate city scale areas (O(10 km)) with high resolution within street canyons in certain areas of interests necessitates different grid resolutions in different part of the simulated area. General purpose computational fluid dynamics codes typically employ unstructured refined grids while mesoscale meteorological models more often employ nesting of computational domains. ELMM is a large eddy simulation model for the atmospheric boundary layer. It employs orthogonal uniform grids and for this reason domain nesting was chosen as the approach for simulations in multiple scales. Domains are implemented as sets of MPI processes which communicate with each other as in a normal non-nested run, but also with processes from another (outer/inner) domain. It should stressed that the duration of solution of time-steps in the outer and in the inner domain must be synchronized, so that the processes do not have to wait for the completion of their boundary conditions. This can achieved by assigning an appropriate number of CPUs to each domain, and to gain high efficiency. When nesting is applied for large eddy simulation, the inner domain receives inflow boundary conditions which lack turbulent motions not represented by the outer grid. ELMM remedies this by optional adding of turbulent fluctuations to the inflow using the efficient method of Xie and Castro (2008). The spatial scale of these fluctuations is in the subgrid-scale of the outer grid and their intensity will be estimated from the subgrid turbulent kinetic energy in the outer grid.