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Sample records for non-canonical local structure

  1. RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs

    Science.gov (United States)

    Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

    2017-02-01

    Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.

  2. Body-fixed orbit-attitude hovering control over an asteroid using non-canonical Hamiltonian structure

    Science.gov (United States)

    Wang, Yue; Xu, Shijie

    2015-12-01

    The orbit-attitude hovering means that both the position and attitude of the spacecraft are kept to be stationary in the asteroid body-fixed frame. The orbit-attitude hovering is discussed in the framework of the gravitationally coupled orbit-attitude dynamics, also called the full dynamics, in which the spacecraft is modeled as a rigid body to take into account the gravitational orbit-attitude coupling naturally. A feedback hovering control law is proposed by using the non-canonical Hamiltonian structure of the problem, which is consisted of two potential shapings and one energy dissipation. The first potential shaping is to create an artificial equilibrium at the desired hovering position-attitude. Then, the second potential shaping modifies the potential further so that the artificial equilibrium is a minimum of the modified Hamiltonian on the invariant manifold. Finally, the energy dissipation leads the motion to converge asymptotically to the minimum of the modified Hamiltonian, i.e., the artificial equilibrium for hovering. The feasibility of the hovering control law is verified through numerical simulations. The proposed hovering control law has a simple form and can be implemented by the spacecraft autonomously with little computation. This feature can be attributed to the utilization of the Hamiltonian structure and natural dynamical behaviors of the system in the control law design.

  3. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.

    Directory of Open Access Journals (Sweden)

    Ivana Nemčovičová

    2013-03-01

    Full Text Available The TRAIL (TNF-related apoptosis inducing ligand death receptors (DRs of the tumor necrosis factor receptor superfamily (TNFRSF can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways.

  4. Structure of human cytomegalovirus UL141 binding to TRAIL-R2 reveals novel, non-canonical death receptor interactions.

    Science.gov (United States)

    Nemčovičová, Ivana; Benedict, Chris A; Zajonc, Dirk M

    2013-03-01

    The TRAIL (TNF-related apoptosis inducing ligand) death receptors (DRs) of the tumor necrosis factor receptor superfamily (TNFRSF) can promote apoptosis and regulate antiviral immunity by maintaining immune homeostasis during infection. In turn, human cytomegalovirus (HCMV) expresses immunomodulatory proteins that down-regulate cell surface expression of TNFRSF members as well as poliovirus receptor-related proteins in an effort to inhibit host immune effector pathways that would lead to viral clearance. The UL141 glycoprotein of human cytomegalovirus inhibits host defenses by blocking cell surface expression of TRAIL DRs (by retention in ER) and poliovirus receptor CD155, a nectin-like Ig-fold molecule. Here we show that the immunomodulatory function of HCMV UL141 is associated with its ability to bind diverse proteins, while utilizing at least two distinct binding sites to selectively engage TRAIL DRs or CD155. Binding studies revealed high affinity interaction of UL141 with both TRAIL-R2 and CD155 and low affinity binding to TRAIL-R1. We determined the crystal structure of UL141 bound to TRAIL-R2 at 2.1 Å resolution, which revealed that UL141 forms a homodimer that engages two TRAIL-R2 monomers 90° apart to form a heterotetrameric complex. Our structural and biochemical data reveal that UL141 utilizes its Ig-domain to facilitate non-canonical death receptor interactions while UL141 partially mimics the binding site of TRAIL on TRAIL-R2, which we found to be distinct from that of CD155. Moreover, UL141 also binds to an additional surface patch on TRAIL-R2 that is distinct from the TRAIL binding site. Therefore, the breadth of UL141-mediated effects indicates that HCMV has evolved sophisticated strategies to evade the immune system by modulating multiple effector pathways.

  5. Importin α1 Mediates Yorkie Nuclear Import via an N-terminal Non-canonical Nuclear Localization Signal.

    Science.gov (United States)

    Wang, Shimin; Lu, Yi; Yin, Meng-Xin; Wang, Chao; Wu, Wei; Li, Jinhui; Wu, Wenqing; Ge, Ling; Hu, Lianxin; Zhao, Yun; Zhang, Lei

    2016-04-08

    The Hippo signaling pathway controls organ size by orchestrating cell proliferation and apoptosis. When the Hippo pathway was inactivated, the transcriptional co-activator Yorkie translocates into the nucleus and forms a complex with transcription factor Scalloped to promote the expression of Hippo pathway target genes. Therefore, the nuclear translocation of Yorkie is a critical step in Hippo signaling. Here, we provide evidence that the N-terminal 1-55 amino acids of Yorkie, especially Arg-15, were essential for its nuclear localization. By mass spectrometry and biochemical analyses, we found that Importin α1 can directly interact with the Yorkie N terminus and drive Yorkie into the nucleus. Further experiments show that the upstream component Hippo can inhibit Importin α1-mediated Yorkie nuclear import. Taken together, we identified a potential nuclear localization signal at the N-terminal end of Yorkie as well as a critical role for Importin α1 in Yorkie nuclear import.

  6. Mono and trimethine cyanines Cyan 40 and Cyan 2 as probes for highly selective fluorescent detection of non-canonical DNA structures.

    Science.gov (United States)

    Kovalska, Vladyslava B; Losytskyy, Mykhaylo Yu; Yarmoluk, Sergiy M; Lubitz, Irit; Kotlyar, Alexander B

    2011-01-01

    Two of earlier reported dsDNA sensitive cyanine dyes-monomethine Cyan 40 and meso-substituted trimethine Cyan 2 were studied for their ability to interact with non-canonical DNA conformations. These dyes were characterized by spectral-luminescent methods in the presence of G-quadruplex, triplex and dsDNA motifs. We have demonstrated that Cyan 2 binds strongly and preferentially to triple- and quadruple-stranded DNA forms that results in a strong enhancement of the dye fluorescence, as compared to dsDNA, while Cyan 40 form fluorescent complexes preferentially only with the triplex form. Highly fluorescent complexes of Cyan 2 with DNA triplexes and G-quadruplexes and Cyan 40 with DNA triplexes are very stable and do not dissociate during gel electrophoresis, leading to preferential staining of the above DNA forms in gels. The data presented point to the intercalation mechanism of the Cyan 2 binding to G4-DNA, while the complexes of Cyan 40 and Cyan 2 with triplex DNA are believed to be formed via groove binding mode. The Cyan dyes can provide a highly sensitive method for detection and quantification of non-canonical structures in genome.

  7. Body-fixed orbit-attitude hovering at equilibria near an asteroid using non-canonical Hamiltonian structure

    CERN Document Server

    Wang, Yue

    2014-01-01

    Orbit-attitude hovering of a spacecraft at the natural relative equilibria in the body-fixed frame of a uniformly rotating asteroid is discussed in the framework of the full spacecraft dynamics, in which the spacecraft is modeled as a rigid body with the gravitational orbit-attitude coupling. In this hovering model, both the position and attitude of the spacecraft are kept to be stationary in the asteroid body-fixed frame. A Hamiltonian structure-based feedback control law is proposed to stabilize the relative equilibria of the full dynamics to achieve the orbit-attitude hovering. The control law is consisted of two parts: potential shaping and energy dissipation. The potential shaping is to make the relative equilibrium a minimum of the modified Hamiltonian on the invariant manifold by modifying the potential artificially. With the energy-Casimir method, it is shown that the unstable relative equilibrium can always be stabilized in the Lyapunov sense by the potential shaping with sufficiently large feedback ...

  8. Structure and specificity of a new class of Ca(2+) independent housekeeping sortase from Streptomyces avermitilis provides insights into its non-canonical substrate preference.

    Science.gov (United States)

    Das, Sreetama; Pawale, Vijaykumar S; Dadireddy, Venkatareddy; Singh, Avinash Kumar; Ramakumar, Suryanarayanarao; Roy, Rajendra P

    2017-03-07

    Surface proteins in Gram-positive bacteria are incorporated into the cell wall through a peptide ligation reaction catalyzed by transpeptidase sortase. Six main classes (A-F) of sortase have been identified of which class A sortase is meant for housekeeping functions. The prototypic housekeeping sortase A (SaSrtA) from Staphylococcus aureus cleaves LPXTG-containing proteins at the scissile T-G peptide bond and ligates Protein-LPXT to the terminal Gly residue of the nascent cross-bridge of peptidoglycan Lipid II precursor. Sortase-mediated ligation ('sortagging') of LPXTG-containing substrates and Gly-terminated nucleophiles occurs in vitro as well as in cellulo in the presence of Ca(2+) and has been applied extensively for protein conjugations. Although majority of applications emanate from SaSrtA, low catalytic efficiency, LPXTG specificity restriction, and Ca(2+) requirement (particularly for in cellulo applications) remains a drawback. Given that Gram-positive bacterial genomes encode a variety of sortases, natural sortase mining can be a viable complementary approach akin to engineering of wild type SaSrtA. Here we describe the structure and specificity of a new class E sortase (SavSrtE) annotated to perform housekeeping roles in Streptomyces avermitilis Biochemical experiments define the attributes of an optimum peptide substrate, demonstrate Ca(2+)-independent activity and provide insights about contrasting functional characteristics of SavSrtE and SaSrtA. Crystal structure, substrate docking and mutagenesis experiments have identified a critical residue that dictates the preference for a non-canonical LAXTG recognition motif over LPXTG. These results have implications for rational tailoring of substrate tolerance in sortases. Besides, Ca(2+) independent orthogonal specificity of SavSrtE is likely to expand the sortagging toolkit.

  9. Update on non-canonical microRNAs

    OpenAIRE

    2014-01-01

    Non-canonical microRNAs are a recently-discovered subset of microRNAs. They structurally and functionally resemble canonical miRNAs, but were found to follow distinct maturation pathways, typically bypassing one or more steps of the classic canonical biogenesis pathway. Non-canonical miRNAs were found to have diverse origins, including introns, snoRNAs, endogenous shRNAs and tRNAs. Our knowledge about their functions remains relatively primitive; however, many interesting discoveries have tak...

  10. Update on non-canonical microRNAs

    Science.gov (United States)

    Abdelfattah, Ahmed Maher; Park, Chanhyun

    2015-01-01

    Non-canonical microRNAs are a recently-discovered subset of microRNAs. They structurally and functionally resemble canonical miRNAs, but were found to follow distinct maturation pathways, typically bypassing one or more steps of the classic canonical biogenesis pathway. Non-canonical miRNAs were found to have diverse origins, including introns, snoRNAs, endogenous shRNAs and tRNAs. Our knowledge about their functions remains relatively primitive; however, many interesting discoveries have taken place in the past few years. They have been found to take part in several cellular processes, such as immune response and stem cell proliferation. Adversely, their deregulation has pathologic effects on several different tissues, which strongly suggests an integral role for non-canonical miRNAs in disease pathogenesis. In this review, we discuss the recently-discovered functional characteristics of non-canonical miRNAs and illustrate their principal maturation pathways as well as debating their potential role in multiple cellular processes. PMID:25372759

  11. De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies.

    Science.gov (United States)

    Karamitros, Timokratis; Harrison, Ian; Piorkowska, Renata; Katzourakis, Aris; Magiorkinis, Gkikas; Mbisa, Jean Lutamyo

    2016-01-01

    Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging. To improve the assembly of HHV-1 genomes we have employed a hybrid genome assembly protocol using data from two sequencing technologies: the short-read Roche 454 and the long-read Oxford Nanopore MinION sequencers. We sequenced 18 HHV-1 cell culture-isolated clinical specimens collected from immunocompromised patients undergoing antiviral therapy. The susceptibility of the samples to several antivirals was determined by plaque reduction assay. Hybrid genome assembly resulted in a decrease in the number of contigs in 6 out of 7 samples and an increase in N(G)50 and N(G)75 of all 7 samples sequenced by both technologies. The approach also enhanced the detection of non-canonical contigs including a rearrangement between the unique (UL) and repeat (T/IRL) sequence regions of one sample that was not detectable by assembly of 454 reads alone. We detected several known and novel resistance-associated mutations in UL23 and UL30 genes. Genome-wide genetic variability ranged from assembly of accurate, full-length HHV-1 genomes will be useful in determining genetic determinants of drug resistance, virulence, pathogenesis and viral evolution. The numerous, complex repeat regions of the HHV-1 genome currently remain a barrier towards this goal.

  12. Splitting K-symplectic methods for non-canonical separable Hamiltonian problems

    Science.gov (United States)

    Zhu, Beibei; Zhang, Ruili; Tang, Yifa; Tu, Xiongbiao; Zhao, Yue

    2016-10-01

    Non-canonical Hamiltonian systems have K-symplectic structures which are preserved by K-symplectic numerical integrators. There is no universal method to construct K-symplectic integrators for arbitrary non-canonical Hamiltonian systems. However, in many cases of interest, by using splitting, we can construct explicit K-symplectic methods for separable non-canonical systems. In this paper, we identify situations where splitting K-symplectic methods can be constructed. Comparative numerical experiments in three non-canonical Hamiltonian problems show that symmetric/non-symmetric splitting K-symplectic methods applied to the non-canonical systems are more efficient than the same-order Gauss' methods/non-symmetric symplectic methods applied to the corresponding canonicalized systems; for the non-canonical Lotka-Volterra model, the splitting algorithms behave better in efficiency and energy conservation than the K-symplectic method we construct via generating function technique. In our numerical experiments, the favorable energy conservation property of the splitting K-symplectic methods is apparent.

  13. Non-canonical modulators of nuclear receptors.

    Science.gov (United States)

    Tice, Colin M; Zheng, Ya-Jun

    2016-09-01

    Like G protein-coupled receptors (GPCRs) and protein kinases, nuclear receptors (NRs) are a rich source of pharmaceutical targets. Over 80 NR-targeting drugs have been approved for 18 NRs. The focus of drug discovery in NRs has hitherto been on identifying ligands that bind to the canonical ligand binding pockets of the C-terminal ligand binding domains (LBDs). Due to the development of drug resistance and selectivity concerns, there has been considerable interest in exploring other, non-canonical ligand binding sites. Unfortunately, the potencies of compounds binding at other sites have generally not been sufficient for clinical development. However, the situation has changed dramatically over the last 3years, as compounds with sufficient potency have been reported for several NR targets. Here we review recent developments in this area from a medicinal chemistry point of view in the hope of stimulating further interest in this area of research.

  14. The non-canonical functions of the heme oxygenases.

    Science.gov (United States)

    Vanella, Luca; Barbagallo, Ignazio; Tibullo, Daniele; Forte, Stefano; Zappalà, Agata; Li Volti, Giovanni

    2016-10-18

    Heme oxygenase (HO) isoforms catalyze the conversion of heme to carbon monoxide (CO) and biliverdin with a concurrent release of iron, which can drive the synthesis of ferritin for iron sequestration. Most of the studies so far were directed at evaluating the protective effect of these enzymes because of their ability to generate antioxidant and antiapoptotic molecules such as CO and bilirubin. Recent evidences are suggesting that HO may possess other important physiological functions, which are not related to its enzymatic activity and for which we would like to introduce for the first time the term "non canonical functions". Recent evidence suggest that both HO isoforms may form protein-protein interactions (i.e. cytochrome P450, adiponectin, CD91) thus serving as chaperone-like protein. In addition, truncated HO-1 isoform was localized in the nuclear compartment under certain experimental conditions (i.e. excitotoxicity, hypoxia) regulating the activity of important nuclear transcription factors (i.e. Nrf2) and DNA repair. In the present review, we discuss three potential signaling mechanisms that we refer to as the non-canonical functions of the HO isoforms: protein-protein interaction, intracellular compartmentalization, and extracellular secretion. The aim of the present review is to describe each of this mechanism and all the aspects warranting additional studies in order to unravel all the functions of the HO system.

  15. Extension of warm inflation to non-canonical scalar fields

    CERN Document Server

    Zhang, Xiao-Min

    2014-01-01

    We extend the warm inflationary scenario to the case of the non-canonical scalar fields. The equation of motion and the other basic equations of this new scenario are obtained. The Hubble damped term is enhanced in non-canonical inflation. A linear stability analysis is performed to give the proper slow roll conditions in warm non-canonical inflation. We study the density fluctuations in the new picture and obtain an approximate analytic expression of the power spectrum. The energy scale at the horizon crossing is depressed by both non-canonical effect and thermal effect, so does the tensor-to-scalar ratio. Besides the synergy, the non-canonical effect and the thermal effect are competing in the case of the warm non-canonical inflation.

  16. Non-canonical WNT signalling in the lung

    Science.gov (United States)

    Li, Changgong; Bellusci, Saverio; Borok, Zea; Minoo, Parviz

    2015-01-01

    The role of WNT signalling in metazoan organogenesis has been a topic of widespread interest. In the lung, while the role of canonical WNT signalling has been examined in some detail by multiple studies, the non-canonical WNT signalling has received limited attention. Reliable evidence shows that this important signalling mechanism constitutes a major regulatory pathway in lung development. In addition, accumulating evidence has also shown that the non-canonical WNT pathway is critical for maintaining lung homeostasis and that aberrant activation of this pathway may underlie several debilitating lung diseases. Functional analyses have further revealed that the non-canonical WNT pathway regulates multiple cellular activities in the lung that are dependent on the specific cellular context. In most cell types, non-canonical WNT signalling regulates canonical WNT activity, which is also critical for many aspects of lung biology. This review will summarize what is currently known about the role of non-canonical WNT signalling in lung development, homeostasis and pathogenesis of disease. PMID:26261051

  17. Accretion of the Moon from non-canonical discs.

    Science.gov (United States)

    Salmon, J; Canup, R M

    2014-09-13

    Impacts that leave the Earth-Moon system with a large excess in angular momentum have recently been advocated as a means of generating a protolunar disc with a composition that is nearly identical to that of the Earth's mantle. We here investigate the accretion of the Moon from discs generated by such 'non-canonical' impacts, which are typically more compact than discs produced by canonical impacts and have a higher fraction of their mass initially located inside the Roche limit. Our model predicts a similar overall accretional history for both canonical and non-canonical discs, with the Moon forming in three consecutive steps over hundreds of years. However, we find that, to yield a lunar-mass Moon, the more compact non-canonical discs must initially be more massive than implied by prior estimates, and only a few of the discs produced by impact simulations to date appear to meet this condition. Non-canonical impacts require that capture of the Moon into the evection resonance with the Sun reduced the Earth-Moon angular momentum by a factor of 2 or more. We find that the Moon's semi-major axis at the end of its accretion is approximately 7R⊕, which is comparable to the location of the evection resonance for a post-impact Earth with a 2.5 h rotation period in the absence of a disc. Thus, the dynamics of the Moon's assembly may directly affect its ability to be captured into the resonance.

  18. Accretion of the Moon from non-canonical disks

    CERN Document Server

    Salmon, Julien

    2014-01-01

    Impacts that leave the Earth-Moon system with a large excess in angular momentum have recently been advocated as a means of generating a protolunar disc with a composition that is nearly identical to that of the Earth's mantle. We here investigate the accretion of the Moon from discs generated by such "non-canonical" impacts, which are typically more compact than discs produced by canonical impacts and have a higher fraction of their mass initially located inside the Roche limit. Our model predicts a similar overall accretional history for both canonical and non-canonical discs, with the Moon forming in three consecutive steps over hundreds of years. However, we find that, to yield a lunar-mass Moon, the more compact non-canonical discs must initially be more massive than implied by prior estimates, and only a few of the discs produced by impact simulations to date appear to meet this condition. Non-canonical impacts require that capture of the Moon into the evection resonance with the Sun reduced the Earth-M...

  19. Non-canonical Stat3 signaling in cancer.

    Science.gov (United States)

    Srivastava, Jaya; DiGiovanni, John

    2016-12-01

    Stat3 is a member of the signal transducers and activators of transcription family and is a known regulator of essential biologic processes including angiogenesis, apoptosis, cell cycle progression, and cell migration. Canonical Stat3-mediated signaling involves tyrosine phosphorylation on specific residues that leads to homodimerization and translocation to the nucleus. For many years it was presumed that most, if not all, of the functions of Stat3, both normal and aberrant, were due to the canonical cytokine and growth factor signaling mechanisms. Recent studies suggest that Stat3 functions through alternate non-canonical pathways to bring about some of these biological functions both in normal cells as well as during cancer development and progression. A number of studies have now shown that Stat3 has a function in mitochondria and that unphosphorylated Stat3 (uStat3) can also function as a transcription factor broadening the potential mechanisms involved in Stat3 action. In this review article, we discuss these two main non-canonical functions of Stat3 and their potential roles in oncogenesis. Given the many facets of Stat3 signaling, additional comprehensive investigations are required to fully understand the role of non-canonical Stat3 signaling in cancer and whether these pathways can be targeted for cancer prevention and treatment. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  20. Variational principle and phase space measure in non-canonical coordinates

    Directory of Open Access Journals (Sweden)

    Sergi, A

    2005-11-01

    Full Text Available Non-canonical equations of motion are derived from a variational principle written in symplectic form. The invariant measure of phase space and the covariant expression for the entropy are derived from non-canonical transformations of coordinates. This shows that the geometry of non-canonical phase space is non trivial even if dynamics has no compressibility.

  1. Mechanisms of Non-canonical Activation of Ataxia Telangiectasia Mutated.

    Science.gov (United States)

    Khoronenkova, S V

    2016-12-01

    ATM is a master regulator of the cellular response to DNA damage. The classical mechanism of ATM activation involves its monomerization in response to DNA double-strand breaks, resulting in ATM-dependent phosphorylation of more than a thousand substrates required for cell cycle progression, DNA repair, and apoptosis. Here, new experimental evidence for non-canonical mechanisms of ATM activation in response to stimuli distinct from DNA double-strand breaks is discussed. It includes cytoskeletal changes, chromatin modifications, RNA-DNA hybrids, and DNA single-strand breaks. Noncanonical ATM activation may be important for the pathology of the multisystemic disease Ataxia Telangiectasia.

  2. Non-canonical signaling of the PTH receptor

    Science.gov (United States)

    Vilardaga, Jean-Pierre; Gardella, Thomas J.; Wehbi, Vanessa L.; Feinstein, Timothy N.

    2012-01-01

    The classical model of arrestin-mediated desensitization of cell-surface G protein-coupled receptors (GPCRs) is thought to be universal. However, this paradigm is incompatible with recent reports that the parathyroid hormone (PTH) receptor (PTHR), a crucial GPCR for bone and mineral ion metabolism, sustains GS activity and continues to generate cAMP for prolonged periods after ligand-wash-out; during these periods the receptor is observed mainly in endosomes, associated with the bound ligand, GS and β-arrestins. In this review, we discuss possible molecular mechanisms underlying sustained signaling by the PTHR, including modes of signal generation and attenuation within endosomes, as well as the biological relevance of such non-canonical signaling. PMID:22709554

  3. Production of non-canonical sentences in agrammatic aphasia: limits in representation or rule application?

    Science.gov (United States)

    Burchert, Frank; Meissner, Nadine; De Bleser, Ria

    2008-02-01

    The study reported here compares two linguistically informed hypotheses on agrammatic sentence production, the TPH [Friedmann, N., & Grodzinsky, Y. (1997). Tense and agreement in agrammatic production: Pruning the syntactic tree. Brain and Language, 56, 397-425.] and the DOP [Bastiaanse, R., & van Zonneveld, R. (2005). Sentence production with verbs of alternating transitivity in agrammatic Broca's aphasia. Journal of Neurolinguistics, 18, 59-66]. To explain impaired production of non-canonical sentences in agrammatism, the TPH basically relies on deleted or pruned clause structure positions in the left periphery, whereas the DOP appeals to limitations in the application of movement rules. Certain non-canonical sentences such as object-questions and object-relative clauses require the availability of nodes in the left periphery as well as movement to these nodes. In languages with relatively fixed word order such as English, the relevant test cases generally involve a coincidence of left periphery and movement, such that the predictions of the TPH and the DOP are identical although for different reasons. In languages with relatively free word order such as German, on the other hand, it is possible to devise specific tests of the different predictions due to the availability of scrambling. Scrambled object sentences, for example, do not involve the left periphery but do require application of movement in a domain below the left periphery. A study was conducted with German agrammatic subjects which elicited canonical sentences without object movement and non-canonical scrambled sentences with object movement. The results show that agrammatic speakers have a particular problem with the production of scrambled sentences. Further evidence reported in the study from spontaneous speech, elicitation of object relatives, questions and passives and with different agrammatic subjects confirms that non-canonical sentences are generally harder to produce for agrammatics. These

  4. Rational design of a non-canonical "sticky-ended" collagen triple helix.

    Science.gov (United States)

    Jalan, Abhishek A; Jochim, Katherine A; Hartgerink, Jeffrey D

    2014-05-28

    In a canonical collagen triple helix, three peptides self-assemble into a supercoiled motif with a one-amino-acid offset between the peptide chains. Design of triple helices that contain more than one residue offset is lucrative, as it leaves the non-covalent interactions unsatisfied at the termini and renders the termini "sticky" to further self-assemble into collagen-like nanofibers. Here we use lysine-glutamate axial salt-bridges to design a heterotrimeric collagen triple helix, ABC-1, containing a non-canonical offset of four residues between the peptide chains. The four-residue offset is necessary to prevent aggregation, which would prevent characterization of the non-canonical chain arrangement at the molecular level by NMR spectroscopy. A second heterotrimer, ABC-2, also stabilized by axial salt-bridges, is designed containing a canonical one-amino-acid offset to facilitate comparison of structure and stability by CD and NMR. ABC-1 and ABC-2 demonstrate our ability to modulate chain offset in a collagen triple helix. This lays the groundwork to design longer, and therefore stickier, offsets allowing access to a new class of collagen-related nanostructures.

  5. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jianyuan [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Qin, Hong [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543, USA; Liu, Jian [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; He, Yang [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Zhang, Ruili [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026, China; Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026, China; Sun, Yajuan [LSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, P.O. Box 2719, Beijing 100190, China

    2015-11-01

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint arXiv: 1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave. (C) 2015 AIP Publishing LLC.

  6. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, Jianyuan; Liu, Jian; He, Yang; Zhang, Ruili [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Key Laboratory of Geospace Environment, CAS, Hefei, Anhui 230026 (China); Qin, Hong, E-mail: hongqin@ustc.edu.cn [School of Nuclear Science and Technology and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Plasma Physics Laboratory, Princeton University, Princeton, New Jersey 08543 (United States); Sun, Yajuan [LSEC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, P.O. Box 2719, Beijing 100190 (China)

    2015-11-15

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithms conserve a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a structure-preserving splitting method discovered by He et al. [preprint http://arxiv.org/abs/arXiv:1505.06076 (2015)], which produces five exactly soluble sub-systems, and high-order structure-preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom on massively parallel supercomputers. The algorithms have been tested and verified by the two physics problems, i.e., the nonlinear Landau damping and the electron Bernstein wave.

  7. Explicit high-order non-canonical symplectic particle-in-cell algorithms for Vlasov-Maxwell systems

    CERN Document Server

    Xiao, Jianyuan; Liu, Jian; He, Yang; Zhang, Ruili; Sun, Yajuan

    2015-01-01

    Explicit high-order non-canonical symplectic particle-in-cell algorithms for classical particle-field systems governed by the Vlasov-Maxwell equations are developed. The algorithm conserves a discrete non-canonical symplectic structure derived from the Lagrangian of the particle-field system, which is naturally discrete in particles. The electromagnetic field is spatially-discretized using the method of discrete exterior calculus with high-order interpolating differential forms for a cubic grid. The resulting time-domain Lagrangian assumes a non-canonical symplectic structure. It is also gauge invariant and conserves charge. The system is then solved using a splitting method discovered by He et al., which produces five exactly-soluable sub-systems, and high-order structure- preserving algorithms follow by combinations. The explicit, high-order, and conservative nature of the algorithms is especially suitable for long-term simulations of particle-field systems with extremely large number of degrees of freedom ...

  8. Complete Hamiltonian analysis of cosmological perturbations at all orders II: non-canonical scalar field

    Science.gov (United States)

    Nandi, Debottam; Shankaranarayanan, S.

    2016-10-01

    In this work, we present a consistent Hamiltonian analysis of cosmological perturbations for generalized non-canonical scalar fields. In order to do so, we introduce a new phase-space variable that is uniquely defined for different non-canonical scalar fields. We also show that this is the simplest and efficient way of expressing the Hamiltonian. We extend the Hamiltonian approach of [1] to non-canonical scalar field and obtain an unique expression of speed of sound in terms of phase-space variable. In order to invert generalized phase-space Hamilton's equations to Euler-Lagrange equations of motion, we prescribe a general inversion formulae and show that our approach for non-canonical scalar field is consistent. We also obtain the third and fourth order interaction Hamiltonian for generalized non-canonical scalar fields and briefly discuss the extension of our method to generalized Galilean scalar fields.

  9. Complete Hamiltonian analysis of cosmological perturbations at all orders II: Non-canonical scalar field

    CERN Document Server

    Nandi, Debottam

    2016-01-01

    In this work, we present a consistent Hamiltonian analysis of cosmological perturbations for generalized non-canonical scalar fields. In order to do so, we introduce a new phase-space variable that is uniquely defined for different non-canonical scalar fields. We also show that this is the simplest and efficient way of expressing the Hamiltonian. We extend the Hamiltonian approach of [arXiv:1512.02539] to non-canonical scalar field and obtain a new definition of speed of sound in phase-space. In order to invert generalized phase-space Hamilton's equations to Euler-Lagrange equations of motion, we prescribe a general inversion formulae and show that our approach for non-canonical scalar field is consistent. We also obtain the third and fourth order interaction Hamiltonian for generalized non-canonical scalar fields and briefly discuss the extension of our method to generalized Galilean scalar fields.

  10. Red-Shifted Aequorin Variants Incorporating Non-Canonical Amino Acids: Applications in In Vivo Imaging.

    Directory of Open Access Journals (Sweden)

    Kristen M Grinstead

    Full Text Available The increased importance of in vivo diagnostics has posed new demands for imaging technologies. In that regard, there is a need for imaging molecules capable of expanding the applications of current state-of-the-art imaging in vivo diagnostics. To that end, there is a desire for new reporter molecules capable of providing strong signals, are non-toxic, and can be tailored to diagnose or monitor the progression of a number of diseases. Aequorin is a non-toxic photoprotein that can be used as a sensitive marker for bioluminescence in vivo imaging. The sensitivity of aequorin is due to the fact that bioluminescence is a rare phenomenon in nature and, therefore, it does not suffer from autofluorescence, which contributes to background emission. Emission of bioluminescence in the blue-region of the spectrum by aequorin only occurs when calcium, and its luciferin coelenterazine, are bound to the protein and trigger a biochemical reaction that results in light generation. It is this reaction that endows aequorin with unique characteristics, making it ideally suited for a number of applications in bioanalysis and imaging. Herein we report the site-specific incorporation of non-canonical or non-natural amino acids and several coelenterazine analogues, resulting in a catalog of 72 cysteine-free, aequorin variants which expand the potential applications of these photoproteins by providing several red-shifted mutants better suited to use in vivo. In vivo studies in mouse models using the transparent tissue of the eye confirmed the activity of the aequorin variants incorporating L-4-iodophehylalanine and L-4-methoxyphenylalanine after injection into the eye and topical addition of coelenterazine. The signal also remained localized within the eye. This is the first time that aequorin variants incorporating non-canonical amino acids have shown to be active in vivo and useful as reporters in bioluminescence imaging.

  11. Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations.

    Science.gov (United States)

    Seligmann, Hervé

    2016-01-01

    Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s). Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R) detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides), and from transcripts systematically (a) deleting mono-, dinucleotides after trinucleotides (delRNAs), (b) exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A) produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.

  12. Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations

    Directory of Open Access Journals (Sweden)

    Hervé Seligmann

    2016-01-01

    Full Text Available Proteomic MS/MS mass spectrometry detections are usually biased towards peptides cleaved by experimentally added digestion enzyme(s. Hence peptides resulting from spontaneous degradation and natural proteolysis usually remain undetected. Previous analyses of tryptic human proteome data (cleavage after K, R detected non-canonical tryptic peptides translated according to tetra- and pentacodons (codons expanded by silent mono- and dinucleotides, and from transcripts systematically (a deleting mono-, dinucleotides after trinucleotides (delRNAs, (b exchanging nucleotides according to 23 bijective transformations. Nine symmetric and fourteen asymmetric nucleotide exchanges (X ↔ Y, e.g. A ↔ C; and X → Y → Z → X, e.g. A → C → G → A produce swinger RNAs. Here unbiased reanalyses of these proteomic data detect preferentially non-canonical tryptic peptides despite assuming random cleavage. Unbiased analyses couldn't reconstruct experimental tryptic digestion if most detected non-canonical peptides were false positives. Detected non-tryptic non-canonical peptides map preferentially on corresponding, previously described non-canonical transcripts, as for tryptic non-canonical peptides. Hence unbiased analyses independently confirm previous trypsin-biased analyses that showed translations of del- and swinger RNA and expanded codons. Accounting for natural proteolysis completes trypsin-biased mitopeptidome analyses, independently confirms non-canonical transcriptions and translations.

  13. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

    Science.gov (United States)

    Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun

    2016-03-01

    The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.

  14. TRIM24 Links a Non-canonical Histone Signature to Breast Cancer

    Energy Technology Data Exchange (ETDEWEB)

    W Tsai; Z Wang; T Yiu; K Akdemir; W Xia; S Winter; C Tsai; X Shi; D Schwarzer; et al.

    2011-12-31

    Recognition of modified histone species by distinct structural domains within 'reader' proteins plays a critical role in the regulation of gene expression. Readers that simultaneously recognize histones with multiple marks allow transduction of complex chromatin modification patterns into specific biological outcomes. Here we report that chromatin regulator tripartite motif-containing 24 (TRIM24) functions in humans as a reader of dual histone marks by means of tandem plant homeodomain (PHD) and bromodomain (Bromo) regions. The three-dimensional structure of the PHD-Bromo region of TRIM24 revealed a single functional unit for combinatorial recognition of unmodified H3K4 (that is, histone H3 unmodified at lysine 4, H3K4me0) and acetylated H3K23 (histone H3 acetylated at lysine 23, H3K23ac) within the same histone tail. TRIM24 binds chromatin and oestrogen receptor to activate oestrogen-dependent genes associated with cellular proliferation and tumour development. Aberrant expression of TRIM24 negatively correlates with survival of breast cancer patients. The PHD-Bromo of TRIM24 provides a structural rationale for chromatin activation through a non-canonical histone signature, establishing a new route by which chromatin readers may influence cancer pathogenesis.

  15. Canonical and non-canonical barriers facing antimiR cancer therapeutics.

    Science.gov (United States)

    Cheng, Christopher J; Saltzman, W Mark; Slack, Frank J

    2013-01-01

    Once considered genetic "oddities", microRNAs (miRNAs) are now recognized as key epigenetic regulators of numerous biological processes, including some with a causal link to the pathogenesis, maintenance, and treatment of cancer. The crux of small RNA-based therapeutics lies in the antagonism of potent cellular targets; the main shortcoming of the field in general, lies in ineffective delivery. Inhibition of oncogenic miRNAs is a relatively nascent therapeutic concept, but as with predecessor RNA-based therapies, success hinges on delivery efficacy. This review will describes the canonical (e.g. pharmacokinetics and clearance, cellular uptake, endosome escape, etc.) and non-canonical (e.g. spatial localization and accessibility of miRNA, technical limitations of miRNA inhibition, off-target impacts, etc.) challenges to the delivery of antisense-based anti-miRNA therapeutics (i.e. antimiRs) for the treatment of cancer. Emphasis will be placed on how the current leading antimiR platforms-ranging from naked chemically modified oligonucleotides to nanoscale delivery vehicles-are affected by and overcome these barriers. The perplexity of antimiR delivery presents both engineering and biological hurdles that must be overcome in order to capitalize on the extensive pharmacological benefits of antagonizing tumor-associated miRNAs.

  16. A non-canonical peptide synthetase adenylates 3-methyl-2-oxovaleric acid for auriculamide biosynthesis

    Directory of Open Access Journals (Sweden)

    Daniel Braga

    2016-12-01

    Full Text Available Auriculamide is the first natural product known from the predatory bacterium Herpetosiphon aurantiacus. It is composed of three unusual building blocks, including the non-proteinogenic amino acid 3-chloro-L-tyrosine, the α-hydroxy acid L-isoleucic acid, and a methylmalonyl-CoA-derived ethane unit. A candidate genetic locus for auriculamide biosynthesis was identified and encodes four enzymes. Among them, the non-canonical 199 kDa four-domain nonribosomal peptide synthetase, AulA, is extraordinary in that it features two consecutive adenylation domains. Here, we describe the functional characterization of the recombinantly produced AulA. The observed activation of 3-methyl-2-oxovaleric acid by the enzyme supports the hypothesis that it participates in the biosynthesis of auriculamide. An artificially truncated version of AulA that lacks the first adenylation domain activated this substrate like the full-length enzyme which shows that the first adenylation domain is dispensable. Additionally, we provide evidence that the enzyme tolerates structural variation of the substrate. α-Carbon substituents significantly affected the substrate turnover. While all tested aliphatic α-keto acids were accepted by the enzyme and minor differences in chain size and branches did not interfere with the enzymatic activity, molecules with methylene α-carbons led to low turnover. Such enzymatic plasticity is an important attribute to help in the perpetual search for novel molecules and to access a greater structural diversity by mutasynthesis.

  17. Complex phylogenetic distribution of a non-canonical genetic code in green algae

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2010-10-01

    Full Text Available Abstract Background A non-canonical nuclear genetic code, in which TAG and TAA have been reassigned from stop codons to glutamine, has evolved independently in several eukaryotic lineages, including the ulvophycean green algal orders Dasycladales and Cladophorales. To study the phylogenetic distribution of the standard and non-canonical genetic codes, we generated sequence data of a representative set of ulvophycean green algae and used a robust green algal phylogeny to evaluate different evolutionary scenarios that may account for the origin of the non-canonical code. Results This study demonstrates that the Dasycladales and Cladophorales share this alternative genetic code with the related order Trentepohliales and the genus Blastophysa, but not with the Bryopsidales, which is sister to the Dasycladales. This complex phylogenetic distribution whereby all but one representative of a single natural lineage possesses an identical deviant genetic code is unique. Conclusions We compare different evolutionary scenarios for the complex phylogenetic distribution of this non-canonical genetic code. A single transition to the non-canonical code followed by a reversal to the canonical code in the Bryopsidales is highly improbable due to the profound genetic changes that coincide with codon reassignment. Multiple independent gains of the non-canonical code, as hypothesized for ciliates, are also unlikely because the same deviant code has evolved in all lineages. Instead we favor a stepwise acquisition model, congruent with the ambiguous intermediate model, whereby the non-canonical code observed in these green algal orders has a single origin. We suggest that the final steps from an ambiguous intermediate situation to a non-canonical code have been completed in the Trentepohliales, Dasycladales, Cladophorales and Blastophysa but not in the Bryopsidales. We hypothesize that in the latter lineage an initial stage characterized by translational ambiguity was

  18. Natural chymotrypsin-like-cleaved human mitochondrial peptides confirm tetra-, pentacodon, non-canonical RNA translations.

    Science.gov (United States)

    Seligmann, Hervé

    2016-09-01

    Mass spectra of human mitochondrial peptides match non-canonical transcripts systematically (a) deleting mono/dinucleotides after trinucleotides (delRNA), (b) exchanging nucleotides (swinger RNA), translated according to tri, (c) tetra- and pentacodons (codons expanded by a 4th (and 5th) silent nucleotide(s)). Swinger transcriptions are 23 bijective transformations, nine symmetric (XY, e.g. AC) and fourteen asymmetric exchanges (X->Y->Z->X, e.g. A->C->G->A). Here, proteomic analyses assuming cleavage after W,Y, F (chymotrypsin-like, for trypsinized samples) detect fewer chymotrypsinized than trypsinized peptides. Detected non-canonical peptides map preferentially on detected non-canonical RNAs for chymotrypsinized peptides, as previously found for trypsinized peptides. This suggests residual natural chymotrypsin-like digestion detectable within experimentally trypsinized peptide data. Some trypsinized peptides are detected twice, by analyses assuming trypsin, and those assuming chymotrypsin cleavages. They have higher spectra counts than peptides detected only once, meaning that abundant peptides are more frequently detected, but detection certainties resemble those for peptides detected only once. Analyses assuming 'incorrect' digestions are inadequate negative controls for digestion enzymes naturally active in biological samples. Chymotrypsin-analyses confirm non-canonical transcriptions/translations independently of results obtained assuming trypsinization, increase non-canonical peptidome coverage, indicating mitogenome-encoding of yet undetected proteins.

  19. Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification

    Science.gov (United States)

    Kugel, Susann; Baunach, Martin; Baer, Philipp; Ishida-Ito, Mie; Sundaram, Srividhya; Xu, Zhongli; Groll, Michael; Hertweck, Christian

    2017-06-01

    Terpenoid natural products comprise a wide range of molecular architectures that typically result from C-C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis. The crystal structure of XiaF with bound FADH2 (at 2.4 Å resolution) and phylogenetic analyses reveal that XiaF is, surprisingly, most closely related to xenobiotic-degrading enzymes. Biotransformation assays show that XiaF is a designated indole hydroxylase that can be used for the production of indigo and indirubin. We unveil a cryptic hydroxylation step that sets the basis for terpenoid cyclization and suggest that the cyclase has evolved from xenobiotics detoxification enzymes.

  20. Generalized second law of thermodynamics for non-canonical scalar field model with corrected-entropy

    Science.gov (United States)

    Das, Sudipta; Debnath, Ujjal; Mamon, Abdulla Al

    2015-10-01

    In this work, we have considered a non-canonical scalar field dark energy model in the framework of flat FRW background. It has also been assumed that the dark matter sector interacts with the non-canonical dark energy sector through some interaction term. Using the solutions for this interacting non-canonical scalar field dark energy model, we have investigated the validity of generalized second law (GSL) of thermodynamics in various scenarios using first law and area law of thermodynamics. For this purpose, we have assumed two types of horizons viz apparent horizon and event horizon for the universe and using first law of thermodynamics, we have examined the validity of GSL on both apparent and event horizons. Next, we have considered two types of entropy-corrections on apparent and event horizons. Using the modified area law, we have examined the validity of GSL of thermodynamics on apparent and event horizons under some restrictions of model parameters.

  1. Generalized Second Law of Thermodynamics for Non-canonical Scalar Field Model with Corrected-Entropy

    CERN Document Server

    Das, Sudipta; Mamon, Abdulla Al

    2015-01-01

    In this work, we have considered a non-canonical scalar field dark energy model in the framework of flat FRW background. It has also been assumed that the dark matter sector interacts with the non-canonical dark energy sector through some interaction term. Using the solutions for this interacting non-canonical scalar field dark energy model, we have investigated the validity of generalized second law (GSL) of thermodynamics in various scenarios using first law and area law of thermodynamics. For this purpose, we have assumed two types of horizons viz apparent horizon and event horizon for the universe and using first law of thermodynamics, we have examined the validity of GSL on both apparent and event horizons. Next, we have considered two types of entropy-corrections on apparent and event horizons. Using the modified area law, we have examined the validity of GSL of thermodynamics on apparent and event horizons under some restrictions of model parameters.

  2. Generalized second law of thermodynamics for non-canonical scalar field model with corrected-entropy

    Energy Technology Data Exchange (ETDEWEB)

    Das, Sudipta; Mamon, Abdulla Al [Visva-Bharati, Department of Physics, Santiniketan (India); Debnath, Ujjal [Indian Institute of Engineering Science and Technology, Department of Mathematics, Shibpur, Howrah (India)

    2015-10-15

    In this work, we have considered a non-canonical scalar field dark energy model in the framework of flat FRW background. It has also been assumed that the dark matter sector interacts with the non-canonical dark energy sector through some interaction term. Using the solutions for this interacting non-canonical scalar field dark energy model, we have investigated the validity of generalized second law (GSL) of thermodynamics in various scenarios using first law and area law of thermodynamics. For this purpose, we have assumed two types of horizons viz apparent horizon and event horizon for the universe and using first law of thermodynamics, we have examined the validity of GSL on both apparent and event horizons. Next, we have considered two types of entropy-corrections on apparent and event horizons. Using the modified area law, we have examined the validity of GSL of thermodynamics on apparent and event horizons under some restrictions of model parameters. (orig.)

  3. Non-Canonical Hh Signaling in Cancer—Current Understanding and Future Directions

    Directory of Open Access Journals (Sweden)

    Dongsheng Gu

    2015-08-01

    Full Text Available As a major regulatory pathway for embryonic development and tissue patterning, hedgehog signaling is not active in most adult tissues, but is reactivated in a number of human cancer types. A major milestone in hedgehog signaling in cancer is the Food and Drug Administration (FDA approval of a smoothened inhibitor Vismodegib for treatment of basal cell carcinomas. Vismodegib can block ligand-mediated hedgehog signaling, but numerous additional clinical trials have failed to show significant improvements in cancer patients. Amounting evidence indicate that ligand-independent hedgehog signaling plays an essential role in cancer. Ligand-independent hedgehog signaling, also named non-canonical hedgehog signaling, generally is not sensitive to smoothened inhibitors. What we know about non-canonical hedgehog signaling in cancer, and how should we prevent its activation? In this review, we will summarize recent development of non-canonical hedgehog signaling in cancer, and will discuss potential ways to prevent this type of hedgehog signaling.

  4. Power Spectra beyond the Slow Roll Approximation in Theories with Non-Canonical Kinetic Terms

    CERN Document Server

    van de Bruck, Carsten

    2014-01-01

    We derive analytical expressions for the power spectra at the end of inflation in theories with two inflaton fields and non-canonical kinetic terms. We find that going beyond the slow-roll approximation is necessary and that the nature of the non-canonical terms have an important impact on the final power spectra at the end of inflation. We study five models numerically and find excellent agreement with our analytical results. Our results emphasise the fact that going beyond the slow-roll approximation is important in times of high-precision data coming from cosmological observations.

  5. Study of non-canonical scalar field model using various parametrizations of dark energy equation of state

    Energy Technology Data Exchange (ETDEWEB)

    Al Mamon, Abdulla; Das, Sudipta [Visva-Bharati, Department of Physics, Santiniketan (India)

    2015-06-15

    In this present work, we try to build up a cosmological model using a non-canonical scalar field within the framework of a spatially flat FRW space-time. In this context, we have considered four different parametrizations of the equation of state parameter of the non-canonical scalar field. Under this scenario, analytical solutions for various cosmological parameters have been found out. It has been found that the deceleration parameter shows a smooth transition from a positive value to some negative value which indicates that the universe was undergoing an early deceleration followed by late time acceleration which is essential for the structure formation of the universe. With these four parametrizations, the future evolution of the models are also discussed. It has been found that one of the models (Generalized Chaplygin gas model, GCG) mimics the concordance ΛCDM in the near future, whereas two other models (CPL and JBP) diverge due to future singularity. Finally, we have studied these theoretical models with the latest datasets from SN Ia + H(z) + BAO/CMB. (orig.)

  6. A non-canonical mismatch repair pathway in prokaryotes

    Science.gov (United States)

    Castañeda-García, A.; Prieto, A. I.; Rodríguez-Beltrán, J.; Alonso, N.; Cantillon, D.; Costas, C.; Pérez-Lago, L.; Zegeye, E. D.; Herranz, M.; Plociński, P.; Tonjum, T.; García de Viedma, D.; Paget, M.; Waddell, S. J.; Rojas, A. M.; Doherty, A. J.; Blázquez, J.

    2017-01-01

    Mismatch repair (MMR) is a near ubiquitous pathway, essential for the maintenance of genome stability. Members of the MutS and MutL protein families perform key steps in mismatch correction. Despite the major importance of this repair pathway, MutS–MutL are absent in almost all Actinobacteria and many Archaea. However, these organisms exhibit rates and spectra of spontaneous mutations similar to MMR-bearing species, suggesting the existence of an alternative to the canonical MutS–MutL-based MMR. Here we report that Mycobacterium smegmatis NucS/EndoMS, a putative endonuclease with no structural homology to known MMR factors, is required for mutation avoidance and anti-recombination, hallmarks of the canonical MMR. Furthermore, phenotypic analysis of naturally occurring polymorphic NucS in a M. smegmatis surrogate model, suggests the existence of M. tuberculosis mutator strains. The phylogenetic analysis of NucS indicates a complex evolutionary process leading to a disperse distribution pattern in prokaryotes. Together, these findings indicate that distinct pathways for MMR have evolved at least twice in nature. PMID:28128207

  7. Agonistic and antagonistic roles for TNIK and MINK in non-canonical and canonical Wnt signalling.

    Directory of Open Access Journals (Sweden)

    Alexander Mikryukov

    Full Text Available Wnt signalling is a key regulatory factor in animal development and homeostasis and plays an important role in the establishment and progression of cancer. Wnt signals are predominantly transduced via the Frizzled family of serpentine receptors to two distinct pathways, the canonical ß-catenin pathway and a non-canonical pathway controlling planar cell polarity and convergent extension. Interference between these pathways is an important determinant of cellular and phenotypic responses, but is poorly understood. Here we show that TNIK (Traf2 and Nck-interacting kinase and MINK (Misshapen/NIKs-related kinase MAP4K signalling kinases are integral components of both canonical and non-canonical pathways in Xenopus. xTNIK and xMINK interact and are proteolytically cleaved in vivo to generate Kinase domain fragments that are active in signal transduction, and Citron-NIK-Homology (CNH Domain fragments that are suppressive. The catalytic activity of the Kinase domain fragments of both xTNIK and xMINK mediate non-canonical signalling. However, while the Kinase domain fragments of xTNIK also mediate canonical signalling, the analogous fragments derived from xMINK strongly antagonize this signalling. Our data suggest that the proteolytic cleavage of xTNIK and xMINK determines their respective activities and is an important factor in controlling the balance between canonical and non-canonical Wnt signalling in vivo.

  8. Non-canonical NF-κB signaling in rheumatoid arthritis: Dr Jekyll and Mr Hyde?

    Science.gov (United States)

    Noort, Ae R; Tak, Paul P; Tas, Sander W

    2015-01-28

    The nuclear factor-κB (NF-κB) family of transcription factors is essential for the expression of pro-inflammatory cytokines, but can also induce regulatory pathways. NF-κB can be activated via two distinct pathways: the classical or canonical pathway, and the alternative or non-canonical pathway. It is well established that the canonical NF-κB pathway is essential both in acute inflammatory responses and in chronic inflammatory diseases, including rheumatoid arthritis (RA). Although less extensively studied, the non-canonical NF-κB pathway is not only central in lymphoid organ development and adaptive immune responses, but is also thought to play an important role in the pathogenesis of RA. Importantly, this pathway appears to have cell type-specific functions and, since many different cell types are involved in the pathogenesis of RA, it is difficult to predict the net overall contribution of the non-canonical NF-κB pathway to synovial inflammation. In this review, we describe the current understanding of non-canonical NF-κB signaling in various important cell types in the context of RA and consider the relevance to the pathogenesis of the disease. In addition, we discuss current drugs targeting this pathway, as well as future therapeutic prospects.

  9. Both canonical and non-canonical Wnt signaling independently promote stem cell growth in mammospheres.

    Directory of Open Access Journals (Sweden)

    Alexander M Many

    Full Text Available The characterization of mammary stem cells, and signals that regulate their behavior, is of central importance in understanding developmental changes in the mammary gland and possibly for targeting stem-like cells in breast cancer. The canonical Wnt/β-catenin pathway is a signaling mechanism associated with maintenance of self-renewing stem cells in many tissues, including mammary epithelium, and can be oncogenic when deregulated. Wnt1 and Wnt3a are examples of ligands that activate the canonical pathway. Other Wnt ligands, such as Wnt5a, typically signal via non-canonical, β-catenin-independent, pathways that in some cases can antagonize canonical signaling. Since the role of non-canonical Wnt signaling in stem cell regulation is not well characterized, we set out to investigate this using mammosphere formation assays that reflect and quantify stem cell properties. Ex vivo mammosphere cultures were established from both wild-type and Wnt1 transgenic mice and were analyzed in response to manipulation of both canonical and non-canonical Wnt signaling. An increased level of mammosphere formation was observed in cultures derived from MMTV-Wnt1 versus wild-type animals, and this was blocked by treatment with Dkk1, a selective inhibitor of canonical Wnt signaling. Consistent with this, we found that a single dose of recombinant Wnt3a was sufficient to increase mammosphere formation in wild-type cultures. Surprisingly, we found that Wnt5a also increased mammosphere formation in these assays. We confirmed that this was not caused by an increase in canonical Wnt/β-catenin signaling but was instead mediated by non-canonical Wnt signals requiring the receptor tyrosine kinase Ror2 and activity of the Jun N-terminal kinase, JNK. We conclude that both canonical and non-canonical Wnt signals have positive effects promoting stem cell activity in mammosphere assays and that they do so via independent signaling mechanisms.

  10. Macrophages Mediate a Switch between Canonical and Non-Canonical Wnt Pathways in Canine Mammary Tumors

    Science.gov (United States)

    Król, Magdalena; Mucha, Joanna; Majchrzak, Kinga; Homa, Agata; Bulkowska, Małgorzata; Majewska, Alicja; Gajewska, Małgorzata; Pietrzak, Marta; Perszko, Mikołaj; Romanowska, Karolina; Pawłowski, Karol; Manuali, Elisabetta; Hellmen, Eva; Motyl, Tomasz

    2014-01-01

    Objective According to the current hypothesis, tumor-associated macrophages (TAMs) are “corrupted” by cancer cells and subsequently facilitate, rather than inhibit, tumor metastasis. Because the molecular mechanisms of cancer cell–TAM interactions are complicated and controversial we aimed to better define this phenomenon. Methods and Results Using microRNA microarrays, Real-time qPCR and Western blot we showed that co-culture of canine mammary tumor cells with TAMs or treatment with macrophage-conditioned medium inhibited the canonical Wnt pathway and activated the non-canonical Wnt pathway in tumor cells. We also showed that co-culture of TAMs with tumor cells increased expression of canonical Wnt inhibitors in TAMs. Subsequently, we demonstrated macrophage-induced invasive growth patterns and epithelial–mesenchymal transition of tumor cells. Validation of these results in canine mammary carcinoma tissues (n = 50) and xenograft tumors indicated the activation of non-canonical and canonical Wnt pathways in metastatic tumors and non-metastatic malignancies, respectively. Activation of non-canonical Wnt pathway correlated with number of TAMs. Conclusions We demonstrated that TAMs mediate a “switch” between canonical and non-canonical Wnt signaling pathways in canine mammary tumors, leading to increased tumor invasion and metastasis. Interestingly, similar changes in neoplastic cells were observed in the presence of macrophage-conditioned medium or live macrophages. These observations indicate that rather than being “corrupted” by cancer cells, TAMs constitutively secrete canonical Wnt inhibitors that decrease tumor proliferation and development, but as a side effect, they induce the non-canonical Wnt pathway, which leads to tumor metastasis. These data challenge the conventional understanding of TAM–cancer cell interactions. PMID:24404146

  11. Non-canonical roles of tRNAs and tRNA mimics in bacterial cell biology.

    Science.gov (United States)

    Katz, Assaf; Elgamal, Sara; Rajkovic, Andrei; Ibba, Michael

    2016-08-01

    Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl-tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl-tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond translation include synthetic, regulatory and information functions within the cell. Here we provide an overview of the non-canonical roles of tRNAs and their mimics in bacteria, and discuss some of the common themes that arise when comparing these different functions.

  12. Non-Canonical EZH2 Transcriptionally Activates RelB in Triple Negative Breast Cancer

    Science.gov (United States)

    Lawrence, Cortney L.; Baldwin, Albert S.

    2016-01-01

    Enhancer of zeste homology 2 (EZH2) is the methyltransferase component of the polycomb repressive complex (PRC2) which represses gene transcription via histone H3 trimethylation at lysine 23 (H3K27me3). EZH2 activity has been linked with oncogenesis where it is thought to block expression of certain tumor suppressors. Relative to a role in cancer, EZH2 functions to promote self-renewal and has been shown to be important for the tumor-initiating cell (TIC) phenotype in breast cancer. Recently a non-canonical role for EZH2 has been identified where it promotes transcriptional activation of certain genes. Here we show that EZH2, through a methyltransferase-independent mechanism, promotes the transcriptional activation of the non-canonical NF-κB subunit RelB to drive self-renewal and the TIC phenotype of triple-negative breast cancer cells. PMID:27764181

  13. Ambiguities in second-order cosmological perturbations for non-canonical scalar fields

    CERN Document Server

    Appignani, Corrado; Shankaranarayanan, S

    2010-01-01

    Over the last few years, it was realised that non-canonical scalar fields can lead to the accelerated expansion in the early universe. The primordial spectrum in these scenarios not only shows near scale-invariance consistent with CMB observations,but also large primordial non-Gaussianity. Second-order perturbation theory is the primary theoretical tool to investigate such non-Gaussianity. However, it is still uncertain which quantities are gauge-invariant at second-order and their physical understanding therefore remains unclear. As an attempt to understand second order quantities, we consider a general non-canonical scalar field, minimally coupled to gravity, on the unperturbed FRW background where metric fluctuations are neglected a priori. In this simplified set-up, we show that there arise ambiguities in the expressions of physically relevant quantities, such as the effective speeds of the perturbations. Further, the stress tensor and energy density display a potential instability which is not present at...

  14. Non-canonical two-field inflation to order $\\xi^2$

    CERN Document Server

    Wang, Yun-Chao

    2016-01-01

    In non-canonical two-field inflation models, deviations from the canonical model can be captured by a parameter $\\xi$. We show this parameter is usually one half of the slow-roll order and analytically calculate the primordial power spectra to the precision of order $\\xi^2$. The super-horizon perturbations are studied with an improved method, which gives a correction of order $\\xi$. Three typical examples demonstrate that our analytical formulae of power spectra fit well with numerical simulation.

  15. The dark sector from interacting canonical and non-canonical scalar fields

    Energy Technology Data Exchange (ETDEWEB)

    De Souza, Rudinei C; Kremer, Gilberto M, E-mail: kremer@Fisica.ufpr.b [Departamento de Fisica, Universidade Federal do Parana, Curitiba (Brazil)

    2010-09-07

    In this work general models with interactions between two canonical scalar fields and between one non-canonical (tachyon type) and one canonical scalar field are investigated. The potentials and couplings to the gravity are selected through the Noether symmetry approach. These general models are employed to describe interactions between dark energy and dark matter, with the fields being constrained by the astronomical data. The cosmological solutions of some cases are compared with the observed evolution of the late Universe.

  16. Dark Sector from Interacting Canonical and Non-Canonical Scalar Fields

    CERN Document Server

    de Souza, Rudinei C

    2010-01-01

    In this work it is investigated general models with interactions between two canonical scalar fields and between one non-canonical (tachyon-type) and one canonical scalar field. The potentials and couplings to the gravity are selected through the Noether symmetry approach. These general models are employed to describe interactions between dark energy and dark matter, with the fields being constrained by the astronomical data. The cosmological solutions of some cases are compared with the observed evolution of the late Universe.

  17. Non-Canonical Statistics of a Spin-Boson Model: Theory and Exact Monte-Carlo Simulations

    CERN Document Server

    Lee, Chee Kong; Gong, Jiangbin

    2012-01-01

    Equilibrium canonical distribution in statistical mechanics assumes weak system-bath coupling (SBC). In real physical situations this assumption can be invalid and equilibrium quantum statistics of the system may be non-canonical. By exploiting both polaron transformation and perturbation theory in a spin-boson model, an analytical treatment is advocated to study non-canonical statistics of a two-level system at arbitrary temperature and for arbitrary SBC strength, yielding theoretical results in agreement with exact Monte-Carlo simulations. In particular, the eigen-representation of system's reduced density matrix is used to quantify non-canonical statistics as well as the quantumness of the open system. For example, it is found that irrespective of SBC strength, non-canonical statistics enhances as temperature decreases but vanishes at high temperature.

  18. A note on second-order perturbations of non-canonical scalar fields

    CERN Document Server

    Appignani, Corrado; Shankaranarayanan, S

    2009-01-01

    We study second-order perturbations for a general non-canonical scalar field, minimally coupled to gravity, on the unperturbed FRW background, where metric fluctuations are neglected a priori. By employing different approaches to cosmological perturbation theory, we show that, even in this simplified set-up, there arise ambiguities in the expressions of physically relevant quantities, such as the effective speed of the perturbations, and the stress tensor and energy density display a potential instability which is not present at linear order. We also discuss the significance of our analysis in light of the possible linearization instability of these fields about the FRW background.

  19. The Non-Adiabatic Pressure Perturbation and Non-Canonical Kinetic Terms in Multifield Inflation

    CERN Document Server

    van de Bruck, C

    2012-01-01

    The evolution of the non-adiabatic pressure perturbation during inflation driven by two scalar fields is studied numerically for three different types of models. In the first model, the fields have standard kinetic terms. The other two models considered feature non-canonical kinetic terms; the first containing two fields which are coupled via their kinetic terms, and the second where one field has the standard kinetic term with the other field being a DBI field. We find that the evolution and the final amplitude of the non-adiabatic pressure perturbation depends strongly on the kinetic terms.

  20. Dynamical Characteristics of a Non-canonical Scalar-Torsion Model of Dark Energy

    Science.gov (United States)

    Banijamali, A.; Ghasemi, E.

    2016-08-01

    In this paper, we analyze the phase-space of a model of dark energy in which a non-canonical scalar field (tachyon) non-minimally coupled to torsion scalar in the framework of teleparallelism. Scalar field potential and non-minimal coupling function are chosen as V( ϕ) = V 0 ϕ n and f( ϕ) = ϕ N , respectively. We obtain a critical point that behaves like a stable or saddle point depending on the values of N and n. Additionally we find an unstable critical line. We have shown such a behavior of critical points using numerical computations and phase-space trajectories explicitly.

  1. Non-canonical Glucocorticoid Receptor Transactivation of gilz by Alcohol Suppresses Cell Inflammatory Response

    Science.gov (United States)

    Ng, Hang Pong; Jennings, Scott; Wang, Jack; Molina, Patricia E.; Nelson, Steve; Wang, Guoshun

    2017-01-01

    Acute alcohol exposure suppresses cell inflammatory response. The underlying mechanism has not been fully defined. Here we report that alcohol was able to activate glucocorticoid receptor (GR) signaling in the absence of glucocorticoids (GCs) and upregulated glucocorticoid-induced leucine zipper (gilz), a prominent GC-responsive gene. Such a non-canonical activation of GR was not blocked by mifepristone, a potent GC competitor. The proximal promoter of gilz, encompassing five GC-responsive elements (GREs), was incorporated and tested in a luciferase reporter system. Deletion and/or mutation of the GREs abrogated the promoter responsiveness to alcohol. Thus, the GR–GRE interaction transduced the alcohol action on gilz. Alcohol induced GR nuclear translocation, which was enhanced by the alcohol dehydrogenase inhibitor fomepizole, suggesting that it was alcohol, not its metabolites, that engendered the effect. Gel mobility shift assay showed that unliganded GR was able to bind GREs and such interaction withstood clinically relevant levels of alcohol. GR knockout via CRISPR/Cas9 gene targeting or GILZ depletion via small RNA interference diminished alcohol suppression of cell inflammatory response to LPS. Thus, a previously unrecognized, non-canonical GR activation of gilz is involved in alcohol modulation of cell immune response. PMID:28638383

  2. Non-canonical Glucocorticoid Receptor Transactivation of gilz by Alcohol Suppresses Cell Inflammatory Response

    Directory of Open Access Journals (Sweden)

    Hang Pong Ng

    2017-06-01

    Full Text Available Acute alcohol exposure suppresses cell inflammatory response. The underlying mechanism has not been fully defined. Here we report that alcohol was able to activate glucocorticoid receptor (GR signaling in the absence of glucocorticoids (GCs and upregulated glucocorticoid-induced leucine zipper (gilz, a prominent GC-responsive gene. Such a non-canonical activation of GR was not blocked by mifepristone, a potent GC competitor. The proximal promoter of gilz, encompassing five GC-responsive elements (GREs, was incorporated and tested in a luciferase reporter system. Deletion and/or mutation of the GREs abrogated the promoter responsiveness to alcohol. Thus, the GR–GRE interaction transduced the alcohol action on gilz. Alcohol induced GR nuclear translocation, which was enhanced by the alcohol dehydrogenase inhibitor fomepizole, suggesting that it was alcohol, not its metabolites, that engendered the effect. Gel mobility shift assay showed that unliganded GR was able to bind GREs and such interaction withstood clinically relevant levels of alcohol. GR knockout via CRISPR/Cas9 gene targeting or GILZ depletion via small RNA interference diminished alcohol suppression of cell inflammatory response to LPS. Thus, a previously unrecognized, non-canonical GR activation of gilz is involved in alcohol modulation of cell immune response.

  3. Lifting locally homogeneous geometric structures

    CERN Document Server

    McKay, Benjamin

    2011-01-01

    We prove that under some purely algebraic conditions every locally homogeneous structure modelled on some homogeneous space is induced by a locally homogeneous structure modelled on a different homogeneous space.

  4. A Putative Non-Canonical Ras-Like GTPase from P. falciparum: Chemical Properties and Characterization of the Protein.

    Directory of Open Access Journals (Sweden)

    Annette Kaiser

    Full Text Available During its development the malaria parasite P. falciparum has to adapt to various different environmental contexts. Key cellular mechanisms involving G-protein coupled signal transduction chains are assumed to act at these interfaces. Heterotrimeric G-proteins are absent in Plasmodium. We here describe the first cloning and expression of a putative, non-canonical Ras-like G protein (acronym PfG from Plasmodium. PfG reveals an open reading frame of 2736 bp encoding a protein of 912 amino acids with a theoretical pI of 8.68 and a molecular weight of 108.57 kDa. Transcript levels and expression are significantly increased in the erythrocytic phase in particular during schizont and gametocyte formation. Most notably, PfG has GTP binding capacity and GTPase activity due to an EngA2 domain present in small Ras-like GTPases in a variety of Bacillus species and Mycobacteria. By contrast, plasmodial PfG is divergent from any human alpha-subunit. PfG was expressed in E. coli as a histidine-tagged fusion protein and was stable only for 3.5 hours. Purification was only possible under native conditions by Nickel-chelate chromatography and subsequent separation by Blue Native PAGE. Binding of a fluorescent GTP analogue BODIPY® FL guanosine 5'O-(thiotriphosphate was determined by fluorescence emission. Mastoparan stimulated GTP binding in the presence of Mg2+. GTPase activity was determined colorimetrically. Activity expressed as absolute fluorescence was 50% higher for the human paralogue than the activity of the parasitic enzyme. The PfG protein is expressed in the erythrocytic stages and binds GTP after immunoprecipitation. Immunofluorescence using specific antiserum suggests that PfG localizes to the parasite cytosol. The current data suggest that the putitative, Ras-like G-protein might be involved in a non-canonical signaling pathway in Plasmodium. Research on the function of PfG with respect to pathogenesis and antimalarial chemotherapy is currently

  5. Non-Canonical Wnt Predominates in Activated Rat Hepatic Stellate Cells, Influencing HSC Survival and Paracrine Stimulation of Kupffer Cells.

    Directory of Open Access Journals (Sweden)

    Laura Corbett

    Full Text Available The Wnt system is highly complex and is comprised of canonical and non-canonical pathways leading to the activation of gene expression. Our aim was to examine changes in the expression of Wnt ligands and regulators during hepatic stellate cell (HSC transdifferentiation and assess the relative contributions of the canonical and non-canonical Wnt pathways in fibrogenic activated HSC. The expression profile of Wnt ligands and regulators in HSC was not supportive for a major role for β-catenin-dependent canonical Wnt signalling, this verified by inability to induce Topflash reporter activity in HSC even when expressing a constitutive active β-catenin. We detected expression of Wnt5a in activated HSC which can signal via non-canonical mechanisms and showed evidence for non-canonical signalling in these cells involving phosphorylation of Dvl2 and pJNK. Stimulation of HSC or Kupffer cells with Wnt5a regulated HSC apoptosis and expression of TGF-β1 and MCP1 respectively. We were unable to confirm a role for β-catenin-dependent canonical Wnt in HSC and instead propose autocrine and paracrine functions for Wnts expressed by activated HSC via non-canonical pathways. The data warrant detailed investigation of Wnt5a in liver fibrosis.

  6. Expanding the genetic code of Salmonella with non-canonical amino acids

    Science.gov (United States)

    Gan, Qinglei; Lehman, Brent P.; Bobik, Thomas A.; Fan, Chenguang

    2016-01-01

    The diversity of non-canonical amino acids (ncAAs) endows proteins with new features for a variety of biological studies and biotechnological applications. The genetic code expansion strategy, which co-translationally incorporates ncAAs into specific sites of target proteins, has been applied in many organisms. However, there have been only few studies on pathogens using genetic code expansion. Here, we introduce this technique into the human pathogen Salmonella by incorporating p-azido-phenylalanine, benzoyl-phenylalanine, acetyl-lysine, and phosphoserine into selected Salmonella proteins including a microcompartment shell protein (PduA), a type III secretion effector protein (SteA), and a metabolic enzyme (malate dehydrogenase), and demonstrate practical applications of genetic code expansion in protein labeling, photocrosslinking, and post-translational modification studies in Salmonella. This work will provide powerful tools for a wide range of studies on Salmonella. PMID:28008993

  7. KLF4 transcriptionally activates non-canonical WNT5A to control epithelial stratification.

    Science.gov (United States)

    Tetreault, Marie-Pier; Weinblatt, Daniel; Shaverdashvili, Khvaramze; Yang, Yizeng; Katz, Jonathan P

    2016-05-17

    Epithelial differentiation and stratification are essential for normal homeostasis, and disruption of these processes leads to both injury and cancer. The zinc-finger transciption factor KLF4 is a key driver of epithelial differentiation, yet the mechanisms and targets by which KLF4 controls differentiation are not well understood. Here, we define WNT5A, a non-canonical Wnt ligand implicated in epithelial differentiation, repair, and cancer, as a direct transcriptional target that is activated by KLF4 in squamous epithelial cells. Further, we demonstrate functionally that WNT5A mediates KLF4 control of epithelial differentiation and stratification, as treatment of keratinocytes with WNT5A rescues defective epithelial stratification resulting from KLF4 loss. Finally, we show that the small GTPase CDC42 is regulated by KLF4 in a WNT5A dependent manner. As such, we delineate a novel pathway for epithelial differentiation and stratification and define potential therapeutic targets for epithelial diseases.

  8. Non-Canonical Phase-Space Noncommutativity and the Kantowski-Sachs singularity for Black Holes

    CERN Document Server

    Bastos, Catarina; Dias, Nuno Costa; Prata, João Nuno

    2010-01-01

    We consider a cosmological model based upon a non-canonical noncommutative extension of the Heisenberg-Weyl algebra to address the thermodynamical stability and the singularity problem of both the Schwarzschild and the Kantowski-Sachs black holes. The interior of the black hole is modelled by a noncommutative extension of the Wheeler-DeWitt equation. We compute the temperature and entropy of a Kantowski-Sachs black hole and compare our results with the Hawking values. Again, the noncommutativity in the momenta sector allows us to have a minimum in the potential, which is relevant in order to apply the Feynman-Hibbs procedure. For Kantowski-Sachs black holes, the same model is shown to generate a non-unitary dynamics, predicting vanishing total probability in the neighborhood of the singularity. This result effectively regularizes the Kantowski-Sachs singularity and generalizes a similar result, previously obtained for the case of Schwarzschild black hole.

  9. XEDAR activates the non-canonical NF-κB pathway

    Energy Technology Data Exchange (ETDEWEB)

    Verhelst, Kelly, E-mail: Kelly.Verhelst@irc.VIB-UGent.be [Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent (Belgium); Department of Biomedical Molecular Biology, Ghent University, Ghent (Belgium); Gardam, Sandra, E-mail: s.gardam@garvan.org.au [Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent (Belgium); Department of Biomedical Molecular Biology, Ghent University, Ghent (Belgium); Borghi, Alice, E-mail: Alice.Borghi@irc.VIB-UGent.be [Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent (Belgium); Department of Biomedical Molecular Biology, Ghent University, Ghent (Belgium); Kreike, Marja, E-mail: Marja.Kreike@irc.VIB-UGent.be [Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent (Belgium); Department of Biomedical Molecular Biology, Ghent University, Ghent (Belgium); Carpentier, Isabelle, E-mail: Isabelle.Carpentier@irc.VIB-UGent.be [Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent (Belgium); Department of Biomedical Molecular Biology, Ghent University, Ghent (Belgium); Beyaert, Rudi, E-mail: Rudi.Beyaert@irc.VIB-UGent.be [Inflammation Research Center, Unit of Molecular Signal Transduction in Inflammation, VIB, Ghent (Belgium); Department of Biomedical Molecular Biology, Ghent University, Ghent (Belgium)

    2015-09-18

    Members of the tumor necrosis factor receptor (TNFR) superfamily are involved in a number of physiological and pathological responses by activating a wide variety of intracellular signaling pathways. The X-linked ectodermal dysplasia receptor (XEDAR; also known as EDA2R or TNFRSF27) is a member of the TNFR superfamily that is highly expressed in ectodermal derivatives during embryonic development and binds to ectodysplasin-A2 (EDA-A2), a member of the TNF family that is encoded by the anhidrotic ectodermal dysplasia (EDA) gene. Although XEDAR was first described in the year 2000, its function and molecular mechanism of action is still largely unclear. XEDAR has been reported to activate canonical nuclear factor κB (NF-κB) signaling and mitogen-activated protein (MAP) kinases. Here we report that XEDAR is also able to trigger the non-canonical NF-κB pathway, characterized by the processing of p100 (NF-κB2) into p52, followed by nuclear translocation of p52 and RelB. We provide evidence that XEDAR-induced p100 processing relies on the binding of XEDAR to TRAF3 and TRAF6, and requires the kinase activity of NIK and IKKα. We also show that XEDAR stimulation results in NIK accumulation and that p100 processing is negatively regulated by TRAF3, cIAP1 and A20. - Highlights: • XEDAR activates the non-canonical NF-κB pathway. • XEDAR-induced processing of p100 depends on XEDAR interaction with TRAF3 and TRAF6. • XEDAR-induced processing of p100 depends on NIK and IKKα activity. • Overexpression of XEDAR leads to NIK accumulation. • XEDAR-induced processing of p100 is negatively regulated by TRAF3 cIAP1 and A20.

  10. Study of parametrized dark energy models with a general non-canonical scalar field

    Energy Technology Data Exchange (ETDEWEB)

    Al Mamon, Abdulla; Das, Sudipta [Visva-Bharati, Department of Physics, Santiniketan (India)

    2016-03-15

    In this paper, we consider various dark energy models in the framework of a non-canonical scalar field with a Lagrangian density of the form L(φ, X) = f(φ)X ((X)/(M{sup 4}{sub Pl})){sup α-1} - V(φ), which provides the standard canonical scalar field model for α = 1 and f(φ) = 1. In this particular non-canonical scalar field model, we carry out the analysis for α = 2. We then obtain cosmological solutions for constant as well as variable equation of state parameter (ω{sub φ}(z)) for dark energy. We also perform the data analysis for three different functional forms of ω{sub φ}(z) by using the combination of SN Ia, BAO, and CMB datasets.We have found that for all the choices of ω{sub φ}(z), the SN Ia + CMB/BAO dataset favors the past decelerated and recent accelerated expansion phase of the universe. Furthermore, using the combined dataset, we have observed that the reconstructed results of ω{sub φ}(z) and q(z) are almost choice independent and the resulting cosmological scenarios are in good agreement with the ΛCDM model (within the 1σ confidence contour). We have also derived the form of the potentials for each model and the resulting potentials are found to be a quartic potential for constant ω{sub φ} and a polynomial in φ for variable ω{sub φ}. (orig.)

  11. IFN signaling: how a non-canonical model led to the development of IFN mimetics

    Directory of Open Access Journals (Sweden)

    Howard M Johnson

    2013-07-01

    Full Text Available The classical model of cytokine signaling dominates our view of specific gene activation by cytokines such as the interferons (IFNs. The importance of the model extends beyond cytokines and applies to hormones such as growth hormone (GH and insulin, and growth factors such as epidermal growth factor (EGF and fibroblast growth factor (FGF. According to this model, ligand activates the cell via interaction with the extracellular domain of the receptor. This results in activation of receptor or receptor-associated tyrosine kinases, primarily of the Janus kinase (JAK family, phosphorylation and dimerization of the STAT transcription factors, which dissociate from the receptor cytoplasmic domain and translocate to the nucleus. This view ascribes no further role to the ligand, JAK kinase, or receptor in either specific gene activation or the associated epigenetic events. The presence of dimeric STATs in the nucleus essentially explains it all. Our studies have resulted in the development of a non-canonical, more complex model of IFNγ signaling that is akin to that of steroid hormone/steroid receptor signaling. We have shown that ligand, receptor, activated JAKs and STATs are associated with specific gene activation, where the receptor subunit IFNGR1 functions as a co-transcription factor and the JAKs are involved in associated epigenetic events. We found that the type I IFN system functions similarly. The fact that GH receptor, insulin receptor, EGF receptor, and FGF receptor undergo nuclear translocation upon ligand binding suggests that they may also function similarly. The steroid hormone/steroid receptor nature of type I and II IFN signaling provides insight into the specificity of signaling by members of cytokine families. The non-canonical model could also provide better understanding to more complex cytokine families such as those of IL-2 and IL-12, whose members often use the same JAKs and STATs, but also have different functions and

  12. The Non-canonical Tetratricopeptide Repeat (TPR) Domain of Fluorescent (FLU) Mediates Complex Formation with Glutamyl-tRNA Reductase.

    Science.gov (United States)

    Zhang, Min; Zhang, Feilong; Fang, Ying; Chen, Xuemin; Chen, Yuhong; Zhang, Wenxia; Dai, Huai-En; Lin, Rongcheng; Liu, Lin

    2015-07-10

    The tetratricopeptide repeat (TPR)-containing protein FLU is a negative regulator of chlorophyll biosynthesis in plants. It directly interacts through its TPR domain with glutamyl-tRNA reductase (GluTR), the rate-limiting enzyme in the formation of δ-aminolevulinic acid (ALA). Delineation of how FLU binds to GluTR is important for understanding the molecular basis for FLU-mediated repression of synthesis of ALA, the universal tetrapyrrole precursor. Here, we characterize the FLU-GluTR interaction by solving the crystal structures of the uncomplexed TPR domain of FLU (FLU(TPR)) at 1.45-Å resolution and the complex of the dimeric domain of GluTR bound to FLU(TPR) at 2.4-Å resolution. Three non-canonical TPR motifs of each FLU(TPR) form a concave surface and clamp the helix bundle in the C-terminal dimeric domain of GluTR. We demonstrate that a 2:2 FLU(TPR)-GluTR complex is the functional unit for FLU-mediated GluTR regulation and suggest that the formation of the FLU-GluTR complex prevents glutamyl-tRNA, the GluTR substrate, from binding with this enzyme. These results also provide insights into the spatial regulation of ALA synthesis by the membrane-located FLU protein.

  13. DRB2, DRB3 and DRB5 function in a non-canonical microRNA pathway in Arabidopsis thaliana.

    Science.gov (United States)

    Eamens, Andrew L; Wook Kim, Ki; Waterhouse, Peter M

    2012-10-01

    DOUBLE-STRANDED RNA BINDING (DRB) proteins have been functionally characterized in viruses, prokaryotes and eukaryotes and are involved in all aspects of RNA biology. Arabidopsis thaliana (Arabidopsis) encodes five closely related DRB proteins, DRB1 to DRB5. DRB1 and DRB4 are required by DICER-LIKE (DCL) proteins DCL1 and DCL4 to accurately and efficiently process structurally distinct double-stranded RNA (dsRNA) precursor substrates in the microRNA (miRNA) and trans-acting small-interfering RNA (tasiRNA) biogenesis pathways respectively. We recently reported that DRB2 is also involved in the biogenesis of specific miRNA subsets. ( 1) Furthermore, the severity of the developmental phenotype displayed by the drb235 triple mutant plant, compared with those expressed by either drb2, drb3 and drb5 single mutants, or double mutant combinations thereof, indicates that DRB3 and DRB5 function in the same non-canonical miRNA pathway as DRB2. Through the use of our artificial miRNA (amiRNA) plant expression vector, pBlueGreen ( 2) (,) ( 3) we demonstrate here that unlike DRB2, DRB3 and DRB5 are not involved in the dsRNA processing stages of the miRNA biogenesis pathway, but are required to mediate RNA silencing of target genes of DRB2-associated miRNAs.

  14. A non-canonical function of eukaryotic elongation factor 1A1: regulation of interleukin-6 expression.

    Science.gov (United States)

    Schulz, Ingo; Engel, Claudia; Niestroj, André J; Kehlen, Astrid; Rahfeld, Jens-Ulrich; Kleinschmidt, Martin; Lehmann, Karola; Roßner, Steffen; Demuth, Hans-Ulrich

    2014-05-01

    Interleukin-6 is one of the most prominent triggers of inflammatory processes. We have shown recently that heteroarylketones (HAKs) interfere with stimulated interleukin-6 expression in astrocytes by suppression of STAT3 phosphorylation at serine 727. Surprisingly, this effect is not based on the inhibition of STAT3-relevant kinases. Therefore, we here used the structurally modified HAK compound biotin-HAK-3 in a reverse chemical approach to identify the relevant molecular target in UV-mediated cross-linking experiments. Employing streptavidin-specific 2D-immunoblotting followed by mass spectrometry we identified nine proteins putatively interacting with biotin-HAK-3. After co-immunoprecipitation, co-immunofluorescence, surface plasmon resonance analyses and RNAi-mediated knock-down, the eukaryotic elongation factor 1A1 (eEF1A1) was verified as the relevant target of HAK bioactivity. eEF1A1 forms complexes with STAT3 and PKCδ, which are crucial for STAT3(S727) phosphorylation and for NF-κB/STAT3-enhanced interleukin-6 expression. Furthermore, the intracellular HAK accumulation is strongly dependent on eEF1A1 expression. Taken together, the results reveal a novel molecular mechanism for a non-canonical role of eEF1A1 in signal transduction via direct modulation of kinase-dependent phosphorylation events.

  15. Molecular cloning and characterization of a novel isoform of the non-canonical poly(A) polymerase PAPD7

    Energy Technology Data Exchange (ETDEWEB)

    Ogami, Koichi; Cho, Rihe [Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603 (Japan); Hoshino, Shin-ichi, E-mail: hoshino@phar.nagoya-cu.ac.jp [Department of Biological Chemistry, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya 467-8603 (Japan)

    2013-03-01

    Highlights: ► So far, only an enzymatically inactive isoform of PAPD7 was reported. ► The novel isoform: PAPD7 l shows robust nucleotidyl transferase activity. ► The newly identified amino terminal region is required for the activity. ► PAPD7 l localizes to the nucleoplasm. ► The N terminal region identified is also required for the nuclear localization. - Abstract: Non-canonical poly(A) polymerases (ncPAPs) catalyze the addition of poly(A) tail to the 3′ end of RNA to play pivotal roles in the regulation of gene expression and also in quality control. Here we identified a novel isoform of the 7th member of ncPAPs: PAPD7 (PAPD7 l), which contains 230 extra amino acids at the amino terminus of the previously identified PAPD7 (PAPD7 s). In sharp contrast to the inactive PAPD7 s, PAPD7 l showed robust nucleotidyl transferase activity when tethered to an RNA. A region required for the activity was localized to 187–219 aa, and this region was also required for the nuclear retention of PAPD7 l. Western blot analysis revealed that 94 kDa band (corresponding to PAPD7 l) but not 62 kDa band (corresponding to PAPD7 s) detected by PAPD7 antibody was specifically depleted by treatment with PAPD7 siRNA in both HeLa and U2OS cells. These results suggest that PAPD7 l is the major and active isoform of PAPD7 expressed in cells.

  16. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity

    Directory of Open Access Journals (Sweden)

    Joshua R. Kane

    2015-05-01

    Full Text Available HIV-1 encodes the accessory protein Vif, which hijacks a host Cullin-RING ubiquitin ligase (CRL complex as well as the non-canonical cofactor CBFβ, to antagonize APOBEC3 antiviral proteins. Non-canonical cofactor recruitment to CRL complexes by viral factors, to date, has only been attributed to HIV-1 Vif. To further study this phenomenon, we employed a comparative approach combining proteomic, biochemical, structural, and virological techniques to investigate Vif complexes across the lentivirus genus, including primate (HIV-1 and simian immunodeficiency virus macaque [SIVmac] and non-primate (FIV, BIV, and MVV viruses. We find that CBFβ is completely dispensable for the activity of non-primate lentiviral Vif proteins. Furthermore, we find that BIV Vif requires no cofactor and that MVV Vif requires a novel cofactor, cyclophilin A (CYPA, for stable CRL complex formation and anti-APOBEC3 activity. We propose modular conservation of Vif complexes allows for potential exaptation of functions through the acquisition of non-CRL-associated host cofactors while preserving anti-APOBEC3 activity.

  17. Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.

    Science.gov (United States)

    Kane, Joshua R; Stanley, David J; Hultquist, Judd F; Johnson, Jeffrey R; Mietrach, Nicole; Binning, Jennifer M; Jónsson, Stefán R; Barelier, Sarah; Newton, Billy W; Johnson, Tasha L; Franks-Skiba, Kathleen E; Li, Ming; Brown, William L; Gunnarsson, Hörður I; Adalbjornsdóttir, Adalbjorg; Fraser, James S; Harris, Reuben S; Andrésdóttir, Valgerður; Gross, John D; Krogan, Nevan J

    2015-05-26

    HIV-1 encodes the accessory protein Vif, which hijacks a host Cullin-RING ubiquitin ligase (CRL) complex as well as the non-canonical cofactor CBFβ, to antagonize APOBEC3 antiviral proteins. Non-canonical cofactor recruitment to CRL complexes by viral factors, to date, has only been attributed to HIV-1 Vif. To further study this phenomenon, we employed a comparative approach combining proteomic, biochemical, structural, and virological techniques to investigate Vif complexes across the lentivirus genus, including primate (HIV-1 and simian immunodeficiency virus macaque [SIVmac]) and non-primate (FIV, BIV, and MVV) viruses. We find that CBFβ is completely dispensable for the activity of non-primate lentiviral Vif proteins. Furthermore, we find that BIV Vif requires no cofactor and that MVV Vif requires a novel cofactor, cyclophilin A (CYPA), for stable CRL complex formation and anti-APOBEC3 activity. We propose modular conservation of Vif complexes allows for potential exaptation of functions through the acquisition of non-CRL-associated host cofactors while preserving anti-APOBEC3 activity.

  18. Markedness and Salience in Language Contact and Second-Language Acquisition: Evidence from a Non-Canonical Contact Language.

    Science.gov (United States)

    Deumert, Ana

    2003-01-01

    Argues that the study of contact varieties of a language are relevant to understanding of second language acquisition and use, because non-canonical contact languages are often situated on a continuum between pidginization and the more general processes of untutored second language acquisition. Data on participle regularization in Namibian Black…

  19. A Non-Canonical NRPS Is Involved in the Synthesis of Fungisporin and Related Hydrophobic Cyclic Tetrapeptides in Penicillium chrysogenum

    NARCIS (Netherlands)

    Ali, Hazrat; Ries, Marco I.; Lankhorst, Peter P.; van der Hoeven, Rob A. M.; Schouten, Olaf L.; Noga, Marek; Hankemeier, Thomas; van Peij, Noel N. M. E.; Bovenberg, Roel A. L.; Vreeken, Rob J.; Driessen, Arnold J. M.

    2014-01-01

    The filamentous fungus Penicillium chrysogenum harbors an astonishing variety of nonribosomal peptide synthetase genes, which encode proteins known to produce complex bioactive metabolites from simple building blocks. Here we report a novel non-canonical tetra-modular nonribosomal peptide synthetase

  20. Prospects of In vivo Incorporation of non-canonical amino acids for the chemical diversification of antimicrobial peptides

    NARCIS (Netherlands)

    Baumann, Tobias; Nickling, Jessica H; Bartholomae, Maike; Buivydas, Andrius; Kuipers, Oscar P; Budisa, Nediljko

    2017-01-01

    The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-natu

  1. Emerging Non-Canonical Functions and Regulation by p53: p53 and Stemness.

    Science.gov (United States)

    Olivos, David J; Mayo, Lindsey D

    2016-11-26

    Since its discovery nearly 40 years ago, p53 has ascended to the forefront of investigated genes and proteins across diverse research disciplines and is recognized most exclusively for its role in cancer as a tumor suppressor. Levine and Oren (2009) reviewed the evolution of p53 detailing the significant discoveries of each decade since its first report in 1979. In this review, we will highlight the emerging non-canonical functions and regulation of p53 in stem cells. We will focus on general themes shared among p53's functions in non-malignant stem cells and cancer stem-like cells (CSCs) and the influence of p53 on the microenvironment and CSC niche. We will also examine p53 gain of function (GOF) roles in stemness. Mutant p53 (mutp53) GOFs that lead to survival, drug resistance and colonization are reviewed in the context of the acquisition of advantageous transformation processes, such as differentiation and dedifferentiation, epithelial-to-mesenchymal transition (EMT) and stem cell senescence and quiescence. Finally, we will conclude with therapeutic strategies that restore wild-type p53 (wtp53) function in cancer and CSCs, including RING finger E3 ligases and CSC maintenance. The mechanisms by which wtp53 and mutp53 influence stemness in non-malignant stem cells and CSCs or tumor-initiating cells (TICs) are poorly understood thus far. Further elucidation of p53's effects on stemness could lead to novel therapeutic strategies in cancer research.

  2. Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline.

    Science.gov (United States)

    Sangrithi, Mahesh N; Royo, Helene; Mahadevaiah, Shantha K; Ojarikre, Obah; Bhaw, Leena; Sesay, Abdul; Peters, Antoine H F M; Stadler, Michael; Turner, James M A

    2017-02-06

    Somatic X dosage compensation requires two mechanisms: X inactivation balances X gene output between males (XY) and females (XX), while X upregulation, hypothesized by Ohno and documented in vivo, balances X gene with autosomal gene output. Whether X dosage compensation occurs in germ cells is unclear. We show that mouse and human germ cells exhibit non-canonical X dosage states that differ from the soma and between the sexes. Prior to genome-wide reprogramming, X upregulation is present, consistent with Ohno's hypothesis. Subsequently, however, it is erased. In females, erasure follows loss of X inactivation, causing X dosage excess. Conversely, in males, erasure leads to permanent X dosage decompensation. Sex chromosomally abnormal models exhibit a "sex-reversed" X dosage state: XX males, like XX females, develop X dosage excess, while XO females, like XY males, develop X dosage decompensation. Thus, germline X dosage compensation states are determined by X chromosome number, not phenotypic sex. These unexpected differences in X dosage compensation states between germline and soma offer unique perspectives on sex chromosome infertility.

  3. Non-canonical Wnt4 prevents skeletal aging and inflammation by inhibiting NF-κB

    Science.gov (United States)

    Yu, Bo; Chang, Jia; Liu, Yunsong; Li, Jiong; Kevork, Kareena; Al-Hezaimi, Khalid; Graves, Dana T; Park, No-Hee; Wang, Cun-Yu

    2014-01-01

    Aging-related bone loss and osteoporosis affect millions of patients worldwide. Chronic inflammation associated with aging and arthritis promotes bone resorption and impairs bone formation. Here we show that Wnt4 attenuated bone loss in osteoporosis and skeletal aging by inhibiting nuclear factor-kappa B (NF-κB) via non-canonical Wnt signaling. Transgenic mice expressing Wnt4 from osteoblasts were significantly protected from bone loss and chronic inflammation induced by ovariectomy, tumor necrosis factor or natural aging. In addition to promoting bone formation, Wnt4 could inhibit osteoclast formation and bone resorption. Mechanistically, Wnt4 inhibited transforming growth factor beta-activated kinase 1-mediated NF-κB activation in macrophages and osteoclast precursors independent of β-catenin. Moreover, recombinant Wnt4 proteins were able to alleviate osteoporotic bone loss and inflammation by inhibiting NF-κB in vivo. Taken together, our results suggest that Wnt4 might be used as a therapeutic agent for treating osteoporosis by attenuating NF-κB. PMID:25108526

  4. Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome.

    Directory of Open Access Journals (Sweden)

    Naomi L Bogenschutz

    Full Text Available Eukaryotic DNA replication initiates from multiple sites on each chromosome called replication origins (origins. In the budding yeast Saccharomyces cerevisiae, origins are defined at discrete sites. Regular spacing and diverse firing characteristics of origins are thought to be required for efficient completion of replication, especially in the presence of replication stress. However, a S. cerevisiae chromosome III harboring multiple origin deletions has been reported to replicate relatively normally, and yet how an origin-deficient chromosome could accomplish successful replication remains unknown. To address this issue, we deleted seven well-characterized origins from chromosome VI, and found that these deletions do not cause gross growth defects even in the presence of replication inhibitors. We demonstrated that the origin deletions do cause a strong decrease in the binding of the origin recognition complex. Unexpectedly, replication profiling of this chromosome showed that DNA replication initiates from non-canonical loci around deleted origins in yeast. These results suggest that replication initiation can be unexpectedly flexible in this organism.

  5. Swinger RNA self-hybridization and mitochondrial non-canonical swinger transcription, transcription systematically exchanging nucleotides.

    Science.gov (United States)

    Seligmann, Hervé

    2016-06-21

    Stem-loop hairpins punctuate mitochondrial post-transcriptional processing. Regulation of mitochondrial swinger transcription, transcription producing RNAs matching the mitogenome only assuming systematic exchanges between nucleotides (23 bijective transformations along 9 symmetric exchanges XY, e.g. AG, and 14 asymmetric exchanges X>Y>Z>X, e.g. A>G>C>A) remains unknown. Does swinger RNA self-hybridization regulate swinger, as regular, transcription? Groups of 8 swinger transformations share canonical self-hybridization properties within each group, group 0 includes identity (regular) transcription. The human mitogenome has more stem-loop hairpins than randomized sequences for all groups. Group 2 transformations reveal complementarity of the light strand replication origin (OL) loop and a neighboring tRNA gene, detecting the longtime presumed OL/tRNA homology. Non-canonical G=U pairings in hairpins increases with swinger RNA detection. These results confirm biological relevancy of swinger-transformed DNA/RNA, independently of, and in combination with, previously detected swinger DNA/RNA and swinger peptides. Swinger-transformed mitogenomes include unsuspected multilayered information.

  6. Cbx8 Acts Non-canonically with Wdr5 to Promote Mammary Tumorigenesis.

    Science.gov (United States)

    Chung, Chi-Yeh; Sun, Zhen; Mullokandov, Gavriel; Bosch, Almudena; Qadeer, Zulekha A; Cihan, Esma; Rapp, Zachary; Parsons, Ramon; Aguirre-Ghiso, Julio A; Farias, Eduardo F; Brown, Brian D; Gaspar-Maia, Alexandre; Bernstein, Emily

    2016-07-12

    Chromatin-mediated processes influence the development and progression of breast cancer. Using murine mammary carcinoma-derived tumorspheres as a functional readout for an aggressive breast cancer phenotype, we performed a loss-of-function screen targeting 60 epigenetic regulators. We identified the Polycomb protein Cbx8 as a key regulator of mammary carcinoma both in vitro and in vivo. Accordingly, Cbx8 is overexpressed in human breast cancer and correlates with poor survival. Our genomic analyses revealed that Cbx8 positively regulates Notch signaling by maintaining H3K4me3 levels on Notch-network gene promoters. Ectopic expression of Notch1 partially rescues tumorsphere formation in Cbx8-depleted cells. We find that Cbx8 associates with non-PRC1 complexes containing the H3K4 methyltransferase complex component WDR5, which together regulate Notch gene expression. Thus, our study implicates a key non-canonical role for Cbx8 in promoting breast tumorigenesis.

  7. Cbx8 Acts Non-canonically with Wdr5 to Promote Mammary Tumorigenesis

    Directory of Open Access Journals (Sweden)

    Chi-Yeh Chung

    2016-07-01

    Full Text Available Chromatin-mediated processes influence the development and progression of breast cancer. Using murine mammary carcinoma-derived tumorspheres as a functional readout for an aggressive breast cancer phenotype, we performed a loss-of-function screen targeting 60 epigenetic regulators. We identified the Polycomb protein Cbx8 as a key regulator of mammary carcinoma both in vitro and in vivo. Accordingly, Cbx8 is overexpressed in human breast cancer and correlates with poor survival. Our genomic analyses revealed that Cbx8 positively regulates Notch signaling by maintaining H3K4me3 levels on Notch-network gene promoters. Ectopic expression of Notch1 partially rescues tumorsphere formation in Cbx8-depleted cells. We find that Cbx8 associates with non-PRC1 complexes containing the H3K4 methyltransferase complex component WDR5, which together regulate Notch gene expression. Thus, our study implicates a key non-canonical role for Cbx8 in promoting breast tumorigenesis.

  8. A Non-canonical Transferred DNA Insertion at the BRI 1 Locus in Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Zhong Zhao; Yan Zhu; Mathieu Erhardt; Ying Ruan; Wen-Hui Shen

    2009-01-01

    Agrobacterium-mediated transformation is widely used in transgenic plant englnserlng and has been proven to be a powerful tool for insertional mutagenesis of the plant genome.The transferred DNA (T-DNA) from Agrobacterlum is Integrated into the plant genome through illegitimate recombination between the T-DNA and the plant DNA.Contrasting to the canonical insertion,here we report on a locus showing a complex mutation associated with T-DNA insertion at the BRI 1 gene in Arabidopsis thaliana.We obtained a mutant line,named salade for its phenotype of dwarf stature and proliferating rosette,Molecular charactedzation of this mutant revealed that in addition to T-DNA a non.T.DNA-Iocalized transposon from bacteda was inserted in the Arabidopsis genome and that a region of more than 11.5 kb of the Arebidopsis genome was deleted at the insertion site.The deleted region contains the brassinosteroid receptor gene BRI 1 and the transcdption factor gene WRKY13.Our finding reveals non-canonical T-DNA insertion,implicating horizontal gene transfer and cautioning the use of T-DNA as mutagen in transgenic research.

  9. Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells.

    Science.gov (United States)

    Zhang, Yilan; Ge, Xianglian; Yang, Fayu; Zhang, Liping; Zheng, Jiayong; Tan, Xuefang; Jin, Zi-Bing; Qu, Jia; Gu, Feng

    2014-06-23

    CRISPR/Cas9-mediated DNA cleavage (CCMDC) is becoming increasingly used for efficient genome engineering. Proto-spacer adjacent motif (PAM) adjacent to target sequence is one of the key components in the design of CCMDC strategies. It has been reported that NAG sequences are the predominant non-canonical PAM for CCMDC at the human EMX locus, but it is not clear whether it is universal at other loci. In the present study, we attempted to use a GFP-reporter system to comprehensively and quantitatively test the efficiency of CCMDC with non-canonical PAMs in human cells. The initial results indicated that the effectiveness of NGA PAM for CCMDC is much higher than that of other 14 PAMs including NAG. Then we further designed another three pairs of NGG, NGA and NAG PAMs at different locations in the GFP gene and investigated the corresponding DNA cleavage efficiency. We observed that one group of NGA PAMs have a relatively higher DNA cleavage efficiency, while the other groups have lower efficiency, compared with the corresponding NAG PAMs. Our study clearly demonstrates that NAG may not be the universally predominant non-canonical PAM for CCMDC in human cells. These findings raise more concerns over off-target effects in CRISPR/Cas9-mediated genome engineering.

  10. A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

    Directory of Open Access Journals (Sweden)

    Omi Shizue

    2010-11-01

    Full Text Available Abstract Background Proteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are found in many important structural and signaling complexes, and are generally thought to interact with their protein partners through a C-terminal consensus sequence. We undertook a comprehensive search for protein partners of all individual PDZ domains in C. elegans to characterize their function and mode of interaction. Results Coupling high-throughput yeast two-hybrid screens with extensive validation by co-affinity purification, we defined a domain-orientated interactome map. This integrates PDZ domain proteins in numerous cell-signaling pathways and shows that PDZ domain proteins are implicated in an unexpectedly wide range of cellular processes. Importantly, we uncovered a high frequency of non-canonical interactions, not involving the C-terminus of the protein partner, which were directly confirmed in most cases. We completed our study with the generation of a yeast array representing the entire set of PDZ domains from C. elegans and provide a proof-of-principle for its application to the discovery of PDZ domain targets for any protein or peptide of interest. Conclusions We provide an extensive domain-centered dataset, together with a clone resource, that will help future functional study of PDZ domains. Through this unbiased approach, we revealed frequent non-canonical interactions between PDZ domains and their protein partners that will require a re-evaluation of this domain's molecular function. [The protein interactions from this publication have been submitted to the IMEx (http://www.imexconsortium.org consortium through IntAct (PMID: 19850723 and assigned the identifier IM-14654

  11. Canonicalizable gyrocenter and structure-preserving geometric algorithms for the Vlasov-Maxwell system

    Science.gov (United States)

    Qin, Hong

    2016-10-01

    Littlejohn's introduction of the non-canonical symplectic structure for the gyrocenter dynamics revolutionized plasma kinetic theory. The discovery of the non-canonical symplectic algorithm for gyrocenters initiated the search for symplectic algorithms for the gyrokinetic system. This effort is enforced by the recent discovery of canonical and non-canonical symplectic algorithms for the Vlasov-Maxwell (VM) system. However, symplectic algorithms for the gyrokinetic system remain elusive despite intense effort. In retrospect, the success of the symplectic algorithms for the VM system can be attributed to its global canonicalizability. Darboux's theorem ensures that any symplectic structure is locally canonicalizable, but not necessarily globally. Indeed, Littlejohn's gyrocenter is not globally canonicalizable. In this talk, I will show to construct a different gyrocenter that is globally canonicalizable. It should be a good starting point for developing symplectic algorithms for the gyrokinetic system. Research supported by the U.S. Department of Energy (DE-AC02-09CH11466).

  12. Local measurement for structural health monitoring

    Institute of Scientific and Technical Information of China (English)

    G.Z.Qi; Guo Xun; Qi Xiaozhai; W. Dong; P.Chang

    2005-01-01

    Localized nature of damage in structures requires local measurements for structural health monitoring. The local measurement means to measure the local, usually higher modes of the vibration in a structure. Three fundamental issues about the local measurement for structural health monitoring including (1) the necessity of making local measurement, (2) the difficulty of making local measurement and (3) how to make local measurement are addressed in this paper. The results from both the analysis and the tests show that the local measurement can successfully monitor the structural health status as long as the local modes are excited. Unfortunately, the results also illustrate that it is difficult to excite local modes in a structure.Therefore, in order to carry structural health monitoring into effect, we must (1) ensure that the local modes are excited, and (2) deploy enough sensors in a structure so that the local modes can be monitored.

  13. Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells

    OpenAIRE

    Yilan Zhang; Xianglian Ge; Fayu Yang; Liping Zhang; Jiayong Zheng; Xuefang Tan; Zi-Bing Jin; Jia Qu; Feng Gu

    2014-01-01

    CRISPR/Cas9 -mediated DNA cleavage (CCMDC) is becoming increasingly used for efficient genome engineering. Proto-spacer adjacent motif (PAM) adjacent to target sequence is one of the key components in the design of CCMDC strategies. It has been reported that NAG sequences are the predominant non-canonical PAM for CCMDC at the human EMX locus, but it is not clear whether it is universal at other loci. In the present study, we attempted to use a GFP-reporter system to comprehensively and quanti...

  14. Components of the canonical and non-canonical Wnt pathways are not mis-expressed in pituitary tumors.

    Directory of Open Access Journals (Sweden)

    Leandro Machado Colli

    Full Text Available INTRODUCTION: Canonical and non-canonical Wnt pathways are involved in the genesis of multiple tumors; however, their role in pituitary tumorigenesis is mostly unknown. OBJECTIVE: This study evaluated gene and protein expression of Wnt pathways in pituitary tumors and whether these expression correlate to clinical outcome. MATERIALS AND METHODS: Genes of the WNT canonical pathway: activating ligands (WNT11, WNT4, WNT5A, binding inhibitors (DKK3, sFRP1, β-catenin (CTNNB1, β-catenin degradation complex (APC, AXIN1, GSK3β, inhibitor of β-catenin degradation complex (AKT1, sequester of β-catenin (CDH1, pathway effectors (TCF7, MAPK8, NFAT5, pathway mediators (DVL-1, DVL-2, DVL-3, PRICKLE, VANGL1, target genes (MYB, MYC, WISP2, SPRY1, TP53, CCND1; calcium dependent pathway (PLCB1, CAMK2A, PRKCA, CHP; and planar cell polarity pathway (PTK7, DAAM1, RHOA were evaluated by QPCR, in 19 GH-, 18 ACTH-secreting, 21 non-secreting (NS pituitary tumors, and 5 normal pituitaries. Also, the main effectors of canonical (β-catenin, planar cell polarity (JNK, and calcium dependent (NFAT5 Wnt pathways were evaluated by immunohistochemistry. RESULTS: There are no differences in gene expression of canonical and non-canonical Wnt pathways between all studied subtypes of pituitary tumors and normal pituitaries, except for WISP2, which was over-expressed in ACTH-secreting tumors compared to normal pituitaries (4.8x; p = 0.02, NS pituitary tumors (7.7x; p = 0.004 and GH-secreting tumors (5.0x; p = 0.05. β-catenin, NFAT5 and JNK proteins showed no expression in normal pituitaries and in any of the pituitary tumor subtypes. Furthermore, no association of the studied gene or protein expression was observed with tumor size, recurrence, and progressive disease. The hierarchical clustering showed a regular pattern of genes of the canonical and non-canonical Wnt pathways randomly distributed throughout the dendrogram. CONCLUSIONS: Our data reinforce previous reports

  15. Bose realization for non-canonical representations of the symplectic group Sp(4) contains SU(2)xU(1)

    Energy Technology Data Exchange (ETDEWEB)

    Tello-Llanos, R.A. [Departamento de Formacion General y Ciencias Basicas, Universidad Simon Bolivar, Caracas (Venezuela)]. E-mail: rtello@usb.ve

    2002-02-01

    A new method is formulated for the construction of arbitrary unitary irreducible representations of the compact symplectic group Sp(4){approx}O(5) in orthonormal bases which are reduced with respect to the non-canonical group chain Sp(4) contains SU(2)xU(1). The method is based on a realization of the algebra of generators and basis states by means of a system of Bose creation and annihilation operators. As an illustration, some series of representations with multiplicities equal to, or less than, three are given in explicit algebraic form. (author)

  16. A non-canonical NRPS is involved in the synthesis of fungisporin and related hydrophobic cyclic tetrapeptides in Penicillium chrysogenum.

    Directory of Open Access Journals (Sweden)

    Hazrat Ali

    Full Text Available The filamentous fungus Penicillium chrysogenum harbors an astonishing variety of nonribosomal peptide synthetase genes, which encode proteins known to produce complex bioactive metabolites from simple building blocks. Here we report a novel non-canonical tetra-modular nonribosomal peptide synthetase (NRPS with microheterogenicity of all involved adenylation domains towards their respective substrates. By deleting the putative gene in combination with comparative metabolite profiling various unique cyclic and derived linear tetrapeptides were identified which were associated with this NRPS, including fungisporin. In combination with substrate predictions for each module, we propose a mechanism for a 'trans-acting' adenylation domain.

  17. A non-canonical NRPS is involved in the synthesis of fungisporin and related hydrophobic cyclic tetrapeptides in Penicillium chrysogenum.

    Science.gov (United States)

    Ali, Hazrat; Ries, Marco I; Lankhorst, Peter P; van der Hoeven, Rob A M; Schouten, Olaf L; Noga, Marek; Hankemeier, Thomas; van Peij, Noël N M E; Bovenberg, Roel A L; Vreeken, Rob J; Driessen, Arnold J M

    2014-01-01

    The filamentous fungus Penicillium chrysogenum harbors an astonishing variety of nonribosomal peptide synthetase genes, which encode proteins known to produce complex bioactive metabolites from simple building blocks. Here we report a novel non-canonical tetra-modular nonribosomal peptide synthetase (NRPS) with microheterogenicity of all involved adenylation domains towards their respective substrates. By deleting the putative gene in combination with comparative metabolite profiling various unique cyclic and derived linear tetrapeptides were identified which were associated with this NRPS, including fungisporin. In combination with substrate predictions for each module, we propose a mechanism for a 'trans-acting' adenylation domain.

  18. Protein structure search and local structure characterization

    Directory of Open Access Journals (Sweden)

    Ku Shih-Yen

    2008-08-01

    Full Text Available Abstract Background Structural similarities among proteins can provide valuable insight into their functional mechanisms and relationships. As the number of available three-dimensional (3D protein structures increases, a greater variety of studies can be conducted with increasing efficiency, among which is the design of protein structural alphabets. Structural alphabets allow us to characterize local structures of proteins and describe the global folding structure of a protein using a one-dimensional (1D sequence. Thus, 1D sequences can be used to identify structural similarities among proteins using standard sequence alignment tools such as BLAST or FASTA. Results We used self-organizing maps in combination with a minimum spanning tree algorithm to determine the optimum size of a structural alphabet and applied the k-means algorithm to group protein fragnts into clusters. The centroids of these clusters defined the structural alphabet. We also developed a flexible matrix training system to build a substitution matrix (TRISUM-169 for our alphabet. Based on FASTA and using TRISUM-169 as the substitution matrix, we developed the SA-FAST alignment tool. We compared the performance of SA-FAST with that of various search tools in database-scale search tasks and found that SA-FAST was highly competitive in all tests conducted. Further, we evaluated the performance of our structural alphabet in recognizing specific structural domains of EGF and EGF-like proteins. Our method successfully recovered more EGF sub-domains using our structural alphabet than when using other structural alphabets. SA-FAST can be found at http://140.113.166.178/safast/. Conclusion The goal of this project was two-fold. First, we wanted to introduce a modular design pipeline to those who have been working with structural alphabets. Secondly, we wanted to open the door to researchers who have done substantial work in biological sequences but have yet to enter the field of protein

  19. Bioinformatics and molecular dynamics simulation study of L1 stalk non-canonical rRNA elements: kink-turns, loops, and tetraloops.

    Science.gov (United States)

    Krepl, Miroslav; Réblová, Kamila; Koča, Jaroslav; Sponer, Jiří

    2013-05-09

    The L1 stalk is a prominent mobile element of the large ribosomal subunit. We explore the structure and dynamics of its non-canonical rRNA elements, which include two kink-turns, an internal loop, and a tetraloop. We use bioinformatics to identify the L1 stalk RNA conservation patterns and carry out over 11.5 μs of MD simulations for a set of systems ranging from isolated RNA building blocks up to complexes of L1 stalk rRNA with the L1 protein and tRNA fragment. We show that the L1 stalk tetraloop has an unusual GNNA or UNNG conservation pattern deviating from major GNRA and YNMG RNA tetraloop families. We suggest that this deviation is related to a highly conserved tertiary contact within the L1 stalk. The available X-ray structures contain only UCCG tetraloops which in addition differ in orientation (anti vs syn) of the guanine. Our analysis suggests that the anti orientation might be a mis-refinement, although even the anti interaction would be compatible with the sequence pattern and observed tertiary interaction. Alternatively, the anti conformation may be a real substate whose population could be pH-dependent, since the guanine syn orientation requires protonation of cytosine in the tertiary contact. In absence of structural data, we use molecular modeling to explore the GCCA tetraloop that is dominant in bacteria and suggest that the GCCA tetraloop is structurally similar to the YNMG tetraloop. Kink-turn Kt-77 is unusual due to its 11-nucleotide bulge. The simulations indicate that the long bulge is a stalk-specific eight-nucleotide insertion into consensual kink-turn only subtly modifying its structural dynamics. We discuss a possible evolutionary role of helix H78 and a mechanism of L1 stalk interaction with tRNA. We also assess the simulation methodology. The simulations provide a good description of the studied systems with the latest bsc0χOL3 force field showing improved performance. Still, even bsc0χOL3 is unable to fully stabilize an essential

  20. PfAP2Tel, harbouring a non-canonical DNA-binding AP2 domain, binds to Plasmodium falciparum telomeres.

    Science.gov (United States)

    Sierra-Miranda, Miguel; Vembar, Shruthi S; Delgadillo, Dulce María; Ávila-López, P A; Vargas, Miguel; Hernandez-Rivas, Rosaura

    2017-04-04

    The telomeres of the malaria parasite Plasmodium falciparum are essential not only for chromosome end maintenance during blood stage development in humans but also to generate genetic diversity by facilitating homologous recombination of subtelomeric, multigene virulence families such as var and rifin. However, other than the telomerase PfTERT, proteins that act at P. falciparum telomeres are poorly characterized. To isolate components that bind to telomeres, we performed oligonucleotide pulldowns and electromobility shift assays with a telomeric DNA probe and identified a non-canonical member of the ApiAP2 family of transcription factors, PfAP2Tel (encoded by PF3D7_0622900), as a component of the P. falciparum telomere-binding protein complex. PfAP2Tel is expressed throughout the intra-erythrocytic life cycle and localizes to the nuclear periphery, co-localizing with telomeric clusters. Furthermore, EMSAs using the recombinant protein demonstrated direct binding of PfAP2Tel to telomeric repeats in vitro, while genome-wide chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) corroborated the high specificity of this protein to telomeric ends of all 14 chromosomes in vivo. Taken together, our data describe a novel function for ApiAP2 proteins at chromosome ends and open new avenues to study the molecular machinery that regulates telomere function in P. falciparum.

  1. Src promotes castration-recurrent prostate cancer through androgen receptor-dependent canonical and non-canonical transcriptional signatures

    Science.gov (United States)

    Chattopadhyay, Indranil; Wang, Jianmin; Qin, Maochun; Gao, Lingqiu; Holtz, Renae; Vessella, Robert L.; Leach, Robert W.; Gelman, Irwin H.

    2017-01-01

    Progression of prostate cancer (PC) to castration-recurrent growth (CRPC) remains dependent on sustained expression and transcriptional activity of the androgen receptor (AR). A major mechanism contributing to CRPC progression is through the direct phosphorylation and activation of AR by Src-family (SFK) and ACK1 tyrosine kinases. However, the AR-dependent transcriptional networks activated by Src during CRPC progression have not been elucidated. Here, we show that activated Src (Src527F) induces androgen-independent growth in human LNCaP cells, concomitant with its ability to induce proliferation/survival genes normally induced by dihydrotestosterone (DHT) in androgen-dependent LNCaP and VCaP cells. Src induces additional gene signatures unique to CRPC cell lines, LNCaP-C4-2 and CWR22Rv1, and to CRPC LuCaP35.1 xenografts. By comparing the Src-induced AR-cistrome and/or transcriptome in LNCaP to those in CRPC and LuCaP35.1 tumors, we identified an 11-gene Src-regulated CRPC signature consisting of AR-dependent, AR binding site (ARBS)-associated genes whose expression is altered by DHT in LNCaP[Src527F] but not in LNCaP cells. The differential expression of a subset (DPP4, BCAT1, CNTNAP4, CDH3) correlates with earlier PC metastasis onset and poorer survival, with the expression of BCAT1 required for Src-induced androgen-independent proliferation. Lastly, Src enhances AR binding to non-canonical ARBS enriched for FOXO1, TOP2B and ZNF217 binding motifs; cooperative AR/TOP2B binding to a non-canonical ARBS was both Src- and DHT-sensitive and correlated with increased levels of Src-induced phosphotyrosyl-TOP2B. These data suggest that CRPC progression is facilitated via Src-induced sensitization of AR to intracrine androgen levels, resulting in the engagement of canonical and non-canonical ARBS-dependent gene signatures. PMID:28055971

  2. Recent Developments of Engineered Translational Machineries for the Incorporation of Non-Canonical Amino Acids into Polypeptides

    Directory of Open Access Journals (Sweden)

    Naohiro Terasaka

    2015-03-01

    Full Text Available Genetic code expansion and reprogramming methodologies allow us to incorporate non-canonical amino acids (ncAAs bearing various functional groups, such as fluorescent groups, bioorthogonal functional groups, and post-translational modifications, into a desired position or multiple positions in polypeptides both in vitro and in vivo. In order to efficiently incorporate a wide range of ncAAs, several methodologies have been developed, such as orthogonal aminoacyl-tRNA-synthetase (AARS–tRNA pairs, aminoacylation ribozymes, frame-shift suppression of quadruplet codons, and engineered ribosomes. More recently, it has been reported that an engineered translation system specifically utilizes an artificially built genetic code and functions orthogonally to naturally occurring counterpart. In this review we summarize recent advances in the field of ribosomal polypeptide synthesis containing ncAAs.

  3. Non-canonical NF-κB activation and abnormal B cell accumulation in mice expressing ubiquitin protein ligase-inactive c-IAP2.

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    Dietrich B Conze

    Full Text Available Chromosomal translocations between loci encoding MALT1 and c-IAP2 are common in MALT lymphomas. The resulting fusion proteins lack the c-IAP2 RING domain, the region responsible for its ubiquitin protein ligase (E3 activity. Ectopic expression of the fusion protein activates the canonical NF-κB signaling cascade, but how it does so is controversial and how it promotes MALT lymphoma is unknown. Considering recent reports implicating c-IAP1 and c-IAP2 E3 activity in repression of non-canonical NF-κB signaling, we asked if the c-IAP2/MALT fusion protein can initiate non-canonical NF-κB activation. Here we show that in addition to canonical activation, the fusion protein stabilizes NIK and activates non-canonical NF-κB. Canonical but not non-canonical activation depended on MALT1 paracaspase activity, and expression of E3-inactive c-IAP2 activated non-canonical NF-κB. Mice in which endogenous c-IAP2 was replaced with an E3-inactive mutant accumulated abnormal B cells with elevated non-canonical NF-κB and had increased numbers of B cells with a marginal zone phenotype, gut-associated lymphoid hyperplasia, and other features of MALT lymphoma. Thus, the c-IAP2/MALT1 fusion protein activates NF-κB by two distinct mechanisms, and loss of c-IAP2 E3 activity in vivo is sufficient to induce abnormalities common to MALT lymphoma.

  4. Non-canonical microRNAs miR-320 and miR-702 promote proliferation in Dgcr8-deficient embryonic stem cells

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    Kim, Byeong-Moo [Department of Medicine/GI Unit, Massachusetts General Hospital, Boston, MA 02114 (United States); Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States); Choi, Michael Y., E-mail: mchoi@partners.org [Department of Medicine/GI Unit, Massachusetts General Hospital, Boston, MA 02114 (United States); Department of Medicine, Harvard Medical School, Boston, MA 02115 (United States); Harvard Stem Cell Institute, Boston, MA 02114 (United States)

    2012-09-21

    Highlights: Black-Right-Pointing-Pointer Embryonic stem cells (ESCs) lacking non-canonical miRNAs proliferate slower. Black-Right-Pointing-Pointer miR-320 and miR-702 are two non-canonical miRNAs expressed in ESCs. Black-Right-Pointing-Pointer miR-320 and miR-702 promote proliferation of Dgcr8-deficient ESCs. Black-Right-Pointing-Pointer miR-320 targets p57 and helps to release Dgcr8-deficient ESCs from G1 arrest. Black-Right-Pointing-Pointer miR-702 targets p21 and helps to release Dgcr8-deficient ESCs from G1 arrest. -- Abstract: MicroRNAs are known to contribute significantly to stem cell phenotype by post-transcriptionally regulating gene expression. Most of our knowledge of microRNAs comes from the study of canonical microRNAs that require two sequential cleavages by the Drosha/Dgcr8 heterodimer and Dicer to generate mature products. In contrast, non-canonical microRNAs bypass the cleavage by the Drosha/Dgcr8 heterodimer within the nucleus but still require cytoplasmic cleavage by Dicer. The function of non-canonical microRNAs in embryonic stem cells (ESCs) remains obscure. It has been hypothesized that non-canonical microRNAs have important roles in ESCs based upon the phenotypes of ESC lines that lack these specific classes of microRNAs; Dicer-deficient ESCs lacking both canonical and non-canonical microRNAs have much more severe proliferation defect than Dgcr8-deficient ESCs lacking only canonical microRNAs. Using these cell lines, we identified two non-canonical microRNAs, miR-320 and miR-702, that promote proliferation of Dgcr8-deficient ESCs by releasing them from G1 arrest. This is accomplished by targeting the 3 Prime -untranslated regions of the cell cycle inhibitors p57 and p21 and thereby inhibiting their expression. This is the first report of the crucial role of non-canonical microRNAs in ESCs.

  5. Localized structure of Euglena bioconvection

    Science.gov (United States)

    Iima, Makoto; Shoji, Erika; Awazu, Akinori; Nishimori, Hiraku; Izumi, Shunsuke; Hiroshima University Collaboration

    2013-11-01

    Bioconvection of a suspension of Euglena gracilis, a photosensitive flagellate whose body length is approximately 50 micrometers, was experimentally studied. Under strong light intensity, Euglena has a negative phototaxis; they tend to go away from the light source. When the bright illumination is given from the bottom, a large scale spatio-temporal pattern is generated as a result of interaction between Euglena and surrounding flow. Recently, localized convection pattern had been reported, however, the generation process and interaction of the localized convection cells has not been analyzed. We performed experimental study to understand the localization mechanism, in particular, the onset of bioconvection and lateral localization behavior due to phototaxis. Experiments started from different initial condition suggests a bistability near the onset of the convection as binary fluid convection that also shows localized convection cells. Dynamics of localized convections cells, which is similar to the binary fluid convection case although the basic equations are not the same, is also reported.

  6. A non canonical subtilase attenuates the transcriptional activation of defence responses in Arabidopsis thaliana

    Science.gov (United States)

    Serrano, Irene; Buscaill, Pierre; Audran, Corinne; Pouzet, Cécile; Jauneau, Alain; Rivas, Susana

    2016-01-01

    Proteases play crucial physiological functions in all organisms by controlling the lifetime of proteins. Here, we identified an atypical protease of the subtilase family [SBT5.2(b)] that attenuates the transcriptional activation of plant defence independently of its protease activity. The SBT5.2 gene produces two distinct transcripts encoding a canonical secreted subtilase [SBT5.2(a)] and an intracellular protein [SBT5.2(b)]. Concomitant to SBT5.2(a) downregulation, SBT5.2(b) expression is induced after bacterial inoculation. SBT5.2(b) localizes to endosomes where it interacts with and retains the defence-related transcription factor MYB30. Nuclear exclusion of MYB30 results in its reduced transcriptional activation and, thus, suppressed resistance. sbt5.2 mutants, with abolished SBT5.2(a) and SBT5.2(b) expression, display enhanced defence that is suppressed in a myb30 mutant background. Moreover, overexpression of SBT5.2(b), but not SBT5.2(a), in sbt5.2 plants reverts the phenotypes displayed by sbt5.2 mutants. Overall, we uncover a regulatory mode of the transcriptional activation of defence responses previously undescribed in eukaryotes. DOI: http://dx.doi.org/10.7554/eLife.19755.001 PMID:27685353

  7. Dissecting non-canonical interactions in frameshift-stimulating mRNA pseudoknots

    Energy Technology Data Exchange (ETDEWEB)

    Cornish, Peter V. [University of Illinois at Urbana-Champaign, Department of Physics (United States); Giedroc, David P. [2128 TAMU, Texas A and M University, Department of Biochemistry and Biophysics (United States); Hennig, Mirko [Scripps Research Institute, MB33, Department of Molecular Biology (United States)], E-mail: hennig@musc.edu

    2006-07-15

    A variety of powerful NMR experiments have been introduced over the last few years that allow for the direct identification of different combinations of donor and acceptor atoms involved in hydrogen bonds in biomolecules. This ability to directly observe tertiary structural hydrogen bonds in solution tremendously facilitates structural studies of nucleic acids. We show here that an adiabatic HNN-COSY pulse scheme permits observation and measurement of J(N,N) couplings for nitrogen sites that are separated by up to 140 ppm in a single experiment at a proton resonance frequency of 500 MHz. Crucial hydrogen bond acceptor sites in nucleic acids, such as cytidine N3 nitrogens, can be unambiguously identified even in the absence of detectable H41 and H42 amino protons using a novel triple-resonance two-dimensional experiment, denoted H5(C5C4)N3. The unambiguous identification of amino nitrogen donor and aromatic nitrogen acceptor sites associated with both major groove as well as minor groove triple base pairs reveal the details of hydrogen bonding networks that stabilize the complex architecture of frameshift-stimulating mRNA pseudoknots. Another key tertiary interaction involving a 2'-OH hydroxyl proton that donates a hydrogen bond to an aromatic nitrogen acceptor in a cis Watson-Crick/sugar edge interaction can also be directly detected using a quantitative J(H,N) {sup 1}H,{sup 15}N-HSQC experiment.

  8. TWEAK activates the non-canonical NFkappaB pathway in murine renal tubular cells: modulation of CCL21.

    Directory of Open Access Journals (Sweden)

    Ana B Sanz

    Full Text Available TWEAK is a member of the TNF superfamily of cytokines that contribute to kidney tubulointerstitial injury. It has previously been reported that TWEAK induces transient nuclear translocation of RelA and expression of RelA-dependent cytokines in renal tubular cells. Additionally, TWEAK induced long-lasting NFkappaB activation suggestive of engagement of the non-canonical NFkappaB pathway. We now explore TWEAK-induced activation of NFkappaB2 and RelB, as well as expression of CCL21, a T-cell chemotactic factor, in cultured murine tubular epithelial cells and in healthy kidneys in vivo. In cultured tubular cells, TWEAK and TNFalpha activated different DNA-binding NFkappaB complexes. TWEAK-induced sustained NFkappaB activation was associated with NFkappaB2 p100 processing to p52 via proteasome and nuclear translocation and DNA-binding of p52 and RelB. TWEAK, but not TNFalpha used as control, induced a delayed increase in CCL21a mRNA (3.5+/-1.22-fold over control and CCL21 protein (2.5+/-0.8-fold over control, which was prevented by inhibition of the proteasome, or siRNA targeting of NIK or RelB, but not by RelA inhibition with parthenolide. A second NFkappaB2-dependent chemokine, CCL19, was upregulates by TWEAK, but not by TNFalpha. However, both cytokines promoted chemokine RANTES expression (3-fold mRNA at 24 h. In vivo, TWEAK induced nuclear NFkappaB2 and RelB translocation and CCL21a mRNA (1.5+/-0.3-fold over control and CCL21 protein (1.6+/-0.5-fold over control expression in normal kidney. Increased tubular nuclear RelB and tubular CCL21 expression in acute kidney injury were decreased by neutralization (2+/-0.9 vs 1.3+/-0.6-fold over healthy control or deficiency of TWEAK (2+/-0.9 vs 0.8+/-0.6-fold over healthy control. Moreover, anti-TWEAK treatment prevented the recruitment of T cells to the kidney in this model (4.1+/-1.4 vs 1.8+/-1-fold over healthy control. Our results thus identify TWEAK as a regulator of non-canonical NFkappa

  9. TWEAK Activates the Non-Canonical NFκB Pathway in Murine Renal Tubular Cells: Modulation of CCL21

    Science.gov (United States)

    Sanz, Ana B.; Sanchez-Niño, Maria D.; Izquierdo, Maria C.; Jakubowski, Aniela; Justo, Pilar; Blanco-Colio, Luis M.; Ruiz-Ortega, Marta; Selgas, Rafael; Egido, Jesús; Ortiz, Alberto

    2010-01-01

    TWEAK is a member of the TNF superfamily of cytokines that contribute to kidney tubulointerstitial injury. It has previously been reported that TWEAK induces transient nuclear translocation of RelA and expression of RelA-dependent cytokines in renal tubular cells. Additionally, TWEAK induced long-lasting NFκB activation suggestive of engagement of the non-canonical NFκB pathway. We now explore TWEAK-induced activation of NFκB2 and RelB, as well as expression of CCL21, a T-cell chemotactic factor, in cultured murine tubular epithelial cells and in healthy kidneys in vivo. In cultured tubular cells, TWEAK and TNFα activated different DNA-binding NFκB complexes. TWEAK-induced sustained NFκB activation was associated with NFκB2 p100 processing to p52 via proteasome and nuclear translocation and DNA-binding of p52 and RelB. TWEAK, but not TNFα used as control), induced a delayed increase in CCL21a mRNA (3.5±1.22-fold over control) and CCL21 protein (2.5±0.8-fold over control), which was prevented by inhibition of the proteasome, or siRNA targeting of NIK or RelB, but not by RelA inhibition with parthenolide. A second NFκB2-dependent chemokine, CCL19, was upregulates by TWEAK, but not by TNFα. However, both cytokines promoted chemokine RANTES expression (3-fold mRNA at 24 h). In vivo, TWEAK induced nuclear NFκB2 and RelB translocation and CCL21a mRNA (1.5±0.3-fold over control) and CCL21 protein (1.6±0.5-fold over control) expression in normal kidney. Increased tubular nuclear RelB and tubular CCL21 expression in acute kidney injury were decreased by neutralization (2±0.9 vs 1.3±0.6-fold over healthy control) or deficiency of TWEAK (2±0.9 vs 0.8±0.6-fold over healthy control). Moreover, anti-TWEAK treatment prevented the recruitment of T cells to the kidney in this model (4.1±1.4 vs 1.8±1-fold over healthy control). Our results thus identify TWEAK as a regulator of non-canonical NFκB activation and CCL21 expression in tubular cells thus promoting

  10. The NAV2 homolog Sickie regulates F-actin-mediated axonal growth in Drosophila mushroom body neurons via the non-canonical Rac-Cofilin pathway.

    Science.gov (United States)

    Abe, Takashi; Yamazaki, Daisuke; Murakami, Satoshi; Hiroi, Makoto; Nitta, Yohei; Maeyama, Yuko; Tabata, Tetsuya

    2014-12-01

    The Rac-Cofilin pathway is essential for cytoskeletal remodeling to control axonal development. Rac signals through the canonical Rac-Pak-LIMK pathway to suppress Cofilin-dependent axonal growth and through a Pak-independent non-canonical pathway to promote outgrowth. Whether this non-canonical pathway converges to promote Cofilin-dependent F-actin reorganization in axonal growth remains elusive. We demonstrate that Sickie, a homolog of the human microtubule-associated protein neuron navigator 2, cell-autonomously regulates axonal growth of Drosophila mushroom body (MB) neurons via the non-canonical pathway. Sickie was prominently expressed in the newborn F-actin-rich axons of MB neurons. A sickie mutant exhibited axonal growth defects, and its phenotypes were rescued by exogenous expression of Sickie. We observed phenotypic similarities and genetic interactions among sickie and Rac-Cofilin signaling components. Using the MARCM technique, distinct F-actin and phospho-Cofilin patterns were detected in developing axons mutant for sickie and Rac-Cofilin signaling regulators. The upregulation of Cofilin function alleviated the axonal defect of the sickie mutant. Epistasis analyses revealed that Sickie suppresses the LIMK overexpression phenotype and is required for Pak-independent Rac1 and Slingshot phosphatase to counteract LIMK. We propose that Sickie regulates F-actin-mediated axonal growth via the non-canonical Rac-Cofilin pathway in a Slingshot-dependent manner.

  11. Zebrafish colgate/hdac1 functions in the non-canonical Wnt pathway during axial extension and in Wnt-independent branchiomotor neuron migration.

    Science.gov (United States)

    Nambiar, Roopa M; Ignatius, Myron S; Henion, Paul D

    2007-01-01

    Vertebrate gastrulation involves the coordinated movements of populations of cells. These movements include cellular rearrangements in which cells polarize along their medio-lateral axes leading to cell intercalations that result in elongation of the body axis. Molecular analysis of this process has implicated the non-canonical Wnt/Frizzled signaling pathway that is similar to the planar cell polarity pathway (PCP) in Drosophila. Here we describe a zebrafish mutant, colgate (col), which displays defects in the extension of the body axis and the migration of branchiomotor neurons. Activation of the non-canonical Wnt/PCP pathway in these mutant embryos by overexpressing DeltaNdishevelled, rho kinase2 and van gogh-like protein 2 (vangl2) rescues the extension defects suggesting that col acts as a positive regulator of the non-canonical Wnt/PCP pathway. Further, we show that col normally regulates the caudal migration of nVII facial hindbrain branchiomotor neurons and that the mutant phenotype can be rescued by misexpression of vangl2 independent of the Wnt/PCP pathway. We cloned the col locus and found that it encodes histone deacetylase1 (hdac1). Our previous results and studies by others have implicated hdac1 in repressing the canonical Wnt pathway. Here, we demonstrate novel roles for zebrafish hdac1 in activating non-canonical Wnt/PCP signaling underlying axial extension and in promoting Wnt-independent caudal migration of a subset of hindbrain branchiomotor neurons.

  12. Statins activate the canonical hedgehog-signaling and aggravate non-cirrhotic portal hypertension, but inhibit the non-canonical hedgehog signaling and cirrhotic portal hypertension.

    Science.gov (United States)

    Uschner, Frank E; Ranabhat, Ganesh; Choi, Steve S; Granzow, Michaela; Klein, Sabine; Schierwagen, Robert; Raskopf, Esther; Gautsch, Sebastian; van der Ven, Peter F M; Fürst, Dieter O; Strassburg, Christian P; Sauerbruch, Tilman; Diehl, Anna Mae; Trebicka, Jonel

    2015-09-28

    Liver cirrhosis but also portal vein obstruction cause portal hypertension (PHT) and angiogenesis. This study investigated the differences of angiogenesis in cirrhotic and non-cirrhotic PHT with special emphasis on the canonical (Shh/Gli) and non-canonical (Shh/RhoA) hedgehog pathway. Cirrhotic (bile duct ligation/BDL; CCl4 intoxication) and non-cirrhotic (partial portal vein ligation/PPVL) rats received either atorvastatin (15 mg/kg; 7d) or control chow before sacrifice. Invasive hemodynamic measurement and Matrigel implantation assessed angiogenesis in vivo. Angiogenesis in vitro was analysed using migration and tube formation assay. In liver and vessel samples from animals and humans, transcript expression was analyzed using RT-PCR and protein expression using Western blot. Atorvastatin decreased portal pressure, shunt flow and angiogenesis in cirrhosis, whereas atorvastatin increased these parameters in PPVL rats. Non-canonical Hh was upregulated in experimental and human liver cirrhosis and was blunted by atorvastatin. Moreover, atorvastatin blocked the non-canonical Hh-pathway RhoA dependently in activated hepatic steallate cells (HSCs). Interestingly, hepatic and extrahepatic Hh-pathway was enhanced in PPVL rats, which resulted in increased angiogenesis. In summary, statins caused contrary effects in cirrhotic and non-cirrhotic portal hypertension. Atorvastatin inhibited the non-canonical Hh-pathway and angiogenesis in cirrhosis. In portal vein obstruction, statins enhanced the canonical Hh-pathway and aggravated PHT and angiogenesis.

  13. Deoxycholic acid mediates non-canonical EGFR-MAPK activation through the induction of calcium signaling in colon cancer cells.

    Science.gov (United States)

    Centuori, Sara M; Gomes, Cecil J; Trujillo, Jesse; Borg, Jamie; Brownlee, Joshua; Putnam, Charles W; Martinez, Jesse D

    2016-07-01

    Obesity and a western diet have been linked to high levels of bile acids and the development of colon cancer. Specifically, increased levels of the bile acid deoxycholic acid (DCA), an established tumor promoter, has been shown to correlate with increased development of colorectal adenomas and progression to carcinoma. Herein we investigate the mechanism by which DCA leads to EGFR-MAPK activation, a candidate mechanism by which DCA may promote colorectal tumorigenesis. DCA treated colon cancer cells exhibited strong and prolonged activation of ERK1/2 when compared to EGF treatment alone. We also showed that DCA treatment prevents EGFR degradation as opposed to the canonical EGFR recycling observed with EGF treatment. Moreover, the combination of DCA and EGF treatment displayed synergistic activity, suggesting DCA activates MAPK signaling in a non-canonical manner. Further evaluation showed that DCA treatment increased intracellular calcium levels and CAMKII phosphorylation, and that blocking calcium with BAPTA-AM abrogated MAPK activation induced by DCA, but not by EGF. Finally we showed that DCA-induced CAMKII leads to MAPK activation through the recruitment of c-Src. Taken together, we demonstrated that DCA regulates MAPK activation through calcium signaling, an alternative mechanism not previously recognized in human colon cancer cells. Importantly, this mechanism allows for EGFR to escape degradation and thus achieve a constitutively active state, which may explain its tumor promoting effects.

  14. Non-canonical 3'-5' extension of RNA with prebiotically plausible ribonucleoside 2',3'-cyclic phosphates.

    Science.gov (United States)

    Mutschler, Hannes; Holliger, Philipp

    2014-04-09

    Ribonucleoside 2',3'-cyclic phosphates (N>p's) are generated by multiple prebiotically plausible processes and are credible building blocks for the assembly of early RNA oligomers. While N>p's can be polymerized into short RNAs by non-enzymatic processes with variable efficiency and regioselectivity, no enzymatic route for RNA synthesis had been described. Here we report such a non-canonical 3'-5' nucleotidyl transferase activity. We engineered a variant of the hairpin ribozyme to catalyze addition of all four N>p's (2',3'-cyclic A-, G-, U-, and CMP) to the 5'-hydroxyl termini of RNA strands with 5' nucleotide addition enhanced in all cases by eutectic ice phase formation at -7 °C. We also observed 5' addition of 2',3'-cyclic phosphate-activated β-nicotinamide adenine dinucleotide (NAD>p) and ACA>p RNA trinucleotide, and multiple additions of GUCCA>p RNA pentamers. Our results establish a new mode of RNA 3'-5' extension with implications for RNA oligomer synthesis from prebiotic nucleotide pools.

  15. Canonical and Non-Canonical Aspects of JAK–STAT Signaling: Lessons from Interferons for Cytokine Responses

    Science.gov (United States)

    Majoros, Andrea; Platanitis, Ekaterini; Kernbauer-Hölzl, Elisabeth; Rosebrock, Felix; Müller, Mathias; Decker, Thomas

    2017-01-01

    Janus kinase (JAK)–signal transducer and activator of transcription (STAT) signal transduction mediates cytokine responses. Canonical signaling is based on STAT tyrosine phosphorylation by activated JAKs. Downstream of interferon (IFN) receptors, activated JAKs cause the formation of the transcription factors IFN-stimulated gene factor 3 (ISGF3), a heterotrimer of STAT1, STAT2 and interferon regulatory factor 9 (IRF9) subunits, and gamma interferon-activated factor (GAF), a STAT1 homodimer. In recent years, several deviations from this paradigm were reported. These include kinase-independent JAK functions as well as extra- and intranuclear activities of U-STATs without phosphotyrosines. Additionally, transcriptional control by STAT complexes resembling neither GAF nor ISGF3 contributes to transcriptome changes in IFN-treated cells. Our review summarizes the contribution of non-canonical JAK–STAT signaling to the innate antimicrobial immunity imparted by IFN. Moreover, we touch upon functions of IFN pathway proteins beyond the IFN response. These include metabolic functions of IRF9 as well as the regulation of natural killer cell activity by kinase-dead TYK2 and different phosphorylation isoforms of STAT1. PMID:28184222

  16. Allosteric Regulation of Serine Protease HtrA2 through Novel Non-Canonical Substrate Binding Pocket

    Science.gov (United States)

    Singh, Nitu; Gadewal, Nikhil; Chaganti, Lalith K.; Sastry, G. Madhavi; Bose, Kakoli

    2013-01-01

    HtrA2, a trimeric proapoptotic serine protease is involved in several diseases including cancer and neurodegenerative disorders. Its unique ability to mediate apoptosis via multiple pathways makes it an important therapeutic target. In HtrA2, C-terminal PDZ domain upon substrate binding regulates its functions through coordinated conformational changes the mechanism of which is yet to be elucidated. Although allostery has been found in some of its homologs, it has not been characterized in HtrA2 so far. Here, with an in silico and biochemical approach we have shown that allostery does regulate HtrA2 activity. Our studies identified a novel non-canonical selective binding pocket in HtrA2 which initiates signal propagation to the distal active site through a complex allosteric mechanism. This non-classical binding pocket is unique among HtrA family proteins and thus unfolds a novel mechanism of regulation of HtrA2 activity and hence apoptosis. PMID:23457469

  17. Allosteric regulation of serine protease HtrA2 through novel non-canonical substrate binding pocket.

    Directory of Open Access Journals (Sweden)

    Pruthvi Raj Bejugam

    Full Text Available HtrA2, a trimeric proapoptotic serine protease is involved in several diseases including cancer and neurodegenerative disorders. Its unique ability to mediate apoptosis via multiple pathways makes it an important therapeutic target. In HtrA2, C-terminal PDZ domain upon substrate binding regulates its functions through coordinated conformational changes the mechanism of which is yet to be elucidated. Although allostery has been found in some of its homologs, it has not been characterized in HtrA2 so far. Here, with an in silico and biochemical approach we have shown that allostery does regulate HtrA2 activity. Our studies identified a novel non-canonical selective binding pocket in HtrA2 which initiates signal propagation to the distal active site through a complex allosteric mechanism. This non-classical binding pocket is unique among HtrA family proteins and thus unfolds a novel mechanism of regulation of HtrA2 activity and hence apoptosis.

  18. Evidence for a non-canonical role of HDAC5 in regulation of the cardiac Ncx1 and Bnp genes

    Science.gov (United States)

    Harris, Lillianne G.; Wang, Sabina H.; Mani, Santhosh K.; Kasiganesan, Harinath; Chou, C. James; Menick, Donald R.

    2016-01-01

    Class IIa histone deacetylases (HDACs) are very important for tissue specific gene regulation in development and pathology. Because class IIa HDAC catalytic activity is low, their exact molecular roles have not been fully elucidated. Studies have suggested that class IIa HDACs may serve as a scaffold to recruit the catalytically active class I HDAC complexes to their substrate. Here we directly address whether the class IIa HDAC, HDAC5 may function as a scaffold to recruit co-repressor complexes to promoters. We examined two well-characterized cardiac promoters, the sodium calcium exchanger (Ncx1) and the brain natriuretic peptide (Bnp) whose hypertrophic upregulation is mediated by both class I and IIa HDACs. Selective inhibition of class IIa HDACs did not prevent adrenergic stimulated Ncx1 upregulation, however HDAC5 knockout prevented pressure overload induced Ncx1 upregulation. Using the HDAC5(-/-) mouse we show that HDAC5 is required for the interaction of the HDAC1/2/Sin3a co-repressor complexes with the Nkx2.5 and YY1 transcription factors and critical for recruitment of the HDAC1/Sin3a co-repressor complex to either the Ncx1 or Bnp promoter. Our novel findings support a non-canonical role of class IIa HDACs in the scaffolding of transcriptional regulatory complexes, which may be relevant for therapeutic intervention for pathologies. PMID:26704971

  19. Wnt3a regulates proliferation and migration of HUVEC via canonical and non-canonical Wnt signaling pathways

    Energy Technology Data Exchange (ETDEWEB)

    Samarzija, Ivana [Friedrich Miescher Institute for Biomedical Research, Basel (Switzerland); Sini, Patrizia [Cancer and Infection Research Area, AstraZeneca Pharmaceuticals, Macclesfield (United Kingdom); Schlange, Thomas [Bayer Schering Pharma AG, Wuppertal (Germany); MacDonald, Gwen [Friedrich Miescher Institute for Biomedical Research, Basel (Switzerland); Hynes, Nancy E., E-mail: Nancy.Hynes@fmi.ch [Friedrich Miescher Institute for Biomedical Research, Basel (Switzerland)

    2009-08-28

    Untangling the signaling pathways involved in endothelial cell biology is of central interest for the development of antiangiogenesis based therapies. Here we report that Wnt3a induces the proliferation and migration of HUVECs, but does not affect their survival. Wnt3a-induced proliferation was VEGFR signaling independent, but reduced upon CamKII inhibition. In a search for the downstream mediators of Wnt3a's effects on HUVEC biology, we found that Wnt3a treatment leads to phosphorylation of DVL3 and stabilization of {beta}-catenin. Moreover, under the same conditions we observed an upregulation in c-MYC, TIE-2 and GJA1 mRNA transcripts. Although treatment of HUVECs with Wnt5a induced DVL3 phosphorylation, we did not observe any of the other effects seen upon Wnt3a stimulation. Taken together, our data indicate that Wnt3a induces canonical and non-canonical Wnt signaling in HUVECs, and stimulates their proliferation and migration.

  20. Distinct pathways for modification of the bacterial cell wall by non-canonical D-amino acids.

    Science.gov (United States)

    Cava, Felipe; de Pedro, Miguel A; Lam, Hubert; Davis, Brigid M; Waldor, Matthew K

    2011-07-26

    Production of non-canonical D-amino acids (NCDAAs) in stationary phase promotes remodelling of peptidoglycan (PG), the polymer that comprises the bacterial cell wall. Impairment of NCDAAs production leads to excessive accumulation of PG and hypersensitivity to osmotic shock; however, the mechanistic bases for these phenotypes were not previously determined. Here, we show that incorporation of NCDAAs into PG is a critical means by which NCDAAs control PG abundance and strength. We identified and reconstituted in vitro two (of at least three) distinct processes that mediate NCDAA incorporation. Diverse bacterial phyla incorporate NCDAAs into their cell walls, either through periplasmic editing of the mature PG or via incorporation into PG precursor subunits in the cytosol. Production of NCDAAs in Vibrio cholerae requires the stress response sigma factor RpoS, suggesting that NCDAAs may aid bacteria in responding to varied environmental challenges. The widespread capacity of diverse bacteria, including non-producers, to incorporate NCDAAs suggests that these amino acids may serve as both autocrine- and paracrine-like regulators of chemical and physical properties of the cell wall in microbial communities.

  1. A role for NRAGE in NF-kappaB activation through the non-canonical BMP pathway.

    Science.gov (United States)

    Matluk, Nicholas; Rochira, Jennifer A; Karaczyn, Aldona; Adams, Tamara; Verdi, Joseph M

    2010-01-25

    Previous studies have linked neurotrophin receptor-interacting MAGE protein to the bone morphogenic protein signaling pathway and its effect on p38 mediated apoptosis of neural progenitor cells via the XIAP-Tak1-Tab1 complex. Its effect on NF-kappaB has yet to be explored. Herein we report that NRAGE, via the same XIAP-Tak1-Tab1 complex, is required for the phosphorylation of IKK -alpha/beta and subsequent transcriptional activation of the p65 subunit of NF-kappaB. Ablation of endogenous NRAGE by siRNA inhibited NF-kappaB pathway activation, while ablation of Tak1 and Tab1 by morpholino inhibited overexpression of NRAGE from activating NF-kappaB. Finally, cytokine profiling of an NRAGE over-expressing stable line revealed the expression of macrophage migration inhibitory factor. Modulation of NRAGE expression revealed novel roles in regulating NF-kappaB activity in the non-canonical bone morphogenic protein signaling pathway. The expression of macrophage migration inhibitory factor by bone morphogenic protein -4 reveals novel crosstalk between an immune cytokine and a developmental pathway.

  2. A role for NRAGE in NF-κB activation through the non-canonical BMP pathway

    Directory of Open Access Journals (Sweden)

    Karaczyn Aldona

    2010-01-01

    Full Text Available Abstract Background Previous studies have linked neurotrophin receptor-interacting MAGE protein to the bone morphogenic protein signaling pathway and its effect on p38 mediated apoptosis of neural progenitor cells via the XIAP-Tak1-Tab1 complex. Its effect on NF-κB has yet to be explored. Results Herein we report that NRAGE, via the same XIAP-Tak1-Tab1 complex, is required for the phosphorylation of IKK -α/β and subsequent transcriptional activation of the p65 subunit of NF-κB. Ablation of endogenous NRAGE by siRNA inhibited NF-κB pathway activation, while ablation of Tak1 and Tab1 by morpholino inhibited overexpression of NRAGE from activating NF-κB. Finally, cytokine profiling of an NRAGE over-expressing stable line revealed the expression of macrophage migration inhibitory factor. Conclusion Modulation of NRAGE expression revealed novel roles in regulating NF-κB activity in the non-canonical bone morphogenic protein signaling pathway. The expression of macrophage migration inhibitory factor by bone morphogenic protein -4 reveals novel crosstalk between an immune cytokine and a developmental pathway.

  3. Notch-induced Asb2 expression promotes protein ubiquitination by forming non-canonical E3 ligase complexes

    Institute of Scientific and Technical Information of China (English)

    Lei Nie; Ying Zhao; Wei Wu; Yuan-Zheng Yang; Hong-Cheng Wang; Xiao-Hong Sun

    2011-01-01

    Notch signaling controls multiple developmental processes, thus demanding versatile functions. We have previously shown that this may be partly achieved by accelerating ubiquitin-mediated degradation of important regulators of differentiation. However, the underlying mechanism was unknown. We now find that Notch signaling transcriptionally activates the gene encoding ankyrin-repeat SOCS box-containing protein 2(Asb2). Asb2 promotes the ubiquidnation of Notch targets such as E2A and Janus kinase(Jak)2, and a dominant-negative(DN)mutant of Asb2blocks Notch-induced degradation of these proteins. Asb2 likely binds Jak2 directly but associates with E2A through Skp2. We next provide evidence to suggest that Asb2 bridges the formation of non-canonical cullin-based complexes through interaction with not only ElonginB/C and Cullin(Cul)5, but also the F-box-containing protein, Skp2, which is known to associate with Skpl and Cull. Consistently, ablating the function of Cull or Cu15 using DN mutants or siRNAs protected both E2A and Jak2 from Asb2-mediated or Notch-induced degradation. By shifting monomeric E3ligase complexes to dimeric forms through activation of Asb2 transcription, Notch could effectively control the turnover of a variety of substrates and it exerts diverse effects on cell proliferation and differentiation.

  4. Enhancing community detection by local structural information

    CERN Document Server

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

    2016-01-01

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

  5. Combinatorics of locally optimal RNA secondary structures.

    Science.gov (United States)

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles).

  6. Non-canonical Cajal bodies form in the nucleus of late stage avian oocytes lacking functional nucleolus.

    Science.gov (United States)

    Khodyuchenko, Tatiana; Gaginskaya, Elena; Krasikova, Alla

    2012-07-01

    In the somatic cell nucleus, there are several universal domains such as nucleolus, SC35-domains, Cajal bodies (CBs) and histone locus bodies (HLBs). Among them, CBs were described more than 100 years ago; however, we still do not have a final understanding of their nature and biological significance. The giant nucleus of avian and amphibian growing oocytes represents an advantageous model for analysis of functions and biogenesis of various nuclear domains. Nevertheless, in large-sized avian oocytes that contain transcriptionally active lampbrush chromosomes, CB-like organelles have not been identified yet. Here we demonstrate that in the pigeon (Columba livia) oocyte nucleus, characterized by absence of any functional nucleoli, extrachromosomal spherical bodies contain TMG-capped spliceosomal snRNAs, core proteins of Sm snRNPs and the protein coilin typical for CBs, but not splicing factor SC35 nor the histone pre-mRNA 3'-end processing factor symplekin. The results establish that coilin-rich nuclear organelles in pigeon late-stage oocyte are not the equivalents of HLBs but belong to a group of CBs. At the same time, they do not contain the snoRNP/scaRNP protein fibrillarin involved in 2'-O-methylation of snoRNAs and snRNAs. Thus, the nucleus of late-stage pigeon oocytes houses CB-like organelles that have an unusual molecular composition and are implicated in the snRNP biogenesis pathway. These data demonstrate that snRNP-rich non-canonical CBs can form in the absence of nucleolus. We argue that pigeon oocytes represent a new promising model to investigate CB modular organization, functions and formation mechanism.

  7. Prospects of In vivo Incorporation of Non-canonical Amino Acids for the Chemical Diversification of Antimicrobial Peptides

    Science.gov (United States)

    Baumann, Tobias; Nickling, Jessica H.; Bartholomae, Maike; Buivydas, Andrius; Kuipers, Oscar P.; Budisa, Nediljko

    2017-01-01

    The incorporation of non-canonical amino acids (ncAA) is an elegant way for the chemical diversification of recombinantly produced antimicrobial peptides (AMPs). Residue- and site-specific installation methods in several bacterial production hosts hold great promise for the generation of new-to-nature AMPs, and can contribute to tackle the ongoing emergence of antibiotic resistance in pathogens. Especially from a pharmacological point of view, desirable improvements span pH and protease resistance, solubility, oral availability and circulation half-life. Although the primary focus of this report is on ribosomally synthesized and post-translationally modified peptides (RiPPs), we have included selected cases of peptides produced by solid phase peptide synthesis to comparatively show the potential and impact of ncAA introduction. Generally speaking, the introduction of ncAAs in recombinant AMPs delivers novel levels of chemical diversification. Cotranslationally incorporated, they can take part in AMP biogenesis either through direction interaction with elements of the post-translational modification (PTM) machinery or as untargeted sites with unique physicochemical properties and chemical handles for further modification. Together with genetic libraries, genome mining and processing by PTM machineries, ncAAs present not a mere addition to this process, but a highly diverse pool of building blocks to significantly broaden the chemical space of this valuable class of molecules. This perspective summarizes new developments of ncAA containing peptides. Challenges to be resolved in order to reach large-scale pharmaceutical production of these promising compounds and prospects for future developments are discussed. PMID:28210246

  8. Locally homogeneous structures on Hopf surfaces

    CERN Document Server

    McKay, Benjamin

    2009-01-01

    We study holomorphic locally homogeneous geometric structures modelled on line bundles over the projective line. We classify these structures on primary Hopf surfaces. We write out the developing map and holonomy morphism of each of these structures explicitly on each primary Hopf surface.

  9. MiRNA-335 suppresses neuroblastoma cell invasiveness by direct targeting of multiple genes from the non-canonical TGF-β signalling pathway.

    Science.gov (United States)

    Lynch, Jennifer; Fay, Joanna; Meehan, Maria; Bryan, Kenneth; Watters, Karen M; Murphy, Derek M; Stallings, Raymond L

    2012-05-01

    Transforming growth factor-β (TGF-β) signaling regulates many diverse cellular activities through both canonical (SMAD-dependent) and non-canonical branches, which includes the mitogen-activated protein kinase (MAPK), Rho-like guanosine triphosphatase and phosphatidylinositol-3-kinase/AKT pathways. Here, we demonstrate that miR-335 directly targets and downregulates genes in the TGF-β non-canonical pathways, including the Rho-associated coiled-coil containing protein (ROCK1) and MAPK1, resulting in reduced phosphorylation of downstream pathway members. Specifically, inhibition of ROCK1 and MAPK1 reduces phosphorylation levels of the motor protein myosin light chain (MLC) leading to a significant inhibition of the invasive and migratory potential of neuroblastoma cells. Additionally, miR-335 targets the leucine-rich alpha-2-glycoprotein 1 (LRG1) messenger RNA, which similarly results in a significant reduction in the phosphorylation status of MLC and a decrease in neuroblastoma cell migration and invasion. Thus, we link LRG1 to the migratory machinery of the cell, altering its activity presumably by exerting its effect within the non-canonical TGF-β pathway. Moreover, we demonstrate that the MYCN transcription factor, whose coding sequence is highly amplified in a particularly clinically aggressive neuroblastoma tumor subtype, directly binds to a region immediately upstream of the miR-335 transcriptional start site, resulting in transcriptional repression. We conclude that MYCN contributes to neuroblastoma cell migration and invasion, by directly downregulating miR-335, resulting in the upregulation of the TGF-β signaling pathway members ROCK1, MAPK1 and putative member LRG1, which positively promote this process. Our results provide novel insight into the direct regulation of TGF-β non-canonical signaling by miR-335, which in turn is downregulated by MYCN.

  10. Pro-apoptotic Chemotherapeutic Drugs Induce Non-canonical Processing and Release of IL-1β via Caspase-8 in Dendritic Cells#

    OpenAIRE

    Antonopoulos, Christina; El Sanadi, Caroline; Kaiser, William J.; Mocarski, Edward S.; Dubyak, George R.

    2013-01-01

    The identification of non-canonical (caspase-1 independent) pathways for IL-1β production has unveiled an intricate interplay between inflammatory and death-inducing signaling platforms. We found a heretofore unappreciated role for caspase-8 as a major pathway for IL-1β processing and release in murine bone marrow-derived dendritic cells (BMDC) co-stimulated with TLR4 agonists and pro-apoptotic chemotherapeutic agents such as doxorubicin (Dox) or staurosporine (STS). The ability of Dox to sti...

  11. Combinatorics of locally optimal RNA secondary structures

    CERN Document Server

    Clote, Peter

    2011-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 \\cdot n^{-3/2} \\cdot 2.618034^n$. To provide a better understanding of the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are {\\em locally optimal}, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the {\\em saturated} structures, for which we have previously shown that asymptotically, there are $1.07427\\cdot n^{-3/2} \\cdot 2.35467^n$ many saturated structures for a sequence of length $n$. In this paper, we consider the {\\em base stacking energy model}, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, ...

  12. Introduction: Dissipative localized structures in extended systems

    Science.gov (United States)

    Tlidi, Mustapha; Taki, Majid; Kolokolnikov, Theodore

    2007-09-01

    Localized structures belong to the class of dissipative structures found far from equilibrium. Contributions from the most representative groups working on a various fields of natural science such as biology, chemistry, plant ecology, mathematics, optics, and laser physics are presented. The aim of this issue is to gather specialists from these fields towards a cross-fertilization among these active areas of research and thereby to present an overview of the state of art in the formation and the characterization of dissipative localized structures. Nonlinear optics and laser physics have an important part in this issue because of potential applications in information technology. In particular, localized structures could be used as "bits" for parallel information storage and processing.

  13. Polarization properties of localized structures in VCSELs

    Science.gov (United States)

    Averlant, Etienne; Tlidi, Mustapha; Ackemann, Thorsten; Thienpont, Hugo; Panajotov, Krassimir

    2016-04-01

    Broad area Vertical-Cavity Surface-Emitting Lasers (VCSELs) have peculiar polarization properties which are a field of study by itself.1-3 These properties have already been used for localized structure generation, in a simple configuration, where only one polarization component was used.4 Here, we present new experimental and theoretical results on the complex polarization behavior of localized structures generated in an optically-injected broad area VCSEL. A linear stability analysis of the spin-flip VCSEL model is performed for the case of broad area devices, in a restrained and experimentally relevant parameter set. Numerical simulations are performed, in one and two dimensions. They reveal existence of vector localized structures. These structures have a complex polarization state, which is not simply a linear polarization following the one of the optical injection. Experimental results confirm theoretical predictions. Applications of this work can lead to the encoding of small color images in the polarization state of an ensemble of localized structures at the surface of a broad area VCSEL.

  14. Non-canonical CRL4A/4B(CDT2 interacts with RAD18 to modulate post replication repair and cell survival.

    Directory of Open Access Journals (Sweden)

    Sarah Sertic

    Full Text Available The Cullin-4(CDT2 E3 ubiquitin ligase plays an essential role in DNA replication origin licensing directing degradation of several licensing factors at the G1/S transition in order to prevent DNA re-replication. Recently a RAD18-independent role of Cullin-4(CDT2 in PCNA monoubiquitylation has been proposed. In an effort to better understand the function of Cullin-4(CDT2 E3 ubiquitin ligase in mammalian Post-Replication Repair during an unperturbed S-phase, we show that down-regulation of Cullin-4(CDT2 leads to two distinguishable independent phenotypes in human cells that unveil at least two independent roles of Cullin-4(CDT2 in S-phase. Apart from the re-replication preventing activity, we identified a non-canonical Cullin-4(CDT2 complex, containing both CUL4A and CUL4B, associated to the COP9 signalosome, that controls a RAD18-dependent damage avoidance pathway essential during an unperturbed S-phase. Indeed, we show that the non-canonical Cullin-4A/4B(CDT2 complex binds to RAD18 and it is required to modulate RAD18 protein levels onto chromatin and the consequent dynamics of PCNA monoubiquitylation during a normal S-phase. This function prevents replication stress, ATR hyper-signaling and, ultimately, apoptosis. A very similar PRR regulatory mechanism has been recently described for Spartan. Our findings uncover a finely regulated process in mammalian cells involving Post-Replication Repair factors, COP9 signalosome and a non-canonical Cullin4-based E3 ligase which is essential to tolerate spontaneous damage and for cell survival during physiological DNA replication.

  15. Non-canonical peroxisome targeting signals: identification of novel PTS1 tripeptides and characterization of enhancer elements by computational permutation analysis

    Directory of Open Access Journals (Sweden)

    Chowdhary Gopal

    2012-08-01

    Full Text Available Abstract Background High-accuracy prediction tools are essential in the post-genomic era to define organellar proteomes in their full complexity. We recently applied a discriminative machine learning approach to predict plant proteins carrying peroxisome targeting signals (PTS type 1 from genome sequences. For Arabidopsis thaliana 392 gene models were predicted to be peroxisome-targeted. The predictions were extensively tested in vivo, resulting in a high experimental verification rate of Arabidopsis proteins previously not known to be peroxisomal. Results In this study, we experimentally validated the predictions in greater depth by focusing on the most challenging Arabidopsis proteins with unknown non-canonical PTS1 tripeptides and prediction scores close to the threshold. By in vivo subcellular targeting analysis, three novel PTS1 tripeptides (QRL>, SQM>, and SDL> and two novel tripeptide residues (Q at position −3 and D at pos. -2 were identified. To understand why, among many Arabidopsis proteins carrying the same C-terminal tripeptides, these proteins were specifically predicted as peroxisomal, the residues upstream of the PTS1 tripeptide were computationally permuted and the changes in prediction scores were analyzed. The newly identified Arabidopsis proteins were found to contain four to five amino acid residues of high predicted targeting enhancing properties at position −4 to −12 in front of the non-canonical PTS1 tripeptide. The identity of the predicted targeting enhancing residues was unexpectedly diverse, comprising besides basic residues also proline, hydroxylated (Ser, Thr, hydrophobic (Ala, Val, and even acidic residues. Conclusions Our computational and experimental analyses demonstrate that the plant PTS1 tripeptide motif is more diverse than previously thought, including an increasing number of non-canonical sequences and allowed residues. Specific targeting enhancing elements can be predicted for particular sequences

  16. Local atomic structure in cubic stabilized zirconia

    Energy Technology Data Exchange (ETDEWEB)

    Villella, P.; Conradson, S. D.; Espinosa-Faller, F. J.; Foltyn, S. R.; Sickafus, K. E.; Valdez, J. A.; Degueldre, C. A.

    2001-09-01

    X-ray-absorption fine structure measurements have been used to elucidate the local atomic structure of quaternary Zr, Y, Er, Ce/U cubic stabilized zirconia. These compounds display more complicated local environments than those reported for simpler binary systems. While the shortest cation-O distances are similar to those found in the binary cubic stabilized compounds, responding to the different sizes of the cations, we have identified large distortions in the first-shell oxygen distribution involving long, 2.8--3.2 {angstrom} cation-O distances that are similar to those found in the amorphous phase of zirconium. The cation-cation distributions are also found to be quite complicated (non-Gaussian) and element specific. The U-near neighbor distances are expanded relative to the Ce ions for which it substitutes, consistent with the larger size of the actinide, and the U-cation distribution is also more complicated. In terms of the effects of this substitution on the other cation sites, the local environment around Y is altered while the Zr and Er local environments remain unchanged. These results point out the importance of collective and correlated interactions between the different pairs of cations and the host lattice that are mediated by the local strain fields generated by the different cations. The presence of pair-specific couplings has not been commonly included in previous analyses and may have implications for the stabilization mechanisms of cubic zirconia.

  17. Automatic Tool for Local Assembly Structures

    Energy Technology Data Exchange (ETDEWEB)

    2016-10-11

    Whole community shotgun sequencing of total DNA (i.e. metagenomics) and total RNA (i.e. metatranscriptomics) has provided a wealth of information in the microbial community structure, predicted functions, metabolic networks, and is even able to reconstruct complete genomes directly. Here we present ATLAS (Automatic Tool for Local Assembly Structures) a comprehensive pipeline for assembly, annotation, genomic binning of metagenomic and metatranscriptomic data with an integrated framework for Multi-Omics. This will provide an open source tool for the Multi-Omic community at large.

  18. Canonical Wnt signaling protects hippocampal neurons from Aβ oligomers: role of non-canonical Wnt-5a/Ca2+ in mitochondrial dynamics

    Science.gov (United States)

    Silva-Alvarez, Carmen; Arrázola, Macarena S.; Godoy, Juan A.; Ordenes, Daniela; Inestrosa, Nibaldo C.

    2013-01-01

    Alzheimer's disease (AD) is the most common type of age-related dementia. The disease is characterized by a progressive loss of cognitive abilities, severe neurodegeneration, synaptic loss and mitochondrial dysfunction. The Wnt signaling pathway participates in the development of the central nervous system and growing evidence indicates that Wnts also regulate the function of the adult nervous system. We report here, that indirect activation of canonical Wnt/β-catenin signaling using Bromoindirubin-30-Oxime (6-BIO), an inhibitor of glycogen synthase kinase-3β, protects hippocampal neurons from amyloid-β (Aβ) oligomers with the concomitant blockade of neuronal apoptosis. More importantly, activation with Wnt-5a, a non-canonical Wnt ligand, results in the modulation of mitochondrial dynamics, preventing the changes induced by Aβ oligomers (Aβo) in mitochondrial fission-fusion dynamics and modulates Bcl-2 increases induced by oligomers. The canonical Wnt-3a ligand neither the secreted Frizzled-Related Protein (sFRP), a Wnt scavenger, did not prevent these effects. In contrast, some of the Aβ oligomer effects were blocked by Ryanodine. We conclude that canonical Wnt/β-catenin signaling controls neuronal survival, and that non-canonical Wnt/Ca2+signaling modulates mitochondrial dysfunction. Since mitochondrial dysfunction is present in neurodegenerative diseases, the therapeutic possibilities of the activation of Wnt signaling are evident. PMID:23805073

  19. Muscle fiber type specific activation of the slow myosin heavy chain 2 promoter by a non-canonical E-box.

    Science.gov (United States)

    Weimer, Kristina; DiMario, Joseph X

    2016-01-22

    Different mechanisms control skeletal muscle fiber type gene expression at specific times in vertebrate development. Embryonic myogenesis leading to formation of primary muscle fibers in avian species is largely directed by myoblast cell commitment to the formation of diverse fiber types. In contrast, development of different secondary fiber types during fetal myogenesis is partly determined by neural influences. In both primary and secondary chicken muscle fibers, differential expression of the slow myosin heavy chain 2 (MyHC2) gene distinguishes fast from fast/slow muscle fibers. This study focused on the transcriptional regulation of the slow MyHC2 gene in primary myotubes formed from distinct fast/slow and fast myogenic cell lineages. Promoter deletion analyses identified a discrete 86 bp promoter segment that conferred fiber type, lineage-specific gene expression in fast/slow versus fast myoblast derived primary myotubes. Sequence analysis and promoter activity assays determined that this segment contains two functional cis-regulatory elements. One element is a non-canonical E-box, and electromobility shift assays demonstrated that both cis-elements interacted with the E-protein, E47. The results indicate that primary muscle fiber type specific expression of the slow MyHC2 gene is controlled by a novel mechanism involving a transcriptional complex that includes E47 at a non-canonical E-box.

  20. Simulating Structure Formation of the Local Universe

    CERN Document Server

    Heß, Steffen; Gottloeber, Stefan

    2013-01-01

    In this work we present cosmological N-body simulations of the Local Universe with initial conditions constrained by the Two-Micron Redshift Survey (2MRS) within a cubic volume of 180 Mpc/h side-length centred at the Local Group. We use a self-consistent Bayesian based approach to explore the joint parameter space of primordial density fluctuations and peculiar velocity fields, which are compatible with the 2MRS galaxy distribution after cosmic evolution. This method (the KIGEN-code) includes the novel ALPT (Augmented Lagrangian Perturbation Theory) structure formation model which combines second order LPT (2LPT) on large scales with the spherical collapse model on small scales. Furthermore we describe coherent flows with 2LPT and include a dispersion term to model fingers-of-god (fogs) arising from virialised structures. These implementations are crucial to avoid artificial filamentary structures, which appear when using a structure formation model with 2LPT and data with compressed fogs. We assume LCDM cosm...

  1. The Structure of the Local Hot Bubble

    Science.gov (United States)

    Liu, W.; Chiao, M.; Collier, M. R.; Cravens, T.; Galeazzi, M.; Koutroumpa, D.; Kuntz, K. D.; Lallement, R.; Lepri, S. T.; McCammon, Dan; hide

    2016-01-01

    Diffuse X-rays from the Local Galaxy (DXL) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the Diffuse X-ray Background and study the properties of the Local Hot Bubble (LHB). Based on the results from the DXL mission, we quantified and removed the contribution of SWCX to the diffuse X-ray background measured by the ROSAT All Sky Survey. The cleaned maps were used to investigate the physical properties of the LHB. Assuming thermal ionization equilibrium, we measured a highly uniform temperature distributed around kT = 0.097 keV +/- 0.013 keV (FWHM) +/- 0.006 keV(systematic). We also generated a thermal emission measure map and used it to characterize the three-dimensional (3D) structure of the LHB, which we found to be in good agreement with the structure of the local cavity measured from dust and gas.

  2. The Structure of the Local Hot Bubble

    CERN Document Server

    Liu, W; Collier, M R; Cravens, T; Galeazzi, M; Koutroumpa, D; Kuntz, K D; Lallement, R; Lepri, S T; McCammon, D; Morgan, K; Porter, F S; Snowden, S L; Thomas, N E; Uprety, Y; Ursino, E; Walsh, B M

    2016-01-01

    DXL (Diffuse X-rays from the Local Galaxy) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the Diffuse X-ray Background and study the properties of the Local Hot Bubble (LHB). Based on the results from the DXL mission, we quantified and removed the contribution of SWCX to the diffuse X-ray background measured by the ROSAT All Sky Survey (RASS). The "cleaned" maps were used to investigate the physical properties of the LHB. Assuming thermal ionization equilibrium, we measured a highly uniform temperature distributed around kT=0.097 keV+/-0.013 keV (FWHM)+/-0.006 keV (systematic). We also generated a thermal emission measure map and used it to characterize the three-dimensional (3D) structure of the LHB which we found to be in good agreement with the structure of the local cavity measured from dust and gas.

  3. The Structure of the Local Hot Bubble

    Science.gov (United States)

    Liu, W.; Chiao, M.; Collier, M. R.; Cravens, T.; Galeazzi, M.; Koutroumpa, D.; Kuntz, K. D.; Lallement, R.; Lepri, S. T.; McCammon, D.; Morgan, K.; Porter, F. S.; Snowden, S. L.; Thomas, N. E.; Uprety, Y.; Ursino, E.; Walsh, B. M.

    2017-01-01

    Diffuse X-rays from the Local Galaxy (DXL) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the Diffuse X-ray Background and study the properties of the Local Hot Bubble (LHB). Based on the results from the DXL mission, we quantified and removed the contribution of SWCX to the diffuse X-ray background measured by the ROSAT All Sky Survey. The “cleaned” maps were used to investigate the physical properties of the LHB. Assuming thermal ionization equilibrium, we measured a highly uniform temperature distributed around kT = 0.097 keV ± 0.013 keV (FWHM) ± 0.006 keV (systematic). We also generated a thermal emission measure map and used it to characterize the three-dimensional (3D) structure of the LHB, which we found to be in good agreement with the structure of the local cavity measured from dust and gas.

  4. The Meckel-Gruber syndrome protein TMEM67 controls basal body positioning and epithelial branching morphogenesis in mice via the non-canonical Wnt pathway.

    Science.gov (United States)

    Abdelhamed, Zakia A; Natarajan, Subaashini; Wheway, Gabrielle; Inglehearn, Christopher F; Toomes, Carmel; Johnson, Colin A; Jagger, Daniel J

    2015-06-01

    Ciliopathies are a group of developmental disorders that manifest with multi-organ anomalies. Mutations in TMEM67 (MKS3) cause a range of human ciliopathies, including Meckel-Gruber and Joubert syndromes. In this study we describe multi-organ developmental abnormalities in the Tmem67(tm1Dgen/H1) knockout mouse that closely resemble those seen in Wnt5a and Ror2 knockout mice. These include pulmonary hypoplasia, ventricular septal defects, shortening of the body longitudinal axis, limb abnormalities, and cochlear hair cell stereociliary bundle orientation and basal body/kinocilium positioning defects. The basal body/kinocilium complex was often uncoupled from the hair bundle, suggesting aberrant basal body migration, although planar cell polarity and apical planar asymmetry in the organ of Corti were normal. TMEM67 (meckelin) is essential for phosphorylation of the non-canonical Wnt receptor ROR2 (receptor-tyrosine-kinase-like orphan receptor 2) upon stimulation with Wnt5a-conditioned medium. ROR2 also colocalises and interacts with TMEM67 at the ciliary transition zone. Additionally, the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay. Cultured lungs of Tmem67 mutant mice failed to respond to stimulation of epithelial branching morphogenesis by Wnt5a. Wnt5a also inhibited both the Shh and canonical Wnt/β-catenin signalling pathways in wild-type embryonic lung. Pulmonary hypoplasia phenotypes, including loss of correct epithelial branching morphogenesis and cell polarity, were rescued by stimulating the non-canonical Wnt pathway downstream of the Wnt5a-TMEM67-ROR2 axis by activating RhoA. We propose that TMEM67 is a receptor that has a main role in non-canonical Wnt signalling, mediated by Wnt5a and ROR2, and normally represses Shh signalling. Downstream therapeutic targeting of the Wnt5a-TMEM67-ROR2 axis might, therefore, reduce or prevent pulmonary hypoplasia in ciliopathies and other congenital conditions.

  5. The Meckel-Gruber syndrome protein TMEM67 controls basal body positioning and epithelial branching morphogenesis in mice via the non-canonical Wnt pathway

    Directory of Open Access Journals (Sweden)

    Zakia A. Abdelhamed

    2015-06-01

    Full Text Available Ciliopathies are a group of developmental disorders that manifest with multi-organ anomalies. Mutations in TMEM67 (MKS3 cause a range of human ciliopathies, including Meckel-Gruber and Joubert syndromes. In this study we describe multi-organ developmental abnormalities in the Tmem67tm1Dgen/H1 knockout mouse that closely resemble those seen in Wnt5a and Ror2 knockout mice. These include pulmonary hypoplasia, ventricular septal defects, shortening of the body longitudinal axis, limb abnormalities, and cochlear hair cell stereociliary bundle orientation and basal body/kinocilium positioning defects. The basal body/kinocilium complex was often uncoupled from the hair bundle, suggesting aberrant basal body migration, although planar cell polarity and apical planar asymmetry in the organ of Corti were normal. TMEM67 (meckelin is essential for phosphorylation of the non-canonical Wnt receptor ROR2 (receptor-tyrosine-kinase-like orphan receptor 2 upon stimulation with Wnt5a-conditioned medium. ROR2 also colocalises and interacts with TMEM67 at the ciliary transition zone. Additionally, the extracellular N-terminal domain of TMEM67 preferentially binds to Wnt5a in an in vitro binding assay. Cultured lungs of Tmem67 mutant mice failed to respond to stimulation of epithelial branching morphogenesis by Wnt5a. Wnt5a also inhibited both the Shh and canonical Wnt/β-catenin signalling pathways in wild-type embryonic lung. Pulmonary hypoplasia phenotypes, including loss of correct epithelial branching morphogenesis and cell polarity, were rescued by stimulating the non-canonical Wnt pathway downstream of the Wnt5a-TMEM67-ROR2 axis by activating RhoA. We propose that TMEM67 is a receptor that has a main role in non-canonical Wnt signalling, mediated by Wnt5a and ROR2, and normally represses Shh signalling. Downstream therapeutic targeting of the Wnt5a-TMEM67-ROR2 axis might, therefore, reduce or prevent pulmonary hypoplasia in ciliopathies and other congenital

  6. Identification of p62/SQSTM1 as a component of non-canonical Wnt VANGL2-JNK signalling in breast cancer.

    Science.gov (United States)

    Puvirajesinghe, Tania M; Bertucci, François; Jain, Ashish; Scerbo, Pierluigi; Belotti, Edwige; Audebert, Stéphane; Sebbagh, Michael; Lopez, Marc; Brech, Andreas; Finetti, Pascal; Charafe-Jauffret, Emmanuelle; Chaffanet, Max; Castellano, Rémy; Restouin, Audrey; Marchetto, Sylvie; Collette, Yves; Gonçalvès, Anthony; Macara, Ian; Birnbaum, Daniel; Kodjabachian, Laurent; Johansen, Terje; Borg, Jean-Paul

    2016-01-12

    The non-canonical Wnt/planar cell polarity (Wnt/PCP) pathway plays a crucial role in embryonic development. Recent work has linked defects of this pathway to breast cancer aggressiveness and proposed Wnt/PCP signalling as a therapeutic target. Here we show that the archetypal Wnt/PCP protein VANGL2 is overexpressed in basal breast cancers, associated with poor prognosis and implicated in tumour growth. We identify the scaffold p62/SQSTM1 protein as a novel VANGL2-binding partner and show its key role in an evolutionarily conserved VANGL2-p62/SQSTM1-JNK pathway. This proliferative signalling cascade is upregulated in breast cancer patients with shorter survival and can be inactivated in patient-derived xenograft cells by inhibition of the JNK pathway or by disruption of the VANGL2-p62/SQSTM1 interaction. VANGL2-JNK signalling is thus a potential target for breast cancer therapy.

  7. A phenotypic screen in zebrafish identifies a novel small-molecule inducer of ectopic tail formation suggestive of alterations in non-canonical Wnt/PCP signaling.

    Directory of Open Access Journals (Sweden)

    Evelien Gebruers

    Full Text Available Zebrafish have recently emerged as an attractive model for the in vivo bioassay-guided isolation and characterization of pharmacologically active small molecules of natural origin. We carried out a zebrafish-based phenotypic screen of over 3000 plant-derived secondary metabolite extracts with the goal of identifying novel small-molecule modulators of the BMP and Wnt signaling pathways. One of the bioactive plant extracts identified in this screen - Jasminum gilgianum, an Oleaceae species native to Papua New Guinea - induced ectopic tails during zebrafish embryonic development. As ectopic tail formation occurs when BMP or non-canonical Wnt signaling is inhibited during the tail protrusion process, we suspected a constituent of this extract to act as a modulator of these pathways. A bioassay-guided isolation was carried out on the basis of this zebrafish phenotype, identifying para-coumaric acid methyl ester (pCAME as the active compound. We then performed an in-depth phenotypic analysis of pCAME-treated zebrafish embryos, including a tissue-specific marker analysis of the secondary tails. We found pCAME to synergize with the BMP-inhibitors dorsomorphin and LDN-193189 in inducing ectopic tails, and causing convergence-extension defects in compound-treated embryos. These results indicate that pCAME may interfere with non-canonical Wnt signaling. Inhibition of Jnk, a downstream target of Wnt/PCP signaling (via morpholino antisense knockdown and pharmacological inhibition with the kinase inhibitor SP600125 phenocopied pCAME-treated embryos. However, immunoblotting experiments revealed pCAME to not directly inhibit Jnk-mediated phosphorylation of c-Jun, suggesting additional targets of SP600125, and/or other pathways, as possibly being involved in the ectopic tail formation activity of pCAME. Further investigation of pCAME's mechanism of action will help determine this compound's pharmacological utility.

  8. Targeting non-canonical nuclear factor-κB signalling attenuates neovascularization in a novel 3D model of rheumatoid arthritis synovial angiogenesis.

    Science.gov (United States)

    Maracle, Chrissta X; Kucharzewska, Paulina; Helder, Boy; van der Horst, Corine; Correa de Sampaio, Pedro; Noort, Ae-Ri; van Zoest, Katinka; Griffioen, Arjan W; Olsson, Henric; Tas, Sander W

    2017-02-01

    Angiogenesis is crucial in RA disease progression. Lymphotoxin β receptor (LTβR)-induced activation of the non-canonical nuclear factor-κB (NF-κB) pathway via NF-κB-inducing kinase (NIK) has been implicated in this process. Consequently, inhibition of this pathway may hold therapeutic potential in RA. We describe a novel three-dimensional (3D) model of synovial angiogenesis incorporating endothelial cells (ECs), RA fibroblast-like synoviocytes (RAFLSs) and RA synovial fluid (RASF) to further investigate the contributions of NF-κB in this process. Spheroids consisting of RAFLSs and ECs were stimulated with RASF, the LTβR ligands LTβ and LIGHT, or growth factor bFGF and VEGF, followed by quantification of EC sprouting using confocal microscopy and digital image analysis. Next, the effects of anginex, NIK-targeting siRNA (siNIK), LTβR-Ig fusion protein (baminercept) and a novel pharmacological NIK inhibitor were investigated. RASF significantly promoted sprout formation, which was blocked by the established angiogenesis inhibitor anginex (P factors (P model of synovial angiogenesis incorporating RAFLSs, ECs and RASF that mimics the in vivo situation. Using this system, we demonstrate that non-canonical NF-κB signalling promotes neovascularization and show that this model is useful for dissecting relative contributions of signalling pathways in specific cell types to angiogenic responses and for testing pharmacological inhibitors of angiogenesis. © The Author 2016. Published by Oxford University Press on behalf of the British Society for Rheumatology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Evidence of non-canonical NOTCH signaling: Delta-like 1 homolog (DLK1) directly interacts with the NOTCH1 receptor in mammals.

    Science.gov (United States)

    Traustadóttir, Gunnhildur Ásta; Jensen, Charlotte H; Thomassen, Mads; Beck, Hans Christian; Mortensen, Sussi B; Laborda, Jorge; Baladrón, Victoriano; Sheikh, Søren P; Andersen, Ditte C

    2016-04-01

    Canonical NOTCH signaling, known to be essential for tissue development, requires the Delta-Serrate-LAG2 (DSL) domain for NOTCH to interact with its ligand. However, despite lacking DSL, Delta-like 1 homolog (DLK1), a protein that plays a significant role in mammalian development, has been suggested to interact with NOTCH1 and act as an antagonist. This non-canonical interaction is, however controversial, and evidence for a direct interaction, still lacking in mammals. In this study, we elucidated the putative DLK1-NOTCH1 interaction in a mammalian context. Taking a global approach and using Dlk1(+/+) and Dlk1(-/-) mouse tissues at E16.5, we demonstrated that several NOTCH signaling pathways indeed are affected by DLK1 during tissue development, and this was supported by a lower activation of NOTCH1 protein in Dlk1(+/+) embryos. Likewise, but using a distinct Dlk1-manipulated (siRNA) setup in a mammalian cell line, NOTCH signaling was substantially inhibited by DLK1. Using a mammalian two-hybrid system, we firmly established that the effect of DLK1 on NOTCH signaling was due to a direct interaction between DLK1 and NOTCH1. By careful dissection of this mechanism, we found this interaction to occur between EGF domains 5 and 6 of DLK1 and EGF domains 10-15 of NOTCH1. Thus, our data provide the first evidence for a direct interaction between DLK1 and NOTCH1 in mammals, and substantiate that non-canonical NOTCH ligands exist, adding to the complexity of NOTCH signaling.

  10. Chlamydia trachomatis protein CT009 is a structural and functional homolog to the key morphogenesis component RodZ and interacts with division septal plane localized MreB

    Science.gov (United States)

    Kemege, Kyle E.; Hickey, John M.; Barta, Michael L.; Wickstrum, Jason; Balwalli, Namita; Lovell, Scott; Battaile, Kevin P.; Hefty, P. Scott

    2015-01-01

    Summary Cell division in Chlamydiae is poorly understood as apparent homologs to most conserved bacterial cell division proteins are lacking and presence of elongation (rod shape) associated proteins indicate non-canonical mechanisms may be employed. The rod-shape determining protein MreB has been proposed as playing a unique role in chlamydial cell division. In other organisms, MreB is part of an elongation complex that requires RodZ for proper function. A recent study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence similarity to RodZ. The studies herein expand on those observations through protein structure, mutagenesis, and cellular localization analyses. Structural analysis indicated that CT009 shares high level of structural similarity to RodZ, revealing the conserved orientation of two residues critical for MreB interaction. Substitutions eliminated MreB protein interaction and partial complementation provided by CT009 in RodZ deficient E. coli. Cellular localization analysis of CT009 showed uniform membrane staining in Chlamydia. This was in contrast to the localization of MreB, which was restricted to predicted septal planes. MreB localization to septal planes provides direct experimental observation for the role of MreB in cell division and supports the hypothesis that it serves as a functional replacement for FtsZ in Chlamydia. PMID:25382739

  11. Community detection using global and local structural information

    Indian Academy of Sciences (India)

    Hai-Long Yan; Ju Xiang; Xiao-Yu Zhang; Jun-Feng Fan; Fang Chane; Gen-Yi Fu; Er-Min Guo; Xin-Guang Hu; Ke Hu; Ru-Min Wang

    2013-01-01

    Community detection is of considerable importance for understanding both the structure and function of complex networks. In this paper, we introduced the general procedure of the community detection algorithms using global and local structural information, where the edge betweenness and the local similarity measures respectively based on local random walk dynamics and local cyclic structures were used. The algorithms were tested on artificial and real-world networks. The results clearly show that all the algorithms have excellent performance in the tests and the local similarity measure based on local random walk dynamics is superior to that based on local cyclic structures.

  12. NMR and the local structure of relaxors

    Directory of Open Access Journals (Sweden)

    Blinc R.

    2002-01-01

    Full Text Available The relaxor transition in cubic perovskite relaxors (PMN, PSN and PST and tungsten bronze relaxor (SBN has been studied by NMR. The observed spectra are composed of a narrow -1/2 « 1/2 central transition superimposed on a broad background due to satellite transitions. The chemical heterogeneity, responsible for relaxor properties, is reflected here in the structure of the central transition part. The latter is composed of two components, one due to ordered and the other due to disordered regions. Despite of the fact that the macroscopic symmetry does not change when relaxor transition occurs, a non-zero quadruple coupling constant determined from NMR clearly demonstrates the broken local symmetry.

  13. TNFα modulates Fibroblast Growth Factor Receptor 2 gene expression through the pRB/E2F1 pathway: identification of a non-canonical E2F binding motif.

    Directory of Open Access Journals (Sweden)

    Sirio D'Amici

    Full Text Available Interactions between epithelium and mesenchyme during wound healing are not fully understood, but Fibroblast Growth Factors (FGFs and their receptors FGFRs are recognized as key elements. FGFR2 gene encodes for two splicing transcript variants, FGFR2-IIIb or Keratinocyte Growth Factor Receptor (KGFR and FGFR2-IIIc, which differ for tissue localization and ligand specificity. Proinflammatory cytokines play an essential role in the regulation of epithelial-mesenchymal interactions, and have been indicated to stimulate FGFs production. Here we demonstrated that upregulation of FGFR2 mRNA and protein expression is induced by the proinflammatory cytokines Tumor Necrosis Factor-α, Interleukin-1β and Interleukin 2. Furthermore, we found that TNFα determines FGFR2 transcriptional induction through activation of pRb, mediated by Raf and/or p38 pathways, and subsequent release of the transcription factor E2F1. Experiments based on FGFR2 promoter serial deletions and site-directed mutagenesis allowed us to identify a minimal responsive element that retains the capacity to be activated by E2F1. Computational analysis indicated that this element is a non-canonical E2F responsive motif. Thus far, the molecular mechanisms of FGFR2 upregulation during wound healing or in pathological events are not known. Our data suggest that FGFR2 expression can be modulated by local recruitment of inflammatory cytokines. Furthermore, since alterations in FGFR2 expression have been linked to the pathogenesis of certain human cancers, these findings could also provide elements for diagnosis and potential targets for novel therapeutic approaches.

  14. Local Government Structure and Capacities in Europe

    NARCIS (Netherlands)

    Nemec, J.; Vries, M.S. de

    2015-01-01

    This article argues that the local government capacities and local government performance in Europe clearly rank this continent to the most developed world areas from the point of local democracy. The background factors explaining this situation have a multidimensional character and one can identify

  15. Local Government Structure and Capacities in Europe

    NARCIS (Netherlands)

    Nemec, J.; Vries, M.S. de

    2015-01-01

    This article argues that the local government capacities and local government performance in Europe clearly rank this continent to the most developed world areas from the point of local democracy. The background factors explaining this situation have a multidimensional character and one can identify

  16. Induction of CXC chemokines in human mesenchymal stemcells by stimulation with secreted frizzled-related proteinsthrough non-canonical Wnt signaling

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    AIM To investigate the effect of secreted frizzledrelatedproteins (sFRPs) on CXC chemokine expressionin human mesenchymal stem cells (hMSCs).METHODS: CXC chemokines such as CXCL5 andCXCL8 are induced in hMSCs during differentiation withosteogenic differentiation medium (OGM) and may beinvolved in angiogenic stimulation during bone repair.hMSCs were treated with conditioned medium (CM) fromL-cells expressing non-canonical Wnt5a protein, or withcontrol CM from wild type L-cells, or directly with sFRPsfor up to 10 d in culture. mRNA expression levels of bothCXCL5 and CXCL8 were quantitated by real-time reversetranscriptase-polymerase chain reaction and secretedprotein levels of these proteins determined by ELISA.Dose- (0-500 ng/mL) and time-response curves weregenerated for treatment with sFRP1. Signal transductionpathways were explored by western blot analysis withpan- or phosphorylation-specific antibodies, through useof specific pathway inhibitors, and through use of siRNAstargeting specific frizzled receptors (Fzd)-2 and 5 or the receptor tyrosine kinase-like orphan receptor-2 (RoR2)prior to treatment with sFRPs.RESULTS: CM from L-cells expressing Wnt5a, a noncanonicalWnt, stimulated an increase in CXCL5 mRNAexpression and protein secretion in comparison to controlL-cell CM. sFRP1, which should inhibit both canonicaland non-canonical Wnt signaling, surprisingly enhancedthe expression of CXCL5 at 7 and 10 d. Dickkopf1, aninhibitor of canonical Wnt signaling prevented the sFRPstimulatedinduction of CXCL5 and actually inhibitedbasal levels of CXCL5 expression at 7 but not at 10 d posttreatment. In addition, all four sFRPs isoforms inducedCXCL8 expression in a dose- and time-dependent mannerwith maximum expression at 7 d with treatment at 150ng/mL. The largest increases in CXCL5 expression wereseen from stimulation with sFRP1 or sFRP2. Analysis ofmitogen-activated protein kinase signaling pathwaysin the presence of OGM showed sFRP1

  17. Importance of Local Structural Variations on Recrystallization

    DEFF Research Database (Denmark)

    Juul Jensen, Dorte; Lin, Fengxiang; Zhang, Yubin

    2013-01-01

    Effects of local variations in the deformation microstructure on subsequent recrystallization are discussed and illustrated by three examples. The three examples consider local variations on different length scales and are: 1. Effects of local variations in the deformation microstructure on the f...... on the formation of protrusions on migrating boundaries. 2. Effects of an inhomogeneous spatial distribution of second phase particles on growth. 3. Effects of stored energy and orientation variations on recrystallization kinetics. © (2013) Trans Tech Publications, Switzerland....

  18. Local Government Structure and Capacities in Europe

    OpenAIRE

    Nemec, J.; Vries, M.S. de

    2015-01-01

    This article argues that the local government capacities and local government performance in Europe clearly rank this continent to the most developed world areas from the point of local democracy. The background factors explaining this situation have a multidimensional character and one can identify as core positive factors the relative economic wealth, high human development, the long historical tradition of the subsidiarity principle in most parts of Europe, and the regulatory function of t...

  19. In-frame amber stop codon replacement mutagenesis for the directed evolution of proteins containing non-canonical amino acids: identification of residues open to bio-orthogonal modification.

    Directory of Open Access Journals (Sweden)

    James A J Arpino

    Full Text Available Expanded genetic code approaches are a powerful means to add new and useful chemistry to proteins at defined residues positions. One such use is the introduction of non-biological reactive chemical handles for site-specific biocompatible orthogonal conjugation of proteins. Due to our currently limited information on the impact of non-canonical amino acids (nAAs on the protein structure-function relationship, rational protein engineering is a "hit and miss" approach to selecting suitable sites. Furthermore, dogma suggests surface exposed native residues should be the primary focus for introducing new conjugation chemistry. Here we describe a directed evolution approach to introduce and select for in-frame codon replacement to facilitate engineering proteins with nAAs. To demonstrate the approach, the commonly reprogrammed amber stop codon (TAG was randomly introduced in-frame in two different proteins: the bionanotechnologically important cyt b(562 and therapeutic protein KGF. The target protein is linked at the gene level to sfGFP via a TEV protease site. In absence of a nAA, an in-frame TAG will terminate translation resulting in a non-fluorescent cell phenotype. In the presence of a nAA, TAG will encode for nAA incorporation so instilling a green fluorescence phenotype on E. coli. The presence of endogenously expressed TEV proteases separates in vivo target protein from its fusion to sfGFP if expressed as a soluble fusion product. Using this approach, we incorporated an azide reactive handle and identified residue positions amenable to conjugation with a fluorescence dye via strain-promoted azide-alkyne cycloaddition (SPAAC. Interestingly, best positions for efficient conjugation via SPAAC were residues whose native side chain were buried through analysis of their determined 3D structures and thus may not have been chosen through rational protein engineering. Molecular modeling suggests these buried native residues could become partially

  20. Non-canonical PRC1.1 Targets Active Genes Independent of H3K27me3 and Is Essential for Leukemogenesis

    Directory of Open Access Journals (Sweden)

    Vincent van den Boom

    2016-01-01

    Full Text Available Polycomb proteins are classical regulators of stem cell self-renewal and cell lineage commitment and are frequently deregulated in cancer. Here, we find that the non-canonical PRC1.1 complex, as identified by mass-spectrometry-based proteomics, is critically important for human leukemic stem cells. Downmodulation of PRC1.1 complex members, like the DNA-binding subunit KDM2B, strongly reduces cell proliferation in vitro and delays or even abrogates leukemogenesis in vivo in humanized xenograft models. PRC1.1 components are significantly overexpressed in primary AML CD34+ cells. Besides a set of genes that is targeted by PRC1 and PRC2, ChIP-seq studies show that PRC1.1 also binds a distinct set of genes that are devoid of H3K27me3, suggesting a gene-regulatory role independent of PRC2. This set encompasses genes involved in metabolism, which have transcriptionally active chromatin profiles. These data indicate that PRC1.1 controls specific genes involved in unique cell biological processes required for leukemic cell viability.

  1. Identification of p62/SQSTM1 as a component of non-canonical Wnt VANGL2–JNK signalling in breast cancer

    Science.gov (United States)

    Puvirajesinghe, Tania M.; Bertucci, François; Jain, Ashish; Scerbo, Pierluigi; Belotti, Edwige; Audebert, Stéphane; Sebbagh, Michael; Lopez, Marc; Brech, Andreas; Finetti, Pascal; Charafe-Jauffret, Emmanuelle; Chaffanet, Max; Castellano, Rémy; Restouin, Audrey; Marchetto, Sylvie; Collette, Yves; Gonçalvès, Anthony; Macara, Ian; Birnbaum, Daniel; Kodjabachian, Laurent; Johansen, Terje; Borg, Jean-Paul

    2016-01-01

    The non-canonical Wnt/planar cell polarity (Wnt/PCP) pathway plays a crucial role in embryonic development. Recent work has linked defects of this pathway to breast cancer aggressiveness and proposed Wnt/PCP signalling as a therapeutic target. Here we show that the archetypal Wnt/PCP protein VANGL2 is overexpressed in basal breast cancers, associated with poor prognosis and implicated in tumour growth. We identify the scaffold p62/SQSTM1 protein as a novel VANGL2-binding partner and show its key role in an evolutionarily conserved VANGL2–p62/SQSTM1–JNK pathway. This proliferative signalling cascade is upregulated in breast cancer patients with shorter survival and can be inactivated in patient-derived xenograft cells by inhibition of the JNK pathway or by disruption of the VANGL2–p62/SQSTM1 interaction. VANGL2–JNK signalling is thus a potential target for breast cancer therapy. PMID:26754771

  2. An amino acid depleted cell-free protein synthesis system for the incorporation of non-canonical amino acid analogs into proteins.

    Science.gov (United States)

    Singh-Blom, Amrita; Hughes, Randall A; Ellington, Andrew D

    2014-05-20

    Residue-specific incorporation of non-canonical amino acids into proteins is usually performed in vivo using amino acid auxotrophic strains and replacing the natural amino acid with an unnatural amino acid analog. Herein, we present an efficient amino acid depleted cell-free protein synthesis system that can be used to study residue-specific replacement of a natural amino acid by an unnatural amino acid analog. This system combines a simple methodology and high protein expression titers with a high-efficiency analog substitution into a target protein. To demonstrate the productivity and efficacy of a cell-free synthesis system for residue-specific incorporation of unnatural amino acids in vitro, we use this system to show that 5-fluorotryptophan and 6-fluorotryptophan substituted streptavidin retain the ability to bind biotin despite protein-wide replacement of a natural amino acid for the amino acid analog. We envisage this amino acid depleted cell-free synthesis system being an economical and convenient format for the high-throughput screening of a myriad of amino acid analogs with a variety of protein targets for the study and functional characterization of proteins substituted with unnatural amino acids when compared to the currently employed in vivo methodologies.

  3. Regulation of natural competence by the orphan two-component system sensor kinase ChiS involves a non-canonical transmembrane regulator in Vibrio cholerae.

    Science.gov (United States)

    Yamamoto, Shouji; Mitobe, Jiro; Ishikawa, Takahiko; Wai, Sun Nyunt; Ohnishi, Makoto; Watanabe, Haruo; Izumiya, Hidemasa

    2014-01-01

    In Vibrio cholerae, 41 chitin-inducible genes, including the genes involved in natural competence for DNA uptake, are governed by the orphan two-component system (TCS) sensor kinase ChiS. However, the mechanism by which ChiS controls the expression of these genes is currently unknown. Here, we report the involvement of a novel transcription factor termed 'TfoS' in this process. TfoS is a transmembrane protein that contains a large periplasmic domain and a cytoplasmic AraC-type DNA-binding domain, but lacks TCS signature domains. Inactivation of tfoS abolished natural competence as well as transcription of the tfoR gene encoding a chitin-induced small RNA essential for competence gene expression. A TfoS fragment containing the DNA-binding domain specifically bound to and activated transcription from the tfoR promoter. Intracellular TfoS levels were unaffected by disruption of chiS and coexpression of TfoS and ChiS in Escherichia coli recovered transcription of the chromosomally integrated tfoR::lacZ gene, suggesting that TfoS is post-translationally modulated by ChiS during transcriptional activation; however, this regulation persisted when the canonical phosphorelay residues of ChiS were mutated. The results presented here suggest that ChiS operates a chitin-induced non-canonical signal transduction cascade through TfoS, leading to transcriptional activation of tfoR.

  4. PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A Site Usage

    Directory of Open Access Journals (Sweden)

    Hun-Way Hwang

    2016-04-01

    Full Text Available Accurate and precise annotation of 3′ UTRs is critical for understanding how mRNAs are regulated by microRNAs (miRNAs and RNA-binding proteins (RBPs. Here, we describe a method, poly(A binding protein-mediated mRNA 3′ end retrieval by crosslinking immunoprecipitation (PAPERCLIP, that shows high specificity for mRNA 3′ ends and compares favorably with existing 3′ end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A sites, the majority of which contain a downstream GUKKU motif. Furthermore, in the mouse brain, PAPERCLIP discovers extended 3′ UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts, including one in Atp2b2 that is evolutionarily conserved in humans and results in the gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo.

  5. Lithium promotes neural precursor cell proliferation: evidence for the involvement of the non-canonical GSK-3β-NF-AT signaling

    Directory of Open Access Journals (Sweden)

    Qu Zhaoxia

    2011-05-01

    Full Text Available Abstract Lithium, a drug that has long been used to treat bipolar disorder and some other human pathogenesis, has recently been shown to stimulate neural precursor growth. However, the involved mechanism is not clear. Here, we show that lithium induces proliferation but not survival of neural precursor cells. Mechanistic studies suggest that the effect of lithium mainly involved activation of the transcription factor NF-AT and specific induction of a subset of proliferation-related genes. While NF-AT inactivation by specific inhibition of its upstream activator calcineurin antagonized the effect of lithium on the proliferation of neural precursor cells, specific inhibition of the NF-AT inhibitor GSK-3β, similar to lithium treatment, promoted neural precursor cell proliferation. One important function of lithium appeared to increase inhibitory phosphorylation of GSK-3β, leading to GSK-3β suppression and subsequent NF-AT activation. Moreover, lithium-induced proliferation of neural precursor cells was independent of its role in inositol depletion. These findings not only provide mechanistic insights into the clinical effects of lithium, but also suggest an alternative therapeutic strategy for bipolar disorder and other neural diseases by targeting the non-canonical GSK-3β-NF-AT signaling.

  6. Towards a Viable Local Government Structure in Nigeria:

    African Journals Online (AJOL)

    M.P._Ezekiel & D.O_Oriakhogba

    local government structure under the Nigerian constitutional framework with a .... socialization and participation of the people of the locality in the governance of ... 22 R. M. Bird, and E. Slack, Urban Finance in Canada, John Wiley and Sons, ...

  7. Towards structural controllability of local-world networks

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Shiwen, E-mail: sunsw80@126.com [Tianjin Key Laboratory of Intelligence Computing and Novel Software Technology, Tianjin University of Technology, Tianjin 300384 (China); Key Laboratory of Computer Vision and System (Tianjin University of Technology), Ministry of Education, Tianjin 300384 (China); Ma, Yilin; Wu, Yafang; Wang, Li; Xia, Chengyi [Tianjin Key Laboratory of Intelligence Computing and Novel Software Technology, Tianjin University of Technology, Tianjin 300384 (China); Key Laboratory of Computer Vision and System (Tianjin University of Technology), Ministry of Education, Tianjin 300384 (China)

    2016-05-20

    Controlling complex networks is of vital importance in science and engineering. Meanwhile, local-world effect is an important ingredient which should be taken into consideration in the complete description of real-world complex systems. In this letter, structural controllability of a class of local-world networks is investigated. Through extensive numerical simulations, firstly, effects of local world size M and network size N on structural controllability are examined. For local-world networks with sparse topological configuration, compared to network size, local-world size can induce stronger influence on controllability, however, for dense networks, controllability is greatly affected by network size and local-world effect can be neglected. Secondly, relationships between controllability and topological properties are analyzed. Lastly, the robustness of local-world networks under targeted attacks regarding structural controllability is discussed. These results can help to deepen the understanding of structural complexity and connectivity patterns of complex systems. - Highlights: • Structural controllability of a class of local-world networks is investigated. • For sparse local-world networks, compared to network size, local-world size can bring stronger influence on controllability. • For dense networks, controllability is greatly affected by network size and the effect of local-world size can be neglected. • Structural controllability against targeted node attacks is discussed.

  8. The Local Product Theorem for bihamiltonian structures

    CERN Document Server

    Turiel, Francisco-Javier

    2011-01-01

    In this work one proves that, around each point of a dense open set (regular points), a real analytic or holomorphic bihamiltonian structure decomposes into a product of a Kronecker bihamiltonian structure and a symplectic one if a necessary condition on the characteristic polynomial of the symplectic factor holds. Moreover we give an example of bihamiltonian structure for showing that this result does not extend to the $C^\\infty$-category. Thus a classical problem on the geometric theory of bihamiltonian structures is solved at almost every point.

  9. IFNβ/TNFα synergism induces a non-canonical STAT2/IRF9-dependent pathway triggering a novel DUOX2 NADPH Oxidase-mediated airway antiviral response

    Institute of Scientific and Technical Information of China (English)

    Karin Fink; Lydie Martin; Esperance Mukawera; Stéfany Chartier; Xavier De Deken; Emmanuelle Brochiero; Fran(c)oise Miot

    2013-01-01

    Airway epithelial cells are key initial innate immune responders in the fight against respiratory viruses,primarily via the secretion of antiviral and proinflammatory cytokines that act in an autocrine/paracrine fashion to trigger the establishment of an antiviral state.It is currently thought that the early antiviral state in airway epithelial cells primarily relies on IFNβ secretion and the subsequent activation of the interferon-stimulated gene factor 3 (ISGF3) transcription factor complex,composed of STAT1,STAT2 and IRF9,which regulates the expression of a panoply of interferon-stimulated genes encoding proteins with antiviral activities.However,the specific pathways engaged by the synergistic action of different cytokines during viral infections,and the resulting physiological outcomes are still ill-defined.Here,we unveil a novel delayed antiviral response in the airways,which is initiated by the synergistic autocrine/paracrine action of IFNβ and TNFα,and signals through a non-canonical STAT2-and IRF9-dependent,but STAT1-independent cascade.This pathway ultimately leads to the late induction of the DUOX2 NADPH oxidase expression.Importantly,our study uncovers that the development of the antiviral state relies on DUOX2-dependent H2O2 production.Key antiviral pathways are often targeted by evasion strategies evolved by various pathogenic viruses.In this regard,the importance of the novel DUOX2-dependent antiviral pathway is further underlined by the observation that the human respiratory syncytial virus is able to subvert DUOX2 induction.

  10. Enhancing community detection by using local structural information

    Science.gov (United States)

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

    2016-03-01

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

  11. Wave localization in randomly disordered periodic layered piezoelectric structures

    Institute of Scientific and Technical Information of China (English)

    Fengming Li; Yuesheng Wang; Chao Hu; Wenhu Huang

    2006-01-01

    Considering the mechnoelectrical coupling,the localization of SH-waves in disordered periodic layered piezoelectric structures is studied.The waves propagating in directions normal and tangential to the layers are considered.The transfer matrices between two consecutive unit cells are obtained according to the continuity conditions.The expressions of localization factor and localization length in the disordered periodic structures are presented.For the disordered periodic piezoelectric structures,the numerical results of localization factor and localization length are presented and discussed.It can be seen from the results that the fequency passbands and stopbands appear for the ordered periodic structures and the wave localization phenomenon occurs in the disordered periodic ones,and the larger the coefficient of variation is,the greater the degree of wave localization is.The widths of stopbands in the ordered periodic structures are very narrow when the properties of the consecutive piezoelectric materials are similar and the intervals of stopbands become broader when a certain material parameter has large changes.For the wave propagating in the direction normal to the layers the localization length has less dependence on the frequency,but for the wave propagating in the direction tangential to the layers the localization length is strongly dependent on the frequency.

  12. Guanine quadruplex structures localize to heterochromatin

    NARCIS (Netherlands)

    R.F. Hoffmann; Y.M. Moshkin (Yuri); Mouton, S. (Stijn); Grzeschik, N.A. (Nicola A.); R.D. Kalicharan (Ruby); J. Kuipers (Jeroen); Wolters, A.H.G. (Anouk H.G.); Nishida, K. (Kazuki); A.V. Romashchenko; Postberg, J. (Jan); Lipps, H. (Hans); E. Berezikov (Eugene); O.C.M. Sibon (Ody); B.N.G. Giepmans (Ben); Lansdorp, P.M. (Peter M.)

    2016-01-01

    textabstractIncreasing amounts of data support a role for guanine quadruplex (G4) DNA and RNA structures in various cellular processes. We stained different organisms with monoclonal antibody 1H6 specific for G4 DNA. Strikingly, immuno-electron microscopy showed exquisite specificity for heterochrom

  13. Guanine quadruplex structures localize to heterochromatin

    NARCIS (Netherlands)

    Hoffmann, Roland F.; Moshkin, Yuri M.; Mouton, Stijn; Grzeschik, Nicola A.; Kalicharan, Ruby D.; Kuipers, Jeroen; Wolters, Anouk H. G.; Nishida, Kazuki; Romashchenko, Aleksander V.; Postberg, Jan; Lipps, Hans; Berezikov, Eugene; Sibon, Ody C. M.; Giepmans, Ben N. G.; Lansdorp, Peter M.

    2016-01-01

    Increasing amounts of data support a role for guanine quadruplex (G4) DNA and RNA structures in various cellular processes. We stained different organisms with monoclonal antibody 1H6 specific for G4 DNA. Strikingly, immuno-electron microscopy showed exquisite specificity for heterochromatin.

  14. Shaped input distributions for structural damage localization

    DEFF Research Database (Denmark)

    Ulriksen, Martin Dalgaard; Bernal, Dionisio; Damkilde, Lars

    2017-01-01

    Given a structure in a state with any type of perturbation, the steady-state vibrational response will be identical to that in the unperturbed state if the perturbation is rendered dormant and, of course, if the load distribution is the same in the two states. Guided by this principle, a damage l...

  15. Local structure of self-affine sets

    CERN Document Server

    Bandt, Christoph

    2011-01-01

    The structure of a self-similar set with open set condition does not change under magnification. For self-affine sets the situation is completely different. We consider planar self-affine Cantor sets E of the type studied by Bedford, McMullen, Gatzouras and Lalley, for which the projection onto the horizontal axis is an interval. We show that within small square neighborhoods of almost each point x in E, with respect to many product measures on address space, E is well approximated by product sets of an interval and a Cantor set. Even though E is totally disconnected, the limit sets have the product structure with interval fibres, reminiscent to the view of attractors of chaotic differentiable dynamical systems.

  16. Dynamics of localized structures in vector waves

    CERN Document Server

    Hernández-García, E; Colet, P; San Miguel, M; Hernandez-Garcia, Emilio; Hoyuelos, Miguel; Colet, Pere; Miguel, Maxi San

    1999-01-01

    Dynamical properties of topological defects in a twodimensional complex vector field are considered. These objects naturally arise in the study of polarized transverse light waves. Dynamics is modeled by a Vector Complex Ginzburg-Landau Equation with parameter values appropriate for linearly polarized laser emission. Creation and annihilation processes, and selforganization of defects in lattice structures, are described. We find "glassy" configurations dominated by vectorial defects and a melting process associated to topological-charge unbinding.

  17. Local Atomic Structure of Piperidyl Nd Dithiocarbamate

    Institute of Scientific and Technical Information of China (English)

    吴忠华; 李前树; 等

    1999-01-01

    The atomic structure of a novel rare earth complex consisting of Nd and the sulfur-containing ligand pipdtc (C5H10NCS2-) has been studied with extended x-ray absortpiton fine structure(EXAFS) and x-ray diffraction techniques.The complex of formula Nd(pipdtc)4N(CH3)4 crystallizaes in the monoclinic space group P21/n with the following lattice parameters,a=22.685(2),b=20.332(2),c=17.1270(10)A,β=100.570(10)°.Z=8,the calculated density is 1.47g/cm3,A new derivative method is used to remove the piost-edge absorption background including the multielectron excitation effect.The EXAFS results demonstrate that there are about eight S and four O atoms around Nd with the Nd-S bond length of 2.916A and the Nd-O bond length of 2.415A,respectively.This implies that the powder of this complex is not stable and is easy to oxidize in air.The possible change of structure before and after oxidation is discussed.

  18. A Novel Local Structure Descriptor for Color Image Retrieval

    Directory of Open Access Journals (Sweden)

    Zhiyong Zeng

    2016-02-01

    Full Text Available A novel local structure descriptor (LSD for color image retrieval is proposed in this paper. Local structures are defined based on a similarity of edge orientation, and LSD is constructed using the underlying colors in local structures with similar edge direction. LSD can effectively combine color, texture and shape as a whole for image retrieval. LSH integrates the advantages of both statistical and structural texture description methods, and it possesses high indexing capability and low dimensionality. In addition, the proposed feature extraction algorithm does not need to train on a large scale training datasets, and it can extract local structure histogram based on LSD. The experimental results on the Corel image databases show that the descriptor has a better image retrieval performance than other descriptors.

  19. Band structures and localization properties of aperiodic layered phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yan Zhizhong, E-mail: zzyan@bit.edu.cn [Department of Applied Mathematics, Beijing Institute of Technology, Beijing 100081 (China); Zhang Chuanzeng [Department of Civil Engineering, University of Siegen, D-57078 Siegen (Germany)

    2012-03-15

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  20. Band structures and localization properties of aperiodic layered phononic crystals

    Science.gov (United States)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  1. Non-local currents and the structure of eigenstates in planar discrete systems with local symmetries

    Energy Technology Data Exchange (ETDEWEB)

    Röntgen, M., E-mail: mroentge@physnet.uni-hamburg.de [Zentrum für optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Morfonios, C.V., E-mail: christian.morfonios@physnet.uni-hamburg.de [Zentrum für optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Diakonos, F.K., E-mail: fdiakono@phys.uoa.gr [Department of Physics, University of Athens, GR-15771 Athens (Greece); Schmelcher, P., E-mail: pschmelc@physnet.uni-hamburg.de [Zentrum für optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)

    2017-05-15

    Local symmetries are spatial symmetries present in a subdomain of a complex system. By using and extending a framework of so-called non-local currents that has been established recently, we show that one can gain knowledge about the structure of eigenstates in locally symmetric setups through a Kirchhoff-type law for the non-local currents. The framework is applicable to all discrete planar Schrödinger setups, including those with non-uniform connectivity. Conditions for spatially constant non-local currents are derived and we explore two types of locally symmetric subsystems in detail, closed-loops and one-dimensional open ended chains. We find these systems to support locally similar or even locally symmetric eigenstates. - Highlights: • We extend the framework of non-local currents to discrete planar systems. • Structural information about the eigenstates is gained. • Conditions for the constancy of non-local currents are derived. • We use the framework to design two types of example systems featuring locally symmetric eigenstates.

  2. Structural Health Monitoring Based on Combined Structural Global and Local Frequencies

    Directory of Open Access Journals (Sweden)

    Jilin Hou

    2014-01-01

    Full Text Available This paper presents a parameter estimation method for Structural Health Monitoring based on the combined measured structural global frequencies and structural local frequencies. First, the global test is experimented to obtain the low order modes which can reflect the global information of the structure. Secondly, the mass is added on the member of structure to increase the local dynamic characteristic and to make the member have local primary frequency, which belongs to structural local frequency and is sensitive to local parameters. Then the parameters of the structure can be optimized accurately using the combined structural global frequencies and structural local frequencies. The effectiveness and accuracy of the proposed method are verified by the experiment of a space truss.

  3. Comparative integromics on non-canonical WNT or planar cell polarity signaling molecules: transcriptional mechanism of PTK7 in colorectal cancer and that of SEMA6A in undifferentiated ES cells.

    Science.gov (United States)

    Katoh, Masuko; Katoh, Masaru

    2007-09-01

    Non-canonical WNT and planar cell polarity (PCP) are overlapping but distinct signaling pathways, which control convergent extension, neural tube closure, orientation of cilia and sensory hair cells, axon guidance, and cell motility. Non-canonical WNT signals, regulated by the interaction of WNT, WNT antagonist, Frizzled and ROR2, are transduced to JNK, ROCK, PKC, MAP3K7, and NFAT signaling cascades. PCP signals, regulated by the interaction of VANGL-PRICKLE complex, CELSR and Frizzled-DVL complex, are transduced to JNK, ROCK, and other uncharacterized signaling cascades. PTK7 signaling, regulated by SEMA6 and Plexin-A family members, affects PCP pathway through VANGL. Here, integrative genomic analyses on WNT5A, WNT5B, WNT11, FZD3, FZD6, ROR1, ROR2, RYK, CELSR1, CELSR2, CELSR3, VANGL1, VANGL2, PRICKLE1, PRICKLE2, PTK7, SEMA6A, SEMA6B, SEMA6C and SEMA6D were carried out. PTK7 and SEMA6A were expressed in undifferentiated embryonic stem (ES) cells, SEMA6A in endodermal progenitors, CELSR1, VANGL1 and PTK7 in gastrointestinal tumors. CELSR2, PRICKLE2 and SEMA6C were expressed in fetal brain, CELSR2, PRICKLE1 and SEMA6A in adult brain, WNT5A and CELSR3 in adult brain tumors. These facts indicate class switches of non-canonical WNT or PCP signaling molecules during embryogenesis and carcinogenesis. TCF/LEF-, SP1-, and 5 bHLH-binding sites within human PTK7 promoter were conserved in chimpanzee, rhesus monkey, mouse, and rat PTK7 orthologs, which explained the mechanism of PTK7 upregulation in colorectal cancer. NANOG-, SOX2-, and POU5F1 (OCT3/OCT4)-binding sites within intron 1 of the human SEMA6A gene were conserved in chimpanzee, rhesus monkey, mouse, and rat SEMA6A orthologs, which explained the mechanism of SEMA6A upregulation in undifferentiated ES cells. Most of non-canonical WNT or PCP signaling molecules, except PTK7 and SEMA6A, were not frequently expressed in undifferentiated human ES cells. Non-canonical WNT or PCP signaling pathway, activated to orchestrate

  4. Strain localization and percolation of stable structure in amorphous solids

    OpenAIRE

    Shi, Yunfeng; Falk, Michael L.

    2005-01-01

    Spontaneous strain localization occurs during mechanical tests of a model amorphous solid simulated using molecular dynamics. The degree of localization depends upon the extent of structural relaxation prior to mechanical testing. In the most rapidly quenched samples higher strain rates lead to increased localization, while the more gradually quenched samples exhibit the opposite strain rate dependence. This transition coincides with the k-core percolation of atoms with quasi-crystal-like sho...

  5. Local structural modeling for implementation of optimal active damping

    Science.gov (United States)

    Blaurock, Carl A.; Miller, David W.

    1993-09-01

    Local controllers are good candidates for active control of flexible structures. Local control generally consists of low order, frequency benign compensators using collocated hardware. Positive real compensators and plant transfer functions ensure that stability margins and performance robustness are high. The typical design consists of an experimentally chosen gain on a fixed form controller such as rate feedback. The resulting compensator performs some combination of damping (dissipating energy) and structural modification (changing the energy flow paths). Recent research into structural impedance matching has shown how to optimize dissipation based on the local behavior of the structure. This paper investigates the possibility of improving performance by influencing global energy flow, using local controllers designed using a global performance metric.

  6. Semifolded Localized Structures in Three-Dimensional Soliton Systems

    Institute of Scientific and Technical Information of China (English)

    FANG Jian-Ping; ZHENG Chun-Long; CHEN Li-Qun

    2004-01-01

    By means ora Painlevé-Backlund transformation and a multi-linear variable separation approach, abundant localized coherent excitations of the three-dimensional Broer-Kaup-Kupershmidt system with variable coefficients are derived. There are possible phase shifts for the interactions of the three-dimensional novel localized structures discussed in this paper.

  7. Semifolded Localized Structures in Three-Dimensional Soliton Systems

    Institute of Scientific and Technical Information of China (English)

    FANGJian-Ping; ZHENGChun-Long; CHENLi-Qun

    2004-01-01

    By means ofa Painlev6 Backlund transformation and a multi-linear variable separation approach, abundant localized coherent excitations of the three-dimensional Broer Kaup Kupershmidt system with variable coeft~cients are derived. There are possible phase shifts for the interactions of the three-dimensional novel localized structures discussed in this paper.

  8. Local Influence Analysis of Nonlinear Structural Equation Models

    Science.gov (United States)

    Lee, Sik-Yum; Tang, Nian-Sheng

    2004-01-01

    By regarding the latent random vectors as hypothetical missing data and based on the conditional expectation of the complete-data log-likelihood function in the EM algorithm, we investigate assessment of local influence of various perturbation schemes in a nonlinear structural equation model. The basic building blocks of local influence analysis…

  9. Mapping chemical performance on molecular structures using locally interpretable explanations

    CERN Document Server

    Whitmore, Leanne S; Hudson, Corey M

    2016-01-01

    In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for classifying biologically produced fuel compounds with regard to Research Octane Number. This method of "painting" locally interpretable explanations onto 2-D chemical structures replicates the chemical intuition of synthetic chemists, allowing researchers in the field to directly accept, reject, inform and evaluate decisions underlying inscrutably complex quantitative structure-activity relationship models.

  10. A generative, probabilistic model of local protein structure

    DEFF Research Database (Denmark)

    Boomsma, Wouter; Mardia, Kanti V.; Taylor, Charles C.;

    2008-01-01

    Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative...... conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence-structure correlations in the native state...

  11. Localized Structures Embedded in the Eigenfunctions of Chaotic Hamiltonian Systems

    CERN Document Server

    Vergini, E G

    1998-01-01

    We study quantum localization phenomena in chaotic systems with a parameter. The parametric motion of energy levels proceeds without crossing any other and the defined avoided crossings quantify the interaction between states. We propose the elimination of avoided crossings as the natural mechanism to uncover localized structures. We describe an efficient method for the elimination of avoided crossings in chaotic billiards and apply it to the stadium billiard. We find many scars of short periodic orbits revealing the skeleton on which quantum mechanics is built. Moreover, we have observed strong interaction between similar localized structures.

  12. Local structure-preserving algorithms for partial differential equations

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    In this paper, we discuss the concept of local structure-preserving algorithms (SPAs) for partial differential equations, which are the natural generalization of the corresponding global SPAs. Local SPAs for the problems with proper boundary conditions are global SPAs, but the inverse is not necessarily valid. The concept of the local SPAs can explain the difference between different SPAs and provide a basic theory for analyzing and constructing high performance SPAs. Furthermore, it enlarges the applicable scopes of SPAs. We also discuss the application and the construction of local SPAs and derive several new SPAs for the nonlinear Klein-Gordon equation.

  13. Local structure preserving sparse coding for infrared target recognition

    Science.gov (United States)

    Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

    2017-01-01

    Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. PMID:28323824

  14. Two-dimensional localized structures in harmonically forced oscillatory systems

    Science.gov (United States)

    Ma, Y.-P.; Knobloch, E.

    2016-12-01

    Two-dimensional spatially localized structures in the complex Ginzburg-Landau equation with 1:1 resonance are studied near the simultaneous presence of a steady front between two spatially homogeneous equilibria and a supercritical Turing bifurcation on one of them. The bifurcation structures of steady circular fronts and localized target patterns are computed in the Turing-stable and Turing-unstable regimes. In particular, localized target patterns grow along the solution branch via ring insertion at the core in a process reminiscent of defect-mediated snaking in one spatial dimension. Stability of axisymmetric solutions on these branches with respect to axisymmetric and nonaxisymmetric perturbations is determined, and parameter regimes with stable axisymmetric oscillons are identified. Direct numerical simulations reveal novel depinning dynamics of localized target patterns in the radial direction, and of circular and planar localized hexagonal patterns in the fully two-dimensional system.

  15. Measurement of local relative displacements in large structures

    DEFF Research Database (Denmark)

    Tesauro, Angelo; Eder, Martin Alexander; Nielsen, Magda

    2014-01-01

    This paper presents a novel measurement technique to measure local relative displacements between parts of large-scale structures. The measured deformations can be of significant importance for fracture analyses in many different types of structures in general, and for adhesive connections...... in particular. The measurement of small local relative displacements in structures subjected to large global deformations is complex and hardly feasible with conventional measurement methods. Therefore, a Small Displacement Measurement System (SDMS) has been devised. The SDMS is based on stereo photogrammetry...... and capable of measuring 3D local displacements with a high degree of accuracy. In this article, the technique is used to measure local deformations in the vicinity of the adhesive trailing edge joint of a wind turbine rotor blade. The SDMS results correspond well with another independent measurement method....

  16. Local interaction of light with periodic photonic structures

    NARCIS (Netherlands)

    Flück, Eliane

    2003-01-01

    Photonic crystals are structures with a strong relation between geometry and op- tical properties. The application of near-field methods is a new and challenging approach to investigate the local optical properties of photonic crystals. The op- tical signals obtained in crystal structures of various

  17. Local structure studies using the pair distribution function

    Directory of Open Access Journals (Sweden)

    Bordet Pierre

    2015-01-01

    Full Text Available The pair distribution analysis method is a fast spreading structural analysis method allowing to go beyond classical crystallographic analysis by providing quantitative information about local as well as meso-structure. It based on powder diffraction data fourier transformed to direct space. We will present here the main characteristics of the method, and its domain of application.

  18. Damage localization in offshore structures using shaped inputs

    DEFF Research Database (Denmark)

    Ulriksen, Martin Dalgaard; Bernal, Dionisio; Nielsen, Morten Eggert

    2017-01-01

    Input shaping is an active control procedure by which vibrations in a structural subdomain are suppressed. Recently, a scheme based on shaped inputs has been proposed for damage localization purposes; cast on the premise that the vibration signature of a structural domain in a damaged phase will ...

  19. Deriving quantum theory from its local structure and reversibility.

    Science.gov (United States)

    de la Torre, Gonzalo; Masanes, Lluís; Short, Anthony J; Müller, Markus P

    2012-08-31

    We investigate the class of physical theories with the same local structure as quantum theory but potentially different global structure. It has previously been shown that any bipartite correlations generated by such a theory can be simulated in quantum theory but that this does not hold for tripartite correlations. Here we explore whether imposing an additional constraint on this space of theories-that of dynamical reversibility-will allow us to recover the global quantum structure. In the particular case in which the local systems are identical qubits, we show that any theory admitting at least one continuous reversible interaction must be identical to quantum theory.

  20. An online substructure identification method for local structural health monitoring

    Science.gov (United States)

    Hou, Jilin; Jankowski, Łukasz; Ou, Jinping

    2013-09-01

    This paper proposes a substructure isolation method, which uses time series of measured local response for online monitoring of substructures. The proposed monitoring process consists of two key steps: construction of the isolated substructure, and its identification. The isolated substructure is an independent virtual structure, which is numerically isolated from the global structure by placing virtual supports on the interface. First, the isolated substructure is constructed by a specific linear combination of time series of its measured local responses. Then, the isolated substructure is identified using its local natural frequencies extracted from the combined responses. The substructure is assumed to be linear; the outside part of the global structure can have any characteristics. The method has no requirements on the initial state of the structure, and so the process can be carried out repetitively for online monitoring. Online isolation and monitoring is illustrated in a numerical example with a frame model, and then verified in a cantilever beam experiment.

  1. Reconstruction of biofilm images: combining local and global structural parameters

    Energy Technology Data Exchange (ETDEWEB)

    Resat, Haluk; Renslow, Ryan S.; Beyenal, Haluk

    2014-10-20

    Digitized images can be used for quantitative comparison of biofilms grown under different conditions. Using biofilm image reconstruction, it was previously found that biofilms with a completely different look can have nearly identical structural parameters and that the most commonly utilized global structural parameters were not sufficient to uniquely define these biofilms. Here, additional local and global parameters are introduced to show that these parameters considerably increase the reliability of the image reconstruction process. Assessment using human evaluators indicated that the correct identification rate of the reconstructed images increased from 50% to 72% with the introduction of the new parameters into the reconstruction procedure. An expanded set of parameters especially improved the identification of biofilm structures with internal orientational features and of structures in which colony sizes and spatial locations varied. Hence, the newly introduced structural parameter sets helped to better classify the biofilms by incorporating finer local structural details into the reconstruction process.

  2. Local thermal energy as a structural indicator in glasses

    Science.gov (United States)

    Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

    2017-07-01

    Identifying heterogeneous structures in glasses—such as localized soft spots—and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses—an intrinsic signature of glassy frustration—anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal ω4ω4 density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field—a “softness field”—is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

  3. New Fractal Localized Structures in Boiti-Leon-Pempinelli System

    Institute of Scientific and Technical Information of China (English)

    MAZheng-Yi; ZHUJia-Min; ZHENGChun-Long

    2004-01-01

    A novel phenomenon that the localized coherent structures of a (2+1)-dimensional physical model possess fractal behaviors is revealed. To clarify the interesting phenomenon, we take the (2+1)-dimensional Boiti Leon-Pempinelli system as a concrete example. Starting from an extended homogeneous balance approach, a general solution of the system is derived. From which some special localized excitations with fractal behaviors are obtained by introducin gsome types of lower-dimensional fractal patterns.

  4. Sampling Realistic Protein Conformations Using Local Structural Bias

    DEFF Research Database (Denmark)

    Hamelryck, Thomas Wim; Kent, John T.; Krogh, A.

    2006-01-01

    are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded......The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which...... in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications...

  5. Influences of consolidation processes on local paper structure

    Science.gov (United States)

    Sung, Yongjoo

    The accurate measurement of the structural parameters such as thickness, grammage, apparent density and surface topography, and the proper evaluation of the variation of each parameter, are very important not only for predicting the end use properties of the paper, but also for diagnosing the pa permaking processes. The difficulty of the measurement of thickness at fine scale ˜1 mm has been an impediment to the understanding of local paper structure. To address this problem, a twin laser profilometer instrument (TLP) for non-contacting measurement of local thickness and surface topography was developed, characterized and calibrated in this work. The fundamental relationships between structural parameters were reexamined with various handsheet samples. The effects of wet pressing on the local paper structure were evaluated using laboratory static press and commercial press felts. The different press pressure had no significant influence on the local density variation of the handsheet samples. The influences of felts on the surface topography were also successfully observed. The different densification effects of soft nip and hard nip calendering processes were evaluated by direct comparison of structural parameters before and after processing. The much higher selective reduction in local thickness (larger reduction for the thicker area) by the hard nip calendering process resulted in different relationships between structural parameters. The various periodic variations in the paper structure were also detected, analyzed and identified. The effects of different forming elements such as the conventional foil system and the velocity induced drainage (VID) system on the paper structure and end use properties were evaluated with pilot machine trials and commercial product produced using different forming elements. Generally, the VID samples showed better formation, less two sidedness in the fine distribution through thickness direction, and less densification during

  6. Local Linearizability for Concurrent Container-Type Data Structures

    OpenAIRE

    Haas, Andreas; Henzinger, Thomas A.; Holzer, Andreas; Kirsch, Christoph M.; Lippautz, Michael; Payer, Hannes; Sezgin, Ali; Sokolova, Ana; Veith, Helmut

    2016-01-01

    The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizabi...

  7. Cosmic Flows and the Structure of the Local Universe

    Science.gov (United States)

    Steinmetz, Matthias

    2016-03-01

    The Local Volume is the area of the cosmos we can analyze in most detail with respect to the properties of its galaxy population, their abundance, their inner structure, their distribution, and their formation. Indeed, many challenges of the cosmological concordance model such as the substructure crisis or the surprising occurrence of vast planes of satellite galaxies are intimately linked to observations of the local galaxy population. However, owing to the peculiar environment of our Milky Way system and its cosmic neighborhood, the Local Volume may also be severely biased. Cosmography, i.e. the reconstruction of the local cosmic web from cosmic flows, and constrained simulations of structure formation as a tool to produce simulated local group analogues provide a powerful method to analyze and quantify these biases. Possible applications include the analysis of the local distribution of dwarf galaxies around luminous galaxies and the characterization of the mass accretion history of these objects. Thanks to the extension of galaxy velocity data out to distances in excess of 200Mpc, we are now capable to reconstruct the 3D matter distribution out to these distances, thus constraining the formation history of object such as the Virgo Cluster.

  8. Local structure analysis in ab initio liquid water

    Science.gov (United States)

    Santra, Biswajit; DiStasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    2015-09-01

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps - a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.

  9. Local structure of numerically generated worm hole spacetime.

    Science.gov (United States)

    Siino, M.

    The author investigates the evolution of the apparent horizons in a numerically gererated worm hole spacetime. The behavior of the apparent horizons is affected by the dynamics of the matter field. By using the local mass of the system, he interprets the evolution of the worm hole structure.

  10. Local Structure of Numerically Generated Worm Hole Spacetime

    OpenAIRE

    Nambu, Yasusada; Siino, Masaru

    1993-01-01

    We investigate the evolution of the apparent horizons in a numerically gererated worm hole spacetime. The behavior of the apparent horizons is affected by the dynamics of the matter field. By using the local mass of the system, we interpret the evolution of the worm hole structure. Figures are available by mail to author.

  11. DELORES - A System for Detection and Localization of Structural Damages

    DEFF Research Database (Denmark)

    Johansen, Rasmus Johan; Ulriksen, Martin Dalgaard; Damkilde, Lars

    2016-01-01

    of the dynamic damage locating vector (DDLV) and the stochastic dynamic damage locating vector (SDDLV) methods, which include an outlier analysis scheme for a more unambiguous localization of potential damages. The (S)DDLV methods are model-based, which means that a mechanical model of the healthy structure...

  12. Local Structure of Numerically Generated Worm Hole Spacetime

    CERN Document Server

    Nambu, Y; Nambu, Yasusada; Siino, Masaru

    1993-01-01

    We investigate the evolution of the apparent horizons in a numerically gererated worm hole spacetime. The behavior of the apparent horizons is affected by the dynamics of the matter field. By using the local mass of the system, we interpret the evolution of the worm hole structure. Figures are available by mail to author.

  13. The distribution of Elongation Factor-1 Alpha (EF-1alpha), Elongation Factor-Like (EFL), and a non-canonical genetic code in the ulvophyceae: discrete genetic characters support a consistent phylogenetic framework.

    Science.gov (United States)

    Gile, Gillian H; Novis, Philip M; Cragg, David S; Zuccarello, Giuseppe C; Keeling, Patrick J

    2009-01-01

    The systematics of the green algal class Ulvophyceae have been difficult to resolve with ultrastructural and molecular phylogenetic analyses. Therefore, we investigated relationships among ulvophycean orders by determining the distribution of two discrete genetic characters previously identified only in the order Dasycladales. First, Acetabularia acetabulum uses the core translation GTPase Elongation Factor 1alpha (EF-1alpha) while most Chlorophyta instead possess the related GTPase Elongation Factor-Like (EFL). Second, the nuclear genomes of dasycladaleans A. acetabulum and Batophora oerstedii use a rare non-canonical genetic code in which the canonical termination codons TAA and TAG instead encode glutamine. Representatives of Ulvales and Ulotrichales were found to encode EFL, while Caulerpales, Dasycladales, Siphonocladales, and Ignatius tetrasporus were found to encode EF-1alpha, in congruence with the two major lineages previously proposed for the Ulvophyceae. The EF-1alpha of I. tetrasporus supports its relationship with Caulerpales/Dasycladales/Siphonocladales, in agreement with ultrastructural evidence, but contrary to certain small subunit rRNA analyses that place it with Ulvales/Ulotrichales. The same non-canonical genetic code previously described in A. acetabulum was observed in EF-1alpha sequences from Parvocaulis pusillus (Dasycladales), Chaetomorpha coliformis, and Cladophora cf. crinalis (Siphonocladales), whereas Caulerpales use the universal code. This supports a sister relationship between Siphonocladales and Dasycladales and further refines our understanding of ulvophycean phylogeny.

  14. Local magnetic structure determination using polarized neutron holography

    Energy Technology Data Exchange (ETDEWEB)

    Szakál, Alex, E-mail: szakal.alex@wigner.mta.hu; Markó, Márton, E-mail: marko.marton@wigner.mta.hu; Cser, László, E-mail: cser.laszlo@wigner.mta.hu [Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest (Hungary)

    2015-05-07

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  15. Local Exact Pattern Matching for Non-Fixed RNA Structures.

    Science.gov (United States)

    Amit, Mika; Backofen, Rolf; Heyne, Steffen; Landau, Gad M; Möhl, Mathias; Otto, Christina; Will, Sebastian

    2014-01-01

    Detecting local common sequence-structure regions of RNAs is a biologically important problem. Detecting such regions allows biologists to identify functionally relevant similarities between the inspected molecules. We developed dynamic programming algorithms for finding common structure-sequence patterns between two RNAs. The RNAs are given by their sequence and a set of potential base pairs with associated probabilities. In contrast to prior work on local pattern matching of RNAs, we support the breaking of arcs. This allows us to add flexibility over matching only fixed structures; potentially matching only a similar subset of specified base pairs. We present an O(n(3)) algorithm for local exact pattern matching between two nested RNAs, and an O(n(3) log n) algorithm for one nested RNA and one bounded-unlimited RNA. In addition, an algorithm for approximate pattern matching is introduced that for two given nested RNAs and a number k, finds the maximal local pattern matching score between the two RNAs with at most k mismatches in O(n(3)k(2)) time. Finally, we present an O(n(3)) algorithm for finding the most similar subforest between two nested RNAs.

  16. Recognition of Local DNA Structures by p53 Protein.

    Science.gov (United States)

    Brázda, Václav; Coufal, Jan

    2017-02-10

    p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.

  17. Parametric localized modes in quadratic nonlinear photonic structures

    DEFF Research Database (Denmark)

    Sukhorukov, Andrey A.; Kivshar, Yuri S.; Bang, Ole;

    2001-01-01

    We analyze two-color spatially localized nonlinear modes formed by parametrically coupled fundamental and second-harmonic fields excited at quadratic (or chi2) nonlinear interfaces embedded in a linear layered structure-a quadratic nonlinear photonic crystal. For a periodic lattice of nonlinear...... interfaces, we derive an effective discrete model for the amplitudes of the fundamental and second-harmonic waves at the interfaces (the so-called discrete chi2 equations) and find, numerically and analytically, the spatially localized solutions-discrete gap solitons. For a single nonlinear interface...... in a linear superlattice, we study the properties of two-color localized modes, and describe both similarities to and differences from quadratic solitons in homogeneous media....

  18. Dynamics of Localized Structures in Systems with Broken Parity Symmetry

    CERN Document Server

    Javaloyes, J; Marconi, M; Giudici, M

    2016-01-01

    A great variety of nonlinear dissipative systems are known to host structures having a correlation range much shorter than the size of the system. The dynamics of these Localized Structures (LSs) have been investigated so far in situations featuring parity symmetry. In this letter we extend this analysis to systems lacking of this property. We show that the LS drifting speed in a parameter varying landscape is not simply proportional to the parameter gradient, as found in parity preserving situations. The symmetry breaking implies a new contribution to the velocity field which is a function of the parameter value, thus leading to a new paradigm for LSs manipulation. We illustrate this general concept by studying the trajectories of the LSs found in a passively mode-locked laser operated in the localization regime. Moreover, the lack of parity affects significantly LSs interactions which are governed by asymmetrical repulsive forces.

  19. Alfvénic localized structures in partially ionized plasmas

    Science.gov (United States)

    Borhanian, Jafar; Rezaei, Arash

    2017-02-01

    The existence and dynamics of Alfvénic localized structures are investigated in partially ionized plasmas. We have employed the Hall magnetohydrodynamics model for partially ionized plasmas and shown that the evolution of a weakly nonlinear and weakly dispersive Alfvén wave is governed by a derivative nonlinear Schrödinger (DNLS) type equation. In the Hall effect domination limit, this equation reduces to a standard DNLS equation that possesses localized solutions in the form of solitons and rogue waves. The dependence of the profile of these structures on the Hall parameter is addressed. When the ohmic and ambipolar effects are small but finite in comparison to the Hall effect, the evolution equation takes the form of a perturbed DNLS equation. In this limit, the dynamics of envelope soliton solution is examined by means of the soliton perturbation method, the moment method, to be precise.

  20. Local structure co-occurrence pattern for image retrieval

    Science.gov (United States)

    Zhang, Ke; Zhang, Fan; Lu, Jia; Lu, Yinghua; Kong, Jun; Zhang, Ming

    2016-03-01

    Image description and annotation is an active research topic in content-based image retrieval. How to utilize human visual perception is a key approach to intelligent image feature extraction and representation. This paper has proposed an image feature descriptor called the local structure co-occurrence pattern (LSCP). LSCP extracts the whole visual perception for an image by building a local binary structure, and it is represented by a color-shape co-occurrence matrix which explores the relationship of multivisual feature spaces according to visual attention mechanism. As a result, LSCP not only describes low-level visual features integrated with texture feature, color feature, and shape feature but also bridges high-level semantic comprehension. Extensive experimental results on an image retrieval task on the benchmark datasets, corel-10,000, MIT VisTex, and INRIA Holidays, have demonstrated the usefulness, effectiveness, and robustness of the proposed LSCP.

  1. Local Structure and Magnetism of (Ga,Mn)As

    CERN Document Server

    AUTHOR|(CDS)2093111; Temst, Kristiaan

    Throughout the years, dilute magnetic semiconductors (DMS) have emerged as promising materials for semiconductor-based spintronics. In particular, (Ga,Mn)As has become the model system in which to explore the physics of carrier-mediated ferromagnetism in semiconductors and the associated spintronic phenomena, with a number of interesting functionalities and demonstrated proof-of-concept devices. It constitutes the perfect example of how the magnetic behavior of DMS materials is strongly influenced by local structure. In this thesis, we address key aspects of the interplay between local structure and ferromagnetism of (Ga,Mn)As. We unambiguously identify the lattice site occupied by interstitial Mn as the tetrahedral interstitial site with As nearest neighbors T(As). We show, furthermore, that the T(As) is the most energetically favorable site regardless of the interstitial atom forming or not complexes with substitutional Mn. We also evaluate the thermal stability of both interstitial and substitutional Mn si...

  2. The local spiral structure of the Milky Way.

    Science.gov (United States)

    Xu, Ye; Reid, Mark; Dame, Thomas; Menten, Karl; Sakai, Nobuyuki; Li, Jingjing; Brunthaler, Andreas; Moscadelli, Luca; Zhang, Bo; Zheng, Xingwu

    2016-09-01

    The nature of the spiral structure of the Milky Way has long been debated. Only in the last decade have astronomers been able to accurately measure distances to a substantial number of high-mass star-forming regions, the classic tracers of spiral structure in galaxies. We report distance measurements at radio wavelengths using the Very Long Baseline Array for eight regions of massive star formation near the Local spiral arm of the Milky Way. Combined with previous measurements, these observations reveal that the Local Arm is larger than previously thought, and both its pitch angle and star formation rate are comparable to those of the Galaxy's major spiral arms, such as Sagittarius and Perseus. Toward the constellation Cygnus, sources in the Local Arm extend for a great distance along our line of sight and roughly along the solar orbit. Because of this orientation, these sources cluster both on the sky and in velocity to form the complex and long enigmatic Cygnus X region. We also identify a spur that branches between the Local and Sagittarius spiral arms.

  3. Cosmic structure and dynamics of the local Universe

    Science.gov (United States)

    Kitaura, Francisco-Shu; Erdoǧdu, Pirin; Nuza, Sebastián. E.; Khalatyan, Arman; Angulo, Raul E.; Hoffman, Yehuda; Gottlöber, Stefan

    2012-11-01

    We present a cosmography analysis of the local Universe based on the recently released Two-Micron All-Sky Redshift Survey catalogue. Our method is based on a Bayesian Networks Machine Learning algorithm (the KIGEN-code) which self-consistently samples the initial density fluctuations compatible with the observed galaxy distribution and a structure formation model given by second-order Lagrangian perturbation theory (2LPT). From the initial conditions we obtain an ensemble of reconstructed density and peculiar velocity fields which characterize the local cosmic structure with high accuracy unveiling non-linear structures like filaments and voids in detail. Coherent redshift-space distortions are consistently corrected within 2LPT. From the ensemble of cross-correlations between the reconstructions and the galaxy field and the variance of the recovered density fields, we find that our method is extremely accurate up to k˜ 1 h Mpc-1 and still yields reliable results down to scales of about 3-4 h-1 Mpc. The motion of the Local Group we obtain within ˜80 h-1 Mpc (vLG = 522 ± 86 km s-1, lLG = 291° ± 16°, bLG = 34° ± 8°) is in good agreement with measurements derived from the cosmic microwave background and from direct observations of peculiar motions and is consistent with the predictions of ΛCDM.

  4. Cosmic Structure and Dynamics of the Local Universe

    CERN Document Server

    Kitaura, Francisco-Shu; Nuza, Sebastian E; Khalatyan, Arman; Angulo, Raul E; Hoffman, Yehuda; Gottloeber, Stefan

    2012-01-01

    We present a cosmography analysis of the Local Universe based on the recently released Two-Micron All-Sky Redshift Survey (2MRS). Our method is based on a Bayesian Networks Machine Learning algorithm (the Kigen-code) which self-consistently samples the initial density fluctuations compatible with the observed galaxy distribution and a structure formation model given by second order Lagrangian perturbation theory (2LPT). From the initial conditions we obtain an ensemble of reconstructed density and peculiar velocity fields which characterize the local cosmic structure with high accuracy unveiling nonlinear structures like filaments and voids in detail. Coherent redshift space distortions are consistently corrected within 2LPT. From the ensemble of cross-correlations between the reconstructions and the galaxy field and the variance of the recovered density fields we find that our method is extremely accurate up to k ~ 1 h Mpc^-1 and still yields reliable results up to k ~ 2 h Mpc^-1. The motion of the local gro...

  5. Hypo-analytic structures local theory (PMS-40)

    CERN Document Server

    Treves, François

    2014-01-01

    In Hypo-Analytic Structures Franois Treves provides a systematic approach to the study of the differential structures on manifolds defined by systems of complex vector fields. Serving as his main examples are the elliptic complexes, among which the De Rham and Dolbeault are the best known, and the tangential Cauchy-Riemann operators. Basic geometric entities attached to those structures are isolated, such as maximally real submanifolds and orbits of the system. Treves discusses the existence, uniqueness, and approximation of local solutions to homogeneous and inhomogeneous equations and delimits their supports. The contents of this book consist of many results accumulated in the last decade by the author and his collaborators, but also include classical results, such as the Newlander-Nirenberg theorem. The reader will find an elementary description of the FBI transform, as well as examples of its use. Treves extends the main approximation and uniqueness results to first-order nonlinear equations by means of ...

  6. Persistent Near-Surface Flow Structures from Local Helioseismology

    CERN Document Server

    Howe, R; Baker, D; Harra, L; van Driel-Gesztelyi, L; Bogart, R S

    2015-01-01

    Near-surface flows measured by the ring-diagram technique of local helioseismology show structures that persist over multiple rotations. We examine these phenomena using data from the {\\em Global Oscillation Network Group} (GONG) and the {\\em Helioseismic and Magnetic Imager} (HMI) and show that a correlation analysis of the structures can be used to estimate the rotation rate as a function of latitude, giving a result consistent with the near-surface rate from global helioseismology and slightly slower than that obtained from a similar analysis of the surface magnetic field strength. At latitudes of 60$^{\\circ}$ and above the HMI flow data reveal a strong signature of a two-sided zonal flow structure. This signature may be related to recent reports of "giant cells" in solar convection.

  7. The local structure of transition metal doped semiconducting boron carbides

    Energy Technology Data Exchange (ETDEWEB)

    Liu Jing; Dowben, P A [Department of Physics and Astronomy and the Nebraska Center for Materials and Nanoscience, Behlen Laboratory of Physics, University of Nebraska-Lincoln, PO Box 880111, Lincoln, NE 68588-0111 (United States); Luo Guangfu; Mei Waining [Department of Physics, University of Nebraska at Omaha, Omaha, NE 68182-0266 (United States); Kizilkaya, Orhan [J. Bennett Johnston Sr. Center for Advanced Microstructures and Devices, Louisiana State University, 6980 Jefferson Hwy., Baton Rouge LA 70806 (United States); Shepherd, Eric D; Brand, J I [College of Engineering, and the Nebraska Center for Materials and Nanoscience, N209 Walter Scott Engineering Center, 17th and Vine Streets, University of Nebraska-Lincoln, Lincoln, NE 68588-0511 (United States)

    2010-03-03

    Transition metal doped boron carbides produced by plasma enhanced chemical vapour deposition of orthocarborane (closo-1,2-C{sub 2}B{sub 10}H{sub 12}) and 3d metal metallocenes were investigated by performing K-edge extended x-ray absorption fine structure and x-ray absorption near edge structure measurements. The 3d transition metal atom occupies one of the icosahedral boron or carbon atomic sites within the icosahedral cage. Good agreement was obtained between experiment and models for Mn, Fe and Co doping, based on the model structures of two adjoined vertex sharing carborane cages, each containing a transition metal. The local spin configurations of all the 3d transition metal doped boron carbides, Ti through Cu, are compared using cluster and/or icosahedral chain calculations, where the latter have periodic boundary conditions.

  8. The local spiral structure of the Milky Way

    CERN Document Server

    Xu, Ye; Dame, Thomas; Menten, Karl; Sakai, Nobuyuki; Li, Jingjing; Brunthaler, Andreas; Moscadelli, Luca; Zhang, Bo; Zheng, Xingwu

    2016-01-01

    The nature of the spiral structure of the Milky Way has long been debated. Only in the last decade have astronomers been able to accurately measure distances to a substantial number of high-mass star-forming regions, the classic tracers of spiral structure in galaxies. We report distance measurements at radio wavelengths using the Very Long Baseline Array for eight regions of massive star formation near the Local spiral arm of the Milky Way. Combined with previous measurements, these observations reveal that the Local Arm is larger than previously thought, and both its pitch angle and star formation rate are comparable to those of the Galaxy's major spiral arms, such as Sagittarius and Perseus. Toward the constellation Cygnus, sources in the Local Arm extend for a great distance along our line of sight and roughly along the solar orbit. Because of this orientation, these sources cluster both on the sky and in velocity to form the complex and long enigmatic Cygnus X region. We also identify a spur that branche...

  9. Role of nonlinear localized structures and turbulence in magnetized plasma

    Science.gov (United States)

    Pathak, Neha; Yadav, Nitin; Uma, R.; Sharma, R. P.

    2016-09-01

    In the present study, we have analyzed the field localization of kinetic Alfvén wave (KAW) due to the presence of background density perturbation, which are assumed to be originated by the three dimensionally propagating low frequency KAW. These localized structures play an important role for energy transportation at smaller scales in the dispersion range of magnetic power spectrum. For the present model, governing dynamic equations of high frequency pump KAW and low frequency KAW has been derived by considering ponderomotive nonlinearity. Further, these coupled equations have been numerically solved to analyze the resulting localized structures of pump KAW and magnetic power spectrum in the magnetopause regime. Numerically calculated spectrum exhibits inertial range having spectral index of -3/2 followed by steeper scaling; this steepening in the turbulent spectrum is a signature of energy transportation from larger to smaller scales. In this way, the proposed mechanism, which is based on nonlinear wave-wave interaction, may be useful for understanding the particle acceleration and turbulence in magnetopause.

  10. Measuring capital market efficiency: Global and local correlations structure

    Science.gov (United States)

    Kristoufek, Ladislav; Vosvrda, Miloslav

    2013-01-01

    We introduce a new measure for capital market efficiency. The measure takes into consideration the correlation structure of the returns (long-term and short-term memory) and local herding behavior (fractal dimension). The efficiency measure is taken as a distance from an ideal efficient market situation. The proposed methodology is applied to a portfolio of 41 stock indices. We find that the Japanese NIKKEI is the most efficient market. From a geographical point of view, the more efficient markets are dominated by the European stock indices and the less efficient markets cover mainly Latin America, Asia and Oceania. The inefficiency is mainly driven by a local herding, i.e. a low fractal dimension.

  11. Structural eigenfrequency optimization based on local sub-domain "frequencies"

    DEFF Research Database (Denmark)

    Pedersen, Pauli; Pedersen, Niels Leergaard

    2013-01-01

    The engineering approach of fully stressed design is a practical tool with a theoretical foundation. The analog approach to structural eigenfrequency optimization is presented here with its theoretical foundation. A numerical redesign procedure is proposed and illustrated with examples.......For the ideal case, an optimality criterion is fulfilled if the design have the same sub-domain ”frequency” (local Rayleigh quotient). Sensitivity analysis shows an important relation between squared system eigenfrequency and squared local sub-domain frequency for a given eigenmode. Higher order...... eigenfrequencies may also be controlled in this manner.The presented examples are based on 2D finite element models with the use of subspace iteration for analysis and a recursive design procedure based on the derived optimality condition. The design that maximize a frequency depend on the total amount...

  12. Characterizing structural transitions using localized free energy landscape analysis.

    Directory of Open Access Journals (Sweden)

    Nilesh K Banavali

    Full Text Available BACKGROUND: Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes. METHODOLOGY/PRINCIPAL FINDINGS: Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom. CONCLUSIONS/SIGNIFICANCE: The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

  13. Investigation of nanogap localized field enhancement in gold plasmonic structures

    Science.gov (United States)

    Debu, Desalegn Tadesse; Bauman, Stephen; Saylor, Cameron; Novak, Eric; French, David; Herzog, Joseph

    2015-03-01

    Nanogaps between plasmonic structures allow confining the localized electric field with moreenhancements. Based on previously implemented two-step lithography process, we introducea nano-masking technique to fabricate nanostructrues and nanogaps for various geometrical patterns. This new method can fabricate gold nanostructures as well as nanogaps that are less than 10nm, below the limiting scale of lithography. Simulation from finite element method (FEM) shows strong gap dependence of optical properties and peak enhancement of these devices. The fabricated plasmonic nanostructure provides wide range of potential future application including highly sensitive optical antenna, surface enhanced Raman spectroscopy and biosensing.

  14. Structure and chromosomal localization of the human thrombospondin gene.

    Science.gov (United States)

    Wolf, F W; Eddy, R L; Shows, T B; Dixit, V M

    1990-04-01

    Thrombospondin (THBS1) is a large modular glycoprotein component of the extracellular matrix and contains a variety of distinct domains, including three repeating subunits (types I, II, and III) that share homology to an assortment of other proteins. Determination of THBS1 gene structure has revealed that the type I repeat modules are encoded by symmetrical exons and that the heparin-binding domain is encoded by a single exon. To further elucidate the higher level organization of THBS1, the gene was localized to the q11-qter region of chromosome 15.

  15. The local structure theorem for real spherical varieties

    DEFF Research Database (Denmark)

    Knop, Friedrich; Krötz, Bernhard; Schlichtkrull, Henrik

    2015-01-01

    Let G be an algebraic real reductive group and Z a real spherical G -variety, that is, it admits an open orbit for a minimal parabolic subgroup P . We prove a local structure theorem for Z . In the simplest case where Z is homogeneous, the theorem provides an isomorphism of the open P -orbit...... with a bundle Q×LS . Here Q is a parabolic subgroup with Levi decomposition L⋉U , and S is a homogeneous space for a quotient D=L/Ln of L , where Ln⊆L is normal, such that D is compact modulo center....

  16. Local structure probes of nanoscale heterogeneity in crystalline materials.

    Science.gov (United States)

    Conradson, S; Espinosa, F; Villella, P

    2001-03-01

    In the conventional model of condensed matter increasing numbers of defects break down the order and ultimately convert perfect periodic crystals into aperiodic glasses. Local structure probes of a variety of materials with non-stoichiometric compositions, multiple degenerate ordering modes, or other symmetry breaking factors identify multiple ordered arrangements of atoms that render the materials heterogeneous on the nanometer scale. While exerting apparently negligible effects on bulk properties, this heterogeneity or phase separation does influence correlated or collective properties such as magnetism and phase stability.

  17. Local structure of Eu3+ ions in fluorophosphate laser glass

    Indian Academy of Sciences (India)

    P Babu; R Vijaya; Kyoung Hyuk Jang; Hyo Jin Seo; V Lavin; C K Jayasankar

    2010-11-01

    A fluorophosphate laser glass doped with 1.0 mol% of Eu3+ ions has been prepared and studied by site-selective spectroscopy to explore the local structure of Eu3+ ions. Site-selective 50 → 71,2 emission spectra have been measured under resonant excitation to the 50 level at different wavelengths within the 70 → 50 band at 16 K. Using the Stark level positions of the 71 and 72 levels, crystal-field analysis has been carried out. The results suggest the existence of a unique kind of site for all the environments of Eu3+ ions in this glass.

  18. Local structure of nanosized tungstates revealed by evolutionary algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Timoshenko, Janis; Anspoks, Andris; Kuzmin, Alexei [Institute of Solid State Physics, University of Latvia, Riga (Latvia); Kalinko, Alexandr [Institute of Solid State Physics, University of Latvia, Riga (Latvia); Synchrotron SOLEIL, l' Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette (France)

    2015-02-01

    Nanostructured tungstates, such as CoWO{sub 4} and CuWO{sub 4}, are very promising catalytic materials, particularly for photocatalytic oxidation of water. The high catalytic activity of tungstate nanoparticles partially is a result of their extremely small sizes, and, consequently, high surface-to-volume ratio. Therefore their properties depend strongly on the atomic structure, which differ significantly from that of the bulk material. X-ray absorption spectroscopy is a powerful technique to address the challenging problem of the local structure determination in nanomaterials. In order to fully exploit the structural information contained in X-ray absorption spectra, in this study we employ a novel evolutionary algorithm (EA) for the interpretation of the Co and Cu K-edges as well as the W L{sub 3}-edge extended X-ray absorption fine structure (EXAFS) of nanosized CoWO{sub 4} and CuWO{sub 4}. The combined EA-EXAFS approach and simultaneous analysis of the W L{sub 3} and Co(Cu) K-edge EXAFS spectra allowed us for the first time to obtain a 3D structure model of the tungstate nanoparticles and to explore in details the effect of size, temperature and transition metal type. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  19. Vacuum arc localization in CLIC prototype radio frequency accelerating structures

    CERN Document Server

    AUTHOR|(CDS)2091976; Koivunen, Visa

    2016-04-04

    A future linear collider capable of reaching TeV collision energies should support accelerating gradients beyond 100 MV/m. At such high fields, the occurrence of vacuum arcs have to be mitigated through conditioning, during which an accelerating structure’s resilience against breakdowns is slowly increased through repeated radio frequency pulsing. Conditioning is very time and resource consuming, which is why developing more efficient procedures is desirable. At CERN, conditioning related research is conducted at the CLIC high-power X-band test stands. Breakdown localization is an important diagnostic tool of accelerating structure tests. Abnormal position distributions highlight issues in structure design, manufacturing or operation and may consequently help improve these processes. Additionally, positioning can provide insight into the physics of vacuum arcs. In this work, two established positioning methods based on the time-difference-ofarrival of radio frequency waves are extended. The first method i...

  20. A local algorithm for detecting community structures in dynamic networks

    CERN Document Server

    Massaro, Emanuele; Guazzini, Andrea; Passarella, Andrea; Bagnoli, Franco

    2013-01-01

    The emergence and the global adaptation of mobile devices has influenced human interactions at the individual, community, and social levels leading to the so called Cyber-Physical World (CPW) convergence scenario [1]. One of the most important features of CPW is the possibility of exploiting information about the structure of social communities of users, that manifest through joint movement patterns and frequency of physical co-location: mobile devices of users that belong to the same social community are likely to "see" each other (and thus be able to communicate through ad hoc networking techniques) more frequently and regularly than devices outside of the community. In mobile opportunistic networks, this fact can be exploited, for example, to optimize networking operations such as forwarding and dissemination of messages. In this paper we present a novel local cognitive-inspired algorithm for revealing the structure of these dynamic social networks by exploiting information about physical encounters, logge...

  1. Embrittlement and Flow Localization in Reactor Structural Materials

    Energy Technology Data Exchange (ETDEWEB)

    Xianglin Wu; Xiao Pan; James Stubbins

    2006-10-06

    Many reactor components and structural members are made from metal alloys due, in large part, to their strength and ability to resist brittle fracture by plastic deformation. However, brittle fracture can occur when structural material cannot undergo extensive, or even limited, plastic deformation due to irradiation exposure. Certain irradiation conditions lead to the development of a damage microstructure where plastic flow is limited to very small volumes or regions of material, as opposed to the general plastic flow in unexposed materials. This process is referred to as flow localization or plastic instability. The true stress at the onset of necking is a constant regardless of the irradiation level. It is called 'critical stress' and this critical stress has strong temperature dependence. Interrupted tensile testes of 316L SS have been performed to investigate the microstructure evolution and competing mechanism between mechanic twinning and planar slip which are believed to be the controlling mechanism for flow localization. Deformation twinning is the major contribution of strain hardening and good ductility for low temperatures, and the activation of twinning system is determined by the critical twinning stress. Phases transform and texture analyses are also discussed in this study. Finite element analysis is carried out to complement the microstructural analysis and for the prediction of materaials performance with and without stress concentration and irradiation.

  2. A local immunization strategy for networks with overlapping community structure

    Science.gov (United States)

    Taghavian, Fatemeh; Salehi, Mostafa; Teimouri, Mehdi

    2017-02-01

    Since full coverage treatment is not feasible due to limited resources, we need to utilize an immunization strategy to effectively distribute the available vaccines. On the other hand, the structure of contact network among people has a significant impact on epidemics of infectious diseases (such as SARS and influenza) in a population. Therefore, network-based immunization strategies aim to reduce the spreading rate by removing the vaccinated nodes from contact network. Such strategies try to identify more important nodes in epidemics spreading over a network. In this paper, we address the effect of overlapping nodes among communities on epidemics spreading. The proposed strategy is an optimized random-walk based selection of these nodes. The whole process is local, i.e. it requires contact network information in the level of nodes. Thus, it is applicable to large-scale and unknown networks in which the global methods usually are unrealizable. Our simulation results on different synthetic and real networks show that the proposed method outperforms the existing local methods in most cases. In particular, for networks with strong community structures, high overlapping membership of nodes or small size communities, the proposed method shows better performance.

  3. Topology Optimization of Continuum Structures with Local Stress Constraints

    DEFF Research Database (Denmark)

    Duysinx, Pierre; Bendsøe, Martin P

    1997-01-01

    We introduce an extension of current technologies for topology optimization of continuum structures which allows for treating local stress criteria. We first consider relevant stress criteria for porous composite materials, initially by studying the stress states of the so-called rank~2 layered m...... of the stress constraints is used. We describe the mathematical programming approach that is used to solve the numerical optimization problems, and show results for a number of example applications.......We introduce an extension of current technologies for topology optimization of continuum structures which allows for treating local stress criteria. We first consider relevant stress criteria for porous composite materials, initially by studying the stress states of the so-called rank~2 layered...... materials. Then, an empirical model is proposed for the power law materials (also called SIMP materials). In a second part, solution aspects of topology problems are considered. To deal with the so-called 'singularity' phenomenon of stress constraints in topology design, an $\\epsilon$ constraint relaxation...

  4. Local structural ordering in surface-confined liquid crystals

    Science.gov (United States)

    Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

    2017-06-01

    The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

  5. Local structure and local conduction paths in amorphous (In,Ga,Hf)-ZnO semiconductor thin films

    Science.gov (United States)

    Yang, Dong-Seok; Cheol Lee, Jae; Chung, JaeGwan; Lee, Eunha; Anass, Benayad; Sung, Nark-Eon; Min Lee, Jay; Jae Kang, Hee

    2012-10-01

    The local structure and local conduction paths of Ga-In-Zn-O (GIZO) and Hf-In-Zn-O (HIZO) amorphous thin films were investigated by the extended X-ray absorption fine structure (EXAFS). We found that the local hindrance paths of In-Ga and In-Hf exist in the conduction paths of amorphous GIZO and HIZO semiconductor thin films, respectively.

  6. Matt: local flexibility aids protein multiple structure alignment.

    Directory of Open Access Journals (Sweden)

    Matthew Menke

    2008-01-01

    Full Text Available Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists, an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global performance is competitive with the other programs on Homstrad, but outperforms the other programs on SABmark, a benchmark of multiple structure alignments of proteins with more distant homology. On both datasets, Matt demonstrates an ability to better align the ends of alpha-helices and beta-strands, an important characteristic of any structure alignment program intended to help construct a structural template library for threading approaches to the inverse protein-folding problem. The related question of whether Matt alignments can be used to distinguish distantly homologous structure pairs from pairs of proteins that are not homologous is also considered. For this purpose, a p-value score based on the length of the common core

  7. Structure and local charging of electromigrated Au nanocontacts

    Science.gov (United States)

    Arnold, D.; Marz, M.; Schneider, S.; Hoffmann-Vogel, R.

    2017-02-01

    We study the structure and the electronic properties of Au nanocontacts created by controlled electromigration of thin film devices, a method frequently used to contact molecules. In contrast to electromigration testing, a current is applied in a cyclic fashion and during each cycle the resistance increase of the metal upon heating is used to avoid thermal runaway. In this way, nanometer sized-gaps are obtained. The thin film devices with an optimized structure at the origin of the electromigration process are made by shadow evaporation without contamination by organic materials. Defining rounded edges and a thinner area in the center of the device allow to pre-determine the location where the electromigration takes place. Scanning force microscopy images of the pristine Au film and electromigrated contact show its grainy structure. Through electromigration, a 1.5 μm-wide slit is formed, with extensions only on the anode side that had previously not been observed in narrower structures. It is discussed whether this could be explained by asymmetric heating of both electrodes. New grains are formed in the slit and on the extensions on both, the anode and the cathode side. The smaller structures inside the slit lead to an electrode distance below 150 nm. Kelvin probe force microscopy images show a local work function difference with fluctuations of 70 mV on the metal before electromigration. Between the electrodes, disconnected through electromigration, a work function difference of 3.2 V is observed due to charging. Some of the grains newly formed by electromigration are electrically disconnected from the electrodes.

  8. Structural plasticity of the nuclear envelope and the endoplasmic reticulum

    Directory of Open Access Journals (Sweden)

    Sheval E. V.

    2014-09-01

    Full Text Available The nuclear envelope is a double membrane structure, continuous with endoplasmic reticulum, and the morphological organization of both these structures is quite conservative. However, nuclear envelope and endoplasmic reticulum demonstrate distinct structural plasticity, i. e., based on common organization, cells may form various non-canonical membrane structures that are observed only in specialized types of cells or appear in different pathologies. In this review, we will discuss the mechanisms of the biogenesis of such non-canonical structures, and the possible role of this plasticity in the development of pathological processes.

  9. Local structure of solid Rb at megabar pressures

    Energy Technology Data Exchange (ETDEWEB)

    De Panfilis, S. [Centre for Life Nano Science IIT@Sapienza, Istituto Italiano di Tecnologia, I-00161 Roma (Italy); Gorelli, F.; Santoro, M. [INO-CNR and LENS, I-50019 Sesto Fiorentino, Firenze (Italy); Ulivi, L. [ISC-CNR, I-50019 Sesto Fiorentino, Firenze (Italy); Gregoryanz, E. [School of Physics and Astronomy, Centre for Science Under Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Irifune, T.; Shinmei, T. [Geodynamics Research Center, Ehime University, Matsuyama 790-8577 (Japan); Kantor, I.; Mathon, O.; Pascarelli, S. [European Synchrotron Radiation Facility, F-38043 Grenoble (France)

    2015-06-07

    We have investigated the local and electronic structure of solid rubidium by means of x-ray absorption spectroscopy up to 101.0 GPa, thus doubling the maximum investigated experimental pressure. This study confirms the predicted stability of phase VI and was completed by the combination of two pivotal instrumental solutions. On one side, we made use of nanocrystalline diamond anvils, which, contrary to the more commonly used single crystal diamond anvils, do not generate sharp Bragg peaks (glitches) at specific energies that spoil the weak fine structure oscillations in the x-ray absorption cross section. Second, we exploited the performance of a state-of-the-art x-ray focussing device yielding a beam spot size of 5 × 5 μm{sup 2}, spatially stable over the entire energy scan. An advanced data analysis protocol was implemented to extract the pressure dependence of the structural parameters in phase VI of solid Rb from 51.2 GPa up to the highest pressure. A continuous reduction of the nearest neighbour distances was observed, reaching about 6% over the probed pressure range. We also discuss a phenomenological model based on the Einstein approximation to describe the pressure behaviour of the mean-square relative displacement. Within this simplified scheme, we estimate the Grüneisen parameter for this high pressure Rb phase to be in the 1.3–1.5 interval.

  10. Local atomic structures of single-component metallic glasses

    Science.gov (United States)

    Trady, Salma; Hasnaoui, Abdellatif; Mazroui, M.'hammed; Saadouni, Khalid

    2016-10-01

    In this study we examine the structural properties of single-component metallic glasses of aluminum. We use a molecular dynamics simulation based on semi-empirical many-body potential, derived from the embedded atom method (EAM). The radial distribution function (RDF), common neighbors analysis method (CNA), coordination number analysis (CN) and Voronoi tessellation are used to characterize the metal's local structure during the heating and cooling (quenching). The simulation results reveal that the melting temperature depends on the heating rate. In addition, atomic visualization shows that the structure of aluminum after fast quenching is in a glassy state, confirmed quantitatively by the splitting of the second peak of the radial distribution function, and by the appearance of icosahedral clusters observed via CNA technique. On the other hand, the Wendt-Abraham parameters are calculated to determine the glass transition temperature (Tg), which depends strongly on the cooling rate; it increases while the cooling rate increases. On the basis of CN analysis and Voronoi tessellation, we demonstrate that the transition from the Al liquid to glassy state is mainly due to the formation of distorted and perfect icosahedral clusters.

  11. Local causal structures, Hadamard states and the principle of local covariance in quantum field theory

    Energy Technology Data Exchange (ETDEWEB)

    Dappiaggi, Claudio [Erwin Schroedinger Institut fuer Mathematische Physik, Wien (Austria); Pinamonti, Nicola [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Porrmann, Martin [KwaZulu-Natal Univ. (South Africa). Quantum Research Group, School of Physics; National Institute for Theoretical Physics, Durban (South Africa)

    2010-01-15

    In the framework of the algebraic formulation, we discuss and analyse some new features of the local structure of a real scalar quantum field theory in a strongly causal spacetime. In particular we use the properties of the exponential map to set up a local version of a bulk-to-boundary correspondence. The bulk is a suitable subset of a geodesic neighbourhood of any but fixed point p of the underlying background, while the boundary is a part of the future light cone having p as its own tip. In this regime, we provide a novel notion for the extended *-algebra of Wick polynomials on the said cone and, on the one hand, we prove that it contains the information of the bulk counterpart via an injective *-homomorphism while, on the other hand, we associate to it a distinguished state whose pull-back in the bulk is of Hadamard form. The main advantage of this point of view arises if one uses the universal properties of the exponential map and of the light cone in order to show that, for any two given backgrounds M and M{sup '} and for any two subsets of geodesic neighbourhoods of two arbitrary points, it is possible to engineer the above procedure such that the boundary extended algebras are related via a restriction homomorphism. This allows for the pull-back of boundary states in both spacetimes and, thus, to set up a machinery which permits the comparison of expectation values of local field observables in M and M{sup '}. (orig.)

  12. Local causal structures, Hadamard states and the principle of local covariance in quantum field theory

    Energy Technology Data Exchange (ETDEWEB)

    Dappiaggi, Claudio [Erwin Schroedinger Institut fuer Mathematische Physik, Wien (Austria); Pinamonti, Nicola [Hamburg Univ. (Germany). 2. Inst. fuer Theoretische Physik; Porrmann, Martin [KwaZulu-Natal Univ. (South Africa). Quantum Research Group, School of Physics; National Institute for Theoretical Physics, Durban (South Africa)

    2010-01-15

    In the framework of the algebraic formulation, we discuss and analyse some new features of the local structure of a real scalar quantum field theory in a strongly causal spacetime. In particular we use the properties of the exponential map to set up a local version of a bulk-to-boundary correspondence. The bulk is a suitable subset of a geodesic neighbourhood of any but fixed point p of the underlying background, while the boundary is a part of the future light cone having p as its own tip. In this regime, we provide a novel notion for the extended *-algebra of Wick polynomials on the said cone and, on the one hand, we prove that it contains the information of the bulk counterpart via an injective *-homomorphism while, on the other hand, we associate to it a distinguished state whose pull-back in the bulk is of Hadamard form. The main advantage of this point of view arises if one uses the universal properties of the exponential map and of the light cone in order to show that, for any two given backgrounds M and M{sup '} and for any two subsets of geodesic neighbourhoods of two arbitrary points, it is possible to engineer the above procedure such that the boundary extended algebras are related via a restriction homomorphism. This allows for the pull-back of boundary states in both spacetimes and, thus, to set up a machinery which permits the comparison of expectation values of local field observables in M and M{sup '}. (orig.)

  13. Cosmological parameter dependence in local string theories of structure formation

    CERN Document Server

    Copeland, E J; Steer, D A; Magueijo, Joao

    2000-01-01

    We perform the most accurate study to date of the dependence on cosmological parameters of structure formation with local cosmic strings. The crucial new ingredients are the inclusion of the effects of gravitational backreaction on the evolution of the network, and the accurate evolution of the network through the radiation to matter transition. Our work re-iterates the fact that expanding Universe numerical simulations only probe a transient regime, and we incorporate our results into the unequal time correlators recently measured. We then compute the CMB and CDM fluctuations' power spectra for various values of the Hubble constant $H_0$ and baryon fraction $\\Omega_b$. We find that, whereas the dependence on $\\Omega_b$ is negligible, there is still a strong dependence on $H_0$.

  14. Quantum correlations and light localization in disordered nanophotonic structures

    DEFF Research Database (Denmark)

    Smolka, Stephan

    This thesis reports results on quantum properties of light in multiple-scattering nano-structured materials. Spatial quantum correlations of photons are demonstrated experimentally that are induced by multiple scattering of squeezed light and of purely quantum origin. By varying the quantum state...... of the light source, positive and negative spatial quantum correlations are observed. Angular-resolved measurements of multiply scattered photons show the innite range of the correlation function in the diusive regime. The multiply scattered light is characterized in frequency-resolved quantum noise...... photon uctuations that is larger than the predicted enhancement of the backscattered light intensity. Characterizing the quantum properties of multiply scattered light forms the basis for studies of quantum interference and quantum entanglement in disordered media. Anderson localization of light...

  15. Compare local pocket and global protein structure models by small structure patterns

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns; and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11; 669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://www.cbrc.kaust.edu.sa/prosta/

  16. Human estrogen sulfotransferase gene (STE): Cloning, structure, and chromosomal localization

    Energy Technology Data Exchange (ETDEWEB)

    Her, Chengtao; Aksoy, I.A.; Weinshilboum, M. [Mayo Foundation, Rochester, MI (United States)] [and others

    1995-09-01

    Sulfation is an important pathway in the metabolism of estrogens. We recently cloned a human liver estrogen sulfotransferase (EST) cDNA. We have now determined the structure and chromosomal localization of the EST gene, STE, as a step toward molecular genetic studies of the regulation of EST in humans. STE spans approximately 20 kb and consists of 8 exons, ranging in length from 95 to 181 bp. The locations of most exon-intron splice junctions within STE are identical to those found in a human phenol ST (PST) gene, STM, and in a rat PST gene. In addition, the locations of five STE introns are also conserved in the human dehydroepiandrosterone (DBEA) ST gene, STD. The 5{prime} flanking region of STE contains one CCAAT and two TATA sequences. The location of one of the TATA box elements is in excellent agreement with the site of transcription initiation as determined by 5{prime}-rapid amplification of cDNA ends. STE was mapped to human chromosome 4q13.1 by fluorescence in situ hybridization. Cloning and structural characterization of STE will now make it possible to study potential molecular genetic mechanisms involved in the regulation of EST in human tissues. 50 refs., 6 figs., 1 tab.

  17. Local structure of the magnetotail current sheet: 2001 Cluster observations

    Directory of Open Access Journals (Sweden)

    A. Runov

    2006-03-01

    Full Text Available Thirty rapid crossings of the magnetotail current sheet by the Cluster spacecraft during July-October 2001 at a geocentric distance of 19 RE are examined in detail to address the structure of the current sheet. We use four-point magnetic field measurements to estimate electric current density; the current sheet spatial scale is estimated by integration of the translation velocity calculated from the magnetic field temporal and spatial derivatives. The local normal-related coordinate system for each case is defined by the combining Minimum Variance Analysis (MVA and the curlometer technique. Numerical parameters characterizing the plasma sheet conditions for these crossings are provided to facilitate future comparisons with theoretical models. Three types of current sheet distributions are distinguished: center-peaked (type I, bifurcated (type II and asymmetric (type III sheets. Comparison to plasma parameter distributions show that practically all cases display non-Harris-type behavior, i.e. interior current peaks are embedded into a thicker plasma sheet. The asymmetric sheets with an off-equatorial current density peak most likely have a transient nature. The ion contribution to the electric current rarely agrees with the current computed using the curlometer technique, indicating that either the electron contribution to the current is strong and variable, or the current density is spatially or temporally structured.

  18. Band gaps in grid structure with periodic local resonator subsystems

    Science.gov (United States)

    Zhou, Xiaoqin; Wang, Jun; Wang, Rongqi; Lin, Jieqiong

    2017-09-01

    The grid structure is widely used in architectural and mechanical field for its high strength and saving material. This paper will present a study on an acoustic metamaterial beam (AMB) based on the normal square grid structure with local resonators owning both flexible band gaps and high static stiffness, which have high application potential in vibration control. Firstly, the AMB with variable cross-section frame is analytically modeled by the beam-spring-mass model that is provided by using the extended Hamilton’s principle and Bloch’s theorem. The above model is used for computing the dispersion relation of the designed AMB in terms of the design parameters, and the influences of relevant parameters on band gaps are discussed. Then a two-dimensional finite element model of the AMB is built and analyzed in COMSOL Multiphysics, both the dispersion properties of unit cell and the wave attenuation in a finite AMB have fine agreement with the derived model. The effects of design parameters of the two-dimensional model in band gaps are further examined, and the obtained results can well verify the analytical model. Finally, the wave attenuation performances in three-dimensional AMBs with equal and unequal thickness are presented and discussed.

  19. Cell-free synthesis of functional human epidermal growth factor receptor: Investigation of ligand-independent dimerization in Sf21 microsomal membranes using non-canonical amino acids

    Science.gov (United States)

    Quast, Robert B.; Ballion, Biljana; Stech, Marlitt; Sonnabend, Andrei; Varga, Balázs R.; Wüstenhagen, Doreen A.; Kele, Péter; Schiller, Stefan M.; Kubick, Stefan

    2016-01-01

    Cell-free protein synthesis systems represent versatile tools for the synthesis and modification of human membrane proteins. In particular, eukaryotic cell-free systems provide a promising platform for their structural and functional characterization. Here, we present the cell-free synthesis of functional human epidermal growth factor receptor and its vIII deletion mutant in a microsome-containing system derived from cultured Sf21 cells. We provide evidence for embedment of cell-free synthesized receptors into microsomal membranes and asparagine-linked glycosylation. Using the cricket paralysis virus internal ribosome entry site and a repetitive synthesis approach enrichment of receptors inside the microsomal fractions was facilitated thereby providing analytical amounts of functional protein. Receptor tyrosine kinase activation was demonstrated by monitoring receptor phosphorylation. Furthermore, an orthogonal cell-free translation system that provides the site-directed incorporation of p-azido-L-phenylalanine is characterized and applied to investigate receptor dimerization in the absence of a ligand by photo-affinity cross-linking. Finally, incorporated azides are used to generate stable covalently linked receptor dimers by strain-promoted cycloaddition using a novel linker system. PMID:27670253

  20. The model of local mode analysis for structural acoustics of box structures

    Science.gov (United States)

    Ngai, King-Wah

    Structure-borne noise is a new noise pollution problem emerging from railway concrete box structures in Hong Kong. Its low frequency noise with intermittent effect can cause considerable nuisance to neighborhoods. The tonal noise peaks in this low frequency range should be one of the important factors in structure-borne noise analysis. In the acoustic field, the deterministic analysis of all the resonant modes of vibration is generally considered as not practical. Many acoustic experts use the statistical energy analysis as the main tool for the noise investigation whereas the application of the experimental modal analysis in the structural acoustic problem is comparatively rare. In the past, most studies mainly focused on the structure-borne noise measurement and analysis. The detail study of the cause of structure-borne noise is lack, especially for the rectangular concrete box structure. In this dissertation, an experimental and analytical approach is adopted to study a typical concrete box model. This thesis aims at confirming the importance of modal analysis in the structure-borne noise study and then at identifying the local vibration modes along the cross-section of box structure. These local modes are responsible for the structure-borne noise radiation. The findings of this study suggest that the web of viaduct cross-section is not as rigid as assumed in the conventional viaduct design and the web face is likely to be more flexible in the vertical displacement of the concrete viaduct. Two types of local vibration modes along the cross-section are identified: the centre mode and the web mode. At the top panel of the viaduct, the centre mode has movement in the middle but not at the edges. The web mode has movement at the edges with the middle fixed. The combined centre and web mode has been found to be important in the structural acoustics of the concrete box structure. In the actual concrete viaduct, the coincidence frequency is especially low (often around

  1. Heterotrimeric G-protein, Gα16, is a critical downstream effector of non-canonical Wnt signaling and a potent inhibitor of transformed cell growth in non small cell lung cancer.

    Directory of Open Access Journals (Sweden)

    Sreedevi Avasarala

    Full Text Available G-protein-coupled receptors (GPCR are the largest family of cell surface molecules that play important role/s in a number of biological and pathological processes including cancers. Earlier studies have highlighted the importance of Wnt7a signaling via its cognate receptor Frizzled9, a GPCR, in inhibition of cell proliferation, anchorage-independent growth, and reversal of transformed phenotype in non small cell lung cancer primarily through activation of the tumor suppressor, PPARγ. However, the G-protein effectors that couple to this important tumor suppressor pathway have not been identified, and are of potential therapeutic interest. In this study, by using two independent Wnt7a/Frizzled9-specific read-outs, we identify Gα16 as a novel downstream effector of Wnt7a/Frizzled9 signaling. Interestingly, Gα16 expression is severely down-regulated, both at the messenger RNA levels and protein levels, in many non small cell lung cancer cell lines. Additionally, through gene-specific knock-downs and expression of GTPase-deficient forms (Q212L of Gα16, we also establish Gα16 as a novel regulator of non small cell lung cancer cell proliferation and anchorage-independent cell growth. Taken together, our data not only establish the importance of Gα16 as a critical downstream effector of the non-canonical Wnt signaling pathway but also as a potential therapeutic target for the treatment of non small cell lung cancer.

  2. Local Structural Distortion Induced Uniaxial Negative Thermal Expansion in Nanosized Semimetal Bismuth.

    Science.gov (United States)

    Li, Qiang; Zhu, He; Zheng, Lirong; Fan, Longlong; Ren, Yang; Chen, Jun; Deng, Jinxia; Xing, Xianran

    2016-11-01

    The corrugated layer structure bismuth has been successfully tailored into negative thermal expansion along c axis by size effect. Pair distribution function and extended X-ray absorption fine structure are combined to reveal the local structural distortion for nanosized bismuth. The comprehensive method to identify the local structure of nanomaterials can benefit the regulating and controlling of thermal expansion in nanodivices.

  3. Local genetic structure in a white-bearded manakin population.

    Science.gov (United States)

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present.

  4. Crustal structure beneath the southern Korean Peninsula from local earthquakes

    Science.gov (United States)

    Kim, Kwang-Hee; Park, Jung-Ho; Park, Yongcheol; Hao, Tian-Yao; Kim, Han-Joon

    2017-02-01

    The three-dimensional subsurface structure beneath the southern Korean Peninsula is poorly known, even though such information could be key in verifying or rejecting several competing models of the tectonic evolution of East Asia. We constructed a three-dimensional velocity model of the upper crust beneath the southern Korean Peninsula using 19,935 P-wave arrivals from 747 earthquakes recorded by high-density local seismic networks. Results show significant lateral and vertical variations: velocity increases from northwest to southeast at shallow depths, and significant velocity variations are observed across the South Korea Tectonic Line between the Okcheon Fold Belt and the Youngnam Massif. Collision between the North China and South China blocks during the Early Cretaceous might have caused extensive deformation and the observed negative velocity anomalies in the region. The results of the tomographic inversion, combined with the findings of previous studies of Bouguer and isostatic gravity anomalies, indicate the presence of high-density material in the upper and middle crust beneath the Gyeongsang Basin in the southeastern Korean Peninsula. Although our results partially support the indentation tectonic model, it is still premature to discard other tectonic evolution models because our study only covers the southern half of the peninsula.

  5. Historic timber skeleton structures and the local seismic culture

    Science.gov (United States)

    Bostenaru, M.

    2009-04-01

    This presentation deals with the employment of timber skeleton structure and the local seismic culture. After the 1755 earthquake in the reconstruction of Lisbon a type of building with timber skeleton and masonry infill called "gaiola pombalina" was promoted, since this was designed to better resists earthquakes. "Gaiola" means cage, and it was also named after the Marques de Pombal who introduced it in the reconstruction following the earthquake. The „gaiola pombalina" presents a timber skeleton with Saint Andrew crosses in the interior walls with masonry infill and thick masonry load bearing walls loosing in thickness to the upper floors in the exterior walls. The masonry can fall out during earthquakes but the building remains staying given the interior timber skeleton. The type of buildings with timber structure and (masonry) infill behaved well in earthquakes in various parts of the earth, like Nepal (the dhaji dewary type), Pakistan, Turkey (the himiş type after the 1999 earthquake) [both latter types were researched by Langenbach, www.conservationtech.com and www.traditional-is-modern.net] and also in Germany after the 1356 earthquake (the Southern German subtype of Fachwerk). Also in Italy a subtype called "casa baraccata" was promoted in a construction code to a similar time (following the 1783 earthquake in Southern Italy, see Tobriner 1983) as that of the "gaiola pombalina", the time of the Baroque, when town planning acquired another status. Unlike at the "gaiola pombalina" the "casa baraccata" the timber skeleton is at the exterior walls. For this reason this type of buildings is considered to be an expression of the local seismic culture. However, this type of buildings is common also for areas where seismic risk is not an issue, like half-timbered in England and the northern subtype of Fachwerk in Northern Germany, and in some high seismic risk regions with mountains and timber resources like Romania is not spread. Given these premises the author

  6. Evidence of non-canonical NOTCH signaling

    DEFF Research Database (Denmark)

    Traustadóttir, Gunnhildur Ásta; Jensen, Charlotte H; Thomassen, Mads

    2016-01-01

    Dlk1(+/+) and Dlk1(-/-) mouse tissues at E16.5, we demonstrated that several NOTCH signaling pathways indeed are affected by DLK1 during tissue development, and this was supported by a lower activation of NOTCH1 protein in Dlk1(+/+) embryos. Likewise, but using a distinct Dlk1-manipulated (si...

  7. Strength through structure: visualization and local assessment of the trabecular bone structure

    Energy Technology Data Exchange (ETDEWEB)

    Raeth, C; Monetti, R; Bauer, J; Sidorenko, I [Max-Planck Institut fuer Extraterrestrische Physik, Giessenbachstrasse 1, 85748 Garching (Germany); Mueller, D [Department of Radiology, Technische Universitaet Muenchen, Klinikum rechts der Isar, Ismaninger Strasse 22, 81675 Munich (Germany); Matsuura, M [Institute of Anatomy, Ludwig Maximilians Universitaet Muenchen, Pettenkoferstrasse 11, 80336 Muenchen (Germany); Lochmueller, E-M [Department of Gynaecology I, Ludwig Maximilians Universitaet Muenchen, Maistrasse 11, 80337 Muenchen (Germany); Zysset, P [Institute for Lightweight Design and Structural Biomechanics, Vienna University of Technology (TU-Wien), Gusshausstrasse 27-29, 1040 Wien (Austria); Eckstein, F [Paracelsus Medical University Salzburg, Strubergasse 21, 5020 Salzburg (Austria)], E-mail: cwr@mpe.mpg.de

    2008-12-15

    The visualization and subsequent assessment of the inner human bone structures play an important role for better understanding the disease- or drug-induced changes of bone in the context of osteoporosis giving prospect for better predictions of bone strength and thus of the fracture risk of osteoporotic patients. In this work, we show how the complex trabecular bone structure can be visualized using {mu}CT imaging techniques at an isotropic resolution of 26 {mu}m. We quantify these structures by calculating global and local topological and morphological measures, namely Minkowski functionals (MFs) and utilizing the (an-)isotropic scaling index method (SIM) and by deriving suitable texture measures based on MF and SIM. Using a sample of 151 specimens taken from human vertebrae in vitro, we correlate the texture measures with the mechanically measured maximum compressive strength (MCS), which quantifies the strength of the bone probe, by using Pearson's correlation coefficient. The structure parameters derived from the local measures yield good correlations with the bone strength as measured in mechanical tests. We investigate whether the performance of the texture measures depends on the MCS value by selecting different subsamples according to MCS. Considering the whole sample the results for the newly defined parameters are better than those obtained for the standard global histomorphometric parameters except for bone volume/total volume (BV/TV). If a subsample consisting only of weak bones is analysed, the local structural analysis leads to similar and even better correlations with MCS as compared to BV/TV. Thus, the MF and SIM yield additional information about the stability of the bone especially in the case of weak bones, which corroborates the hypothesis that the bone structure (and not only its mineral mass) constitutes an important component of bone stability.

  8. Expectation and Locality Effects in German Verb-final Structures.

    Science.gov (United States)

    Levy, Roger P; Keller, Frank

    2013-02-01

    Probabilistic expectations and memory limitations are central factors governing the real-time comprehension of natural language, but how the two factors interact remains poorly understood. One respect in which the two factors have come into theoretical conflict is the documentation of both locality effects, in which more dependents preceding a governing verb increase processing difficulty at the verb, and anti-locality effects, in which more preceding dependents facilitate processing at the verb. However, no controlled study has previously demonstrated both locality and anti-locality effects in the same type of dependency relation within the same language. Additionally, many previous demonstrations of anti-locality effects have been potentially confounded with lexical identity, plausibility, and sentence position. Here, we provide new evidence of both locality and anti-locality effects in the same type of dependency relation in a single language-verb-final constructions in German-while controlling for lexical identity, plausibility, and sentence position. In main clauses, we find clear anti-locality effects, with the presence of a preceding dative argument facilitating processing at the final verb; in subject-extracted relative clauses with identical linear ordering of verbal dependents, we find both anti-locality and locality effects, with processing facilitated when the verb is preceded by a dative argument alone, but hindered when the verb is preceded by both the dative argument and an adjunct. These results indicate that both expectations and memory limitations need to be accounted for in any complete theory of online syntactic comprehension.

  9. The emergence of a coherent structure for coherent structures: localized states in nonlinear systems

    OpenAIRE

    Dawes, Jonathan

    2010-01-01

    Coherent structures emerge from the dynamics of many kinds of dissipative, externally driven, nonlinear systems, and continue to provoke new questions that challenge our physical and mathematical understanding. In one specific sub-class of such problems, where a pattern-forming, or `Turing', instability occurs, rapid progress has been made recently in our understanding of the formation of localized states: patches of regular pattern surrounded by the unpatterned homogeneous background state. ...

  10. Superpose3D: a local structural comparison program that allows for user-defined structure representations.

    Directory of Open Access Journals (Sweden)

    Pier Federico Gherardini

    Full Text Available Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D.

  11. Alignment-free local structural search by writhe decomposition

    OpenAIRE

    2010-01-01

    Motivation: Rapid methods for protein structure search enable biological discoveries based on flexibly defined structural similarity, unleashing the power of the ever greater number of solved protein structures. Projection methods show promise for the development of fast structural database search solutions. Projection methods map a structure to a point in a high-dimensional space and compare two structures by measuring distance between their projected points. These methods offer a tremendous...

  12. Alternative Measured-Service Rate Structures for Local Telephone Service,

    Science.gov (United States)

    1980-06-01

    Pricing," American Economic Review , Vol. 60, 1970, pp. 265-283. Cosgrove, J. G. and P. G. Linhart, "Customer Choices Under Local Measured Telephone...November 1976. "Optimal Pricing of Local Telephone Service," American Economic Review , Vol. 68, September 1978, pp. 517-537. , "Economic Issues in

  13. A special kind of local structure in the CMB intensity maps: duel peak structure

    Institute of Scientific and Technical Information of China (English)

    Hao Liu; Ti-Pei Li

    2009-01-01

    We study the local structure of Cosmic Microwave Background (CMB) tem-perature maps released by the Wilkinson Microwave Anisotropy Probe (WMAP) team, and find a new kind of structure, which can be described as follows: a peak (or valley) of average temperature is often followed by a peak of temperature fluctuation that is 4° away. This structure is important for the following reasons: both the well known cold spot detected by Cruz et al. and the hot spot detected by Vielva et al. with the same technology (the third spot in their article) have such structure; more spots that are similar to them can be found on CMB maps and they also tend to be significant cold/hot spots; if we change the 4° characteristic into an artificial one, such as 3° or 5°, there will be less "similar spots", and the temperature peaks or valleys will be less significant. The presented "sim-ilar spots" have passed a strict consistency test which requires them to be significant on at least three different CMB temperature maps. We hope that this article could arouse some interest in the relationship of average temperature with temperature fluctuation in local areas; meanwhile, we are also trying to find an explanation for it which might be important to CMB observation and theory.

  14. Average and local structure of selected metal deuterides

    Energy Technology Data Exchange (ETDEWEB)

    Soerby, Magnus H.

    2005-07-01

    at ambient and low temperatures. The Switendick criterion is always fulfilled. The local deuterium arrangement in the disordered cubic phase at 298 K resemble that of the ordered monoclinic low-temperature phase at 150 K for length scales up to 4 Aa or three coordination spheres. The nearest and next-nearest deuterium neighbours are statically displaced from their average positions to adapt interatomic distances in better agreement with those in the ordered structure. There are no significant differences in the short-range order around the onset temperature for ordering (252 K and 248 K) as compared to that observed at 298 K. (Author)

  15. Rich Localized Coherent Structures of the (2+1)-Dimensional Broer-Kaup-Kupershmidt Equation

    Institute of Scientific and Technical Information of China (English)

    LI Hua-Mei

    2003-01-01

    Using a Backlund transformation and the variable separation approach, we find there exist abundant localized coherent structures for the (2 + 1)-dimensional Broer-Kaup-Kupershmidt (BKK) system. The abundance of the localized structures for the model is introduced by the entrance of an arbitrary function of the seed solution. For some specialselections of the arbitrary function, it is shown that the localized structures of the BKK equation may be dromions, lumps, ring solitons, peakons, or fractal solitons etc.

  16. Lightfront holography and area density of entropy associated with quantum localization on wedge-horizon

    Energy Technology Data Exchange (ETDEWEB)

    Schroer, Bert [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)]. E-mail: schroer@cbpf.br

    2002-08-01

    The lightfront quantization of the 70s is reviewed in the more rigorous setting of lightfront (LF) restriction of free fields in which the lightfront is considered to be linear extension of the upper causal horizon of a wedge region. Particular attention is given to the change of localization structure in passing from the wedge to its horizon which results in the emergence of a transverse quantum mechanical substructure of the QFT on the horizon and its lightfront extension. The vacuum fluctuations of QFT on the LF are compressed into the direction of the lightray (where they become associated with a chiral QFT) and lead to the notion of area density of a 'split localization' entropy. To overcome the limitation of this restriction approach and include interacting theories with non-canonical short distance behavior, we introduce a new concept of algebraic lightfront holography which uses ideas of algebraic QFT, in particular the modular structure of its associated local operator algebras. In this way the localization properties of LF degrees of freedom including the absence of transverse vacuum fluctuations are confirmed to be stable against interactions. The important universality aspect of lightfront holography is emphasized. Only in this way one is able to extract from the 'split-localization' entropy a split-independent additive entropy-like measure of the entanglement of the vacuum upon restriction to the horizon algebra. (author)

  17. Local Large-Scale Structure and the Assumption of Homogeneity

    Science.gov (United States)

    Keenan, Ryan C.; Barger, Amy J.; Cowie, Lennox L.

    2016-10-01

    Our recent estimates of galaxy counts and the luminosity density in the near-infrared (Keenan et al. 2010, 2012) indicated that the local universe may be under-dense on radial scales of several hundred megaparsecs. Such a large-scale local under-density could introduce significant biases in the measurement and interpretation of cosmological observables, such as the inferred effects of dark energy on the rate of expansion. In Keenan et al. (2013), we measured the K-band luminosity density as a function of distance from us to test for such a local under-density. We made this measurement over the redshift range 0.01 0.07, we measure an increasing luminosity density that by z ~ 0.1 rises to a value of ~ 1.5 times higher than that measured locally. This implies that the stellar mass density follows a similar trend. Assuming that the underlying dark matter distribution is traced by this luminous matter, this suggests that the local mass density may be lower than the global mass density of the universe at an amplitude and on a scale that is sufficient to introduce significant biases into the measurement of basic cosmological observables. At least one study has shown that an under-density of roughly this amplitude and scale could resolve the apparent tension between direct local measurements of the Hubble constant and those inferred by Planck team. Other theoretical studies have concluded that such an under-density could account for what looks like an accelerating expansion, even when no dark energy is present.

  18. Long term structural dynamics of mechanical systems with local nonlinearities

    NARCIS (Netherlands)

    Fey, R.H.B.; Campen, D.H. van; Kraker, A. de

    1996-01-01

    This paper deals with the long term behavior of periodically excited mechanical systems consisting of linear components and local nonlinearities. The number of degrees of freedom of the linear components is reduced by applying a component mode synthesis technique. Lyapunov exponents are used to iden

  19. The elastic response of sandwich structures to local loading

    NARCIS (Netherlands)

    Koysin, V.; Skvortsov, Vitaly; Krahmalev, Sergey; Shipsha, Andrey

    2004-01-01

    The paper addresses the elastic response of sandwich panels to local static and dynamic loading. The bottom face is assumed to be clamped, so that the overall bending is eliminated. The governing equations are derived using the static Lamé equations for the core and the thin plate Kirchoff–Love

  20. Global Local Structural Optimization of Transportation Aircraft Wings

    NARCIS (Netherlands)

    Ciampa, P.D.; Nagel, B.; Van Tooren, M.J.L.

    2010-01-01

    The study presents a multilevel optimization methodology for the preliminary structural design of transportation aircraft wings. A global level is defined by taking into account the primary wing structural components (i.e., ribs, spars and skin) which are explicitly modeled by shell layered finite e

  1. DELORES - A System for Detection and Localization of Structural Damages

    DEFF Research Database (Denmark)

    Johansen, Rasmus Johan; Ulriksen, Martin Dalgaard; Damkilde, Lars

    2016-01-01

    Today, structural inspections of large structures, like wind turbines, bridges, etc., are often performed manually by highly trained personnel. Obviously, this inspection approach is both extremely costly and tedious, for which reason this paper provides a presentation of an alternative approach ...

  2. Global/local methods research using a common structural analysis framework

    Science.gov (United States)

    Knight, Norman F., Jr.; Ransom, Jonathan B.; Griffin, O. H., Jr.; Thompson, Danniella M.

    1991-01-01

    Methodologies for global/local stress analysis are described including both two- and three-dimensional analysis methods. These methods are being developed within a common structural analysis framework. Representative structural analysis problems are presented to demonstrate the global/local methodologies being developed.

  3. Effects of broadband ultraviolet B on non-canonical Wnt pathways in human epidermal melanocytes%宽谱中波紫外线对人表皮黑素细胞非经典Wnt通路的作用研究

    Institute of Scientific and Technical Information of China (English)

    王辉; 林彤; 王千秋

    2015-01-01

    , CCK-8 assay was performed to evaluate the proliferative activity of melanocytes, dopa oxidation assay to estimate the activity of tyrosinase, and sodium hydroxide (NaOH)-lysis method was used to determine melanin content.Real-time fluorescence-based quantitative PCR was conducted to measure the mRNA expressions of genes involved in non-canonical Wnt pathways in melanocytes after irradiation with BB-UVB at 30, 50 and 100 mJ/cm2.Western blot was carried out to determine the expressions of proteins involved in non-canonical Wnt pathways in melanocytes before and after irradiation with BB-UVB of 100 mJ/cm2.The melanocytes receiving no treatment served as the control group.Statistical analysis was carried out by one-way analysis of variance followed by least significant difference (LSD)-t test for multiple group comparisons and by the independent sample t test for two-group comparisons.Results After irradiation with BB-UVB at 10-300 mJ/cm2, the proliferative activity of melanocytes was gradually reduced compared with the control group (all P < 0.05), and the survival rate of melanocytes was less than 50% when the irradiation dose of BB-UVB was higher than 100 mJ/cm2.Furthermore, tyrosinase activity gradually increased in melanocytes after irradiation with BB-UVB at 10-100 mJ/cm2 compared with the control group, and the increase was statistically significant at the radiation dose of 100 mJ/cm2 (P < 0.05).Compared with the control group, the WIF-1 mRNA expression level decreased, while c-Jun N-terminal kinase (JNK), microphthalmia-associated transcription factor (MITF), Ras-related C3 botulinum toxin substrate 1 (RAC 1) and tyrosinase (TYR) mRNA expression levels increased in melanocytes after irradiation with BB-UVB at 30, 50 and 100 mJ/cm2 (all P < 0.05);the WNT5A mRNA expression significantly decreased in melanocytes irradiated with 30 and 50 mJ/cm2 BB-UVB, but increased in those irradiated with 100 mJ/cm2 BB-UVB (all P < 0.05).The radiation with 100 mJ/cm2 BB

  4. Oscillation structure of localized perturbations in modulationally unstable media

    Science.gov (United States)

    Biondini, Gino; Li, Sitai; Mantzavinos, Dionyssios

    2016-12-01

    We characterize the properties of the asymptotic stage of modulational instability arising from localized perturbations of a constant background, including the number and location of the individual peaks in the oscillation region. We show that, for long times, the solution tends to an ensemble of classical (i.e., sech-shaped) solitons of the focusing nonlinear Schrödinger equation (as opposed to the various breatherlike solutions of the same equation with a nonzero background). We also confirm the robustness of the theoretical results by comparing the analytical predictions with careful numerical simulations with a variety of initial conditions, which confirm that the evolution of modulationally unstable media in the presence of localized initial perturbations is indeed described by the same asymptotic state.

  5. Local chiral potentials and the structure of light nuclei

    CERN Document Server

    Piarulli, Maria; Schiavilla, Rocco; Kievsky, Alejandro; Lovato, Alessandro; Marcucci, Laura E; Pieper, Steven C; Viviani, Michele; Wiringa, Robert B

    2016-01-01

    We present fully local versions of the minimally non-local nucleon-nucleon potentials constructed in a previous paper [M.\\ Piarulli {\\it et al.}, Phys.\\ Rev.\\ C {\\bf 91}, 024003 (2015)], and use them in hypersperical-harmonics and quantum Monte Carlo calculations of ground and excited states of $^3$H, $^3$He, $^4$He, $^6$He, and $^6$Li nuclei. The long-range part of these local potentials includes one- and two-pion exchange contributions without and with $\\Delta$-isobars in the intermediate states up to order $Q^3$ ($Q$ denotes generically the low momentum scale) in the chiral expansion, while the short-range part consists of contact interactions up to order $Q^4$. The low-energy constants multiplying these contact interactions are fitted to the 2013 Granada database in two different ranges of laboratory energies, either 0--125 MeV or 0--200 MeV, and to the deuteron binding energy and $nn$ singlet scattering length. Fits to these data are performed for three models characterized by long- and short-range cutof...

  6. Remote sensing image segmentation using local sparse structure constrained latent low rank representation

    Science.gov (United States)

    Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

    2016-09-01

    Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

  7. Local structure of oxygen-deficient Yttrium oxide

    Institute of Scientific and Technical Information of China (English)

    CHENG Xue-Rui; DAI Hai-Yang; QI Ze-Ming; WANG Yu-Yin; ZHANG Guo-Bin

    2013-01-01

    Yttrium oxide thin films have been deposited on Si (100) substrate by using pulsed laser deposition (PLD) method.X-ray diffraction (XRD),hard and soft X-ray absorption spectroscopy (XAFS) are employed to investigate the origin of oxygen vacancies and their influence on the structure and atomic distributions.The XRD results indicate that the Y2O3 thin films strongly orient the (111) axis of the cubic structure.Analyses on the Y K-edge extended X-ray absorption fine structures reveal that the coordination number of Y atoms decreases and the bond length of Y-O contracts due to the loss of oxygen atoms.The X-ray absorption near edge structure analysis together with a theoretical approach further confirms the oxygen vacancies formation and their possible location.

  8. Local Crystalline Structure in an Amorphous Protein Dense Phase.

    Science.gov (United States)

    Greene, Daniel G; Modla, Shannon; Wagner, Norman J; Sandler, Stanley I; Lenhoff, Abraham M

    2015-10-20

    Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumin precipitate particles salted out with ammonium sulfate. We found that the ovalbumin phase-separates into core-shell particles with a core radius of ∼2 μm and shell thickness of ∼0.5 μm. Within this shell region, nanostructures comprised of crystallites of ovalbumin self-assemble into a well-defined bicontinuous network with branches ∼12 nm thick. These results demonstrate that the protein gel is comprised in part of nanocrystalline protein.

  9. Magnetic polaritons in metamagnet layered structures: Spectra and localization properties

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, C.A.A. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil); Albuquerque, E.L. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil)], E-mail: eudenilson@dfte.ufrn.br; Anselmo, D.H.A.L. [Departamento de Fisica, Universidade Federal do Rio Grande do Norte, 59072-970 Natal-RN (Brazil); Vasconcelos, M.S. [Departamento de Ciencias Exatas, Centro Federal de Educacao Tecnologica do Maranhao, 65025-001 Sao Luis-MA (Brazil)

    2008-02-11

    The magnetic polariton propagation in metamagnet layered structures is theoretically studied by using a transfer matrix approach. The layered structures considered here are made up by the stacking of two different layers (also known as building blocks, named A and B), where one of them is a metamagnetic thin film (A), while the other is a non-magnetic insulator thin layer (B). We take into account both the antiferromagnetic (AFM) and ferromagnetic (FM) phases of the metamagnetic material. For the periodic arrangement, the bulk modes are characterized by two large symmetric bands, with non-reciprocal surface modes between them. The quasiperiodic metamagnetic structure is then built up by following the Fibonacci sequence, whose long-range order effect is then investigated, giving rise to an interesting self-similar spectra and a power-law profile.

  10. Identification of local variations within secondary structures of proteins.

    Science.gov (United States)

    Kumar, Prasun; Bansal, Manju

    2015-05-01

    Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C(α) atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely α-helices, 310-helices, π-helices, extended β-strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.php.

  11. SEISMIC RANDOM VIBRATION ANALYSIS OF LOCALLY NONLINEAR STRUCTURES

    Institute of Scientific and Technical Information of China (English)

    ZhaoYan; LinJiahao; ZhangYahui; AnWei

    2003-01-01

    A nonlinear seismic analysis method for complex frame structures subjected to stationary random ground excitations is proposed. The nonlinear elasto-plastic behaviors may take place only on a small part of the structure. The Bouc-Wen differential equation model is used to model the hysteretic characteristics of the nonlinear components. The Pseudo Excitation Method (PEM) is used in solving the linearized random differential equations to replace the solution of the less efficient Lyapunov equation. Numerical results of a real bridge show that .the method proposed is effective for practical engineering analysis.

  12. Defect Structure of Localized Excitons in a WSe2 Monolayer

    KAUST Repository

    Zhang, Shuai

    2017-07-26

    The atomic and electronic structure of intrinsic defects in a WSe2 monolayer grown on graphite was revealed by low temperature scanning tunneling microscopy and spectroscopy. Instead of chalcogen vacancies that prevail in other transition metal dichalcogenide materials, intrinsic defects in WSe2 arise surprisingly from single tungsten vacancies, leading to the hole (p-type) doping. Furthermore, we found these defects to dominate the excitonic emission of the WSe2 monolayer at low temperature. Our work provided the first atomic-scale understanding of defect excitons and paved the way toward deciphering the defect structure of single quantum emitters previously discovered in the WSe2 monolayer.

  13. Improving hybrid statistical and physical forcefields through local structure enumeration.

    Science.gov (United States)

    Conway, Patrick; DiMaio, Frank

    2016-08-01

    Forcefields used in biomolecular simulations are comprised of energetic terms that are physical in nature, based on parameter fitting to quantum mechanical simulation or experimental data, or statistical, drawing off high-resolution structural data to describe distributions of molecular features. Combining the two in a single forcefield is challenging, since physical terms describe some, but not all, of the observed statistics, leading to double counting. In this manuscript, we develop a general scheme for correcting statistical potentials used in combination with physical terms. We apply these corrections to the sidechain torsional potential used in the Rosetta all-atom forcefield. We show the approach identifies instances of double-counted interactions, including electrostatic interactions between sidechain and nearby backbone, and steric interactions between neighboring Cβ atoms within secondary structural elements. Moreover, this scheme allows for the inclusion of intraresidue physical terms, previously turned off to avoid overlap with the statistical potential. Combined, these corrections lead to a forcefield with improved performance on several structure prediction tasks, including rotamer prediction and native structure discrimination.

  14. Local Reasoning about Programs that Alter Data Structures

    DEFF Research Database (Denmark)

    O'Hearn, Peter W.; Reynolds, John Clifton; Yang, Hongseok

    2001-01-01

    We describe an extension of Hoare's logic for reasoning about programs that alter data structures. We consider a low-level storage model based on a heap with associated lookup, update, allocation and deallocation operations, and unrestricted address arithmetic. The assertion language is based...

  15. local

    Directory of Open Access Journals (Sweden)

    Abílio Amiguinho

    2005-01-01

    Full Text Available The process of socio-educational territorialisation in rural contexts is the topic of this text. The theme corresponds to a challenge to address it having as main axis of discussion either the problem of social exclusion or that of local development. The reasons to locate the discussion in this last field of analysis are discussed in the first part of the text. Theoretical and political reasons are there articulated because the question is about projects whose intentions and practices call for the political both in the theoretical debate and in the choices that anticipate intervention. From research conducted for several years, I use contributions that aim at discuss and enlighten how school can be a potential locus of local development. Its identification and recognition as local institution (either because of those that work and live in it or because of those that act in the surrounding context are crucial steps to progressively constitute school as a partner for development. The promotion of the local values and roots, the reconstruction of socio-personal and local identities, the production of sociabilities and the equation and solution of shared problems were the dimensions of a socio-educative intervention, markedly globalising. This scenario, as it is argued, was also, intentionally, one of transformation and of deliberate change of school and of the administration of the educative territoires.

  16. Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm.

    Science.gov (United States)

    Lehtonen, J V; Denessiouk, K; May, A C; Johnson, M S

    1999-02-15

    We have developed a generic tool for the automatic identification of regions of local structural similarity in unrelated proteins having different folds, as well as for defining more global similarities that result from homologous protein structures. The computer program GENFIT has evolved from the genetic algorithm-based three-dimensional protein structure comparison program GA_FIT. GENFIT, however, can locate and superimpose regions of local structural homology regardless of their position in a pair of structures, the fold topology, or the chain direction. Furthermore, it is possible to restrict the search to a volume centered about a region of interest (e.g., catalytic site, ligand-binding site) in two protein structures. We present a number of examples to illustrate the function of the program, which is a parallel processing implementation designed for distribution to multiple machines over a local network or to run on a single multiprocessor computer.

  17. Transcription inactivation through local refolding of the RNA polymerase structure

    Energy Technology Data Exchange (ETDEWEB)

    Belogurov, Georgiy A.; Vassylyeva, Marina N.; Sevostyanova, Anastasiya; Appleman, James R.; Xiang, Alan X.; Lira, Ricardo; Webber, Stephen E.; Klyuyev, Sergiy; Nudler, Evgeny; Artsimovitch, Irina; Vassylyev, Dmitry G.; (OSU); (UAB); (Anadys); (NYUSM)

    2009-02-12

    Structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding. Myxopyronin inhibits bacterial RNA polymerase (RNAP) by an unknown mechanism. Here we report the structure of dMyx - a desmethyl derivative of myxopyronin B - complexed with a Thermus thermophilus RNAP holoenzyme. The antibiotic binds to a pocket deep inside the RNAP clamp head domain, which interacts with the DNA template in the transcription bubble. Notably, binding of dMyx stabilizes refolding of the {beta}'-subunit switch-2 segment, resulting in a configuration that might indirectly compromise binding to, or directly clash with, the melted template DNA strand. Consistently, footprinting data show that the antibiotic binding does not prevent nucleation of the promoter DNA melting but instead blocks its propagation towards the active site. Myxopyronins are thus, to our knowledge, a first structurally characterized class of antibiotics that target formation of the pre-catalytic transcription initiation complex - the decisive step in gene expression control. Notably, mutations designed in switch-2 mimic the dMyx effects on promoter complexes in the absence of antibiotic. Overall, our results indicate a plausible mechanism of the dMyx action and a stepwise pathway of open complex formation in which core enzyme mediates the final stage of DNA melting near the transcription start site, and that switch-2 might act as a molecular checkpoint for DNA loading in response to regulatory signals or antibiotics. The universally conserved switch-2 may have the same role in all multisubunit RNAPs.

  18. A Dual Mechanism Controls Nuclear Localization in the Atypical Basic-Helix-Loop-Helix Protein PAR1 of Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Anahit Galstyan; Jordi Bou-Torrent; Irma Roig-Villanova; Jaime F. Martínez-García

    2012-01-01

    PAR1 is an atypical basic-helix-loop-helix (bHLH) protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor.Consistently with this function,PAR1 has to be in the nucleus to display biological activity.Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus.However,truncated forms of PAR1 lacking this region still display biological activity,implying that PAR1 has additional mechanisms to localize into the nucleus.In this work,we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins,which led us to suggest that PAR1 contains a non-canonical nuclear localization signal (NLS) in the N-terminal region.By overexpressing truncated and mutated derivatives of PAR1,we have also investigated the importance of other regions of PAR1,such as the acidic and the extended HLH dimerization domains,for its nuclear localization.We found that,in the absence of the N-terminal region,a functional HLH domain is required for nuclear localization.Our results suggest the existence of a dual mechanism for PAR1 nuclear localization:(1) one mediated by the N-terminal non-consensus NLS and (2) a second one that involves interaction with other proteins via the dimerization domain.

  19. The local structure of europium-lead-borate glass ceramics

    Science.gov (United States)

    Rada, S.; Pascuta, P.; Culea, M.; Maties, V.; Rada, M.; Barlea, M.; Culea, E.

    2009-04-01

    Glass ceramics in the xEu 2O 3(100 - x)[3B 2O 3·PbO] system with 0 ⩽ x ⩽ 50 mol% have been prepared using the melt quenching method, succeeded by heat treatment applied at 625 °C and 675 °C, respectively, for 48 h. The influence of europium ions on structural behavior of the lead-borate glass ceramics has been investigated using infrared spectroscopy and DFT calculations. The addition of europium ions into the host glass ceramics matrix leads to an increase of the glass network polymerization due to the replacement of B sbnd O sbnd B bonds by the more resistant B sbnd O sbnd Pb bonds. The structural evolution of the studied glass ceramics with the gradual increase of the europium oxide content up to 50 mol% could be explained by considering that the excess of oxygen may be accommodated by the formation of [PbO 4] structural units. Then, the formation of different ionic complexes of the lead ions will decrease the rate of crystal growth and the conversion of the glass into crystalline material becomes more difficult, in agreement to the X-ray data.

  20. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure.

    Science.gov (United States)

    Timoshenko, Janis; Shivhare, Atal; Scott, Robert W J; Lu, Deyu; Frenkel, Anatoly I

    2016-07-20

    We adopted ab initio X-ray absorption near edge structure (XANES) modeling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modeling, where the candidate structures are known, and the inverse modeling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by revealing the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  1. Study of local structure and magnetism in high-T(sub c) copper oxide superconductors

    Science.gov (United States)

    Budnick, J. I.; Tan, Z.; Filipkowski, M.; Niedermayer, CH.; Glueckler, H.; Simon, R.; Golnik, A.; Rauer, M.; Recknagel, E.; Weidinger, A.

    1990-01-01

    The muon spin rotation (MUSR) study of local magnetism of Sr-doped La2CuO4 is reviewed. Emphasis is placed on magnetic order as detected by local and bulk probes with local atomic environments studied by x ray absorption fine structure (XAFS). Correlations between the MUSR study of local magnetic ordering and the bulk magnetization study are presented along with a discussion of the dependence upon oxygen stoichiometry. Results are presented for both superconducting phases and magnetic phases. Recent data which reveals the existence of local magnetic ordering in the hydrogen-doped YBa2Cu3O7 system are also discussed.

  2. Topology optimization of fail-safe structures using a simplified local damage model

    DEFF Research Database (Denmark)

    Jansen, Miche; Lombaert, Geert; Schevenels, Mattias;

    2014-01-01

    Topology optimization of mechanical structures often leads to efficient designs which resemble statically determinate structures. These economical structures are especially vulnerable to local loss of stiffness due to material failure. This paper therefore addresses local failure of continuum...... with a fixed shape. The damage scenarios are taken into account by means of a minimax formulation of the optimization problem which minimizes the worst case performance.The detrimental influence of local failure on the nominal design is demonstrated in two representative examples: a cantilever beam optimized...

  3. Sea urchin vault structure, composition, and differential localization during development

    Directory of Open Access Journals (Sweden)

    Dickey-Sims Carrie

    2005-02-01

    Full Text Available Abstract Background Vaults are intriguing ribonucleoprotein assemblies with an unknown function that are conserved among higher eukaryotes. The Pacific coast sea urchin, Strongylocentrotus purpuratus, is an invertebrate model organism that is evolutionarily closer to humans than Drosophila and C. elegans, neither of which possesses vaults. Here we compare the structures of sea urchin and mammalian vaults and analyze the subcellular distribution of vaults during sea urchin embryogenesis. Results The sequence of the sea urchin major vault protein (MVP was assembled from expressed sequence tags and genome traces, and the predicted protein was found to have 64% identity and 81% similarity to rat MVP. Sea urchin MVP includes seven ~50 residue repeats in the N-terminal half of the protein and a predicted coiled coil domain in the C-terminus, as does rat MVP. A cryoelectron microscopy (cryoEM reconstruction of isolated sea urchin vaults reveals the assembly to have a barrel-shaped external structure that is nearly identical to the rat vault structure. Analysis of the molecular composition of the sea urchin vault indicates that it contains components that may be homologs of the mammalian vault RNA component (vRNA and protein components (VPARP and TEP1. The sea urchin vault appears to have additional protein components in the molecular weight range of 14–55 kDa that might correspond to molecular contents. Confocal experiments indicate a dramatic relocalization of MVP from the cytoplasm to the nucleus during sea urchin embryogenesis. Conclusions These results are suggestive of a role for the vault in delivering macromolecules to the nucleus during development.

  4. The Structure of the Local Interstellar Medium V: Electron Densities

    CERN Document Server

    Redfield, Seth

    2008-01-01

    We present a comprehensive survey of CII* absorption detections toward stars within 100 pc in order to measure the distribution of electron densities present in the local interstellar medium (LISM). Using high spectral resolution observations of nearby stars obtained by GHRS and STIS onboard the Hubble Space Telescope, we identify 13 sight lines with 23 individual CII* absorption components, which provide electron density measurements, the vast majority of which are new. We employ several strategies to determine more accurate CII column densities from the saturated CII resonance line, including, constraints of the line width from the optically thin CII* line, constraints from independent temperature measurements of the LISM gas based on line widths of other ions, and third, using measured SII column densities as a proxy for CII column densities. The sample of electron densities appears consistent with a log-normal distribution and an unweighted mean value of n_e(CII_SII) = 0.11^+0.10_-0.05 cm^-3. Seven indivi...

  5. Gene structure and chromosomal localization of plasma kallikrein

    Energy Technology Data Exchange (ETDEWEB)

    Beaubien, G.; Mbikay, M.; Chretien, M.; Seidah, N.G. (Clinical Research Institute of Montreal, Quebec (Canada)); Rosinski-Chupin, I. (Inst. Pasteur, Paris (France)); Mattei, M.G. (Groupe hospitalier de a Timone, Marseille (France))

    1991-02-12

    Plasma kallikrein (Fletcher factor) is a hepatic serine proteinase that participates in the early phase of blood coagulation. From two genomic libraries, the authors succeeded to isolate four overlapping clones representing the entire rat plasma kallikrein gene. Using selective DNA sequencing, polymerase chain reactions, and restriction mapping, the authors demonstrated that the gene for rat plasma kallikrein was 22 kb in length. Similar to human factor XI the authors also found that the plasma kallikrein gene is composed of 15 exons and 14 introns. A potential transcription initiation step was determined by a novel application of the polymerase chain reaction technique. Computer analysis of the 5{prime}-promoter region of this gene revealed some putative control elements that might regulate the rat plasma kallikrein gene expression. These data and the results of chromosomal localization reported in the present study for mouse (chromosome 8) and human (chromosome 4) plasma kallikrein genes strongly corroborate a genic duplication event from a common ancestor to both plasma kallikrein and factor XI.

  6. Structural Damage Detection Using Frequency Domain Error Localization.

    Science.gov (United States)

    1994-12-01

    113 rn ~l-,I T X ~oy Ul C 114 APPENDIX D. FE MODEL / COMPUTER CODES The following is a brief description of MATLAB routines employed in this thesis...R.R., Structural Dynamics, An Introduction to Computer Methods , pp. 383-387, John Wiley and Sons, Inc., 1981. 8. Guyan , R.J., "Reduction of Stiffness...official policy or position of the Department of Defense or the U.S. Government. 12a. DISTRIBUTION/AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE

  7. Understanding Protein-Protein Interactions Using Local Structural Features

    DEFF Research Database (Denmark)

    Planas-Iglesias, Joan; Bonet, Jaume; García-García, Javier;

    2013-01-01

    Protein-protein interactions (PPIs) play a relevant role among the different functions of a cell. Identifying the PPI network of a given organism (interactome) is useful to shed light on the key molecular mechanisms within a biological system. In this work, we show the role of structural features...... (loops and domains) to comprehend the molecular mechanisms of PPIs. A paradox in protein-protein binding is to explain how the unbound proteins of a binary complex recognize each other among a large population within a cell and how they find their best docking interface in a short timescale. We use...

  8. Prosodic realizations of global and local structure and rhetorical relations in read aloud news reports

    NARCIS (Netherlands)

    Ouden, J.N. den; Noordman, L.G.M.; Terken, J.M.B.

    2009-01-01

    The aim of this research is to study effects of global and local structure of texts and of rhetorical relations between sentences on the prosodic realization of sentences in read aloud text. Twenty texts were analyzed using Rhetorical Structure Theory. Based on these analyses, the global structure i

  9. Study on the local atomic structure of germanium in organic germanium compounds by EXAFS

    Institute of Scientific and Technical Information of China (English)

    1999-01-01

    Organic germanium compounds have been extensively applied in medicine as tonics,In this paper,the local structures of two organic germanium compounds,carboxyethylgermanium sesquioxide and polymeric germanium glutamate,were determined by EXAFS.The structure parameters including coordination numbers and bond lengths were reported,and possible structure patterns were discussed.

  10. The local structure of mixed-ion perovskites

    CERN Document Server

    Shuvaeva, V A; Azuma, Y; Yagi, K; Sakaue, K; Terauchi, H; Raevski, I P; Zhuchkov, K; Antipin, M Y

    2003-01-01

    The temperature-dependent Nb K-edge absorption spectra of several mixed-ion Pb-containing perovskite compounds were analysed to determine the Nb displacement and to trace its changes through the phase transitions. Both extended x-ray absorption fine structure (EXAFS) and the pre-edge region of the spectra were involved in the analysis. The results show that, in the compounds studied, Nb occupies an off-centre position with symmetry lower than that implied by macroscopic symmetry. The magnitude and direction of the Nb off-centre displacement do not display any noticeable temperature change and are not affected by the change in macroscopic symmetry. The Nb-O distribution and its temperature evolution do not show any distinct dependence on the degree of compositional ordering and properties of the samples.

  11. Theoretical model for assessing properties of local structures in metalloprotein

    Science.gov (United States)

    Koyimatu, M.; Shimahara, H.; Iwayama, M.; Sugimori, K.; Kawaguchi, K.; Saito, H.; Nagao, H.

    2013-02-01

    For model structures containing two aromatic rings such as the indole of Trp5 and the imidazole of His64 in human carbonic anhydrase (hCAII), the location and orientation of the rings with regard to each other contribute to the magnitude of the entire interaction energy. Here the energetic contribution of the indole ring of Trp5 on the imidazole ring of the "out" conformation of His64 were calculated to compare with that of the alternative "in" conformation of His64 by using the MP2/6-311++G(d,p)//B3LYP/6-31G(d,p) method. We suggest that 1) Trp5 and the "out" conformation of His64 are predicted to form a stack of planar parallel rings via π-stacking interaction and 2) the energy is 1.73-1.83 kcal/mol to stabilize the "out" conformation, compared with the "in" conformation.

  12. Seismic data filtering using non-local means algorithm based on structure tensor

    Science.gov (United States)

    Yang, Shuai; Chen, Anqing; Chen, Hongde

    2017-05-01

    Non-Local means algorithm is a new and effective filtering method. It calculates weights of all similar neighborhoods' center points relative to filtering point within searching range by Gaussian weighted Euclidean distance between neighborhoods, then gets filtering point's value by weighted average to complete the filtering operation. In this paper, geometric distance of neighborhood's center point is taken into account in the distance measure calculation, making the non-local means algorithm more reasonable. Furthermore, in order to better protect the geometry structure information of seismic data, we introduce structure tensor that can depict the local geometrical features of seismic data. The coherence measure, which reflects image local contrast, is extracted from the structure tensor, is integrated into the non-local means algorithm to participate in the weight calculation, the control factor of geometry structure similarity is added to form a non-local means filtering algorithm based on structure tensor. The experimental results prove that the algorithm can effectively restrain noise, with strong anti-noise and amplitude preservation effect, improving PSNR and protecting structure information of seismic image. The method has been successfully applied in seismic data processing, indicating that it is a new and effective technique to conduct the structure-preserved filtering of seismic data.

  13. From local pixel structure to global image super-resolution: a new face hallucination framework.

    Science.gov (United States)

    Hu, Yu; Lam, Kin-Man; Qiu, Guoping; Shen, Tingzhi

    2011-02-01

    We have developed a new face hallucination framework termed from local pixel structure to global image super-resolution (LPS-GIS). Based on the assumption that two similar face images should have similar local pixel structures, the new framework first uses the input low-resolution (LR) face image to search a face database for similar example high-resolution (HR) faces in order to learn the local pixel structures for the target HR face. It then uses the input LR face and the learned pixel structures as priors to estimate the target HR face. We present a three-step implementation procedure for the framework. Step 1 searches the database for K example faces that are the most similar to the input, and then warps the K example images to the input using optical flow. Step 2 uses the warped HR version of the K example faces to learn the local pixel structures for the target HR face. An effective method for learning local pixel structures from an individual face, and an adaptive procedure for fusing the local pixel structures of different example faces to reduce the influence of warping errors, have been developed. Step 3 estimates the target HR face by solving a constrained optimization problem by means of an iterative procedure. Experimental results show that our new method can provide good performances for face hallucination, both in terms of reconstruction error and visual quality; and that it is competitive with existing state-of-the-art methods.

  14. Local atomic structure modulations activate metal oxide as electrocatalyst for hydrogen evolution in acidic water.

    Science.gov (United States)

    Li, Yu Hang; Liu, Peng Fei; Pan, Lin Feng; Wang, Hai Feng; Yang, Zhen Zhong; Zheng, Li Rong; Hu, P; Zhao, Hui Jun; Gu, Lin; Yang, Hua Gui

    2015-08-19

    Modifications of local structure at atomic level could precisely and effectively tune the capacity of materials, enabling enhancement in the catalytic activity. Here we modulate the local atomic structure of a classical but inert transition metal oxide, tungsten trioxide, to be an efficient electrocatalyst for hydrogen evolution in acidic water, which has shown promise as an alternative to platinum. Structural analyses and theoretical calculations together indicate that the origin of the enhanced activity could be attributed to the tailored electronic structure by means of the local atomic structure modulations. We anticipate that suitable structure modulations might be applied on other transition metal oxides to meet the optimal thermodynamic and kinetic requirements, which may pave the way to unlock the potential of other promising candidates as cost-effective electrocatalysts for hydrogen evolution in industry.

  15. A matrix structured LED backlight system with 2D-DHT local dimming method

    Science.gov (United States)

    Liu, Jia; Li, Yang; Du, Sidan

    To reduce the number of the drivers in the conventional local dimming method for LCDs, a novel LED backlight local dimming system is proposed in this paper. The backlight of this system is generated by 2D discrete Hadamard transform and its matrix structured LED modules. Compared with the conventional 2D local dimming method, the proposed method costs much fewer drivers but with little degradation.

  16. The averaging of non-local Hamiltonian structures in Whitham's method

    CERN Document Server

    Maltsev, A Y

    1999-01-01

    We consider the m-phase Whitham's averaging method and propose the procedure of "averaging" of non-local Hamiltonian structures. The procedure is based on the existence of sufficient number of local commuting integrals of the system and gives the Poisson bracket of Ferapontov type for the Whitham system. The method can be considered as the generalization of the Dubrovin-Novikov procedure for the local field-theoretical brackets.

  17. Local reversibility and entanglement structure of many-body ground states

    CERN Document Server

    Kuwahara, Tomotaka; Amico, Luigi; Vedral, Vlatko

    2015-01-01

    The low-temperature physics of quantum many-body systems is largely governed by the structure of their ground states. Minimizing the energy of local interactions, ground states often reflect strong properties of locality such as the area law for entanglement entropy and the exponential decay of correlations between spatially separated observables. In this letter we present a novel characterization of locality in quantum states, which we call `local reversibility'. It characterizes the type of operations that are needed to reverse the action of a general disturbance on the state. We prove that unique ground states of gapped local Hamiltonian are locally reversible. This way, we identify new fundamental features of many-body ground states, which cannot be derived from the aforementioned properties. We use local reversibility to distinguish between states enjoying microscopic and macroscopic quantum phenomena. To demonstrate the potential of our approach, we prove specific properties of ground states, which are ...

  18. High-density localization of active molecules using Structured Sparse Model and Bayesian Information Criterion.

    Science.gov (United States)

    Quan, Tingwei; Zhu, Hongyu; Liu, Xiaomao; Liu, Yongfeng; Ding, Jiuping; Zeng, Shaoqun; Huang, Zhen-Li

    2011-08-29

    Localization-based super-resolution microscopy (or called localization microscopy) rely on repeated imaging and localization of active molecules, and the spatial resolution enhancement of localization microscopy is built upon the sacrifice of its temporal resolution. Developing algorithms for high-density localization of active molecules is a promising approach to increase the speed of localization microscopy. Here we present a new algorithm called SSM_BIC for such purpose. The SSM_BIC combines the advantages of the Structured Sparse Model (SSM) and the Bayesian Information Criterion (BIC). Through simulation and experimental studies, we evaluate systematically the performance between the SSM_BIC and the conventional Sparse algorithm in high-density localization of active molecules. We show that the SSM_BIC is superior in processing single molecule images with weak signal embedded in strong background.

  19. Origin of heterogeneous dynamics in local molecular structures of ionic liquids.

    Science.gov (United States)

    Sha, Maolin; Liu, Yusheng; Dong, Huaze; Luo, Fabao; Jiang, Fangling; Tang, Zhongfeng; Zhu, Guanglai; Wu, Guozhong

    2016-11-04

    Room-temperature ionic liquids (ILs) are generally considered as structurally heterogeneous with inherent polar/apolar phase separation. However, even after a decade of research, local dynamics in the heterogeneous structures of ILs remain neglected. Such local dynamics may influence the ion transport of electrolytes, as well as the reaction rate of solvents. In this study, we performed molecular dynamics simulation to analyze the local dynamics for the structural heterogeneity of ILs. Calculations of the diffusion, reorientation, and association dynamics showed a distinct heterogeneous dynamics between the polar and apolar regions of ILs. Further studies demonstrated that such local dynamic differences originate from local structural heterogeneity. Different energy barriers determine a predominant fast reorientation dynamics in apolar regions and a locally vibrating behavior in polar regions. Additionally, we suggested a new jumping mechanism to clarify the dynamic heterogeneity of ions in the polar regions. The results will help determine the origin of the heterogeneous dynamics in IL local structures and provide a theoretical basis for tuning the dynamic properties of ILs used as electrolytes or reaction solvents.

  20. A hierarchical method for structural topology design problems with local stress and displacement constraints

    DEFF Research Database (Denmark)

    Stolpe, Mathias; Stidsen, Thomas K.

    2005-01-01

    of minimizing the weight of a structure subject to displacement and local design-dependent stress constraints. The method iteratively solves a sequence of problems of increasing size of the same type as the original problem. The problems are defined on a design mesh which is initially coarse...... from global optimization, which have only recently become available, for solving the problems in the sequence. Numerical examples of topology design problems of continuum structures with local stress and displacement constraints are presented....

  1. A hierarchical method for discrete structural topology design problems with local stress and displacement constraints

    DEFF Research Database (Denmark)

    Stolpe, Mathias; Stidsen, Thomas K.

    2007-01-01

    of minimizing the weight of a structure subject to displacement and local design-dependent stress constraints. The method iteratively treats a sequence of problems of increasing size of the same type as the original problem. The problems are defined on a design mesh which is initially coarse...... from global optimization, which have only recently become available, for solving the problems in the sequence. Numerical examples of topology design problems of continuum structures with local stress and displacement constraints are presented....

  2. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

    OpenAIRE

    Levin, Igor; Vanderah, Terrell

    2008-01-01

    The functional responses (e. g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure-a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale-the so-called "nanostructure problem...

  3. Local Synthesis of Carbon Nanotubes in Silicon Microsystems: The Effect of Temperature Distribution on Growth Structure

    Directory of Open Access Journals (Sweden)

    Knut E. Aasmundtveit

    2013-07-01

    Full Text Available Local synthesis and direct integration of carbon nanotubes (CNTs into microsystems is a promising method for producing CNT-based devices in a single step, low-cost, and wafer-level, CMOS/MEMS-compatible process. In this report, the structure of the locally grown CNTs are studied by transmission imaging in scanning electron microscopy—S(TEM. The characterization is performed directly on the microsystem, without any post-synthesis processing required. The results show an effect of temperature on the structure of CNTs: high temperature favors thin and regular structures, whereas low temperature favors “bamboo-like” structures.

  4. Deciphering the shape and deformation of secondary structures through local conformation analysis

    Directory of Open Access Journals (Sweden)

    Camproux Anne-Claude

    2011-02-01

    Full Text Available Abstract Background Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation. Results Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartments (surface, core and interface reveals that secondary structures tend to adopt preferential conformations that differ among the compartments. The local description of secondary structures highlights that curved conformations are preferred on the surface while straight ones are preferred in the core. Interfaces display a mixture of local conformations either preferred in core or surface. The analysis of the structural letters transition occurring between protein-bound and unbound conformations shows that the deformation of secondary structure is tightly linked to the compartment preference of the local conformations. Conclusion The conformation of secondary structures can be further analysed and detailed thanks to a structural alphabet which allows a better description of protein surface, core and interface in terms of secondary structures' shape and deformation. Induced-fit modification tendencies described here should be valuable information to identify and characterize regions under strong structural constraints for functional reasons.

  5. Disruption of Higher Order DNA Structures in Friedreich's Ataxia (GAA)(n) Repeats by PNA or LNA Targeting

    DEFF Research Database (Denmark)

    Bergquist, Helen; Rocha, Cristina S. J.; Alvarez-Asencio, Ruben;

    2016-01-01

    Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigen......Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated...

  6. Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

    Directory of Open Access Journals (Sweden)

    Levin, Igor

    2008-11-01

    Full Text Available The functional responses (e. g., dielectric, magnetic, catalytic, etc. of many industrially-relevant materials are controlled by their local structure-a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale-the so-called "nanostructure problem"-at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem-an ultimate frontier in materials characterization-necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed "institute" would provide an intellectual infrastructure for local structure determination by (1 developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2, (2 connecting industrial and academic users with experts in measurement techniques, (3

  7. Local structure study of the orbital order/disorder transition in LaMnO3

    Science.gov (United States)

    Thygesen, Peter M. M.; Young, Callum A.; Beake, Edward O. R.; Romero, Fabio Denis; Connor, Leigh D.; Proffen, Thomas E.; Phillips, Anthony E.; Tucker, Matthew G.; Hayward, Michael A.; Keen, David A.; Goodwin, Andrew L.

    2017-05-01

    We use a combination of neutron and x-ray total scattering measurements together with pair distribution function (PDF) analysis to characterize the variation in local structure across the orbital order/disorder transition in LaMnO3. Our experimental data are inconsistent with a conventional order/disorder description of the transition, and reflect instead the existence of a discontinuous change in local structure between ordered and disordered states. Within the orbital ordered regime, the neutron and x-ray PDFs are best described by a local structure model with the same local orbital arrangements as those observed in the average (long-range) crystal structure. We show that a variety of meaningfully different local orbital arrangement models can give fits of comparable quality to the experimental PDFs collected within the disordered regime; nevertheless, our data show a subtle but consistent preference for the anisotropic Potts model proposed previously [M. R. Ahmed and G. A. Gehring, Phys. Rev. B 79, 174106 (2009), 10.1103/PhysRevB.79.174106]. The key implications of this model are electronic and magnetic isotropy together with the loss of local inversion symmetry at the Mn site. We conclude with a critical assessment of the interpretation of PDF measurements when characterizing local symmetry breaking in functional materials.

  8. Adjoint-tomography for a Local Surface Structure: Methodology and a Blind Test

    Science.gov (United States)

    Kubina, Filip; Michlik, Filip; Moczo, Peter; Kristek, Jozef; Stripajova, Svetlana

    2017-04-01

    We have developed a multiscale full-waveform adjoint-tomography method for local surface sedimentary structures with complicated interference wavefields. The local surface sedimentary basins and valleys are often responsible for anomalous earthquake ground motions and corresponding damage in earthquakes. In many cases only relatively small number of records of a few local earthquakes is available for a site of interest. Consequently, prediction of earthquake ground motion at the site has to include numerical modeling for a realistic model of the local structure. Though limited, the information about the local structure encoded in the records is important and irreplaceable. It is therefore reasonable to have a method capable of using the limited information in records for improving a model of the local structure. A local surface structure and its interference wavefield require a specific multiscale approach. In order to verify our inversion method, we performed a blind test. We obtained synthetic seismograms at 8 receivers for 2 local sources, complete description of the sources, positions of the receivers and material parameters of the bedrock. We considered the simplest possible starting model - a homogeneous halfspace made of the bedrock. Using our inversion method we obtained an inverted model. Given the starting model, synthetic seismograms simulated for the inverted model are surprisingly close to the synthetic seismograms simulated for the true structure in the target frequency range up to 4.5 Hz. We quantify the level of agreement between the true and inverted seismograms using the L2 and time-frequency misfits, and, more importantly for earthquake-engineering applications, also using the goodness-of-fit criteria based on the earthquake-engineering characteristics of earthquake ground motion. We also verified the inverted model for other source-receiver configurations not used in the inversion.

  9. Ultrahigh resolution imaging of local structural distortions in intergrowth tungsten bronzes.

    Science.gov (United States)

    Kirkland, A I; Sloan, J; Haigh, S

    2007-01-01

    Details of the local structure of a complex tungsten bronze, K(x)WO(3) have been determined using focal series exit wave reconstruction. Octahedral rotations in different structural regions of the same crystal have been directly measured from the exit wave phase and correlated with variations in cation occupancy determined from the exit wave modulus.

  10. Localized structures and front propagation in the Lengyel-Epstein model

    DEFF Research Database (Denmark)

    Jensen, O.; Pannbacker, Viggo Ole; Mosekilde, Erik

    1994-01-01

    Pattern selection, localized structure formation, and front propagation are analyzed within the framework of a model for the chlorine dioxide-iodine-malonic acid reaction that represents a key to understanding recently obtained Turing structures. This model is distinguished from previously studied...

  11. Local structure of the Ce3+ ion the yellow emitting phosphor YAG:Ce

    NARCIS (Netherlands)

    Ghigna, P.; Pin, S.; Ronda, C.; Speghini, A.; Piccinelli, F.; Bettinelli, M.

    2011-01-01

    The local structure of the Ce3+ ion in the yellow emitting YAG:Ce phosphor has been studied by Extended X-ray Absorption Fine Structurespectroscopy in the 300−20 K temperature range. It has evidenced that the dopant Ce3+ replaces Y3+ in the garnet structure, giving rise to a significant expan

  12. Local structure information by EXAFS analysis using two algorithms for Fourier transform calculation

    Energy Technology Data Exchange (ETDEWEB)

    Aldea, N; Pintea, S; Rednic, V [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania); Matei, F [University of Agricultural Sciences and Veterinary Medicine, 3-5 Calea Manastur, 400372 Cluj-Napoca (Romania); Hu Tiandou; Xie Yaning, E-mail: nicolae.aldea@itim-cj.r [Beijing Synchrotron Radiation Facilities of Beijing Electron Positron Collider National Laboratory (China)

    2009-08-01

    The present work is a comparison study between different algorithms of Fourier transform for obtaining very accurate local structure results using Extended X-ray Absorption Fine Structure technique. In this paper we focus on the local structural characteristics of supported nickel catalysts and Fe{sub 3}O{sub 4} core-shell nanocomposites. The radial distribution function could be efficiently calculated by the fast Fourier transform when the coordination shells are well separated while the Filon quadrature gave remarkable results for close-shell coordination.

  13. Temperature influence on the global and local structure of the chromia supported nickel catalysts

    Energy Technology Data Exchange (ETDEWEB)

    Pintea, Stelian; Rednic, Vasile; Marginean, Petru; Aldea, Nicolae [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania); Xie Yaning, E-mail: stelian.pintea@itim-cj.r [Beijing Synchrotron Radiation Facilities of Beijing Electron Positron Collider National Laboratory (China)

    2009-08-01

    The changes induced by the heat treatment on the global and the local structures of the supported nickel catalysts are investigated. The global structure parameters were obtained by processing the X-ray diffraction patterns of the samples using the Scherrer formula. The local structure parameters were determined by X-ray absorption spectra processing. Both types of measurements were carried out using synchrotron radiation. The nickel catalysts supported on chromia were prepared by coprecipitation method. The nickel/chromium atomic percent was 70/30. After preparation, the samples were thermally treated for three hours at 350, 650 and 950{sup 0}C. A strong correlation between previous catalytic activity information and the global and local structure is evidenced. Also the correlation between the nickel crystallite size and the active metal-oxide support interaction is discussed.

  14. PLACE AND ROLE OF THE STRUCTURAL FUNDS IN THE LOCAL BUDGET REVENUES

    Directory of Open Access Journals (Sweden)

    CRISTINEL ICHIM

    2016-06-01

    Full Text Available In this study we aim to analyse the place and role manifested within local budgets of Romania by a new category of revenues available to local authorities namely those from the Structural and Cohesion Funds of the EU. At the beginning of our scientific approach we have outlined the scope of local government revenues highlighting that in the section development of local budgets are also set off funds from the European Union. The research continues with a characterization of the structural funds in which, on the one hand, we have emphasized their importance to the development of territorial administrative units in Romania and on the other hand we showed some difficulties arising in the process of absorption of European funds. The analysis of financial resources from the EU funds within the local budgets from Romania is the last part of the article and is based on the quantitative analysis of the budget indicator, "amounts of the EU in the payments made and pre-financing" from existing data in the Statistical Yearbook of Romania, and highlights the place occupied by such income within local public revenues. This analysis shows that local public authorities from Romania have made significant progress in terms of accessing European funds, their share in total revenues of local budgets increased during 2008-2014.

  15. CheShift-2 resolves a local inconsistency between two X-ray crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Sue, Shih-Che [Scripps Research Institute, Department of Molecular Biology (United States); Fraser, James S. [University of California, California Institute of Quantitative Biosciences (QB3) and Department of Cellular and Molecular Pharmacology (United States); Scheraga, Harold A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Dyson, H. Jane, E-mail: dyson@scripps.edu [Scripps Research Institute, Department of Molecular Biology (United States)

    2012-10-15

    Since chemical shifts provide important and relatively accessible information about protein structure in solution, a Web server, CheShift-2, was developed for structure interrogation, based on a quantum mechanics database of {sup 13}C{sup {alpha}} chemical shifts. We report the application of CheShift-2 to a local inconsistency between two X-ray crystal structures (PDB IDs 1IKN and 1NFI) of the complex between the p65/p50 heterodimer of NF{kappa}B and its inhibitor I{kappa}B{alpha}. The availability of NMR resonance assignments that included the region of the inconsistency provided an opportunity for independent validation of the CheShift-2 server. Application of the server showed that the {sup 13}C{sup {alpha}} chemical shifts measured for the Gly270-Pro281 sequence close to the C-terminus of I{kappa}B{alpha} were unequivocally consistent with the backbone structure modeled in the 1IKN structure, and were inconsistent with the 1NFI structure. Previous NOE measurements had demonstrated that the position of a tryptophan ring in the region immediately N-terminal in this region was not consistent with either structure. Subsequent recalculation of the local structure in this region, based on the electron density of the deposited structure factors for 1IKN, confirmed that the local backbone structure was best modeled by 1IKN, but that the rotamer of Trp258 is consistent with the 1NFI structure, including the presence of a hydrogen bond between the ring N{epsilon}H of Trp258 and the backbone carbonyl group of Gln278. The consensus between all of these measures suggests that the CheShift-2 server operates well under circumstances in which backbone chemical shifts are available but where local plasticity may render X-ray structural data ambiguous.

  16. The analysis of space time structure in QCD vacuum, I: localization vs global behavior in local observables and Dirac eigenmodes

    Science.gov (United States)

    Horváth, Ivan

    2005-03-01

    The structure of QCD vacuum can be studied from first principles using lattice-regularized theory. This line of research entered a qualitatively new phase recently, wherein the space-time structure (at least for some quantities) can be directly observed in configurations dominating the QCD path integral, i.e., without any subjective processing of typical configurations. This approach to QCD vacuum structure does not rely on any proposed picture of QCD vacuum but rather attempts to characterize this structure in a model-independent manner, so that a coherent physical picture of the vacuum can emerge when such unbiased numerical information accumulates to a sufficient degree. An important part of this program is to develop a set of suitable quantitative characteristics describing the space-time structure in a meaningful and physically relevant manner. One of the basic pertinent issues here is whether QCD vacuum dynamics can be understood in terms of localized vacuum objects, or whether such objects behave as inherently global entities. The first direct studies of vacuum structure strongly support the latter. In this paper, we develop a formal framework which allows to answer this question in a quantitative manner. We discuss in detail how to apply this approach to Dirac eigenmodes and to basic scalar and pseudoscalar composites of gauge fields (action density and topological charge density). The approach is illustrated numerically on overlap Dirac zero modes and near-zero modes. This illustrative data provides direct quantitative evidence supporting our earlier arguments for the global nature of QCD Dirac eigenmodes.

  17. Protein Classification Based on Analysis of Local Sequence-Structure Correspondence

    Energy Technology Data Exchange (ETDEWEB)

    Zemla, A T

    2006-02-13

    The goal of this project was to develop an algorithm to detect and calculate common structural motifs in compared structures, and define a set of numerical criteria to be used for fully automated motif based protein structure classification. The Protein Data Bank (PDB) contains more than 33,000 experimentally solved protein structures, and the Structural Classification of Proteins (SCOP) database, a manual classification of these structures, cannot keep pace with the rapid growth of the PDB. In our approach called STRALCP (STRucture Alignment based Clustering of Proteins), we generate detailed information about global and local similarities between given set of structures, identify similar fragments that are conserved within analyzed proteins, and use these conserved regions (detected structural motifs) to classify proteins.

  18. Local structure studies of Fe2TeO6 using x-ray absorption spectroscopy

    Science.gov (United States)

    Singh, Harishchandra; Yadav, A. K.

    2016-05-01

    In the present study, we have performed EXAFS measurements on powder samples of Fe2TeO6 (FTO) to probe the local structure surrounding at the Fe site. The structural parameters (atomic coordination and lattice parameters) of FTO used for simulation of theoretical EXAFS spectra of the samples have been obtained from Rietveld refined structure on synchrotron X-ray Diffraction (SXRD) data. Quite similar and satisfactory structural parameters have been obtained from both the study, indicating goodness of synchrotron structural analysis over EXAFS analysis. SXRD and EXAFS results shows absence of any secondary phase proves current synthesis superior over reported techniques.

  19. INTERCONNECTIONS BETWEEN THE ECONOMIC STRUCTURE OF LOCAL SPENDING AND ECONOMIC GROWTH IN ROMANIA

    Directory of Open Access Journals (Sweden)

    Bilan Irina

    2015-07-01

    Full Text Available The issue of the effects of government interventions, explicitly of the taxes and expenditures of local public authorities, has generated substantial debate over time, and still gives rise to numerous controversies in theory and practice. Following the Keynesian path of reasoning, it is, at least theoretically, admitted that it is possible to influence the socio-economic activities and support for economic growth by means of government spending, but different other factors act towards enhancing or, on the contrary, impeding the achievement of the desired effects. From this point of view, the delimitation of competences and public expenditure responsibilities between different levels of government raises the issue of some possible different effects of the central and local governments’ interventions. As the macroeconomic stabilization function is usually associated with central governments, and the contribution of local governments often is of lesser importance, less attention is paid to the effectiveness of local administrative actions. In such a context, the paper aims to empirically evaluate the effects of the economic structure of local public expenditures on the local (territorial economic growth in Romania, over the period 2007 to 2012. The analysis has been conducted at the level of the 42 Romanian counties and on annual data collected from both international and national sources (World Bank, INSSE, The Romanian Ministry of Regional Development and Public Administration.The general method of estimation is the fixed effects estimation technique for panel data models. Our empirical approach is of absolute novelty, especially for Romania, where previous empirical studies have been focusing on the assessment of the overall effects of general government spending. The main findings of our study are that local public expenditures have a negative impact on territorial economic growth, confirmed both for overall expenditures and for various

  20. Mining Local Specialties for Travelers by Leveraging Structured and Unstructured Data

    Directory of Open Access Journals (Sweden)

    Kai Jiang

    2012-01-01

    Full Text Available Recently, many local review websites such as Yelp are emerging, which have greatly facilitated people's daily life such as cuisine hunting. However they failed to meet travelers' demands because travelers are more concerned about a city's local specialties instead of the city's high ranked restaurants. To solve this problem, this paper presents a local specialty mining algorithm, which utilizes both the structured data from local review websites and the unstructured user-generated content (UGC from community Q&A websites, and travelogues. The proposed algorithm extracts dish names from local review data to build a document for each city, and applies tfidf weighting algorithm on these documents to rank dishes. Dish-city correlations are calculated from unstructured UGC, and combined with the tfidf ranking score to discover local specialties. Finally, duplicates in the local specialty mining results are merged. A recommendation service is built to present local specialties to travelers, along with specialties' associated restaurants, Q&A threads, and travelogues. Experiments on a large data set show that the proposed algorithm can achieve a good performance, and compared to using local review data alone, leveraging unstructured UGC can boost the mining performance a lot, especially in large cities.

  1. Reductions of locally conformal symplectic structures and de Rham cohomology tangent to a foliation

    CERN Document Server

    Domitrz, Wojciech

    2008-01-01

    We propose a produre of reduction a locally conformal symplectic structure. This procedure of reduction can be applied to wide class of submanifolds. There are no local obstructions for this procedure. But there are global obstructions. We find a necessary and sufficient condition when this reduction holds in terms of the special kind of de Rham cohomology class (tangent to the characteristic foliation) of the Lee form.

  2. Relations between structural properties and synchronizability on local world dynamical networks

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In this paper, the effects of various structural properties on the synchronization of coupled oscillators with local-world coupling configurations are investigated. It is found that for local world networks, the larger heterogeneity of the degree distribution, the enhanced interconnection of nodes, and the increased clustering do not improve the synchronizability of dynamical systems. On the contrary, the increase of the maximum betweenness centrality appears to be responsible for the decrease of the synchronizability.

  3. Identification, characterization and evolution of non-local quasi-Lagrangian structures in turbulence

    Institute of Scientific and Technical Information of China (English)

    Yue Yang

    2016-01-01

    The recent progress on non-local Lagrangian and quasi-Lagrangian structures in turbulence is reviewed. The quasi-Lagrangian structures, e.g., vortex surfaces in vis-cous flow, gas-liquid interfaces in multi-phase flow, and flame fronts in premixed combustion, can show essential Lagrangian following properties, but they are able to have topological changes in the temporal evolution. In addition, they can represent or influence the turbulent flow field. The challenges for the investigation of the non-local structures include their identification, characterization, and evolution. The improving understanding of the quasi-Lagrangian struc-tures is expected to be helpful to elucidate crucial dynamics and develop structure-based predictive models in turbulence.

  4. Analysis of transverse Anderson localization in refractive index structures with customized random potential

    CERN Document Server

    Boguslawski, Martin; Armijo, Julien; Diebel, Falko; Rose, Patrick; Denz, Cornelia

    2013-01-01

    We present a method to demonstrate Anderson localization in an optically induced randomized potential. By usage of computer controlled spatial light modulators, we are able to implement fully randomized nondiffracting beams of variable structural size in order to control the modulation length (photonic grain size) as well as the depth (disorder strength) of a random potential induced in a photorefractive crystal. In particular, we quantitatively analyze the localization length of light depending on these two parameters and find that they are crucial influencing factors on the propagation behavior leading to variably strong localization. Thus, we corroborate that transverse light localization in a random refractive index landscape strongly depends on the character of the potential, allowing for a flexible regulation of the localization strength by adapting the optical induction configuration.

  5. Prediction of Local Quality of Protein Structure Models Considering Spatial Neighbors in Graphical Models

    Science.gov (United States)

    Shin, Woong-Hee; Kang, Xuejiao; Zhang, Jian; Kihara, Daisuke

    2017-01-01

    Protein tertiary structure prediction methods have matured in recent years. However, some proteins defy accurate prediction due to factors such as inadequate template structures. While existing model quality assessment methods predict global model quality relatively well, there is substantial room for improvement in local quality assessment, i.e. assessment of the error at each residue position in a model. Local quality is a very important information for practical applications of structure models such as interpreting/designing site-directed mutagenesis of proteins. We have developed a novel local quality assessment method for protein tertiary structure models. The method, named Graph-based Model Quality assessment method (GMQ), explicitly considers the predicted quality of spatially neighboring residues using a graph representation of a query protein structure model. GMQ uses conditional random field as its core of the algorithm, and performs a binary prediction of the quality of each residue in a model, indicating if a residue position is likely to be within an error cutoff or not. The accuracy of GMQ was improved by considering larger graphs to include quality information of more surrounding residues. Moreover, we found that using different edge weights in graphs reflecting different secondary structures further improves the accuracy. GMQ showed competitive performance on a benchmark for quality assessment of structure models from the Critical Assessment of Techniques for Protein Structure Prediction (CASP). PMID:28074879

  6. Correlation between locally deformed structure and oxide film properties in austenitic stainless steel irradiated with neutrons

    Science.gov (United States)

    Chimi, Yasuhiro; Kitsunai, Yuji; Kasahara, Shigeki; Chatani, Kazuhiro; Koshiishi, Masato; Nishiyama, Yutaka

    2016-07-01

    To elucidate the mechanism of irradiation-assisted stress corrosion cracking (IASCC) in high-temperature water for neutron-irradiated austenitic stainless steels (SSs), the locally deformed structures, the oxide films formed on the deformed areas, and their correlation were investigated. Tensile specimens made of irradiated 316L SSs were strained 0.1%-2% at room temperature or at 563 K, and the surface structures and crystal misorientation among grains were evaluated. The strained specimens were immersed in high-temperature water, and the microstructures of the oxide films on the locally deformed areas were observed. The appearance of visible step structures on the specimens' surface depended on the neutron dose and the applied strain. The surface oxides were observed to be prone to increase in thickness around grain boundaries (GBs) with increasing neutron dose and increasing local strain at the GBs. No penetrative oxidation was observed along GBs or along surface steps.

  7. Study on near-wall turbulence structures with local Reynolds stress

    Institute of Scientific and Technical Information of China (English)

    LiLI; ChunxiaoXU; GuixiangCUI; ZhaoshunZHANG

    2000-01-01

    The direct-numerical-simulated channel turbulence is analyzed with twodimensional wavelet transform. Considering the relation between turbulence coherent structure and Reynolds stress in near wall region, the local Reynolds stress (LRS) is defined.A new method for extracting coherent signals from turbulence based on the LRS is developed. Velocity fluctuations are decomposed to coherent signals and background signals. It is found that the scaling exponents of coherent signals have a considerable deviation from the Kolmogorov scaling law q/3 (K41 theory), while that, of background signals is very close to q/3. It is confirmed that coherent signals are mainly responsible for the anomalous scalings.Locally characterized by the positive peaks of LRS, the typical structures in near wall regionare obtained by conditional statistical averaging. It is shown that the local character of near-wall turbulence structures can be effectively described with LRS.

  8. A bouquet of DNA structures: Emerging diversity

    Directory of Open Access Journals (Sweden)

    Mahima Kaushik

    2016-03-01

    Full Text Available Structural polymorphism of DNA has constantly been evolving from the time of illustration of the double helical model of DNA by Watson and Crick. A variety of non-canonical DNA structures have constantly been documented across the globe. DNA attracted worldwide attention as a carrier of genetic information. In addition to the classical Watson–Crick duplex, DNA can actually adopt diverse structures during its active participation in cellular processes like replication, transcription, recombination and repair. Structures like hairpin, cruciform, triplex, G-triplex, quadruplex, i-motif and other alternative non-canonical DNA structures have been studied at length and have also shown their in vivo occurrence. This review mainly focuses on non-canonical structures adopted by DNA oligonucleotides which have certain prerequisites for their formation in terms of sequence, its length, number and orientation of strands along with varied solution conditions. This conformational polymorphism of DNA might be the basis of different functional properties of a specific set of DNA sequences, further giving some insights for various extremely complicated biological phenomena. Many of these structures have already shown their linkages with diseases like cancer and genetic disorders, hence making them an extremely striking target for structure-specific drug designing and therapeutic applications.

  9. Correlation between locally deformed structure and oxide film properties in austenitic stainless steel irradiated with neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Chimi, Yasuhiro, E-mail: chimi.yasuhiro@jaea.go.jp [Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan); Kitsunai, Yuji [Nippon Nuclear Fuel Development, 2163 Narita-cho, Oarai-machi, Higashi-ibaraki-gun, Ibaraki 311-1313 (Japan); Kasahara, Shigeki [Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan); Chatani, Kazuhiro; Koshiishi, Masato [Nippon Nuclear Fuel Development, 2163 Narita-cho, Oarai-machi, Higashi-ibaraki-gun, Ibaraki 311-1313 (Japan); Nishiyama, Yutaka [Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan)

    2016-07-15

    To elucidate the mechanism of irradiation-assisted stress corrosion cracking (IASCC) in high-temperature water for neutron-irradiated austenitic stainless steels (SSs), the locally deformed structures, the oxide films formed on the deformed areas, and their correlation were investigated. Tensile specimens made of irradiated 316L SSs were strained 0.1%–2% at room temperature or at 563 K, and the surface structures and crystal misorientation among grains were evaluated. The strained specimens were immersed in high-temperature water, and the microstructures of the oxide films on the locally deformed areas were observed. The appearance of visible step structures on the specimens' surface depended on the neutron dose and the applied strain. The surface oxides were observed to be prone to increase in thickness around grain boundaries (GBs) with increasing neutron dose and increasing local strain at the GBs. No penetrative oxidation was observed along GBs or along surface steps. - Highlights: • Visible step structures depend on the neutron dose and the applied strain. • Local strain at grain boundaries was accumulated with the neutron dose. • Oxide thickness increases with neutron dose and local strain at grain boundaries. • No penetrative oxidation was observed along grain boundaries or surface steps.

  10. Local structure of multiferroic RMn 2O 5: Important role of the R site

    Science.gov (United States)

    Tyson, T. A.; Chen, Z.; DeLeon, M. A.; Yoong, S.; Cheong, S.-W.

    2009-06-01

    The temperature and magnetic field dependent local structure of RMn 2O 5 systems was examined. While no significant displacements of the Mn ions are observed, it is found that the R-O distribution exhibits changes at low temperature which are possibly related to the changes in the electric polarization. Density functional computations are used to explore the system dynamics and to link the local structural measurements with anomalous changes in the infrared absorption spectra. The anomalous R-O distribution and observed coupling to magnetic fields point to the need to properly treat the 4f electrons on the R sites in these systems.

  11. Exotic Localized Coherent Structures of the (2+1)-Dimensional Dispersive Long-Wave Equation

    Institute of Scientific and Technical Information of China (English)

    ZHANG JieFang

    2002-01-01

    This article is concerned with the extended homogeneous balance method for studying thc abundantlocalized solution structures in the (2-k1)-dimensional dispersive long-wave equations uty + xx + (u2)xy/2 = 0, ηt +(u + u + uxy)x = 0. Starting from the homogeneous balance method, we find that the richness of the localized coherentstructures of the model is caused by the entrance of two variable-separated arbitrary functions. For some special selectionsof the arbitrary functions, it is shown that the localized structures of the model may be dromions, lumps, breathers,instantons and ring solitons.

  12. Crystal structures of bacterial lipoprotein localization factors, LolA and LolB

    OpenAIRE

    Takeda, Kazuki; Miyatake, Hideyuki; Yokota, Naoko; Matsuyama, Shin-ichi; Tokuda, Hajime; Miki, Kunio

    2003-01-01

    Lipoproteins having a lipid-modified cysteine at the N-terminus are localized on either the inner or the outer membrane of Escherichia coli depending on the residue at position 2. Five Lol proteins involved in the sorting and membrane localization of lipoprotein are highly conserved in Gram-negative bacteria. We determined the crystal structures of a periplasmic chaperone, LolA, and an outer membrane lipoprotein receptor, LolB. Despite their dissimilar amino acid sequences, the structures of ...

  13. Pose Estimation using Local Structure-Specific Shape and Appearance Context

    DEFF Research Database (Denmark)

    Buch, Anders Glent; Kraft, Dirk; Kämäräinen, Joni-Kristian

    2013-01-01

    We address the problem of estimating the alignment pose between two models using structure-specific local descriptors. Our descriptors are generated using a combination of 2D image data and 3D contextual shape data, resulting in a set of semi-local descriptors containing rich appearance and shape...... information for both edge and texture structures. This is achieved by defining feature space relations which describe the neighborhood of a descriptor. By quantitative evaluations, we show that our descriptors provide high discriminative power compared to state of the art approaches. In addition, we show how...

  14. Acoustic emission localization on ship hull structures using a deep learning approach

    DEFF Research Database (Denmark)

    Georgoulas, George; Kappatos, Vassilios; Nikolakopoulos, George

    2016-01-01

    In this paper, deep belief networks were used for localization of acoustic emission events on ship hull structures. In order to avoid complex and time consuming implementations, the proposed approach uses a simple feature extraction module, which significantly reduces the extremely high dimension......In this paper, deep belief networks were used for localization of acoustic emission events on ship hull structures. In order to avoid complex and time consuming implementations, the proposed approach uses a simple feature extraction module, which significantly reduces the extremely high...

  15. Acoustic emission localization on ship hull structures using a deep learning approach

    DEFF Research Database (Denmark)

    Georgoulas, George; Kappatos, Vassilios; Nikolakopoulos, George

    2016-01-01

    In this paper, deep belief networks were used for localization of acoustic emission events on ship hull structures. In order to avoid complex and time consuming implementations, the proposed approach uses a simple feature extraction module, which significantly reduces the extremely high dimension......In this paper, deep belief networks were used for localization of acoustic emission events on ship hull structures. In order to avoid complex and time consuming implementations, the proposed approach uses a simple feature extraction module, which significantly reduces the extremely high...

  16. Discussions on equivalent solutions and localized structures via the mapping method based on Riccati equation

    Science.gov (United States)

    Xu, Ling; Cheng, Xuan; Dai, Chao-Qing

    2015-12-01

    Although the mapping method based on Riccati equation was proposed to obtain variable separation solutions many years ago, two important problems have not been studied: i) the equivalence of variable separation solutions by means of the mapping method based on Riccati equation with the radical sign combined ansatz; and ii) lack of physical meanings for some localized structures constructed by variable separation solutions. In this paper, we re-study the (2+1)-dimensional Boiti-Leon-Pempinelli equation via the mapping method based on Riccati equation and prove that nine types of variable separation solutions are actually equivalent to each other. Moreover, we also re-study localized structures constructed by variable separation solutions. Results indicate that some localized structures reported in the literature are lacking real values due to the appearance of the divergent and un-physical phenomenon for the initial field. Therefore, we must be careful with the initial field to avoid the appearance of some un-physical or even divergent structures in it when we construct localized structures for the potential field.

  17. Modular localization and the holistic structure of causal quantum theory, a historical perspective

    Science.gov (United States)

    Schroer, Bert

    2015-02-01

    Recent insights into the conceptual structure of localization in QFT (modular localization) led to clarifications of old unsolved problems. The oldest one is the Einstein-Jordan conundrum which led Jordan in 1925 to the discovery of quantum field theory. This comparison of fluctuations in subsystems of heat bath systems (Einstein) with those resulting from the restriction of the QFT vacuum state to an open subvolume (Jordan) leads to a perfect analogy; the globally pure vacuum state becomes upon local restriction a strongly impure KMS state. This phenomenon of localization-caused thermal behavior as well as the vacuum-polarization clouds at the causal boundary of the localization region places localization in QFT into a sharp contrast with quantum mechanics and justifies the attribute "holstic". In fact it positions the E-J Gedankenexperiment into the same conceptual category as the cosmological constant problem and the Unruh Gedankenexperiment. The holistic structure of QFT resulting from "modular localization" also leads to a revision of the conceptual origin of the crucial crossing property which entered particle theory at the time of the bootstrap S-matrix approach but suffered from incorrect use in the S-matrix settings of the dual model and string theory. The new holistic point of view, which strengthens the autonomous aspect of QFT, also comes with new messages for gauge theory by exposing the clash between Hilbert space structure and localization and presenting alternative solutions based on the use of stringlocal fields in Hilbert space. Among other things this leads to a reformulation of the Englert-Higgs symmetry breaking mechanism.

  18. Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs

    Directory of Open Access Journals (Sweden)

    Ricardo eFlores

    2012-06-01

    Full Text Available As a consequence of two unique physical properties, small size and circularity, viroid RNAs do not code for proteins and thus depend on RNA sequence/structural motifs for interacting with host proteins that mediate their invasion, replication, spread, and circumvention of defensive barriers. Viroid genomes fold up on themselves adopting collapsed secondary structures wherein stretches of nucleotides stabilized by Watson-Crick pairs are flanked by apparently unstructured loops. However, compelling data show that they are instead stabilized by alternative non-canonical pairs and that specific loops in the rod-like secondary structure, characteristic of Potato spindle tuber viroid and most other members of the family Pospiviroidae, are critical for replication and systemic trafficking. In contrast, rather than folding into a rod-like secondary structure, most members of the family Avsunvioidae adopt multibranched conformations occasionally stabilized by kissing loop interactions critical for viroid viability in vivo. Besides these most stable secondary structures, viroid RNAs alternatively adopt during replication transient metastable conformations containing elements of local higher-order structure, prominent among which are the hammerhead ribozymes catalyzing a key replicative step in the family Avsunvioidae, and certain conserved hairpins that also mediate replication steps in the family Pospiviroidae. Therefore, different RNA structures ⎯either global or local ⎯ determine different functions, thus highlighting the need for in-depth structural studies on viroid RNAs.

  19. Mechanistic insight into the interaction of BLM helicase with intra-strand G-quadruplex structures

    DEFF Research Database (Denmark)

    Chatterjee, Sujoy; Zagelbaum, Jennifer; Savitsky, Pavel;

    2014-01-01

    Bloom syndrome is an autosomal recessive disorder caused by mutations in the RecQ family helicase BLM that is associated with growth retardation and predisposition to cancer. BLM helicase has a high specificity for non-canonical G-quadruplex (G4) DNA structures, which are formed by G-rich DNA...

  20. Structure in the 3D Galaxy Distribution: II. Voids and Watersheds of Local Maxima and Minima

    CERN Document Server

    Way, M J; Scargle, Jeffrey D

    2014-01-01

    The major uncertainties in studies of the multi-scale structure of the Universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian Blocks and self organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium Simulation and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. The resulting sizes follow continuous multi-scale distributions with no indication of the presence of a discrete hierarchy. We also int...

  1. Geometrical structure, multifractal spectra and localized optical modes of aperiodic Vogel spirals.

    Science.gov (United States)

    Trevino, Jacob; Liew, Seng Fatt; Noh, Heeso; Cao, Hui; Dal Negro, Luca

    2012-01-30

    We present a numerical study of the structural properties, photonic density of states and bandedge modes of Vogel spiral arrays of dielectric cylinders in air. Specifically, we systematically investigate different types of Vogel spirals obtained by the modulation of the divergence angle parameter above and below the golden angle value (≈137.507°). We found that these arrays exhibit large fluctuations in the distribution of neighboring particles characterized by multifractal singularity spectra and pair correlation functions that can be tuned between amorphous and random structures. We also show that the rich structural complexity of Vogel spirals results in a multifractal photonic mode density and isotropic bandedge modes with distinctive spatial localization character. Vogel spiral structures offer the opportunity to create novel photonic devices that leverage radially localized and isotropic bandedge modes to enhance light-matter coupling, such as optical sensors, light sources, concentrators, and broadband optical couplers.

  2. Local Structure and Short-Range Order in a NiCoCr Solid Solution Alloy

    Science.gov (United States)

    Zhang, F. X.; Zhao, Shijun; Jin, Ke; Xue, H.; Velisa, G.; Bei, H.; Huang, R.; Ko, J. Y. P.; Pagan, D. C.; Neuefeind, J. C.; Weber, W. J.; Zhang, Yanwen

    2017-05-01

    Multielement solid solution alloys are intrinsically disordered on the atomic scale, and many of their advanced properties originate from the local structural characteristics. The local structure of a NiCoCr solid solution alloy is measured with x-ray or neutron total scattering and extended x-ray absorption fine structure (EXAFS) techniques. The atomic pair distribution function analysis does not exhibit an observable structural distortion. However, an EXAFS analysis suggests that the Cr atoms are favorably bonded with Ni and Co in the solid solution alloys. This short-range order (SRO) may make an important contribution to the low values of the electrical and thermal conductivities of the Cr-alloyed solid solutions. In addition, an EXAFS analysis of Ni ion irradiated samples reveals that the degree of SRO in NiCoCr alloys is enhanced after irradiation.

  3. Prevention of brittle fracture of steel structures by controlling the local stress and strain fields

    Directory of Open Access Journals (Sweden)

    Moyseychik Evgeniy Alekseevich

    Full Text Available In the article the author offers a classification of the methods to increase the cold resistance of steel structural shapes with a focus on the regulation of local fields of internal stresses and strains to prevent brittle fracture of steel structures. The need of a computer thermography is highlighted not only for visualization of temperature fields on the surface, but also to control the fields of residual stresses and strains in a controlled element.

  4. Tuning LDA+U for electron localization and structure at oxygen vacancies in ceria.

    Science.gov (United States)

    Castleton, C W M; Kullgren, J; Hermansson, K

    2007-12-28

    We examine the real space structure and the electronic structure (particularly Ce4f electron localization) of oxygen vacancies in CeO(2) (ceria) as a function of U in density functional theory studies with the rotationally invariant forms of the LDA+U and GGA+U functionals. The four nearest neighbor Ce ions always relax outwards, with those not carrying localized Ce4f charge moving furthest. Several quantification schemes show that the charge starts to become localized at U approximately 3 eV and that the degree of localization reaches a maximum at approximately 6 eV for LDA+U or at approximately 5.5 eV for GGA+U. For higher U it decreases rapidly as charge is transferred onto second neighbor O ions and beyond. The localization is never into atomic corelike states; at maximum localization about 80-90% of the Ce4f charge is located on the two nearest neighboring Ce ions. However, if we look at the total atomic charge we find that the two ions only make a net gain of (0.2-0.4)e each, so localization is actually very incomplete, with localization of Ce4f electrons coming at the expense of moving other electrons off the Ce ions. We have also revisited some properties of defect-free ceria and find that with LDA+U the crystal structure is actually best described with U=3-4 eV, while the experimental band structure is obtained with U=7-8 eV. (For GGA+U the lattice parameters worsen for U>0 eV, but the band structure is similar to LDA+U.) The best overall choice is U approximately 6 eV with LDA+U and approximately 5.5 eV for GGA+U, since the localization is most important, but a consistent choice for both CeO(2) and Ce(2)O(3), with and without vacancies, is hard to find.

  5. Hybrid local FEM/global LISA modeling of damped guided wave propagation in complex composite structures

    Science.gov (United States)

    Shen, Yanfeng; Cesnik, Carlos E. S.

    2016-09-01

    This paper presents a new hybrid modeling technique for the efficient simulation of guided wave generation, propagation, and interaction with damage in complex composite structures. A local finite element model is deployed to capture the piezoelectric effects and actuation dynamics of the transmitter, while the global domain wave propagation and interaction with structural complexity (structure features and damage) are solved utilizing a local interaction simulation approach (LISA). This hybrid approach allows the accurate modeling of the local dynamics of the transducers and keeping the LISA formulation in an explicit format, which facilitates its readiness for parallel computing. The global LISA framework was extended through the 3D Kelvin-Voigt viscoelasticity theory to include anisotropic damping effects for composite structures, as an improvement over the existing LISA formulation. The global LISA framework was implemented using the compute unified device architecture running on graphic processing units. A commercial preprocessor is integrated seamlessly with the computational framework for grid generation and material property allocation to handle complex structures. The excitability and damping effects are successfully captured by this hybrid model, with experimental validation using the scanning laser doppler vibrometry. To demonstrate the capability of our hybrid approach for complex structures, guided wave propagation and interaction with a delamination in a composite panel with stiffeners is presented.

  6. Study on the Analytical Behaviour of Concrete Structure Against Local Impact of Hard Missile

    Directory of Open Access Journals (Sweden)

    Ahmad Mujahid Ahmad Zaidi

    2011-07-01

    Full Text Available Concrete is basic construction material used for almost all kind of structure. However, in the majority essential structures such as nuclear plants, Power plants, Weapon Industries, weapons storage places, water retaining structures like dams, highways barriers, bridges, & etc., concrete structures have to be designed as self-protective structure which can afford any disaster or consciously engendered unpleasant incidents such as incident occurs in nuclear plants, incident in any essential industry, terrorist attack, Natural disasters like tsunami and etc missile attack, and local impact damage generated by kinetic missiles dynamic loading (steel rods, steel pipes, turbine blades, etc.. This paper inquisitively is paying attention on verdict of the recent development in formulating analytical behavior of concrete and reinforced concrete structures against local impact effect generated by hard missile with and without the influence of dimensional analysis based on dominant non-dimensional parameters, various nose shape factors at normal and certain inclined oblique angles. The paper comprises the analytical models and methods for predicting penetration, and perforation of concrete and reinforced concrete. The fallout conquer from this study can be used for making design counsel and design procedures for seminal the dynamic retort of the concrete targets to foil local impact damage.

  7. The organization of mineral exploitation and the relationship to urban structures and local business development

    DEFF Research Database (Denmark)

    Hendriksen, Kåre; Hoffmann, Birgitte; Jørgensen, Ulrik

    2013-01-01

    The paper explores relations between mining and urban structures as these are decisive for involving the local workforce and developing local businesses. A major challenge for Greenland is the on-going decoupling between existing settlements and the main export industry based on marine living...... resources. Because Greenland, as other Arctic regions, are structured in relatively isolated island economies with only modest trade between the settlements and no possibility of commuting, a number of settlements are left without substantial industrial base. Administration of the settlement becomes...... of the resources using immigrant and migrant labour, working intensively over a period of time, while living in shantytowns. Both local and international experiences show that such an organization of work life is not attractive for the population, and that it often provides significant human and social challenges...

  8. Pressure-Induced Local Structure Distortions in Cu(pyz)F(2)(H(2)O)(2)

    Energy Technology Data Exchange (ETDEWEB)

    J Musfeldt; Z Liu; S Li; J Kang; C Lee; P Jena; J Manson; J Schlueter; G Carr; M Whangbo

    2011-12-31

    We employed infrared spectroscopy along with complementary lattice dynamics and spin density calculations to investigate pressure-driven local structure distortions in the copper coordination polymer Cu(pyz)F{sub 2}(H{sub 2}O){sub 2}. Here, pyz is pyrazine. Our study reveals rich and fully reversible local lattice distortions that buckle the pyrazine ring, disrupt the bc-plane O-H {hor_ellipsis} F hydrogen-bonding network, and reinforce magnetic property switching. The resiliency of the soft organic ring is a major factor in the stability of this material. Interestingly, the collective character of the lattice vibrations masks direct information on the Cu-N and Cu-O linkages through the series of pressure-induced Jahn-Teller axis switching transitions, although Cu-F bond softening is clearly identified above 3 GPa. These findings illustrate the importance of combined bulk and local probe techniques for microscopic structure determination in complex materials.

  9. Pressure Induced Local Structure Distortions in Cu(pyz)F2(H2O)2

    Energy Technology Data Exchange (ETDEWEB)

    Musfeldt, J.L.; Carr, G.; Liu, Z.; Li, S.; Kang, C.L., Jena, P.; Manson, J.L.; Schlueter, J.A. Whangbo, M.H.

    2011-06-06

    We employed infrared spectroscopy along with complementary lattice dynamics and spin density calculations to investigate pressure-driven local structure distortions in the copper coordination polymer Cu(pyz)F{sub 2}(H{sub 2}O){sub 2}. Here, pyz is pyrazine. Our study reveals rich and fully reversible local lattice distortions that buckle the pyrazine ring, disrupt the bc-plane O-H {hor_ellipsis} F hydrogen-bonding network, and reinforce magnetic property switching. The resiliency of the soft organic ring is a major factor in the stability of this material. Interestingly, the collective character of the lattice vibrations masks direct information on the Cu-N and Cu-O linkages through the series of pressure-induced Jahn-Teller axis switching transitions, although Cu-F bond softening is clearly identified above 3 GPa. These findings illustrate the importance of combined bulk and local probe techniques for microscopic structure determination in complex materials.

  10. Heterogeneity of Global and Local Connectivity in Spatial Network Structures of World Migration

    CERN Document Server

    Danchev, Valentin

    2016-01-01

    We examine world migration as a social-spatial network of countries connected via movements of people. We assess how multilateral migratory relationships at global, regional, and local scales coexist ("glocalization"), divide ("polarization"), or form an interconnected global system ("globalization"). To do this, we decompose the world migration network (WMN) into communities---sets of countries with denser than expected migration connections---and characterize their pattern of local (i.e., intracommunity) and global (i.e., intercommunity) connectivity. We distinguish community signatures---"cave", "biregional", and "bridging"---with distinct migration patterns, spatial network structures, temporal dynamics, and underlying antecedents. Cave communities are tightly-knit, enduring structures that tend to channel local migration between contiguous countries; biregional communities are likely to merge migration between two distinct geographic regions (e.g., North Africa and Europe); and bridging communities have ...

  11. Strong nonlocal coupling stabilizes localized structures: an analysis based on front dynamics.

    Science.gov (United States)

    Fernandez-Oto, C; Clerc, M G; Escaff, D; Tlidi, M

    2013-04-26

    We investigate the effect of strong nonlocal coupling in bistable spatially extended systems by using a Lorentzian-like kernel. This effect through front interaction drastically alters the space-time dynamics of bistable systems by stabilizing localized structures in one and two dimensions, and by affecting the kinetics law governing their behavior with respect to weak nonlocal and local coupling. We derive an analytical formula for the front interaction law and show that the kinetics governing the formation of localized structures obeys a law inversely proportional to their size to some power. To illustrate this mechanism, we consider two systems, the Nagumo model describing population dynamics and nonlinear optics model describing a ring cavity filled with a left-handed material. Numerical solutions of the governing equations are in close agreement with analytical predictions.

  12. Magnetic Doppler imaging considering atmospheric structure modifications due to local abundances: a luxury or a necessity?

    CERN Document Server

    Kochukhov, O; Shulyak, D

    2012-01-01

    Magnetic Doppler imaging is currently the most powerful method of interpreting high-resolution spectropolarimetric observations of stars. This technique has revealed the presence of unexpected small-scale magnetic fields on the surfaces of Ap stars. These studies were recently criticisied by Stift et al. (2012), who claimed that magnetic inversions are not robust and are undermined by neglecting a feedback on the Stokes line profiles from the local atmospheric structure in the regions of enhanced metal abundance. We show that Stift et al. misinterpreted published magnetic Doppler imaging results and neglected some of the most fundamental principles behind magnetic mapping. We demonstrate that the variation of atmospheric structure across the surface of a star with chemical spots affects the local continuum intensity but is negligible for the normalised local Stokes profiles. For the disk-integrated spectra of an Ap star with extreme abundance variations, we find that the assumption of a mean model atmosphere ...

  13. Exciton Localization in Extended {\\pi}-electron Systems: Comparison of Linear and Cyclic Structures

    CERN Document Server

    Thiessen, Alexander; Jester, Stefan-S; Aggarwal, A Vikas; Idelson, Alissa; Bange, Sebastian; Vogelsang, Jan; Höger, Sigurd; Lupton, John M

    2015-01-01

    We employ five {\\pi}-conjugated model materials of different molecular shape --- oligomers and cyclic structures --- to investigate the extent of exciton self-trapping and torsional motion of the molecular framework following optical excitation. Our studies combine steady-state and transient fluorescence spectroscopy in the ensemble with measurements of polarization anisotropy on single molecules, supported by Monte Carlo simulations. The dimer exhibits a significant spectral red-shift within $\\sim$ 100 ps after photoexcitation which is attributed to torsional relaxation. This relaxation mechanism is inhibited in the structurally rigid macrocyclic analogue. However, both systems show a high degree of exciton localization but with very different consequences: while in the macrocycle the exciton localizes randomly on different parts of the ring, scrambling polarization memory, in the dimer, localization leads to a deterministic exciton position with luminescence characteristics of a dipole. Monte Carlo simulati...

  14. Localized Polymerization Using Single Photon Photoinitiators in Two-photon process for Fabricating Subwavelength Structures

    CERN Document Server

    Ummethala, Govind; Chaudhary, Raghvendra P; Hawal, Suyog; Saxena, Sumit; Shukla, Shobha

    2016-01-01

    Localized polymerization in subwavelength volumes using two photon dyes has now become a well-established method for fabrication of subwavelength structures. Unfortunately, the two photon absorption dyes used in such process are not only expensive but also proprietary. LTPO-L is an inexpensive, easily available single photon photoinitiator and has been used extensively for single photon absorption of UV light for polymerization. These polymerization volumes however are not localized and extend to micron size resolution having limited applications. We have exploited high quantum yield of radicals of LTPO-Lfor absorption of two photons to achieve localized polymerization in subwavelength volumes, much below the diffraction limit. Critical concentration (10wt%) of LTPO-Lin acrylate (Sartomer) was found optimal to achieve subwavelength localized polymerization and has been demonstrated by fabricating 2D/3D complex nanostructures and functional devices such as variable polymeric gratings with nanoscaled subwavelen...

  15. Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation.

    NARCIS (Netherlands)

    Marle-Koster, van E.; Hefer, C.A.; Nel, L.H.; Groenen, M.A.M.

    2008-01-01

    In this study microsatellite markers were applied to investigate the genetic diversity and population structure of the six local chicken lines kept in the “Fowls for Africa” program, for better clarification of parameters for breed differentiation and genetic conservation of this valuable resource.

  16. On the robustness of the localized spatiotemporal structures in electron-positron-ion plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Mahajan, S.M. [Univ. of Texas, Austin, TX (United States). Institute for Fusion Studies; Berezhiani, V.I. [Univ. of Texas, Austin, TX (United States). Institute for Fusion Studies]|[Institute of Physics, Tbilisi (Russian Federation). Dept. of Plasma Physics; Miklaszewski, R. [Institute of Plasma Physics and Laser Microfusion, Warsaw (Poland)

    1998-04-01

    It is shown that, in an electron-positron plasma with a small fraction of ions, large-amplitude localized spatiotemporal structures (light bullets) can be readily generated and sustained. These light bullets are found to be exceptionally robust: they can emerge from a large variety of initial field distributions and are remarkably stable.

  17. Observation of electro-activated localized structures in broad area VCSELs

    CERN Document Server

    Parravicini, J; Columbo, L; Prati, F; Rizza, C; Tissoni, G; Agranat, A J; DelRe, E

    2014-01-01

    We demonstrate experimentally the electro-activation of a localized optical structure in a coherently driven broad-area vertical-cavity surface-emitting laser (VCSEL) operated below threshold. Control is achieved by electro-optically steering a writing beam through a pre-programmable switch based on a photorefractive funnel waveguide.

  18. Localization to Chromosomes of Structural Genes for the Major Protease Inhibitors of Barley Grains

    DEFF Research Database (Denmark)

    Hejgaard, Jørn; Bjørn, S.E.; Nielsen, Gunnar Gissel

    1984-01-01

    Wheat-barley chromosome addition lines were compared by isoelectric focusing of protein extracts to identify chromosomes carrying loci for the major immunochemically distinct protease inhibitors of barley grains. Structural genes for the following inhibitors were localized: an inhibitor of both...

  19. Local atomic arrangements and lattice distortions in layered Ge-Sb-Te crystal structures

    Science.gov (United States)

    Lotnyk, Andriy; Ross, Ulrich; Bernütz, Sabine; Thelander, Erik; Rauschenbach, Bernd

    2016-05-01

    Insights into the local atomic arrangements of layered Ge-Sb-Te compounds are of particular importance from a fundamental point of view and for data storage applications. In this view, a detailed knowledge of the atomic structure in such alloys is central to understanding the functional properties both in the more commonly utilized amorphous-crystalline transition and in recently proposed interfacial phase change memory based on the transition between two crystalline structures. Aberration-corrected scanning transmission electron microscopy allows direct imaging of local arrangement in the crystalline lattice with atomic resolution. However, due to the non-trivial influence of thermal diffuse scattering on the high-angle scattering signal, a detailed examination of the image contrast requires comparison with theoretical image simulations. This work reveals the local atomic structure of trigonal Ge-Sb-Te thin films by using a combination of direct imaging of the atomic columns and theoretical image simulation approaches. The results show that the thin films are prone to the formation of stacking disorder with individual building blocks of the Ge2Sb2Te5, Ge1Sb2Te4 and Ge3Sb2Te6 crystal structures intercalated within randomly oriented grains. The comparison with image simulations based on various theoretical models reveals intermixed cation layers with pronounced local lattice distortions, exceeding those reported in literature.

  20. Design Optimization of Laminated Composite Structures with Many Local Strength Criteria

    DEFF Research Database (Denmark)

    Lund, Erik

    2012-01-01

    This paper presents different strategies for handling very many local strength criteria in structural optimization of laminated composites. Global strength measures using Kreisselmeier-Steinhauser or p-norm functions are introduced for patch-wise parameterizations, and the efficiency of the methods...

  1. Assessment of the local SAR Distortion by Major Anatomical Structures in a Cylindrical Neck Phantom

    NARCIS (Netherlands)

    M.M. Paulides (Maarten); D.H.M. Wielheesen (Dennis); J. van der Zee (Jill); G.C. van Rhoon (Gerard)

    2005-01-01

    textabstractThe objective of this work is to gain insight in the distortions on the local SAR distribution by various major anatomical structures in the neck. High resolution 3D FDTD calculations based on a variable grid are made for a semi-3D generic phantom based on average dimensions obtained fro

  2. New Exact Solutions and Localized Structures for (3+1)-Dimensional Burgers System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jing-Shang; LI Jiang-Bo; MA Song-Hua; REN Qing-Bao; FANG Jian-Ping; ZHENG Chun-Long

    2008-01-01

    With an extended mapping approach and a linear variable separation method, new families of variable separation solutions (including solitary wave solutions, periodic wave solutions, and rational function solutions) with arbitrary functions for (3+1)-dimensional Burgers system is derived. Based on the derived excitations, we obtain some novel localized coherent structures and study the interactions between solitons.

  3. Locally self-consistent Green’s function approach to the electronic structure problem

    DEFF Research Database (Denmark)

    Abrikosov, I.A.; Simak, S.I.; Johansson, B.;

    1997-01-01

    The locally self-consistent Green's function (LSGF) method is an order-N method for calculation of the electronic structure of systems with an arbitrary distribution of atoms of different kinds on an underlying crystal lattice. For each atom Dyson's equation is used to solve the electronic multiple...

  4. Residual dent in locally loaded foam core sandwich structures – Analysis and use for NDI

    NARCIS (Netherlands)

    Koysin, V.; Shipsha, Andrey

    2008-01-01

    This paper addresses the residual denting in the face sheet and corresponding core damage in a locally loaded flat sandwich structure with foam core. The problem is analytically considered in the context of elastic bending of the face sheet accompanied by non-linear deformation of the crushed foam

  5. Types and concentrations of metal ions affect local structure and dynamics of RNA

    Science.gov (United States)

    Wang, Jun; Xiao, Yi

    2016-10-01

    The roles that metal ions play in the structure and dynamics of RNA molecules are long-standing problems that have been studied extensively but are still not well understood. Here we show that metal ions have distributions around RNA molecules that strongly depend on the types and concentrations of the metal ions and also the electrostatic surface of the molecule. In particular, the ion distributions may not balance all the local electronegativity of the molecule. These ion distributions do not only greatly affect local structures but also lead to different local dynamics of RNA. We studied the effects of different ion solutions on the structure and dynamics of RNA by taking the pre Q1 riboswitch aptamer domain as an illustrative example and using molecular dynamics simulations. Since the local structures and dynamics of RNAs are important to their functions, our results also indicate that the selection of proper ion conditions is necessary to model them correctly, in contrast to the use of diverse ion solutions in current molecular dynamics simulations.

  6. Local temperature redistribution and structural transition during joule-heating-driven conductance switching in VO2.

    Science.gov (United States)

    Kumar, Suhas; Pickett, Matthew D; Strachan, John Paul; Gibson, Gary; Nishi, Yoshio; Williams, R Stanley

    2013-11-13

    Joule-heating induced conductance-switching is studied in VO2 , a Mott insulator. Complementary in situ techniques including optical characterization, blackbody microscopy, scanning transmission X-ray microscopy (STXM) and numerical simulations are used. Abrupt redistribution in local temperature is shown to occur upon conductance-switching along with a structural phase transition, at the same current.

  7. Impacts of Information Subsidies and Community Structure on Local Press Coverage of Environmental Contamination.

    Science.gov (United States)

    Griffin, Robert J.; Dunwoody, Sharon

    1995-01-01

    Finds that a press kit sent by an environmental group to midwestern newspapers influenced them to delegate local staff to cover the story. Indicates that the press's function to report or raise issues concerning industrial toxic releases and related health risks is tempered by community structure and particularly by community reliance on…

  8. Local structural investigation of SmFeAsO1 - xFx high temperature superconductors

    Science.gov (United States)

    Malavasi, Lorenzo; Artioli, Gianluca A.; Kim, Hyunjeong; Maroni, Beatrice; Joseph, Boby; Ren, Yang; Proffen, Thomas; Billinge, Simon J. L.

    2011-07-01

    A strong revitalization of the field of high temperature superconductivity (HTSC) has been induced recently by the discovery of TC around 26 K in F-doped LaFeAsO iron pnictides. Starting from this discovery, a huge amount of experimental data have been accumulated. This important corpus of results will allow the development of suitable theoretical models aimed at describing the basic electronic structure properties and nature of superconducting states in these fascinating new systems. A close correlation between structural features and physical properties of the normal and superconducting states has already been demonstrated in the current literature. Advanced theoretical models are also based on the close correlation with structural properties and in particular with the Fe-As tetrahedral array. As for other complex materials, a deeper understanding of their structure-properties correlation requires a full knowledge of the atomic arrangement within the structure. Here we report an investigation of the local structure in the SmFeAsO1 - xFx system carried out by means of x-ray total scattering measurements and pair distribution function analysis. The results presented indicate that the local structure of these HTSC significantly differs from the average structure determined by means of traditional diffraction techniques, in particular the distribution of Fe-As bond lengths. In addition, a model for describing the observed discrepancies is presented.

  9. Local structural investigation of SmFeAsO₁₋xF(x) high temperature superconductors.

    Science.gov (United States)

    Malavasi, Lorenzo; Artioli, Gianluca A; Kim, Hyunjeong; Maroni, Beatrice; Joseph, Boby; Ren, Yang; Proffen, Thomas; Billinge, Simon J L

    2011-07-13

    A strong revitalization of the field of high temperature superconductivity (HTSC) has been induced recently by the discovery of T(C) around 26 K in F-doped LaFeAsO iron pnictides. Starting from this discovery, a huge amount of experimental data have been accumulated. This important corpus of results will allow the development of suitable theoretical models aimed at describing the basic electronic structure properties and nature of superconducting states in these fascinating new systems. A close correlation between structural features and physical properties of the normal and superconducting states has already been demonstrated in the current literature. Advanced theoretical models are also based on the close correlation with structural properties and in particular with the Fe-As tetrahedral array. As for other complex materials, a deeper understanding of their structure-properties correlation requires a full knowledge of the atomic arrangement within the structure. Here we report an investigation of the local structure in the SmFeAsO₁₋ xF(x) system carried out by means of x-ray total scattering measurements and pair distribution function analysis. The results presented indicate that the local structure of these HTSC significantly differs from the average structure determined by means of traditional diffraction techniques, in particular the distribution of Fe-As bond lengths. In addition, a model for describing the observed discrepancies is presented.

  10. Decoupling local mechanics from large-scale structure in modular metamaterials.

    Science.gov (United States)

    Yang, Nan; Silverberg, Jesse L

    2017-04-04

    A defining feature of mechanical metamaterials is that their properties are determined by the organization of internal structure instead of the raw fabrication materials. This shift of attention to engineering internal degrees of freedom has coaxed relatively simple materials into exhibiting a wide range of remarkable mechanical properties. For practical applications to be realized, however, this nascent understanding of metamaterial design must be translated into a capacity for engineering large-scale structures with prescribed mechanical functionality. Thus, the challenge is to systematically map desired functionality of large-scale structures backward into a design scheme while using finite parameter domains. Such "inverse design" is often complicated by the deep coupling between large-scale structure and local mechanical function, which limits the available design space. Here, we introduce a design strategy for constructing 1D, 2D, and 3D mechanical metamaterials inspired by modular origami and kirigami. Our approach is to assemble a number of modules into a voxelized large-scale structure, where the module's design has a greater number of mechanical design parameters than the number of constraints imposed by bulk assembly. This inequality allows each voxel in the bulk structure to be uniquely assigned mechanical properties independent from its ability to connect and deform with its neighbors. In studying specific examples of large-scale metamaterial structures we show that a decoupling of global structure from local mechanical function allows for a variety of mechanically and topologically complex designs.

  11. Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis.

    Science.gov (United States)

    Ding, Hang

    2014-01-01

    Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

  12. Characterization of local complex structures in a recurrence plot to improve nonlinear dynamic discriminant analysis

    Science.gov (United States)

    Ding, Hang

    2014-01-01

    Structures in recurrence plots (RPs), preserving the rich information of nonlinear invariants and trajectory characteristics, have been increasingly analyzed in dynamic discrimination studies. The conventional analysis of RPs is mainly focused on quantifying the overall diagonal and vertical line structures through a method, called recurrence quantification analysis (RQA). This study extensively explores the information in RPs by quantifying local complex RP structures. To do this, an approach was developed to analyze the combination of three major RQA variables: determinism, laminarity, and recurrence rate (DLR) in a metawindow moving over a RP. It was then evaluated in two experiments discriminating (1) ideal nonlinear dynamic series emulated from the Lorenz system with different control parameters and (2) data sets of human heart rate regulations with normal sinus rhythms (n = 18) and congestive heart failure (n = 29). Finally, the DLR was compared with seven major RQA variables in terms of discriminatory power, measured by standardized mean difference (DSMD). In the two experiments, DLR resulted in the highest discriminatory power with DSMD = 2.53 and 0.98, respectively, which were 7.41 and 2.09 times the best performance from RQA. The study also revealed that the optimal RP structures for the discriminations were neither typical diagonal structures nor vertical structures. These findings indicate that local complex RP structures contain some rich information unexploited by RQA. Therefore, future research to extensively analyze complex RP structures would potentially improve the effectiveness of the RP analysis in dynamic discrimination studies.

  13. Identification and characterization of multiple conserved nuclear localization signals within adenovirus E1A

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, Kris S.; Cohen, Michael J.; Fonseca, Greg J.; Todorovic, Biljana; King, Cason R. [Department of Microbiology and Immunology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6 (Canada); Yousef, Ahmed F. [Department of Chemical and Environmental Engineering, Masdar Institute, Abu Dhabi (United Arab Emirates); Zhang, Zhiying [College of Animal Science and Technologies, Northwest A and F University, Yangling, Shaanxi 712100 (China); Mymryk, Joe S., E-mail: jmymryk@uwo.ca [Department of Microbiology and Immunology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6 (Canada); Department of Oncology, Western University, London Regional Cancer Program, London, ON, Canada N6A 4L6 (Canada)

    2014-04-15

    The human adenovirus 5 (HAdV-5) E1A protein has a well defined canonical nuclear localization signal (NLS) located at its C-terminus. We used a genetic assay in the yeast Saccharomyces cerevisiae to demonstrate that the canonical NLS is present and functional in the E1A proteins of each of the six HAdV species. This assay also detects a previously described non-canonical NLS within conserved region 3 and a novel active NLS within the N-terminal/conserved region 1 portion of HAdV-5 E1A. These activities were also present in the E1A proteins of each of the other five HAdV species. These results demonstrate that, despite substantial differences in primary sequence, HAdV E1A proteins are remarkably consistent in that they contain one canonical and two non-canonical NLSs. By utilizing independent mechanisms, these multiple NLSs ensure nuclear localization of E1A in the infected cell. - Highlights: • HAdV E1A uses multiple mechanisms for nuclear import. • We identified an additional non-canonical NLS in the N-terminal/CR1 portion of E1A. • The new NLS does not contact importin-alpha directly. • All NLSs are functionally conserved in the E1A proteins of all 6 HAdV species.

  14. Machine-learning approach for local classification of crystalline structures in multiphase systems

    Science.gov (United States)

    Dietz, C.; Kretz, T.; Thoma, M. H.

    2017-07-01

    Machine learning is one of the most popular fields in computer science and has a vast number of applications. In this work we will propose a method that will use a neural network to locally identify crystal structures in a mixed phase Yukawa system consisting of fcc, hcp, and bcc clusters and disordered particles similar to plasma crystals. We compare our approach to already used methods and show that the quality of identification increases significantly. The technique works very well for highly disturbed lattices and shows a flexible and robust way to classify crystalline structures that can be used by only providing particle positions. This leads to insights into highly disturbed crystalline structures.

  15. Local structure in the disordered solid solution of cis- and trans-perinones

    DEFF Research Database (Denmark)

    Teteruk, Jaroslav L.; Glinnemann, Juergen; Heyse, Winfried;

    2016-01-01

    The cis- and trans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures of cis-perinone (Pigment Red 194) and trans-perinone (Pigment Orange 34) and exhibits a combined positional....... The crystal structure of the solid solution was determined by single-crystal X-ray analysis. Extensive lattice-energy minimizations with force-field and DFT-D methods were carried out on combinatorially complete sets of ordered models. For the disordered systems, local structures were calculated, including...

  16. Nuclear Enhanced X-ray Maximum Entropy Method Used to Analyze Local Distortions in Simple Structures

    DEFF Research Database (Denmark)

    Christensen, Sebastian; Bindzus, Niels; Christensen, Mogens

    the ideal, undistorted rock-salt structure. NEXMEM employs a simple procedure to normalize extracted structure factors to the atomic form factors. The NDD is reconstructed by performing maximum entropy calculations on the normalized structure factors. NEXMEM has been validated by testing against simulated....... In addition, we have applied NEXMEM to multi-temperature synchrotron powder X-ray diffraction collected on PbX. Based on powder diffraction data, our study demonstrates that NEXMEM successfully improves the atomic resolution over standard MEM. This new tool aids our understanding of the local distortions...

  17. Identification and localization of the structural proteins of anguillid herpesvirus 1

    Directory of Open Access Journals (Sweden)

    van Beurden Steven J

    2011-10-01

    Full Text Available Abstract Many of the known fish herpesviruses have important aquaculture species as their natural host, and may cause serious disease and mortality. Anguillid herpesvirus 1 (AngHV-1 causes a hemorrhagic disease in European eel, Anguilla anguilla. Despite their importance, fundamental molecular knowledge on fish herpesviruses is still limited. In this study we describe the identification and localization of the structural proteins of AngHV-1. Purified virions were fractionated into a capsid-tegument and an envelope fraction, and premature capsids were isolated from infected cells. Proteins were extracted by different methods and identified by mass spectrometry. A total of 40 structural proteins were identified, of which 7 could be assigned to the capsid, 11 to the envelope, and 22 to the tegument. The identification and localization of these proteins allowed functional predictions. Our findings include the identification of the putative capsid triplex protein 1, the predominant tegument protein, and the major antigenic envelope proteins. Eighteen of the 40 AngHV-1 structural proteins had sequence homologues in related Cyprinid herpesvirus 3 (CyHV-3. Conservation of fish herpesvirus structural genes seemed to be high for the capsid proteins, limited for the tegument proteins, and low for the envelope proteins. The identification and localization of the structural proteins of AngHV-1 in this study adds to the fundamental knowledge of members of the Alloherpesviridae family, especially of the Cyprinivirus genus.

  18. Connecting the dots: how local structure affects global integration in infants.

    Science.gov (United States)

    Palomares, Melanie; Pettet, Mark; Vildavski, Vladimir; Hou, Chuan; Norcia, Anthony

    2010-07-01

    Glass patterns are moirés created from a sparse random-dot field paired with its spatially shifted copy. Because discrimination of these patterns is not based on local features, they have been used extensively to study global integration processes. Here, we investigated whether 4- to 5.5-month-old infants are sensitive to the global structure of Glass patterns by measuring visual-evoked potentials. Although we found strong responses to the appearance of the constituent dots, we found sensitivity to the global structure of the Glass patterns in the infants only over a very limited range of spatial separation. In contrast, we observed robust responses in the infants when we connected the dot pairs of the Glass pattern with lines. Moreover, both infants and adults showed differential responses to exchanges between line patterns portraying different global structures. A control study varying luminance contrast in adults suggests that infant sensitivity to global structure is not primarily limited by reduced element visibility. Together our results suggest that the insensitivity to structure in conventional Glass patterns is due to inefficiencies in extracting the local orientation cues generated by the dot pairs. Once the local orientations are made unambiguous or when the interpolation span is small, infants can integrate these signals over the image.

  19. Efficient tracker based on sparse coding with Euclidean local structure-based constraint

    Institute of Scientific and Technical Information of China (English)

    WANG Hongyuan; ZHANG Ji; CHEN Fuhua

    2016-01-01

    Sparse coding ( SC) based visual tracking ( l1⁃tracker) is gaining increasing attention, and many related algorithms are developed. In these algorithms, each candidate region is sparsely represented as a set of target tem⁃plates. However, the structure connecting these candidate regions is usually ignored. Lu proposed an NLSSC⁃tracker with non⁃local self⁃similarity sparse coding to address this issue, which has a high computational cost. In this study, we propose an Euclidean local⁃structure constraint based sparse coding tracker with a smoothed Euclidean local structure. With this tracker, the optimization procedure is transformed to a small⁃scale l1⁃optimization problem, sig⁃nificantly reducing the computational cost. Extensive experimental results on visual tracking demonstrate the effectiveness and efficiency of the proposed algorithm.

  20. Self-organization of amphiphilic macromolecules with local helix structure in concentrated solutions.

    Science.gov (United States)

    Glagolev, M K; Vasilevskaya, V V; Khokhlov, A R

    2012-08-28

    Concentrated solutions of amphiphilic macromolecules with local helical structure were studied by means of molecular dynamic simulations. It is shown that in poor solvent the macromolecules are assembled into wire-like aggregates having complex core-shell structure. The core consists of a hydrophobic backbone of the chains which intertwine around each other. It is protected by the shell of hydrophilic side groups. In racemic mixture of right-hand and left-hand helix macromolecules the wire-like complex is a chain of braid bundles of macromolecules with the same chirality stacking at their ends. The average number of macromolecules in the wire cross-section is close to that of separate bundles observed in dilute solutions of such macromolecules. The effects described here could serve as a simple model of self-organization in solutions of macromolecules with local helical structure.

  1. Local kernel nonparametric discriminant analysis for adaptive extraction of complex structures

    Science.gov (United States)

    Li, Quanbao; Wei, Fajie; Zhou, Shenghan

    2017-05-01

    The linear discriminant analysis (LDA) is one of popular means for linear feature extraction. It usually performs well when the global data structure is consistent with the local data structure. Other frequently-used approaches of feature extraction usually require linear, independence, or large sample condition. However, in real world applications, these assumptions are not always satisfied or cannot be tested. In this paper, we introduce an adaptive method, local kernel nonparametric discriminant analysis (LKNDA), which integrates conventional discriminant analysis with nonparametric statistics. LKNDA is adept in identifying both complex nonlinear structures and the ad hoc rule. Six simulation cases demonstrate that LKNDA have both parametric and nonparametric algorithm advantages and higher classification accuracy. Quartic unilateral kernel function may provide better robustness of prediction than other functions. LKNDA gives an alternative solution for discriminant cases of complex nonlinear feature extraction or unknown feature extraction. At last, the application of LKNDA in the complex feature extraction of financial market activities is proposed.

  2. Experimental Study on Local Mass Transfer of Structured Packing with the Method of Flow Visualization

    Institute of Scientific and Technical Information of China (English)

    张燕来; 朱慧铭; 尹秋响

    2011-01-01

    A chromochemical reactive mass transfer technique has been employed to study local mass transfer characteristics of structured packing. This technology adopted by experiment is an Ammonia Adsorption Method (AAM) that yields the surface distribution of transferred mass by analyzing the color distribution on a filter paper with the results of the color chemical reaction. A digital image processing technology is applied for data visualiza-tion. The three-dimensional plot of the local mass transfer coefficients shows that there exist three peak values on different positions of a unit cell of structured packing. In order to improve mass transfer efficiency of the structured packing, one piece of baffle is added between packing sheets. As a result, the average mass transfer coefficient increases by (10 20)% and the pressure drop decreases by (15-55)%.

  3. Local topological modeling of glass structure and radiation-induced rearrangements in connected networks

    Energy Technology Data Exchange (ETDEWEB)

    Hobbs, L.W. [Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, Cambridge, MA (United States); Jesurum, C.E. [Massachusetts Institute of Technology, Dept. of Mathematics, Cambridge, MA (United States); Pulim, V. [Massachusetts Institute of Technology, Lab. for Computer Science, Cambridge, MA (United States)

    1997-07-01

    Topology is shown to govern the arrangement of connected structural elements in network glasses such as silica and related radiation-amorphized network compounds: A topological description of such topologically-disordered arrangements is possible which utilizes a characteristic unit of structure--the local cluster--not far in scale from the unit cells in crystalline arrangements. Construction of credible glass network structures and their aberration during cascade disordering events during irradiation can be effected using local assembly rules based on modification of connectivity-based assembly rules derived for crystalline analogues. These topological approaches may provide useful complementary information to that supplied by molecular dynamics about re-ordering routes and final configurations in irradiated glasses. (authors)

  4. Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure

    Science.gov (United States)

    Campo, Matteo; Speck, Thomas

    2016-08-01

    We study numerically the crystallization of a hard-sphere mixture with 8% polydispersity. Although often used as a model glass former, for small system sizes we observe crystallization in molecular dynamics simulations. This opens the possibility to study the competition between crystallization and structural relaxation of the melt, which typically is out of reach due to the disparate timescales. We quantify the dependence of relaxation and crystallization times on density and system size. For one density and system size we perform a detailed committor analysis to investigate the suitability of local structures as order parameters to describe the crystallization process. We find that local structures are strongly correlated with generic bond order and add little information to the reaction coordinate.

  5. Strong influence of regional species pools on continent-wide structuring of local communities

    DEFF Research Database (Denmark)

    Lessard, Jean-Philippe; Borregaard, Michael Krabbe; Fordyce, James A.;

    2012-01-01

    of communities along climatic gradients. We find that the average phylogenetic relatedness of species in ant communities decreases from tropical to temperate regions, but the strength of this relationship depends on the level of ecological realism in the definition of source pools. We conclude that the evolution......There is a long tradition in ecology of evaluating the relative contribution of the regional species pool and local interactions on the structure of local communities. Similarly, a growing number of studies assess the phylogenetic structure of communities, relative to that in the regional species...... pool, to examine the interplay between broad-scale evolutionary and fine-scale ecological processes. Finally, a renewed interest in the influence of species source pools on communities has shown that the definition of the source pool influences interpretations of patterns of community structure. We use...

  6. Effective 3D protein structure prediction with local adjustment genetic-annealing algorithm.

    Science.gov (United States)

    Zhang, Xiao-Long; Lin, Xiao-Li

    2010-09-01

    The protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing the energy function. The protein folding structure prediction is computationally challenging and has been shown to be NP-hard problem when the 3D off-lattice AB model is employed. In this paper, the local adjustment genetic-annealing (LAGA) algorithm was used to search the ground state of 3D offlattice AB model for protein folding structure. The algorithm included an improved crossover strategy and an improved mutation strategy, where a local adjustment strategy was also used to enhance the searching ability. The experiments were carried out with the Fibonacci sequences. The experimental results demonstrate that the LAGA algorithm appears to have better performance and accuracy compared to the previous methods.

  7. Localization and fractal spectra of optical phonon modes in quasiperiodic structures

    Science.gov (United States)

    Anselmo, D. H. A. L.; Dantas, A. L.; Medeiros, S. K.; Albuquerque, E. L.; Freire, V. N.

    2005-04-01

    The dispersion relation and localization profile of confined optical phonon modes in quasiperiodic structures, made up of nitride semiconductor materials, are analyzed through a transfer-matrix approach. The quasiperiodic structures are characterized by the nature of their Fourier spectrum, which can be dense pure point (Fibonacci sequences) or singular continuous (Thue-Morse and Double-period sequences). These substitutional sequences are described in terms of a series of generations that obey peculiar recursion relations and/or inflation rules. We present a quantitative analysis of the localization and magnitude of the allowed band widths in the optical phonons spectra of these quasiperiodic structures, as well as how they scale as a function of the number of generations of the sequences.

  8. Strain properties analysis and wireless collection system of PVDF for structural local health monitoring of civil engineering structures

    Science.gov (United States)

    Yu, Yan; Wang, Yang; Dong, Weijie; Jin, Yajing; Ou, Jinping

    2009-07-01

    For large civil engineering structures and base establishments, for example, bridges, super-high buildings, long-span space structures, offshore platforms and pipe systems of water & gas supply, their lives are up to a few decades or centuries. Damaged by environmental loads, fatigue effects, corrosion effects and material aging, these structures experience inevitably such side effects as damage accumulation, resistance reduction and even accidents. The traditional civil structure is a kind of passive one, whose performance and status are unpredictable to a great extent, but the informatics' introduction breaks a new path to obtain the status of the structure, thus it is an important research direction to evaluate and improve reliability of civil structures by the use of monitoring and health diagnosis technique, and this also assures the security of service for civil engineering structures. Smart material structure, originated from the aerospace sector, has been a research hotspot in civil engineering, medicine, shipping, and so on. For structural health monitoring of civil engineering, the research about high-performance sensing unit of smart material structure is very important, and this will possibly push further the development and application of monitoring and health diagnosis techniques. At present, piezoelectric materials are one of the most widely used sensing materials among the research of smart material structures. As one of the piezoelectric materials, PVDF(Polyvinylidene Fluoride)film is widely considered for the advantages of low cost, good mechanical ability, high sensibility, the ability of being easily placed and resistance of corrosion. However, only a few studies exit about building a mature monitoring system using PVDF. In this paper, for the sake of using PVDF for sensing unit for structural local monitoring of civil engineering, the strain sensing properties of PVDF are studied in detail. Firstly, the operating mechanism of PVDF is analyzed

  9. Emergence of Coherent Localized Structures in Shear Deformations of Temperature Dependent Fluids

    Science.gov (United States)

    Katsaounis, Theodoros; Olivier, Julien; Tzavaras, Athanasios E.

    2016-12-01

    Shear localization occurs in various instances of material instability in solid mechanics and is typically associated with Hadamard-instability for an underlying model. While Hadamard instability indicates the catastrophic growth of oscillations around a mean state, it does not by itself explain the formation of coherent structures typically observed in localization. The latter is a nonlinear effect and its analysis is the main objective of this article. We consider a model that captures the main mechanisms observed in high strain-rate deformation of metals, and describes shear motions of temperature dependent non-Newtonian fluids. For a special dependence of the viscosity on the temperature, we carry out a linearized stability analysis around a base state of uniform shearing solutions, and quantitatively assess the effects of the various mechanisms affecting the problem: thermal softening, momentum diffusion and thermal diffusion. Then, we turn to the nonlinear model, and construct localized states—in the form of similarity solutions—that emerge as coherent structures in the localization process. This justifies a scenario for localization that is proposed on the basis of asymptotic analysis in uc(Katsaounis) and uc(Tzavaras) (SIAM J Appl Math 69:1618-1643, 2009).

  10. Emergence of coherent localized structures in shear deformations of temperature dependent fluids

    KAUST Repository

    Katsaounis, Theodoros

    2016-11-25

    Shear localization occurs in various instances of material instability in solid mechanics and is typically associated with Hadamard-instability for an underlying model. While Hadamard instability indicates the catastrophic growth of oscillations around a mean state, it does not by itself explain the formation of coherent structures typically observed in localization. The latter is a nonlinear effect and its analysis is the main objective of this article. We consider a model that captures the main mechanisms observed in high strain-rate deformation of metals, and describes shear motions of temperature dependent non-Newtonian fluids. For a special dependence of the viscosity on the temperature, we carry out a linearized stability analysis around a base state of uniform shearing solutions, and quantitatively assess the effects of the various mechanisms affecting the problem: thermal softening, momentum diffusion and thermal diffusion. Then, we turn to the nonlinear model, and construct localized states - in the form of similarity solutions - that emerge as coherent structures in the localization process. This justifies a scenario for localization that is proposed on the basis of asymptotic analysis in \\\\cite{KT}.

  11. Functional annotation by identification of local surface similarities: a novel tool for structural genomics

    Directory of Open Access Journals (Sweden)

    Zanzoni Andreas

    2005-08-01

    Full Text Available Abstract Background Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in the sequence. Hence, functional annotation by means of sequence or fold similarity is not adequate for such cases. Results We describe a method for the function-related annotation of protein structures by means of the detection of local structural similarity with a library of annotated functional sites. An automatic procedure was used to annotate the function of local surface regions. Next, we employed a sequence-independent algorithm to compare exhaustively these functional patches with a larger collection of protein surface cavities. After tuning and validating the algorithm on a dataset of well annotated structures, we applied it to a list of protein structures that are classified as being of unknown function in the Protein Data Bank. By this strategy, we were able to provide functional clues to proteins that do not show any significant sequence or global structural similarity with proteins in the current databases. Conclusion This method is able to spot structural similarities associated to function-related similarities, independently on sequence or fold resemblance, therefore is a valuable tool for the functional analysis of uncharacterized proteins. Results are available at http://cbm.bio.uniroma2.it/surface/structuralGenomics.html

  12. Structural and contextual dimensions of Iranian primary health care system at local level.

    Science.gov (United States)

    Zanganeh Baygi, Mehdi; Seyedin, Hesam; Salehi, Masoud; Jafari Sirizi, Mehdi

    2015-01-01

    In recent years, family physician plan was established as the main strategy of health system in Iran, while organizational structure of the primary health care system has remained the same as thirty years ago. This study was performed to illustrate structural and contextual dimensions of organizational structure and relationship between them in Iranian primary health care system at local level. A cross-sectional quantitative study was conducted from January to June 2013, during which 121 questionnaires were distributed among senior and junior managers of city health centers at Medical Sciences universities in Iran. Validity of the questionnaire was confirmed by experts (CVI = 0.089 and CVR more than 0.85) and Cronbach α was utilized for reliability (α = 0.904). We used multistage sampling method in this study and analysis of the data was performed by SPSS software using different tests. Local level of primary health care system in Iran had mechanical structure, but in contextual dimensions the results showed different types. There was a significant relationship between structural and contextual dimensions (r = 0.642, P value structural dimensions. Because of the changes in goals and strategies of Iranian health system in recent years, it is urgently recommended to reform the current structure to increase efficiency and effectiveness of the system.

  13. Cultural order and participatory local development: structure for the occupational therapist practice

    Directory of Open Access Journals (Sweden)

    Ricardo Lopes Correia

    2016-01-01

    Full Text Available The Cultural Order is understood as the expression of a game of interdependencies determinations between local and global social groups, pairs identified by productions, values and behavior that consciously guide the life projects and the expansion of a collective freedom. Based on a Social Science research and with theoretical mark of Nobert Elias and Amartya Sen, this article aims to present a theoretical-practice structure of the approach in participatory local development- PLD to the occupational therapist surround by the construction of collective life projects, in order to operationalize in the practice of the community question, understood as the strengths that singularize the participation. We discuss the use of the PLD approach to the occupational therapist in a flexible structure, aiming to guarantee its domain, the Human Occupation, and the set of interventions, technologies, sustained in the management of the activities of daily living. The approach in participatory local development presents itself as an important structural outline to the community actions, and it is the occupational therapist role to be an articulator of the Local Cultural Order dimensions, to deal with the target population their work processes of continuity in collective life projects and expansion of freedom.

  14. Structural and functional characterization of human telomerase RNA processing and cajal body localization signals.

    Science.gov (United States)

    Theimer, Carla A; Jády, Beáta E; Chim, Nicholas; Richard, Patricia; Breece, Katherine E; Kiss, Tamás; Feigon, Juli

    2007-09-21

    The RNA component of human telomerase (hTR) includes H/ACA and CR7 domains required for 3' end processing, localization, and accumulation. The terminal loop of the CR7 domain contains the CAB box (ugAG) required for targeting of scaRNAs to Cajal bodies (CB) and an uncharacterized sequence required for accumulation and processing. To dissect out the contributions of the CR7 stem loop to hTR processing and localization, we solved the solution structures of the 3' terminal stem loops of hTR CR7 and U64 H/ACA snoRNA, and the 5' terminal stem loop of U85 C/D-H/ACA scaRNA. These structures, together with analysis of localization, processing, and accumulation of hTRs containing nucleotide substitutions in the CR7 domain, identified the sequence and structural requirements of the hTR processing and CB localization signals and showed that these signals are functionally independent. Further, 3' end processing was found to be a prerequisite for translocation of hTR to CBs.

  15. Local Structure in Ab Initio Liquid Water: Signatures of Amorphous Phases

    Science.gov (United States)

    Santra, Biswajit; Distasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyze the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I), was unimodal with most water molecules characterized by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water This work was supported by the DOE: DE-SC0008626, DE-SC0005180.

  16. BAYESIAN LOCAL INFLUENCE ASSESSMENTS IN A GROWTH CURVE MODEL WITH GENERAL COVARIANCE STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The objective of this paper is to present a Bayesian approach based on Kullback Leibler divergence for assessing local influence in a growth curve model with general covariance structure.Under certain prior distribution assumption,the Kullback-Leibler divergence is used to measure the influence of some minor perturbation on the posterior distribution of unknown parameter.This leads to the diagnostic statistic for detecting which response is locally influential.As an application,the common covariance-weighted perturbation scheme is thoroughly considered.

  17. Local structure of temperature and pH-sensitive colloidal microgels

    Energy Technology Data Exchange (ETDEWEB)

    Nigro, Valentina, E-mail: nigro@fis.uniroma3.it; Bruni, Fabio; Ricci, Maria Antonietta [Dipartimento di Scienze, Sezione di Nanoscienze, Università degli Studi Roma Tre, Via della Vasca Navale 84, I-00146 Roma (Italy); Angelini, Roberta; Ruzicka, Barbara [Istituto dei Sistemi Complessi del Consiglio Nazionale delle Ricerche (ISC-CNR) UOS Sapienza and Dipartimento di Fisica, Sapienza Università, Pz.le Aldo Moro 5, I-00185 Roma (Italy); Bertoldo, Monica [Istituto per i Processi Chimico-Fisici del Consiglio Nazionale delle Ricerche (IPCF-CNR), Area della Ricerca, Via G. Moruzzi 1, I-56124 Pisa (Italy); Castelvetro, Valter [Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via G. Moruzzi 3, I-56126 Pisa (Italy); Rogers, Sarah [ISIS-STFC, Rutherford Appleton Laboratory, Chilton, Oxon OX11 0QX (United Kingdom)

    2015-09-21

    The temperature dependence of the local intra-particle structure of colloidal microgel particles, composed of interpenetrated polymer networks, has been investigated by small-angle neutron scattering at different pH and concentrations, in the range (299÷315) K, where a volume phase transition from a swollen to a shrunken state takes place. Data are well described by a theoretical model that takes into account the presence of both interpenetrated polymer networks and cross-linkers. Two different behaviors are found across the volume phase transition. At neutral pH and T ≈ 307 K, a sharp change of the local structure from a water rich open inhomogeneous interpenetrated polymer network to a homogeneous porous solid-like structure after expelling water is observed. Differently, at acidic pH, the local structure changes almost continuously. These findings demonstrate that a fine control of the pH of the system allows to tune the sharpness of the volume-phase transition.

  18. Rearrangement dynamics in colloidal particle packings identified through local structure and machine-learning

    Science.gov (United States)

    Davidson, Zoey S.; Still, Tim; Gratale, Matthew D.; Ma, Xiaoguang; Schoenholz, Samuel S.; Sussman, Daniel M.; Liu, A. J.; Yodh, A. G.

    We explore the connection between measures of local structure and particle rearrangements in soft thermal quasi-two-dimensional colloidal systems employing a machine learning approach. Local structure is characterized by two and three point structure functions that measure radial and angular distributions of particles, and rearrangements are identified by a measure of change in average colloidal particle position. By generating labeled training data, we can extract the features of these functions that contribute to the likelihood of a rearrangement. In particular, we use a machine-learning algorithm to construct a decision function in the form of a scalar field we call softness that with high accuracy labels regions of particles more likely to rearrange. Thus, we can predict dynamic rearrangements from the instantaneous local structure. The softness field remains a good predictor when we vary the packing fraction between training and test data sets. In glassy samples, the softness field can identify aging as particles become less likely to undergo cage rearrangements. We gratefully acknowledge financial support through NSF DMR12-05463, MRSEC DMR11-20901, NASA NNX08AO0G, and DE-FG02-05ER46199.

  19. Protein subcellular localization prediction based on compartment-specific features and structure conservation

    Directory of Open Access Journals (Sweden)

    Lo Allan

    2007-09-01

    Full Text Available Abstract Background Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; thus, computational approaches become highly desirable. Extensive studies of localization prediction have led to the development of several methods including composition-based and homology-based methods. However, their performance might be significantly degraded if homologous sequences are not detected. Moreover, methods that integrate various features could suffer from the problem of low coverage in high-throughput proteomic analyses due to the lack of information to characterize unknown proteins. Results We propose a hybrid prediction method for Gram-negative bacteria that combines a one-versus-one support vector machines (SVM model and a structural homology approach. The SVM model comprises a number of binary classifiers, in which biological features derived from Gram-negative bacteria translocation pathways are incorporated. In the structural homology approach, we employ secondary structure alignment for structural similarity comparison and assign the known localization of the top-ranked protein as the predicted localization of a query protein. The hybrid method achieves overall accuracy of 93.7% and 93.2% using ten-fold cross-validation on the benchmark data sets. In the assessment of the evaluation data sets, our method also attains accurate prediction accuracy of 84.0%, especially when testing on sequences with a low level of homology to the training data. A three-way data split procedure is also incorporated to prevent overestimation of the predictive performance. In addition, we show that the prediction accuracy should be approximately 85% for non-redundant data sets of sequence identity less than 30%. Conclusion Our results demonstrate that biological features derived from Gram-negative bacteria translocation

  20. Local Structure Analysis and Interface Layer Effect of Phase-Change Recording Material Using Actual Media

    Science.gov (United States)

    Nakai, Tsukasa; Yoshiki, Masahiko; Satoh, Yasuhiro; Ashida, Sumio

    2008-07-01

    The influences of the interface layer on crystal structure, the local atomic arrangement, and the electronic and chemical structure of a GeBiTe (GBT) phase-change recording material have been investigated using X-ray diffraction (XRD), X-ray absorption fine structure (XAFS), and hard X-ray photoelectron spectroscopy (HX-PES) methods using actual rewritable high-speed HD DVD media without special sample processing. XRD results showed that the crystal structure of laser-crystallized GBT alloy in the actual HD DVD media is the same as that of GeSbTe (GST) alloy, which has a NaCl-type structure. No differences between samples with and without interface layers were found. The lattice constant of GBT is larger than that of GST. Bi increases the lattice constant of GST with respect to the Bi substitution ratio of Sb. According to HX-PES, the DOS of in the recording film amorphous state with an interface layer is closer to that of the crystalline state than the recording film without an interface layer. From XAFS results, clear differences between amorphous (Amo.) and crystalline states (Cry.) were observed. The interatomic distance of amorphous recording material is independent of the existence of an interface layer. On the other hand, the coordination number varied slightly due to the presence of the interface layer. Therefore, the electronic state of the recording layer changes because of the interface layer, although the local structure changes only slightly except for the coordination number. Combining these results, we conclude that the interface layer changes the electronic state of the recording layer and promotes crystallization, but only affects the local structure of the atomic arrangement slightly.

  1. Local structure, composition, and crystallization mechanism of a model two-phase "composite nanoglass"

    Science.gov (United States)

    Chattopadhyay, Soma; Kelly, S. D.; Shibata, Tomohiro; Balasubramanian, M.; Srinivasan, S. G.; Du, Jincheng; Banerjee, Rajarshi; Ayyub, Pushan

    2016-02-01

    We report a detailed study of the local composition and structure of a model, bi-phasic nanoglass with nominal stoichiometry Cu55Nb45. Three dimensional atom probe data suggest a nanoscale-phase-separated glassy structure having well defined Cu-rich and Nb-rich regions with a characteristic length scale of ≈3 nm. However, extended x-ray absorption fine structure analysis indicates subtle differences in the local environments of Cu and Nb. While the Cu atoms displayed a strong tendency to cluster and negligible structural order beyond the first coordination shell, the Nb atoms had a larger fraction of unlike neighbors (higher chemical order) and a distinctly better-ordered structural environment (higher topological order). This provides the first experimental indication that metallic glass formation may occur due to frustration arising from the competition between chemical ordering and clustering. These observations are complemented by classical as well as ab initio molecular dynamics simulations. Our study indicates that these nanoscale phase-separated glasses are quite distinct from the single phase nanoglasses (studied by Gleiter and others) in the following three respects: (i) they contain at least two structurally and compositionally distinct, nanodispersed, glassy phases, (ii) these phases are separated by comparatively sharp inter-phase boundaries, and (iii) thermally induced crystallization occurs via a complex, multi-step mechanism. Such materials, therefore, appear to constitute a new class of disordered systems that may be called a composite nanoglass.

  2. Local structure, composition, and crystallization mechanism of a model two-phase “composite nanoglass”

    Energy Technology Data Exchange (ETDEWEB)

    Chattopadhyay, Soma; Shibata, Tomohiro [CSRRI-IIT, MRCAT, Sector 10, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Kelly, S. D. [EXAFS Analysis, Bolingbrook, Illinois 60440 (United States); Balasubramanian, M. [Sector 20 XOR, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Srinivasan, S. G.; Du, Jincheng; Banerjee, Rajarshi [Department of Materials Science and Engineering, University of North Texas, Denton, Texas 76203-5017 (United States); Ayyub, Pushan, E-mail: pushan@tifr.res.in [Department of Condensed Matter Physics and Materials Science, Tata Institute of Fundamental Research, Mumbai 400005 (India)

    2016-02-14

    We report a detailed study of the local composition and structure of a model, bi-phasic nanoglass with nominal stoichiometry Cu{sub 55}Nb{sub 45}. Three dimensional atom probe data suggest a nanoscale-phase-separated glassy structure having well defined Cu-rich and Nb-rich regions with a characteristic length scale of ≈3 nm. However, extended x-ray absorption fine structure analysis indicates subtle differences in the local environments of Cu and Nb. While the Cu atoms displayed a strong tendency to cluster and negligible structural order beyond the first coordination shell, the Nb atoms had a larger fraction of unlike neighbors (higher chemical order) and a distinctly better-ordered structural environment (higher topological order). This provides the first experimental indication that metallic glass formation may occur due to frustration arising from the competition between chemical ordering and clustering. These observations are complemented by classical as well as ab initio molecular dynamics simulations. Our study indicates that these nanoscale phase-separated glasses are quite distinct from the single phase nanoglasses (studied by Gleiter and others) in the following three respects: (i) they contain at least two structurally and compositionally distinct, nanodispersed, glassy phases, (ii) these phases are separated by comparatively sharp inter-phase boundaries, and (iii) thermally induced crystallization occurs via a complex, multi-step mechanism. Such materials, therefore, appear to constitute a new class of disordered systems that may be called a composite nanoglass.

  3. Local structure in the disordered solid solution of cis- and trans-perinones.

    Science.gov (United States)

    Teteruk, Jaroslav L; Glinnemann, Jürgen; Heyse, Winfried; Johansson, Kristoffer E; van de Streek, Jacco; Schmidt, Martin U

    2016-06-01

    The cis- and trans-isomers of the polycyclic aromatic compound perinone, C26H12N4O2, form a solid solution (Vat Red 14). This solid solution is isotypic to the crystal structures of cis-perinone (Pigment Red 194) and trans-perinone (Pigment Orange 34) and exhibits a combined positional and orientational disorder: In the crystal, each molecular position is occupied by either a cis- or trans-perinone molecule, both of which have two possible molecular orientations. The structure of cis-perinone exhibits a twofold orientational disorder, whereas the structure of trans-perinone is ordered. The crystal structure of the solid solution was determined by single-crystal X-ray analysis. Extensive lattice-energy minimizations with force-field and DFT-D methods were carried out on combinatorially complete sets of ordered models. For the disordered systems, local structures were calculated, including preferred local arrangements, ordering lengths, and probabilities for the arrangement of neighbouring molecules. The superposition of the atomic positions of all energetically favourable calculated models corresponds well with the experimentally determined crystal structures, explaining not only the atomic positions, but also the site occupancies and anisotropic displacement parameters.

  4. Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs

    Directory of Open Access Journals (Sweden)

    Wang Zhouxi

    2013-02-01

    Full Text Available Abstract Background The prediction of biochemical function from the 3D structure of a protein has proved to be much more difficult than was originally foreseen. A reliable method to test the likelihood of putative annotations and to predict function from structure would add tremendous value to structural genomics data. We report on a new method, Structurally Aligned Local Sites of Activity (SALSA, for the prediction of biochemical function based on a local structural match at the predicted catalytic or binding site. Results Implementation of the SALSA method is described. For the structural genomics protein PY01515 (PDB ID 2aqw from Plasmodium yoelii, it is shown that the putative annotation, Orotidine 5'-monophosphate decarboxylase (OMPDC, is most likely correct. SALSA analysis of YP_001304206.1 (PDB ID 3h3l, a putative sugar hydrolase from Parabacteroides distasonis, shows that its active site does not bear close resemblance to any previously characterized member of its superfamily, the Concanavalin A-like lectins/glucanases. It is noted that three residues in the active site of the thermophilic beta-1,4-xylanase from Nonomuraea flexuosa (PDB ID 1m4w, Y78, E87, and E176, overlap with POOL-predicted residues of similar type, Y168, D153, and E232, in YP_001304206.1. The substrate recognition regions of the two proteins are rather different, suggesting that YP_001304206.1 is a new functional type within the superfamily. A structural genomics protein from Mycobacterium avium (PDB ID 3q1t has been reported to be an enoyl-CoA hydratase (ECH, but SALSA analysis shows a poor match between the predicted residues for the SG protein and those of known ECHs. A better local structural match is obtained with Anabaena beta-diketone hydrolase (ABDH, a known β-diketone hydrolase from Cyanobacterium anabaena (PDB ID 2j5s. This suggests that the reported ECH function of the SG protein is incorrect and that it is more likely a β-diketone hydrolase. Conclusions

  5. Microheterogeneous Structure of Local Melted Zones in the Process of Explosive Welding

    Science.gov (United States)

    Greenberg, Bella A.; Ivanov, Mikhail A.; Inozemtsev, Alexei V.; Patselov, Alexander M.; Pushkin, Mark S.; Vlasova, Alisa M.

    2015-08-01

    The dispersed structures formed in the process of explosive welding and solidification after melting were investigated in areas near the interface. It was shown that melting can be initiated by particles flying away as a result of granulating fragmentation. This is the fastest process during explosive welding, which is similar to fragmentation in conventional explosions with the formation of fragments but occurring in the presence of a barrier. The reaction between the particles and their environment may lead to local heating sufficient for melting. This is confirmed by the observation of numerous particles of the refractory phase within the local melted zones. In the absence of mutual solubility of the initial phases, the solidified local melted zones are to a certain extent analogous to colloidal solutions of immiscible liquids. Correlations between the typical temperatures were obtained that determine the conditions for the formation of various types of colloidal solutions.

  6. TAP score: torsion angle propensity normalization applied to local protein structure evaluation

    Directory of Open Access Journals (Sweden)

    Battistutta Roberto

    2007-05-01

    Full Text Available Abstract Background Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging. Results A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at http://protein.cribi.unipd.it/tap/. Conclusion A novel procedure for energy normalization (TAP has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination.

  7. Delay-induced depinning of localized structures in a spatially inhomogeneous Swift-Hohenberg model

    Science.gov (United States)

    Tabbert, Felix; Schelte, Christian; Tlidi, Mustapha; Gurevich, Svetlana V.

    2017-03-01

    We report on the dynamics of localized structures in an inhomogeneous Swift-Hohenberg model describing pattern formation in the transverse plane of an optical cavity. This real order parameter equation is valid close to the second-order critical point associated with bistability. The optical cavity is illuminated by an inhomogeneous spatial Gaussian pumping beam and subjected to time-delayed feedback. The Gaussian injection beam breaks the translational symmetry of the system by exerting an attracting force on the localized structure. We show that the localized structure can be pinned to the center of the inhomogeneity, suppressing the delay-induced drift bifurcation that has been reported in the particular case where the injection is homogeneous, assuming a continuous wave operation. Under an inhomogeneous spatial pumping beam, we perform the stability analysis of localized solutions to identify different instability regimes induced by time-delayed feedback. In particular, we predict the formation of two-arm spirals, as well as oscillating and depinning dynamics caused by the interplay of an attracting inhomogeneity and destabilizing time-delayed feedback. The transition from oscillating to depinning solutions is investigated by means of numerical continuation techniques. Analytically, we use an order parameter approach to derive a normal form of the delay-induced Hopf bifurcation leading to an oscillating solution. Additionally we model the interplay of an attracting inhomogeneity and destabilizing time delay by describing the localized solution as an overdamped particle in a potential well generated by the inhomogeneity. In this case, the time-delayed feedback acts as a driving force. Comparing results from the later approach with the full Swift-Hohenberg model, we show that the approach not only provides an instructive description of the depinning dynamics, but also is numerically accurate throughout most of the parameter regime.

  8. On the local integrability of almost-product structures defined by space-time metrics

    CERN Document Server

    Delphenich, D H

    2016-01-01

    The splitting of the tangent bundle of space-time into temporal and spatial sub-bundles defines an almost-product structure. In particular, any space-time metric can be locally expressed in time-orthogonal form, in such a way that whether or not that almost-product structure is locally generated by a coordinate chart is a matter of the integrability of the Pfaff equation that the temporal 1-form of that expression for the metric defines. When one applies that analysis to the known exact solutions to the Einstein field equations, one finds that many of the common ones are completely-integrable, although some of the physically-interesting ones are not.

  9. The phase diagram of molybdenum at extreme conditions and the role of local liquid structures

    Energy Technology Data Exchange (ETDEWEB)

    Ross, M

    2008-08-15

    Recent DAC measurements made of the Mo melting curve by the x-ray diffraction studies confirms that, up to at least 110 GPa (3300K) melting is directly from bcc to liquid, evidence that there is no basis for a speculated bcc-hcp or fcc transition. An examination of the Poisson Ratio, obtained from shock sound speed measurements, provides evidence that the 210 GPa (4100K) transition detected from shock experiments is a continuation of the bcc-liquid melting, but is from a bcc-to a solid-like mixed phase rather than to liquid. Calculations, modeled to include the free energy of liquid local structures, predict that the transition from the liquid to the mixed phase is near 150 GPa(3500K). The presence of local structures provides the simplest and most direct explanation for the Mo phase diagram, and the low melting slopes.

  10. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions

    Science.gov (United States)

    Rahrig, Ryan R.; Leontis, Neocles B.; Zirbel, Craig L.

    2010-01-01

    Motivation: Comparing 3D structures of homologous RNA molecules yields information about sequence and structural variability. To compare large RNA 3D structures, accurate automatic comparison tools are needed. In this article, we introduce a new algorithm and web server to align large homologous RNA structures nucleotide by nucleotide using local superpositions that accommodate the flexibility of RNA molecules. Local alignments are merged to form a global alignment by employing a maximum clique algorithm on a specially defined graph that we call the ‘local alignment’ graph. Results: The algorithm is implemented in a program suite and web server called ‘R3D Align’. The R3D Align alignment of homologous 3D structures of 5S, 16S and 23S rRNA was compared to a high-quality hand alignment. A full comparison of the 16S alignment with the other state-of-the-art methods is also provided. The R3D Align program suite includes new diagnostic tools for the structural evaluation of RNA alignments. The R3D Align alignments were compared to those produced by other programs and were found to be the most accurate, in comparison with a high quality hand-crafted alignment and in conjunction with a series of other diagnostics presented. The number of aligned base pairs as well as measures of geometric similarity are used to evaluate the accuracy of the alignments. Availability: R3D Align is freely available through a web server http://rna.bgsu.edu/R3DAlign. The MATLAB source code of the program suite is also freely available for download at that location. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: r-rahrig@onu.edu PMID:20929913

  11. Structural Health Monitoring of Wind Turbine Blades: Acoustic Source Localization Using Wireless Sensor Networks

    Directory of Open Access Journals (Sweden)

    Omar Mabrok Bouzid

    2015-01-01

    Full Text Available Structural health monitoring (SHM is important for reducing the maintenance and operation cost of safety-critical components and systems in offshore wind turbines. This paper proposes an in situ wireless SHM system based on an acoustic emission (AE technique. By using this technique a number of challenges are introduced due to high sampling rate requirements, limitations in the communication bandwidth, memory space, and power resources. To overcome these challenges, this paper focused on two elements: (1 the use of an in situ wireless SHM technique in conjunction with the utilization of low sampling rates; (2 localization of acoustic sources which could emulate impact damage or audible cracks caused by different objects, such as tools, bird strikes, or strong hail, all of which represent abrupt AE events and could affect the structural health of a monitored wind turbine blade. The localization process is performed using features extracted from aliased AE signals based on a developed constraint localization model. To validate the performance of these elements, the proposed system was tested by testing the localization of the emulated AE sources acquired in the field.

  12. Impact localization on composite structures using time difference and MUSIC approach

    Science.gov (United States)

    Zhong, Yongteng; Xiang, Jiawei

    2017-05-01

    1-D uniform linear array (ULA) has the shortcoming of the half-plane mirror effect, which does not allow discriminating between a target placed above the array and a target placed below the array. This paper presents time difference (TD) and multiple signal classification (MUSIC) based omni-directional impact localization on a large stiffened composite structure using improved linear array, which is able to perform omni-directional 360° localization. This array contains 2M+3 PZT sensors, where 2M+1 PZT sensors are arranged as a uniform linear array, and the other two PZT sensors are placed above and below the array. Firstly, the arrival times of impact signals observed by the other two sensors are determined using the wavelet transform. Compared with each other, the direction range of impact source can be decided in general, 0°to 180° or 180°to 360°. And then, two dimensional multiple signal classification (2D-MUSIC) based spatial spectrum formula using the uniform linear array is applied for impact localization by the general direction range. When the arrival times of impact signals observed by upper PZT is equal to that of lower PZT, the direction can be located in x axis (0°or 180°). And time difference based MUSIC method is present to locate impact position. To verify the proposed approach, the proposed approach is applied to a composite structure. The localization results are in good agreement with the actual impact occurring positions.

  13. Scale-adaptive tensor algebra for local many-body methods of electronic structure theory

    Energy Technology Data Exchange (ETDEWEB)

    Liakh, Dmitry I [ORNL

    2014-01-01

    While the formalism of multiresolution analysis (MRA), based on wavelets and adaptive integral representations of operators, is actively progressing in electronic structure theory (mostly on the independent-particle level and, recently, second-order perturbation theory), the concepts of multiresolution and adaptivity can also be utilized within the traditional formulation of correlated (many-particle) theory which is based on second quantization and the corresponding (generally nonorthogonal) tensor algebra. In this paper, we present a formalism called scale-adaptive tensor algebra (SATA) which exploits an adaptive representation of tensors of many-body operators via the local adjustment of the basis set quality. Given a series of locally supported fragment bases of a progressively lower quality, we formulate the explicit rules for tensor algebra operations dealing with adaptively resolved tensor operands. The formalism suggested is expected to enhance the applicability and reliability of local correlated many-body methods of electronic structure theory, especially those directly based on atomic orbitals (or any other localized basis functions).

  14. Local Impact Simulation of SC Wall Structures using Aircraft Engine Projectile

    Energy Technology Data Exchange (ETDEWEB)

    Chung, Chulhun; Lee, Jungwhee; Lee, Hanjoo [Dankook Univ., Yongin (Korea, Republic of); Jung, Raeyoung; Hyun, Changhun [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

    2013-05-15

    SC wall structure developed for nuclear power plant buildings consists of plain concrete and two steel plates on both surface of the concrete, while RC structure consists of re bar and concrete. SC structure has higher scabbing resistance than RC structure due to the action of steel plate on the rear side of impact. Therefore SC structure is known as more effective structure from the viewpoint of aircraft crash than RC structure. However, most of the recent researches and experiments about local impact damage deal with RC structures, and the effect of re bar and steel plate is not considered reasonably. Although Walter et al. and Make-work et al. suggested a formula for evaluating perforation depth of steel plate covered RC walls, most of the previous researches about SC structure are focused on perforation and scabbing due to the impact of hard projectile, rather than soft projectile such as an aircraft. In this research a soft projectile, i. e. aircraft engine, is utilized for impact simulation of RC and SC walls. To evaluate local damage of SC wall structures, parametric study with the variables of wall thickness and steel ratio of the cover plate is performed, and the results are compared with those of RC structures. Since scabbing was prevented by the steel plates, penetration mode of damage was observed in SC walls while scabbing damage was occurred in RC walls. It is confirmed that the rear steel plate not only contains concrete debris, but also reduces the internal damage of the concrete walls. Penetration depth of SC walls did not largely vary due to the increasing steel ratio, and similar results to RC walls were observed when the wall thickness is larger than a certain value since the impact resistance of SC wall is mainly governed by the thickness of concrete part. Therefore, it is expected that similar level of impact resistance to RC structure can be produced with the minimum thickness of steel plates of SC structure. According to these results, SC

  15. Spatiotemporal Chaos, Localized Structures and Synchronization in the Vector Complex Ginzburg-Landau Equation

    CERN Document Server

    Hernández-García, E; Colet, P; Montagne, R; Miguel, M S; Hernandez-Garcia, Emilio; Hoyuelos, Miguel; Colet, Pere; Montagne, Raul; Miguel, Maxi San

    1999-01-01

    We study the spatiotemporal dynamics, in one and two spatial dimensions, of two complex fields which are the two components of a vector field satisfying a vector form of the complex Ginzburg-Landau equation. We find synchronization and generalized synchronization of the spatiotemporally chaotic dynamics. The two kinds of synchronization can coexist simultaneously in different regions of the space, and they are mediated by localized structures. A quantitative characterization of the degree of synchronization is given in terms of mutual information measures.

  16. Nanoelectromechanics of Inorganic and Biological Systems: From Structural Imaging to Local Functionalities

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, Brian [University College, Dublin; Kalinin, Sergei V [ORNL; Jesse, Stephen [ORNL; Thompson, G. L. [Clemson University; Vertegel, Alexey [ORNL; Hohlbauch, Sophia [Asylum Research, Santa Barbara, CA; Proksch, Roger [Asylum Research, Santa Barbara, CA

    2008-01-01

    Coupling between electrical and mechanical phenomena is extremely common in inorganic materials, and nearly ubiquitous in biological systems, underpinning phenomena and devices ranging from SONAR to cardiac activity and hearing. This paper briefly summarizes the Scanning Probe Microscopy (SPM) approach, referred to as Piezoresponse Force Microscopy (PFM), for probing electromechanical coupling on the nanometer scales, and delineates some existing and emerging applications to probe local structure and functionality in inorganic ferroelectrics, calcified and connective tissues, and complex biosystems based on electromechanical detection.

  17. Observation of highly localized structures in a Faraday experiment with highly dissipative fluids

    Science.gov (United States)

    Cabeza, C.; Gibiat, V.; Negreira, C.

    2003-09-01

    We present an experimental study about the Faraday instability using a highly dissipative fluid. The fluid layer is excited with a vertical periodic acceleration field. In this regimen of high viscosity and shallow fluid depth, we have found two very interesting phenomena. On the one hand, we observed a periodicity windows appearing after the whole classical crispation, on the other hand highly spatially localized structures are generated within the periodicity window that propagates on fluid surface.

  18. Model-based Leakage Localization in Drinking Water Distribution Networks using Structured Residuals

    OpenAIRE

    Rosich, Albert; Puig, Vicenç

    2013-01-01

    In this paper, a new model based approach to leakage localization in drinking water networks is proposed based on generating a set of structured residuals. The residual evaluation is based on a numerical method based on an enhanced Newton-Raphson algorithm. The proposed method is suitable for water network systems because the non-linearities of the model make impossible to derive analytical residuals. Furthermore, the computed residuals are designed so that leaks are decoupled, which impro...

  19. Local deformation method for measuring element tension in space deployable structures

    Directory of Open Access Journals (Sweden)

    Belov Sergey

    2017-01-01

    Full Text Available The article describes the local deformation method to determine the tension of cord and thin membrane elements in space deployable structure as antenna reflector. Possible measuring instrument model, analytical and numerical solutions and experimental results are presented. The boundary effects on measurement results of metallic mesh reflector surface tension are estimated. The study case depicting non-uniform reflector surface tension is considered.

  20. Structures et dynamiques spatiales des villes portuaires: du local au mondial

    Directory of Open Access Journals (Sweden)

    César Ducruet

    2005-04-01

    Full Text Available More than other cities, port cities must constantly adapt to a rapidly changing international trade environment. This adaptation is spurred by their ties to both maritime and land networks and by specific spatio-functional relations between cities and ports, from the local to the global level. For comparative purposes, this paper proposes a new way to interpret the basic structures and trends underlying these complex, and sometimes contradictory, ties.

  1. The local structure and optical absorption characteristic investigation on Fe doped TiO2 nanoparticles

    CERN Document Server

    Zhao, Tianxing; Huang, Junheng; He, Jinfu; Liu, Qinghua; Pan, Zhiyun; Wu, Ziyu

    2014-01-01

    The local structures and optical absorption characteristic of Fe doped TiO2 nanoparticles synthesized by the sol-gel method were characterized by X-ray Diffraction (XRD), X-ray absorption fine structure spectroscopy (XAFS) and UV-Vis absorption spectroscopy (UV-Vis). XRD patterns show that all Fe-doped TiO2 samples have the characteristic anatase structure. Accurate Fe and Ti K-edge EXAFS analysis further reveal that all Fe atoms replace Ti atoms in the anatase lattice. The analysis of UV-Vis data shows a red shift to the visible range. According to the above results, we claim that substitutional Fe atoms lead to the formation of structural defects and new intermediate energy levels appear, narrowing the band gap and extending the optical absorption edge towards the visible region.

  2. AFM characterization of the shape of surface structures with localization factor.

    Science.gov (United States)

    Bonyár, Attila

    2016-08-01

    Although with the use of scanning probe microscopy (SPM) methods the topographical imaging of surfaces is now widely available, the characterization of surface structures, especially their shape, and the processes which change these features is not trivial with the existing surface describing parameters. In this work the application of a parameter called localization factor is demonstrated for the quantitative characterization of surface structures and for processes which alter the shape of these structures. The theory and optimal operation range of this parameter are discussed with three application examples: microstructure characterization of gold thin films, characterization of the changes in the grain structure of these films during thermal annealing, and finally, characterization of the oxidation processes on a polished tin surface.

  3. Local structure and magnetism of Co3 + in wurtzite Co:ZnO

    Science.gov (United States)

    Henne, Bastian; Ney, Verena; Lumetzberger, Julia; Ollefs, Katharina; Wilhelm, Fabrice; Rogalev, Andrei; Ney, Andreas

    2017-02-01

    The structural and magnetic properties of 30% and 50% Co-doped ZnO have been investigated in order to determine the influence of the presence of Co3 + as a potential p -type dopant. For 30% doping, Co3 + could be stabilized in the wurtzite lattice of ZnO without phase separation by providing high oxygen partial pressures during growth. At 50% Co concentration, the crystal lattice destabilizes. X-ray absorption spectroscopy and simulations are used to substantiate the valence and local structure of Co3 +. Integral and element selective magnetometry reveals uncompensated antiferromagnetism of the Co atoms irrespective of being present as Co2 + or Co3 +.

  4. Spatial Object Aggregation Based on Data Structure,Local Triangulation and Hierarchical Analyzing Method

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This paper focuses on the methods and process of spatial aggregation based on semantic and geometric characteristics of spatial objects and relations among the objects with the help of spatial data structure (Formal Data Structure),the Local Constrained Delaunay Triangulations and semantic hierarchy.The adjacent relation among connected objects and unconnected objects has been studied through constrained triangle as elementary processing unit in aggregation operation.The hierarchical semantic analytical matrix is given for analyzing the similarity between objects types and between objects.Several different cases of aggregation have been presented in this paper.

  5. Local-global alignment for finding 3D similarities in protein structures

    Science.gov (United States)

    Zemla, Adam T.

    2011-09-20

    A method of finding 3D similarities in protein structures of a first molecule and a second molecule. The method comprises providing preselected information regarding the first molecule and the second molecule. Comparing the first molecule and the second molecule using Longest Continuous Segments (LCS) analysis. Comparing the first molecule and the second molecule using Global Distance Test (GDT) analysis. Comparing the first molecule and the second molecule using Local Global Alignment Scoring function (LGA_S) analysis. Verifying constructed alignment and repeating the steps to find the regions of 3D similarities in protein structures.

  6. Local Structure of Ge/Si(100) Self-Assembled Quantum Dot

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Local structure of uncapped and Si-capped Ge quantum dots grownon Si(100) has been probed by X-ray absorption fine structure spectroscopy. It is found that the uncapped Ge dots are partially oxidized and partially alloyed with Si. The amount of Ge present in the Ge phase is found to be about 20-30%. In the Si-capped sample, Ge is found to be dissolved in silicon, the fraction of Ge atoms existing as pure Ge phase being not more than 10%.

  7. Probing the local, electronic and magnetic structure of matter under extreme conditions of temperature and pressure

    DEFF Research Database (Denmark)

    Torchio, R.; Boccato, S.; Cerantola, V.;

    2016-01-01

    In this paper we present recent achievements in the field of investigation of the local, electronic and magnetic structure of the matter under extreme conditions of pressure and temperature. These results were obtained thanks to the coupling of a compact laser heating system to the energy......-dispersive XAS technique available on the ID24 beamline at the ESRF synchrotron. The examples chosen concern the melting and the liquid structure of 3d metals and alloys under high pressures (HPs) and the observation of temperature-induced spin crossover in FeCO3 at HP....

  8. Near-Field Sound Localization Based on the Small Profile Monaural Structure

    Directory of Open Access Journals (Sweden)

    Youngwoong Kim

    2015-11-01

    Full Text Available The acoustic wave around a sound source in the near-field area presents unconventional properties in the temporal, spectral, and spatial domains due to the propagation mechanism. This paper investigates a near-field sound localizer in a small profile structure with a single microphone. The asymmetric structure around the microphone provides a distinctive spectral variation that can be recognized by the dedicated algorithm for directional localization. The physical structure consists of ten pipes of different lengths in a vertical fashion and rectangular wings positioned between the pipes in radial directions. The sound from an individual direction travels through the nearest open pipe, which generates the particular fundamental frequency according to the acoustic resonance. The Cepstral parameter is modified to evaluate the fundamental frequency. Once the system estimates the fundamental frequency of the received signal, the length of arrival and angle of arrival (AoA are derived by the designed model. From an azimuthal distance of 3–15 cm from the outer body of the pipes, the extensive acoustic experiments with a 3D-printed structure show that the direct and side directions deliver average hit rates of 89% and 73%, respectively. The closer positions to the system demonstrate higher accuracy, and the overall hit rate performance is 78% up to 15 cm away from the structure body.

  9. Structure in the 3D Galaxy Distribution. II. Voids and Watersheds of Local Maxima and Minima

    Science.gov (United States)

    Way, M. J.; Gazis, P. R.; Scargle, Jeffrey D.

    2015-01-01

    The major uncertainties in studies of the multi-scale structure of the universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies, we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian blocks, and self-organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium simulation, and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. We also introduce a void finder that utilizes a method to assemble Delaunay tetrahedra into connected structures and characterizes regions empty of galaxies in the source catalog.

  10. STRUCTURE IN THE 3D GALAXY DISTRIBUTION. II. VOIDS AND WATERSHEDS OF LOCAL MAXIMA AND MINIMA

    Energy Technology Data Exchange (ETDEWEB)

    Way, M. J. [Also at NASA Goddard Institute for Space Studies, 2880 Broadway, New York, NY 10025, USA. (United States); Gazis, P. R.; Scargle, Jeffrey D., E-mail: Michael.J.Way@nasa.gov, E-mail: PGazis@sbcglobal.net, E-mail: Jeffrey.D.Scargle@nasa.gov [NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035 (United States)

    2015-01-20

    The major uncertainties in studies of the multi-scale structure of the universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of these methodological dependencies, we have carried out 12 different analyses defining structures in various ways. This has been done in a purely geometrical way by utilizing the HOP algorithm as a unique parameter-free method of assigning groups of galaxies to local density maxima or minima. From three density estimation techniques (smoothing kernels, Bayesian blocks, and self-organizing maps) applied to three data sets (the Sloan Digital Sky Survey Data Release 7, the Millennium simulation, and randomly distributed points) we tabulate information that can be used to construct catalogs of structures connected to local density maxima and minima. We also introduce a void finder that utilizes a method to assemble Delaunay tetrahedra into connected structures and characterizes regions empty of galaxies in the source catalog.

  11. Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)

    2007-01-01

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

  12. Probing into the local structure of quadrupolar spin systems with MRFM

    Science.gov (United States)

    Verhagen, Rieko; Hilbers, Cees; Kentgens, Arno; van Kempen, Herman

    2001-03-01

    Magnetic Resonance Force Microscopy is a method to enhance the sensitivity of conventional inductive Nuclear Magnetic Resonance. It combines the advantages of Atomic Force Microscopy with those of NMR, resulting in a method that has both high spatial resolution and sub-surface sensitivity. This gives the capability of 3D imaging and/or spectral characterization of nanoscale structures. We have adapted a conventional MRFM probe to observe nuclei other than protons. The objective of this modification lays in the possibility to observe nuclear spins with spin quantum numbers other than 1/2. In an external magnetic field (Zeeman interaction), these nuclei have multiple spin-transitions with equal energy differences, causing a single spectral line. However, the nuclei have a quadrupole moment and therefore interact with the electrical field gradient caused by charge distributions in the local environment. This shifts the spin energy levels differently so that several transitions occur at different NMR frequencies. The quadrupolar interaction can be used as a probe for obtaining information on the local structure. Since the quadrupolar splitting can be large compared to the spectral resolution of the MRFM detection method it may be imaged using MRFM. We present some methods and first results of MRFM on quadrupolar spin systems, specifically ^23Na (S=3/2) at 4.2T. It is shown that the method is capable of observing the splitting and may obtain local disorders in the lattice structure by scanning the sample.

  13. Exciton Localization in Extended π-Electron Systems: Comparison of Linear and Cyclic Structures.

    Science.gov (United States)

    Thiessen, Alexander; Würsch, Dominik; Jester, Stefan-S; Aggarwal, A Vikas; Idelson, Alissa; Bange, Sebastian; Vogelsang, Jan; Höger, Sigurd; Lupton, John M

    2015-07-30

    We employ five π-conjugated model materials of different molecular shape-oligomers and cyclic structures-to investigate the extent of exciton self-trapping and torsional motion of the molecular framework following optical excitation. Our studies combine steady state and transient fluorescence spectroscopy in the ensemble with measurements of polarization anisotropy on single molecules, supported by Monte Carlo simulations. The dimer exhibits a significant spectral red shift within ∼100 ps after photoexcitation which is attributed to torsional relaxation. This relaxation mechanism is inhibited in the structurally rigid macrocyclic analogue. However, both systems show a high degree of exciton localization but with very different consequences: while, in the macrocycle, the exciton localizes randomly on different parts of the ring, scrambling polarization memory, in the dimer, localization leads to a deterministic exciton position with luminescence characteristics of a dipole. Monte Carlo simulations allow us to quantify the structural difference between the emitting and absorbing units of the π-conjugated system in terms of disorder parameters.

  14. Structural imperfections and attendant localized/itinerant ferromagnetism in ZnO nanoparticles

    Science.gov (United States)

    Yang, Chao-Yao; Lu, Yi-Hsuan; Lin, Wei-Hao; Lee, Min-Han; Hsu, Yung-Jung; Tseng, Yuan-Chieh

    2014-08-01

    Using synchrotron-based x-ray magnetic spectroscopy, we report a study focusing on the local symmetry of Cu-dopant and resultant structural imperfections in mediating Cu-doped ZnO nanoparticles' ferromagnetism (FM). Prepared by an antisolvent method, Cu appeared to preferably populate on the basal plane of ZnO with a local symmetry of [CuO4]. This unique symmetry was antiferromagnetic in nature, while electronically and structurally coupled to surrounded oxygen vacancies (Vo) that yielded a localized FM, because of a strong dependency on the number/location of the [CuO4] symmetry. Surprisingly, the FM of undoped but oxygen-deficient ZnO appeared to be more itinerant and long-range, where Vo percolated the FM effectively and isotropically through oxygen's delocalized orbital. By adopting the approach of structural imperfection, this study clearly identifies Vo's (defect's) true characters in mediating the FM of magnetic semiconductors which has been thought of as a long-standing debate, and thus provides a different thinking about the traditional extrinsic ferromagnetic-tuning in the semiconductors. It even illuminates recent research concerning the intrinsic FM of low-dimensional systems that contain defects but non-magnetic elements.

  15. Efficient determination of soft spots in amorphous solids using local structural information

    Science.gov (United States)

    Cubuk, Ekin; Schoenholz, Samuel; Malone, Brad; Liu, Andrea; Kaxiras, Efthimios

    2014-03-01

    Structural defects such as dislocations are also flow defects that control plastic flow in crystalline solids. In disordered solids, it is more challenging to identify such local regions that are susceptible to rearrangement. We propose an extremely fast method for identifying soft spots with high accuracy, which scales linearly with number of particles. We achieve this by training a supervised learning model with instances of local neighborhoods and their subsequent plastic flow behavior. By characterizing local neighborhoods with not just one structural quantity, such as bond orientational order, but a combination of multiple structural quantities, we are able to identify a population of regions that correlates just as strongly with rearrangements as do soft spots calculated from vibrational modes. This method does not require knowledge of the interparticle interactions and can readily be applied to experiments that measure the positions of constituent particles in a disordered packing. Furthermore, this also allows for the prediction of plastic behavior in systems like lithiated amorphous silicon, which is important for addressing the durability issues encountered in recent work on improving lithium-ion batteries.

  16. Protein structure alignment and fast similarity search using local shape signatures.

    Science.gov (United States)

    Can, Tolga; Wang, Yuan-Fang

    2004-03-01

    We present a new method for conducting protein structure similarity searches, which improves on the efficiency of some existing techniques. Our method is grounded in the theory of differential geometry on 3D space curve matching. We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful. The invariancy of the shape signatures allows us to improve similarity searching efficiency by adopting a hierarchical coarse-to-fine strategy. We index the shape signatures using an efficient hashing-based technique. With the help of this technique we screen out unlikely candidates and perform detailed pairwise alignments only for a small number of candidates that survive the screening process. Contrary to other hashing based techniques, our technique employs domain specific information (not just geometric information) in constructing the hash key, and hence, is more tuned to the domain of biology. Furthermore, the invariancy, localization, and compactness of the shape signatures allow us to utilize a well-known local sequence alignment algorithm for aligning two protein structures. One measure of the efficacy of the proposed technique is that we were able to perform structure alignment queries 36 times faster (on the average) than a well-known method while keeping the quality of the query results at an approximately similar level.

  17. The Future of the Local Large Scale Structure: the roles of Dark Matter and Dark Energy

    CERN Document Server

    Hoffman, Yehuda; Yepes, Gustavo; Dover, Yaniv

    2007-01-01

    We study the distinct effects of Dark Matter and Dark Energy on the future evolution of nearby large scale structures using constrained N-body simulations. We contrast a model of Cold Dark Matter and a Cosmological Constant (LCDM) with an Open CDM (OCDM) model with the same matter density Omega_m =0.3 and the same Hubble constant h=0.7. Already by the time the scale factor increased by a factor of 6 (29 Gyr from now in LCDM; 78 Gyr from now in OCDM) the comoving position of the Local Group is frozen. Well before that epoch the two most massive members of the Local Group, the Milky Way and Andromeda (M31), will merge. However, as the expansion rates of the scale factor in the two models are different, the Local Group will be receding in physical coordinates from Virgo exponentially in a LCDM model and at a roughly constant velocity in an OCDM model. More generally, in comoving coordinates the future large scale structure will look like a sharpened image of the present structure: the skeleton of the cosmic web ...

  18. Effect of oxygen deficiency on electronic properties and local structure of amorphous tantalum oxide thin films

    Energy Technology Data Exchange (ETDEWEB)

    Denny, Yus Rama [Department of Physics Education, University of Sultan Ageng Tirtayasa, Banten 42435 (Indonesia); Firmansyah, Teguh [Department of Electrical Engineering, University of Sultan Ageng Tirtayasa, Banten 42435 (Indonesia); Oh, Suhk Kun [Department of Physics, Chungbuk National University, Cheongju 28644 (Korea, Republic of); Kang, Hee Jae, E-mail: hjkang@cbu.ac.kr [Department of Physics, Chungbuk National University, Cheongju 28644 (Korea, Republic of); Yang, Dong-Seok [Department of Physics Education, Chungbuk National University, Cheongju 28644 (Korea, Republic of); Heo, Sung; Chung, JaeGwan; Lee, Jae Cheol [Analytical Engineering Center, Samsung Advanced Institute of Technology, Suwon 16678 (Korea, Republic of)

    2016-10-15

    Highlights: • The effect of oxygen flow rate on electronic properties and local structure of tantalum oxide thin films was studied. • The oxygen deficiency induced the nonstoichiometric state a-TaOx. • A small peak at 1.97 eV above the valence band side appeared on nonstoichiometric Ta{sub 2}O{sub 5} thin films. • The oxygen flow rate can change the local electronic structure of tantalum oxide thin films. - Abstract: The dependence of electronic properties and local structure of tantalum oxide thin film on oxygen deficiency have been investigated by means of X-ray photoelectron spectroscopy (XPS), Reflection Electron Energy Loss Spectroscopy (REELS), and X-ray absorption spectroscopy (XAS). The XPS results showed that the oxygen flow rate change results in the appearance of features in the Ta 4f at the binding energies of 23.2 eV, 24.4 eV, 25.8, and 27.3 eV whose peaks are attributed to Ta{sup 1+}, Ta{sup 2+}, Ta{sup 3+}/Ta{sup 4+}, and Ta{sup 5+}, respectively. The presence of nonstoichiometric state from tantalum oxide (TaOx) thin films could be generated by the oxygen vacancies. In addition, XAS spectra manifested both the increase of coordination number of the first Ta-O shell and a considerable reduction of the Ta-O bond distance with the decrease of oxygen deficiency.

  19. Structure, localization and histone binding properties of nuclear-associated nucleosome assembly protein from Plasmodium falciparum

    Directory of Open Access Journals (Sweden)

    Maier Alexander G

    2010-04-01

    Full Text Available Abstract Background Nucleosome assembly proteins (NAPs are histone chaperones that are crucial for the shuttling and incorporation of histones into nucleosomes. NAPs participate in the assembly and disassembly of nucleosomes thus contributing to chromatin structure organization. The human malaria parasite Plasmodium falciparum contains two nucleosome assembly proteins termed PfNapL and PfNapS. Methods Three-dimensional crystal structure of PfNapS has been determined and analysed. Gene knockout and localization studies were also performed on PfNapS using transfection studies. Fluorescence spectroscopy was performed to identify histone-binding sites on PfNapS. Extensive sequence and structural comparisons were done with the crystal structures available for NAP/SET family of proteins. Results Crystal structure of PfNapS shares structural similarity with previous structures from NAP/SET family. Failed attempts to knock-out the gene for PfNapS from malaria parasite suggest essentiality in the parasite. GFP-fused PfNapS fusion protein targeting indicates cellular localization of PfNapS in the parasite nucleus. Fluorescence spectroscopy data suggest that PfNapS interacts with core histones (tetramer, octamer, H3, H4, H2A and H2B at a different site from its interaction with linker histone H1. This analysis illustrates two regions on the PfNapS dimer as the possible sites for histone recognition. Conclusions This work presents a thorough analysis of the structural, functional and regulatory attributes of PfNapS from P. falciparum with respect to previously studied histone chaperones.

  20. Network community structure alterations in adult schizophrenia: identification and localization of alterations.

    Science.gov (United States)

    Lerman-Sinkoff, Dov B; Barch, Deanna M

    2016-01-01

    A growing body of literature suggests functional connectivity alterations in schizophrenia. While findings have been mixed, evidence points towards a complex pattern of hyper-connectivity and hypo-connectivity. This altered connectivity can be represented and analyzed using the mathematical frameworks provided by graph and information theory to represent functional connectivity data as graphs comprised of nodes and edges linking the nodes. One analytic technique in this framework is the determination and analysis of network community structure, which is the grouping of nodes into linked communities or modules. This data-driven technique finds a best-fit structure such that nodes in a given community have greater connectivity with nodes in their community than with nodes in other communities. These community structure representations have been found to recapitulate known neural-systems in healthy individuals, have been used to identify novel functional systems, and have identified and localized community structure alterations in a childhood onset schizophrenia cohort. In the present study, we sought to determine whether community structure alterations were present in an adult onset schizophrenia cohort while stringently controlling for sources of imaging artifacts. Group level average graphs in healthy controls and individuals with schizophrenia exhibited visually similar network community structures and high amounts of normalized mutual information (NMI). However, testing of individual subject community structures identified small but significant alterations in community structure with alterations being driven by changes in node community membership in the somatosensory, auditory, default mode, salience, and subcortical networks.

  1. Rethinking the Changing Structures of Rural Local Government--State Power, Rural Politics and Local Political Strategies?

    Science.gov (United States)

    Pemberton, Simon; Goodwin, Mark

    2010-01-01

    There is a notable absence in contemporary rural studies--of both a theoretical and empirical nature--concerning the changing nature of rural local government. Despite the scale and significance of successive rounds of local government reorganisation in the UK, very little has been written on this topic from a rural perspective. Instead research…

  2. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images

    Directory of Open Access Journals (Sweden)

    Paul Grégory

    2010-07-01

    Full Text Available Abstract Background Sub-cellular structures interact in numerous direct and indirect ways in order to fulfill cellular functions. While direct molecular interactions crucially depend on spatial proximity, other interactions typically result in spatial correlations between the interacting structures. Such correlations are the target of microscopy-based co-localization analysis, which can provide hints of potential interactions. Two complementary approaches to co-localization analysis can be distinguished: intensity correlation methods capitalize on pattern discovery, whereas object-based methods emphasize detection power. Results We first reinvestigate the classical co-localization measure in the context of spatial point pattern analysis. This allows us to unravel the set of implicit assumptions inherent to this measure and to identify potential confounding factors commonly ignored. We generalize object-based co-localization analysis to a statistical framework involving spatial point processes. In this framework, interactions are understood as position co-dependencies in the observed localization patterns. The framework is based on a model of effective pairwise interaction potentials and the specification of a null hypothesis for the expected pattern in the absence of interaction. Inferred interaction potentials thus reflect all significant effects that are not explained by the null hypothesis. Our model enables the use of a wealth of well-known statistical methods for analyzing experimental data, as demonstrated on synthetic data and in a case study considering virus entry into live cells. We show that the classical co-localization measure typically under-exploits the information contained in our data. Conclusions We establish a connection between co-localization and spatial interaction of sub-cellular structures by formulating the object-based interaction analysis problem in a spatial statistics framework based on nearest-neighbor distance

  3. ARX model-based damage sensitive features for structural damage localization using output-only measurements

    Science.gov (United States)

    Roy, Koushik; Bhattacharya, Bishakh; Ray-Chaudhuri, Samit

    2015-08-01

    The study proposes a set of four ARX model (autoregressive model with exogenous input) based damage sensitive features (DSFs) for structural damage detection and localization using the dynamic responses of structures, where the information regarding the input excitation may not be available. In the proposed framework, one of the output responses of a multi-degree-of-freedom system is assumed as the input and the rest are considered as the output. The features are based on ARX model coefficients, Kolmogorov-Smirnov (KS) test statistical distance, and the model residual error. At first, a mathematical formulation is provided to establish the relation between the change in ARX model coefficients and the normalized stiffness of a structure. KS test parameters are then described to show the sensitivity of statistical distance of ARX model residual error with the damage location. The efficiency of the proposed set of DSFs is evaluated by conducting numerical studies involving a shear building and a steel moment-resisting frame. To simulate the damage scenarios in these structures, stiffness degradation of different elements is considered. It is observed from this study that the proposed set of DSFs is good indicator for damage location even in the presence of damping, multiple damages, noise, and parametric uncertainties. The performance of these DSFs is compared with mode shape curvature-based approach for damage localization. An experimental study has also been conducted on a three-dimensional six-storey steel moment frame to understand the performance of these DSFs under real measurement conditions. It has been observed that the proposed set of DSFs can satisfactorily localize damage in the structure.

  4. Local atomic structure in tetragonal pure ZrO{sub 2} nanopowders

    Energy Technology Data Exchange (ETDEWEB)

    Acuna, Leandro M.; Lamas, Diego G.; Fuentes, Rodolfo O.; Fabregas, Ismael O. [CITEFA-CONICET, Villa Martelli, Provincia de Buenos Aires (AR). CINSO (Centro de Investigaciones en Solidos); Fantini, Marcia C.A.; Craievich, Aldo F. [Universidade de Sao Paulo (Brazil). Inst. de Fisica; Prado, Rogerio J. [Universidade Federal de Mato Grosso (UFMT), Cuiaba (Brazil). Inst. de Fisica

    2010-04-15

    The local atomic structures around the Zr atom of pure (undoped) ZrO{sub 2} nanopowders with different average crystallite sizes, ranging from 7 to 40 nm, have been investigated. The nanopowders were synthesized by different wetchemical routes, but all exhibit the high-temperature tetragonal phase stabilized at room temperature, as established by synchrotron radiation X-ray diffraction. The extended X-ray absorption fine structure (EXAFS) technique was applied to analyze the local structure around the Zr atoms. Several authors have studied this system using the EXAFS technique without obtaining a good agreement between crystallographic and EXAFS data. In this work, it is shown that the local structure of ZrO{sub 2} nanopowders can be described by a model consisting of two oxygen subshells (4+4 atoms) with different Zr-O distances, in agreement with those independently determined by X-ray diffraction. However, the EXAFS study shows that the second oxygen subshell exhibits a Debye-Waller (DW) parameter much higher than that of the first oxygen subshell, a result that cannot be explained by the crystallographic model accepted for the tetragonal phase of zirconia-based materials. However, as proposed by other authors, the difference in the DW parameters between the two oxygen subshells around the Zr atoms can be explained by the existence of oxygen displacements perpendicular to the z direction; these mainly affect the second oxygen subshell because of the directional character of the EXAFS DW parameter, in contradiction to the crystallographic value. It is also established that this model is similar to another model having three oxygen subshells, with a 4+2+2 distribution of atoms, with only one DW parameter for all oxygen subshells. Both models are in good agreement with the crystal structure determined by X-ray diffraction experiments. (orig.)

  5. The effect of static and dynamic spatially structured disturbances on a locally dispersing population.

    Science.gov (United States)

    Hiebeler, David E; Morin, Benjamin R

    2007-05-01

    Previous models of locally dispersing populations have shown that in the presence of spatially structured fixed habitat heterogeneity, increasing local spatial autocorrelation in habitat generally has a beneficial effect on such populations, increasing equilibrium population density. It has also been shown that with large-scale disturbance events which simultaneously affect contiguous blocks of sites, increasing spatial autocorrelation in the disturbances has a harmful effect, decreasing equilibrium population density. Here, spatial population models are developed which include both of these spatially structured exogenous influences, to determine how they interact with each other and with the endogenously generated spatial structure produced by the population dynamics. The models show that when habitat is fragmented and disturbance occurs at large spatial scales, the population cannot persist no matter how large its birth rate, an effect not seen in previous simpler models of this type. The behavior of the model is also explored when the local autocorrelation of habitat heterogeneity and disturbance events are equal, i.e. the two effects occur at the same spatial scale. When this scale parameter is very small, habitat fragmentation prevents the population from persisting because sites attempting to reproduce will drop most of their offspring on unsuitable sites; when the parameter is very large, large-scale disturbance events drive the population to extinction. Population levels reach their maximum at intermediate values of the scale parameter, and the critical values in the model show that the population will persist most easily at these intermediate scales of spatial influences. The models are investigated via spatially explicit stochastic simulations, traditional (infinite-dispersal) and improved (local-dispersal) mean-field approximations, and pair approximations.

  6. Propagation of localized structures in relativistic magnetized electron-positron plasmas using particle-in-cell simulations

    Energy Technology Data Exchange (ETDEWEB)

    López, Rodrigo A. [Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Concepción 4070386 (Chile); Muñoz, Víctor [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Viñas, Adolfo F. [Geospace Physics Laboratory, Heliophysics Science Division, NASA Goddard Space Flight Center, Greenbelt, Maryland 20771 (United States); Valdivia, Juan A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Santiago 9170124 (Chile)

    2015-09-15

    We use a particle-in-cell simulation to study the propagation of localized structures in a magnetized electron-positron plasma with relativistic finite temperature. We use as initial condition for the simulation an envelope soliton solution of the nonlinear Schrödinger equation, derived from the relativistic two fluid equations in the strongly magnetized limit. This envelope soliton turns out not to be a stable solution for the simulation and splits in two localized structures propagating in opposite directions. However, these two localized structures exhibit a soliton-like behavior, as they keep their profile after they collide with each other due to the periodic boundary conditions. We also observe the formation of localized structures in the evolution of a spatially uniform circularly polarized Alfvén wave. In both cases, the localized structures propagate with an amplitude independent velocity.

  7. Correlative infrared-electron nanoscopy reveals the local structure-conductivity relationship in zinc oxide nanowires.

    Science.gov (United States)

    Stiegler, J M; Tena-Zaera, R; Idigoras, O; Chuvilin, A; Hillenbrand, R

    2012-01-01

    High-resolution characterization methods play a key role in the development, analysis and optimization of nanoscale materials and devices. Because of the various material properties, only a combination of different characterization techniques provides a comprehensive understanding of complex functional materials. Here we introduce correlative infrared-electron nanoscopy, a novel method yielding transmission electron microscope and infrared near-field images of one and the same nanostructure. While transmission electron microscopy provides structural information up to the atomic level, infrared near-field imaging yields nanoscale maps of chemical composition and conductivity. We demonstrate the method's potential by studying the relation between conductivity and crystal structure in ZnO nanowire cross-sections. The combination of infrared conductivity maps and the local crystal structure reveals a radial free-carrier gradient, which inversely correlates to the density of extended crystalline defects. Our method opens new avenues for studying the local interplay between structure, conductivity and chemical composition in widely different material systems.

  8. Correlative infrared-electron nanoscopy reveals the local structure-conductivity relationship in zinc oxide nanowires

    Science.gov (United States)

    Stiegler, J. M.; Tena-Zaera, R.; Idigoras, O.; Chuvilin, A.; Hillenbrand, R.

    2012-10-01

    High-resolution characterization methods play a key role in the development, analysis and optimization of nanoscale materials and devices. Because of the various material properties, only a combination of different characterization techniques provides a comprehensive understanding of complex functional materials. Here we introduce correlative infrared-electron nanoscopy, a novel method yielding transmission electron microscope and infrared near-field images of one and the same nanostructure. While transmission electron microscopy provides structural information up to the atomic level, infrared near-field imaging yields nanoscale maps of chemical composition and conductivity. We demonstrate the method's potential by studying the relation between conductivity and crystal structure in ZnO nanowire cross-sections. The combination of infrared conductivity maps and the local crystal structure reveals a radial free-carrier gradient, which inversely correlates to the density of extended crystalline defects. Our method opens new avenues for studying the local interplay between structure, conductivity and chemical composition in widely different material systems.

  9. In situ KPFM imaging of local photovoltaic characteristics of structured organic photovoltaic devices.

    Science.gov (United States)

    Watanabe, Satoshi; Fukuchi, Yasumasa; Fukasawa, Masako; Sassa, Takafumi; Kimoto, Atsushi; Tajima, Yusuke; Uchiyama, Masanobu; Yamashita, Takashi; Matsumoto, Mutsuyoshi; Aoyama, Tetsuya

    2014-02-12

    Here, we discuss the local photovoltaic characteristics of a structured bulk heterojunction, organic photovoltaic devices fabricated with a liquid carbazole, and a fullerene derivative based on analysis by scanning kelvin probe force microscopy (KPFM). Periodic photopolymerization induced by an interference pattern from two laser beams formed surface relief gratings (SRG) in the structured films. The surface potential distribution in the SRGs indicates the formation of donor and acceptor spatial distribution. Under illumination, the surface potential reversibly changed because of the generation of fullerene anions and hole transport from the films to substrates, which indicates that we successfully imaged the local photovoltaic characteristics of the structured photovoltaic devices. Using atomic force microscopy, we confirmed the formation of the SRG because of the material migration to the photopolymerized region of the films, which was induced by light exposure through photomasks. The structuring technique allows for the direct fabrication and the control of donor and acceptor spatial distribution in organic photonic and electronic devices with minimized material consumption. This in situ KPFM technique is indispensable to the fabrication of nanoscale electron donor and electron acceptor spatial distribution in the devices.

  10. Experimental observation of stochastic, periodic, and localized light structures in a brillouin cavity system

    Science.gov (United States)

    Ding, Yingchun; Feng, Qi; Zhang, Bin; Liu, Zhongxuan; Tang, Xin; Lin, Chengyou; Chen, Zhaoyang

    2017-06-01

    It has been an important research subject to find new nonlinear optical phenomena. In this paper, we report the experimental observation of stochastic, periodic, and localized light structures in a super long single-mode standard fiber with external optical feedback provided by the fiber end. The end facet reflection provides an analogous Fabry-Perot stimulated Brillouin resonator cavity. By increasing the pump power to exceed stimulated Brillouin scattering threshold, we observed light structures exhibiting extremely rich temporal-pulse characteristics that had never been reported in literature before, including supercontinuum background generation, the localization of periodic optical structure formation, fission, and compression. These optical structures are of period-doubling distribution and have different recurrence rates. What is more interesting is that we have observed sets of low frequency bipolar cycle-pulse trains that is often seen in the electrical field and hardly seen in pure optical system. Real-time specification of dynamical temporal regimes of laser operation may bring new insight into rich underlying nonlinear physics of practical fiber cavity systems. Therefore, some new nonlinear optical phenomena have been observed.

  11. Local structures of ionic liquids in the presence of gold under high pressures

    Directory of Open Access Journals (Sweden)

    Hai-Chou Chang

    2013-03-01

    Full Text Available The interactions between ionic liquid ([EMI][TFS] and gold surfaces have been investigated via the application of pressures up to ca. 2 GPa. Comparing the spectral features of [EMI][TFS]/gold with those of pure [EMI][TFS], no appreciable changes of C-H bands in the presence of gold powders were observed under ambient pressure. Nevertheless, the imidazolium C-H bands display red shifts in frequency as the [EMI][TFS] / Au mixture was compressed to the pressure above 1.4 GPa and a new alkyl C-H band at ca. 3016 cm−1 was also revealed. These spectral changes, being related to the addition of gold powders and pressure elevation, should be attributed to the local structural changes of C-H groups caused by pressure-enhanced interfacial interactions between [EMI][TFS] and Au. Gold powders tend to induce the changes in hydrogen bonding structures of imidazolium C2-H group under high pressures. The pressure-dependent spectral features in the asymmetric SO3 stretching region display band-narrowing and minor local structural changes induced by the presence of gold particles under high pressures. These observations suggest that Au powders perturb structural equilibrium of C-H groups of cations under high pressures.

  12. Diversity, population structure, and evolution of local peach cultivars in China identified by simple sequence repeats.

    Science.gov (United States)

    Shen, Z J; Ma, R J; Cai, Z X; Yu, M L; Zhang, Z

    2015-01-15

    The fruit peach originated in China and has a history of domestication of more than 4000 years. Numerous local cultivars were selected during the long course of cultivation, and a great morphological diversity exists. To study the diversity and genetic background of local peach cultivars in China, a set of 158 accessions from different ecological regions, together with 27 modern varieties and 10 wild accessions, were evaluated using 49 simple sequence repeats (SSRs) covering the peach genome. Broad diversity was also observed in local cultivars at the SSR level. A total of 648 alleles were amplified with an average of 13.22 observed alleles per locus. The number of genotypes detected ranged from 9 (UDP96015) to 58 (BPPCT008) with an average of 27.00 genotypes per marker. Eight subpopulations divided by STRUCTURE basically coincided with the dendrogram of genetic relationships and could be explained by the traditional groups. The 8 subpopulations were juicy honey peach, southwestern peach I, wild peach, Buddha peach + southwestern peach II, northern peach, southern crisp peach, ornamental peach, and Prunus davidiana + P. kansuensis. Most modern varieties carried the genetic backgrounds of juicy honey peach and southwestern peach I, while others carried diverse genetic backgrounds, indicating that local cultivars were partly used in modern breeding programs. Based on the traditional evolution pathway, a modified pathway for the development of local peach cultivars in China was proposed using the genetic background of subpopulations that were identified by SSRs. Current status and prospects of utilization of Chinese local peach cultivars were also discussed according to the SSR information.

  13. Prediction of Global and Localized Damage and Future Reliability for RC Structures subject to Earthquakes

    DEFF Research Database (Denmark)

    Köyluoglu, H.U.; Nielsen, Søren R.K.; Cakmak, A.S.;

    1997-01-01

    The paper deals with the prediction of global and localized damage and the future reliability estimation of partly damaged reinforced concrete (RC) structures under seismic excitation. Initially, a global maximum softening damage indicator is considered based on the variation of the eigenfrequency...... of the first mode due to the stiffness and strength deterioration of the structure. The hysteresis of the first mode is modelled by a Clough and Johnston hysteretic oscillator with a degrading elastic fraction of the restoring force. The linear parameters of the model are assumed to be known, measured before....... The proposed model is next generalized for the MDOF system. Using the adapted models for the structure and the global damage state, the global damage in a future earthquake can then be estimated when a suitable earthquake model is applied. The performance of the model is illustrated on RC frames which were...

  14. Prediction of Global and Localized Damage and Future Reliability for RC Structures subject to Earthquakes

    DEFF Research Database (Denmark)

    Köyluoglu, H.U.; Nielsen, Søren R.K.; Cakmak, A.S.;

    1994-01-01

    The paper deals with the prediction of global and localized damage and the future reliability estimation of partly damaged reinforced concrete (RC) structures under seismic excitation. Initially, a global maximum softening damage indicator is considered based on the variation of the eigenfrequency...... of the first mode due to the stiffness and strength deterioration of the structure. The hysteresis of the first mode is modelled by a Clough and Johnston hysteretic oscillator with a degrading elastic fraction of the restoring force. The linear parameters of the model are assumed to be known, measured before....... The proposed model is next generalized for the MDOF system. Using the adapted models for the structure and the global damage state, the global damage in a future earthquake can then be estimated when a suitable earthquake model is applied. The performance of the model is illustrated on RC frames which were...

  15. Local concurrent error detection and correction in data structures using virtual backpointers

    Science.gov (United States)

    Li, Chung-Chi Jim; Chen, Paul Peichuan; Fuchs, W. Kent

    1989-01-01

    A new technique, based on virtual backpointers, for local concurrent error detection and correction in linked data strutures is presented. Two new data structures, the Virtual Double Linked List, and the B-tree with Virtual Backpointers, are described. For these structures, double errors can be detected in 0(1) time and errors detected during forward moves can be corrected in 0(1) time. The application of a concurrent auditor process to data structure error detection and correction is analyzed, and an implementation is described, to determine the effect on mean time to failure of a multi-user shared database system. The implementation utilizes a Sequent shared memory multiprocessor system operating on a shared database of Virtual Double Linked Lists.

  16. Text localization using standard deviation analysis of structure elements and support vector machines

    Directory of Open Access Journals (Sweden)

    Zagoris Konstantinos

    2011-01-01

    Full Text Available Abstract A text localization technique is required to successfully exploit document images such as technical articles and letters. The proposed method detects and extracts text areas from document images. Initially a connected components analysis technique detects blocks of foreground objects. Then, a descriptor that consists of a set of suitable document structure elements is extracted from the blocks. This is achieved by incorporating an algorithm called Standard Deviation Analysis of Structure Elements (SDASE which maximizes the separability between the blocks. Another feature of the SDASE is that its length adapts according to the requirements of the application. Finally, the descriptor of each block is used as input to a trained support vector machines that classify the block as text or not. The proposed technique is also capable of adjusting to the text structure of the documents. Experimental results on benchmarking databases demonstrate the effectiveness of the proposed method.

  17. Local structures of ions at ion-exchange resin/solution interface.

    Science.gov (United States)

    Harada, Makoto; Okada, Tetsuo

    2005-08-26

    The local structures of Cl- and Br- in anion-exchange resins have been studied by X-ray absorption fine structure (XAFS), and separation selectivity is discussed on the basis of results. When two different anion-exchange resins having trimethylammonium and dimethylammonium groups as anion-exchange groups are employed for ion-exchange experiments, slightly higher Br- selectivity has been obtained with the former. XAFS has indicated that the average hydration numbers for a given anion is not affected by the structure of the ion-exchange group, but that the extent of ion-association between the anion and the ion-exchange groups depends on the type of the ion-exchange group. Shorter interaction distance (and in turn stronger ion-association) has been confirmed for the dimethylammonium-type resin, and is consistent with lower Br- selectivity of this resin.

  18. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

    Science.gov (United States)

    Lee, Hui Sun; Im, Wonpil

    2016-04-01

    Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/.

  19. Fusion of multichannel local and global structural cues for photo aesthetics evaluation.

    Science.gov (United States)

    Luming Zhang; Yue Gao; Zimmermann, Roger; Qi Tian; Xuelong Li

    2014-03-01

    Photo aesthetic quality evaluation is a fundamental yet under addressed task in computer vision and image processing fields. Conventional approaches are frustrated by the following two drawbacks. First, both the local and global spatial arrangements of image regions play an important role in photo aesthetics. However, existing rules, e.g., visual balance, heuristically define which spatial distribution among the salient regions of a photo is aesthetically pleasing. Second, it is difficult to adjust visual cues from multiple channels automatically in photo aesthetics assessment. To solve these problems, we propose a new photo aesthetics evaluation framework, focusing on learning the image descriptors that characterize local and global structural aesthetics from multiple visual channels. In particular, to describe the spatial structure of the image local regions, we construct graphlets small-sized connected graphs by connecting spatially adjacent atomic regions. Since spatially adjacent graphlets distribute closely in their feature space, we project them onto a manifold and subsequently propose an embedding algorithm. The embedding algorithm encodes the photo global spatial layout into graphlets. Simultaneously, the importance of graphlets from multiple visual channels are dynamically adjusted. Finally, these post-embedding graphlets are integrated for photo aesthetics evaluation using a probabilistic model. Experimental results show that: 1) the visualized graphlets explicitly capture the aesthetically arranged atomic regions; 2) the proposed approach generalizes and improves four prominent aesthetic rules; and 3) our approach significantly outperforms state-of-the-art algorithms in photo aesthetics prediction.

  20. Local adaptation in Trinidadian guppies alters stream ecosystem structure at landscape scales despite high environmental variability

    Science.gov (United States)

    Simon, Troy N.; Bassar, Ronald D.; Binderup, Andrew J.; Flecker, Alex S.; Freeman, Mary C.; Gilliam, James F.; Marshall, Michael C.; Thomas, Steve A.; Travis, Joseph; Reznick, David N.; Pringle, Catherine M.

    2017-01-01

    While previous studies have shown that evolutionary divergence alters ecological processes in small-scale experiments, a major challenge is to assess whether such evolutionary effects are important in natural ecosystems at larger spatial scales. At the landscape scale, across eight streams in the Caroni drainage, we found that the presence of locally adapted populations of guppies (Poecilia reticulata) is associated with reduced algal biomass and increased invertebrate biomass, while the opposite trends were true in streams with experimentally introduced populations of non-locally adapted guppies. Exclusion experiments conducted in two separate reaches of a single stream showed that guppies with locally adapted phenotypes significantly reduced algae with no effect on invertebrates, while non-adapted guppies had no effect on algae but significantly reduced invertebrates. These divergent effects of phenotype on stream ecosystems are comparable in strength to the effects of abiotic factors (e.g., light) known to be important drivers of ecosystem condition. They also corroborate the results of previous experiments conducted in artificial streams. Our results demonstrate that local adaptation can produce phenotypes with significantly different effects in natural ecosystems at a landscape scale, within a tropical watershed, despite high variability in abiotic factors: five of the seven physical and chemical parameters measured across the eight study streams varied by more than one order of magnitude. Our findings suggest that ecosystem structure is, in part, an evolutionary product and not simply an ecological pattern.

  1. Automated foveola localization in retinal 3D-OCT images using structural support vector machine prediction.

    Science.gov (United States)

    Liu, Yu-Ying; Ishikawa, Hiroshi; Chen, Mei; Wollstein, Gadi; Schuman, Joel S; Rehg, James M

    2012-01-01

    We develop an automated method to determine the foveola location in macular 3D-OCT images in either healthy or pathological conditions. Structural Support Vector Machine (S-SVM) is trained to directly predict the location of the foveola, such that the score at the ground truth position is higher than that at any other position by a margin scaling with the associated localization loss. This S-SVM formulation directly minimizes the empirical risk of localization error, and makes efficient use of all available training data. It deals with the localization problem in a more principled way compared to the conventional binary classifier learning that uses zero-one loss and random sampling of negative examples. A total of 170 scans were collected for the experiment. Our method localized 95.1% of testing scans within the anatomical area of the foveola. Our experimental results show that the proposed method can effectively identify the location of the foveola, facilitating diagnosis around this important landmark.

  2. Structural damage localization by outlier analysis of signal-processed mode shapes - Analytical and experimental validation

    Science.gov (United States)

    Ulriksen, M. D.; Damkilde, L.

    2016-02-01

    Contrary to global modal parameters such as eigenfrequencies, mode shapes inherently provide structural information on a local level. Therefore, this particular modal parameter and its derivatives are utilized extensively for damage identification. Typically, more or less advanced mathematical methods are employed to identify damage-induced discontinuities in the spatial mode shape signals, hereby, potentially, facilitating damage detection and/or localization. However, by being based on distinguishing damage-induced discontinuities from other signal irregularities, an intrinsic deficiency in these methods is the high sensitivity towards measurement noise. In the present paper, a damage localization method which, compared to the conventional mode shape-based methods, has greatly enhanced robustness towards measurement noise is proposed. The method is based on signal processing of a spatial mode shape by means of continuous wavelet transformation (CWT) and subsequent application of a generalized discrete Teager-Kaiser energy operator (GDTKEO) to identify damage-induced mode shape discontinuities. In order to evaluate whether the identified discontinuities are in fact damage-induced, outlier analysis is conducted by applying the Mahalanobis metric to major principal scores of the sensor-located bands of the signal-processed mode shape. The method is tested analytically and benchmarked with other mode shape-based damage localization approaches on the basis of a free-vibrating beam and validated experimentally in the context of a residential-sized wind turbine blade subjected to an impulse load.

  3. Structural phase-dependent hole localization and transport in bismuth vanadate

    Science.gov (United States)

    Kweon, Kyoung E.; Hwang, Gyeong S.

    2013-05-01

    We present theoretical evidence for the phase dependence of hole localization and transport in bismuth vanadate (BiVO4). Our hybrid density-functional theory calculations predict that, in the tetragonal phase [tetragonal scheelite BiVO4 (ts-BiVO4)], an excess hole tends to localize around a BiO8 polyhedron with strong lattice distortion, whereas, in the monoclinic phase [monoclinic scheelite BiVO4 (ms-BiVO4)], it spreads over many lattice sites. The phase-dependent behavior is likely related to the higher structural stability of ms-BiVO4 than ts-BiVO4, which may suppress hole-induced lattice distortions. Our study also demonstrates that the relatively weakly localized hole in ms-BiVO4 undergoes faster diffusion compared to the case of ts-BiVO4, irrespective of the fact that the degrees of localization and mobility vary depending on the choice of exchange-correlation functional. The mobility difference may provide an explanation for the enhanced photocatalytic activity of ms-BiVO4 over ts-BiVO4 for water oxidation, considering that the increased mobility would lead to an increase in the hole current to the catalyst surface.

  4. Structure-Based Local Search Heuristics for Circuit-Level Boolean Satisfiability

    CERN Document Server

    Belov, Anton

    2011-01-01

    This work focuses on improving state-of-the-art in stochastic local search (SLS) for solving Boolean satisfiability (SAT) instances arising from real-world industrial SAT application domains. The recently introduced SLS method CRSat has been shown to noticeably improve on previously suggested SLS techniques in solving such real-world instances by combining justification-based local search with limited Boolean constraint propagation on the non-clausal formula representation form of Boolean circuits. In this work, we study possibilities of further improving the performance of CRSat by exploiting circuit-level structural knowledge for developing new search heuristics for CRSat. To this end, we introduce and experimentally evaluate a variety of search heuristics, many of which are motivated by circuit-level heuristics originally developed in completely different contexts, e.g., for electronic design automation applications. To the best of our knowledge, most of the heuristics are novel in the context of SLS for S...

  5. Local equivalent welding element to predict the welding deformations of plate-type structures

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Considering the Heat Affected Zone (HAZ) of welding joint, the residual strain be-haviors of material under constraint and temperature circulation, as well as the activating mechanism of welding process, this paper addresses a new type welding element for numerical simulation of welding deformation, which is called the LEWE (the local equivalent welding element). This element can describe the basic char-acteristics of welded seam: the local position points of inherent strain, the equiva-lent size, the bending radius (or bending angle) from inherent strain, etc. It could be used to predict the welding deformation of plate-type structure. The comparisons between the computed deflection of welded plate and its experiment measurement are present. The results showed that the LEWE possesses a potential to simulate the deformation of welding process high-efficiently and precisely.

  6. High-order spoof localized surface plasmons supported on a complementary metallic spiral structure

    Science.gov (United States)

    Gao, Zhen; Gao, Fei; Zhang, Baile

    2016-01-01

    We experimentally demonstrate that multiple high-order spoof localized surface plasmons (spoof-LSPs) modes can be supported on a complementary metallic spiral structure, which were absent in the previously reported spoof-LSPs modes. Through exact numerical simulations and near-field imaging experiments, we directly observe these high-order spoof-LSPs modes at microwave frequencies. We also show that these higher-order spoof-LSPs modes exhibit larger frequency shifts caused by the local environmental refractive index change than the previously reported low-order spoof-LSPs modes. Hence the complementary MSS may find potential applications as plasmonic sensor in the microwave and terahertz frequencies. PMID:27079658

  7. Boundary-locality and perturbative structure of entanglement spectra in gapped systems.

    Science.gov (United States)

    Alba, Vincenzo; Haque, Masudul; Läuchli, Andreas M

    2012-06-01

    The entanglement between two parts of a many-body system can be characterized in detail by the entanglement spectrum. Focusing on gapped phases of several one-dimensional systems, we show how this spectrum is dominated by contributions from the boundary between the parts. This contradicts the view of an "entanglement Hamiltonian" as a bulk entity. The boundary-local nature of the entanglement spectrum is clarified through its hierarchical level structure, through the combination of two single-boundary spectra to form a two-boundary spectrum, and finally through consideration of dominant eigenfunctions of the entanglement Hamiltonian. We show consequences of boundary-locality for perturbative calculations of the entanglement spectrum.

  8. Fine structure of type-I edge-localized modes in the steep gradient region.

    Science.gov (United States)

    Kurzan, B; Murmann, H D; Neuhauser, J

    2005-09-30

    Fast, high resolution multichannel Thomson scattering is used to quantitatively determine plasma perturbations induced by type-I edge-localized modes (ELMs) in the low-field side edge of ASDEX Upgrade H-mode plasmas. 2D snapshots of temperature and density, deduced from the laser light scattered in a vertically elongated, poloidal array of 5 x 10 scattering volumes, are obtained in the hot, steep edge gradient zone, which is difficult to access by other diagnostics. Local maxima and minima with large amplitude are identified during ELMs and even in the precursor phase, both in density and temperature. Interpreting these structures as footprints of approximately field aligned helical modes in accordance with previous experimental and theoretical work, toroidal mode numbers between 8 and 20 are obtained, roughly consistent with corresponding scrape-off layer and divertor measurements.

  9. Cross flow response of a cylindrical structure under local shear flow

    Directory of Open Access Journals (Sweden)

    Yoo-Chul Kim

    2009-12-01

    Full Text Available The VIV (Vortex-Induced Vibration analysis of a flexible cylindrical structure under locally strong shear flow is presented. The model is made of Teflon and has 9.5m length, 0.0127m diameter, and 0.001m wall thickness. 11 2-dimensional accelerometers are installed along the model. The experiment has been conducted at the ocean engineering basin in the University of Tokyo in which uniform current can be generated. The model is installed at about 30 degree of slope and submerged by almost overall length. Local shear flow is made by superposing uniform current and accelerated flow generated by an impeller. The results of frequency and modal analysis are presented.

  10. Generalized Pipek-Mezey orbital localization method for electronic structure calculations employing periodic boundary conditions

    CERN Document Server

    Jónsson, Elvar Ö; Puska, Martti; Jónsson, Hannes

    2016-01-01

    An implementation of the generalized Pipek-Mezey method [Lehtola, S.; J\\'onsson, H. J. Chem. Theory Comput. 2014, 10, 642] for generating localized orbitals in periodic systems, i.e. Wannier functions, is described. The projector augmented wave (PAW) formalism for the representation of atomic core electrons is included in the implementation, which has been developed within the atomic simulation environment (ASE) software library. The implementation supports several different kinds of representations for the wave function, including real-space grids, plane waves or a linear combination of atomic orbitals. The implementation is tailored to the GPAW program but can easily be adapted to use output from various other electronic structure software packages such as ABINIT, NWChem, or VASP through interfaces in ASE. Generalized Pipek-Mezey Wannier functions (PMWF) are presented for both isolated molecules, as well as systems with periodicity in one, two and three dimensions. The method gives a set of highly localized...

  11. The RNAsnp web server: predicting SNP effects on local RNA secondary structure.

    Science.gov (United States)

    Sabarinathan, Radhakrishnan; Tafer, Hakim; Seemann, Stefan E; Hofacker, Ivo L; Stadler, Peter F; Gorodkin, Jan

    2013-07-01

    The function of many non-coding RNA genes and cis-regulatory elements of messenger RNA largely depends on the structure, which is in turn determined by their sequence. Single nucleotide polymorphisms (SNPs) and other mutations may disrupt the RNA structure, interfere with the molecular function and hence cause a phenotypic effect. RNAsnp is an efficient method to predict the effect of SNPs on local RNA secondary structure based on the RNA folding algorithms implemented in the Vienna RNA package. The SNP effects are quantified in terms of empirical P-values, which, for computational efficiency, are derived from extensive pre-computed tables of distributions of substitution effects as a function of gene length and GC content. Here, we present a web service that not only provides an interface for RNAsnp but also features a graphical output representation. In addition, the web server is connected to a local mirror of the UCSC genome browser database that enables the users to select the genomic sequences for analysis and visualize the results directly in the UCSC genome browser. The RNAsnp web server is freely available at: http://rth.dk/resources/rnasnp/.

  12. Phylogeny, genetic relationships and population structure of five Italian local chicken breeds

    Directory of Open Access Journals (Sweden)

    Simone Ceccobelli

    2013-09-01

    Full Text Available Number and population size of local chicken breeds in Italy is considered to be critical. Molecular data can be used to provide reliable insight into the diversity of chicken breeds. The first aim of this study was to investigate the maternal genetic origin of five Italian local chicken breeds (Ancona, Livorno, Modenese, Romagnola and Valdarnese bianca based on mitochondrial DNA (mtDNA information. Secondly, the extent of the genetic diversity, population structure and the genetic relationships among these chicken populations, by using 27 microsatellite markers, were assessed. To achieve these targets, a 506 bp fragment of the D-loop region was sequenced in 50 chickens of the five breeds. Eighteen variable sites were observed which defined 12 haplotypes. They were assigned to three clades and two maternal lineages. Results indicated that 90% of the haplotypes are related to clade E, which has been described to originate from the Indian subcontinent. For the microsatellite analysis, 137 individual blood samples from the five Italian breeds were included. A total of 147 alleles were detected at 27 microsatellite loci. The five Italian breeds showed a slightly higher degree of inbreeding (FIS=0.08 than the commercial populations that served as reference. Structure analysis showed a separation of the Italian breeds from the reference populations. A further sub-clustering allowed discriminating among the five different Italian breeds. This research provides insight into population structure, relatedness and variability of the five studied breeds.

  13. Modal Strain Energy Based Structural Damage Localization for Offshore Platform using Simulated and Measured Data

    Institute of Scientific and Technical Information of China (English)

    WANG Shuqing; LIU Fushun; ZHANG Min

    2014-01-01

    Modal strain energy based methods for damage detection have received much attention. However, most of published articles use numerical methods and some studies conduct modal tests with simple 1D or 2D structures to verify the damage detection algorithms. Only a few studies utilize modal testing data from 3D frame structures. Few studies conduct performance comparisons between two different modal strain energy based methods. The objective of this paper is to investigate and compare the effectiveness of a traditional modal strain energy method (Stubbs index) and a recently developed modal strain energy decomposition (MSED) method for damage localization, for such a purpose both simulated and measured data from an offshore platform model being used. Particularly, the mode shapes used in the damage localization are identified and synthesized from only two measurements of one damage scenario because of the limited number of sensors. The two methods were first briefly reviewed. Next, using a 3D offshore platform model, the damage detection algorithms were implemented with different levels of damage severities for both single damage and multiple damage cases. Finally, a physical model of an offshore steel platform was constructed for modal testing and for validat-ing the applicability. Results indicate that the MSED method outperforms the Stubbs index method for structural damage detection.

  14. Dynamic morphometric characterization of local connective tissue network structure in humans using ultrasound

    Directory of Open Access Journals (Sweden)

    Konofagou Elisa E

    2007-06-01

    Full Text Available Abstract Background In humans, connective tissue forms a complex, interconnected network throughout the body that may have mechanosensory, regulatory and signaling functions. Understanding these potentially important phenomena requires non-invasive measurements of collagen network structure that can be performed in live animals or humans. The goal of this study was to show that ultrasound can be used to quantify dynamic changes in local connective tissue structure in vivo. We first performed combined ultrasound and histology examinations of the same tissue in two subjects undergoing surgery: in one subject, we examined the relationship of ultrasound to histological images in three dimensions; in the other, we examined the effect of a localized tissue perturbation using a previously developed robotic acupuncture needling technique. In ten additional non-surgical subjects, we quantified changes in tissue spatial organization over time during needle rotation vs. no rotation using ultrasound and semi-variogram analyses. Results 3-D renditions of ultrasound images showed longitudinal echogenic sheets that matched with collagenous sheets seen in histological preparations. Rank correlations between serial 2-D ultrasound and corresponding histology images resulted in high positive correlations for semi-variogram ranges computed parallel (r = 0.79, p Conclusion The combination of ultrasound and semi-variogram analyses allows quantitative assessment of dynamic changes in the structure of human connective tissue in vivo.

  15. Classification of trabeculae into three-dimensional rodlike and platelike structures via local inertial anisotropy

    Science.gov (United States)

    Vasilić, Branimir; Rajapakse, Chamith S.; Wehrli, Felix W.

    2009-01-01

    Trabecular bone microarchitecture is a significant determinant of the bone’s mechanical properties and is thus of major clinical relevance in predicting fracture risk. The three-dimensional nature of trabecular bone is characterized by parameters describing scale, topology, and orientation of structural elements. However, none of the current methods calculates all three types of parameters simultaneously and in three dimensions. Here the authors present a method that produces a continuous classification of voxels as belonging to platelike or rodlike structures that determines their orientation and estimates their thickness. The method, dubbed local inertial anisotropy (LIA), treats the image as a distribution of mass density and the orientation of trabeculae is determined from a locally calculated tensor of inertia at each voxel. The orientation entropies of rods and plates are introduced, which can provide new information about microarchitecture not captured by existing parameters. The robustness of the method to noise corruption, resolution reduction, and image rotation is demonstrated. Further, the method is compared with established three-dimensional parameters including the structure-model index and topological surface-to-curve ratio. Finally, the method is applied to data acquired in a previous translational pilot study showing that the trabecular bone of untreated hypogonadal men is less platelike than that of their eugonadal peers. PMID:19673224

  16. The Structure, Density, and Local Environment Distribution in Ab Initio Liquid Water

    Science.gov (United States)

    Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

    2014-03-01

    We have performed extensive ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions in the canonical (NVT) and isothermal-isobaric (NPT) ensembles to understand the individual and collective importance of exact exchange, van der Waals interactions, and nuclear quantum effects on the structural properties of liquid water. AIMD simulations which include these effects result in oxygen-oxygen radial distribution functions which are in excellent agreement with experiments and a liquid water structure having an equilibrium density within 1% of the experimental value of 1 g/cm3. A detailed analysis of the distribution of local structure in ambient liquid water has revealed that the inherent potential energy surface is bimodal with respect to high- and low-density molecular environments, consistent with the existence of polymorphism in the amorphous phases of water. With these findings in mind, the methodology presented herein overcomes the well-known limitations of semi-local density functional theory (GGA-DFT) providing a detailed and accurate microscopic description of ambient liquid water. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500.

  17. Dynamic behavior of acoustic metamaterials and metaconfigured structures with local oscillators

    Science.gov (United States)

    Manimala, James Mathew

    Dynamic behavior of acoustic metamaterials (AM) and metaconfigured structures (MCS) with various oscillator-type microstructures or local attachments was investigated. AM derive their unusual elastic wave manipulation capabilities not just from material constituents but more so from engineered microstructural configurations. Depending on the scale of implementation, these "microstructures" may be deployed as microscopic inclusions in metacomposites or even as complex endo-structures within load-bearing exo-structures in MCS. The frequency-dependent negative effective-mass exhibited by locally resonant microstructures when considered as a single degree of freedom system was experimentally verified using a structure with an internal mass-spring resonator. AM constructed by incorporating resonators in a host material display spatial attenuation of harmonic stress waves within a tunable bandgap frequency range. An apparent damping coefficient was derived to compare the degree of attenuation achieved in these wholly elastic AM to equivalent conventionally damped models illustrating their feasibility as stiff structures that simultaneously act as effective damping elements. Parametric studies were performed using simulations to design and construct MCS with attached resonators for dynamic load mitigation applications. 98% payload isolation at resonance (7 Hz) was experimentally attained using a low-frequency vibration isolator with tip-loaded cantilever beam resonators. Pendulum impact tests on a resonator stack substantiated a peak transmitted stress reduction of about 60% and filtering of the resonator frequencies in the transmitted spectrum. Drop-tower tests were done to gauge the shock mitigation performance of an AM-inspired infrastructural building-block with internal resonators. Proof-of-concept experiments using an array of multifunctional resonators demonstrate the possibility of integrating energy harvesting and transducer capabilities. Stress wave attenuation

  18. Local population structure of Plasmodium: impact on malaria control and elimination

    Directory of Open Access Journals (Sweden)

    Chenet Stella M

    2012-12-01

    Full Text Available Abstract Background Regardless of the growing interest in detecting population structures in malarial parasites, there have been limited discussions on how to use this concept in control programmes. In such context, the effects of the parasite population structures will depend on interventions’ spatial or temporal scales. This investigation explores the problem of identifying genetic markers, in this case microsatellites, to unveil Plasmodium genetic structures that could affect decisions in the context of elimination. The study was performed in a low-transmission area, which offers a good proxy to better understand problems associated with surveillance at the final stages of malaria elimination. Methods Plasmodium vivax samples collected in Tumeremo, Venezuela, between March 2003 and November 2004 were analysed. Since Plasmodium falciparum also circulates in many low endemic areas, P. falciparum samples from the same locality and time period were included for comparison. Plasmodium vivax samples were assayed for an original set of 25 microsatellites and P. falciparum samples were assayed for 12 microsatellites. Results Not all microsatellite loci assayed offered reliable local data. A complex temporal-cluster dynamics is found in both P. vivax and P. falciparum. Such dynamics affect the numbers and the type of microsatellites required for identifying individual parasites or parasite clusters when performing cross-sectional studies. The minimum number of microsatellites required to differentiate circulating P. vivax clusters differs from the minimum number of hyper-variable microsatellites required to distinguish individuals within these clusters. Regardless the extended number of microsatellites used in P. vivax, it was not possible to separate all individual infections. Conclusions Molecular surveillance has great potential; however, it requires preliminary local studies in order to properly interpret the emerging patterns in the context of

  19. Assignment Confidence in Localization of the Hand Motor Cortex: Comparison of Structural Imaging With Functional MRI.

    Science.gov (United States)

    Sahin, Neslin; Mohan, Suyash; Maralani, Pejman J; Duddukuri, Srikalyan; O'Rourke, Donald M; Melhem, Elias R; Wolf, Ronald L

    2016-12-01

    The purpose of this study was to assign confidence levels to structural MRI and functional MRI (fMRI) for localization of the primary motor cortex. Ninety-one fMRI studies with at least one motor task (178 hemispheres) were identified. Three anatomic assessments were used to localize the primary motor cortex: relation between the superior frontal sulcus and precentral sulcus; cortical thickness; and configuration of the precentral knob. In 105 hemispheres, interreader agreement was assessed for two investigators with different experience levels. Confidence ratings from 0 to 5 (0, no confidence; 5, 100% confidence) were assigned for fMRI and each anatomic localization method. Cortical thickness had the highest confidence rating (mean, 4.90 ± 0.47 [SD]) with only one failure. The relation between the superior frontal sulcus and precentral sulcus had the lowest confidence rating (4.33 ± 0.91) with three failures. The greatest statistical significance was observed for the cortical thickness and superior frontal sulcus-precentral sulcus methods (post hoc Bonferroni test, p Confidence rating scores were significantly higher for the cortical thickness sign than for fMRI results (4.72 ± 0.54) for a single motor task (post hoc Bonferroni test, p = 0.006); however, the mean confidence rating for fMRI improved to 4.87 ± 0.36 when additional motor tasks were performed. Interreader differences were least for the cortical thickness sign (paired t test, t = 4.25, p confidence regarding localization of the primary motor cortex; however, localization of motor function is more specific when combined with fMRI findings. Multiple techniques can be used to increase confidence in identifying the hand motor cortex.

  20. Electronic structure and local magnetism of 3d-5d impurity substituted CeFe2

    Science.gov (United States)

    Das, Rakesh; Das, G. P.; Srivastava, S. K.

    2016-04-01

    We present here a systematic first-principles study of electronic structure and local magnetic properties of Ce[Fe0.75M0.25]2 compounds, where M is a 3d, 4d or 5d transition or post-transition element, using the generalized gradient approximation of the density functional theory. The d-f band hybridizations existing in CeFe2 get modified by the impurity M in an orderly manner across a period for each impurity series: the hybridization is strongest for the Mn group impurity in the period and gets diminished on either side of it. The weakening of the d-f hybridization strength is also associated with a relative localization of the Ce 4f states with respect to the delocalized 4f states in CeFe2. The above effects are most prominent for 3d impurity series, while for 4d and 5d impurities, the hybridizations and relocalizations are relatively weak due primarily to the relatively extended nature of 4d and 5d wavefunctions. The Ce local moment is found to decrease from the CeFe2 value in proportion to the strength of relocalization, thus following almost the same orderly trend as obeyed by the d-f hybridization. Further, depending on the way the spin-up and spin-down densities of states of an impurity shift relative to the Fermi energy, the impurity local moments are highest for Mn or Fe group, reduce on either side, become zero for Ni to Ga, and are small but negative for V and Ti. The Ce hyperfine field is found to follow the M local moment in a linear fashion, and vice-versa.