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Sample records for chromatin higher-order structure

  1. Neutron scattering studies on chromatin higher-order structure

    Energy Technology Data Exchange (ETDEWEB)

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V. [Brookhaven National Laboratory, Upton, NY (United States)

    1994-12-31

    We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.

  2. ISWI regulates higher-order chromatin structure and histone H1 assembly in vivo.

    Directory of Open Access Journals (Sweden)

    Davide F V Corona

    2007-09-01

    Full Text Available Imitation SWI (ISWI and other ATP-dependent chromatin-remodeling factors play key roles in transcription and other processes by altering the structure and positioning of nucleosomes. Recent studies have also implicated ISWI in the regulation of higher-order chromatin structure, but its role in this process remains poorly understood. To clarify the role of ISWI in vivo, we examined defects in chromosome structure and gene expression resulting from the loss of Iswi function in Drosophila. Consistent with a broad role in transcriptional regulation, the expression of a large number of genes is altered in Iswi mutant larvae. The expression of a dominant-negative form of ISWI leads to dramatic alterations in higher-order chromatin structure, including the apparent decondensation of both mitotic and polytene chromosomes. The loss of ISWI function does not cause obvious defects in nucleosome assembly, but results in a significant reduction in the level of histone H1 associated with chromatin in vivo. These findings suggest that ISWI plays a global role in chromatin compaction in vivo by promoting the association of the linker histone H1 with chromatin.

  3. Higher-order chromatin structure in DSB induction, repair and misrepair.

    Science.gov (United States)

    Falk, Martin; Lukasova, Emilie; Kozubek, Stanislav

    2010-01-01

    Double-strand breaks (DSBs), continuously introduced into DNA by cell metabolism, ionizing radiation and some chemicals, are the biologically most deleterious type of genome damage, and must be accurately repaired to protect genomic integrity, ensure cell survival, and prevent carcinogenesis. Although a huge amount of information has been published on the molecular basis and biological significance of DSB repair, our understanding of DSB repair and its spatiotemporal arrangement is still incomplete. In particular, the role of higher-order chromatin structure in DSB induction and repair, movement of DSBs and the mechanism giving rise to chromatin exchanges, and many other currently disputed questions are discussed in this review. Finally, a model explaining the formation of chromosome translocations is proposed.

  4. A new non-catalytic role for ubiquitin ligase RNF8 in unfolding higher-order chromatin structure

    DEFF Research Database (Denmark)

    Luijsterburg, Martijn S; Acs, Klara; Ackermann, Leena;

    2012-01-01

    The ubiquitin ligases RNF8 and RNF168 orchestrate DNA damage signalling through the ubiquitylation of histone H2A and the recruitment of downstream repair factors. Here, we demonstrate that RNF8, but not RNF168 or the canonical H2A ubiquitin ligase RNF2, mediates extensive chromatin decondensatio...

  5. Higher Order Hessian Structures on Manifolds

    Indian Academy of Sciences (India)

    R David Kumar

    2005-08-01

    In this paper we define th order Hessian structures on manifolds and study them. In particular, when =3, we make a detailed study and establish a one-to-one correspondence between third-order Hessian structures and a certain class of connections on the second-order tangent bundle of a manifold. Further, we show that a connection on the tangent bundle of a manifold induces a connection on the second-order tangent bundle. Also we define second-order geodesics of special second-order connection which gives a geometric characterization of symmetric third-order Hessian structures.

  6. Modulation of Higher Order Chromatin Conformation in Mammalian Cell Nuclei Can Be Mediated by Polyamines and Divalent Cations.

    Directory of Open Access Journals (Sweden)

    Ashwat Visvanathan

    Full Text Available The organisation of the large volume of mammalian genomic DNA within cell nuclei requires mechanisms to regulate chromatin compaction involving the reversible formation of higher order structures. The compaction state of chromatin varies between interphase and mitosis and is also subject to rapid and reversible change upon ATP depletion/repletion. In this study we have investigated mechanisms that may be involved in promoting the hyper-condensation of chromatin when ATP levels are depleted by treating cells with sodium azide and 2-deoxyglucose. Chromatin conformation was analysed in both live and permeabilised HeLa cells using FLIM-FRET, high resolution fluorescence microscopy and by electron spectroscopic imaging microscopy. We show that chromatin compaction following ATP depletion is not caused by loss of transcription activity and that it can occur at a similar level in both interphase and mitotic cells. Analysis of both live and permeabilised HeLa cells shows that chromatin conformation within nuclei is strongly influenced by the levels of divalent cations, including calcium and magnesium. While ATP depletion results in an increase in the level of unbound calcium, chromatin condensation still occurs even in the presence of a calcium chelator. Chromatin compaction is shown to be strongly affected by small changes in the levels of polyamines, including spermine and spermidine. The data are consistent with a model in which the increased intracellular pool of polyamines and divalent cations, resulting from depletion of ATP, bind to DNA and contribute to the large scale hyper-compaction of chromatin by a charge neutralisation mechanism.

  7. H2 O2-induced higher order chromatin degradation: A novel mechanism of oxidative genotoxicity

    Indian Academy of Sciences (India)

    Gregory W Konat

    2003-02-01

    The genotoxicity of reactive oxygen species (ROS) is well established. The underlying mechanism involves oxidation of DNA by ROS. However, we have recently shown that hydrogen peroxide (H2O2), the major mediator of oxidative stress, can also cause genomic damage indirectly. Thus, H2O2 at pathologically relevant concentrations rapidly induces higher order chromatin degradation (HOCD), i.e. enzymatic excision of chromatin loops and their oligomers at matrix-attachment regions. The activation of endonuclease that catalyzes HOCD is a signalling event triggered specifically by H2O2. The activation is not mediated by an influx of calcium ions, but resting concentrations of intracellular calcium ions are required for the maintenance of the endonuclease in an active form. Although H2O2-induced HOCD can efficiently dismantle the genome leading to cell death, under sublethal oxidative stress conditions H2O2-induced HOCD may be the major source of somatic mutations.

  8. Common themes and cell type specific variations of higher order chromatin arrangements in the mouse

    Directory of Open Access Journals (Sweden)

    Cremer Thomas

    2005-12-01

    Full Text Available Abstract Background Similarities as well as differences in higher order chromatin arrangements of human cell types were previously reported. For an evolutionary comparison, we now studied the arrangements of chromosome territories and centromere regions in six mouse cell types (lymphocytes, embryonic stem cells, macrophages, fibroblasts, myoblasts and myotubes with fluorescence in situ hybridization and confocal laser scanning microscopy. Both species evolved pronounced differences in karyotypes after their last common ancestors lived about 87 million years ago and thus seem particularly suited to elucidate common and cell type specific themes of higher order chromatin arrangements in mammals. Results All mouse cell types showed non-random correlations of radial chromosome territory positions with gene density as well as with chromosome size. The distribution of chromosome territories and pericentromeric heterochromatin changed during differentiation, leading to distinct cell type specific distribution patterns. We exclude a strict dependence of these differences on nuclear shape. Positional differences in mouse cell nuclei were less pronounced compared to human cell nuclei in agreement with smaller differences in chromosome size and gene density. Notably, the position of chromosome territories relative to each other was very variable. Conclusion Chromosome territory arrangements according to chromosome size and gene density provide common, evolutionary conserved themes in both, human and mouse cell types. Our findings are incompatible with a previously reported model of parental genome separation.

  9. Cohesin is required for higher-order chromatin conformation at the imprinted IGF2-H19 locus.

    Directory of Open Access Journals (Sweden)

    Raffaella Nativio

    2009-11-01

    Full Text Available Cohesin is a chromatin-associated protein complex that mediates sister chromatid cohesion by connecting replicated DNA molecules. Cohesin also has important roles in gene regulation, but the mechanistic basis of this function is poorly understood. In mammalian genomes, cohesin co-localizes with CCCTC binding factor (CTCF, a zinc finger protein implicated in multiple gene regulatory events. At the imprinted IGF2-H19 locus, CTCF plays an important role in organizing allele-specific higher-order chromatin conformation and functions as an enhancer blocking transcriptional insulator. Here we have used chromosome conformation capture (3C assays and RNAi-mediated depletion of cohesin to address whether cohesin affects higher order chromatin conformation at the IGF2-H19 locus in human cells. Our data show that cohesin has a critical role in maintaining CTCF-mediated chromatin conformation at the locus and that disruption of this conformation coincides with changes in IGF2 expression. We show that the cohesin-dependent, higher-order chromatin conformation of the locus exists in both G1 and G2 phases of the cell cycle and is therefore independent of cohesin's function in sister chromatid cohesion. We propose that cohesin can mediate interactions between DNA molecules in cis to insulate genes through the formation of chromatin loops, analogous to the cohesin mediated interaction with sister chromatids in trans to establish cohesion.

  10. Higher-order structure and epidemic dynamics in clustered networks

    CERN Document Server

    Ritchie, Martin; House, Thomas; Kiss, Istvan Z

    2013-01-01

    Clustering is typically measured by the ratio of triangles to all triples, open or closed. Generating clustered networks, and how clustering affects dynamics on networks, is reasonably well understood for certain classes of networks \\cite{vmclust, karrerclust2010}, e.g., networks composed of lines and non-overlapping triangles. In this paper we show that it is possible to generate networks which, despite having the same degree distribution and equal clustering, exhibit different higher-order structure, specifically, overlapping triangles and other order-four (a closed network motif composed of four nodes) structures. To distinguish and quantify these additional structural features, we develop a new network metric capable of measuring order-four structure which, when used alongside traditional network metrics, allows us to more accurately describe a network's topology. Three network generation algorithms are considered: a modified configuration model and two rewiring algorithms. By generating homogeneous netwo...

  11. Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

    DEFF Research Database (Denmark)

    Ebert, Grit; Steininger, Anne; Weißmann, Robert

    2014-01-01

    in order to gain insights into the mutual relationship of SDs and chromatin topology. RESULTS: Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different...

  12. p63 and Brg1 control developmentally regulated higher-order chromatin remodelling at the epidermal differentiation complex locus in epidermal progenitor cells

    Science.gov (United States)

    Mardaryev, Andrei N.; Gdula, Michal R.; Yarker, Joanne L.; Emelianov, Vladimir N.; Poterlowicz, Krzysztof; Sharov, Andrey A.; Sharova, Tatyana Y.; Scarpa, Julie A.; Chambon, Pierre; Botchkarev, Vladimir A.; Fessing, Michael Y.

    2014-01-01

    Chromatin structural states and their remodelling, including higher-order chromatin folding and three-dimensional (3D) genome organisation, play an important role in the control of gene expression. The role of 3D genome organisation in the control and execution of lineage-specific transcription programmes during the development and differentiation of multipotent stem cells into specialised cell types remains poorly understood. Here, we show that substantial remodelling of the higher-order chromatin structure of the epidermal differentiation complex (EDC), a keratinocyte lineage-specific gene locus on mouse chromosome 3, occurs during epidermal morphogenesis. During epidermal development, the locus relocates away from the nuclear periphery towards the nuclear interior into a compartment enriched in SC35-positive nuclear speckles. Relocation of the EDC locus occurs prior to the full activation of EDC genes involved in controlling terminal keratinocyte differentiation and is a lineage-specific, developmentally regulated event controlled by transcription factor p63, a master regulator of epidermal development. We also show that, in epidermal progenitor cells, p63 directly regulates the expression of the ATP-dependent chromatin remodeller Brg1, which binds to distinct domains within the EDC and is required for relocation of the EDC towards the nuclear interior. Furthermore, Brg1 also regulates gene expression within the EDC locus during epidermal morphogenesis. Thus, p63 and its direct target Brg1 play an essential role in remodelling the higher-order chromatin structure of the EDC and in the specific positioning of this locus within the landscape of the 3D nuclear space, as required for the efficient expression of EDC genes in epidermal progenitor cells during skin development. PMID:24346698

  13. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

    The Third Edition of Chromatin: Structure and Function brings the reader up-to-date with the remarkable progress in chromatin research over the past three years. It has been extensively rewritten to cover new material on chromatin remodeling, histone modification, nuclear compartmentalization, DNA methylation, and transcriptional co-activators and co-repressors. The book is written in a clear and concise fashion, with 60 new illustrations. Chromatin: Structure and Function provides the reader with a concise and coherent account of the nature, structure, and assembly of chromatin and its active

  14. Switchable photooxygenation catalysts that sense higher-order amyloid structures

    Science.gov (United States)

    Taniguchi, Atsuhiko; Shimizu, Yusuke; Oisaki, Kounosuke; Sohma, Youhei; Kanai, Motomu

    2016-10-01

    Proteins can misfold into amyloid structures that are associated with diseases; however, the same proteins often have important biological roles. To degrade selectively the amyloid form without affecting the fraction of functional protein is, therefore, an attractive goal. Here we report target-state-dependent photooxygenation catalysts that are active only when bound to the cross-β-sheet structure that is characteristic of pathogenic aggregated amyloid proteins. We show these catalysts can selectively oxygenate the amyloid form of amyloid β-protein (Aβ) 1-42 in the presence of non-amyloid off-target substrates. Furthermore, photooxygenation with a catalyst that bears an Aβ-binding peptide attenuated the Aβ pathogenicity in the presence of cells. We also show that selective photooxygenation is generally applicable to other amyloidogenic proteins (amylin, insulin, β2-microglobulin, transthyretin and α-synuclein) and does not affect the physiologically functional non-aggregate states of these proteins. This is the first report of an artificial catalyst that can be selectively and reversibly turned on and off depending on the structure and aggregation state of the substrate protein.

  15. A Higher Order Analysis of the Factor Structure of the Myers-Briggs Type Indicator.

    Science.gov (United States)

    Johnson, William L.; Mauzey, Edward; Johnson, Annabel M.; Murphy, Stanley D.; Zimmerman, Kurt J.

    2001-01-01

    Examines the higher order structure of Form G of the Myers Briggs Type Indicator. A third order component analysis of a sample (N=926) found two higher order components. This higher order analysis contributes to the research literature pertaining to the generalized structure of the personality measure. (Contains 44 references and 1 table.) (GCP)

  16. Orthogonal Higher Order Structure of the WISC-IV Spanish Using Hierarchical Exploratory Factor Analytic Procedures

    Science.gov (United States)

    McGill, Ryan J.; Canivez, Gary L.

    2016-01-01

    As recommended by Carroll, the present study examined the factor structure of the Wechsler Intelligence Scale for Children-Fourth Edition Spanish (WISC-IV Spanish) normative sample using higher order exploratory factor analytic techniques not included in the WISC-IV Spanish Technical Manual. Results indicated that the WISC-IV Spanish subtests were…

  17. Factors Affecting Higher Order Thinking Skills of Students: A Meta-Analytic Structural Equation Modeling Study

    Science.gov (United States)

    Budsankom, Prayoonsri; Sawangboon, Tatsirin; Damrongpanit, Suntorapot; Chuensirimongkol, Jariya

    2015-01-01

    The purpose of the research is to develop and identify the validity of factors affecting higher order thinking skills (HOTS) of students. The thinking skills can be divided into three types: analytical, critical, and creative thinking. This analysis is done by applying the meta-analytic structural equation modeling (MASEM) based on a database of…

  18. The Higher Order Factor Structure and Gender Invariance of the Pathological Narcissism Inventory

    Science.gov (United States)

    Wright, Aidan G. C.; Lukowitsky, Mark R.; Pincus, Aaron L.; Conroy, David E.

    2010-01-01

    The Pathological Narcissism Inventory (PNI) is a recently developed multidimensional inventory for the assessment of pathological narcissism. The authors describe and report the results of two studies that investigate the higher order factor structure and gender invariance of the PNI. The results of the first study indicate that the PNI has a…

  19. Simple NMR methods for evaluating higher order structures of monoclonal antibody therapeutics with quinary structure.

    Science.gov (United States)

    Chen, Kang; Long, Dianna S; Lute, Scott C; Levy, Michaella J; Brorson, Kurt A; Keire, David A

    2016-09-01

    Monoclonal antibody (mAb) drugs constitute the largest class of protein therapeutics currently on the market. Correctly folded protein higher order structure (HOS), including quinary structure, is crucial for mAb drug quality. The quinary structure is defined as the association of quaternary structures (e.g., oligomerized mAb). Here, several commonly available analytical methods, i.e., size-exclusion-chromatography (SEC) FPLC, multi-angle light scattering (MALS), circular dichroism (CD), NMR and multivariate analysis, were combined and modified to yield a complete profile of HOS and comparable metrics. Rituximab and infliximab were chosen for method evaluation because both IgG1 molecules are known to be homologous in sequence, superimposable in Fab crystal structure and identical in Fc structure. However, herein the two are identified to be significantly different in quinary structure in addition to minor secondary structure differences. All data collectively showed rituximab was mostly monomeric while infliximab was in mono-oligomer equilibrium driven by its Fab fragment. The quinary structure differences were qualitatively inferred from the less used but more reproducible dilution-injection-SEC-FPLC curve method. Quantitative principal component analysis (PCA) was performed on NMR spectra of either the intact or the in-situ enzymatic-digested mAb samples. The cleavage reactions happened directly in NMR tubes without further separation, which greatly enhanced NMR spectra quality and resulted in larger inter- and intra-lot variations based on PCA. The new in-situ enzymatic digestion method holds potential in identifying structural differences on larger therapeutic molecules using NMR.

  20. Aromatic Interactions Promote Self-association of Collagen Triple-helical Peptides to Higher Order Structures

    OpenAIRE

    Kar, Karunakar; Ibrar, Sajjad; Nanda, Vikas; Getz, Todd M.; Kunapuli, Satya P.; Brodsky, Barbara

    2009-01-01

    Aromatic residues are relatively rare within the collagen triple-helix, but they appear to play a specialized role in higher order structure and function. The role of aromatic amino acids in the self-assembly of triple-helical peptides was investigated in terms of the kinetics of self-association, the nature of aggregated species formed, and the ability of these species to activate platelet aggregation. The presence of aromatic residues on both ends of a type IV collagen model peptide is obse...

  1. Phase structure of the $O(2)$ ghost model with higher-order gradient term

    CERN Document Server

    Péli, Z; Sailer, K

    2016-01-01

    The phase structure and the infrared behaviour of the Euclidean 3-dimensional $O(2)$ symmetric ghost scalar field model with higher-order derivative term has been investigated in Wegner and Houghton's renormalization group framework. The symmetric phase in which no ghost condensation occurs and the phase with restored symmetry but with a transient presence of a ghost condensate have been identified. Finiteness of the correlation length at the phase boundary hints to a phase transition of first order. The results are compared with those for the ordinary $O(2)$ symmetric scalar field model.

  2. Structure of chromatin in spermatozoa.

    Science.gov (United States)

    Björndahl, Lars; Kvist, Ulrik

    2014-01-01

    The specialized structure of the sperm chromatin has a dual function - first to protect the DNA from damage during storage and transport to the oocyte, and then to enable a rapid and complete unpacking of the undamaged paternal genome in the ooplasm. It is evident that zinc has a pivotal role in maintaining the structural stability and in enabling a rapid decondensation at the appropriate time. It is important for the sperm chromatin structure that the spermatozoa are ejaculated together with the zinc-rich prostatic secretion. Early exposure to zinc-binding seminal vesicular fluid can deplete the sperm chromatin of zinc and most likely induce surplus formation of disulfide bridges, likely to cause incomplete and delayed decondensation of the sperm chromatin in the oocyte. A premature decrease in sperm chromatin structure stability is likely to increase the risk for damage to the DNA due to increased access to the genome for DNA damaging compounds. The status of the sperm chromatin structure can vary in vitro depending on the exposure to zinc-depleting conditions when spermatozoa are stored in semen after ejaculation. When sperm DNA damage tests are evaluated and validated, it is therefore essential to also take into account the dynamics of zinc-dependent and zinc-independent sperm chromatin stability.

  3. Higher order structure of short immunostimulatory oligonucleotides studied by atomic force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Klein, Dionne C.G., E-mail: dionne.c.g.klein@ntnu.no [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway); Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Latz, Eicke [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 (United States); Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn (Germany); Espevik, Terje [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Stokke, Bjorn T. [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway)

    2010-05-15

    Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.

  4. 高阶布尔网络的结构%Structure of higher order Boolean networks*

    Institute of Scientific and Technical Information of China (English)

    李志强; 赵寅; 程代展

    2011-01-01

    The higher order Boolean (control) network is introduced and its topological structure is studied.Using semi-tensor product of matrices,its dynamics is converted into two algebraic forms,which are standard discrete-time dynamic systems.The one-to-one correspondence of the network dynamics and its first algebraic form is proved,and certain topological structures,including fixed points,cycles,and transient time,of higher order Boolean (control) networks are revealed.The relationship between the original system and its second algebraic form is also studied.%介绍高阶布尔(控制)网络,并研究了其拓扑结构.以矩阵的半张量积作为工具,把高阶布尔网络的动态过程转化为2种标准离散事件动态系统的代数形式.证明了高阶布尔网络和第1代数形式的一一对应关系,并由此得到其拓扑结构(不动点、极限圈以及暂态期等).还研究了高阶布尔网络系统与它第2代数形式的关系.

  5. Design and construction of higher-order structure and function in proteinosome-based protocells.

    Science.gov (United States)

    Huang, Xin; Patil, Avinash J; Li, Mei; Mann, Stephen

    2014-06-25

    The design and construction of higher-order structure and function in proteinosome microcompartments enclosed by a cross-linked membrane of amphiphilic bovine serum albumin/poly(N-isopropylacrylamide) (BSA-NH2/PNIPAAm) nanoconjugates is described. Three structure/function relationships are investigated: (i) differential chemical cross-linking for the control of membrane disassembly and regulated release of encapsulated genetic polymers; (ii) enzyme-mediated hydrogel structuring of the internal microenvironment to increase mechanical robustness and generate a molecularly crowded reaction environment; and (iii) self-production of a membrane-enclosing outer hydrogel wall for generating protease-resistant forms of the protein-polymer protocells. Our results highlight the potential of integrating aspects of supramolecular and polymer chemistry into the design and construction of novel bioinspired microcompartments as a step toward small-scale materials systems based on synthetic cellularity.

  6. Aromatic Interactions Promote Self-association of Collagen Triple-helical Peptides to Higher Order Structures

    Science.gov (United States)

    Kar, Karunakar; Ibrar, Sajjad; Nanda, Vikas; Getz, Todd M.; Kunapuli, Satya P.; Brodsky, Barbara

    2009-01-01

    Aromatic residues are relatively rare within the collagen triple-helix, but they appear to play a specialized role in higher order structure and function. The role of aromatic amino acids in the self-assembly of triple-helical peptides was investigated in terms of the kinetics of self-association, the nature of aggregated species formed, and the ability of these species to activate platelet aggregation. The presence of aromatic residues on both ends of a type IV collagen model peptide is observed to greatly accelerate the kinetics of self-association, decreasing the lag time and leading to insoluble, well defined linear fibrils as well as small soluble aggregates. Both macroscopic visible aggregates and small multi-molecular complexes in solution are capable of inducing platelet aggregation through the glycoprotein VI receptor on platelets. Proline-aromatic CH⋯π interactions are often observed within globular proteins and in protein complexes, and examination of molecular packing in the crystal structure of the integrin binding collagen peptide shows Phe interacts with Pro/Hyp in a neighboring triple-helical molecule. An intermolecular interaction between aromatic amino acids and imino acids within the triple-helix is also supported by the observed inhibitory effect of isolated Phe amino acids on the self-association of (Pro-Hyp-Gly)10. Given the high fraction of Pro and Hyp residues on the surface of collagen molecules, it is likely that imino acid-aromatic CH⋯π interactions are important in formation of higher order structure. It is suggested that the catalysis of type I collagen fibrillogenesis by non-helical telopeptides is due to specific intermolecular CH⋯π interactions between aromatic residues in the telopeptides and Pro/Hyp residues within the triple-helix. PMID:19610672

  7. Effects of fast neutrons on chromatin: dependence on chromatin structure

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L. [Dept. of Molecular Genetics, V. Babes National Inst., Bd. Timisoara, Bucharest (Romania); Constantinescu, B. [Dept. of Cyclotron, H. Hulubei National Inst., Bucharest (Romania); Gazdaru, D. [Dept. of Biophysics, Physics Faculty, Univ. of Bucharest (Romania)

    2002-07-01

    The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)

  8. Mathematical Structure of Anomalous Dimensions and QCD Wilson Coefficients in Higher Order

    Science.gov (United States)

    Blümlein, J.

    2004-10-01

    The alternating and non-alternating harmonic sums and other algebraic objects of the same equivalence class are connected by algebraic relations which are induced by the product of these quantities and which depend on their index class rather than on their value. We show how to find a basis of the associated algebra. The length of the basis l is found to be ⩽1/d, where d is the depth of the sums considered and is given by the 2nd WITT formula. It can be also determined counting the LYNDON words of the respective index set. There are two further classes of relations: structural relations between NIELSEN-type integrals and relations due to the specific structure of Feynman diagrams which lead to a considerable reduction of the set of basic functions. The relations derived can be used to simplify results of higher order calculations in QED and QCD. We also report on results calculating the 16th non-singlet moment of unpolarized structure functions at 3-loop order in the MS¯ scheme.

  9. Mathematical structure of anomalous dimensions and QCD Wilson coefficients in higher order

    Energy Technology Data Exchange (ETDEWEB)

    Bluemlein, J. [Deutsches Elektronen Synchrotron, DESY, Platanenallee 6, D-15738 Zeuthen (Germany)

    2004-10-01

    The alternating and non-alternating harmonic sums and other algebraic objects of the same equivalence class are connected by algebraic relations which are induced by the product of these quantities and which depend on their index class rather than on their value. We show how to find a basis of the associated algebra. The length of the basis l is found to be =<1/d, where d is the depth of the sums considered and is given by the 2nd Witt formula. It can be also determined counting the Lyndon words of the respective index set. There are two further classes of relations: structural relations between Nielsen-type integrals and relations due to the specific structure of Feynman diagrams which lead to a considerable reduction of the set of basic functions. The relations derived can be used to simplify results of higher order calculations in QED and QCD. We also report on results calculating the 16th non-singlet moment of unpolarized structure functions at 3-loop order in the MS-bar scheme.

  10. Structural damage detection using higher-order finite elements and a scanning laser vibrometer

    Science.gov (United States)

    Jin, Si

    In contrast to conventional non-destructive evaluation methods, dynamics-based damage detection methods are capable of rapid integrity evaluation of large structures and have received considerable attention from aerospace, mechanical, and civil engineering communities in recent years. However, the identifiable damage size using dynamics-based methods is determined by the number of sensors used, level of measurement noise, accuracy of structural models, and signal processing techniques. In this thesis we study dynamics of structures with damage and then derive and experimentally verify new model-independent structural damage detection methods that can locate small damage to structures. To find sensitive damage detection parameters we develop a higher-order beam element that enforces the continuity of displacements, slopes, bending moments, and shear forces at all nodes, and a higher-order rectangular plate element that enforces the continuity of displacements, slopes, and bending and twisting moments at all nodes. These two elements are used to study the dynamics of beams and plates. Results show that high-order spatial derivatives of high-frequency modes are important sensitive parameters that can locate small structural damage. Unfortunately the most powerful and popular structural modeling technique, the finite element method, is not accurate in predicting high-frequency responses. Hence, a model-independent method using dynamic responses obtained from high density measurements is concluded to be the best approach. To increase measurement density and reduce noise a Polytec PI PSV-200 scanning laser vibrometer is used to provide non-contact, dense, and accurate measurements of structural vibration velocities. To avoid the use of structural models and to extract sensitive detection parameters from experimental data, a brand-new structural damage detection method named BED (Boundary-Effect Detection) is developed for pinpointing damage locations using Operational

  11. Self-association of collagen triple helic peptides into higher order structures.

    Science.gov (United States)

    Kar, Karunakar; Amin, Priyal; Bryan, Michael A; Persikov, Anton V; Mohs, Angela; Wang, Yuh-Hwa; Brodsky, Barbara

    2006-11-03

    Interest in self-association of peptides and proteins is motivated by an interest in the mechanism of physiologically higher order assembly of proteins such as collagen as well as the mechanism of pathological aggregation such as beta-amyloid formation. The triple helical form of (Pro-Hyp-Gly)(10), a peptide that has proved a useful model for molecular features of collagen, was found to self-associate, and its association properties are reported here. Turbidity experiments indicate that the triple helical peptide self-assembles at neutral pH via a nucleation-growth mechanism, with a critical concentration near 1 mM. The associated form is more stable than individual molecules by about 25 degrees C, and the association is reversible. The rate of self-association increases with temperature, supporting an entropically favored process. After self-association, (Pro-Hyp-Gly)(10) forms branched filamentous structures, in contrast with the highly ordered axially periodic structure of collagen fibrils. Yet a number of characteristics of triple helix assembly for the peptide resemble those of collagen fibril formation. These include promotion of fibril formation by neutral pH and increasing temperature; inhibition by sugars; and a requirement for hydroxyproline. It is suggested that these similar features for peptide and collagen self-association are based on common lateral underlying interactions between triple helical molecules mediated by hydrogen-bonded hydration networks involving hydroxyproline.

  12. Thermo-Elastic Analysis of Internally Cooled Structures Using a Higher Order Theory

    Science.gov (United States)

    Arnold, Steven M.; Bednarcyk, Brett A.; Aboudi, Jacob

    2001-01-01

    This paper presents the results of a study on the thermomechanical behavior of internally cooled silicon nitride structures. Silicon nitride is under consideration for elevated temperature aerospace engine applications. and techniques for lowering the operating temperature of structures composed of this material are under development. Lowering the operating temperature provides a large payoff in terms of fatigue life and may be accomplished through the use of thermal barrier coatings (TBC's) and the novel concept of included cooling channels. Herein, an in-depth study is performed on the behavior of a flame-impinged silicon nitride plate with a TBC and internal channels cooled by forced air. The analysis is performed using the higher order theory for functionally graded materials (HOTFGM), which has been developed through NASA Glenn Research Center funding over the past several years. HOTFGM was chosen over the traditional finite element approach as a prelude to an examination of functionally graded silicon nitride structures for which HOTFGM is ideally suited. To accommodate the analysis requirement% of the internally cooled plate problem, two crucial enhancements were made to the two-dimensional Cartesian-based version of HOTFGM. namely, incorporation of internal boundary capabilities and incorporation of convective boundary conditions. Results indicate the viability and large benefits of cooling the plate via forced air through cooling channels. Furthermore, cooling can positively impact the stress and displacement fields present in the plate, yielding an additional payoff in terms of fatigue life. Finally, a spin-off capability resulted from inclusion of internal boundaries within HOTFGM; the ability to simulate the thermo-elastic response of structures with curved surfaces. This new capability is demonstrated, and through comparison with an analytical solution, shown to be viable and accurate.

  13. Higher-order massive neutrino perturbations in large-scale structure

    CERN Document Server

    Führer, Florian

    2014-01-01

    We develop a higher-order perturbation theory for large-scale structure formation involving a free-streaming hot or warm dark matter species. We focus on the case of mixed cold dark matter and massive neutrinos, although our approach is applicable also to a single warm dark matter species. In order to capture the suppressed growth of neutrino density perturbations on small scales, we account for the full momentum dependence of the phase space distribution using the Vlaslov equation, and derive from it a formal closed-form nonlinear equation for the neutrino density. Using a systematic perturbative expansion of this equation we compute high-order corrections to the neutrino density contrast without the explicit need to track the perturbed neutrino momentum distribution. We calculate the leading-order total matter bispectrum for several neutrino masses. Using our result as a benchmark, we test the accuracy of the fluid approximation and a linear approximation used in perturbative and N-body analyses, as well as...

  14. Continued stabilization of the nuclear higher-order structure of post-mitotic neurons in vivo.

    Directory of Open Access Journals (Sweden)

    Janeth Alva-Medina

    Full Text Available BACKGROUND: Cellular terminal differentiation (TD correlates with a permanent exit from the cell cycle and so TD cells become stably post-mitotic. However, TD cells express the molecular machinery necessary for cell proliferation that can be reactivated by experimental manipulation, yet it has not been reported the stable proliferation of any type of reactivated TD cells. Neurons become post-mitotic after leaving the ventricular zone. When neurons are forced to reenter the cell cycle they invariably undergo cell death. Wider evidence indicates that the post-mitotic state cannot solely depend on gene products acting in trans, otherwise mutations in the corresponding genes may lead to reentry and completion of the cell cycle in TD cells, but this has not been observed. In the interphase, nuclear DNA of metazoan cells is organized in supercoiled loops anchored to a nuclear nuclear matrix (NM. The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS. We have previously compared the NHOS of aged rat hepatocytes with that of early post-mitotic rat neurons and our results indicated that a very stable NHOS is a common feature of both senescent and post-mitotic cells in vivo. PRINCIPAL FINDINGS: In the present work we compared the NHOS in rat neurons from different post-natal ages. Our results show that the trend towards further stabilization of the NHOS in neurons continues throughout post-natal life. This phenomenon occurs in absence of overt changes in the post-mitotic state and transcriptional activity of neurons, suggesting that it is independent of functional constraints. CONCLUSIONS: Apparently the continued stabilization of the NHOS as a function of time is basically determined by thermodynamic and structural constraints. We discuss how the resulting highly stable NHOS of neurons may be the structural, non-genetic basis of their permanent and irreversible post-mitotic state.

  15. Continued Stabilization of the Nuclear Higher-Order Structure of Post-Mitotic Neurons In Vivo

    Science.gov (United States)

    Alva-Medina, Janeth; Maya-Mendoza, Apolinar; Dent, Myrna A. R.; Aranda-Anzaldo, Armando

    2011-01-01

    Background Cellular terminal differentiation (TD) correlates with a permanent exit from the cell cycle and so TD cells become stably post-mitotic. However, TD cells express the molecular machinery necessary for cell proliferation that can be reactivated by experimental manipulation, yet it has not been reported the stable proliferation of any type of reactivated TD cells. Neurons become post-mitotic after leaving the ventricular zone. When neurons are forced to reenter the cell cycle they invariably undergo cell death. Wider evidence indicates that the post-mitotic state cannot solely depend on gene products acting in trans, otherwise mutations in the corresponding genes may lead to reentry and completion of the cell cycle in TD cells, but this has not been observed. In the interphase, nuclear DNA of metazoan cells is organized in supercoiled loops anchored to a nuclear nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS). We have previously compared the NHOS of aged rat hepatocytes with that of early post-mitotic rat neurons and our results indicated that a very stable NHOS is a common feature of both senescent and post-mitotic cells in vivo. Principal Findings In the present work we compared the NHOS in rat neurons from different post-natal ages. Our results show that the trend towards further stabilization of the NHOS in neurons continues throughout post-natal life. This phenomenon occurs in absence of overt changes in the post-mitotic state and transcriptional activity of neurons, suggesting that it is independent of functional constraints. Conclusions Apparently the continued stabilization of the NHOS as a function of time is basically determined by thermodynamic and structural constraints. We discuss how the resulting highly stable NHOS of neurons may be the structural, non-genetic basis of their permanent and irreversible post-mitotic state. PMID:21731716

  16. Chromatin structure regulates gene conversion.

    Directory of Open Access Journals (Sweden)

    W Jason Cummings

    2007-10-01

    Full Text Available Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vlambda pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205, expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vlambda donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vlambda array, and altered the outcome of Vlambda diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences.

  17. SANS spectra of the fractal supernucleosomal chromatin structure models

    Science.gov (United States)

    Ilatovskiy, Andrey V.; Lebedev, Dmitry V.; Filatov, Michael V.; Petukhov, Michael G.; Isaev-Ivanov, Vladimir V.

    2012-03-01

    The eukaryotic genome consists of chromatin—a nucleoprotein complex with hierarchical architecture based on nucleosomes, the organization of higher-order chromatin structures still remains unknown. Available experimental data, including SANS spectra we had obtained for whole nuclei, suggested fractal nature of chromatin. Previously we had built random-walk supernucleosomal models (up to 106 nucleosomes) to interpret our SANS spectra. Here we report a new method to build fractal supernucleosomal structure of a given fractal dimension or two different dimensions. Agreement between calculated and experimental SANS spectra was significantly improved, especially for model with two fractal dimensions—3 and 2.

  18. Higher-order nonlinear effects on wave structures in a multispecies plasma with nonisothermal electrons

    Energy Technology Data Exchange (ETDEWEB)

    Gill, Tarsem Singh [Dept. of Physics, Guru Nanak Dev Univ., Amritsar (India); Bala, Parveen [Dept. of Math. Stat. and Physics, Punjab Agricultural Univ., Ludhiana (India); Kaur, Harvinder [Dept. of Physics, Khalsa Coll., Amritsar (India)

    2010-04-15

    In the present investigation, we have studied ion-acoustic solitary waves in a plasma consisting of warm positive and negative ions and nonisothermal electron distribution. We have used reductive perturbation theory (RPT) and derived a dispersion relation which supports only two ion-acoustic modes, viz. slow and fast. The expression for phase velocities of these modes is observed to be a function of parameters like nonisothermality, charge and mass ratio, and relative temperature of ions. A modified Korteweg-de Vries (KdV) equation with a (1+1/2) nonlinearity, also known as Schamel-mKdV model, is derived. RPT is further extended to include the contribution of higher-order terms. The results of numerical computation for such contributions are shown in the form of graphs in different parameter regimes for both, slow and fast ion-acoustic solitary waves having several interesting features. For the departure from the isothermally distributed electrons, a generalized KdV equation is derived and solved. It is observed that both rarefactive and compressive solitons exist for the isothermal case. However, nonisothermality supports only the compressive type of solitons in the given parameter regime. (orig.)

  19. Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

    Institute of Scientific and Technical Information of China (English)

    Iouri Chepelev; Gang Wei; Dara Wangsa; Qingsong Tang; Keji Zhao

    2012-01-01

    Recent epigenomic studies have predicted thousands of potential enhancers in the human genome.However,there has not been systematic characterization of target promoters for these potential enhancers.Using H3K4me2 as a mark for active enhancers,we identified genome-wide EP interactions in human CD4+ T cells.Among the 6 520 longdistance chromatin interactions,we identify 2 067 enhancers that interact with 1 619 promoters and enhance their expression.These enhancers exist in accessible chromatin regions and are associated with various histone modifications and polymerase Ⅱ binding.The promoters with interacting enhancers are expressed at higher levels than those without interacting enhancers,and their expression levels are positively correlated with the number of interacting enhancers.Interestingly,interacting promoters are co-expressed in a tissue-specific manner.We also find that chromosomes are organized into multiple levels of interacting domains.Our results define a global view of EP interactions and provide a data set to further understand mechanisms of enhancer targeting and long-range chromatin organization.The Gene Expression Omnibus accession number for the raw and analyzed chromatin interaction data is GSE32677.

  20. Sequence dependence of kinetics and morphology of collagen model peptide self-assembly into higher order structures

    OpenAIRE

    Kar, Karunakar; Wang, Yuh-Hwa; Brodsky, Barbara

    2008-01-01

    The process of self-assembly of the triple-helical peptide (Pro-Hyp-Gly)10 into higher order structure resembles the nucleation-growth mechanism of collagen fibril formation in many features, but the irregular morphology of the self-assembled peptide contrasts with the ordered fibers and networks formed by collagen in vivo. The amino acid sequence in the central region of the (Pro-Hyp-Gly)10 peptide was varied and found to affect the kinetics of self-assembly and nature of the higher order st...

  1. On modeling micro-structural evolution using a higher order strain gradient continuum theory

    DEFF Research Database (Denmark)

    El-Naaman, S. A.; Nielsen, K. L.; Niordson, C. F.

    2016-01-01

    Published experimental measurements on deformed metal crystals show distinct pattern formation, in which dislocations are arranged in wall and cell structures. The distribution of dislocations is highly non-uniform, which produces discontinuities in the lattice rotations. Modeling the experimenta......Published experimental measurements on deformed metal crystals show distinct pattern formation, in which dislocations are arranged in wall and cell structures. The distribution of dislocations is highly non-uniform, which produces discontinuities in the lattice rotations. Modeling...... a proper treatment of the back stress enables dislocation wall and cell structure type response in the adopted framework....

  2. Higher-order proton structure corrections to the Lamb shift in muonic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Carlson, Carl E. [Helmholtz Institut Mainz, Johannes Gutenberg-Universitaet, D-55099 Mainz (Germany); Department of Physics, College of William and Mary, Williamsburg, Virginia 23187 (United States); Vanderhaeghen, Marc [Institut fuer Kernphysik, Johannes Gutenberg-Universitaet, D-55099 Mainz (Germany)

    2011-08-15

    The recent conundrum with the proton charge radius inspires reconsideration of the corrections that enter into determinations of the proton size. We study the two-photon proton-structure corrections, with special consideration of the nonpole subtraction term in the dispersion relation and using fits to modern data to evaluate the energy contributions. We find that individual contributions change more than the total and present results with error estimates.

  3. Higher order proton structure corrections to the Lamb shift in muonic hydrogen

    CERN Document Server

    Carlson, Carl E

    2011-01-01

    The recent conundrum with the proton charge radius inspires reconsideration of the corrections that enter into determinations of the proton size. We study the two-photon proton-structure corrections, with special consideration of the non-pole subtraction term in the dispersion relation, and using fits to modern data to evaluate the energy contributions. We find that individual contributions change more than the total, and present results with error estimates.

  4. A generative spike train model with time-structured higher order correlations

    Directory of Open Access Journals (Sweden)

    James eTrousdale

    2013-07-01

    Full Text Available Emerging technologies are revealing the spiking activity in ever larger neural ensembles. Frequently, this spiking is far from independent, with correlations in the spike times of different cells. Understanding how such correlations impact the dynamics and function of neural ensembles remains an important open problem.Here we describe a new, generative model for correlated spike trains that can exhibit many of the features observed in data. Extending prior work in mathematical finance, this generalized thinning and shift (GTaS model creates marginally Poisson spike trains with diverse temporal correlation structures.We give several examples which highlight the model's flexibility and utility. For instance, we use it to examine how a neural network responds to highly structured patterns of inputs.We then show that the GTaS model is analytically tractable, and derive cumulant densities of all orders in terms of model parameters. The GTaS framework can therefore be an important tool in the experimental and theoretical exploration of neural dynamics.

  5. On the structure of characteristic surfaces related with partial differential equations of first and higher orders. Part 1

    Directory of Open Access Journals (Sweden)

    Natalia K. Prykarpatska

    2005-01-01

    Full Text Available The geometric structure of characteristic surfaces related with partial differential equations of first and higher orders is studied making use the vector field technique on hypersurfaces. It is shown, that corresponding characteristics are defined uniquely up to some smooth tensor fields, thereby supplying additional information about the suitable set of their solutions. In particular, it may be very useful for studying asymptotic properties of solutions to our partial differential equations under some boundary conditions.

  6. Sequence dependence of kinetics and morphology of collagen model peptide self-assembly into higher order structures

    Science.gov (United States)

    Kar, Karunakar; Wang, Yuh-Hwa; Brodsky, Barbara

    2008-01-01

    The process of self-assembly of the triple-helical peptide (Pro-Hyp-Gly)10 into higher order structure resembles the nucleation-growth mechanism of collagen fibril formation in many features, but the irregular morphology of the self-assembled peptide contrasts with the ordered fibers and networks formed by collagen in vivo. The amino acid sequence in the central region of the (Pro-Hyp-Gly)10 peptide was varied and found to affect the kinetics of self-assembly and nature of the higher order structure formed. Single amino acid changes in the central triplet produced irregular higher order structures similar to (Pro-Hyp-Gly)10, but the rate of self-association was markedly delayed by a single change in one Pro to Ala or Leu. The introduction of a Hyp-rich hydrophobic sequence from type IV collagen resulted in a more regular suprastructure of extended fibers that sometimes showed supercoiling and branching features similar to those seen for type IV collagen in the basement membrane network. Several peptides, where central Pro-Hyp sequences were replaced by charged residues or a nine-residue hydrophobic region from type III collagen, lost the ability to self-associate under standard conditions. The inability to self-assemble likely results from loss of imino acids, and lack of an appropriate distribution of hydrophobic/electrostatic residues. The effect of replacement of a single Gly residue was also examined, as a model for collagen diseases such as osteogenesis imperfecta and Alport syndrome. Unexpectedly, the Gly to Ala replacement interfered with self-assembly of (Pro-Hyp-Gly)10, while the peptide with a Gly to Ser substitution self-associated to form a fibrillar structure. PMID:18441232

  7. Computational strategies to address chromatin structure problems

    Science.gov (United States)

    Perišić, Ognjen; Schlick, Tamar

    2016-06-01

    While the genetic information is contained in double helical DNA, gene expression is a complex multilevel process that involves various functional units, from nucleosomes to fully formed chromatin fibers accompanied by a host of various chromatin binding enzymes. The chromatin fiber is a polymer composed of histone protein complexes upon which DNA wraps, like yarn upon many spools. The nature of chromatin structure has been an open question since the beginning of modern molecular biology. Many experiments have shown that the chromatin fiber is a highly dynamic entity with pronounced structural diversity that includes properties of idealized zig-zag and solenoid models, as well as other motifs. This diversity can produce a high packing ratio and thus inhibit access to a majority of the wound DNA. Despite much research, chromatin’s dynamic structure has not yet been fully described. Long stretches of chromatin fibers exhibit puzzling dynamic behavior that requires interpretation in the light of gene expression patterns in various tissue and organisms. The properties of chromatin fiber can be investigated with experimental techniques, like in vitro biochemistry, in vivo imagining, and high-throughput chromosome capture technology. Those techniques provide useful insights into the fiber’s structure and dynamics, but they are limited in resolution and scope, especially regarding compact fibers and chromosomes in the cellular milieu. Complementary but specialized modeling techniques are needed to handle large floppy polymers such as the chromatin fiber. In this review, we discuss current approaches in the chromatin structure field with an emphasis on modeling, such as molecular dynamics and coarse-grained computational approaches. Combinations of these computational techniques complement experiments and address many relevant biological problems, as we will illustrate with special focus on epigenetic modulation of chromatin structure.

  8. HOTCFGM-1D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Through-Thickness Functionally Graded Microstructures

    Science.gov (United States)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    1998-01-01

    The objective of this three-year project was to develop and deliver to NASA Lewis one-dimensional and two-dimensional higher-order theories, and related computer codes, for the analysis, optimization and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, blisk blades). To satisfy this objective, a quasi one-dimensional version of the higher-order theory, HOTCFGM-1D, and four computer codes based on this theory, for the analysis, design and optimization of cylindrical structural components functionally graded in the radial direction were developed. The theory is applicable to thin multi-phased composite shell/cylinders subjected to macroscopically axisymmetric thermomechanical and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial and circumferential directions, and arbitrarily distributed in the radial direction, thereby allowing functional grading of the internal reinforcement in this direction.

  9. Characteristic effect of an anticancer dinuclear platinum(II) complex on the higher-order structure of DNA.

    Science.gov (United States)

    Kida, Naoko; Katsuda, Yousuke; Yoshikawa, Yuko; Komeda, Seiji; Sato, Takaji; Saito, Yoshihiro; Chikuma, Masahiko; Suzuki, Mari; Imanaka, Tadayuki; Yoshikawa, Kenichi

    2010-06-01

    It is known that a 1,2,3-triazolato-bridged dinuclear platinum(II) complex, [{cis-Pt(NH(3))(2)}(2)(micro-OH)(micro-1,2,3-ta-N (1),N (2))](NO(3))(2) (AMTA), shows high in vitro cytotoxicity against several human tumor cell lines and circumvents cross-resistance to cisplatin. In the present study, we examined a dose- and time-dependent effect of AMTA on the higher-order structure of a large DNA, T4 phage DNA (166 kbp), by adapting single-molecule observation with fluorescence microscopy. It was found that AMTA induces the shrinking of DNA into a compact state with a much higher potency than cisplatin. From a quantitative analysis of the Brownian motion of individual DNA molecules in solution, it became clear that the density of a DNA segment in the compact state is about 2,000 times greater than that in the absence of AMTA. Circular dichroism spectra suggested that AMTA causes a transition from the B to the C form in the secondary structure of DNA, which is characterized by fast and slow processes. Electrophoretic measurements indicated that the binding of AMTA to supercoiled DNA induces unwinding of the double helix. Our results indicate that AMTA acts on DNA through both electrostatic interaction and coordination binding; the former causes a fast change in the secondary structure from the B to the C form, whereas the latter promotes shrinking in the higher-order structure as a relatively slow kinetic process. The shrinking effect of AMTA on DNA is attributable to the possible increase in the number of bridges along a DNA molecule. It is concluded that AMTA interacts with DNA in a manner markedly different from that of cisplatin.

  10. Aromatic interactions promote self-association of collagen triple-helical peptides to higher-order structures.

    Science.gov (United States)

    Kar, Karunakar; Ibrar, Sajjad; Nanda, Vikas; Getz, Todd M; Kunapuli, Satya P; Brodsky, Barbara

    2009-08-25

    Aromatic residues are relatively rare within the collagen triple helix, but they appear to play a specialized role in higher-order structure and function. The role of aromatic amino acids in the self-assembly of triple-helical peptides was investigated in terms of the kinetics of self-association, the nature of aggregated species formed, and the ability of these species to activate platelet aggregation. The presence of aromatic residues on both ends of a type IV collagen model peptide is observed to greatly accelerate the kinetics of self-association, decreasing the lag time and leading to insoluble, well-defined linear fibrils as well as small soluble aggregates. Both macroscopic visible aggregates and small multimolecular complexes in solution are capable of inducing platelet aggregation through the glycoprotein VI receptor on platelets. Proline-aromatic CH...pi interactions are often observed within globular proteins and in protein complexes, and examination of molecular packing in the crystal structure of the integrin binding collagen peptide shows Phe interacts with Pro/Hyp in a neighboring triple-helical molecule. An intermolecular interaction between aromatic amino acids and imino acids within the triple helix is also supported by the observed inhibitory effect of isolated Phe amino acids on the self-association of (Pro-Hyp-Gly)(10). Given the high fraction of Pro and Hyp residues on the surface of collagen molecules, it is likely that imino acid-aromatic CH...pi interactions are important in formation of higher-order structure. We suggest that the catalysis of type I collagen fibrillogenesis by nonhelical telopeptides is due to specific intermolecular CH...pi interactions between aromatic residues in the telopeptides and Pro/Hyp residues within the triple helix.

  11. Exploring item and higher order factor structure with the Schmid-Leiman solution: syntax codes for SPSS and SAS.

    Science.gov (United States)

    Wolff, Hans-Georg; Preising, Katja

    2005-02-01

    To ease the interpretation of higher order factor analysis, the direct relationships between variables and higher order factors may be calculated by the Schmid-Leiman solution (SLS; Schmid & Leiman, 1957). This simple transformation of higher order factor analysis orthogonalizes first-order and higher order factors and thereby allows the interpretation of the relative impact of factor levels on variables. The Schmid-Leiman solution may also be used to facilitate theorizing and scale development. The rationale for the procedure is presented, supplemented by syntax codes for SPSS and SAS, since the transformation is not part of most statistical programs. Syntax codes may also be downloaded from www.psychonomic.org/archive/.

  12. Chromatin structure and evolution in the human genome

    Directory of Open Access Journals (Sweden)

    Dunlop Malcolm G

    2007-05-01

    Full Text Available Abstract Background Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time. Results In this study we have shown that, paradoxically, synonymous site divergence (dS at non-CpG sites is highest in regions of open chromatin, primarily as a result of an increased number of transitions, while the rates of other traditional measures of mutation (intergenic, intronic and ancient repeat divergence as well as SNP density are highest in closed regions of the genome. Analysis of human-chimpanzee divergence across intron-exon boundaries indicates that although genes in relatively open chromatin generally display little selection at their synonymous sites, those in closed regions show markedly lower divergence at their fourfold degenerate sites than in neighbouring introns and intergenic regions. Exclusion of known Exonic Splice Enhancer hexamers has little affect on the divergence observed at fourfold degenerate sites across chromatin categories; however, we show that closed chromatin is enriched with certain classes of ncRNA genes whose RNA secondary structure may be particularly important. Conclusion We conclude that, overall, non-CpG mutation rates are lowest in open regions of the genome and that regions of the genome with a closed chromatin structure have the highest background mutation rate. This might reflect lower rates of DNA damage or enhanced DNA repair processes in regions of open chromatin. Our results also indicate that dS is a poor

  13. CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement

    Institute of Scientific and Technical Information of China (English)

    Ann J Feeney; Jiyoti Verma-Gaur

    2012-01-01

    The CTCF/cohesin complex regulates higher order chromatin structure by creating long-range chromatin loops and by insulating neighboring genes from each other.The lymphocyte antigen receptor loci have large numbers of CTCF/cohesin binding sites,and recent studies demonstrate that the CTCF/cohesin complex plays several important roles in regulating the process of V(D)J recombination at these megabase-sized receptor loci.

  14. Higher Order Spreading Models

    CERN Document Server

    Argyros, S A; Tyros, K

    2012-01-01

    We introduce the higher order spreading models associated to a Banach space $X$. Their definition is based on $\\ff$-sequences $(x_s)_{s\\in\\ff}$ with $\\ff$ a regular thin family and the plegma families. We show that the higher order spreading models of a Banach space $X$ form an increasing transfinite hierarchy $(\\mathcal{SM}_\\xi(X))_{\\xi<\\omega_1}$. Each $\\mathcal{SM}_\\xi (X)$ contains all spreading models generated by $\\ff$-sequences $(x_s)_{s\\in\\ff}$ with order of $\\ff$ equal to $\\xi$. We also provide a study of the fundamental properties of the hierarchy.

  15. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression

    DEFF Research Database (Denmark)

    Almassalha, Luay M; Tiwari, A; Ruhoff, P T;

    2017-01-01

    in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D...... show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating...

  16. Elucidating the higher-order structure of biopolymers by structural probing and mass spectrometry: MS3D

    Science.gov (United States)

    Fabris, Daniele; Yu, Eizadora T.

    2010-01-01

    Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers, but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown substrates or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns, and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures, while highlighting common elements, salient distinctions, and complementary capabilities exhibited by methods employed in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological substrates. PMID:20648672

  17. Higher-Order Hierarchies

    DEFF Research Database (Denmark)

    Ernst, Erik

    2003-01-01

    . Finally, it must be possible to write generic code that works on every hierarchy derived from the hierarchy for which it was written. This paper presents a language design that supports such a notion of higher-order hierarchies. It has been implemented in context of a full-fledged, statically typed...... be possible to create hierarchies incrementally based on existing hierarchies, such that commonalities are expressed via reuse, not duplication. Second, the hierarchies must themselves be organized into hierarchies, such that their relationships are made explicit and can be exploited in a type safe manner...... language....

  18. Structural studies of chromatin and chromosomes. Progress report, March 15--September 15, 1997

    Energy Technology Data Exchange (ETDEWEB)

    Bradbury, E.M.

    1997-11-01

    This study focused on the following: (1) the structure of chromatin and chromosomes by neutron and x-ray scatter and atomic force microscope; (2) the architecture of human sperm and the structure of sperm by atomic force microscopy (AFM); (3) genome-architecture and higher-order structures in human sperm nuclei; and (4) the effects of histone modifications on the structure of nucleosomes by protein DNA crosslinking method.

  19. Higher Order Mode Fibers

    DEFF Research Database (Denmark)

    Israelsen, Stine Møller

    to implement a nonlinear chirp which is a first time demonstration. The results are modelled using coupled mode theory and it is shown that the conversion bandwidth may be increased more than four fold. In the final part of the thesis, imaging as a characterization tool for HOMs is considered. Three different......This PhD thesis considers higher order modes (HOMs) in optical fibers. That includes their excitation and characteristics. Within the last decades, HOMs have been applied both for space multiplexing in optical communications, group velocity dispersion management and sensing among others....... The research presented in this thesis falls in three parts. In the first part, a first time demonstration of the break of the azimuthal symmetry of the Bessel-like LP0X modes is presented. This effect, known as the bowtie effect, causes the mode to have an azimuthal dependence as well as a quasi...

  20. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression

    Science.gov (United States)

    Almassalha, L. M.; Tiwari, A.; Ruhoff, P. T.; Stypula-Cyrus, Y.; Cherkezyan, L.; Matsuda, H.; Dela Cruz, M. A.; Chandler, J. E.; White, C.; Maneval, C.; Subramanian, H.; Szleifer, I.; Roy, H. K.; Backman, V.

    2017-01-01

    Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis. PMID:28117353

  1. The Global Relationship between Chromatin Physical Topology, Fractal Structure, and Gene Expression.

    Science.gov (United States)

    Almassalha, L M; Tiwari, A; Ruhoff, P T; Stypula-Cyrus, Y; Cherkezyan, L; Matsuda, H; Dela Cruz, M A; Chandler, J E; White, C; Maneval, C; Subramanian, H; Szleifer, I; Roy, H K; Backman, V

    2017-01-24

    Most of what we know about gene transcription comes from the view of cells as molecular machines: focusing on the role of molecular modifications to the proteins carrying out transcriptional reactions at a loci-by-loci basis. This view ignores a critical reality: biological reactions do not happen in an empty space, but in a highly complex, interrelated, and dense nanoenvironment that profoundly influences chemical interactions. We explored the relationship between the physical nanoenvironment of chromatin and gene transcription in vitro. We analytically show that changes in the fractal dimension, D, of chromatin correspond to simultaneous increases in chromatin accessibility and compaction heterogeneity. Using these predictions, we demonstrate experimentally that nanoscopic changes to chromatin D within thirty minutes correlate with concomitant enhancement and suppression of transcription. Further, we show that the increased heterogeneity of physical structure of chromatin due to increase in fractal dimension correlates with increased heterogeneity of gene networks. These findings indicate that the higher order folding of chromatin topology may act as a molecular-pathway independent code regulating global patterns of gene expression. Since physical organization of chromatin is frequently altered in oncogenesis, this work provides evidence pairing molecular function to physical structure for processes frequently altered during tumorigenesis.

  2. Investigation of the Factor Structure of the Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV): Exploratory and Higher Order Factor Analyses

    Science.gov (United States)

    Canivez, Gary L.; Watkins, Marley W.

    2010-01-01

    The present study examined the factor structure of the Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV; D. Wechsler, 2008a) standardization sample using exploratory factor analysis, multiple factor extraction criteria, and higher order exploratory factor analysis (J. Schmid & J. M. Leiman, 1957) not included in the WAIS-IV Technical…

  3. Higher order structure in the 3'-minor domain of small subunit ribosomal RNAs from a gram negative bacterium, a gram positive bacterium and a eukaryote

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A

    1983-01-01

    . Several unusual structural features were detected. Multiple G X A pairings in two of the putative helices, which are compatible with phylogenetic sequence comparisons, are strongly supported by the occurrence of cobra venom ribonuclease cuts adjacent to, and in one case between, these pairings. Evidence......An experimental approach was used to determine and compare the highest order structure within the 150 to 200 nucleotides at the 3'-ends of the RNAs from the small ribosomal subunits of Escherichia coli, Bacillus stearothermophilus and Saccharomyces cerevisiae. Chemical reagents were employed...... of additional higher order structure in the renatured free RNA. It can be concluded that a high level of conservation of higher order structure has occurred during the evolution of the gram negative and gram positive eubacteria and the eukaryote in both the double helical regions and the "unstructured" regions...

  4. Impact of chromatin structure on PR signaling

    DEFF Research Database (Denmark)

    Grøntved, Lars; Hager, Gordon L

    2012-01-01

    The progesterone receptor (PR) interacts with chromatin in a highly dynamic manner that requires ongoing chromatin remodeling, interaction with chaparones and activity of the proteasome. Here we discuss dynamic interaction of steroid receptor with chromatin, with special attention not only to PR...

  5. X-ray Crystallographic Structures of Trimers and Higher-Order Oligomeric Assemblies of a Peptide Derived from Aβ17–36

    OpenAIRE

    Spencer, Ryan K.; Li, Hao; Nowick, James S.

    2014-01-01

    A peptide derived from Aβ17–36 crystallizes to form trimers that further associate to form higher-order oligomers. The trimers consist of three highly twisted β-hairpins in a triangular arrangement. Two trimers associate face-to-face in the crystal lattice to form a hexamer; four trimers in a tetrahedral arrangement about a central cavity form a dodecamer. These structures provide a working model for the structures of oligomers associated with neurodegeneration in Alzheimer’s disease.

  6. 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...

  7. 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...

  8. Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

    KAUST Repository

    Chawla, Mohit

    2013-10-10

    The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).

  9. Gain analysis of higher-order-mode amplification in a dielectric-implanted multi-beam traveling wave structure

    Energy Technology Data Exchange (ETDEWEB)

    Gee, Anthony; Shin, Young-Min

    2013-01-01

    A multi-beam traveling wave amplifier designed with an overmoded staggered double grating array was examined by small signal analysis combined with simulation. Eigenmode and S-parameter analyses show that the 2cm long slow wave structure (SWS) has 1-5dB insertion loss over the passband (TM31 mode) with ~28% cold bandwidth. Analytic gain calculation indicates that in the SWS, TM31-mode is amplified with 15–20 dB/beam at 64–84GHz with three elliptical beams of 10kV and 150mA/beam, which was compared with particle-in-cell (PIC) simulations. PIC analysis on the analysis of instability with zero-input driving excitations demonstrated that background noises and non-operating lower order modes are noticeably suppressed by implanting equidistant dielectric absorbers; the overmoded structure only allowed the desired 3rd order mode to propagate in the structure. The designed circuit structure can be widely applied to multi-beam devices for high power RF generation.

  10. Impact of chromatin structures on DNA processing for genomic analyses.

    Directory of Open Access Journals (Sweden)

    Leonid Teytelman

    Full Text Available Chromatin has an impact on recombination, repair, replication, and evolution of DNA. Here we report that chromatin structure also affects laboratory DNA manipulation in ways that distort the results of chromatin immunoprecipitation (ChIP experiments. We initially discovered this effect at the Saccharomyces cerevisiae HMR locus, where we found that silenced chromatin was refractory to shearing, relative to euchromatin. Using input samples from ChIP-Seq studies, we detected a similar bias throughout the heterochromatic portions of the yeast genome. We also observed significant chromatin-related effects at telomeres, protein binding sites, and genes, reflected in the variation of input-Seq coverage. Experimental tests of candidate regions showed that chromatin influenced shearing at some loci, and that chromatin could also lead to enriched or depleted DNA levels in prepared samples, independently of shearing effects. Our results suggested that assays relying on immunoprecipitation of chromatin will be biased by intrinsic differences between regions packaged into different chromatin structures - biases which have been largely ignored to date. These results established the pervasiveness of this bias genome-wide, and suggested that this bias can be used to detect differences in chromatin structures across the genome.

  11. Higher order structure of chromosomes.

    Science.gov (United States)

    Okada, T A; Comings, D E

    1979-04-01

    Isolated Chinese hamster metaphase chromosomes were resuspended in 4 M ammonium acetate and spread on a surface of distilled water or 0.15 to 0.5 M ammonium acetate. The DNA was released in the form of a regular series of rosettes connected by interrossette DNA. The mean length of the rosette DNA was 14 micron, similar to the mean length of 10 micron for chromomere DNA of Drosophila polytene chromosomes. The mean interrosette DNA was 4.2 micron. SDS gel electrophoresis of the chromosomal nonhistone proteins showed them to be very similar to nuclear nonhistone proteins except for the presence of more actin and tubulin. Nuclear matrix proteins were present in the chromosomes and may play a role in forming the rosettes. Evidence that the rosette pattern is artifactual versus the possibility that it represents a real organizational substructure of the chromosomes is reviewed.

  12. Technical decision making with higher order structure data: utilization of differential scanning calorimetry to elucidate critical protein structural changes resulting from oxidation.

    Science.gov (United States)

    Arthur, Kelly K; Dinh, Nikita; Gabrielson, John P

    2015-04-01

    Differential scanning calorimetry (DSC) is a useful tool for monitoring thermal stability of the molecular conformation of proteins. Here, we present an example of the sensitivity of DSC to changes in stability arising from a common chemical degradation pathway, oxidation. This Note is part of a series of industry case studies demonstrating the application of higher order structure data for technical decision making. For this study, six protein products from three structural classes were evaluated at multiple levels of oxidation. For each protein, the melting temperature (Tm ) decreased linearly as a function of oxidation; however, differences in the rate of change in Tm , as well as differences in domain Tm stability were observed across and within structural classes. For one protein, analysis of the impact of oxidation on protein function was also performed. For this protein, DSC was shown to be a leading indicator of decreased antigen binding suggesting a subtle conformation change may be underway that can be detected using DSC prior to any observable impact on product potency. Detectable changes in oxidized methionine by mass spectrometry (MS) occurred at oxidation levels below those with a detectable conformational or functional impact. Therefore, by using MS, DSC, and relative potency methods in concert, the intricate relationship between a primary structural modification, changes in conformational stability, and functional impact can be elucidated.

  13. Telomere Chromatin Condensation Assay (TCCA): a novel approach to study structural telomere integrity.

    Science.gov (United States)

    Gonzalez-Vasconcellos, Iria; Alonso-Rodríguez, Silvia; López-Baltar, Isidoro; Fernández, José Luis

    2015-01-01

    Telomeres, the DNA-protein complexes located at the end of linear eukaryotic chromosomes are essential for genome stability. Improper higher-order chromatin organization at the chromosome ends can give rise to telomeric recombination and genomic instability. We report the development of an assay to quantify differences in the condensation of telomeric chromatin, thereby offering new opportunities to study telomere biology and stability. We have combined a DNA nuclease digestion with a quantitative PCR (qPCR) assay of telomeric DNA, which we term the Telomere Chromatin Condensation Assay (TCCA). By quantifying the relative quantities of telomeric DNA that are progressively digested with the exonuclease Bal 31 the method can discriminate between different levels of telomeric chromatin condensation. The structural chromatin packaging at telomeres shielded against exonuclease digestion delivered an estimate, which we term Chromatin Protection Factor (CPF) that ranged from 1.7 to 2.3 fold greater than that present in unpacked DNA. The CPF was significantly decreased when cell cultures were incubated with the DNA hypomethylating agent 5-azacytidine, demonstrating the ability of the TCCA assay to discriminate between packaging levels of telomeric DNA.

  14. A cross-cultural study of the higher-order structures underlying personality disorders in French-speaking Africa and Switzerland.

    Science.gov (United States)

    Rigozzi, Christine; Rossier, Jérôme; Dahourou, Donatien; Adjahouisso, Marcel; Ah-Kion, Jennifer; Amoussou-Yeye, Denis; Barry, Oumar; Bhowon, Uma; Bouatta, Cherifa; Cissé, Daouda Dougoumalé; Mbodji, Mamadou; Meyer de Stadelhofen, Franz; Minga, David Minga; Tseung, Caroline Ng; Ondongo, François; Romdhane, Mohamed Nouri; Sfayhi, Nicole; Tsokini, Dieudonné; Verardi, Sabrina

    2009-04-01

    Most studies about the higher-order dimensions to be considered in order to parsimoniously describe Personality Disorders (PDs) have identified between two and four factors but there is still no consensus about their exact number. In this context, the cultural stability of these structures might be a criterion to be considered. The aim of this study was to identify stable higher-order structures of PD traits in a French-speaking African and Swiss sample (N = 2,711). All subjects completed the IPDE screening questionnaire. Using Everett's criterion and conducting a series of principal component analyses, a cross-culturally stable two- and four-factor structure were identified, associated with a total congruence coefficient of .98 and .94, respectively, after Procrustes rotation. Moreover, these two structures were also highly replicable across the four African regions considered, North Africa, West Africa, Central Africa, and Mauritius, with a mean total congruence coefficient of .97 and .87, respectively. The four-factor structure presented the advantage of being similar to Livesely's four components and of describing the ten PDs more accurately.

  15. Higher-order organization of complex networks.

    Science.gov (United States)

    Benson, Austin R; Gleich, David F; Leskovec, Jure

    2016-07-08

    Networks are a fundamental tool for understanding and modeling complex systems in physics, biology, neuroscience, engineering, and social science. Many networks are known to exhibit rich, lower-order connectivity patterns that can be captured at the level of individual nodes and edges. However, higher-order organization of complex networks--at the level of small network subgraphs--remains largely unknown. Here, we develop a generalized framework for clustering networks on the basis of higher-order connectivity patterns. This framework provides mathematical guarantees on the optimality of obtained clusters and scales to networks with billions of edges. The framework reveals higher-order organization in a number of networks, including information propagation units in neuronal networks and hub structure in transportation networks. Results show that networks exhibit rich higher-order organizational structures that are exposed by clustering based on higher-order connectivity patterns.

  16. Higher-order risk vulnerability

    OpenAIRE

    Huang,Xiaoping; Stapleton, Richard Christopher

    2017-01-01

    We add an independent unfair background risk to higher-order risk-taking models in the current literature and examine its interaction with the main risk under consideration. Parallel to the well-known concept of risk vulnerability, which is defined by Gollier and Pratt (Econometrica 64:1109–1123, 1996), an agent is said to have a type of higher-order risk vulnerability if adding an independent unfair background risk to wealth raises his level of this type of higher-order risk aversion. We der...

  17. Effect of DNA groove binder distamycin A upon chromatin structure.

    Directory of Open Access Journals (Sweden)

    Parijat Majumder

    Full Text Available BACKGROUND: Distamycin A is a prototype minor groove binder, which binds to B-form DNA, preferentially at A/T rich sites. Extensive work in the past few decades has characterized the binding at the level of double stranded DNA. However, effect of the same on physiological DNA, i.e. DNA complexed in chromatin, has not been well studied. Here we elucidate from a structural perspective, the interaction of distamycin with soluble chromatin, isolated from Sprague-Dawley rat. METHODOLOGY/PRINCIPAL FINDINGS: Chromatin is a hierarchical assemblage of DNA and protein. Therefore, in order to characterize the interaction of the same with distamycin, we have classified the system into various levels, according to the requirements of the method adopted, and the information to be obtained. Isothermal titration calorimetry has been employed to characterize the binding at the levels of chromatin, chromatosome and chromosomal DNA. Thermodynamic parameters obtained thereof, identify enthalpy as the driving force for the association, with comparable binding affinity and free energy for chromatin and chromosomal DNA. Reaction enthalpies at different temperatures were utilized to evaluate the change in specific heat capacity (ΔCp, which, in turn, indicated a possible binding associated structural change. Ligand induced structural alterations have been monitored by two complementary methods--dynamic light scattering, and transmission electron microscopy. They indicate compaction of chromatin. Using transmission electron microscopy, we have visualized the effect of distamycin upon chromatin architecture at di- and trinucleosome levels. Our results elucidate the simultaneous involvement of linker bending and internucleosomal angle contraction in compaction process induced by distamycin. CONCLUSIONS/SIGNIFICANCE: We summarize here, for the first time, the thermodynamic parameters for the interaction of distamycin with soluble chromatin, and elucidate its effect on

  18. HOTCFGM-2D: A Coupled Higher-Order Theory for Cylindrical Structural Components with Bi-Directionally Components with Bi-Directionally Graded Microstructures

    Science.gov (United States)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    2000-01-01

    The objective of this two-year project was to develop and deliver to the NASA-Glenn Research Center a two-dimensional higher-order theory, and related computer codes, for the analysis and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, brisk blades). To satisfy this objective, two-dimensional version of the higher-order theory, HOTCFGM-2D, and four computer codes based on this theory, for the analysis and design of structural components functionally graded in the radial and circumferential directions were developed in the cylindrical coordinate system r-Theta-z. This version of the higher-order theory is a significant generalization of the one-dimensional theory, HOTCFGM-1D, developed during the FY97 for the analysis and design of cylindrical structural components with radially graded microstructures. The generalized theory is applicable to thin multi-phased composite shells/cylinders subjected to steady-state thermomechanical, transient thermal and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial direction, and arbitrarily distributed in the radial and circumferential direction, thereby allowing functional grading of the internal reinforcement in the r-Theta plane. The four computer codes fgmc3dq.cylindrical.f, fgmp3dq.cylindrical.f, fgmgvips3dq.cylindrical.f, and fgmc3dq.cylindrical.transient.f are research-oriented codes for investigating the effect of functionally graded architectures, as well as the properties of the multi-phase reinforcement, in thin shells subjected to thermomechanical and inertial loading, on the internal temperature, stress and (inelastic) strain fields. The reinforcement distribution in the radial and circumferential directions is specified by the user. The thermal

  19. Sperm chromatin structure and male fertility: biological and clinical aspects

    Institute of Scientific and Technical Information of China (English)

    J. Erenpreiss; M. Spano; J. Erenpreisa; M. Bungum; A. Giwercman

    2006-01-01

    Aim: Sperm chromatin/DNA integrity is essential for the accurate transmission of paternal genetic information, and normal sperm chromatin structure is important for sperm fertilizing ability. The routine examination of semen, which includes sperm concentration, motility and morphology, does not identify defects in sperm chromatin structure. The origin of sperm DNA damage and a variety of methods for its assessment are described. Evaluation of sperm DNA damage appears to be a useful tool for assessing male fertility potential both in vivo and in vitro. The possible impact of sperm DNA defects on the offspring is also discussed.

  20. Investigation of the factor structure of the Wechsler Adult Intelligence Scale--Fourth Edition (WAIS-IV): exploratory and higher order factor analyses.

    Science.gov (United States)

    Canivez, Gary L; Watkins, Marley W

    2010-12-01

    The present study examined the factor structure of the Wechsler Adult Intelligence Scale--Fourth Edition (WAIS-IV; D. Wechsler, 2008a) standardization sample using exploratory factor analysis, multiple factor extraction criteria, and higher order exploratory factor analysis (J. Schmid & J. M. Leiman, 1957) not included in the WAIS-IV Technical and Interpretation Manual (D. Wechsler, 2008b). Results indicated that the WAIS-IV subtests were properly associated with the theoretically proposed first-order factors, but all but one factor-extraction criterion recommended extraction of one or two factors. Hierarchical exploratory analyses with the Schmid and Leiman procedure found that the second-order g factor accounted for large portions of total and common variance, whereas the four first-order factors accounted for small portions of total and common variance. It was concluded that the WAIS-IV provides strong measurement of general intelligence, and clinical interpretation should be primarily at that level.

  1. Chromatin structure and DNA damage repair

    Directory of Open Access Journals (Sweden)

    Dinant Christoffel

    2008-11-01

    Full Text Available Abstract The integrity of the genome is continuously challenged by both endogenous and exogenous DNA damaging agents. These damaging agents can induce a wide variety of lesions in the DNA, such as double strand breaks, single strand breaks, oxidative lesions and pyrimidine dimers. The cell has evolved intricate DNA damage response mechanisms to counteract the genotoxic effects of these lesions. The two main features of the DNA damage response mechanisms are cell-cycle checkpoint activation and, at the heart of the response, DNA repair. For both damage signalling and repair, chromatin remodelling is most likely a prerequisite. Here, we discuss current knowledge on chromatin remodelling with respect to the cellular response to DNA damage, with emphasis on the response to lesions resolved by nucleotide excision repair. We will discuss the role of histone modifications as well as their displacement or exchange in nucleotide excision repair and make a comparison with their requirement in transcription and double strand break repair.

  2. Control of chromatin structure by long noncoding RNA

    Science.gov (United States)

    Böhmdorfer, Gudrun; Wierzbicki, Andrzej T.

    2015-01-01

    Long noncoding RNA (lncRNA) is a pivotal factor regulating various aspects of genome activity. Genome regulation via DNA methylation and posttranslational histone modifications is a well-documented function of lncRNA in plants, fungi, and animals. Here, we summarize evidence showing that lncRNA also controls chromatin structure including nucleosome positioning and chromosome looping. We focus on data from plant experimental systems, discussed in the context of other eukaryotes. We explain the mechanisms of lncRNA-controlled chromatin remodeling and the implications of the functional interplay between noncoding transcription and several different chromatin remodelers. We propose that the unique properties of RNA make it suitable for controlling chromatin modifications and structure. PMID:26410408

  3. The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes.

    Science.gov (United States)

    Silva-Santiago, Evangelina; Pardo, Juan Pablo; Hernández-Muñoz, Rolando; Aranda-Anzaldo, Armando

    2017-01-15

    During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific.

  4. Nonlocal higher order evolution equations

    KAUST Repository

    Rossi, Julio D.

    2010-06-01

    In this article, we study the asymptotic behaviour of solutions to the nonlocal operator ut(x, t)1/4(-1)n-1 (J*Id -1)n (u(x, t)), x ∈ ℝN, which is the nonlocal analogous to the higher order local evolution equation vt(-1)n-1(Δ)nv. We prove that the solutions of the nonlocal problem converge to the solution of the higher order problem with the right-hand side given by powers of the Laplacian when the kernel J is rescaled in an appropriate way. Moreover, we prove that solutions to both equations have the same asymptotic decay rate as t goes to infinity. © 2010 Taylor & Francis.

  5. Glycoforms of Immunoglobulin G Based Biopharmaceuticals Are Differentially Cleaved by Trypsin Due to the Glycoform Influence on Higher-Order Structure.

    Science.gov (United States)

    Falck, David; Jansen, Bas C; Plomp, Rosina; Reusch, Dietmar; Haberger, Markus; Wuhrer, Manfred

    2015-09-01

    It has been reported that glycosylation can influence the proteolytic cleavage of proteins. A thorough investigation of this phenomenon was conducted for the serine protease trypsin, which is essential in many proteomics workflows. Monoclonal and polyclonal immunoglobulin G biopharmaceuticals were employed as model substances, which are highly relevant for the bioanalytical applications. Relative quantitation of glycopeptides derived from the conserved Fc-glycosylation site allowed resolution of biases on the level of individual glycan compositions. As a result, a strong preferential digestion of high mannose, hybrid, alpha2-3-sialylated and bisected glycoforms was observed over the most abundant neutral, fucosylated glycoforms. Interestingly, this bias was, to a large extent, dependent on the intact higher order structure of the antibodies and, consequently, was drastically reduced in denatured versus intact antibodies. In addition, a cleavage protocol with acidic denaturation was tested, which featured reduced hands-on time and toxicity while showing highly comparable results to a published denaturation, reduction, and alkylation based protocol.

  6. Organization into Higher Ordered Ring Structures Counteracts Membrane Binding of IM30, a Protein Associated with Inner Membranes in Chloroplasts and Cyanobacteria.

    Science.gov (United States)

    Heidrich, Jennifer; Wulf, Verena; Hennig, Raoul; Saur, Michael; Markl, Jürgen; Sönnichsen, Carsten; Schneider, Dirk

    2016-07-15

    The IM30 (inner membrane-associated protein of 30 kDa), also known as the Vipp1 (vesicle-inducing protein in plastids 1), has a crucial role in thylakoid membrane biogenesis and maintenance. Recent results suggest that the protein binds peripherally to membranes containing negatively charged lipids. However, although IM30 monomers interact and assemble into large oligomeric ring complexes with different numbers of monomers, it is still an open question whether ring formation is crucial for membrane interaction. Here we show that binding of IM30 rings to negatively charged phosphatidylglycerol membrane surfaces results in a higher ordered membrane state, both in the head group and in the inner core region of the lipid bilayer. Furthermore, by using gold nanorods covered with phosphatidylglycerol layers and single particle spectroscopy, we show that not only IM30 rings but also lower oligomeric IM30 structures interact with membranes, although with higher affinity. Thus, ring formation is not crucial for, and even counteracts, membrane interaction of IM30.

  7. Dynamic structures of intact chicken erythrocyte chromatins as studied by 1H-31P cross-polarization NMR.

    Science.gov (United States)

    Akutsu, H; Nishimoto, S; Kyogoku, Y

    1994-08-01

    The dynamic properties of DNA in intact chicken erythrocyte cells, nuclei, nondigested chromatins, digested soluble chromatins, H1, H5-depleted soluble chromatins and nucleosome cores were investigated by means of single-pulse and 1H-31P cross-polarization NMR. The temperature dependence of the phosphorus chemical shift anisotropy was identical for the former three in the presence of 3 mM MgCl2, suggesting that the local higher order structure is identical for these chromatins. The intrinsic phosphorus chemical shift anisotropy of the nucleosome cores was -159 ppm. The chemical shift anisotropy of DNA in the chromatins can be further averaged by the motion of the linker DNA. The spin-lattice relaxation time in the rotating frame of the proton spins (T1p) of the nondigested chromatins was measured at various locking fields. The result was analyzed on the assumption of the isotropic motion to get a rough value of the correlation time of the motion efficient for the relaxation, which was eventually ascribed to the segmental motion of the linker DNA with restricted amplitude. The 30 nm filament structure induced by NaCl was shown to be dynamically different from that induced by MgCl2. Side-by-side compaction of 30-nm filaments was suggested to be induced in the MgCl2 concentration range higher than 0.3 mM. Biological significance of the dynamic structure was discussed in connection with the results obtained.

  8. Higher-Order Program Generation

    DEFF Research Database (Denmark)

    Rhiger, Morten

    to the disproportion between general programs that can be executed in several contexts and their specialized counterparts that can be executed efficiently. However, stand-alone partial evaluation is usually too costly when a program must be specialized at run time. We introduce a collection of byte-code combinators...... for OCaml, a dialect of ML, that provides run-time code generation for OCaml programs. We apply these byte-code combinators in semantics-directed compilation for an imperative language and in run-time specialization using type-directed partial evaluation. Finally, we present an approach to compiling goal......This dissertation addresses the challenges of embedding programming languages, specializing generic programs to specific parameters, and generating specialized instances of programs directly as executable code. Our main tools are higher-order programming techniques and automatic program generation...

  9. Chromatin Structure of Epstein-Barr Virus Latent Episomes.

    Science.gov (United States)

    Lieberman, Paul M

    2015-01-01

    EBV latent infection is characterized by a highly restricted pattern of viral gene expression. EBV can establish latent infections in multiple different tissue types with remarkable variation and plasticity in viral transcription and replication. During latency, the viral genome persists as a multi-copy episome, a non-integrated-closed circular DNA with nucleosome structure similar to cellular chromosomes. Chromatin assembly and histone modifications contribute to the regulation of viral gene expression, DNA replication, and episome persistence during latency. This review focuses on how EBV latency is regulated by chromatin and its associated processes.

  10. Chromatin Structure in Cell Differentiation, Aging and Cancer

    NARCIS (Netherlands)

    S. Kheradmand Kia (Sima)

    2009-01-01

    textabstractChromatin is the structure that the eukaryotic genome is packaged into, allowing over a metre of DNA to fit into the small volume of the nucleus. It is composed of DNA and proteins, most of which are histones. This DNA-protein complex is the template for a number of essential cell proces

  11. Analogy, higher order thinking, and education.

    Science.gov (United States)

    Richland, Lindsey Engle; Simms, Nina

    2015-01-01

    Analogical reasoning, the ability to understand phenomena as systems of structured relationships that can be aligned, compared, and mapped together, plays a fundamental role in the technology rich, increasingly globalized educational climate of the 21st century. Flexible, conceptual thinking is prioritized in this view of education, and schools are emphasizing 'higher order thinking', rather than memorization of a cannon of key topics. The lack of a cognitively grounded definition for higher order thinking, however, has led to a field of research and practice with little coherence across domains or connection to the large body of cognitive science research on thinking. We review literature on analogy and disciplinary higher order thinking to propose that relational reasoning can be productively considered the cognitive underpinning of higher order thinking. We highlight the utility of this framework for developing insights into practice through a review of mathematics, science, and history educational contexts. In these disciplines, analogy is essential to developing expert-like disciplinary knowledge in which concepts are understood to be systems of relationships that can be connected and flexibly manipulated. At the same time, analogies in education require explicit support to ensure that learners notice the relevance of relational thinking, have adequate processing resources available to mentally hold and manipulate relations, and are able to recognize both the similarities and differences when drawing analogies between systems of relationships.

  12. Analysis of chromatin structure at meiotic DSB sites in yeasts.

    Science.gov (United States)

    Hirota, Kouji; Fukuda, Tomoyuki; Yamada, Takatomi; Ohta, Kunihiro

    2009-01-01

    One of the major features of meiosis is a high frequency of homologous recombination that not only confers genetic diversity to a successive generation but also ensures proper segregation of chromosomes. Meiotic recombination is initiated by DNA double-strand breaks that require many proteins including the catalytic core, Spo11. In this regard, like transcription and repair, etc., recombination is hindered by a compacted chromatin structure because trans-acting factors cannot easily access the DNA. Such inhibitory effects must be alleviated prior to recombination initiation. Indeed, a number of groups showed that chromatin around recombination hotspots is less condensed, by using nucleases as a probe to assess local DNA accessibility. Here we describe a method to analyze chromatin structure of a recombination hotspot in the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. This method, combining micrococcal nuclease (MNase) digestion ofchromatin DNA and subsequent Southern blotting, is expected to provide information as to chromatin context around a hotspot. Moreover, by virtue of MNase preferentially targeting linker DNA, positions of several nucleosomes surrounding a hotspot can also be determined. Our protocol is a very powerful way to analyze several-kb regions of interest and can be applied to other purposes.

  13. HDAC up-regulation in early colon field carcinogenesis is involved in cell tumorigenicity through regulation of chromatin structure.

    Directory of Open Access Journals (Sweden)

    Yolanda Stypula-Cyrus

    Full Text Available Normal cell function is dependent on the proper maintenance of chromatin structure. Regulation of chromatin structure is controlled by histone modifications that directly influence chromatin architecture and genome function. Specifically, the histone deacetylase (HDAC family of proteins modulate chromatin compaction and are commonly dysregulated in many tumors, including colorectal cancer (CRC. However, the role of HDAC proteins in early colorectal carcinogenesis has not been previously reported. We found HDAC1, HDAC2, HDAC3, HDAC5, and HDAC7 all to be up-regulated in the field of human CRC. Furthermore, we observed that HDAC2 up-regulation is one of the earliest events in CRC carcinogenesis and observed this in human field carcinogenesis, the azoxymethane-treated rat model, and in more aggressive colon cancer cell lines. The universality of HDAC2 up-regulation suggests that HDAC2 up-regulation is a novel and important early event in CRC, which may serve as a biomarker. HDAC inhibitors (HDACIs interfere with tumorigenic HDAC activity; however, the precise mechanisms involved in this process remain to be elucidated. We confirmed that HDAC inhibition by valproic acid (VPA targeted the more aggressive cell line. Using nuclease digestion assays and transmission electron microscopy imaging, we observed that VPA treatment induced greater changes in chromatin structure in the more aggressive cell line. Furthermore, we used the novel imaging technique partial wave spectroscopy (PWS to quantify nanoscale alterations in chromatin. We noted that the PWS results are consistent with the biological assays, indicating a greater effect of VPA treatment in the more aggressive cell type. Together, these results demonstrate the importance of HDAC activity in early carcinogenic events and the unique role of higher-order chromatin structure in determining cell tumorigenicity.

  14. HDAC up-regulation in early colon field carcinogenesis is involved in cell tumorigenicity through regulation of chromatin structure.

    Science.gov (United States)

    Stypula-Cyrus, Yolanda; Damania, Dhwanil; Kunte, Dhananjay P; Cruz, Mart Dela; Subramanian, Hariharan; Roy, Hemant K; Backman, Vadim

    2013-01-01

    Normal cell function is dependent on the proper maintenance of chromatin structure. Regulation of chromatin structure is controlled by histone modifications that directly influence chromatin architecture and genome function. Specifically, the histone deacetylase (HDAC) family of proteins modulate chromatin compaction and are commonly dysregulated in many tumors, including colorectal cancer (CRC). However, the role of HDAC proteins in early colorectal carcinogenesis has not been previously reported. We found HDAC1, HDAC2, HDAC3, HDAC5, and HDAC7 all to be up-regulated in the field of human CRC. Furthermore, we observed that HDAC2 up-regulation is one of the earliest events in CRC carcinogenesis and observed this in human field carcinogenesis, the azoxymethane-treated rat model, and in more aggressive colon cancer cell lines. The universality of HDAC2 up-regulation suggests that HDAC2 up-regulation is a novel and important early event in CRC, which may serve as a biomarker. HDAC inhibitors (HDACIs) interfere with tumorigenic HDAC activity; however, the precise mechanisms involved in this process remain to be elucidated. We confirmed that HDAC inhibition by valproic acid (VPA) targeted the more aggressive cell line. Using nuclease digestion assays and transmission electron microscopy imaging, we observed that VPA treatment induced greater changes in chromatin structure in the more aggressive cell line. Furthermore, we used the novel imaging technique partial wave spectroscopy (PWS) to quantify nanoscale alterations in chromatin. We noted that the PWS results are consistent with the biological assays, indicating a greater effect of VPA treatment in the more aggressive cell type. Together, these results demonstrate the importance of HDAC activity in early carcinogenic events and the unique role of higher-order chromatin structure in determining cell tumorigenicity.

  15. Regulation of chromatin structure by poly(ADP-ribosylation

    Directory of Open Access Journals (Sweden)

    Sascha eBeneke

    2012-09-01

    Full Text Available The interaction of DNA with proteins in the context of chromatin has to be tightly regulated to achieve so different tasks as packaging, transcription, replication and repair. The very rapid and transient post-translational modification of proteins by poly(ADP-ribose has been shown to take part in all four. Originally identified as immediate cellular answer to a variety of genotoxic stresses, already early data indicated the ability of this highly charged nucleic acid-like polymer to modulate nucleosome structure, the basic unit of chromatin. At the same time the enzyme responsible for synthesizing poly(ADP-ribose, the zinc-finger protein poly(ADP-ribose polymerase-1 (PARP1, was shown to control transcription initiation as basic factor TFIIC within the RNA-polymerase II machinery. Later research focused more on PARP-mediated regulation of DNA repair and cell death, but in the last few years, transcription as well as chromatin modulation has re-appeared on the scene. This review will discuss the impact of PARP1 on transcription and transcription factors, its implication in chromatin remodeling for DNA repair and probably also replication, and its role in controlling epigenetic events such as DNA methylation and the functionality of the insulator protein CCCTC-binding factor.

  16. Light scattering measurements supporting helical structures for chromatin in solution.

    Science.gov (United States)

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model.

  17. Repression and activation by multiprotein complexes that alter chromatin structure.

    Science.gov (United States)

    Kingston, R E; Bunker, C A; Imbalzano, A N

    1996-04-15

    Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.

  18. SU(3) Polyakov Linear $\\sigma$-Model in Magnetic Field: Thermodynamics, Higher-Order Moments, Chiral Phase Structure and Meson Masses

    CERN Document Server

    Tawfik, Abdel Nasser

    2015-01-01

    Effects of external magnetic field on various properties of the quantum chromodynamics under extreme conditions of temperature and density have been analysed. To this end, we use SU(3) Polyakov linear sigma-model and assume that the external magnetic field eB adds some restrictions to the quarks energy due to the existence of free charges in the plasma phase. In doing this, we apply the Landau theory of quantization. This requires an additional temperature to drive the system through the chiral phase-transition. Accordingly, the dependence of the critical temperature of chiral and confinement phase-transitions on the magnetic field is characterized. Based on this, we have studied the thermal evolution of thermodynamic quantities and the first four higher-order moment of particle multiplicity. Having all these calculations, we have studied the effects of magnetic field on chiral phase-transition. We found that both critical temperature T_c and critical chemical potential increase with increasing the magnetic f...

  19. SU(3) Polyakov linear-σ model in magnetic fields: Thermodynamics, higher-order moments, chiral phase structure, and meson masses

    Science.gov (United States)

    Tawfik, Abdel Nasser; Magdy, Niseem

    2015-01-01

    Effects of an external magnetic field on various properties of quantum chromodynamics (QCD) matter under extreme conditions of temperature and density (chemical potential) have been analyzed. To this end, we use SU(3) Polyakov linear-σ model and assume that the external magnetic field (e B ) adds some restrictions to the quarks' energy due to the existence of free charges in the plasma phase. In doing this, we apply the Landau theory of quantization, which assumes that the cyclotron orbits of charged particles in a magnetic field should be quantized. This requires an additional temperature to drive the system through the chiral phase transition. Accordingly, the dependence of the critical temperature of chiral and confinement phase transitions on the magnetic field is characterized. Based on this, we have studied the thermal evolution of thermodynamic quantities (energy density and trace anomaly) and the first four higher-order moment of particle multiplicity. Having all these calculations, we have studied the effects of the magnetic field on the chiral phase transition. We found that both critical temperature Tc and critical chemical potential increase with increasing magnetic field, e B . Last but not least, the magnetic effects of the thermal evolution of four scalar and four pseudoscalar meson states are studied. We concluded that the meson masses decrease as the temperature increases up to Tc. Then, the vacuum effect becomes dominant and rapidly increases with the temperature T . At low T , the scalar meson masses normalized to the lowest Matsubara frequency rapidly decrease as T increases. Then, starting from Tc, we find that the thermal dependence almost vanishes. Furthermore, the meson masses increase with increasing magnetic field. This gives a characteristic phase diagram of T vs external magnetic field e B . At high T , we find that the masses of almost all meson states become temperature independent. It is worthwhile to highlight that the various meson

  20. Biphasic Chromatin Structure and FISH Signals Reflect Intranuclear Order

    Directory of Open Access Journals (Sweden)

    Jyoti P. Chaudhuri

    2005-01-01

    Full Text Available Background and Aim: One of the two parental allelic genes may selectively be expressed, regulated by imprinting, X-inactivation or by other less known mechanisms. This study aims to reflect on such genetic mechanisms. Materials and Methods: Slides from short term cultures or direct smears of blood, bone marrow and amniotic fluids were hybridized with FISH probes singly, combined or sequentially. Two to three hundred cells were examined from each preparation. Results and Aignificance: A small number of cells (up to about 5%, more frequent in leukemia cases, showed the twin features: (1 nuclei with biphasic chromatin, one part decondensed and the other condensed; and (2 homologous FISH signals distributed equitably in those two regions. The biphasic chromatin structure with equitable distribution of the homologous FISH signals may correspond to the two sets of chromosomes, supporting observations on ploidywise intranuclear order. The decondensed chromatin may relate to enhanced transcriptions or advanced replications. Conclusions: Transcriptions of only one of the two parental genomes cause allelic exclusion. Genomes may switch with alternating monoallelic expression of biallelic genes as an efficient genetic mechanism. If genomes fail to switch, allelic exclusion may lead to malignancy. Similarly, a genome-wide monoallelic replication may tilt the balance of heterozygosity resulting in aneusomy, initiating early events in malignant transformation and in predicting cancer mortality.

  1. Chromatin structure and ATRX function in mouse oocytes.

    Science.gov (United States)

    De La Fuente, Rabindranath; Baumann, Claudia; Viveiros, Maria M

    2012-01-01

    Differentiation of chromatin structure and function during oogenesis is essential to confer the mammalian oocyte with meiotic and developmental potential. Errors in chromosome segregation during female meiosis and subsequent transmission of an abnormal chromosome complement (aneuploidy) to the early conceptus are one of the leading causes of pregnancy loss in women. The chromatin remodeling protein ATRX (α-thalassemia mental retardation X-linked) has recently emerged as a critical factor involved in heterochromatin formation at mammalian centromeres during meiosis. In mammalian oocytes, ATRX binds to centromeric heterochromatin domains where it is required for accurate chromosome segregation. Loss of ATRX function induces abnormal meiotic chromosome morphology, reduces histone H3 phosphorylation, and promotes a high incidence of aneuploidy associated with severely reduced fertility. The presence of centromeric breaks during the transition to the first mitosis in the early embryo indicates that the role of ATRX in chromosome segregation is mediated through an epigenetic mechanism involving the maintenance of chromatin modifications associated with pericentric heterochromatin (PCH) formation and chromosome condensation. This is consistent with the existence of a potential molecular link between centromeric and PCH in the epigenetic control of centromere function and maintenance of chromosome stability in mammalian oocytes. Dissecting the molecular mechanisms of ATRX function during meiosis will have important clinical implications towards uncovering the epigenetic factors contributing to the onset of aneuploidy in the human oocyte.

  2. Evaluation of sperm chromatin structure in boar semen

    Directory of Open Access Journals (Sweden)

    Banaszewska Dorota

    2015-06-01

    Full Text Available This study was an attempt to evaluate sperm chromatin structure in the semen of insemination boars. Preparations of semen were stained with acridine orange, aniline blue, and chromomycin A3. Abnormal protamination occurred more frequently in young individuals whose sexual development was not yet complete, but may also be an individual trait. This possibility is important to factor into the decision regarding further exploitation of insemination boars. Thus a precise assessment of abnormalities in the protamination process would seem to be expedient as a tool supplementing morphological and molecular evaluation of semen. Disruptions in nucleoprotein structure can be treated as indicators of the biological value of sperm cells.

  3. Higher order mode optical fiber Raman amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten; Friis, Søren Michael Mørk; Usuga Castaneda, Mario A.;

    2016-01-01

    We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations.......We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations....

  4. Challenges in higher order mode Raman amplifiers

    DEFF Research Database (Denmark)

    Rottwitt, Karsten; Nielsen, Kristian; Friis, Søren Michael Mørk;

    2015-01-01

    A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed......A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed...

  5. Higher order resonances in dynamical systems

    CERN Document Server

    Contopoulos, George

    1978-01-01

    It is shown that the appearance of higher order resonances (that produce higher order islands on a surface of section), is not an indication of non-integrability. Examples are given and a method is described for constructing integrable Hamiltonians with higher order resonances. (11 refs).

  6. Higher-order structure in the 3'-terminal domain VI of the 23 S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus

    DEFF Research Database (Denmark)

    Garrett, R A; Christensen, A; Douthwaite, S

    1984-01-01

    subdomains. The 5' subdomain has been conserved during evolution and appears to be functionally important for the binding of the EF-1 X GTP X aminoacyl-tRNA complex in eukaryotes. The 3' subdomain has diverged widely between eubacteria and eukaryotes, and has produced the 4.5 S RNA in the chloroplast...... ribonuclease from Naja naja oxiana, and the relatively unstructured and accessible sequences were detected with the single-strand-specific ribonucleases A, T1 and T2. The data enabled the three secondary structural models, proposed for the E. coli 23 S RNAs, to be examined critically and it was concluded...

  7. Two's company, three (or more) is a simplex : Algebraic-topological tools for understanding higher-order structure in neural data.

    Science.gov (United States)

    Giusti, Chad; Ghrist, Robert; Bassett, Danielle S

    2016-08-01

    The language of graph theory, or network science, has proven to be an exceptional tool for addressing myriad problems in neuroscience. Yet, the use of networks is predicated on a critical simplifying assumption: that the quintessential unit of interest in a brain is a dyad - two nodes (neurons or brain regions) connected by an edge. While rarely mentioned, this fundamental assumption inherently limits the types of neural structure and function that graphs can be used to model. Here, we describe a generalization of graphs that overcomes these limitations, thereby offering a broad range of new possibilities in terms of modeling and measuring neural phenomena. Specifically, we explore the use of simplicial complexes: a structure developed in the field of mathematics known as algebraic topology, of increasing applicability to real data due to a rapidly growing computational toolset. We review the underlying mathematical formalism as well as the budding literature applying simplicial complexes to neural data, from electrophysiological recordings in animal models to hemodynamic fluctuations in humans. Based on the exceptional flexibility of the tools and recent ground-breaking insights into neural function, we posit that this framework has the potential to eclipse graph theory in unraveling the fundamental mysteries of cognition.

  8. X波段加速管中高阶模电场分布的测试%Higher Order Mode Measurements in a XBand Accelerating Structure

    Institute of Scientific and Technical Information of China (English)

    肖利苓; 梁宇中; 童德春; 张化一

    2001-01-01

    介绍了一种用于测试X波段加速管中高阶模电场分布的笼子式微扰体的研制与标定. 该微型扰动体通过专门设计加工的固定装置,在尼龙线表面平行沉积溅射数根金属丝膜制成. 利用一标准圆柱腔,对笼子式扰动体的扰动因子进行了定标,证实金属丝笼子式扰动体与同外形尺寸的金属圆筒相比,具有高分辨率、高灵敏度的优点. 采用笼子式扰动体测试了一根长30cm的X波段加速管中TM110模的纵向电场分布.%A metallic cage made by sputtering silver film onto a thin nylon thread through a specially designed fixture is used as perturbing object to measure the higher modes in a Xband accelerating structure. The fabrication and calibration of the cage are described in this paper. It is found that this type of perturbation object has the advantages of high sensitivity and high resolution. Using the cage as bead, the longitudinal electric fields of TM110 mode in a Xband 30cm structure are obtained with bead pull measurements.

  9. RNA is an integral component of chromatin that contributes to its structural organization.

    Directory of Open Access Journals (Sweden)

    Antonio Rodríguez-Campos

    Full Text Available Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA(- and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with alpha-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.

  10. Focus and Higher-Order Unification

    CERN Document Server

    Gardent, C; Gardent, Claire; Kohlhase, Michael

    1996-01-01

    Pulman has shown that Higher--Order Unification (HOU) can be used to model the interpretation of focus. In this paper, we extend the unification--based approach to cases which are often seen as a test--bed for focus theory: utterances with multiple focus operators and second occurrence expressions. We then show that the resulting analysis favourably compares with two prominent theories of focus (namely, Rooth's Alternative Semantics and Krifka's Structured Meanings theory) in that it correctly generates interpretations which these alternative theories cannot yield. Finally, we discuss the formal properties of the approach and argue that even though HOU need not terminate, for the class of unification--problems dealt with in this paper, HOU avoids this shortcoming and is in fact computationally tractable.

  11. Higher order mechanics on graded bundles

    Science.gov (United States)

    Bruce, Andrew James; Grabowska, Katarzyna; Grabowski, Janusz

    2015-05-01

    In this paper we develop a geometric approach to higher order mechanics on graded bundles in both, the Lagrangian and Hamiltonian formalism, via the recently discovered weighted algebroids. We present the corresponding Tulczyjew triple for this higher order situation and derive in this framework the phase equations from an arbitrary (also singular) Lagrangian or Hamiltonian, as well as the Euler-Lagrange equations. As important examples, we geometrically derive the classical higher order Euler-Lagrange equations and analogous reduced equations for invariant higher order Lagrangians on Lie groupoids.

  12. The structure of the core NuRD repression complex provides insights into its interaction with chromatin.

    Science.gov (United States)

    Millard, Christopher J; Varma, Niranjan; Saleh, Almutasem; Morris, Kyle; Watson, Peter J; Bottrill, Andrew R; Fairall, Louise; Smith, Corinne J; Schwabe, John W R

    2016-04-21

    The NuRD complex is a multi-protein transcriptional corepressor that couples histone deacetylase and ATP-dependent chromatin remodelling activities. The complex regulates the higher-order structure of chromatin, and has important roles in the regulation of gene expression, DNA damage repair and cell differentiation. HDACs 1 and 2 are recruited by the MTA1 corepressor to form the catalytic core of the complex. The histone chaperone protein RBBP4, has previously been shown to bind to the carboxy-terminal tail of MTA1. We show that MTA1 recruits a second copy of RBBP4. The crystal structure reveals an extensive interface between MTA1 and RBBP4. An EM structure, supported by SAXS and crosslinking, reveals the architecture of the dimeric HDAC1:MTA1:RBBP4 assembly which forms the core of the NuRD complex. We find evidence that in this complex RBBP4 mediates interaction with histone H3 tails, but not histone H4, suggesting a mechanism for recruitment of the NuRD complex to chromatin.

  13. Static Complexity Analysis of Higher Order Programs

    DEFF Research Database (Denmark)

    Avery, James Emil; Kristiansen, Lars; Moyen, Jean-Yves

    2009-01-01

    The overall goal of the research presented in this paper is to find^M automatic methods for static complexity analysis of higher order^M programs.......The overall goal of the research presented in this paper is to find^M automatic methods for static complexity analysis of higher order^M programs....

  14. Higher-Order (Non-)Modularity

    DEFF Research Database (Denmark)

    Appel, Claus; van Oostrom, Vincent; Simonsen, Jakob Grue

    2010-01-01

    We show that, contrary to the situation in first-order term rewriting, almost none of the usual properties of rewriting are modular for higher-order rewriting, irrespective of the higher-order rewriting format. We show that for the particular format of simply typed applicative term rewriting syst...

  15. Higher-order mode photonic crystal based nanofluidic sensor

    Science.gov (United States)

    Peng, Wang; Chen, Youping; Ai, Wu

    2017-01-01

    A higher-order photonic crystal (PC) based nanofluidic sensor, which worked at 532 nm, was designed and demonstrated. A systematical and detailed method for sculpturing a PC sensor for a given peak wavelength value (PWV) and specified materials was illuminated. It was the first time that the higher order mode was used to design PC based nanofluidic sensor, and the refractive index (RI) sensitivity of this sensor had been verified with FDTD simulation software from Lumerical. The enhanced electrical field of higher order mode structure was mostly confined in the channel area, where the enhance field is wholly interacting with the analytes in the channels. The comparison of RI sensitivity between fundamental mode and higher order mode shows the RI variation of higher order mode is 124.5 nm/RIU which is much larger than the fundamental mode. The proposed PC based nanofluidic structure pioneering a novel style for future optofluidic design.

  16. Assaying chromatin structure and remodeling by restriction enzyme accessibility

    OpenAIRE

    Trotter, Kevin W.; Archer, Trevor K.

    2012-01-01

    The packaging of eukaryotic DNA into nucleosomes, the fundamental unit of chromatin, creates a barrier to nuclear processes, such as transcription, DNA replication, recombination, and repair(1). This obstructive nature of chromatin can be overcome by the enzymatic activity of chromatin remodeling complexes which creates a more favorable environment for the association of essential factors and regulators to sequences within target genes. Here we describe a detailed approach for analyzing chrom...

  17. PU.1 Level-Directed Chromatin Structure Remodeling at the Irf8 Gene Drives Dendritic Cell Commitment

    Directory of Open Access Journals (Sweden)

    Jörg Schönheit

    2013-05-01

    Full Text Available Dendritic cells (DCs are essential regulators of immune responses; however, transcriptional mechanisms that establish DC lineage commitment are poorly defined. Here, we report that the PU.1 transcription factor induces specific remodeling of the higher-order chromatin structure at the interferon regulatory factor 8 (Irf8 gene to initiate DC fate choice. An Irf8 reporter mouse enabled us to pinpoint an initial progenitor stage at which DCs separate from other myeloid lineages in the bone marrow. In the absence of Irf8, this progenitor undergoes DC-to-neutrophil reprogramming, indicating that DC commitment requires an active, Irf8-dependent escape from alternative myeloid lineage potential. Mechanistically, myeloid Irf8 expression depends on high PU.1 levels, resulting in local chromosomal looping and activation of a lineage- and developmental-stage-specific cis-enhancer. These data delineate PU.1 as a concentration-dependent rheostat of myeloid lineage selection by controlling long-distance contacts between regulatory elements and suggest that specific higher-order chromatin remodeling at the Irf8 gene determines DC differentiation.

  18. Synchrotron radiation of higher order soliton

    CERN Document Server

    Driben, Rodislav; Efimov, Anatoly

    2015-01-01

    We demonstrate radiation mechanism exhibited by higher order soliton. In a course of its evolution higher order soliton emits polychromatic radiation resulting in appearance of multipeak frequency comb like spectral band. The shape and spectral position of this band can be effectively controlled by the relative strength of the third order dispersion. An analytical description is completely corroborated by numerical simulations. An analogy between this radiation and the radiation of moving charges is presented. For longer pulses the described effect persists also under the action of higher order perturbations such as Raman and self-steepening.

  19. Inverstigation of chromatin folding patterns by atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    ZHANGYi; OUYANGZhenqian; 等

    1999-01-01

    The chromatin folding patterns in air and liquid were studied by atomic force microscopy(AFM),A gentle water-air interface method was adopted to spread chromatin from interphase nucleus of chicken erythrocyte.The chromatin was absorbed on APS-mica surface and studied with AFM,Beads-on a-string were observed and many higher-order structrues such as superbeads with dimensions 40-60nm in diameter and 4-7nm in height were found to string together to make chromation fibers.When sample spreading and absorbing time were shortened.higher-order chromatin fibers with 60-120nm in width were observed in air as well as under water environment.These chromatin structures may reflect chromatin folding patterns in the living cells.

  20. Higher-order techniques in computational electromagnetics

    CERN Document Server

    Graglia, Roberto D

    2016-01-01

    Higher-Order Techniques in Computational Electromagnetics explains 'high-order' techniques that can significantly improve the accuracy, computational cost, and reliability of computational techniques for high-frequency electromagnetics, such as antennas, microwave devices and radar scattering applications.

  1. On higher order relations in Fedosov supermanifolds

    Energy Technology Data Exchange (ETDEWEB)

    Lavrov, P M; Radchenko, O V [Tomsk State Pedagogical University, 634041 Tomsk (Russian Federation)

    2006-05-26

    Higher order relations existing in normal coordinates between affine extensions of the symplectic curvature tensor and basic objects for any Fedosov supermanifolds are derived. Representation of these relations in general coordinates is discussed.

  2. Higher order relations in Fedosov supermanifolds

    CERN Document Server

    Lavrov, P M

    2005-01-01

    Higher order relations existing in normal coordinates between affine extensions of the curvature tensor and basic objects for any Fedosov supermanifolds are derived. Representation of these relations in general coordinates is discussed.

  3. The shades of gray of the chromatin fiber: recent literature provides new insights into the structure of chromatin.

    Science.gov (United States)

    Ausió, Juan

    2015-01-01

    The chromatin fiber consists of a string of nucleosomes connected by linker DNA regions. The hierarchy of folding of this fiber within the cell has long been controversial, and the existence of an originally described 30 nm fiber has been debated and reviewed extensively. This review contextualizes two recent papers on this topic that suggest the 30 nm fiber to be an over-simplification. The idealized model from the first study provides good insight into the constraints and histone participation in the maintenance of the fiber structure. The second paper provides a theoretical description of a more realistic view of the highly heterogeneous and dynamic chromatin organization in the in vivo setting. It is now time to abandon the highly regular "one start" solenoidal 30 nm structure and replace it with a more realistic highly dynamic, polymorphic fiber.

  4. Higher Order Cumulants in Colorless Partonic Plasma

    CERN Document Server

    Cherif, S; Ladrem, M

    2016-01-01

    Any physical system considered to study the QCD deconfinement phase transition certainly has a finite volume, so the finite size effects are inevitably present. This renders the location of the phase transition and the determination of its order as an extremely difficult task, even in the simplest known cases. In order to identify and locate the colorless QCD deconfinement transition point in finite volume $T_{0}(V)$, a new approach based on the finite-size cumulant expansion of the order parameter and the $\\mathscr{L}_{m,n}$-Method is used.We have shown that both cumulants of higher order and their ratios, associated to the thermodynamical fluctuations of the order parameter, in QCD deconfinement phase transition behave in a particular enough way revealing pronounced oscillations in the transition region. The sign structure and the oscillatory behavior of these in the vicinity of the deconfinement phase transition point might be a sensitive probe and may allow one to elucidate their relation to the QCD phase...

  5. The serenity of the meditating mind: a cross-cultural psychometric study on a two-factor higher order structure of mindfulness, its effects, and mechanisms related to mental health among experienced meditators.

    Directory of Open Access Journals (Sweden)

    Ulrich S Tran

    Full Text Available OBJECTIVE: To investigate the psychometric and structural properties of the Five Facets Mindfulness Questionnaire (FFMQ among meditators, to develop a short form, and to examine associations of mindfulness with mental health and the mechanisms of mindfulness. METHODS: Two independent samples were used, a German (n = 891 and a Spanish (n = 393 meditator sample, practicing various meditation styles. Structural and psychometric properties of the FFMQ were investigated with multigroup confirmatory factor analysis and exploratory structural equation modeling. Associations with mental health and mechanisms of mindfulness were examined with path analysis. RESULTS: The derived short form broadly matched a previous item selection in samples of non-meditators. Self-regulated Attention and Orientation to Experience governed the facets of mindfulness on a higher-order level. Higher-order factors of mindfulness and meditation experience were negatively associated with symptoms of depression and anxiety, and perceived stress. Decentering and nonattachment were the most salient mechanisms of mindfulness. Aspects of emotion regulation, bodily awareness, and nonattachment explained the effects of mindfulness on depression and anxiety. CONCLUSIONS: A two-component conceptualization for the FFMQ, and for the study of mindfulness as a psychological construct, is recommended for future research. Mechanisms of mindfulness need to be examined in intervention studies.

  6. A Note On Higher Order Grammar

    CERN Document Server

    Gluzberg, Victor

    2009-01-01

    Both syntax-phonology and syntax-semantics interfaces in Higher Order Grammar (HOG) are expressed as axiomatic theories in higher-order logic (HOL), i.e. a language is defined entirely in terms of provability in the single logical system. An important implication of this elegant architecture is that the meaning of a valid expression turns out to be represented not by a single, nor even by a few "discrete" terms (in case of ambiguity), but by a "continuous" set of logically equivalent terms. The note is devoted to precise formulation and proof of this observation.

  7. Feynman rules of higher-order poles in CHY construction

    Science.gov (United States)

    Huang, Rijun; Feng, Bo; Luo, Ming-xing; Zhu, Chuan-Jie

    2016-06-01

    In this paper, we generalize the integration rules for scattering equations to situations where higher-order poles are present. We describe the strategy to deduce the Feynman rules of higher-order poles from known analytic results of simple CHY-integrands, and propose the Feynman rules for single double pole and triple pole as well as duplex-double pole and triplex-double pole structures. We demonstrate the validation and strength of these rules by ample non-trivial examples.

  8. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins

    KAUST Repository

    Bigeard, Jean

    2014-07-10

    In eukaryotes, most of the DNA is located in the nucleus where it is organized with histone proteins in a higher order structure as chromatin. Chromatin and chromatin-associated proteins contribute to DNA-related processes such as replication and transcription as well as epigenetic regulation. Protein functions are often regulated by PTMs among which phosphorylation is one of the most abundant PTM. Phosphorylation of proteins affects important properties, such as enzyme activity, protein stability, or subcellular localization. We here describe the main specificities of protein phosphorylation in plants and review the current knowledge on phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. We also outline some future challenges to further elucidate protein phosphorylation and chromatin regulation.

  9. Frontiers of higher order fuzzy sets

    CERN Document Server

    Tahayori, Hooman

    2015-01-01

    Frontiers of Higher Order Fuzzy Sets, strives to improve the theoretical aspects of general and Interval Type-2 fuzzy sets and provides a unified representation theorem for higher order fuzzy sets. Moreover, the book elaborates on the concept of gradual elements and their integration with the higher order fuzzy sets. This book also introduces new frameworks for information granulation based on general T2FSs, IT2FSs, Gradual elements, Shadowed sets and rough sets. In particular, the properties and characteristics of the new proposed frameworks are studied. Such new frameworks are shown to be more capable to be exploited in real applications. Higher order fuzzy sets that are the result of the integration of general T2FSs, IT2FSs, gradual elements, shadowed sets and rough sets will be shown to be suitable to be applied in the fields of bioinformatics, business, management, ambient intelligence, medicine, cloud computing and smart grids. Presents new variations of fuzzy set frameworks and new areas of applicabili...

  10. Higher-Order Components for Grid Programming

    CERN Document Server

    Dünnweber, Jan

    2009-01-01

    Higher-Order Components were developed within the CoreGRID European Network of Excellence and have become an optional extension of the popular Globus middleware. This book provides the reader with hands-on experience, describing a collection of example applications from various fields of science and engineering, including biology and physics.

  11. Dynamical symmetry and higher-order interactions

    Energy Technology Data Exchange (ETDEWEB)

    Van Isacker, P. [Grand Accelerateur National d' Ions Lourds (GANIL), 14 - Caen (France)

    1999-07-01

    It is shown that the concept of dynamical symmetry is enriched by increasing the order the interactions between the constituent particles of a given many-body-system. The idea is illustrated with an analysis of higher-order interactions in the interacting boson model. (author)

  12. Higher Order Thinking in the Dance Studio

    Science.gov (United States)

    Moffett, Ann-Thomas

    2012-01-01

    The author identifies higher order thinking as an essential component of dance training for students of all ages and abilities. Weaving together insights from interviews with experts in the field of dance education with practical pedagogical applications within an Improvisation and Composition class for talented and gifted youth, this article…

  13. Human motion perception: Higher-order organization

    Science.gov (United States)

    Kaiser, Mary K.; Proffitt, Dennis R.

    1990-01-01

    An overview is given of higher-order motion perception and organization. It is argued that motion is sufficient to fully specify a number of environmental properties, including: depth order, three-dimensional form, object displacement, and dynamics. A grammar of motion perception is proposed; applications of this work for display design are discussed.

  14. A Higher-Order Colon Translation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Nielsen, Lasse R.

    2000-01-01

    A lambda-encoding such as the CPS transformation gives rise to administrative redexes. In his seminal article ``Call-by-name, call-by-value and the lambda-calculus'', 25 years ago, Plotkin tackled administrative reductions using a so-called ``colon translation.'' 10 years ago, Danvy and Filinski...... integrated administrative reductions in the CPS transformation, making it operate in one pass. The technique applies to other lambda-encodings (e.g., variants of CPS), but we do not see it used in practice--instead, Plotkin's colon translation appears to be favored. Therefore, in an attempt to link both...... techniques, we recast Plotkin's proof of Indifference and Simulation to the higher-order specification of the one-pass CPS transformation. To this end, we extend his colon translation from first order to higher order...

  15. A Higher-Order Colon Translation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Nielsen, Lasse Reichstein

    2001-01-01

    A lambda-encoding such as the CPS transformation gives rise to administrative redexes. In his seminal article ``Call-by-name, call-by-value and the lambda-calculus'', 25 years ago, Plotkin tackled administrative reductions using a so-called ``colon translation.'' 10 years ago, Danvy and Filinski...... integrated administrative reductions in the CPS transformation, making it operate in one pass. The technique applies to other lambda-encodings (e.g., variants of CPS), but we do not see it used in practice--instead, Plotkin's colon translation appears to be favored. Therefore, in an attempt to link both...... techniques, we recast Plotkin's proof of Indifference and Simulation to the higher-order specification of the one-pass CPS transformation. To this end, we extend his colon translation from first order to higher order...

  16. Higher-Order Mentalising and Executive Functioning.

    Science.gov (United States)

    2015-11-01

    Higher-order mentalising is the ability to represent the beliefs and desires of other people at multiple, iterated levels - a capacity that sets humans apart from other species. However, there has not yet been a systematic attempt to determine what cognitive processes underlie this ability. Here we present three correlational studies assessing the extent to which performance on higher-order mentalising tasks relates to emotion recognition, self-reported empathy and self-inhibition. In Study 1a and 1b, examining emotion recognition and empathy, a relationship was identified between individual differences in the ability to mentalise and an emotion recognition task (the Reading the Mind in the Eyes task), but no correlation was found with the Empathy Quotient, a self-report scale of empathy. Study 2 investigated whether a relationship exists between individual mentalising abilities and four different forms of self-inhibition: motor inhibition, executive inhibition, automatic imitation and temporal discounting. Results demonstrate that only temporal discounting performance relates to mentalising ability; suggesting that cognitive skills relevant to representation of the minds of others' are not influenced by the ability to perform more basic inhibition. Higher-order mentalising appears to rely on the cognitive architecture that serves both low-level social cognition (emotion recognition), and complex forms of inhibition.

  17. Higher-Order Aberrations in Myopic Eyes

    Directory of Open Access Journals (Sweden)

    Farid Karimian

    2010-01-01

    Full Text Available Purpose: To evaluate the correlation between refractive error and higher-order aberrations (HOAs in patients with myopic astigmatism. Methods: HOAs were measured using the Zywave II aberrometer over a 6 mm pupil. Correlations between HOAs and myopia, astigmatism, and age were analyzed. Results: One hundred and twenty-six eyes of 63 subjects with mean age of 26.4±5.9 years were studied. Mean spherical equivalent refractive error and refractive astigmatism were -4.94±1.63 D and 0.96±1.06 D, respectively. The most common higher-order aberration was primary horizontal trefoil with mean value of 0.069±0.152 μm followed by spherical aberration (-0.064±0.130 μm and primary vertical coma (-0.038±0.148 μm. As the order of aberration increased from third to fifth, its contribution to total HOA decreased: 53.9% for third order, 31.9% for fourth order, and 14.2% for fifth order aberrations. Significant correlations were observed between spherical equivalent refractive error and primary horizontal coma (R=0.231, P=0.022, and root mean square (RMS of spherical aberration (R=0.213, P=0.031; between astigmatism and RMS of total HOA (R=0.251, P=0.032, RMS of fourth order aberration (R=0.35, P<0.001, and primary horizontal coma (R=0.314, P=0.004. Spherical aberration (R=0.214, P=0.034 and secondary vertical coma (R=0.203, P=0.031 significantly increased with age. Conclusion: Primary horizontal trefoil, spherical aberration and primary vertical coma are the predominant higher-order aberrations in eyes with myopic astigmatism.

  18. Data on force-dependent structural changes of chromatin fibers measured with magnetic tweezers

    Directory of Open Access Journals (Sweden)

    Fan-Tso Chien

    2014-12-01

    Full Text Available The compaction of chromatin fibers regulates the accessibility of embedded DNA, highly associated with transcriptional activities [1]. Single molecule force spectroscopy has revealed the great details of the structural changes of chromatin fibers in the presence of external exerted force [2–7]. However, most of the studies focus on a specific force regime [2,3,8,9]. The data here show force-extension (FE traces of chromatin fibers as measured with magnetic tweezers, covering the force regime from 0 pN to 27 pN. Those traces provide information for further studies at varied force regimes.

  19. The regular state in higher order gravity

    Science.gov (United States)

    Cotsakis, Spiros; Kadry, Seifedine; Trachilis, Dimitrios

    2016-08-01

    We consider the higher-order gravity theory derived from the quadratic Lagrangian R + 𝜖R2 in vacuum as a first-order (ADM-type) system with constraints, and build time developments of solutions of an initial value formulation of the theory. We show that all such solutions, if analytic, contain the right number of free functions to qualify as general solutions of the theory. We further show that any regular analytic solution which satisfies the constraints and the evolution equations can be given in the form of an asymptotic formal power series expansion.

  20. Higher Order Equations and Constituent Fields

    Science.gov (United States)

    Barci, D. G.; Bollini, C. G.; Oxman, L. E.; Rocca, M.

    We consider a simple wave equation of fourth degree in the D'Alembertian operator. It contains the main ingredients of a general Lorentz-invariant higher order equation, namely, a normal bradyonic sector, a tachyonic state and a pair of complex conjugate modes. The propagators are respectively the Feynman causal function and three Wheeler-Green functions (half-advanced and half-retarded). The latter are Lorentz-invariant and consistent with the elimination of tachyons and complex modes from free asymptotic states. We also verify the absence of absorptive parts from convolutions involving Wheeler propagators.

  1. Higher-Order Gauss-Bonnet Cosmology

    CERN Document Server

    Capozziello, Salvatore; Makarenko, Andrey N

    2014-01-01

    We study cosmological models derived from higher-order Gauss-Bonnet gravity $F(R,G)$ by using the Lagrange multiplier approach without assuming the presence of additional fields with the exception of standard perfect fluid matter. The presence of Lagrange multipliers reduces the number of allowed solutions. We need to introduce compatibility conditions of the FRW equations, which impose strict restrictions on the metric or require the introduction of additional exotic matter. Several classes of $F(R,G)$ models are generated and discussed.

  2. Adaptive filtering using Higher Order Statistics (HOS

    Directory of Open Access Journals (Sweden)

    Abdelghani Manseur

    2012-03-01

    Full Text Available The performed job, in this study, consists in studying adaptive filters and higher order statistics (HOS to ameliorate their performances, by extension of linear case to non linear filters via Volterra series. This study is, principally, axed on: „ Choice of the adaptation step and convergence conditions. „ Convergence rate. „ Adaptive variation of the convergence factor, according to the input signal. The obtained results, with real signals, have shown computationally efficient and numerically stable algorithms for adaptive nonlinear filtering while keeping relatively simple computational complexity.

  3. Enhanced higher order parametric x radiation production

    Science.gov (United States)

    Dinova, Kay L.

    1992-12-01

    This thesis examines parametric x-radiation (PXR) which is the Bragg scattering of the virtual photons associated with the Coulomb field of relativistic charged particle from the atomic planes of a crystal. Higher order parametric x-radiation from the (002) planes of a thick mosaic graphite crystal have been observed. The raw PXR data was collected using a SiLi detector and a Pulse Height Analyzer (PHA) software program. The data was corrected for various effects including attenuation, detector drift, and efficiency. The absolute number of photons per electron was obtained by using the fluorescent x-ray yield from a tin foil backing on the graphite crystal to determine the LINAC current. The number of photons per electron observed greatly exceeds the expected values. Comparison of the ratio of intensity of a given order to the first order I(n)/I(I) to the theoretical ratio shows that the ratios increase with order. Not only is the absolute intensity greater than expected, but the higher orders (compared to the first order) are larger than expected. Lastly, the intensity for various crystal angle orientations and a fixed detector angle was measured.

  4. Higher order assortativity in complex networks

    CERN Document Server

    Arcagni, Alberto; Stefani, Silvana; Torriero, Anna

    2016-01-01

    Assortativity was first introduced by Newman and has been extensively studied and applied to many real world networked systems since then. Assortativity is a graph metrics and describes the tendency of high degree nodes to be directly connected to high degree nodes and low degree nodes to low degree nodes. It can be interpreted as a first order measure of the connection between nodes, i.e. the first autocorrelation of the degree-degree vector. Even though assortativity has been used so extensively, to the author's knowledge, no attempt has been made to extend it theoretically. This is the scope of our paper. We will introduce higher order assortativity by extending the Newman index based on a suitable choice of the matrix driving the connections. Higher order assortativity will be defined for paths, shortest paths, random walks of a given time length, connecting any couple of nodes. The Newman assortativity is achieved for each of these measures when the matrix is the adjacency matrix, or, in other words, the...

  5. Stochastic Models for Phylogenetic Trees on Higher-order Taxa

    CERN Document Server

    Aldous, David; Popovic, Lea

    2007-01-01

    Simple stochastic models for phylogenetic trees on species have been well studied. But much paleontology data concerns time series or trees on higher-order taxa, and any broad picture of relationships between extant groups requires use of higher-order taxa. A coherent model for trees on (say) genera should involve both a species-level model and a model for the classification scheme by which species are assigned to genera. We present a general framework for such models, and describe three alternate classification schemes. Combining with the species-level model of Aldous-Popovic (2005), one gets models for higher-order trees, and we initiate analytic study of such models. In particular we derive formulas for the lifetime of genera, for the distribution of number of species per genus, and for the offspring structure of the tree on genera.

  6. Higher-Order Item Response Models for Hierarchical Latent Traits

    Science.gov (United States)

    Huang, Hung-Yu; Wang, Wen-Chung; Chen, Po-Hsi; Su, Chi-Ming

    2013-01-01

    Many latent traits in the human sciences have a hierarchical structure. This study aimed to develop a new class of higher order item response theory models for hierarchical latent traits that are flexible in accommodating both dichotomous and polytomous items, to estimate both item and person parameters jointly, to allow users to specify…

  7. Conformal higher-order viscoelastic fluid mechanics

    CERN Document Server

    Fukuma, Masafumi

    2012-01-01

    We present a generally covariant formulation of conformal higher-order viscoelastic fluid mechanics with strain allowed to take arbitrarily large values. We give a general prescription to determine the dynamics of a relativistic viscoelastic fluid in a way consistent with the hypothesis of local thermodynamic equilibrium and the second law of thermodynamics. We then elaborately study the transient time scales at which the strain almost relaxes and becomes proportional to the gradients of velocity. We particularly show that a conformal second-order fluid with all possible parameters in the constitutive equations can be obtained without breaking the hypothesis of local thermodynamic equilibrium, if the conformal fluid is defined as the long time limit of a conformal second-order viscoelastic system. We also discuss how local thermodynamic equilibrium could be understood in the context of the fluid/gravity correspondence.

  8. Conformal higher-order viscoelastic fluid mechanics

    Science.gov (United States)

    Fukuma, Masafumi; Sakatani, Yuho

    2012-06-01

    We present a generally covariant formulation of conformal higher-order viscoelastic fluid mechanics with strain allowed to take arbitrarily large values. We give a general prescription to determine the dynamics of a relativistic viscoelastic fluid in a way consistent with the hypothesis of local thermodynamic equilibrium and the second law of thermodynamics. We then elaborately study the transient time scales at which the strain almost relaxes and becomes proportional to the gradients of velocity. We particularly show that a conformal second-order fluid with all possible parameters in the constitutive equations can be obtained without breaking the hypothesis of local thermodynamic equilibrium, if the conformal fluid is defined as the long time limit of a conformal second-order viscoelastic system. We also discuss how local thermodynamic equilibrium could be understood in the context of the fluid/gravity correspondence.

  9. Synthetic CpG islands reveal DNA sequence determinants of chromatin structure

    Science.gov (United States)

    Wachter, Elisabeth; Quante, Timo; Merusi, Cara; Arczewska, Aleksandra; Stewart, Francis; Webb, Shaun; Bird, Adrian

    2014-01-01

    The mammalian genome is punctuated by CpG islands (CGIs), which differ sharply from the bulk genome by being rich in G + C and the dinucleotide CpG. CGIs often include transcription initiation sites and display ‘active’ histone marks, notably histone H3 lysine 4 methylation. In embryonic stem cells (ESCs) some CGIs adopt a ‘bivalent’ chromatin state bearing simultaneous ‘active’ and ‘inactive’ chromatin marks. To determine whether CGI chromatin is developmentally programmed at specific genes or is imposed by shared features of CGI DNA, we integrated artificial CGI-like DNA sequences into the ESC genome. We found that bivalency is the default chromatin structure for CpG-rich, G + C-rich DNA. A high CpG density alone is not sufficient for this effect, as A + T-rich sequence settings invariably provoke de novo DNA methylation leading to loss of CGI signature chromatin. We conclude that both CpG-richness and G + C-richness are required for induction of signature chromatin structures at CGIs. DOI: http://dx.doi.org/10.7554/eLife.03397.001 PMID:25259796

  10. 基于NMR指纹谱相关分析的生物类似药高级结构评价%Higher Order Structure Assessment of Biosimilars Based on the Correlation of NMR Spectral Fingerprints

    Institute of Scientific and Technical Information of China (English)

    许美凤; 方均建; 董芳霆; 颜贤忠

    2015-01-01

    A procedure based on the1H NMR fingerprints of biologics was established for the assessment of higher order structure of biosimilar samples. The global correlation coefficientsr andR2 of binned NMR spectra were used to quantify structural similarity between biosimilars and originators, and a local correlation analysis method was used to find out the specific regions that contribute to the structure differences. This method was applied to the quantitative assessment of daptomycin, a lipopeptide antibiotic with a molecular weight of 1 620, by comparing the higher order structure of the biosimilar active pharmaceutical ingredient (API), its injection and originator injection Cubicin. The results showed that there were significant spectral differences among daptomycin samples, indicating structural differences between daptomycin originator and its biosimilars. Local correlation analysis further revealed the specific spectral regions that contributed to these differences. The method was also applied to a monoclonal antibody drug Trastuzumab, which is a large protein with a molecular weight of 145 423.1H NMR spectra of the originator drug Herceptin and four lots of its biosimilar were recorded and binned for statistical analysis. The correlation coefficientsr andR2 showed that Trastuzumab biosimilars seem to be highly similar to Herceptin. These results demonstrated that the combination of NMR fingerprints and statistical analysis is a powerful and robust technique in biosimilar quality control.%建立了基于1H NMR指纹技术的生物类似药高级结构相似性分析方法,利用相关系数r和决定系数R2定量评估生物类似药与其原研药的结构相似度。将该方法应用在一种分子量为1620的抗菌性脂肽达托霉素上,比较了其类似药的活性原料成分(API)、类似药制剂与原研药克必信的高级结构相似性。实验结果显示,3个达托霉素样品的谱图存在显著差异,表明达托霉素类似药与

  11. Aspects of general higher-order gravities

    CERN Document Server

    Bueno, Pablo; Min, Vincent S; Visser, Manus R

    2016-01-01

    We study several aspects of higher-order gravities constructed from general contractions of the Riemann tensor and the metric in arbitrary dimensions. First, we use the fast-linearization procedure presented in arXiv:1607.06463 to obtain the equations satisfied by the metric perturbation modes on a maximally symmetric background in the presence of matter and to classify $\\mathcal{L}($Riemann$)$ theories according to their spectrum. Then, we linearize all theories up to quartic order in curvature and use this result to construct quartic versions of Einsteinian cubic gravity (ECG). In addition, we show that the most general cubic gravity constructed in a dimension-independent way and which does not propagate the ghost-like spin-2 mode (but can propagate the scalar) is a linear combination of $f($Lovelock$)$ invariants, plus the ECG term, plus a New ghost-free gravity term. Next, we construct the generalized Newton potential and the Post-Newtonian parameter $\\gamma$ for general $\\mathcal{L}($Riemann$)$ gravities...

  12. Chromatin structure of repeating CTG/CAG and CGG/CCG sequences in human disease.

    Science.gov (United States)

    Wang, Yuh-Hwa

    2007-05-01

    In eukaryotic cells, chromatin structure organizes genomic DNA in a dynamic fashion, and results in regulation of many DNA metabolic processes. The CTG/CAG and CGG/CCG repeating sequences involved in several neuromuscular degenerative diseases display differential abilities for the binding of histone octamers. The effect of the repeating DNA on nucleosome assembly could be amplified as the number of repeats increases. Also, CpG methylation, and sequence interruptions within the triplet repeats exert an impact on the formation of nucleosomes along these repeating DNAs. The two most common triplet expansion human diseases, myotonic dystrophy 1 and fragile X syndrome, are caused by the expanded CTG/CAG and CGG/CCG repeats, respectively. In addition to the expanded repeats and CpG methylation, histone modifications, chromatin remodeling factors, and noncoding RNA have been shown to coordinate the chromatin structure at both myotonic dystrophy 1 and fragile X loci. Alterations in chromatin structure at these two loci can affect transcription of these disease-causing genes, leading to disease symptoms. These observations have brought a new appreciation that a full understanding of disease gene expression requires a knowledge of the structure of the chromatin domain within which the gene resides.

  13. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...... reassembly on nascent DNA strands. The aim of this review is to discuss how histones - new and old - are handled at the replication fork, highlighting new mechanistic insights and revisiting old paradigms....

  14. Distributed probing of chromatin structure in vivo reveals pervasive chromatin accessibility for expressed and non-expressed genes during tissue differentiation in C. elegans

    Directory of Open Access Journals (Sweden)

    Sha Ky

    2010-08-01

    Full Text Available Abstract Background Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underlying genomic DNA, the epigenome influences the cell's transcriptome and ultimately its function. Existing genomic methods for analyzing cell-type-specific changes in chromatin generally involve two elements: (i a source for purified cells (or nuclei of distinct types, and (ii a specific treatment that partitions or degrades chromatin by activity or structural features. For many cell types of great interest, such assays are limited by our inability to isolate the relevant cell populations in an organism or complex tissue containing an intertwined mixture of other cells. This limitation has confined available knowledge of chromatin dynamics to a narrow range of biological systems (cell types that can be sorted/separated/dissected in large numbers and tissue culture models or to amalgamations of diverse cell types (tissue chunks, whole organisms. Results Transgene-driven expression of DNA/chromatin modifying enzymes provides one opportunity to query chromatin structures in expression-defined cell subsets. In this work we combine in vivo expression of a bacterial DNA adenine methyltransferase (DAM with high throughput sequencing to sample tissue-specific chromatin accessibility on a genome-wide scale. We have applied the method (DALEC: Direct Asymmetric Ligation End Capture towards mapping a cell-type-specific view of genome accessibility as a function of differentiated state. Taking advantage of C. elegans strains expressing the DAM enzyme in diverse tissues (body wall muscle, gut, and hypodermis, our efforts yield a genome-wide dataset measuring chromatin accessibility at each of 538,000 DAM target sites in the C. elegans (diploid genome. Conclusions Validating the DALEC mapping results, we observe a strong association

  15. Comparative structural biology of the genome: nano-scale imaging of single nucleus from different kingdoms reveals the common physicochemical property of chromatin with a 40 nm structural unit.

    Science.gov (United States)

    Kobori, Toshiro; Kodama, Mami; Hizume, Kohji; Yoshimura, Shige H; Ohtani, Toshio; Takeyasu, Kunio

    2006-01-01

    Genome function is closely linked to the higher-order chromatin structures. To reveal a structural basis for the interphase chromatin organization, the 'on-substrate' lysis procedure was applied to nuclei isolated from human HeLa cells, chicken erythrocyte cells and yeast Schizosaccharomyces pombe, which possessed different intrinsic properties of the genomes such as histone composition and inter-nucleosomal distance. The isolated nuclei on a coverslip were successively treated with a detergent and a high-salt solution to extract the nuclear membrane and the nucleoplasm, and therefore, atomic force microscopy (AFM) visualized the structural changes in response to the lysis procedure. After the nucleoplasm was extracted, AFM clarified that chromatin fibers, approximately 40 nm in width, were partially released out of the nuclei and that the other chromatin still remaining in the nuclei was composed of granular structures with diameter of 80-100 nm. Thus, these results suggest that the approximately 40 nm fiber would be a stable structural unit and fold the 80-100 nm granules into a one-step higher unit. A common mechanism could be implied regardless of the intrinsic properties of the eukaryotic genomes.

  16. Global chromatin fibre compaction in response to DNA damage

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, Charlotte [Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Hayward, Richard L. [Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Breakthrough Research Unit, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Gilbert, Nick, E-mail: Nick.Gilbert@ed.ac.uk [Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom); Breakthrough Research Unit, The University of Edinburgh, Edinburgh EH4 2XR (United Kingdom)

    2011-11-04

    Highlights: Black-Right-Pointing-Pointer Robust KAP1 phosphorylation in response to DNA damage in HCT116 cells. Black-Right-Pointing-Pointer DNA repair foci are found in soluble chromatin. Black-Right-Pointing-Pointer Biophysical analysis reveals global chromatin fibre compaction after DNA damage. Black-Right-Pointing-Pointer DNA damage is accompanied by rapid linker histone dephosphorylation. -- Abstract: DNA is protected by packaging it into higher order chromatin fibres, but this can impede nuclear processes like DNA repair. Despite considerable research into the factors required for signalling and repairing DNA damage, it is unclear if there are concomitant changes in global chromatin fibre structure. In human cells DNA double strand break (DSB) formation triggers a signalling cascade resulting in H2AX phosphorylation ({gamma}H2AX), the rapid recruitment of chromatin associated proteins and the subsequent repair of damaged sites. KAP1 is a transcriptional corepressor and in HCT116 cells we found that after DSB formation by chemicals or ionising radiation there was a wave of, predominantly ATM dependent, KAP1 phosphorylation. Both KAP1 and phosphorylated KAP1 were readily extracted from cells indicating they do not have a structural role and {gamma}H2AX was extracted in soluble chromatin indicating that sites of damage are not attached to an underlying structural matrix. After DSB formation we did not find a concomitant change in the sensitivity of chromatin fibres to micrococcal nuclease digestion. Therefore to directly investigate higher order chromatin fibre structures we used a biophysical sedimentation technique based on sucrose gradient centrifugation to compare the conformation of chromatin fibres isolated from cells before and after DNA DSB formation. After damage we found global chromatin fibre compaction, accompanied by rapid linker histone dephosphorylation, consistent with fibres being more regularly folded or fibre deformation being stabilized by

  17. Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP

    DEFF Research Database (Denmark)

    Muratcioglu, Serena; Presman, Diego M; Pooley, John R

    2015-01-01

    The glucocorticoid receptor (GR) is a steroid-hormone-activated transcription factor that modulates gene expression. Transcriptional regulation by the GR requires dynamic receptor binding to specific target sites located across the genome. This binding remodels the chromatin structure to allow...... interaction with other transcription factors. Thus, chromatin remodeling is an essential component of GR-mediated transcriptional regulation, and understanding the interactions between these molecules at the structural level provides insights into the mechanisms of how GR and chromatin remodeling cooperate...

  18. Salt and divalent cations affect the flexible nature of the natural beaded chromatin structure

    DEFF Research Database (Denmark)

    Christiansen, Gunna; Griffith, J

    1977-01-01

    A natural chromatin containing simian virus 40 (SV40) DNA and histone has been used to examine changes in chromatin structure caused by various physical and chemical treatments. We find that histone H1 depleted chromatin is more compact in solutions of 0.15M NaCl or 2 mM MgCl2 than in 0.01 M Na......Cl or 0.6M NaCL, and is compact in 0.01 M NaCl solutions if histone H 1 is present. Even high concentrations of urea did not alter the fundamental beaded structure, consisting of 110A beads of 200 base pair content, each joined by thin DNA bridges of 50 base pairs. The physical bead observed by EM...... therefore contains more DNA than the 140 base pair "core particle". The natural variation in the bridge length is consistent with the broad bands observed after nuclease digestion of chromatin. Chromatin prepared for EM without fixation containing long 20A to 30A fibers possibly complexed with protein....

  19. Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses

    Directory of Open Access Journals (Sweden)

    Ana Paula Santos

    2017-01-01

    Full Text Available The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.

  20. Coactivators p300 and CBP maintain the identity of mouse embryonic stem cells by mediating long-range chromatin structure.

    Science.gov (United States)

    Fang, Fang; Xu, Yifeng; Chew, Kai-Khen; Chen, Xi; Ng, Huck-Hui; Matsudaira, Paul

    2014-07-01

    Master transcription factors Oct4, Sox2, and Nanog are required to maintain the pluripotency and self-renewal of embryonic stem cells (ESCs) by regulating a specific transcriptional network. A few other transcription factors have been shown to be important in ESCs by interacting with these master transcription factors; however, little is known about the transcriptional mechanisms regulated by coregulators (coactivators and corepressors). In this study, we examined the function of two highly homologous coactivators, p300 and CREB-binding protein (CBP), in ESCs. We find that these two coactivators play redundant roles in maintaining the undifferentiated state of ESCs. They are recruited by Nanog through physical interaction to Nanog binding loci, mediating the formation of long-range chromatin looping structures, which is essential to maintain ESC-specific gene expression. Further functional studies reveal that the p300/CBP binding looping fragments contain enhancer activities, suggesting that the formation of p300/CBP-mediated looping structures may recruit distal enhancers to create a concentration of factors for the transcription activation of genes that are involved in self-renewal and pluripotency. Overall, these results provide a total new insight into the transcriptional regulation mechanism of coactivators p300 and CBP in ESCs, which is important in maintaining self-renewal and pluripotency, by mediating the formation of higher order chromosome structures.

  1. Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics

    Directory of Open Access Journals (Sweden)

    Monica Soldi

    2013-03-01

    Full Text Available Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.

  2. Higher order gravity theories and their black hole solutions

    CERN Document Server

    Charmousis, Christos

    2008-01-01

    We discuss a particular higher order gravity theory, Lovelock theory, that generalises in higher dimensions, general relativity. After briefly motivating modifications of gravity, we will introduce the theory in question and we will argue that it is a unique, mathematically sensible, and physically interesting extension of general relativity. We will see, by using the formalism of differential forms, the relation of Lovelock gravity to differential geometry and topology of even dimensional manifolds. We will then discuss a generic staticity theorem, which will give us the charged static black hole solutions. We will examine their asymptotic behavior, analyse their horizon structure and briefly their thermodynamics. We will then examine the distributional matching conditions for Lovelock theory. We will see how induced 4 dimensional Einstein-Hilbert terms result on the brane geometry from the higher order Lovelock terms. With the junction conditions at hand, we will go back to the black hole solutions and give...

  3. Mathematical model of the chromatin structure of the nuclei of blood cells

    Science.gov (United States)

    Nikitaev, V. G.; Nagornov, O. V.; Pronichev, A. N.; Dmitrieva, V. V.; Polyakov, E. V.

    2017-01-01

    This paper describes the model of images of the nuclei of blood cells for research informative texture features in the diagnostics of acute leukemias on the basis of computer microscopy. The proposed model allows to simulate the structure of chromatin and factors distorting the signal in the formation of image.

  4. At the intersection of non-coding transcription, DNA repair, chromatin structure, and cellular senescence

    Directory of Open Access Journals (Sweden)

    Ryosuke eOhsawa

    2013-07-01

    Full Text Available It is well accepted that non-coding RNAs play a critical role in regulating gene expression. Recent paradigm-setting studies are now revealing that non-coding RNAs, other than microRNAs, also play intriguing roles in the maintenance of chromatin structure, in the DNA damage response, and in adult human stem cell aging. In this review, we will discuss the complex inter-dependent relationships among non-coding RNA transcription, maintenance of genomic stability, chromatin structure and adult stem cell senescence. DNA damage-induced non-coding RNAs transcribed in the vicinity of the DNA break regulate recruitment of the DNA damage machinery and DNA repair efficiency. We will discuss the correlation between non-coding RNAs and DNA damage repair efficiency and the potential role of changing chromatin structures around double-strand break sites. On the other hand, induction of non-coding RNA transcription from the repetitive Alu elements occurs during human stem cell aging and hinders efficient DNA repair causing entry into senescence. We will discuss how this fine balance between transcription and genomic instability may be regulated by the dramatic changes to chromatin structure that accompany cellular senescence.

  5. Higher-Order and Symbolic Computation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Mason, Ian

    2008-01-01

    HOL is a logic of total functions, one must explicitly address the termination of functions that are not primitive recursive. In "Flow-sensitive Type Systems and the Ambient Calculus," Torben Amtoft reports on what apperar to be the first type-based flow-sensitive topological analysis of ambient......-calculus programs, historically. The anaylsis determines the possible locations of ambients and mirrors the temporla sequencing of actions in the structure of types....

  6. Higher Order Macro Coefficients in Periodic Homogenization

    Energy Technology Data Exchange (ETDEWEB)

    Conca, Carlos; San Martin, Jorge [Departamento de IngenierIa Matematica, Facultad de Ciencias Fisicas y Matematicas, Universidad de Chile and Centro de Modelamiento Matematico, UMR 2071 CNRS-UChile, Casilla 170/3 - Correo 3, Santiago (Chile); Smaranda, Loredana [Department of Mathematics, Faculty of Mathematics and Computer Science, University of Pitesti, 110040 Pitesti, Str. Targu din Vale Nr.1, Arges (Romania); Vanninathan, Muthusamy, E-mail: cconca@dim.uchile.cl, E-mail: jorge@dim.uchile.cl, E-mail: smaranda@dim.uchile.cl, E-mail: vanni@math.tifrbng.res.in [TIFR-CAM, Post Bag 6503, GKVK Post, Bangalore - 560065 (India)

    2011-09-15

    A first set of macro coefficients known as the homogenized coefficients appear in the homogenization of PDE on periodic structures. If energy is increased or scale is decreased, these coefficients do not provide adequate approximation. Using Bloch decomposition, it is first realized that the above coefficients correspond to the lowest energy and the largest scale. This naturally paves the way to introduce other sets of macro coefficients corresponding to higher energies and lower scales which yield better approximation. The next task is to compare their properties with those of the homogenized coefficients. This article reviews these developments along with some new results yet to be published.

  7. Circulating chromatin-anti-chromatin antibody complexes bind with high affinity to dermo-epidermal structures in murine and human lupus nephritis

    DEFF Research Database (Denmark)

    Fismen, S; Hedberg, A; Fenton, K A;

    2009-01-01

    (NZBxNZW)F1 and MRL-lpr/lpr mice and from five patients with lupus nephritis were analysed by immunofluorescence, immune electron microscopy (IEM) and co-localization TUNEL IEM. Affinity of chromatin fragments for membrane structures was determined by surface plasmon resonance. Results demonstrated (i...

  8. 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

  9. Concept Mapping for Higher Order Thinking

    Directory of Open Access Journals (Sweden)

    Susan Marie Zvacek

    2013-02-01

    Full Text Available Engineering education is facing a changing world in which how one thinks is becoming more important than what one thinks; that is, our course content is important but constantly changing and we need to help students learn how to think about that content.Today’s students have grown accustomed to immediate rewards, multi-channel stimuli, and rapid-fire communications.  As a result, they are often impatient and suffer a lack of focus. When reflection is called for in the learning process - a time consuming practice - students may find it difficult to overcome the conflict between their typically speedy management of priorities and the focused, time-intensive thinking required to acquire a strong foundation of declarative knowledge.Therefore, the exploration of tools to facilitate the formation of deep knowledge structures is essential. One instructional strategy that shows promise is the use of concept mapping, a learning activity that requires students to explain their understanding of important ideas and the relationships among those ideas.  This paper describes a pilot project to integrate concept mapping into a Mechanical Engineering Course and the preliminary results of that project.This project has been established within the Working Group of “Tools for Developing High Order Thinking Skills”, of the Portuguese Society for Engineering Education, in which the first author is the leader and the other two co-authors, are working group members

  10. Chromatin structure, epigenetic mechanisms and long-range interactions in the human insulin locus.

    Science.gov (United States)

    Xu, Z; Lefevre, G M; Felsenfeld, G

    2012-10-01

    Regulation of gene expression in eukaryotes is largely dependent on variations in chromatin structure. More recently, it has become clear that this may involve not only local chromatin organization but also distant regulatory elements that participate in large-scale chromatin architecture within the nucleus. We describe recent methods that make possible the detection of such structures and apply them to analysis of the human insulin (INS) locus in pancreatic islets. We show that the INS gene is part of an extended 'open' chromatin domain that includes adjacent genes as well. We also find that in islets, the INS promoter is in physical contact with distant sites on the same human chromosome and notably, with the SYT8 gene, located nearly 300 kb away. The strength of the contact between INS and SYT8 is increased by glucose, and this results in stimulation of SYT8 expression. Inhibition of INS transcription decreases SYT8 expression. Furthermore, downregulation of SYT8 results in decreased secretion of insulin. Our results thus establish the existence of a regulatory network between the INS gene and other distant genes through long-range physical interactions, and suggest that such networks may have general importance for insulin biology and diabetes.

  11. Structure and Function of SWI/SNF Chromatin Remodeling Complexes and Mechanistic Implications for Transcription

    OpenAIRE

    Tang, Liling; Nogales, Eva; Ciferri, Claudio

    2010-01-01

    ATP-dependent chromatin remodeling complexes are specialized protein machinery able to restructure the nucleosome to make its DNA accessible during transcription, replication and DNA repair. During the past few years structural biologists have defined the architecture and dynamics of some of these complexes using electron microscopy, shedding light on the mechanisms of action of these important complexes. In this paper we review the existing structural information on the SWI/SNF family of the...

  12. Higher-order polarization singularitites in tailored vector beams

    Science.gov (United States)

    Otte, E.; Alpmann, C.; Denz, C.

    2016-07-01

    Higher-order polarization singularities embedded in tailored vector beams are introduced and experimentally realized. As holographic modulation allows to define order and location of any vectorial singularity, the surrounding vector field can be dynamically shaped. We demonstrate light fields associated with flowers or spider webs due to regular and even irregular patterns of the orientation of polarization ellipses. Beyond that, not yet investigated hybrid structures are introduced that allow generating networks of flowers and webs in very close vicinity. Our results pave the way to applications of singular optics in spatially extended, optimized optical tweezing and high-resolution imaging.

  13. A Higher Order Godunov Method for Radiation Hydrodynamics: Radiation Subsystem

    CERN Document Server

    Sekora, Michael

    2009-01-01

    A higher order Godunov method for the radiation subsystem of radiation hydrodynamics is presented. A key ingredient of the method is the direct coupling of stiff source term effects to the hyperbolic structure of the system of conservation laws; it is composed of a predictor step that is based on Duhamel's principle and a corrector step that is based on Picard iteration. The method is second order accurate in both time and space, unsplit, asymptotically preserving, and uniformly well behaved from the photon free streaming (hyperbolic) limit through the weak equilibrium diffusion (parabolic) limit and to the strong equilibrium diffusion (hyperbolic) limit. Numerical tests demonstrate second order convergence across various parameter regimes.

  14. The Emerging Roles of ATP-Dependent Chromatin Remodeling Enzymes in Nucleotide Excision Repair

    Directory of Open Access Journals (Sweden)

    Wioletta Czaja

    2012-09-01

    Full Text Available DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo.

  15. Generalizations of Euler Numbers and Euler Numbers of Higher Order

    Institute of Scientific and Technical Information of China (English)

    LUOQiu-ming; QIFeng

    2005-01-01

    The purpose of this paper is to define the generalized Euler numbers and the generalized Euler numbers of higher order, their recursion formula and some properties were established, accordingly Euler numbers and Euler numbers of higher order were extended.

  16. HIGHER ORDER MULTIVARIABLE NORLUND EULER-BERNOULLI POLYNOMIALS

    Institute of Scientific and Technical Information of China (English)

    刘国栋

    2002-01-01

    The definitions of higher order multivariable Norlund Euler polynomials and Norlund Bernoulli polynomials are presented and some of their important properties are expounded. Some identities involving recurrence sequences and higher order multivariable Norlund Euler-Bernoulli polynomials are established.

  17. Conceptualizing and Assessing Higher-Order Thinking in Reading

    Science.gov (United States)

    Afflerbach, Peter; Cho, Byeong-Young; Kim, Jong-Yun

    2015-01-01

    Students engage in higher-order thinking as they read complex texts and perform complex reading-related tasks. However, the most consequential assessments, high-stakes tests, are currently limited in providing information about students' higher-order thinking. In this article, we describe higher-order thinking in relation to reading. We provide a…

  18. Distinct differences in chromatin structure at subtelomeric X and Y' elements in budding yeast.

    Directory of Open Access Journals (Sweden)

    Xuefeng Zhu

    Full Text Available In Saccharomyces cerevisiae, all ends of telomeric DNA contain telomeric repeats of (TG(1-3, but the number and position of subtelomeric X and Y' repeat elements vary. Using chromatin immunoprecipitation and genome-wide analyses, we here demonstrate that the subtelomeric X and Y' elements have distinct structural and functional properties. Y' elements are transcriptionally active and highly enriched in nucleosomes, whereas X elements are repressed and devoid of nucleosomes. In contrast to X elements, the Y' elements also lack the classical hallmarks of heterochromatin, such as high Sir3 and Rap1 occupancy as well as low levels of histone H4 lysine 16 acetylation. Our analyses suggest that the presence of X and Y' elements govern chromatin structure and transcription activity at individual chromosome ends.

  19. Chromatin dynamics in plants

    NARCIS (Netherlands)

    Fransz, P.F.; Jong, de J.H.

    2002-01-01

    Recent studies in yeast, animals and plants have provided major breakthroughs in unraveling the molecular mechanism of higher-order gene regulation. In conjunction with the DNA code, proteins that are involved in chromatin remodeling, histone modification and epigenetic imprinting form a large netwo

  20. Changes in large-scale chromatin structure and function during oogenesis: a journey in company with follicular cells.

    Science.gov (United States)

    Luciano, Alberto M; Franciosi, Federica; Dieci, Cecilia; Lodde, Valentina

    2014-09-01

    The mammalian oocyte nucleus or germinal vesicle (GV) exhibits characteristic chromatin configurations, which are subject to dynamic modifications through oogenesis. Aim of this review is to highlight how changes in chromatin configurations are related to both functional and structural modifications occurring in the oocyte nuclear and cytoplasmic compartments. During the long phase of meiotic arrest at the diplotene stage, the chromatin enclosed within the GV is subjected to several levels of regulation. Morphologically, the chromosomes lose their individuality and form a loose chromatin mass. The decondensed configuration of chromatin then undergoes profound rearrangements during the final stages of oocyte growth that are tightly associated with the acquisition of meiotic and developmental competence. Functionally, the discrete stages of chromatin condensation are characterized by different level of transcriptional activity, DNA methylation and covalent histone modifications. Interestingly, the program of chromatin rearrangement is not completely intrinsic to the oocyte, but follicular cells exert their regulatory actions through gap junction mediated communications and intracellular messenger dependent mechanism(s). With this in mind and since oocyte growth mostly relies on the bidirectional interaction with the follicular cells, a connection between cumulus cells gene expression profile and oocyte developmental competence, according to chromatin configuration is proposed. This analysis can help in identifying candidate genes involved in the process of oocyte developmental competence acquisition and in providing non-invasive biomarkers of oocyte health status that can have important implications in treating human infertility as well as managing breeding schemes in domestic mammals.

  1. Time-Discrete Higher-Order ALE Formulations: Stability

    KAUST Repository

    Bonito, Andrea

    2013-01-01

    Arbitrary Lagrangian Eulerian (ALE) formulations deal with PDEs on deformable domains upon extending the domain velocity from the boundary into the bulk with the purpose of keeping mesh regularity. This arbitrary extension has no effect on the stability of the PDE but may influence that of a discrete scheme. We examine this critical issue for higher-order time stepping without space discretization. We propose time-discrete discontinuous Galerkin (dG) numerical schemes of any order for a time-dependent advection-diffusion-model problem in moving domains, and study their stability properties. The analysis hinges on the validity of the Reynold\\'s identity for dG. Exploiting the variational structure and assuming exact integration, we prove that our conservative and nonconservative dG schemes are equivalent and unconditionally stable. The same results remain true for piecewise polynomial ALE maps of any degree and suitable quadrature that guarantees the validity of the Reynold\\'s identity. This approach generalizes the so-called geometric conservation law to higher-order methods. We also prove that simpler Runge-Kutta-Radau methods of any order are conditionally stable, that is, subject to a mild ALE constraint on the time steps. Numerical experiments corroborate and complement our theoretical results. © 2013 Society for Industrial and Applied Mathematics.

  2. Structure and function insights into the NuRD chromatin remodeling complex.

    Science.gov (United States)

    Torchy, Morgan P; Hamiche, Ali; Klaholz, Bruno P

    2015-07-01

    Transcription regulation through chromatin compaction and decompaction is regulated through various chromatin-remodeling complexes such as nucleosome remodeling and histone deacetylation (NuRD) complex. NuRD is a 1 MDa multi-subunit protein complex which comprises many different subunits, among which histone deacetylases HDAC1/2, ATP-dependent remodeling enzymes CHD3/4, histone chaperones RbAp46/48, CpG-binding proteins MBD2/3, the GATAD2a (p66α) and/or GATAD2b (p66β) and specific DNA-binding proteins MTA1/2/3. Here, we review the currently known crystal and NMR structures of these subunits, the functional data and their relevance for biomedical research considering the implication of NuRD subunits in cancer and various other diseases. The complexity of this macromolecular assembly, and its poorly understood mode of interaction with the nucleosome, the repeating unit of chromatin, illustrate that this complex is a major challenge for structure-function relationship studies which will be tackled best by an integrated biology approach.

  3. LINE retrotransposon RNA is an essential structural and functional epigenetic component of a core neocentromeric chromatin.

    Directory of Open Access Journals (Sweden)

    Anderly C Chueh

    2009-01-01

    Full Text Available We have previously identified and characterized the phenomenon of ectopic human centromeres, known as neocentromeres. Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres. Recent studies have indicated that neocentromere formation provides a major mechanism for centromere repositioning, karyotype evolution, and speciation. Using a marker chromosome mardel(10 containing a neocentromere formed at the normal chromosomal 10q25 region, we have previously mapped a 330-kb CENP-A-binding domain and described an increased prevalence of L1 retrotransposons in the underlying DNA sequences of the CENP-A-binding clusters. Here, we investigated the potential role of the L1 retrotransposons in the regulation of neocentromere activity. Determination of the transcriptional activity of a panel of full-length L1s (FL-L1s across a 6-Mb region spanning the 10q25 neocentromere chromatin identified one of the FL-L1 retrotransposons, designated FL-L1b and residing centrally within the CENP-A-binding clusters, to be transcriptionally active. We demonstrated the direct incorporation of the FL-L1b RNA transcripts into the CENP-A-associated chromatin. RNAi-mediated knockdown of the FL-L1b RNA transcripts led to a reduction in CENP-A binding and an impaired mitotic function of the 10q25 neocentromere. These results indicate that LINE retrotransposon RNA is a previously undescribed essential structural and functional component of the neocentromeric chromatin and that retrotransposable elements may serve as a critical epigenetic determinant in the chromatin remodelling events leading to neocentromere formation.

  4. Fractal Characterization of Chromatin Decompaction in Live Cells.

    Science.gov (United States)

    Yi, Ji; Stypula-Cyrus, Yolanda; Blaha, Catherine S; Roy, Hemant K; Backman, Vadim

    2015-12-01

    Chromatin organization has a fundamental impact on the whole spectrum of genomic functions. Quantitative characterization of the chromatin structure, particularly at submicron length scales where chromatin fractal globules are formed, is critical to understanding this structure-function relationship. Such analysis is currently challenging due to the diffraction-limited resolution of conventional light microscopy. We herein present an optical approach termed inverse spectroscopic optical coherence tomography to characterize the mass density fractality of chromatin, and we apply the technique to observe chromatin decompaction in live cells. The technique makes it possible for the first time, to our knowledge, to sense intracellular morphology with length-scale sensitivity from ∼30 to 450 nm, thus primarily probing the higher-order chromatin structure, without resolving the actual structures. We used chromatin decompaction due to inhibition of histone deacytelases and measured the subsequent changes in the fractal dimension of the intracellular structure. The results were confirmed by transmission electron microscopy and confocal fluorescence microscopy.

  5. TM6, a novel nuclear matrix attachment region, enhances its flanking gene expression through influencing their chromatin structure.

    Science.gov (United States)

    Ji, Lusha; Xu, Rui; Lu, Longtao; Zhang, Jiedao; Yang, Guodong; Huang, Jinguang; Wu, Changai; Zheng, Chengchao

    2013-08-01

    Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.

  6. Analytical Higher-Order Model for Flexible and Stretchable Sensors

    Institute of Scientific and Technical Information of China (English)

    ZHANG Yongfang; ZHU Hongbin; LIU Cheng; LIU Xu; LIU Fuxi; L Yanjun

    2015-01-01

    The stretchable sensor wrapped around a foldable airfoil or embedded inside of it has great potential for use in the monitoring of the structural status of the foldable airfoil. The design methodology is important to the development of the stretchable sensor for status monitoring on the foldable airfoil. According to the requirement of mechanical flexibility of the sensor, the combined use of a layered flexible structural formation and a strain isolation layer is implemented. An analytical higher-order model is proposed to predict the stresses of the strain-isolation layer based on the shear-lag model for the safe design of the flexible and stretchable sensors. The normal stress and shear stress equations in the constructed structure of the sensors are obtained by the proposed model. The stress distribution in the structure is investigated when bending load is applied to the structures. The numerical results show that the proposed model can predict the variation of normal stress and shear stress along the thickness of the strain-isolation (polydimethylsiloxane) layer accurately. The results by the proposed model are in good agreement with the finite element method, in which the normal stress is variable while the shear stress is invariable along the thickness direction of strain-isolation layer. The high-order model is proposed to predict the stresses of the layered structure of the flexible and stretchable sensor for monitoring the status of the foldable airfoil.

  7. Skinner-Rusk unified formalism for higher-order systems

    Science.gov (United States)

    Prieto-Martínez, Pedro Daniel; Román-Roy, Narciso

    2012-07-01

    The Lagrangian-Hamiltonian unified formalism of R. Skinner and R. Rusk was originally stated for autonomous dynamical systems in classical mechanics. It has been generalized for non-autonomous first-order mechanical systems, first-order and higher-order field theories, and higher-order autonomous systems. In this work we present a generalization of this formalism for higher-order non-autonomous mechanical systems.

  8. Higher order mode analysis of the SPL cavities

    CERN Document Server

    Schuh, M; Tuckmantel, J; Welsch, CP

    2010-01-01

    Higher Order Modes (HOMs) can severely limit the operation of superconducting cavities in a linac with high beam current, high duty factor and complex pulse structure. The full HOM spectrum has to be analyzed in order to identify potentially dangerous modes already during the design phase and to define their damping requirements. For this purpose a dedicated beam simulation code focused on beam-HOMinteraction was developed, taking into account important effects like the HOMfrequency spread, beam input jitter, different chopping patterns, as well as klystron and alignment errors. Here, the code is used to investigate in detail the HOM properties of the cavities foreseen in the Superconducting Proton Linac (SPL) at CERN and their potential to drive beam instabilities. Special attention is given to HOM excitation by chopped pulses with high repetition rate.

  9. Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions.

    Science.gov (United States)

    Schep, Alicia N; Buenrostro, Jason D; Denny, Sarah K; Schwartz, Katja; Sherlock, Gavin; Greenleaf, William J

    2015-11-01

    Transcription factors canonically bind nucleosome-free DNA, making the positioning of nucleosomes within regulatory regions crucial to the regulation of gene expression. Using the assay of transposase accessible chromatin (ATAC-seq), we observe a highly structured pattern of DNA fragment lengths and positions around nucleosomes in Saccharomyces cerevisiae, and use this distinctive two-dimensional nucleosomal "fingerprint" as the basis for a new nucleosome-positioning algorithm called NucleoATAC. We show that NucleoATAC can identify the rotational and translational positions of nucleosomes with up to base-pair resolution and provide quantitative measures of nucleosome occupancy in S. cerevisiae, Schizosaccharomyces pombe, and human cells. We demonstrate the application of NucleoATAC to a number of outstanding problems in chromatin biology, including analysis of sequence features underlying nucleosome positioning, promoter chromatin architecture across species, identification of transient changes in nucleosome occupancy and positioning during a dynamic cellular response, and integrated analysis of nucleosome occupancy and transcription factor binding.

  10. Adaptive Integral Method for Higher Order Method of Moments

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Meincke, Peter

    2008-01-01

    The adaptive integral method (AIM) is combined with the higher order method of moments (MoM) to solve integral equations. The technique takes advantage of the low computational complexity and memory requirements of the AIM and the reduced number of unknowns and higher order convergence of higher...... order basis functions. The classical AIM is appropriately modified to allow larger discretization elements and, consequently, higher basis function expansion orders. Numerical examples based on the higher order hierarchical Legendre basis functions show the advantages of the proposed technique over...... the classical AIM based on low-order basis functions in terms of memory and computational time....

  11. Higher Order Diffraction Characteristics of Fiber Bragg Grating

    Directory of Open Access Journals (Sweden)

    Sunita P. Ugale

    2013-02-01

    Full Text Available The effect of grating saturation on higher order diffraction characteristic of FBG is investigated by using Coupled mode theory. Grating saturation effects were considered in the index distribution model showing the significant influence on the coupling process and hence on the reflectivity characteristics of FBG. Maximum reflectivity curves for first and higher order diffraction of FBG are plotted for different values of saturation coefficient. The effect of change in length and change in refractive index are studied. The behavior of grating for higher order of diffraction is totally different than first order of diffraction. In saturated gratings, the higher order diffraction can be utilized for multiparameter sensing

  12. Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging.

    Science.gov (United States)

    Cherstvy, A G; Teif, V B

    2013-06-01

    Chromatin domains formed in vivo are characterized by different types of 3D organization of interconnected nucleosomes and architectural proteins. Here, we quantitatively test a hypothesis that the similarities in the structure of chromatin fibers (which we call "structural homology") can affect their mutual electrostatic and protein-mediated bridging interactions. For example, highly repetitive DNA sequences in heterochromatic regions can position nucleosomes so that preferred inter-nucleosomal distances are preserved on the surfaces of neighboring fibers. On the contrary, the segments of chromatin fiber formed on unrelated DNA sequences have different geometrical parameters and lack structural complementarity pivotal for stable association and cohesion. Furthermore, specific functional elements such as insulator regions, transcription start and termination sites, and replication origins are characterized by strong nucleosome ordering that might induce structure-driven iterations of chromatin fibers. We propose that shape-specific protein-bridging interactions facilitate long-range pairing of chromatin fragments, while for closely-juxtaposed fibers electrostatic forces can in addition yield fine-tuned structure-specific recognition and pairing. These pairing effects can account for some features observed for mitotic and inter-phase chromatins.

  13. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

    Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

  14. Higher-order phase transitions on financial markets

    Science.gov (United States)

    Kasprzak, A.; Kutner, R.; Perelló, J.; Masoliver, J.

    2010-08-01

    Statistical and thermodynamic properties of the anomalous multifractal structure of random interevent (or intertransaction) times were thoroughly studied by using the extended continuous-time random walk (CTRW) formalism of Montroll, Weiss, Scher, and Lax. Although this formalism is quite general (and can be applied to any interhuman communication with nontrivial priority), we consider it in the context of a financial market where heterogeneous agent activities can occur within a wide spectrum of time scales. As the main general consequence, we found (by additionally using the Saddle-Point Approximation) the scaling or power-dependent form of the partition function, Z(q'). It diverges for any negative scaling powers q' (which justifies the name anomalous) while for positive ones it shows the scaling with the general exponent τ(q'). This exponent is the nonanalytic (singular) or noninteger power of q', which is one of the pilar of higher-order phase transitions. In definition of the partition function we used the pausing-time distribution (PTD) as the central one, which takes the form of convolution (or superstatistics used, e.g. for describing turbulence as well as the financial market). Its integral kernel is given by the stretched exponential distribution (often used in disordered systems). This kernel extends both the exponential distribution assumed in the original version of the CTRW formalism (for description of the transient photocurrent measured in amorphous glassy material) as well as the Gaussian one sometimes used in this context (e.g. for diffusion of hydrogen in amorphous metals or for aging effects in glasses). Our most important finding is the third- and higher-order phase transitions, which can be roughly interpreted as transitions between the phase where high frequency trading is most visible and the phase defined by low frequency trading. The specific order of the phase transition directly depends upon the shape exponent α defining the stretched

  15. On the fractional counterpart of the higher-order equations

    CERN Document Server

    D'Ovidio, Mirko

    2011-01-01

    In this work we study the solutions to some fractional higher-order equations. Special cases in which time-fractional derivatives take integer values are also examined and the explicit solutions are presented. Such solutions can be expressed by means of the transition laws of stable subordinators and their inverse processes. In particular we establish connections between fractional and higher-order equations.

  16. Numbers of Subnormal Solutions for Higher Order Periodic Differential Equations

    Institute of Scientific and Technical Information of China (English)

    Zong Xuan CHEN; Kwang Ho SHON

    2011-01-01

    In this paper,we estimate the number of subnormal solutions for higher order linear periodic differential equations,and estimate the growth of subnormal solutions and all other solutions.We also give a representation of subnormal solutions of a class of higher order linear periodic differential equations.

  17. Conservation Laws in Higher-Order Nonlinear Optical Effects

    CERN Document Server

    Kim, J; Shin, H J; Kim, Jongbae

    1999-01-01

    Conservation laws of the nonlinear Schrödinger equation are studied in the presence of higher-order nonlinear optical effects including the third-order dispersion and the self-steepening. In a context of group theory, we derive a general expression for infinitely many conserved currents and charges of the coupled higher-order nonlinear Schrödinger equation. The first few currents and charges are also presented explicitly. Due to the higher-order effects, conservation laws of the nonlinear Schrödinger equation are violated in general. The differences between the types of the conserved currents for the Hirota and the Sasa-Satsuma equations imply that the higher-order terms determine the inherent types of conserved quantities for each integrable cases of the higher-order nonlinear Schrödinger equation.

  18. Replication domains are self-interacting structural chromatin units of human chromosomes

    Science.gov (United States)

    Arneodo, Alain

    2011-03-01

    In higher eukaryotes, the absence of specific sequence motifs marking the origins of replication has been a serious hindrance to the understanding of the mechanisms that regulate the initiation and the maintenance of the replication program in different cell types. In silico analysis of nucleotide compositional skew has predicted the existence, in the germline, of replication N-domains bordered by putative replication origins and where the skew decreases rather linearly as the signature of a progressive inversion of the average fork polarity. Here, from the demonstration that the average fork polarity can be directly extracted from the derivative of replication timing profiles, we develop a wavelet-based pattern recognition methodology to delineate replication U-domains where the replication timing profile is shaped as a U and its derivative as a N. Replication U-domains are robustly found in seven cell lines as covering a significant portion (40-50%) of the human genome where the replication timing data actually displays some plasticity between cell lines. The early replication initiation zones at U-domains borders are found to be hypersensitive to DNase I cleavage, to be associated with transcriptional activity and to present a significant enrichment in insular-binding proteins CTCF, the hallmark of an open chromatin structure. A comparative analysis of genome-wide chromatin interaction (HiC) data shows that replication-U domains correspond to self-interacting structural high order chromatin units of megabase characteristic size. Taken together, these findings provide evidence that the epigenetic compartmentalization of the human genome into autonomous replication U-domains comes along with an extensive remodelling of the threedimensional chromosome architecture during development or in specific diseases. The observed cell specific conservation of the replication timing between the human and mouse genomes strongly suggests that this chromosome organization into

  19. ATRX in chromatin assembly and genome architecture during development and disease.

    Science.gov (United States)

    Bérubé, Nathalie G

    2011-10-01

    The regulation of genome architecture is essential for a variety of fundamental cellular phenomena that underlie the complex orchestration of mammalian development. The ATP-dependent chromatin remodeling protein ATRX is emerging as a key regulatory component of nucleosomal dynamics and higher order chromatin conformation. Here we provide an overview of the role of ATRX at chromatin and during development, and discuss recent studies exposing a repertoire of ATRX functions at heterochromatin, in gene regulation, and during mitosis and meiosis. Exciting new progress on several fronts suggest that ATRX operates in histone variant deposition and in the modulation of higher order chromatin structure. Not surprisingly, dysfunction or absence of ATRX protein has devastating consequences on embryonic development and leads to human disease.

  20. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure.

    Directory of Open Access Journals (Sweden)

    Nicolas M Berbenetz

    2010-09-01

    Full Text Available Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers positions nucleosomes adjacent to the origin to promote replication origin function.

  1. Fine analysis of the chromatin structure of yeast RNA polymerase Ⅱ transcription teminators

    Institute of Scientific and Technical Information of China (English)

    HUGENGXI; YUNHUAYU; 等

    1992-01-01

    In order to study the functional structure of the transcription terminators and the mechanism of temination,a survey of the chromatin structure,including the location of DNase I hypersensitive sites and the nucleosome arrangement,of yeast ADH1 and FLP terminators was made.The results show that there is no relationship between the function of the terminators and the existence of DNase I hypersensitive sites.However,it is found that there is always a nucleosmoe at the immediate upstream of the transcriptional termination sites.As a control,the chromatin structures of the pBR322 DNA fragments on the yeast shutter vectors are also investigated at the same time.The random nucleosome arrangement on the bacterial DNA in yesast agrees with the published reports.A new hypothesis,about the mechanism of transcriptional termination is put forward and the reason of different nucleosome arrengement on the DNAs which are originally from different species in yeast is discussed.

  2. Higher-order graph wavelets and sparsity on circulant graphs

    Science.gov (United States)

    Kotzagiannidis, Madeleine S.; Dragotti, Pier Luigi

    2015-08-01

    The notion of a graph wavelet gives rise to more advanced processing of data on graphs due to its ability to operate in a localized manner, across newly arising data-dependency structures, with respect to the graph signal and underlying graph structure, thereby taking into consideration the inherent geometry of the data. In this work, we tackle the problem of creating graph wavelet filterbanks on circulant graphs for a sparse representation of certain classes of graph signals. The underlying graph can hereby be data-driven as well as fixed, for applications including image processing and social network theory, whereby clusters can be modelled as circulant graphs, respectively. We present a set of novel graph wavelet filter-bank constructions, which annihilate higher-order polynomial graph signals (up to a border effect) defined on the vertices of undirected, circulant graphs, and are localised in the vertex domain. We give preliminary results on their performance for non-linear graph signal approximation and denoising. Furthermore, we provide extensions to our previously developed segmentation-inspired graph wavelet framework for non-linear image approximation, by incorporating notions of smoothness and vanishing moments, which further improve performance compared to traditional methods.

  3. A Recurrence Relation Approach to Higher Order Quantum Superintegrability

    Directory of Open Access Journals (Sweden)

    Ernie G. Kalnins

    2011-03-01

    Full Text Available We develop our method to prove quantum superintegrability of an integrable 2D system, based on recurrence relations obeyed by the eigenfunctions of the system with respect to separable coordinates. We show that the method provides rigorous proofs of superintegrability and explicit constructions of higher order generators for the symmetry algebra. We apply the method to 5 families of systems, each depending on a parameter k, including most notably the caged anisotropic oscillator, the Tremblay, Turbiner and Winternitz system and a deformed Kepler-Coulomb system, and we give proofs of quantum superintegrability for all rational values of k, new for 4 of these systems. In addition, we show that the explicit information supplied by the special function recurrence relations allows us to prove, for the first time in 4 cases, that the symmetry algebra generated by our lowest order symmetries closes and to determine the associated structure equations of the algebras for each k. We have no proof that our generating symmetries are of lowest possible order, but we have no counterexamples, and we are confident we can can always find any missing generators from our raising and lowering operator recurrences. We also get for free, one variable models of the action of the symmetry algebra in terms of difference operators. We describe how the Stäckel transform acts and show that it preserves the structure equations.

  4. Non-rigid registration using higher-order mutual information

    Science.gov (United States)

    Rueckert, D.; Clarkson, M. J.; Hill, D. L. G.; Hawkes, D. J.

    2000-03-01

    Non-rigid registration of multi-modality images is an important tool for assessing temporal and structural changesbetween images. For rigid registration, voxel similarity measures like mutual information have been shown to alignimages from different modalities accurately and robustly. For non-rigid registration, mutual information can besensitive to local variations of intensity which in MR images may be caused by RF inhomogeneity. The reasonfor the sensitivity of mutual information towards intensity variations stems from the fact that mutual informationignores any spatial information. In this paper we propose an extension of the mutual information framework whichincorporates spatial information about higher-order image structure into the registration process and has the potentialto improve the accuracy and robustness of non-rigid registration in the presence of intensity variations. We haveapplied the non-rigid registration algorithm to a number of simulated MR brain images of a digital phantom whichhave been degraded by a simulated intensity shading and a known deformation. In addition, we have applied thealgorithm for the non-rigid registration of eight pre- and post-operative brain MR images which were acquired withan interventional MR scanner and therefore have substantial intensity shading due to RF field inhomogeneities. Inall cases the second-order estimate of mutual information leads to robust and accurate registration.

  5. Modeling Human Behaviour with Higher Order Logic: Insider Threats

    DEFF Research Database (Denmark)

    Boender, Jaap; Ivanova, Marieta Georgieva; Kammuller, Florian;

    2014-01-01

    to and implemented in Higher Order Logic. We validate this working hypothesis by revisiting Weber’s understanding explanation. We focus on constructive realism in the context of logical explanation. We review Higher Order Logic (HOL) as a foundation for computer science and summarize its use of theories relating...... it to the sociological process of logical explanation. As a case study on modeling human behaviour, we present the modeling and analysis of insider threats as a Higher Order Logic theory in Isabelle/HOL. We show how each of the three step process of sociological explanation can be seen in our modeling of insider’s state...

  6. Solution of Higher-Order ODEs Using Backward Difference Method

    Directory of Open Access Journals (Sweden)

    Mohamed Bin Suleiman

    2011-01-01

    Full Text Available The current numerical technique for solving a system of higher-order ordinary differential equations (ODEs is to reduce it to a system of first-order equations then solving it using first-order ODE methods. Here, we propose a method to solve higher-order ODEs directly. The formulae will be derived in terms of backward difference in a constant stepsize formulation. The method developed will be validated by solving some higher-order ODEs directly with constant stepsize. To simplify the evaluations of the integration coefficients, we find the relationship between various orders. The result presented confirmed our hypothesis.

  7. Higher-order harmonics of general limited diffraction Bessel beams

    Science.gov (United States)

    Ding, De-Sheng; Huang, Jin-Huang

    2016-12-01

    In this paper, we extensively study the higher-order harmonic generation of the general limited diffraction m-th-order Bessel beam. The analysis is based on successive approximations of the Khokhlov-Zabolotskaya-Kuznetsov (KZK) equation. Asymptotic expansions are presented for higher-order harmonic Bessel beams in near and far fields. The validity of asymptotic approximation is also analyzed. The higher-order harmonic of the Bessel beam with the lowest zero-order is taken as a special example. Project supported by the National Natural Science Foundation of China (Grant Nos. 11074038 and 11374051).

  8. Exposure to Hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    David eRoquis

    2014-07-01

    Full Text Available Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharziasis, a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the 20th century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited. Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modification were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.

  9. Sperm chromatin structure assay (SCSA): a tool in diagnosis and treatment of infertility

    Institute of Scientific and Technical Information of China (English)

    Mona Bungum; Leif Bungum; Aleksander Giwercman

    2011-01-01

    Diagnosis of male infertility has mainly been based on the World Health Organization (WHO) manual-based semen parameter's concentration,motility and morphology.It has,however,become apparent that none of these parameters are reliable markers for evaluation of the fertility potential of a couple.A search for better markers has led to an increased focus on sperm chromatin integrity testing in fertility work-up and assisted reproductive techniques.During the last couple of decades,numerous sperm DNA integrity tests have been developed.These are claimed to be characterized by a lower intraindividual variation,less intralaboratory and interlaboratory variation and thus less subjective than the conventional sperm analysis.However,not all the sperm chromatin integrity tests have yet been shown to be of clinical value.So far,the test that has been found to have the most stable clinical threshold values in relation to fertility is the sperm chromatin structure assay (SCSA),a flow cytometric test that measures the susceptibility of sperm DNA to acid-induced DNA denaturation in situ.Sperm DNA fragmentation as measured by SCSA has shown to be an independent predictor of successful pregnancy in first pregnancy planners as well as in couples undergoing intrauterine insemination,and can be used as a tool in investigation,counseling and treatment of involuntary childlessness.More conflicting data exist regarding the role of sperm DNA fragmentation in relation to fertilization,pre-embryo development and pregnancy outcome in in vitrofertilization and intracytoplasmic sperm injection (ICSI).

  10. Higher order microfibre modes for dielectric particle trapping and propulsion

    CERN Document Server

    Maimaiti, Aili; Sergides, Marios; Gusachenko, Ivan; Chormaic, Síle Nic

    2014-01-01

    Optical manipulation in the vicinity of optical micro- and nanofibres has shown potential across several fields in recent years, including microparticle control, and cold atom probing and trapping. To date, most work has focussed on propagation of the fundamental mode through the fibre. However, along the maximum mode intensity axis, higher order modes have a longer evanescent field extension and larger field amplitude at the fibre waist compared to the fundamental mode, opening up new possibilities for optical manipulation and particle trapping. In this work, we demonstrate a microfibre/optical tweezers compact system for trapping and propelling dielectric particles based on the excitation of the first group of higher order modes at the fibre waist. Single polystyrene particles were trapped and propelled in the evanescent fields of higher order and fundamental modes near the surface of microfibres. Speed enhancement of particle propulsion was observed for the higher order modes compared to the fundamental mo...

  11. On Doubly Degenerate Quasilinear Parabolic Equations of Higher Order

    Institute of Scientific and Technical Information of China (English)

    Zhen Hai LIU

    2005-01-01

    We deal with the existence of periodic solutions for doubly degenerate quasilinear parabolic equations of higher order, which can degenerate, on a part of the boundary, on a segment in the interior of the domain and in time.

  12. Unambiguous formalism for higher order Lagrangian field theories

    Energy Technology Data Exchange (ETDEWEB)

    Campos, Cedric M; De Leon, Manuel; De Diego, David MartIn [Instituto de Ciencias Matematicas, CSIC-UAM-UC3M-UCM, Serrano 123, 28006 Madrid (Spain); Vankerschaver, Joris [Control and Dynamical Systems, California Institute of Technology, CA (United States)], E-mail: cedricmc@imaff.cfmac.csic.es, E-mail: mdeleon@imaff.cfmac.csic.es, E-mail: d.martin@imaff.cfmac.csic.es, E-mail: jv@caltech.edu

    2009-11-27

    The aim of this paper is to propose an unambiguous intrinsic formalism for higher order field theories which avoids the arbitrariness in the generalization of the conventional description of field theories, and implies the existence of different Cartan forms and Legendre transformations. We propose a differential-geometric setting for the dynamics of a higher order field theory, based on the Skinner and Rusk formalism for mechanics. This approach incorporates aspects of both the Lagrangian and the Hamiltonian description, since the field equations are formulated using the Lagrangian on a higher order jet bundle and the canonical multisymplectic form on its affine dual. As both of these objects are uniquely defined, the Skinner-Rusk approach has the advantage that it does not suffer from the arbitrariness in conventional descriptions. The result is that we obtain a unique and global intrinsic version of the Euler-Lagrange equations for higher order field theories. Several examples illustrate our construction.

  13. Development of a core confidence-higher order construct.

    Science.gov (United States)

    Stajkovic, Alexander D

    2006-11-01

    The author develops core confidence as a higher order construct and suggests that a core confidence-higher order construct--not addressed by extant work motivation theories--is helpful in better understanding employee motivation in today's rapidly changing organizations. Drawing from psychology (social, clinical, and developmental) and social anthropology, the author develops propositions regarding the relationships between core confidence and performance, attitudes, and subjective well-being. The core confidence-higher order construct is proposed to be manifested by hope, self-efficacy, optimism, and resilience. The author reasons that these four variables share a common confidence core (a higher order construct) and may be considered as its manifestations. Suggestions for future research and implications of the work are discussed.

  14. Demand-Driven Higher-Order Fixpoint Iteration

    DEFF Research Database (Denmark)

    Rosendahl, Mads

    Our aim is to show that techniques from higher-order strictness analysis may be used as a general algorithmic principle in a functional programming language. Certain problems may be expressed as the search for the least solution that satisfy certain given properties. This is often done using some...... kind of fixpoint iteration. We will present a fixpoint operation that can be used for second-order functions and extend this to higher-order functions. The technique is based on using partial function graphs to represent higher-order objects. The main problem in finding fixpoints for higher......-order functions is to establish a notion of {\\em neededness} so as to restrict the iteration to those parts of the function that may influence the result. This is here done through a uniform extension of the domain of values with need information. The result is an iteration strategy which will terminate if base...

  15. Dual equivalence in models with higher-order derivatives

    CERN Document Server

    Bazeia, D; Nascimento, J R S; Ribeiro, R F; Wotzasek, C

    2003-01-01

    We introduce a class of higher-order derivative models in (2,1) space-time dimensions. The models are described by a vector field, and contain a Proca-like mass term which prevents gauge invariance. We use the gauge embedding procedure to generate another class of higher-order derivative models, gauge-invariant and dual to the former class. We also show that the gauge embedding approach works appropriately when the vector field couples with fermionic matter.

  16. All-fiber Raman Probe using Higher Order Modes

    DEFF Research Database (Denmark)

    Larsen, Stine Højer Møller; Rishøj, Lars Søgaard; Rottwitt, Karsten

    2013-01-01

    We demonstrate the first all-fiber Raman probe utilizing higher order modes for the excitation. The spectrum of cyclohexane is measured using both the fundamental mode as well as in-fiber-generated Bessel-like modes.......We demonstrate the first all-fiber Raman probe utilizing higher order modes for the excitation. The spectrum of cyclohexane is measured using both the fundamental mode as well as in-fiber-generated Bessel-like modes....

  17. Slice Energy in Higher Order Gravity Theories and Conformal Transformations

    CERN Document Server

    Cotsakis, S

    2004-01-01

    We show that there is a generic transport of energy between the scalar field generated by the conformal transformation of higher order gravity theories and the matter component. We give precise relations of this exchange and show that, unless we are in a stationary spacetime, slice energy is not generically conserved. These results translate into statements about the relative behaviour of ordinary matter, dark matter and dark energy in the context of higher order gravity.

  18. Linear matrix differential equations of higher-order and applications

    Directory of Open Access Journals (Sweden)

    Mustapha Rachidi

    2008-07-01

    Full Text Available In this article, we study linear differential equations of higher-order whose coefficients are square matrices. The combinatorial method for computing the matrix powers and exponential is adopted. New formulas representing auxiliary results are obtained. This allows us to prove properties of a large class of linear matrix differential equations of higher-order, in particular results of Apostol and Kolodner are recovered. Also illustrative examples and applications are presented.

  19. Exploiting Higher-order Derivatives in Computational Optimal Control

    OpenAIRE

    Ross, I. Michael; Rea, Jeremy; Fahroo, Fariba

    2002-01-01

    Proceedings of the 10th Mediterranean Conference on Control and Automation -- MED 2002 , Lisbon, Portugal, July7 9-12, 2002 To facilitate generation of real-time solutions to nonlinear optimal control problems, we present a new way of approximating higher-order derivatives that arise in control systems. A Legendre pseudospectral method is presented to efficiently and accurately discretize optimal control problems governed by higher-order dynamical constraints. For mechanical systems, a re...

  20. Higher-Order Quantum-Inspired Genetic Algorithms

    OpenAIRE

    Nowotniak, Robert; Kucharski, Jacek

    2014-01-01

    This paper presents a theory and an empirical evaluation of Higher-Order Quantum-Inspired Genetic Algorithms. Fundamental notions of the theory have been introduced, and a novel Order-2 Quantum-Inspired Genetic Algorithm (QIGA2) has been presented. Contrary to all QIGA algorithms which represent quantum genes as independent qubits, in higher-order QIGAs quantum registers are used to represent genes strings which allows modelling of genes relations using quantum phenomena. Performance comparis...

  1. Higher order derivatives of R-Jacobi polynomials

    Science.gov (United States)

    Das, Sourav; Swaminathan, A.

    2016-06-01

    In this work, the R-Jacobi polynomials defined on the nonnegative real axis related to F-distribution are considered. Using their Sturm-Liouville system higher order derivatives are constructed. Orthogonality property of these higher ordered R-Jacobi polynomials are obtained besides their normal form, self-adjoint form and hypergeometric representation. Interesting results on the Interpolation formula and Gaussian quadrature formulae are obtained with numerical examples.

  2. Higher-order web link analysis using multilinear algebra.

    Energy Technology Data Exchange (ETDEWEB)

    Kenny, Joseph P.; Bader, Brett William (Sandia National Laboratories, Albuquerque, NM); Kolda, Tamara Gibson

    2005-07-01

    Linear algebra is a powerful and proven tool in web search. Techniques, such as the PageRank algorithm of Brin and Page and the HITS algorithm of Kleinberg, score web pages based on the principal eigenvector (or singular vector) of a particular non-negative matrix that captures the hyperlink structure of the web graph. We propose and test a new methodology that uses multilinear algebra to elicit more information from a higher-order representation of the hyperlink graph. We start by labeling the edges in our graph with the anchor text of the hyperlinks so that the associated linear algebra representation is a sparse, three-way tensor. The first two dimensions of the tensor represent the web pages while the third dimension adds the anchor text. We then use the rank-1 factors of a multilinear PARAFAC tensor decomposition, which are akin to singular vectors of the SVD, to automatically identify topics in the collection along with the associated authoritative web pages.

  3. Higher order statistical frequency domain decomposition for operational modal analysis

    Science.gov (United States)

    Nita, G. M.; Mahgoub, M. A.; Sharyatpanahi, S. G.; Cretu, N. C.; El-Fouly, T. M.

    2017-02-01

    Experimental methods based on modal analysis under ambient vibrational excitation are often employed to detect structural damages of mechanical systems. Many of such frequency domain methods, such as Basic Frequency Domain (BFD), Frequency Domain Decomposition (FFD), or Enhanced Frequency Domain Decomposition (EFFD), use as first step a Fast Fourier Transform (FFT) estimate of the power spectral density (PSD) associated with the response of the system. In this study it is shown that higher order statistical estimators such as Spectral Kurtosis (SK) and Sample to Model Ratio (SMR) may be successfully employed not only to more reliably discriminate the response of the system against the ambient noise fluctuations, but also to better identify and separate contributions from closely spaced individual modes. It is shown that a SMR-based Maximum Likelihood curve fitting algorithm may improve the accuracy of the spectral shape and location of the individual modes and, when combined with the SK analysis, it provides efficient means to categorize such individual spectral components according to their temporal dynamics as coherent or incoherent system responses to unknown ambient excitations.

  4. A general higher-order remap algorithm for ALE calculations

    Energy Technology Data Exchange (ETDEWEB)

    Chiravalle, Vincent P [Los Alamos National Laboratory

    2011-01-05

    A numerical technique for solving the equations of fluid dynamics with arbitrary mesh motion is presented. The three phases of the Arbitrary Lagrangian Eulerian (ALE) methodology are outlined: the Lagrangian phase, grid relaxation phase and remap phase. The Lagrangian phase follows a well known approach from the HEMP code; in addition the strain rate andflow divergence are calculated in a consistent manner according to Margolin. A donor cell method from the SALE code forms the basis of the remap step, but unlike SALE a higher order correction based on monotone gradients is also added to the remap. Four test problems were explored to evaluate the fidelity of these numerical techniques, as implemented in a simple test code, written in the C programming language, called Cercion. Novel cell-centered data structures are used in Cercion to reduce the complexity of the programming and maximize the efficiency of memory usage. The locations of the shock and contact discontinuity in the Riemann shock tube problem are well captured. Cercion demonstrates a high degree of symmetry when calculating the Sedov blast wave solution, with a peak density at the shock front that is similar to the value determined by the RAGE code. For a flyer plate test problem both Cercion and FLAG give virtually the same velocity temporal profile at the target-vacuum interface. When calculating a cylindrical implosion of a steel shell, Cercion and FLAG agree well and the Cercion results are insensitive to the use of ALE.

  5. Role of ATRX in chromatin structure and function: implications for chromosome instability and human disease.

    Science.gov (United States)

    De La Fuente, Rabindranath; Baumann, Claudia; Viveiros, Maria M

    2011-08-01

    Functional differentiation of chromatin structure is essential for the control of gene expression, nuclear architecture, and chromosome stability. Compelling evidence indicates that alterations in chromatin remodeling proteins play an important role in the pathogenesis of human disease. Among these, α-thalassemia mental retardation X-linked protein (ATRX) has recently emerged as a critical factor involved in heterochromatin formation at mammalian centromeres and telomeres as well as facultative heterochromatin on the murine inactive X chromosome. Mutations in human ATRX result in an X-linked neurodevelopmental condition with various degrees of gonadal dysgenesis (ATRX syndrome). Patients with ATRX syndrome may exhibit skewed X chromosome inactivation (XCI) patterns, and ATRX-deficient mice exhibit abnormal imprinted XCI in the trophoblast cell line. Non-random or skewed XCI can potentially affect both the onset and severity of X-linked disease. Notably, failure to establish epigenetic modifications associated with the inactive X chromosome (Xi) results in several conditions that exhibit genomic and chromosome instability such as fragile X syndrome as well as cancer development. Insight into the molecular mechanisms of ATRX function and its interacting partners in different tissues will no doubt contribute to our understanding of the pathogenesis of ATRX syndrome as well as the epigenetic origins of aneuploidy. In turn, this knowledge will be essential for the identification of novel drug targets and diagnostic tools for cancer progression as well as the therapeutic management of global epigenetic changes commonly associated with malignant neoplastic transformation.

  6. Methods for Analyzing the Role of DNA Methylation and Chromatin Structure in Regulating T Lymphocyte Gene Expression

    Directory of Open Access Journals (Sweden)

    Lu Qianjin

    2004-01-01

    Full Text Available Chromatin structure, determined in part by DNA methylation, is established during differentiation and prevents expression of genes unnecessary for the function of a given cell type. We reported that DNA methylation and chromatin structure contributes to lymphoid-specific ITGAL (CD11a and PRF1 (perforin expression. We used bisulfite sequencing to compare methylation patterns in the ITGAL promoter and 5' flanking region of T cells and fibroblasts, and in the PRF1 promoter and upstream enhancer of CD4+ and CD8+ T cells with fibroblasts. The effects of methylation on promoter function were tested using regional methylation of reporter constructs, and confirmed by DNA methyltransferase inhibition. The relationship between DNA methylation and chromatin structure was analyzed by DNaseI hypersensitivity. Herein we described the methods and results in greater detail.

  7. Reprogramming chromatin

    DEFF Research Database (Denmark)

    Ehrensberger, Andreas Hasso; Svejstrup, Jesper Qualmann

    2012-01-01

    attributed to high kinetic barriers that affect all cells equally and can only be overcome by rare stochastic events. The barriers to reprogramming are likely to involve transformations of chromatin state because (i) inhibitors of chromatin-modifying enzymes can enhance the efficiency of reprogramming...... and (ii) knockdown or knock-out of chromatin-modifying enzymes can lower the efficiency of reprogramming. Here, we review the relationship between chromatin state transformations (chromatin reprogramming) and cellular reprogramming, with an emphasis on transcription factors, chromatin remodeling factors...

  8. Dynamics and control of higher-order nonholonomic systems

    Science.gov (United States)

    Rubio Hervas, Jaime

    A theoretical framework is established for the control of higher-order nonholonomic systems, defined as systems that satisfy higher-order nonintegrable constraints. A model for such systems is developed in terms of differential-algebraic equations defined on a higher-order tangent bundle. A number of control-theoretic properties such as nonintegrability, controllability, and stabilizability are presented. Higher-order nonholonomic systems are shown to be strongly accessible and, under certain conditions, small time locally controllable at any equilibrium. There are important examples of higher-order nonholonomic systems that are asymptotically stabilizable via smooth feedback, including space vehicles with multiple slosh modes and Prismatic-Prismatic-Revolute (PPR) robots moving open liquid containers, as well as an interesting class of systems that do not admit asymptotically stabilizing continuous static or dynamic state feedback. Specific assumptions are introduced to define this class, which includes important examples of robotic systems. A discontinuous nonlinear feedback control algorithm is developed to steer any initial state to the equilibrium at the origin. The applicability of the theoretical development is illustrated through two examples: control of a planar PPR robot manipulator subject to a jerk constraint and control of a point mass moving on a constant torsion curve in a three dimensional space.

  9. Objective Reduction Solutions to Higher-Order Boussinesq System in (2+1)-Dimensions

    Institute of Scientific and Technical Information of China (English)

    HU Ya-Hong; ZHENG Chun-Long

    2009-01-01

    With the help of an objective reduction approach (ORA), abundant exact solutions of (2+1)-dimensional higher-order Boussinesq system (including some hyperboloid function solutions, trigonometric function solutions, and a rational function solution) are obtained. It is shown that some novel soliton structures, like single linearity soliton structure, breath soliton structure, single linearity y-periodic solitary wave structure, libration dromion structure, and kink-like multisoliton structure with actual physical meaning exist in the (2+1)-dimensional higher-order Bonssinesq system.

  10. Histone variants: key players of chromatin.

    Science.gov (United States)

    Biterge, Burcu; Schneider, Robert

    2014-06-01

    Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.

  11. Higher-order modulation instability in nonlinear fiber optics.

    Science.gov (United States)

    Erkintalo, Miro; Hammani, Kamal; Kibler, Bertrand; Finot, Christophe; Akhmediev, Nail; Dudley, John M; Genty, Goëry

    2011-12-16

    We report theoretical, numerical, and experimental studies of higher-order modulation instability in the focusing nonlinear Schrödinger equation. This higher-order instability arises from the nonlinear superposition of elementary instabilities, associated with initial single breather evolution followed by a regime of complex, yet deterministic, pulse splitting. We analytically describe the process using the Darboux transformation and compare with experiments in optical fiber. We show how a suitably low frequency modulation on a continuous wave field induces higher-order modulation instability splitting with the pulse characteristics at different phases of evolution related by a simple scaling relationship. We anticipate that similar processes are likely to be observed in many other systems including plasmas, Bose-Einstein condensates, and deep water waves.

  12. Higher-order theories from the minimal length

    Science.gov (United States)

    Dias, M.; Hoff da Silva, J. M.; Scatena, E.

    2016-06-01

    We show that the introduction of a minimal length in the context of noncommutative space-time gives rise (after some considerations) to higher-order theories. We then explicitly demonstrate how these higher-derivative theories appear as a generalization of the standard electromagnetism and general relativity by applying a consistent procedure that modifies the original Maxwell and Einstein-Hilbert actions. In order to set a bound on the minimal length, we compare the deviations from the inverse-square law with the potentials obtained in the higher-order theories and discuss the validity of the results. The introduction of a quantum bound for the minimal length parameter β in the higher-order QED allows us to lower the actual limits on the parameters of higher-derivative gravity by almost half of their order of magnitude.

  13. Higher-order theories from the minimal length

    CERN Document Server

    Dias, Marco; Scatena, Eslley

    2016-01-01

    We show that the introduction of a minimal length in the context of non-commutative spacetime gives rise (after some considerations) to higher-order theories. We then explicitly demonstrate how these higher-derivative theories appear as a generalization of the standard electromagnetism and general relativity by applying a consistent procedure that modifies the original Maxwell and Einstein-Hilbert actions. In order to set a bound on the minimal length, we compare the deviations from the inverse-square law with the potentials obtained in the higher-order theories and discuss the validity of the results. The introduction of a quantum bound for the minimal length parameter $\\sqrt{\\beta}$ in the higher-order QED allows us to lower the actual limits on the parameters of higher-derivative gravity by almost half of their order of magnitude.

  14. Should evolutionary geneticists worry about higher-order epistasis?

    Science.gov (United States)

    Weinreich, Daniel M; Lan, Yinghong; Wylie, C Scott; Heckendorn, Robert B

    2013-12-01

    Natural selection drives evolving populations up the fitness landscape, the projection from nucleotide sequence space to organismal reproductive success. While it has long been appreciated that topographic complexities on fitness landscapes can arise only as a consequence of epistatic interactions between mutations, evolutionary genetics has mainly focused on epistasis between pairs of mutations. Here we propose a generalization to the classical population genetic treatment of pairwise epistasis that yields expressions for epistasis among arbitrary subsets of mutations of all orders (pairwise, three-way, etc.). Our approach reveals substantial higher-order epistasis in almost every published fitness landscape. Furthermore we demonstrate that higher-order epistasis is critically important in two systems we know best. We conclude that higher-order epistasis deserves empirical and theoretical attention from evolutionary geneticists.

  15. Higher-order discrete variational problems with constraints

    Science.gov (United States)

    Colombo, Leonardo; Martín de Diego, David; Zuccalli, Marcela

    2013-09-01

    An interesting family of geometric integrators for Lagrangian systems can be defined using discretizations of the Hamilton's principle of critical action. This family of geometric integrators is called variational integrators. In this paper, we derive new variational integrators for higher-order Lagrangian mechanical system subjected to higher-order constraints. From the discretization of the variational principles, we show that our methods are automatically symplectic and, in consequence, with a very good energy behavior. Additionally, the symmetries of the discrete Lagrangian imply that momentum is conserved by the integrator. Moreover, we extend our construction to variational integrators where the Lagrangian is explicitly time-dependent. Finally, some motivating applications of higher-order problems are considered; in particular, optimal control problems for explicitly time-dependent underactuated systems and an interpolation problem on Riemannian manifolds.

  16. Higher-Order Smoothing:A Novel Semantic Smoothing Method for Text Classification

    Institute of Scientific and Technical Information of China (English)

    Mitat Poyraz; Zeynep Hilal Kilimci; Murat Can Ganiz

    2014-01-01

    It is known that latent semantic indexing (LSI) takes advantage of implicit higher-order (or latent) structure in the association of terms and documents. Higher-order relations in LSI capture “latent semantics”. These findings have inspired a novel Bayesian framework for classification named Higher-Order Naive Bayes (HONB), which was introduced previously, that can explicitly make use of these higher-order relations. In this paper, we present a novel semantic smoothing method named Higher-Order Smoothing (HOS) for the Naive Bayes algorithm. HOS is built on a similar graph based data representation of the HONB which allows semantics in higher-order paths to be exploited. We take the concept one step further in HOS and exploit the relationships between instances of different classes. As a result, we move beyond not only instance boundaries, but also class boundaries to exploit the latent information in higher-order paths. This approach improves the parameter estimation when dealing with insufficient labeled data. Results of our extensive experiments demonstrate the value of HOS on several benchmark datasets.

  17. Higher-order Kerr effect and harmonic cascading in gases

    CERN Document Server

    Bache, Morten; Minardi, Stefano

    2012-01-01

    The higher-order Kerr effect (HOKE) has been recently advocated to explain measurements of the saturation of the nonlinear refractive index in gases. Here we show that cascaded third-harmonic generation results in an effective fifth order nonlinearity that is negative and significant. Higher-order harmonic cascading will also occur from the HOKE, and the cascading contributions may significantly modify the observed nonlinear index change. At lower wavelengths cascading increases the HOKE saturation intensity, while for longer wavelengths cascading will decrease the HOKE saturation intensity.

  18. Interference of selective higher-order modes in optical fibers

    Institute of Scientific and Technical Information of China (English)

    Li Enbang; Peng Gangding

    2007-01-01

    The interference of selective higher-order modes in optical fibers is investigated both theoretically and experimentally.It has been demonstrated that by coupling the LP01 mode in a step-index single-mode fiber(SMF)to the LPom modes in step-index muhimode fibers(MMFs)with different parameters,one can selectively generate higher-order modes and construct all-fiber interferometers.The research presented in this paper forms a basis of a new type of fiber devices with potential applications in fiber sensing,optical fiber communications,and optical signal processing.

  19. Higher-order Laplace equations and hyper-Cauchy distributions

    CERN Document Server

    Orsingher, Enzo

    2012-01-01

    In this paper we introduce new distributions which are solutions of higher-order Laplace equations. It is proved that their densities can be obtained by folding and symmetrizing Cauchy distributions. Another class of probability laws related to higher-order Laplace equations is obtained by composing pseudo-processes with positively-skewed Cauchy distributions which produce asymmetric Cauchy densities in the odd-order case. A special attention is devoted to the third-order Laplace equation where the connection between the Cauchy distribution and the Airy functions is obtained and analyzed.

  20. Higher order nonlinearity and synchronization of quantum cascade lasers

    Institute of Scientific and Technical Information of China (English)

    Taraprasad Chattopadhyay; Prosenjit Bhattacharyya

    2011-01-01

    This paper presents a closed-form analysis of the synchronization phenomenon of the quantum cascade laser (QCL). The analysis has been made with considering higher order nonlinearity of the modal gain of the QCL. The frequency response characteristics of the synchronized QCL along with the stability of the locked state, the effect of nonlinearity on the lockband of the QCL and the amplitude limiting action of the locked QCL have been calculated. The analysis demonstrates the effect of higher order nonlinearity on the properties of the synchronized QCL.

  1. Summation of Higher Order Effects using the Renormalization Group Equation

    CERN Document Server

    Elias, V; Sherry, T N

    2004-01-01

    The renormalization group (RG) is known to provide information about radiative corrections beyond the order in perturbation theory to which one has calculated explicitly. We first demonstrate the effect of the renormalization scheme used on these higher order effects determined by the RG. Particular attention is payed to the relationship between bare and renormalized quantities. Application of the method of characteristics to the RG equation to determine higher order effects is discussed, and is used to examine the free energy in thermal field theory, the relationship between the bare and renormalized coupling and the effective potential in massless scalar electrodynamics.

  2. Detection of small target using recursive higher order statistics

    Science.gov (United States)

    Hou, Wang; Sun, Hongyuan; Lei, Zhihui

    2014-02-01

    In this paper, a recursive higher order statistics algorithm is proposed for small target detection in temporal domain. Firstly, the background of image sequence is normalized. Then, the higher order statistics are recursively solved in image sequence to obtain the feature image. Finally, the feature image is segmented with threshold to detect the small target. To validate the algorithm proposed in this paper, five simulated and one semi-simulation image sequences are created. The ROC curves are employed for evaluation of experimental results. Experiment results show that our method is very effective for small target detection.

  3. The Cauchy problem for higher order abstract differential equations

    CERN Document Server

    Xiao, Ti-Jun

    1998-01-01

    This monograph is the first systematic exposition of the theory of the Cauchy problem for higher order abstract linear differential equations, which covers all the main aspects of the developed theory. The main results are complete with detailed proofs and established recently, containing the corresponding theorems for first and incomplete second order cases and therefore for operator semigroups and cosine functions. They will find applications in many fields. The special power of treating the higher order problems directly is demonstrated, as well as that of the vector-valued Laplace transforms in dealing with operator differential equations and operator families. The reader is expected to have a knowledge of complex and functional analysis.

  4. Threshold resummation and higher order effects in QCD

    Energy Technology Data Exchange (ETDEWEB)

    Ringer, Felix Maximilian

    2015-06-26

    Quantum chromodynamics (QCD) is a quantum field theory that describes the strong interactions between quarks and gluons, the building blocks of all hadrons. Thanks to the experimental progress over the past decades, there has been an ever-growing need for QCD precision calculations for scattering processes involving hadrons. For processes at large momentum transfer, perturbative QCD offers a systematic approach for obtaining precise predictions. This approach relies on two key concepts: the asymptotic freedom of QCD and factorization. In a perturbative calculation at higher orders, the infrared cancellation between virtual and real emission diagrams generally leaves behind logarithmic contributions. In many observables relevant for hadronic scattering these logarithms are associated with a kinematic threshold and are hence known as ''threshold logarithms''. They become large when the available phase space for real gluon emission shrinks. In order to obtain a reliable prediction from QCD, the threshold logarithms need to be taken into account to all orders in the strong coupling constant, a procedure known as ''threshold resummation''. The main focus of my PhD thesis is on studies of QCD threshold resummation effects beyond the next-to-leading logarithmic order. Here we primarily consider the production of hadron pairs in hadronic collisions as an example. In addition, we also consider hadronic jet production, which is particularly interesting for the phenomenology at the LHC. For both processes, we fully take into account the non-trivial QCD color structure of the underlying partonic hard- scattering cross sections. We find that threshold resummation leads to sizable numerical effects in the kinematic regimes relevant for comparisons to experimental data.

  5. A Structural Basis for BRD2/4-Mediated Host Chromatin Interaction and Oligomer Assembly of Kaposi Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus LANA Proteins

    Science.gov (United States)

    Krausze, Joern; Richter, Ulrike; Adler, Heiko; Fedorov, Roman; Pietrek, Marcel; Rückert, Jessica; Ritter, Christiane; Schulz, Thomas F.; Lührs, Thorsten

    2013-01-01

    Kaposi sarcoma-associated herpesvirus (KSHV) establishes a lifelong latent infection and causes several malignancies in humans. Murine herpesvirus 68 (MHV-68) is a related γ2-herpesvirus frequently used as a model to study the biology of γ-herpesviruses in vivo. The KSHV latency-associated nuclear antigen (kLANA) and the MHV68 mLANA (orf73) protein are required for latent viral replication and persistence. Latent episomal KSHV genomes and kLANA form nuclear microdomains, termed ‘LANA speckles’, which also contain cellular chromatin proteins, including BRD2 and BRD4, members of the BRD/BET family of chromatin modulators. We solved the X-ray crystal structure of the C-terminal DNA binding domains (CTD) of kLANA and MHV-68 mLANA. While these structures share the overall fold with the EBNA1 protein of Epstein-Barr virus, they differ substantially in their surface characteristics. Opposite to the DNA binding site, both kLANA and mLANA CTD contain a characteristic lysine-rich positively charged surface patch, which appears to be a unique feature of γ2-herpesviral LANA proteins. Importantly, kLANA and mLANA CTD dimers undergo higher order oligomerization. Using NMR spectroscopy we identified a specific binding site for the ET domains of BRD2/4 on kLANA. Functional studies employing multiple kLANA mutants indicate that the oligomerization of native kLANA CTD dimers, the characteristic basic patch and the ET binding site on the kLANA surface are required for the formation of kLANA ‘nuclear speckles’ and latent replication. Similarly, the basic patch on mLANA contributes to the establishment of MHV-68 latency in spleen cells in vivo. In summary, our data provide a structural basis for the formation of higher order LANA oligomers, which is required for nuclear speckle formation, latent replication and viral persistence. PMID:24146614

  6. The dynamics of individual nucleosomes controls the chromatin condensation pathway: direct AFM visualization of variant chromatin

    CERN Document Server

    Montel, Fabien; Castelnovo, Martin; Bednar, Jan; Dimitrov, Stefan; Angelov, Dimitar; Faivre-Moskalenko, Cendrine

    2009-01-01

    Chromatin organization and dynamics is studied in this work at scales ranging from single nucleosome to nucleosomal array by using a unique combination of biochemical assays, single molecule imaging technique and numerical modeling. We demonstrate that a subtle modification in the nucleosome structure induced by the histone variant H2A.Bbd drastically modifies the higher order organization of the nucleosomal arrays. Importantly, as directly visualized by AFM, conventional H2A nucleosomal arrays exhibit specific local organization, in contrast to H2A.Bbd arrays, which show ?beads on a string? structure. The combination of systematic image analysis and theoretical modeling allows a quantitative description relating the observed gross structural changes of the arrays to their local organization. Our results strongly suggest that higher-order organization of H1-free nucleosomal arrays is mainly determined by the fluctuation properties of individual nucleosomes. Moreover, numerical simulations suggest the existenc...

  7. Extracting the jet azimuthal anisotropy from higher order cumulants

    CERN Document Server

    Lokhtin, Igor P; Snigirev, A M

    2003-01-01

    We analyze the method for calculation of a coefficient of jet azimuthal anisotropy without reconstruction of the nuclear reaction plane considering the higher order correlators between the azimuthal position of jet axis and the angles of particles not incorporated in the jet. The reliability of this technique in the real physical situation under LHC conditions is illustrated.

  8. Higher-order momentum distributions and locally affine LDDMM registration

    DEFF Research Database (Denmark)

    Sommer, Stefan Horst; Nielsen, Mads; Darkner, Sune;

    2013-01-01

    higher-order momentum distributions in the large deformation diffeomorphic metric mapping (LDDMM) registration framework. While the zeroth-order moments previously used in LDDMM only describe local displacement, the first-order momenta that are proposed here represent a basis that allows local...

  9. Decidable Fragments of a Higher Order Calculus with Locations

    DEFF Research Database (Denmark)

    Hüttel, Hans; Godskesen, Jens Christian; Haagensen, Bjørn

    2009-01-01

    Homer is a higher order process calculus with locations. In this paper we study Homer in the setting of the semantic finite control property, which is a finite reachability criterion that implies decidability of barbed bisimilarity. We show that strong and weak barbed bisimilarity are undecidable...... control π-calculus in Homer....

  10. Meta-Logical Reasoning in Higher-Order Logic

    DEFF Research Database (Denmark)

    Villadsen, Jørgen; Schlichtkrull, Anders; Hess, Andreas Viktor

    The semantics of first-order logic (FOL) can be described in the meta-language of higher-order logic (HOL). Using HOL one can prove key properties of FOL such as soundness and completeness. Furthermore, one can prove sentences in FOL valid using the formalized FOL semantics. To aid in the constru...

  11. First Measurements of Higher Order Optics Parameters in the LHC

    CERN Document Server

    Vanbavinckhove, G; Bartolini, R; Calaga, R; Giovannozzi, M; Maclean, E H; Miyamoto, R; Schmidt, F; Tomas, R

    2011-01-01

    Higher order effects can play an important role in the performance of the LHC. Lack of knowledge of these pa- rameters can increase the tune footprint and compromise the beam lifetime. First measurements of these parameters at injection and flattop have been conducted. Detailed sim- ulations are compared to the measurements together with discussions on the measurement limitations.

  12. Higher-Order Integral Equation Methods in Computational Electromagnetics

    DEFF Research Database (Denmark)

    Jørgensen, Erik; Meincke, Peter

    Higher-order integral equation methods have been investigated. The study has focused on improving the accuracy and efficiency of the Method of Moments (MoM) applied to electromagnetic problems. A new set of hierarchical Legendre basis functions of arbitrary order is developed. The new basis...

  13. RECURSIVE CLASSIFICATION OF MQAM SIGNALS BASED ON HIGHER ORDER CUMULANTS

    Institute of Scientific and Technical Information of China (English)

    Chen Weidong; Yang Shaoquan

    2002-01-01

    A new feature based on higher order cumulants is proposed for classification of MQAM signals. Theoretical analysis justify that the new feature is invariant with respect to translation (shift), scale and rotation transform of signal constellations, and can suppress color or white additive Gaussian noise. Computer simulation shows that the proposed recursive orderreduction based classification algorithm can classify MQAM signals with any order.

  14. Higher-Order Coloured Unification and Natural Language Semantics

    CERN Document Server

    Gardent, C; Gardent, Claire; Kohlhase, Michael

    1996-01-01

    In this paper, we show that Higher-Order Coloured Unification - a form of unification developed for automated theorem proving - provides a general theory for modeling the interface between the interpretation process and other sources of linguistic, non semantic information. In particular, it provides the general theory for the Primary Occurrence Restriction which (Dalrymple, Shieber and Pereira, 1991)'s analysis called for.

  15. Building Higher-Order Markov Chain Models with EXCEL

    Science.gov (United States)

    Ching, Wai-Ki; Fung, Eric S.; Ng, Michael K.

    2004-01-01

    Categorical data sequences occur in many applications such as forecasting, data mining and bioinformatics. In this note, we present higher-order Markov chain models for modelling categorical data sequences with an efficient algorithm for solving the model parameters. The algorithm can be implemented easily in a Microsoft EXCEL worksheet. We give a…

  16. Improved Multilevel Fast Multipole Method for Higher-Order discretizations

    DEFF Research Database (Denmark)

    Borries, Oscar Peter; Meincke, Peter; Jorgensen, Erik;

    2014-01-01

    The Multilevel Fast Multipole Method (MLFMM) allows for a reduced computational complexity when solving electromagnetic scattering problems. Combining this with the reduced number of unknowns provided by Higher-Order discretizations has proven to be a difficult task, with the general conclusion b...

  17. Multilevel Fast Multipole Method for Higher Order Discretizations

    DEFF Research Database (Denmark)

    Borries, Oscar Peter; Meincke, Peter; Jorgensen, Erik;

    2014-01-01

    The multi-level fast multipole method (MLFMM) for a higher order (HO) discretization is demonstrated on high-frequency (HF) problems, illustrating for the first time how an efficient MLFMM for HO can be achieved even for very large groups. Applying several novel ideas, beneficial to both lower or...

  18. Numerical modeling of higher order magnetic moments in UXO discrimination

    Science.gov (United States)

    Sanchez, V.; Yaoguo, L.; Nabighian, M.N.; Wright, D.L.

    2008-01-01

    The surface magnetic anomaly observed in unexploded ordnance (UXO) clearance is mainly dipolar, and consequently, the dipole is the only magnetic moment regularly recovered in UXO discrimination. The dipole moment contains information about the intensity of magnetization but lacks information about the shape of the target. In contrast, higher order moments, such as quadrupole and octupole, encode asymmetry properties of the magnetization distribution within the buried targets. In order to improve our understanding of magnetization distribution within UXO and non-UXO objects and to show its potential utility in UXO clearance, we present a numerical modeling study of UXO and related metallic objects. The tool for the modeling is a nonlinear integral equation describing magnetization within isolated compact objects of high susceptibility. A solution for magnetization distribution then allows us to compute the magnetic multipole moments of the object, analyze their relationships, and provide a depiction of the anomaly produced by different moments within the object. Our modeling results show the presence of significant higher order moments for more asymmetric objects, and the fields of these higher order moments are well above the noise level of magnetic gradient data. The contribution from higher order moments may provide a practical tool for improved UXO discrimination. ?? 2008 IEEE.

  19. Higher Order Language Competence and Adolescent Mental Health

    Science.gov (United States)

    Cohen, Nancy J.; Farnia, Fataneh; Im-Bolter, Nancie

    2013-01-01

    Background: Clinic and community-based epidemiological studies have shown an association between child psychopathology and language impairment. The demands on language for social and academic adjustment shift dramatically during adolescence and the ability to understand the nonliteral meaning in language represented by higher order language…

  20. Higher-Order Hierarchical Legendre Basis Functions in Applications

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter;

    2007-01-01

    degree of orthogonality. The basis functions are well-suited for solution of complex electromagnetic problems involving multiple homogeneous or inhomogeneous dielectric regions, metallic surfaces, layered media, etc. This paper presents real-life complex antenna radiation problems modeled...... with electromagnetic simulation tools based on the higher-order hierarchical Legendre basis functions....

  1. Higher Order Risk Attitudes, Demographics, and Financial Decisions

    NARCIS (Netherlands)

    Noussair, C.N.; Trautmann, S.T.; van de Kuilen, G.

    2011-01-01

    We conduct an experiment to study the prevalence of the higher order risk attitudes of prudence and temperance, in a large demographically representative sample, as well as in a sample of undergraduate students. Participants make pairwise choices between lotteries of the form proposed by Eeckhoudt a

  2. Abstract Operators and Higher-order Linear Partial Differential Equation

    Institute of Scientific and Technical Information of China (English)

    BI Guang-qing; BI Yue-kai

    2011-01-01

    We summarize several relevant principles for the application of abstract operators in partial differential equations,and combine abstract operators with the Laplace transform.Thus we have developed the theory of partial differential equations of abstract operators and obtained the explicit solutions of initial value problems for a class of higher-order linear partial differential equations.

  3. Systematic determination of replication activity type highlights interconnections between replication, chromatin structure and nuclear localization.

    Directory of Open Access Journals (Sweden)

    Shlomit Farkash-Amar

    Full Text Available DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR. Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR. Our algorithm, ARTO (Analysis of Replication Timing and Organization, uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10-25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are

  4. Visualization and processing of higher order descriptors for multi-valued data

    CERN Document Server

    Schultz, Thomas

    2015-01-01

    Modern imaging techniques and computational simulations yield complex multi-valued data that require higher-order mathematical descriptors. This book addresses topics of importance when dealing with such data, including frameworks for image processing, visualization, and statistical analysis of higher-order descriptors. It also provides examples of the successful use of higher-order descriptors in specific applications and a glimpse of the next generation of diffusion MRI. To do so, it combines contributions on new developments, current challenges in this area, and state-of-the-art surveys.   Compared to the increasing importance of higher-order descriptors in a range of applications, tools for analysis and processing are still relatively hard to come by. Even though application areas such as medical imaging, fluid dynamics, and structural mechanics are very different in nature they face many shared challenges. This book provides an interdisciplinary perspective on this topic with contributions from key rese...

  5. Beam interactions with surface waves and higher-order modes in oversized backward wave oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Ogura, Kazuo; Kojima, Akihiko; Kawabe, Fumiaki; Yambe, Kiyoyuki [Niigata University, Niigata (Japan); Amin, Ruhul [Islamic University of Technology, Gazipur (Bangladesh)

    2014-10-15

    Beam interactions with surface waves and higher-order modes in an oversized backward wave oscillator (BWO) are studied. In addition to the well-known Cherenkov interaction, the slow cyclotron interaction occurs due to transverse perturbations of the electron beam. The Cherenkov interaction dominates the slow cyclotron interaction. Growth rates of both the interactions for the higher order modes are small compared with those for the surface-wave modes in an oversized BWO. The coaxial slow-wave structure exhibits a reduced number of higher-order modes, which consequently reduces the mode competition problem and improves beam interactions with higher order modes. For higher values of beam currents, the slow cyclotron wave grows at a faster rate than the Cherenkov waves.

  6. Higher order QCD corrections in small x physics

    Energy Technology Data Exchange (ETDEWEB)

    Chachamis, G.

    2006-11-15

    We study higher order QCD corrections in small x Physics. The numerical implementation of the full NLO photon impact factor is the remaining necessary piece for the testing of the NLO BFKL resummation against data from physical processes, such as {gamma}{sup *}{gamma}{sup *} collisions. We perform the numerical integration over phase space for the virtual corrections to the NLO photon impact factor. This, along with the previously calculated real corrections, makes feasible in the near future first estimates for the {gamma}*{gamma}* total cross section, since the convolution of the full impact factor with the NLO BFKL gluon Green's function is now straightforward. The NLO corrections for the photon impact factor are sizeable and negative. In the second part of this thesis, we estimate higher order correction to the BK equation. We are mainly interested in whether partonic saturation delays or not in rapidity when going beyond the leading order. In our investigation, we use the so called 'rapidity veto' which forbid two emissions to be very close in rapidity, to 'switch on' higher order corrections to the BK equation. From analytic and numerical analysis, we conclude that indeed saturation does delay in rapidity when higher order corrections are taken into account. In the last part, we investigate higher order QCD corrections as additional corrections to the Electroweak (EW) sector. The question of whether BFKL corrections are of any importance in the Regge limit for the EW sector seems natural; although they arise in higher loop level, the accumulation of logarithms in energy s at high energies, cannot be dismissed without an investigation. We focus on the process {gamma}{gamma}{yields}ZZ. We calculate the pQCD corrections in the forward region at leading logarithmic (LL) BFKL accuracy, which are of the order of few percent at the TeV energy scale. (orig.)

  7. Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

    OpenAIRE

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes ...

  8. Simulation of Radiation-Induced Damage Distribution to evaluate Models for Higher-Order Chromosome Organisation

    NARCIS (Netherlands)

    T.A. Knoch (Tobias); P. Quicken (Peter); G. Kreth (Gregor); W. Friedland (Werner); A.A. Friedl (Anna)

    2003-01-01

    textabstractThe structure of chromatin at the level of the 30 nm fibre has been studied in considerable detail, but little is known about how this fibre is arranged within the interphase chromosome territory. Over the years, various polymer models were developed to simulate chromosome structure, for

  9. Initial Semantics for higher-order typed syntax in Coq

    Directory of Open Access Journals (Sweden)

    Benedikt Ahrens

    2011-01-01

    Full Text Available Initial Semantics aims at characterizing the syntax associated to a signature as the initial object of some category. We present an initial semantics result for typed higher-order syntax together with its formalization in the Coq proof assistant. The main theorem was first proved on paper in the second author’s PhD thesis in 2010, and verified formally shortly afterwards.To a simply–typed binding signature S over a fixed set T of object types we associate a category called the category of representations of S. We show that this category has an initial object Sigma(S, i.e. an object Sigma(S from which there is precisely one morphism i_R : Sigma(S -> R to any object R of this category. From its construction it will be clear that the object Sigma(S merits the name abstract syntax associated to S: it is given by an inductive set – parametrized by a set of free variables and dependent on object types – the type of whose constructors are each given by the arities of the signature S.Our theorem is implemented and proved correct in the proof assistant Coq through heavy use of dependent types. The approach through monads gives rise to an implementation of syntax where both terms and variables are intrinsically typed, i.e. where the object types are rejected in the meta–level types. Terms are implemented as a Coq data type – which play the role of sets – dependent on an object type as well as on a type family of free variables.This article is to be seen as a research article rather than about the formalization of a classical mathematical result. The nature of our theorem – involving lengthy, technical proofs and complicated algebraic structures – makes it particularly interesting for formal verification. Our goal is to promote the use of computer theorem provers as research tools, and, accordingly, a new way of publishing mathematical results: a parallel description of a theorem and its formalization should allow the verification of

  10. Higher order moments of lensing convergence - I. Estimate from simulations

    CERN Document Server

    Vicinanza, M; Maoli, R; Scaramella, R; Er, X

    2016-01-01

    Large area lensing surveys are expected to make it possible to use cosmic shear tomography as a tool to severely constrain cosmological parameters. To this end, one typically relies on second order statistics such as the two - point correlation fucntion and its Fourier counterpart, the power spectrum. Moving a step forward, we wonder whether and to which extent higher order stastistics can improve the lensing Figure of Merit (FoM). In this first paper of a series, we investigate how second, third and fourth order lensing convergence moments can be measured and use as probe of the underlying cosmological model. We use simulated data and investigate the impact on moments estimate of the map reconstruction procedure, the cosmic variance, and the intrinsic ellipticity noise. We demonstrate that, under realistic assumptions, it is indeed possible to use higher order moments as a further lensing probe.

  11. Higher Order Kernels and Locally Affine LDDMM Registration

    CERN Document Server

    Sommer, Stefan; Darkner, Sune; Pennec, Xavier

    2011-01-01

    To achieve sparse description that allows intuitive analysis, we aim to represent deformation with a basis containing interpretable elements, and we wish to use elements that have the description capacity to represent the deformation compactly. We accomplish this by introducing higher order kernels in the LDDMM registration framework. The kernels allow local description of affine transformations and subsequent compact description of non-translational movement and of the entire non-rigid deformation. This is obtained with a representation that contains directly interpretable information from both mathematical and modeling perspectives. We develop the mathematical construction behind the higher order kernels, we show the implications for sparse image registration and deformation description, and we provide examples of how the capacity of the kernels enables registration with a very low number of parameters. The capacity and interpretability of the kernels lead to natural modeling of articulated movement, and th...

  12. Practical Programming with Higher-Order Encodings and Dependent Types

    DEFF Research Database (Denmark)

    Poswolsky, Adam; Schürmann, Carsten

    2008-01-01

    Higher-order abstract syntax (HOAS) refers to the technique of representing variables of an object-language using variables of a meta-language. The standard first-order alternatives force the programmer to deal with superficial concerns such as substitutions, whose implementation is often routine......, tedious, and error-prone. In this paper, we describe the underlying calculus of Delphin. Delphin is a fully implemented functional-programming language supporting reasoning over higher-order encodings and dependent types, while maintaining the benefits of HOAS. More specifically, just as representations...... utilizing HOAS free the programmer from concerns of handling explicit contexts and substitutions, our system permits programming over such encodings without making these constructs explicit, leading to concise and elegant programs. To this end our system distinguishes bindings of variables intended...

  13. Toddlers infer higher-order relational principles in causal learning.

    Science.gov (United States)

    Walker, Caren M; Gopnik, Alison

    2014-01-01

    Children make inductive inferences about the causal properties of individual objects from a very young age. When can they infer higher-order relational properties? In three experiments, we examined 18- to 30-month-olds' relational inferences in a causal task. Results suggest that at this age, children are able to infer a higher-order relational causal principle from just a few observations and use this inference to guide their own subsequent actions and bring about a novel causal outcome. Moreover, the children passed a revised version of the relational match-to-sample task that has proven very difficult for nonhuman primates. The findings are considered in light of their implications for understanding the nature of relational and causal reasoning, and their evolutionary origins.

  14. Statistics of predictions with missing higher order corrections

    CERN Document Server

    Berthier, Laure

    2016-01-01

    Effective operators have been used extensively to understand small deviations from the Standard Model in the search for new physics. So far there has been no general method to fit for small parameters when higher order corrections in these parameters are present but unknown. We present a new technique that solves this problem, allowing for an exact p-value calculation under the assumption that higher order theoretical contributions can be treated as gaussian distributed random variables. The method we propose is general, and may be used in the analysis of any perturbative theoretical prediction, ie.~truncated power series. We illustrate this new method by performing a fit of the Standard Model Effective Field Theory parameters, which include eg.~anomalous gauge and four-fermion couplings.

  15. Comparison Criteria for Nonlinear Functional Dynamic Equations of Higher Order

    Directory of Open Access Journals (Sweden)

    Taher S. Hassan

    2016-01-01

    Full Text Available We will consider the higher order functional dynamic equations with mixed nonlinearities of the form xnt+∑j=0Npjtϕγjxφjt=0, on an above-unbounded time scale T, where n≥2, xi(t≔ri(tϕαixi-1Δ(t,  i=1,…,n-1,   with  x0=x,  ϕβ(u≔uβsgn⁡u, and α[i,j]≔αi⋯αj. The function φi:T→T is a rd-continuous function such that limt→∞φi(t=∞ for j=0,1,…,N. The results extend and improve some known results in the literature on higher order nonlinear dynamic equations.

  16. Higher order theories and their relationship with noncommutativity

    Energy Technology Data Exchange (ETDEWEB)

    Sánchez-Santos, Oscar, E-mail: oscarsanbuzz@yahoo.com.mx [Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, C.P. 09340, México D.F., México (Mexico); Vergara, José David, E-mail: vergara@nucleares.unam.mx [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Apartado Postal 70-543, C.P. 04510, México D.F., México (Mexico)

    2014-06-13

    We present a relationship between noncommutativity and higher order time derivative theories using a perturbation method. We make a generalization of the Chern–Simons quantum mechanics for higher order time derivatives. This model presents noncommutativity in a natural way when we project to low-energy physical states without the necessity of taking the strong field limit. We quantize the theory using a Bopp's shift of the noncommutative variables and we obtain a spectrum without negative energies, under the perturbation limits. In addition, we extent the model to high order time derivatives and noncommutativity with variable dependent parameter. - Highlights: • We show a relationship between high order derivative theories and noncommutativity. • The noncommutativity appears when we project to low-energy physical states. • We extend the model to high order time derivatives. • We include cases with variable dependent noncommutative parameter.

  17. Promoting higher order thinking skills using inquiry-based learning

    Science.gov (United States)

    Madhuri, G. V.; S. S. N Kantamreddi, V.; Goteti, L. N. S. Prakash

    2012-05-01

    Active learning pedagogies play an important role in enhancing higher order cognitive skills among the student community. In this work, a laboratory course for first year engineering chemistry is designed and executed using an inquiry-based learning pedagogical approach. The goal of this module is to promote higher order thinking skills in chemistry. Laboratory exercises are designed based on Bloom's taxonomy and a just-in-time facilitation approach is used. A pre-laboratory discussion outlining the theory of the experiment and its relevance is carried out to enable the students to analyse real-life problems. The performance of the students is assessed based on their ability to perform the experiment, design new experiments and correlate practical utility of the course module with real life. The novelty of the present approach lies in the fact that the learning outcomes of the existing experiments are achieved through establishing a relationship with real-world problems.

  18. Unusual chromatin structural organization in the sperm head of a murid rodent from southern Africa: the red veld rat, Aethomys chrysophilus type B.

    Science.gov (United States)

    Breed, W G

    1997-11-01

    The structural organization of the chromatin of cauda epididymal spermatozoa of the red veld rat Aethomys chrysophilus type B was investigated by fluorescence microscopy after staining with DNA specific dyes and by transmission electron microscopy after incubation with Triton X100, dithiothreitol, and SDS. Staining with DNA dyes showed variation in intensity of fluorescence of the sperm chromatin, with an anterior spherical region staining far more intensely than the surrounding chromatin. Transmission electron microscopy of these spermatozoa indicated that this region was composed of cords and fibres. This chromatin region dispersed more readily than the surrounding chromatin when spermatozoa were incubated with the detergents, and it is suggested that, unlike the rest of the sperm chromatin, it may be a histone-rich region, with protamine(s) being either scarce or absent.

  19. Higher order relativistic galaxy number counts: dominating terms

    CERN Document Server

    Nielsen, Jeppe Trøst

    2016-01-01

    We review the number counts to second order concentrating on the terms which dominate on sub horizon scales. We re-derive the result for these terms and compare it with the different versions found in the literature. We generalize our derivation to higher order terms, especially the third order number counts which are needed to compute the 1-loop contribution to the power spectrum.

  20. 1957-2007: 50 Years of Higher Order Programming Languages

    OpenAIRE

    Alen Lovrenčić; Mario Konecki; Tihomir Orehovački

    2009-01-01

    Fifty years ago one of the greatest breakthroughs in computer programming and in the history of computers happened -- the appearance of FORTRAN, the first higher-order programming language. From that time until now hundreds of programming languages were invented, different programming paradigms were defined, all with the main goal to make computer programming easier and closer to as many people as possible. Many battles were fought among scientists as well as among developers around concepts ...

  1. Higher-order conditioning and the retrosplenial cortex.

    Science.gov (United States)

    Todd, Travis P; Huszár, Roman; DeAngeli, Nicole E; Bucci, David J

    2016-09-01

    The retrosplenial cortex (RSC) is known to contribute to contextual and spatial learning and memory. This is consistent with its well-established connectivity; the RSC is located at the interface of visuo-spatial association areas and the parahippocampal-hippocampal memory system. However, the RSC also contributes to learning and memory for discrete cues. For example, both permanent lesions and temporary inactivation of the RSC have been shown to impair sensory preconditioning, a form of higher-order conditioning. The purpose of the present experiment was to examine the role of the RSC in a closely related higher-order conditioning paradigm: second-order conditioning. Sham and RSC lesioned rats received first-order conditioning in which one visual stimulus (V1) was paired with footshock and one visual stimulus (V2) was not. Following first-order conditioning, one auditory stimulus (A1) was then paired with V1 and a second auditory stimulus (A2) was paired with V2. Although lesions of the RSC impaired the first-order discrimination, they had no impact on the acquisition of second-order conditioning. Thus, the RSC does not appear necessary for acquisition/expression of second-order fear conditioning. The role of the RSC in higher-order conditioning, as well as a possible dissociation from the hippocampus, is discussed.

  2. Wave Transformation Modeling with Effective Higher-Order Finite Elements

    Directory of Open Access Journals (Sweden)

    Tae-Hwa Jung

    2016-01-01

    Full Text Available This study introduces a finite element method using a higher-order interpolation function for effective simulations of wave transformation. Finite element methods with a higher-order interpolation function usually employ a Lagrangian interpolation function that gives accurate solutions with a lesser number of elements compared to lower order interpolation function. At the same time, it takes a lot of time to get a solution because the size of the local matrix increases resulting in the increase of band width of a global matrix as the order of the interpolation function increases. Mass lumping can reduce computation time by making the local matrix a diagonal form. However, the efficiency is not satisfactory because it requires more elements to get results. In this study, the Legendre cardinal interpolation function, a modified Lagrangian interpolation function, is used for efficient calculation. Diagonal matrix generation by applying direct numerical integration to the Legendre cardinal interpolation function like conducting mass lumping can reduce calculation time with favorable accuracy. Numerical simulations of regular, irregular and solitary waves using the Boussinesq equations through applying the interpolation approaches are carried out to compare the higher-order finite element models on wave transformation and examine the efficiency of calculation.

  3. Higher Order Mode Coupler Heating in Continuous Wave Operation

    Science.gov (United States)

    Solyak, N.; Awida, M.; Hocker, A.; Khabibobulline, T.; Lunin, A.

    Electromagnetic heating due to higher order modes (HOM) propagation is particularly a concern for continuous wave (CW) particle accelerator machines. Power on the order of several watts could flow out of the cavity's HOM ports in CW operations. The upgrade of the Linac Coherent Light Source (LCLS-II) at SLAC requires a major modification of the design of the higher order mode (HOM) antenna and feed through of the conventional ILC elliptical 9-cell cavity in order to utilize it for LCLS-II. The HOM antenna is required to bear higher RF losses, while relatively maintaining the coupling level of the higher order modes. In this paper, we present a detailed analysis of the heating expected in the HOM coupler with a thorough thermal quench study in comparison with the conventional ILC design. We discuss also how the heat will be removed from the cavity through RF cables with specially designed cooling straps. Finally, we report on the latest experimental results of cavity testing in vertical and horizontal cryostats.

  4. Ectopically tethered CP190 induces large-scale chromatin decondensation

    Science.gov (United States)

    Ahanger, Sajad H.; Günther, Katharina; Weth, Oliver; Bartkuhn, Marek; Bhonde, Ramesh R.; Shouche, Yogesh S.; Renkawitz, Rainer

    2014-01-01

    Insulator mediated alteration in higher-order chromatin and/or nucleosome organization is an important aspect of epigenetic gene regulation. Recent studies have suggested a key role for CP190 in such processes. In this study, we analysed the effects of ectopically tethered insulator factors on chromatin structure and found that CP190 induces large-scale decondensation when targeted to a condensed lacO array in mammalian and Drosophila cells. In contrast, dCTCF alone, is unable to cause such a decondensation, however, when CP190 is present, dCTCF recruits it to the lacO array and mediates chromatin unfolding. The CP190 induced opening of chromatin may not be correlated with transcriptional activation, as binding of CP190 does not enhance luciferase activity in reporter assays. We propose that CP190 may mediate histone modification and chromatin remodelling activity to induce an open chromatin state by its direct recruitment or targeting by a DNA binding factor such as dCTCF.

  5. Chromatin assembly using Drosophila systems.

    Science.gov (United States)

    Fyodorov, Dmitry V; Levenstein, Mark E

    2002-05-01

    To successfully study chromatin structure and activity in vitro, it is essential to have a chromatin assembly system that will prepare extended nucleosome arrays with highly defined protein content that resemble bulk chromatin isolated from living cell nuclei in terms of periodicity and nucleosome positioning. The Drosophila ATP-dependent chromatin assembly system described in this unit meets these requirements. The end product of the reaction described here has highly periodic extended arrays with physiologic spacing and positioning of the nucleosomes.

  6. Dynamic Nucleosome Movement Provides Structural Information of Topological Chromatin Domains in Living Human Cells

    Science.gov (United States)

    Shinkai, Soya; Nozaki, Tadasu; Maeshima, Kazuhiro

    2016-01-01

    The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory. We analytically show that the mean-squared displacement (MSD) of nucleosome fluctuations within CDs is subdiffusive. The diffusion coefficient and the subdiffusive exponent depend on the structural information of CDs. This analytical result enabled us to extract information from the single-nucleosome imaging data for HeLa cells. Our observation that the MSD is lower at the nuclear periphery region than the interior region indicates that CDs in the heterochromatin-rich nuclear periphery region are more compact than those in the euchromatin-rich interior region with respect to the fractal dimensions as well as the size. Finally, we evaluated that the average size of CDs is in the range of 100–500 nm and that the relaxation time of nucleosome movement within CDs is a few seconds. Our results provide physical and dynamic insights into the genome architecture in living cells. PMID:27764097

  7. Unifying refinement and hoare-style reasoning in a logic for higher-order concurrency

    DEFF Research Database (Denmark)

    Turon, Aaron; Dreyer, Derek; Birkedal, Lars

    2013-01-01

    Modular programming and modular verification go hand in hand, but most existing logics for concurrency ignore two crucial forms of modularity: *higher-order functions*, which are essential for building reusable components, and *granularity abstraction*, a key technique for hiding the intricacies...... of fine-grained concurrent data structures from the clients of those data structures. In this paper, we present CaReSL, the first logic to support the use of granularity abstraction for modular verification of higher-order concurrent programs. After motivating the features of CaReSL through a variety...

  8. Higher order asymptotic fields for mode Ⅰ crack in functionally gradient material

    Institute of Scientific and Technical Information of China (English)

    DAI Yao; YAN Xiu-fa

    2005-01-01

    Higher order stress fields for a mode Ⅰ crack perpendicular to the direction of property variation in a functionally gradient material(FGM), which has an exponential variation of elastic modulus along the gradient direction, were obtained through an asymptotic analysis. The Poisson's ratio of the FGMs was assumed to be constant throughout the analysis. The first five terms in the asymptotic expansions of crack tip stress fields were derived to bring out the influence of nonhomogeneity on the structure of the stress field explicitly. The analysis reveals that only the higher order terms in the expansion are influenced by the material nonhomogeneity. Moreover, it can be seen from expressions of higher order stress fields that at least three terms must be considered in the case of FGMs in order to explicitly account for the nonhomogeneity effects on the structure of crack tip stress fields.

  9. Higher-order-mode fiber optimized for energetic soliton propagation.

    Science.gov (United States)

    Pedersen, Martin E V; Cheng, Ji; Charan, Kriti; Wang, Ke; Xu, Chris; Grüner-Nielsen, Lars; Jakobsen, Dan

    2012-08-15

    We describe the design optimization of a higher-order-mode (HOM) fiber for energetic soliton propagation at wavelengths below 1300 nm. A new HOM fiber is fabricated according to our design criteria. The HOM fiber is pumped at 1045 nm by an energetic femtosecond fiber laser. The soliton self-frequency shift process shifts the center wavelength of the soliton to 1085 nm. The soliton has a temporal duration of 216 fs and a pulse energy of 6.3 nJ. The demonstrated pulse energy is approximately six times higher than the previous record in a solid core fiber at wavelengths below 1300 nm.

  10. A higher-order duration calculus and its completeness

    Institute of Scientific and Technical Information of China (English)

    詹乃军

    2000-01-01

    This paper studies how to describe the real-time behaviour of programs using duration calculus. Since program variables are interpreted as functions over time in real-time programming, and it is inevitable to introduce quantifications over program variables in order to describe local variable declaration and declare local channel and so on. Therefore to establish a higher-order duration calculus (HDC) is necessary. We first establish HDC, then show some real-time properties of programs in terms of HDC, and then, prove that HDC is complete on abstract domains under the assumption that all program variables vary finitely.

  11. Higher-order photon correlations in pulsed photonic crystal nanolasers

    CERN Document Server

    Elvira, David; Verma, V; Braive, Remy; Beaudoin, Gregoire; Robert-Philip, Isabelle; Sagnes, Isabelle; Baek, Burm; Nam, Sae Woo; Dauler, Eric A; Abram, Izo; Stevens, Martin J; Beveratos, Alexios

    2011-01-01

    We report on the higher-order photon correlations of a high-$\\beta$ nanolaser under pulsed excitation at room temperature. Using a multiplexed four-element superconducting single photon detector we measured g$^{(n)}(\\vec{0})$ with $n$=2,3,4. All orders of correlation display partially chaotic statistics, even at four times the threshold excitation power. We show that this departure from coherence and Poisson statistics is due to the quantum fluctuations associated with the small number of dipoles and photons involved in the lasing process.

  12. Higher order temporal finite element methods through mixed formalisms.

    Science.gov (United States)

    Kim, Jinkyu

    2014-01-01

    The extended framework of Hamilton's principle and the mixed convolved action principle provide new rigorous weak variational formalism for a broad range of initial boundary value problems in mathematical physics and mechanics. In this paper, their potential when adopting temporally higher order approximations is investigated. The classical single-degree-of-freedom dynamical systems are primarily considered to validate and to investigate the performance of the numerical algorithms developed from both formulations. For the undamped system, all the algorithms are symplectic and unconditionally stable with respect to the time step. For the damped system, they are shown to be accurate with good convergence characteristics.

  13. Femtosecond filamentation in air and higher-order nonlinearities

    CERN Document Server

    Kolesik, M; Moloney, J V

    2010-01-01

    According to a recent experiment, the instantaneous electronic Kerr effect in air exhibits a strong intensity dependence, the nonlinear refractive index switching sign and crossing over from a self-focusing to a de-focusing nonlinearity. A subsequent theoretical work has demonstrated that this has paradigm-changing consequences for the understanding of filamentation in air, so it is important to subject the idea of higher-order nonlinearities to stringent tests. Here we use numerical modeling to propose an experiment capable of discriminating between the standard and the new intensity-dependent Kerr-effect models.

  14. Stability and convergence of a higher order rational difference Equation

    CERN Document Server

    Gazor, Hamid

    2011-01-01

    In this paper the asymptotic stability of equilibria and periodic points of the following higher order rational difference Equation x_{n+1} =(alpha x_{n-k})/(1+x_{n}...x_{n-k}), k>=1, n=0,1,... is studied where the parameters ?alpha, betta, and gamma are positive real numbers, and the initial conditions x_{-k}, ..., x_{0} are given arbitrary real numbers. The forbidden set of this equation is found and then, the order reduction method is used to facilitate the analysis of its asymptotic dynamics

  15. Radiation by solitons due to higher-order dispersion

    DEFF Research Database (Denmark)

    Karpman, V.I.

    1993-01-01

    We consider the Korteweg-de Vries (KdV) and nonlinear Schrodinger (NS) equations with higher-order derivative terms describing dispersive corrections. Conditions of existence of stationary and radiating solitons of the fifth-order KdV equation are obtained. An asymptotic time-dependent solution...... to the latter equation, describing the soliton radiation, is found. The radiation train may be in front as well as behind the soliton, depending on the sign of dispersion. The change rate of the soliton due to the radiation is calculated. A modification of the WKB method, that permits one to describe...

  16. Isotropic Stars in Higher-Order Torsion Scalar Theories

    Directory of Open Access Journals (Sweden)

    Gamal G. L. Nashed

    2016-01-01

    Full Text Available Two different nondiagonal tetrad spaces reproducing spherically symmetric spacetime are applied to the field equations of higher-order torsion scalar theories. Assuming the existence of conformal Killing vector, two isotropic solutions are derived. We show that the first solution is not stable while the second one confirms a stable behavior. We also discuss the construction of the stellar model and show that one of our solutions is capable of such construction while the other is not. Finally, we discuss the generalized Tolman-Oppenheimer-Volkoff and show that one of our models has a tendency to equilibrium.

  17. Isotropic stars in higher-order torsion scalar theories

    CERN Document Server

    Nashed, Gamal G L

    2016-01-01

    Two tetrad spaces reproducing spherically symmetric spacetime are applied to the equations of motion of higher-order torsion theories. Assuming the existence of conformal Killing vector, two isotropic solutions are derived. We show that the first solution is not stable while the second one confirms a stable behavior. We also discuss the construction of the stellar model and show that one of our solution capable of such construction while the other cannot. Finally, we discuss the generalized Tolman-Oppenheimer-Volkoff and show that one of our models has a tendency to equilibrium.

  18. Squeezing of higher order Hermite-Gauss modes

    DEFF Research Database (Denmark)

    Lassen, Mikael Østergaard

    2008-01-01

    The present paper gives an overview of the experimental generation of squeezing in higher order Hermite-Gaussian modes with an optical parametric ampli¯er (OPA). This work was awarded with The European Optical Society (EOS) price 2007. The purpose of the prize is to encourage a European dimension...... in research in pure and applied optics. The EOS prize is awarded based on the selection criteria of high professionalism, academic and technical quality. Following the EOS Prize rules, the conditions for eligibility are that the work was performed in Europe and that it is published under the auspices...

  19. Higher Order Mode Properties of Superconducting Two-Spoke Cavities

    Energy Technology Data Exchange (ETDEWEB)

    Hopper, C. S.; Delayen, J. R.; Olave, R. G.

    2011-07-01

    Multi-Spoke cavities lack the cylindrical symmetry that many other cavity types have, which leads to a more complex Higher Order Mode (HOM) spectrum. In addition, spoke cavities offer a large velocity acceptance which means we must perform a detailed analysis of the particle velocity dependence for each mode's R/Q. We present here a study of the HOM properties of two-spoke cavities designed for high-velocity applications. Frequencies, R/Q and field profiles of HOMs have been calculated and are reported.

  20. Higher-order chaotic oscillator using active bessel filter

    DEFF Research Database (Denmark)

    Lindberg, Erik; Mykolaitis, Gytis; Bumelien, Skaidra;

    2010-01-01

    A higher-order oscillator, including a nonlinear unit and an 8th-order low-pass active Bessel filter is described. The Bessel unit plays the role of "three-in-one": a delay line, an amplifier and a filter. Results of hardware experiments and numerical simulation are presented. Depending on the pa...... on the parameters of the nonlinear unit the oscillator operates either in a one-scroll or two-scroll mode. Two positive Lyapunov exponents, found at larger values of the negative slopes of the nonlinear function, characterize the oscillations as hyperchaotic....

  1. Laser-PlasmaWakefield Acceleration with Higher Order Laser Modes

    Energy Technology Data Exchange (ETDEWEB)

    Geddes, C.G.R.; Cormier-Michel, E.; Esarey, E.; Schroeder, C.B.; Mullowney, P.; Paul, K.; Cary, J.R.; Leemans, W.P.

    2010-06-01

    Laser-plasma collider designs point to staging of multiple accelerator stages at the 10 GeV level, which are to be developed on the upcoming BELLA laser, while Thomson Gamma source designs use GeV stages, both requiring efficiency and low emittance. Design and scaling of stages operating in the quasi-linear regime to address these needs are presented using simulations in the VORPAL framework. In addition to allowing symmetric acceleration of electrons and positrons, which is important for colliders, this regime has the property that the plasma wakefield is proportional to the transverse gradient of the laser intensity profile. We demonstrate use of higher order laser modes to tailor the laser pulse and hence the transverse focusing forces in the plasma. In particular, we show that by using higher order laser modes, we can reduce the focusing fields and hence increase the matched electron beam radius, which is important to increased charge and efficiency, while keeping the low bunch emittance required for applications.

  2. Higher-Order Spectrum in Understanding Nonlinearity in EEG Rhythms

    Directory of Open Access Journals (Sweden)

    Cauchy Pradhan

    2012-01-01

    Full Text Available The fundamental nature of the brain's electrical activities recorded as electroencephalogram (EEG remains unknown. Linear stochastic models and spectral estimates are the most common methods for the analysis of EEG because of their robustness, simplicity of interpretation, and apparent association with rhythmic behavioral patterns in nature. In this paper, we extend the use of higher-order spectrum in order to indicate the hidden characteristics of EEG signals that simply do not arise from random processes. The higher-order spectrum is an extension Fourier spectrum that uses higher moments for spectral estimates. This essentially nullifies all Gaussian random effects, therefore, can reveal non-Gaussian and nonlinear characteristics in the complex patterns of EEG time series. The paper demonstrates the distinguishing features of bispectral analysis for chaotic systems, filtered noises, and normal background EEG activity. The bispectrum analysis detects nonlinear interactions; however, it does not quantify the coupling strength. The squared bicoherence in the nonredundant region has been estimated to demonstrate nonlinear coupling. The bicoherence values are minimal for white Gaussian noises (WGNs and filtered noises. Higher bicoherence values in chaotic time series and normal background EEG activities are indicative of nonlinear coupling in these systems. The paper shows utility of bispectral methods as an analytical tool in understanding neural process underlying human EEG patterns.

  3. Chromatin computation.

    Directory of Open Access Journals (Sweden)

    Barbara Bryant

    Full Text Available In living cells, DNA is packaged along with protein and RNA into chromatin. Chemical modifications to nucleotides and histone proteins are added, removed and recognized by multi-functional molecular complexes. Here I define a new computational model, in which chromatin modifications are information units that can be written onto a one-dimensional string of nucleosomes, analogous to the symbols written onto cells of a Turing machine tape, and chromatin-modifying complexes are modeled as read-write rules that operate on a finite set of adjacent nucleosomes. I illustrate the use of this "chromatin computer" to solve an instance of the Hamiltonian path problem. I prove that chromatin computers are computationally universal--and therefore more powerful than the logic circuits often used to model transcription factor control of gene expression. Features of biological chromatin provide a rich instruction set for efficient computation of nontrivial algorithms in biological time scales. Modeling chromatin as a computer shifts how we think about chromatin function, suggests new approaches to medical intervention, and lays the groundwork for the engineering of a new class of biological computing machines.

  4. Sequence information encoded in DNA that may influence long-range chromatin structure correlates with human chromosome functions.

    Directory of Open Access Journals (Sweden)

    Taichi E Takasuka

    Full Text Available Little is known about the possible function of the bulk of the human genome. We have recently shown that long-range regular oscillation in the motif non-T, A/T, G (VWG existing at ten-nucleotide multiples influences large-scale nucleosome array formation. In this work, we have determined the locations of all 100 kb regions that are predicted to form distinctive chromatin structures throughout each human chromosome (except Y. Using these data, we found that a significantly greater fraction of 300 kb sequences lacked annotated transcripts in genomic DNA regions > or = 300 kb that contained nearly continuous chromatin organizing signals than in control regions. We also found a relationship between the meiotic recombination frequency and the presence of strong VWG chromatin organizing signals. Large (> or = 300 kb genomic DNA regions having low average recombination frequency are enriched in chromatin organizing signals. As additional controls, we show using chromosome 1 that the VWG motif signals are not enriched in randomly selected DNA regions having the mean size of the recombination coldspots, and that non-VWG motif sets do not generate signals that are enriched in recombination coldspots. We also show that tandemly repeated alpha satellite DNA contains strong VWG signals for the formation of distinctive nucleosome arrays, consistent with the low recombination activity of centromeres. Our correlations cannot be explained simply by variations in the GC content. Our findings suggest that a specific set of periodic DNA motifs encoded in genomic DNA, which provide signals for chromatin organization, influence human chromosome function.

  5. Proper orthogonal decomposition-based spectral higher-order stochastic estimation

    Energy Technology Data Exchange (ETDEWEB)

    Baars, Woutijn J., E-mail: wbaars@unimelb.edu.au [Department of Mechanical Engineering, The University of Melbourne, Melbourne, Victoria 3010 (Australia); Tinney, Charles E. [Center for Aeromechanics Research, The University of Texas at Austin, Austin, Texas 78712 (United States)

    2014-05-15

    A unique routine, capable of identifying both linear and higher-order coherence in multiple-input/output systems, is presented. The technique combines two well-established methods: Proper Orthogonal Decomposition (POD) and Higher-Order Spectra Analysis. The latter of these is based on known methods for characterizing nonlinear systems by way of Volterra series. In that, both linear and higher-order kernels are formed to quantify the spectral (nonlinear) transfer of energy between the system's input and output. This reduces essentially to spectral Linear Stochastic Estimation when only first-order terms are considered, and is therefore presented in the context of stochastic estimation as spectral Higher-Order Stochastic Estimation (HOSE). The trade-off to seeking higher-order transfer kernels is that the increased complexity restricts the analysis to single-input/output systems. Low-dimensional (POD-based) analysis techniques are inserted to alleviate this void as POD coefficients represent the dynamics of the spatial structures (modes) of a multi-degree-of-freedom system. The mathematical framework behind this POD-based HOSE method is first described. The method is then tested in the context of jet aeroacoustics by modeling acoustically efficient large-scale instabilities as combinations of wave packets. The growth, saturation, and decay of these spatially convecting wave packets are shown to couple both linearly and nonlinearly in the near-field to produce waveforms that propagate acoustically to the far-field for different frequency combinations.

  6. A reduced-rank approach for implementing higher-order Volterra filters

    Science.gov (United States)

    O. Batista, Eduardo L.; Seara, Rui

    2016-12-01

    The use of Volterra filters in practical applications is often limited by their high computational burden. To cope with this problem, many strategies for implementing Volterra filters with reduced complexity have been proposed in the open literature. Some of these strategies are based on reduced-rank approaches obtained by defining a matrix of filter coefficients and applying the singular value decomposition to such a matrix. Then, discarding the smaller singular values, effective reduced-complexity Volterra implementations can be obtained. The application of this type of approach to higher-order Volterra filters (considering orders greater than 2) is however not straightforward, which is especially due to some difficulties encountered in the definition of higher-order coefficient matrices. In this context, the present paper is devoted to the development of a novel reduced-rank approach for implementing higher-order Volterra filters. Such an approach is based on a new form of Volterra kernel implementation that allows decomposing higher-order kernels into structures composed only of second-order kernels. Then, applying the singular value decomposition to the coefficient matrices of these second-order kernels, effective implementations for higher-order Volterra filters can be obtained. Simulation results are presented aiming to assess the effectiveness of the proposed approach.

  7. Multiple higher-order stop gaps in infrared polymer photonic crystals.

    Science.gov (United States)

    Straub, M; Ventura, M; Gu, M

    2003-07-25

    Engineering of stop gaps between higher photonic bands provides an alternative to miniaturization of photonic crystals. Femtosecond laser microfabrication of highly correlated void channel polymer microstructures results in photonic crystals with large stop gaps and a multitude of higher-order gaps in the mid- and near-infrared spectral regions. The gap wavelengths obey Bragg's law. Consistent with theory, varying the woodpile structure unit cell allows for tuning the number of higher-order gaps, and transitions from mere resonant Bragg scattering to stop band total reflection are observed.

  8. Higher-Order Markov Tag-Topic Models for Tagged Documents and Images

    CERN Document Server

    Zeng, Jia; Cheung, William K; Li, Chun-Hung

    2011-01-01

    This paper studies the topic modeling problem of tagged documents and images. Higher-order relations among tagged documents and images are major and ubiquitous characteristics, and play positive roles in extracting reliable and interpretable topics. In this paper, we propose the tag-topic models (TTM) to depict such higher-order topic structural dependencies within the Markov random field (MRF) framework. First, we use the novel factor graph representation of latent Dirichlet allocation (LDA)-based topic models from the MRF perspective, and present an efficient loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Second, we propose the factor hypergraph representation of TTM, and focus on both pairwise and higher-order relation modeling among tagged documents and images. Efficient loopy BP algorithm is developed to learn TTM, which encourages the topic labeling smoothness among tagged documents and images. Extensive experimental results confirm the incorporation of highe...

  9. Higher-order adaptive finite-element methods for Kohn-Sham density functional theory

    CERN Document Server

    Motamarri, Phani; Leiter, Kenneth; Knap, Jaroslaw; Gavini, Vikram

    2012-01-01

    We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn-Sham density-functional theory (DFT).To this end, we develop an \\emph{a priori} mesh adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss-Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn-Sham DFT problem. Our studies suggest that staggering computational savings---of the order of $1000-$fold---can be realized, for both all-electron and pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems stu...

  10. Role of chromatin structure modulation by the histone deacetylase inhibitor trichostatin A on the radio-sensitivity of ataxia telangiectasia

    Energy Technology Data Exchange (ETDEWEB)

    Meschini, Roberta, E-mail: meschini@unitus.it; Morucci, Elisa; Berni, Andrea; Lopez-Martinez, Wilner; Palitti, Fabrizio

    2015-07-15

    Highlights: • Role of chromatin compaction on chromosomal instability. • Reduced radiation-induced clastogenicity in Ataxia telangiectasia cell lines. • Histone tails hyperacetylation reduces heterochromatin content favouring DSBs repair. - Abstract: At present, a lot is known about biochemical aspects of double strand breaks (DBS) repair but how chromatin structure affects this process and the sensitivity of DNA to DSB induction is still an unresolved question. Ataxia telangiectasia (A-T) patients are characterised by very high sensitivity to DSB-inducing agents such as ionising radiation. This radiosensitivity is revealed with an enhancement of chromosomal instability as a consequence of defective DNA repair for a small fraction of breaks located in the heterochromatin, where they are less accessible. Besides, recently it has been reported that Ataxia Telangiectasia Mutated (ATM) mediated signalling modifies chromatin structure. In order to study the impact of chromatin compaction on the chromosomal instability of A-T cells, the response to trichostatin-A, an histone deacetylase inhibitor, in normal and A-T lymphoblastoid cell lines was investigated testing its effect on chromosomal aberrations, cell cycle progression, DNA damage and repair after exposure to X-rays. The results suggest that the response to both trichostatin-A pre- and continuous treatments is independent of the presence of either functional or mutated ATM protein, as the reduction of chromosomal damage was found also in the wild-type cell line. The presence of trichostatin-A before exposure to X-rays could give rise to prompt DNA repair functioning on chromatin structure already in an open conformation. Differently, trichostatin-A post-treatment causing hyperacetylation of histone tails and reducing the heterochromatic DNA content might diminish the requirement for ATM and favour DSBs repair reducing chromosomal damage only in A-T cells. This fact could suggest that trichostatin-A post

  11. Experimental validation of the Higher-Order Theory approach for sandwich panels with flexible core materials

    NARCIS (Netherlands)

    Straalen, IJ.J. van

    2000-01-01

    During tthe 1990's the higher-order theory was developed by Frostig to enable detailed stress analyses of sandwich panel structures. To investigate the potentials of this approach experiments are performed on sandwich panels made of thin steel faces and mineral wool or polystyrene core material. A p

  12. Performance-Based Task Assessment of Higher-Order Proficiencies in Redesigned STEM High Schools

    Science.gov (United States)

    Ernst, Jeremy V.; Glennie, Elizabeth; Li, Songze

    2017-01-01

    This study explored student abilities in applying conceptual knowledge when presented with structured performance tasks. Specifically, the study gauged proficiency in higher-order applications of students enrolled in earth and environmental science or biology. The student sample was drawn from a Redesigned STEM high school model where a tested…

  13. Higher order branching of periodic orbits from polynomial isochrones

    Directory of Open Access Journals (Sweden)

    B. Toni

    1999-09-01

    Full Text Available We discuss the higher order local bifurcations of limit cycles from polynomial isochrones (linearizable centers when the linearizing transformation is explicitly known and yields a polynomial perturbation one-form. Using a method based on the relative cohomology decomposition of polynomial one-forms complemented with a step reduction process, we give an explicit formula for the overall upper bound of branch points of limit cycles in an arbitrary $n$ degree polynomial perturbation of the linear isochrone, and provide an algorithmic procedure to compute the upper bound at successive orders. We derive a complete analysis of the nonlinear cubic Hamiltonian isochrone and show that at most nine branch points of limit cycles can bifurcate in a cubic polynomial perturbation. Moreover, perturbations with exactly two, three, four, six, and nine local families of limit cycles may be constructed.

  14. Higher order mode propagation in nonuniform circular ducts

    Science.gov (United States)

    Cho, Y. C.; Ingard, K. U.

    1980-01-01

    This paper presents an analytical investigation of higher order mode propagation in a nonuniform circular duct without mean flow. An approximate wave equation is derived on the assumptions that the duct cross section varies slowly and that mode conversion is negligible. Exact closed form solutions are obtained for a particular class of converging-diverging circular duct which is here referred to as 'circular cosh duct'. Numerical results are presentd in terms of the transmission loss for the various duct shapes and frequencies. The results are applicable to studies of multimodal propagation as well as single mode propagation. The results are also applicable to studies of sound radiation from certain types of contoured inlet ducts, or of sound propagation in a converging-diverging duct of somewhat different shape from a cosh duct.

  15. Inflationary scenarios in Starobinsky model with higher order corrections

    Energy Technology Data Exchange (ETDEWEB)

    Artymowski, Michał [Institute of Physics, Jagiellonian University,Łojasiewicza 11, 30-348 Kraków (Poland); Lalak, Zygmunt [Institute of Theoretical Physics, Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland); Lewicki, Marek [Institute of Theoretical Physics, Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland); Michigan Center for Theoretical Physics, University of Michigan,450 Church Street, Ann Arbor MI 48109 (United States)

    2015-06-17

    We consider the Starobinsky inflation with a set of higher order corrections parametrised by two real coefficients λ{sub 1} ,λ{sub 2}. In the Einstein frame we have found a potential with the Starobinsky plateau, steep slope and possibly with an additional minimum, local maximum or a saddle point. We have identified three types of inflationary behaviour that may be generated in this model: i) inflation on the plateau, ii) at the local maximum (topological inflation), iii) at the saddle point. We have found limits on parameters λ{sub i} and initial conditions at the Planck scale which enable successful inflation and disable eternal inflation at the plateau. We have checked that the local minimum away from the GR vacuum is stable and that the field cannot leave it neither via quantum tunnelling nor via thermal corrections.

  16. Mixed Higher Order Variational Model for Image Recovery

    Directory of Open Access Journals (Sweden)

    Pengfei Liu

    2014-01-01

    Full Text Available A novel mixed higher order regularizer involving the first and second degree image derivatives is proposed in this paper. Using spectral decomposition, we reformulate the new regularizer as a weighted L1-L2 mixed norm of image derivatives. Due to the equivalent formulation of the proposed regularizer, an efficient fast projected gradient algorithm combined with monotone fast iterative shrinkage thresholding, called, FPG-MFISTA, is designed to solve the resulting variational image recovery problems under majorization-minimization framework. Finally, we demonstrate the effectiveness of the proposed regularization scheme by the experimental comparisons with total variation (TV scheme, nonlocal TV scheme, and current second degree methods. Specifically, the proposed approach achieves better results than related state-of-the-art methods in terms of peak signal to ratio (PSNR and restoration quality.

  17. Towards regularized higher-order computations in QFT without DREG

    CERN Document Server

    Sborlini, German F R; Hernandez-Pinto, Roger; Rodrigo, German

    2016-01-01

    In this talk, we review the basis of the loop-tree duality theorem, which allows to rewrite loop scattering amplitudes in terms of tree-level like objects. Since the loop measure is converted into a phase-space one, both virtual and real contributions are expressible using the same integration variables. A physically motivated momentum mapping allows to generate the real emission process starting from the Born kinematics and the loop momenta. The integrand-level combination leads to regular functions, which can be integrated without using dimensional regularization (DREG) and correctly reproduce the finite higher-order corrections to physical observables. We explain the implementation of this novel approach to compute some benchmark physical processes, and we show how to deal with both infrared and ultraviolet divergences in four space-time dimensions.

  18. Special issue of Higher-Order and Symbolic Computation

    DEFF Research Database (Denmark)

    Danvy, Olivier

    , they should have a large range of applicability for a large class of specifications or programs. Only general ideas could become the basis for an automatic system for program development. Bob’s APTS system is indeed the incarnation of most of the techniques he proposed (cf. Leonard and Heitmeyer...... at the Courant Institute in New York, the members of the IFIP Working Group 2.1, and the people at the various Universities he visited, including the University of Copenhagen and the University of Wisconsin. All his friends and colleagues, enjoyed Bob’s talks and presentations. His ideas and his visions...... on program development and programming methodology were a source of enthusiasm, strength, and inspiration. His dedication to research and teaching is for us all an example to follow. The articles in this issue of Higher-Order and Symbolic Computation were contributed and formally reviewed, and they reflect...

  19. Higher Order Reentrant Post Modes in Cylindrical Cavities

    CERN Document Server

    McAllister, Ben T; Parker, Stephen R; Tobar, Michael E

    2016-01-01

    Reentrant cavities are microwave resonant devices employed in a number of different areas of physics. They are appealing due to their simple frequency tuning mechanism, which offers large tuning ranges. Reentrant cavities are, in essence, 3D lumped LC circuits consisting of a conducting central post embedded in a resonant cavity. The lowest order reentrant mode (which transforms from the TM010 mode) has been extensively studied in past publications. In this work we show the existence of higher order reentrant post modes (which transform from the TM01n mode family). We characterize these new modes in terms of their frequency tuning, filling factors and quality factors, as well as discuss some possible applications of these modes in fundamental physics tests.

  20. Dependable software through higher-order strategic programming.

    Energy Technology Data Exchange (ETDEWEB)

    Winter, Victor Lono (University of Nebraska at Omaha); Fraij, Fares (University of Texas at El Paso); Roach, Steve (University of Texas at El Paso)

    2004-03-01

    Program transformation is a restricted form of software construction that can be amenable to formal verification. When successful, the nature of the evidence provided by such a verification is considered strong and can constitute a major component of an argument that a high-consequence or safety-critical system meets its dependability requirements. This article explores the application of novel higher-order strategic programming techniques to the development of a portion of a class loader for a restricted implementation of the Java Virtual Machine (JVM). The implementation is called the SSP and is intended for use in high-consequence safety-critical embedded systems. Verification of the strategic program using ACL2 is also discussed.

  1. Recognition of higher order patterns in proteins: immunologic kernels.

    Directory of Open Access Journals (Sweden)

    Robert D Bremel

    Full Text Available By applying analysis of the principal components of amino acid physical properties we predicted cathepsin cleavage sites, MHC binding affinity, and probability of B-cell epitope binding of peptides in tetanus toxin and in ten diverse additional proteins. Cross-correlation of these metrics, for peptides of all possible amino acid index positions, each evaluated in the context of a ±25 amino acid flanking region, indicated that there is a strongly repetitive pattern of short peptides of approximately thirty amino acids each bounded by cathepsin cleavage sites and each comprising B-cell linear epitopes, MHC-I and MHC-II binding peptides. Such "immunologic kernel" peptides comprise all signals necessary for adaptive immunologic cognition, response and recall. The patterns described indicate a higher order spatial integration that forms a symbolic logic coordinating the adaptive immune system.

  2. Higher-order techniques for some problems of nonlinear control

    Directory of Open Access Journals (Sweden)

    Sarychev Andrey V.

    2002-01-01

    Full Text Available A natural first step when dealing with a nonlinear problem is an application of some version of linearization principle. This includes the well known linearization principles for controllability, observability and stability and also first-order optimality conditions such as Lagrange multipliers rule or Pontryagin's maximum principle. In many interesting and important problems of nonlinear control the linearization principle fails to provide a solution. In the present paper we provide some examples of how higher-order methods of differential geometric control theory can be used for the study nonlinear control systems in such cases. The presentation includes: nonlinear systems with impulsive and distribution-like inputs; second-order optimality conditions for bang–bang extremals of optimal control problems; methods of high-order averaging for studying stability and stabilization of time-variant control systems.

  3. Podolsky`s higher-order electromagnetism from first principles

    Energy Technology Data Exchange (ETDEWEB)

    Accioly, A. [Sao Paulo, Univ. Estadual Paulista (Brazil). Instituto de Fisica Teorica; Mukai, H. [Maringa, Fundacao Universidade Estadual de Maringa (Brazil). Dept. de Fisica

    1997-07-01

    Podolsky`s higher-order field equations are obtained by generalizing the laws of Podolsky`s electrostatics, which follow from Coulomb`s generalized law and superposition, to be consistent with special relativity. In addition, it is necessary to take into account the independence of the observed charge of a particle on tis speed. It is also shown that the gauge-independent term concerning the Feynman propagator for Podolsky`s generalized electrodynamics has a good ultraviolet behaviour at the expense of a negative metric massive ghost which, contrary to what is currently assumed in the literature, is non-tachyonic. A brief discussion on Podolsky`s characteristic length is presented as well.

  4. A higher-order theory of emotional consciousness

    Science.gov (United States)

    LeDoux, Joseph E.; Brown, Richard

    2017-01-01

    Emotional states of consciousness, or what are typically called emotional feelings, are traditionally viewed as being innately programmed in subcortical areas of the brain, and are often treated as different from cognitive states of consciousness, such as those related to the perception of external stimuli. We argue that conscious experiences, regardless of their content, arise from one system in the brain. In this view, what differs in emotional and nonemotional states are the kinds of inputs that are processed by a general cortical network of cognition, a network essential for conscious experiences. Although subcortical circuits are not directly responsible for conscious feelings, they provide nonconscious inputs that coalesce with other kinds of neural signals in the cognitive assembly of conscious emotional experiences. In building the case for this proposal, we defend a modified version of what is known as the higher-order theory of consciousness. PMID:28202735

  5. Higher order numerical differentiation on the Infinity Computer

    CERN Document Server

    Sergeyev, Yaroslav D

    2012-01-01

    There exist many applications where it is necessary to approximate numerically derivatives of a function which is given by a computer procedure. In particular, all the fields of optimization have a special interest in such a kind of information. In this paper, a new way to do this is presented for a new kind of a computer -- the Infinity Computer -- able to work numerically with finite, infinite, and infinitesimal numbers. It is proved that the Infinity Computer is able to calculate values of derivatives of a higher order for a wide class of functions represented by computer procedures. It is shown that the ability to compute derivatives of arbitrary order automatically and accurate to working precision is an intrinsic property of the Infinity Computer related to its way of functioning. Numerical examples illustrating the new concepts and numerical tools are given.

  6. Higher order statistical moment application for solar PV potential analysis

    Science.gov (United States)

    Basri, Mohd Juhari Mat; Abdullah, Samizee; Azrulhisham, Engku Ahmad; Harun, Khairulezuan

    2016-10-01

    Solar photovoltaic energy could be as alternative energy to fossil fuel, which is depleting and posing a global warming problem. However, this renewable energy is so variable and intermittent to be relied on. Therefore the knowledge of energy potential is very important for any site to build this solar photovoltaic power generation system. Here, the application of higher order statistical moment model is being analyzed using data collected from 5MW grid-connected photovoltaic system. Due to the dynamic changes of skewness and kurtosis of AC power and solar irradiance distributions of the solar farm, Pearson system where the probability distribution is calculated by matching their theoretical moments with that of the empirical moments of a distribution could be suitable for this purpose. On the advantage of the Pearson system in MATLAB, a software programming has been developed to help in data processing for distribution fitting and potential analysis for future projection of amount of AC power and solar irradiance availability.

  7. SU(2) Higher-order effective quark interactions from polarization

    Science.gov (United States)

    Braghin, Fábio L.

    2016-10-01

    Higher order quark effective interactions are found for SU(2) flavor by departing from a non-local quark-quark interaction. By integrating out a component of the quark field, the determinant is expanded in chirally symmetric and symmetry breaking effective interactions up to the fifth order in the quark bilinears. The resulting coupling constants are resolved in the leading order of the longwavelength limit and exact numerical ratios between several of these coupling constants are obtained in the large quark mass limit. In this level, chiral invariant interactions only show up in even powers of the quark bilinears, i.e. O(ψ bar ψ) 2 n (n = 1 , 2 , 3 , . .), whereas (explicit) chiral symmetry breaking terms emerge as O(ψ bar ψ) n being always proportional to some power of the Lagrangian quark mass.

  8. Higher Order Variability Properties of Accreting Black Holes

    CERN Document Server

    Maccarone, T J; Maccarone, Thomas J.; Coppi, Paolo S.

    2002-01-01

    To better constrain the emission mechanism underlying the hard state of galactic black hole candidates, we use high-time resolution RXTE lightcurves for Cyg X-1 and GX 399-4 to compute two higher order variability statistics for these objects, the skewness and the Fourier bispectrum. Similar analyses, in particular using the skewness measure, have been attempted before, but the photon collection area of RXTE allows us to present results of much greater statistical significance. The results for the two objects are qualitatively similar, reinforcing the idea that the same basic mechanisms are at work in both. We find a significantly positive skewness for variability timescales less than $\\sim 1 $ second, and a {\\it negative} skewness for timescale $1- 5 $ sec. Such a skewness pattern cannot be reproduced by the simplest shot variability models where individual shots have a fixed profile and intensity and are uncorrelated in time. Further evidence against simple shot models comes from the significant detection o...

  9. Chemical Freeze-Out and Higher Order Multiplicity Moments

    CERN Document Server

    Tawfik, A

    2013-01-01

    We calculate the non-normalized moments of the particle multiplicity within the framework of the hadron resonance gas (HRG) model. At finite chemical potential $\\mu$, a non-monotonic behavior is observed in the thermal evolution of third order moment (skewness $S$) and the higher order ones as well. Among others, this observation likely reflects dynamical fluctuations and strong correlations. The signatures of non-monotonicity in the normalized fourth order moment (kurtosis $\\kappa$) and its products get very clear. Based on these findings, we introduce a novel condition characterizing the universal freeze-out curve. The chemical freeze-out parameters $T$ and $\\mu$ are described by vanishing $\\kappa\\, \\sigma^2$ or equivalently $m_4=3\\,\\chi^2$, where $\\sigma$, $\\chi$ and $m_4$ are the standard deviation, susceptibility and fourth order moment, respectively. The fact that the HRG model is not able to release information about criticality related to the confinement and chiral dynamics should not veil the observa...

  10. Research on Life Signals Detection Based on Higher Order Statistics

    Directory of Open Access Journals (Sweden)

    Jian-Jun Li

    2012-10-01

    Full Text Available The life signals are built on harmonic mode for their low frequency, quasi-periodicity, low SNR, and the easy submerged in strong clutter noise. The method for detecting life signal based on adaptive filter and high order statistics is presented, in which neither the Gaussian supposition of the observed signal, nor a prior information about the waveform and arrival time of the observed signal is necessary. The principle of method is to  separate the spectrum of input signal into many narrow frequency bands, whose Sub-band signal  is followed by a short-time estimation of higher-order statistics so as to suppress Gaussian noises. Simulated results show that the method can effectively detect life signals from noise with good convergence speed and stability, and greatly improve the signal quality with respect to LMS method.

  11. Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts.

    Science.gov (United States)

    Magistri, Marco; Faghihi, Mohammad Ali; St Laurent, Georges; Wahlestedt, Claes

    2012-08-01

    In the decade following the publication of the Human Genome, noncoding RNAs (ncRNAs) have reshaped our understanding of the broad landscape of genome regulation. During this period, natural antisense transcripts (NATs), which are transcribed from the opposite strand of either protein or non-protein coding genes, have vaulted to prominence. Recent findings have shown that NATs can exert their regulatory functions by acting as epigenetic regulators of gene expression and chromatin remodeling. Here, we review recent work on the mechanisms of epigenetic modifications by NATs and their emerging role as master regulators of chromatin states. Unlike other long ncRNAs, antisense RNAs usually regulate their counterpart sense mRNA in cis by bridging epigenetic effectors and regulatory complexes at specific genomic loci. Understanding the broad range of effects of NATs will shed light on the complex mechanisms that regulate chromatin remodeling and gene expression in development and disease.

  12. Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics

    Science.gov (United States)

    Aguilar, Carlos A.; Craighead, Harold G.

    2013-10-01

    Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin -- a dynamic complex of nucleic acids and proteins -- is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.

  13. FGF signalling regulates chromatin organisation during neural differentiation via mechanisms that can be uncoupled from transcription.

    Directory of Open Access Journals (Sweden)

    Nishal S Patel

    Full Text Available Changes in higher order chromatin organisation have been linked to transcriptional regulation; however, little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals. Here we analyse changes in chromatin organisation as neural differentiation progresses, exploiting the clear spatial separation of the temporal events of differentiation along the elongating body axis of the mouse embryo. Combining fluorescence in situ hybridisation with super-resolution structured illumination microscopy, we show that chromatin around key differentiation gene loci Pax6 and Irx3 undergoes both decompaction and displacement towards the nuclear centre coincident with transcriptional onset. Conversely, down-regulation of Fgf8 as neural differentiation commences correlates with a more peripheral nuclear position of this locus. During normal neural differentiation, fibroblast growth factor (FGF signalling is repressed by retinoic acid, and this vitamin A derivative is further required for transcription of neural genes. We show here that exposure to retinoic acid or inhibition of FGF signalling promotes precocious decompaction and central nuclear positioning of differentiation gene loci. Using the Raldh2 mutant as a model for retinoid deficiency, we further find that such changes in higher order chromatin organisation are dependent on retinoid signalling. In this retinoid deficient condition, FGF signalling persists ectopically in the elongating body, and importantly, we find that inhibiting FGF receptor (FGFR signalling in Raldh2-/- embryos does not rescue differentiation gene transcription, but does elicit both chromatin decompaction and nuclear position change. These findings demonstrate that regulation of higher order chromatin organisation during differentiation in the embryo can be uncoupled from the machinery that promotes transcription and, for the first time, identify FGF as an extrinsic signal that

  14. Estrogen induces global reorganization of chromatin structure in human breast cancer cells.

    Directory of Open Access Journals (Sweden)

    Raphaël Mourad

    Full Text Available In the cell nucleus, each chromosome is confined to a chromosome territory. This spatial organization of chromosomes plays a crucial role in gene regulation and genome stability. An additional level of organization has been discovered at the chromosome scale: the spatial segregation into open and closed chromatins to form two genome-wide compartments. Although considerable progress has been made in our knowledge of chromatin organization, a fundamental issue remains the understanding of its dynamics, especially in cancer. To address this issue, we performed genome-wide mapping of chromatin interactions (Hi-C over the time after estrogen stimulation of breast cancer cells. To biologically interpret these interactions, we integrated with estrogen receptor α (ERα binding events, gene expression and epigenetic marks. We show that gene-rich chromosomes as well as areas of open and highly transcribed chromatins are rearranged to greater spatial proximity, thus enabling genes to share transcriptional machinery and regulatory elements. At a smaller scale, differentially interacting loci are enriched for cancer proliferation and estrogen-related genes. Moreover, these loci are correlated with higher ERα binding events and gene expression. Taken together these results reveal the role of a hormone--estrogen--on genome organization, and its effect on gene regulation in cancer.

  15. Estrogen induces global reorganization of chromatin structure in human breast cancer cells.

    Science.gov (United States)

    Mourad, Raphaël; Hsu, Pei-Yin; Juan, Liran; Shen, Changyu; Koneru, Prasad; Lin, Hai; Liu, Yunlong; Nephew, Kenneth; Huang, Tim H; Li, Lang

    2014-01-01

    In the cell nucleus, each chromosome is confined to a chromosome territory. This spatial organization of chromosomes plays a crucial role in gene regulation and genome stability. An additional level of organization has been discovered at the chromosome scale: the spatial segregation into open and closed chromatins to form two genome-wide compartments. Although considerable progress has been made in our knowledge of chromatin organization, a fundamental issue remains the understanding of its dynamics, especially in cancer. To address this issue, we performed genome-wide mapping of chromatin interactions (Hi-C) over the time after estrogen stimulation of breast cancer cells. To biologically interpret these interactions, we integrated with estrogen receptor α (ERα) binding events, gene expression and epigenetic marks. We show that gene-rich chromosomes as well as areas of open and highly transcribed chromatins are rearranged to greater spatial proximity, thus enabling genes to share transcriptional machinery and regulatory elements. At a smaller scale, differentially interacting loci are enriched for cancer proliferation and estrogen-related genes. Moreover, these loci are correlated with higher ERα binding events and gene expression. Taken together these results reveal the role of a hormone--estrogen--on genome organization, and its effect on gene regulation in cancer.

  16. Scintillations of higher-order laser beams in non-Kolmogorov medium.

    Science.gov (United States)

    Baykal, Yahya

    2014-04-01

    In an atmospheric medium that shows a non-Kolmogorov turbulence behavior, the variation of the on-axis scintillation index is evaluated when higher-order laser modes are used as the excitation. The Rytov method is employed together with the equivalent structure constant, which makes our results valid in weak turbulence. In the limiting case, our solution correctly reduces to the known scintillation index of the Gaussian beam in Kolmogorov turbulence. For all the higher-order even modes, increase in the power law exponent, α of the non-Kolmogorov spectrum is found to increase the scintillations. When the source size of the higher-order modes is large, higher-order even modes attain almost the same scintillation index values for all α. However, for small source sizes, being valid for any realization of the non-Kolmogorov spectrum, the scintillations decrease as the mode order becomes large. The changes in the propagation distance, structure constant, and the wavelength do not vary these trends.

  17. Higher order SVD analysis for dynamic texture synthesis.

    Science.gov (United States)

    Costantini, Roberto; Sbaiz, Luciano; Süsstrunk, Sabine

    2008-01-01

    Videos representing flames, water, smoke, etc., are often defined as dynamic textures: "textures" because they are characterized by the redundant repetition of a pattern and "dynamic" because this repetition is also in time and not only in space. Dynamic textures have been modeled as linear dynamic systems by unfolding the video frames into column vectors and describing their trajectory as time evolves. After the projection of the vectors onto a lower dimensional space by a singular value decomposition (SVD), the trajectory is modeled using system identification techniques. Synthesis is obtained by driving the system with random noise. In this paper, we show that the standard SVD can be replaced by a higher order SVD (HOSVD), originally known as Tucker decomposition. HOSVD decomposes the dynamic texture as a multidimensional signal (tensor) without unfolding the video frames on column vectors. This is a more natural and flexible decomposition, since it permits us to perform dimension reduction in the spatial, temporal, and chromatic domain, while standard SVD allows for temporal reduction only. We show that for a comparable synthesis quality, the HOSVD approach requires, on average, five times less parameters than the standard SVD approach. The analysis part is more expensive, but the synthesis has the same cost as existing algorithms. Our technique is, thus, well suited to dynamic texture synthesis on devices limited by memory and computational power, such as PDAs or mobile phones.

  18. Predicting perceptual learning from higher-order cortical processing.

    Science.gov (United States)

    Wang, Fang; Huang, Jing; Lv, Yaping; Ma, Xiaoli; Yang, Bin; Wang, Encong; Du, Boqi; Li, Wu; Song, Yan

    2016-01-01

    Visual perceptual learning has been shown to be highly specific to the retinotopic location and attributes of the trained stimulus. Recent psychophysical studies suggest that these specificities, which have been associated with early retinotopic visual cortex, may in fact not be inherent in perceptual learning and could be related to higher-order brain functions. Here we provide direct electrophysiological evidence in support of this proposition. In a series of event-related potential (ERP) experiments, we recorded high-density electroencephalography (EEG) from human adults over the course of learning in a texture discrimination task (TDT). The results consistently showed that the earliest C1 component (68-84ms), known to reflect V1 activity driven by feedforward inputs, was not modulated by learning regardless of whether the behavioral improvement is location specific or not. In contrast, two later posterior ERP components (posterior P1 and P160-350) over the occipital cortex and one anterior ERP component (anterior P160-350) over the prefrontal cortex were progressively modified day by day. Moreover, the change of the anterior component was closely correlated with improved behavioral performance on a daily basis. Consistent with recent psychophysical and imaging observations, our results indicate that perceptual learning can mainly involve changes in higher-level visual cortex as well as in the neural networks responsible for cognitive functions such as attention and decision making.

  19. Higher Order Modes Excitation of Micro Cantilever Beams

    KAUST Repository

    Jaber, Nizar

    2014-05-01

    In this study, we present analytical and experimental investigation of electrically actuated micro cantilever based resonators. These devices are fabricated using polyimide and coated with chrome and gold layers from both sides. The cantilevers are highly curled up due to stress gradient, which is a common imperfection in surface micro machining. Using a laser Doppler vibrometer, we applied a noise signal to experimentally find the first four resonance frequencies. Then, using a data acquisition card, we swept the excitation frequency around the first four natural modes of vibrations. Theoretically, we derived a reduced order model using the Galerkin method to simulate the dynamics of the system. Extensive numerical analysis and computations were performed. The numerical analysis was able to provide good matching with experimental values of the resonance frequencies. Also, we proved the ability to excite higher order modes using partial electrodes with shapes that resemble the shape of the mode of interest. Such micro-resonators are shown to be promising for applications in mass and gas sensing.

  20. Chemical freeze-out and higher order multiplicity moments

    Energy Technology Data Exchange (ETDEWEB)

    Tawfik, A., E-mail: a.tawfik@eng.mti.edu.eg

    2014-02-15

    We calculate the non-normalized moments of the particle multiplicity within the framework of the hadron resonance gas (HRG) model. At finite chemical potential μ, a non-monotonic behavior is observed in the thermal evolution of third order moment (skewness S) and the higher order ones as well. The signatures of non-monotonicity in the normalized fourth order moment (kurtosis κ) and its products get very clear. Among others, this observation likely reflects dynamical fluctuations and strong correlations. Based on these findings, we introduce the physics of the universal freeze-out curve. It is found that the chemical freeze-out parameters T and μ are described by vanishing κσ{sup 2} or equivalently m{sub 4}=3χ{sup 2}, where σ, χ and m{sub 4} are the standard deviation, susceptibility and fourth order moment, respectively. The fact that the HRG model is not able to release information about criticality related to the confinement and chiral dynamics should not veil the observations related to the chemical freeze-out. Recent lattice QCD studies strongly advocate the main conclusion of the present paper.

  1. Near integrability of kink lattice with higher order interactions

    CERN Document Server

    Jiang, Yunguo; He, Song

    2016-01-01

    In the paper, we make use of Manton's analytical method to investigate the force between kink and the anti-kink with large distance in $1+1$ dimensional field theory. The related potential has infinite order corrections of exponential pattern, and coefficients for each order are determined. These coefficients can also be obtained by solving the equation of the fluctuation around the vacuum. At the lowest order, the kink lattice represents the Toda lattice. With higher order correction terms, the kink lattice can represent one kind of the generic Toda lattice. With only two sites, the kink lattice is classically integrable. If the number of sites of the lattice is larger than two, the kink lattice is not integrable but a near integrable system. We take use of the Flaschka's variables to study the Lax pair of the kink lattice. These Flaschka's variables have interesting algebraic relations and the non-integrability can be manifested. We also discussed the higher Hamiltonians for the deformed open Toda lattice, ...

  2. A higher-order nonlocal elasticity and strain gradient theory and its applications in wave propagation

    Science.gov (United States)

    Lim, C. W.; Zhang, G.; Reddy, J. N.

    2015-05-01

    In recent years there have been many papers that considered the effects of material length scales in the study of mechanics of solids at micro- and/or nano-scales. There are a number of approaches and, among them, one set of papers deals with Eringen's differential nonlocal model and another deals with the strain gradient theories. The modified couple stress theory, which also accounts for a material length scale, is a form of a strain gradient theory. The large body of literature that has come into existence in the last several years has created significant confusion among researchers about the length scales that these various theories contain. The present paper has the objective of establishing the fact that the length scales present in nonlocal elasticity and strain gradient theory describe two entirely different physical characteristics of materials and structures at nanoscale. By using two principle kernel functions, the paper further presents a theory with application examples which relates the classical nonlocal elasticity and strain gradient theory and it results in a higher-order nonlocal strain gradient theory. In this theory, a higher-order nonlocal strain gradient elasticity system which considers higher-order stress gradients and strain gradient nonlocality is proposed. It is based on the nonlocal effects of the strain field and first gradient strain field. This theory intends to generalize the classical nonlocal elasticity theory by introducing a higher-order strain tensor with nonlocality into the stored energy function. The theory is distinctive because the classical nonlocal stress theory does not include nonlocality of higher-order stresses while the common strain gradient theory only considers local higher-order strain gradients without nonlocal effects in a global sense. By establishing the constitutive relation within the thermodynamic framework, the governing equations of equilibrium and all boundary conditions are derived via the variational

  3. Response spectrum method for extreme wave loading with higher order components of drag force

    Science.gov (United States)

    Reza, Tabeshpour Mohammad; Mani, Fatemi Dezfouli; Mohammad Ali, Dastan Diznab; Saied, Mohajernasab; Saied, Seif Mohammad

    2017-01-01

    Response spectra of fixed offshore structures impacted by extreme waves are investigated based on the higher order components of the nonlinear drag force. In this way, steel jacket platforms are simplified as a mass attached to a light cantilever cylinder and their corresponding deformation response spectra are estimated by utilizing a generalized single degree of freedom system. Based on the wave data recorded in the Persian Gulf region, extreme wave loading conditions corresponding to different return periods are exerted on the offshore structures. Accordingly, the effect of the higher order components of the drag force is considered and compared to the linearized state for different sea surface levels. When the fundamental period of the offshore structure is about one third of the main period of wave loading, the results indicate the linearized drag term is not capable of achieving a reliable deformation response spectrum.

  4. Emotion recognition from EEG using higher order crossings.

    Science.gov (United States)

    Petrantonakis, Panagiotis C; Hadjileontiadis, Leontios J

    2010-03-01

    Electroencephalogram (EEG)-based emotion recognition is a relatively new field in the affective computing area with challenging issues regarding the induction of the emotional states and the extraction of the features in order to achieve optimum classification performance. In this paper, a novel emotion evocation and EEG-based feature extraction technique is presented. In particular, the mirror neuron system concept was adapted to efficiently foster emotion induction by the process of imitation. In addition, higher order crossings (HOC) analysis was employed for the feature extraction scheme and a robust classification method, namely HOC-emotion classifier (HOC-EC), was implemented testing four different classifiers [quadratic discriminant analysis (QDA), k-nearest neighbor, Mahalanobis distance, and support vector machines (SVMs)], in order to accomplish efficient emotion recognition. Through a series of facial expression image projection, EEG data have been collected by 16 healthy subjects using only 3 EEG channels, namely Fp1, Fp2, and a bipolar channel of F3 and F4 positions according to 10-20 system. Two scenarios were examined using EEG data from a single-channel and from combined-channels, respectively. Compared with other feature extraction methods, HOC-EC appears to outperform them, achieving a 62.3% (using QDA) and 83.33% (using SVM) classification accuracy for the single-channel and combined-channel cases, respectively, differentiating among the six basic emotions, i.e., happiness, surprise, anger, fear, disgust, and sadness. As the emotion class-set reduces its dimension, the HOC-EC converges toward maximum classification rate (100% for five or less emotions), justifying the efficiency of the proposed approach. This could facilitate the integration of HOC-EC in human machine interfaces, such as pervasive healthcare systems, enhancing their affective character and providing information about the user's emotional status (e.g., identifying user's emotion

  5. Higher order variability properties of accreting black holes

    Science.gov (United States)

    Maccarone, Thomas J.; Coppi, Paolo S.

    2002-11-01

    To better constrain the emission mechanism underlying the hard state of galactic black hole candidates, we use high-time resolution RXTE light curves for Cyg X-1 and GX 339-4 to compute two higher order variability statistics for these objects, the skewness and the Fourier bispectrum. Similar analyses, in particular using the skewness measure, have been attempted previously, but the photon collection area of RXTE allows us to present results of much greater statistical significance. The results for the two objects are qualitatively similar, reinforcing the idea that the same basic mechanisms are at work in both. We find a significantly positive skewness for variability time-scales less than ~1 s, and a negative skewness for time-scales from 1 to 5 s. Such a skewness pattern cannot be reproduced by the simplest shot variability models where individual shots have a fixed profile and intensity and are uncorrelated in time. Further evidence against simple-shot models comes from the significant detection of a non-zero bicoherence for Fourier periods ~0.1-10 s, implying that significant coupling does exist between variations on these time-scales. We discuss how current popular models for variability in black hole systems can be modified to match these observations. Using simulated light curves, we suggest that the most likely way to reproduce this observed behaviour is to have the variability come in groups of many shots, with the number of shots per unit time fitting an envelope function that has a rapid rise and a slow decay, while the individual shots have a slow rise and a rapid decay. Invoking a finite-energy reservoir that is depleted by each shot is a natural way of producing the required shot correlations.

  6. 1957-2007: 50 Years of Higher Order Programming Languages

    Directory of Open Access Journals (Sweden)

    Alen Lovrenčić

    2009-06-01

    Full Text Available Fifty years ago one of the greatest breakthroughs in computer programming and in the history of computers happened -- the appearance of FORTRAN, the first higher-order programming language. From that time until now hundreds of programming languages were invented, different programming paradigms were defined, all with the main goal to make computer programming easier and closer to as many people as possible. Many battles were fought among scientists as well as among developers around concepts of programming, programming languages and paradigms. It can be said that programming paradigms and programming languages were very often a trigger for many changes and improvements in computer science as well as in computer industry. Definitely, computer programming is one of the cornerstones of computer science.Today there are many tools that give a help in the process of programming, but there is still a programming tasks that can be solved only manually. Therefore, programming is still one of the most creative parts of interaction with computers.Programmers should chose programming language in accordance to task they have to solve, but very often, they chose it in accordance to their personal preferences, their beliefs and many other subjective reasons.Nevertheless, the market of programming languages can be merciless to languages as history was merciless to some people, even whole nations. Programming languages and developers get born, live and die leaving more or less tracks and successors, and not always the best survives. The history of programming languages is closely connected to the history of computers and computer science itself. Every single thing from one of them has its reflexions onto the other. This paper gives a short overview of last fifty years of computer programming and computer programming languages, but also gives many ideas that influenced other aspects of computer science. Particularly, programming paradigms are described, their

  7. Higher-order singletons, partially massless fields, and their boundary values in the ambient approach

    Energy Technology Data Exchange (ETDEWEB)

    Bekaert, Xavier [Laboratoire de Mathématiques et Physique Théorique, Unité Mixte de Recherche 7350 du CNRS, Fédération de Recherche 2964 Denis Poisson, Université François Rabelais, Parc de Grandmont, 37200 Tours (France); Grigoriev, Maxim, E-mail: grig@lpi.ru [Tamm Theory Department, Lebedev Physics Institute, Leninsky prospect 53, 119991 Moscow (Russian Federation)

    2013-11-11

    Using ambient space we develop a fully gauge and o(d,2)-covariant approach to boundary values of AdS{sub d+1} gauge fields. It is applied to the study of (partially) massless fields in the bulk and (higher-order) conformal scalars, i.e. singletons, as well as (higher-depth) conformal gauge fields on the boundary. In particular, we identify the corresponding generalized Fradkin–Tseytlin equations as obstructions to the extension of the off-shell boundary value to the bulk, generalizing the usual considerations for the holographic anomalies to the partially massless fields. We also relate the background fields for the higher-order singleton to the boundary values of partially massless fields and prove the appropriate generalization of the Flato–Fronsdal theorem, which is in agreement with the known structure of symmetries for the higher-order wave operator. All these facts support the following generalization of the higher-spin holographic duality: the O(N) model at a multicritical isotropic Lifshitz point should be dual to the theory of partially massless symmetric tensor fields described by the Vasiliev equations based on the higher-order singleton symmetry algebra.

  8. Higher-order spectra for identification of nonlinear modal coupling

    Science.gov (United States)

    Hickey, Daryl; Worden, Keith; Platten, Michael F.; Wright, Jan R.; Cooper, Jonathan E.

    2009-05-01

    Over the past four decades considerable work has been done in the area of power spectrum estimation. The information contained within the power spectrum relates to a signal's autocorrelation or 'second-order statistics'. The power spectrum provides a complete statistical description of a Gaussian process; however, a problem with this information is that it is phase blind. This problem is addressed if one turns to a system's frequency response function (FRF). The FRF graphs the magnitude and phase of the frequency response of a system; in order to do this it requires information regarding the frequency content of the input and output signals. Situations arise in science and engineering whereby signal analysts are required to look beyond second-order statistics and analyse a signal's higher-order statistics (HOS). HOS or spectra give information on a signal's deviation from Gaussianity and consequently are a good indicator function for the presence of nonlinearity within a system. One of the main problems in nonlinear system identification is that of high modal density. Many modelling schemes involve making some expansion of the nonlinear restoring force in terms of polynomial or other basis terms. If more than one degree-of-freedom is involved this becomes a multivariate problem and the number of candidate terms in the expansion grows explosively with the order of nonlinearity and the number of degrees-of-freedom. This paper attempts to use HOS to detect and qualify nonlinear behaviour for a number of symmetrical and asymmetrical systems over a range of degrees-of-freedom. In doing so the paper also attempts to show that HOS are a more sensitive tool than the FRF in detecting nonlinearity. Furthermore, the object of this paper is to try and identify which modes couple in a nonlinear manner in order to reduce the number of candidate coupling terms, for a model, as much as possible. The bispectrum method has previously been applied to simple low-DOF systems with high

  9. Analysis of Higher Order Channel Dropping Tunneling Processes in Photonic Crystals

    Institute of Scientific and Technical Information of China (English)

    FU Jian; HE Sai-Ling

    2000-01-01

    A theoretical analysis is given for a higher order channel drop tunneling structure composed of two horizontal channels and a resonator system with two vertical multi-mode cavities in a two- or three-dimensional photonic crystal. Criteria for a complete transfer are derived for the application of wavelength division multiplexing. Compared to the resonator system with two single-mode cavities or a single multi-mode cavity, the present resonator system improves the transport properties.

  10. The structure of the nucleosome core particle of chromatin in chicken erythrocytes visualized by using atomic force microscopy

    Institute of Scientific and Technical Information of China (English)

    ZHAOHUI; YIZHANG; 等

    1999-01-01

    The structure of the nuclosome core particle of chromatin in chicken erythrocytes has been examined by using AFM.The 146 bp of DNA wrapped twice around the core histone octamer are clearly visualized.Both the ends of entry/exit of linker DNA are also demonstrated.The dimension of the nucleosome core particles is - 1-4 nm in height and - 13-22 nm in width.In addition,superbeads (width of - 48-57 nm,height of - 2-3 nm )are occasionally revealed,two turns of DNA around the core particles are also detected.

  11. Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin

    Directory of Open Access Journals (Sweden)

    Mora Xavier

    2007-05-01

    Full Text Available Abstract Background Histone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes in physiological salt (0.14 M NaCl at constant stoichiometry. Results The H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin. Conclusion H1 subtypes freely exchange in vitro between chromatin binding sites in physiological salt (0.14 M NaCl. The large differences in relative affinity of the H1 subtypes for

  12. Conformal Invariance of Higher-Order Lagrange Systems by Lie Point Transformation

    Institute of Scientific and Technical Information of China (English)

    HUANG Wei-Li; CAI Jian-Le

    2011-01-01

    Conformal invariance and conserved quantities for a higher-order Lagrange system by Lie point transformation of groups are studied. The differential equation of motion for the higher-order Lagrange system is introduced. The definition of conformal invariance for the system together with its determining equations and conformal factor are provided. The necessary and sufficient condition that the system's conformal invariance would be Lie symmetry by the infinitesimal one-parameter point transformation group is deduced. The conserved quantity of the system is derived using the structural equation satisfied by the gauge function. An example of a higher-order mechanical system is offered to illustrate the application of the result.%Conformal invariance and conserved quantities for a higher-order Lagrange system by Lie point transformation of groups are studied.The differential equation of motion for the higher-order Lagrange system is introduced.The definition of conformal invariance for the system together with its determining equations and conformal factor are provided.The necessary and sufficient condition that the system's conformal invariance would be Lie symmetry by the infinitesimal one-parameter point transformation group is deduced.The conserved quantity of the system is derived using the structural equation satisfied by the gauge function.An example of a higher-order mechanical system is offered to illustrate the application of the result.Since the Noether theorem was published in 1918,[1] the symmetry and conserved quantity for a dynamical system play important roles in the fields of modern science and technology,and some important results have been gained so far.[2-21] Conformal invariance is a modern method for finding conserved quantities.In 1997,Galiullin etal.[22] studied conformal invariance of Birkhoff systems under special infinitesimal transformations.In recent years,we have discussed the conformal invariance of Lie symmetry for Lagrange systems

  13. Modulations of prolactin and growth hormone gene expression and chromatin structure in cultured rat pituitary cells.

    OpenAIRE

    Levy-Wilson, B

    1983-01-01

    I have measured the effect of hormones and other regulatory factors present in the serum component of the culture medium on the levels of growth hormone and prolactin mRNAs in rat pituitary (GH4) cells. Hybridization of cytoplasmic RNA with growth hormone or prolactin cDNA clones indicate that serum depletion reduces significantly the amount of these two mRNAs. The localization of these two genes in chromatin was also analysed using micrococcal nuclease as a probe. At intermediate levels of d...

  14. Robust rooftop extraction from visible band images using higher order CRF

    KAUST Repository

    Li, Er

    2015-08-01

    In this paper, we propose a robust framework for building extraction in visible band images. We first get an initial classification of the pixels based on an unsupervised presegmentation. Then, we develop a novel conditional random field (CRF) formulation to achieve accurate rooftops extraction, which incorporates pixel-level information and segment-level information for the identification of rooftops. Comparing with the commonly used CRF model, a higher order potential defined on segment is added in our model, by exploiting region consistency and shape feature at segment level. Our experiments show that the proposed higher order CRF model outperforms the state-of-the-art methods both at pixel and object levels on rooftops with complex structures and sizes in challenging environments. © 1980-2012 IEEE.

  15. Nested Hoare Triples and Frame Rules for Higher-order Store

    CERN Document Server

    Schwinghammer, Jan; Reus, Bernhard; Yang, Hongseok

    2011-01-01

    Separation logic is a Hoare-style logic for reasoning about programs with heap-allocated mutable data structures. As a step toward extending separation logic to high-level languages with ML-style general (higher-order) storage, we investigate the compatibility of nested Hoare triples with several variations of higher-order frame rules. The interaction of nested triples and frame rules can be subtle, and the inclusion of certain frame rules is in fact unsound. A particular combination of rules can be shown consistent by means of a Kripke model where worlds live in a recursively defined ultrametric space. The resulting logic allows us to elegantly prove programs involving stored code. In particular, using recursively defined assertions, it leads to natural specifications and proofs of invariants required for dealing with recursion through the store.

  16. On the Polarization of non-Guassian optical quantum field: higher-order optical-polarization

    CERN Document Server

    Singh, Ravi S

    2013-01-01

    Polarization of light signifies transversal, anisotropic and asymmetrical statistical property of electromagnetic radiation about direction of propagation. Traditionally, optical-polarization is characterized by Stokes theory susceptible to be insufficient in assessing polarization structure of optical quantum fields and, also, does not decipher twin characteristic polarization parameters (ratio of real amplitudes and difference in phases). An alternative way, in spirit of classical description of optical-polarization, is introduced which can be generalized to deal higher-order polarization of quantum light, particularly, prepared in non-Guassian Schrodinger Cat or Cat-like states and entangled bi-modal coherent states. On account of pseudo mono-modal or multi-modal nature of such optical quantum field, higher-order polarization is seen to be highly sensitive to the basis of description.

  17. A Higher-Order Neural Network Design for Improving Segmentation Performance in Medical Image Series

    Science.gov (United States)

    Selvi, Eşref; Selver, M. Alper; Güzeliş, Cüneyt; Dicle, Oǧuz

    2014-03-01

    Segmentation of anatomical structures from medical image series is an ongoing field of research. Although, organs of interest are three-dimensional in nature, slice-by-slice approaches are widely used in clinical applications because of their ease of integration with the current manual segmentation scheme. To be able to use slice-by-slice techniques effectively, adjacent slice information, which represents likelihood of a region to be the structure of interest, plays critical role. Recent studies focus on using distance transform directly as a feature or to increase the feature values at the vicinity of the search area. This study presents a novel approach by constructing a higher order neural network, the input layer of which receives features together with their multiplications with the distance transform. This allows higher-order interactions between features through the non-linearity introduced by the multiplication. The application of the proposed method to 9 CT datasets for segmentation of the liver shows higher performance than well-known higher order classification neural networks.

  18. Transcriptional networks and chromatin remodeling controlling adipogenesis

    DEFF Research Database (Denmark)

    Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne

    2012-01-01

    remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications...

  19. Higher-order adaptive finite-element methods for Kohn–Sham density functional theory

    Energy Technology Data Exchange (ETDEWEB)

    Motamarri, P. [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Nowak, M.R. [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Leiter, K.; Knap, J. [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States); Gavini, V., E-mail: vikramg@umich.edu [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)

    2013-11-15

    We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688

  20. Structural basis of H2A.Z recognition by SRCAP chromatin-remodeling subunit YL1.

    Science.gov (United States)

    Liang, Xiaoping; Shan, Shan; Pan, Lu; Zhao, Jicheng; Ranjan, Anand; Wang, Feng; Zhang, Zhuqiang; Huang, Yingzi; Feng, Hanqiao; Wei, Debbie; Huang, Li; Liu, Xuehui; Zhong, Qiang; Lou, Jizhong; Li, Guohong; Wu, Carl; Zhou, Zheng

    2016-04-01

    Histone variant H2A.Z, a universal mark of dynamic nucleosomes flanking gene promoters and enhancers, is incorporated into chromatin by SRCAP (SWR1), an ATP-dependent, multicomponent chromatin-remodeling complex. The YL1 (Swc2) subunit of SRCAP (SWR1) plays an essential role in H2A.Z recognition, but how it achieves this has been unclear. Here, we report the crystal structure of the H2A.Z-binding domain of Drosophila melanogaster YL1 (dYL1-Z) in complex with an H2A.Z-H2B dimer at 1.9-Å resolution. The dYL1-Z domain adopts a new whip-like structure that wraps over H2A.Z-H2B, and preferential recognition is largely conferred by three residues in loop 2, the hyperacidic patch and the extended αC helix of H2A.Z. Importantly, this domain is essential for deposition of budding yeast H2A.Z in vivo and SRCAP (SWR1)-catalyzed histone H2A.Z replacement in vitro. Our studies distinguish YL1-Z from known H2A.Z chaperones and suggest a hierarchical mechanism based on increasing binding affinity facilitating H2A.Z transfer from SRCAP (SWR1) to the nucleosome.

  1. Multilevel Higher-Order Item Response Theory Models

    Science.gov (United States)

    Huang, Hung-Yu; Wang, Wen-Chung

    2014-01-01

    In the social sciences, latent traits often have a hierarchical structure, and data can be sampled from multiple levels. Both hierarchical latent traits and multilevel data can occur simultaneously. In this study, we developed a general class of item response theory models to accommodate both hierarchical latent traits and multilevel data. The…

  2. Higher-Order Theory for Functionally Graded Materials

    Science.gov (United States)

    Aboudi, J.; Pindera, M. J.; Arnold, Steven M.

    2001-01-01

    Functionally graded materials (FGM's) are a new generation of engineered materials wherein the microstructural details are spatially varied through nonuniform distribution of the reinforcement phase(s). Engineers accomplish this by using reinforcements with different properties, sizes, and shapes, as well as by interchanging the roles of the reinforcement and matrix phases in a continuous manner (ref. 1). The result is a microstructure that produces continuously or discretely changing thermal and mechanical properties at the macroscopic or continuum scale. This new concept of engineering the material's microstructure marks the beginning of a revolution both in the materials science and mechanics of materials areas since it allows one, for the first time, to fully integrate the material and structural considerations into the final design of structural components. Functionally graded materials are ideal candidates for applications involving severe thermal gradients, ranging from thermal structures in advanced aircraft and aerospace engines to computer circuit boards. Owing to the many variables that control the design of functionally graded microstructures, full exploitation of the FGM's potential requires the development of appropriate modeling strategies for their response to combined thermomechanical loads. Previously, most computational strategies for the response of FGM's did not explicitly couple the material's heterogeneous microstructure with the structural global analysis. Rather, local effective or macroscopic properties at a given point within the FGM were first obtained through homogenization based on a chosen micromechanics scheme and then subsequently used in a global thermomechanical analysis.

  3. Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP.

    Science.gov (United States)

    Muratcioglu, Serena; Presman, Diego M; Pooley, John R; Grøntved, Lars; Hager, Gordon L; Nussinov, Ruth; Keskin, Ozlem; Gursoy, Attila

    2015-09-15

    The glucocorticoid receptor (GR) is a steroid-hormone-activated transcription factor that modulates gene expression. Transcriptional regulation by the GR requires dynamic receptor binding to specific target sites located across the genome. This binding remodels the chromatin structure to allow interaction with other transcription factors. Thus, chromatin remodeling is an essential component of GR-mediated transcriptional regulation, and understanding the interactions between these molecules at the structural level provides insights into the mechanisms of how GR and chromatin remodeling cooperate to regulate gene expression. This study suggests models for the assembly of the SWI/SNF-A (SWItch/Sucrose-NonFermentable) complex and its interaction with the GR. We used the PRISM algorithm (PRotein Interactions by Structural Matching) to predict the three-dimensional complex structures of the target proteins. The structural models indicate that BAF57 and/or BAF250 mediate the interaction between the GR and the SWI/SNF-A complex, corroborating experimental data. They further suggest that a BAF60a/BAF155 and/or BAF60a/BAF170 interaction is critical for association between the core and variant subunits. Further, we model the interaction between GR and CCAAT-enhancer-binding proteins (C/EBPs), since the GR can regulate gene expression indirectly by interacting with other transcription factors like C/EBPs. We observe that GR can bind to bZip domains of the C/EBPα homodimer as both a monomer and dimer of the DNA-binding domain. In silico mutagenesis of the predicted interface residues confirm the importance of these residues in binding. In vivo analysis of the computationally suggested mutations reveals that double mutations of the leucine residues (L317D+L335D) may disrupt the interaction between GR and C/EBPα. Determination of the complex structures of the GR is of fundamental relevance to understanding its interactions and functions, since the function of a protein or a

  4. Special issue of Higher-Order and Symbolic Computation

    DEFF Research Database (Denmark)

    Circular Programs to Deforest in Accumulating Parameters" proposes a technique to eliminate intermediate data structures from consumer/producer pairs with accumulators. A key problem of accumulators is that they capture intermediate data and require multiple traversals. The author solves this problem...... by integrating the techniques of deforestation and tupling with circular programs. A preliminary version of this work was presented at ASIA-PEPM 02....

  5. Visualization of chromatin folding patterns in chicken erythrocytes by atomic force microscopy (AFM)

    Institute of Scientific and Technical Information of China (English)

    QIANRUOLAN; ZHENGXIALIU; 等

    1997-01-01

    The organization of the higher order structure of chromatin in chicken erythrocytes has been examined with tapping-mode scanning force microscopy under conditions close to their native envirinment.Reproducible highresolution AFM images of chromatin compaction at several levels can be demonstrated.An extended beads-on-astring (width of - 15-20nm,height of - 2-3nm for each individual nucleosome) can be consistently observed.Furthermore,superbeade (width of - 40nm,height of - 7nm) are demonstrated.Visualization of the solenoid conformation at the level of 30nm chromatin fiber is attained either by using AFM or by using electron microscopy.In addition,tightly coiled chromatin fibers (- 50-60nm and - 90-110nm) can be revealed.Our data suggest that the chromatin in the interphase nucleus of chicken erythrocyte represents a high-order conformation and AFM provides useful high-resolution structural information concerning the folding pattern of interphase chromatin fibers.

  6. Biophysical studies of cholesterol effects on chromatin.

    Science.gov (United States)

    Silva, Isabel T G; Fernandes, Vinicius; Souza, Caio; Treptow, Werner; Santos, Guilherme Martins

    2017-03-22

    Changes in chromatin structure regulate gene expression and genome maintenance. Molecules that bind to the nucleosome, the complex of DNA and histone proteins, are key modulators of chromatin structure. Previous work indicated that cholesterol, a ubiquitous cellular lipid, may bind to chromatin in vivo, suggesting a potential function for lipids in modulating chromatin architecture. However, the molecular mechanisms of cholesterol action on chromatin structure have remained unclear. Here, we explored the biophysical impact of cholesterol on nucleosome and chromatin fibers reconstituted in vitro and characterized in silico the cholesterol binding to nucleosome. Our findings support that cholesterol assists 10nm and 30nm chromatin formation and induces folding of long chromatin fibers as a result of direct interaction of the cholesterol to six nucleosomal binding sites.

  7. Discovery of higher order modes in a cylindrical reentrant-ring cavity resonator

    CERN Document Server

    Fan, Y; Carvalho, N C; Floch, J-M Le; Shan, Q; Tobar, M E

    2013-01-01

    Rigorous analysis of the properties of resonant modes in a reentrant cavity structure comprising of a post and ring is undertaken and verified experimentally. In particular for the first time we show the existence of higher order reentrant cavity modes in such a structure. Results show this cavity has a better displacement sensitivity compared to the common fundamental mode in a reentrant cylindrical cavity with just a single post. Thus, this type of cavity has the potential to operate as a highly sensitive transducer for a variety of precision measurement applications.

  8. Slat Noise Predictions Using Higher-Order Finite-Difference Methods on Overset Grids

    Science.gov (United States)

    Housman, Jeffrey A.; Kiris, Cetin

    2016-01-01

    Computational aeroacoustic simulations using the structured overset grid approach and higher-order finite difference methods within the Launch Ascent and Vehicle Aerodynamics (LAVA) solver framework are presented for slat noise predictions. The simulations are part of a collaborative study comparing noise generation mechanisms between a conventional slat and a Krueger leading edge flap. Simulation results are compared with experimental data acquired during an aeroacoustic test in the NASA Langley Quiet Flow Facility. Details of the structured overset grid, numerical discretization, and turbulence model are provided.

  9. Higher-order principal component pursuit via tensor approximation and convex optimization

    Institute of Scientific and Technical Information of China (English)

    Sijia Cai; Ping Wang; Linhao Li; Chuhan Zhang

    2014-01-01

    Recovering the low-rank structure of data matrix from sparse errors arises in the principal component pursuit (PCP). This paper exploits the higher-order generalization of matrix recovery, named higher-order principal component pursuit (HOPCP), since it is critical in multi-way data analysis. Unlike the convexification (nuclear norm) for matrix rank function, the tensorial nuclear norm is stil an open problem. While existing preliminary works on the tensor completion field provide a viable way to indicate the low complexity estimate of tensor, therefore, the paper focuses on the low multi-linear rank tensor and adopt its convex relaxation to formulate the convex optimization model of HOPCP. The paper further propose two algorithms for HOPCP based on alternative minimization scheme: the augmented Lagrangian alternating di-rection method (ALADM) and its truncated higher-order singular value decomposition (ALADM-THOSVD) version. The former can obtain a high accuracy solution while the latter is more efficient to handle the computational y intractable problems. Experimental re-sults on both synthetic data and real magnetic resonance imaging data show the applicability of our algorithms in high-dimensional tensor data processing.

  10. Some classes of gravitational shock waves from higher order theories of gravity

    Science.gov (United States)

    Oikonomou, V. K.

    2017-02-01

    We study the gravitational shock wave generated by a massless high energy particle in the context of higher order gravities of the form F(R,R_{μν}R^{μν},R_{μναβ}R^{μν αβ}). In the case of F(R) gravity, we investigate the gravitational shock wave solutions corresponding to various cosmologically viable gravities, and as we demonstrate the solutions are rescaled versions of the Einstein-Hilbert gravity solution. Interestingly enough, other higher order gravities result to the general relativistic solution, except for some specific gravities of the form F(R_{μν}R^{μν}) and F(R,R_{μν}R^{μν}), which we study in detail. In addition, when realistic Gauss-Bonnet gravities of the form R+F(G) are considered, the gravitational shock wave solutions are identical to the general relativistic solution. Finally, the singularity structure of the gravitational shock waves solutions is studied, and it is shown that the effect of higher order gravities makes the singularities milder in comparison to the general relativistic solutions, and in some particular cases the singularities seem to be absent.

  11. Electroweak higher-order effects and theoretical uncertainties in deep-inelastic neutrino scattering

    CERN Document Server

    Diener, K P O; Hollik, W

    2005-01-01

    A previous calculation of electroweak O(alpha) corrections to deep-inelastic neutrino scattering, as e.g. measured by NuTeV and NOMAD, is supplemented by higher-order effects. In detail, we take into account universal two-loop effects from \\Delta\\alpha and \\Delta\\rho as well as higher-order final-state photon radiation off muons in the structure function approach. Moreover, we make use of the recently released O(alpha)-improved parton distributions MRST2004QED and identify the relevant QED factorization scheme, which is DIS like. As a technical byproduct, we describe slicing and subtraction techniques for an efficient calculation of a new type of real corrections that are induced by the generated photon distribution. A numerical discussion of the higher-order effects suggests that the remaining theoretical uncertainty from unknown electroweak corrections is dominated by non-universal two-loop effects and is of the order 0.0003 when translated into a shift in sin^2\\theta_W=1-MW^2/MZ^2. The O(alpha) corrections...

  12. Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation

    Science.gov (United States)

    Nguyen, Carvell T.; Gonzales, Felicidad A.; Jones, Peter A.

    2001-01-01

    Silencing of tumor-suppressor genes by hypermethylation of promoter CpG islands is well documented in human cancer and may be mediated by methyl-CpG-binding proteins, like MeCP2, that are associated in vivo with chromatin modifiers and transcriptional repressors. However, the exact dynamic between methylation and chromatin structure in the regulation of gene expression is not well understood. In this study, we have analyzed the methylation status and chromatin structure of three CpG islands in the p14(ARF)/p16(INK4A) locus in a series of normal and cancer cell lines using methylation-sensitive digestion, MspI accessibility in intact nuclei and chromatin immunoprecipitation (ChIP) assays. We demonstrate the existence of an altered chromatin structure associated with the silencing of tumor-suppressor genes in human cancer cell lines involving CpG island methylation, chromatin condensation, histone deacetylation and MeCP2 binding. The data showed that MeCP2 could bind to methylated CpG islands in both promoters and exons; MeCP2 does not interfere with transcription when bound at an exon, suggesting a more generalized role for the protein beyond transcriptional repression. In the absence of methylation, it is demonstrated that CpG islands located in promoters versus exons display marked differences in the levels of acetylation of associated histone H3, suggesting that chromatin remodeling can be achieved by methylation-independent processes and perhaps explaining why non-promoter CpG islands are more susceptible to de novo methylation than promoter islands. PMID:11713309

  13. Histone H3 lysine 14 (H3K14) acetylation facilitates DNA repair in a positioned nucleosome by stabilizing the binding of the chromatin Remodeler RSC (Remodels Structure of Chromatin).

    Science.gov (United States)

    Duan, Ming-Rui; Smerdon, Michael J

    2014-03-21

    Histone H3 acetylation is induced by UV damage in yeast and may play an important role in regulating the repair of UV photolesions in nucleosome-loaded genomic loci. However, it remains elusive how H3 acetylation facilitates repair. We generated a strongly positioned nucleosome containing homogeneously acetylated H3 at Lys-14 (H3K14ac) and investigated possible mechanisms by which H3K14 acetylation modulates repair. We show that H3K14ac does not alter nucleosome unfolding dynamics or enhance the repair of UV-induced cyclobutane pyrimidine dimers by UV photolyase. Importantly, however, nucleosomes with H3K14ac have a higher affinity for purified chromatin remodeling complex RSC (Remodels the Structure of Chromatin) and show greater cyclobutane pyrimidine dimer repair compared with unacetylated nucleosomes. Our study indicates that, by anchoring RSC, H3K14 acetylation plays an important role in the unfolding of strongly positioned nucleosomes during repair of UV damage.

  14. Automated higher-order calculations: Status and prospects

    CERN Document Server

    Ossola, Giovanni

    2015-01-01

    In this presentation we review the current status in the automated evaluation of scattering amplitudes, with particular attention to the developments related with NLO calculations, which led to the construction of powerful multi-purpose computational tools. After a general overview, we will devote a short section to describe the GoSam framework for NLO calculations and its application to the production of Higgs boson plus jets. We will then briefly comment on the challenges presented by NNLO calculations, whose structure is considerably more complicated. Finally, we will describe some of the features of the integrand-reduction techniques beyond NLO, an alternative promising approach to multi-loop calculations which is currently under development.

  15. Quantitative FLIM-FRET Microscopy to Monitor Nanoscale Chromatin Compaction In Vivo Reveals Structural Roles of Condensin Complexes

    Directory of Open Access Journals (Sweden)

    David Llères

    2017-02-01

    Full Text Available How metazoan genomes are structured at the nanoscale in living cells and tissues remains unknown. Here, we adapted a quantitative FRET (Förster resonance energy transfer-based fluorescence lifetime imaging microscopy (FLIM approach to assay nanoscale chromatin compaction in living organisms. Caenorhabditis elegans was chosen as a model system. By measuring FRET between histone-tagged fluorescent proteins, we visualized distinct chromosomal regions and quantified the different levels of nanoscale compaction in meiotic cells. Using RNAi and repetitive extrachromosomal array approaches, we defined the heterochromatin state and showed that its architecture presents a nanoscale-compacted organization controlled by Heterochromatin Protein-1 (HP1 and SETDB1 H3-lysine-9 methyltransferase homologs in vivo. Next, we functionally explored condensin complexes. We found that condensin I and condensin II are essential for heterochromatin compaction and that condensin I additionally controls lowly compacted regions. Our data show that, in living animals, nanoscale chromatin compaction is controlled not only by histone modifiers and readers but also by condensin complexes.

  16. Using oocyte nuclei for studies on chromatin structure and gene expression.

    Science.gov (United States)

    Sommerville, John

    2010-05-01

    The giant nucleus of amphibian oocytes is generally referred to as the germinal vesicle (GV). Its size allows relatively easy manual isolation from the rest of the oocyte and also presents a large target in situ for microinjection of macromolecules including plasmid DNA, RNA species, antibodies and other proteins and even whole organelles, including somatic cell nuclei. Thus the use of GVs is excellent for two major types of study: the function of endogenous nuclear processes such as gene transcription, RNA processing and intra-nuclear dynamics; and the use of the nuclear components to effect processes such as chromatin assembly, expression of foreign genes and nucleocytoplasmic transport of injected biomolecules. This article outlines some basic techniques appropriate for GV studies, particularly the preparation of oocytes for microinjection and the isolation of germinal vesicles into an oil phase. As an aid to the targeting of the GV within the nucleus, descriptions are given of the use of oocytes from albino animals.

  17. Higher-order-mode damper as beam-position monitors; Higher-Order-Mode Daempfer als Stahllagemonitore

    Energy Technology Data Exchange (ETDEWEB)

    Peschke, C.

    2006-03-15

    In the framework of this thesis a beam-position monitor was developed, which can only because of the signals from the HOM dampers of a linear-accelerator structure determine the beam position with high accuracy. For the unique determination of the beam position in the plane a procedure was developed, which uses the amplitudes and the start-phase difference between a dipole mode and a higher monopole mode. In order tocheck the suitability of the present SBLC-HOM damper as beam position monitor three-dimensional numerical field calculations in the frequency and time range and measurements on the damper cell were performed. For the measurements without beam a beam simulator was constructed, which allows computer-driven measurements with variable depositions of the simulated beam with a resolution of 1.23 {mu}m. Because the complete 6 m long, 180-cell accelerator structure was not available for measurements and could also with the available computers not be three-dimensionally simulated simulated, a one-dimensional equivalent-circuit based model of the multi-cell was studied. The equivalent circuits with 879 concentrated components regards the detuning from cell to cell, the cell losses, the damper losses, and the beam excitation in dependence on the deposition. the measurements and simulations let a resolution of the ready beam-position monitor on the 180-cell in the order of magnitude of 1-10 {mu}m and a relative accuracy smaller 6.2% be expected.

  18. Exploratory movement generates higher-order information that is sufficient for accurate perception of scaled egocentric distance.

    Directory of Open Access Journals (Sweden)

    Bruno Mantel

    Full Text Available Body movement influences the structure of multiple forms of ambient energy, including optics and gravito-inertial force. Some researchers have argued that egocentric distance is derived from inferential integration of visual and non-visual stimulation. We suggest that accurate information about egocentric distance exists in perceptual stimulation as higher-order patterns that extend across optics and inertia. We formalize a pattern that specifies the egocentric distance of a stationary object across higher-order relations between optics and inertia. This higher-order parameter is created by self-generated movement of the perceiver in inertial space relative to the illuminated environment. For this reason, we placed minimal restrictions on the exploratory movements of our participants. We asked whether humans can detect and use the information available in this higher-order pattern. Participants judged whether a virtual object was within reach. We manipulated relations between body movement and the ambient structure of optics and inertia. Judgments were precise and accurate when the higher-order optical-inertial parameter was available. When only optic flow was available, judgments were poor. Our results reveal that participants perceived egocentric distance from the higher-order, optical-inertial consequences of their own exploratory activity. Analysis of participants' movement trajectories revealed that self-selected movements were complex, and tended to optimize availability of the optical-inertial pattern that specifies egocentric distance. We argue that accurate information about egocentric distance exists in higher-order patterns of ambient energy, that self-generated movement can generate these higher-order patterns, and that these patterns can be detected and used to support perception of egocentric distance that is precise and accurate.

  19. The Chd Family of Chromatin Remodelers

    OpenAIRE

    Marfella, Concetta G.A.; Imbalzano, Anthony N.

    2007-01-01

    Chromatin remodeling enzymes contribute to the dynamic changes that occur in chromatin structure during cellular processes such as transcription, recombination, repair, and replication. Members of the chromodomain helicase DNA-binding (Chd) family of enzymes belong to the SNF2 superfamily of ATP-dependent chromatin remodelers. The Chd proteins are distinguished by the presence of two N-terminal chromodomains that function as interaction surfaces for a variety of chromatin components. Genetic,...

  20. Higher-order Mode Calculations, predictions and Overview of Damping Schemes for ERLs

    Energy Technology Data Exchange (ETDEWEB)

    Robert Rimmer

    2005-03-19

    This paper gives a brief review of computational methods for calculating higher-order mode (HOM) impedances for RF structures, the cases for which they are appropriate and some comparisons with measurements. An overview of damping schemes suitable for moderate to high current energy recovered linacs (ERL's), is presented, with a discussion of the pro's and con's of each. The influence of number of cells per cavity, cell shape and cell-to-cell coupling are described. The Jefferson Lab Ampere-class cryomodule concept is presented as an example and the issue of HOM power is highlighted.

  1. Higher-order mode calculations, predictions and overview of damping schemes for energy recovering linacs

    Energy Technology Data Exchange (ETDEWEB)

    Rimmer, R.A. [Jefferson Laboratory, 12000 Jefferson Avenue, Newport News, VA 23606 (United States)]. E-mail: rarimmer@jlab.org

    2006-02-01

    This paper gives a brief review of computational methods for calculating higher-order mode (HOM) impedances for RF structures, the cases for which they are appropriate and some comparisons with measurements. An overview of damping schemes suitable for moderate to high current energy recovered linacs (ERLs), is presented, with a discussion of the pro's and con's of each. The influence of number of cells per cavity, cell shape and cell-to-cell coupling are described. The Jefferson Lab Ampere-class cryomodule concept is presented as an example and the issue of HOM power is highlighted.

  2. Simulation of Airborne Antenna Array Layout Problems Using Parallel Higher-Order MoM

    Directory of Open Access Journals (Sweden)

    Zhongchao Lin

    2014-01-01

    Full Text Available The parallel higher-order Method of Moments based on message passing interface (MPI has been successfully used to analyze the changes in radiation patterns of a microstrip patch array antenna mounted on different positions of an airplane. The block-partitioned scheme for the large dense MoM matrix and a block-cyclic matrix distribution scheme are designed to achieve excellent load balance and high parallel efficiency. Numerical results demonstrate that the rigorous parallel Method of Moments can efficiently and accurately solve large complex electromagnetic problems with composite structures.

  3. Constructing higher order DNA origami arrays using DNA junctions of anti-parallel/parallel double crossovers

    Science.gov (United States)

    Ma, Zhipeng; Park, Seongsu; Yamashita, Naoki; Kawai, Kentaro; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

    2016-06-01

    DNA origami provides a versatile method for the construction of nanostructures with defined shape, size and other properties; such nanostructures may enable a hierarchical assembly of large scale architecture for the placement of other nanomaterials with atomic precision. However, the effective use of these higher order structures as functional components depends on knowledge of their assembly behavior and mechanical properties. This paper demonstrates construction of higher order DNA origami arrays with controlled orientations based on the formation of two types of DNA junctions: anti-parallel and parallel double crossovers. A two-step assembly process, in which preformed rectangular DNA origami monomer structures themselves undergo further self-assembly to form numerically unlimited arrays, was investigated to reveal the influences of assembly parameters. AFM observations showed that when parallel double crossover DNA junctions are used, the assembly of DNA origami arrays occurs with fewer monomers than for structures formed using anti-parallel double crossovers, given the same assembly parameters, indicating that the configuration of parallel double crossovers is not energetically preferred. However, the direct measurement by AFM force-controlled mapping shows that both DNA junctions of anti-parallel and parallel double crossovers have homogeneous mechanical stability with any part of DNA origami.

  4. A Herpesviral Lytic Protein Regulates the Structure of Latent Viral Chromatin

    Directory of Open Access Journals (Sweden)

    Priya Raja

    2016-05-01

    Full Text Available Latent infections by viruses usually involve minimizing viral protein expression so that the host immune system cannot recognize the infected cell through the viral peptides presented on its cell surface. Herpes simplex virus (HSV, for example, is thought to express noncoding RNAs such as latency-associated transcripts (LATs and microRNAs (miRNAs as the only abundant viral gene products during latent infection. Here we describe analysis of HSV-1 mutant viruses, providing strong genetic evidence that HSV-infected cell protein 0 (ICP0 is expressed during establishment and/or maintenance of latent infection in murine sensory neurons in vivo. Studies of an ICP0 nonsense mutant virus showed that ICP0 promotes heterochromatin and latent and lytic transcription, arguing that ICP0 is expressed and functional. We propose that ICP0 promotes transcription of LATs during establishment or maintenance of HSV latent infection, much as it promotes lytic gene transcription. This report introduces the new concept that a lytic viral protein can be expressed during latent infection and can serve dual roles to regulate viral chromatin to optimize latent infection in addition to its role in epigenetic regulation during lytic infection. An additional implication of the results is that ICP0 might serve as a target for an antiviral therapeutic acting on lytic and latent infections.

  5. Generation of higher order Gauss-Laguerre modes in single-pass 2nd harmonic generation

    DEFF Research Database (Denmark)

    Buchhave, Preben; Tidemand-Lichtenberg, Peter

    2008-01-01

    We present a realistic method for dynamic simulation of the development of higher order modes in second harmonic generation. The deformation of the wave fronts due to the nonlinear interaction is expressed by expansion in higher order Gauss-Laguerre modes.......We present a realistic method for dynamic simulation of the development of higher order modes in second harmonic generation. The deformation of the wave fronts due to the nonlinear interaction is expressed by expansion in higher order Gauss-Laguerre modes....

  6. On the Identities of Symmetry for the -Euler Polynomials of Higher Order

    Directory of Open Access Journals (Sweden)

    Park KyoungHo

    2009-01-01

    Full Text Available The main purpose of this paper is to investigate several further interesting properties of symmetry for the multivariate -adic fermionic integral on . From these symmetries, we can derive some recurrence identities for the -Euler polynomials of higher order, which are closely related to the Frobenius-Euler polynomials of higher order. By using our identities of symmetry for the -Euler polynomials of higher order, we can obtain many identities related to the Frobenius-Euler polynomials of higher order.

  7. On the expressiveness and decidability of higher-order process calculi

    NARCIS (Netherlands)

    Lanese, Ivan; Perez, Jorge A.; Sangiorgi, Davide; Schmitt, Alan

    2011-01-01

    In higher-order process calculi, the values exchanged in communications may contain processes. A core calculus of higher-order concurrency is studied; it has only the operators necessary to express higher-order communications: input prefix, process output, and parallel composition. By exhibiting a d

  8. Higher order hierarchical discretization scheme for surface integral equations for layered media

    DEFF Research Database (Denmark)

    Jørgensen, Erik; Kim, Oleksiy S.; Meincke, Peter;

    2004-01-01

    equation. This higher order MoM solution comprises higher order curved patches for the geometry modeling and higher order hierarchical basis functions for expansion of the electric surface current density. Due to the hierarchical property of the basis functions, the order of the expansion can be selected...

  9. Molecular Behavior of DNA Origami in Higher-Order Self-Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Li, Zhe [Arizona State Univ., Tempe, AZ (United States); Liu, Minghui [Arizona State Univ., Tempe, AZ (United States); Lei, Wang [Arizona State Univ., Tempe, AZ (United States); Shandong Univ., Jinan (China); Nangreave, Jeanette [Arizona State Univ., Tempe, AZ (United States); Yan, Hao [Arizona State Univ., Tempe, AZ (United States); Liu, Yan [Arizona State Univ., Tempe, AZ (United States)

    2010-09-08

    DNA-based self-assembly is a unique method for achieving higher-order molecular architectures made possible by the fact that DNA is a programmable information-coding polymer. In the past decade, two main types of DNA nanostructures have been developed: branch-shaped DNA tiles with small dimensions (commonly up to ~20 nm) and DNA origami tiles with larger dimensions (up to ~100 nm). Here we aimed to determine the important factors involved in the assembly of DNA origami superstructures. We constructed a new series of rectangular-shaped DNA origami tiles in which parallel DNA helices are arranged in a zigzag pattern when viewed along the DNA helical axis, a design conceived in order to relax an intrinsic global twist found in the original planar, rectangular origami tiles. Self-associating zigzag tiles were found to form linear arrays in both diagonal directions, while planar tiles showed significant growth in only one direction. Although the series of zigzag tiles were designed to promote two-dimensional array formation, one-dimensional linear arrays and tubular structures were observed instead. We discovered that the dimensional aspect ratio of the origami unit tiles and intertile connection design play important roles in determining the final products, as revealed by atomic force microscopy imaging. This study provides insight into the formation of higher-order structures from self-assembling DNA origami tiles, revealing their unique behavior in comparison with conventional DNA tiles having smaller dimensions.

  10. 基于高阶位移场理论的多孔金属圆柱壳结构响应研究%Research on Structural Response of Metallic Lattice Tube Based on Higher-Order Field Displacement (HOFD) Theory

    Institute of Scientific and Technical Information of China (English)

    张凯; 邓子辰; 王博

    2013-01-01

    A metallic cylindrical lattice tube under internal pressure was analyzed by using the HODF theory .The response of the structure was obtained and compared with that obtained by using the FEM analysis .By using the homogenization method , three cylindrical lattice tubs , whose lattice types were Triangle , Square, and Kagome re-spectively , under internal pressure were homogenized to be orthotropic material and calculated by HODF theory . The HODF theoretical results and the FEM results were respectively obtained and their comparisons show that the differences are very small .The radial displacement and axial displacement obtained with HODF theory are nearly the same as the respective displacements obtained with FEM .The errors in radial stress , hoop stress and radial strain are relatively small .The ratios of the displacements obtained respectively with HODF theory and FEM are calculated and the patterns of these respective ratios are nearly the same .The results of Triangle and Kagome are better than the results of Square .The comparison and analysis of calculated results confirm preliminarily that the higher-order displacement theory can be used to calculate the correct responses of the metallic cylindrical lattice tube under internal pressure .%基于高阶位移场理论研究了简支条件棱镜型圆柱壳体在内压力作用下的结构响应。首先,建立承受内压圆柱壳体的平衡方程,计算在该载荷作用下的各项同性材料的响应,与弹性力学理论解进行对比,验证所得平衡方程的正确性。采用均匀化方法,将正方形,三角形和Kagome 3种多孔金属圆柱壳体等效为正交各向异性的材料,计算了在内压下的结构响应,并与有限元计算结果进行对比,结果表明文中方法所得结果与有限元的结果非常接近,计算得到的径向位移和轴向应变与有限元的计算基本相同,径向应力,环向应力和径向应变等结

  11. Lagrange-type modeling of continuous dielectric permittivity variation in double-higher-order volume integral equation method

    Science.gov (United States)

    Chobanyan, E.; Ilić, M. M.; Notaroš, B. M.

    2015-05-01

    A novel double-higher-order entire-domain volume integral equation (VIE) technique for efficient analysis of electromagnetic structures with continuously inhomogeneous dielectric materials is presented. The technique takes advantage of large curved hexahedral discretization elements—enabled by double-higher-order modeling (higher-order modeling of both the geometry and the current)—in applications involving highly inhomogeneous dielectric bodies. Lagrange-type modeling of an arbitrary continuous variation of the equivalent complex permittivity of the dielectric throughout each VIE geometrical element is implemented, in place of piecewise homogeneous approximate models of the inhomogeneous structures. The technique combines the features of the previous double-higher-order piecewise homogeneous VIE method and continuously inhomogeneous finite element method (FEM). This appears to be the first implementation and demonstration of a VIE method with double-higher-order discretization elements and conformal modeling of inhomogeneous dielectric materials embedded within elements that are also higher (arbitrary) order (with arbitrary material-representation orders within each curved and large VIE element). The new technique is validated and evaluated by comparisons with a continuously inhomogeneous double-higher-order FEM technique, a piecewise homogeneous version of the double-higher-order VIE technique, and a commercial piecewise homogeneous FEM code. The examples include two real-world applications involving continuously inhomogeneous permittivity profiles: scattering from an egg-shaped melting hailstone and near-field analysis of a Luneburg lens, illuminated by a corrugated horn antenna. The results show that the new technique is more efficient and ensures considerable reductions in the number of unknowns and computational time when compared to the three alternative approaches.

  12. Higher-order rational solitons and rogue-like wave solutions of the (2 + 1)-dimensional nonlinear fluid mechanics equations

    Science.gov (United States)

    Wen, Xiao-Yong; Yan, Zhenya

    2017-02-01

    The novel generalized perturbation (n, M)-fold Darboux transformations (DTs) are reported for the (2 + 1)-dimensional Kadomtsev-Petviashvili (KP) equation and its extension by using the Taylor expansion of the Darboux matrix. The generalized perturbation (1 , N - 1) -fold DTs are used to find their higher-order rational solitons and rogue wave solutions in terms of determinants. The dynamics behaviors of these rogue waves are discussed in detail for different parameters and time, which display the interesting RW and soliton structures including the triangle, pentagon, heptagon profiles, etc. Moreover, we find that a new phenomenon that the parameter (a) can control the wave structures of the KP equation from the higher-order rogue waves (a ≠ 0) into higher-order rational solitons (a = 0) in (x, t)-space with y = const . These results may predict the corresponding dynamical phenomena in the models of fluid mechanics and other physically relevant systems.

  13. From higher order thinking to higher order behavior: exploring the relationship between early cognitive skills and social competence in black boys.

    Science.gov (United States)

    Scott, Kristin M; Barbarin, Oscar A; Brown, Jeffrey M

    2013-01-01

    This study examines the relations of higher order (i.e., abstract) thinking (HOT) skills to specific domains of social competence in Black boys (n = 108) attending publicly sponsored prekindergarten (pre-K) programs. Data for the study were collected as part of the National Center for Early Development and Learning (NCEDL) Multi-State Study, a national, longitudinal study examining the quality and outcomes in a representative sample of publicly sponsored pre-K programs in six states (N = 240). Pre-K and kindergarten teachers rated randomly selected children on measures of abstract thinking, self-regulation, and social functioning at the beginning and end of each school year. Applying structural equation modeling, compared with earlier time points, HOT measured in the fall of kindergarten significantly predicted each of the domains of social competence in the spring of kindergarten, with the exception of peer social skills, while controlling for general cognitive ability. Results suggest that early intervention to improve HOT may be an effective and more focused approach to address concerns about Black boys' early social competencies in specific domains and potentially reduce the risk of later social difficulties.

  14. Effect of Chromatin Structure on the Extent and Distribution of DNA Double Strand Breaks Produced by Ionizing Radiation; Comparative Study of hESC and Differentiated Cells Lines.

    Science.gov (United States)

    Venkatesh, Priyanka; Panyutin, Irina V; Remeeva, Evgenia; Neumann, Ronald D; Panyutin, Igor G

    2016-01-02

    Chromatin structure affects the extent of DNA damage and repair. Thus, it has been shown that heterochromatin is more protective against DNA double strand breaks (DSB) formation by ionizing radiation (IR); and that DNA DSB repair may proceed differently in hetero- and euchromatin regions. Human embryonic stem cells (hESC) have a more open chromatin structure than differentiated cells. Here, we study the effect of chromatin structure in hESC on initial DSB formation and subsequent DSB repair. DSB were scored by comet assay; and DSB repair was assessed by repair foci formation via 53BP1 antibody staining. We found that in hESC, heterochromatin is confined to distinct regions, while in differentiated cells it is distributed more evenly within the nuclei. The same dose of ionizing radiation produced considerably more DSB in hESC than in differentiated derivatives, normal human fibroblasts; and one cancer cell line. At the same time, the number of DNA repair foci were not statistically different among these cells. We showed that in hESC, DNA repair foci localized almost exclusively outside the heterochromatin regions. We also noticed that exposure to ionizing radiation resulted in an increase in heterochromatin marker H3K9me3 in cancer HT1080 cells, and to a lesser extent in IMR90 normal fibroblasts, but not in hESCs. These results demonstrate the importance of chromatin conformation for DNA protection and DNA damage repair; and indicate the difference of these processes in hESC.

  15. Predicting chromatin architecture from models of polymer physics.

    Science.gov (United States)

    Bianco, Simona; Chiariello, Andrea M; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario

    2017-01-09

    We review the picture of chromatin large-scale 3D organization emerging from the analysis of Hi-C data and polymer modeling. In higher mammals, Hi-C contact maps reveal a complex higher-order organization, extending from the sub-Mb to chromosomal scales, hierarchically folded in a structure of domains-within-domains (metaTADs). The domain folding hierarchy is partially conserved throughout differentiation, and deeply correlated to epigenomic features. Rearrangements in the metaTAD topology relate to gene expression modifications: in particular, in neuronal differentiation models, topologically associated domains (TADs) tend to have coherent expression changes within architecturally conserved metaTAD niches. To identify the nature of architectural domains and their molecular determinants within a principled approach, we discuss models based on polymer physics. We show that basic concepts of interacting polymer physics explain chromatin spatial organization across chromosomal scales and cell types. The 3D structure of genomic loci can be derived with high accuracy and its molecular determinants identified by crossing information with epigenomic databases. In particular, we illustrate the case of the Sox9 locus, linked to human congenital disorders. The model in-silico predictions on the effects of genomic rearrangements are confirmed by available 5C data. That can help establishing new diagnostic tools for diseases linked to chromatin mis-folding, such as congenital disorders and cancer.

  16. Spatio-chromatic adaptation via higher-order canonical correlation analysis of natural images.

    Directory of Open Access Journals (Sweden)

    Michael U Gutmann

    Full Text Available Independent component and canonical correlation analysis are two general-purpose statistical methods with wide applicability. In neuroscience, independent component analysis of chromatic natural images explains the spatio-chromatic structure of primary cortical receptive fields in terms of properties of the visual environment. Canonical correlation analysis explains similarly chromatic adaptation to different illuminations. But, as we show in this paper, neither of the two methods generalizes well to explain both spatio-chromatic processing and adaptation at the same time. We propose a statistical method which combines the desirable properties of independent component and canonical correlation analysis: It finds independent components in each data set which, across the two data sets, are related to each other via linear or higher-order correlations. The new method is as widely applicable as canonical correlation analysis, and also to more than two data sets. We call it higher-order canonical correlation analysis. When applied to chromatic natural images, we found that it provides a single (unified statistical framework which accounts for both spatio-chromatic processing and adaptation. Filters with spatio-chromatic tuning properties as in the primary visual cortex emerged and corresponding-colors psychophysics was reproduced reasonably well. We used the new method to make a theory-driven testable prediction on how the neural response to colored patterns should change when the illumination changes. We predict shifts in the responses which are comparable to the shifts reported for chromatic contrast habituation.

  17. Higher order modes excitation of electrostatically actuated clamped–clamped microbeams: experimental and analytical investigation

    KAUST Repository

    Jaber, Nizar

    2016-01-06

    © 2016 IOP Publishing Ltd. In this study, we demonstrate analytically and experimentally the excitations of the higher order modes of vibrations in electrostatically actuated clamped-clamped microbeam resonators. The concept is based on using partial electrodes with shapes that induce strong excitation of the mode of interest. The devices are fabricated using polyimide as a structural layer coated with nickel from the top and chrome and gold layers from the bottom. Experimentally, frequency sweeps with different electro-dynamical loading conditions are shown to demonstrate the excitation of the higher order modes of vibration. Using a half electrode, the second mode is excited with high amplitude of vibration compared with almost zero response using the full electrode. Also, using a two-third electrode configuration is shown to amplify the third mode resonance amplitude compared with the full electrode under the same electrical loading conditions. An analytical model is developed based on the Euler-Bernollui beam model and the Galerkin method to simulate the device response. Good agreement between the simulation results and the experimental data is reported.

  18. Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects

    Science.gov (United States)

    Song, Yong-Shun; Shu, Yao-Gen; Zhou, Xin; Ou-Yang, Zhong-Can; Li, Ming

    2017-01-01

    The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite a few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in the 1970s and the basic idea was widely accepted by later models. However, all these models did not systematically investigate the dominant factor on DNAP fidelity, i.e. the higher-order terminal effects through which the polymerization pathway and the proofreading pathway coordinate to achieve high fidelity. In this paper, we propose a new and comprehensive kinetic model of DNAP based on some recent experimental observations, which includes previous models as special cases. We present a rigorous and unified treatment of the corresponding steady-state kinetic equations of any-order terminal effects, and derive analytical expressions for fidelity in terms of kinetic parameters under bio-relevant conditions. These expressions offer new insights on how the higher-order terminal effects contribute substantially to the fidelity in an order-by-order way, and also show that the polymerization-and-proofreading mechanism is dominated only by very few key parameters. We then apply these results to calculate the fidelity of some real DNAPs, which are in good agreements with previous intuitive estimates given by experimentalists.

  19. Improvements to local projective noise reduction through higher order and multiscale refinements

    Science.gov (United States)

    Moore, Jack Murdoch; Small, Michael; Karrech, Ali

    2015-06-01

    The broad spectrum characteristic of signals from nonlinear systems obstructs noise reduction techniques developed for linear systems. Local projection was developed to reduce noise while preserving nonlinear deterministic structures, and a second order refinement to local projection which was proposed ten years ago does so particularly effectively. It involves adjusting the origin of the projection subspace to better accommodate the geometry of the attractor. This paper describes an analytic motivation for the enhancement from which follows further higher order and multiple scale refinements. However, the established enhancement is frequently as or more effective than the new filters arising from solely geometric considerations. Investigation of the way that measurement errors reinforce or cancel throughout the refined local projection procedure explains the special efficacy of the existing enhancement, and leads to a new second order refinement offering widespread gains. Different local projective filters are found to be best suited to different noise levels. At low noise levels, the optimal order increases as noise increases. At intermediate levels second order tends to be optimal, while at high noise levels prototypical local projection is most effective. The new higher order filters perform better relative to established filters for longer signals or signals corresponding to higher dimensional attractors.

  20. First and Higher Order Effects on Zero Order Radiative Transfer Model

    Science.gov (United States)

    Neelam, M.; Mohanty, B.

    2014-12-01

    Microwave radiative transfer model are valuable tool in understanding the complex land surface interactions. Past literature has largely focused on local sensitivity analysis for factor priotization and ignoring the interactions between the variables and uncertainties around them. Since land surface interactions are largely nonlinear, there always exist uncertainties, heterogeneities and interactions thus it is important to quantify them to draw accurate conclusions. In this effort, we used global sensitivity analysis to address the issues of variable uncertainty, higher order interactions, factor priotization and factor fixing for zero-order radiative transfer (ZRT) model. With the to-be-launched Soil Moisture Active Passive (SMAP) mission of NASA, it is very important to have a complete understanding of ZRT for soil moisture retrieval to direct future research and cal/val field campaigns. This is a first attempt to use GSA technique to quantify first order and higher order effects on brightness temperature from ZRT model. Our analyses reflect conditions observed during the growing agricultural season for corn and soybeans in two different regions in - Iowa, U.S.A and Winnipeg, Canada. We found that for corn fields in Iowa, there exist significant second order interactions between soil moisture, surface roughness parameters (RMS height and correlation length) and vegetation parameters (vegetation water content, structure and scattering albedo), whereas in Winnipeg, second order interactions are mainly due to soil moisture and vegetation parameters. But for soybean fields in both Iowa and Winnipeg, we found significant interactions only to exist between soil moisture and surface roughness parameters.

  1. Cross-ratio Identities and Higher-order Poles of CHY-integrand

    CERN Document Server

    Cardona, Carlos; Gomez, Humberto; Huang, Rijun

    2016-01-01

    The evaluation of generic Cachazo-He-Yuan(CHY)-integrands is a big challenge and efficient computational methods are in demand for practical evaluation. In this paper, we propose a systematic decomposition algorithm by using cross-ratio identities, which provides an analytic and easy to implement method for the evaluation of any CHY-integrand. This algorithm aims to decompose a given CHY-integrand containing higher-order poles as a linear combination of CHY-integrands with only simple poles in a finite number of steps, which ultimately can be trivially evaluated by integration rules of simple poles. To make the method even more efficient for CHY-integrands with large number of particles and complicated higher-order pole structures, we combine the $\\Lambda$-algorithm and the cross-ratio identities, and as a by-product it provides us a way to deal with CHY-integrands where the $\\Lambda$-algorithm was not applicable in its original formulation.

  2. Substance and artifact in the higher-order factors of the Big Five.

    Science.gov (United States)

    McCrae, Robert R; Yamagata, Shinji; Jang, Kerry L; Riemann, Rainer; Ando, Juko; Ono, Yutaka; Angleitner, Alois; Spinath, Frank M

    2008-08-01

    J. M. Digman (1997) proposed that the Big Five personality traits showed a higher-order structure with 2 factors he labeled alpha and beta. These factors have been alternatively interpreted as heritable components of personality or as artifacts of evaluative bias. Using structural equation modeling, the authors reanalyzed data from a cross-national twin study and from American cross-observer studies and analyzed new multimethod data from a German twin study. In all analyses, artifact models outperformed substance models by root-mean-square error of approximation criteria, but models combining both artifact and substance were slightly better. These findings suggest that the search for the biological basis of personality traits may be more profitably focused on the 5 factors themselves and their specific facets, especially in monomethod studies.

  3. Two-photon or higher-order absorbing optical materials and methods of use

    Science.gov (United States)

    Marder, Seth (Inventor); Perry, Joseph (Inventor)

    2012-01-01

    Compositions capable of simultaneous two-photon absorption and higher order absorptivities are provided. Compounds having a donor-pi-donor or acceptor-pi-acceptor structure are of particular interest, where the donor is an electron donating group, acceptor is an electron accepting group, and pi is a pi bridge linking the donor and/or acceptor groups. The pi bridge may additionally be substituted with electron donating or withdrawing groups to alter the absorptive wavelength of the structure. Also disclosed are methods of generating an excited state of such compounds through optical stimulation with light using simultaneous absorption of photons of energies individually insufficient to achieve an excited state of the compound, but capable of doing so upon simultaneous absorption of two or more such photons. Applications employing such methods are also provided, including controlled polymerization achieved through focusing of the light source(s) used.

  4. Sequential changes in chromatin structure during transcriptional activation in the beta globin LCR and its target gene.

    Science.gov (United States)

    Kim, Kihoon; Kim, AeRi

    2010-09-01

    Chromatin structure is modulated during transcriptional activation. The changes include the association of transcriptional activators, formation of hypersensitive sites and covalent modifications of histones. To understand the order of the various changes accompanying transcriptional activation, we analyzed the mouse beta globin gene, which is transcriptionally inducible in erythroid MEL cells over a time course of HMBA treatment. Transcription of the globin genes requires the locus control region (LCR) consisting of several hypersensitive sites (HSs). Erythroid specific transcriptional activators such as NF-E2, GATA-1, TAL1 and EKLF were associated with the LCR in the uninduced state before transcriptional activation. The HSs of the LCR were formed in this state as revealed by high sensitivity to DNase I and MNase attack. However the binding of transcriptional activators and the depletion of histones were observed in the promoter of the beta globin gene only after transcriptional activation. In addition, various covalent histone modifications were sequentially detected in lysine residues of histone H3 during the activation. Acetylation of K9, K36 and K27 was notable in both LCR HSs and gene after induction but before transcriptional initiation. Inactive histone marks such as K9me2, K36me2 and K27me2 were removed coincident with transcriptional initiation in the gene region. Taken together, these results indicate that LCR has a substantially active structure in the uninduced state while transcriptional activation serially adds active marks, including histone modifications, and removes inactive marks in the target gene of the LCR.

  5. Structural changes in single chromatin fibers induced by tension and torsion

    NARCIS (Netherlands)

    Meng, He

    2014-01-01

    Since the discovery of the right-handed helical structure of DNA, 61 years have passed. The DNA molecule, which encodes genetic information, is also found twisted into coils. This extra twist of the helical structure, called supercoiling, plays important roles in both DNA compaction and gene regul

  6. Generation of infrared supercontinuum radiation: spatial mode dispersion and higher-order mode propagation in ZBLAN step-index fibers

    DEFF Research Database (Denmark)

    Ramsay, Jacob Søndergaard; Dupont, Sune Vestergaard Lund; Johansen, Mikkel Willum;

    2013-01-01

    Using femtosecond upconversion we investigate the time and wavelength structure of infrared supercontinuum generation. It is shown that radiation is scattered into higher order spatial modes (HOMs) when generating a supercontinuum using fibers that are not single-moded, such as a step-index ZBLAN...... not include scattering into HOMs, and including this provides an extra degree of freedom for tailoring supercontinuum sources....

  7. Analysis of Buried Dielectric Objects Using Higher-Order MoM for Volume Integral Equations

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Meincke, Peter; Breinbjerg, Olav

    2004-01-01

    A higher-order method of moments (MoM) is applied to solve a volume integral equation for dielectric objects in layered media. In comparison to low-order methods, the higher-order MoM, which is based on higher-order hierarchical Legendre vector basis functions and curvilinear hexahedral elements......, requires considerably less number of unknowns and multilayer Green's function calculations for an accurate solution....

  8. Mathematics Teachers’ Interpretation of Higher-Order Thinking in Bloom’s Taxonomy

    OpenAIRE

    Tony Thompson

    2008-01-01

    This study investigated mathematics teachers’ interpretation of higher-order thinking in Bloom’s Taxonomy. Thirty-two high school mathematics teachers from the southeast U.S. were asked to (a) define lower- and higher-order thinking, (b) identify which thinking skills in Bloom’s Taxonomy represented lower- and higher-order thinking, and (c) create an Algebra I final exam item representative of each thinking skill. Results indicate that mathematics teachers have difficulty interpreting the thi...

  9. Numerical calculation of beam shifts for higher-order Laguerre-Gaussian beams upon transmission

    Science.gov (United States)

    Prajapati, Chandravati

    2017-04-01

    We study numerically the spatial and angular contributions to Goos-Hänchen (GH) and Imbert-Fedorov (IF) shifts for higher-order (| l | ≥ 1) Laguerre-Gaussian (LG) beams upon transmission from a planar interface separating two media. Two kinds of spin-orbit interaction and their role in beam shifts are discussed. Firstly, the interaction between the spin and intrinsic orbital angular momentum (OAM) of the LG beam that produces polarization dependent angular shift which is further coupled to the angular momentum structure of the beam and gives rise to spatial shift in orthogonal direction. Secondly, the interaction between the intrinsic and extrinsic OAM of the beam which produces polarization independent transverse shift, called orbital-Hall effect (OHE). Since the angular and spatial shifts are coupled and the angular shift is dependent on the beam waist, the beam shifts can be tuned to maximize or reduce the resultant shifts for LG beams.

  10. Sensitivity analysis of complex coupled systems extended to second and higher order derivatives

    Science.gov (United States)

    Sobieszczanski-Sobieski, Jaroslaw

    1989-01-01

    In design of engineering systems, the what if questions often arise such as: what will be the change of the aircraft payload, if the wing aspect ratio is incremented by 10 percent. Answers to such questions are commonly sought by incrementing the pertinent variable, and reevaluating the major disciplinary analyses involved. These analyses are contributed by engineering disciplines that are, usually, coupled, as are the aerodynamics, structures, and performance in the context of the question above. The what if questions can be answered precisely by computation of the derivatives. A method for calculation of the first derivatives has been developed previously. An algorithm is presented for calculation of the second and higher order derivatives.

  11. A comparison of different methods to implement higher order derivatives of density functionals

    Energy Technology Data Exchange (ETDEWEB)

    van Dam, Hubertus J.J. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-05-18

    Density functional theory is the dominant approach in electronic structure methods today. To calculate properties higher order derivatives of the density functionals are required. These derivatives might be implemented manually,by automatic differentiation, or by symbolic algebra programs. Different authors have cited different reasons for using the particular method of their choice. This paper presents work where all three approaches were used and the strengths and weaknesses of each approach are considered. It is found that all three methods produce code that is suffficiently performanted for practical applications, despite the fact that our symbolic algebra generated code and our automatic differentiation code still have scope for significant optimization. The automatic differentiation approach is the best option for producing readable and maintainable code.

  12. Double Quarter Wave Crab Cavity Field Profile Analysis and Higher Order Mode Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Marques, Carlos [Brookhaven National Lab. (BNL), Upton, NY (United States). Accelerator R and D Div.; Stony Brook Univ., NY (United States). Physics and Astronomy Dept.; Xiao, B. P. [Brookhaven National Lab. (BNL), Upton, NY (United States). Accelerator R and D Div.; Belomestnykh, S. [Brookhaven National Lab. (BNL), Upton, NY (United States). Accelerator R and D Div.; Stony Brook Univ., NY (United States). Physics and Astronomy Dept.

    2014-06-01

    The Large Hadron Collider (LHC) is underway for a major upgrade to increase its luminosity by an order of magnitude beyond its original design specifications. This novel machine configuration known as the High Luminosity LHC (HL-LHC) will rely on various innovative technologies including very compact and ultra-precise superconducting crab cavities for beam rotation. A double quarter wave crab cavity (DQWCC) has been designed at Brookhaven National Laboratory for the HL-LHC. This cavity as well as the structural support components were fabricated and assembled at Niowave. The field profile of the crabbing mode for the DQWCC was investigated using a phase shift bead pulling technique and compared with simulated results to ensure proper operation or discover discrepancies from modeled results and/or variation in fabrication tolerances. Higher-Order Mode (HOM) characterization was also performed and correlated with simulations.

  13. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a distinc

  14. Structural analysis of interphase X-chromatin based on statistical shape theory

    NARCIS (Netherlands)

    Yang, S.; Illner, D.; Teller, K.; Solovei, I.; van Driel, R.; Joffe, B.; Cremer, T.; Eils, R.; Rohr, K.

    2008-01-01

    The 3D folding structure formed by different genomic regions of a chromosome is still poorly understood. So far, only relatively simple geometric features, like distances and angles between different genomic regions, have been evaluated. This work is concerned with more complex geometric properties,

  15. Single Molecule Studies of Chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Jeans, C; Thelen, M P; Noy, A

    2006-02-06

    In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.

  16. A review of higher order strain gradient theories of plasticity: Origins, thermodynamics and connections with dislocation mechanics

    Indian Academy of Sciences (India)

    Suman Guha; Sandeep Sangal; Sumit Basu

    2015-06-01

    In this paper we review developments in higher order strain gradient theories. Several variants of these theories have been proposed in order to explain the effects of size on plastic properties that are manifest in several experiments with micron sized metallic structures. It is generally appreciated that the size effect arises from the storage of geometrically necessary dislocations (GNDs) over and above the statistically stored dislocations (SSDs) required for homogeneous deformations. We review developments that show that the GNDs result from the non-homogeneous nature of the deformation field. Though the connection between GNDs and strain gradients are established in the framework of single crystal plasticity, generalisations to polycrystal plasticity has been made. Strain gradient plasticity inherently involves an intrinsic length scale. In our review, we show, through a few illustrative problems, that conventional plasticity solutions can always be reduced to a scale independent form. The same problems are solved with a simple higher order strain gradient formulation to capture the experimentally observed size effects. However, higher order theories need to be thermodynamically consistent. It has recently been shown that only a few of the existing theories pass this test. We review a few that do. Higher order theories require higher order boundary conditions that enable us to model effects of dislocation storage at impermeable boundaries. But these additional boundary conditions also lead to unique conceptual issues that are not encountered in conventional theories. We review attempts at resolving these issues pertaining to higher order boundary conditions. Finally, we review the future of such theories, their relevance and experimental validation.

  17. Wavelet and Higher order statistics as a tool for revealing Electromagnetic precursors of Earthquakes

    Science.gov (United States)

    Sondhiya, Deepak Kumar; Gwal, Ashok Kumar; Kumar, Sushil

    2016-07-01

    In recent years a number of scientists have reported correlations between observations of electromagnetic radiation and earthquakes. These observation of seismo-electromagnetic waves have been made both on the ground in the earthquake regions and by spacecraft over earthquake regions. In this work an attempt to develop a complex approach to the problem of searching for electromagnetic earthquake precursor signatures is made on the basis of DEMETER satellite observation.The main focus is concerned with the analysis of electric field data in Very Low Frequency (VLF) range using wavelet transform and higher order statistics. We observed electromagnetic turbulence in VLF range resulting from three earthquakes occurred at Keplulauan, Talud, Indonesia form 2009-2011.It is probably due to generation of electric field in a forthcoming earthquake's epicentral zone and penetrating in to the ionosphere. Large value of kurtosis shows the higher level of intermittence in the VLF signal before earthquake. It is possible to conjecture that the sources of this intermittence are the Coherent Structure (CS). For the better understanding of this behavior skewness parameter are used. The high energy at the large scales of the VLF turbulence due the earthquake preparation process contributes to creation of CS in the VLF signal. The results discussed were obtained during a very quiet time and therefore no ionospheric and magnetospheric sources of perturbation were expected. The statistical behavior of the signal (intermittent) and the shape of the spectra suggest that turbulence observed during this event is of the Kolmogorov type. Keywords: Turbulence, Higher order statistics and wave-wave interaction

  18. Power Efficient Higher Order Sliding Mode Control of SR Motor for Speed Control Applications

    Directory of Open Access Journals (Sweden)

    Muhammad Rafiq

    2011-05-01

    Full Text Available This paper presents a novel scheme for speed regulation/tracking of Switched Reluctance (SR motors based on Higher-Order Sliding-Mode technique. In particular, a Second-Order Sliding-Mode Controller (SOSMC based on Super Twisting algorithm is devel-oped. Owing to the peculiar structural properties of SRM, torque produced by each motor phase is a function of phase current as well as rotor position. More importantly, unlike many other motors the polarity of the phase torque in SR motors is solely determined by the rotor position and is independent of the polarity of the applied voltage or phase current. The proposed controller takes advantage of this property and incorporates a commutation scheme which, at any time instant, selects only those motor phases for the computation of control law, which can contribute torque of the desired polarity at that instant. This feature helps in achieving the desired speed regulation/tracking objective in a power efficient manner as control efforts are applied through selective phases and counterproductive phases are left un-energized. This approach also minimizes the power loss in the motor windings thus reducing the heat generation within the motor. In order to highlight the advantages of Higher-Order Sliding-Mode controllers, a classical First-Order Sliding-Mode controller (FOSMC is also developed and applied to the same system. The comparison of the two schemes shows much reduced chattering in case of SOSMC. The performance of the proposed SOSMC controller for speed regulation is also compared with that of another sliding mode speed controller published in the literature.

  19. Cauchy Problem for Quasilinear Hyperbolic Systems with Higher Order Dissipative Terms

    Institute of Scientific and Technical Information of China (English)

    Wei-guo Zhang

    2003-01-01

    In this paper, the author studies the global existence, singularities and life span of smooth solutions of the Cauchy problem for a class of quasilinear hyperbolic systems with higher order dissipative terms and gives their applications to nonlinear wave equations with higher order dissipative terms.

  20. Teaching Higher Order Thinking in the Introductory MIS Course: A Model-Directed Approach

    Science.gov (United States)

    Wang, Shouhong; Wang, Hai

    2011-01-01

    One vision of education evolution is to change the modes of thinking of students. Critical thinking, design thinking, and system thinking are higher order thinking paradigms that are specifically pertinent to business education. A model-directed approach to teaching and learning higher order thinking is proposed. An example of application of the…

  1. On the Higher Power Sums of Reciprocal Higher-Order Sequences

    Directory of Open Access Journals (Sweden)

    Zhengang Wu

    2014-01-01

    Full Text Available Let {un} be a higher-order linear recursive sequence. In this paper, we use the properties of error estimation and the analytic method to study the reciprocal sums of higher power of higher-order sequences. Then we establish several new and interesting identities relating to the infinite and finite sums.

  2. From "Hello" to Higher-Order Thinking: The Effect of Coaching and Feedback on Online Chats

    Science.gov (United States)

    Stein, David S.; Wanstreet, Constance E.; Slagle, Paula; Trinko, Lynn A.; Lutz, Michelle

    2013-01-01

    This exploratory study examined the effect of a coaching and feedback intervention in teaching presence and social presence on higher-order thinking in an online community of inquiry. Coaching occurred before each chat, and feedback was provided immediately afterwards. The findings suggest that over time, the frequency of higher-order thinking…

  3. Generalized q-Euler Numbers and Polynomials of Higher Order and Some Theoretic Identities

    Directory of Open Access Journals (Sweden)

    T. Kim

    2010-01-01

    Full Text Available We give a new construction of the q-Euler numbers and polynomials of higher order attached to Dirichlet's character χ. We derive some theoretic identities involving the generalized q-Euler numbers and polynomials of higher order.

  4. Ability, Breadth, and Parsimony in Computational Models of Higher-Order Cognition

    Science.gov (United States)

    Cassimatis, Nicholas L.; Bello, Paul; Langley, Pat

    2008-01-01

    Computational models will play an important role in our understanding of human higher-order cognition. How can a model's contribution to this goal be evaluated? This article argues that three important aspects of a model of higher-order cognition to evaluate are (a) its ability to reason, solve problems, converse, and learn as well as people do;…

  5. Higher-order blackhole solutions in N=2 supergravity and Calabi-Yau string backgrounds

    NARCIS (Netherlands)

    Behrndt, K.; Cardoso, G.L.; de Wit, B.Q.P.J.; Lüst, D.; Mohaupt, T.; Sabra, W.A.

    1998-01-01

    Based on special geometry, we consider corrections to N=2 extremal black-hole solutions and their entropies originating from higher-order derivative terms in N=2 supergravity. These corrections are described by a holomorphic function, and the higher-order black-hole solutions can be expressed in ter

  6. Higher-Order Beta Matching with Solutions in Long Beta-Eta Normal Form

    DEFF Research Database (Denmark)

    Støvring, Kristian

    2006-01-01

    up to beta-eta equivalence is a long-standing open problem.We show that higher-order matching up to beta-eta equivalence is decidable if and only if a restricted form of higher-order matching up to beta equivalence is decidable: the restriction is that solutions must be in long beta-eta normal form....

  7. Analysis of Scattering by Inhomogeneous Dielectric Objects Using Higher-Order Hierarchical MoM

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter;

    2003-01-01

    developed higher-order hierarchical Legendre basis functions for expansion of the electric flux density and higher-order geometry modeling. An unstructured mesh composed by trilinear (8-node) and/or curved (27-node) hexahedral elements is used to represent the dielectric object accurately. It is shown...

  8. An Analysis of Higher-Order Thinking on Algebra I End-of-Course Tests

    Science.gov (United States)

    Thompson, Tony

    2011-01-01

    This research provides insight into one US state's effort to incorporate higher-order thinking on its Algebra I End-of-Course tests. To facilitate the inclusion of higher-order thinking, the state used "Dimensions of Thinking" (Marzano et al., 1988) and "Bloom's Taxonomy" (Bloom et al., 1956). An analysis of Algebra I test items found that the…

  9. Higher order antibunching and subpossonian photon statistics in five wave mixing process

    CERN Document Server

    Verma, Amit

    2009-01-01

    We have investigated the possibility of observing higher order antibunching (HOA) and higher order subpossonian photon statistics (HOSPS) in five wave mixing and third harmonic generation process. It had been shown that both processes satisfy the criteria of HOA and HOSPS. Further, some observations on the nature of interaction which produces HOA and HOSPS are reported.

  10. An Analysis of Higher-Order Thinking on Algebra I End-of-Course Tests

    Science.gov (United States)

    Thompson, Tony

    2011-01-01

    This research provides insight into one US state's effort to incorporate higher-order thinking on its Algebra I End-of-Course tests. To facilitate the inclusion of higher-order thinking, the state used "Dimensions of Thinking" (Marzano et al., 1988) and "Bloom's Taxonomy" (Bloom et al., 1956). An analysis of Algebra I test…

  11. From virus structure to chromatin: X-ray diffraction to three-dimensional electron microscopy.

    Science.gov (United States)

    Klug, Aaron

    2010-01-01

    Early influences led me first to medical school with a view to microbiology, but I felt the lack of a deeper foundation and changed to chemistry, which in turn led me to physics and mathematics. I moved to the University of Cape Town to work on the X-ray crystallography of some small organic compounds. I developed a new method of using molecular structure factors to solve the crystal structure, which won me a research studentship to Trinity College Cambridge and the Cavendish Laboratory. There I worked on the austenite-pearlite transition in steel. This is governed by the dissipation of latent heat, and I ended up numerically solving partial differential equations. I used the idea of nucleation and growth during the phase change, which had its echo when I later tackled the assembly of Tobacco mosaic virus (TMV) from its constituent RNA and protein subunits. I wanted to move on to X-ray structure analysis of large biological molecules and obtained a Nuffield Fellowship to work in J.D. Bernal's department at Birkbeck College, London. There, I met Rosalind Franklin, who had taken up the study of TMV. I was able to interpret some of Franklin's beautiful X-ray diffraction patterns of the virus particle. From then on, my fate was sealed. After Franklin's untimely death in 1958, I moved in 1962 to the newly built MRC Laboratory of Molecular Biology in Cambridge, which, under Max Perutz, housed the original MRC unit from the Cavendish Laboratory. I was thus privileged to join the Laboratory at an early stage in its expansion and consequently able to take advantage of, and to help build up, its then unique environment of intellectual and technological sophistication. There I have remained ever since.

  12. [Changes in the chromatin structure of lymphoid cells under the influence of low-intensity extremely high-frequency electromagnetic radiation against the background of inflammatory process].

    Science.gov (United States)

    Gapeev, A B; Romanova, N A; Chemeris, N K

    2011-01-01

    Using the alkaline single cell gel electrophoresis technique (comet assay), changes in chromatin structure of peripheral blood leukocytes and peritoneal neutrophils have been studied in mice exposed to low-intensity extremely high-frequency electromagnetic radiation (42.2 GHz, 0.1 mW/cm2, 20 min at 1 h after induction of inflammation) against the background of the systemic inflammatory process. It was revealed that the exposure of mice with the developing inflammation leads to a pronounced decrease in the level of DNA damage to peripheral blood leukocytes and peritoneal neutrophils. It is supposed that the changes in the chromatin structure of lymphoid cells have a genoprotective character in the inflammatory process and can underlie the mechanisms of realization of antiinflammatory effects of the electromagnetic radiation.

  13. Tunneling dynamics of Bose-Einstein condensates with higher-order interactions in optical lattice

    Institute of Scientific and Technical Information of China (English)

    Tie Lu; Xue Ju-Kui

    2011-01-01

    The nonlinear Landau-Zener tunneling and nonlinear Rabi oscillations of Bose-Einstein condensate (BEC) with higher-order atomic interaction between the Bloch bands in an accelerating optical lattice are discussed.Within the two-level model,the tunneling probability of BEC with higher-order atomic interaction between Bloch bands is obtained.We finds that the tunneling rate is closely related to the higher-order atomic interaction.Furthermore,the nonlinear Rabi oscillations of BEC with higher-order atomic interaction between the bands are discussed by imposing a periodic modulation on the level bias.Analytical expressions of the critical higher-order atomic interaction for suppressing/enhancing the Rabi oscillations are obtained.It is shown that the critical value strongly depends on the modulation parameters (i.e.,the modulation amplitude and frequency) and the strength of periodic potential.

  14. Vision improvement by correcting higher-order aberrations with customized soft contact lenses in keratoconic eyes

    Science.gov (United States)

    Sabesan, Ramkumar; Jeong, Tae Moon; Carvalho, Luis; Cox, Ian G.; Williams, David R.; Yoon, Geunyoung

    2007-04-01

    Higher-order aberration correction in abnormal eyes can result in significant vision improvement, especially in eyes with abnormal corneas. Customized optics such as phase plates and customized contact lenses are one of the most practical, nonsurgical ways to correct these ocular higher-order aberrations. We demonstrate the feasibility of correcting higher-order aberrations and improving visual performance with customized soft contact lenses in keratoconic eyes while compensating for the static decentration and rotation of the lens. A reduction of higher-order aberrations by a factor of 3 on average was obtained in these eyes. The higher-order aberration correction resulted in an average improvement of 2.1 lines in visual acuity over the conventional correction of defocus and astigmatism alone.

  15. Numerical Models of Higher-Order Boussinesq Equations and Comparisons with Laboratory Measurement

    Institute of Scientific and Technical Information of China (English)

    邹志利; 张晓莉

    2001-01-01

    Nonlinear water wave propagation passing a submerged shelf is studied experimentally and numerically. The applicability of two different wave propagation models has been investigated. One is higher-order Boussinesq equationsderived by Zou (1999) and the other is the classic Boussinesq equations. Physical experiments are conducted, three differ-ent front slopes (1:10, 1:5 and 1:2) of the shelf are set up in the experiment and their effects on wave propagation are in-vestigated. Comparisons of numerical results with test data are made, the model of higher-order Boussinesq equationsagrees much better with the measurements than the model of the classical Boussinesq equations. The results show thatthe higher-order Boussinesq equations can also be applied to the steeper slope case although the mild slope assumption isemployed in the derivation of the higher order terms of higher order Boussinesq equations.

  16. Bose-Einstein Condensates in Optical Lattices with Higher-Order Interactions

    Institute of Scientific and Technical Information of China (English)

    张爱霞; 薛具奎

    2012-01-01

    The higher-order interactions of Bose-Einstein condensate in multi-dimensional optical lattices are discussed both analytically and numerically.It is demonstrated that the effects of the higher-order atomic interactions on the sound speed and the stabilities of Bloch waves strongly depend on the lattice strength.In the presence of higher-order effects,tighter and high-dimensional lattices are confirmed to be two positive factors for maintaining the system's energetic stability,and the dynamical instability of Bloch waves can take place simultaneously with the energetic instability.In addition,we find that the higher-order interactions exhibit a long-range behavior and the long-lived coherent Bloch oscillations in a tilted optical lattice exist.Our results provide an effective way to probe the higher-order interactions in optical lattices.

  17. Mathematics Teachers’ Interpretation of Higher-Order Thinking in Bloom’s Taxonomy

    Directory of Open Access Journals (Sweden)

    Tony Thompson

    2008-07-01

    Full Text Available This study investigated mathematics teachers’ interpretation of higher-order thinking in Bloom’s Taxonomy. Thirty-two high school mathematics teachers from the southeast U.S. were asked to (a define lower- and higher-order thinking, (b identify which thinking skills in Bloom’s Taxonomy represented lower- and higher-order thinking, and (c create an Algebra I final exam item representative of each thinking skill. Results indicate that mathematics teachers have difficulty interpreting the thinking skills in Bloom’s Taxonomy and creating test items for higher-order thinking. Alternatives to using Bloom’s Taxonomy to help mathematics teachers assess for higher-order thinking are discussed.

  18. Optimal Control and higher-order mechanics for systems with symmetries

    CERN Document Server

    Colombo, Leonardo; de Diego, David Martin

    2012-01-01

    In this paper we will develop and design numerical methods for optimal control problems for a class of underactuated Lagrangian mechanical systems where the configuration manifold is a trivial principal bundle . We will construct these geometric integrators using discrete variational calculus, deriving a discrete version of the higher-order Euler-Lagrange equations on trivial principal bundles. The analysis applies to systems subject to higher-order constraints (that is, depending of higher-order derivatives as, for example, the acceleration). Interesting applications as, for instance, a discrete derivation of the Euler-Lagrange equations for higher-order Lagrangians and higher-order reduced Lagrangians, respectively, are shown. We find interesting applications both in the optimal control of an underactuated vehicle and the well-known plate ball problem seen as an optimization problem with nonholonomic constraints .

  19. Construction of special eye models for investigation of chromatic and higher-order aberrations of eyes.

    Science.gov (United States)

    Zhai, Yi; Wang, Yan; Wang, Zhaoqi; Liu, Yongji; Zhang, Lin; He, Yuanqing; Chang, Shengjiang

    2014-01-01

    An achromatic element eliminating only longitudinal chromatic aberration (LCA) while maintaining transverse chromatic aberration (TCA) is established for the eye model, which involves the angle formed by the visual and optical axis. To investigate the impacts of higher-order aberrations on vision, the actual data of higher-order aberrations of human eyes with three typical levels are introduced into the eye model along visual axis. Moreover, three kinds of individual eye models are established to investigate the impacts of higher-order aberrations, chromatic aberration (LCA+TCA), LCA and TCA on vision under the photopic condition, respectively. Results show that for most human eyes, the impact of chromatic aberration on vision is much stronger than that of higher-order aberrations, and the impact of LCA in chromatic aberration dominates. The impact of TCA is approximately equal to that of normal level higher-order aberrations and it can be ignored when LCA exists.

  20. Ocular higher-order aberrations features analysis after corneal refractive surgery

    Institute of Scientific and Technical Information of China (English)

    WANG Yan; ZHAO Kan-xing; HE Ji-chang; JIN Ying; ZUO Tong

    2007-01-01

    -3 in LASIK was higher and C5+1 and C5+3 were lower than those in the PRK group. C40 (spherical aberration) values were similar between PRK and LASIK, however, C3-1 and C31 (coma) in LASIK were higher than those in PRK, but these differences are of no statistical significance.Conclusions PRK and LASIK may increase ocular higher-order aberrations, but they both have their own features.The difference between the two types of surgery may be correlated with the change of the corneal shape, the conversion of biodynamics, the healing of the corneal cut, and re-structured corneal epithelium and/or the stroma.

  1. Advances in chromatin remodeling and human disease.

    Science.gov (United States)

    Cho, Kyoung Sang; Elizondo, Leah I; Boerkoel, Cornelius F

    2004-06-01

    Epigenetic factors alter phenotype without changing genotype. A primary molecular mechanism underlying epigenetics is the alteration of chromatin structure by covalent DNA modifications, covalent histone modifications, and nucleosome reorganization. Remodeling of chromatin structure regulates DNA methylation, replication, recombination, and repair as well as gene expression. As these functions would predict, dysfunction of the proteins that remodel chromatin causes an array of multi-system disorders and neoplasias. Insights from these diseases suggest that during embryonic and fetal life, environmental distortions of chromatin remodeling encode a 'molecular memory' that predispose the individual to diseases in adulthood.

  2. Coloration using higher order optical interference in the wing pattern of the Madagascan sunset moth.

    Science.gov (United States)

    Yoshioka, S; Nakano, T; Nozue, Y; Kinoshita, S

    2008-04-06

    Colour patterns of animals' bodies are usually produced by the spatial distribution of pigments with different colours. However, some animals use the spatial variation of colour-producing microstructures. We have studied one distinctive example of such structurally produced colour patterns, the wing of the Madagascan sunset moth, to clarify the physical rules that underlie the colour variation. It is known that the iridescent wing scale of the sunset moth has the alternate air-cuticle multilayer structure that causes optical interference. The microscopic and optical investigations of various parts of the wing have confirmed that the thickness of the cuticle layers within the scale largely varies to produce the colour pattern. However, it varies in very different ways between the dorsal and ventral sides of the hind wing; the thickness gradually varies on the dorsal side from scale to scale, while the abrupt changes are found on the ventral side to form distinctive borders between differently coloured areas. It is also revealed that an unusual coloration mechanism is involved in the green part of the ventral hind wing: the colour is caused by higher order optical interference of the highly non-ideal multilayer structure. The physical mechanism of the colour pattern formation is briefly discussed with the several mathematical models proposed so far.

  3. Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.

    Science.gov (United States)

    Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman

    2016-08-02

    During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called "superdomains," such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called "superloops." DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4 We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.

  4. Geometric Integrators for Higher-Order Variational Systems and Their Application to Optimal Control

    Science.gov (United States)

    Colombo, Leonardo; Ferraro, Sebastián; Martín de Diego, David

    2016-12-01

    Numerical methods that preserve geometric invariants of the system, such as energy, momentum or the symplectic form, are called geometric integrators. In this paper we present a method to construct symplectic-momentum integrators for higher-order Lagrangian systems. Given a regular higher-order Lagrangian L:T^{(k)}Q→ R with k≥ 1, the resulting discrete equations define a generally implicit numerical integrator algorithm on T^{(k-1)}Q× T^{(k-1)}Q that approximates the flow of the higher-order Euler-Lagrange equations for L. The algorithm equations are called higher-order discrete Euler-Lagrange equations and constitute a variational integrator for higher-order mechanical systems. The general idea for those variational integrators is to directly discretize Hamilton's principle rather than the equations of motion in a way that preserves the invariants of the original system, notably the symplectic form and, via a discrete version of Noether's theorem, the momentum map. We construct an exact discrete Lagrangian L_d^e using the locally unique solution of the higher-order Euler-Lagrange equations for L with boundary conditions. By taking the discrete Lagrangian as an approximation of L_d^e, we obtain variational integrators for higher-order mechanical systems. We apply our techniques to optimal control problems since, given a cost function, the optimal control problem is understood as a second-order variational problem.

  5. The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure.

    Directory of Open Access Journals (Sweden)

    Robert J Lake

    2014-04-01

    Full Text Available Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects, and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases. Accumulating evidence suggests that CSB functions in transcription regulation, in addition to its roles in DNA repair, and those defects in this transcriptional activity might contribute to the clinical features of Cockayne syndrome. Transcription profiling studies have so far uncovered CSB-dependent effects on gene expression; however, the direct targets of CSB's transcriptional activity remain largely unknown. In this paper, we report the first comprehensive analysis of CSB genomic occupancy during replicative cell growth. We found that CSB occupancy sites display a high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, we found that CSB occupancy is enriched at sites containing the TPA-response element. Consistent with this binding site preference, we show that CSB and the transcription factor c-Jun can be found in the same protein-DNA complex, suggesting that c-Jun can target CSB to specific genomic regions. In support of this notion, we observed decreased CSB occupancy of TPA-response elements when c-Jun levels were diminished. By modulating CSB abundance, we found that CSB can influence the expression of nearby genes and impact nucleosome positioning in the vicinity of its binding site. These results indicate that CSB can be targeted to specific genomic loci by sequence-specific transcription factors to regulate transcription and local chromatin structure. Additionally, comparison of CSB occupancy sites with the MSigDB Pathways database suggests that CSB might function in peroxisome proliferation, EGF receptor transactivation, G protein signaling and NF-κB activation, shedding new light on the possible causes and mechanisms of Cockayne syndrome.

  6. Solving Nonstiff Higher Order Odes Using Variable Order Step Size Backward Difference Directly

    Directory of Open Access Journals (Sweden)

    Ahmad Fadly Nurullah Rasedee

    2014-01-01

    Full Text Available The current numerical techniques for solving a system of higher order ordinary differential equations (ODEs directly calculate the integration coefficients at every step. Here, we propose a method to solve higher order ODEs directly by calculating the integration coefficients only once at the beginning of the integration and if required once more at the end. The formulae will be derived in terms of backward difference in a constant step size formulation. The method developed will be validated by solving some higher order ODEs directly using variable order step size. To simplify the evaluations of the integration coefficients, we find the relationship between various orders. The results presented confirmed our hypothesis.

  7. Verifying object-oriented programs with higher-order separation logic in Coq

    DEFF Research Database (Denmark)

    Bengtson, Jesper; Jensen, Jonas Braband; Sieczkowski, Filip;

    2011-01-01

    We present a shallow Coq embedding of a higher-order separation logic with nested triples for an object-oriented programming language. Moreover, we develop novel specification and proof patterns for reasoning in higher-order separation logic with nested triples about programs that use interfaces...... and interface inheritance. In particular, we show how to use the higher-order features of the Coq formalisation to specify and reason modularly about programs that (1) depend on some unknown code satisfying a specification or that (2) return objects conforming to a certain specification. All of our results have...

  8. Higher order capacity statistics of multi-hop transmission systems over Rayleigh fading channels

    KAUST Repository

    Yilmaz, Ferkan

    2012-03-01

    In this paper, we present an exact analytical expression to evaluate the higher order statistics of the channel capacity for amplify and forward (AF) multihop transmission systems operating over Rayleigh fading channels. Furthermore, we present simple and efficient closed-form expression to the higher order moments of the channel capacity of dual hop transmission system with Rayleigh fading channels. In order to analyze the behavior of the higher order capacity statistics and investigate the usefulness of the mathematical analysis, some selected numerical and simulation results are presented. Our results are found to be in perfect agreement. © 2012 IEEE.

  9. Adaptive Integral Method for Higher-Order Hierarchical Method of Moments

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Meincke, Peter

    2006-01-01

    complexity and memory requirements of AIM with the reduced number of unknowns and higher-order convergence of higher-order hierarchical Legendre basis functions. Numerical examples given show the advantages of the proposed technique over AIM based on low-order basis functions in terms of memory......The Adaptive Integral Method (AIM) is applied to solve the volume integral equation in conjunction with the higher-order Method of Moments (MoM). The classical AIM is modified for larger discretization cells to take advantage of higher-order MoM. The technique combines the low computational...... and computational time. Several preconditioning techniques applied to AIM for volume integral equations are considered....

  10. Deformation from symmetry for Schrodinger equations of higher order on unbounded domains

    Directory of Open Access Journals (Sweden)

    Addolorata Salvatore

    2003-06-01

    Full Text Available By means of a perturbation method recently introduced by Bolle, we discuss the existence of infinitely many solutions for a class of perturbed symmetric higher order Schrodinger equations with non-homogeneous boundary data on unbounded domains.

  11. The Need to Deliver Higher-Order Skills in the Context of Marketing in SMEs

    Science.gov (United States)

    Copley, Paul

    2013-01-01

    It is argued that the delivery of learning and the development of skills and competences are central to SME success; and there appears to be a requirement for higher-order education and training that can deliver a

  12. A new approach for global controllability of higher order Boolean control network.

    Science.gov (United States)

    Chen, Hao; Sun, Jitao

    2013-03-01

    Using the semi-tensor product, the global control problem of the higher order Boolean control network with avoiding set is considered. First, the number of different control sequences that drive the higher order Boolean control network from the initial state to the destination state while avoiding undesirable set is provided. Then, the definition of global controllability of higher order Boolean control network is given. Third, by using the classical theory of nonnegative matrices, the necessary and sufficient condition for the global controllability of higher order Boolean control network with avoiding set is presented. Furthermore, a sufficient condition for k fixed-time global controllability of the system is also obtained. At last, an example is given to illustrate the main results.

  13. Time-periodic Solution to a Nonlinear Parabolic Type Equation of Higher Order

    Institute of Scientific and Technical Information of China (English)

    Yan-ping Wang; You-lin Zhang

    2008-01-01

    In this paper, the existence and uniqueness of time-periodic generalized solutions and time-periodic classical solutions to a class of parabolic type equation of higher order are proved by Gaierkin method.

  14. STRATEGIES FOR IMPROVING HIGHER ORDER THINKING SKILLS IN TEACHING AND LEARNING OF DESIGN AND TECHNOLOGY EDUCATION

    Directory of Open Access Journals (Sweden)

    Caleb Chidozie Chinedu

    2015-12-01

    Full Text Available Higher order thinking skills (HOTS should be an integral part of teaching and learning especially at the higher education level. Thinking skills lessons should be part of the curriculum if students are to solve problems individually, cooperatively and creatively. Teachers on the other hand must be conversant with relevant techniques needed for teaching higher order thinking. An in-depth review of literature reveals that teachers are faced with the problem of how to prepare and teach higher order thinking skills in design and technology education. This paper is a library based work; and data were collected from textbooks, journal articles and internet search. The paper critically examined existing practices in the teaching of higher order thinking skills in design and technology education. Some of the key features mentioned were the use of concept, inferences, visualization, and schemas, among others. Recommendations for practice change were made regarding the development of HOTS.

  15. MULTIPLE POSITIVE SOLUTIONS TO BVPS FOR HIGHER ORDER NONLINEAR DIFFERENTIAL EQUATIONS IN BANACH SPACES

    Institute of Scientific and Technical Information of China (English)

    戚仕硕

    2001-01-01

    In this article,the author employs the conical expansion and compression fixed point principle and the fixed point index theory to show that there exist at least two positive solutions for a higher order BVP.

  16. A Content Analysis of General Chemistry Laboratory Manuals for Evidence of Higher-Order Cognitive Tasks

    Science.gov (United States)

    Domin, Daniel S.

    1999-01-01

    The science laboratory instructional environment is ideal for fostering the development of problem-solving, manipulative, and higher-order thinking skills: the skills needed by today's learner to compete in an ever increasing technology-based society. This paper reports the results of a content analysis of ten general chemistry laboratory manuals. Three experiments from each manual were examined for evidence of higher-order cognitive activities. Analysis was based upon the six major cognitive categories of Bloom's Taxonomy of Educational Objectives: knowledge, comprehension, application, analysis, synthesis, and evaluation. The results of this study show that the overwhelming majority of general chemistry laboratory manuals provide tasks that require the use of only the lower-order cognitive skills: knowledge, comprehension, and application. Two of the laboratory manuals were disparate in having activities that utilized higher-order cognition. I describe the instructional strategies used within these manuals to foster higher-order cognitive development.

  17. SATB1 Mediates Long-Range Chromatin Interactions: A Dual Regulator of Anti-Apoptotic BCL2 and Pro-Apoptotic NOXA Genes.

    Science.gov (United States)

    Yang, Yin; Wang, Zongdan; Sun, Luan; Shao, Lipei; Yang, Nan; Yu, Dawei; Zhang, Xin; Han, Xiao; Sun, Yujie

    2015-01-01

    Aberrant expression of special AT-rich binding protein 1 (SATB1), a global genomic organizer, has been associated with various cancers, which raises the question of how higher-order chromatin structure contributes to carcinogenesis. Disruption of apoptosis is one of the hallmarks of cancer. We previously demonstrated that SATB1 mediated specific long-range chromosomal interactions between the mbr enhancer located within 3'-UTR of the BCL2 gene and the promoter to regulate BCL2 expression during early apoptosis. In the present study, we used chromosome conformation capture (3C) assays and molecular analyses to further investigate the function of the SATB1-mediated higher-order chromatin structure in co-regulation of the anti-apoptotic BCL2 gene and the pro-apoptotic NOXA gene located 3.4Mb downstream on Chromosome 18. We demonstrated that the mbr enhancer spatially juxtaposed the promoters of BCL2 and NOXA genes through SATB1-mediated chromatin-loop in Jurkat cells. Decreased SATB1 levels switched the mbr-BCL2 loop to mbr-NOXA loop, and thus changed expression of these two genes. The SATB1-mediated dynamic switch of the chromatin loop structures was essential for the cooperative expression of the BCL2 and NOXA genes in apoptosis. Notably, the role of SATB1 was specific, since inhibition of SATB1 degradation by caspase-6 inhibitor or caspase-6-resistant SATB1 mutant reversed expression of BCL-2 and NOXA in response to apoptotic stimulation. This study reveals the critical role of SATB1-organized higher-order chromatin structure in regulating the dynamic equilibrium of apoptosis-controlling genes with antagonistic functions and suggests that aberrant SATB1 expression might contribute to cancer development by disrupting the co-regulated genes in apoptosis pathways.

  18. On higher order radiative corrections to elastic electron–proton scattering

    Energy Technology Data Exchange (ETDEWEB)

    Arbuzov, A. B., E-mail: arbuzov@theor.jinr.ru [Bogoliubov Laboratory of Theoretical Physics, JINR, 141980, Dubna (Russian Federation); Department of Higher Mathematics, Dubna State University, 141982, Dubna (Russian Federation); Kopylova, T. V. [Department of Higher Mathematics, Dubna State University, 141982, Dubna (Russian Federation)

    2015-12-18

    QED radiative corrections to elastic electron–proton scattering at low energies are discussed. Corrections to the electron line and effects due to vacuum polarization are computed. Higher order effects are estimated for the conditions of the experiment on the electric and magnetic proton form factors by the A1 Collaboration. Calculations are performed within the next-to-leading approximation. The inclusion of the higher order effects can affect the value of the proton charge radius extracted from the experimental data.

  19. On higher order radiative corrections to elastic electron-proton scattering

    Energy Technology Data Exchange (ETDEWEB)

    Arbuzov, A.B. [Bogoliubov Laboratory of Theoretical Physics, Dubna (Russian Federation); Dubna State University, Department of Higher Mathematics, Dubna (Russian Federation); Kopylova, T.V. [Dubna State University, Department of Higher Mathematics, Dubna (Russian Federation)

    2015-12-15

    QED radiative corrections to elastic electron-proton scattering at low energies are discussed. Corrections to the electron line and effects due to vacuum polarization are computed. Higher order effects are estimated for the conditions of the experiment on the electric and magnetic proton form factors by the A1 Collaboration. Calculations are performed within the next-to-leading approximation. The inclusion of the higher order effects can affect the value of the proton charge radius extracted from the experimental data. (orig.)

  20. Higher-order terms in sensitivity analysis through a differential approach

    Energy Technology Data Exchange (ETDEWEB)

    Dubi, A.; Dudziak, D.J.

    1981-06-01

    A differential approach to sensitivity analysis has been developed that eliminates some difficulties existing in previous work. The new development leads to simple explicit expressions for the first-order perturbation as well as any higher-order terms. The higher-order terms are dependent only on differentials of the transport operator, the unperturbed flux, the adjoint flux, and the unperturbed Green's function of the system.

  1. PRECONDITIONING HIGHER ORDER FINITE ELEMENT SYSTEMS BY ALGEBRAIC MULTIGRID METHOD OF LINEAR ELEMENTS

    Institute of Scientific and Technical Information of China (English)

    Yun-qing Huang; Shi Shu; Xi-jun Yu

    2006-01-01

    We present and analyze a robust preconditioned conjugate gradient method for the higher order Lagrangian finite element systems of a class of elliptic problems. An auxiliary linear element stiffness matrix is chosen to be the preconditioner for higher order finite elements. Then an algebraic multigrid method of linear finite element is applied for solving the preconditioner. The optimal condition number which is independent of the mesh size is obtained. Numerical experiments confirm the efficiency of the algorithm.

  2. Ultra-compact Higher-Order-Mode Pass Filter in a Silicon Waveguide

    DEFF Research Database (Denmark)

    Guan, Xiaowei; Frandsen, Lars Hagedorn; Ding, Yunhong

    2015-01-01

    An 3.7 μm long higher-order-mode pass filter with an extinction ratio larger than 20 dB is demonstrated in a 1D corrugated silicon multimode waveguide......An 3.7 μm long higher-order-mode pass filter with an extinction ratio larger than 20 dB is demonstrated in a 1D corrugated silicon multimode waveguide...

  3. Higher-order Schrödinger and Hartree–Fock equations

    Energy Technology Data Exchange (ETDEWEB)

    Carles, Rémi, E-mail: Remi.Carles@math.cnrs.fr [IMAG, UMR5149, CNRS and University Montpellier, CC051, 34095 Montpellier (France); Lucha, Wolfgang, E-mail: Wolfgang.Lucha@oeaw.ac.at [Institute for High Energy Physics, Austrian Academy of Sciences, Nikolsdorfergasse 18, A-1050 Vienna (Austria); Moulay, Emmanuel, E-mail: emmanuel.moulay@univ-poitiers.fr [XLIM (UMR-CNRS 7252), University Poitiers, 11 Blvd. Marie et Pierre Curie, BP 30179, 86962 Futuroscope Chasseneuil Cedex (France)

    2015-12-15

    The domain of validity of the higher-order Schrödinger equations is analyzed for harmonic-oscillator and Coulomb potentials as typical examples. Then, the Cauchy theory for higher-order Hartree–Fock equations with bounded and Coulomb potentials is developed. Finally, the existence of associated ground states for the odd-order equations is proved. This renders these quantum equations relevant for physics.

  4. An undular bore solution for the higher-order Korteweg-de Vries equation

    Energy Technology Data Exchange (ETDEWEB)

    Marchant, T R [School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, 2522, NSW (Australia); Smyth, N F [School of Mathematics, University of Edinburgh, The King' s Buildings, Mayfield Road, Edinburgh, EH9 3JZ (United Kingdom)

    2006-09-15

    Undular bores describe the evolution and smoothing out of an initial step in mean height and are frequently observed in both oceanographic and meteorological applications. The undular bore solution for the higher-order Korteweg-de Vries (KdV) equation is derived, using an asymptotic transformation which relates the KdV equation and its higher-order counterpart. The higher-order KdV equation considered includes all possible third-order correction terms (where the KdV equation retains second-order terms). The asymptotic transformation is then applied to the KdV undular bore solution to obtain the higher-order undular bore. Examples of higher-order undular bores, describing both surface and internal waves, are presented. Key properties, such as the amplitude and speed of the lead soliton and the width of the bore, are found. An excellent comparison is obtained between the analytical and numerical solutions. Also, it is illustrated how an asymptotic transformation and numerical solutions can be combined to generate hybrid asymptotic-numerical solutions, thus avoiding the severe instabilities associated with numerical schemes for the higher-order KdV equation. (letter to the editor)

  5. Questions for assessing higher-order cognitive skills: it's not just Bloom's.

    Science.gov (United States)

    Lemons, Paula P; Lemons, J Derrick

    2013-01-01

    We present an exploratory study of biologists' ideas about higher-order cognition questions. We documented the conversations of biologists who were writing and reviewing a set of higher-order cognition questions. Using a qualitative approach, we identified the themes of these conversations. Biologists in our study used Bloom's Taxonomy to logically analyze questions. However, biologists were also concerned with question difficulty, the length of time required for students to address questions, and students' experience with questions. Finally, some biologists demonstrated an assumption that questions should have one correct answer, not multiple reasonable solutions; this assumption undermined their comfort with some higher-order cognition questions. We generated a framework for further research that provides an interpretation of participants' ideas about higher-order questions and a model of the relationships among these ideas. Two hypotheses emerge from this framework. First, we propose that biologists look for ways to measure difficulty when writing higher-order questions. Second, we propose that biologists' assumptions about the role of questions in student learning strongly influence the types of higher-order questions they write.

  6. Modeling and analysis of smart piezoelectric beams using simple higher order shear deformation theory

    Science.gov (United States)

    Adnan Elshafei, M.; Alraiess, Fuzy

    2013-03-01

    In the current work, a finite element formulation is developed for modeling and analysis of isotropic as well as orthotropic composite beams with distributed piezoelectric actuators subjected to both mechanical and electrical loads. The proposed model is developed based on a simple higher order shear deformation theory where the displacement field equations in the model account for a parabolic distribution of the shear strain and the nonlinearity of in-plane displacements across the thickness and subsequently the shear correction factor is not involved. The virtual displacement method is used to formulate the equations of motion of the structure system. The model is valid for both segmented and continuous piezoelectric elements, which can be either surface bonded or embedded in the laminated beams. A two-node element with four mechanical degrees of freedom in addition to one electrical degree of freedom for each node is used in the finite element formulation. The electric potential is considered as a function of the thickness and the length of the beam element. A MATLAB code is developed to compute the static deformation and free vibration parameters of the beams with distributed piezoelectric actuators. The obtained results from the proposed model are compared with the available analytical results and the finite element results of other researchers.

  7. 高阶非局部变分模型%Higher-order nonlocal variational model

    Institute of Scientific and Technical Information of China (English)

    李亚峰; 冯象初

    2012-01-01

    To describe the nonlocal structure of images better and remove noise, this paper proposes a higher-order nonlocal variational model by defining a new weighted function. Theoretical analysis and numerical experiments are presented to demonstrate the performance of the proposed model, which is better than the original in terms of both PSNR and visual perception. As a result, the new model keeps the advantages of the nonlocal variational model, while it can preserve image features better.%为了更好地描述图像的非局部结构并抑制噪声,通过定义新的权函数,提出了一个高阶非局部变分模型.理论分析和实验结果表明,相比于非局部平均去噪算子和非局部变分模型,提出的高阶非局部变分模型在去噪结果上有更高的信噪比和更好的视觉效果.因此,新模型保持了非局部变分模型的优点,同时能够更好地保留图像特征.

  8. Object representation for multi-beam sonar image using local higher-order statistics

    Science.gov (United States)

    Li, Haisen; Gao, Jue; Du, Weidong; Zhou, Tian; Xu, Chao; Chen, Baowei

    2017-01-01

    Multi-beam sonar imaging has been widely used in various underwater tasks such as object recognition and object tracking. Problems remain, however, when the sonar images are characterized by low signal-to-noise ratio, low resolution, and amplitude alterations due to viewpoint changes. This paper investigates the capacity of local higher-order statistics (HOS) to represent objects in multi-beam sonar images. The Weibull distribution has been used for modeling the background of the image. Local HOS involving skewness is estimated using a sliding computational window, thus generating the local skewness image of which a square structure is associated with a potential object. The ability of object representation with different signal-to-noise ratio (SNR) between object and background is analyzed, and the choice of the computational window size is discussed. In the case of the object with high SNR, a novel algorithm based on background estimation is proposed to reduce side lobe and retain object regions. The performance of object representation has been evaluated using real data that provided encouraging results in the case of the object with low amplitude, high side lobes, or large fluctuant amplitude. In conclusion, local HOS provides more reliable and stable information relating to the potential object and improves the object representation in multi-beam sonar image.

  9. Higher Order and Harmonic Corrections to the Quasi-de Sitter Inflation

    CERN Document Server

    Mohsenzadeh, M

    2016-01-01

    Since the trans-Planckian considerations can be associated with the re-definition of the initial vacuum, we investigate further the influence of trans-planckian physics on the spectra produced by initial quasi-de Sitter (dS) state during inflation. Recently, we have introduced asymptotic-dS mode to study the scale dependency of power spectrum during inflation. In this paper, we calculate the trans-Planckian corrections to the spectra resulted from that initial mode. As expected the modified spectra consisting of higher order corrections associated to the type of the geometry and harmonic terms sensitive to the fluctuations of space-time(or gravitational waves) during inflation. The corrections are tiny at far past time limit, but may have very important effects on the formation of large scale structure. Also, the results are always valid for any asymptotic dS space-time and particularly coincide the conventional results for the dS and flat space-time.

  10. Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment

    Energy Technology Data Exchange (ETDEWEB)

    Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)

    2015-11-01

    Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.

  11. Changeability of sperm chromatin structure during liquid storage of ovine semen in milk-egg yolk- and soybean lecithin-based extenders and their relationships to field-fertility.

    Science.gov (United States)

    Khalifa, Tarek; Lymberopoulos, Aristotelis

    2013-12-01

    The aim of this experiment was to study the effect of semen extender on sperm chromatin structure and to correlate chromatin integrity with field-fertility of preserved ram semen. Ejaculates of at least 2 × 10(9) sperm/ml and 70 % progressive motility were collected using an artificial vagina from Chios rams (n = 11, 4-6 years old), split-diluted to 1 × 10(9) sperm/ml with milk-egg yolk- and soybean lecithin (Ovixcell®)-based extenders, packaged in 0.5-ml straws and examined after 6, 24 and 48 h of storage at 5 ± 1 °C. Evaluation endpoints were computer-assisted sperm motion analysis, fluorescence-based analysis of chromatin structure by chromomycin A3 and acridine orange assays, and 65-day pregnancy rate (PR) of 34- to 36-h preserved semen after intra-cervical insemination of ewes (n = 154) in progestagen-synchronized estrus. Neither extender nor storage time had any influence on incidence of decondensed chromatin. Unlike Ovixcell® extender, deterioration of sperm motility (P egg yolk extender. Sperm motility accounted for 14.4-18.5 % of variations in chromatin integrity (P egg yolk-stored semen. Nevertheless, PR differed between rams (14.3-71.4 %; P egg yolk extender in preserving chromatin stability and motility. Chromatin defects are negatively associated with sperm fertility.

  12. Chromatin is wonderful stuff.

    NARCIS (Netherlands)

    R. van Driel

    2007-01-01

    Chromatin molecules have properties that set them aside from all other biomacromolecules in the cell. (i) Chromosomes, which are single chromatin molecules, are the largest macromolecules in eukaryotic cells. (ii) Chromatin molecules carry the cell's genetic and epigenetic information and all contro

  13. Reshaping chromatin after DNA damage: the choreography of histone proteins.

    Science.gov (United States)

    Polo, Sophie E

    2015-02-13

    DNA damage signaling and repair machineries operate in a nuclear environment where DNA is wrapped around histone proteins and packaged into chromatin. Understanding how chromatin structure is restored together with the DNA sequence during DNA damage repair has been a topic of intense research. Indeed, chromatin integrity is central to cell functions and identity. However, chromatin shows remarkable plasticity in response to DNA damage. This review presents our current knowledge of chromatin dynamics in the mammalian cell nucleus in response to DNA double strand breaks and UV lesions. I provide an overview of the key players involved in regulating histone dynamics in damaged chromatin regions, focusing on histone chaperones and their concerted action with histone modifiers, chromatin remodelers and repair factors. I also discuss how these dynamics contribute to reshaping chromatin and, by altering the chromatin landscape, may affect the maintenance of epigenetic information.

  14. Chromatin dynamics resolved with force spectroscopy

    NARCIS (Netherlands)

    Chien, Fan-Tso

    2011-01-01

    In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases t

  15. Higher-order Peregrine combs and Peregrine walls for the variable-coefficient Lenells-Fokas equation

    Science.gov (United States)

    Wang, Zi-Qi; Wang, Xin; Wang, Lei; Sun, Wen-Rong; Qi, Feng-Hua

    2017-02-01

    In this paper, we study the variable-coefficient Lenells-Fokas (LF) model. Under large periodic modulations in the variable coefficients of the LF model, the generalized Akhmediev breathers develop into the breather multiple births (BMBs) from which we obtain the Peregrine combs (PCs). The PCs can be considered as the limiting case of the BMBs and be transformed into the Peregrine walls (PWs) with a specific amplitude of periodic modulation. We further investigate the spatiotemporal characteristics of the PCs and PWs analytically. Based on the second-order breather and rogue-wave solutions, we derive the corresponding higher-order structures (higher-order PCs and PWs) under proper periodic modulations. What is particularly noteworthy is that the second-order PC can be converted into the Peregrine pyramid which exhibits the higher amplitude and thickness. Our results could be helpful for the design of experiments in the optical fiber communications.

  16. Investigation of Fano resonances induced by higher order plasmon modes on a circular nano-disk with an elongated cavity

    KAUST Repository

    Amin, Muhammad Ruhul

    2012-08-10

    In this paper, a planar metallic nanostructure design, which supports two distinct Fano resonances in its extinction cross-section spectrum under normally incident and linearly polarized electromagnetic field, is proposed. The proposed design involves a circular disk embedding an elongated cavity; shifting and rotating the cavity break the symmetry of the structure with respect to the incident field and induce higher order plasmon modes. As a result, Fano resonances are generated in the visible spectrum due to the destructive interference between the sub-radiant higher order modes and super-radiant the dipolar mode. The Fano resonances can be tuned by varying the cavity\\'s width and the rotation angle. An RLC circuit, which is mathematically equivalent to a mass-spring oscillator, is proposed to model the optical response of the nanostructure design.

  17. Supernova, baryon acoustic oscillations, and CMB surface distance constraints on f(G) higher order gravity models

    CERN Document Server

    Moldenhauer, Jacob; Thompson, John; Easson, Damien A

    2010-01-01

    We consider recently proposed higher order gravity models where the action is built from the Einstein-Hilbert action plus a function f(G) of the Gauss-Bonnet invariant. The models were previously shown to pass physical acceptability conditions as well as solar system tests. In this paper, we compare the models to combined data sets of supernovae, baryon acoustic oscillations, and constraints from the CMB surface of last scattering. We find that the models provide fits to the data that are close to those of the LCDM concordance model. The results provide a pool of higher order gravity models that pass these tests and need to be compared to constraints from large scale structure and full CMB analysis.

  18. Higher order aberrations in amblyopic children and their role in refractory amblyopia

    Directory of Open Access Journals (Sweden)

    Arnaldo Dias-Santos

    2014-12-01

    Full Text Available Objective: Some studies have hypothesized that an unfavourable higher order aberrometric profile could act as an amblyogenic mechanism and may be responsible for some amblyopic cases that are refractory to conventional treatment or cases of “idiopathic” amblyopia. This study compared the aberrometric profile in amblyopic children to that of children with normal visual development and compared the aberrometric profile in corrected amblyopic eyes and refractory amblyopic eyes with that of healthy eyes. Methods: Cross-sectional study with three groups of children – the CA group (22 eyes of 11 children with unilateral corrected amblyopia, the RA group (24 eyes of 13 children with unilateral refractory amblyopia and the C group (28 eyes of 14 children with normal visual development. Higher order aberrations were evaluated using an OPD-Scan III (NIDEK. Comparisons of the aberrometric profile were made between these groups as well as between the amblyopic and healthy eyes within the CA and RA groups. Results: Higher order aberrations with greater impact in visual quality were not significantly higher in the CA and RA groups when compared with the C group. Moreover, there were no statistically significant differences in the higher order aberrometric profile between the amblyopic and healthy eyes within the CA and RA groups. Conclusions: Contrary to lower order aberrations (e.g., myopia, hyperopia, primary astigmatism, higher order aberrations do not seem to be involved in the etiopathogenesis of amblyopia. Therefore, these are likely not the cause of most cases of refractory amblyopia.

  19. An efficient higher-order PML in WLP-FDTD method for time reversed wave simulation

    Science.gov (United States)

    Wei, Xiao-Kun; Shao, Wei; Ou, Haiyan; Wang, Bing-Zhong

    2016-09-01

    Derived from a stretched coordinate formulation, a higher-order complex frequency shifted (CFS) perfectly matched layer (PML) is proposed for the unconditionally stable finite-difference time-domain (FDTD) method based on weighted Laguerre polynomials (WLPs). The higher-order PML is implemented with an auxiliary differential equation (ADE) approach. In order to further improve absorbing performance, the parameter values of stretching functions in the higher-order PML are optimized by the multi-objective genetic algorithm (MOGA). The optimal solutions can be chosen from the Pareto front for trading-off between two independent objectives. It is shown in a numerical test that the higher-order PML is efficient in terms of attenuating propagating waves and reducing late time reflections. Moreover, the higher-order PML can be placed very close to the wall when analyzing the channel characteristics of time reversal (TR) waves in a multipath indoor environment. Numerical examples of TR wave propagation demonstrate the availability of the proposed method.

  20. Performance of Higher Order Campbell methods, Part II: calibration and experimental application

    Science.gov (United States)

    Elter, Zs.; de Izarra, G.; Filliatre, P.; Jammes, C.; Pázsit, I.

    2016-11-01

    Applying Higher Order Campbelling methods in neutron flux monitoring with fission chambers is advantageous due to their capabilities to suppress the impact of unwanted noises and signal contributions (such as gamma radiation). This work aims to verify through experimental results that the basic assumptions behind the Higher Order Campelling methods are valid in critical reactors. The experiments, reported in this work, were performed at the MINERVE reactor in Cadarache. It is shown that the calibration of a fission chamber and the associated electronic system is possible in higher order mode. With the use of unbiased cumulant estimators and with digital processing, it is shown that over a wide count rate range, accurate count rate estimation can be achieved based on signal samples of a few ms, which is a significant progress compared to similar experimental results in the literature. The difference between the count rate estimated by pulse counting and by the Higher Order Campelling is less than 4%. The work also investigates the possibility of monitoring transient events. For this purpose, a control rod drop event was followed in Higher Order Campbelling mode.

  1. Simplification of the Flux Function for a Higher-order Gas-kinetic Evolution Model

    CERN Document Server

    Zhou, Guangzhao; Liu, Feng

    2016-01-01

    The higher-order gas-kinetic scheme for solving the Navier-Stokes equations has been studied in recent years. In addition to the use of higher-order reconstruction techniques, many terms are used in the Taylor expansion of the gas distribution functions. Therefore, a large number of coefficients need to be determined in the calculation of the time evolution of the gas distribution function at cell interfaces. As a consequence, the higher-order flux function takes much more computational time than that of a second-order gas-kinetic scheme. This paper aims to simplify the evolution model by two steps. Firstly, the coefficients related to the higher-order spatial and temporal derivatives of a distribution function are redefined to reduce the computational cost. Secondly, based on the physical analysis, some terms can be removed without loss of accuracy. Through the simplifications, the computational efficiency of the higher-order scheme is increased significantly. In addition, a self-adaptive numerical viscosity...

  2. Diffusion-driven looping provides a consistent framework for chromatin organization.

    Directory of Open Access Journals (Sweden)

    Manfred Bohn

    Full Text Available Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei.

  3. Epigenetic phenomena, chromatin dynamics, and gene expression. New theoretical approaches in the study of living systems.

    Science.gov (United States)

    Boi, Luciano

    2008-01-01

    This paper is aimed at exploring the genome at the level beyond that of DNA sequence alone. We stress the fact that the level of genes is not the sole "reality" in the living world, for there are different epigenetic processes that profoundly affect change in living systems. Moreover, epigenetics very likely influences the course of evolution and the unfolding of life. We further attempt to investigate how the genome is dynamically organized into the nuclear space within the cell. We mainly focus on analyses of higher order nuclear architecture and the dynamic interactions of chromatin with other nuclear components. We especially want to know how epigenetic phenomena influences genes expression and chromosome functions. The proper understanding of these processes require new concepts and approaches be introduced and developed. In particular, we think that research in biology has to shift from only describing molecular and local features of living systems to studying the regulatory networks of interactions among gene pathways, the folding and dynamics of chromatin structure and how environmental factors affects the behavior of organisms. There are essential components of biological information on living organisms which cannot be portrayed in the DNA sequence alone. In a post-genomic era, the importance of chromatin/epigenetic interface has become increasingly apparent. One of the purposes of current research should be to highlight the enormous impact of chromatin organization and dynamics on epigenetic phenomena, and, conversely, to emphasize the important role that epigenetic phenomena play in gene expression and cell regulation.

  4. Glucocorticoid receptor and nuclear factor kappa-b affect three-dimensional chromatin organization

    NARCIS (Netherlands)

    Kuznetsova, T.; Wang, S.Y.; Rao, N.A.; Mandoli, A.; Martens, J.H.; Rother, N; Aartse, A.; Groh, L.; Janssen-Megens, E.M.; Li, G.; Ruan, Y.; Logie, C.; Stunnenberg, H.G.

    2015-01-01

    BACKGROUND: The impact of signal-dependent transcription factors, such as glucocorticoid receptor and nuclear factor kappa-b, on the three-dimensional organization of chromatin remains a topic of discussion. The possible scenarios range from remodeling of higher order chromatin architecture by activ

  5. A Stable Higher Order Space-Time Galerkin Scheme for Time Domain Integral Equations

    CERN Document Server

    Pray, A J; Nair, N V; Cools, K; Bağcı, H; Shanker, B

    2014-01-01

    Stability of time domain integral equation (TDIE) solvers has remained an elusive goal for many years. Advancement of this research has largely progressed on four fronts: (1) Exact integration, (2) Lubich quadrature, (3) smooth temporal basis functions, and (4) Space-time separation of convolutions with the retarded potential. The latter method was explored in [Pray et al. IEEE TAP 2012]. This method's efficacy in stabilizing solutions to the time domain electric field integral equation (TD-EFIE) was demonstrated on first order surface descriptions (flat elements) in tandem with 0th order functions as the temporal basis. In this work, we develop the methodology necessary to extend to higher order surface descriptions as well as to enable its use with higher order temporal basis functions. These higher order temporal basis functions are used in a Galerkin framework. A number of results that demonstrate convergence, stability, and applicability are presented.

  6. On the selection of tuning methodology of FOPID controllers for the control of higher order processes.

    Science.gov (United States)

    Das, Saptarshi; Saha, Suman; Das, Shantanu; Gupta, Amitava

    2011-07-01

    In this paper, a comparative study is done on the time and frequency domain tuning strategies for fractional order (FO) PID controllers to handle higher order processes. A new fractional order template for reduced parameter modelling of stable minimum/non-minimum phase higher order processes is introduced and its advantage in frequency domain tuning of FOPID controllers is also presented. The time domain optimal tuning of FOPID controllers have also been carried out to handle these higher order processes by performing optimization with various integral performance indices. The paper highlights on the practical control system implementation issues like flexibility of online autotuning, reduced control signal and actuator size, capability of measurement noise filtration, load disturbance suppression, robustness against parameter uncertainties etc. in light of the above tuning methodologies.

  7. Isomorphisms of types in the presence of higher-order references

    CERN Document Server

    Clairambault, Pierre

    2011-01-01

    We investigate the problem of type isomorphisms in a programming language with higher-order references. We first recall the game-theoretic model of higher-order references by Abramsky, Honda and McCusker. Solving an open problem by Laurent, we show that two finitely branching arenas are isomorphic if and only if they are geometrically the same, up to renaming of moves (Laurent's forest isomorphism). We deduce from this an equational theory characterizing isomorphisms of types in a finitary language with higher order references. We show however that Laurent's conjecture does not hold on infinitely branching arenas, yielding a non-trivial type isomorphism in the extension of this language with natural numbers.

  8. Investigating higher order modes effects on thermionic RF gun transverse emittance

    Science.gov (United States)

    Rajabi, A.; Shokri, B.; Feghhi, S. A. H.

    2017-02-01

    As the excitation of higher order modes in high gradient accelerating cavities of the RF gun negatively influences electron beam quality, in the present work a theory is obtained based on generalizing Panofsky-Wenzel theorem to study the effect of transverse magnetic modes on transverse emittance growth of the RF gun. Based on this theory, the impact of higher order modes on transverse momentum is investigated. Based on analysis and simulation results, it is shown that different RF modes result in divergence or convergence effects on beam transverse dynamics. The presence of dipole and quadrupole modes can enhance the transverse emittance by 320 % and 450 % , respectively. The compound effect of the presence of two higher order modes results in 470 % transverse emittance growth.

  9. Higher-order effects on self-similar parabolic pulse in the microstructured fibre amplifier

    Institute of Scientific and Technical Information of China (English)

    Liu Wei-Ci; Xu Wen-Cheng; Feng Jie; Chen Wei-Cheng; Li Shu-Xian; Lin Song-Hao

    2008-01-01

    By considering higher-order effects, the properties of self-similar parabolic pulses propagating in the microstructured fibre amplifier with a normal group-velocity dispersion have been investigated. The numerical results indicate that the higher-order effects can badly distort self-similar parabolic pulse shape and optical spectrum, and at the same time the peak shift and oscillation appear, while the pulse still reveals highly linear chirp but grows into asymmetry. The influence of different higher-order effects on self-similar parabolic pulse propagation has been analysed. It shows thatthe self-steepening plays a more important role. We can manipulate the geometrical parameters of the microstructured fibre amplifier to gain a suitable dispersion and nonlinearity coefficient which will keep high-quality self-similar parabolic pulse propagation. These results are significant for the further study of self-similar parabolic pulse propagation.

  10. Higher-order-statistics-based radial basis function networks for signal enhancement.

    Science.gov (United States)

    Lin, Bor-Shyh; Lin, Bor-Shing; Chong, Fok-Ching; Lai, Feipei

    2007-05-01

    In this paper, a higher-order-statistics (HOS)-based radial basis function (RBF) network for signal enhancement is introduced. In the proposed scheme, higher order cumulants of the reference signal were used as the input of HOS-based RBF. An HOS-based supervised learning algorithm, with mean square error obtained from higher order cumulants of the desired input and the system output as the learning criterion, was used to adapt weights. The motivation is that the HOS can effectively suppress Gaussian and symmetrically distributed non-Gaussian noise. The influence of a Gaussian noise on the input of HOS-based RBF and the HOS-based learning algorithm can be mitigated. Simulated results indicate that HOS-based RBF can provide better performance for signal enhancement under different noise levels, and its performance is insensitive to the selection of learning rates. Moreover, the efficiency of HOS-based RBF under the nonstationary Gaussian noise is stable.

  11. Regularity properties of fiber derivatives associated with higher-order mechanical systems

    Science.gov (United States)

    Colombo, Leonardo; Prieto-Martínez, Pedro Daniel

    2016-08-01

    The aim of this work is to study fiber derivatives associated to Lagrangian and Hamiltonian functions describing the dynamics of a higher-order autonomous dynamical system. More precisely, given a function in T∗T(k-1)Q, we find necessary and sufficient conditions for such a function to describe the dynamics of a kth-order autonomous dynamical system, thus being a kth-order Hamiltonian function. Then, we give a suitable definition of (hyper)regularity for these higher-order Hamiltonian functions in terms of their fiber derivative. In addition, we also study an alternative characterization of the dynamics in Lagrangian submanifolds in terms of the solutions of the higher-order Euler-Lagrange equations.

  12. A finite deformation theory of higher-order gradient crystal plasticity

    DEFF Research Database (Denmark)

    Kuroda, Mitsutoshi; Tvergaard, Viggo

    2008-01-01

    crystal plasticity that is based on an assumption of the existence of higher-order stresses. Furthermore, a boundary-value problem for simple shear of a constrained thin strip is studied numerically, and some characteristic features of finite deformation are demonstrated through a comparison to a solution......For higher-order gradient crystal plasticity, a finite deformation formulation is presented. The theory does not deviate much from the conventional crystal plasticity theory. Only a back stress effect and additional differential equations for evolution of the geometrically necessary dislocation...... (GND) densities supplement the conventional theory within a non-work-conjugate framework in which there is no need to introduce higher-order microscopic stresses that would be work-conjugate to slip rate gradients. We discuss its connection to a work-conjugate type of finite deformation gradient...

  13. Design and Application of Strategies/Tactics in Higher Order Logics

    Science.gov (United States)

    Archer, Myla (Editor); diVito, Ben (Editor); Munoz, Cesar (Editor)

    2003-01-01

    This Proceedings includes both a paper from the implementors of PVS providing guidance for PVS strategy writers and a tutorial on PVS strategy writing distilled from the experience of three PVS users who have written extensive sets of PVS user strategies. Following these are three full papers from the higher-order logic theorem proving community that discuss PVS strategies to enhance arithmetic and other interactive reasoning in PVS; implementing first-order tactics in higher-order provers; and a proposed technique for specifying small step semantics that can be used in multiple higher order logic theorem provers, with illustrations from both Coq and PVS. The Proceedings concludes with three position papers for a panel session that discuss three settings in which development of PVS strategies is worth while.

  14. Chromatin domain boundaries: insulators and beyond

    Institute of Scientific and Technical Information of China (English)

    Gong Hong WEI; De Pei LIU; Chih Chuan LIANG

    2005-01-01

    The eukaryotic genome is organized into functionally and structurally distinct domains, representing regulatory units for gene expression and chromosome behavior. DNA sequences that mark the border between adjacent domains are the insulators or boundary elements, which are required in maintenance of the function of different domains. Some insulators need others enable to play insulation activity. Chromatin domains are defined by distinct sets of post-translationally modified histones. Recent studies show that these histone modifications are also involved in establishment of sharp chromatin boundaries in order to prevent the spreading of distinct domains. Additionally, in some loci, the high-order chromatin structures for long-range looping interactions also have boundary activities, suggesting a correlation between insulators and chromatin loop domains. In this review, we will discuss recent progress in the field of chromatin domain boundaries.

  15. Linearization of a warped $f(R)$ theory in the higher-order frame

    CERN Document Server

    Zhong, Yuan

    2016-01-01

    The linearization of a type of $f(R)$ gravity is studied directly in the higher-order frame for an arbitrary five-dimensional warped space-time background. The quadratic actions of the normal modes of the scalar, vector and tensor perturbations are derived, and compared to those obtained in the Einstein frame. We find that the corresponding quadratic actions are equivalent. From the point of view of the higher-order frame, the best gauge choice is the curvature gauge, under which the linear perturbation of the scalar curvature is zero, and all the perturbation equations reduce to second order.

  16. Dynamic control of higher-order modes in hollow-core photonic crystal fibers.

    Science.gov (United States)

    Euser, T G; Whyte, G; Scharrer, M; Chen, J S Y; Abdolvand, A; Nold, J; Kaminski, C F; Russell, P St J

    2008-10-27

    We present a versatile method for selective mode coupling into higher-order modes of photonic crystal fibers, using holograms electronically generated by a spatial light modulator. The method enables non-mechanical and completely repeatable changes in the coupling conditions. We have excited higher order modes up to LP(31) in hollow-core photonic crystal fibers. The reproducibility of the coupling allows direct comparison of the losses of different guided modes in both hollow-core bandgap and kagome-lattice photonic crystal fibers. Our results are also relevant to applications in which the intensity distribution of the light inside the fiber is important, such as particle- or atom-guidance.

  17. A TWO-SCALE HIGHER-ORDER FINITE ELEMENT DISCRETIZATION FOR SCHRODINGER EQUATION

    Institute of Scientific and Technical Information of China (English)

    Huajie Chen; Fang Liu; Aihui Zhou

    2009-01-01

    In this paper,a two-scale higher-order finite element discretization scheme is proposed and analyzed for a Schr(o)dinger equation on tensor product domains.With the scheme,the solution of the eigenvalue problem on a fine grid can be reduced to an eigenvalue problem on a much coarser grid together with some eigenvalue problems on partially fine grids.It is shown theoretically and numerically that the proposed two-scale higher-order scheme not only significantly reduces the number of degrees of freedom but also produces very accurate approximations.

  18. Higher Order Modeling in Hybrid Approaches to the Computation of Electromagnetic Fields

    Science.gov (United States)

    Wilton, Donald R.; Fink, Patrick W.; Graglia, Roberto D.

    2000-01-01

    Higher order geometry representations and interpolatory basis functions for computational electromagnetics are reviewed. Two types of vector-valued basis functions are described: curl-conforming bases, used primarily in finite element solutions, and divergence-conforming bases used primarily in integral equation formulations. Both sets satisfy Nedelec constraints, which optimally reduce the number of degrees of freedom required for a given order. Results are presented illustrating the improved accuracy and convergence properties of higher order representations for hybrid integral equation and finite element methods.

  19. Improvement on polynomial Wigner-Ville distribution for detecting higher-order polynomial phase signal

    Institute of Scientific and Technical Information of China (English)

    Tan Xiaogang; Wei Ping; Li Liping

    2009-01-01

    To detect higher order polynomial phase signals (HOPPSs), the smoothed-pseudo polynomial Wigner-Ville distribution (SP-PWVD), an improved version of the polynomial Wigner-Ville distribution (PWVD), is pre-sented using a separable kernel. By adjusting the lengths of the functions in the kernel, the balance between resolution retaining and interference suppressing can be adjusted conveniently. The proposed method with merits of interference terms reduction and noise suppression can provide time frequency representation of better readability and more accurate instantaneous frequency (IF) estimation with higher order SP-PWVD. The performance of the SP-PWVD is verified by computer simulations.

  20. In-medium QCD sum rules for D mesons: A projection method for higher order contributions

    CERN Document Server

    Buchheim, Thomas; Kampfer, Burkhard

    2014-01-01

    D mesons serve as excellent probes of hot and/or dense strongly interacting matter. They can provide insight into the restoration of chiral symmetry. The chiral condensate as well as other chirally odd condensates, such as certain four-quark condensates, are linked to order parameters of spontaneous chiral symmetry breaking. Thus, the evaluation of these higher order condensate contributions in the framework of QCD sum rules is of high interest. We present a general method for projecting Lorentz indices of ground state expectation values providing a crucial step towards a comprehensive calculation of higher order corrections to the operator product expansion of hadrons, especially D mesons, in a strongly interacting medium.