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.
Internal and higher-order structure of chromatin nu bodies
Energy Technology Data Exchange (ETDEWEB)
Olins, D E
1977-01-01
Based upon current biophysical data (including recent laser-Raman studies) of isolated nu bodies and inner histones, we have proposed that the chromatin subunit consists of a DNA-rich outer domain surrounding a protein core composed of ..cap alpha..-helical-rich histone globular regions, close-packed with dihedral point-group symmetry. Analysis of the effects of urea on isolated nu bodies suggest that these two domains respond differently: the DNA-rich shell exhibits noncooperative destabilization; the protein core undergoes cooperative destabilization. This differential response of the two regions of a nu body to a simple chemical perturbant (i.e., urea) may furnish a model for the conformational differences in nu bodies postulated for active chromatin. Nu bodies are believed to organize into 20-30 nm higher-order fibers in condensed regions of chromatin. However, the integrity of subunits in these thick fibers has recently been seriously challenged. Evidence from our laboratory, presented here, confirms that the 20-30 nm chromatin fibers consists of a close-packing of nu bodies. The chromatin subunits, therefore, retain their integrity within the higher-order fibers.
Higher order chromatin structure: bridging physics and biology
Fudenberg, Geoffrey; Mirny, Leonid A.
2012-01-01
Recent advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of high-order interph...
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.
Higher-order chromatin structure in DSB induction, repair and misrepair
Czech Academy of Sciences Publication Activity Database
Falk, Martin; Lukášová, Emilie; Kozubek, Stanislav
2010-01-01
Roč. 704, 1-3 (2010), s. 88-100. ISSN 1383-5742 R&D Projects: GA MŠk ME 919; GA AV ČR(CZ) IAA500040802; GA AV ČR(CZ) 1QS500040508 Grant ostatní: GA MŠk(CZ) LC535 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA double strand breaks * DSB repair * higher-order chromatin structure Subject RIV: BO - Biophysics Impact factor: 8.741, year: 2010
Hydrogen peroxide mediates higher order chromatin degradation.
Bai, H; Konat, G W
2003-01-01
Although a large body of evidence supports a causative link between oxidative stress and neurodegeneration, the mechanisms are still elusive. We have recently demonstrated that hydrogen peroxide (H(2)O(2)), the major mediator of oxidative stress triggers higher order chromatin degradation (HOCD), i.e. excision of chromatin loops at the matrix attachment regions (MARs). The present study was designed to determine the specificity of H(2)O(2) in respect to HOCD induction. Rat glioma C6 cells were exposed to H(2)O(2) and other oxidants, and the fragmentation of genomic DNA was assessed by field inversion gel electrophoresis (FIGE). S1 digestion before FIGE was used to detect single strand fragmentation. The exposure of C6 cells to H(2)O(2) induced a rapid and extensive HOCD. Thus, within 30 min, total chromatin was single strandedly digested into 50 kb fragments. Evident HOCD was elicited by H(2)O(2) at concentrations as low as 5 micro M. HOCD was mostly reversible during 4-8h following the removal of H(2)O(2) from the medium indicating an efficient relegation of the chromatin fragments. No HOCD was induced by H(2)O(2) in isolated nuclei indicating that HOCD-endonuclease is activated indirectly by cytoplasmic signal pathways triggered by H(2)O(2). The exposure of cells to a synthetic peroxide, i.e. tert-butyrylhydroperoxide (tBH) also induced HOCD, but to a lesser extent than H(2)O(2). Contrary to the peroxides, the exposure of cells to equitoxic concentration of hypochlorite and spermine NONOate, a nitric oxide generator, failed to induce rapid HOCD. These results indicate that rapid HOCD is not a result of oxidative stress per se, but is rather triggered by signaling cascades initiated specifically by H(2)O(2). Furthermore, the rapid and extensive HOCD was observed in several rat and human cell lines challenged with H(2)O(2), indicating that the process is not restricted to glial cells, but rather represents a general response of cells to H(2)O(2). PMID:12421592
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
. Interestingly, RNF8-mediated recruitment of CHD4 and subsequent chromatin remodelling were independent of the ubiquitin-ligase activity of RNF8, but involved a non-canonical interaction with the forkhead-associated (FHA) domain. Our study reveals a new mechanism of chromatin remodelling-assisted ubiquitylation......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 decondensation...
Directory of Open Access Journals (Sweden)
Lisa Herr
Full Text Available We present a new approach to model dose rate effects on cell killing after photon radiation based on the spatio-temporal clustering of DNA double strand breaks (DSBs within higher order chromatin structures of approximately 1-2 Mbp size, so called giant loops. The main concept of this approach consists of a distinction of two classes of lesions, isolated and clustered DSBs, characterized by the number of double strand breaks induced in a giant loop. We assume a low lethality and fast component of repair for isolated DSBs and a high lethality and slow component of repair for clustered DSBs. With appropriate rates, the temporal transition between the different lesion classes is expressed in terms of five differential equations. These allow formulating the dynamics involved in the competition of damage induction and repair for arbitrary dose rates and fractionation schemes. Final cell survival probabilities are computable with a cell line specific set of three parameters: The lethality for isolated DSBs, the lethality for clustered DSBs and the half-life time of isolated DSBs. By comparison with larger sets of published experimental data it is demonstrated that the model describes the cell line dependent response to treatments using either continuous irradiation at a constant dose rate or to split dose irradiation well. Furthermore, an analytic investigation of the formulation concerning single fraction treatments with constant dose rates in the limiting cases of extremely high or low dose rates is presented. The approach is consistent with the Linear-Quadratic model extended by the Lea-Catcheside factor up to the second moment in dose. Finally, it is shown that the model correctly predicts empirical findings about the dose rate dependence of incidence probabilities for deterministic radiation effects like pneumonitis and the bone marrow syndrome. These findings further support the general concepts on which the approach is based.
Generalized structure of higher order nonclassicality
International Nuclear Information System (INIS)
A generalized notion of higher order nonclassicality (in terms of higher order moments) is introduced. Under this generalized framework of higher order nonclassicality, conditions of higher order squeezing and higher order subpoissonian photon statistics are derived. A simpler form of the Hong-Mandel higher order squeezing criterion is derived under this framework by using an operator ordering theorem introduced by us in [A. Pathak, J. Phys. A 33 (2000) 5607]. It is also generalized for multi-photon Bose operators of Brandt and Greenberg. Similarly, condition for higher order subpoissonian photon statistics is derived by normal ordering of higher powers of number operator. Further, with the help of simple density matrices, it is shown that the higher order antibunching (HOA) and higher order subpoissonian photon statistics (HOSPS) are not the manifestation of the same phenomenon and consequently it is incorrect to use the condition of HOA as a test of HOSPS. It is also shown that the HOA and HOSPS may exist even in absence of the corresponding lower order phenomenon. Binomial state, nonlinear first order excited squeezed state (NLESS) and nonlinear vacuum squeezed state (NLVSS) are used as examples of quantum state and it is shown that these states may show higher order nonclassical characteristics. It is observed that the Binomial state which is always antibunched, is not always higher order squeezed and NLVSS which shows higher order squeezing does not show HOSPS and HOA. The opposite is observed in NLESS and consequently it is established that the HOSPS and HOS are two independent signatures of higher order nonclassicality.
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.
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.
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.
Stable static structures in models with higher-order derivatives
International Nuclear Information System (INIS)
We investigate the presence of static solutions in generalized models described by a real scalar field in four-dimensional space–time. We study models in which the scalar field engenders higher-order derivatives and spontaneous symmetry breaking, inducing the presence of domain walls. Despite the presence of higher-order derivatives, the models keep to equations of motion second-order differential equations, so we focus on the presence of first-order equations that help us to obtain analytical solutions and investigate linear stability on general grounds. We then illustrate the general results with some specific examples, showing that the domain wall may become compact and that the zero mode may split. Moreover, if the model is further generalized to include k-field behavior, it may contribute to split the static structure itself
DEFF Research Database (Denmark)
Ebert, Grit; Steininger, Anne; Weißmann, Robert;
2014-01-01
three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the...... the chromosome 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...
Revealing Higher Order Protein Structure Using Mass Spectrometry
Chait, Brian T.; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P.; Shi, Yi
2016-04-01
The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope.
Revealing Higher Order Protein Structure Using Mass Spectrometry
Chait, Brian T.; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P.; Shi, Yi
2016-06-01
The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope.
Chromatin structure and DNA damage
International Nuclear Information System (INIS)
This dissertation examines the structure and structural transitions of chromatin in relation to DNA damage. The ability of intact and histone H1 depleted chromatin fibers to fold into higher ordered structures in vitro was examined following DNA photodamage introduced by two different agents. (1) 254-nm UV radiation and (2) trimethylpsoralen (plus near-UV radiation). Both agents are highly specific for DNA and form adducts predicted to cause different degrees of distortion in the DNA helix. The salt-induced structural transitions of intact and histone H1 depleted chromatin fibers were monitored by both analytical ultracentrifugation and light scattering. Our results show that even in the presence of extremely large, nonphysiological amounts of photodamage by either agent the ability of chromatin to fold into higher ordered structures is not affected. The compact, 30 nm fiber must therefore be able to accommodate a large amount of DNA damage without any measurable changes in the overall size or degree of compaction of this structure. The distribution of pyrimidine dimers was mapped at the single nucleotide level in nucleosome core DNA from UV-irradiated mononucleosomes, chromatin fibers, and human cells in culture using the 3' → 5' exonuclease activity of T4 DNA polymerase
Chromatin Structure and Function
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
Structure tuning and its effect on higher order modes
International Nuclear Information System (INIS)
Coarse tuning of multi-cell linac structures is required to achieve the correct accelerator mode frequency and a flat field profile at room temperature. Fine tuning is required to adjust the frequency during operation at low temperatures. Our newly fabricated 1300 MHz CERN/DESY type structures incorporate longitudinal stiffening bars for reduction of microphonic effects. In this paper we evaluate the use of longitudinal rods as a means of coarse tuning and achieving a flat field profile, and report the effect of fine tuning by end cell deformation on high order modes. (Author) 5 figs., 3 refs
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…
International Nuclear Information System (INIS)
An admittance-based structure health monitoring method with a higher-order resonant circuit is proposed and investigated in this paper, with the advantage of increased damage detection sensitivity. The change of the stiffness or mass in the structure due to damage can be detected by measuring the admittance from the piezoelectric transducer adhered to the host structure. It is known that designing an inductive circuitry, together with the piezoelectric capacitance, can introduce an additional resonance and yield enhanced sensitivity. In this paper, based on the electrical–mechanical analogy, a novel higher-order resonant circuit is designed and optimized to significantly improve the damage detection capability, i.e. increasing the admittance magnitude and its sensitivity to damage. Theoretical analyses and simulations are carried out. The results show that the peak admittance magnitude is increased by 74 dB for the higher-order circuit without electrical damping and 46 dB with electrical damping, when comparing with the second-order circuit system. The damage detection sensitivity is increased by 33 dB and 36 dB for a stiffness change of 0.5% and 1%, respectively, by using the proposed higher-order circuit, when comparing with the second-order circuit system, and even more when comparing with the traditional method with only a resistor. (paper)
Study of Higher Order Modes in Superconducting Accelerating Structures for Linac Applications
Schuh, Marcel; Welsch, C P
2011-01-01
Higher Order Modes (HOMs) can severely limit the operation of superconducting cavities in a linear accelerator with high beam current, high duty factor and complex pulse structure. Therefore, the full HOM spectrum has to be analysed in detail to identify potentially dangerous modes already during the design phase and to define their damping requirements. For this purpose a dedicated beam dynamics simulation code, Simulation of higher order Mode Dynamics (SMD), focusing on beam-HOM interaction, has been developed in the frame of this project. SMD allows to analyse the beam behaviour under the presence of HOMs, taking into account many important effects, such as for example the HOM frequency spread, beam input jitter, different chopping patterns, as well as klystron and alignment errors. SMD is used to investigate in detail into the effects of HOMs in the Superconducting Proton Linac (SPL) at CERN and in particular their potential to drive beam instabili- ties in the longitudinal and transverse direction. Based...
Scholtes, Ingo; Garas, Antonios
2015-01-01
Recent research on temporal networks has highlighted the limitations of a static network perspective for our understanding of complex systems with dynamic topologies. In particular, recent works have shown that i) the specific order in which links occur in real-world temporal networks affects causality structures and thus the evolution of dynamical processes, and ii) higher-order aggregate representations of temporal networks can be used to analytically study the effect of these order correlations on dynamical processes. In this article we analyze the effect of order correlations on path-based centrality measures in real-world temporal networks. Analyzing temporal equivalents of betweenness, closeness and reach centrality in six empirical temporal networks, we first show that an analysis of the commonly used static, time-aggregated representation can give misleading results about the actual importance of nodes. We further study higher-order time-aggregated networks, a recently proposed generalization of the c...
The role of Bni5 in the regulation of septin higher-order structure formation.
Patasi, Csilla; Godočíková, Jana; Michlíková, Soňa; Nie, Yan; Káčeriková, Radka; Kválová, Katarína; Raunser, Stefan; Farkašovský, Marian
2015-12-01
Septins are a family of conserved cytoskeletal proteins playing an essential role in cytokinesis and in many other cellular processes in fungi and animals. In budding yeast Saccharomyces cerevisiae, septins form filaments and higher-order structures at the mother-bud neck depending on the particular stage of the cell cycle. Septin structures at the division plane serve as a scaffold to recruit the proteins required for particular cellular processes. The formation and localization of septin structures at particular stages of the cell cycle also determine functionality of these proteins. Many different proteins participate in regulating septin assembly. Despite recent developments, we are only beginning to understand how specific protein-protein interactions lead to changes in the polymerization of septin filaments or assembly of higher-order structures. Here, using fluorescence and electron microscopy, we found that Bni5 crosslinks septin filaments into networks by bridging pairs or multiple filaments, forming structures that resemble railways. Furthermore, Bni5 appears to be a substrate of the Elm1 protein kinase in vitro. Moreover, Elm1 induces in the presence of Bni5 disassembly of long septin filaments, suggesting that these proteins may participate in the hourglass to double ring transition. This work gives new insight into the regulatory role of Bni5 in the structural changes of septins. PMID:26351911
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...
Phase structure of the $O(2)$ ghost model with higher-order gradient term
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.
Gaussian higher Order Derivative based Structural Enhancement of Digital Bone X-Ray Images
Directory of Open Access Journals (Sweden)
Raka Kundu
2011-01-01
Full Text Available A novel method for enhancement of digital X-ray images of bones is presented in this paper. It has come to observation that the proposed method based on the Gaussian higher order derivative shows an appreciable enhancement of edges in digital X-ray images of bones that can be used for detection of various bone deformities as well as for the better understanding of the bone structure. We have achieved a level of improvement in distinguishing the bone information from the other parts of the digital X-ray images.
Analysis of Higher Order Modes in Large Superconducting Radio Frequency Accelerating Structures
Galek, Tomasz; Brackebusch, Korinna; Van Rienen, Ursula
2015-01-01
Superconducting radio frequency cavities used for accelerating charged particle beams are commonly used in accelerator facilities around the world. The design and optimization of modern superconducting RF cavities requires intensive numerical simulations. Vast number of operational parameters must be calculated to ensure appropriate functioning of the accelerating structures. In this study, we primarily focus on estimation and behavior of higher order modes in superconducting RF cavities connected in chains. To calculate large RF models the state-space concatenation scheme, an efficient hybrid method, is employed.
International Nuclear Information System (INIS)
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.
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.
Protein-protein interactions in a higher-order structure direct lambda site-specific recombination.
Thompson, J F; de Vargas, L M; Skinner, S E; Landy, A
1987-06-01
The highly directional site-specific recombination of bacteriophage lambda is tightly regulated by the binding of three different proteins to a complex array of sites. The manner in which these reactions are both stimulated and inhibited by co-operative binding of proteins to specific sites on the P arm of attP and AttR has been elucidated by correlation of nuclease protection with recombination studies of both wild-type and mutant DNAs. In addition to co-operative forces, there is a specific competitive interaction that allows the protein-DNA complex to serve as a "biological switch". This switch does not depend upon the simple occlusion of DNA binding sites by neighboring proteins; but, rather, the outcome of this competition is dependent on long-range interactions that vary between the higher-order structures of attP and attR. These higher-order structures are dependent on cooperative interactions involving three proteins binding to five or more sites. PMID:2958633
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.
Design and construction of higher-order structure and function in proteinosome-based protocells.
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. PMID:24905973
Lermyte, Frederik; Sobott, Frank
2015-08-01
Top-down sequencing approaches are becoming ever more popular for protein characterization, due to the ability to distinguish and characterize different protein isoforms. Under non-denaturing conditions, electron transfer dissociation (ETD) can furthermore provide important information on the exposed surface of proteins or complexes, thereby contributing to the characterization of their higher-order structure. Here, we investigate this approach using top-down ETD of tetrameric hemoglobin, concanavalin A, and alcohol dehydrogenase combined with ion mobility (IM) on a commercially available quadrupole/ion mobility/time-of-flight instrument (Waters Synapt G2). By applying supplemental activation in the transfer cell (post-IM), we release ETD fragments and attain good sequence coverage in the exposed terminal regions of the protein. We investigate the correlation between observed sites of fragmentation with regions of solvent accessibility, as derived from the crystal structure. Ion acceleration prior to ETD is also used to cause collision-induced unfolding (CIU) of the complexes without monomer ejection, as evidenced by the IM profiles. These partially unfolded tetramers show efficient fragmentation in some regions which are not sequenced under more gentle MS conditions. We show that by increasing CIU in small increments and monitoring the changes in the fragmentation pattern, it is possible to follow the initial steps of gas-phase protein unfolding. Fragments from partially unfolded protein complexes are released immediately after electron transfer, prior to IM (they do not share the drift time of their precursor), and observed without the need for supplemental activation. This is further evidence that the higher-order structure in these protein regions has been disrupted. PMID:26081219
Wang, L. F.; Lin, Y. Z.; Higo, T.
2002-04-01
In order to obtain high luminosity and energy efficiency in future linear colliders, most designs for e + and e - collisions in the TeV range will use multi-bunch operation. Therefore, the study of higher order modes excited by previous bunches in the train becomes very important for the optimal design of the accelerator components. Many designs have used tapered disk-loaded waveguides for acceleration. Various numerical methods have been used for the modal analysis of the structure. In this paper, a high-precision eigenmode-computation analysis based on a variational method will be discussed. It allows for rounding the edge of a disk hole without any approximation in shape treatment and calculates the exactly synchronous modes. It converges much faster than the mesh-based computer code SUPERFISH. Good agreement was observed between the results of the variational method and those of other methods.
Wang, L F; Higo, T
2002-01-01
In order to obtain high luminosity and energy efficiency in future linear colliders, most designs for e sup + and e sup - collisions in the TeV range will use multi-bunch operation. Therefore, the study of higher order modes excited by previous bunches in the train becomes very important for the optimal design of the accelerator components. Many designs have used tapered disk-loaded waveguides for acceleration. Various numerical methods have been used for the modal analysis of the structure. In this paper, a high-precision Eigenmode-computation analysis based on a variational method will be discussed. It allows for rounding the edge of a disk hole without any approximation in shape treatment and calculates the exactly synchronous modes. It converges much faster than the mesh-based computer code SUPERFISH. Good agreement was observed between the results of the variational method and those of other methods.
Structural damage detection using higher-order finite elements and a scanning laser vibrometer
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
Higher-order massive neutrino perturbations in large-scale structure
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...
Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew D.; Brodbelt, Jennifer S.
2009-01-01
Isoguanine (2-oxo-6-amino-guanine), a natural but non-standard base, exhibits unique self-association properties compared to its isomer, guanine, and results in formation of different higher order DNA structures. In this work, the higher order structures formed by oligonucleotides containing guanine repeats or isoguanine repeats after annealing in solutions containing various cations are evaluated by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy. ...
Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure
Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii; Fabris, Daniele
2014-07-01
Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.
Scholtes, Ingo; Wider, Nicolas; Garas, Antonios
2016-03-01
Despite recent advances in the study of temporal networks, the analysis of time-stamped network data is still a fundamental challenge. In particular, recent studies have shown that correlations in the ordering of links crucially alter causal topologies of temporal networks, thus invalidating analyses based on static, time-aggregated representations of time-stamped data. These findings not only highlight an important dimension of complexity in temporal networks, but also call for new network-analytic methods suitable to analyze complex systems with time-varying topologies. Addressing this open challenge, here we introduce a novel framework for the study of path-based centralities in temporal networks. Studying betweenness, closeness and reach centrality, we first show than an application of these measures to time-aggregated, static representations of temporal networks yields misleading results about the actual importance of nodes. To overcome this problem, we define path-based centralities in higher-order aggregate networks, a recently proposed generalization of the commonly used static representation of time-stamped data. Using data on six empirical temporal networks, we show that the resulting higher-order measures better capture the true, temporal centralities of nodes. Our results demonstrate that higher-order aggregate networks constitute a powerful abstraction, with broad perspectives for the design of new, computationally efficient data mining techniques for time-stamped relational data.
Coming to terms with chromatin structure.
Even-Faitelson, Liron; Hassan-Zadeh, Vahideh; Baghestani, Zahra; Bazett-Jones, David P
2016-03-01
Chromatin, once thought to serve only as a means to package DNA, is now recognized as a major regulator of gene activity. As a result of the wide range of methods used to describe the numerous levels of chromatin organization, the terminology that has emerged to describe these organizational states is often imprecise and sometimes misleading. In this review, we discuss our current understanding of chromatin architecture and propose terms to describe the various biochemical and structural states of chromatin. PMID:26223534
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.
International Nuclear Information System (INIS)
Radioadapted chicken embryo cells (X-irradiation in ovo with 10 cGy at the 14th day of development with priming periods of 24 h) were treated in vitro by challenge doses of 14 different DNA- and/or chromatin-interactive agents, including X-rays. A decrease in the cellular damage, as measured by scheduled DNA synthesis, was only observed with X-irradiation. Sedimentation of nucleoids as well as viscosity of alkaline lysates from ethidium bromide (0.35-400 μg/ml)-, vovobiocin (125-1800 μg/ml)-, and hyperthermia (30 min at 43 and 45 )-treated cells suggest a higher tendency of radioadapted cells to undergo positive DNA supercoiling. When DNA from adapted and non-adapted chicken embryo cells was used as substrate, neither its digestion by DNase I nor the inhibition of DNase I activity by various DNA-interactive agents was changed in primed cells. From the previous investigations as well as from the present results it is concluded that an increase of tightening of protein-DNA interactions within the nuclear matrix is a molecular determinant of the elevated radiation resistance in radioadapted chicken embryo cells. (orig.)
Flora, David B.; Finkel, Eli J.; Foshee, Vangie A.
2003-01-01
Studied the higher order factor structure of a self-control test developed by H. Grasmick and others (1993). Results for 1,966 eighth and ninth graders show that the self-control test may provide more valid measurement of the constructs it was designed to measure than previous research suggested. (SLD)
Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures.
Li, Rui; Zhu, Hongliang; Luo, Yunbo
2016-01-01
Although thousands of long non-coding RNAs (lncRNAs) have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure-function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq), selective 2'-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq), parallel analysis of RNA structure (PARS), and fragmentation sequencing (FragSeq). The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level. PMID:27196897
Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures
Directory of Open Access Journals (Sweden)
Rui Li
2016-05-01
Full Text Available Although thousands of long non-coding RNAs (lncRNAs have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure–function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq, selective 2′-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq, parallel analysis of RNA structure (PARS, and fragmentation sequencing (FragSeq. The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level.
Computational strategies to address chromatin structure problems.
Perišić, Ognjen; Schlick, Tamar
2016-01-01
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. PMID:27345617
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 the...... experimentally observed micro-structural behavior, within a framework based on continuous field quantities, poses obvious challenges, since the evolution of dislocation structures is inherently a discrete and discontinuous process. This challenge, in particular, motivates the present study, and the aim is to...
Mondal, Samiran; Begum, Nasim A; Hu, Wenjun; Honjo, Tasuku
2016-03-15
Activation-induced cytidine deaminase (AID) is essential for the somatic hypermutation (SHM) and class-switch recombination (CSR) of Ig genes. Although both the N and C termini of AID have unique functions in DNA cleavage and recombination, respectively, during SHM and CSR, their molecular mechanisms are poorly understood. Using a bimolecular fluorescence complementation (BiFC) assay combined with glycerol gradient fractionation, we revealed that the AID C terminus is required for a stable dimer formation. Furthermore, AID monomers and dimers form complexes with distinct heterogeneous nuclear ribonucleoproteins (hnRNPs). AID monomers associate with DNA cleavage cofactor hnRNP K whereas AID dimers associate with recombination cofactors hnRNP L, hnRNP U, and Serpine mRNA-binding protein 1. All of these AID/ribonucleoprotein associations are RNA-dependent. We propose that AID's structure-specific cofactor complex formations differentially contribute to its DNA-cleavage and recombination functions. PMID:26929374
Bulovyatov, Alexander
2010-01-01
The band structure computation turns into solving a family of Maxwell eigenvalue problems on the periodicity domain. The discretization is done by the finite element method with special higher order H(curl)- and H1-conforming modified elements. The eigenvalue problem is solved by a preconditioned iterative eigenvalue solver with a projection onto the divergence-free vector fields. As a preconditioner we use the parallel multigrid method with a special Hiptmair smoother.
Computational strategies to address chromatin structure problems
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.
Energy Technology Data Exchange (ETDEWEB)
Emamuddin, M. [National University, Gazipur (Bangladesh); Yasmin, S.; Mamun, A. A. [Jahangirnagar University, Savar, Dhaka (Bangladesh)
2014-06-15
The Gardner equation, showing the existence of compressive and rarefactive dust-acoustic (DA) solitons in a nonextensive dusty plasma (containing negatively charged dust, Maxwellian ions and two-temperature electrons following a q-nonextensive distribution) beyond the K-dV (Korteweg-de Vries) limit, is derived and numerically solved. The basic features of the DA Gardner solitons (GSs) associated with positive and negative potentials are found to exist beyond the K-dV limit, and the K-dV and modified K-dV (mK-dV) solitons have been compared with the DAGSs by considering the effects of two-temperature electron's nonextensivity. Depending on the nonextensive parameter q, the DAGSs have been found to exhibit negative (positive) potential solitons for q < q{sub c} (q > q{sub c}) (where q{sub c} is the critical value of q). The results obtained from this analysis can be utilized and should be very effective for understanding the localized nonlinear structures, the DAGSs, in different astrophysical and cosmological scenarios (viz. stellar polytropes, quark-gluon plasma, protoneutron stars, etc.).
Higher order structure analysis of nano-materials by spectral reflectance of laser-plasma soft x-ray
International Nuclear Information System (INIS)
We have proposed a new experimental arrangement to measure spectral reflectance of nano-materials for analyzing higher order structure with laser-plasma soft x-rays. Structure modification of annealed Mo/Si multilayers and a nylon-6/clay hybrid with poor periodicity was investigated. The measurement of the spectral reflectance of soft x-rays from laser-produced plasma was found to be a useful method for the structure analysis of nano-materials, especially those of rather poor periodicity
Dromion and Multi-soliton Structures of the (2+1)-Dimensional Higher-Order Broer-Kaup System
Institute of Scientific and Technical Information of China (English)
林机
2002-01-01
Using the standard truncated Painlevé analysis and the Backlund transformation, we can obtain many significant exact soliton solutions of the (2+1)-dimensional higher-order Broer-Kaup (HBK) system. A special type of soliton solution is described by the variable coefficient heat-conduction-like equation. The inclusion of three arbitrary functions in the general expressions of the solitons makes the solitons of the (2+1)-dimensional HBK system possess abundant structures such as solitofT solutions, multi-dromion solutions, ring solitons and so on.
Golay, Philippe; Lecerf, Thierry
2011-03-01
According to the most widely accepted Cattell-Horn-Carroll (CHC) model of intelligence measurement, each subtest score of the Wechsler Intelligence Scale for Adults (3rd ed.; WAIS-III) should reflect both 1st- and 2nd-order factors (i.e., 4 or 5 broad abilities and 1 general factor). To disentangle the contribution of each factor, we applied a Schmid-Leiman orthogonalization transformation (SLT) to the standardization data published in the French technical manual for the WAIS-III. Results showed that the general factor accounted for 63% of the common variance and that the specific contributions of the 1st-order factors were weak (4.7%-15.9%). We also addressed this issue by using confirmatory factor analysis. Results indicated that the bifactor model (with 1st-order group and general factors) better fit the data than did the traditional higher order structure. Models based on the CHC framework were also tested. Results indicated that a higher order CHC model showed a better fit than did the classical 4-factor model; however, the WAIS bifactor structure was the most adequate. We recommend that users do not discount the Full Scale IQ when interpreting the index scores of the WAIS-III because the general factor accounts for the bulk of the common variance in the French WAIS-III. The 4 index scores cannot be considered to reflect only broad ability because they include a strong contribution of the general factor. PMID:21171782
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
On higher order Fourier analysis
Szegedy, Balazs
2012-01-01
We develop a theory of higher order structures in compact abelian groups. In the frame of this theory we prove general inverse theorems and regularity lemmas for Gowers's uniformity norms. We put forward an algebraic interpretation of the notion "higher order Fourier analysis" in terms of continuous morphisms between structures called compact $k$-step nilspaces. As a byproduct of our results we obtain a new type of limit theory for functions on abelian groups in the spirit of the so-called graph limit theory. Our proofs are based on an exact (non-approximative) version of higher order Fourier analysis which appears on ultra product groups.
International Nuclear Information System (INIS)
Higher order modes (HOMs) are one of the reasons for beam current limitations and beam lifetime in synchrotron light sources such as INDUS-2. At higher beam current, the HOMs of the RF cavity may resonate with the beam frequencies (in the beam spectrum) leading to beam instability. Therefore, knowledge of the HOMs of an RF cavity is a necessary part of operations for any synchrotron source. INDUS-2 synchrotron source has 4 elliptically shaped RF cavities, which are operated at a fundamental frequency of 505.812 MHz. The RF cavity HOM spectrum is very sensitive to its conducting surface, which is affected mainly by the thermal loading and tuner movement. An accurate estimation of the cavity frequency spectrum with realistic boundary conditions is possible by a combined (coupled) electromagnetic-thermal-structural analysis. The methodology adopted for this coupled simulation is explained in this paper. The HOM spectrum and electromagnetic parameters of INDUS-2 cavity are simulated using 3D electromagnetic high frequency finite element method in ANSYS. The simulated data sets are compared with the cold model test data of the RF cavities for validation of the numerical simulations. Further, the observed spectra of the INDUS-2 electron beam at various stored beam currents and energies are also studied to find parasitic HOMs. Indicative HOM observations and the simulation data results can be used for shifting the harmful modes.
DEFF Research Database (Denmark)
Ernst, Erik
2003-01-01
This paper introduces the notion of higher-order inheritance hierarchies. They are useful because they provide well-known benefits of object-orientation at the level of entire hierarchies-benefits which are not available with current approaches. Three facets must be adressed: First, it must...... 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....... 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...
International Nuclear Information System (INIS)
According to their physical characteristics, protons and ion beams promise a revolution in cancer radiotherapy. Curing protocols however reflect rather the empirical knowledge than experimental data on DNA repair. This especially holds for the spatio-temporal organization of repair processes in the context of higher-order chromatin structure—the problematics addressed in this work. The consequences for the mechanism of chromosomal translocations are compared for gamma rays and proton beams. - Highlights: ► The majority of DSBs are repaired individually close to the sites of their origin. ► Decondensation of damaged chromatin domains can potentiate clustering of lesions. ► DSB clustering might increase the risk of chromatin translocation. ► Distances of lesions and higher-order chromatin structure influence DSB clustering. ► The conclusions seem to hold both for DSB damage caused by γ-radiation and protons
Wang, Guanbo; Kaltashov, Igor A.
2014-01-01
Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting fact...
Role of histone modifications in defining chromatin structure and function.
Gelato, Kathy A; Fischle, Wolfgang
2008-04-01
Chromosomes in eukaryotic cell nuclei are not uniformly organized, but rather contain distinct chromatin elements, with each state having a defined biochemical structure and biological function. These are recognizable by their distinct architectures and molecular components, which can change in response to cellular stimuli or metabolic requirements. Chromatin elements are characterized by the fundamental histone and DNA components, as well as other associated non-histone proteins and factors. Post-translational modifications of histone proteins in particular often correlate with a specific chromatin structure and function. Patterns of histone modifications are implicated as having a role in directing the level of chromatin compaction, as well as playing roles in multiple functional pathways directing the readout of distinct regions of the genome. We review the properties of various chromatin elements and the apparent links of histone modifications with chromatin organization and functional output. PMID:18225984
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).
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.
Nuclear visions enhanced: chromatin structure, organization and dynamics
Meshorer, Eran; Herrmann, Harald; Raška, Ivan
2011-01-01
The EMBO Workshop on ‘Chromatin Structure, Organization and Dynamics' took place in April 2011 in Prague, Czech Republic. Participants presented data on the generation of models of the genome, working to correlate changes in the organization of chromatin with the functional state of the genome.
International Nuclear Information System (INIS)
Seeds and seedlings of pea have been irradiated between zero to 300 Gy doses of 60Co gamma-irradiation and examinations were carried out on the chromatin of shoots of 1-week-old etiolated seedlings. There was only a slight change in the gross composition of chromatin after irradiation (in the mass ratios of DNA:RNA:histone:non-histone proteins). Separation of histones, however, showed that after 300 Gy irradiation the quantity of H1 histones decreased by 33% after seed irradiation and 43% after seedling irradiation. The ratio of H1 subfractions also changed. Enzymes DNAase II and micrococcal nuclease digested the chromatin of the irradiated sample 30% faster than the unirradiated one. Transcription kinetics of chromatin showed a gradual decrease of Ksub(m) value on increasing doses of irradiation. There was, however, no difference in the rate of transcription of DNAs, isolated from the chromatin of the control and irradiated samples. Protease and RNAase activity of whole shoots showed enhancement after irradiation. These data suggest that irradiation of either seeds or seedlings results in loosening of the seedling chromatin structure, while there is no change in basic nucleosomal structure. The specific degradation or dissociation of histone H1, localized in the internucleosomal region may be responsible for these changes in the higher order structure of chromatin. This may explain the easier accessibility of chromatin to DNAase II after irradiation and the more tightly bound RNA polymerase, exhibited in decreasing Ksub(m) values. (Auth.)
Saintomé, Carole; Amrane, Samir; Mergny, Jean-Louis; Alberti, Patrizia
2016-04-01
DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and protein-binding assays), we show that the (GGGTTA)7GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45°C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higher-order structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium. PMID:26762980
International Nuclear Information System (INIS)
Ionizing radiations are known to challenge the integrity of the genome by inducing several lesions like double strand breaks, single strand breaks and oxidative base damage in the DNA. Human cells have evolved efficient DNA repair processes in response to DNA damage by which the integrity of genome is maintained. Emerging evidence indicates that various modulations to chromatin structure are centrally important to many aspects of the DNA damage response (DDR). DNA is compacted and packed in the form of chromatin in eukaryotic cells, the basic unit of chromatin is the nucleosome core particle, which consists of ∼ 146 base pairs of DNA wrapped in two left-handed superhelical turns around an octamer of histone proteins. Higher order chromatin packaging acts as a barrier to the detection and repair of DNA damage. Hence, chromatin reorganization is thought to play a crucial role in cellular responses to DNA damage by making damaged sites more accessible to repair as well as transcriptional machinery of the cell. Dynamic light scattering (DLS) is a sensitive and non invasive tool to study the dynamics of biomolecules in solution. Changes in the conformation of chromatin on exposure to gamma radiation were measured in the form of average hydrodynamic diameter of chromatin fragments in irradiated and control cells. In the present study we have used Dynamic Light Scattering (PLS) as a tool to analyze radiation induced conformational changes in the structure of native chromatin in peripheral blood mononuclear cells (PBMCs) at resting stage (G0). Dose response experiments carried out on 10 individuals have shown a significant difference in the average hydrodynamic diameter of chromatin fibers in different dose groups. Our results have also shown significant changes in the chromatin size at low dose groups (25 cGy and 50 cGy) as compared to higher doses. Inter-individual variations in the chromatin dynamics were clearly demonstrated
Higher-order organization of complex networks.
Benson, Austin R; Gleich, David F; Leskovec, Jure
2016-07-01
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. PMID:27387949
Impact of chromatin structure on PR signaling
DEFF Research Database (Denmark)
Grøntved, Lars; Hager, Gordon L
2012-01-01
but also to the glucocorticoid receptor (GR), as these receptors share many similarities regarding interaction with, and remodeling of, chromatin. Both receptors can bind nucleosomal DNA and have accordingly been described as pioneering factors. However recent genomic approaches (ChIP-seq and DHS...
DEFF Research Database (Denmark)
Garrett, R A; Christensen, A; Douthwaite, S
1984-01-01
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 that......An experimental approach was used to determine, and compare, the higher-order structure within domain VI of the 23 S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus. This domain, which encompasses approximately 300 nucleotides at the 3' end of the RNAs, consists of two large...... ribosomes of flowering plants. The structure of domain VI within the eubacterial RNAs was probed with chemical reagents in order to establish the degree of stacking and/or accessibility of each adenosine, cytidine and guanosine residue; the double-helical segments were localized with the cobra venom...
Pan, Jingxi; Zhang, Suping; Parker, Carol E; Borchers, Christoph H
2014-09-17
Characterization of the higher-order structure and structural dynamics of proteins is crucial for in-depth understanding of their functions. Amide hydrogen/deuterium exchange (HDX), monitored by mass spectrometry (MS), is now a popular technique for measuring protein higher-order structural changes. Although the proteolysis-based HDX-MS approach is most commonly used, the "top-down" approach, which fragments intact proteins directly using electron-based dissociation, is becoming an important alternative and has several advantages. However, the commonly used top-down strategies are direct-infusion based and thus can only be used with volatile buffers. This has meant that the "top-down" approach could not be used for studying proteins under physiological conditions-the very conditions which are often very important for preserving a protein's native structure and function. More complex proteins such as those with disulfide bonds present another challenge. Therefore, there is significant interest in developing novel top-down HDX methods that are applicable to all types of protein samples. In this paper, we show how top-down electron capture dissociation and subzero temperature HPLC can be combined and used for this purpose. This method keeps the back-exchange level as low as 2% and has no limitations in terms of protein type and sample solution conditions. Close to single-residue level protein structural information can be generated. The new method is validated through comparison with NMR data using calmodulin as a model protein. Its capability of determining structural changes in therapeutic antibodies (Herceptin) is also demonstrated. PMID:25152011
Higher-Order Program Generation
DEFF Research Database (Denmark)
Rhiger, Morten
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...... infrastructure of higher-order functions, types, and modules. Furthermore, it has been observed that embedded programs can be restricted to those having simple types using a technique called ``phantom types''. We prove, using an idealized higher-order language, that such an embedding is sound (i.e., when all...... completeness proof is shown by induction over object-language terms. Furthermore, we address the use of Haskell and Standard ML as meta-languages. Normalization functions, as embodied in type-directed partial evaluation, map a simply-typed higher-order value into a representation of its long beta-eta normal...
Wang, Lei; Zhu, Yu-Jie; Qi, Feng-Hua; Li, Min; Guo, Rui
2015-06-01
In this paper, the nonautonomous Lenells-Fokas (LF) model is investigated. The modulational instability analysis of the solutions with variable coefficients in the presence of a small perturbation is studied. Higher-order soliton, breather, earthwormon, and rogue wave solutions of the nonautonomous LF model are derived via the n-fold variable-coefficient Darboux transformation. The solitons and earthwormons display the elastic collisions. It is found that the nonautonomous LF model admits the higher-order periodic rogue waves, composite rogue waves (rogue wave pair), and oscillating rogue waves, whose dynamics can be controlled by the inhomogeneous nonlinear parameters. Based on the second-order rogue wave, a diamond structure consisting of four first-order rogue waves is observed. In addition, the semirational solutions (the mixed rational-exponential solutions) of the nonautonomous LF model are obtained, which can be used to describe the interactions between the rogue waves and breathers. Our results could be helpful for the design of experiments in the optical fiber communications. PMID:26117105
Higher Order Theories and Noncommutativity
International Nuclear Information System (INIS)
In this work we show a relationship between noncommutativity and higher order theories. Starting from an extension of the Chern-Simons model with higher order time derivatives and using perturbation theory, we found that this model contains intrinsically noncommutativity in the velocities and coordinates. We solve the model both at the classical and quantum level and we show the implications of the noncommutativity in the theory.
Chromatin structure modulates DNA repair by photolyase in vivo.
Suter, B.; Livingstone-Zatchej, M; Thoma, F
1997-01-01
Yeast and many other organisms use nucleotide excision repair (NER) and photolyase in the presence of light (photoreactivation) to repair cyclobutane pyrimidine dimers (CPDs), a major class of DNA lesions generated by UV light. To study the role of photoreactivation at the chromatin level in vivo, we used yeast strains which contained minichromosomes (YRpTRURAP, YRpCS1) with well-characterized chromatin structures. The strains were either proficient (RAD1) or deficient (rad1 delta) in NER. In...
Matthaeus, W. H.; Wan, M.; Osman, K.; Servidio, S.; Oughton, S.; Dmitruk, P.; Greco, A.
2010-12-01
“Universality” in hydrodynamic turbulence usually refers to the existence of unique statistical distributions that are obtained as the Reynolds number tends to infinity. In such cases the hierarchy of structure functions would approach particular functional forms, implying for example a standard form of the energy spectrum. Magnetohydrodynamics (MHD) is more complex for several reasons. First, there are several spectral fluxes and several types of cascades, including inverse and direct cascades. Second, there are several additional dimensionless parameters, including the ratio of magnetic Reynolds number to Reynolds number, the ratio of kinetic to magnetic energy, and when cross helicity is nonzero, the ratio of two fundamental lengths scales - one for each Elsasser field. For these reasons it is doubtful that there are universal MHD turbulence statistics, in the usual sense. Recent simulation work supports this conclusion, as very similar initial energy spectra can lead to very different time evolution depending on details of initial conditions. We suggest here another approach to finding unifying principles for MHD turbulence. We begin with discussion of spontaneous generation of distinctive local correlations, including those corresponding to Beltrami, Alfvenic and force-free states. An argument is outlined as to how these correlations require certain higher order correlations to be generated. In real space these correspond to generation of region of reduced nonlinearity. Spatial patches of correlation may be separated by quasi-discontinuous jumps in the local parameters. This gives rise, e.g., to frequent appearance of “tangential discontinuities” due to formation of current sheets (and the possibility of reconnection) between adjacent quasi-relaxed flux tubes. Recent evidence supports the view that (1) the generation of high wavenumber nonGaussian statistics is a signature of these local rapid relaxation processes, (2) distinctive correlations form in
International Nuclear Information System (INIS)
The higher twist contributions to the deeply inelastic structure functions Fp2(x,Q2) and Fd2(x,Q2) for larger values of the Bjorken variable x are extracted extrapolating the twist-2 contributions measured in the large W2 region to the region 4 GeV2≤W2 ≤12.5 GeV2 applying target mass corrections. We compare the results for the NLO, NNLO and N3LO analyzes and include also the large x at N4LO to the Wilson coefficients. A gradual lowering of the higher twist contributions going from NLO to N4LO is observed, which stresses the importance of higher order corrections. (orig.)
Higher order differential-integral microphone arrays.
Abhayapala, Thushara D; Gupta, Aastha
2010-05-01
This paper develops theory to design higher order directional microphone arrays. The proposed higher order designs have similar inter sensor spacings as traditional first and second order differential arrays. The Jacobi-Anger expansion is used to exploit the underlying structure of microphone signals from pairs of closely spaced sensors. Specifically, the difference and sum of these microphone signals are processed to design the novel directional array. PMID:21117719
Higher order anisotropies in hydrodynamics
Csanad, M; Lokos, S; Bagoly, A
2015-01-01
In the last years it has been revealed that if measuring relative to higher order event planes $\\Psi_n$, higher order flow coefficients $v_n$ for $n>2$ can be measured. It also turned out that Bose-Einstein (HBT) correlation radii also show 3rd order oscillations if measured versus the third order event plane $\\Psi_3$. In this paper we investigate how these observables can be described via analytic hydro solutions and hydro parameterizations. We also investigate the time evolution of asymmetry coefficients and the mixing of velocity field asymmetries and density asymmetries.
Chromatin structure near transcriptionally active genes
International Nuclear Information System (INIS)
Hypersensitive domains are the most prominent features of transcriptionally active chromatin. In the case of the β/sup A/-globin gene, it seems likely that two or more protein factors are capable of binding to the DNA so tightly that the nucleosome is prevented from binding. We have shown that nucleosomes, once bound in the assembly process in vitro, cannot be displaced. The interaction of the 5S gene transcription factor TFIIIA with its target DNA also is blocked by histones, and it has been suggested that the activation of the gene must occur during replication, before histones are reassembled on the DNA. We suppose that a similar mechanism may govern the binding of the hypersensitivity factors. It should be noted that nucleosomes are excluded not only from the sites to which the factors bind, but also from the regions between the two domains and at either side. 12 refs., 6 figs
Sheval, E V; Prusov, A N; Kireev, I I; Fais, D; Polyakov, V Yu
2002-01-01
The method of chromatin photo-stabilization by the action of visible light in the presence of ethidium bromide was used for investigation of higher-level chromatin structures in isolated nuclei. As a model we used rat hepatocyte nuclei isolated in buffers which stabilized or destabilized nuclear matrix. Several higher-level chromatin structures were visualized: 100nm globules-chromomeres, chains of chromomeres-chromonemata, aggregates of chromomeres-blocks of condensed chromatin. All these structures were completely destroyed by 2M NaCl extraction independent of the matrix state, and DNA was extruded from the residual nuclei (nuclear matrices) into a halo. These results show that nuclear matrix proteins do not play the main role in the maintenance of higher-level chromatin structures. Preliminary irradiation led to the reduction of the halo width in the dose-dependent manner. In regions of condensed chromatin of irradiated nucleoids there were discrete complexes consisting of DNA fibers radiating from an electron-dense core and resembling the decondensed chromomeres or the rosette-like structures. As shown by the analysis of proteins bound to irradiated nuclei upon high-salt extraction, irradiation presumably stabilized the non-histone proteins. These results suggest that in interphase nuclei loop domains are folded into discrete higher-level chromatin complexes (chromomeres). These complexes are possibly maintained by putative non-histone proteins, which are extracted with high-salt buffers from non-irradiated nuclei. PMID:12127937
Nonlocal higher order evolution equations
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.
International Nuclear Information System (INIS)
To assess the influence of chromatin structure on the frequency of radiation-induced DNA strand breaks, the alkaline unwinding technique was applied to nuclear and nucleoid monolayers. These chromatin substrates were prepared by treating human fibroblasts grown as monolayers with the nonionic detergent Triton X-100 and varying concentrations of cations. The chromatin structure was modified either by a stepwise removal of DNA-bound proteins by extraction in increasing concentrations of monovalent salt, or by the addition or deletion of mono- and divalent cations to condense or decondense the chromatin, respectively. It was found that the stepwise removal of DNA-bound proteins from the chromatin dramatically increased the frequency of radiation-induced DNA strand breaks. The DNA-bound proteins showed a qualitative difference in their ability to protect the DNA where proteins removed by salt concentrations above 1.0 M exerted the greatest protection. Furthermore, the frequency of radiation-induced DNA strand breaks was found to be 6 times lower in condensed chromatin than in decondensed chromatin and about 80 times lower than in protein-depleted chromatin. It is concluded that the presence of DNA-bound proteins and the folding of the chromatin into higher-order structures protect the DNA against radiation-induced strand breaks
Resilience and higher order thinking
Ioan Fazey
2010-01-01
To appreciate, understand, and tackle chronic global social and environmental problems, greater appreciation of the importance of higher order thinking is required. Such thinking includes personal epistemological beliefs (PEBs), i.e., the beliefs people hold about the nature of knowledge and how something is known. These beliefs have profound implications for the way individuals relate to each other and the world, such as how people understand complex social-ecological systems. Resilience thi...
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. PMID:27226585
Complex higher order derivative theories
International Nuclear Information System (INIS)
In this work is considered a complex scalar field theory with higher order derivative terms and interactions. A procedure is developed to quantize consistently this system avoiding the presence of negative norm states. In order to achieve this goal the original real scalar high order field theory is extended to a complex space attaching a complex total derivative to the theory. Next, by imposing reality conditions the complex theory is mapped to a pair of interacting real scalar field theories without the presence of higher derivative terms.
Carlet, Claude; Freibert, Finley; Guilley, Sylvain; Kiermaier, Michael; Kim, Jon-Lark; Solé, Patrick
2014-01-01
We introduce {\\bf complementary information set codes} of higher-order. A binary linear code of length $tk$ and dimension $k$ is called a complementary information set code of order $t$ ($t$-CIS code for short) if it has $t$ pairwise disjoint information sets. The duals of such codes permit to reduce the cost of masking cryptographic algorithms against side-channel attacks. As in the case of codes for error correction, given the length and the dimension of a $t$-CIS code, we look for the high...
Resilience and Higher Order Thinking
Directory of Open Access Journals (Sweden)
Ioan Fazey
2010-09-01
Full Text Available To appreciate, understand, and tackle chronic global social and environmental problems, greater appreciation of the importance of higher order thinking is required. Such thinking includes personal epistemological beliefs (PEBs, i.e., the beliefs people hold about the nature of knowledge and how something is known. These beliefs have profound implications for the way individuals relate to each other and the world, such as how people understand complex social-ecological systems. Resilience thinking is an approach to environmental stewardship that includes a number of interrelated concepts and has strong foundations in systemic ways of thinking. This paper (1 summarizes a review of educational psychology literature on PEBs, (2 explains why resilience thinking has potential to facilitate development of more sophisticated PEBs, (3 describes an example of a module designed to teach resilience thinking to undergraduate students in ways conducive to influencing PEBs, and (4 discusses a pilot study that evaluates the module's impact. Theoretical and preliminary evidence from the pilot evaluation suggests that resilience thinking which is underpinned by systems thinking has considerable potential to influence the development of more sophisticated PEBs. To be effective, however, careful consideration of how resilience thinking is taught is required. Finding ways to encourage students to take greater responsibility for their own learning and ensuring close alignment between assessment and desired learning outcomes are particularly important.
Light scattering measurements supporting helical structures for chromatin in solution.
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. PMID:662693
Higher-order dielectrophoresis of nonspherical particles
Nili, Hossein; Green, Nicolas G.
2014-06-01
Higher-order terms of dielectrophoretic (DEP) force are commonly ignored by invoking the simplifying dipole approximation. Concurrently, the trend towards micro- and nano-electrode structures in DEP design is bringing about an increasing number of instances where the approximation is expected to lose reliability. The case is severe for nonspherical particles (the shape of many biological particles) due to the shape-dependent nature of dielectric polarization. However, there is a lack of analytical means to determine multipole moments of nonspherical particles, numerical calculations of the same are regarded as unreliable, and there is a prevalence for higher-order force considerations to be ignored. As a result, the dipole approximation is used and/or nonspherical particles are approximated as spheres. This work proves the inefficacy of current qualitative criteria for the reliability of the dipole approximation and presents a quantitative substitute, with verified accuracy, that enables precise determination of the extent to which the dipole approximation would be reliable, and if found unreliable, corrects the approximation by adding second- and third-order terms of the DEP force. The effects of field nonuniformity, electrode design, and particle shape and aspect ratio on the significance of higher-order DEP forces is quantitatively analyzed. The results show that higher-order DEP forces are indeed of substantially increased significance for nonspherical particles; in the cases examined in this work, multipolar terms are seen to constitute more than 40% of the total force on ellipsoidal and cylindrical particles. It is further shown that approximating nonspherical particles as spheres of similar dimensions is subject to substantial error. Last, the substantial importance of the electrode design in influencing higher-order forces is shown.
Chromatin structure analysis based on a hierarchic texture model.
Wolf, G; Beil, M; Guski, H
1995-02-01
The quantification of chromatin structures is an important part of nuclear grading of malignant and premalignant lesions. In order to achieve high accuracy, computerized image analysis systems have been applied in this process. Chromatin texture analysis of cell nuclei requires a suitable texture model. A hierarchic model seemed to be most compatible for this purpose. It assumes that texture consists of homogeneous regions (textons). Based on this model, two approaches to texture segmentation and feature extraction were investigated using sections of cervical tissue. We examined the reproducibility of the measurement under changing optical conditions. The coefficients of variations of the texture features ranged from 2.1% to 16.9%. The features were tested for their discriminating capability in a pilot study including 30 cases of cervical dysplasia and carcinoma. The overall classification accuracy reached 65%. This study presents an automated technique for texture analysis that is similar to human perception. PMID:7766266
Higher-Order and Symbolic Computation
DEFF Research Database (Denmark)
Danvy, Olivier; Mason, Ian
2008-01-01
series of implementaions that properly account for multiple invocations of the derivative-taking opeatro. In "Adapting Functional Programs to Higher-Order Logic," Scott Owens and Konrad Slind present a variety of examples of terminiation proofs of functional programs written in HOL proof systems. Since......-calculus programs, historically. The anaylsis determines the possible locations of ambients and mirrors the temporla sequencing of actions in the structure of types....
Li, Cynthia H; Nguyen, Xichdao; Narhi, Linda; Chemmalil, Letha; Towers, Edward; Muzammil, Salman; Gabrielson, John; Jiang, Yijia
2011-11-01
Circular dichroism (CD) spectroscopy is routinely used in the biopharmaceutical industry to study the effects of manufacturing, formulation, and storage conditions on protein conformation and stability, and these results are often included in regulatory filings. In this context, the purpose of CD spectroscopy is often to verify that a change in the formulation or manufacturing process of a product has not produced a change in the conformation of a protein. A comparison of two or more spectra is often required to confirm that the protein's structure has been maintained. Traditionally, such comparisons have been qualitative in nature, based on visually inspecting the overlaid spectra. However, visual assessment is inherently subjective and therefore prone to error. Furthermore, recent requests from regulatory agencies to demonstrate the suitability of the CD spectroscopic method for the purpose of comparing spectra have highlighted the need to appropriately qualify CD spectroscopy for characterization of biopharmaceutical protein products. In this study, we use a numerical spectral comparison approach to establish the precision of the CD spectroscopic method and to demonstrate that it is suitable for protein structural characterization in numerous biopharmaceutical applications. PMID:21732370
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.
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...
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...... 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....
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.
Higher Order Architecture of Collections of Objects
NILS A. BAAS
2014-01-01
We show that on an arbitrary collection of objects there is a wide variety of higher order architectures governed by hyperstructures. Higher order gluing, local to global processes, fusion of collections, bridges and higher order types are discussed. We think that these types of architectures may have interesting applications in many areas of science.
Tran, Ulrich S.; Cebolla i Martí, Ausiàs Josep; Gluck, Tobias M.; Soler, Joaquim; Javier Garcia-Campayo; Theresa von Moy
2014-01-01
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 confirma...
Logical Reasoning for Higher-Order Functions with Local State
Yoshida, Nobuko; Honda, Kohei; Berger, Martin
2008-01-01
We introduce an extension of Hoare logic for call-by-value higher-order functions with ML-like local reference generation. Local references may be generated dynamically and exported outside their scope, may store higher-order functions and may be used to construct complex mutable data structures. This primitive is captured logically using a predicate asserting reachability of a reference name from a possibly higher-order datum and quantifiers over hidden references. We explore the logic's des...
DEFF Research Database (Denmark)
Douthwaite, S; Christensen, A; Garrett, R A
1983-01-01
, T2 and S1. The data enabled the various minimal secondary structural models, proposed for the 3'-regions of the E. coli and S. cerevisiae RNAs, to be critically examined, and to demonstrate that the main common features of these models are correct. The results also reveal the presence and position...... "unstructured" regions. 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......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 to...
Higher order Fourier analysis as an algebraic theory II
Szegedy, Balazs
2009-01-01
Our approach to higher order Fourier analysis is to study the ultra product of finite (or compact) Abelian groups on which a new algebraic theory appears. This theory has consequences on finite (or compact) groups usually in the form of approximative statements. The present paper is the second part of a paper in which higher order characters and decompositions were introduced. We generalize the concept of the Pontrjagin dual group and introduce higher order versions of it. We study the algebraic structure of the higher order dual groups. We prove a simple formula for the Gowers uniformity norms in terms of higher order decompositions. We present a simple spectral algorithm to produce higher order decompositions. We briefly study a multi linear version of Fourier analysis. Along these lines we obtain new inverse theorems for Gowers's norms.
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.
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. PMID:27287487
Higher order mechanics on graded bundles
International Nuclear Information System (INIS)
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. (paper)
Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics
Monica Soldi; Alessandro Cuomo; Michael Bremang; Tiziana Bonaldi
2013-01-01
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, re...
Static Complexity Analysis of Higher Order Programs
DEFF Research Database (Denmark)
Avery, James Emil; Kristiansen, Lars; Moyen, Jean-Yves
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....
DEFF Research Database (Denmark)
Appel, Claus; van Oostrom, Vincent; Simonsen, Jakob Grue
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...... systems modularity of confluence, normalization, and termination can be recovered by imposing suitable linearity constraints....
Difference equations in massive higher order calculations
International Nuclear Information System (INIS)
The calculation of massive 2-loop operator matrix elements, required for the higher order Wilson coefficients for heavy flavor production in deeply inelastic scattering, leads to new types of multiple infinite sums over harmonic sums and related functions, which depend on the Mellin parameter N. We report on the solution of these sums through higher order difference equations using the summation package Sigma. (orig.)
Higher-order optical-polarization
Singh, Ravi S.; Prakash, Hari
2011-01-01
Polarization properties of optical field in Schr\\"odinger Cat states or Even- or Odd-Coherent states are investigated by generalizing usual concept of optical-polarization to render the concept of Higher-order optical-polarization. It is observed that Higher-order optical-polarization is a basis-dependent property of optical field.
Exploring Higher-Order Gravitational Waves
Arcos, H; Pereira, J G
2015-01-01
In addition to the usual linear gravitational waves in transverse-traceless coordinates, higher-order gravitational field equations, as well as their corresponding solutions, are explicitly obtained. It is found that higher-order waves do not represent corrections to the first-order wave. In contrast, all higher than second-order solutions do represent corrections to the second-order wave, a property that makes the first-order gravitational wave to stand apart from higher-order waves. Furthermore, although the first-order solution is transverse and traceless, all higher-order solutions are not. As a consequence, the whole solution is neither transverse nor traceless, a result that could eventually have important consequences for quantum gravity, and in particular for the definition of graviton itself. Some additional properties and features of these higher-order gravitational waves are explored and discussed.
Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins
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.
Synchrotron radiation of higher order soliton
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.
Resonant radiation from oscillating higher order solitons.
Driben, R; Yulin, A V; Efimov, A
2015-07-27
We present radiation mechanism exhibited by a higher order soliton. In a course of its evolution the higher-order soliton emits polychromatic radiation resulting in formation 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 corroborated by numerical simulations. It is shown that for longer pulses the described effect persists also under the action of higher order perturbations such as Raman and self-steepening. PMID:26367574
Insights into Chromatin Structure and Dynamics in Plants
Directory of Open Access Journals (Sweden)
Stefanie Rosa
2013-11-01
Full Text Available The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.
Unsupervised pattern discovery in human chromatin structure through genomic segmentation.
Hoffman, Michael M; Buske, Orion J; Wang, Jie; Weng, Zhiping; Bilmes, Jeff A; Noble, William Stafford
2012-05-01
We trained Segway, a dynamic Bayesian network method, simultaneously on chromatin data from multiple experiments, including positions of histone modifications, transcription-factor binding and open chromatin, all derived from a human chronic myeloid leukemia cell line. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, transcriptional regulator CTCF-binding regions and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/proj/segway/. PMID:22426492
Higher-order techniques in computational electromagnetics
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.
Synchrotron radiation of higher order soliton
Driben, Rodislav; Yulin, Alexey; 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 cha...
Higher-Order Tensors in Diffusion Imaging
Schultz, Thomas; Fuster, Andrea; Ghosh, Aurobrata; Deriche, Rachid; Florack, Luc; Lek-Heng, Lim
2013-01-01
International audience Diffusion imaging is a noninvasive tool for probing the microstructure of fibrous nerve and muscle tissue. Higher-order tensors provide a powerful mathematical language to model and analyze the large and complex data that is generated by its modern variants such as High Angular Resolution Diffusion Imaging (HARDI) or Diffusional Kurtosis Imaging. This survey gives a careful introduction to the foundations of higher-order tensor algebra, and explains how some concepts...
On higher order estimates in quantum electrodynamics
Matte, Oliver
2009-01-01
We propose a new method to derive certain higher order estimates in quantum electrodynamics. Our method is particularly convenient in the application to the non-local semi-relativistic models of quantum electrodynamics as it avoids the use of iterated commutator expansions. We re-derive higher order estimates obtained earlier by Fr\\"ohlich, Griesemer, and Schlein and prove new estimates for a non-local molecular no-pair operator.
Higher Order Cumulants in Colorless Partonic Plasma
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...
Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains.
Tiana, Guido; Amitai, Assaf; Pollex, Tim; Piolot, Tristan; Holcman, David; Heard, Edith; Giorgetti, Luca
2016-03-29
Experiments based on chromosome conformation capture have shown that mammalian genomes are partitioned into topologically associating domains (TADs), within which the chromatin fiber preferentially interacts. TADs may provide three-dimensional scaffolds allowing genes to contact their appropriate distal regulatory DNA sequences (e.g., enhancers) and thus to be properly regulated. Understanding the cell-to-cell and temporal variability of the chromatin fiber within TADs, and what determines them, is thus of great importance to better understand transcriptional regulation. We recently described an equilibrium polymer model that can accurately predict cell-to-cell variation of chromosome conformation within single TADs, from chromosome conformation capture-based data. Here we further analyze the conformational and energetic properties of our model. We show that the chromatin fiber within TADs can easily fluctuate between several conformational states, which are hierarchically organized and are not separated by important free energy barriers, and that this is facilitated by the fact that the chromatin fiber within TADs is close to the onset of the coil-globule transition. We further show that in this dynamic state the properties of the chromatin fiber, and its contact probabilities in particular, are determined in a nontrivial manner not only by site-specific interactions between strongly interacting loci along the fiber, but also by nonlocal correlations between pairs of contacts. Finally, we use live-cell experiments to measure the dynamics of the chromatin fiber in mouse embryonic stem cells, in combination with dynamical simulations, and predict that conformational changes within one TAD are likely to occur on timescales that are much shorter than the duration of one cell cycle. This suggests that genes and their regulatory elements may come together and disassociate several times during a cell cycle. These results have important implications for transcriptional
Chromatin remodeling, development and disease
International Nuclear Information System (INIS)
Development is a stepwise process in which multi-potent progenitor cells undergo lineage commitment, differentiation, proliferation and maturation to produce mature cells with restricted developmental potentials. This process is directed by spatiotemporally distinct gene expression programs that allow cells to stringently orchestrate intricate transcriptional activation or silencing events. In eukaryotes, chromatin structure contributes to developmental progression as a blueprint for coordinated gene expression by actively participating in the regulation of gene expression. Changes in higher order chromatin structure or covalent modification of its components are considered to be critical events in dictating lineage-specific gene expression during development. Mammalian cells utilize multi-subunit nuclear complexes to alter chromatin structure. Histone-modifying complex catalyzes covalent modifications of histone tails including acetylation, methylation, phosphorylation and ubiquitination. ATP-dependent chromatin remodeling complex, which disrupts histone-DNA contacts and induces nucleosome mobilization, requires energy from ATP hydrolysis for its catalytic activity. Here, we discuss the diverse functions of ATP-dependent chromatin remodeling complexes during mammalian development. In particular, the roles of these complexes during embryonic and hematopoietic development are reviewed in depth. In addition, pathological conditions such as tumor development that are induced by mutation of several key subunits of the chromatin remodeling complex are discussed, together with possible mechanisms that underlie tumor suppression by the complex
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.
Vilenchik, M; Benimetsky, L; Kolbanovsky, A; Miller, P; Stein, C A
2001-04-01
We have demonstrated the formation of higher-order structures (presumably tetraplexes) by an 18-mer phosphorothioate antisense c-myb oligodeoxyribonucleotide that has been shown to have activity in the treatment of leukemia xenograft models. Although not observable by conventionally employed techniques, such as PAGE and dimethyl sulfate (DMS) protection, the formation of such higher-order structures by this oligonucleotide was revealed by several techniques. These included capillary gel electrophoresis (CGE), which demonstrated the presence of molecules with greatly increased retention time compared with the monomer; magnetic circular dichroism spectroscopy, which demonstrated a band at 290 nm, a characteristic of antiparallel tetraplexes; and fluorescence energy transfer measurements. For the last, the 18-mer phosphorothioate oligonucleotide was synthesized with a 5'-fluorescein group. Similar to the molecular beacon model, its fluorescence was quenched when combined in solution with tetraplex-forming oligomers that contained a 3'-Dabcyl moiety. 7-Deazaguanosine inhibits the formation of tetraplexes by eliminated Hoogsteen base pair interactions. The wild-type and 7-deazaguanosine-substituted antisense c-myb oligomers differentially downregulated the expression of the c-myb proto-oncogene in K562 and HL60 cells, with the wild-type oligomer being the least active. The 18-mer c-myb molecule can, therefore, form highly complex structures, whose analysis in solution cannot be limited to examination of slab gel electrophoresis results alone. PMID:11334144
International Nuclear Information System (INIS)
Our objective was to evaluate alterations in sperm chromatin structure in men occupationally exposed to a mixture of organophosphorus pesticides (OP) because these alterations have been proposed to compromise male fertility and offspring development. Chromatin susceptibility to in situ acid-induced denaturation structure was assessed by the sperm chromatin structure assay (SCSA). Urinary levels of alkylphosphates (DAP) were used to assess exposure. Diethylthiophosphate (DETP) was the most frequent OP metabolite found in urine samples indicating that compounds derived from thiophosphoric acid were mainly used. Chromatin structure was altered in most samples. About 75% of semen samples were classified as having poor fertility potential (>30% of Percentage of DNA Fragmentation Index [DFI%]), whereas individuals without OP occupational exposure showed average DFI% values of 9.9%. Most parameters of conventional semen analysis were within normality except for the presence of immature cells (IGC) in which 82% of the samples were above reference values. There were significant direct associations between urinary DETP concentrations and mean DFI and SD-DFI but marginally (P = 0.079) with DFI%, after adjustment for potential confounders, including IGC. This suggests that OP exposure alters sperm chromatin condensation, which could be reflected in an increased number of cells with greater susceptibility to DNA denaturation. This study showed that human sperm chromatin is a sensitive target to OP exposure and may contribute to adverse reproductive outcomes. Further studies on the relevance of protein phosphorylation as a possible mechanism by which OP alter sperm chromatin are required
Structural plasticity of single chromatin fibers revealed by torsional manipulation
Bancaud, Aurelien; Barbi, Maria; Wagner, Gaudeline; Allemand, Jean-Francois; Mozziconacci, Julien; Lavelle, Christophe; Croquette, Vincent; Victor, Jean-Marc; Prunell, Ariel; Viovy, Jean-Louis
2006-01-01
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, which are determined by the crossing status of the entry/exit DNAs (positive, null or negative). Torsional strain, in displacing that equilibrium, extensively reorganizes the fiber architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin, and may provide the ground to better understand the dynamic binding of most chromatin-associated proteins.
Czech Academy of Sciences Publication Activity Database
Ježková, L.; Falk, Martin; Falková, Iva; Davídková, Marie; Bačíková, Alena; Štefančíková, Lenka; Vachelová, Jana; Michaelidesová, Anna; Lukášová, Emilie; Boreyko, A.; Krasavin, E.; Kozubek, Stanislav
2014-01-01
Roč. 83, SI (2014), s. 128-136. ISSN 0969-8043 R&D Projects: GA MŠk(CZ) EE2.3.30.0030; GA ČR(CZ) GBP302/12/G157; GA ČR(CZ) GAP302/10/1022; GA ČR(CZ) GBP108/12/G108; GA MŠk(CZ) LD12039; GA MŠk(CZ) LD12008 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : DNA double-strand breaks * Higher-order chromatin structure and DSB repair * Formation of chromosomal translocations Subject RIV: BO - Biophysics; BO - Biophysics (UJF-V) Impact factor: 1.231, year: 2014
Renormalization methods for higher order differential equations
International Nuclear Information System (INIS)
We adapt methodology of statistical mechanics and quantum field theory to approximate solutions to an arbitrary order ordinary differential equation boundary value problem by a second-order equation. In particular, we study equations involving the derivative of a double-well potential such as u − u3 or − u + 2u3. Using momentum (Fourier) space variables we average over short length scales and demonstrate that the higher order derivatives can be neglected within the first cumulant approximation, once length is properly renormalized, yielding an approximation to solutions of the higher order equation from the second order. The results are confirmed using numerical computations. Additional numerics confirm that the main role of the higher order derivatives is in rescaling the length. (paper)
Feynman Rules of Higher-order Poles in CHY Construction
Huang, Rijun; Luo, Ming-xing; Zhu, Chuan-Jie
2016-01-01
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.
Higher order Godunov schemes for isothermal hydrodynamics
Balsara, Dinshaw S.
1994-01-01
In this paper we construct higher order Godunov schemes for isothermal flow. Isothermal hydrodynamics serves as a good representation for several systems of astrophysical interest. The schemes designed here have second-order accuracy in space and time and some are third-order accurate for advection. Moreover, several ingredients of these schemes are essential components of even higher order. The methods designed here have excellent ability to represent smooth flow yet capture shocks with high resolution. Several test problems are presented. The algorithms presented here are compared with other algorithms having a comparable formal order of accuracy.
Breastfeeding twins and higher-order multiples.
Gromada, K K; Spangler, A K
1998-01-01
The benefits of breastfeeding for pre-term and full-term infants are well documented. Breastfeeding facilitates maternal-infant attachment, provides optimal infant nutrition and immunologic protection, and minimizes economic impact. These benefits are multiplied with twins and higher-order multiples, who often are born at risk. Supporting a mother as she initiates and continues to breastfeed one infant requires specific knowledge and skills. Health professionals need additional knowledge and skills if they are to provide appropriate assessment, intervention, and support when a mother breastfeeds twins or higher-order multiples. PMID:9684207
Critical Cosmology in Higher Order Gravity
Kan, Nahomi; Shiraishi, Kiyoshi
2012-01-01
We construct the higher order terms of curvatures in Lagrangians of the scale factor for the Friedmann-Lemaitre-Robertson-Walker universe, which are linear in the second derivative of the scale factor with respect to cosmic time. It is shown that they are composed from the Lovelock tensors at the first step; iterative construction yields arbitrarily high order terms. The relation to the former work on higher order gravity is discussed. Despite the absence of scalar degrees of freedom in cosmological models which come from our Lagrangian, it is shown that an inflationary behavior of the scale factor can be found. The application to the thick brane solutions is also studied.
A Note On Higher Order Grammar
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.
Kurtz, Katryn Lucille
2008-01-01
[eng] The study of chromatin structure in several simple sperm models of increasing complexity was performed. Species demonstrating different types of sperm nuclear protein transitions and structural changes in spermatic chromatin during spermiogenesis were selected as models for comparison: "H" (non-histone proteins are removed), "H->P" (protamine displaces histones), and "H->Pp->P" (precursor protamine displaces histones, and subsequently is converted into the mature protamine). This study ...
Higher-Order Minimal Functional Graphs
DEFF Research Database (Denmark)
Jones, Neil D; Rosendahl, Mads
1994-01-01
We present a minimal function graph semantics for a higher-order functional language with applicative evaluation order. The semantics captures the intermediate calls performed during the evaluation of a program. This information may be used in abstract interpretation as a basis for proving the...
Canonical Quantization of Higher-Order Lagrangians
Directory of Open Access Journals (Sweden)
Khaled I. Nawafleh
2011-01-01
Full Text Available After reducing a system of higher-order regular Lagrangian into first-order singular Lagrangian using constrained auxiliary description, the Hamilton-Jacobi function is constructed. Besides, the quantization of the system is investigated using the canonical path integral approximation.
Hawking temperature and higher order tunnelling calculations
Chatterjee, Bhramar
2009-01-01
Hawking radiation has recently been explained in terms of tunnelling across the black hole horizon in a Hamilton-Jacobi framework. Higher order calculations using both usual and non-singular coordinates are found to change the tunnelling amplitude, but this change is not a simple alteration of the Hawking temperature.
Higher order antibunching in intermediate states
International Nuclear Information System (INIS)
Since the introduction of binomial state as an intermediate state, different intermediate states have been proposed. Different nonclassical effects have also been reported in these intermediate states. But till now higher order antibunching is predicted in only one type of intermediate state, which is known as shadowed negative binomial state. Recently we have shown that the higher order antibunching is not a rare phenomenon [P. Gupta, P. Pandey, A. Pathak, J. Phys. B 39 (2006) 1137]. To establish our earlier claim further, here we have shown that the higher order antibunching can be seen in different intermediate states, such as binomial state, reciprocal binomial state, hypergeometric state, generalized binomial state, negative binomial state and photon added coherent state. We have studied the possibility of observing the higher order subpoissonian photon statistics in different limits of intermediate states. The effects of different control parameters on the depth of non classicality have also been studied in this connection and it has been shown that the depth of nonclassicality can be tuned by controlling various physical parameters
Frontiers of higher order fuzzy sets
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...
Higher-Order Components for Grid Programming
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.
Logical Reasoning for Higher-Order Functions with Local State
Yoshida, Nobuko; Berger, Martin
2008-01-01
We introduce an extension of Hoare logic for call-by-value higher-order functions with ML-like local reference generation. Local references may be generated dynamically and exported outside their scope, may store higher-order functions and may be used to construct complex mutable data structures. This primitive is captured logically using a predicate asserting reachability of a reference name from a possibly higher-order datum and quantifiers over hidden references. We explore the logic's descriptive and reasoning power with non-trivial programming examples combining higher-order procedures and dynamically generated local state. Axioms for reachability and local invariant play a central role for reasoning about the examples.
Directory of Open Access Journals (Sweden)
Valeria Visone
2014-09-01
Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.
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.
Energy Technology Data Exchange (ETDEWEB)
Bluemlein, J.; Boettcher, H.
2008-02-15
The higher twist contributions to the deeply inelastic structure functions F{sup p}{sub 2}(x,Q{sup 2}) and F{sup d}{sub 2}(x,Q{sup 2}) for larger values of the Bjorken variable x are extracted extrapolating the twist-2 contributions measured in the large W{sup 2} region to the region 4 GeV{sup 2}{<=}W{sup 2} {<=}12.5 GeV{sup 2} applying target mass corrections. We compare the results for the NLO, NNLO and N{sup 3}LO analyzes and include also the large x at N{sup 4}LO to the Wilson coefficients. A gradual lowering of the higher twist contributions going from NLO to N{sup 4}LO is observed, which stresses the importance of higher order corrections. (orig.)
Unsupervised pattern discovery in human chromatin structure through genomic segmentation
Hoffman, Michael M.; Buske, Orion J; Wang, Jie; Weng, Zhiping; Bilmes, Jeff A.; Noble, William Stafford
2012-01-01
We applied a dynamic Bayesian network method that identifies joint patterns from multiple functional genomics experiments to ChIP-seq histone modification and transcription factor data, and DNaseI-seq and FAIRE-seq open chromatin readouts from the human cell line K562. In an unsupervised fashion, we identified patterns associated with transcription start sites, gene ends, enhancers, CTCF elements, and repressed regions. Software and genome browser tracks are at http://noble.gs.washington.edu/...
Chromatin structure and epigenetics of tumour cells: A review
Czech Academy of Sciences Publication Activity Database
Bártová, Eva; Krejčí, Jana; Hájek, R.; Harničarová, Andrea; Kozubek, Stanislav
2009-01-01
Roč. 9, č. 1 (2009), s. 51-61. ISSN 1871-529X R&D Projects: GA AV ČR(CZ) 1QS500040508; GA ČR(CZ) GA204/06/0978 Grant ostatní: GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : tumour cells * chromatin * radiation Subject RIV: BO - Biophysics
Chromatin structure in relation to telomere length maintenance in plants
Czech Academy of Sciences Publication Activity Database
Fajkus, Jiří; Mozgová, I.; Procházková Schrumpfová, P.; Majerová, E.; Fojtová, M.
Zürich, 2009. s. 1. [European Workshop on Plant Chromatin. 03.09.2009-04.09.2009, Zürich] R&D Projects: GA ČR(CZ) GD204/08/H054; GA ČR(CZ) GA204/08/1530; GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : telomere * HMGB1 protein * DNA methylation Subject RIV: BO - Biophysics
Structural plasticity of single chromatin fibers revealed by torsional manipulation
Bancaud, Aurelien; Silva, Natalia Conde e; Barbi, Maria; Wagner, Gaudeline; Allemand, Jean-Francois; Mozziconacci, Julien; Lavelle, Christophe; Croquette, Vincent; Victor, Jean-Marc; Prunell, Ariel; Viovy, Jean-Louis
2007-01-01
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucle...
Czech Academy of Sciences Publication Activity Database
Falk, Martin; Lukášová, Emilie; Faretta, M.; Dellino, I.; Kozubek, Stanislav; Pellici, G. I.; Kozubek, Michal; Rochi, M.
Brno : Masarykova univerzita v Brně, 2004 - (Kozubek, S.; Kozubek, M.), s. 8-23 ISBN 80-210-3560-9. [Biophysics of the Genome. Brno (CZ), 12.10.2004-13.10.2004] R&D Projects: GA MZd NC6987; GA AV ČR IAA1065203; GA AV ČR IBS5004010; GA AV ČR IAA5004306; GA ČR GA202/02/0804; GA MŠk ME 565 Institutional research plan: CEZ:AV0Z5004920 Keywords : acute promyelocytic leukemia * PML bodies * higher order chromatin structure Subject RIV: BO - Biophysics
Performance assessment of higher order thinking.
Griffin, Patrick
2014-01-01
This article describes a study investigating the effect of intervention on student problem solving and higher order competency development using a series of complex numeracy performance tasks (Airasian and Russell, 2008). The tasks were sequenced to promote and monitor student development towards hypothetico-deductive reasoning. Using Rasch partial credit analysis (Wright and Masters, 1982) to calibrate the tasks and analysis of residual gain scores to examine the effect of class and school membership, the study illustrates how directed intervention can improve students' higher order competency skills. This paper demonstrates how the segmentation defined by Wright and Masters can offer a basis for interpreting the construct underlying a test and how segment definitions can deliver targeted interventions. Implications for teacher intervention and teaching mentor schemes are considered. The article also discusses multilevel regression models that differentiate class and school effects, and describes a process for generating, testing and using value added models. PMID:24518581
Higher-Order Pushdown Systems with Data
Directory of Open Access Journals (Sweden)
Paweł Parys
2012-10-01
Full Text Available We propose a new extension of higher-order pushdown automata, which allows to use an infinite alphabet. The new automata recognize languages of data words (instead of normal words, which beside each its letter from a finite alphabet have a data value from an infinite alphabet. Those data values can be loaded to the stack of the automaton, and later compared with some farther data values on the input. Our main purpose for introducing these automata is that they may help in analyzing normal automata (without data. As an example, we give a proof that deterministic automata with collapse can recognize more languages than deterministic automata without collapse. This proof is simpler than in the no-data case. We also state a hypothesis how the new automaton model can be related to the original model of higher-order pushdown automata.
Higher Order Force Gradient Symplectic Algorithms
Chin, S A; Chin, Siu A.; Kidwell, Donald W.
2000-01-01
We show that a recently discovered fourth order symplectic algorithm, which requires one evaluation of force gradient in addition to three evaluations of the force, when iterated to higher order, yielded algorithms that are far superior to similarly iterated higher order algorithms based on the standard Forest-Ruth algorithm. We gauge the accuracy of each algorithm by comparing the step-size independent error functions associated with energy conservation and the rotation of the Laplace-Runge-Lenz vector when solving a highly eccentric Kepler problem. For orders 6, 8, 10 and 12, the new algorithms are approximately a factor of $10^3$, $10^4$, $10^4$ and $10^5$ better.
Sophisticated Thinking: Higher Order Thinking Skills
Elena Tikhonova; Natalia Kudinova
2015-01-01
The information-based society determines that the key factor to achieve success is the development of sophisticated thinking. That said, the thinking process cannot be just a mere imitation of cognitive work, since the digital age requires the authentic skills of working with a flow of information that is being constantly updated. This paper deals with the last stage of the study devoted to the development of sophisticated thinking. It focuses on the enhancement of higher order thinking sk...
Cosmologies from higher-order string corrections
Tsujikawa, Shinji
2006-01-01
We study cosmologies based on low-energy effective string theory with higher-order string corrections to a tree-level action and with a modulus scalar field (dilaton or compactification modulus). In the presence of such corrections it is possible to construct nonsingular cosmological solutions in the context of Pre-Big-Bang and Ekpyrotic universes. We review the construction of nonsingular bouncing solutions and resulting density perturbations in Pre-Big-Bang and Ekpyrotic models. We also dis...
Intentional binding and higher order agency experience
Moore, James W; Haggard, Patrick
2010-01-01
Recent research has shown that human instrumental action is associated with systematic changes in time perception: The interval between a voluntary action and an outcome is perceived as shorter than the interval between a physically similar involuntary movement and an outcome. The study by, Ebert and Wegner (2010) suggests that this change in time perception is related to higher order agency experience. Notwithstanding certain issues arising from their study, which are discussed, we believe i...
Higher-order methods for relativistic magnetohydrodynamics
Núñez-de la Rosa, Jonatan; Munz, Claus-Dieter
2014-01-01
A higher-order finite volume method based on WENO7 reconstruction for solving the relativistic magnetohydrodynamics equations in two-dimensional domains is presented. In the presence of strong shocks, a WENO3 reconstruction is used instead. The time discretization is performed by a Strong Stability-Preserving Runge-Kutta method of fourth order. Numerical results include the Orszag-Tang vortex, the Rotor problem and the Spherical Blast Wave problem.
Tiano, L; Chessa, M G; Carrara, S; Tagliafierro, G; Delmonte Corrado, M U
1999-01-01
The chromatin structure dynamics of the Colpoda inflata macronucleus have been investigated in relation to its functional condition, concerning chromatin body extrusion regulating activity. Samples of 2- and 25-day-old resting cysts derived from a standard culture, and of 1-year-old resting cysts derived from a senescent culture, were examined by means of histogram analysis performed on acquired optical microscopy images. Three groups of histograms were detected in each sample. Histogram classification, clustering and matching were assessed in order to obtain the mean histogram of each group. Comparative analysis of the mean histogram showed a similarity in the grey level range of 25-day- and 1-year-old cysts, unlike the wider grey level range found in 2-day-old cysts. Moreover, the respective mean histograms of the three cyst samples appeared rather similar in shape. All this implies that macronuclear chromatin structural features of 1-year-old cysts are common to both cyst standard cultures. The evaluation of the acquired images and their respective histograms evidenced a dynamic state of the macronuclear chromatin, appearing differently condensed in relation to the chromatin body extrusion regulating activity of the macronucleus. The coexistence of a chromatin-decondensed macronucleus with a pycnotic extrusion body suggests that chromatin unable to decondense, thus inactive, is extruded. This finding, along with the presence of chromatin structural features common to standard and senescent cyst populations, supports the occurrence of 'rejuvenated' cell lines from 1-year-old encysted senescent cells, a phenomenon which could be a result of accomplished macronuclear renewal. PMID:10439214
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.
Ward identities of higher order Virasoro algebra
International Nuclear Information System (INIS)
The general formulations of primary fields versus quasi-primary ones in the context of high order Virasoro algebra (HOVA) and the corresponding Ward identity are explored. The primary fields of conformal spins up to 8 are given in terms of quasi-primary fields, and the general features of the higher order expressions are also discussed. It is observed that the local fields, either primary of quasi-primary, carry the same numbers of central charges, and not all the primary fields contribute to the anomalies in the Ward identities. (author). 6 refs
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.
Lewellen, John W.
2001-04-01
Traditional photocathode rf gun design is based around the use of TM0,1,0-mode cavities. This is typically done in the interest of obtaining the highest possible gradient per unit supplied rf power and for historical reasons. In a multicell, aperture-coupled photoinjector, however, the gun as a whole is produced from strongly coupled cavities oscillating in a π mode. This design requires very careful preparation and tuning, as the field balance and resonant frequencies are easily disturbed. Side-coupled designs are often avoided because of the dipole modes introduced into the cavity fields. This paper proposes the use of a single higher-order mode rf cavity in order to generate the desired on-axis fields. It is shown that the field experienced by a beam in a higher-order mode rf gun is initially very similar to traditional 1.5- or 2.5-cell π-mode gun fields, and projected performance in terms of beam quality is also comparable. The new design has the advantages of much greater ease of fabrication, immunity from coupled-cell effects, and simpler tuning procedures. Because of the gun geometry, the possibility also exists for improved temperature stabilization and cooling for high duty-cycle applications.
Theorem Proving In Higher Order Logics
Carreno, Victor A. (Editor); Munoz, Cesar A.; Tahar, Sofiene
2002-01-01
The TPHOLs International Conference serves as a venue for the presentation of work in theorem proving in higher-order logics and related areas in deduction, formal specification, software and hardware verification, and other applications. Fourteen papers were submitted to Track B (Work in Progress), which are included in this volume. Authors of Track B papers gave short introductory talks that were followed by an open poster session. The FCM 2002 Workshop aimed to bring together researchers working on the formalisation of continuous mathematics in theorem proving systems with those needing such libraries for their applications. Many of the major higher order theorem proving systems now have a formalisation of the real numbers and various levels of real analysis support. This work is of interest in a number of application areas, such as formal methods development for hardware and software application and computer supported mathematics. The FCM 2002 consisted of three papers, presented by their authors at the workshop venue, and one invited talk.
Higher order assortativity in complex networks
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...
Replicating chromatin: a tale of histones
DEFF Research Database (Denmark)
Groth, Anja
2009-01-01
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.......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...
International Nuclear Information System (INIS)
The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 x 10-1 to 10-4 A-1 with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 μm and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm
Equivalent Higher-order Guiding-center Hamiltonian Theories
Brizard, A J
2016-01-01
Equivalent guiding-center Hamiltonian theories are constructed based on higher-order Lie-transform perturbation methods. Higher-order guiding-center theories are distinguished on the basis of whether correction terms associated with magnetic-field nonuniformity appear either in the guiding-center symplectic (Poisson-bracket) structure, in the guiding-center Hamiltonian, or both. These theories are called equivalent because they describe the same guiding-center magnetic-moment invariant. The present work presents the detailed derivations of results that were summarized in a recent paper by Tronko and Brizard [Phys. Plasmas 22, 112507 (2015)].
Fourier transform infrared spectroscopic analysis of sperm chromatin structure and DNA stability.
Oldenhof, H; Schütze, S; Wolkers, W F; Sieme, H
2016-05-01
Sperm chromatin structure and condensation determine accessibility for damage, and hence success of fertilization and development. The aim of this study was to reveal characteristic spectral features coinciding with abnormal sperm chromatin packing (i.e., DNA-protein interactions) and decreased fertility, using Fourier transform infrared spectroscopy. Chromatin structure in spermatozoa obtained from different stallions was investigated. Furthermore, spermatozoa were exposed to oxidative stress, or treated with thiol-oxidizing and disulfide-reducing agents, to alter chromatin structure and packing. Spectroscopic studies were corroborated with flow cytometric analyses using the DNA-intercalating fluorescent dye acridine orange. Decreased fertility of individuals correlated with increased abnormal sperm morphology and decreased stability toward induced DNA damage. Treatment with the disulfide reducing agent dithiothreitol resulted in increased sperm chromatin decondensation and DNA accessibility, similar as found for less mature epididymal spermatozoa. In situ infrared spectroscopic analysis revealed that characteristic bands arising from the DNA backbone (ν1230, ν1086, ν1051 cm(-1) ) changed in response to induced oxidative damage, water removal, and decondensation. This coincided with changes in the amide-I region (intensity at ν1620 vs. ν1640 cm(-1) ) denoting concomitant changes in protein secondary structure. Reduction in protein disulfide bonds resulted in a decreased value of the asymmetric to symmetric phosphate band intensity (ν1230/ν1086 cm(-1) ), suggesting that this band ratio is sensitive for the degree of chromatin condensation. Moreover, when analyzing spermatozoa from different individuals, it was found that the asymmetric/symmetric phosphate band ratio negatively correlated with the percentage of morphologically abnormal spermatozoa. PMID:26916383
A higher order Blokh-Zyablov propagation rule for higher order nets
Dick, Josef
2012-01-01
Higher order nets were introduced by Dick as a generalisation of classical $(t,m,s)$-nets, which are point sets frequently used in quasi-Monte Carlo integration algorithms. Essential tools in finding such point sets of high quality are propagation rules, which make it possible to generate new higher order nets from existing higher order nets and even classical $(t,m,s)$-nets. Such propagation rules for higher order nets were first considered by the authors in [J. Dick, P. Kritzer. Duality theory and propagation rules for generalized digital nets. Math. Comp. 79, 993--1017, 2010] and further developed in [J. Baldeaux, J. Dick, F. Pillichshammer. Duality theory and propagation rules for higher order nets. Discrete Math. 311, 362--386, 2011]. In [E.L. Blokh, V.V. Zyablov. Coding of generalized concatenated codes. Problems of Information Transmission, 10, 218--222, 1974] Blokh and Zyablov established a very general propagation rule for linear codes. This propagation rule has been extended to $(t,m,s)$-nets by Sch...
DEFF Research Database (Denmark)
Fismen, S; Hedberg, A; Fenton, K A;
2009-01-01
Murine and human lupus nephritis are characterized by glomerular deposits of electron-dense structures (EDS). Dominant components of EDS are chromatin fragments and IgG antibodies. Whether glomerular EDS predispose for similar deposits in skin is unknown. We analysed (i) whether dermo...... (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...... were present in capillary lumina in glomeruli and skin of all nephritic individuals. Thus, chromatin-IgG complexes accounting for lupus nephritis seem to reach skin through circulation, but other undetermined factors are required for these complexes to deposit within skin membranes....
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.
Symbolic Backwards-Reachability Analysis for Higher-Order Pushdown Systems
Hague, Matthew; Ong, C. -H. Luke
2008-01-01
Higher-order pushdown systems (PDSs) generalise pushdown systems through the use of higher-order stacks, that is, a nested "stack of stacks" structure. These systems may be used to model higher-order programs and are closely related to the Caucal hierarchy of infinite graphs and safe higher-order recursion schemes. We consider the backwards-reachability problem over higher-order Alternating PDSs (APDSs), a generalisation of higher-order PDSs. This builds on and extends previous work on pushdo...
Interaction and conformational changes of chromatin with divalent ions.
Borochov, N; Ausio, J; Eisenberg, H
1984-01-01
We have investigated the interaction of divalent ions with chromatin towards a closer understanding of the role of metal ions in the cell nucleus. The first row transition metal ion chlorides MnCl2, CoCl2, NiCl2 and CuCl2 lead to precipitation of chicken erythrocyte chromatin at a significantly lower concentration than the alkali earth metal chlorides MgCl2, CaCl2 and BaCl2. A similar distinction can be made for the compaction of chromatin to the "30 nm" solenoid higher order structure which ...
Adams, Peter D
2007-01-01
Cellular senescence is an important tumor suppression process, and a possible contributor to tissue aging. Senescence is accompanied extensive changes in chromatin structure. In particular, many senescent cells accumulate specialized domains of facultative heterochromatin, called Senescence Associated Heterochromatin Foci (SAHF), which are thought to repress expression of proliferation-promoting genes, thereby contributing to senescence-associated proliferation arrest. This article reviews ou...
A Higher Order Godunov Method for Radiation Hydrodynamics: Radiation Subsystem
Sekora, Michael; Stone, James
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 ...
Zhukotskiĭ, A V; Shchegolev, A I; Butusova, N N; Nemirovskiĭ, L E; Kogan, E M
1985-06-01
Geometric and optical parameters of chromatin of hepatocyte nuclei have been examined before (UV, lambda = 265 nm) and after gallocyanine staining. Quantitative parameters of the chromatin structure in the same nuclei measured in situ by a scanning microscope-photometer (step size 0.125 micron) before and after staining were equal. Tinctorial properties of chromatin granules (condensed part of the nuclear material) and its diffuse part were different. It is suggested that the difference between granules and the nongranular part of chromatin is not only of optical but also of chemical nature. PMID:2410060
Energy Technology Data Exchange (ETDEWEB)
Peng, Jamy C.
2007-05-05
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
Higher order asymptotics for the Hirota equation via Deift–Zhou higher order theory
Energy Technology Data Exchange (ETDEWEB)
Huang, Lin, E-mail: huangl12@fudan.edu.cn [School of Mathematical Sciences, Fudan University, Shanghai 200433 (China); Xu, Jian, E-mail: jianxu02@gmail.com [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Fan, En-gui, E-mail: faneg@fudan.edu.cn [School of Mathematical Sciences, Fudan University, Shanghai 200433 (China)
2015-01-02
In this paper, the Deift–Zhou higher order asymptotic theory is used to further establish the full asymptotic expansion for the solution of the Hirota equation to all order, as t→∞. The method is rigorous and does not rely on an a priori ansatz for the form of the solution. - Highlights: • Give RHP for Hirota equation. • Systemically apply Deift–Zhou theory. • Give full asymptotics for Hirota equation.
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
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...
Evaluation of expressions involving higher order derivations
Grossman, Robert
1990-01-01
The local geometric properties of a nonlinear control system defined by vector fields E(sub 1),..., E(sub M) are determined by the algebraic properties of the iterated Lie brackets of the E(sub j)'s. The problem of rewriting expressions is examined involving the E(sub j)'s in terms of the D(sub mu)'s in such a way as to handle effectively any cancellation occurring due to commuting of the D(sub mu)'s. A data structure is introduced which allows us to organize the computation to take advantage of the symmetries in the expression and reduce the operation count.
Higher Order Macro Coefficients in Periodic Homogenization
Conca, Carlos; San Martin, Jorge; Smaranda, Loredana; Vanninathan, Muthusamy
2011-09-01
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.
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.
DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure
International Nuclear Information System (INIS)
Interstitial Telomeric Sequences (ITS) are over-involved in spontaneous and radiationinduced chromosome aberrations in chinese hamster cells. We have performed a study to investigate the origin of their instability, spontaneously or after low doses irradiation. Our results demonstrate that ITS have a particular chromatin structure: short nucleotide repeat length, less compaction of the 30 nm chromatin fiber, presence of G-quadruplex structures. These features would modulate breaks production and would favour the recruitment of alternative DNA repair mechanisms, which are prone to produce chromosome aberrations. These pathways could be at the origin of chromosome aberrations in ITS whereas NHEJ and HR Double Strand Break repair pathways are rather required for a correct repair in these regions. (author)
Chromatin structure implicated in activation of HIV-1 gene expression by ultraviolet light
International Nuclear Information System (INIS)
We have investigated the effects of different DNA-damaging agents on HIV-1 gene expression. We find that agents that produce bulky DNA lesions, similar to those induced by ultraviolet light (UV), all dramatically increase HIV-1 gene expression, whereas agents that produce primarily base damage and DNA breakage, such as ionizing radiation, have little or no effect. We show that these effects are independent of DNA synthesis per se and do not require DNA nucleotide excision repair. The drug novobiocin effectively prevents the UV activation process, consistent with the idea that a change in DNA chromatin structure may be required. We suggest that a transient decondensation of chromatin structure, an early step in DNA nucleotide excision repair but not in base excision repair, may be the triggering mechanism. The decondensation may allow the transcriptional machinery better access to the HIV-1 promoter region, thereby increasing gene expression
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
Mauermann, M; Uppenkamp, S; van Hengel, PWJ; Kollmeier, B
1999-01-01
Critical experiments were performed in order to validate the two-source hypothesis of distortion product otoacoustic emissions (DPOAE) generation. Measurements of the spectral fine structure of DPOAE in response to stimulation with two sinusoids have been:performed with normal-hearing subjects. The
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. PMID:25028181
Higher-order polarization singularitites in tailored vector beams
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.
A Higher Order Godunov Method for Radiation Hydrodynamics: Radiation Subsystem
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.
Chromatin structure and ionizing-radiation-induced chromosome aberrations
International Nuclear Information System (INIS)
The possible influence of chromatic structure or activity on chromosomal radiosensitivity was studied. A cell line was isolated which contained some 105 copies of an amplified plasmid in a single large mosquito artificial chromosome (MAC). This chromosome was hypersensitive to DNase I. Its radiosensitivity was some three fold greater than normal mosquito chromosomes in the same cell. In cultured human cells irradiated during G0, the initial breakage frequency in chromosome 4, 19 and the euchromatic and heterochromatic portions of the Y chromosome were measured over a wide range of doses by inducing Premature Chromosome Condensation (PCC) immediately after irradiation with Cs-137 gamma rays. No evidence was seen that Y heterochromatin or large fragments of it remained unbroken. The only significant deviation from the expected initial breakage frequency per Gy per unit length of chromosome was that observed for the euchromatic portion of the Y chromosome, with breakage nearly twice that expected. The development of aberrations involving X and Y chromosomes at the first mitosis after irradation was also studied. Normal female cells sustained about twice the frequency of aberrations involving X chromosomes for a dose of 7.3 Gy than the corresponding male cells. Fibroblasts from individuals with supernumerary X chromosomes did not show any further increase in X aberrations for this dos. The frequency of aberrations involving the heterochromatic portion of the long arm of the Y chromosome was about what would be expected for a similar length of autosome, but the euchromatic portion of the Y was about 3 times more radiosensitive per unit length. 5-Azacytidine treatment of cultured human female fibroblasts or fibroblasts from a 49,XXXXY individual, reduced the methylation of cytosine residues in DNA, and resulted in an increased chromosomal radiosensitivity in general, but it did not increase the frequency of aberrations involving the X chromosomes
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.
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. PMID:26314830
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...
Widmer, R. M.; Lezzi, M.; Koller, Th.
1987-01-01
We have analysed by micrococcus nuclease digestion the chromatin structure of genes in the Balbiani ring (BR) regions of a Chironomus cell line. Gel electrophoresis of the DNA fragments reveals a repeating structure which consists of two repeat sizes, a long repeat seen in the large fragments and a small repeat seen in the small fragments. The two repeats hardly overlap, except in a narrow transition zone which is at a different fragment size in the BR 2.2 and the BR 2.1 gene. The sizes of th...
Time-Discrete Higher-Order ALE Formulations: Stability
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.
Institute of Scientific and Technical Information of China (English)
Li Xi-Zeng; Su Bao-Xia; Chai Lu
2004-01-01
It is found that the two-mode output quantum electromagnetic field in two-mode squeezed states exhibits higherorder squeezing to all even orders, and the degree of higher-order squeezing is greater than that of the second-order.The higher-order squeezed parameter and squeezed limit due to the modulation frequency are investigated. The smaller the modulation frequency is, the stronger the degree of higher-order squeezing becomes. Furthermore, the higher-order uncertainty relations in two-mode squeezed states are presented for the first time. The product of higher-order noise moments is related to even order number N and the squeeze factor r.
Replication domains are self-interacting structural chromatin units of human chromosomes
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
Genome instability in the context of chromatin structure and fragile sites
Czech Academy of Sciences Publication Activity Database
Bártová, Eva; Galiová-Šustáčková, Gabriela; Legartová, Soňa; Stixová, Lenka; Jugová, Alžbeta; Kozubek, Stanislav
2010-01-01
Roč. 20, č. 3 (2010), s. 181-194. ISSN 1045-4403 R&D Projects: GA MŠk ME 919; GA ČR(CZ) GAP302/10/1022 Grant ostatní: GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * fragile sites * chromatin structure Subject RIV: BO - Biophysics Impact factor: 4.111, year: 2010
International Nuclear Information System (INIS)
Purpose: The open structure of euchromatin renders it susceptible to DNA damage by ionizing radiation (IR) compared with compact heterochromatin. The effect of chromatin configuration on the efficacy of Auger electron radiotherapy was investigated. Methods and Materials: Chromatin structure was altered in MDA-MB-468 and 231-H2N human breast cancer cells by suberoylanilide hydroxamic acid (SAHA), 5-aza-2-deoxycytidine, or hypertonic treatment. The extent and duration of chromatin structural changes were evaluated using the micrococcal nuclease assay. DNA damage (γH2AX assay) and clonogenic survival were evaluated after exposure to 111In-DTPA-hEGF, an Auger electron-emitting radiopharmaceutical, or IR. The intracellular distribution of 111In-DTPA-hEGF after chromatin modification was investigated in cell fractionation experiments. Results: Chromatin remained condensed for up to 20 minutes after NaCl and in a relaxed state 24 hours after SAHA treatment. The number of γH2AX foci per cell was greater in MDA-MB-468 and 231-H2N cells after IR (0.5 Gy) plus SAHA (1 μM) compared with IR alone (16 ± 0.6 and 14 ± 0.3 vs. 12 ± 0.4 and 11 ± 0.2, respectively). More γH2AX foci were observed in MDA-MB-468 and 231-H2N cells exposed to 111In-DTPA-hEGF (6 MBq/μg) plus SAHA vs. 111In-DTPA-hEGF alone (11 ± 0.3 and 12 ± 0.7 vs. 9 ± 0.4 and 7 ± 0.3, respectively). 5-aza-2-deoxycytidine enhanced the DNA damage caused by IR and 111In-DTPA-hEGF. Clonogenic survival was reduced in MDA-MB-468 and 231-H2N cells after IR (6 Gy) plus SAHA (1 μM) vs. IR alone (0.6% ± 0.01 and 0.3% ± 0.2 vs. 5.8% ± 0.2 and 2% ± 0.1, respectively) and after 111In-DTPA-hEGF plus SAHA compared to 111In-DTPA-hEGF alone (21% ± 0.4% and 19% ± 4.6 vs. 33% ± 2.3 and 32% ± 3.7). SAHA did not affect 111In-DTPA-hEGF nuclear localization. Hypertonic treatment resulted in fewer γH2AX foci per cell after IR and 111In-DTPA-hEGF compared to controls but did not significantly alter clonogenic survival
Higher-Order Generalized Invexity in Control Problems
Directory of Open Access Journals (Sweden)
S. K. Padhan
2011-01-01
Full Text Available We introduce a higher-order duality (Mangasarian type and Mond-Weir type for the control problem. Under the higher-order generalized invexity assumptions on the functions that compose the primal problems, higher-order duality results (weak duality, strong duality, and converse duality are derived for these pair of problems. Also, we establish few examples in support of our investigation.
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.
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).
Higher-order phase transitions on financial markets
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
Promoting Higher Order Thinking Skills Using Inquiry-Based Learning
Madhuri, G. V.; Kantamreddi, V. S. S. N; Prakash Goteti, L. N. S.
2012-01-01
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…
Introduction to Higher Order Spatial Statistics in Cosmology
Szapudi, István
2005-01-01
In this lecture notes I concentrate on the classic and widely applicable characterization of higher order statistics by joint moments, a.k.a. higher order correlation functions, and directly related statistics. I put special emphasis on recent results, especially the connection of spatial statistics with symmetries.
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...
Stationary Probability Vectors of Higher-order Markov Chains
Li, Chi-Kwong; Zhang, Shixiao
2013-01-01
We consider the higher-order Markov Chain, and characterize the second order Markov chains admitting every probability distribution vector as a stationary vector. The result is used to construct Markov chains of higher-order with the same property. We also study conditions under which the set of stationary vectors of the Markov chain has a certain affine dimension.
Tran, Ulrich S.; Cebolla i Martí, Ausiàs Josep; Tobias M. Glück; Soler Ribaudi, Joaquim; García Campayo, Javier; von Moy, Theresa
2014-01-01
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 multigrou...
Higher-order Dirac solitons in binary waveguide arrays
International Nuclear Information System (INIS)
We study optical analogues of higher-order Dirac solitons (HODSs) in binary waveguide arrays. Like higher-order solitons obtained from the well-known nonlinear Schrödinger equation governing the pulse propagation in an optical fiber, these HODSs have amplitude profiles which are numerically shown to be periodic over large propagation distances. At the same time, HODSs possess some unique features. Firstly, the period of a HODS depends on its order parameter. Secondly, the discrete nature in binary waveguide arrays imposes the upper limit on the order parameter of HODSs. Thirdly, the order parameter of HODSs can vary continuously in a certain range. - Highlights: • Higher-order Dirac solitons in nonlinear binary waveguide arrays are numerically demonstrated. • Amplitude profiles of higher-order Dirac solitons are periodic during propagation. • The period of higher-order Dirac solitons decreases when the soliton order increases
Higher-order Dirac solitons in binary waveguide arrays
Energy Technology Data Exchange (ETDEWEB)
Tran, Truong X., E-mail: Truong.Tran@mpl.mpg.de [Department of Physics, Le Quy Don University, 236 Hoang Quoc Viet str., 10000 Hanoi (Viet Nam); Max Planck Institute for the Science of Light, Günther-Scharowsky str. 1, 91058 Erlangen (Germany); Duong, Dũng C. [Department of Physics, Le Quy Don University, 236 Hoang Quoc Viet str., 10000 Hanoi (Viet Nam)
2015-10-15
We study optical analogues of higher-order Dirac solitons (HODSs) in binary waveguide arrays. Like higher-order solitons obtained from the well-known nonlinear Schrödinger equation governing the pulse propagation in an optical fiber, these HODSs have amplitude profiles which are numerically shown to be periodic over large propagation distances. At the same time, HODSs possess some unique features. Firstly, the period of a HODS depends on its order parameter. Secondly, the discrete nature in binary waveguide arrays imposes the upper limit on the order parameter of HODSs. Thirdly, the order parameter of HODSs can vary continuously in a certain range. - Highlights: • Higher-order Dirac solitons in nonlinear binary waveguide arrays are numerically demonstrated. • Amplitude profiles of higher-order Dirac solitons are periodic during propagation. • The period of higher-order Dirac solitons decreases when the soliton order increases.
Conservation Laws in Higher-Order Nonlinear Optical Effects
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.
Neural classifiers for learning higher-order correlations
International Nuclear Information System (INIS)
Studies by various authors suggest that higher-order networks can be more powerful and biologically more plausible with respect to the more traditional multilayer networks. These architecture make explicit use of nonlinear interactions between input variables in the form of higher-order units or product units. If it is known a priori that the problem to be implemented possesses a given set of invariances like in the translation, rotation, and scale invariant recognition problems, those invariances can be encoded, thus eliminating all higher-order terms which are incompatible with the invariances. In general, however, it is a serious set-back that the complexity of learning increases exponentially with the size of inputs. This paper reviews higher-order networks and introduces an implicit representation in which learning complexity is mainly decided by the number of higher-order terms to be learned and increases only linearly with the input size
CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells
Handoko, Lusy; Xu, Han; Li, Guoliang; Ngan, Chew Yee; Chew, Elaine; Schnapp, Marie; Lee, Charlie Wah Heng; Ye, Chaopeng; Ping, Joanne Lim Hui; Mulawadi, Fabianus; Wong, Eleanor; Sheng, Jianpeng; Zhang, Yubo; Poh, Thompson; Chan, Chee Seng; Kunarso, Galih; Shahab, Atif; Bourque, Guillaume; Cacheux-Rataboul, Valere; Sung, Wing-Kin; Ruan, Yijun; Wei, Chia-Lin
2011-01-01
Mammalian genomes are viewed as functional organizations that orchestrate spatial and temporal gene regulation. CTCF, the most characterized insulator-binding protein, has been implicated as a key genome organizer. Yet, little is known about CTCF-associated higher order chromatin structures at a global scale. Here, we applied Chromatin Interaction Analysis by Paired-End-Tag sequencing to elucidate the CTCF-chromatin interactome in pluripotent cells. From this analysis, 1,480 cis and 336 trans interacting loci were identified with high reproducibility and precision. Associating these chromatin interaction loci with their underlying epigenetic states, promoter activities, enhancer binding and nuclear lamina occupancy, we uncovered five distinct chromatin domains that suggest potential new models of CTCF function in chromatin organization and transcriptional control. Specifically, CTCF interactions demarcate chromatin-nuclear membrane attachments and influence proper gene expression through extensive crosstalk between promoters and regulatory elements. This highly complex nuclear organization offers insights towards the unifying principles governing genome plasticity and function. PMID:21685913
Higher-order Fourier analysis over finite fields and applications
Hatami, Pooya
Higher-order Fourier analysis is a powerful tool in the study of problems in additive and extremal combinatorics, for instance the study of arithmetic progressions in primes, where the traditional Fourier analysis comes short. In recent years, higher-order Fourier analysis has found multiple applications in computer science in fields such as property testing and coding theory. In this thesis, we develop new tools within this theory with several new applications such as a characterization theorem in algebraic property testing. One of our main contributions is a strong near-equidistribution result for regular collections of polynomials. The densities of small linear structures in subsets of Abelian groups can be expressed as certain analytic averages involving linear forms. Higher-order Fourier analysis examines such averages by approximating the indicator function of a subset by a function of bounded number of polynomials. Then, to approximate the average, it suffices to know the joint distribution of the polynomials applied to the linear forms. We prove a near-equidistribution theorem that describes these distributions for the group F(n/p) when p is a fixed prime. This fundamental fact was previously known only under various extra assumptions about the linear forms or the field size. We use this near-equidistribution theorem to settle a conjecture of Gowers and Wolf on the true complexity of systems of linear forms. Our next application is towards a characterization of testable algebraic properties. We prove that every locally characterized affine-invariant property of functions f : F(n/p) → R with n∈ N, is testable. In fact, we prove that any such property P is proximity-obliviously testable. More generally, we show that any affine-invariant property that is closed under subspace restrictions and has "bounded complexity" is testable. We also prove that any property that can be described as the property of decomposing into a known structure of low
Quantitative research on higher order harmonics in metrology beamline
Institute of Scientific and Technical Information of China (English)
Hongjun ZHOU; Jinjin ZHENG; Tonglin HUO; Guobin ZHANG; Zeming QI; Pengfei ZHONG
2008-01-01
The synchrotron radiation spectra of the spherical grating monochromator (SGM) working in the soft X-ray and VUV region are often contaminated by significant amounts of higher order harmonics. They cannot be suppressed completely by suitable filters. Higher order contributions in the spectral radiation standard and metrology beamline were researched using transmission grating (made in-house) and IRD AXUV100G (USA) photodiode detector. The exit beam was dispersed with the transmission grating behind the exit slit of the monochromator, and the contributions of the different orders were analyzed. The higher order distributions were quantitatively determined for three gratings with line densities of 1800, 600 and 200 l/mm.Experiment results show that in wavelengths between 5 nm and 15 nm the contributions of the higher orders to the detector signal are restricted to less than 7% even without the use of filters. In wavelength regions between 5 nm and 34 nm, the contributions of the higher orders to the detector signal are less than 14% with proper Al, Si3N4 and Zr filters, and after being modified by quantum efficiency of the detector, the higher order contributions are restricted to less than 6.5%. The study also shows that higher orders are almost totally suppressed by MgF2 filter when the wavelength ranges between 115-140 nm.
Mata-Garrido, Jorge; Casafont, Iñigo; Tapia, Olga; Berciano, Maria T; Lafarga, Miguel
2016-01-01
There is growing evidence that defective DNA repair in neurons with accumulation of DNA lesions and loss of genome integrity underlies aging and many neurodegenerative disorders. An important challenge is to understand how neurons can tolerate the accumulation of persistent DNA lesions without triggering the apoptotic pathway. Here we study the impact of the accumulation of unrepaired DNA on the chromatin architecture, kinetics of the DNA damage response and transcriptional activity in rat sensory ganglion neurons exposed to 1-to-3 doses of ionizing radiation (IR). In particular, we have characterized the structural, molecular and transcriptional compartmentalization of unrepaired DNA in persistent DNA damaged foci (PDDF). IR induced the formation of numerous transient foci, which repaired DNA within the 24 h post-IR, and a 1-to-3 PDDF. The latter concentrate DNA damage signaling and repair factors, including γH2AX, pATM, WRAP53 and 53BP1. The number and size of PDDF was dependent on the doses of IR administered. The proportion of neurons carrying PDDF decreased over time of post-IR, indicating that a slow DNA repair occurs in some foci. The fine structure of PDDF consisted of a loose network of unfolded 30 nm chromatin fiber intermediates, which may provide a structural scaffold accessible for DNA repair factors. Furthermore, the transcription assay demonstrated that PDDF are transcriptionally silent, although transcription occurred in flanking euchromatin. Therefore, the expression of γH2AX can be used as a reliable marker of gene silencing in DNA damaged neurons. Moreover, PDDF were located in repressive nuclear environments, preferentially in the perinucleolar domain where they were frequently associated with Cajal bodies or heterochromatin clumps forming a structural triad. We propose that the sequestration of unrepaired DNA in discrete PDDF and the transcriptional silencing can be essential to preserve genome stability and prevent the synthesis of
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...
Higher order Lie-Baecklund symmetries of evolution equations
International Nuclear Information System (INIS)
We have considered in detail the analysis of higher order Lie-Baecklund symmetries for some representative nonlinear evolution equations. Until now all such symmetry analyses have been restricted only to the first order of the infinitesimal parameter. But the existence of Baecklund transformation (which can be shown to be an overall sum of higher order Lie-Baecklund symmetries) makes it necessary to search for such higher order Lie-Baecklund symmetries directly without taking recourse to the Baecklund transformation or inverse scattering technique. (author)
Higher-order graph wavelets and sparsity on circulant graphs
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.
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.
Image Segmentation Using Higher-Order Correlation Clustering.
Kim, Sungwoong; Yoo, Chang D; Nowozin, Sebastian; Kohli, Pushmeet
2014-09-01
In this paper, a hypergraph-based image segmentation framework is formulated in a supervised manner for many high-level computer vision tasks. To consider short- and long-range dependency among various regions of an image and also to incorporate wider selection of features, a higher-order correlation clustering (HO-CC) is incorporated in the framework. Correlation clustering (CC), which is a graph-partitioning algorithm, was recently shown to be effective in a number of applications such as natural language processing, document clustering, and image segmentation. It derives its partitioning result from a pairwise graph by optimizing a global objective function such that it simultaneously maximizes both intra-cluster similarity and inter-cluster dissimilarity. In the HO-CC, the pairwise graph which is used in the CC is generalized to a hypergraph which can alleviate local boundary ambiguities that can occur in the CC. Fast inference is possible by linear programming relaxation, and effective parameter learning by structured support vector machine is also possible by incorporating a decomposable structured loss function. Experimental results on various data sets show that the proposed HO-CC outperforms other state-of-the-art image segmentation algorithms. The HO-CC framework is therefore an efficient and flexible image segmentation framework. PMID:26352230
Higher order microfibre modes for dielectric particle trapping and propulsion
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...
Guo, Li; Feng, Yingang; Zhang, Zhenfeng; Yao, Hongwei; Luo, Yuanming; Wang, Jinfeng; Huang, Li
2007-01-01
Archaea contain a variety of chromatin proteins consistent with the evolution of different genome packaging mechanisms. Among the two main kingdoms in the Archaea, Euryarchaeota synthesize histone homologs, whereas Crenarchaeota have not been shown to possess a chromatin protein conserved at the kingdom level. We report the identification of Cren7, a novel family of chromatin proteins highly conserved in the Crenarchaeota. A small, basic, methylated and abundant protein, Cren7 displays a high...
A novel higher order sliding mode control scheme
Defoort, Michael; Floquet, Thierry; Kökösy, Annemarie; Perruquetti, Wilfrid
2009-01-01
A higher order sliding mode control algorithm is proposed for a class of uncertain multi-input multi-output nonlinear systems. This problem can be viewed as the finite time stabilization of a higher order input-output dynamic system with bounded uncertainties. The developed control scheme is based on geometric homogeneity and sliding mode control. The proposed procedure provides explicit conditions on the controller parameters and guarantees robustness against uncertainties. An illustrative e...
Dual equivalence in models with higher-order derivatives
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.
Equivalence of Reductions in Higher-Order Rewriting
Bruggink, H.J.S.
2008-01-01
Higher-order rewriting is a symbiosis of two classical rewriting paradigms: the Lambda calculus, which features higher-order variables and variable binding, and first-order term rewriting, which features algebraic pattern matching. It is a powerful tool to study the meta-theory of declarative programming languages, such as Prolog and Haskell, on the one hand, and theorem provers and proof assistants, such as Isabelle, on the other. In this dissertation the notion of equivalence of reductions...
A Calculus of Higher-Order Distributed Components
Stefani, Jean-Bernard
2003-01-01
This report presents a calculus for higher-order distributed components, the Kell calculus. The calculus can be understood as a direct extension of the higher-order -calculus with programmable locations. The report illustrates the expressive power of the Kell calculus by encoding several process calculi with explicit locations, including Mobile Ambients, the Distributed Join calculus and the . The latter encoding demonstrates that the Kell calculus retains the expressive power of the but in a...
Higher order Fourier analysis as an algebraic theory I
Szegedy, Balazs
2009-01-01
Ergodic theory, Higher order Fourier analysis and the hyper graph regularity method are three possible approaches to Szemer\\'edi type theorems in abelian groups. In this paper we develop an algebraic theory that creates a connection between these approaches. Our main method is to take the ultra product of abelian groups and to develop a precise algebraic theory of higher order characters on it. These results then can be turned back into approximative statements about finite Abelian groups.
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....
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.
Directory of Open Access Journals (Sweden)
Sujit eRoy
2014-09-01
Full Text Available Plant cells are subject to high levels of DNA damage resulting from plant’s obligatory dependence on sunlight and the associated exposure to environmental stresses like solar UV radiation, high soil salinity, drought, chilling injury and other air and soil pollutants including heavy metals and metabolic byproducts from endogenous processes. The irreversible DNA damages, generated by the environmental and genotoxic stresses affect plant growth and development, reproduction and crop productivity. Thus, for maintaining genome stability, plants have developed an extensive array of mechanisms for the detection and repair of DNA damages. This review will focus recent advances in our understanding of mechanisms regulating plant genome stability in the context of repairing of double stand breaks and chromatin structure maintenance.
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.
General relativity and gauge gravity theories of higher order
International Nuclear Information System (INIS)
It is a short review of today's gauge gravity theories and their relations with Einstein General Relativity. The conceptions of construction of the gauge gravity theories with higher derivatives are analyzed. GR is regarded as the gauge gravity theory corresponding to the choice of G∞4 as the local gauge symmetry group and the symmetrical tensor of rank two gμν as the field variable. Using the mathematical technique, single for all fundamental interactions (namely variational formalism for infinite Lie groups), we can obtain Einstein's theory as the gauge theory without any changes. All other gauge approaches lead to non-Einstein theories of gravity. But above-mentioned mathematical technique permits us to construct the gauge gravity theory of higher order (for instance SO (3,1)-gravity) so that all vacuum solutions of Einstein equations are the solutions of the SO (3,1)-gravity theory. The structure of equations of SO(3,1)-gravity becomes analogous to Weeler-Misner geometrodynamics one
Spectral imaging to visualize higher-order genomic organization.
Sawyer, Iain A; Shevtsov, Sergei P; Dundr, Miroslav
2016-05-01
A concern in the field of genomics is the proper interpretation of large, high-throughput sequencing datasets. The use of DNA FISH followed by high-content microscopy is a valuable tool for validation and contextualization of frequently occurring gene pairing events at the single-cell level identified by deep sequencing. However, these techniques possess certain limitations. Firstly, they do not permit the study of colocalization of many gene loci simultaneously. Secondly, the direct assessment of the relative position of many clustered gene loci within their respective chromosome territories is impossible. Thus, methods are required to advance the study of higher-order nuclear and cellular organization. Here, we describe a multiplexed DNA FISH technique combined with indirect immunofluorescence to study the relative position of 6 distinct genomic or cellular structures. This can be achieved in a single hybridization step using spectral imaging during image acquisition and linear unmixing. Here, we detail the use of this method to quantify gene pairing between highly expressed spliceosomal genes and compare these data to randomly positioned in silico simulated gene clusters. This is a potentially universally applicable approach for the validation of 3C-based technologies, deep imaging of spatial organization within the nucleus and global cellular organization. PMID:27167405
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.
A Simplified Algorithm for Inverting Higher Order Diffusion Tensors
Directory of Open Access Journals (Sweden)
Laura Astola
2014-11-01
Full Text Available In Riemannian geometry, a distance function is determined by an inner product on the tangent space. In Riemann–Finsler geometry, this distance function can be determined by a norm. This gives more freedom on the form of the so-called indicatrix or the set of unit vectors. This has some interesting applications, e.g., in medical image analysis, especially in diffusion weighted imaging (DWI. An important application of DWI is in the inference of the local architecture of the tissue, typically consisting of thin elongated structures, such as axons or muscle fibers, by measuring the constrained diffusion of water within the tissue. From high angular resolution diffusion imaging (HARDI data, one can estimate the diffusion orientation distribution function (dODF, which indicates the relative diffusivity in all directions and can be represented by a spherical polynomial. We express this dODF as an equivalent spherical monomial (higher order tensor to directly generalize the (second order diffusion tensor approach. To enable efficient computation of Riemann–Finslerian quantities on diffusion weighted (DW-images, such as the metric/norm tensor, we present a simple and efficient algorithm to invert even order spherical monomials, which extends the familiar inversion of diffusion tensors, i.e., symmetric matrices.
Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks.
Chambers, Brendan; MacLean, Jason N
2016-08-01
Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex. Circuit dynamics emerge from complex interactions of interconnected neurons, necessitating that links between connectivity and dynamics be evaluated at the network level. Here we map propagating activity in large neuronal ensembles from mouse neocortex and compare it to a recurrent network model, where connectivity can be precisely measured and manipulated. We find that a dynamical feature dominates statistical descriptions of propagating activity for both neocortex and the model: convergent clusters comprised of fan-in triangle motifs, where two input neurons are themselves connected. Fan-in triangles coordinate the timing of presynaptic inputs during ongoing activity to effectively generate postsynaptic spiking. As a result, paradoxically, fan-in triangles dominate the statistics of spike propagation even in randomly connected recurrent networks. Interplay between higher-order synaptic connectivity and the integrative properties of neurons constrains the structure of network dynamics and shapes the routing of information in neocortex. PMID:27542093
A Model of Repetitive-DNA-Organized Chromatin Network of Interphase Chromosomes
Directory of Open Access Journals (Sweden)
Shao-Jun Tang
2012-03-01
Full Text Available During interphase, chromosomes are relatively de-condensed in the nuclear space. Interphase chromosomes are known to occupy nuclear space in a non-random manner (chromosome territory; however, their internal structures are poorly defined. In particular, little is understood about the molecular mechanisms that govern the internal organization of interphase chromosomes. The author recently proposed that pairing (or interaction of repetitive DNA-containing chromatin regions is a critical driving force that specifies the higher-order organization of eukaryotic chromosomes. Guided by this theoretical framework and published experimental data on the structure of interphase chromosomes and the spatial distribution of repetitive DNA in interphase nuclei, I postulate here a molecular structure of chromatin organization in interphase chromosomes. According to this model, an interphase chromosome is a chromatin mesh (or lattice that is formed by repeat pairing (RP. The mesh consists of two types of structural components: chromosome nodes and loose chromatin fibers. Chromosome nodes are DNA repeat assemblies (RAs that are formed via RP, while loose fibers include chromatin loops that radiate from the nodes. Different loops crosslink by RPs and form a large integrated chromatin network. I suggest that the organization of the chromatin network of a given interphase chromosome is intrinsically specified by the distribution of repetitive DNA elements on the linear chromatin. The stability of the organization is governed by the collection of RA-formed nodes, and the dynamics of the organization is driven by the assembling and disassembling of the nodes.
Higher-order Brunnian structures and possible physical realizations
DEFF Research Database (Denmark)
A. Baas, Nils; V. Fedorov, D.; S. Jensen, A.;
2014-01-01
We consider few-body bound state systems and provide precise definitions of Borromean and Brunnian systems. The initial concepts are more than a hundred years old and originated in mathematical knot-theory as purely geometric considerations. About thirty years ago they were generalized and applied......, and condensed matter systems. Appearance is not excluded. However, both the form and the strengths of the interactions must be rather special. The most promising subfields for present searches would be in cold atoms because of external control of effective interactions, or perhaps in condensed-matter systems...
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.
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...... with the new basis functions enables an efficient iterative solution of higher-order MoM systems. Iterative solution methods incorporate a matrix preconditioner and four preconditioners are presented here; two of these are found in existing works and the other two are adaptations of existing preconditioners......M. The existing hybrid technique employs low-order basis functions and flat patches. This technique is extended here to the case of higher-order hierarchical Legendre basis functions and curved patches. The required memory and the computation time of the new higherorder hybrid PO-MoM are typically reduced...
Higher-order theories from the minimal length
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.
Higher-order theories from the minimal length
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.
Optimized higher-order automatic differentiation for the Faddeeva function
Charpentier, Isabelle
2016-08-01
Considerable research efforts have been directed at implementing the Faddeeva function w(z) and its derivatives with respect to z, but these did not consider the key computing issue of a possible dependence of z on some variable t. The general case is to differentiate the compound function w(z(t)) = w ∘ z(t) with respect to t by applying the chain rule for a first order derivative, or Faà di Bruno's formula for higher-order ones. Higher-order automatic differentiation (HOAD) is an efficient and accurate technique for derivative calculation along scientific computing codes. Although codes are available for w(z) , a special symbolic HOAD is required to compute accurate higher-order derivatives for w ∘ z(t) in an efficient manner. A thorough evaluation is carried out considering a nontrivial case study in optics to support this assertion.
Pushdown Control-Flow Analysis of Higher-Order Programs
Earl, Christopher; Van Horn, David
2010-01-01
Context-free approaches to static analysis gain precision over classical approaches by perfectly matching returns to call sites---a property that eliminates spurious interprocedural paths. Vardoulakis and Shivers's recent formulation of CFA2 showed that it is possible (if expensive) to apply context-free methods to higher-order languages and gain the same boost in precision achieved over first-order programs. To this young body of work on context-free analysis of higher-order programs, we contribute a pushdown control-flow analysis framework, which we derive as an abstract interpretation of a CESK machine with an unbounded stack. One instantiation of this framework marks the first polyvariant pushdown analysis of higher-order programs; another marks the first polynomial-time analysis. In the end, we arrive at a framework for control-flow analysis that can efficiently compute pushdown generalizations of classical control-flow analyses.
An Implementation of the Language Lambda Prolog Organized around Higher-Order Pattern Unification
Qi, Xiaochu
2009-01-01
This thesis concerns the implementation of Lambda Prolog, a higher-order logic programming language that supports the lambda-tree syntax approach to representing and manipulating formal syntactic objects. Lambda Prolog achieves its functionality by extending a Prolog-like language by using typed lambda terms as data structures that it then manipulates via higher-order unification and some new program-level abstraction mechanisms. These additional features raise new implementation questions th...
Breaking the symmetry for enhanced higher-order mode delocalization
Stutzki, Fabian; Jansen, Florian; Jauregui, Cesar; Limpert, Jens; Tünnermann, Andreas
2014-03-01
Large-pitch fibers (LPFs) have enabled the current records for average power, pulse energy and pulse peak power in ultra-fast fiber laser systems. In this paper the working principle of LPFs, which is based on higher-order mode delocalization, is numerically analyzed paying special attention to thermal effects and index mismatch. An enhanced design concept is proposed with a reduced symmetry to improve the delocalization of higher-order modes. This enhanced design has been obtained by transferring the most important characteristics of spiral geometries to a common hexagonal lattice.
A Testing Theory for a Higher-Order Cryptographic Language
Koutavas, Vasileios; Hennessy, Matthew
We study a higher-order concurrent language with cryptographic primitives, for which we develop a sound and complete, first-order testing theory for the preservation of safety properties. Our theory is based on co-inductive set simulations over transitions in a first-order Labelled Transition System. This keeps track of the knowledge of the observer, and treats transmitted higher-order values in a symbolic manner, thus obviating the quantification over functional contexts. Our characterisation provides an attractive proof technique, and we illustrate its usefulness in proofs of equivalence, including cases where bisimulation theory does not apply.
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.
The Cauchy problem for higher order abstract differential equations
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.
Higher order energy transfer. Quantum electrodynamical calculations and graphical representation
International Nuclear Information System (INIS)
In Chapter 1, a novel method of calculating quantum electrodynamic amplitudes is formulated using combinatorial theory. This technique is used throughout instead of conventional time-ordered methods. A variety of hyperspaces are discussed to highlight isomorphism between a number of A generalisation of Pascal's triangle is shown to be beneficial in determining the form of hyperspace graphs. Chapter 2 describes laser assisted resonance energy transfer (LARET), a higher order perturbative contribution to the well-known process resonance energy transfer, accommodating an off resonance auxiliary laser field to stimulate the migration. Interest focuses on energy exchanges between two uncorrelated molecular species, as in a system where molecules are randomly oriented. Both phase-weighted and standard isotropic averaging are required for the calculations. Results are discussed in terms of a laser intensity-dependent mechanism. Identifying the applied field regime where LARET should prove experimentally significant, transfer rate increases of up to 30% are predicted. General results for three-center energy transfer are elucidated in chapter 3. Cooperative and accretive mechanistic pathways are identified with theory formulated to elicit their role in a variety of energy transfer phenomena and their relative dominance. In multichromophoric the interplay of such factors is analysed with regard to molecular architectures. The alignments and magnitudes of donor and acceptor transition moments and polarisabilities prove to have profound effects on achievable pooling efficiency for linear configurations. Also optimum configurations are offered. In ionic lattices, although both mechanisms play significant roles in pooling and cutting processes, only the accretive is responsible for sensitisation. The local, microscopic level results are used to gauge the lattice response, encompassing concentration and structural effects. (author)
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.
Threshold resummation and higher order effects in QCD
International Nuclear Information System (INIS)
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.
Numerical methods of higher order of accuracy for incompressible flows
Czech Academy of Sciences Publication Activity Database
Kozel, K.; Louda, Petr; Příhoda, Jaromír
2010-01-01
Roč. 80, č. 8 (2010), s. 1734-1745. ISSN 0378-4754 Institutional research plan: CEZ:AV0Z20760514 Keywords : higher order methods * upwind methods * backward-facing step Subject RIV: BK - Fluid Dynamics Impact factor: 0.812, year: 2010
Numerical modeling of higher order magnetic moments in UXO discrimination
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.
Building Higher-Order Markov Chain Models with EXCEL
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…
Inverse and higher-order processes of internal conversion
International Nuclear Information System (INIS)
Monoenergetic positron emission, nuclear excitation by positron annihilation, and nuclear excitation by free electron capture in laser-induced plasma are described as inverse internal conversion. As a higher-order process, electron bridge is considered. The experimental possibilities for the latter two processes for highly ionized ions are discussed. (author)
Developing Higher-Order Thinking Skills through WebQuests
Polly, Drew; Ausband, Leigh
2009-01-01
In this study, 32 teachers participated in a year-long professional development project related to technology integration in which they designed and implemented a WebQuest. This paper describes the extent to which higher-order thinking skills (HOTS) and levels of technology implementation (LoTI) occur in the WebQuests that participants designed.…
Multilevel Fast Multipole Method for Higher Order Discretizations
DEFF Research Database (Denmark)
Borries, Oscar Peter; Meincke, Peter; Jorgensen, Erik; Hansen, Per Christian
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...
Validating variational principle for higher order theory of gravity
Ruz, Soumendranath; Sarkar, Kaushik; Sk., Nayem; Sanyal, Abhik Kumar
2015-01-01
Metric variation of higher order theory of gravity requires to fix the Ricci scalar in addition to the metric tensor at the boundary. Fixing Ricci scalar at the boundary implies that the classical solutions are fixed once and forever to the de-Sitter or anti de-Sitter solutions. Here, we justify such requirement from the standpoint of Noether Symmetry.
Higher-Order Latent Trait Models for Cognitive Diagnosis
de la Torre, Jimmy; Douglas, Jeffrey A.
2004-01-01
Higher-order latent traits are proposed for specifying the joint distribution of binary attributes in models for cognitive diagnosis. This approach results in a parsimonious model for the joint distribution of a high-dimensional attribute vector that is natural in many situations when specific cognitive information is sought but a less informative…
Lorentz-Invariance Violation with Higher-Order Operators
Reyes, Carlos M
2016-01-01
In this work, in the light of the developments for indefinite metric theories made by Lee and Wick, we study perturbative unitarity in a Lorentz-invariance violating QED model with higher-order operators. We show that by following the Lee-Wick prescription it is possible to preserve unitarity in the model at one-loop order in the coupling.
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...
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...... finite control π-calculus in Homer....
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...
Higher-Order Coloured Unification and Natural Language Semantics
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.
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.
Visualization and processing of higher order descriptors for multi-valued data
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...
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.
Higher order QCD corrections in small x physics
International Nuclear Information System (INIS)
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 γ*γ* 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 γ*γ* 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 γγ→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.)
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.)
Robin, Jérôme D; Magdinier, Frédérique
2016-01-01
Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains. We will discuss here the impact of A-type Lamins loss on alterations of chromatin organization and formation of chromatin domains and how disorganization of the lamina contributes to the patho-physiology of premature aging syndromes. PMID:27602048
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
Higher order mode excitations in gyro-amplifiers
Nguyen, K. T.; Calame, J. P.; Danly, B. G.; Levush, B.; Garven, M.; Antonsen, T.
2001-05-01
In gyro-devices, a nonlinear output taper is often employed as the transition from the near cutoff radius of the interaction circuit to a much larger output waveguide. The tapers are usually designed to avoid passive mode conversion, and thus do not consider the effect of a bunched beam. However, recent simulations with the self-consistent MAGY code [Botton et al., IEEE Trans. Plasma Sci. 26, 882 (1998)] indicate that higher order mode interactions with the bunched electron beam can substantially compromise the mode purity of the rf output. The interaction in the taper region is traveling wave in nature, and is strongly dependent on the residual beam bunching characteristics resulting from the upstream operating mode interaction. An experiment has been performed to quantify the rf output mode content from a Ka-band gyroklystron. The agreement between salient theoretical and measured rf output characteristics confirms the existence of higher order mode excitation in output tapers as predicted by theory.
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≔uβsgnu, 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.
Higher Order Kernels and Locally Affine LDDMM Registration
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...
Promoting higher order thinking skills using inquiry-based learning
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.
Higher order moments of lensing convergence - I. Estimate from simulations
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.
Speckle reduction via higher order total variation approach.
Wensen Feng; Hong Lei; Yang Gao
2014-04-01
Multiplicative noise (also known as speckle) reduction is a prerequisite for many image-processing tasks in coherent imaging systems, such as the synthetic aperture radar. One approach extensively used in this area is based on total variation (TV) regularization, which can recover significantly sharp edges of an image, but suffers from the staircase-like artifacts. In order to overcome the undesirable deficiency, we propose two novel models for removing multiplicative noise based on total generalized variation (TGV) penalty. The TGV regularization has been mathematically proven to be able to eliminate the staircasing artifacts by being aware of higher order smoothness. Furthermore, an efficient algorithm is developed for solving the TGV-based optimization problems. Numerical experiments demonstrate that our proposed methods achieve state-of-the-art results, both visually and quantitatively. In particular, when the image has some higher order smoothness, our methods outperform the TV-based algorithms. PMID:24808350
Higher Order Feature Set For Underwater Noise Classification
Directory of Open Access Journals (Sweden)
Mohankumar K
2014-12-01
Full Text Available The development of intelligent systems for classification of underwater noise sources has been a field of research interest for decades. Such systems include the extraction of features from the received signals, followed by the application of suitable classification algorithms. Most of the existing feature extraction methods rely on the classical power spectral methods, which may fail to provide information pertaining to the deviations from linearity and Gaussianity of stochastic processes. Hence, many recent research efforts focus on higher order spectral methods in order to prevail over such limitations. This paper makes use of bispectrum, which is a higher order spectrum of order three, in order to extract a set of robust features for the classification of underwater noise sources. An SVM classifier is used for evaluating the performance of the feature set.
Numerical Analysis of Higher Order Discontinuous Galerkin Finite Element methods
Hartmann, Ralf
2008-01-01
After the introduction in Section 1 this lecture starts off with recalling well-known results from the numerical analysis of the continuous finite element methods. In particular, we recall a priori error estimates in the energy norm and the L2-norm including their proofs for higher order standard finite element methods of Poisson's equation in Section 2 and for the standard and the streamline diffusion finite element method of the linear advection equation in Section 3. ...
1957-2007: 50 Years of Higher Order Programming Languages
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 ...
Higher-Order Finite Element Modeling with Curvilinear Elements
Czech Academy of Sciences Publication Activity Database
Karban, P.; Mach, F.; Doležel, Ivo
Gliwice : Silesian University of Technology, 2011, s. 5-6. ISBN 978-83-85940-33-3. [INTERNATIONAL CONFERENCE ON FUNDAMENTALS OF ELECTROTECHNICS AND CIRCUIT THEORY /34./. Ustroň (PL), 18.05.2011-21.05.2011] R&D Projects: GA ČR(CZ) GAP102/11/0498 Institutional research plan: CEZ:AV0Z20570509 Keywords : automatic adaptivity * higher-order finite element method * curvilinear elements Subject RIV: JA - Electronics ; Optoelectronics, Electrical Engineering
Accessing higher order correlations by time-multiplexing
Avenhaus, M; Chekhova, M V; Silberhorn, C
2009-01-01
We experimentally measured higher order normalized correlation functions (nCF) of pulsed light with a time-multiplexing-detector. We demonstrate excellent performance of our device by verifying unity valued nCF up to the eight order for coherent light, and factorial dependence of the nCF for pseudo-thermal light. We applied our measurement technique to a type-II parametric downconversion source to investigate mutual two-mode correlation properties and ascertain non-classicality.
Applying quantitative semantics to higher-order quantum computing
Pagani, Michele; Selinger, Peter; Valiron, Benoît
2013-01-01
Finding a denotational semantics for higher order quantum computation is a long-standing problem in the semantics of quantum programming languages. Most past approaches to this problem fell short in one way or another, either limiting the language to an unusably small finitary fragment, or giving up important features of quantum physics such as entanglement. In this paper, we propose a denotational semantics for a quantum lambda calculus with recursion and an infinite data type, using constru...
BENDING ANALYSIS OF COMPOSITE PLATES USING HIGHER ORDER THEORY
N UPENDRA; B. Sidda Reddy; K TIRUPATI REDDY; AJAY KUMAR REDDY K
2013-01-01
In this paper, an analytical formulation and solutions are developed to investigate the bending characteristics of laminated composite plates based on higher order shear deformation theory. The equation ofmotion of laminated plates is deduced using Hamilton’s principle. Closed-form solutions are obtained by using the Navier’s technique for simply supported boundary conditions. The effect of side to thickness ratio, aspect ratio, degree of orthotropic, stacking sequence ad no of layers on defl...
The Key Exchange Cryptosystem Used With Higher Order Diophantine Equations
Harry Yosh
2011-01-01
One-way functions are widely used for encrypting the secret in public key cryptography, although they are regarded as plausibly one-way but have not been proven so. Here we discuss the public key cryptosystem based on the system of higher order Diophantine equations. In this system those Diophantine equations are used as public keys for sender and recipient, and sender can recover the secret from the Diophantine equation returned from recipient with a trapdoor. In general the system of Diopha...
Sequential High-Resolution Direction Finding From Higher Order Statistics
Birot, Gwénaël; Albera, Laurent; Chevalier, Pascal
2010-01-01
12 pages International audience The classical higher order MUSIC-like methods based on a simultaneous search for all Directions Of Arrival (DOA's) show i) a capacity for processing underdetermined mixtures of sources, ii) a high robustness with respect to both a Gaussian noise with unknown spatial coherence and modeling errors, and iii) a better resolution than algorithms based on second order statistics. However, these methods have some limits: for a finite number of samples, they show...
Higher order relativistic galaxy number counts: dominating terms
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.
Evaluation of corneal higher order aberrations in normal topographic patterns
Mirzajani, Ali; Aghataheri, Sattar; Ghoreishi, Mohammad; Jafarzadepour, Ebrahim; Mohammadinia, Mohadese
2016-01-01
Purpose This study reports the characteristics of corneal higher order aberrations (HOAs) in eyes with normal topographic pattern using the Pentacam scheimpflug system. Methods In this prospective, observational, comparative study, 165 eyes of 97 patients separated into five groups based on corneal topographic patterns were enrolled. All eyes received a comprehensive ophthalmologic examination including corneal tomographic analysis with the Pentacam system. Keratometry, corneal cylinder, and ...
Mathematical reasoning with higher-order anti-unifcation
Guhe, Markus; Pease, Alison; Smaill, Alan; Schmidt, Martin; Gust, Helmar; Kühnberger, Kai-Uwe; Krumnack, Ulf
2010-01-01
We show how heuristic-driven theory projection (HDTP, a method based on higher-order anti-unification) can be used to model analogical reasoning in mathematics. More precisely, HDTP provides the framework for a model of the inductive analogy-making process involved in establishing the fundamental concepts of arithmetic. This process is a crucial component for being able to generalise from the concrete experiences that humans have due to their embodied and embedded nature. Such generalisations...
Higher order mode dampers for the KAON booster cavity
International Nuclear Information System (INIS)
A prototype higher order mode (HOM) damper cavity has been designed and tested on a ferrite tuned booster cavity proposed for the KAON factory at TRIUMF. The damper cavity has been designed to keep the overall length minimum and has been optimized by using SUPERFISH code. Low level signal measurements of unloaded and loaded Q of the booster cavity without and with the damper cavity respectively have been reported and it has been demonstrated that nearly all modes up to 1 GHz which couple to the accelerating gap are damped by the mode damper. In order to reduce the coupling at the booster fundamental frequencies by this type of damper, a new concept of damping higher order modes in the KAON booster cavity by employing a high-pass filter is presented. Conceptual design, prototype realization of such a filter in coaxial form and measurements of damping are outlined. Preliminary measurements show that the higher order modes up to 900 MHz are damped significantly with very little power absorption at the fundamental frequencies
Painting a Clearer Picture of Chromatin.
Finn, Elizabeth H; Misteli, Tom; Shachar, Sigal
2016-02-22
Elucidating chromatin's 3D shape is critical to understanding its function, but the fine structure of chromatin domains remains poorly resolved. In a recent report in Nature, Boettiger et al. (2016) visualize chromatin in super-resolution, gaining unprecedented insight into chromatin architecture. PMID:26906730
Thakar, Amit; Sylar, Elise; Flynn, Francis W
2012-12-01
The tachykinin, neurokinin 3 receptor (NK3R) is a g-protein coupled receptor that is broadly distributed in the nervous system and exerts its diverse physiological actions through multiple signaling pathways. Despite the role of the receptor system in a range of biological functions, the effects of NK3R activation on chromatin dynamics and gene expression have received limited attention. The present work determined the effects of senktide, a selective NK3R agonist, on chromatin organization, acetylation, and gene expression, using qRT-PCR, in a hypothalamic cell line (CLU 209) that expresses the NK3R. Senktide (1 nM, 10nM) caused a relaxation of chromatin, an increase in global acetylation of histone H3 and H4, and an increase in the expression of a common set of genes involved in cell signaling, cell growth, and synaptic plasticity. Pretreatment with histone acetyltransferase (HAT) inhibitor (garcinol and 2-methylene y-butylactone), that inhibits p300, p300/CREB binding protein (CBP) associated factor (PCAF), and GCN 5, prevented the senktide-induced increase in expression of most, but not all, of the genes upregulated in response to 1 nM and 10nM senktide. Treatment with 100 nM had the opposite effect: a reduction in chromatin relaxation and decreased acetylation. The expression of four genes was significantly decreased and the HAT inhibitor had a limited effect in blocking the upregulation of genes in response to 100 nM senktide. Activation of the NK3R appears to recruit multiple pathways, including acetylation, and possibly histone deactylases, histone methylases, or DNA methylases to affect chromatin structure and gene expression. PMID:22985858
International Nuclear Information System (INIS)
Inhibition of herpes simplex virus (HSV) thymidine kinase (TK) gene transcription (pHSV-106, pML-BPV-TK4) by DNA methylation is an indirect effect, which occurs with a latency period of ∼ 8 hr microinjection of the DNA into TK- rat 2 and mouse LTK- cells. The authors have strong evidence that chromatin formation is critical for the transition of the injected DNA from methylation insensitivity to methylation sensitivity. Chromatin was reconstituted in vitro by using methylated and mock-methylated HSV TK DNA and purified chicken histone octamers. After microinjection, the methylated chromatin was always biologically inactive, as tested by autoradiography of the cells after incubation with [3H]thymidine and by RNA dot blot analysis. However, in transformed cell lines, reactivation of the methylated chromatic occurred after treatment with 5-azacytidine. Furthermore, integration of the TK chromatin into the host genome is not required to block expression of the methylated TK gene. Mouse cells that contained the pML-BPV-TK4 chromatin permanently in an episomal state also did not support TK gene expression as long as the TK DNA remained methylated
International Nuclear Information System (INIS)
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
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
Shimada, T.; Inokuchi, K; Nienhuis, A W
1987-01-01
The effect of in vitro methylation on the function and chromatin structure of the human dihydrofolate reductase (DHFR) promoter linked to the DHFR coding sequences (minigene) was studied after DNA-mediated gene transfer into DHFR- CHO cells. Methylation of HhaI sites reduced the transforming frequency to about 10% of control, whereas methylation of HpaII sites had a less significant effect. The integrated genes were demethylated at specific sites in the promoter sequence, namely, HpaII sites ...
Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics
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.
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
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.
Higher order bulk characteristic parameters of asymmetric nuclear matter
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
The bulk parameters characterizing the energy of symmetric nuclear matter and the symmetry energy defined at normal nuclear density ρ0 provide important information on the equation of state (EOS) of isospin asymmetric nuclear matter. While significant progress has been made in determining some lower order bulk characteristic parameters, such as the energy E0(ρ0) and incompress ibility K0 of symmetric nuclear matter as well as the symmetry energy Esym(ρ0) and its slope parameter L, yet the higher order bulk characteristic parameters are still poorly known. Here, we analyze the correlations between the lower and higher order bulk char acteristic parameters within the framework of Skyrme Hartree-Fock energy density functional and then estimate the values of some higher order bulk characteristic parameters. In particular, we obtain J0 = (-355±95) MeV and I0 = (1473±680) MeV for the third order and fourth-order derivative parameters of symmetric nuclear matter at ρ0 and Ksym = (-100 ± 165) MeV, Jsym = (224 ± 385) MeV, Isym = (-1309 ± 2025) MeV for the curvature parameter, third-order and fourth-order derivative parameters of the symmetry energy at ρ0, using the empirical constraints on E0(ρ0), K0, Esym(ρ0), L, and the isoscalar and isovector nucleon effective masses. Furthermore, our results indicate that the three parameters E0(ρ0), K0, and J0 can reasonably characterize the EOS of symmetric nuclear matter up to 2ρ0 while the symmetry energy up to 2ρ0 can be well described by Esym(ρ0), L, and Ksym.
PARP-1 Regulates Chromatin Structure and Transcription Through a KDM5B-Dependent Pathway
Krishnakumar, Raga; Kraus, W. Lee
2010-01-01
PARP-1 is an abundant nuclear enzyme that regulates gene expression, although the underlying mechanisms are unclear. We examined the interplay between PARP-1, histone 3 lysine 4 trimethylation (H3K4me3), and linker histone H1 in the chromatin-dependent control of transcription. We show that PARP-1 is required for a series of molecular outcomes at the promoters of PARP-1 regulated genes, leading to a permissive chromatin environment that allows loading of the RNA Pol II machinery. PARP-1 does ...
Relations in Higher-Order Fuzzy Logic I,II
Czech Academy of Sciences Publication Activity Database
Běhounek, Libor; Cintula, Petr
Linz : Johannes Kepler Universität, 2005 - (Gottwald, S.; Hájek, P.; Höhle, U.; Klement, E.). s. 10-15 [Linz Seminar on Fuzzy Set Theory /26./. 01.02.2005-05.02.2005, Linz] R&D Projects: GA MŠk OC 274.001; GA AV ČR KJB100300502 Grant ostatní: COST(XE) Action 274 TARSKI Institutional research plan: CEZ:AV0Z10300504 Keywords : formal fuzzy logic * fuzzy set * foundations of fuzzy mathematics * LPi logic * higher-order fuzzy logic * fuzzy type theory * multi-sorted fuzzy logic Subject RIV: BA - General Mathematics
The Complexity of Model Checking Higher-Order Fixpoint Logic
DEFF Research Database (Denmark)
Axelsson, Roland; Lange, Martin; Somla, Rafal
2007-01-01
Higher Order Fixpoint Logic (HFL) is a hybrid of the simply typed λ-calculus and the modal μ-calculus. This makes it a highly expressive temporal logic that is capable of expressing various interesting correctness properties of programs that are not expressible in the modal μ-calculus. This paper...... of solving rather large parity games of small index. As a consequence of this we obtain an ExpTime upper bound on the expression complexity of each HFLk,m. The lower bound is established by a reduction from the word problem for alternating (k-1)-fold exponential space bounded Turing Machines. As a...
The commutativity of quantized first- and higher-order Hamiltonians
International Nuclear Information System (INIS)
The key point of the Hamiltonian formalism of Toda molecules is the commutativity of the Hamiltonians (tr yk, tr yl)=0, where y in GL(n) and (,) is a Poisson bracket associated with the classical r-matrix. To quantize the Toda molecule, we have to consider the q-analogue of the above formula. In this paper, we show the commutativity of the quantized first- and higher-order Hamiltonians (trq Xm, trq X)=0, where X is a matrix of quantum group GLq(n). (author)
Higher Order Aberration and Astigmatism in Children with Hyperopic Amblyopia
Choi, Seung Kwon; Chang, Ji Woong
2016-01-01
Purpose To investigate the changes in corneal higher-order aberration (HOA) during amblyopia treatment and the correlation between HOA and astigmatism in hyperopic amblyopia children. Methods In this retrospective study, a total of 72 eyes from 72 patients ranging in age from 38 to 161 months were included. Patients were divided into two groups based on the degree of astigmatism. Corneal HOA was measured using a KR-1W aberrometer at the initial visit and at 3-, 6-, and 12-month follow-ups. Co...
Initial Semantics for higher-order typed syntax in Coq
Benedikt Ahrens; Julianna Zsido
2010-01-01
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 rep...
Higher-Order Separation Logic in Isabelle/HOLCF
DEFF Research Database (Denmark)
Varming, Carsten; Birkedal, Lars
2008-01-01
language. This follows the definitional approach common in HOL theorem provers, i.e., the soundness of our model only relies on the soundness of Isabelle/HOL [6]. We use our formalization to give a formally verified proof of Cheney's copying garbage collector [4] using a tagged representation of objects....... The proof generalizes the results in [2]. The proof uses an encoding of the separation logic formula this(h) to capture the heap from before the garbage collection and thus shows another novel use of higher-order separation logic....
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...
BENDING ANALYSIS OF COMPOSITE PLATES USING HIGHER ORDER THEORY
Directory of Open Access Journals (Sweden)
N UPENDRA
2013-10-01
Full Text Available In this paper, an analytical formulation and solutions are developed to investigate the bending characteristics of laminated composite plates based on higher order shear deformation theory. The equation ofmotion of laminated plates is deduced using Hamilton’s principle. Closed-form solutions are obtained by using the Navier’s technique for simply supported boundary conditions. The effect of side to thickness ratio, aspect ratio, degree of orthotropic, stacking sequence ad no of layers on deflection and stresses are investigated. The results predicted by the present theory are in good agreement with the solutions of other plate theories available in the literature.
Practical Programming with Higher-Order Encodings and Dependent Types
DEFF Research Database (Denmark)
Poswolsky, Adam; Schürmann, Carsten
2008-01-01
, 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...... for instantiation from those that will remain uninstantiated, utilizing a variation of Miller and Tiu’s ∇-quantifier [1]....
Modeling Human Behaviour with Higher Order Logic: Insider Threats
DEFF Research Database (Denmark)
Boender, Jaap; Ivanova, Marieta Georgieva; Kammuller, Florian;
2014-01-01
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......In this paper, we approach the problem of modeling the human component in technical systems with a view on the difference between the use of model and theory in sociology and computer science. One aim of this essay is to show that building of theories and models for sociology can be compared to and...
Tight focusing of higher orders Laguerre-Gaussian modes
Savelyev, Dmitry A.; Khonina, Svetlana N.; Golub, Ilya
2016-04-01
The spatial redistribution of the contribution of different electric field components provides a decrease in the size of the central focal spot for higher orders Laguerre-Gaussian modes. It was shown that when sharply focusing laser beams with vortex or special binary phase plate, a sub-wavelength light localization of separate vector field components is possible for any polarization type. This fact should be considered for the interaction of laser radiation with materials selectively sensitive to lateral and longitudinal components of the electromagnetic field.
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.
Isotropic stars in higher-order torsion scalar theories
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.
Programming real-time executives in higher order language
Foudriat, E. C.
1982-01-01
Methods by which real-time executive programs can be implemented in a higher order language are discussed, using HAL/S and Path Pascal languages as program examples. Techniques are presented by which noncyclic tasks can readily be incorporated into the executive system. Situations are shown where the executive system can fail to meet its task scheduling and yet be able to recover either by rephasing the clock or stacking the information for later processing. The concept of deadline processing is shown to enable more effective mixing of time and information synchronized systems.
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.
Inhibitory control gains from higher-order cognitive strategy training.
Motes, Michael A; Gamino, Jacquelyn F; Chapman, Sandra B; Rao, Neena K; Maguire, Mandy J; Brier, Matthew R; Kraut, Michael A; Hart, John
2014-02-01
The present study examined the transfer of higher-order cognitive strategy training to inhibitory control. Middle school students enrolled in a comprehension- and reasoning-focused cognitive strategy training program and passive controls participated. The training program taught students a set of steps for inferring essential gist or themes from materials. Both before and after training or a comparable duration in the case of the passive controls, participants completed a semantically cued Go/No-Go task that was designed to assess the effects of depth of semantic processing on response inhibition and components of event-related potentials (ERP) related to response inhibition. Depth of semantic processing was manipulated by varying the level of semantic categorization required for response selection and inhibition. The SMART-trained group showed inhibitory control gains and changes in fronto-central P3 ERP amplitudes on inhibition trials; whereas, the control group did not. The results provide evidence of the transfer of higher-order cognitive strategy training to inhibitory control and modulation of ERPs associated with semantically cued inhibitory control. The findings are discussed in terms of implications for cognitive strategy training, models of cognitive abilities, and education. PMID:24286804
Orchestration of Molecular Information through Higher Order Chemical Recognition
Frezza, Brian M.
Broadly defined, higher order chemical recognition is the process whereby discrete chemical building blocks capable of specifically binding to cognate moieties are covalently linked into oligomeric chains. These chains, or sequences, are then able to recognize and bind to their cognate sequences with a high degree of cooperativity. Principally speaking, DNA and RNA are the most readily obtained examples of this chemical phenomenon, and function via Watson-Crick cognate pairing: guanine pairs with cytosine and adenine with thymine (DNA) or uracil (RNA), in an anti-parallel manner. While the theoretical principles, techniques, and equations derived herein apply generally to any higher-order chemical recognition system, in practice we utilize DNA oligomers as a model-building material to experimentally investigate and validate our hypotheses. Historically, general purpose information processing has been a task limited to semiconductor electronics. Molecular computing on the other hand has been limited to ad hoc approaches designed to solve highly specific and unique computation problems, often involving components or techniques that cannot be applied generally in a manner suitable for precise and predictable engineering. Herein, we provide a fundamental framework for harnessing high-order recognition in a modular and programmable fashion to synthesize molecular information process networks of arbitrary construction and complexity. This document provides a solid foundation for routinely embedding computational capability into chemical and biological systems where semiconductor electronics are unsuitable for practical application.
On theories of gravitation with higher-order field equations
International Nuclear Information System (INIS)
Weyl and Eddington suggested three alternative general relativistic theories of gravitation with fourth-order field equations which in empty space admit the Schwarzschild metric as a solution. These theories, like Einstein's, follow from a variational principle and thus imply differential identities. If, as in Einstein's theory the sources are taken to be proportional to the energy-momentum tensor Tsup(μν), these identities imply the vanishing of the covariant divergence of Tsup(μν). It is shown here that in the presence of extended sources, Weyl's and Eddington's theories (as well as all other higher-order metric theories derivable from an action principle) contradict Newton's law of gravitation in the nonrelativistic limit. To entail this law would require a modification of the source term of the field equations which in general is not compatible with Tsup(μν)sub(;ν) = 0; alternatively, one could require only asymptotic agreement with Newton's law, which is compatable with supplementary higher-order terms in Einstein's equations, but which requires the introduction of universal constants of the dimensions of length. None of the generalizations of Einstein's equations considered here admits Birkhoff's theorem. (author)
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.
Chromatin structure of Asparagales telomeres - old story with a new end?
Czech Academy of Sciences Publication Activity Database
Sýkorová, Eva; Skleničková, Marie; Lim, K. Y.; Leitch, A. R.; Fajkus, Jiří
London: Biochemical Society, 2004. s. 17. [EMBO Workshop / Harden Conference /58./ - Telemeres and Genome Stability . 03.04.2004-07.04.2004, Cambridge] R&D Projects: GA ČR GA204/02/0027; GA ČR GP204/04/P105 Keywords : alternative telomeres in plants * chromatin * nucleosome Subject RIV: BO - Biophysics
Directory of Open Access Journals (Sweden)
Benjamin Staude
2010-07-01
Full Text Available The extent to which groups of neurons exhibit higher-order correlations in their spiking activity is a controversial issue in current brain research. A major difficulty is that currently available tools for the analysis of massively parallel spike trains (N>10 for higher-order correlations typically require vast sample sizes. While multiple single-cell recordings become increasingly available, experimental approaches to investigate the role of higher-order correlations suffer from the limitations of available analysis techniques. We have recently presented a novel method for cumulant-based inference of higher-order correlations (CuBIC that detects correlations of higher order even from relatively short data stretches of length T=10-100 s. CuBIC employs the compound Poisson process (CPP as a statistical model for the population spike counts, and assumes spike trains to be stationary in the analyzed data stretch. In the present study, we describe a non-stationary version of the CPP by decoupling the correlation structure from the spiking intensity of the population. This allows us to adapt CuBIC to time-varying firing rates. Numerical simulations reveal that the adaptation corrects for false positive inference of correlations in data with pure rate co-variation, while allowing for temporal variations of the firing rates has a surprisingly small effect on CuBICs sensitivity for correlations.
Interactions and Strings in Higher Order Anisotropic and Inhomogeneous Superspaces and Isospaces
Vacaru, S I
1997-01-01
The monograph gives a general geometric background of the theory of field interactions, strings and diffusion processes on spaces, superspaces and isospaces with higher order anisotropy and inhomogenity. Our approach proceeds by developing the concept of higher order anisotropic superspace which unify the logical and mathematical aspects of modern Kaluza-Klein theories and generalized Lagrange and Finsler geometry and leads to modelling of physical processes on higher order fiber bundles provided with nonlinear and distingushed connections and metric structures. The view adopted in the monograph is that a general field theory should incorporate all possible anisotropic and stochastic manifestations of classical and quantum interactions and, in consequence, a corresponding modification of basic principles and mathematical methods in formulation of physical theories. This book can be also considered as a pedagogical survey on the mentioned subjects.
Rapidity window dependences of higher order cumulants and diffusion master equation
International Nuclear Information System (INIS)
We study the rapidity window dependences of higher order cumulants of conserved charges observed in relativistic heavy ion collisions. The time evolution and the rapidity window dependence of the non-Gaussian fluctuations are described by the diffusion master equation. Analytic formulas for the time evolution of cumulants in a rapidity window are obtained for arbitrary initial conditions. We discuss that the rapidity window dependences of the non-Gaussian cumulants have characteristic structures reflecting the non-equilibrium property of fluctuations, which can be observed in relativistic heavy ion collisions with the present detectors. It is argued that various information on the thermal and transport properties of the hot medium can be revealed experimentally by the study of the rapidity window dependences, especially by the combined use, of the higher order cumulants. Formulas of higher order cumulants for a probability distribution composed of sub-probabilities, which are useful for various studies of non-Gaussian cumulants, are also presented
The higher order Rogue Wave solutions of the Gerdjikov-Ivanov equation
Guo, Lijuan; Zhang, Yongshuai; Xu, Shuwei; Wu, Zhiwei; He, Jingsong(Department of Mathematics and Ningbo Collabrative Innovation Center of Nonlinear Harzard System of Ocean and Atmosphere, Ningbo University, Ningbo 315211, China)
2013-01-01
We construct higher order rogue wave solutions for the Gerdjikov-Ivanov equation explicitly in term of determinant expression. Dynamics of both soliton and non-soliton solutions is discussed. A family of solutions with distinct structures are presented, which are new to the Gerdjikov-Ivanov equation.
Higher order modes and multipactor discharge in superconducting cavity of eLINAC accelerator
International Nuclear Information System (INIS)
The dependence of electrodynamic characteristics of higher order modes on the geometric sizes of last cells of the structure and beam channel tubes has been investigated. The sizes that allow reducing the influence of locked modes have been obtained. A multipactor discharge in a single-cell test cavity has been studied
Visualizing Higher Order Finite Elements: FY05 Yearly Report.
Energy Technology Data Exchange (ETDEWEB)
Thompson, David; Pebay, Philippe Pierre
2005-11-01
This report contains an algorithm for decomposing higher-order finite elementsinto regions appropriate for isosurfacing and proves the conditions under which thealgorithm will terminate. Finite elements are used to create piecewise polynomialapproximants to the solution of partial differential equations for which no analyticalsolution exists. These polynomials represent fields such as pressure, stress, and mo-mentim. In the past, these polynomials have been linear in each parametric coordinate.Each polynomial coefficient must be uniquely determined by a simulation, and thesecoefficients are called degrees of freedom. When there are not enough degrees of free-dom, simulations will typically fail to produce a valid approximation to the solution.Recent work has shown that increasing the number of degrees of freedom by increas-ing the order of the polynomial approximation (instead of increasing the number offinite elements, each of which has its own set of coefficients) can allow some typesof simulations to produce a valid approximation with many fewer degrees of freedomthan increasing the number of finite elements alone. However, once the simulation hasdetermined the values of all the coefficients in a higher-order approximant, tools donot exist for visual inspection of the solution.This report focuses on a technique for the visual inspection of higher-order finiteelement simulation results based on decomposing each finite element into simplicialregions where existing visualization algorithms such as isosurfacing will work. Therequirements of the isosurfacing algorithm are enumerated and related to the placeswhere the partial derivatives of the polynomial become zero. The original isosurfacingalgorithm is then applied to each of these regions in turn.3 AcknowledgementThe authors would like to thank David Day and Louis Romero for their insight into poly-nomial system solvers and the LDRD Senior Council for the opportunity to pursue thisresearch. The authors were
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 in...... a simple and general way the radiation of KdV and NS, as well as other types. of solitons, is developed. From the WKB approach it follows that the soliton radiation is a result of a tunneling transformation of the non-linearly self-trapped wave into the free-propagating radiation....
MHD stability analysis using higher order spline functions
International Nuclear Information System (INIS)
The eigenvalue problem of the linearized magnetohydrodynamic (MHD) equation is formulated by using higher order spline functions as the base functions of Ritz-Galerkin approximation. When the displacement vector normal to the magnetic surface (in the magnetic surface) is interpolated by B-spline functions of degree p1 (degree p2), which is continuously c1-th (c2-th) differentiable on neighboring finite elements, the sufficient conditions for the good approximation is given by p1≥p2+1, c1≤c2+1, (c1≥1, p2≥c2≥0). The influence of the numerical integration upon the convergence of calculated eigenvalues is discussed. (author)
Relations in Higher-order Fuzzy Logic III
Czech Academy of Sciences Publication Activity Database
Bodenhofer, U.; Běhounek, Libor; Cintula, Petr
Linz : Johannes Kepler Universität, 2005 - (Gottwald, S.; Hájek, P.; Höhle, U.; Klement, E.). s. 20-22 [Linz Seminar on Fuzzy Set Theory /26./. 01.02.2005-05.02.2005, Linz] R&D Projects: GA MŠk OC 274.001; GA AV ČR KJB100300502; GA ČR GD401/03/H047 Grant ostatní: COST(XE) Action 274 TARSKI Institutional research plan: CEZ:AV0Z10300504 Source of funding: V - iné verejné zdroje Keywords : formal fuzzy logic * fuzzy set * foundations of fuzzy mathematics * LPi logic * higher-order fuzzy logic * fuzzy type theory * multi-sorted fuzzy logic Subject RIV: BA - General Mathematics
Special issue of Higher-Order and Symbolic Computation
DEFF Research Database (Denmark)
Danvy, Olivier
the development of new techniques for the derivation of algorithms and programs using the transformational methodology. Starting from specifications written in a set theoretical language, using suitable algebraic or logical formulas, the programmer should transform them, possibly in various steps....... Leonard and Heitmeyer’s contribution in this issue). Only general techniques may become part of a new programming methodology and this was what, ultimately, Bob was looking for and wanted to propose. Bob’s colleagues and friends are all very happy to have been working and sharing ideas with him. In...... 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...
Scalar brane backgrounds in higher order curvature gravity
Charmousis, C; Dufaux, J F; Charmousis, Christos; Davis, Stephen C.; Dufaux, Jean-Francois
2003-01-01
We investigate maximally symmetric brane world solutions with a scalar field. Five-dimensional bulk gravity is described by a general lagrangian which yields field equations containing no higher than second order derivatives. This includes the Gauss-Bonnet combination for the graviton. Stability and gravitational properties of such solutions are considered, and we particularily emphasise the modifications induced by the higher order terms. In particular it is shown that higher curvature corrections to Einstein theory can give rise to instabilities in brane world solutions. A method for analytically obtaining the general solution for such actions is outlined. Genericaly, the requirement of a finite volume element together with the absence of a naked singularity in the bulk imposes fine-tuning of the brane tension. A model with a moduli scalar field is analysed in detail and we address questions of instability and non-singular self-tuning solutions. In particular, we discuss a case with a normalisable zero mode...
SPHS: Smoothed Particle Hydrodynamics with a higher order dissipation switch
Read, J I
2011-01-01
We present a novel implementation of Smoothed Particle Hydrodynamics (SPHS) that uses the spatial derivative of the velocity divergence as a higher order dissipation switch. Our switch -- which is second order accurate -- detects flow convergence before it occurs. If particle trajectories are going to cross, we switch on the usual SPH artificial viscosity, as well as conservative dissipation in all advected fluid quantities (for example, the entropy). The viscosity and dissipation terms (that are numerical errors) are designed to ensure that all fluid quantities remain single-valued as particles approach one another, to respect conservation laws, and to vanish on a given physical scale as the resolution is increased. SPHS alleviates a number of known problems with `classic' SPH, successfully resolving mixing, and recovering numerical convergence with increasing resolution. An additional key advantage is that -- treating the particle mass similarly to the entropy -- we are able to use multimass particles, givi...
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.
MHD stability analysis using higher order spline functions
Energy Technology Data Exchange (ETDEWEB)
Ida, Akihiro [Department of Energy Engineering and Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi (Japan); Todoroki, Jiro; Sanuki, Heiji
1999-04-01
The eigenvalue problem of the linearized magnetohydrodynamic (MHD) equation is formulated by using higher order spline functions as the base functions of Ritz-Galerkin approximation. When the displacement vector normal to the magnetic surface (in the magnetic surface) is interpolated by B-spline functions of degree p{sub 1} (degree p{sub 2}), which is continuously c{sub 1}-th (c{sub 2}-th) differentiable on neighboring finite elements, the sufficient conditions for the good approximation is given by p{sub 1}{>=}p{sub 2}+1, c{sub 1}{<=}c{sub 2}+1, (c{sub 1}{>=}1, p{sub 2}{>=}c{sub 2}{>=}0). The influence of the numerical integration upon the convergence of calculated eigenvalues is discussed. (author)
A higher-order Robert-Asselin type time filter
Li, Yong; Trenchea, Catalin
2014-02-01
The Robert-Asselin (RA) time filter combined with leapfrog scheme is widely used in numerical models of weather and climate. It successfully suppresses the spurious computational mode associated with the leapfrog method, but it also weakly dampens the physical mode and degrades the numerical accuracy. The Robert-Asselin-Williams (RAW) time filter is a modification of the RA filter that reduces the undesired numerical damping of RA filter and increases the accuracy. We propose a higher-order Robert-Asselin (hoRA) type time filter which effectively suppresses the computational modes and achieves third-order accuracy with the same storage requirement as RAW filter. Like RA and RAW filters, the hoRA filter is non-intrusive, and so it would be easily implementable. The leapfrog scheme with hoRA filter is almost as accurate, stable and efficient as the intrusive third-order Adams-Bashforth (AB3) method.
Inflationary scenarios in Starobinsky model with higher order corrections
Artymowski, Michal; Lewicki, Marek
2015-01-01
We consider the Starobinsky inflation with a set of higher order corrections parametrised by two real coefficients $\\lambda_1, \\lambda_2$. 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 $\\lambda_i$ 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.
SU(2) higher-order effective quark interactions from polarization
Braghin, Fábio L
2016-01-01
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 fifh 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. ${\\cal O}(\\bpsi \\psi)^{2 n}$ ($n=1,2,3,..$), and chiral symmetry breaking terms emerge as ${\\cal O}(\\bpsi \\psi)^{n}$.
Higher-Order Finite Element Solutions of Option Prices
DEFF Research Database (Denmark)
Raahauge, Peter
2004-01-01
Kinks and jumps in the payoff function of option contracts prevent an effectiveimplementation of higher-order numerical approximation methods. Moreover, thederivatives (the greeks) are not easily determined around such singularities, even withstandard lower-order methods. This paper suggests a...... transformation to turn the originalill-conditioned pricing problem into a well-behaved numerical problem. For astandard test case, both vanilla- and binary call price functions are approximated with(tensor) B-splines of up to 10'th order. Polynomial convergence rates of orders up toapproximately 10 are obtained...... for prices as well as for first and second order derivatives(delta and gamma). Unlike similar studies, numerical approximation errors aremeasured both as weighted averages and in the supnorm over a state space includingtime-to-maturities down to a split second.KEYWORDS: Numerical option pricing...
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.
The Key Exchange Cryptosystem Used With Higher Order Diophantine Equations
Directory of Open Access Journals (Sweden)
Harry Yosh
2011-03-01
Full Text Available One-way functions are widely used for encrypting the secret in public key cryptography, although theyare regarded as plausibly one-way but have not been proven so.Here we discuss the public key cryptosystem based on the system of higher order Diophantine equations.In this system those Diophantine equations are used as public keys for sender and recipient, and bothsender and recipient can obtain the shared secret through a trapdoor, while attackers must solve thoseDiophantine equations without trapdoor. Thus the scheme of this cryptosystem might be considered torepresent a possible one-way function.We also discuss the problem on implementation, which is caused from additional complexity necessaryfor constructing Diophantine equations in order to prevent from attacking by tamperers.
Higher order correlation beams in atmosphere under strong turbulence conditions.
Avetisyan, H; Monken, C H
2016-02-01
Higher order correlation beams, that is, two-photon beams obtained from the process of spontaneous parametric down-conversion pumped by Hermite-Gauss or Laguerre-Gauss beams of any order, can be used to encode information in many modes, opening the possibility of quantum communication with large alphabets. In this paper we calculate, analytically, the fourth-order correlation function for the Hermite-Gauss and Laguerre-Gauss coherent and partially coherent correlation beams propagating through a strong turbulent medium. We show that fourth-order correlation functions for correlation beams have, under certain conditions, expressions similar to those of intensities of classical beams and are degraded by turbulence in a similar way as the classical beams. Our results can be useful in establishing limits for the use of two-photon beams in quantum communications with larger alphabets under atmospheric turbulence. PMID:26906808
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.
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.
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.
A Hypergraph-Based Reduction for Higher-Order Binary Markov Random Fields.
Fix, Alexander; Gruber, Aritanan; Boros, Endre; Zabih, Ramin
2015-07-01
Higher-order Markov Random Fields, which can capture important properties of natural images, have become increasingly important in computer vision. While graph cuts work well for first-order MRF's, until recently they have rarely been effective for higher-order MRF's. Ishikawa's graph cut technique [1], [2] shows great promise for many higher-order MRF's. His method transforms an arbitrary higher-order MRF with binary labels into a first-order one with the same minima. If all the terms are submodular the exact solution can be easily found; otherwise, pseudoboolean optimization techniques can produce an optimal labeling for a subset of the variables. We present a new transformation with better performance than [1], [2], both theoretically and experimentally. While [1], [2] transforms each higher-order term independently, we use the underlying hypergraph structure of the MRF to transform a group of terms at once. For n binary variables, each of which appears in terms with k other variables, at worst we produce n non-submodular terms, while [1], [2] produces O(nk). We identify a local completeness property under which our method perform even better, and show that under certain assumptions several important vision problems (including common variants of fusion moves) have this property. We show experimentally that our method produces smaller weight of non-submodular edges, and that this metric is directly related to the effectiveness of QPBO [3]. Running on the same field of experts dataset used in [1], [2] we optimally label significantly more variables (96 versus 80 percent) and converge more rapidly to a lower energy. Preliminary experiments suggest that some other higher-order MRF's used in stereo [4] and segmentation [5] are also locally complete and would thus benefit from our work. PMID:26352447
Topoisomerase II–DNA complexes trapped by ICRF-193 perturb chromatin structure
Germe, Thomas; Hyrien, Olivier
2005-01-01
DNA topoisomerase II (topo II) is involved in unlinking replicating DNA and organizing mitotic chromosomes. Topo II is the target of many antitumour drugs. Topo II inhibition results in extensive catenation of newly replicated DNA and may potentially perturb chromatin assembly. Here, we show that the topo II inhibitor ICRF-193 does not prevent the bulk of nucleosome deposition, but perturbs nucleosome spacing in Xenopus egg extracts. This is due to the trapping of topo II-closed clamps on the...
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
Higher-Order Finite Elements for Computing Thermal Radiation
Gould, Dana C.
2004-01-01
Two variants of the finite-element method have been developed for use in computational simulations of radiative transfers of heat among diffuse gray surfaces. Both variants involve the use of higher-order finite elements, across which temperatures and radiative quantities are assumed to vary according to certain approximations. In this and other applications, higher-order finite elements are used to increase (relative to classical finite elements, which are assumed to be isothermal) the accuracies of final numerical results without having to refine computational meshes excessively and thereby incur excessive computation times. One of the variants is termed the radiation sub-element (RSE) method, which, itself, is subject to a number of variations. This is the simplest and most straightforward approach to representation of spatially variable surface radiation. Any computer code that, heretofore, could model surface-to-surface radiation can incorporate the RSE method without major modifications. In the basic form of the RSE method, each finite element selected for use in computing radiative heat transfer is considered to be a parent element and is divided into sub-elements for the purpose of solving the surface-to-surface radiation-exchange problem. The sub-elements are then treated as classical finite elements; that is, they are assumed to be isothermal, and their view factors and absorbed heat fluxes are calculated accordingly. The heat fluxes absorbed by the sub-elements are then transferred back to the parent element to obtain a radiative heat flux that varies spatially across the parent element. Variants of the RSE method involve the use of polynomials to interpolate and/or extrapolate to approximate spatial variations of physical quantities. The other variant of the finite-element method is termed the integration method (IM). Unlike in the RSE methods, the parent finite elements are not subdivided into smaller elements, and neither isothermality nor other
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
Higher order effects in electroweak theory 1981-12 (KEK)
International Nuclear Information System (INIS)
This is a brief report on the higher order or loop effects in electroweak theory. The discussion is based on the Weinberg Salam model and QCD. The loop correction to weak interaction is described. The renormalization conditions were applied to physical parameters, α(QED), M(W) and M(Z). It is expected to obtain experimentally the values of M(W) and M(Z) with the accuracy of 0.1 percent. In this scheme, the parameters were fixed loop by loop. The correction was evaluated along the present on-shell scheme. The general estimation of the order of correction was performed. The evaluation of the size of terms in one-loop correction was made. The examples of one loop analysis are presented. The leading logarithmic correction such as α ln(m2 q2/M2) is discussed. The system was described by H(eff) with the local operator O(i), in which the propagator of heavy particles was contracted. The effective interaction was obtained as C(i) (q2) O(i), where C(i)(q2) satisfies a proper equation of a renormalization group. As the practical examples, μ-decay, charged current and neutral current were studied. The correction to electron neutral current and the shift of M(W) and M(Z) were numerically obtained. Comments on quark mass and the uncertainty of sin2(theta) from the νN reaction are presented. (Kato, T.)
Invariants of Velocities, and Higher Order Grassmann Bundles
Grigore, D R; Grigore, Dan Radu; Krupka, Demeter
1997-01-01
An $(r,n)$-velocity is an $r$-jet with source at $0 \\in \\R^n$, and target in a manifold $Y$. An $(r,n)$-velocity is said to be regular, if it has a representative which is an immersion at $0 \\in \\R^{n}$. The manifold $T^{r}_{n}Y$ of $(r,n)$-velocities as well as its open, $L^{r}_{n}$-invariant, dense submanifold $\\Imm T^{r}_{n}Y$ of regular $(r,n)$-velocities, are endowed with a natural action of the differential group $L^{r}_{n}$ of invertible $r$-jets with source and target $0 \\in \\R^{n}$. In this paper, we describe all continuous, $L^{r}_{n}$-invariant, real-valued functions on $T^{r}_{n}Y$ and T^{r}_{n}Y$ in an explicit, recurrent form. To this purpose, higher order Grassmann bundles are considered as the corresponding quotients $P^{r}_{n}Y = that nontrivial $L^{r}_{n}$-invariants on $\\Imm T^{r}_{n}Y$ cannot be continuously extended onto $T^{r}_{n}Y$.
SPHS: smoothed particle hydrodynamics with a higher order dissipation switch
Read, J. I.; Hayfield, T.
2012-06-01
We present a novel implementation of smoothed particle hydrodynamics that uses the spatial derivative of the velocity divergence as a higher order dissipation switch. Our switch - which is second order accurate - detects flow convergence before it occurs. If particle trajectories are going to cross, we switch on the usual SPH artificial viscosity, as well as conservative dissipation in all advected fluid quantities (e.g. the entropy). The viscosity and dissipation terms (that are numerical errors) are designed to ensure that all fluid quantities remain single valued as particles approach one another, to respect conservation laws, and to vanish on a given physical scale as the resolution is increased. SPHS alleviates a number of known problems with 'classic' SPH, successfully resolving mixing, and recovering numerical convergence with increasing resolution. An additional key advantage is that - treating the particle mass similarly to the entropy - we are able to use multimass particles, giving significantly improved control over the refinement strategy. We present a wide range of code tests including the Sod shock tube, Sedov-Taylor blast wave, Kelvin-Helmholtz Instability, the 'blob test' and some convergence tests. Our method performs well on all tests, giving good agreement with analytic expectations.
Higher-order Statistics of Weak Lensing Shear and Flexion
Munshi, Dipak; Heavens, Alan; Coles, Peter; Cooray, Asantha
2010-01-01
Owing to their more extensive sky coverage and tighter control on systematic errors, future deep weak lensing surveys should provide a better statistical picture of the dark matter clustering beyond the level of the power spectrum. In this context, the study of non-Gaussianity induced by gravity can help tighten constraints on the background cosmology by breaking parameter degeneracies, as well as throwing light on the nature of dark matter, dark energy or alternative gravity theories. Analysis of the shear or flexion properties of such maps is more complicated than the simpler case of the convergence due to the spinorial nature of the fields involved. Here we develop analytical tools for the study of higher-order statistics such as the bispectrum (or trispectrum) directly using such maps at different source redshift. The statistics we introduce can be constructed from cumulants of the shear or flexions, involving the cross-correlation of squared and cubic maps at different redshifts. Typically, the low signa...
Comparison of higher order moment spectrum estimation techniques
McAloon, Jeffrey F.
1993-09-01
This thesis compares the detection performance of the 1-1/2 D instantaneous power spectrum (1-1/2 D (sub ips)), the bispectrum, the instantaneous higher-order moment slice (IHOMS) method, and the spectrogram for multi-component stationary signals, harmonically related stationary signals, and multi-component linear FM signals corrupted by additive white Gaussian noise. In addition, a determination of the relative processing gain between the 1-1/2 D(sub ips) method and the spectrogram is made for stationary signals in noise. The results of this thesis show that 1-1/2 D(sub ips) has a processing gain advantage over that of the spectrogram for a range of input SNR that depends upon the size of the data window. Under some conditions, the bispectrum can detect both harmonic coupling and phase coupling between the components of multi-component signals. IHOMS' ability to detect linear chirps in noise is limited to chirps having different slew rates, and the method has a significantly greater computational cost than both the spectrogram and 1- 1/2 D(sub ips).
Higher Order Modes Excitation of Micro Cantilever Beams
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.
Higher order finite element analysis of thick composite laminates
Goering, J.; Kim, H. J.
1992-01-01
A higher order, sub-parametric, laminated, 3D solid finite element was used for the analysis of very thick laminated composite plates. The geometry of this element is defined by four nodes in the X-Y plane which define a prism of material through the thickness of the laminate. There are twenty-four degrees of freedom at each node; translations at the upper and lower surfaces of the laminate in each of the three coordinate directions, and the derivatives of these translations with respect to each coordinate. This choice of degrees of freedom leads to displacement and strain compatibility at the corners. Stacking sequence effects are accounted for by explicitly integrating the strain energy density through the thickness of the element. The laminated solid element was combined with a gap-contact element to analyze thick laminated composite lugs loaded through flexible pins. The resulting model accounts for pin bending effects that produce non-uniform bearing stresses through the thickness of the lug. A thick composite lug experimental test program was performed, and provided data that was used to validate the analytical model. Two lug geometries and three stacking sequences were tested.
Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci.
Bonifer, C; Hecht, A; Saueressig, H; Winter, D M; Sippel, A E
1991-10-01
It is hypothesized that nuclear DNA is organized in topologically constrained loop domains defining basic units of higher order chromatin structure. Our studies are performed in order to investigate the functional relevance of this structural subdivision of eukaryotic chromatin for the control of gene expression. We used the chicken lysozyme gene locus as a model to examine the relation between chromatin structure and gene function. Several structural features of the lysozyme locus are known: the extension of the region of general DNAasel sensitivity of the active gene, the location of DNA-sequences with high affinity for the nuclear matrix in vitro, and the position of DNAasel hypersensitive chromatin sites (DHSs). The pattern of DHSs changes depending on the transcriptional status of the gene. Functional studies demonstrated that DHSs mark the position of cis-acting regulatory elements. Additionally, we discovered a novel cis-activity of the border regions of the DNAasel sensitive domain (A-elements). By eliminating the position effect on gene expression usually observed when genes are randomly integrated into the genome after transfection, A-elements possibly serve as punctuation marks for a regulatory chromatin domain. Experiments using transgenic mice confirmed that the complete structurally defined lysozyme gene domain behaves as an independent regulatory unit, expressing the gene in a tissue specific and position independent manner. These expression features were lost in transgenic mice carrying a construct, in which the A-elements as well as an upstream enhancer region were deleted, indicating the lack of a locus activation function on this construct. Experiments are designed in order to uncover possible hierarchical relationships between the different cis-acting regulatory elements for stepwise gene activation during cell differentiation. We are aiming at the definition of the basic structural and functional requirements for position independent and high
Generalized Flows for Optimal Inference in Higher Order MRF-MAP.
Arora, Chetan; Banerjee, Subhashis; Kalra, Prem Kumar; Maheshwari, S N
2015-07-01
Use of higher order clique potentials in MRF-MAP problems has been limited primarily because of the inefficiencies of the existing algorithmic schemes. We propose a new combinatorial algorithm for computing optimal solutions to 2 label MRF-MAP problems with higher order clique potentials. The algorithm runs in time O(2(k)n(3)) in the worst case (k is size of clique and n is the number of pixels). A special gadget is introduced to model flows in a higher order clique and a technique for building a flow graph is specified. Based on the primal dual structure of the optimization problem, the notions of the capacity of an edge and a cut are generalized to define a flow problem. We show that in this flow graph, when the clique potentials are submodular, the max flow is equal to the min cut, which also is the optimal solution to the problem. We show experimentally that our algorithm provides significantly better solutions in practice and is hundreds of times faster than solution schemes like Dual Decomposition [1], TRWS [2] and Reduction [3], [4], [5]. The framework represents a significant advance in handling higher order problems making optimal inference practical for medium sized cliques. PMID:26352442
Higher-order Chebyshev rational approximation method (CRAM)
International Nuclear Information System (INIS)
The burnup equations can in principle be solved by computing the exponential of the burnup matrix. However, due to the difficult numerical characteristics of burnup matrices, the problem is extremely stiff, and the matrix exponential solution was long considered infeasible for an entire burnup system containing over a thousand nuclides. After discovering that the eigenvalues of burnup matrices are generally confined to a region near the negative real axis, the Chebyshev rational approximation method (CRAM) was introduced as a novel method to solve the burnup equations. It can be characterized as the best rational function on the negative real axis and it has been shown to be capable of simultaneously solving an entire burnup system both accurately and efficiently. The main difficulty in using CRAM for computing the matrix exponential is determining the coefficients of the rational function for a given approximation order. Some polynomial CRAM coefficients have been published in 1984, and based on these literature values, CRAM approximations up to the order 16 have been thus far applied in burnup calculations. The topic of this paper is the computation of CRAM approximations and their application to burnup equations. A Remez-type method utilizing the equioscillation property of best approximations is used to construct the CRAM approximants for approximation orders 1,. . . , 50. Numerical results are presented for a large burnup system and for a decay system. It is demonstrated that higher-order CRAM can be used to accurately solve the burnup equations even with time steps of the order of millions of years. (author)
Separating higher-order nonlinearities in transient absorption microscopy
Wilson, Jesse W.; Anderson, Miguel; Park, Jong Kang; Fischer, Martin C.; Warren, Warren S.
2015-08-01
The transient absorption response of melanin is a promising optically-accessible biomarker for distinguishing malignant melanoma from benign pigmented lesions, as demonstrated by earlier experiments on thin sections from biopsied tissue. The technique has also been demonstrated in vivo, but the higher optical intensity required for detecting these signals from backscattered light introduces higher-order nonlinearities in the transient response of melanin. These components that are higher than linear with respect to the pump or the probe introduce intensity-dependent changes to the overall response that complicate data analysis. However, our data also suggest these nonlinearities might be advantageous to in vivo imaging, in that different types of melanins have different nonlinear responses. Therefore, methods to separate linear from nonlinear components in transient absorption measurements might provide additional information to aid in the diagnosis of melanoma. We will discuss numerical methods for analyzing the various nonlinear contributions to pump-probe signals, with the ultimate objective of real time analysis using digital signal processing techniques. To that end, we have replaced the lock-in amplifier in our pump-probe microscope with a high-speed data acquisition board, and reprogrammed the coprocessor field-programmable gate array (FPGA) to perform lock-in detection. The FPGA lock-in offers better performance than the commercial instrument, in terms of both signal to noise ratio and speed. In addition, the flexibility of the digital signal processing approach enables demodulation of more complicated waveforms, such as spread-spectrum sequences, which has the potential to accelerate microscopy methods that rely on slow relaxation phenomena, such as photo-thermal and phosphorescence lifetime imaging.
Bignold, L P
2002-01-01
Nuclear chromatin patterns are used to distinguish normal and abnormal cells in histopathology and cytopathology. However, many chromatin pattern features are affected by aspects of tissue processing, especially fixation. Major effects of aldehyde and/or ethanol fixation on nuclei in the living state include shrinkage, chromatin aggregation and production of a 'chromatinic rim'. The mechanisms of these effects are poorly understood. In the past, possible mechanisms of fixation-induced morphological change have been considered only in terms of the theoretical model of the nucleus, which involves only a random tangle of partly unfolded chromosomes contained within the nuclear membrane. Such a model provides no basis for chromatin to be associated with the nuclear envelope, and hence no obvious clue to a mechanism for the formation of the 'chromatinic rim' in fixed nuclei. In recent years, two new models of nuclear structure have been described. The nuclear membrane-bound, chromosomal-domain model is based on the discoveries of chromatin-nuclear membrane attachments and of the localisation of the chromatin of each chromosome within discrete, exclusive parts of the nucleus (the 'domain' of each partly unfolded chromosome). The nuclear matrix/scaffold model is based on the discovery of relatively insoluble proteins in nuclei, which it suggests forms a 'matrix' and modulates gene expression by affecting transcription of DNA. Here, a hypothesis for fixation-associated chromatin pattern formation based mainly on the first model but partially relying on the second, is presented. The hypothesis offers explanations of the variations of appearance of nuclei according to fixation (especially air-drying versus wet-fixation with formaldehyde, glutaraldehyde or ethanol); the appearances of the nuclei of more metabolically active versus less metabolically active cells of the same type; the appearances of nuclei after fixation with osmium tetroxide; and of the marked central
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.
Higher-order adaptive finite-element methods for orbital-free density functional theory
International Nuclear Information System (INIS)
In the present work, we study various numerical aspects of higher-order finite-element discretizations of the non-linear saddle-point formulation of orbital-free density-functional theory. We first investigate the robustness of viable solution schemes by analyzing the solvability conditions of the discrete problem. We find that a staggered solution procedure where the potential fields are computed consistently for every trial electron-density is a robust solution procedure for higher-order finite-element discretizations. We next study the convergence properties of higher-order finite-element discretizations of orbital-free density functional theory by considering benchmark problems that include calculations involving both pseudopotential as well as Coulomb singular potential fields. Our numerical studies suggest close to optimal rates of convergence on all benchmark problems for various orders of finite-element approximations considered in the present study. We finally investigate the computational efficiency afforded by various higher-order finite-element discretizations, which constitutes the main aspect of the present work, by measuring the CPU time for the solution of discrete equations on benchmark problems that include large Aluminum clusters. In these studies, we use mesh coarse-graining rates that are derived from error estimates and an a priori knowledge of the asymptotic solution of the far-field electronic fields. Our studies reveal a significant 100–1000 fold computational savings afforded by the use of higher-order finite-element discretization, alongside providing the desired chemical accuracy. We consider this study as a step towards developing a robust and computationally efficient discretization of electronic structure calculations using the finite-element basis.
International Nuclear Information System (INIS)
Trypsin is the enzyme commonly used to prepare single cell suspensions from monolayer and spheroid cultures, both to determine survival and to assay DNA damage. Trypsin induces rounding, dissociation and radiosensitization of anchorage-dependent cells. Radiosensitivity and chromatin structure were compared between trypsin-treated (0.05%) round V79 cells from monolayers and spheroids vs. untreated spread monolayer cells in situ. The fluorescent halo technique was used to measure the changes in DNA supercoiling in nucleoids isolated from control and irradiated round and spread cells. Maximal halo diameters, the amount of initial and residual radiation-induced SNA damage and the radiosensitivity were higher in round cells than in spread monolayer V79 cells. The effects on cellular radiosensitivity and maximal halo diameter of other agents which also round and dissociate cells, e.g. 0.25% trypsin, pronase E and a non-enzymatic cell-dissociation solution, were similar to those of 0.05% trypsin. In LY-S cells, which are anchorage-independent, DNA loop size, the initial amount of DNA damage and radiosensitivity were not affected by trypsin. We suggest that the higher radiosensitivity of anchorage-dependent cells under immediate trypsinization and plating conditions, compared to cells with postirradiation in situ repair incubation, is due to correlated changes in cell shape and chromatin structure. (author)
Higher-Order, Space-Time Adaptive Finite Volume Methods: Algorithms, Analysis and Applications
Energy Technology Data Exchange (ETDEWEB)
Minion, Michael
2014-04-29
The four main goals outlined in the proposal for this project were: 1. Investigate the use of higher-order (in space and time) finite-volume methods for fluid flow problems. 2. Explore the embedding of iterative temporal methods within traditional block-structured AMR algorithms. 3. Develop parallel in time methods for ODEs and PDEs. 4. Work collaboratively with the Center for Computational Sciences and Engineering (CCSE) at Lawrence Berkeley National Lab towards incorporating new algorithms within existing DOE application codes.
Querying and Merging Heterogeneous Data by Approximate Joins on Higher-Order Terms
S. Price; Flach, PA
2008-01-01
Integrating heterogeneous data from sources as diverse as web pages, digital libraries, knowledge bases, the Semantic Web and databases is an open problem. The ultimate aim of our work is to be able to query such heterogeneous data sources as if their data were conveniently held in a single relational database. Pursuant to this aim, we propose a generalisation of joins from the relational database model to enable joins on arbitrarily complex structured data in a higher-order representation. B...
In-service teacher education: asking questions for higher order thinking in visual literacy
Visvaganthie Moodley
2013-01-01
The kinds of questions teachers ask may thwart or promote learner high-order thinking; teachers themselves must have expertise in questioning skills to promote higher order cognition among learners. Drawing on experiential knowledge of assessment, and as an English-teaching professional development programme (PDP) facilitator, I demonstrate that within the framework of a carefully structured subject-specific PDP, teachers can be taught how to enhance thinking skills in the English visual lite...
A Relational Algebra for Basic Terms in a Higher-Order Logic:Technical Report CSTR-13-004
Price, Simon; Flach, Peter A.
2013-01-01
We define a relational algebra on basic terms, strongly typed terms in a higher-order logic, that are well suited to the representation of heterogeneous data, irrespective of whether the data originated from relational, unstructured, semi-structured or structured sources. This higher-order generalisation of the relational model has potential applications in NoSQL databases and Big Variety, Big Data applications.
Alamia, Andrea; Solopchuk, Oleg; D'Ausilio, Alessandro; Van Bever, Violette; Fadiga, Luciano; Olivier, Etienne; Zénon, Alexandre
2016-03-01
Because Broca's area is known to be involved in many cognitive functions, including language, music, and action processing, several attempts have been made to propose a unifying theory of its role that emphasizes a possible contribution to syntactic processing. Recently, we have postulated that Broca's area might be involved in higher-order chunk processing during implicit learning of a motor sequence. Chunking is an information-processing mechanism that consists of grouping consecutive items in a sequence and is likely to be involved in all of the aforementioned cognitive processes. Demonstrating a contribution of Broca's area to chunking during the learning of a nonmotor sequence that does not involve language could shed new light on its function. To address this issue, we used offline MRI-guided TMS in healthy volunteers to disrupt the activity of either the posterior part of Broca's area (left Brodmann's area [BA] 44) or a control site just before participants learned a perceptual sequence structured in distinct hierarchical levels. We found that disruption of the left BA 44 increased the processing time of stimuli representing the boundaries of higher-order chunks and modified the chunking strategy. The current results highlight the possible role of the left BA 44 in building up effector-independent representations of higher-order events in structured sequences. This might clarify the contribution of Broca's area in processing hierarchical structures, a key mechanism in many cognitive functions, such as language and composite actions. PMID:26765778
Radiation Heat Transfer Between Diffuse-Gray Surfaces Using Higher Order Finite Elements
Gould, Dana C.
2000-01-01
This paper presents recent work on developing methods for analyzing radiation heat transfer between diffuse-gray surfaces using p-version finite elements. The work was motivated by a thermal analysis of a High Speed Civil Transport (HSCT) wing structure which showed the importance of radiation heat transfer throughout the structure. The analysis also showed that refining the finite element mesh to accurately capture the temperature distribution on the internal structure led to very large meshes with unacceptably long execution times. Traditional methods for calculating surface-to-surface radiation are based on assumptions that are not appropriate for p-version finite elements. Two methods for determining internal radiation heat transfer are developed for one and two-dimensional p-version finite elements. In the first method, higher-order elements are divided into a number of sub-elements. Traditional methods are used to determine radiation heat flux along each sub-element and then mapped back to the parent element. In the second method, the radiation heat transfer equations are numerically integrated over the higher-order element. Comparisons with analytical solutions show that the integration scheme is generally more accurate than the sub-element method. Comparison to results from traditional finite elements shows that significant reduction in the number of elements in the mesh is possible using higher-order (p-version) finite elements.
Lv, Zhan-Jun; Wang, Xiu-Fang; Zhai, Yu; Song, Shu-Xia
2003-01-01
Although the set of genes is virtually the same in all tissues,differential gene expression is appeared in cells of different kinds. Differentiation and ageing are associated with regulation of gene expression that is a fundamental mechanism in eukaryotic development and survival. The sensitivity to DNase I of actively transcribed genes seems to be a general phenomenon. The purpose of the study is to test whether RNAs obtained from different organs or cells can enhance susceptibility of albumin gene to DNase I digestion in BALB/c mouse brain chromatin assembled.RNAs extracted from rat liver, lung, kidney, brain, tRNA from yeast and synthesized RNAs (23 nt completed with mouse alb gene) were added to a system of chromatin reconstitution that was achieved by dialysis from high ionic strength solution. Assembled chromatin was digested with DNase I (12.5 microg/mL) at 20 degrees for 1 min, then PCR assay was used to detect the level of albumin gene digested. PCR products (1200 bp) were run on a 6% polyacylamide gel and analyzed by silver stain assay. RNAs from different organs and synthesized RNAs all increased the sensitivity of albumin gene to DNase I attack in mouse assembled chromatin. The effect was more obvious in liver and lung RNAs than in kidney and brain ones. tRNA from yeast did not enhance the sensitivity of albumin gene to DNase I digestion. RNA increased albumin gene sensitivity to DNase I in a dose-dependent manner. We report here for the first time that RNAs can enhance susceptibility of albumin gene to DNase I digestion. The effect is associated with RNA sources or sequences. It is generally agreed that the formation of gene sensitivity to DNase I, by unfolding of a tightly packed chromatin fiber, is the first step in gene activation, then RNAs that recognize complementary DNA sequences may be the specific factors that affect DNA supercoiling and determine the sensitivity of gene to DNase I digestion. Here we describes "RNA Population Gene Activating
Igaz, Nóra; Kovács, Dávid; Rázga, Zsolt; Kónya, Zoltán; Boros, Imre M; Kiricsi, Mónika
2016-10-01
Histone deacetylase (HDAC) inhibitors are considered as novel therapeutic agents inducing cell cycle arrest and apoptotic cell death in various cancer cells. Inhibition of deacetylase activity results in a relaxed chromatin structure thereby rendering the genetic material more vulnerable to DNA targeting agents that could be exploited by combinational cancer therapy. The unique potential of silver nanoparticles (AgNPs) in tumor therapy relies on the generation of reactive radicals which trigger oxidative stress, DNA damage and apoptosis in cancer cells. The revolutionary application of AgNPs as chemotherapeutical drugs seems very promising, nevertheless the exact molecular mechanisms of AgNP action in combination with other anti-cancer agents have yet to be elucidated in details before clinical administrations. As a step towards this we investigated the combinational effect of HDAC inhibition and AgNP administration in HeLa cervical cancer cells. We identified synergistic inhibition of cancer cell growth and migration upon combinational treatments. Here we report that the HDAC inhibitor Trichostatin A enhances the DNA targeting capacity and apoptosis inducing efficacy of AgNPs most probably due to its effect on chromatin condensation. These results point to the potential benefits of combinational application of HDAC inhibitors and AgNPs in novel cancer medication protocols. PMID:27434153
Impact of Chromatin on HIV Replication
Agosto, Luis M.; Matthew Gagne; Henderson, Andrew J.
2015-01-01
Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.
Robust rooftop extraction from visible band images using higher order CRF
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.
Higher-order chromatin domains link eQTLs with the expression of far-away genes
Duggal, Geet; Wang, Hao; Kingsford, Carl
2013-01-01
Distal expression quantitative trait loci (distal eQTLs) are genetic mutations that affect the expression of genes genomically far away. However, the mechanisms that cause a distal eQTL to modulate gene expression are not yet clear. Recent high-resolution chromosome conformation capture experiments along with a growing database of eQTLs provide an opportunity to understand the spatial mechanisms influencing distal eQTL associations on a genome-wide scale. We test the hypothesis that spatial p...
Directory of Open Access Journals (Sweden)
Hua Wong
Full Text Available In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.
Higher order Hamiltonian fluid reduction of Vlasov equation
Perin, Maxime; Morrison, Philip; Tassi, Emanuele
2014-01-01
From the Hamiltonian structure of the Vlasov equation, we build a Hamiltonian model for the first three moments of the Vlasov distribution function, namely, the density, the momentum density and the specific internal energy. We derive the Poisson bracket of this model from the Poisson bracket of the Vlasov equation, and we discuss the associated Casimir invariants.
2012-01-01
Although it is well known that chromosomes are non-randomly organized during interphase, it is not completely clear whether higher-order chromatin structure is transmitted from mother to daughter cells. Therefore, we addressed the question of how chromatin is rearranged during interphase and whether heterochromatin pattern is transmitted after mitosis. We additionally tested the similarity of chromatin arrangement in sister interphase nuclei. We noticed a very active cell rotation during inte...
Higher-order probabilistic perceptrons as Bayesian inference engines
International Nuclear Information System (INIS)
This letter makes explicit a structural connection between the Bayes optimal classifier operating on K binary input variables and corresponding two-layer perceptron having normalized output activities and couplings from input to output units of all orders up to K. Given a large and unbiased training set and an effective learning algorithm, such a neural network should be able to learn the statistics of the classification problem and match the a posteriori probabilities given by the Bayes optimal classifier. (author). 18 refs
Special issue of Higher-Order and Symbolic Computation
DEFF Research Database (Denmark)
. "Using 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....
Spectroscopic study of laser irradiated chromatin
Energy Technology Data Exchange (ETDEWEB)
Radu, Liliana, E-mail: liliana1radu@gmail.com [V. Babes National Institute, Department of Molecular Genetics and Radiobiology (Romania); Mihailescu, I. [National Institute for Lasers, Plasma and Radiation Physics, Department of Lasers (Romania); Gazdaru, Doina [Faculty of Physics, Bucharest University, Department of Biophysics (Romania); Preoteasa, V. [V. Babes National Institute, Department of Molecular Genetics and Radiobiology (Romania)
2013-04-15
The effects of three UV excimer laser radiations, with wavelengths of 193, 248 and 282 nm respectively, on the structure of chromatin (the complex of deoxyribonucleic acid with proteins that exists in eukaryotic cells nuclei) were investigated. The chromatin was extracted from livers of Winstar rats. The spectroscopic methods used are: fluorescence (Foerster) resonance energy transfer (FRET), time resolved fluorescence and steady-state fluorescence. A chromatin deoxyribonucleic acid radiolysis, a chromatin proteins damage and a change of the global chromatin structure on lasers action were indicated by this study. It exists some small differences between the actions of these three laser radiations.
Higher order beam jitter in the SLC linac
International Nuclear Information System (INIS)
The pulse-to-pulse behavior of the beams in the SLC linac is dominated by wakefields which can amplify any other sources of jitter. A strong focusing lattice combined with BNS damping controls the amplitude of oscillations which otherwise would grow exponentially. Measurements of oscillation amplitude along the linac show beam motion that is up to six times larger than that expected from injection jitter. A search for possible sources of jitter within the linac uncovered some problems such as structure jitter at 8 to 12 Hz, pump vibrations at 59 Hz and 1 Hz aliasing by the feedback systems. These account for only a small fraction of the observed jitter which is dominantly white noise. No source has yet been fully identified but possible candidates are dark current in the linac structures (not confirmed by experiment) or subtle correlations in injection jitter. An example would be a correlated x-z jitter with no net offset visible on the beam position monitors at injection. Such a correlation would cause jitter growth along the linac as wakefields from the head of the bunch deflect the core and tail of the bunch. Estimates of the magnitude of this effect and some possible sources are discussed in this paper. (author)
Higher-order-mode damper as beam-position monitors
International Nuclear Information System (INIS)
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 μm. 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 μm and a relative accuracy smaller 6.2% be expected
Power grid higher-order harmonics estimation with multilayer perceptrons
Nguyen, Thien Minh; Wira, Patrice
2015-12-01
This work proposes a new neural approach based on the structure of a Multi-Layer Perceptron (MLP) for identifying current harmonics in power systems. The learning approach is based on several MLP, adopts the Fourier decomposition of a signal and a training set generated from harmonic waveforms is used to calculate the weights. After training, each MLP is able to identify two coefficients for each harmonic term of the input signal. The effectiveness of the new approach is evaluated by experiments. Results show that the proposed MLPs of the new approach enable to identify effectively the amplitudes of harmonic terms from the signals under noisy condition. Results are compared to other and recent MLP approaches. The new approach can be applied in harmonic compensation strategies by being implement in an active power filter to ensure the power quality in electrical power systems.
Higher-order gravitational lensing reconstruction using Feynman diagrams
Energy Technology Data Exchange (ETDEWEB)
Jenkins, Elizabeth E.; Manohar, Aneesh V.; Yadav, Amit P.S. [Department of Physics, University of California at San Diego, La Jolla, CA 92093 (United States); Waalewijn, Wouter J., E-mail: ejenkins@ucsd.edu, E-mail: amanohar@ucsd.edu, E-mail: W.J.Waalewijn@uva.nl, E-mail: ayadav@physics.ucsd.edu [Nikhef, Theory Group, Science Park 105, 1098 XG, Amsterdam (Netherlands)
2014-09-01
We develop a method for calculating the correlation structure of the Cosmic Microwave Background (CMB) using Feynman diagrams, when the CMB has been modified by gravitational lensing, Faraday rotation, patchy reionization, or other distorting effects. This method is used to calculate the bias of the Hu-Okamoto quadratic estimator in reconstructing the lensing power spectrum up to O (φ{sup 4}) in the lensing potential φ. We consider both the diagonal noise TT TT, EB EB, etc. and, for the first time, the off-diagonal noise TT TE, TB EB, etc. The previously noted large O (φ{sup 4}) term in the second order noise is identified to come from a particular class of diagrams. It can be significantly reduced by a reorganization of the φ expansion. These improved estimators have almost no bias for the off-diagonal case involving only one B component of the CMB, such as EE EB.
Higher-Order Gravitational Lensing Reconstruction using Feynman Diagrams
Jenkins, Elizabeth E; Waalewijn, Wouter J; Yadav, Amit P S
2014-01-01
We develop a method for calculating the correlation structure of the Cosmic Microwave Background (CMB) using Feynman diagrams, when the CMB has been modified by gravitational lensing, Faraday rotation, patchy reionization, or other distorting effects. This method is used to calculate the bias of the Hu-Okamoto quadratic estimator in reconstructing the lensing power spectrum up to O(\\phi^4) in the lensing potential $\\phi$. We consider both the diagonal noise TTTT, EBEB, etc. and, for the first time, the off-diagonal noise TTTE, TBEB, etc. The previously noted large O(\\phi^4) term in the second order noise is identified to come from a particular class of diagrams. It can be significantly reduced by a reorganization of the $\\phi$ expansion. These improved estimators have almost no bias for the off-diagonal case involving only one $B$ component of the CMB, such as EEEB.
Czech Academy of Sciences Publication Activity Database
Falk, Martin; Lukášová, Emilie; Gabrielová, Barbora; Ondřej, Vladan; Kozubek, Stanislav; Kroupová, Iva
La Jolla, 2007. s. 46-46. [Symposium on Biological Complexity: Diseases of Transcription. 11.01.2007-14.01.2007, La Jolla] R&D Projects: GA ČR(CZ) GP204/06/P349; GA MŠk(CZ) 1P05OC084 Institutional research plan: CEZ:AV0Z50040507 Keywords : double-strand breaks (DSB) * DSB-repair * higher-order chromatin structure Subject RIV: BO - Biophysics
International Nuclear Information System (INIS)
Research highlights: → An in vitro reconstitution system was established with isolated nuclei and cytoplasm. → Chromatin fluidities were measured in the system using FRAP. → Chromatin fluidities were higher in the cytoplasm of earlier-stage embryos. → Chromatin fluidities were higher in the earlier-stage nuclei with egg-extract. → Chromatin fluidity may decrease during embryonic development. -- Abstract: Chromatin fluidity, which is one of the indicators of higher-order structures in chromatin, is associated with cell differentiation. However, little is known about the relationships between chromatin fluidity and cell differentiation status in embryonic development. We established an in vitro reconstitution system that uses isolated nuclei and cytoplasmic extracts of Xenopus embryos and a fluorescence recovery after photobleaching assay to measure the fluidities of heterochromatin protein 1 (HP1) and histone H1 during development. The HP1 and H1 fluidities of nuclei isolated from the tailbuds of early tadpole stage (stage 32) embryos in the cytoplasmic extracts of eggs and of late blastula stage (stage 9) embryos were higher than those in the cytoplasmic extracts of mid-neurula stage (stage 15) embryos. The HP1 fluidities of nuclei isolated from animal cap cells of early gastrula stage (stage 10) embryos and from the neural plates of neural stage (stage 20) embryos were higher than those isolated from the tailbuds of stage 32 embryos in egg extracts, whereas the HP1 fluidities of these nuclei were the same in the cytoplasmic extracts of stage 15 embryos. These results suggest that chromatin fluidity is dependent upon both cytoplasmic and nuclear factors and decreases during development.
Energy Technology Data Exchange (ETDEWEB)
Aoki, Ryuta; Inui, Masafumi; Hayashi, Yohei; Sedohara, Ayako [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Okabayashi, Koji [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); ICORP Organ Regeneration Project, Japan Science and Technology Agency (JST), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Ohnuma, Kiyoshi, E-mail: kohnuma@vos.nagaokaut.ac.jp [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Murata, Masayuki [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Asashima, Makoto, E-mail: asashi@bio.c.u-tokyo.ac.jp [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); ICORP Organ Regeneration Project, Japan Science and Technology Agency (JST), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Organ Development Research Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562 (Japan)
2010-09-17
Research highlights: {yields} An in vitro reconstitution system was established with isolated nuclei and cytoplasm. {yields} Chromatin fluidities were measured in the system using FRAP. {yields} Chromatin fluidities were higher in the cytoplasm of earlier-stage embryos. {yields} Chromatin fluidities were higher in the earlier-stage nuclei with egg-extract. {yields} Chromatin fluidity may decrease during embryonic development. -- Abstract: Chromatin fluidity, which is one of the indicators of higher-order structures in chromatin, is associated with cell differentiation. However, little is known about the relationships between chromatin fluidity and cell differentiation status in embryonic development. We established an in vitro reconstitution system that uses isolated nuclei and cytoplasmic extracts of Xenopus embryos and a fluorescence recovery after photobleaching assay to measure the fluidities of heterochromatin protein 1 (HP1) and histone H1 during development. The HP1 and H1 fluidities of nuclei isolated from the tailbuds of early tadpole stage (stage 32) embryos in the cytoplasmic extracts of eggs and of late blastula stage (stage 9) embryos were higher than those in the cytoplasmic extracts of mid-neurula stage (stage 15) embryos. The HP1 fluidities of nuclei isolated from animal cap cells of early gastrula stage (stage 10) embryos and from the neural plates of neural stage (stage 20) embryos were higher than those isolated from the tailbuds of stage 32 embryos in egg extracts, whereas the HP1 fluidities of these nuclei were the same in the cytoplasmic extracts of stage 15 embryos. These results suggest that chromatin fluidity is dependent upon both cytoplasmic and nuclear factors and decreases during development.
Institute of Scientific and Technical Information of China (English)
Li Xi-Zeng; Su Bao-Xia; Chai Lu
2005-01-01
It is found that the field of the combined mode of the probe wave and the phase conjugate wave in the process of non-degenerate four-wave mixing exhibits higher-order squeezing to all even orders. The higher-order squeezed parameter and squeezed limit due to the modulation frequency are investigated. The smaller the modulation frequency is, the stronger the degree of higher-order squeezing becomes. Furthermore, the higher-order uncertainty relations in the process of non-degenerate four-wave mixing are presented for the first time. The product of higher-order noise moments is related to even order number N and the length L of the medium.
International Nuclear Information System (INIS)
The global safety of nuclear power plants is greatly affected by the resistance of internal and external plate and shell-type structures to dynamic loads caused by accidentally generated flying objects, such as parts of failed rotating equipment or ruptured piping, tornado missiles or impacting aircraft engines. This paper describes the development of a linear and nonlinear laminated plate dynamics computer program based on explicit time integration with a special mass matrix diagonalization scheme using a higher-order theory and Co finite elements. A Lagrangian approach is adopted for the geometric nonlinear analysis and the stress and strain descriptions used are those due to Piola-Kirchhoff and Green respectively
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.
Propagation of femtosecond terawatt laser pulses in N2 gas including higher-order Kerr effects
Directory of Open Access Journals (Sweden)
T. W. Huang
2012-12-01
Full Text Available Propagation characteristic of femtosecond terawatt laser pulses in N2 gas with higher-order Kerr effect (HOKE is investigated. Theoretical analysis shows that HOKE acting as Hamiltonian perturbation can destroy the coherent structure of a laser field and result in the appearance of incoherent patterns. Numerical simulations show that in this case two different types of complex structures can appear. It is found that the high-order focusing terms in HOKE can cause continuous phase shift and off-axis evolution of the laser fields when irregular homoclinic orbit crossings of the field in phase space take place. As the laser propagates, small-scale spatial structures rapidly appear and the evolution of the laser field becomes chaotic. The two complex patterns can switch between each other quasi-periodically. Numerical results show that the two complex patterns are associated with the stochastic evolution of the energy contained in the higher-order shorter-wavelength Fourier modes. Such complex patterns, associated with small-scale filaments, may be typical for laser propagation in a HOKE medium.
Analysis of Scattering by Inhomogeneous Dielectric Objects Using Higher-Order Hierarchical MoM
Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter; Breinbjerg, Olav
2003-01-01
An efficient technique for the analysis of electromagnetic scattering by arbitrary shaped inhomogeneous dielectric objects is presented. The technique is based on a higher-order method of moments (MoM) solution of the volume integral equation. This higher-order MoM solution comprises recently 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 curv...
Brain Function and Chromatin Plasticity
Dulac, Catherine
2010-01-01
The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activity and connectivity. Persistent changes in chromatin structure are thought to contribute to mechanisms of epigenetic inheritance. Recent advances in chromatin biology offer new avenues to investig...
Higher-order Convergence Statistics for Three-dimensional Weak Gravitational Lensing
Munshi, Dipak; Coles, Peter
2010-01-01
Weak gravitational lensing on a cosmological scales can provide strong constraints both on the nature of dark matter and the dark energy equation of state. Most current weak lensing studies are restricted to (two-dimensional) projections, but tomographic studies with photometric redshifts have started, and future surveys offer the possibility of probing the evolution of structure with redshift. In future we will be able to probe the growth of structure in 3D and put tighter constraints on cosmological models than can be achieved by the use of galaxy redshift surveys alone. Earlier studies in this direction focused mainly on evolution of the 3D power spectrum, but extension to higher-order statistics can lift degeneracies as well as providing information on primordial non-gaussianity. We present analytical results for specific higher-order descriptors, the bispectrum and trispectrum, as well as collapsed multi-point statistics derived from them, i.e. cumulant correlators. We also compute quantities we call the...
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.
In-service teacher education: asking questions for higher order thinking in visual literacy
Directory of Open Access Journals (Sweden)
Visvaganthie Moodley
2013-01-01
Full Text Available The kinds of questions teachers ask may thwart or promote learner high-order thinking; teachers themselves must have expertise in questioning skills to promote higher order cognition among learners. Drawing on experiential knowledge of assessment, and as an English-teaching professional development programme (PDP facilitator, I demonstrate that within the framework of a carefully structured subject-specific PDP, teachers can be taught how to enhance thinking skills in the English visual literacy (VL learning classroom. Guided by an earlier taxonomy of cognition, and using qualitative methodology, the paper analyses data obtained from: (i observation notes and examination equivalents of 40 teachers from various public schools in Gauteng who were engaged in the Advanced Certificate in Education (ACE, English specialization programme; and (ii a case study of three teachers by means of semi-structured interviews, and a study of their lesson plans and worksheets.The paper examines, specifically, teachers' choice of texts and questions asked, for English second-language learners for the teaching of VL. It concludes by suggesting that if teachers themselves are first engaged in the cognitive processes they wish learners to acquire, they are better positioned to promote higher order among their learners.
Higher Order Moment Spectra Time-Frequency Analysis of the Geophysical Signal
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
On the basis of an introduction of the Wigner Higher-Order spectra(WHOS) and a general class of time-frequency higher-order moment spectra ,the geophysical signal was analyzed using the higher order time-frequency distributions(TFD). Simulation results obtained in this paper show that the higher-order TFD (Wigner Bispectrum,Wigner Trispectrum and Choi-Williams Trispectrum) have much better Time-Frequency Concentration than the second-order TFD ,and the reduced interference higher-order TFD such as CWT can effectively reduce the cross-term in multicomponent signals and simultaneously obtain high time-frequency concentration.
International Nuclear Information System (INIS)
Exponentially growing mammalian cells were exposed to 3.4 MeV alpha particles. The chromatin of cells arrested in G2 by alpha irradiation was severely damaged, though all cells were still capable to condensate their chromatin after fusion with mitotic cells. In addition to the common types of aberrations (breaks, gaps, dicentrics and exchanges) cells were found possessing one or more chromosomes with long stretches of undercondensed chromatin. Repair of these lesions was indicated by site specific unscheduled DNA synthesis and by the observation that condensation of these regions improved during G2 arrest. Furthermore, during G2 arrest the synthesis of two cellular proteins was stimulated. This was studied by two-dimensional gel electrophoresis of 35S-methionine labeled cellular proteins. All these findings provided evidence that radiation-induced G2 arrest is caused by chromatin damage, which prevents regular chromosome condensation for mitosis. (orig./MG)
Thakar, Amit; Sylar, Elise; Flynn, Francis W.
2012-01-01
The tachykinin, neurokinin 3 receptor (NK3R) is a g-protein coupled receptor that is broadly distributed in the nervous system and exerts its diverse physiological actions through multiple signaling pathways. Despite the role of the receptor system in a range of biological functions, the effects of NK3R activation on chromatin dynamics and gene expression have received limited attention. The present work determined the effects of senktide, a selective NK3R agonist, on chromatin organization, ...
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.
Kruithof, Maarten Christiaan
2009-01-01
Animals and plants are build from a large number of cells. These cells continuously respond to signals from outside and inside the cell by producing various kinds of proteins. The blueprints of these proteins are stored in genes. The genes, in cells with a nucleus, are carried in chromosomes: threadlike structures in the nucleus of a cell that become visible when the cell, upon dividing, condenses these structures. Chromosomes consist of roughly two parts: proteins, that take care of the cond...
Improvements to local projective noise reduction through higher order and multiscale refinements
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.
Improvements to local projective noise reduction through higher order and multiscale refinements.
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. PMID:26117108
Cross-ratio Identities and Higher-order Poles of CHY-integrand
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.
International Nuclear Information System (INIS)
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. (paper)
Higher-order exchange interactions leading to metamagnetism in FeRh
Barker, Joseph; Chantrell, Roy W.
2015-09-01
The origin of the metamagnetic antiferromagnetic-ferromagnetic phase transition of FeRh is a subject of debate. Competing explanations invoke magnetovolume effects or a purely thermodynamic transition within the spin system. It is experimentally difficult to observe the changes in the magnetic system and the lattice simultaneously, leading to conflicting evidence over which mechanism causes the phase transition. A noncollinear electronic structure study by Mryasov [Phase Transitions 78, 197 (2005), 10.1080/01411590412331316591] showed that nonlinear behavior of the Rh moment leads to higher-order exchange terms in FeRh. Using atomistic spin dynamics, we show that the phase transition can occur due to the competition between bilinear and the higher-order four spin exchange terms in an effective spin Hamiltonian. The phase transition we see is of first order and shows thermal hysteresis in agreement with experimental observations. Simulating subpicosecond laser heating, we show an agreement with pump-probe experiments with a ferromagnetic response on a picosecond time scale.
Energy Technology Data Exchange (ETDEWEB)
Candel, A.; Kabel, A.; Lee, L.; Li, Z.; Limborg, C.; Ng, C.; Prudencio, E.; Schussman, G.; Uplenchwar, R.; Ko, K.; /SLAC
2009-06-19
Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell) approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.
Higher order modes in superconducting radio frequency resonators for energy recovery linacs
International Nuclear Information System (INIS)
The main scope of this work is the automation of the extraction procedure of the external quality factors of Higher Order Modes (HOMs) in Superconducting Radio Frequency (SRF) cavities. The HOMs are generated by charged particle beams traveling through a SRF cavity at the speed of light. The HOMs decay very slowly, depending on localization inside the structure and cell-to-cell coupling, and may influence succeeding charged particle bunches. Thus it is important, at the SRF cavity design optimization stage, to calculate the external quality factors (Qext) of HOMs. Traveling Poles Elimination (TPE) scheme was used to automatically extract Qext from the transmission spectra and careful eigenmode analysis of the SC cavity was performed to confirm TPE results. The eigenmode analysis also delivers important information about band structure, cell-to-cell coupling of HOMs and allows rapid identification of modes that could interact with the charged particle bunches.
Two-photon or higher-order absorbing optical materials and methods of use
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.
Directory of Open Access Journals (Sweden)
Abdolreza Rastegarnia
2013-01-01
Full Text Available Objective: The aim of the present study was to evaluate three thawing rates on the post thaw motility, viability and chromatin structure of buffalo semen frozen in 0.5-ml straws.Materials and Methods: In this experimental study semen was collected with artificial vagina (42˚C from four buffalo bulls.Split pooled ejaculates (n=4 were extended at 37˚C with a Bioxcell® extender. Semen was cooled to 4˚C within 2 hours, equilibrated at 4˚C for 4 hours, then filled in 0.5 ml French straws, and frozen in programmable cell freezer before plunging into liquid nitrogen. Straws were thawed at water bath temperatures of 37, 50 or 70˚C for 30, 15 and 6 seconds, respectively. Semen was incubated at 37˚C for 2 hours and evaluated for post thaw motility, viability, acrosomal and DNA integrity of spermatozoa. Analysis of variance (ANOVA was used for comparisons of means. When the ANOVA test showed statistical differences, the mean of the treatments were compared using Duncan’s multiple range tests.Results: The initial postthaw motility (0 hour averaged 62.7 ± 7.2%, 73.1 ± 9.77%, and 74.9 ± 8.58% for the three thaw rates, respectively. Kinematic parameters such as average path velocity, linearity and beat/cross frequency in the thaw rate of 70˚C for 6 seconds were superior to other rates studied (p0.05. A positive correlation was detected between sperm motility and thawing rate after two hours incubation times. The percentage of viable spermatozoa and spermatozoa with an intact acrosome and plasma membrane integrity were not different between the groups of samples thawed at different temperatures (p>0.05. The percentage of spermatozoa with chromatin dispersion forthe thaw rate of 70˚C for 6 seconds was significantly higher than for the to other rates studied (p< 0.05. In contrast with motility and viability, the DNA integrity of post thaw spermatozoa remained unaffected during 2 hours incubation.Conclusion: The post thaw motility and kinematic
Chromatin remodelers and their roles in chromatin organization
Strålfors, Annelie
2012-01-01
The DNA in the eukaryotic nucleus is organized into a complex DNA-protein structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around a histone protein octamer. The nucleosomes form a “beads on a string” structure, which can be folded into higherorder structures that allow an extensive degree of DNA compaction. This compaction is so effective that 2 meters of DNA can fit into the human cell nucleus with a ...
Chinone, N.; Yamasue, K.; Hiranaga, Y.; Honda, K.; Cho, Y.
2012-11-01
Scanning nonlinear dielectric microscopy (SNDM) can be used to visualize polarization distributions in ferroelectric materials and dopant profiles in semiconductor devices. Without using a special sharp tip, we achieved an improved lateral resolution in SNDM through the measurement of super-higher-order nonlinearity up to the fourth order. We observed a multidomain single crystal congruent LiTaO3 (CLT) sample, and a cross section of a metal-oxide-semiconductor (MOS) field-effect-transistor (FET). The imaged domain boundaries of the CLT were narrower in the super-higher-order images than in the conventional image. Compared to the conventional method, the super-higher-order method resolved the more detailed structure of the MOSFET.
A Study of Lower-order and Higher-order Questions at Secondary Level
Directory of Open Access Journals (Sweden)
Wilayat Bibi khan
2011-08-01
Full Text Available In classrooms, questioning is one of the most regularly employed teaching strategies. Questioning is considered by many to be the most important tool that teachers have for helping students build understanding and to encourage students to think about and act upon the material that have structured. Questions are asked to individual pupils, to the whole class, to small groups to arouse curiosity, focus attention, develop an active approach, stimulate pupils, structure the task, diagnose difficulties, communicate expectation, help children reflect, develop thinking skills, help group reflection, provoke discussion and show interest in pupils’ ideas. Perhaps few studies have been carried out regarding the levels of classroom questions in Pakistan on this vital aspect of teaching learning process. The main objective of the study was to explore the levels of questions teachers asked during teaching at secondary level using bloom’s taxonomy. It was focused to observe the ratio of lower and higher- order questions. It was an observational study of the descriptive method. The target population comprised all the teachers of Working Folks Grammar School & College Peshawar. Twenty teachers of different subjects teaching at secondary level were randomly selected as sample of the study. Teachers were observed using an observational guide and audio recording were conducted. The researcher focused only the asked questions of the teachers. This study is significant because its findings and conclusions may stimulate teachers to improve their questioning behavior in order to develop and promote higher order thinking abilities. The result of the study showed that so much time was spent with teachers questioning the students. Most of the questions were low- level cognitive questions. Higher- order questions were also observed however, the ratio of these questions was very low. Total percentage of questions during 445 minutes was 60 percent. The whole number of
Gopalan, Sunita; Kasza, Aneta; Xu, Weili; Kiss, Daniel L.; Wilczynska, Katarzyna M.; Rydel, Russell E.; Kordula, Tomasz
2005-01-01
The distal serpin subcluster contains genes encoding α1-antichymotrypsin (ACT), protein C inhibitor (PCI), kallistatin (KAL), and the KAL-like protein that are expressed in hepatocytes but only the act gene is expressed in astrocytes. We show here that the tissue-specific expression of these genes associates with astrocyte- and hepatocyte-specific chromatin structures. In hepatocytes, we identified twelve DNase I-hypersenitive sites (DHS) that were distributed throughout the entire subcluster...
Characterization of the RNA content of chromatin
Mondal, Tanmoy; Rasmussen, Markus; Pandey, Gaurav Kumar; Isaksson, Anders; Kanduri, Chandrasekhar
2010-01-01
Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show s...
Mathematics Teachers’ Interpretation of Higher-Order Thinking in Bloom’s Taxonomy
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...
On the Expressiveness of Polyadic and Synchronous Communication in Higher-Order Process Calculi
Lanese, Ivan; Peréz, Jorge,; Sangiorgi, Davide; Schmitt, Alan
2010-01-01
Higher-order process calculi are calculi in which processes can be communicated. We study the expressiveness of strictly higher-order process calculi, and focus on two issues well-understood for first-order calculi but not in the higher-order setting: synchronous vs. asynchronous communication and polyadic vs. monadic communication. First, and similarly to the first-order setting, synchronous process-passing is shown to be encodable into asynchronous process- passing. Then, the absence of nam...
Directory of Open Access Journals (Sweden)
Wang QL
2009-01-01
Full Text Available A new notion of higher-order weakly generalized adjacent epiderivative for a set-valued map is introduced. By virtue of the epiderivative and weak minimality, a higher-order Mond-Weir type dual problem and a higher-order Wolfe type dual problem are introduced for a constrained set-valued optimization problem, respectively. Then, corresponding weak duality, strong duality, and converse duality theorems are established.
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....
Higher order Godunov methods for general systems of hyperbolic conservation laws
Energy Technology Data Exchange (ETDEWEB)
Bell, J. B.; Colella, P.; Trangenstein, J. A.
1989-06-01
We describe an extension of higher order Godunov methods to general systems of hyperbolic conservation laws. This extension allow the method to be applied to problems that are not strictly hyperbolic and exhibit local linear degeneracies in the wave fields. The method constructs an approximation of the Riemann problem from local wave information. A generalization of the Engquist--Osher flux for systems is then used to compute a numerical flux based on this approximation. This numerical flux replaces the Godunov numerical flux in the algorithm, thereby eliminating the need for a global Riemann problem solution. The additional modifications to the Godunov methodology that are needed to treat loss of strict hyperbolicity are described in detail. THe method is applied to some simple model problems for which the glocal analytic structure is known. The method is also applied to the black-oil model for multiphase flow in petroleum reservoirs. /copyright/ 1989 Academic Press, Inc.
Higher order Godunov methods for general systems of hyperbolic conservation laws
International Nuclear Information System (INIS)
We describe an extension of higher order Godunov methods to general systems of hyperbolic conservation laws. This extension allow the method to be applied to problems that are not strictly hyperbolic and exhibit local linear degeneracies in the wave fields. The method constructs an approximation of the Riemann problem from local wave information. A generalization of the Engquist--Osher flux for systems is then used to compute a numerical flux based on this approximation. This numerical flux replaces the Godunov numerical flux in the algorithm, thereby eliminating the need for a global Riemann problem solution. The additional modifications to the Godunov methodology that are needed to treat loss of strict hyperbolicity are described in detail. The method is applied to some simple model problems for which the glocal analytic structure is known. The method is also applied to the black-oil model for multiphase flow in petroleum reservoirs. copyright 1989 Academic Press, Inc
Mimasu, Ken; Sanz, Verónica; Williams, Ciaran
2016-08-01
We present predictions for the associated production of a Higgs boson at NLO+PS accuracy, including the effect of anomalous interactions between the Higgs and gauge bosons. We present our results in different frameworks, one in which the interaction vertex between the Higgs boson and Standard Model W and Z bosons is parameterized in terms of general Lorentz structures, and one in which Electroweak symmetry breaking is manifestly linear and the resulting operators arise through a six-dimensional effective field theory framework. We present analytic calculations of the Standard Model and Beyond the Standard Model contributions, and discuss the phenomenological impact of the higher order pieces. Our results are implemented in the NLO Monte Carlo program MCFM, and interfaced to shower Monte Carlos through the Powheg box framework.
Tsai, Yu-Cheng; Cooke, Nancy E; Liebhaber, Stephen A
2016-06-01
The relationships of higher order chromatin organization to mammalian gene expression remain incompletely defined. The human Growth Hormone (hGH) multigene cluster contains five gene paralogs. These genes are selectively activated in either the pituitary or the placenta by distinct components of a remote locus control region (LCR). Prior studies have revealed that appropriate activation of the placental genes is dependent not only on the actions of the LCR, but also on the multigene composition of the cluster itself. Here, we demonstrate that the hGH LCR 'loops' over a distance of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes in the cluster. This long-range interaction sequesters the GH genes from the three hCS genes which co-assemble into a tightly packed 'hCS chromatin hub'. Elimination of the long-range looping, via specific deletion of the placental LCR components, triggers a dramatic disruption of the hCS chromatin hub. These data reveal a higher-order structural pathway by which long-range looping from an LCR impacts on local chromatin architecture that is linked to tissue-specific gene regulation within a multigene cluster. PMID:26893355
Higher order hierarchical discretization scheme for surface integral equations for layered media
DEFF Research Database (Denmark)
Jørgensen, Erik; Kim, Oleksiy S.; Meincke, Peter; Breinbjerg, Olav
2004-01-01
This paper presents an efficient technique for the analysis of electromagnetic scattering by arbitrarily shaped perfectly conducting objects in layered media. The technique is based on a higher order method of moments (MoM) solution of the electric field, magnetic field, or combined-field integral...... 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...
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Meincke, Peter; Breinbjerg, Olav;
2007-01-01
applied to transform the VSIE into a system of linear equations. The higher-order MoM provides significant reduction in the number of unknowns in comparison with standard MoM formulations using low-order basis functions, such as RWG functions. Due to the orthogonal nature of the higher-order Legendre......The problem of electromagnetic scattering by composite metallic and dielectric objects is solved using the coupled volume-surface integral equation (VSIE). The method of moments (MoM) based on higher-order hierarchical Legendre basis functions and higher-order curvilinear geometrical elements is...
International Nuclear Information System (INIS)
The of elution of DNA during non-denaturing filter elution (NFE) often correlates with cell sensitivity to radiation. The elution rate is influenced by two cellular factors: chromatin structure and the number of DNA-strand breaks (DSBs) produced in an intact cell by ionizing radiation. To determine which of the above factors is relevant to cell radiosensitivity, four assays were used to measure induction of DNA damage in three cell lines varying in radiosensitivity (V79, CHO, and L5178Y-R). Each of the assays, neutral filter elution (NFE), DNA precipitation, constant (CFGE) and pulsed field gel electrophoresis (PFGE) have different physical basis for DNA damage measurement and might be differently affected by chromatin structure. Three of the methods used to measure DNA double-strand breaks gave different results: NFE was dependent on cell type and location of DNA relative to the replication fork, gel electrophoresis was independent of cell type but was affected by proximity to the replication fork, and the precipitation assay was independent of both cell type and replication status. Pulsed field gel electrophoresis produced the same results and constant field gel electrophoresis for 3 cell lines examined. Only NFE showed differences in sensitivity which correlated with cell survival following irradiation. The results suggest that three is the same initial amount of DSBs in cells from all three lines and that the sensitivity to radiation is determined by some additional factors, probably chromatin structure. (author). 18 refs, 5 figs
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.
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
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.
Teaching Higher Order Thinking in the Introductory MIS Course: A Model-Directed Approach
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…
An Analysis of Higher-Order Thinking on Algebra I End-of-Course Tests
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…
Regularity of solutions to higher-order integrals of the calculus of variations
Ammi, Moulay Rchid Sidi
2007-01-01
We obtain new regularity conditions for problems of calculus of variations with higher-order derivatives. As a corollary, we get non-occurrence of the Lavrentiev phenomenon. Our main regularity result asserts that autonomous integral functionals with a Lagrangian having coercive partial derivatives with respect to the higher-order derivatives admit only minimizers with essentially bounded derivatives.
Multi-domain, higher order level set scheme for 3D image segmentation on the GPU
DEFF Research Database (Denmark)
Sharma, Ojaswa; Zhang, Qin; Anton, François;
2010-01-01
evaluate level set surfaces that are $C^2$ continuous, but are slow due to high computational burden. In this paper, we provide a higher order GPU based solver for fast and efficient segmentation of large volumetric images. We also extend the higher order method to multi-domain segmentation. Our streaming...
Assessing Higher-Order Cognitive Constructs by Using an Information-Processing Framework
Dickison, Philip; Luo, Xiao; Kim, Doyoung; Woo, Ada; Muntean, William; Bergstrom, Betty
2016-01-01
Designing a theory-based assessment with sound psychometric qualities to measure a higher-order cognitive construct is a highly desired yet challenging task for many practitioners. This paper proposes a framework for designing a theory-based assessment to measure a higher-order cognitive construct. This framework results in a modularized yet…
Schraw, Gregory, Ed.; Robinson, Daniel H., Ed.
2011-01-01
This volume examines the assessment of higher order thinking skills from the perspectives of applied cognitive psychology and measurement theory. The volume considers a variety of higher order thinking skills, including problem solving, critical thinking, argumentation, decision making, creativity, metacognition, and self-regulation. Fourteen…
From "Hello" to Higher-Order Thinking: The Effect of Coaching and Feedback on Online Chats
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…
Complete Bell polynomials and new generalized identities for polynomials of higher order
Rubinstein, Boris Y
2009-01-01
The relations between the Bernoulli and Eulerian polynomials of higher order and the complete Bell polynomials are found that lead to new identities for the Bernoulli and Eulerian polynomials and numbers of higher order. General form of these identities is considered and generating function for polynomials satisfying this general identity is found.
Higher Order Thinking Skills among Secondary School Students in Science Learning
Saido, Gulistan Mohammed; Siraj, Saedah; Bin Nordin, Abu Bakar; Al Amedy, Omed Saadallah
2015-01-01
A central goal of science education is to help students to develop their higher order thinking skills to enable them to face the challenges of daily life. Enhancing students' higher order thinking skills is the main goal of the Kurdish Science Curriculum in the Iraqi-Kurdistan region. This study aimed at assessing 7th grade students' higher order…
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.
Even and Odd Charge Coherent States: Higher-Order Nonclassical Properties and Generation Scheme
Duc, Truong Minh; Dinh, Dang Huu; Dat, Tran Quang
2016-06-01
We examine the higher-order nonclassical properties of the even and odd charge coherent states as well as proposing a scheme to generate these states whose modes can freely travel in open space. We show that the even and odd charge coherent states exhibit both higher-order antibunching and higher-order squeezing. While the two-mode higher-order antibunching occurs in any order and essentially depends on the charge number, the two-mode higher-order squeezing appears only in the even orders. We also prove that these states are genuinely entangled, and they can be generated by means of cross-Kerr media, beam splitters, phase shifts and threshold detectors. We find that the fidelity and the corresponding success probability to generate these states are dependent on the correlative parameters.
Tunneling dynamics of Bose—Einstein condensates with higher-order interactions in optical lattice
International Nuclear Information System (INIS)
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. (general)
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.
International Nuclear Information System (INIS)
Electrophoretic spectra of nuclear proteins, as well as of DNA fragments, forming as a result of activation of liver/testis cell nuclear nucleases of channel fishes from ChNPP cooling reservoir, have been investigated. Differences were found between histone H1 and nonhistone fractions of liver/testis chromatin protein tissues. Nuclear nucleases are also tissue-specific and have different activity
Li, Guoliang; Ruan, Xiaoan; Auerbach, Raymond K.; Sandhu, Kuljeet Singh; Zheng, Meizhen; Wang, Ping; Poh, Huay Mei; Goh, Yufen; Lim, Joanne; Zhang, Jingyao; Sim, Hui Shan; Peh, Su Qin; Mulawadi, Fabianus Hendriyan; Ong, Chin Thing; Orlov, Yuriy L.
2012-01-01
Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIA-PET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intra-genic, extra-genic and inter-genic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engage...
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.
International Nuclear Information System (INIS)
We have examined the ability of intact and histone H1 depleted chromatin fibers to fold into higher ordered structures in vitro following DNA damage by two different agents: UV irradiation at 254 nm and trimethylpsoralen plus near-UV light. Both agents damage DNA specifically, yet cause different degrees of unwinding (and possibly bending) of the DNA helix. In addition, trimethylpsoralen forms interstrand DNA cross-links. The structural transitions of intact and histone H1 depleted chromatin fibers, induced by NaCl, were monitored by analytical ultracentrifugation, light scattering, and circular dichroism. Our results indicate that when chromatin fibers contain even large, nonphysiological amounts of DNA photodamage by either agent, the salt-induced folding of these fibers into higher ordered structures is unaffected. The compact 30-nm fiber must therefore be able to accommodate a large amount of DNA photodamage (greater than one UV-induced photoproduct or trimethylpsoralen interstrand cross-link per nucleosome) with little or no change in the overall size or compaction of this structure
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.
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
2016-08-01
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. PMID:27432957
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
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
2016-01-01
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. PMID:27432957
Ultrastructural organization of replicating chromatin in prematurely condensed chromosomes
Directory of Open Access Journals (Sweden)
Arifulin E. A.
2015-08-01
Full Text Available Aim. The ultrastructural aspect of replicating chromatin organization is a matter of dispute. Here, we have analyzed the ultrastructural organization of replication foci using prematurely condensed chromosomes (PCC. Methods. To investigate the ultrastructure of replicating chromatin, we have used correlative light and electron microscopy as well as immunogold staining. Results. Replication in PCC occurs in the gaps between condensed chromatin domains. Using correlative light and electron microscopy, we observed that the replication foci contain decondensed chromatin as well as 80 and 130 nm globules, those were also found in condensed non-replicating chromatin domains. Using immunogolding, we demonstrated that DNA replication in S-phase PCC occurs in loose chromatin on the periphery of dense chromatin domains. Conclusion. Replication in PCC occurred in the decondensed chromatin neighboring the condensed chromatin without formation of special structures.
Shock waves with higher order effects in an electron depleted dusty Plasma
Ghai, Yashika; Singh Saini, Nareshpal; Singh, Manpreet
2016-07-01
Shock waves are characterized as a sudden change in properties of the medium that propagate faster than the speed of sound. A plasma system in which dissipation is dominant over dispersion of the medium, the balance between dissipation and nonlinearity leads to the formation of shock structures. A number of observations and in-situ measurements have confirmed the presence of excess superthermal populations in astrophysical and space plasmas. In fact, two temperature superthermal ion populations have been observed by Geotail spacecraft in earth's magnetotail. Moreover, charging of dust by accumulation of electrons in plasma leads to electron depleted plasma. In present investigation, shocks in an electron depleted dusty plasma with two temperature superthermal ions have been studied by using Burger's equation. Further, to incorporate higher order nonlinear effects, we have derived modified Burger's equation and studied its shock solution. The effects of various physical parameters such as superthermality of ions, kinematic viscosity and dust concentration have been observed on properties of shock structures. The results of present investigation may be useful in understanding the nonlinear structures formed in earth's atmosphere where dust and two temperature superthermal ions are observed.
Multi-domain, higher order level set scheme for 3D image segmentation on the GPU
DEFF Research Database (Denmark)
Sharma, Ojaswa; Zhang, Qin; Anton, François; Bajaj, Chandrajit
evaluate level set surfaces that are $C^2$ continuous, but are slow due to high computational burden. In this paper, we provide a higher order GPU based solver for fast and efficient segmentation of large volumetric images. We also extend the higher order method to multi-domain segmentation. Our streaming......Level set method based segmentation provides an efficient tool for topological and geometrical shape handling. Conventional level set surfaces are only $C^0$ continuous since the level set evolution involves linear interpolation to compute derivatives. Bajaj et al. present a higher order method to...
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...
Modulational instability of a modified Gross-Pitaevskii equation with higher-order nonlinearity.
Qi, Xiu-Ying; Xue, Ju-Kui
2012-07-01
We consider the modulational instability (MI) of Bose-Einstein condensate (BEC) described by a modified Gross-Pitaevskii (GP) equation with higher-order nonlinearity both analytically and numerically. A new explicit time-dependent criterion for exciting the MI is obtained. It is shown that the higher-order term can either suppress or enhance the MI, which is interesting for control of the system instability. Importantly, we predict that with the help of the higher-order nonlinearity, the MI can also take place in a BEC with repulsively contact interactions. The analytical results are confirmed by direct numerical simulations. PMID:23005569
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
An efficient technique for the analysis of electromagnetic scattering by arbitrary shaped inhomogeneous dielectric objects is presented. The technique is based on a higher-order method of moments (MoM) solution of the volume integral equation. This higher-order MoM solution comprises recently...... the condition number of the resulting MoM matrix is reduced by several orders of magnitude in comparison to existing higher-order hierarchical basis functions and, consequently, an iterative solver can be applied even for high expansion orders. Numerical results demonstrate excellent agreement with...
Higher order capacity statistics of multi-hop transmission systems over Rayleigh fading channels
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.
On the Continuity Condition for the Higher-Order VSIE-MoM Formulation
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter;
2004-01-01
A higher-order method of moments (MoM) solution of the volume-surface integral equation (VSIE) based on the higher-order hierarchical Legendre basis functions is presented. The technique is suitable for solving electromagnetic problems involving composite metallic-dielectric objects. Numerical...... examples for a finite FSS show that the explicit enforcement of the continuity condition at a metallic-dielectric interface significantly improves the solution if higher-order basis functions are defined on rather large domains with metallic edges present. This improvement manifests itself in reducing the...
Nuclease Footprints in Sperm Project Past and Future Chromatin Regulatory Events.
Johnson, Graham D; Jodar, Meritxell; Pique-Regi, Roger; Krawetz, Stephen A
2016-01-01
Nuclear remodeling to a condensed state is a hallmark of spermatogenesis. This is achieved by replacement of histones with protamines. Regions retaining nucleosomes may be of functional significance. To determine their potential roles, sperm from wild type and transgenic mice harboring a single copy insert of the human protamine cluster were subjected to Micrococcal Nuclease-seq. CENTIPEDE, a hierarchical Bayesian model, was used to identify multiple spatial patterns, "footprints", of MNase-seq reads along the sperm genome. Regions predicted by CENTIPEDE analysis to be bound by a regulatory factor in sperm were correlated with genomic landmarks and higher order chromatin structure datasets to identify potential roles for these factors in regulating either prior or post spermatogenic, i.e., early embryonic events. This approach linked robust endogenous protamine transcription and transgene suppression to its chromatin environment within topologically associated domains. Of the candidate enhancer-bound regulatory proteins, Ctcf, was associated with chromatin domain boundaries in testes and embryonic stem cells. The continuity of Ctcf binding through the murine germline may permit rapid reconstitution of chromatin organization following fertilization. This likely reflects its preparation for early zygotic genome activation and comparatively accelerated preimplantation embryonic development program observed in mouse as compared to human and bull. PMID:27184706
International Nuclear Information System (INIS)
Studies over the past two decades have clearly shown that reproductive toxicants cause sperm DNA fragmentation. This DNA fragmentation can usually be detected prior to observing alterations of metaphase chromosomes in embryos. Thus, Sperm Chromatin Structure Assay (SCSA)-detected DNA damage is viewed as the molecular precursor to later gross chromosome damage observed under the light microscope. SCSA measurements of animal or human sperm consist of first obtaining a fresh or flash frozen neat semen sample in LN2 or dry ice. Samples are then sent to a SCSA diagnostic laboratory where the samples are thawed, diluted to ∼1-2 x 106 sperm/ml, treated for 30 s with a pH 1.2 detergent buffer and then stained with acridine orange (AO). The low pH partially denatures DNA at the sites of DNA strand breaks and the AO-ssDNA fluoresces red while the AO-dsDNA fluoresces green. Flow cytometry measurements of 5000 sperm/sample provide statistically robust data on the ratio of red to green sperm, the extent of the DNA fragmentation and the standard deviations of measures. Numerous experiments on rodents treated with reproductive toxicants clearly showed that SCSA measures are highly dose responsive and have a very low CV. Different agents that act on germ cells at various stages of development usually showed sperm DNA fragmentation when that germ cell fraction arrived in the epididymis or ejaculate. Some of these treated samples were capable of successful in vitro fertilization but with frequent embryo failure. A 2-year longitudinal study of men living a valley town with a reported abnormal level of infertility and spontaneous miscarriages and also a seasonal atmospheric smog pollution, showed, for the first time, that SCSA measurements of human sperm DNA fragmentation were detectable and correlated with dosage of air pollution while the classical semen measures were not correlated. Also, young men spraying pesticides without protective gear are at an increased risk for elevated
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.
Experimental test of higher-order Laguerre–Gauss modes in the 10 m Glasgow prototype interferometer
International Nuclear Information System (INIS)
Brownian noise of dielectric mirror coatings is expected to be one of the limiting noise sources, at the peak sensitivity, of next generation ground based interferometric gravitational wave (GW) detectors. The use of higher-order Laguerre–Gauss (LG) beams has been suggested to reduce the effect of coating thermal noise in future generations of gravitational wave detectors. In this paper we describe the first test of interferometry with higher-order LG beams in an environment similar to a full-scale gravitational wave detector. We compare the interferometric performance of higher-order LG modes and the fundamental mode beams, injected into a 10 m long suspended cavity that features a finesse of 612, a value chosen to be typical of future gravitational wave detectors. We found that the expected mode degeneracy of the injected LG3,3 beam was resolved into a multiple peak structure, and that the cavity length control signal featured several nearby zero crossings. The break up of the mode degeneracy is due to an astigmatism (defined as |Rcy − Rcx|) of 5.25 ± 0.5 cm on one of our cavity mirrors with a radius of curvature (Rc) of 15 m. This observation agrees well with numerical simulations developed with the FINESSE software. We also report on how these higher-order mode beams respond to the misalignment and mode mismatch present in our 10 m cavity. In general we found the LG3,3 beam to be considerably more susceptible to astigmatism and mode mismatch than a conventional fundamental mode beam. Therefore the potential application of higher-order Laguerre–Gauss beams in future gravitational wave detectors will impose much more stringent requirements on both mode matching and mirror astigmatism. (paper)
Huang, T W; Zhou, C T; He, X T
2013-05-01
Plasma defocusing and higher-order Kerr effects on multiple filamentation and pattern formation of ultrashort laser pulse propagation in air are investigated. Linear analyses and numerical results show that these two saturable nonlinear effects can destroy the coherent evolution of the laser field, and small-scale spatial turbulent structures rapidly appear. For the two-dimensional case, numerical simulations show that blow-up-like solutions, spatial chaos, and pseudorecurrence can appear at higher laser intensities if only plasma defocusing is included. These complex patterns result from the stochastic evolution of the higher- or shorter-wavelength modes of the laser light spectrum. From the viewpoint of nonlinear dynamics, filamentation can be attributed to the modulational instability of these spatial incoherent localized structures. Furthermore, filament patterns associated with multiphoton ionization of the air molecules with and without higher-order Kerr effects are compared. PMID:23767639
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.
Existence Results for Higher-Order Boundary Value Problems on Time Scales
Sang Yanbin; Liu Jian
2009-01-01
By using the fixed-point index theorem, we consider the existence of positive solutions for the following nonlinear higher-order four-point singular boundary value problem on time scales , ; , ; , ; , , where , , , , , , , and is rd-continuous.
Higher-order mass defect analysis for mass spectra of complex organic mixtures.
Roach, Patrick J; Laskin, Julia; Laskin, Alexander
2011-06-15
Higher-order mass defect analysis is introduced as a unique formula assignment and visualization method for the analysis of complex mass spectra. This approach is an extension of the concepts of Kendrick mass transformation widely used for identification of homologous compounds differing only by a number of base units (e.g., CH(2), H(2), O, CH(2)O, etc.) in complex mixtures. We present an iterative renormalization routine for defining higher-order homologous series and multidimensional clustering of mass spectral features. This approach greatly simplifies visualization of complex mass spectra and increases the number of chemical formulas that can be confidently assigned for given mass accuracy. The potential for using higher-order mass defects for data reduction and visualization is shown. Higher-order mass defect analysis is described and demonstrated through third-order analysis of a deisotoped high-resolution mass spectrum of crude oil containing nearly 13,000 peaks. PMID:21526851
The geometry of higher-order Lagrange spaces applications to mechanics and physics
Miron, Radu
1997-01-01
This monograph is devoted to the problem of the geometrizing of Lagrangians which depend on higher-order accelerations It presents a construction of the geometry of the total space of the bundle of the accelerations of order k>=1 A geometrical study of the notion of the higher-order Lagrange space is conducted, and the old problem of prolongation of Riemannian spaces to k-osculator manifolds is solved Also, the geometrical ground for variational calculus on the integral of actions involving higher-order Lagrangians is dealt with Applications to higher-order analytical mechanics and theoretical physics are included as well Audience This volume will be of interest to scientists whose work involves differential geometry, mechanics of particles and systems, calculus of variation and optimal control, optimization, optics, electromagnetic theory, and biology
The Need to Deliver Higher-Order Skills in the Context of Marketing in SMEs
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
Zembrzycki, Andreas; Stocker, Adam M; Leingärtner, Axel; Sahara, Setsuko; Chou, Shen-Ju; Kalatsky, Valery; May, Scott R; Stryker, Michael P; O'Leary, Dennis Dm
2015-01-01
In mammals, the neocortical layout consists of few modality-specific primary sensory areas and a multitude of higher order ones. Abnormal layout of cortical areas may disrupt sensory function and behavior. Developmental genetic mechanisms specify primary areas, but mechanisms influencing higher order area properties are unknown. By exploiting gain-of and loss-of function mouse models of the transcription factor Emx2, we have generated bi-directional changes in primary visual cortex size in vivo and have used it as a model to show a novel and prominent function for genetic mechanisms regulating primary visual area size and also proportionally dictating the sizes of surrounding higher order visual areas. This finding redefines the role for intrinsic genetic mechanisms to concomitantly specify and scale primary and related higher order sensory areas in a linear fashion. PMID:26705332
Higher-order factor analysis and functional regionalization: a case study in South Wales, 1971
Davies, W. K. D.
1980-01-01
A method for functional regionalization based on higher-order factor analysis is proposed. The utility of the method when using alternative factorial procedures is described by reference to a study of journey-to-work flows in South Wales in 1971, in which the stability of the results under alternative factorial procedures is explored. The advantages of the higher-order factorial approach compared with previously suggested methodologies are documented.
Higher order mode of a microstripline fed cylindrical dielectric resonator antenna
Kumar, A. V. Praveen
2016-03-01
A microstrip transmission line can be used to excite the broadside radiating mode of a cylindrical dielectric resonator antenna (CDRA). The same is found to excite considerably well a higher order mode (HOM) as well. However unlike the broadside mode, the higher order mode gives distorted radiation pattern which makes this mode less useful for practical applications. The cause of distortion in the HOM radiation and the dependence of HOM coupling on the microstrip feed line are explored using HFSS simulations.
Caleb Chidozie Chinedu; Oladiran Stephen Olabiyi; Yusri Bin Kamin
2015-01-01
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 o...
The contrasting role of higher order awareness in hypnosis and meditation
Semmens-Wheeler, Rebecca
2013-01-01
Two key questions underpin the research presented here. Firstly, how does altered higher order awareness contribute to hypnotic experience? Secondly, how do meditation and hypnosis differ in terms of the role of higher order awareness? These questions are addressed here in the form of four papers. In the first paper I review the literatures of hypnosis and meditation in order to consider the similarities and differences between meditation and hypnosis in terms of the role of attentional skill...
Lagrangian-Hamiltonian unified formalism for autonomous higher-order dynamical systems
Prieto Martínez, Pedro Daniel; Román Roy, Narciso
2011-01-01
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, as well as for first-order and higher-order field theories. However, a complete generalization to higher-order mechanical systems has yet to be described. In this work, after reviewing the natural geometrical setting and the Lagrangian and Hamiltonian formalisms for highe...
Springer, Andreas
2015-01-01
This work discusses the viability of constructing efficient discontinuous Galerkin time discretizations of higher order for optimal control problems governed by parabolic partial differential equations. In particular, we address the issue of efficient solution of the resulting large implicit time stepping equations and develop two ways of achieving rapid convergence with higher order dG methods in spite of the typically low regularity of solutions when additional inequality constraints are pr...
Higher-Order Income Risk and Social Insurance Policy Over the Business Cycle
Rocio Madera; Fatih Guvenen; David Domeij; Christopher Busch
2015-01-01
This paper studies how higher-order income risk varies over the business cycle as well as the extent to which such risks can be smoothed within households or with government social insurance policies. To provide a broad perspective on these questions, we study panel data on individuals and households from the United States, Germany, and Sweden, covering more than three decades of data for each country. We find that the underlying variation in higher-order risk is remarkably similar across the...
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.
International Nuclear Information System (INIS)
The supersymmetric version of the Stueckelberg Lagrangian of the massive vector superfield leads to an example of higher-order derivative model. The canonical quantization yields massive states which compose two irreducible representations, one physical supermultiplet and another spurious. The origin of the different spurious states are investigated, especially those originating from the higher-order derivative terms. The spurious superfield is found to be decoupled when the supercurrent satisfies some appropriate conditions. (orig.)
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.)
Equivalent representations of higher-order Hamiltonian guiding-center theory
Brizard, Alain J.; Tronko, Natalia
2012-01-01
Two complementary representations of higher-order guiding-center theory are presented, which are distinguished by whether higher-order corrections due to magnetic-field nonuniformity appear in the guiding-center Poisson bracket or the guiding-center Hamiltonian. The equivalence of these two representations implies that the guiding-center gyroaction adiabatic invariant and the guiding-center Hamilton equations of motion are representation-invariants. By using a new perturbative hierarchy in gu...
Das, Saptarshi; Saha, Suman; Das, Shantanu; Gupta, Amitava
2012-01-01
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 modeling 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 orde...
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.
Hencken, Kai; Trautmann, Dirk; Baur, Gerhard
1998-01-01
We present a calculation of higher order effects for the impact parameter dependent probability for single and multiple electron-positron pairs in (peripheral) relativistic heavy ion collisions. Also total cross sections are given for SPS and RHIC energies. We make use of the expression derived recently by several groups where the summation of all higher orders can be done analytically in the high energy limit. An astonishing result is that the cross section, that is, integrating over all imp...
On Prediction of 3d Stress State in Elastic Shell by Higher-order Shell Formulations
Brank, Boštjan; Ibrahimbegović, Adnan; Bohinc, Uroš
2008-01-01
In this work we study the accuracy of modem higher-order shell finite element formulations in computation of 3d stress state in elastic shells. In that sense we compare three higher-order shell models: (i) with seven dislacement-like kinematic parameters, and (ii, iii) with six displacement-like kinematic parameters plus one strain-like kinematic parameter introduced by two different versions of enhanced assumed strain (EAS) concept. The finite element approximations of all shell models are b...
TreatJS: Higher-Order Contracts for JavaScript (Artifact)
Keil, Matthias; Thiemann, Peter
2015-01-01
TreatJS is a language embedded, higher-order contract system for JavaScript which enforces contracts by run-time monitoring. Beyond providing the standard abstractions for building higher-order contracts (base, function, and object contracts), TreatJS's novel contributions are its guarantee of non-interfering contract execution, its systematic approach to blame assignment, its support for contracts in the style of union and intersection types, and its notion of a parameterized contract scope,...
On higher order radiative corrections to elastic electron-proton scattering
Arbuzov, A B
2015-01-01
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 A1 Collaboration. Calculations are performed within the next-to-leading approximation. Inclusion of the higher order effects can affect the value of the proton charge radius extracted from the experimental data.
Higher order harmonic detection for exploring nonlinear interactions with nanoscale resolution
Vasudevan, R. K.; M. Baris Okatan; Rajapaksa, I.; Kim, Y.; Marincel, D.; Trolier-McKinstry, S.; Jesse, S.; Valanoor, N.; Kalinin, S. V.
2013-01-01
Nonlinear dynamics underpin a vast array of physical phenomena ranging from interfacial motion to jamming transitions. In many cases, insight into the nonlinear behavior can be gleaned through exploration of higher order harmonics. Here, a method using band excitation scanning probe microscopy (SPM) to investigate higher order harmonics of the electromechanical response, with nanometer scale spatial resolution is presented. The technique is demonstrated by probing the first three harmonics of...
Glunčić, Matko; Rosandić, Marija; Jelovina, Denis; Dekanić, Krešimir; Vlahović, Ines; Paar, Vladimir
2012-01-01
Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to the functional and structural role within centromere they are also a suitable model for evolutionary stud-ies, because of being subject to concerted evolution. The Global Repeat Map (GRM) algorithm is a convenient computational tool to determine consensus repeat units and their exact size within a given genomic sequence, both of monomeric and higher-order (HOR) type. Using GRM, we identify in Build...
Higher-order weakly nonlinear theory for internal waves in three-layer fluid
Kurkina, O. E.; Kurkin, A. A.; Rouvinskaya, E. A.
2012-04-01
Three-layer stratifications are proved to be a proper approximation of sea water density profile in some basins in the World Ocean with specific hydrological conditions. Some shallow basins such as the Baltic Sea and some river estuaries have more or less continuous three-layer vertical structure caused by the interplay of fresh water discharge to the surface and salt water intrusion in the bottom layers. In order to describe the basic features of the internal wave field in such environments it is necessary to introduce a three-layer model. Such models are considerably more complex than the most popular two-layer systems; however, they represent new dynamical effects and allow for much more analytical progress in their studies compared to the fully stratified situation. In the present study two modes of long internal gravity waves in a three-layer fluid are investigated in the framework of higher-order nonlinear evolutionary equations derived with the use of asymptotic procedure from the governing Euler equations for inviscid incompressible layered medium with "rigid lid" and horizontal impermeable bottom. The equations are written upto the fifth order of the perturbation theory for both interfaces for the waves of both modes: first (fast mode) and second (slow mode, so-called double-humped or varicose). For each equation the coefficients of nonlinearity, dispersion and nonlinear dispersion are expressed explicitly in terms of parameters of this fluid configuration. The behavior and signs of the coefficients are analyzed. The necessary order of the equations is discussed and determined for each case. A few nonlinear asymptotic transformations are proposed to reduce higher-order equations to simpler lower-order or well-known integrable equations (Korteweg - de Vries, Gardner equations). Special attention is paid to the situations when the nonlinear terms of lower orders of perturbation theory can vanish. For such situations particular rescaling is performed in order
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.
Higher Order and Harmonic Corrections to the Quasi-de Sitter Inflation
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.
Magnitude and significance of the higher-order reduced density matrix cumulants
Herbert, John M.
Using full configuration interaction wave functions for Be and LiH, in both minimal and extended basis sets, we examine the absolute magnitude and energetic significance of various contributions to the three-electron reduced density matrix (3-RDM) and its connected (size-consistent) component, the 3-RDM cumulant (3-RDMC). Minimal basis sets are shown to suppress the magnitude of the 3-RDMC in an artificial manner, whereas in extended basis sets, 3-RDMC matrix elements are often comparable in magnitude to the corresponding 3-RDM elements, even in cases where this result is not required by spin angular momentum coupling. Formal considerations suggest that these observations should generalize to higher-order p-RDMs and p-RDMCs (p > 3). This result is discussed within the context of electronic structure methods based on the contracted Schrödinger equation (CSE), as solution of the CSE relies on 3- and 4-RDM ?reconstruction functionals? that neglect the 3-RDMC, the 4-RDMC, or both. Although the 3-RDMC is responsible for at most 0.2% of the total electronic energy in Be and LiH, it accounts for up to 70% of the correlation energy, raising questions regarding whether (and how) the CSE can offer a useful computational methodology.
Functional independence in resting-state connectivity facilitates higher-order cognition.
James, G Andrew; Kearney-Ramos, Tonisha E; Young, Jonathan A; Kilts, Clinton D; Gess, Jennifer L; Fausett, Jennifer S
2016-06-01
Growing evidence suggests that intrinsic functional connectivity (i.e. highly structured patterns of communication between brain regions during wakeful rest) may encode cognitive ability. However, the generalizability of these findings is limited by between-study differences in statistical methodology and cognitive domains evaluated. To address this barrier, we evaluated resting-state neural representations of multiple cognitive domains within a relatively large normative adult sample. Forty-four participants (mean(sd) age=31(10) years; 18 male and 26 female) completed a resting-state functional MRI scan and neuropsychological assessments spanning motor, visuospatial, language, learning, memory, attention, working memory, and executive function performance. Robust linear regression related cognitive performance to resting-state connectivity among 200 a priori determined functional regions of interest (ROIs). Only higher-order cognitions (such as learning and executive function) demonstrated significant relationships between brain function and behavior. Additionally, all significant relationships were negative - characterized by moderately positive correlations among low performers and weak to moderately negative correlations among high performers. These findings suggest that functional independence among brain regions at rest facilitates cognitive performance. Our interpretation is consistent with graph theoretic analyses which represent the brain as independent functional nodes that undergo dynamic reorganization with task demand. Future work will build upon these findings by evaluating domain-specific variance in resting-state neural representations of cognitive impairment among patient populations. PMID:27105037
Siebenlist, U; Durand, D B; Bressler, P; Holbrook, N J; Norris, C A; Kamoun, M.; Kant, J A; Crabtree, G R
1986-01-01
The chromatin structure of the interleukin-2 (IL-2) gene was probed by DNase I treatment of isolated nuclei. The 5' region of the IL-2 gene contains three regions of hypersensitivity to DNase I. When peripheral blood T cells or Jurkat T cells are stimulated with mitogens, IL-2 message is induced, and the promoter region of the IL-2 gene develops an additional hypersensitive site. This suggests that a DNA sequence close to the transcriptional start site is involved in the transduction of the e...
Where splicing joins chromatin
Hnilicová, Jarmila; Staněk, David
2011-01-01
There are numerous data suggesting that two key steps in gene expression—transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and...