Neutron scattering studies on chromatin higher-order structure
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
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.
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
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
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...
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
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
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.
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
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
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
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
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
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…
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
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.
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.
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*
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
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.
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
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
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.
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
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
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
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.
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.
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...
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).
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.
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
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
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...
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
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
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
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
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.
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
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
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
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
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
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.
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...
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
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
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
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....
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
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
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
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
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
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.
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
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
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
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
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.
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
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.
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
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
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...
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
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
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
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
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
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...
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...
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
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
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
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
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
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
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
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
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
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
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
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.
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
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
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
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.
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
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
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
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
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
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
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
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
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
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
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
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.
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.
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
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
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
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
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
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
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
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.