Neutron scattering studies on chromatin higher-order structure
Energy Technology Data Exchange (ETDEWEB)
Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V. [Brookhaven National Laboratory, Upton, NY (United States)
1994-12-31
We have been engaged in studies of the structure and condensation of chromatin into the 30nm filament using small-angle neutron scattering. We have also used deuterated histone H1 to determine its location in the chromatin 30nm filament. Our studies indicate that chromatin condenses with increasing ionic strength to a limiting structure that has a mass per unit length of 6-7 nucleosomes/11 nm. They also show that the linker histone H1/H5 is located in the interior of the chromatin filament, in a position compatible with its binding to the inner face of the nucleosome. Analysis of the mass per unit length as a function of H5 stoichiometry suggests that 5-7 contiguous nucleosomes need to have H5 bound before a stable higher order structure can exist.
Higher order chromatin structure: bridging physics and biology
Fudenberg, Geoffrey; Mirny, Leonid A.
2012-01-01
Recent advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of high-order interph...
ISWI regulates higher-order chromatin structure and histone H1 assembly in vivo.
Directory of Open Access Journals (Sweden)
Davide F V Corona
2007-09-01
Full Text Available Imitation SWI (ISWI and other ATP-dependent chromatin-remodeling factors play key roles in transcription and other processes by altering the structure and positioning of nucleosomes. Recent studies have also implicated ISWI in the regulation of higher-order chromatin structure, but its role in this process remains poorly understood. To clarify the role of ISWI in vivo, we examined defects in chromosome structure and gene expression resulting from the loss of Iswi function in Drosophila. Consistent with a broad role in transcriptional regulation, the expression of a large number of genes is altered in Iswi mutant larvae. The expression of a dominant-negative form of ISWI leads to dramatic alterations in higher-order chromatin structure, including the apparent decondensation of both mitotic and polytene chromosomes. The loss of ISWI function does not cause obvious defects in nucleosome assembly, but results in a significant reduction in the level of histone H1 associated with chromatin in vivo. These findings suggest that ISWI plays a global role in chromatin compaction in vivo by promoting the association of the linker histone H1 with chromatin.
Hydrogen peroxide mediates higher order chromatin degradation.
Bai, H; Konat, G W
2003-01-01
Although a large body of evidence supports a causative link between oxidative stress and neurodegeneration, the mechanisms are still elusive. We have recently demonstrated that hydrogen peroxide (H(2)O(2)), the major mediator of oxidative stress triggers higher order chromatin degradation (HOCD), i.e. excision of chromatin loops at the matrix attachment regions (MARs). The present study was designed to determine the specificity of H(2)O(2) in respect to HOCD induction. Rat glioma C6 cells were exposed to H(2)O(2) and other oxidants, and the fragmentation of genomic DNA was assessed by field inversion gel electrophoresis (FIGE). S1 digestion before FIGE was used to detect single strand fragmentation. The exposure of C6 cells to H(2)O(2) induced a rapid and extensive HOCD. Thus, within 30 min, total chromatin was single strandedly digested into 50 kb fragments. Evident HOCD was elicited by H(2)O(2) at concentrations as low as 5 micro M. HOCD was mostly reversible during 4-8h following the removal of H(2)O(2) from the medium indicating an efficient relegation of the chromatin fragments. No HOCD was induced by H(2)O(2) in isolated nuclei indicating that HOCD-endonuclease is activated indirectly by cytoplasmic signal pathways triggered by H(2)O(2). The exposure of cells to a synthetic peroxide, i.e. tert-butyrylhydroperoxide (tBH) also induced HOCD, but to a lesser extent than H(2)O(2). Contrary to the peroxides, the exposure of cells to equitoxic concentration of hypochlorite and spermine NONOate, a nitric oxide generator, failed to induce rapid HOCD. These results indicate that rapid HOCD is not a result of oxidative stress per se, but is rather triggered by signaling cascades initiated specifically by H(2)O(2). Furthermore, the rapid and extensive HOCD was observed in several rat and human cell lines challenged with H(2)O(2), indicating that the process is not restricted to glial cells, but rather represents a general response of cells to H(2)O(2). PMID:12421592
A new non-catalytic role for ubiquitin ligase RNF8 in unfolding higher-order chromatin structure
DEFF Research Database (Denmark)
Luijsterburg, Martijn S; Acs, Klara; Ackermann, Leena;
2012-01-01
The ubiquitin ligases RNF8 and RNF168 orchestrate DNA damage signalling through the ubiquitylation of histone H2A and the recruitment of downstream repair factors. Here, we demonstrate that RNF8, but not RNF168 or the canonical H2A ubiquitin ligase RNF2, mediates extensive chromatin decondensatio...
Directory of Open Access Journals (Sweden)
Lisa Herr
Full Text Available We present a new approach to model dose rate effects on cell killing after photon radiation based on the spatio-temporal clustering of DNA double strand breaks (DSBs within higher order chromatin structures of approximately 1-2 Mbp size, so called giant loops. The main concept of this approach consists of a distinction of two classes of lesions, isolated and clustered DSBs, characterized by the number of double strand breaks induced in a giant loop. We assume a low lethality and fast component of repair for isolated DSBs and a high lethality and slow component of repair for clustered DSBs. With appropriate rates, the temporal transition between the different lesion classes is expressed in terms of five differential equations. These allow formulating the dynamics involved in the competition of damage induction and repair for arbitrary dose rates and fractionation schemes. Final cell survival probabilities are computable with a cell line specific set of three parameters: The lethality for isolated DSBs, the lethality for clustered DSBs and the half-life time of isolated DSBs. By comparison with larger sets of published experimental data it is demonstrated that the model describes the cell line dependent response to treatments using either continuous irradiation at a constant dose rate or to split dose irradiation well. Furthermore, an analytic investigation of the formulation concerning single fraction treatments with constant dose rates in the limiting cases of extremely high or low dose rates is presented. The approach is consistent with the Linear-Quadratic model extended by the Lea-Catcheside factor up to the second moment in dose. Finally, it is shown that the model correctly predicts empirical findings about the dose rate dependence of incidence probabilities for deterministic radiation effects like pneumonitis and the bone marrow syndrome. These findings further support the general concepts on which the approach is based.
Higher Order Hessian Structures on Manifolds
Indian Academy of Sciences (India)
R David Kumar
2005-08-01
In this paper we define th order Hessian structures on manifolds and study them. In particular, when =3, we make a detailed study and establish a one-to-one correspondence between third-order Hessian structures and a certain class of connections on the second-order tangent bundle of a manifold. Further, we show that a connection on the tangent bundle of a manifold induces a connection on the second-order tangent bundle. Also we define second-order geodesics of special second-order connection which gives a geometric characterization of symmetric third-order Hessian structures.
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Ashwat Visvanathan
Full Text Available The organisation of the large volume of mammalian genomic DNA within cell nuclei requires mechanisms to regulate chromatin compaction involving the reversible formation of higher order structures. The compaction state of chromatin varies between interphase and mitosis and is also subject to rapid and reversible change upon ATP depletion/repletion. In this study we have investigated mechanisms that may be involved in promoting the hyper-condensation of chromatin when ATP levels are depleted by treating cells with sodium azide and 2-deoxyglucose. Chromatin conformation was analysed in both live and permeabilised HeLa cells using FLIM-FRET, high resolution fluorescence microscopy and by electron spectroscopic imaging microscopy. We show that chromatin compaction following ATP depletion is not caused by loss of transcription activity and that it can occur at a similar level in both interphase and mitotic cells. Analysis of both live and permeabilised HeLa cells shows that chromatin conformation within nuclei is strongly influenced by the levels of divalent cations, including calcium and magnesium. While ATP depletion results in an increase in the level of unbound calcium, chromatin condensation still occurs even in the presence of a calcium chelator. Chromatin compaction is shown to be strongly affected by small changes in the levels of polyamines, including spermine and spermidine. The data are consistent with a model in which the increased intracellular pool of polyamines and divalent cations, resulting from depletion of ATP, bind to DNA and contribute to the large scale hyper-compaction of chromatin by a charge neutralisation mechanism.
H2 O2-induced higher order chromatin degradation: A novel mechanism of oxidative genotoxicity
Indian Academy of Sciences (India)
Gregory W Konat
2003-02-01
The genotoxicity of reactive oxygen species (ROS) is well established. The underlying mechanism involves oxidation of DNA by ROS. However, we have recently shown that hydrogen peroxide (H2O2), the major mediator of oxidative stress, can also cause genomic damage indirectly. Thus, H2O2 at pathologically relevant concentrations rapidly induces higher order chromatin degradation (HOCD), i.e. enzymatic excision of chromatin loops and their oligomers at matrix-attachment regions. The activation of endonuclease that catalyzes HOCD is a signalling event triggered specifically by H2O2. The activation is not mediated by an influx of calcium ions, but resting concentrations of intracellular calcium ions are required for the maintenance of the endonuclease in an active form. Although H2O2-induced HOCD can efficiently dismantle the genome leading to cell death, under sublethal oxidative stress conditions H2O2-induced HOCD may be the major source of somatic mutations.
Mardaryev, Andrei N.; Gdula, Michal R.; Yarker, Joanne L.; Emelianov, Vladimir N.; Poterlowicz, Krzysztof; Sharov, Andrey A.; Sharova, Tatyana Y.; Scarpa, Julie A.; Chambon, Pierre; Botchkarev, Vladimir A.; Fessing, Michael Y.
2014-01-01
Chromatin structural states and their remodelling, including higher-order chromatin folding and three-dimensional (3D) genome organisation, play an important role in the control of gene expression. The role of 3D genome organisation in the control and execution of lineage-specific transcription programmes during the development and differentiation of multipotent stem cells into specialised cell types remains poorly understood. Here, we show that substantial remodelling of the higher-order chromatin structure of the epidermal differentiation complex (EDC), a keratinocyte lineage-specific gene locus on mouse chromosome 3, occurs during epidermal morphogenesis. During epidermal development, the locus relocates away from the nuclear periphery towards the nuclear interior into a compartment enriched in SC35-positive nuclear speckles. Relocation of the EDC locus occurs prior to the full activation of EDC genes involved in controlling terminal keratinocyte differentiation and is a lineage-specific, developmentally regulated event controlled by transcription factor p63, a master regulator of epidermal development. We also show that, in epidermal progenitor cells, p63 directly regulates the expression of the ATP-dependent chromatin remodeller Brg1, which binds to distinct domains within the EDC and is required for relocation of the EDC towards the nuclear interior. Furthermore, Brg1 also regulates gene expression within the EDC locus during epidermal morphogenesis. Thus, p63 and its direct target Brg1 play an essential role in remodelling the higher-order chromatin structure of the EDC and in the specific positioning of this locus within the landscape of the 3D nuclear space, as required for the efficient expression of EDC genes in epidermal progenitor cells during skin development. PMID:24346698
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
Switchable photooxygenation catalysts that sense higher-order amyloid structures
Taniguchi, Atsuhiko; Shimizu, Yusuke; Oisaki, Kounosuke; Sohma, Youhei; Kanai, Motomu
2016-10-01
Proteins can misfold into amyloid structures that are associated with diseases; however, the same proteins often have important biological roles. To degrade selectively the amyloid form without affecting the fraction of functional protein is, therefore, an attractive goal. Here we report target-state-dependent photooxygenation catalysts that are active only when bound to the cross-β-sheet structure that is characteristic of pathogenic aggregated amyloid proteins. We show these catalysts can selectively oxygenate the amyloid form of amyloid β-protein (Aβ) 1-42 in the presence of non-amyloid off-target substrates. Furthermore, photooxygenation with a catalyst that bears an Aβ-binding peptide attenuated the Aβ pathogenicity in the presence of cells. We also show that selective photooxygenation is generally applicable to other amyloidogenic proteins (amylin, insulin, β2-microglobulin, transthyretin and α-synuclein) and does not affect the physiologically functional non-aggregate states of these proteins. This is the first report of an artificial catalyst that can be selectively and reversibly turned on and off depending on the structure and aggregation state of the substrate protein.
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…
McGill, Ryan J.; Canivez, Gary L.
2016-01-01
As recommended by Carroll, the present study examined the factor structure of the Wechsler Intelligence Scale for Children-Fourth Edition Spanish (WISC-IV Spanish) normative sample using higher order exploratory factor analytic techniques not included in the WISC-IV Spanish Technical Manual. Results indicated that the WISC-IV Spanish subtests were…
International Nuclear Information System (INIS)
An admittance-based structure health monitoring method with a higher-order resonant circuit is proposed and investigated in this paper, with the advantage of increased damage detection sensitivity. The change of the stiffness or mass in the structure due to damage can be detected by measuring the admittance from the piezoelectric transducer adhered to the host structure. It is known that designing an inductive circuitry, together with the piezoelectric capacitance, can introduce an additional resonance and yield enhanced sensitivity. In this paper, based on the electrical–mechanical analogy, a novel higher-order resonant circuit is designed and optimized to significantly improve the damage detection capability, i.e. increasing the admittance magnitude and its sensitivity to damage. Theoretical analyses and simulations are carried out. The results show that the peak admittance magnitude is increased by 74 dB for the higher-order circuit without electrical damping and 46 dB with electrical damping, when comparing with the second-order circuit system. The damage detection sensitivity is increased by 33 dB and 36 dB for a stiffness change of 0.5% and 1%, respectively, by using the proposed higher-order circuit, when comparing with the second-order circuit system, and even more when comparing with the traditional method with only a resistor. (paper)
Chen, Kang; Long, Dianna S; Lute, Scott C; Levy, Michaella J; Brorson, Kurt A; Keire, David A
2016-09-01
Monoclonal antibody (mAb) drugs constitute the largest class of protein therapeutics currently on the market. Correctly folded protein higher order structure (HOS), including quinary structure, is crucial for mAb drug quality. The quinary structure is defined as the association of quaternary structures (e.g., oligomerized mAb). Here, several commonly available analytical methods, i.e., size-exclusion-chromatography (SEC) FPLC, multi-angle light scattering (MALS), circular dichroism (CD), NMR and multivariate analysis, were combined and modified to yield a complete profile of HOS and comparable metrics. Rituximab and infliximab were chosen for method evaluation because both IgG1 molecules are known to be homologous in sequence, superimposable in Fab crystal structure and identical in Fc structure. However, herein the two are identified to be significantly different in quinary structure in addition to minor secondary structure differences. All data collectively showed rituximab was mostly monomeric while infliximab was in mono-oligomer equilibrium driven by its Fab fragment. The quinary structure differences were qualitatively inferred from the less used but more reproducible dilution-injection-SEC-FPLC curve method. Quantitative principal component analysis (PCA) was performed on NMR spectra of either the intact or the in-situ enzymatic-digested mAb samples. The cleavage reactions happened directly in NMR tubes without further separation, which greatly enhanced NMR spectra quality and resulted in larger inter- and intra-lot variations based on PCA. The new in-situ enzymatic digestion method holds potential in identifying structural differences on larger therapeutic molecules using NMR.
Phase structure of the $O(2)$ ghost model with higher-order gradient term
Péli, Z; Sailer, K
2016-01-01
The phase structure and the infrared behaviour of the Euclidean 3-dimensional $O(2)$ symmetric ghost scalar field model with higher-order derivative term has been investigated in Wegner and Houghton's renormalization group framework. The symmetric phase in which no ghost condensation occurs and the phase with restored symmetry but with a transient presence of a ghost condensate have been identified. Finiteness of the correlation length at the phase boundary hints to a phase transition of first order. The results are compared with those for the ordinary $O(2)$ symmetric scalar field model.
Gaussian higher Order Derivative based Structural Enhancement of Digital Bone X-Ray Images
Directory of Open Access Journals (Sweden)
Raka Kundu
2011-01-01
Full Text Available A novel method for enhancement of digital X-ray images of bones is presented in this paper. It has come to observation that the proposed method based on the Gaussian higher order derivative shows an appreciable enhancement of edges in digital X-ray images of bones that can be used for detection of various bone deformities as well as for the better understanding of the bone structure. We have achieved a level of improvement in distinguishing the bone information from the other parts of the digital X-ray images.
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...
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.
Energy Technology Data Exchange (ETDEWEB)
Klein, Dionne C.G., E-mail: dionne.c.g.klein@ntnu.no [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway); Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Latz, Eicke [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 (United States); Institute of Innate Immunity, University Hospitals, University of Bonn, Sigmund-Freud-Str. 25, 53127 Bonn (Germany); Espevik, Terje [Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489, Trondheim (Norway); Stokke, Bjorn T. [Department of Physics, Norwegian University of Science and Technology, N-7491, Trondheim (Norway)
2010-05-15
Immunostimulatory CpG-DNA activates the innate immune system by binding to Toll-like receptor 9. Structurally different CpG-containing oligonucleotides trigger a different type of immune response while activating the same receptor. We therefore investigated the higher order structure of two different classes of immunostimulatory CpG-DNA. Class A, which contains a partly self-complementary sequence and poly-G ends, forms duplexes and nanoparticles in salt solution, while class B, which does not contain these features and is purely linear, does not form a duplex or nanoparticles. Results obtained here by high-resolution atomic force microscopy of classes A and B CpG-DNA, reflect these differences in secondary structure. Detailed structural analysis of the atomic force microscopy topographs is presented for two different sample preparation methods.
Protein-protein interactions in a higher-order structure direct lambda site-specific recombination.
Thompson, J F; de Vargas, L M; Skinner, S E; Landy, A
1987-06-01
The highly directional site-specific recombination of bacteriophage lambda is tightly regulated by the binding of three different proteins to a complex array of sites. The manner in which these reactions are both stimulated and inhibited by co-operative binding of proteins to specific sites on the P arm of attP and AttR has been elucidated by correlation of nuclease protection with recombination studies of both wild-type and mutant DNAs. In addition to co-operative forces, there is a specific competitive interaction that allows the protein-DNA complex to serve as a "biological switch". This switch does not depend upon the simple occlusion of DNA binding sites by neighboring proteins; but, rather, the outcome of this competition is dependent on long-range interactions that vary between the higher-order structures of attP and attR. These higher-order structures are dependent on cooperative interactions involving three proteins binding to five or more sites. PMID:2958633
高阶布尔网络的结构%Structure of higher order Boolean networks*
Institute of Scientific and Technical Information of China (English)
李志强; 赵寅; 程代展
2011-01-01
The higher order Boolean (control) network is introduced and its topological structure is studied.Using semi-tensor product of matrices,its dynamics is converted into two algebraic forms,which are standard discrete-time dynamic systems.The one-to-one correspondence of the network dynamics and its first algebraic form is proved,and certain topological structures,including fixed points,cycles,and transient time,of higher order Boolean (control) networks are revealed.The relationship between the original system and its second algebraic form is also studied.%介绍高阶布尔（控制）网络,并研究了其拓扑结构.以矩阵的半张量积作为工具,把高阶布尔网络的动态过程转化为2种标准离散事件动态系统的代数形式.证明了高阶布尔网络和第1代数形式的一一对应关系,并由此得到其拓扑结构（不动点、极限圈以及暂态期等）.还研究了高阶布尔网络系统与它第2代数形式的关系.
Design and construction of higher-order structure and function in proteinosome-based protocells.
Huang, Xin; Patil, Avinash J; Li, Mei; Mann, Stephen
2014-06-25
The design and construction of higher-order structure and function in proteinosome microcompartments enclosed by a cross-linked membrane of amphiphilic bovine serum albumin/poly(N-isopropylacrylamide) (BSA-NH2/PNIPAAm) nanoconjugates is described. Three structure/function relationships are investigated: (i) differential chemical cross-linking for the control of membrane disassembly and regulated release of encapsulated genetic polymers; (ii) enzyme-mediated hydrogel structuring of the internal microenvironment to increase mechanical robustness and generate a molecularly crowded reaction environment; and (iii) self-production of a membrane-enclosing outer hydrogel wall for generating protease-resistant forms of the protein-polymer protocells. Our results highlight the potential of integrating aspects of supramolecular and polymer chemistry into the design and construction of novel bioinspired microcompartments as a step toward small-scale materials systems based on synthetic cellularity. PMID:24905973
Effects of fast neutrons on chromatin: dependence on chromatin structure
Energy Technology Data Exchange (ETDEWEB)
Radu, L. [Dept. of Molecular Genetics, V. Babes National Inst., Bd. Timisoara, Bucharest (Romania); Constantinescu, B. [Dept. of Cyclotron, H. Hulubei National Inst., Bucharest (Romania); Gazdaru, D. [Dept. of Biophysics, Physics Faculty, Univ. of Bucharest (Romania)
2002-07-01
The effects of fast neutrons (10-100 Gy) on chromatin extracted from normal (liver of Wistar rats) and tumor (Walker carcinosarcoma maintained on Wistar rats) tissues were compared. The spectroscopic assays used were (i) chromatin intrinsic fluorescence, (ii) time-resolved fluorescence of chromatin-proflavine complexes, and (iii) fluorescence resonance energy transfer (FRET) between dansyl chloride and acridine orange coupled to chromatin. For both normal and tumor chromatin, the intensity of intrinsic fluorescence specific for acidic and basic proteins decreased with increasing dose. The relative contributions of the excited-state lifetime of proflavine bound to chromatin were reduced upon fast-neutron irradiation, indicating a decrease in the proportion of chromatin DNA available for ligand binding. The Forster energy transfer efficiencies were also modified by irradiation. These effects were larger for chromatin from tumor tissue. In the range 0-100 Gy, fast neutrons induced alterations in DNA and acidic and basic proteins, as well as in global chromatin structure. The radiosensitivity of chromatin extracted from tumor tissue seems to be higher than that of chromatin extracted from normal tissue, probably because of its higher euchromatin (loose)-heterochromatin (compact) ratio. (author)
Chromatin structure regulates gene conversion.
Directory of Open Access Journals (Sweden)
W Jason Cummings
2007-10-01
Full Text Available Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vlambda pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205, expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vlambda donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vlambda array, and altered the outcome of Vlambda diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences.
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...
Continued Stabilization of the Nuclear Higher-Order Structure of Post-Mitotic Neurons In Vivo
Alva-Medina, Janeth; Maya-Mendoza, Apolinar; Dent, Myrna A. R.; Aranda-Anzaldo, Armando
2011-01-01
Background Cellular terminal differentiation (TD) correlates with a permanent exit from the cell cycle and so TD cells become stably post-mitotic. However, TD cells express the molecular machinery necessary for cell proliferation that can be reactivated by experimental manipulation, yet it has not been reported the stable proliferation of any type of reactivated TD cells. Neurons become post-mitotic after leaving the ventricular zone. When neurons are forced to reenter the cell cycle they invariably undergo cell death. Wider evidence indicates that the post-mitotic state cannot solely depend on gene products acting in trans, otherwise mutations in the corresponding genes may lead to reentry and completion of the cell cycle in TD cells, but this has not been observed. In the interphase, nuclear DNA of metazoan cells is organized in supercoiled loops anchored to a nuclear nuclear matrix (NM). The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS). We have previously compared the NHOS of aged rat hepatocytes with that of early post-mitotic rat neurons and our results indicated that a very stable NHOS is a common feature of both senescent and post-mitotic cells in vivo. Principal Findings In the present work we compared the NHOS in rat neurons from different post-natal ages. Our results show that the trend towards further stabilization of the NHOS in neurons continues throughout post-natal life. This phenomenon occurs in absence of overt changes in the post-mitotic state and transcriptional activity of neurons, suggesting that it is independent of functional constraints. Conclusions Apparently the continued stabilization of the NHOS as a function of time is basically determined by thermodynamic and structural constraints. We discuss how the resulting highly stable NHOS of neurons may be the structural, non-genetic basis of their permanent and irreversible post-mitotic state. PMID:21731716
Continued stabilization of the nuclear higher-order structure of post-mitotic neurons in vivo.
Directory of Open Access Journals (Sweden)
Janeth Alva-Medina
Full Text Available BACKGROUND: Cellular terminal differentiation (TD correlates with a permanent exit from the cell cycle and so TD cells become stably post-mitotic. However, TD cells express the molecular machinery necessary for cell proliferation that can be reactivated by experimental manipulation, yet it has not been reported the stable proliferation of any type of reactivated TD cells. Neurons become post-mitotic after leaving the ventricular zone. When neurons are forced to reenter the cell cycle they invariably undergo cell death. Wider evidence indicates that the post-mitotic state cannot solely depend on gene products acting in trans, otherwise mutations in the corresponding genes may lead to reentry and completion of the cell cycle in TD cells, but this has not been observed. In the interphase, nuclear DNA of metazoan cells is organized in supercoiled loops anchored to a nuclear nuclear matrix (NM. The DNA-NM interactions define a higher-order structure in the cell nucleus (NHOS. We have previously compared the NHOS of aged rat hepatocytes with that of early post-mitotic rat neurons and our results indicated that a very stable NHOS is a common feature of both senescent and post-mitotic cells in vivo. PRINCIPAL FINDINGS: In the present work we compared the NHOS in rat neurons from different post-natal ages. Our results show that the trend towards further stabilization of the NHOS in neurons continues throughout post-natal life. This phenomenon occurs in absence of overt changes in the post-mitotic state and transcriptional activity of neurons, suggesting that it is independent of functional constraints. CONCLUSIONS: Apparently the continued stabilization of the NHOS as a function of time is basically determined by thermodynamic and structural constraints. We discuss how the resulting highly stable NHOS of neurons may be the structural, non-genetic basis of their permanent and irreversible post-mitotic state.
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.
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. ...
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.
Institute of Scientific and Technical Information of China (English)
Iouri Chepelev; Gang Wei; Dara Wangsa; Qingsong Tang; Keji Zhao
2012-01-01
Recent epigenomic studies have predicted thousands of potential enhancers in the human genome.However,there has not been systematic characterization of target promoters for these potential enhancers.Using H3K4me2 as a mark for active enhancers,we identified genome-wide EP interactions in human CD4+ T cells.Among the 6 520 longdistance chromatin interactions,we identify 2 067 enhancers that interact with 1 619 promoters and enhance their expression.These enhancers exist in accessible chromatin regions and are associated with various histone modifications and polymerase Ⅱ binding.The promoters with interacting enhancers are expressed at higher levels than those without interacting enhancers,and their expression levels are positively correlated with the number of interacting enhancers.Interestingly,interacting promoters are co-expressed in a tissue-specific manner.We also find that chromosomes are organized into multiple levels of interacting domains.Our results define a global view of EP interactions and provide a data set to further understand mechanisms of enhancer targeting and long-range chromatin organization.The Gene Expression Omnibus accession number for the raw and analyzed chromatin interaction data is GSE32677.
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)
On modeling micro-structural evolution using a higher order strain gradient continuum theory
DEFF Research Database (Denmark)
El-Naaman, S. A.; Nielsen, K. L.; Niordson, C. F.
2016-01-01
is to improve the micro-structural response predicted using strain gradient crystal plasticity within a continuum mechanics framework. One approach to modeling the dislocation structures observed is through a back stress formulation, which can be related directly to the strain gradient energy. The present work...... offers an investigation of constitutive equations for the back stress based on both considerations of the gradient energy, but also includes results obtained from a purely phenomenological starting point. The influence of model parameters is brought out in a parametric study, and it is demonstrated how...... a proper treatment of the back stress enables dislocation wall and cell structure type response in the adopted framework....
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
Energy Technology Data Exchange (ETDEWEB)
Emamuddin, M. [National University, Gazipur (Bangladesh); Yasmin, S.; Mamun, A. A. [Jahangirnagar University, Savar, Dhaka (Bangladesh)
2014-06-15
The Gardner equation, showing the existence of compressive and rarefactive dust-acoustic (DA) solitons in a nonextensive dusty plasma (containing negatively charged dust, Maxwellian ions and two-temperature electrons following a q-nonextensive distribution) beyond the K-dV (Korteweg-de Vries) limit, is derived and numerically solved. The basic features of the DA Gardner solitons (GSs) associated with positive and negative potentials are found to exist beyond the K-dV limit, and the K-dV and modified K-dV (mK-dV) solitons have been compared with the DAGSs by considering the effects of two-temperature electron's nonextensivity. Depending on the nonextensive parameter q, the DAGSs have been found to exhibit negative (positive) potential solitons for q < q{sub c} (q > q{sub c}) (where q{sub c} is the critical value of q). The results obtained from this analysis can be utilized and should be very effective for understanding the localized nonlinear structures, the DAGSs, in different astrophysical and cosmological scenarios (viz. stellar polytropes, quark-gluon plasma, protoneutron stars, etc.).
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
Directory of Open Access Journals (Sweden)
Natalia K. Prykarpatska
2005-01-01
Full Text Available The geometric structure of characteristic surfaces related with partial differential equations of first and higher orders is studied making use the vector field technique on hypersurfaces. It is shown, that corresponding characteristics are defined uniquely up to some smooth tensor fields, thereby supplying additional information about the suitable set of their solutions. In particular, it may be very useful for studying asymptotic properties of solutions to our partial differential equations under some boundary conditions.
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.
Dromion and Multi-soliton Structures of the (2+1)-Dimensional Higher-Order Broer-Kaup System
Institute of Scientific and Technical Information of China (English)
林机
2002-01-01
Using the standard truncated Painlevé analysis and the Backlund transformation, we can obtain many significant exact soliton solutions of the (2+1)-dimensional higher-order Broer-Kaup (HBK) system. A special type of soliton solution is described by the variable coefficient heat-conduction-like equation. The inclusion of three arbitrary functions in the general expressions of the solitons makes the solitons of the (2+1)-dimensional HBK system possess abundant structures such as solitofT solutions, multi-dromion solutions, ring solitons and so on.
Pindera, Marek-Jerzy; Aboudi, Jacob
1998-01-01
The objective of this three-year project was to develop and deliver to NASA Lewis one-dimensional and two-dimensional higher-order theories, and related computer codes, for the analysis, optimization and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, blisk blades). To satisfy this objective, a quasi one-dimensional version of the higher-order theory, HOTCFGM-1D, and four computer codes based on this theory, for the analysis, design and optimization of cylindrical structural components functionally graded in the radial direction were developed. The theory is applicable to thin multi-phased composite shell/cylinders subjected to macroscopically axisymmetric thermomechanical and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial and circumferential directions, and arbitrarily distributed in the radial direction, thereby allowing functional grading of the internal reinforcement in this direction.
Chromatin structure and evolution in the human genome
Directory of Open Access Journals (Sweden)
Dunlop Malcolm G
2007-05-01
Full Text Available Abstract Background Evolutionary rates are not constant across the human genome but genes in close proximity have been shown to experience similar levels of divergence and selection. The higher-order organisation of chromosomes has often been invoked to explain such phenomena but previously there has been insufficient data on chromosome structure to investigate this rigorously. Using the results of a recent genome-wide analysis of open and closed human chromatin structures we have investigated the global association between divergence, selection and chromatin structure for the first time. Results In this study we have shown that, paradoxically, synonymous site divergence (dS at non-CpG sites is highest in regions of open chromatin, primarily as a result of an increased number of transitions, while the rates of other traditional measures of mutation (intergenic, intronic and ancient repeat divergence as well as SNP density are highest in closed regions of the genome. Analysis of human-chimpanzee divergence across intron-exon boundaries indicates that although genes in relatively open chromatin generally display little selection at their synonymous sites, those in closed regions show markedly lower divergence at their fourfold degenerate sites than in neighbouring introns and intergenic regions. Exclusion of known Exonic Splice Enhancer hexamers has little affect on the divergence observed at fourfold degenerate sites across chromatin categories; however, we show that closed chromatin is enriched with certain classes of ncRNA genes whose RNA secondary structure may be particularly important. Conclusion We conclude that, overall, non-CpG mutation rates are lowest in open regions of the genome and that regions of the genome with a closed chromatin structure have the highest background mutation rate. This might reflect lower rates of DNA damage or enhanced DNA repair processes in regions of open chromatin. Our results also indicate that dS is a poor
CTCF-cohesin complex: architect of chromatin structure regulates V(D)J rearrangement
Institute of Scientific and Technical Information of China (English)
Ann J Feeney; Jiyoti Verma-Gaur
2012-01-01
The CTCF/cohesin complex regulates higher order chromatin structure by creating long-range chromatin loops and by insulating neighboring genes from each other.The lymphocyte antigen receptor loci have large numbers of CTCF/cohesin binding sites,and recent studies demonstrate that the CTCF/cohesin complex plays several important roles in regulating the process of V(D)J recombination at these megabase-sized receptor loci.
DEFF Research Database (Denmark)
Douthwaite, S; Christensen, A; Garrett, R A
1983-01-01
of additional higher order structure in the renatured free RNA. It can be concluded that a high level of conservation of higher order structure has occurred during the evolution of the gram negative and gram positive eubacteria and the eukaryote in both the double helical regions and the "unstructured" regions...
On higher order Fourier analysis
Szegedy, Balazs
2012-01-01
We develop a theory of higher order structures in compact abelian groups. In the frame of this theory we prove general inverse theorems and regularity lemmas for Gowers's uniformity norms. We put forward an algebraic interpretation of the notion "higher order Fourier analysis" in terms of continuous morphisms between structures called compact $k$-step nilspaces. As a byproduct of our results we obtain a new type of limit theory for functions on abelian groups in the spirit of the so-called graph limit theory. Our proofs are based on an exact (non-approximative) version of higher order Fourier analysis which appears on ultra product groups.
International Nuclear Information System (INIS)
Higher order modes (HOMs) are one of the reasons for beam current limitations and beam lifetime in synchrotron light sources such as INDUS-2. At higher beam current, the HOMs of the RF cavity may resonate with the beam frequencies (in the beam spectrum) leading to beam instability. Therefore, knowledge of the HOMs of an RF cavity is a necessary part of operations for any synchrotron source. INDUS-2 synchrotron source has 4 elliptically shaped RF cavities, which are operated at a fundamental frequency of 505.812 MHz. The RF cavity HOM spectrum is very sensitive to its conducting surface, which is affected mainly by the thermal loading and tuner movement. An accurate estimation of the cavity frequency spectrum with realistic boundary conditions is possible by a combined (coupled) electromagnetic-thermal-structural analysis. The methodology adopted for this coupled simulation is explained in this paper. The HOM spectrum and electromagnetic parameters of INDUS-2 cavity are simulated using 3D electromagnetic high frequency finite element method in ANSYS. The simulated data sets are compared with the cold model test data of the RF cavities for validation of the numerical simulations. Further, the observed spectra of the INDUS-2 electron beam at various stored beam currents and energies are also studied to find parasitic HOMs. Indicative HOM observations and the simulation data results can be used for shifting the harmful modes.
Fabris, Daniele; Yu, Eizadora T.
2010-01-01
Chemical probing represents a very versatile alternative for studying the structure and dynamics of substrates that are intractable by established high-resolution techniques. The implementation of MS-based strategies for the characterization of probing products has not only extended the range of applicability to virtually all types of biopolymers, but has also paved the way for the introduction of new reagents that would not have been viable with traditional analytical platforms. As the availability of probing data is steadily increasing on the wings of the development of dedicated interpretation aids, powerful computational approaches have been explored to enable the effective utilization of such information to generate valid molecular models. This combination of factors has contributed to making the possibility of obtaining actual 3D structures by MS-based technologies (MS3D) a reality. Although approaches for achieving structure determination of unknown substrates or assessing the dynamics of known structures may share similar reagents and development trajectories, they clearly involve distinctive experimental strategies, analytical concerns, and interpretation paradigms. This Perspective offers a commentary on methods aimed at obtaining distance constraints for the modeling of full-fledged structures, while highlighting common elements, salient distinctions, and complementary capabilities exhibited by methods employed in dynamics studies. We discuss critical factors to be addressed for completing effective structural determinations and expose possible pitfalls of chemical methods. We survey programs developed for facilitating the interpretation of experimental data and discuss possible computational strategies for translating sparse spatial constraints into all-atom models. Examples are provided to illustrate how the concerted application of very diverse probing techniques can lead to the solution of actual biological substrates. PMID:20648672
DEFF Research Database (Denmark)
Ernst, Erik
2003-01-01
. Finally, it must be possible to write generic code that works on every hierarchy derived from the hierarchy for which it was written. This paper presents a language design that supports such a notion of higher-order hierarchies. It has been implemented in context of a full-fledged, statically typed...... be possible to create hierarchies incrementally based on existing hierarchies, such that commonalities are expressed via reuse, not duplication. Second, the hierarchies must themselves be organized into hierarchies, such that their relationships are made explicit and can be exploited in a type safe manner...... language....
International Nuclear Information System (INIS)
According to their physical characteristics, protons and ion beams promise a revolution in cancer radiotherapy. Curing protocols however reflect rather the empirical knowledge than experimental data on DNA repair. This especially holds for the spatio-temporal organization of repair processes in the context of higher-order chromatin structure—the problematics addressed in this work. The consequences for the mechanism of chromosomal translocations are compared for gamma rays and proton beams. - Highlights: ► The majority of DSBs are repaired individually close to the sites of their origin. ► Decondensation of damaged chromatin domains can potentiate clustering of lesions. ► DSB clustering might increase the risk of chromatin translocation. ► Distances of lesions and higher-order chromatin structure influence DSB clustering. ► The conclusions seem to hold both for DSB damage caused by γ-radiation and protons
Wang, Guanbo; Kaltashov, Igor A.
2014-01-01
Top-down hydrogen/deuterium exchange (HDX) with mass spectrometric (MS) detection has recently matured to become a potent biophysical tool capable of providing valuable information on higher order structure and conformational dynamics of proteins at an unprecedented level of structural detail. However, the scope of the proteins amenable to the analysis by top-down HDX MS still remains limited, with the protein size and the presence of disulfide bonds being the two most important limiting fact...
Chawla, Mohit
2013-10-10
The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).
Energy Technology Data Exchange (ETDEWEB)
Gee, Anthony; Shin, Young-Min
2013-01-01
A multi-beam traveling wave amplifier designed with an overmoded staggered double grating array was examined by small signal analysis combined with simulation. Eigenmode and S-parameter analyses show that the 2cm long slow wave structure (SWS) has 1-5dB insertion loss over the passband (TM31 mode) with ~28% cold bandwidth. Analytic gain calculation indicates that in the SWS, TM31-mode is amplified with 15–20 dB/beam at 64–84GHz with three elliptical beams of 10kV and 150mA/beam, which was compared with particle-in-cell (PIC) simulations. PIC analysis on the analysis of instability with zero-input driving excitations demonstrated that background noises and non-operating lower order modes are noticeably suppressed by implanting equidistant dielectric absorbers; the overmoded structure only allowed the desired 3rd order mode to propagate in the structure. The designed circuit structure can be widely applied to multi-beam devices for high power RF generation.
Higher order structure of chromosomes.
Okada, T A; Comings, D E
1979-04-01
Isolated Chinese hamster metaphase chromosomes were resuspended in 4 M ammonium acetate and spread on a surface of distilled water or 0.15 to 0.5 M ammonium acetate. The DNA was released in the form of a regular series of rosettes connected by interrossette DNA. The mean length of the rosette DNA was 14 micron, similar to the mean length of 10 micron for chromomere DNA of Drosophila polytene chromosomes. The mean interrosette DNA was 4.2 micron. SDS gel electrophoresis of the chromosomal nonhistone proteins showed them to be very similar to nuclear nonhistone proteins except for the presence of more actin and tubulin. Nuclear matrix proteins were present in the chromosomes and may play a role in forming the rosettes. Evidence that the rosette pattern is artifactual versus the possibility that it represents a real organizational substructure of the chromosomes is reviewed.
Rigozzi, Christine; Rossier, Jérôme; Dahourou, Donatien; Adjahouisso, Marcel; Ah-Kion, Jennifer; Amoussou-Yeye, Denis; Barry, Oumar; Bhowon, Uma; Bouatta, Cherifa; Cissé, Daouda Dougoumalé; Mbodji, Mamadou; Meyer de Stadelhofen, Franz; Minga, David Minga; Tseung, Caroline Ng; Ondongo, François; Romdhane, Mohamed Nouri; Sfayhi, Nicole; Tsokini, Dieudonné; Verardi, Sabrina
2009-04-01
Most studies about the higher-order dimensions to be considered in order to parsimoniously describe Personality Disorders (PDs) have identified between two and four factors but there is still no consensus about their exact number. In this context, the cultural stability of these structures might be a criterion to be considered. The aim of this study was to identify stable higher-order structures of PD traits in a French-speaking African and Swiss sample (N = 2,711). All subjects completed the IPDE screening questionnaire. Using Everett's criterion and conducting a series of principal component analyses, a cross-culturally stable two- and four-factor structure were identified, associated with a total congruence coefficient of .98 and .94, respectively, after Procrustes rotation. Moreover, these two structures were also highly replicable across the four African regions considered, North Africa, West Africa, Central Africa, and Mauritius, with a mean total congruence coefficient of .97 and .87, respectively. The four-factor structure presented the advantage of being similar to Livesely's four components and of describing the ten PDs more accurately.
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
Sperm chromatin structure and male fertility: biological and clinical aspects
Institute of Scientific and Technical Information of China (English)
J. Erenpreiss; M. Spano; J. Erenpreisa; M. Bungum; A. Giwercman
2006-01-01
Aim: Sperm chromatin/DNA integrity is essential for the accurate transmission of paternal genetic information, and normal sperm chromatin structure is important for sperm fertilizing ability. The routine examination of semen, which includes sperm concentration, motility and morphology, does not identify defects in sperm chromatin structure. The origin of sperm DNA damage and a variety of methods for its assessment are described. Evaluation of sperm DNA damage appears to be a useful tool for assessing male fertility potential both in vivo and in vitro. The possible impact of sperm DNA defects on the offspring is also discussed.
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
Impact of chromatin structure on PR signaling
DEFF Research Database (Denmark)
Grøntved, Lars; Hager, Gordon L
2012-01-01
but also to the glucocorticoid receptor (GR), as these receptors share many similarities regarding interaction with, and remodeling of, chromatin. Both receptors can bind nucleosomal DNA and have accordingly been described as pioneering factors. However recent genomic approaches (ChIP-seq and DHS-seq) show...
Pindera, Marek-Jerzy; Aboudi, Jacob
2000-01-01
The objective of this two-year project was to develop and deliver to the NASA-Glenn Research Center a two-dimensional higher-order theory, and related computer codes, for the analysis and design of cylindrical functionally graded materials/structural components for use in advanced aircraft engines (e.g., combustor linings, rotor disks, heat shields, brisk blades). To satisfy this objective, two-dimensional version of the higher-order theory, HOTCFGM-2D, and four computer codes based on this theory, for the analysis and design of structural components functionally graded in the radial and circumferential directions were developed in the cylindrical coordinate system r-Theta-z. This version of the higher-order theory is a significant generalization of the one-dimensional theory, HOTCFGM-1D, developed during the FY97 for the analysis and design of cylindrical structural components with radially graded microstructures. The generalized theory is applicable to thin multi-phased composite shells/cylinders subjected to steady-state thermomechanical, transient thermal and inertial loading applied uniformly along the axial direction such that the overall deformation is characterized by a constant average axial strain. The reinforcement phases are uniformly distributed in the axial direction, and arbitrarily distributed in the radial and circumferential direction, thereby allowing functional grading of the internal reinforcement in the r-Theta plane. The four computer codes fgmc3dq.cylindrical.f, fgmp3dq.cylindrical.f, fgmgvips3dq.cylindrical.f, and fgmc3dq.cylindrical.transient.f are research-oriented codes for investigating the effect of functionally graded architectures, as well as the properties of the multi-phase reinforcement, in thin shells subjected to thermomechanical and inertial loading, on the internal temperature, stress and (inelastic) strain fields. The reinforcement distribution in the radial and circumferential directions is specified by the user. The thermal
Control of chromatin structure by long noncoding RNA
Böhmdorfer, Gudrun; Wierzbicki, Andrzej T.
2015-01-01
Long noncoding RNA (lncRNA) is a pivotal factor regulating various aspects of genome activity. Genome regulation via DNA methylation and posttranslational histone modifications is a well-documented function of lncRNA in plants, fungi, and animals. Here, we summarize evidence showing that lncRNA also controls chromatin structure including nucleosome positioning and chromosome looping. We focus on data from plant experimental systems, discussed in the context of other eukaryotes. We explain the mechanisms of lncRNA-controlled chromatin remodeling and the implications of the functional interplay between noncoding transcription and several different chromatin remodelers. We propose that the unique properties of RNA make it suitable for controlling chromatin modifications and structure. PMID:26410408
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...
A Paraconsistent Higher Order Logic
DEFF Research Database (Denmark)
Villadsen, Jørgen
2004-01-01
of paraconsistent logics in knowledge-based systems, logical semantics of natural language, etc. Higher order logics have the advantages of being expressive and with several automated theorem provers available. Also the type system can be helpful. We present a concise description of a paraconsistent higher order...... logic with countable infinite indeterminacy, where each basic formula can get its own indeterminate truth value (or as we prefer: truth code). The meaning of the logical operators is new and rather different from traditional many-valued logics as well as from logics based on bilattices. The adequacy...
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.
Bruggeman, R.W.; Diamantis, N.
2012-01-01
The spaces of Maass forms of even weight and of arbitrary order are studied. It is shown that, if we allow exponential growth at the cusps, these spaces are as large as algebraic restrictions allow. These results also apply to higher-order holomorphic forms of even weight.
Higher-Order Program Generation
DEFF Research Database (Denmark)
Rhiger, Morten
This dissertation addresses the challenges of embedding programming languages, specializing generic programs to specific parameters, and generating specialized instances of programs directly as executable code. Our main tools are higher-order programming techniques and automatic program generation....... It is our thesis that they synergize well in the development of customizable software. Recent research on domain-specific languages propose to embed them into existing general-purpose languages. Typed higher-order languages have proven especially useful as meta languages because they provide a rich...... to the disproportion between general programs that can be executed in several contexts and their specialized counterparts that can be executed efficiently. However, stand-alone partial evaluation is usually too costly when a program must be specialized at run time. We introduce a collection of byte-code combinators...
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.
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...
Chromatin structure near transcriptionally active genes
International Nuclear Information System (INIS)
Hypersensitive domains are the most prominent features of transcriptionally active chromatin. In the case of the β/sup A/-globin gene, it seems likely that two or more protein factors are capable of binding to the DNA so tightly that the nucleosome is prevented from binding. We have shown that nucleosomes, once bound in the assembly process in vitro, cannot be displaced. The interaction of the 5S gene transcription factor TFIIIA with its target DNA also is blocked by histones, and it has been suggested that the activation of the gene must occur during replication, before histones are reassembled on the DNA. We suppose that a similar mechanism may govern the binding of the hypersensitivity factors. It should be noted that nucleosomes are excluded not only from the sites to which the factors bind, but also from the regions between the two domains and at either side. 12 refs., 6 figs
Falck, David; Jansen, Bas C; Plomp, Rosina; Reusch, Dietmar; Haberger, Markus; Wuhrer, Manfred
2015-09-01
It has been reported that glycosylation can influence the proteolytic cleavage of proteins. A thorough investigation of this phenomenon was conducted for the serine protease trypsin, which is essential in many proteomics workflows. Monoclonal and polyclonal immunoglobulin G biopharmaceuticals were employed as model substances, which are highly relevant for the bioanalytical applications. Relative quantitation of glycopeptides derived from the conserved Fc-glycosylation site allowed resolution of biases on the level of individual glycan compositions. As a result, a strong preferential digestion of high mannose, hybrid, alpha2-3-sialylated and bisected glycoforms was observed over the most abundant neutral, fucosylated glycoforms. Interestingly, this bias was, to a large extent, dependent on the intact higher order structure of the antibodies and, consequently, was drastically reduced in denatured versus intact antibodies. In addition, a cleavage protocol with acidic denaturation was tested, which featured reduced hands-on time and toxicity while showing highly comparable results to a published denaturation, reduction, and alkylation based protocol.
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
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
International Nuclear Information System (INIS)
To assess the influence of chromatin structure on the frequency of radiation-induced DNA strand breaks, the alkaline unwinding technique was applied to nuclear and nucleoid monolayers. These chromatin substrates were prepared by treating human fibroblasts grown as monolayers with the nonionic detergent Triton X-100 and varying concentrations of cations. The chromatin structure was modified either by a stepwise removal of DNA-bound proteins by extraction in increasing concentrations of monovalent salt, or by the addition or deletion of mono- and divalent cations to condense or decondense the chromatin, respectively. It was found that the stepwise removal of DNA-bound proteins from the chromatin dramatically increased the frequency of radiation-induced DNA strand breaks. The DNA-bound proteins showed a qualitative difference in their ability to protect the DNA where proteins removed by salt concentrations above 1.0 M exerted the greatest protection. Furthermore, the frequency of radiation-induced DNA strand breaks was found to be 6 times lower in condensed chromatin than in decondensed chromatin and about 80 times lower than in protein-depleted chromatin. It is concluded that the presence of DNA-bound proteins and the folding of the chromatin into higher-order structures protect the DNA against radiation-induced strand breaks
Chromatin Structure in Cell Differentiation, Aging and Cancer
S. Kheradmand Kia (Sima)
2009-01-01
textabstractChromatin is the structure that the eukaryotic genome is packaged into, allowing over a metre of DNA to fit into the small volume of the nucleus. It is composed of DNA and proteins, most of which are histones. This DNA-protein complex is the template for a number of essential cell proces
McGowan, L. E.; Dahlke, H. E.; Paw U, K. T.
2015-12-01
Snow cover is a critical driver of the Earth's surface energy budget, climate change, and water resources. Variations in snow cover not only affect the energy budget of the land surface but also represent a major water supply source. In California, US estimates of snow depth, extent, and melt in the Sierra Nevada are critical to estimating the amount of water available for both California agriculture and urban users. However, accurate estimates of snow cover and snow melt processes in forested area still remain a challenge. Canopy structure influences the vertical and spatiotemporal distribution of snow, and therefore ultimately determines the degree and extent by which snow alters both the surface energy balance and water availability in forested regions. In this study we use the Advanced Canopy-Atmosphere-Soil algorithm (ACASA), a multi-layer soil-vegetation-atmosphere numerical model, to simulate the effect of different snow-covered canopy structures on the energy budget, and temperature and other scalar profiles within different forest types in the Sierra Nevada, California. ACASA incorporates a higher order turbulence closure scheme which allows the detailed simulation of turbulent fluxes of heat and water vapor as well as the CO2 exchange of several layers within the canopy. As such ACASA can capture the counter gradient fluxes within canopies that may occur frequently, but are typically unaccounted for, in most snow hydrology models. Six different canopy types were modeled ranging from coniferous forests (e.g. most biomass near the ground) to top-heavy (e.g. most biomass near the top of the crown) deciduous forests to multi-layered forest canopies (e.g. mixture of young and mature trees). Preliminary results indicate that the canopy shape and structure associated with different canopy types fundamentally influence the vertical scalar profiles (including those of temperature, moisture, and wind speed) in the canopy and thus alter the interception and snow
Directory of Open Access Journals (Sweden)
Yolanda Stypula-Cyrus
Full Text Available Normal cell function is dependent on the proper maintenance of chromatin structure. Regulation of chromatin structure is controlled by histone modifications that directly influence chromatin architecture and genome function. Specifically, the histone deacetylase (HDAC family of proteins modulate chromatin compaction and are commonly dysregulated in many tumors, including colorectal cancer (CRC. However, the role of HDAC proteins in early colorectal carcinogenesis has not been previously reported. We found HDAC1, HDAC2, HDAC3, HDAC5, and HDAC7 all to be up-regulated in the field of human CRC. Furthermore, we observed that HDAC2 up-regulation is one of the earliest events in CRC carcinogenesis and observed this in human field carcinogenesis, the azoxymethane-treated rat model, and in more aggressive colon cancer cell lines. The universality of HDAC2 up-regulation suggests that HDAC2 up-regulation is a novel and important early event in CRC, which may serve as a biomarker. HDAC inhibitors (HDACIs interfere with tumorigenic HDAC activity; however, the precise mechanisms involved in this process remain to be elucidated. We confirmed that HDAC inhibition by valproic acid (VPA targeted the more aggressive cell line. Using nuclease digestion assays and transmission electron microscopy imaging, we observed that VPA treatment induced greater changes in chromatin structure in the more aggressive cell line. Furthermore, we used the novel imaging technique partial wave spectroscopy (PWS to quantify nanoscale alterations in chromatin. We noted that the PWS results are consistent with the biological assays, indicating a greater effect of VPA treatment in the more aggressive cell type. Together, these results demonstrate the importance of HDAC activity in early carcinogenic events and the unique role of higher-order chromatin structure in determining cell tumorigenicity.
Stypula-Cyrus, Yolanda; Damania, Dhwanil; Kunte, Dhananjay P; Cruz, Mart Dela; Subramanian, Hariharan; Roy, Hemant K; Backman, Vadim
2013-01-01
Normal cell function is dependent on the proper maintenance of chromatin structure. Regulation of chromatin structure is controlled by histone modifications that directly influence chromatin architecture and genome function. Specifically, the histone deacetylase (HDAC) family of proteins modulate chromatin compaction and are commonly dysregulated in many tumors, including colorectal cancer (CRC). However, the role of HDAC proteins in early colorectal carcinogenesis has not been previously reported. We found HDAC1, HDAC2, HDAC3, HDAC5, and HDAC7 all to be up-regulated in the field of human CRC. Furthermore, we observed that HDAC2 up-regulation is one of the earliest events in CRC carcinogenesis and observed this in human field carcinogenesis, the azoxymethane-treated rat model, and in more aggressive colon cancer cell lines. The universality of HDAC2 up-regulation suggests that HDAC2 up-regulation is a novel and important early event in CRC, which may serve as a biomarker. HDAC inhibitors (HDACIs) interfere with tumorigenic HDAC activity; however, the precise mechanisms involved in this process remain to be elucidated. We confirmed that HDAC inhibition by valproic acid (VPA) targeted the more aggressive cell line. Using nuclease digestion assays and transmission electron microscopy imaging, we observed that VPA treatment induced greater changes in chromatin structure in the more aggressive cell line. Furthermore, we used the novel imaging technique partial wave spectroscopy (PWS) to quantify nanoscale alterations in chromatin. We noted that the PWS results are consistent with the biological assays, indicating a greater effect of VPA treatment in the more aggressive cell type. Together, these results demonstrate the importance of HDAC activity in early carcinogenic events and the unique role of higher-order chromatin structure in determining cell tumorigenicity.
Resilience and Higher Order Thinking
Directory of Open Access Journals (Sweden)
Ioan Fazey
2010-09-01
Full Text Available To appreciate, understand, and tackle chronic global social and environmental problems, greater appreciation of the importance of higher order thinking is required. Such thinking includes personal epistemological beliefs (PEBs, i.e., the beliefs people hold about the nature of knowledge and how something is known. These beliefs have profound implications for the way individuals relate to each other and the world, such as how people understand complex social-ecological systems. Resilience thinking is an approach to environmental stewardship that includes a number of interrelated concepts and has strong foundations in systemic ways of thinking. This paper (1 summarizes a review of educational psychology literature on PEBs, (2 explains why resilience thinking has potential to facilitate development of more sophisticated PEBs, (3 describes an example of a module designed to teach resilience thinking to undergraduate students in ways conducive to influencing PEBs, and (4 discusses a pilot study that evaluates the module's impact. Theoretical and preliminary evidence from the pilot evaluation suggests that resilience thinking which is underpinned by systems thinking has considerable potential to influence the development of more sophisticated PEBs. To be effective, however, careful consideration of how resilience thinking is taught is required. Finding ways to encourage students to take greater responsibility for their own learning and ensuring close alignment between assessment and desired learning outcomes are particularly important.
Regulation of chromatin structure by poly(ADP-ribosylation
Directory of Open Access Journals (Sweden)
Sascha eBeneke
2012-09-01
Full Text Available The interaction of DNA with proteins in the context of chromatin has to be tightly regulated to achieve so different tasks as packaging, transcription, replication and repair. The very rapid and transient post-translational modification of proteins by poly(ADP-ribose has been shown to take part in all four. Originally identified as immediate cellular answer to a variety of genotoxic stresses, already early data indicated the ability of this highly charged nucleic acid-like polymer to modulate nucleosome structure, the basic unit of chromatin. At the same time the enzyme responsible for synthesizing poly(ADP-ribose, the zinc-finger protein poly(ADP-ribose polymerase-1 (PARP1, was shown to control transcription initiation as basic factor TFIIC within the RNA-polymerase II machinery. Later research focused more on PARP-mediated regulation of DNA repair and cell death, but in the last few years, transcription as well as chromatin modulation has re-appeared on the scene. This review will discuss the impact of PARP1 on transcription and transcription factors, its implication in chromatin remodeling for DNA repair and probably also replication, and its role in controlling epigenetic events such as DNA methylation and the functionality of the insulator protein CCCTC-binding factor.
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
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 and Symbolic Computation
DEFF Research Database (Denmark)
Danvy, Olivier; Mason, Ian
2008-01-01
series of implementaions that properly account for multiple invocations of the derivative-taking opeatro. In "Adapting Functional Programs to Higher-Order Logic," Scott Owens and Konrad Slind present a variety of examples of terminiation proofs of functional programs written in HOL proof systems. Since......-calculus programs, historically. The anaylsis determines the possible locations of ambients and mirrors the temporla sequencing of actions in the structure of types....
Repression and activation by multiprotein complexes that alter chromatin structure.
Kingston, R E; Bunker, C A; Imbalzano, A N
1996-04-15
Recent studies have provided strong evidence that macromolecular complexes are used in the cell to remodel chromatin structure during activation and to create an inaccessible structure during repression, Although there is not yet any rigorous demonstration that modification of chromatin structure plays a direct, causal role in either activation or repression, there is sufficient smoke to indicate the presence of a blazing inferno nearby. It is clear that complexes that remodel chromatin are tractable in vitro; hopefully this will allow the establishment of systems that provide a direct analysis of the role that remodeling might play in activation. These studies indicate that establishment of functional systems to corroborate the elegant genetic studies on repression might also be tractable. As the mechanistic effects of these complexes are sorted out, it will become important to understand how the complexes are regulated. In many of the instances discussed above, the genes whose products make up these complexes were identified in genetic screens for effects on developmental processes. This implies a regulation of the activity of these complexes in response to developmental cues and further implies that the work to fully understand these complexes will occupy a generation of scientists.
Biphasic Chromatin Structure and FISH Signals Reflect Intranuclear Order
Directory of Open Access Journals (Sweden)
Jyoti P. Chaudhuri
2005-01-01
Full Text Available Background and Aim: One of the two parental allelic genes may selectively be expressed, regulated by imprinting, X-inactivation or by other less known mechanisms. This study aims to reflect on such genetic mechanisms. Materials and Methods: Slides from short term cultures or direct smears of blood, bone marrow and amniotic fluids were hybridized with FISH probes singly, combined or sequentially. Two to three hundred cells were examined from each preparation. Results and Aignificance: A small number of cells (up to about 5%, more frequent in leukemia cases, showed the twin features: (1 nuclei with biphasic chromatin, one part decondensed and the other condensed; and (2 homologous FISH signals distributed equitably in those two regions. The biphasic chromatin structure with equitable distribution of the homologous FISH signals may correspond to the two sets of chromosomes, supporting observations on ploidywise intranuclear order. The decondensed chromatin may relate to enhanced transcriptions or advanced replications. Conclusions: Transcriptions of only one of the two parental genomes cause allelic exclusion. Genomes may switch with alternating monoallelic expression of biallelic genes as an efficient genetic mechanism. If genomes fail to switch, allelic exclusion may lead to malignancy. Similarly, a genome-wide monoallelic replication may tilt the balance of heterozygosity resulting in aneusomy, initiating early events in malignant transformation and in predicting cancer mortality.
Evaluation of sperm chromatin structure in boar semen
Directory of Open Access Journals (Sweden)
Banaszewska Dorota
2015-06-01
Full Text Available This study was an attempt to evaluate sperm chromatin structure in the semen of insemination boars. Preparations of semen were stained with acridine orange, aniline blue, and chromomycin A3. Abnormal protamination occurred more frequently in young individuals whose sexual development was not yet complete, but may also be an individual trait. This possibility is important to factor into the decision regarding further exploitation of insemination boars. Thus a precise assessment of abnormalities in the protamination process would seem to be expedient as a tool supplementing morphological and molecular evaluation of semen. Disruptions in nucleoprotein structure can be treated as indicators of the biological value of sperm cells.
Tawfik, Abdel Nasser
2015-01-01
Effects of external magnetic field on various properties of the quantum chromodynamics under extreme conditions of temperature and density have been analysed. To this end, we use SU(3) Polyakov linear sigma-model and assume that the external magnetic field eB adds some restrictions to the quarks energy due to the existence of free charges in the plasma phase. In doing this, we apply the Landau theory of quantization. This requires an additional temperature to drive the system through the chiral phase-transition. Accordingly, the dependence of the critical temperature of chiral and confinement phase-transitions on the magnetic field is characterized. Based on this, we have studied the thermal evolution of thermodynamic quantities and the first four higher-order moment of particle multiplicity. Having all these calculations, we have studied the effects of magnetic field on chiral phase-transition. We found that both critical temperature T_c and critical chemical potential increase with increasing the magnetic f...
Effects of aluminum and other cations on the structure of brain and liver chromatin.
Walker, P R; LeBlanc, J; Sikorska, M
1989-05-01
The reactivity of aluminum and several other divalent and trivalent metallic cations toward chromatin from rat brain and liver has been investigated. Two criteria are used to determine the relative reactivity of these cations toward chromatin. The first involves the ability of the ions to compact the chromatin fibers to the point where chromatin precipitates. The second criterion measures the ability of cations to interfere with the accessibility of exogenous structural probes (nucleases) to chromatin. Of the divalent cations tested, nickel, cobalt, zinc, cadmium, and mercury were the most reactive toward chromatin, on the basis of their ability to induce precipitation of chromatin in the micromolar concentration range. The divalent cations magnesium, calcium, copper, strontium, and barium were much less effective, although all cations precipitate chromatin if their concentration is increased. Of the trivalent cations tested, aluminum, indium, and gallium were very effective precipitants, whereas iron and scandium were without effect at the concentrations tested. Of all the cations tested, aluminum was the most reactive. Aluminum's ability to alter the structure of chromatin was investigated further by testing its ability to interfere with nuclease accessibility. This test confirmed that aluminum does induce considerable changes in chromatin structure at micromolar concentrations. Furthermore, chromatin from cortical areas of the brain was much more sensitive to aluminum than chromatin from liver. These results are discussed in light of the known toxicity of these cations, with particular emphasis on the possible role of aluminum in Alzheimer's disease. PMID:2752000
Higher order mode optical fiber Raman amplifiers
DEFF Research Database (Denmark)
Rottwitt, Karsten; Friis, Søren Michael Mørk; Usuga Castaneda, Mario A.;
2016-01-01
We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations.......We review higher order mode Raman amplifiers and discuss recent theoretical as well as experimental results including system demonstrations....
Challenges in higher order mode Raman amplifiers
DEFF Research Database (Denmark)
Rottwitt, Karsten; Nielsen, Kristian; Friis, Søren Michael Mørk;
2015-01-01
A higher order Raman amplifier model that take random mode coupling into account ispresented. Mode dependent gain and signal power fluctuations at the output of the higher order modeRaman amplifier are discussed...
Higher order resonances in dynamical systems
Contopoulos, George
1978-01-01
It is shown that the appearance of higher order resonances (that produce higher order islands on a surface of section), is not an indication of non-integrability. Examples are given and a method is described for constructing integrable Hamiltonians with higher order resonances. (11 refs).
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...
DEFF Research Database (Denmark)
Garrett, R A; Christensen, A; Douthwaite, S
1984-01-01
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...... level of structural conservation has occurred throughout the RNA domain during the evolution of the Gram negative and Gram positive bacteria although the thermophile was generally more stable at base-pairs adjacent to the terminal loops....
RNA is an integral component of chromatin that contributes to its structural organization.
Directory of Open Access Journals (Sweden)
Antonio Rodríguez-Campos
Full Text Available Chromatin structure is influenced by multiples factors, such as pH, temperature, nature and concentration of counterions, post-translational modifications of histones and binding of structural non-histone proteins. RNA is also known to contribute to the regulation of chromatin structure as chromatin-induced gene silencing was shown to depend on the RNAi machinery in S. pombe, plants and Drosophila. Moreover, both in Drosophila and mammals, dosage compensation requires the contribution of specific non-coding RNAs. However, whether RNA itself plays a direct structural role in chromatin is not known. Here, we report results that indicate a general structural role for RNA in eukaryotic chromatin. RNA is found associated to purified chromatin prepared from chicken liver, or cultured Drosophila S2 cells, and treatment with RNase A alters the structural properties of chromatin. Our results indicate that chromatin-associated RNAs, which account for 2%-5% of total chromatin-associated nucleic acids, are polyA(- and show a size similar to that of the DNA contained in the corresponding chromatin fragments. Chromatin-associated RNA(s are not likely to correspond to nascent transcripts as they are also found bound to chromatin when cells are treated with alpha-amanitin. After treatment with RNase A, chromatin fragments of molecular weight >3.000 bp of DNA showed reduced sedimentation through sucrose gradients and increased sensitivity to micrococcal nuclease digestion. This structural transition, which is observed both at euchromatic and heterochromatic regions, proceeds without loss of histone H1 or any significant change in core-histone composition and integrity.
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...
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.
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 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.
Higher order mechanics on graded bundles
International Nuclear Information System (INIS)
In this paper we develop a geometric approach to higher order mechanics on graded bundles in both, the Lagrangian and Hamiltonian formalism, via the recently discovered weighted algebroids. We present the corresponding Tulczyjew triple for this higher order situation and derive in this framework the phase equations from an arbitrary (also singular) Lagrangian or Hamiltonian, as well as the Euler–Lagrange equations. As important examples, we geometrically derive the classical higher order Euler–Lagrange equations and analogous reduced equations for invariant higher order Lagrangians on Lie groupoids. (paper)
Static Complexity Analysis of Higher Order Programs
DEFF Research Database (Denmark)
Avery, James Emil; Kristiansen, Lars; Moyen, Jean-Yves
2009-01-01
The overall goal of the research presented in this paper is to find^M automatic methods for static complexity analysis of higher order^M programs.......The overall goal of the research presented in this paper is to find^M automatic methods for static complexity analysis of higher order^M programs....
Higher-order knowledge in computer games
A. Witzel; J.A. Zvesper
2008-01-01
Our main aim is to raise awareness of higher-order knowledge, i.e. knowledge about knowledge, as an issue in simulating realistic non-player characters in computer games. We motivate the importance of higher-order knowledge with arguments, as well as a few examples.We survey existing games and liter
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.
Terry, S.Y.A.; Vallis, K.A.
2012-01-01
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 alte
Inverstigation of chromatin folding patterns by atomic force microscopy
Institute of Scientific and Technical Information of China (English)
ZHANGYi; OUYANGZhenqian; 等
1999-01-01
The chromatin folding patterns in air and liquid were studied by atomic force microscopy(AFM),A gentle water-air interface method was adopted to spread chromatin from interphase nucleus of chicken erythrocyte.The chromatin was absorbed on APS-mica surface and studied with AFM,Beads-on a-string were observed and many higher-order structrues such as superbeads with dimensions 40-60nm in diameter and 4-7nm in height were found to string together to make chromation fibers.When sample spreading and absorbing time were shortened.higher-order chromatin fibers with 60-120nm in width were observed in air as well as under water environment.These chromatin structures may reflect chromatin folding patterns in the living cells.
Ausió, Juan
2015-01-01
The chromatin fiber consists of a string of nucleosomes connected by linker DNA regions. The hierarchy of folding of this fiber within the cell has long been controversial, and the existence of an originally described 30 nm fiber has been debated and reviewed extensively. This review contextualizes two recent papers on this topic that suggest the 30 nm fiber to be an over-simplification. The idealized model from the first study provides good insight into the constraints and histone participation in the maintenance of the fiber structure. The second paper provides a theoretical description of a more realistic view of the highly heterogeneous and dynamic chromatin organization in the in vivo setting. It is now time to abandon the highly regular "one start" solenoidal 30 nm structure and replace it with a more realistic highly dynamic, polymorphic fiber.
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
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.
DEFF Research Database (Denmark)
Appel, Claus; van Oostrom, Vincent; Simonsen, Jakob Grue
2010-01-01
We show that, contrary to the situation in first-order term rewriting, almost none of the usual properties of rewriting are modular for higher-order rewriting, irrespective of the higher-order rewriting format. We show that for the particular format of simply typed applicative term rewriting syst...... systems modularity of confluence, normalization, and termination can be recovered by imposing suitable linearity constraints.......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...
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.
Polymer Physics of the Large-Scale Structure of Chromatin.
Bianco, Simona; Chiariello, Andrea Maria; Annunziatella, Carlo; Esposito, Andrea; Nicodemi, Mario
2016-01-01
We summarize the picture emerging from recently proposed models of polymer physics describing the general features of chromatin large scale spatial architecture, as revealed by microscopy and Hi-C experiments. PMID:27659986
Insights into Chromatin Structure and Dynamics in Plants
Directory of Open Access Journals (Sweden)
Stefanie Rosa
2013-11-01
Full Text Available The packaging of chromatin into the nucleus of a eukaryotic cell requires an extraordinary degree of compaction and physical organization. In recent years, it has been shown that this organization is dynamically orchestrated to regulate responses to exogenous stimuli as well as to guide complex cell-type-specific developmental programs. Gene expression is regulated by the compartmentalization of functional domains within the nucleus, by distinct nucleosome compositions accomplished via differential modifications on the histone tails and through the replacement of core histones by histone variants. In this review, we focus on these aspects of chromatin organization and discuss novel approaches such as live cell imaging and photobleaching as important tools likely to give significant insights into our understanding of the very dynamic nature of chromatin and chromatin regulatory processes. We highlight the contribution plant studies have made in this area showing the potential advantages of plants as models in understanding this fundamental aspect of biology.
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...
Directory of Open Access Journals (Sweden)
Ulrich S Tran
Full Text Available OBJECTIVE: To investigate the psychometric and structural properties of the Five Facets Mindfulness Questionnaire (FFMQ among meditators, to develop a short form, and to examine associations of mindfulness with mental health and the mechanisms of mindfulness. METHODS: Two independent samples were used, a German (n = 891 and a Spanish (n = 393 meditator sample, practicing various meditation styles. Structural and psychometric properties of the FFMQ were investigated with multigroup confirmatory factor analysis and exploratory structural equation modeling. Associations with mental health and mechanisms of mindfulness were examined with path analysis. RESULTS: The derived short form broadly matched a previous item selection in samples of non-meditators. Self-regulated Attention and Orientation to Experience governed the facets of mindfulness on a higher-order level. Higher-order factors of mindfulness and meditation experience were negatively associated with symptoms of depression and anxiety, and perceived stress. Decentering and nonattachment were the most salient mechanisms of mindfulness. Aspects of emotion regulation, bodily awareness, and nonattachment explained the effects of mindfulness on depression and anxiety. CONCLUSIONS: A two-component conceptualization for the FFMQ, and for the study of mindfulness as a psychological construct, is recommended for future research. Mechanisms of mindfulness need to be examined in intervention studies.
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.
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
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.
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.
Feynman rules of higher-order poles in CHY construction
Huang, Rijun; Feng, Bo; Luo, Ming-xing; Zhu, Chuan-Jie
2016-06-01
In this paper, we generalize the integration rules for scattering equations to situations where higher-order poles are present. We describe the strategy to deduce the Feynman rules of higher-order poles from known analytic results of simple CHY-integrands, and propose the Feynman rules for single double pole and triple pole as well as duplex-double pole and triplex-double pole structures. We demonstrate the validation and strength of these rules by ample non-trivial examples.
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.
International Nuclear Information System (INIS)
Our objective was to evaluate alterations in sperm chromatin structure in men occupationally exposed to a mixture of organophosphorus pesticides (OP) because these alterations have been proposed to compromise male fertility and offspring development. Chromatin susceptibility to in situ acid-induced denaturation structure was assessed by the sperm chromatin structure assay (SCSA). Urinary levels of alkylphosphates (DAP) were used to assess exposure. Diethylthiophosphate (DETP) was the most frequent OP metabolite found in urine samples indicating that compounds derived from thiophosphoric acid were mainly used. Chromatin structure was altered in most samples. About 75% of semen samples were classified as having poor fertility potential (>30% of Percentage of DNA Fragmentation Index [DFI%]), whereas individuals without OP occupational exposure showed average DFI% values of 9.9%. Most parameters of conventional semen analysis were within normality except for the presence of immature cells (IGC) in which 82% of the samples were above reference values. There were significant direct associations between urinary DETP concentrations and mean DFI and SD-DFI but marginally (P = 0.079) with DFI%, after adjustment for potential confounders, including IGC. This suggests that OP exposure alters sperm chromatin condensation, which could be reflected in an increased number of cells with greater susceptibility to DNA denaturation. This study showed that human sperm chromatin is a sensitive target to OP exposure and may contribute to adverse reproductive outcomes. Further studies on the relevance of protein phosphorylation as a possible mechanism by which OP alter sperm chromatin are required
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...
Canonical Quantization of Higher-Order Lagrangians
Directory of Open Access Journals (Sweden)
Khaled I. Nawafleh
2011-01-01
Full Text Available After reducing a system of higher-order regular Lagrangian into first-order singular Lagrangian using constrained auxiliary description, the Hamilton-Jacobi function is constructed. Besides, the quantization of the system is investigated using the canonical path integral approximation.
Hawking temperature and higher order tunnelling calculations
Chatterjee, Bhramar
2009-01-01
Hawking radiation has recently been explained in terms of tunnelling across the black hole horizon in a Hamilton-Jacobi framework. Higher order calculations using both usual and non-singular coordinates are found to change the tunnelling amplitude, but this change is not a simple alteration of the Hawking temperature.
Higher-Order Minimal Functional Graphs
DEFF Research Database (Denmark)
Jones, Neil D; Rosendahl, Mads
1994-01-01
We present a minimal function graph semantics for a higher-order functional language with applicative evaluation order. The semantics captures the intermediate calls performed during the evaluation of a program. This information may be used in abstract interpretation as a basis for proving...... the soundness of program analyses. An example of this is the ``closure analysis'' of partial evaluation....
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.
Higher Order Thinking in the Dance Studio
Moffett, Ann-Thomas
2012-01-01
The author identifies higher order thinking as an essential component of dance training for students of all ages and abilities. Weaving together insights from interviews with experts in the field of dance education with practical pedagogical applications within an Improvisation and Composition class for talented and gifted youth, this article…
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.
Superstrings in Higher Order Extensions of Finsler Superspaces
Vacaru, S I
1996-01-01
The work proposes a general background of the theory of field interactions and strings in spaces with higher order anisotropy. Our approach proceeds by developing the concept of higher order anisotropic superspace which unifies the logical and mathematical aspects of modern Kaluza-Klein theories and generalized Lagrange and Finsler geometry and leads to modelling of physical processes on higher order fiber bundles provided with nonlinear and distingushed connections and metric structures. The view adopted here is that a general field theory should incorporate all possible anisotropic and stochastic manifestations of classical and quantum interactions and, in consequence, a corresponding modification of basic principles and mathematical methods in formulation of physical theories. The presentation is divided into two parts. The first five sections cover the higher order anisotropic superspaces. We focus on the geometry of distinguished by nonlinear connection vector superbundles, consider different supersymmet...
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 ...
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
A Higher-Order Colon Translation
DEFF Research Database (Denmark)
Danvy, Olivier; Nielsen, Lasse R.
2000-01-01
integrated administrative reductions in the CPS transformation, making it operate in one pass. The technique applies to other lambda-encodings (e.g., variants of CPS), but we do not see it used in practice--instead, Plotkin's colon translation appears to be favored. Therefore, in an attempt to link both......A lambda-encoding such as the CPS transformation gives rise to administrative redexes. In his seminal article ``Call-by-name, call-by-value and the lambda-calculus'', 25 years ago, Plotkin tackled administrative reductions using a so-called ``colon translation.'' 10 years ago, Danvy and Filinski...... techniques, we recast Plotkin's proof of Indifference and Simulation to the higher-order specification of the one-pass CPS transformation. To this end, we extend his colon translation from first order to higher order...
A Higher-Order Colon Translation
DEFF Research Database (Denmark)
Danvy, Olivier; Nielsen, Lasse Reichstein
2001-01-01
integrated administrative reductions in the CPS transformation, making it operate in one pass. The technique applies to other lambda-encodings (e.g., variants of CPS), but we do not see it used in practice--instead, Plotkin's colon translation appears to be favored. Therefore, in an attempt to link both......A lambda-encoding such as the CPS transformation gives rise to administrative redexes. In his seminal article ``Call-by-name, call-by-value and the lambda-calculus'', 25 years ago, Plotkin tackled administrative reductions using a so-called ``colon translation.'' 10 years ago, Danvy and Filinski...... techniques, we recast Plotkin's proof of Indifference and Simulation to the higher-order specification of the one-pass CPS transformation. To this end, we extend his colon translation from first order to higher order...
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...
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...
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.
Data on force-dependent structural changes of chromatin fibers measured with magnetic tweezers
Directory of Open Access Journals (Sweden)
Fan-Tso Chien
2014-12-01
Full Text Available The compaction of chromatin fibers regulates the accessibility of embedded DNA, highly associated with transcriptional activities [1]. Single molecule force spectroscopy has revealed the great details of the structural changes of chromatin fibers in the presence of external exerted force [2–7]. However, most of the studies focus on a specific force regime [2,3,8,9]. The data here show force-extension (FE traces of chromatin fibers as measured with magnetic tweezers, covering the force regime from 0 pN to 27 pN. Those traces provide information for further studies at varied force regimes.
The regular state in higher order gravity
Cotsakis, Spiros; Kadry, Seifedine; Trachilis, Dimitrios
2016-08-01
We consider the higher-order gravity theory derived from the quadratic Lagrangian R + 𝜖R2 in vacuum as a first-order (ADM-type) system with constraints, and build time developments of solutions of an initial value formulation of the theory. We show that all such solutions, if analytic, contain the right number of free functions to qualify as general solutions of the theory. We further show that any regular analytic solution which satisfies the constraints and the evolution equations can be given in the form of an asymptotic formal power series expansion.
Adaptive filtering using Higher Order Statistics (HOS
Directory of Open Access Journals (Sweden)
Abdelghani Manseur
2012-03-01
Full Text Available The performed job, in this study, consists in studying adaptive filters and higher order statistics (HOS to ameliorate their performances, by extension of linear case to non linear filters via Volterra series. This study is, principally, axed on: „ Choice of the adaptation step and convergence conditions. „ Convergence rate. „ Adaptive variation of the convergence factor, according to the input signal. The obtained results, with real signals, have shown computationally efficient and numerically stable algorithms for adaptive nonlinear filtering while keeping relatively simple computational complexity.
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...
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)].
International Nuclear Information System (INIS)
The chromatin organization in chicken erythrocyte nuclei was studied by small-angle neutron scattering in the scattering-vector range from 1.5 x 10-1 to 10-4 A-1 with the use of the contrast-variation technique. This scattering-vector range corresponds to linear dimensions from 4 nm to 6 μm and covers the whole hierarchy of chromatin structures, from the nucleosomal structure to the entire nucleus. The results of the present study allowed the following conclusions to be drawn: (1) both the chromatin-protein structure and the structure of the nucleic acid component in chicken erythrocyte nuclei have mass-fractal properties, (2) the structure of the protein component of chromatin exhibits a fractal behavior on scales extending over two orders of magnitude, from the nucleosomal size to the size of an entire nucleus, and (3) the structure of the nucleic acid component of chromatin in chicken erythrocyte nuclei is likewise of a fractal nature and has two levels of organization or two phases with the crossover point at about 300-400 nm
Directory of Open Access Journals (Sweden)
Sha Ky
2010-08-01
Full Text Available Abstract Background Tissue differentiation is accompanied by genome-wide changes in the underlying chromatin structure and dynamics, or epigenome. By controlling when, where, and what regulatory factors have access to the underlying genomic DNA, the epigenome influences the cell's transcriptome and ultimately its function. Existing genomic methods for analyzing cell-type-specific changes in chromatin generally involve two elements: (i a source for purified cells (or nuclei of distinct types, and (ii a specific treatment that partitions or degrades chromatin by activity or structural features. For many cell types of great interest, such assays are limited by our inability to isolate the relevant cell populations in an organism or complex tissue containing an intertwined mixture of other cells. This limitation has confined available knowledge of chromatin dynamics to a narrow range of biological systems (cell types that can be sorted/separated/dissected in large numbers and tissue culture models or to amalgamations of diverse cell types (tissue chunks, whole organisms. Results Transgene-driven expression of DNA/chromatin modifying enzymes provides one opportunity to query chromatin structures in expression-defined cell subsets. In this work we combine in vivo expression of a bacterial DNA adenine methyltransferase (DAM with high throughput sequencing to sample tissue-specific chromatin accessibility on a genome-wide scale. We have applied the method (DALEC: Direct Asymmetric Ligation End Capture towards mapping a cell-type-specific view of genome accessibility as a function of differentiated state. Taking advantage of C. elegans strains expressing the DAM enzyme in diverse tissues (body wall muscle, gut, and hypodermis, our efforts yield a genome-wide dataset measuring chromatin accessibility at each of 538,000 DAM target sites in the C. elegans (diploid genome. Conclusions Validating the DALEC mapping results, we observe a strong association
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...
Aspects of general higher-order gravities
Bueno, Pablo; Min, Vincent S; Visser, Manus R
2016-01-01
We study several aspects of higher-order gravities constructed from general contractions of the Riemann tensor and the metric in arbitrary dimensions. First, we use the fast-linearization procedure presented in arXiv:1607.06463 to obtain the equations satisfied by the metric perturbation modes on a maximally symmetric background in the presence of matter and to classify $\\mathcal{L}($Riemann$)$ theories according to their spectrum. Then, we linearize all theories up to quartic order in curvature and use this result to construct quartic versions of Einsteinian cubic gravity (ECG). In addition, we show that the most general cubic gravity constructed in a dimension-independent way and which does not propagate the ghost-like spin-2 mode (but can propagate the scalar) is a linear combination of $f($Lovelock$)$ invariants, plus the ECG term, plus a New ghost-free gravity term. Next, we construct the generalized Newton potential and the Post-Newtonian parameter $\\gamma$ for general $\\mathcal{L}($Riemann$)$ gravities...
Salt and divalent cations affect the flexible nature of the natural beaded chromatin structure
DEFF Research Database (Denmark)
Christiansen, Gunna; Griffith, J
1977-01-01
A natural chromatin containing simian virus 40 (SV40) DNA and histone has been used to examine changes in chromatin structure caused by various physical and chemical treatments. We find that histone H1 depleted chromatin is more compact in solutions of 0.15M NaCl or 2 mM MgCl2 than in 0.01 M Na......Cl or 0.6M NaCL, and is compact in 0.01 M NaCl solutions if histone H 1 is present. Even high concentrations of urea did not alter the fundamental beaded structure, consisting of 110A beads of 200 base pair content, each joined by thin DNA bridges of 50 base pairs. The physical bead observed by EM...... therefore contains more DNA than the 140 base pair "core particle". The natural variation in the bridge length is consistent with the broad bands observed after nuclease digestion of chromatin. Chromatin prepared for EM without fixation containing long 20A to 30A fibers possibly complexed with protein....
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
DEFF Research Database (Denmark)
Fismen, S; Hedberg, A; Fenton, K A;
2009-01-01
Murine and human lupus nephritis are characterized by glomerular deposits of electron-dense structures (EDS). Dominant components of EDS are chromatin fragments and IgG antibodies. Whether glomerular EDS predispose for similar deposits in skin is unknown. We analysed (i) whether dermo...... (NZBxNZW)F1 and MRL-lpr/lpr mice and from five patients with lupus nephritis were analysed by immunofluorescence, immune electron microscopy (IEM) and co-localization TUNEL IEM. Affinity of chromatin fragments for membrane structures was determined by surface plasmon resonance. Results demonstrated (i...... were present in capillary lumina in glomeruli and skin of all nephritic individuals. Thus, chromatin-IgG complexes accounting for lupus nephritis seem to reach skin through circulation, but other undetermined factors are required for these complexes to deposit within skin membranes....
Mass Spectrometry-Based Proteomics for the Analysis of Chromatin Structure and Dynamics
Directory of Open Access Journals (Sweden)
Monica Soldi
2013-03-01
Full Text Available Chromatin is a highly structured nucleoprotein complex made of histone proteins and DNA that controls nearly all DNA-dependent processes. Chromatin plasticity is regulated by different associated proteins, post-translational modifications on histones (hPTMs and DNA methylation, which act in a concerted manner to enforce a specific “chromatin landscape”, with a regulatory effect on gene expression. Mass Spectrometry (MS has emerged as a powerful analytical strategy to detect histone PTMs, revealing interplays between neighbouring PTMs and enabling screens for their readers in a comprehensive and quantitative fashion. Here we provide an overview of the recent achievements of state-of-the-art mass spectrometry-based proteomics for the detailed qualitative and quantitative characterization of histone post-translational modifications, histone variants, and global interactomes at specific chromatin regions. This synopsis emphasizes how the advances in high resolution MS, from “Bottom Up” to “Top Down” analysis, together with the uptake of quantitative proteomics methods by chromatin biologists, have made MS a well-established method in the epigenetics field, enabling the acquisition of original information, highly complementary to that offered by more conventional, antibody-based, assays.
Higher order variational time discretization of optimal control problems
Campos, C M; Ober-Blöbaum, S
2012-01-01
We reconsider the variational integration of optimal control problems for mechanical systems based on a direct discretization of the Lagrange-d'Alembert principle. This approach yields discrete dynamical constraints which by construction preserve important structural properties of the system, like the evolution of the momentum maps or the energy behavior. Here, we employ higher order quadrature rules based on polynomial collocation. The resulting variational time discretization decreases the overall computational effort.
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 ...
Directory of Open Access Journals (Sweden)
Ryosuke eOhsawa
2013-07-01
Full Text Available It is well accepted that non-coding RNAs play a critical role in regulating gene expression. Recent paradigm-setting studies are now revealing that non-coding RNAs, other than microRNAs, also play intriguing roles in the maintenance of chromatin structure, in the DNA damage response, and in adult human stem cell aging. In this review, we will discuss the complex inter-dependent relationships among non-coding RNA transcription, maintenance of genomic stability, chromatin structure and adult stem cell senescence. DNA damage-induced non-coding RNAs transcribed in the vicinity of the DNA break regulate recruitment of the DNA damage machinery and DNA repair efficiency. We will discuss the correlation between non-coding RNAs and DNA damage repair efficiency and the potential role of changing chromatin structures around double-strand break sites. On the other hand, induction of non-coding RNA transcription from the repetitive Alu elements occurs during human stem cell aging and hinders efficient DNA repair causing entry into senescence. We will discuss how this fine balance between transcription and genomic instability may be regulated by the dramatic changes to chromatin structure that accompany cellular senescence.
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...
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 ...
Zhukotskiĭ, A V; Shchegolev, A I; Butusova, N N; Nemirovskiĭ, L E; Kogan, E M
1985-06-01
Geometric and optical parameters of chromatin of hepatocyte nuclei have been examined before (UV, lambda = 265 nm) and after gallocyanine staining. Quantitative parameters of the chromatin structure in the same nuclei measured in situ by a scanning microscope-photometer (step size 0.125 micron) before and after staining were equal. Tinctorial properties of chromatin granules (condensed part of the nuclear material) and its diffuse part were different. It is suggested that the difference between granules and the nongranular part of chromatin is not only of optical but also of chemical nature. PMID:2410060
Energy Technology Data Exchange (ETDEWEB)
Peng, Jamy C.
2007-05-05
Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in
Energy Technology Data Exchange (ETDEWEB)
Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)
2007-01-01
Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in
Higher Order Macro Coefficients in Periodic Homogenization
Conca, Carlos; San Martin, Jorge; Smaranda, Loredana; Vanninathan, Muthusamy
2011-09-01
A first set of macro coefficients known as the homogenized coefficients appear in the homogenization of PDE on periodic structures. If energy is increased or scale is decreased, these coefficients do not provide adequate approximation. Using Bloch decomposition, it is first realized that the above coefficients correspond to the lowest energy and the largest scale. This naturally paves the way to introduce other sets of macro coefficients corresponding to higher energies and lower scales which yield better approximation. The next task is to compare their properties with those of the homogenized coefficients. This article reviews these developments along with some new results yet to be published.
Higher Order Macro Coefficients in Periodic Homogenization
Energy Technology Data Exchange (ETDEWEB)
Conca, Carlos; San Martin, Jorge [Departamento de IngenierIa Matematica, Facultad de Ciencias Fisicas y Matematicas, Universidad de Chile and Centro de Modelamiento Matematico, UMR 2071 CNRS-UChile, Casilla 170/3 - Correo 3, Santiago (Chile); Smaranda, Loredana [Department of Mathematics, Faculty of Mathematics and Computer Science, University of Pitesti, 110040 Pitesti, Str. Targu din Vale Nr.1, Arges (Romania); Vanninathan, Muthusamy, E-mail: cconca@dim.uchile.cl, E-mail: jorge@dim.uchile.cl, E-mail: smaranda@dim.uchile.cl, E-mail: vanni@math.tifrbng.res.in [TIFR-CAM, Post Bag 6503, GKVK Post, Bangalore - 560065 (India)
2011-09-15
A first set of macro coefficients known as the homogenized coefficients appear in the homogenization of PDE on periodic structures. If energy is increased or scale is decreased, these coefficients do not provide adequate approximation. Using Bloch decomposition, it is first realized that the above coefficients correspond to the lowest energy and the largest scale. This naturally paves the way to introduce other sets of macro coefficients corresponding to higher energies and lower scales which yield better approximation. The next task is to compare their properties with those of the homogenized coefficients. This article reviews these developments along with some new results yet to be published.
The Emerging Roles of ATP-Dependent Chromatin Remodeling Enzymes in Nucleotide Excision Repair
Directory of Open Access Journals (Sweden)
Wioletta Czaja
2012-09-01
Full Text Available DNA repair in eukaryotic cells takes place in the context of chromatin, where DNA, including damaged DNA, is tightly packed into nucleosomes and higher order chromatin structures. Chromatin intrinsically restricts accessibility of DNA repair proteins to the damaged DNA and impacts upon the overall rate of DNA repair. Chromatin is highly responsive to DNA damage and undergoes specific remodeling to facilitate DNA repair. How damaged DNA is accessed, repaired and restored to the original chromatin state, and how chromatin remodeling coordinates these processes in vivo, remains largely unknown. ATP-dependent chromatin remodelers (ACRs are the master regulators of chromatin structure and dynamics. Conserved from yeast to humans, ACRs utilize the energy of ATP to reorganize packing of chromatin and control DNA accessibility by sliding, ejecting or restructuring nucleosomes. Several studies have demonstrated that ATP-dependent remodeling activity of ACRs plays important roles in coordination of spatio-temporal steps of different DNA repair pathways in chromatin. This review focuses on the role of ACRs in regulation of various aspects of nucleotide excision repair (NER in the context of chromatin. We discuss current understanding of ATP-dependent chromatin remodeling by various subfamilies of remodelers and regulation of the NER pathway in vivo.
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
Energy Technology Data Exchange (ETDEWEB)
Terry, Samantha Y.A. [CR-UK/MRC Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Oxford (United Kingdom); Vallis, Katherine A., E-mail: katherine.vallis@oncology.ox.ac.uk [CR-UK/MRC Gray Institute for Radiation Oncology and Biology, Department of Oncology, University of Oxford, Oxford (United Kingdom)
2012-07-15
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 ({gamma}H2AX assay) and clonogenic survival were evaluated after exposure to {sup 111}In-DTPA-hEGF, an Auger electron-emitting radiopharmaceutical, or IR. The intracellular distribution of {sup 111}In-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 {gamma}H2AX foci per cell was greater in MDA-MB-468 and 231-H2N cells after IR (0.5 Gy) plus SAHA (1 {mu}M) compared with IR alone (16 {+-} 0.6 and 14 {+-} 0.3 vs. 12 {+-} 0.4 and 11 {+-} 0.2, respectively). More {gamma}H2AX foci were observed in MDA-MB-468 and 231-H2N cells exposed to {sup 111}In-DTPA-hEGF (6 MBq/{mu}g) plus SAHA vs. {sup 111}In-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 {sup 111}In-DTPA-hEGF. Clonogenic survival was reduced in MDA-MB-468 and 231-H2N cells after IR (6 Gy) plus SAHA (1 {mu}M) vs. IR alone (0.6% {+-} 0.01 and 0.3% {+-} 0.2 vs. 5.8% {+-} 0.2 and 2% {+-} 0.1, respectively) and after {sup 111}In-DTPA-hEGF plus SAHA compared to {sup 111}In-DTPA-hEGF alone (21% {+-} 0.4% and 19% {+-} 4.6 vs. 33% {+-} 2.3 and 32% {+-} 3.7). SAHA did not affect {sup 111}In-DTPA-hEGF nuclear localization. Hypertonic treatment resulted in fewer {gamma}H2AX foci per cell
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.
Distinct differences in chromatin structure at subtelomeric X and Y' elements in budding yeast.
Directory of Open Access Journals (Sweden)
Xuefeng Zhu
Full Text Available In Saccharomyces cerevisiae, all ends of telomeric DNA contain telomeric repeats of (TG(1-3, but the number and position of subtelomeric X and Y' repeat elements vary. Using chromatin immunoprecipitation and genome-wide analyses, we here demonstrate that the subtelomeric X and Y' elements have distinct structural and functional properties. Y' elements are transcriptionally active and highly enriched in nucleosomes, whereas X elements are repressed and devoid of nucleosomes. In contrast to X elements, the Y' elements also lack the classical hallmarks of heterochromatin, such as high Sir3 and Rap1 occupancy as well as low levels of histone H4 lysine 16 acetylation. Our analyses suggest that the presence of X and Y' elements govern chromatin structure and transcription activity at individual chromosome ends.
DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure
International Nuclear Information System (INIS)
Interstitial Telomeric Sequences (ITS) are over-involved in spontaneous and radiationinduced chromosome aberrations in chinese hamster cells. We have performed a study to investigate the origin of their instability, spontaneously or after low doses irradiation. Our results demonstrate that ITS have a particular chromatin structure: short nucleotide repeat length, less compaction of the 30 nm chromatin fiber, presence of G-quadruplex structures. These features would modulate breaks production and would favour the recruitment of alternative DNA repair mechanisms, which are prone to produce chromosome aberrations. These pathways could be at the origin of chromosome aberrations in ITS whereas NHEJ and HR Double Strand Break repair pathways are rather required for a correct repair in these regions. (author)
Generalizations of Euler Numbers and Euler Numbers of Higher Order
Institute of Scientific and Technical Information of China (English)
LUOQiu-ming; QIFeng
2005-01-01
The purpose of this paper is to define the generalized Euler numbers and the generalized Euler numbers of higher order, their recursion formula and some properties were established, accordingly Euler numbers and Euler numbers of higher order were extended.
HIGHER ORDER MULTIVARIABLE NORLUND EULER-BERNOULLI POLYNOMIALS
Institute of Scientific and Technical Information of China (English)
刘国栋
2002-01-01
The definitions of higher order multivariable Norlund Euler polynomials and Norlund Bernoulli polynomials are presented and some of their important properties are expounded. Some identities involving recurrence sequences and higher order multivariable Norlund Euler-Bernoulli polynomials are established.
Chromatin structure and ionizing-radiation-induced chromosome aberrations
International Nuclear Information System (INIS)
The possible influence of chromatic structure or activity on chromosomal radiosensitivity was studied. A cell line was isolated which contained some 105 copies of an amplified plasmid in a single large mosquito artificial chromosome (MAC). This chromosome was hypersensitive to DNase I. Its radiosensitivity was some three fold greater than normal mosquito chromosomes in the same cell. In cultured human cells irradiated during G0, the initial breakage frequency in chromosome 4, 19 and the euchromatic and heterochromatic portions of the Y chromosome were measured over a wide range of doses by inducing Premature Chromosome Condensation (PCC) immediately after irradiation with Cs-137 gamma rays. No evidence was seen that Y heterochromatin or large fragments of it remained unbroken. The only significant deviation from the expected initial breakage frequency per Gy per unit length of chromosome was that observed for the euchromatic portion of the Y chromosome, with breakage nearly twice that expected. The development of aberrations involving X and Y chromosomes at the first mitosis after irradation was also studied. Normal female cells sustained about twice the frequency of aberrations involving X chromosomes for a dose of 7.3 Gy than the corresponding male cells. Fibroblasts from individuals with supernumerary X chromosomes did not show any further increase in X aberrations for this dos. The frequency of aberrations involving the heterochromatic portion of the long arm of the Y chromosome was about what would be expected for a similar length of autosome, but the euchromatic portion of the Y was about 3 times more radiosensitive per unit length. 5-Azacytidine treatment of cultured human female fibroblasts or fibroblasts from a 49,XXXXY individual, reduced the methylation of cytosine residues in DNA, and resulted in an increased chromosomal radiosensitivity in general, but it did not increase the frequency of aberrations involving the X chromosomes
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.
Directory of Open Access Journals (Sweden)
Anderly C Chueh
2009-01-01
Full Text Available We have previously identified and characterized the phenomenon of ectopic human centromeres, known as neocentromeres. Human neocentromeres form epigenetically at euchromatic chromosomal sites and are structurally and functionally similar to normal human centromeres. Recent studies have indicated that neocentromere formation provides a major mechanism for centromere repositioning, karyotype evolution, and speciation. Using a marker chromosome mardel(10 containing a neocentromere formed at the normal chromosomal 10q25 region, we have previously mapped a 330-kb CENP-A-binding domain and described an increased prevalence of L1 retrotransposons in the underlying DNA sequences of the CENP-A-binding clusters. Here, we investigated the potential role of the L1 retrotransposons in the regulation of neocentromere activity. Determination of the transcriptional activity of a panel of full-length L1s (FL-L1s across a 6-Mb region spanning the 10q25 neocentromere chromatin identified one of the FL-L1 retrotransposons, designated FL-L1b and residing centrally within the CENP-A-binding clusters, to be transcriptionally active. We demonstrated the direct incorporation of the FL-L1b RNA transcripts into the CENP-A-associated chromatin. RNAi-mediated knockdown of the FL-L1b RNA transcripts led to a reduction in CENP-A binding and an impaired mitotic function of the 10q25 neocentromere. These results indicate that LINE retrotransposon RNA is a previously undescribed essential structural and functional component of the neocentromeric chromatin and that retrotransposable elements may serve as a critical epigenetic determinant in the chromatin remodelling events leading to neocentromere formation.
Fractal Characterization of Chromatin Decompaction in Live Cells.
Yi, Ji; Stypula-Cyrus, Yolanda; Blaha, Catherine S; Roy, Hemant K; Backman, Vadim
2015-12-01
Chromatin organization has a fundamental impact on the whole spectrum of genomic functions. Quantitative characterization of the chromatin structure, particularly at submicron length scales where chromatin fractal globules are formed, is critical to understanding this structure-function relationship. Such analysis is currently challenging due to the diffraction-limited resolution of conventional light microscopy. We herein present an optical approach termed inverse spectroscopic optical coherence tomography to characterize the mass density fractality of chromatin, and we apply the technique to observe chromatin decompaction in live cells. The technique makes it possible for the first time, to our knowledge, to sense intracellular morphology with length-scale sensitivity from ∼30 to 450 nm, thus primarily probing the higher-order chromatin structure, without resolving the actual structures. We used chromatin decompaction due to inhibition of histone deacytelases and measured the subsequent changes in the fractal dimension of the intracellular structure. The results were confirmed by transmission electron microscopy and confocal fluorescence microscopy.
Ji, Lusha; Xu, Rui; Lu, Longtao; Zhang, Jiedao; Yang, Guodong; Huang, Jinguang; Wu, Changai; Zheng, Chengchao
2013-08-01
Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.
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.
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.
Institute of Scientific and Technical Information of China (English)
Li Xi-Zeng; Su Bao-Xia; Chai Lu
2004-01-01
It is found that the two-mode output quantum electromagnetic field in two-mode squeezed states exhibits higherorder squeezing to all even orders, and the degree of higher-order squeezing is greater than that of the second-order.The higher-order squeezed parameter and squeezed limit due to the modulation frequency are investigated. The smaller the modulation frequency is, the stronger the degree of higher-order squeezing becomes. Furthermore, the higher-order uncertainty relations in two-mode squeezed states are presented for the first time. The product of higher-order noise moments is related to even order number N and the squeeze factor r.
Higher-Order Generalized Invexity in Control Problems
Directory of Open Access Journals (Sweden)
S. K. Padhan
2011-01-01
Full Text Available We introduce a higher-order duality (Mangasarian type and Mond-Weir type for the control problem. Under the higher-order generalized invexity assumptions on the functions that compose the primal problems, higher-order duality results (weak duality, strong duality, and converse duality are derived for these pair of problems. Also, we establish few examples in support of our investigation.
Skinner-Rusk unified formalism for higher-order systems
Prieto-Martínez, Pedro Daniel; Román-Roy, Narciso
2012-07-01
The Lagrangian-Hamiltonian unified formalism of R. Skinner and R. Rusk was originally stated for autonomous dynamical systems in classical mechanics. It has been generalized for non-autonomous first-order mechanical systems, first-order and higher-order field theories, and higher-order autonomous systems. In this work we present a generalization of this formalism for higher-order non-autonomous mechanical systems.
Higher order mode analysis of the SPL cavities
Schuh, M; Tuckmantel, J; Welsch, CP
2010-01-01
Higher Order Modes (HOMs) can severely limit the operation of superconducting cavities in a linac with high beam current, high duty factor and complex pulse structure. The full HOM spectrum has to be analyzed in order to identify potentially dangerous modes already during the design phase and to define their damping requirements. For this purpose a dedicated beam simulation code focused on beam-HOMinteraction was developed, taking into account important effects like the HOMfrequency spread, beam input jitter, different chopping patterns, as well as klystron and alignment errors. Here, the code is used to investigate in detail the HOM properties of the cavities foreseen in the Superconducting Proton Linac (SPL) at CERN and their potential to drive beam instabilities. Special attention is given to HOM excitation by chopped pulses with high repetition rate.
DEFF Research Database (Denmark)
Ebert, Grit; Steininger, Anne; Weißmann, Robert;
2014-01-01
of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS: Our study suggests a link of nuclear architecture and the propagation of SDs across...
Some properties of generalized higher-order convexity
Wasowicz, Szymon
2008-01-01
The generalized divided differences are introduced. They are applied to investigate some properties characterizing generalized higher-order convexity. Among others some support-type property is proved.
Higher Order Diffraction Characteristics of Fiber Bragg Grating
Directory of Open Access Journals (Sweden)
Sunita P. Ugale
2013-02-01
Full Text Available The effect of grating saturation on higher order diffraction characteristic of FBG is investigated by using Coupled mode theory. Grating saturation effects were considered in the index distribution model showing the significant influence on the coupling process and hence on the reflectivity characteristics of FBG. Maximum reflectivity curves for first and higher order diffraction of FBG are plotted for different values of saturation coefficient. The effect of change in length and change in refractive index are studied. The behavior of grating for higher order of diffraction is totally different than first order of diffraction. In saturated gratings, the higher order diffraction can be utilized for multiparameter sensing
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
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...
Directory of Open Access Journals (Sweden)
Nicolas M Berbenetz
2010-09-01
Full Text Available Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers positions nucleosomes adjacent to the origin to promote replication origin function.
Fine analysis of the chromatin structure of yeast RNA polymerase Ⅱ transcription teminators
Institute of Scientific and Technical Information of China (English)
HUGENGXI; YUNHUAYU; 等
1992-01-01
In order to study the functional structure of the transcription terminators and the mechanism of temination,a survey of the chromatin structure,including the location of DNase I hypersensitive sites and the nucleosome arrangement,of yeast ADH1 and FLP terminators was made.The results show that there is no relationship between the function of the terminators and the existence of DNase I hypersensitive sites.However,it is found that there is always a nucleosmoe at the immediate upstream of the transcriptional termination sites.As a control,the chromatin structures of the pBR322 DNA fragments on the yeast shutter vectors are also investigated at the same time.The random nucleosome arrangement on the bacterial DNA in yesast agrees with the published reports.A new hypothesis,about the mechanism of transcriptional termination is put forward and the reason of different nucleosome arrengement on the DNAs which are originally from different species in yeast is discussed.
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
Introduction to Higher Order Spatial Statistics in Cosmology
Szapudi, István
2005-01-01
In this lecture notes I concentrate on the classic and widely applicable characterization of higher order statistics by joint moments, a.k.a. higher order correlation functions, and directly related statistics. I put special emphasis on recent results, especially the connection of spatial statistics with symmetries.
Adaptive Integral Method for Higher Order Method of Moments
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Meincke, Peter
2008-01-01
The adaptive integral method (AIM) is combined with the higher order method of moments (MoM) to solve integral equations. The technique takes advantage of the low computational complexity and memory requirements of the AIM and the reduced number of unknowns and higher order convergence of higher...
On the fractional counterpart of the higher-order equations
D'Ovidio, Mirko
2011-01-01
In this work we study the solutions to some fractional higher-order equations. Special cases in which time-fractional derivatives take integer values are also examined and the explicit solutions are presented. Such solutions can be expressed by means of the transition laws of stable subordinators and their inverse processes. In particular we establish connections between fractional and higher-order equations.
Higher-order Dirac solitons in binary waveguide arrays
International Nuclear Information System (INIS)
We study optical analogues of higher-order Dirac solitons (HODSs) in binary waveguide arrays. Like higher-order solitons obtained from the well-known nonlinear Schrödinger equation governing the pulse propagation in an optical fiber, these HODSs have amplitude profiles which are numerically shown to be periodic over large propagation distances. At the same time, HODSs possess some unique features. Firstly, the period of a HODS depends on its order parameter. Secondly, the discrete nature in binary waveguide arrays imposes the upper limit on the order parameter of HODSs. Thirdly, the order parameter of HODSs can vary continuously in a certain range. - Highlights: • Higher-order Dirac solitons in nonlinear binary waveguide arrays are numerically demonstrated. • Amplitude profiles of higher-order Dirac solitons are periodic during propagation. • The period of higher-order Dirac solitons decreases when the soliton order increases
Neural classifiers for learning higher-order correlations
International Nuclear Information System (INIS)
Studies by various authors suggest that higher-order networks can be more powerful and biologically more plausible with respect to the more traditional multilayer networks. These architecture make explicit use of nonlinear interactions between input variables in the form of higher-order units or product units. If it is known a priori that the problem to be implemented possesses a given set of invariances like in the translation, rotation, and scale invariant recognition problems, those invariances can be encoded, thus eliminating all higher-order terms which are incompatible with the invariances. In general, however, it is a serious set-back that the complexity of learning increases exponentially with the size of inputs. This paper reviews higher-order networks and introduces an implicit representation in which learning complexity is mainly decided by the number of higher-order terms to be learned and increases only linearly with the input size
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.
Higher-order Dirac solitons in binary waveguide arrays
Energy Technology Data Exchange (ETDEWEB)
Tran, Truong X., E-mail: Truong.Tran@mpl.mpg.de [Department of Physics, Le Quy Don University, 236 Hoang Quoc Viet str., 10000 Hanoi (Viet Nam); Max Planck Institute for the Science of Light, Günther-Scharowsky str. 1, 91058 Erlangen (Germany); Duong, Dũng C. [Department of Physics, Le Quy Don University, 236 Hoang Quoc Viet str., 10000 Hanoi (Viet Nam)
2015-10-15
We study optical analogues of higher-order Dirac solitons (HODSs) in binary waveguide arrays. Like higher-order solitons obtained from the well-known nonlinear Schrödinger equation governing the pulse propagation in an optical fiber, these HODSs have amplitude profiles which are numerically shown to be periodic over large propagation distances. At the same time, HODSs possess some unique features. Firstly, the period of a HODS depends on its order parameter. Secondly, the discrete nature in binary waveguide arrays imposes the upper limit on the order parameter of HODSs. Thirdly, the order parameter of HODSs can vary continuously in a certain range. - Highlights: • Higher-order Dirac solitons in nonlinear binary waveguide arrays are numerically demonstrated. • Amplitude profiles of higher-order Dirac solitons are periodic during propagation. • The period of higher-order Dirac solitons decreases when the soliton order increases.
Directory of Open Access Journals (Sweden)
David eRoquis
2014-07-01
Full Text Available Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharziasis, a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the 20th century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited. Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modification were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.
Dileep, Vishnu; Rivera-Mulia, Juan Carlos; Sima, Jiao; Gilbert, David M
2015-01-01
Chromosome architecture has received a lot of attention since the recent development of genome-scale methods to measure chromatin interactions (Hi-C), enabling the first sequence-based models of chromosome tertiary structure. A view has emerged of chromosomes as a string of structural units (topologically associating domains; TADs) whose boundaries persist through the cell cycle and development. TADs with similar chromatin states tend to aggregate, forming spatially segregated chromatin compartments. However, high-resolution Hi-C has revealed substructure within TADs (subTADs) that poses a challenge for models that attribute significance to structural units at any given scale. More than 20 years ago, the DNA replication field independently identified stable structural (and functional) units of chromosomes (replication foci) as well as spatially segregated chromatin compartments (early and late foci), but lacked the means to link these units to genomic map units. Genome-wide studies of replication timing (RT) have now merged these two disciplines by identifying individual units of replication regulation (replication domains; RDs) that correspond to TADs and are arranged in 3D to form spatiotemporally segregated subnuclear compartments. Furthermore, classifying RDs/TADs by their constitutive versus developmentally regulated RT has revealed distinct classes of chromatin organization, providing unexpected insight into the relationship between large-scale chromosome structure and function. PMID:26590169
Sperm chromatin structure assay (SCSA): a tool in diagnosis and treatment of infertility
Institute of Scientific and Technical Information of China (English)
Mona Bungum; Leif Bungum; Aleksander Giwercman
2011-01-01
Diagnosis of male infertility has mainly been based on the World Health Organization (WHO) manual-based semen parameter's concentration,motility and morphology.It has,however,become apparent that none of these parameters are reliable markers for evaluation of the fertility potential of a couple.A search for better markers has led to an increased focus on sperm chromatin integrity testing in fertility work-up and assisted reproductive techniques.During the last couple of decades,numerous sperm DNA integrity tests have been developed.These are claimed to be characterized by a lower intraindividual variation,less intralaboratory and interlaboratory variation and thus less subjective than the conventional sperm analysis.However,not all the sperm chromatin integrity tests have yet been shown to be of clinical value.So far,the test that has been found to have the most stable clinical threshold values in relation to fertility is the sperm chromatin structure assay (SCSA),a flow cytometric test that measures the susceptibility of sperm DNA to acid-induced DNA denaturation in situ.Sperm DNA fragmentation as measured by SCSA has shown to be an independent predictor of successful pregnancy in first pregnancy planners as well as in couples undergoing intrauterine insemination,and can be used as a tool in investigation,counseling and treatment of involuntary childlessness.More conflicting data exist regarding the role of sperm DNA fragmentation in relation to fertilization,pre-embryo development and pregnancy outcome in in vitrofertilization and intracytoplasmic sperm injection (ICSI).
Higher-order Fourier analysis over finite fields and applications
Hatami, Pooya
Higher-order Fourier analysis is a powerful tool in the study of problems in additive and extremal combinatorics, for instance the study of arithmetic progressions in primes, where the traditional Fourier analysis comes short. In recent years, higher-order Fourier analysis has found multiple applications in computer science in fields such as property testing and coding theory. In this thesis, we develop new tools within this theory with several new applications such as a characterization theorem in algebraic property testing. One of our main contributions is a strong near-equidistribution result for regular collections of polynomials. The densities of small linear structures in subsets of Abelian groups can be expressed as certain analytic averages involving linear forms. Higher-order Fourier analysis examines such averages by approximating the indicator function of a subset by a function of bounded number of polynomials. Then, to approximate the average, it suffices to know the joint distribution of the polynomials applied to the linear forms. We prove a near-equidistribution theorem that describes these distributions for the group F(n/p) when p is a fixed prime. This fundamental fact was previously known only under various extra assumptions about the linear forms or the field size. We use this near-equidistribution theorem to settle a conjecture of Gowers and Wolf on the true complexity of systems of linear forms. Our next application is towards a characterization of testable algebraic properties. We prove that every locally characterized affine-invariant property of functions f : F(n/p) → R with n∈ N, is testable. In fact, we prove that any such property P is proximity-obliviously testable. More generally, we show that any affine-invariant property that is closed under subspace restrictions and has "bounded complexity" is testable. We also prove that any property that can be described as the property of decomposing into a known structure of low
Quantitative research on higher order harmonics in metrology beamline
Institute of Scientific and Technical Information of China (English)
Hongjun ZHOU; Jinjin ZHENG; Tonglin HUO; Guobin ZHANG; Zeming QI; Pengfei ZHONG
2008-01-01
The synchrotron radiation spectra of the spherical grating monochromator (SGM) working in the soft X-ray and VUV region are often contaminated by significant amounts of higher order harmonics. They cannot be suppressed completely by suitable filters. Higher order contributions in the spectral radiation standard and metrology beamline were researched using transmission grating (made in-house) and IRD AXUV100G (USA) photodiode detector. The exit beam was dispersed with the transmission grating behind the exit slit of the monochromator, and the contributions of the different orders were analyzed. The higher order distributions were quantitatively determined for three gratings with line densities of 1800, 600 and 200 l/mm.Experiment results show that in wavelengths between 5 nm and 15 nm the contributions of the higher orders to the detector signal are restricted to less than 7% even without the use of filters. In wavelength regions between 5 nm and 34 nm, the contributions of the higher orders to the detector signal are less than 14% with proper Al, Si3N4 and Zr filters, and after being modified by quantum efficiency of the detector, the higher order contributions are restricted to less than 6.5%. The study also shows that higher orders are almost totally suppressed by MgF2 filter when the wavelength ranges between 115-140 nm.
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
Demand-Driven Higher-Order Fixpoint Iteration
DEFF Research Database (Denmark)
Rosendahl, Mads
Our aim is to show that techniques from higher-order strictness analysis may be used as a general algorithmic principle in a functional programming language. Certain problems may be expressed as the search for the least solution that satisfy certain given properties. This is often done using some...... kind of fixpoint iteration. We will present a fixpoint operation that can be used for second-order functions and extend this to higher-order functions. The technique is based on using partial function graphs to represent higher-order objects. The main problem in finding fixpoints for higher...
DEFF Research Database (Denmark)
Ehrensberger, Andreas Hasso; Svejstrup, Jesper Qualmann
2012-01-01
attributed to high kinetic barriers that affect all cells equally and can only be overcome by rare stochastic events. The barriers to reprogramming are likely to involve transformations of chromatin state because (i) inhibitors of chromatin-modifying enzymes can enhance the efficiency of reprogramming...... and (ii) knockdown or knock-out of chromatin-modifying enzymes can lower the efficiency of reprogramming. Here, we review the relationship between chromatin state transformations (chromatin reprogramming) and cellular reprogramming, with an emphasis on transcription factors, chromatin remodeling factors...
Directory of Open Access Journals (Sweden)
Lu Qianjin
2004-01-01
Full Text Available Chromatin structure, determined in part by DNA methylation, is established during differentiation and prevents expression of genes unnecessary for the function of a given cell type. We reported that DNA methylation and chromatin structure contributes to lymphoid-specific ITGAL (CD11a and PRF1 (perforin expression. We used bisulfite sequencing to compare methylation patterns in the ITGAL promoter and 5' flanking region of T cells and fibroblasts, and in the PRF1 promoter and upstream enhancer of CD4+ and CD8+ T cells with fibroblasts. The effects of methylation on promoter function were tested using regional methylation of reporter constructs, and confirmed by DNA methyltransferase inhibition. The relationship between DNA methylation and chromatin structure was analyzed by DNaseI hypersensitivity. Herein we described the methods and results in greater detail.
Unambiguous formalism for higher order Lagrangian field theories
Energy Technology Data Exchange (ETDEWEB)
Campos, Cedric M; De Leon, Manuel; De Diego, David MartIn [Instituto de Ciencias Matematicas, CSIC-UAM-UC3M-UCM, Serrano 123, 28006 Madrid (Spain); Vankerschaver, Joris [Control and Dynamical Systems, California Institute of Technology, CA (United States)], E-mail: cedricmc@imaff.cfmac.csic.es, E-mail: mdeleon@imaff.cfmac.csic.es, E-mail: d.martin@imaff.cfmac.csic.es, E-mail: jv@caltech.edu
2009-11-27
The aim of this paper is to propose an unambiguous intrinsic formalism for higher order field theories which avoids the arbitrariness in the generalization of the conventional description of field theories, and implies the existence of different Cartan forms and Legendre transformations. We propose a differential-geometric setting for the dynamics of a higher order field theory, based on the Skinner and Rusk formalism for mechanics. This approach incorporates aspects of both the Lagrangian and the Hamiltonian description, since the field equations are formulated using the Lagrangian on a higher order jet bundle and the canonical multisymplectic form on its affine dual. As both of these objects are uniquely defined, the Skinner-Rusk approach has the advantage that it does not suffer from the arbitrariness in conventional descriptions. The result is that we obtain a unique and global intrinsic version of the Euler-Lagrange equations for higher order field theories. Several examples illustrate our construction.
On Doubly Degenerate Quasilinear Parabolic Equations of Higher Order
Institute of Scientific and Technical Information of China (English)
Zhen Hai LIU
2005-01-01
We deal with the existence of periodic solutions for doubly degenerate quasilinear parabolic equations of higher order, which can degenerate, on a part of the boundary, on a segment in the interior of the domain and in time.
Development of a core confidence-higher order construct.
Stajkovic, Alexander D
2006-11-01
The author develops core confidence as a higher order construct and suggests that a core confidence-higher order construct--not addressed by extant work motivation theories--is helpful in better understanding employee motivation in today's rapidly changing organizations. Drawing from psychology (social, clinical, and developmental) and social anthropology, the author develops propositions regarding the relationships between core confidence and performance, attitudes, and subjective well-being. The core confidence-higher order construct is proposed to be manifested by hope, self-efficacy, optimism, and resilience. The author reasons that these four variables share a common confidence core (a higher order construct) and may be considered as its manifestations. Suggestions for future research and implications of the work are discussed. PMID:17100479
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...
All-fiber Raman Probe using Higher Order Modes
DEFF Research Database (Denmark)
Larsen, Stine Højer Møller; Rishøj, Lars Søgaard; Rottwitt, Karsten
2013-01-01
We demonstrate the first all-fiber Raman probe utilizing higher order modes for the excitation. The spectrum of cyclohexane is measured using both the fundamental mode as well as in-fiber-generated Bessel-like modes.......We demonstrate the first all-fiber Raman probe utilizing higher order modes for the excitation. The spectrum of cyclohexane is measured using both the fundamental mode as well as in-fiber-generated Bessel-like modes....
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.
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.
Higher order aberrations of the eye: Part one
Directory of Open Access Journals (Sweden)
Marsha Oberholzer
2016-03-01
Full Text Available This article is the first in a series of two articles that provide a comprehensive literature review of higher order aberrations (HOAs of the eye. The present article mainly explains the general principles of such HOAs as well as HOAs of importance, and the measuring apparatus used to measure HOAs of the eye. The second article in the series discusses factors contributing to variable results in measurements of HOAs of the eye.Keywords: Higher order aberrations; wavefront aberrations; aberrometer
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...
Linear matrix differential equations of higher-order and applications
Directory of Open Access Journals (Sweden)
Mustapha Rachidi
2008-07-01
Full Text Available In this article, we study linear differential equations of higher-order whose coefficients are square matrices. The combinatorial method for computing the matrix powers and exponential is adopted. New formulas representing auxiliary results are obtained. This allows us to prove properties of a large class of linear matrix differential equations of higher-order, in particular results of Apostol and Kolodner are recovered. Also illustrative examples and applications are presented.
A Simplified Algorithm for Inverting Higher Order Diffusion Tensors
Directory of Open Access Journals (Sweden)
Laura Astola
2014-11-01
Full Text Available In Riemannian geometry, a distance function is determined by an inner product on the tangent space. In Riemann–Finsler geometry, this distance function can be determined by a norm. This gives more freedom on the form of the so-called indicatrix or the set of unit vectors. This has some interesting applications, e.g., in medical image analysis, especially in diffusion weighted imaging (DWI. An important application of DWI is in the inference of the local architecture of the tissue, typically consisting of thin elongated structures, such as axons or muscle fibers, by measuring the constrained diffusion of water within the tissue. From high angular resolution diffusion imaging (HARDI data, one can estimate the diffusion orientation distribution function (dODF, which indicates the relative diffusivity in all directions and can be represented by a spherical polynomial. We express this dODF as an equivalent spherical monomial (higher order tensor to directly generalize the (second order diffusion tensor approach. To enable efficient computation of Riemann–Finslerian quantities on diffusion weighted (DW-images, such as the metric/norm tensor, we present a simple and efficient algorithm to invert even order spherical monomials, which extends the familiar inversion of diffusion tensors, i.e., symmetric matrices.
A general higher-order remap algorithm for ALE calculations
Energy Technology Data Exchange (ETDEWEB)
Chiravalle, Vincent P [Los Alamos National Laboratory
2011-01-05
A numerical technique for solving the equations of fluid dynamics with arbitrary mesh motion is presented. The three phases of the Arbitrary Lagrangian Eulerian (ALE) methodology are outlined: the Lagrangian phase, grid relaxation phase and remap phase. The Lagrangian phase follows a well known approach from the HEMP code; in addition the strain rate andflow divergence are calculated in a consistent manner according to Margolin. A donor cell method from the SALE code forms the basis of the remap step, but unlike SALE a higher order correction based on monotone gradients is also added to the remap. Four test problems were explored to evaluate the fidelity of these numerical techniques, as implemented in a simple test code, written in the C programming language, called Cercion. Novel cell-centered data structures are used in Cercion to reduce the complexity of the programming and maximize the efficiency of memory usage. The locations of the shock and contact discontinuity in the Riemann shock tube problem are well captured. Cercion demonstrates a high degree of symmetry when calculating the Sedov blast wave solution, with a peak density at the shock front that is similar to the value determined by the RAGE code. For a flyer plate test problem both Cercion and FLAG give virtually the same velocity temporal profile at the target-vacuum interface. When calculating a cylindrical implosion of a steel shell, Cercion and FLAG agree well and the Cercion results are insensitive to the use of ALE.
Higher-order web link analysis using multilinear algebra.
Energy Technology Data Exchange (ETDEWEB)
Kenny, Joseph P.; Bader, Brett William (Sandia National Laboratories, Albuquerque, NM); Kolda, Tamara Gibson
2005-07-01
Linear algebra is a powerful and proven tool in web search. Techniques, such as the PageRank algorithm of Brin and Page and the HITS algorithm of Kleinberg, score web pages based on the principal eigenvector (or singular vector) of a particular non-negative matrix that captures the hyperlink structure of the web graph. We propose and test a new methodology that uses multilinear algebra to elicit more information from a higher-order representation of the hyperlink graph. We start by labeling the edges in our graph with the anchor text of the hyperlinks so that the associated linear algebra representation is a sparse, three-way tensor. The first two dimensions of the tensor represent the web pages while the third dimension adds the anchor text. We then use the rank-1 factors of a multilinear PARAFAC tensor decomposition, which are akin to singular vectors of the SVD, to automatically identify topics in the collection along with the associated authoritative web pages.
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
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
Higher-order Brunnian structures and possible physical realizations
DEFF Research Database (Denmark)
A. Baas, Nils; V. Fedorov, D.; S. Jensen, A.;
2014-01-01
We consider few-body bound state systems and provide precise definitions of Borromean and Brunnian systems. The initial concepts are more than a hundred years old and originated in mathematical knot-theory as purely geometric considerations. About thirty years ago they were generalized and applied......, and condensed matter systems. Appearance is not excluded. However, both the form and the strengths of the interactions must be rather special. The most promising subfields for present searches would be in cold atoms because of external control of effective interactions, or perhaps in condensed-matter systems...
Histone variants: key players of chromatin.
Biterge, Burcu; Schneider, Robert
2014-06-01
Histones are fundamental structural components of chromatin. Eukaryotic DNA is wound around an octamer of the core histones H2A, H2B, H3, and H4. Binding of linker histone H1 promotes higher order chromatin organization. In addition to their structural role, histones impact chromatin function and dynamics by, e.g., post-translational histone modifications or the presence of specific histone variants. Histone variants exhibit differential expression timings (DNA replication-independent) and mRNA characteristics compared to canonical histones. Replacement of canonical histones with histone variants can affect nucleosome stability and help to create functionally distinct chromatin domains. In line with this, several histone variants have been implicated in the regulation of cellular processes such as DNA repair and transcriptional activity. In this review, we focus on recent progress in the study of core histone variants H2A.X, H2A.Z, macroH2A, H3.3, and CENP-A, as well as linker histone H1 variants, their functions and their links to development and disease.
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...
Directory of Open Access Journals (Sweden)
Sujit eRoy
2014-09-01
Full Text Available Plant cells are subject to high levels of DNA damage resulting from plant’s obligatory dependence on sunlight and the associated exposure to environmental stresses like solar UV radiation, high soil salinity, drought, chilling injury and other air and soil pollutants including heavy metals and metabolic byproducts from endogenous processes. The irreversible DNA damages, generated by the environmental and genotoxic stresses affect plant growth and development, reproduction and crop productivity. Thus, for maintaining genome stability, plants have developed an extensive array of mechanisms for the detection and repair of DNA damages. This review will focus recent advances in our understanding of mechanisms regulating plant genome stability in the context of repairing of double stand breaks and chromatin structure maintenance.
Objective Reduction Solutions to Higher-Order Boussinesq System in (2+1)-Dimensions
Institute of Scientific and Technical Information of China (English)
HU Ya-Hong; ZHENG Chun-Long
2009-01-01
With the help of an objective reduction approach (ORA), abundant exact solutions of (2+1)-dimensional higher-order Boussinesq system (including some hyperboloid function solutions, trigonometric function solutions, and a rational function solution) are obtained. It is shown that some novel soliton structures, like single linearity soliton structure, breath soliton structure, single linearity y-periodic solitary wave structure, libration dromion structure, and kink-like multisoliton structure with actual physical meaning exist in the (2+1)-dimensional higher-order Bonssinesq system.
Directory of Open Access Journals (Sweden)
Shlomit Farkash-Amar
Full Text Available DNA replication is a highly regulated process, with each genomic locus replicating at a distinct time of replication (ToR. Advances in ToR measurement technology enabled several genome-wide profiling studies that revealed tight associations between ToR and general genomic features and a remarkable ToR conservation in mammals. Genome wide studies further showed that at the hundreds kb-to-megabase scale the genome can be divided into constant ToR regions (CTRs in which the replication process propagates at a faster pace due to the activation of multiple origins and temporal transition regions (TTRs in which the replication process propagates at a slower pace. We developed a computational tool that assigns a ToR to every measured locus and determines its replication activity type (CTR versus TTR. Our algorithm, ARTO (Analysis of Replication Timing and Organization, uses signal processing methods to fit a constant piece-wise linear curve to the measured raw data. We tested our algorithm and provide performance and usability results. A Matlab implementation of ARTO is available at http://bioinfo.cs.technion.ac.il/people/zohar/ARTO/. Applying our algorithm to ToR data measured in multiple mouse and human samples allowed precise genome-wide ToR determination and replication activity type characterization. Analysis of the results highlighted the plasticity of the replication program. For example, we observed significant ToR differences in 10-25% of the genome when comparing different tissue types. Our analyses also provide evidence for activity type differences in up to 30% of the probes. Integration of the ToR data with multiple aspects of chromosome organization characteristics suggests that ToR plays a role in shaping the regional chromatin structure. Namely, repressive chromatin marks, are associated with late ToR both in TTRs and CTRs. Finally, characterization of the differences between TTRs and CTRs, with matching ToR, revealed that TTRs are
Should evolutionary geneticists worry about higher-order epistasis?
Weinreich, Daniel M; Lan, Yinghong; Wylie, C Scott; Heckendorn, Robert B
2013-12-01
Natural selection drives evolving populations up the fitness landscape, the projection from nucleotide sequence space to organismal reproductive success. While it has long been appreciated that topographic complexities on fitness landscapes can arise only as a consequence of epistatic interactions between mutations, evolutionary genetics has mainly focused on epistasis between pairs of mutations. Here we propose a generalization to the classical population genetic treatment of pairwise epistasis that yields expressions for epistasis among arbitrary subsets of mutations of all orders (pairwise, three-way, etc.). Our approach reveals substantial higher-order epistasis in almost every published fitness landscape. Furthermore we demonstrate that higher-order epistasis is critically important in two systems we know best. We conclude that higher-order epistasis deserves empirical and theoretical attention from evolutionary geneticists.
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.
Modeling Human Behaviour with Higher Order Logic: Insider Threats
DEFF Research Database (Denmark)
Boender, Jaap; Ivanova, Marieta Georgieva; Kammuller, Florian;
2014-01-01
In this paper, we approach the problem of modeling the human component in technical systems with a view on the difference between the use of model and theory in sociology and computer science. One aim of this essay is to show that building of theories and models for sociology can be compared...... to and implemented in Higher Order Logic. We validate this working hypothesis by revisiting Weber’s understanding explanation. We focus on constructive realism in the context of logical explanation. We review Higher Order Logic (HOL) as a foundation for computer science and summarize its use of theories relating...... it to the sociological process of logical explanation. As a case study on modeling human behaviour, we present the modeling and analysis of insider threats as a Higher Order Logic theory in Isabelle/HOL. We show how each of the three step process of sociological explanation can be seen in our modeling of insider’s state...
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.
Higher-Order Separation Logic in Isabelle/HOLCF
DEFF Research Database (Denmark)
Varming, Carsten; Birkedal, Lars
2008-01-01
and to show how the higher-order logic enables natural assertions in specifications. To support abstract reasoning we have implemented rules for representation hiding and data abstraction as seen in [1]. The logic is represented as lemmas for reasoning about the denotational semantics of the programming......We formalize higher-order separation logic for a first-order imperative language with procedures and local variables in Isabelle/HOLCF. The assertion language is modeled in such a way that one may use any theory defined in Isabelle/HOLCF to construct assertions, e.g., primitive recursion, least...... or greatest fixed points etc. The higher-order logic ensures that we can show non-trivial algorithms correct without having to extend the semantics of the language as was done previously in verifications based on first-order separation logic [2,20]. We provide non-trivial examples to support this claim...
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.
Montel, Fabien; Castelnovo, Martin; Bednar, Jan; Dimitrov, Stefan; Angelov, Dimitar; Faivre-Moskalenko, Cendrine
2009-01-01
Chromatin organization and dynamics is studied in this work at scales ranging from single nucleosome to nucleosomal array by using a unique combination of biochemical assays, single molecule imaging technique and numerical modeling. We demonstrate that a subtle modification in the nucleosome structure induced by the histone variant H2A.Bbd drastically modifies the higher order organization of the nucleosomal arrays. Importantly, as directly visualized by AFM, conventional H2A nucleosomal arrays exhibit specific local organization, in contrast to H2A.Bbd arrays, which show ?beads on a string? structure. The combination of systematic image analysis and theoretical modeling allows a quantitative description relating the observed gross structural changes of the arrays to their local organization. Our results strongly suggest that higher-order organization of H1-free nucleosomal arrays is mainly determined by the fluctuation properties of individual nucleosomes. Moreover, numerical simulations suggest the existenc...
Higher order nonlinearity and synchronization of quantum cascade lasers
Institute of Scientific and Technical Information of China (English)
Taraprasad Chattopadhyay; Prosenjit Bhattacharyya
2011-01-01
This paper presents a closed-form analysis of the synchronization phenomenon of the quantum cascade laser (QCL). The analysis has been made with considering higher order nonlinearity of the modal gain of the QCL. The frequency response characteristics of the synchronized QCL along with the stability of the locked state, the effect of nonlinearity on the lockband of the QCL and the amplitude limiting action of the locked QCL have been calculated. The analysis demonstrates the effect of higher order nonlinearity on the properties of the synchronized QCL.
The Cauchy problem for higher order abstract differential equations
Xiao, Ti-Jun
1998-01-01
This monograph is the first systematic exposition of the theory of the Cauchy problem for higher order abstract linear differential equations, which covers all the main aspects of the developed theory. The main results are complete with detailed proofs and established recently, containing the corresponding theorems for first and incomplete second order cases and therefore for operator semigroups and cosine functions. They will find applications in many fields. The special power of treating the higher order problems directly is demonstrated, as well as that of the vector-valued Laplace transforms in dealing with operator differential equations and operator families. The reader is expected to have a knowledge of complex and functional analysis.
Higher-order Laplace equations and hyper-Cauchy distributions
Orsingher, Enzo
2012-01-01
In this paper we introduce new distributions which are solutions of higher-order Laplace equations. It is proved that their densities can be obtained by folding and symmetrizing Cauchy distributions. Another class of probability laws related to higher-order Laplace equations is obtained by composing pseudo-processes with positively-skewed Cauchy distributions which produce asymmetric Cauchy densities in the odd-order case. A special attention is devoted to the third-order Laplace equation where the connection between the Cauchy distribution and the Airy functions is obtained and analyzed.
Interference of selective higher-order modes in optical fibers
Institute of Scientific and Technical Information of China (English)
Li Enbang; Peng Gangding
2007-01-01
The interference of selective higher-order modes in optical fibers is investigated both theoretically and experimentally.It has been demonstrated that by coupling the LP01 mode in a step-index single-mode fiber(SMF)to the LPom modes in step-index muhimode fibers(MMFs)with different parameters,one can selectively generate higher-order modes and construct all-fiber interferometers.The research presented in this paper forms a basis of a new type of fiber devices with potential applications in fiber sensing,optical fiber communications,and optical signal processing.
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.
HIGHER ORDER SPECTRAL ANALYSIS IN FAULT DIAGNOSIS OF ROTORS
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
The nonlinear properties of rotating machinery vibration signals are presented. The relationship between faults and quadratic phase coupling is discussed. The mechanism that gives rise to quadratic phase coupling is analyzed, and the coupling models are summarized. As a result, higher order spectra analysis is introduced into fault diagnosis of rotors. A brief review of the properties of higher order spectra is presented. Furthermore, the bicoherence spectrum is employed to extract the features that signify the machinery condition. Experiments show that bicoherence spectrum patterns of different faults are quite different, so it is proposed to identify the faults in rotors.
Threshold resummation and higher order effects in QCD
Energy Technology Data Exchange (ETDEWEB)
Ringer, Felix Maximilian
2015-06-26
Quantum chromodynamics (QCD) is a quantum field theory that describes the strong interactions between quarks and gluons, the building blocks of all hadrons. Thanks to the experimental progress over the past decades, there has been an ever-growing need for QCD precision calculations for scattering processes involving hadrons. For processes at large momentum transfer, perturbative QCD offers a systematic approach for obtaining precise predictions. This approach relies on two key concepts: the asymptotic freedom of QCD and factorization. In a perturbative calculation at higher orders, the infrared cancellation between virtual and real emission diagrams generally leaves behind logarithmic contributions. In many observables relevant for hadronic scattering these logarithms are associated with a kinematic threshold and are hence known as ''threshold logarithms''. They become large when the available phase space for real gluon emission shrinks. In order to obtain a reliable prediction from QCD, the threshold logarithms need to be taken into account to all orders in the strong coupling constant, a procedure known as ''threshold resummation''. The main focus of my PhD thesis is on studies of QCD threshold resummation effects beyond the next-to-leading logarithmic order. Here we primarily consider the production of hadron pairs in hadronic collisions as an example. In addition, we also consider hadronic jet production, which is particularly interesting for the phenomenology at the LHC. For both processes, we fully take into account the non-trivial QCD color structure of the underlying partonic hard- scattering cross sections. We find that threshold resummation leads to sizable numerical effects in the kinematic regimes relevant for comparisons to experimental data.
Higher-Order Hierarchical Legendre Basis Functions in Applications
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter;
2007-01-01
degree of orthogonality. The basis functions are well-suited for solution of complex electromagnetic problems involving multiple homogeneous or inhomogeneous dielectric regions, metallic surfaces, layered media, etc. This paper presents real-life complex antenna radiation problems modeled...... with electromagnetic simulation tools based on the higher-order hierarchical Legendre basis functions....
Numerical modeling of higher order magnetic moments in UXO discrimination
Sanchez, V.; Yaoguo, L.; Nabighian, M.N.; Wright, D.L.
2008-01-01
The surface magnetic anomaly observed in unexploded ordnance (UXO) clearance is mainly dipolar, and consequently, the dipole is the only magnetic moment regularly recovered in UXO discrimination. The dipole moment contains information about the intensity of magnetization but lacks information about the shape of the target. In contrast, higher order moments, such as quadrupole and octupole, encode asymmetry properties of the magnetization distribution within the buried targets. In order to improve our understanding of magnetization distribution within UXO and non-UXO objects and to show its potential utility in UXO clearance, we present a numerical modeling study of UXO and related metallic objects. The tool for the modeling is a nonlinear integral equation describing magnetization within isolated compact objects of high susceptibility. A solution for magnetization distribution then allows us to compute the magnetic multipole moments of the object, analyze their relationships, and provide a depiction of the anomaly produced by different moments within the object. Our modeling results show the presence of significant higher order moments for more asymmetric objects, and the fields of these higher order moments are well above the noise level of magnetic gradient data. The contribution from higher order moments may provide a practical tool for improved UXO discrimination. ?? 2008 IEEE.
Order-sorted Algebraic Specifications with Higher-order Functions
DEFF Research Database (Denmark)
Haxthausen, Anne Elisabeth
1995-01-01
This paper gives a proposal for how order-sorted algebraic specification languages can be extended with higher-order functions. The approach taken is a generalisation to the order-sorted case of an approach given by Mller, Tarlecki and Wirsing for the many-sorted case. The main idea in the proposal...
Higher-order momentum distributions and locally affine LDDMM registration
DEFF Research Database (Denmark)
Sommer, Stefan Horst; Nielsen, Mads; Darkner, Sune;
2013-01-01
description of affine transformations and subsequent compact description of non-translational movement in a globally nonrigid deformation. The resulting representation contains directly interpretable information from both mathematical and modeling perspectives. We develop the mathematical construction...... higher-order momenta lead to natural modeling of articulated movement, and the method promises to be useful for quantifying ventricle expansion and progressing atrophy during Alzheimer's disease....
Inverse and higher-order processes of internal conversion
International Nuclear Information System (INIS)
Monoenergetic positron emission, nuclear excitation by positron annihilation, and nuclear excitation by free electron capture in laser-induced plasma are described as inverse internal conversion. As a higher-order process, electron bridge is considered. The experimental possibilities for the latter two processes for highly ionized ions are discussed. (author)
Validating variational principle for higher order theory of gravity
Ruz, Soumendranath; Sarkar, Kaushik; Sk., Nayem; Sanyal, Abhik Kumar
2015-01-01
Metric variation of higher order theory of gravity requires to fix the Ricci scalar in addition to the metric tensor at the boundary. Fixing Ricci scalar at the boundary implies that the classical solutions are fixed once and forever to the de-Sitter or anti de-Sitter solutions. Here, we justify such requirement from the standpoint of Noether Symmetry.
Lorentz-Invariance Violation with Higher-Order Operators
Reyes, Carlos M
2016-01-01
In this work, in the light of the developments for indefinite metric theories made by Lee and Wick, we study perturbative unitarity in a Lorentz-invariance violating QED model with higher-order operators. We show that by following the Lee-Wick prescription it is possible to preserve unitarity in the model at one-loop order in the coupling.
Higher Order Risk Attitudes, Demographics, and Financial Decisions
Noussair, C.N.; Trautmann, S.T.; van de Kuilen, G.
2011-01-01
We conduct an experiment to study the prevalence of the higher order risk attitudes of prudence and temperance, in a large demographically representative sample, as well as in a sample of undergraduate students. Participants make pairwise choices between lotteries of the form proposed by Eeckhoudt a
Extracting the jet azimuthal anisotropy from higher order cumulants
Lokhtin, Igor P; Snigirev, A M
2003-01-01
We analyze the method for calculation of a coefficient of jet azimuthal anisotropy without reconstruction of the nuclear reaction plane considering the higher order correlators between the azimuthal position of jet axis and the angles of particles not incorporated in the jet. The reliability of this technique in the real physical situation under LHC conditions is illustrated.
Meta-Logical Reasoning in Higher-Order Logic
DEFF Research Database (Denmark)
Villadsen, Jørgen; Schlichtkrull, Anders; Hess, Andreas Viktor
The semantics of first-order logic (FOL) can be described in the meta-language of higher-order logic (HOL). Using HOL one can prove key properties of FOL such as soundness and completeness. Furthermore, one can prove sentences in FOL valid using the formalized FOL semantics. To aid...
Abstract Operators and Higher-order Linear Partial Differential Equation
Institute of Scientific and Technical Information of China (English)
BI Guang-qing; BI Yue-kai
2011-01-01
We summarize several relevant principles for the application of abstract operators in partial differential equations,and combine abstract operators with the Laplace transform.Thus we have developed the theory of partial differential equations of abstract operators and obtained the explicit solutions of initial value problems for a class of higher-order linear partial differential equations.
Multilevel Fast Multipole Method for Higher Order Discretizations
DEFF Research Database (Denmark)
Borries, Oscar Peter; Meincke, Peter; Jorgensen, Erik;
2014-01-01
The multi-level fast multipole method (MLFMM) for a higher order (HO) discretization is demonstrated on high-frequency (HF) problems, illustrating for the first time how an efficient MLFMM for HO can be achieved even for very large groups. Applying several novel ideas, beneficial to both lower...
Decidable Fragments of a Higher Order Calculus with Locations
DEFF Research Database (Denmark)
Hüttel, Hans; Godskesen, Jens Christian; Haagensen, Bjørn;
2009-01-01
Homer is a higher order process calculus with locations. In this paper we study Homer in the setting of the semantic finite control property, which is a finite reachability criterion that implies decidability of barbed bisimilarity. We show that strong and weak barbed bisimilarity are undecidable...... control π-calculus in Homer....
Higher order QCD corrections in small x physics
Energy Technology Data Exchange (ETDEWEB)
Chachamis, G.
2006-11-15
We study higher order QCD corrections in small x Physics. The numerical implementation of the full NLO photon impact factor is the remaining necessary piece for the testing of the NLO BFKL resummation against data from physical processes, such as {gamma}{sup *}{gamma}{sup *} collisions. We perform the numerical integration over phase space for the virtual corrections to the NLO photon impact factor. This, along with the previously calculated real corrections, makes feasible in the near future first estimates for the {gamma}*{gamma}* total cross section, since the convolution of the full impact factor with the NLO BFKL gluon Green's function is now straightforward. The NLO corrections for the photon impact factor are sizeable and negative. In the second part of this thesis, we estimate higher order correction to the BK equation. We are mainly interested in whether partonic saturation delays or not in rapidity when going beyond the leading order. In our investigation, we use the so called 'rapidity veto' which forbid two emissions to be very close in rapidity, to 'switch on' higher order corrections to the BK equation. From analytic and numerical analysis, we conclude that indeed saturation does delay in rapidity when higher order corrections are taken into account. In the last part, we investigate higher order QCD corrections as additional corrections to the Electroweak (EW) sector. The question of whether BFKL corrections are of any importance in the Regge limit for the EW sector seems natural; although they arise in higher loop level, the accumulation of logarithms in energy s at high energies, cannot be dismissed without an investigation. We focus on the process {gamma}{gamma}{yields}ZZ. We calculate the pQCD corrections in the forward region at leading logarithmic (LL) BFKL accuracy, which are of the order of few percent at the TeV energy scale. (orig.)
Higher order QCD corrections in small x physics
International Nuclear Information System (INIS)
We study higher order QCD corrections in small x Physics. The numerical implementation of the full NLO photon impact factor is the remaining necessary piece for the testing of the NLO BFKL resummation against data from physical processes, such as γ*γ* collisions. We perform the numerical integration over phase space for the virtual corrections to the NLO photon impact factor. This, along with the previously calculated real corrections, makes feasible in the near future first estimates for the γ*γ* total cross section, since the convolution of the full impact factor with the NLO BFKL gluon Green's function is now straightforward. The NLO corrections for the photon impact factor are sizeable and negative. In the second part of this thesis, we estimate higher order correction to the BK equation. We are mainly interested in whether partonic saturation delays or not in rapidity when going beyond the leading order. In our investigation, we use the so called 'rapidity veto' which forbid two emissions to be very close in rapidity, to 'switch on' higher order corrections to the BK equation. From analytic and numerical analysis, we conclude that indeed saturation does delay in rapidity when higher order corrections are taken into account. In the last part, we investigate higher order QCD corrections as additional corrections to the Electroweak (EW) sector. The question of whether BFKL corrections are of any importance in the Regge limit for the EW sector seems natural; although they arise in higher loop level, the accumulation of logarithms in energy s at high energies, cannot be dismissed without an investigation. We focus on the process γγ→ZZ. We calculate the pQCD corrections in the forward region at leading logarithmic (LL) BFKL accuracy, which are of the order of few percent at the TeV energy scale. (orig.)
Modular specification and verification for higher-order languages with state
DEFF Research Database (Denmark)
Svendsen, Kasper
The overall topic of this thesis is modular reasoning for higher-order languages with state. The thesis consists of four mostly independent chapters that each deal with a different aspect of reasoning about higher-order languages with state. The unifying theme throughout all four chapters is higher...... structures. To ensure modular reasoning, we need a generic specification that clients can refine with their desired sharing discipline. In the second chapter we present a new higher-order separation logic and a new style of specification that clients can refine with a sharing discipline of their choice...... dependent type theory with effects. The motivation is to take advantage of an existing implementation of a pure dependent type theory to obtain an implementation of a formal proof system based on higher-order separation logic. In particular, we extend the Calculus of Inductive Constructions with monadically...
Beam interactions with surface waves and higher-order modes in oversized backward wave oscillators
Energy Technology Data Exchange (ETDEWEB)
Ogura, Kazuo; Kojima, Akihiko; Kawabe, Fumiaki; Yambe, Kiyoyuki [Niigata University, Niigata (Japan); Amin, Ruhul [Islamic University of Technology, Gazipur (Bangladesh)
2014-10-15
Beam interactions with surface waves and higher-order modes in an oversized backward wave oscillator (BWO) are studied. In addition to the well-known Cherenkov interaction, the slow cyclotron interaction occurs due to transverse perturbations of the electron beam. The Cherenkov interaction dominates the slow cyclotron interaction. Growth rates of both the interactions for the higher order modes are small compared with those for the surface-wave modes in an oversized BWO. The coaxial slow-wave structure exhibits a reduced number of higher-order modes, which consequently reduces the mode competition problem and improves beam interactions with higher order modes. For higher values of beam currents, the slow cyclotron wave grows at a faster rate than the Cherenkov waves.
Visualization and processing of higher order descriptors for multi-valued data
Schultz, Thomas
2015-01-01
Modern imaging techniques and computational simulations yield complex multi-valued data that require higher-order mathematical descriptors. This book addresses topics of importance when dealing with such data, including frameworks for image processing, visualization, and statistical analysis of higher-order descriptors. It also provides examples of the successful use of higher-order descriptors in specific applications and a glimpse of the next generation of diffusion MRI. To do so, it combines contributions on new developments, current challenges in this area, and state-of-the-art surveys. Compared to the increasing importance of higher-order descriptors in a range of applications, tools for analysis and processing are still relatively hard to come by. Even though application areas such as medical imaging, fluid dynamics, and structural mechanics are very different in nature they face many shared challenges. This book provides an interdisciplinary perspective on this topic with contributions from key rese...
Chromatin assembly using Drosophila systems.
Fyodorov, Dmitry V; Levenstein, Mark E
2002-05-01
To successfully study chromatin structure and activity in vitro, it is essential to have a chromatin assembly system that will prepare extended nucleosome arrays with highly defined protein content that resemble bulk chromatin isolated from living cell nuclei in terms of periodicity and nucleosome positioning. The Drosophila ATP-dependent chromatin assembly system described in this unit meets these requirements. The end product of the reaction described here has highly periodic extended arrays with physiologic spacing and positioning of the nucleosomes.
Ectopically tethered CP190 induces large-scale chromatin decondensation
Ahanger, Sajad H.; Günther, Katharina; Weth, Oliver; Bartkuhn, Marek; Bhonde, Ramesh R.; Shouche, Yogesh S.; Renkawitz, Rainer
2014-01-01
Insulator mediated alteration in higher-order chromatin and/or nucleosome organization is an important aspect of epigenetic gene regulation. Recent studies have suggested a key role for CP190 in such processes. In this study, we analysed the effects of ectopically tethered insulator factors on chromatin structure and found that CP190 induces large-scale decondensation when targeted to a condensed lacO array in mammalian and Drosophila cells. In contrast, dCTCF alone, is unable to cause such a decondensation, however, when CP190 is present, dCTCF recruits it to the lacO array and mediates chromatin unfolding. The CP190 induced opening of chromatin may not be correlated with transcriptional activation, as binding of CP190 does not enhance luciferase activity in reporter assays. We propose that CP190 may mediate histone modification and chromatin remodelling activity to induce an open chromatin state by its direct recruitment or targeting by a DNA binding factor such as dCTCF.
Shinkai, Soya; Nozaki, Tadasu; Maeshima, Kazuhiro
2016-01-01
The mammalian genome is organized into submegabase-sized chromatin domains (CDs) including topologically associating domains, which have been identified using chromosome conformation capture-based methods. Single-nucleosome imaging in living mammalian cells has revealed subdiffusively dynamic nucleosome movement. It is unclear how single nucleosomes within CDs fluctuate and how the CD structure reflects the nucleosome movement. Here, we present a polymer model wherein CDs are characterized by fractal dimensions and the nucleosome fibers fluctuate in a viscoelastic medium with memory. We analytically show that the mean-squared displacement (MSD) of nucleosome fluctuations within CDs is subdiffusive. The diffusion coefficient and the subdiffusive exponent depend on the structural information of CDs. This analytical result enabled us to extract information from the single-nucleosome imaging data for HeLa cells. Our observation that the MSD is lower at the nuclear periphery region than the interior region indicates that CDs in the heterochromatin-rich nuclear periphery region are more compact than those in the euchromatin-rich interior region with respect to the fractal dimensions as well as the size. Finally, we evaluated that the average size of CDs is in the range of 100–500 nm and that the relaxation time of nucleosome movement within CDs is a few seconds. Our results provide physical and dynamic insights into the genome architecture in living cells. PMID:27764097
Statistics of predictions with missing higher order corrections
Berthier, Laure
2016-01-01
Effective operators have been used extensively to understand small deviations from the Standard Model in the search for new physics. So far there has been no general method to fit for small parameters when higher order corrections in these parameters are present but unknown. We present a new technique that solves this problem, allowing for an exact p-value calculation under the assumption that higher order theoretical contributions can be treated as gaussian distributed random variables. The method we propose is general, and may be used in the analysis of any perturbative theoretical prediction, ie.~truncated power series. We illustrate this new method by performing a fit of the Standard Model Effective Field Theory parameters, which include eg.~anomalous gauge and four-fermion couplings.
Comparison Criteria for Nonlinear Functional Dynamic Equations of Higher Order
Directory of Open Access Journals (Sweden)
Taher S. Hassan
2016-01-01
Full Text Available We will consider the higher order functional dynamic equations with mixed nonlinearities of the form xnt+∑j=0Npjtϕγjxφjt=0, on an above-unbounded time scale T, where n≥2, xi(t≔ri(tϕαixi-1Δ(t, i=1,…,n-1, with x0=x, ϕβ(u≔uβsgnu, and α[i,j]≔αi⋯αj. The function φi:T→T is a rd-continuous function such that limt→∞φi(t=∞ for j=0,1,…,N. The results extend and improve some known results in the literature on higher order nonlinear dynamic equations.
Higher Order Hierarchical Legendre Basis Functions for Electromagnetic Modeling
DEFF Research Database (Denmark)
Jørgensen, Erik; Volakis, John L.; Meincke, Peter;
2004-01-01
This paper presents a new hierarchical basis of arbitrary order for integral equations solved with the Method of Moments (MoM). The basis is derived from orthogonal Legendre polynomials which are modified to impose continuity of vector quantities between neighboring elements while maintaining most....... In addition, all higher-order terms in the expansion have two vanishing moments.In contrast to existing formulations, these properties allow the use of very high-order basis functions without introducing ill-conditioning of the resulting MoM matrix. Numerical results confirm that the condition number...... of the MoM matrix obtained with this new basis is much lower than existing higher-order interpolatory and hierarchical basis functions. As a consequence of the excellent condition numbers, we demonstrate that even very high-order MoM systems, e.g. 10th order, can be solved efficiently with an iterative...
Higher order moments of lensing convergence - I. Estimate from simulations
Vicinanza, M; Maoli, R; Scaramella, R; Er, X
2016-01-01
Large area lensing surveys are expected to make it possible to use cosmic shear tomography as a tool to severely constrain cosmological parameters. To this end, one typically relies on second order statistics such as the two - point correlation fucntion and its Fourier counterpart, the power spectrum. Moving a step forward, we wonder whether and to which extent higher order stastistics can improve the lensing Figure of Merit (FoM). In this first paper of a series, we investigate how second, third and fourth order lensing convergence moments can be measured and use as probe of the underlying cosmological model. We use simulated data and investigate the impact on moments estimate of the map reconstruction procedure, the cosmic variance, and the intrinsic ellipticity noise. We demonstrate that, under realistic assumptions, it is indeed possible to use higher order moments as a further lensing probe.
Higher-order chaotic oscillator using active bessel filter
DEFF Research Database (Denmark)
Lindberg, Erik; Mykolaitis, Gytis; Bumelien, Skaidra;
2010-01-01
A higher-order oscillator, including a nonlinear unit and an 8th-order low-pass active Bessel filter is described. The Bessel unit plays the role of "three-in-one": a delay line, an amplifier and a filter. Results of hardware experiments and numerical simulation are presented. Depending on the pa......A higher-order oscillator, including a nonlinear unit and an 8th-order low-pass active Bessel filter is described. The Bessel unit plays the role of "three-in-one": a delay line, an amplifier and a filter. Results of hardware experiments and numerical simulation are presented. Depending...... on the parameters of the nonlinear unit the oscillator operates either in a one-scroll or two-scroll mode. Two positive Lyapunov exponents, found at larger values of the negative slopes of the nonlinear function, characterize the oscillations as hyperchaotic....
Higher-Order Integral Equation Methods in Computational Electromagnetics
DEFF Research Database (Denmark)
Jørgensen, Erik; Meincke, Peter
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...... to incorporate edge singularities. Previous works in this area have shown the necessity of singular basis functions and three existing formulations are adapted to the new Legendre basis functions. Numerical experiments show that one formulation is the most accurate as well as the fastest to compute. Using......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...
Promoting higher order thinking skills using inquiry-based learning
Madhuri, G. V.; S. S. N Kantamreddi, V.; Goteti, L. N. S. Prakash
2012-05-01
Active learning pedagogies play an important role in enhancing higher order cognitive skills among the student community. In this work, a laboratory course for first year engineering chemistry is designed and executed using an inquiry-based learning pedagogical approach. The goal of this module is to promote higher order thinking skills in chemistry. Laboratory exercises are designed based on Bloom's taxonomy and a just-in-time facilitation approach is used. A pre-laboratory discussion outlining the theory of the experiment and its relevance is carried out to enable the students to analyse real-life problems. The performance of the students is assessed based on their ability to perform the experiment, design new experiments and correlate practical utility of the course module with real life. The novelty of the present approach lies in the fact that the learning outcomes of the existing experiments are achieved through establishing a relationship with real-world problems.
Higher Order Feature Set For Underwater Noise Classification
Directory of Open Access Journals (Sweden)
Mohankumar K
2014-12-01
Full Text Available The development of intelligent systems for classification of underwater noise sources has been a field of research interest for decades. Such systems include the extraction of features from the received signals, followed by the application of suitable classification algorithms. Most of the existing feature extraction methods rely on the classical power spectral methods, which may fail to provide information pertaining to the deviations from linearity and Gaussianity of stochastic processes. Hence, many recent research efforts focus on higher order spectral methods in order to prevail over such limitations. This paper makes use of bispectrum, which is a higher order spectrum of order three, in order to extract a set of robust features for the classification of underwater noise sources. An SVM classifier is used for evaluating the performance of the feature set.
Higher Order Kernels and Locally Affine LDDMM Registration
Sommer, Stefan; Darkner, Sune; Pennec, Xavier
2011-01-01
To achieve sparse description that allows intuitive analysis, we aim to represent deformation with a basis containing interpretable elements, and we wish to use elements that have the description capacity to represent the deformation compactly. We accomplish this by introducing higher order kernels in the LDDMM registration framework. The kernels allow local description of affine transformations and subsequent compact description of non-translational movement and of the entire non-rigid deformation. This is obtained with a representation that contains directly interpretable information from both mathematical and modeling perspectives. We develop the mathematical construction behind the higher order kernels, we show the implications for sparse image registration and deformation description, and we provide examples of how the capacity of the kernels enables registration with a very low number of parameters. The capacity and interpretability of the kernels lead to natural modeling of articulated movement, and th...
Robin, Jérôme D; Magdinier, Frédérique
2016-01-01
Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains. We will discuss here the impact of A-type Lamins loss on alterations of chromatin organization and formation of chromatin domains and how disorganization of the lamina contributes to the patho-physiology of premature aging syndromes. PMID:27602048
1957-2007: 50 Years of Higher Order Programming Languages
Alen Lovrenčić; Mario Konecki; Tihomir Orehovački
2009-01-01
Fifty years ago one of the greatest breakthroughs in computer programming and in the history of computers happened -- the appearance of FORTRAN, the first higher-order programming language. From that time until now hundreds of programming languages were invented, different programming paradigms were defined, all with the main goal to make computer programming easier and closer to as many people as possible. Many battles were fought among scientists as well as among developers around concepts ...
The Key Exchange Cryptosystem Used With Higher Order Diophantine Equations
Harry Yosh
2011-01-01
One-way functions are widely used for encrypting the secret in public key cryptography, although they are regarded as plausibly one-way but have not been proven so. Here we discuss the public key cryptosystem based on the system of higher order Diophantine equations. In this system those Diophantine equations are used as public keys for sender and recipient, and sender can recover the secret from the Diophantine equation returned from recipient with a trapdoor. In general the system of Diopha...
Evaluation of corneal higher order aberrations in normal topographic patterns
Mirzajani, Ali; Aghataheri, Sattar; Ghoreishi, Mohammad; Jafarzadepour, Ebrahim; Mohammadinia, Mohadese
2016-01-01
Purpose This study reports the characteristics of corneal higher order aberrations (HOAs) in eyes with normal topographic pattern using the Pentacam scheimpflug system. Methods In this prospective, observational, comparative study, 165 eyes of 97 patients separated into five groups based on corneal topographic patterns were enrolled. All eyes received a comprehensive ophthalmologic examination including corneal tomographic analysis with the Pentacam system. Keratometry, corneal cylinder, and ...
Accessing higher order correlations by time-multiplexing
Avenhaus, M; Chekhova, M V; Silberhorn, C
2009-01-01
We experimentally measured higher order normalized correlation functions (nCF) of pulsed light with a time-multiplexing-detector. We demonstrate excellent performance of our device by verifying unity valued nCF up to the eight order for coherent light, and factorial dependence of the nCF for pseudo-thermal light. We applied our measurement technique to a type-II parametric downconversion source to investigate mutual two-mode correlation properties and ascertain non-classicality.
Applying quantitative semantics to higher-order quantum computing
Pagani, Michele; Selinger, Peter; Valiron, Benoît
2013-01-01
Finding a denotational semantics for higher order quantum computation is a long-standing problem in the semantics of quantum programming languages. Most past approaches to this problem fell short in one way or another, either limiting the language to an unusably small finitary fragment, or giving up important features of quantum physics such as entanglement. In this paper, we propose a denotational semantics for a quantum lambda calculus with recursion and an infinite data type, using constru...
Sequential High-Resolution Direction Finding From Higher Order Statistics
Birot, Gwénaël; Albera, Laurent; Chevalier, Pascal
2010-01-01
12 pages International audience The classical higher order MUSIC-like methods based on a simultaneous search for all Directions Of Arrival (DOA's) show i) a capacity for processing underdetermined mixtures of sources, ii) a high robustness with respect to both a Gaussian noise with unknown spatial coherence and modeling errors, and iii) a better resolution than algorithms based on second order statistics. However, these methods have some limits: for a finite number of samples, they show...
Higher order relativistic galaxy number counts: dominating terms
Nielsen, Jeppe Trøst
2016-01-01
We review the number counts to second order concentrating on the terms which dominate on sub horizon scales. We re-derive the result for these terms and compare it with the different versions found in the literature. We generalize our derivation to higher order terms, especially the third order number counts which are needed to compute the 1-loop contribution to the power spectrum.
BENDING ANALYSIS OF COMPOSITE PLATES USING HIGHER ORDER THEORY
N UPENDRA; B. Sidda Reddy; K TIRUPATI REDDY; AJAY KUMAR REDDY K
2013-01-01
In this paper, an analytical formulation and solutions are developed to investigate the bending characteristics of laminated composite plates based on higher order shear deformation theory. The equation ofmotion of laminated plates is deduced using Hamilton’s principle. Closed-form solutions are obtained by using the Navier’s technique for simply supported boundary conditions. The effect of side to thickness ratio, aspect ratio, degree of orthotropic, stacking sequence ad no of layers on defl...
Mathematical reasoning with higher-order anti-unifcation
Guhe, Markus; Pease, Alison; Smaill, Alan; Schmidt, Martin; Gust, Helmar; Kühnberger, Kai-Uwe; Krumnack, Ulf
2010-01-01
We show how heuristic-driven theory projection (HDTP, a method based on higher-order anti-unification) can be used to model analogical reasoning in mathematics. More precisely, HDTP provides the framework for a model of the inductive analogy-making process involved in establishing the fundamental concepts of arithmetic. This process is a crucial component for being able to generalise from the concrete experiences that humans have due to their embodied and embedded nature. Such generalisations...
Higher-order conditioning and the retrosplenial cortex.
Todd, Travis P; Huszár, Roman; DeAngeli, Nicole E; Bucci, David J
2016-09-01
The retrosplenial cortex (RSC) is known to contribute to contextual and spatial learning and memory. This is consistent with its well-established connectivity; the RSC is located at the interface of visuo-spatial association areas and the parahippocampal-hippocampal memory system. However, the RSC also contributes to learning and memory for discrete cues. For example, both permanent lesions and temporary inactivation of the RSC have been shown to impair sensory preconditioning, a form of higher-order conditioning. The purpose of the present experiment was to examine the role of the RSC in a closely related higher-order conditioning paradigm: second-order conditioning. Sham and RSC lesioned rats received first-order conditioning in which one visual stimulus (V1) was paired with footshock and one visual stimulus (V2) was not. Following first-order conditioning, one auditory stimulus (A1) was then paired with V1 and a second auditory stimulus (A2) was paired with V2. Although lesions of the RSC impaired the first-order discrimination, they had no impact on the acquisition of second-order conditioning. Thus, the RSC does not appear necessary for acquisition/expression of second-order fear conditioning. The role of the RSC in higher-order conditioning, as well as a possible dissociation from the hippocampus, is discussed.
Wave Transformation Modeling with Effective Higher-Order Finite Elements
Directory of Open Access Journals (Sweden)
Tae-Hwa Jung
2016-01-01
Full Text Available This study introduces a finite element method using a higher-order interpolation function for effective simulations of wave transformation. Finite element methods with a higher-order interpolation function usually employ a Lagrangian interpolation function that gives accurate solutions with a lesser number of elements compared to lower order interpolation function. At the same time, it takes a lot of time to get a solution because the size of the local matrix increases resulting in the increase of band width of a global matrix as the order of the interpolation function increases. Mass lumping can reduce computation time by making the local matrix a diagonal form. However, the efficiency is not satisfactory because it requires more elements to get results. In this study, the Legendre cardinal interpolation function, a modified Lagrangian interpolation function, is used for efficient calculation. Diagonal matrix generation by applying direct numerical integration to the Legendre cardinal interpolation function like conducting mass lumping can reduce calculation time with favorable accuracy. Numerical simulations of regular, irregular and solitary waves using the Boussinesq equations through applying the interpolation approaches are carried out to compare the higher-order finite element models on wave transformation and examine the efficiency of calculation.
Unifying refinement and hoare-style reasoning in a logic for higher-order concurrency
DEFF Research Database (Denmark)
Turon, Aaron; Dreyer, Derek; Birkedal, Lars
2013-01-01
Modular programming and modular verification go hand in hand, but most existing logics for concurrency ignore two crucial forms of modularity: *higher-order functions*, which are essential for building reusable components, and *granularity abstraction*, a key technique for hiding the intricacies...... of fine-grained concurrent data structures from the clients of those data structures. In this paper, we present CaReSL, the first logic to support the use of granularity abstraction for modular verification of higher-order concurrent programs. After motivating the features of CaReSL through a variety...
Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang
2016-01-01
Ionizing radiation threatens genome integrity by causing DNA damage. Monte Carlo simulation of the interaction of a radiation track structure with DNA provides a powerful tool for investigating the mechanisms of the biological effects. However, the more or less oversimplification of the indirect effect and the inadequate consideration of high-order chromatin structures in current models usually results in discrepancies between simulations and experiments, which undermine the predictive role of the models. Here we present a biophysical model taking into consideration factors that influence indirect effect to simulate radiation-induced DNA strand breaks in eukaryotic cells with high-order chromatin structures. The calculated yields of single-strand breaks and double-strand breaks (DSBs) for photons are in good agreement with the experimental measurements. The calculated yields of DSB for protons and α particles are consistent with simulations by the PARTRAC code, whereas an overestimation is seen compared with the experimental results. The simulated fragment size distributions for 60Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with 60Co irradiation validates our model in simulating photon irradiation. The general agreement found in α particle irradiation encourages model applicability in the high linear energy transfer range. Moreover, we demonstrate the importance of chromatin high-order structures in shaping the spectrum of initial damage.
Higher order bulk characteristic parameters of asymmetric nuclear matter
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
The bulk parameters characterizing the energy of symmetric nuclear matter and the symmetry energy defined at normal nuclear density ρ0 provide important information on the equation of state (EOS) of isospin asymmetric nuclear matter. While significant progress has been made in determining some lower order bulk characteristic parameters, such as the energy E0(ρ0) and incompress ibility K0 of symmetric nuclear matter as well as the symmetry energy Esym(ρ0) and its slope parameter L, yet the higher order bulk characteristic parameters are still poorly known. Here, we analyze the correlations between the lower and higher order bulk char acteristic parameters within the framework of Skyrme Hartree-Fock energy density functional and then estimate the values of some higher order bulk characteristic parameters. In particular, we obtain J0 = (-355±95) MeV and I0 = (1473±680) MeV for the third order and fourth-order derivative parameters of symmetric nuclear matter at ρ0 and Ksym = (-100 ± 165) MeV, Jsym = (224 ± 385) MeV, Isym = (-1309 ± 2025) MeV for the curvature parameter, third-order and fourth-order derivative parameters of the symmetry energy at ρ0, using the empirical constraints on E0(ρ0), K0, Esym(ρ0), L, and the isoscalar and isovector nucleon effective masses. Furthermore, our results indicate that the three parameters E0(ρ0), K0, and J0 can reasonably characterize the EOS of symmetric nuclear matter up to 2ρ0 while the symmetry energy up to 2ρ0 can be well described by Esym(ρ0), L, and Ksym.
Higher order temporal finite element methods through mixed formalisms.
Kim, Jinkyu
2014-01-01
The extended framework of Hamilton's principle and the mixed convolved action principle provide new rigorous weak variational formalism for a broad range of initial boundary value problems in mathematical physics and mechanics. In this paper, their potential when adopting temporally higher order approximations is investigated. The classical single-degree-of-freedom dynamical systems are primarily considered to validate and to investigate the performance of the numerical algorithms developed from both formulations. For the undamped system, all the algorithms are symplectic and unconditionally stable with respect to the time step. For the damped system, they are shown to be accurate with good convergence characteristics.
Higher-order photon correlations in pulsed photonic crystal nanolasers
Elvira, David; Verma, V; Braive, Remy; Beaudoin, Gregoire; Robert-Philip, Isabelle; Sagnes, Isabelle; Baek, Burm; Nam, Sae Woo; Dauler, Eric A; Abram, Izo; Stevens, Martin J; Beveratos, Alexios
2011-01-01
We report on the higher-order photon correlations of a high-$\\beta$ nanolaser under pulsed excitation at room temperature. Using a multiplexed four-element superconducting single photon detector we measured g$^{(n)}(\\vec{0})$ with $n$=2,3,4. All orders of correlation display partially chaotic statistics, even at four times the threshold excitation power. We show that this departure from coherence and Poisson statistics is due to the quantum fluctuations associated with the small number of dipoles and photons involved in the lasing process.
A higher-order duration calculus and its completeness
Institute of Scientific and Technical Information of China (English)
詹乃军
2000-01-01
This paper studies how to describe the real-time behaviour of programs using duration calculus. Since program variables are interpreted as functions over time in real-time programming, and it is inevitable to introduce quantifications over program variables in order to describe local variable declaration and declare local channel and so on. Therefore to establish a higher-order duration calculus (HDC) is necessary. We first establish HDC, then show some real-time properties of programs in terms of HDC, and then, prove that HDC is complete on abstract domains under the assumption that all program variables vary finitely.
Squeezing of higher order Hermite-Gauss modes
DEFF Research Database (Denmark)
Lassen, Mikael Østergaard
2008-01-01
The present paper gives an overview of the experimental generation of squeezing in higher order Hermite-Gaussian modes with an optical parametric ampli¯er (OPA). This work was awarded with The European Optical Society (EOS) price 2007. The purpose of the prize is to encourage a European dimension...... in research in pure and applied optics. The EOS prize is awarded based on the selection criteria of high professionalism, academic and technical quality. Following the EOS Prize rules, the conditions for eligibility are that the work was performed in Europe and that it is published under the auspices...
Special issue of Higher-Order and Symbolic Computation
DEFF Research Database (Denmark)
Danvy, Olivier
on program development and programming methodology were a source of enthusiasm, strength, and inspiration. His dedication to research and teaching is for us all an example to follow. The articles in this issue of Higher-Order and Symbolic Computation were contributed and formally reviewed, and they reflect...... to the development of new techniques for the derivation of algorithms and programs using the transformational methodology. Starting from specifications written in a set theoretical language, using suitable algebraic or logical formulas, the programmer should transform them, possibly in various steps, into runnable...
Programming real-time executives in higher order language
Foudriat, E. C.
1982-01-01
Methods by which real-time executive programs can be implemented in a higher order language are discussed, using HAL/S and Path Pascal languages as program examples. Techniques are presented by which noncyclic tasks can readily be incorporated into the executive system. Situations are shown where the executive system can fail to meet its task scheduling and yet be able to recover either by rephasing the clock or stacking the information for later processing. The concept of deadline processing is shown to enable more effective mixing of time and information synchronized systems.
Higher Order Mode Properties of Superconducting Two-Spoke Cavities
Energy Technology Data Exchange (ETDEWEB)
Hopper, C. S.; Delayen, J. R.; Olave, R. G.
2011-07-01
Multi-Spoke cavities lack the cylindrical symmetry that many other cavity types have, which leads to a more complex Higher Order Mode (HOM) spectrum. In addition, spoke cavities offer a large velocity acceptance which means we must perform a detailed analysis of the particle velocity dependence for each mode's R/Q. We present here a study of the HOM properties of two-spoke cavities designed for high-velocity applications. Frequencies, R/Q and field profiles of HOMs have been calculated and are reported.
BENDING ANALYSIS OF COMPOSITE PLATES USING HIGHER ORDER THEORY
Directory of Open Access Journals (Sweden)
N UPENDRA
2013-10-01
Full Text Available In this paper, an analytical formulation and solutions are developed to investigate the bending characteristics of laminated composite plates based on higher order shear deformation theory. The equation ofmotion of laminated plates is deduced using Hamilton’s principle. Closed-form solutions are obtained by using the Navier’s technique for simply supported boundary conditions. The effect of side to thickness ratio, aspect ratio, degree of orthotropic, stacking sequence ad no of layers on deflection and stresses are investigated. The results predicted by the present theory are in good agreement with the solutions of other plate theories available in the literature.
Higher order asymptotic fields for mode Ⅰ crack in functionally gradient material
Institute of Scientific and Technical Information of China (English)
DAI Yao; YAN Xiu-fa
2005-01-01
Higher order stress fields for a mode Ⅰ crack perpendicular to the direction of property variation in a functionally gradient material(FGM), which has an exponential variation of elastic modulus along the gradient direction, were obtained through an asymptotic analysis. The Poisson's ratio of the FGMs was assumed to be constant throughout the analysis. The first five terms in the asymptotic expansions of crack tip stress fields were derived to bring out the influence of nonhomogeneity on the structure of the stress field explicitly. The analysis reveals that only the higher order terms in the expansion are influenced by the material nonhomogeneity. Moreover, it can be seen from expressions of higher order stress fields that at least three terms must be considered in the case of FGMs in order to explicitly account for the nonhomogeneity effects on the structure of crack tip stress fields.
International Nuclear Information System (INIS)
Inhibition of herpes simplex virus (HSV) thymidine kinase (TK) gene transcription (pHSV-106, pML-BPV-TK4) by DNA methylation is an indirect effect, which occurs with a latency period of ∼ 8 hr microinjection of the DNA into TK- rat 2 and mouse LTK- cells. The authors have strong evidence that chromatin formation is critical for the transition of the injected DNA from methylation insensitivity to methylation sensitivity. Chromatin was reconstituted in vitro by using methylated and mock-methylated HSV TK DNA and purified chicken histone octamers. After microinjection, the methylated chromatin was always biologically inactive, as tested by autoradiography of the cells after incubation with [3H]thymidine and by RNA dot blot analysis. However, in transformed cell lines, reactivation of the methylated chromatic occurred after treatment with 5-azacytidine. Furthermore, integration of the TK chromatin into the host genome is not required to block expression of the methylated TK gene. Mouse cells that contained the pML-BPV-TK4 chromatin permanently in an episomal state also did not support TK gene expression as long as the TK DNA remained methylated
Shimada, T.; Inokuchi, K; Nienhuis, A W
1987-01-01
The effect of in vitro methylation on the function and chromatin structure of the human dihydrofolate reductase (DHFR) promoter linked to the DHFR coding sequences (minigene) was studied after DNA-mediated gene transfer into DHFR- CHO cells. Methylation of HhaI sites reduced the transforming frequency to about 10% of control, whereas methylation of HpaII sites had a less significant effect. The integrated genes were demethylated at specific sites in the promoter sequence, namely, HpaII sites ...
Energy Technology Data Exchange (ETDEWEB)
Meschini, Roberta, E-mail: meschini@unitus.it; Morucci, Elisa; Berni, Andrea; Lopez-Martinez, Wilner; Palitti, Fabrizio
2015-07-15
Highlights: • Role of chromatin compaction on chromosomal instability. • Reduced radiation-induced clastogenicity in Ataxia telangiectasia cell lines. • Histone tails hyperacetylation reduces heterochromatin content favouring DSBs repair. - Abstract: At present, a lot is known about biochemical aspects of double strand breaks (DBS) repair but how chromatin structure affects this process and the sensitivity of DNA to DSB induction is still an unresolved question. Ataxia telangiectasia (A-T) patients are characterised by very high sensitivity to DSB-inducing agents such as ionising radiation. This radiosensitivity is revealed with an enhancement of chromosomal instability as a consequence of defective DNA repair for a small fraction of breaks located in the heterochromatin, where they are less accessible. Besides, recently it has been reported that Ataxia Telangiectasia Mutated (ATM) mediated signalling modifies chromatin structure. In order to study the impact of chromatin compaction on the chromosomal instability of A-T cells, the response to trichostatin-A, an histone deacetylase inhibitor, in normal and A-T lymphoblastoid cell lines was investigated testing its effect on chromosomal aberrations, cell cycle progression, DNA damage and repair after exposure to X-rays. The results suggest that the response to both trichostatin-A pre- and continuous treatments is independent of the presence of either functional or mutated ATM protein, as the reduction of chromosomal damage was found also in the wild-type cell line. The presence of trichostatin-A before exposure to X-rays could give rise to prompt DNA repair functioning on chromatin structure already in an open conformation. Differently, trichostatin-A post-treatment causing hyperacetylation of histone tails and reducing the heterochromatic DNA content might diminish the requirement for ATM and favour DSBs repair reducing chromosomal damage only in A-T cells. This fact could suggest that trichostatin-A post
Higher-Order Spectrum in Understanding Nonlinearity in EEG Rhythms
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Cauchy Pradhan
2012-01-01
Full Text Available The fundamental nature of the brain's electrical activities recorded as electroencephalogram (EEG remains unknown. Linear stochastic models and spectral estimates are the most common methods for the analysis of EEG because of their robustness, simplicity of interpretation, and apparent association with rhythmic behavioral patterns in nature. In this paper, we extend the use of higher-order spectrum in order to indicate the hidden characteristics of EEG signals that simply do not arise from random processes. The higher-order spectrum is an extension Fourier spectrum that uses higher moments for spectral estimates. This essentially nullifies all Gaussian random effects, therefore, can reveal non-Gaussian and nonlinear characteristics in the complex patterns of EEG time series. The paper demonstrates the distinguishing features of bispectral analysis for chaotic systems, filtered noises, and normal background EEG activity. The bispectrum analysis detects nonlinear interactions; however, it does not quantify the coupling strength. The squared bicoherence in the nonredundant region has been estimated to demonstrate nonlinear coupling. The bicoherence values are minimal for white Gaussian noises (WGNs and filtered noises. Higher bicoherence values in chaotic time series and normal background EEG activities are indicative of nonlinear coupling in these systems. The paper shows utility of bispectral methods as an analytical tool in understanding neural process underlying human EEG patterns.
Orchestration of Molecular Information through Higher Order Chemical Recognition
Frezza, Brian M.
Broadly defined, higher order chemical recognition is the process whereby discrete chemical building blocks capable of specifically binding to cognate moieties are covalently linked into oligomeric chains. These chains, or sequences, are then able to recognize and bind to their cognate sequences with a high degree of cooperativity. Principally speaking, DNA and RNA are the most readily obtained examples of this chemical phenomenon, and function via Watson-Crick cognate pairing: guanine pairs with cytosine and adenine with thymine (DNA) or uracil (RNA), in an anti-parallel manner. While the theoretical principles, techniques, and equations derived herein apply generally to any higher-order chemical recognition system, in practice we utilize DNA oligomers as a model-building material to experimentally investigate and validate our hypotheses. Historically, general purpose information processing has been a task limited to semiconductor electronics. Molecular computing on the other hand has been limited to ad hoc approaches designed to solve highly specific and unique computation problems, often involving components or techniques that cannot be applied generally in a manner suitable for precise and predictable engineering. Herein, we provide a fundamental framework for harnessing high-order recognition in a modular and programmable fashion to synthesize molecular information process networks of arbitrary construction and complexity. This document provides a solid foundation for routinely embedding computational capability into chemical and biological systems where semiconductor electronics are unsuitable for practical application.
Laser-PlasmaWakefield Acceleration with Higher Order Laser Modes
Energy Technology Data Exchange (ETDEWEB)
Geddes, C.G.R.; Cormier-Michel, E.; Esarey, E.; Schroeder, C.B.; Mullowney, P.; Paul, K.; Cary, J.R.; Leemans, W.P.
2010-06-01
Laser-plasma collider designs point to staging of multiple accelerator stages at the 10 GeV level, which are to be developed on the upcoming BELLA laser, while Thomson Gamma source designs use GeV stages, both requiring efficiency and low emittance. Design and scaling of stages operating in the quasi-linear regime to address these needs are presented using simulations in the VORPAL framework. In addition to allowing symmetric acceleration of electrons and positrons, which is important for colliders, this regime has the property that the plasma wakefield is proportional to the transverse gradient of the laser intensity profile. We demonstrate use of higher order laser modes to tailor the laser pulse and hence the transverse focusing forces in the plasma. In particular, we show that by using higher order laser modes, we can reduce the focusing fields and hence increase the matched electron beam radius, which is important to increased charge and efficiency, while keeping the low bunch emittance required for applications.
Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics
Aguilar, Carlos A.; Craighead, Harold G.
2013-10-01
Deoxyribonucleic acid (DNA) is the blueprint on which life is based and transmitted, but the way in which chromatin -- a dynamic complex of nucleic acids and proteins -- is packaged and behaves in the cellular nucleus has only begun to be investigated. Epigenetic modifications sit 'on top of' the genome and affect how DNA is compacted into chromatin and transcribed into ribonucleic acid (RNA). The packaging and modifications around the genome have been shown to exert significant influence on cellular behaviour and, in turn, human development and disease. However, conventional techniques for studying epigenetic or conformational modifications of chromosomes have inherent limitations and, therefore, new methods based on micro- and nanoscale devices have been sought. Here, we review the development of these devices and explore their use in the study of DNA modifications, chromatin modifications and higher-order chromatin structures.
Directory of Open Access Journals (Sweden)
Benjamin Staude
2010-07-01
Full Text Available The extent to which groups of neurons exhibit higher-order correlations in their spiking activity is a controversial issue in current brain research. A major difficulty is that currently available tools for the analysis of massively parallel spike trains (N>10 for higher-order correlations typically require vast sample sizes. While multiple single-cell recordings become increasingly available, experimental approaches to investigate the role of higher-order correlations suffer from the limitations of available analysis techniques. We have recently presented a novel method for cumulant-based inference of higher-order correlations (CuBIC that detects correlations of higher order even from relatively short data stretches of length T=10-100 s. CuBIC employs the compound Poisson process (CPP as a statistical model for the population spike counts, and assumes spike trains to be stationary in the analyzed data stretch. In the present study, we describe a non-stationary version of the CPP by decoupling the correlation structure from the spiking intensity of the population. This allows us to adapt CuBIC to time-varying firing rates. Numerical simulations reveal that the adaptation corrects for false positive inference of correlations in data with pure rate co-variation, while allowing for temporal variations of the firing rates has a surprisingly small effect on CuBICs sensitivity for correlations.
Visualizing Higher Order Finite Elements: FY05 Yearly Report.
Energy Technology Data Exchange (ETDEWEB)
Thompson, David; Pebay, Philippe Pierre
2005-11-01
This report contains an algorithm for decomposing higher-order finite elementsinto regions appropriate for isosurfacing and proves the conditions under which thealgorithm will terminate. Finite elements are used to create piecewise polynomialapproximants to the solution of partial differential equations for which no analyticalsolution exists. These polynomials represent fields such as pressure, stress, and mo-mentim. In the past, these polynomials have been linear in each parametric coordinate.Each polynomial coefficient must be uniquely determined by a simulation, and thesecoefficients are called degrees of freedom. When there are not enough degrees of free-dom, simulations will typically fail to produce a valid approximation to the solution.Recent work has shown that increasing the number of degrees of freedom by increas-ing the order of the polynomial approximation (instead of increasing the number offinite elements, each of which has its own set of coefficients) can allow some typesof simulations to produce a valid approximation with many fewer degrees of freedomthan increasing the number of finite elements alone. However, once the simulation hasdetermined the values of all the coefficients in a higher-order approximant, tools donot exist for visual inspection of the solution.This report focuses on a technique for the visual inspection of higher-order finiteelement simulation results based on decomposing each finite element into simplicialregions where existing visualization algorithms such as isosurfacing will work. Therequirements of the isosurfacing algorithm are enumerated and related to the placeswhere the partial derivatives of the polynomial become zero. The original isosurfacingalgorithm is then applied to each of these regions in turn.3 AcknowledgementThe authors would like to thank David Day and Louis Romero for their insight into poly-nomial system solvers and the LDRD Senior Council for the opportunity to pursue thisresearch. The authors were
Directory of Open Access Journals (Sweden)
Nishal S Patel
Full Text Available Changes in higher order chromatin organisation have been linked to transcriptional regulation; however, little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals. Here we analyse changes in chromatin organisation as neural differentiation progresses, exploiting the clear spatial separation of the temporal events of differentiation along the elongating body axis of the mouse embryo. Combining fluorescence in situ hybridisation with super-resolution structured illumination microscopy, we show that chromatin around key differentiation gene loci Pax6 and Irx3 undergoes both decompaction and displacement towards the nuclear centre coincident with transcriptional onset. Conversely, down-regulation of Fgf8 as neural differentiation commences correlates with a more peripheral nuclear position of this locus. During normal neural differentiation, fibroblast growth factor (FGF signalling is repressed by retinoic acid, and this vitamin A derivative is further required for transcription of neural genes. We show here that exposure to retinoic acid or inhibition of FGF signalling promotes precocious decompaction and central nuclear positioning of differentiation gene loci. Using the Raldh2 mutant as a model for retinoid deficiency, we further find that such changes in higher order chromatin organisation are dependent on retinoid signalling. In this retinoid deficient condition, FGF signalling persists ectopically in the elongating body, and importantly, we find that inhibiting FGF receptor (FGFR signalling in Raldh2-/- embryos does not rescue differentiation gene transcription, but does elicit both chromatin decompaction and nuclear position change. These findings demonstrate that regulation of higher order chromatin organisation during differentiation in the embryo can be uncoupled from the machinery that promotes transcription and, for the first time, identify FGF as an extrinsic signal that
Higher-order adaptive finite-element methods for Kohn-Sham density functional theory
Motamarri, Phani; Leiter, Kenneth; Knap, Jaroslaw; Gavini, Vikram
2012-01-01
We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn-Sham density-functional theory (DFT).To this end, we develop an \\emph{a priori} mesh adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss-Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn-Sham DFT problem. Our studies suggest that staggering computational savings---of the order of $1000-$fold---can be realized, for both all-electron and pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems stu...
Interactions and Strings in Higher Order Anisotropic and Inhomogeneous Superspaces and Isospaces
Vacaru, S I
1997-01-01
The monograph gives a general geometric background of the theory of field interactions, strings and diffusion processes on spaces, superspaces and isospaces with higher order anisotropy and inhomogenity. Our approach proceeds by developing the concept of higher order anisotropic superspace which unify the logical and mathematical aspects of modern Kaluza-Klein theories and generalized Lagrange and Finsler geometry and leads to modelling of physical processes on higher order fiber bundles provided with nonlinear and distingushed connections and metric structures. The view adopted in the monograph is that a general field theory should incorporate all possible anisotropic and stochastic manifestations of classical and quantum interactions and, in consequence, a corresponding modification of basic principles and mathematical methods in formulation of physical theories. This book can be also considered as a pedagogical survey on the mentioned subjects.
The higher order Rogue Wave solutions of the Gerdjikov-Ivanov equation
Guo, Lijuan; Zhang, Yongshuai; Xu, Shuwei; Wu, Zhiwei; He, Jingsong(Department of Mathematics and Ningbo Collabrative Innovation Center of Nonlinear Harzard System of Ocean and Atmosphere, Ningbo University, Ningbo 315211, China)
2013-01-01
We construct higher order rogue wave solutions for the Gerdjikov-Ivanov equation explicitly in term of determinant expression. Dynamics of both soliton and non-soliton solutions is discussed. A family of solutions with distinct structures are presented, which are new to the Gerdjikov-Ivanov equation.
Dependable software through higher-order strategic programming.
Energy Technology Data Exchange (ETDEWEB)
Winter, Victor Lono (University of Nebraska at Omaha); Fraij, Fares (University of Texas at El Paso); Roach, Steve (University of Texas at El Paso)
2004-03-01
Program transformation is a restricted form of software construction that can be amenable to formal verification. When successful, the nature of the evidence provided by such a verification is considered strong and can constitute a major component of an argument that a high-consequence or safety-critical system meets its dependability requirements. This article explores the application of novel higher-order strategic programming techniques to the development of a portion of a class loader for a restricted implementation of the Java Virtual Machine (JVM). The implementation is called the SSP and is intended for use in high-consequence safety-critical embedded systems. Verification of the strategic program using ACL2 is also discussed.
Higher order branching of periodic orbits from polynomial isochrones
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B. Toni
1999-09-01
Full Text Available We discuss the higher order local bifurcations of limit cycles from polynomial isochrones (linearizable centers when the linearizing transformation is explicitly known and yields a polynomial perturbation one-form. Using a method based on the relative cohomology decomposition of polynomial one-forms complemented with a step reduction process, we give an explicit formula for the overall upper bound of branch points of limit cycles in an arbitrary $n$ degree polynomial perturbation of the linear isochrone, and provide an algorithmic procedure to compute the upper bound at successive orders. We derive a complete analysis of the nonlinear cubic Hamiltonian isochrone and show that at most nine branch points of limit cycles can bifurcate in a cubic polynomial perturbation. Moreover, perturbations with exactly two, three, four, six, and nine local families of limit cycles may be constructed.
Mixed Higher Order Variational Model for Image Recovery
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Pengfei Liu
2014-01-01
Full Text Available A novel mixed higher order regularizer involving the first and second degree image derivatives is proposed in this paper. Using spectral decomposition, we reformulate the new regularizer as a weighted L1-L2 mixed norm of image derivatives. Due to the equivalent formulation of the proposed regularizer, an efficient fast projected gradient algorithm combined with monotone fast iterative shrinkage thresholding, called, FPG-MFISTA, is designed to solve the resulting variational image recovery problems under majorization-minimization framework. Finally, we demonstrate the effectiveness of the proposed regularization scheme by the experimental comparisons with total variation (TV scheme, nonlocal TV scheme, and current second degree methods. Specifically, the proposed approach achieves better results than related state-of-the-art methods in terms of peak signal to ratio (PSNR and restoration quality.
Scalar brane backgrounds in higher order curvature gravity
Charmousis, C; Dufaux, J F; Charmousis, Christos; Davis, Stephen C.; Dufaux, Jean-Francois
2003-01-01
We investigate maximally symmetric brane world solutions with a scalar field. Five-dimensional bulk gravity is described by a general lagrangian which yields field equations containing no higher than second order derivatives. This includes the Gauss-Bonnet combination for the graviton. Stability and gravitational properties of such solutions are considered, and we particularily emphasise the modifications induced by the higher order terms. In particular it is shown that higher curvature corrections to Einstein theory can give rise to instabilities in brane world solutions. A method for analytically obtaining the general solution for such actions is outlined. Genericaly, the requirement of a finite volume element together with the absence of a naked singularity in the bulk imposes fine-tuning of the brane tension. A model with a moduli scalar field is analysed in detail and we address questions of instability and non-singular self-tuning solutions. In particular, we discuss a case with a normalisable zero mode...
SPHS: Smoothed Particle Hydrodynamics with a higher order dissipation switch
Read, J I
2011-01-01
We present a novel implementation of Smoothed Particle Hydrodynamics (SPHS) that uses the spatial derivative of the velocity divergence as a higher order dissipation switch. Our switch -- which is second order accurate -- detects flow convergence before it occurs. If particle trajectories are going to cross, we switch on the usual SPH artificial viscosity, as well as conservative dissipation in all advected fluid quantities (for example, the entropy). The viscosity and dissipation terms (that are numerical errors) are designed to ensure that all fluid quantities remain single-valued as particles approach one another, to respect conservation laws, and to vanish on a given physical scale as the resolution is increased. SPHS alleviates a number of known problems with `classic' SPH, successfully resolving mixing, and recovering numerical convergence with increasing resolution. An additional key advantage is that -- treating the particle mass similarly to the entropy -- we are able to use multimass particles, givi...
Chemical Freeze-Out and Higher Order Multiplicity Moments
Tawfik, A
2013-01-01
We calculate the non-normalized moments of the particle multiplicity within the framework of the hadron resonance gas (HRG) model. At finite chemical potential $\\mu$, a non-monotonic behavior is observed in the thermal evolution of third order moment (skewness $S$) and the higher order ones as well. Among others, this observation likely reflects dynamical fluctuations and strong correlations. The signatures of non-monotonicity in the normalized fourth order moment (kurtosis $\\kappa$) and its products get very clear. Based on these findings, we introduce a novel condition characterizing the universal freeze-out curve. The chemical freeze-out parameters $T$ and $\\mu$ are described by vanishing $\\kappa\\, \\sigma^2$ or equivalently $m_4=3\\,\\chi^2$, where $\\sigma$, $\\chi$ and $m_4$ are the standard deviation, susceptibility and fourth order moment, respectively. The fact that the HRG model is not able to release information about criticality related to the confinement and chiral dynamics should not veil the observa...
SU(2) Higher-order effective quark interactions from polarization
Braghin, Fábio L.
2016-10-01
Higher order quark effective interactions are found for SU(2) flavor by departing from a non-local quark-quark interaction. By integrating out a component of the quark field, the determinant is expanded in chirally symmetric and symmetry breaking effective interactions up to the fifth order in the quark bilinears. The resulting coupling constants are resolved in the leading order of the longwavelength limit and exact numerical ratios between several of these coupling constants are obtained in the large quark mass limit. In this level, chiral invariant interactions only show up in even powers of the quark bilinears, i.e. O(ψ bar ψ) 2 n (n = 1 , 2 , 3 , . .), whereas (explicit) chiral symmetry breaking terms emerge as O(ψ bar ψ) n being always proportional to some power of the Lagrangian quark mass.
Higher-order techniques for some problems of nonlinear control
Directory of Open Access Journals (Sweden)
Sarychev Andrey V.
2002-01-01
Full Text Available A natural first step when dealing with a nonlinear problem is an application of some version of linearization principle. This includes the well known linearization principles for controllability, observability and stability and also first-order optimality conditions such as Lagrange multipliers rule or Pontryagin's maximum principle. In many interesting and important problems of nonlinear control the linearization principle fails to provide a solution. In the present paper we provide some examples of how higher-order methods of differential geometric control theory can be used for the study nonlinear control systems in such cases. The presentation includes: nonlinear systems with impulsive and distribution-like inputs; second-order optimality conditions for bang–bang extremals of optimal control problems; methods of high-order averaging for studying stability and stabilization of time-variant control systems.
A higher-order Robert-Asselin type time filter
Li, Yong; Trenchea, Catalin
2014-02-01
The Robert-Asselin (RA) time filter combined with leapfrog scheme is widely used in numerical models of weather and climate. It successfully suppresses the spurious computational mode associated with the leapfrog method, but it also weakly dampens the physical mode and degrades the numerical accuracy. The Robert-Asselin-Williams (RAW) time filter is a modification of the RA filter that reduces the undesired numerical damping of RA filter and increases the accuracy. We propose a higher-order Robert-Asselin (hoRA) type time filter which effectively suppresses the computational modes and achieves third-order accuracy with the same storage requirement as RAW filter. Like RA and RAW filters, the hoRA filter is non-intrusive, and so it would be easily implementable. The leapfrog scheme with hoRA filter is almost as accurate, stable and efficient as the intrusive third-order Adams-Bashforth (AB3) method.
SU(2) higher-order effective quark interactions from polarization
Braghin, Fábio L
2016-01-01
Higher order quark effective interactions are found for SU(2) flavor by departing from a non local quark-quark interaction. By integrating out a component of the quark field, the determinant is expanded in chirally symmetric and symmetry breaking effective interactions up to the fifh order in the quark bilinears. The resulting coupling constants are resolved in the leading order of the longwavelength limit and exact numerical ratios between several of these coupling constants are obtained in the large quark mass limit. In this level, chiral invariant interactions only show up in even powers of the quark bilinears, i.e. ${\\cal O}(\\bpsi \\psi)^{2 n}$ ($n=1,2,3,..$), and chiral symmetry breaking terms emerge as ${\\cal O}(\\bpsi \\psi)^{n}$.
The Key Exchange Cryptosystem Used With Higher Order Diophantine Equations
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Harry Yosh
2011-03-01
Full Text Available One-way functions are widely used for encrypting the secret in public key cryptography, although theyare regarded as plausibly one-way but have not been proven so.Here we discuss the public key cryptosystem based on the system of higher order Diophantine equations.In this system those Diophantine equations are used as public keys for sender and recipient, and bothsender and recipient can obtain the shared secret through a trapdoor, while attackers must solve thoseDiophantine equations without trapdoor. Thus the scheme of this cryptosystem might be considered torepresent a possible one-way function.We also discuss the problem on implementation, which is caused from additional complexity necessaryfor constructing Diophantine equations in order to prevent from attacking by tamperers.
Inflationary scenarios in Starobinsky model with higher order corrections
Energy Technology Data Exchange (ETDEWEB)
Artymowski, Michał [Institute of Physics, Jagiellonian University,Łojasiewicza 11, 30-348 Kraków (Poland); Lalak, Zygmunt [Institute of Theoretical Physics, Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland); Lewicki, Marek [Institute of Theoretical Physics, Faculty of Physics, University of Warsaw,ul. Pasteura 5, 02-093 Warsaw (Poland); Michigan Center for Theoretical Physics, University of Michigan,450 Church Street, Ann Arbor MI 48109 (United States)
2015-06-17
We consider the Starobinsky inflation with a set of higher order corrections parametrised by two real coefficients λ{sub 1} ,λ{sub 2}. In the Einstein frame we have found a potential with the Starobinsky plateau, steep slope and possibly with an additional minimum, local maximum or a saddle point. We have identified three types of inflationary behaviour that may be generated in this model: i) inflation on the plateau, ii) at the local maximum (topological inflation), iii) at the saddle point. We have found limits on parameters λ{sub i} and initial conditions at the Planck scale which enable successful inflation and disable eternal inflation at the plateau. We have checked that the local minimum away from the GR vacuum is stable and that the field cannot leave it neither via quantum tunnelling nor via thermal corrections.
Inflationary scenarios in Starobinsky model with higher order corrections
Artymowski, Michal; Lewicki, Marek
2015-01-01
We consider the Starobinsky inflation with a set of higher order corrections parametrised by two real coefficients $\\lambda_1, \\lambda_2$. In the Einstein frame we have found a potential with the Starobinsky plateau, steep slope and possibly with an additional minimum, local maximum or a saddle point. We have identified three types of inflationary behaviour that may be generated in this model: i) inflation on the plateau, ii) at the local maximum (topological inflation), iii) at the saddle point. We have found limits on parameters $\\lambda_i$ and initial conditions at the Planck scale which enable successful inflation and disable eternal inflation at the plateau. We have checked that the local minimum away from the GR vacuum is stable and that the field cannot leave it neither via quantum tunnelling nor via thermal corrections.
Polymer quantization, stability and higher-order time derivative terms
Cumsille, Patricio; Ossandon, Sebastian; Reyes, Camilo
2015-01-01
The stability of higher-order time derivative theories using the polymer extension of quantum mechanics is studied. First, we focus on the well-known Pais-Uhlenbeck model and by casting the theory into the sum of two decoupled harmonic oscillators we show that the energy spectrum is composed with positive and negative energy parts. The Schrodinger quantization of the model with creation and annihilations operators leads to a theory with unbounded Hamiltonian that can be interpreted in terms of normal particles and Lee-Wick-like particles responsible for the instability. We investigate whether the fundamental discreetness implicit in the polymer quantization can regularize the effects of the negative energies introduced by the Lee-Wick-like particles which are associated to a high-energy scale. Precisely, we show that the polymer quantization leads to a positive defined Hamiltonian whose stability is improved as the number of Lee-Wick-like particles grows.
Radiation by solitons due to higher-order dispersion
DEFF Research Database (Denmark)
Karpman, V.I.
1993-01-01
We consider the Korteweg-de Vries (KdV) and nonlinear Schrodinger (NS) equations with higher-order derivative terms describing dispersive corrections. Conditions of existence of stationary and radiating solitons of the fifth-order KdV equation are obtained. An asymptotic time-dependent solution...... to the latter equation, describing the soliton radiation, is found. The radiation train may be in front as well as behind the soliton, depending on the sign of dispersion. The change rate of the soliton due to the radiation is calculated. A modification of the WKB method, that permits one to describe...... in a simple and general way the radiation of KdV and NS, as well as other types. of solitons, is developed. From the WKB approach it follows that the soliton radiation is a result of a tunneling transformation of the non-linearly self-trapped wave into the free-propagating radiation....
Recognition of higher order patterns in proteins: immunologic kernels.
Directory of Open Access Journals (Sweden)
Robert D Bremel
Full Text Available By applying analysis of the principal components of amino acid physical properties we predicted cathepsin cleavage sites, MHC binding affinity, and probability of B-cell epitope binding of peptides in tetanus toxin and in ten diverse additional proteins. Cross-correlation of these metrics, for peptides of all possible amino acid index positions, each evaluated in the context of a ±25 amino acid flanking region, indicated that there is a strongly repetitive pattern of short peptides of approximately thirty amino acids each bounded by cathepsin cleavage sites and each comprising B-cell linear epitopes, MHC-I and MHC-II binding peptides. Such "immunologic kernel" peptides comprise all signals necessary for adaptive immunologic cognition, response and recall. The patterns described indicate a higher order spatial integration that forms a symbolic logic coordinating the adaptive immune system.
Higher Order Variability Properties of Accreting Black Holes
Maccarone, T J; Maccarone, Thomas J.; Coppi, Paolo S.
2002-01-01
To better constrain the emission mechanism underlying the hard state of galactic black hole candidates, we use high-time resolution RXTE lightcurves for Cyg X-1 and GX 399-4 to compute two higher order variability statistics for these objects, the skewness and the Fourier bispectrum. Similar analyses, in particular using the skewness measure, have been attempted before, but the photon collection area of RXTE allows us to present results of much greater statistical significance. The results for the two objects are qualitatively similar, reinforcing the idea that the same basic mechanisms are at work in both. We find a significantly positive skewness for variability timescales less than $\\sim 1 $ second, and a {\\it negative} skewness for timescale $1- 5 $ sec. Such a skewness pattern cannot be reproduced by the simplest shot variability models where individual shots have a fixed profile and intensity and are uncorrelated in time. Further evidence against simple shot models comes from the significant detection o...
Research on Life Signals Detection Based on Higher Order Statistics
Directory of Open Access Journals (Sweden)
Jian-Jun Li
2012-10-01
Full Text Available The life signals are built on harmonic mode for their low frequency, quasi-periodicity, low SNR, and the easy submerged in strong clutter noise. The method for detecting life signal based on adaptive filter and high order statistics is presented, in which neither the Gaussian supposition of the observed signal, nor a prior information about the waveform and arrival time of the observed signal is necessary. The principle of method is to separate the spectrum of input signal into many narrow frequency bands, whose Sub-band signal is followed by a short-time estimation of higher-order statistics so as to suppress Gaussian noises. Simulated results show that the method can effectively detect life signals from noise with good convergence speed and stability, and greatly improve the signal quality with respect to LMS method.
Higher-Order Finite Elements for Computing Thermal Radiation
Gould, Dana C.
2004-01-01
Two variants of the finite-element method have been developed for use in computational simulations of radiative transfers of heat among diffuse gray surfaces. Both variants involve the use of higher-order finite elements, across which temperatures and radiative quantities are assumed to vary according to certain approximations. In this and other applications, higher-order finite elements are used to increase (relative to classical finite elements, which are assumed to be isothermal) the accuracies of final numerical results without having to refine computational meshes excessively and thereby incur excessive computation times. One of the variants is termed the radiation sub-element (RSE) method, which, itself, is subject to a number of variations. This is the simplest and most straightforward approach to representation of spatially variable surface radiation. Any computer code that, heretofore, could model surface-to-surface radiation can incorporate the RSE method without major modifications. In the basic form of the RSE method, each finite element selected for use in computing radiative heat transfer is considered to be a parent element and is divided into sub-elements for the purpose of solving the surface-to-surface radiation-exchange problem. The sub-elements are then treated as classical finite elements; that is, they are assumed to be isothermal, and their view factors and absorbed heat fluxes are calculated accordingly. The heat fluxes absorbed by the sub-elements are then transferred back to the parent element to obtain a radiative heat flux that varies spatially across the parent element. Variants of the RSE method involve the use of polynomials to interpolate and/or extrapolate to approximate spatial variations of physical quantities. The other variant of the finite-element method is termed the integration method (IM). Unlike in the RSE methods, the parent finite elements are not subdivided into smaller elements, and neither isothermality nor other
Scintillations of higher-order laser beams in non-Kolmogorov medium.
Baykal, Yahya
2014-04-01
In an atmospheric medium that shows a non-Kolmogorov turbulence behavior, the variation of the on-axis scintillation index is evaluated when higher-order laser modes are used as the excitation. The Rytov method is employed together with the equivalent structure constant, which makes our results valid in weak turbulence. In the limiting case, our solution correctly reduces to the known scintillation index of the Gaussian beam in Kolmogorov turbulence. For all the higher-order even modes, increase in the power law exponent, α of the non-Kolmogorov spectrum is found to increase the scintillations. When the source size of the higher-order modes is large, higher-order even modes attain almost the same scintillation index values for all α. However, for small source sizes, being valid for any realization of the non-Kolmogorov spectrum, the scintillations decrease as the mode order becomes large. The changes in the propagation distance, structure constant, and the wavelength do not vary these trends.
Invariants of Velocities, and Higher Order Grassmann Bundles
Grigore, D R; Grigore, Dan Radu; Krupka, Demeter
1997-01-01
An $(r,n)$-velocity is an $r$-jet with source at $0 \\in \\R^n$, and target in a manifold $Y$. An $(r,n)$-velocity is said to be regular, if it has a representative which is an immersion at $0 \\in \\R^{n}$. The manifold $T^{r}_{n}Y$ of $(r,n)$-velocities as well as its open, $L^{r}_{n}$-invariant, dense submanifold $\\Imm T^{r}_{n}Y$ of regular $(r,n)$-velocities, are endowed with a natural action of the differential group $L^{r}_{n}$ of invertible $r$-jets with source and target $0 \\in \\R^{n}$. In this paper, we describe all continuous, $L^{r}_{n}$-invariant, real-valued functions on $T^{r}_{n}Y$ and T^{r}_{n}Y$ in an explicit, recurrent form. To this purpose, higher order Grassmann bundles are considered as the corresponding quotients $P^{r}_{n}Y = that nontrivial $L^{r}_{n}$-invariants on $\\Imm T^{r}_{n}Y$ cannot be continuously extended onto $T^{r}_{n}Y$.
SPHS: smoothed particle hydrodynamics with a higher order dissipation switch
Read, J. I.; Hayfield, T.
2012-06-01
We present a novel implementation of smoothed particle hydrodynamics that uses the spatial derivative of the velocity divergence as a higher order dissipation switch. Our switch - which is second order accurate - detects flow convergence before it occurs. If particle trajectories are going to cross, we switch on the usual SPH artificial viscosity, as well as conservative dissipation in all advected fluid quantities (e.g. the entropy). The viscosity and dissipation terms (that are numerical errors) are designed to ensure that all fluid quantities remain single valued as particles approach one another, to respect conservation laws, and to vanish on a given physical scale as the resolution is increased. SPHS alleviates a number of known problems with 'classic' SPH, successfully resolving mixing, and recovering numerical convergence with increasing resolution. An additional key advantage is that - treating the particle mass similarly to the entropy - we are able to use multimass particles, giving significantly improved control over the refinement strategy. We present a wide range of code tests including the Sod shock tube, Sedov-Taylor blast wave, Kelvin-Helmholtz Instability, the 'blob test' and some convergence tests. Our method performs well on all tests, giving good agreement with analytic expectations.
Chemical freeze-out and higher order multiplicity moments
Energy Technology Data Exchange (ETDEWEB)
Tawfik, A., E-mail: a.tawfik@eng.mti.edu.eg
2014-02-15
We calculate the non-normalized moments of the particle multiplicity within the framework of the hadron resonance gas (HRG) model. At finite chemical potential μ, a non-monotonic behavior is observed in the thermal evolution of third order moment (skewness S) and the higher order ones as well. The signatures of non-monotonicity in the normalized fourth order moment (kurtosis κ) and its products get very clear. Among others, this observation likely reflects dynamical fluctuations and strong correlations. Based on these findings, we introduce the physics of the universal freeze-out curve. It is found that the chemical freeze-out parameters T and μ are described by vanishing κσ{sup 2} or equivalently m{sub 4}=3χ{sup 2}, where σ, χ and m{sub 4} are the standard deviation, susceptibility and fourth order moment, respectively. The fact that the HRG model is not able to release information about criticality related to the confinement and chiral dynamics should not veil the observations related to the chemical freeze-out. Recent lattice QCD studies strongly advocate the main conclusion of the present paper.
Higher order effects in electroweak theory 1981-12 (KEK)
International Nuclear Information System (INIS)
This is a brief report on the higher order or loop effects in electroweak theory. The discussion is based on the Weinberg Salam model and QCD. The loop correction to weak interaction is described. The renormalization conditions were applied to physical parameters, α(QED), M(W) and M(Z). It is expected to obtain experimentally the values of M(W) and M(Z) with the accuracy of 0.1 percent. In this scheme, the parameters were fixed loop by loop. The correction was evaluated along the present on-shell scheme. The general estimation of the order of correction was performed. The evaluation of the size of terms in one-loop correction was made. The examples of one loop analysis are presented. The leading logarithmic correction such as α ln(m2 q2/M2) is discussed. The system was described by H(eff) with the local operator O(i), in which the propagator of heavy particles was contracted. The effective interaction was obtained as C(i) (q2) O(i), where C(i)(q2) satisfies a proper equation of a renormalization group. As the practical examples, μ-decay, charged current and neutral current were studied. The correction to electron neutral current and the shift of M(W) and M(Z) were numerically obtained. Comments on quark mass and the uncertainty of sin2(theta) from the νN reaction are presented. (Kato, T.)
Higher-order Statistics of Weak Lensing Shear and Flexion
Munshi, Dipak; Heavens, Alan; Coles, Peter; Cooray, Asantha
2010-01-01
Owing to their more extensive sky coverage and tighter control on systematic errors, future deep weak lensing surveys should provide a better statistical picture of the dark matter clustering beyond the level of the power spectrum. In this context, the study of non-Gaussianity induced by gravity can help tighten constraints on the background cosmology by breaking parameter degeneracies, as well as throwing light on the nature of dark matter, dark energy or alternative gravity theories. Analysis of the shear or flexion properties of such maps is more complicated than the simpler case of the convergence due to the spinorial nature of the fields involved. Here we develop analytical tools for the study of higher-order statistics such as the bispectrum (or trispectrum) directly using such maps at different source redshift. The statistics we introduce can be constructed from cumulants of the shear or flexions, involving the cross-correlation of squared and cubic maps at different redshifts. Typically, the low signa...
Predicting perceptual learning from higher-order cortical processing.
Wang, Fang; Huang, Jing; Lv, Yaping; Ma, Xiaoli; Yang, Bin; Wang, Encong; Du, Boqi; Li, Wu; Song, Yan
2016-01-01
Visual perceptual learning has been shown to be highly specific to the retinotopic location and attributes of the trained stimulus. Recent psychophysical studies suggest that these specificities, which have been associated with early retinotopic visual cortex, may in fact not be inherent in perceptual learning and could be related to higher-order brain functions. Here we provide direct electrophysiological evidence in support of this proposition. In a series of event-related potential (ERP) experiments, we recorded high-density electroencephalography (EEG) from human adults over the course of learning in a texture discrimination task (TDT). The results consistently showed that the earliest C1 component (68-84ms), known to reflect V1 activity driven by feedforward inputs, was not modulated by learning regardless of whether the behavioral improvement is location specific or not. In contrast, two later posterior ERP components (posterior P1 and P160-350) over the occipital cortex and one anterior ERP component (anterior P160-350) over the prefrontal cortex were progressively modified day by day. Moreover, the change of the anterior component was closely correlated with improved behavioral performance on a daily basis. Consistent with recent psychophysical and imaging observations, our results indicate that perceptual learning can mainly involve changes in higher-level visual cortex as well as in the neural networks responsible for cognitive functions such as attention and decision making.
Near integrability of kink lattice with higher order interactions
Jiang, Yunguo; He, Song
2016-01-01
In the paper, we make use of Manton's analytical method to investigate the force between kink and the anti-kink with large distance in $1+1$ dimensional field theory. The related potential has infinite order corrections of exponential pattern, and coefficients for each order are determined. These coefficients can also be obtained by solving the equation of the fluctuation around the vacuum. At the lowest order, the kink lattice represents the Toda lattice. With higher order correction terms, the kink lattice can represent one kind of the generic Toda lattice. With only two sites, the kink lattice is classically integrable. If the number of sites of the lattice is larger than two, the kink lattice is not integrable but a near integrable system. We take use of the Flaschka's variables to study the Lax pair of the kink lattice. These Flaschka's variables have interesting algebraic relations and the non-integrability can be manifested. We also discussed the higher Hamiltonians for the deformed open Toda lattice, ...
Higher Order Modes Excitation of Micro Cantilever Beams
Jaber, Nizar
2014-05-01
In this study, we present analytical and experimental investigation of electrically actuated micro cantilever based resonators. These devices are fabricated using polyimide and coated with chrome and gold layers from both sides. The cantilevers are highly curled up due to stress gradient, which is a common imperfection in surface micro machining. Using a laser Doppler vibrometer, we applied a noise signal to experimentally find the first four resonance frequencies. Then, using a data acquisition card, we swept the excitation frequency around the first four natural modes of vibrations. Theoretically, we derived a reduced order model using the Galerkin method to simulate the dynamics of the system. Extensive numerical analysis and computations were performed. The numerical analysis was able to provide good matching with experimental values of the resonance frequencies. Also, we proved the ability to excite higher order modes using partial electrodes with shapes that resemble the shape of the mode of interest. Such micro-resonators are shown to be promising for applications in mass and gas sensing.
Higher order finite element analysis of thick composite laminates
Goering, J.; Kim, H. J.
1992-01-01
A higher order, sub-parametric, laminated, 3D solid finite element was used for the analysis of very thick laminated composite plates. The geometry of this element is defined by four nodes in the X-Y plane which define a prism of material through the thickness of the laminate. There are twenty-four degrees of freedom at each node; translations at the upper and lower surfaces of the laminate in each of the three coordinate directions, and the derivatives of these translations with respect to each coordinate. This choice of degrees of freedom leads to displacement and strain compatibility at the corners. Stacking sequence effects are accounted for by explicitly integrating the strain energy density through the thickness of the element. The laminated solid element was combined with a gap-contact element to analyze thick laminated composite lugs loaded through flexible pins. The resulting model accounts for pin bending effects that produce non-uniform bearing stresses through the thickness of the lug. A thick composite lug experimental test program was performed, and provided data that was used to validate the analytical model. Two lug geometries and three stacking sequences were tested.
Lim, C. W.; Zhang, G.; Reddy, J. N.
2015-05-01
In recent years there have been many papers that considered the effects of material length scales in the study of mechanics of solids at micro- and/or nano-scales. There are a number of approaches and, among them, one set of papers deals with Eringen's differential nonlocal model and another deals with the strain gradient theories. The modified couple stress theory, which also accounts for a material length scale, is a form of a strain gradient theory. The large body of literature that has come into existence in the last several years has created significant confusion among researchers about the length scales that these various theories contain. The present paper has the objective of establishing the fact that the length scales present in nonlocal elasticity and strain gradient theory describe two entirely different physical characteristics of materials and structures at nanoscale. By using two principle kernel functions, the paper further presents a theory with application examples which relates the classical nonlocal elasticity and strain gradient theory and it results in a higher-order nonlocal strain gradient theory. In this theory, a higher-order nonlocal strain gradient elasticity system which considers higher-order stress gradients and strain gradient nonlocality is proposed. It is based on the nonlocal effects of the strain field and first gradient strain field. This theory intends to generalize the classical nonlocal elasticity theory by introducing a higher-order strain tensor with nonlocality into the stored energy function. The theory is distinctive because the classical nonlocal stress theory does not include nonlocality of higher-order stresses while the common strain gradient theory only considers local higher-order strain gradients without nonlocal effects in a global sense. By establishing the constitutive relation within the thermodynamic framework, the governing equations of equilibrium and all boundary conditions are derived via the variational
Topoisomerase II–DNA complexes trapped by ICRF-193 perturb chromatin structure
Germe, Thomas; Hyrien, Olivier
2005-01-01
DNA topoisomerase II (topo II) is involved in unlinking replicating DNA and organizing mitotic chromosomes. Topo II is the target of many antitumour drugs. Topo II inhibition results in extensive catenation of newly replicated DNA and may potentially perturb chromatin assembly. Here, we show that the topo II inhibitor ICRF-193 does not prevent the bulk of nucleosome deposition, but perturbs nucleosome spacing in Xenopus egg extracts. This is due to the trapping of topo II-closed clamps on the...
Higher-order Chebyshev rational approximation method (CRAM)
International Nuclear Information System (INIS)
The burnup equations can in principle be solved by computing the exponential of the burnup matrix. However, due to the difficult numerical characteristics of burnup matrices, the problem is extremely stiff, and the matrix exponential solution was long considered infeasible for an entire burnup system containing over a thousand nuclides. After discovering that the eigenvalues of burnup matrices are generally confined to a region near the negative real axis, the Chebyshev rational approximation method (CRAM) was introduced as a novel method to solve the burnup equations. It can be characterized as the best rational function on the negative real axis and it has been shown to be capable of simultaneously solving an entire burnup system both accurately and efficiently. The main difficulty in using CRAM for computing the matrix exponential is determining the coefficients of the rational function for a given approximation order. Some polynomial CRAM coefficients have been published in 1984, and based on these literature values, CRAM approximations up to the order 16 have been thus far applied in burnup calculations. The topic of this paper is the computation of CRAM approximations and their application to burnup equations. A Remez-type method utilizing the equioscillation property of best approximations is used to construct the CRAM approximants for approximation orders 1,. . . , 50. Numerical results are presented for a large burnup system and for a decay system. It is demonstrated that higher-order CRAM can be used to accurately solve the burnup equations even with time steps of the order of millions of years. (author)
Energy Technology Data Exchange (ETDEWEB)
Bekaert, Xavier [Laboratoire de Mathématiques et Physique Théorique, Unité Mixte de Recherche 7350 du CNRS, Fédération de Recherche 2964 Denis Poisson, Université François Rabelais, Parc de Grandmont, 37200 Tours (France); Grigoriev, Maxim, E-mail: grig@lpi.ru [Tamm Theory Department, Lebedev Physics Institute, Leninsky prospect 53, 119991 Moscow (Russian Federation)
2013-11-11
Using ambient space we develop a fully gauge and o(d,2)-covariant approach to boundary values of AdS{sub d+1} gauge fields. It is applied to the study of (partially) massless fields in the bulk and (higher-order) conformal scalars, i.e. singletons, as well as (higher-depth) conformal gauge fields on the boundary. In particular, we identify the corresponding generalized Fradkin–Tseytlin equations as obstructions to the extension of the off-shell boundary value to the bulk, generalizing the usual considerations for the holographic anomalies to the partially massless fields. We also relate the background fields for the higher-order singleton to the boundary values of partially massless fields and prove the appropriate generalization of the Flato–Fronsdal theorem, which is in agreement with the known structure of symmetries for the higher-order wave operator. All these facts support the following generalization of the higher-spin holographic duality: the O(N) model at a multicritical isotropic Lifshitz point should be dual to the theory of partially massless symmetric tensor fields described by the Vasiliev equations based on the higher-order singleton symmetry algebra.
Institute of Scientific and Technical Information of China (English)
ZHAOHUI; YIZHANG; 等
1999-01-01
The structure of the nuclosome core particle of chromatin in chicken erythrocytes has been examined by using AFM.The 146 bp of DNA wrapped twice around the core histone octamer are clearly visualized.Both the ends of entry/exit of linker DNA are also demonstrated.The dimension of the nucleosome core particles is - 1-4 nm in height and - 13-22 nm in width.In addition,superbeads (width of - 48-57 nm,height of - 2-3 nm )are occasionally revealed,two turns of DNA around the core particles are also detected.
Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin
Directory of Open Access Journals (Sweden)
Mora Xavier
2007-05-01
Full Text Available Abstract Background Histone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes in physiological salt (0.14 M NaCl at constant stoichiometry. Results The H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin. Conclusion H1 subtypes freely exchange in vitro between chromatin binding sites in physiological salt (0.14 M NaCl. The large differences in relative affinity of the H1 subtypes for
Analysis of Higher Order Channel Dropping Tunneling Processes in Photonic Crystals
Institute of Scientific and Technical Information of China (English)
FU Jian; HE Sai-Ling
2000-01-01
A theoretical analysis is given for a higher order channel drop tunneling structure composed of two horizontal channels and a resonator system with two vertical multi-mode cavities in a two- or three-dimensional photonic crystal. Criteria for a complete transfer are derived for the application of wavelength division multiplexing. Compared to the resonator system with two single-mode cavities or a single multi-mode cavity, the present resonator system improves the transport properties.
Higher-Order, Space-Time Adaptive Finite Volume Methods: Algorithms, Analysis and Applications
Energy Technology Data Exchange (ETDEWEB)
Minion, Michael
2014-04-29
The four main goals outlined in the proposal for this project were: 1. Investigate the use of higher-order (in space and time) finite-volume methods for fluid flow problems. 2. Explore the embedding of iterative temporal methods within traditional block-structured AMR algorithms. 3. Develop parallel in time methods for ODEs and PDEs. 4. Work collaboratively with the Center for Computational Sciences and Engineering (CCSE) at Lawrence Berkeley National Lab towards incorporating new algorithms within existing DOE application codes.
Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci.
Bonifer, C; Hecht, A; Saueressig, H; Winter, D M; Sippel, A E
1991-10-01
It is hypothesized that nuclear DNA is organized in topologically constrained loop domains defining basic units of higher order chromatin structure. Our studies are performed in order to investigate the functional relevance of this structural subdivision of eukaryotic chromatin for the control of gene expression. We used the chicken lysozyme gene locus as a model to examine the relation between chromatin structure and gene function. Several structural features of the lysozyme locus are known: the extension of the region of general DNAasel sensitivity of the active gene, the location of DNA-sequences with high affinity for the nuclear matrix in vitro, and the position of DNAasel hypersensitive chromatin sites (DHSs). The pattern of DHSs changes depending on the transcriptional status of the gene. Functional studies demonstrated that DHSs mark the position of cis-acting regulatory elements. Additionally, we discovered a novel cis-activity of the border regions of the DNAasel sensitive domain (A-elements). By eliminating the position effect on gene expression usually observed when genes are randomly integrated into the genome after transfection, A-elements possibly serve as punctuation marks for a regulatory chromatin domain. Experiments using transgenic mice confirmed that the complete structurally defined lysozyme gene domain behaves as an independent regulatory unit, expressing the gene in a tissue specific and position independent manner. These expression features were lost in transgenic mice carrying a construct, in which the A-elements as well as an upstream enhancer region were deleted, indicating the lack of a locus activation function on this construct. Experiments are designed in order to uncover possible hierarchical relationships between the different cis-acting regulatory elements for stepwise gene activation during cell differentiation. We are aiming at the definition of the basic structural and functional requirements for position independent and high
Bignold, L P
2002-01-01
Nuclear chromatin patterns are used to distinguish normal and abnormal cells in histopathology and cytopathology. However, many chromatin pattern features are affected by aspects of tissue processing, especially fixation. Major effects of aldehyde and/or ethanol fixation on nuclei in the living state include shrinkage, chromatin aggregation and production of a 'chromatinic rim'. The mechanisms of these effects are poorly understood. In the past, possible mechanisms of fixation-induced morphological change have been considered only in terms of the theoretical model of the nucleus, which involves only a random tangle of partly unfolded chromosomes contained within the nuclear membrane. Such a model provides no basis for chromatin to be associated with the nuclear envelope, and hence no obvious clue to a mechanism for the formation of the 'chromatinic rim' in fixed nuclei. In recent years, two new models of nuclear structure have been described. The nuclear membrane-bound, chromosomal-domain model is based on the discoveries of chromatin-nuclear membrane attachments and of the localisation of the chromatin of each chromosome within discrete, exclusive parts of the nucleus (the 'domain' of each partly unfolded chromosome). The nuclear matrix/scaffold model is based on the discovery of relatively insoluble proteins in nuclei, which it suggests forms a 'matrix' and modulates gene expression by affecting transcription of DNA. Here, a hypothesis for fixation-associated chromatin pattern formation based mainly on the first model but partially relying on the second, is presented. The hypothesis offers explanations of the variations of appearance of nuclei according to fixation (especially air-drying versus wet-fixation with formaldehyde, glutaraldehyde or ethanol); the appearances of the nuclei of more metabolically active versus less metabolically active cells of the same type; the appearances of nuclei after fixation with osmium tetroxide; and of the marked central
A Relational Algebra for Basic Terms in a Higher-Order Logic:Technical Report CSTR-13-004
Price, Simon; Flach, Peter A.
2013-01-01
We define a relational algebra on basic terms, strongly typed terms in a higher-order logic, that are well suited to the representation of heterogeneous data, irrespective of whether the data originated from relational, unstructured, semi-structured or structured sources. This higher-order generalisation of the relational model has potential applications in NoSQL databases and Big Variety, Big Data applications.
Alamia, Andrea; Solopchuk, Oleg; D'Ausilio, Alessandro; Van Bever, Violette; Fadiga, Luciano; Olivier, Etienne; Zénon, Alexandre
2016-03-01
Because Broca's area is known to be involved in many cognitive functions, including language, music, and action processing, several attempts have been made to propose a unifying theory of its role that emphasizes a possible contribution to syntactic processing. Recently, we have postulated that Broca's area might be involved in higher-order chunk processing during implicit learning of a motor sequence. Chunking is an information-processing mechanism that consists of grouping consecutive items in a sequence and is likely to be involved in all of the aforementioned cognitive processes. Demonstrating a contribution of Broca's area to chunking during the learning of a nonmotor sequence that does not involve language could shed new light on its function. To address this issue, we used offline MRI-guided TMS in healthy volunteers to disrupt the activity of either the posterior part of Broca's area (left Brodmann's area [BA] 44) or a control site just before participants learned a perceptual sequence structured in distinct hierarchical levels. We found that disruption of the left BA 44 increased the processing time of stimuli representing the boundaries of higher-order chunks and modified the chunking strategy. The current results highlight the possible role of the left BA 44 in building up effector-independent representations of higher-order events in structured sequences. This might clarify the contribution of Broca's area in processing hierarchical structures, a key mechanism in many cognitive functions, such as language and composite actions. PMID:26765778
Directory of Open Access Journals (Sweden)
Dostie Josée
2011-10-01
Full Text Available Abstract Background Long-range interactions between regulatory DNA elements such as enhancers, insulators and promoters play an important role in regulating transcription. As chromatin contacts have been found throughout the human genome and in different cell types, spatial transcriptional control is now viewed as a general mechanism of gene expression regulation. Chromosome Conformation Capture Carbon Copy (5C and its variant Hi-C are techniques used to measure the interaction frequency (IF between specific regions of the genome. Our goal is to use the IF data generated by these experiments to computationally model and analyze three-dimensional chromatin organization. Results We formulate a probabilistic model linking 5C/Hi-C data to physical distances and describe a Markov chain Monte Carlo (MCMC approach called MCMC5C to generate a representative sample from the posterior distribution over structures from IF data. Structures produced from parallel MCMC runs on the same dataset demonstrate that our MCMC method mixes quickly and is able to sample from the posterior distribution of structures and find subclasses of structures. Structural properties (base looping, condensation, and local density were defined and their distribution measured across the ensembles of structures generated. We applied these methods to a biological model of human myelomonocyte cellular differentiation and identified distinct chromatin conformation signatures (CCSs corresponding to each of the cellular states. We also demonstrate the ability of our method to run on Hi-C data and produce a model of human chromosome 14 at 1Mb resolution that is consistent with previously observed structural properties as measured by 3D-FISH. Conclusions We believe that tools like MCMC5C are essential for the reliable analysis of data from the 3C-derived techniques such as 5C and Hi-C. By integrating complex, high-dimensional and noisy datasets into an easy to interpret ensemble of three
Conformal Invariance of Higher-Order Lagrange Systems by Lie Point Transformation
Institute of Scientific and Technical Information of China (English)
HUANG Wei-Li; CAI Jian-Le
2011-01-01
Conformal invariance and conserved quantities for a higher-order Lagrange system by Lie point transformation of groups are studied. The differential equation of motion for the higher-order Lagrange system is introduced. The definition of conformal invariance for the system together with its determining equations and conformal factor are provided. The necessary and sufficient condition that the system's conformal invariance would be Lie symmetry by the infinitesimal one-parameter point transformation group is deduced. The conserved quantity of the system is derived using the structural equation satisfied by the gauge function. An example of a higher-order mechanical system is offered to illustrate the application of the result.%Conformal invariance and conserved quantities for a higher-order Lagrange system by Lie point transformation of groups are studied.The differential equation of motion for the higher-order Lagrange system is introduced.The definition of conformal invariance for the system together with its determining equations and conformal factor are provided.The necessary and sufficient condition that the system's conformal invariance would be Lie symmetry by the infinitesimal one-parameter point transformation group is deduced.The conserved quantity of the system is derived using the structural equation satisfied by the gauge function.An example of a higher-order mechanical system is offered to illustrate the application of the result.Since the Noether theorem was published in 1918,[1] the symmetry and conserved quantity for a dynamical system play important roles in the fields of modern science and technology,and some important results have been gained so far.[2-21] Conformal invariance is a modern method for finding conserved quantities.In 1997,Galiullin etal.[22] studied conformal invariance of Birkhoff systems under special infinitesimal transformations.In recent years,we have discussed the conformal invariance of Lie symmetry for Lagrange systems
Visualization of chromatin folding patterns in chicken erythrocytes by atomic force microscopy （AFM）
Institute of Scientific and Technical Information of China (English)
QIANRUOLAN; ZHENGXIALIU; 等
1997-01-01
The organization of the higher order structure of chromatin in chicken erythrocytes has been examined with tapping-mode scanning force microscopy under conditions close to their native envirinment.Reproducible highresolution AFM images of chromatin compaction at several levels can be demonstrated.An extended beads-on-astring (width of - 15-20nm,height of - 2-3nm for each individual nucleosome) can be consistently observed.Furthermore,superbeade (width of - 40nm,height of - 7nm) are demonstrated.Visualization of the solenoid conformation at the level of 30nm chromatin fiber is attained either by using AFM or by using electron microscopy.In addition,tightly coiled chromatin fibers (- 50-60nm and - 90-110nm) can be revealed.Our data suggest that the chromatin in the interphase nucleus of chicken erythrocyte represents a high-order conformation and AFM provides useful high-resolution structural information concerning the folding pattern of interphase chromatin fibers.
Symbolic Reachability Analysis of Higher-Order Context-Free Processes
Bouajjani, Ahmed
2007-01-01
We consider the problem of symbolic reachability analysis of higher-order context-free processes. These models are generalizations of the context-free processes (also called BPA processes) where each process manipulates a data structure which can be seen as a nested stack of stacks. Our main result is that, for any higher-order context-free process, the set of all predecessors of a given regular set of configurations is regular and effectively constructible. This result generalizes the analogous result which is known for level 1 context-free processes. We show that this result holds also in the case of backward reachability analysis under a regular constraint on configurations. As a corollary, we obtain a symbolic model checking algorithm for the temporal logic E(U,X) with regular atomic predicates, i.e., the fragment of CTL restricted to the EU and EX modalities.
Robust rooftop extraction from visible band images using higher order CRF
Li, Er
2015-08-01
In this paper, we propose a robust framework for building extraction in visible band images. We first get an initial classification of the pixels based on an unsupervised presegmentation. Then, we develop a novel conditional random field (CRF) formulation to achieve accurate rooftops extraction, which incorporates pixel-level information and segment-level information for the identification of rooftops. Comparing with the commonly used CRF model, a higher order potential defined on segment is added in our model, by exploiting region consistency and shape feature at segment level. Our experiments show that the proposed higher order CRF model outperforms the state-of-the-art methods both at pixel and object levels on rooftops with complex structures and sizes in challenging environments. © 1980-2012 IEEE.
Nested Hoare Triples and Frame Rules for Higher-order Store
Schwinghammer, Jan; Reus, Bernhard; Yang, Hongseok
2011-01-01
Separation logic is a Hoare-style logic for reasoning about programs with heap-allocated mutable data structures. As a step toward extending separation logic to high-level languages with ML-style general (higher-order) storage, we investigate the compatibility of nested Hoare triples with several variations of higher-order frame rules. The interaction of nested triples and frame rules can be subtle, and the inclusion of certain frame rules is in fact unsound. A particular combination of rules can be shown consistent by means of a Kripke model where worlds live in a recursively defined ultrametric space. The resulting logic allows us to elegantly prove programs involving stored code. In particular, using recursively defined assertions, it leads to natural specifications and proofs of invariants required for dealing with recursion through the store.
Duan, Ming-Rui; Smerdon, Michael J
2014-03-21
Histone H3 acetylation is induced by UV damage in yeast and may play an important role in regulating the repair of UV photolesions in nucleosome-loaded genomic loci. However, it remains elusive how H3 acetylation facilitates repair. We generated a strongly positioned nucleosome containing homogeneously acetylated H3 at Lys-14 (H3K14ac) and investigated possible mechanisms by which H3K14 acetylation modulates repair. We show that H3K14ac does not alter nucleosome unfolding dynamics or enhance the repair of UV-induced cyclobutane pyrimidine dimers by UV photolyase. Importantly, however, nucleosomes with H3K14ac have a higher affinity for purified chromatin remodeling complex RSC (Remodels the Structure of Chromatin) and show greater cyclobutane pyrimidine dimer repair compared with unacetylated nucleosomes. Our study indicates that, by anchoring RSC, H3K14 acetylation plays an important role in the unfolding of strongly positioned nucleosomes during repair of UV damage.
Nguyen, Carvell T.; Gonzales, Felicidad A.; Jones, Peter A.
2001-01-01
Silencing of tumor-suppressor genes by hypermethylation of promoter CpG islands is well documented in human cancer and may be mediated by methyl-CpG-binding proteins, like MeCP2, that are associated in vivo with chromatin modifiers and transcriptional repressors. However, the exact dynamic between methylation and chromatin structure in the regulation of gene expression is not well understood. In this study, we have analyzed the methylation status and chromatin structure of three CpG islands in the p14(ARF)/p16(INK4A) locus in a series of normal and cancer cell lines using methylation-sensitive digestion, MspI accessibility in intact nuclei and chromatin immunoprecipitation (ChIP) assays. We demonstrate the existence of an altered chromatin structure associated with the silencing of tumor-suppressor genes in human cancer cell lines involving CpG island methylation, chromatin condensation, histone deacetylation and MeCP2 binding. The data showed that MeCP2 could bind to methylated CpG islands in both promoters and exons; MeCP2 does not interfere with transcription when bound at an exon, suggesting a more generalized role for the protein beyond transcriptional repression. In the absence of methylation, it is demonstrated that CpG islands located in promoters versus exons display marked differences in the levels of acetylation of associated histone H3, suggesting that chromatin remodeling can be achieved by methylation-independent processes and perhaps explaining why non-promoter CpG islands are more susceptible to de novo methylation than promoter islands. PMID:11713309
Higher-order adaptive finite-element methods for Kohn–Sham density functional theory
Energy Technology Data Exchange (ETDEWEB)
Motamarri, P. [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Nowak, M.R. [Department of Electrical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Leiter, K.; Knap, J. [U.S. Army Research Labs, Aberdeen Proving Ground, Aberdeen, MD 21001 (United States); Gavini, V., E-mail: vikramg@umich.edu [Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)
2013-11-15
We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposed solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688
Higher-Order Theory for Functionally Graded Materials
Aboudi, J.; Pindera, M. J.; Arnold, Steven M.
2001-01-01
Functionally graded materials (FGM's) are a new generation of engineered materials wherein the microstructural details are spatially varied through nonuniform distribution of the reinforcement phase(s). Engineers accomplish this by using reinforcements with different properties, sizes, and shapes, as well as by interchanging the roles of the reinforcement and matrix phases in a continuous manner (ref. 1). The result is a microstructure that produces continuously or discretely changing thermal and mechanical properties at the macroscopic or continuum scale. This new concept of engineering the material's microstructure marks the beginning of a revolution both in the materials science and mechanics of materials areas since it allows one, for the first time, to fully integrate the material and structural considerations into the final design of structural components. Functionally graded materials are ideal candidates for applications involving severe thermal gradients, ranging from thermal structures in advanced aircraft and aerospace engines to computer circuit boards. Owing to the many variables that control the design of functionally graded microstructures, full exploitation of the FGM's potential requires the development of appropriate modeling strategies for their response to combined thermomechanical loads. Previously, most computational strategies for the response of FGM's did not explicitly couple the material's heterogeneous microstructure with the structural global analysis. Rather, local effective or macroscopic properties at a given point within the FGM were first obtained through homogenization based on a chosen micromechanics scheme and then subsequently used in a global thermomechanical analysis.
Igaz, Nóra; Kovács, Dávid; Rázga, Zsolt; Kónya, Zoltán; Boros, Imre M; Kiricsi, Mónika
2016-10-01
Histone deacetylase (HDAC) inhibitors are considered as novel therapeutic agents inducing cell cycle arrest and apoptotic cell death in various cancer cells. Inhibition of deacetylase activity results in a relaxed chromatin structure thereby rendering the genetic material more vulnerable to DNA targeting agents that could be exploited by combinational cancer therapy. The unique potential of silver nanoparticles (AgNPs) in tumor therapy relies on the generation of reactive radicals which trigger oxidative stress, DNA damage and apoptosis in cancer cells. The revolutionary application of AgNPs as chemotherapeutical drugs seems very promising, nevertheless the exact molecular mechanisms of AgNP action in combination with other anti-cancer agents have yet to be elucidated in details before clinical administrations. As a step towards this we investigated the combinational effect of HDAC inhibition and AgNP administration in HeLa cervical cancer cells. We identified synergistic inhibition of cancer cell growth and migration upon combinational treatments. Here we report that the HDAC inhibitor Trichostatin A enhances the DNA targeting capacity and apoptosis inducing efficacy of AgNPs most probably due to its effect on chromatin condensation. These results point to the potential benefits of combinational application of HDAC inhibitors and AgNPs in novel cancer medication protocols. PMID:27434153
Using oocyte nuclei for studies on chromatin structure and gene expression.
Sommerville, John
2010-05-01
The giant nucleus of amphibian oocytes is generally referred to as the germinal vesicle (GV). Its size allows relatively easy manual isolation from the rest of the oocyte and also presents a large target in situ for microinjection of macromolecules including plasmid DNA, RNA species, antibodies and other proteins and even whole organelles, including somatic cell nuclei. Thus the use of GVs is excellent for two major types of study: the function of endogenous nuclear processes such as gene transcription, RNA processing and intra-nuclear dynamics; and the use of the nuclear components to effect processes such as chromatin assembly, expression of foreign genes and nucleocytoplasmic transport of injected biomolecules. This article outlines some basic techniques appropriate for GV studies, particularly the preparation of oocytes for microinjection and the isolation of germinal vesicles into an oil phase. As an aid to the targeting of the GV within the nucleus, descriptions are given of the use of oocytes from albino animals.
Higher-order chromatin domains link eQTLs with the expression of far-away genes
Duggal, Geet; Wang, Hao; Kingsford, Carl
2013-01-01
Distal expression quantitative trait loci (distal eQTLs) are genetic mutations that affect the expression of genes genomically far away. However, the mechanisms that cause a distal eQTL to modulate gene expression are not yet clear. Recent high-resolution chromosome conformation capture experiments along with a growing database of eQTLs provide an opportunity to understand the spatial mechanisms influencing distal eQTL associations on a genome-wide scale. We test the hypothesis that spatial p...
Higher-order probabilistic perceptrons as Bayesian inference engines
International Nuclear Information System (INIS)
This letter makes explicit a structural connection between the Bayes optimal classifier operating on K binary input variables and corresponding two-layer perceptron having normalized output activities and couplings from input to output units of all orders up to K. Given a large and unbiased training set and an effective learning algorithm, such a neural network should be able to learn the statistics of the classification problem and match the a posteriori probabilities given by the Bayes optimal classifier. (author). 18 refs
Higher order methods for convection-diffusion problems
Murphy, J. D.; Prenter, P. M.
This paper applies C1 cubic Hermite polynomials embedded in an orthogonal collocation scheme to the spatial discretization of the unsteady nonlinear Burgers equation as a model of the equations of fluid mechanics. The temporal discretization is carried out by means of either a noniterative finite difference or an iterative finite difference procedure. Results of this method are compared with those of a second-order finite difference scheme and a splined-cubic Taylor's series scheme. Stability limits are derived and the matrix structure of the several schemes are compared.
Impact of Chromatin on HIV Replication
Agosto, Luis M.; Matthew Gagne; Henderson, Andrew J.
2015-01-01
Chromatin influences Human Immunodeficiency Virus (HIV) integration and replication. This review highlights critical host factors that influence chromatin structure and organization and that also impact HIV integration, transcriptional regulation and latency. Furthermore, recent attempts to target chromatin associated factors to reduce the HIV proviral load are discussed.
From Second to Higher Order Tensors in Diffusion-MRI
Ghosh, Aurobrata; Deriche, Rachid
Diffusion MRI, which is sensitive to the Brownian motion of molecules, has become today an excellent medical tool for probing the tissue micro-structure of cerebral white matter in vivo and non-invasively. It makes it possible to reconstruct fiber pathways and segment major fiber bundles that reflect the structures in the brain which are not visible to other non-invasive imaging modalities. Since this is possible without operating on the subject, but by integrating partial information from Diffusion Weighted Images into a reconstructed ‘complete’ image of diffusion, Diffusion MRI opens a whole new domain of image processing. Here we shall explore the role that tensors play in the mathematical model. We shall primarily deal with Cartesian tensors and begin with 2nd order tensors, since these are at the core of Diffusion Tensor Imaging. We shall then explore higher and even ordered symmetric tensors, that can take into account more complex micro-geometries of biological tissues such as axonal crossings in the white matter.
Electroweak higher-order effects and theoretical uncertainties in deep-inelastic neutrino scattering
Diener, K P O; Hollik, W
2005-01-01
A previous calculation of electroweak O(alpha) corrections to deep-inelastic neutrino scattering, as e.g. measured by NuTeV and NOMAD, is supplemented by higher-order effects. In detail, we take into account universal two-loop effects from \\Delta\\alpha and \\Delta\\rho as well as higher-order final-state photon radiation off muons in the structure function approach. Moreover, we make use of the recently released O(alpha)-improved parton distributions MRST2004QED and identify the relevant QED factorization scheme, which is DIS like. As a technical byproduct, we describe slicing and subtraction techniques for an efficient calculation of a new type of real corrections that are induced by the generated photon distribution. A numerical discussion of the higher-order effects suggests that the remaining theoretical uncertainty from unknown electroweak corrections is dominated by non-universal two-loop effects and is of the order 0.0003 when translated into a shift in sin^2\\theta_W=1-MW^2/MZ^2. The O(alpha) corrections...
Higher-Order Gravitational Lensing Reconstruction using Feynman Diagrams
Jenkins, Elizabeth E; Waalewijn, Wouter J; Yadav, Amit P S
2014-01-01
We develop a method for calculating the correlation structure of the Cosmic Microwave Background (CMB) using Feynman diagrams, when the CMB has been modified by gravitational lensing, Faraday rotation, patchy reionization, or other distorting effects. This method is used to calculate the bias of the Hu-Okamoto quadratic estimator in reconstructing the lensing power spectrum up to O(\\phi^4) in the lensing potential $\\phi$. We consider both the diagonal noise TTTT, EBEB, etc. and, for the first time, the off-diagonal noise TTTE, TBEB, etc. The previously noted large O(\\phi^4) term in the second order noise is identified to come from a particular class of diagrams. It can be significantly reduced by a reorganization of the $\\phi$ expansion. These improved estimators have almost no bias for the off-diagonal case involving only one $B$ component of the CMB, such as EEEB.
Automated higher-order calculations: Status and prospects
Ossola, Giovanni
2015-01-01
In this presentation we review the current status in the automated evaluation of scattering amplitudes, with particular attention to the developments related with NLO calculations, which led to the construction of powerful multi-purpose computational tools. After a general overview, we will devote a short section to describe the GoSam framework for NLO calculations and its application to the production of Higgs boson plus jets. We will then briefly comment on the challenges presented by NNLO calculations, whose structure is considerably more complicated. Finally, we will describe some of the features of the integrand-reduction techniques beyond NLO, an alternative promising approach to multi-loop calculations which is currently under development.
Directory of Open Access Journals (Sweden)
Hua Wong
Full Text Available In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.
2012-01-01
Although it is well known that chromosomes are non-randomly organized during interphase, it is not completely clear whether higher-order chromatin structure is transmitted from mother to daughter cells. Therefore, we addressed the question of how chromatin is rearranged during interphase and whether heterochromatin pattern is transmitted after mitosis. We additionally tested the similarity of chromatin arrangement in sister interphase nuclei. We noticed a very active cell rotation during inte...
Chromatin Immunoprecipitation.
Wiehle, Laura; Breiling, Achim
2016-01-01
Chromatin immunoprecipitation (ChIP) is a valuable method to investigate protein-DNA interactions in vivo. Since its discovery it has been indispensable to identify binding sites and patterns of a variety of DNA-interacting proteins, such as transcription factors and regulators, modified histones, and epigenetic modifiers. The Polycomb repressors were the first proteins that have been mapped using this technique, which provided the mechanistic basis for the understanding of their biological function. Cross-linked (XChIP) or native (NChIP) chromatin from tissues or cultured cells is fragmented and the protein of interest is immunoprecipitated using a specific antibody. The co-precipitated DNA is then purified and subjected to analysis by region-specific PCR, DNA microarray (ChIP-on-chip), or next-generation sequencing (ChIP-seq). The assay can therefore produce information about the localization of the analyzed protein at specific candidate loci or throughout the entire genome. In this chapter, we provide a detailed protocol of the basic standard ChIP assay and some remarks about variations. PMID:27659971
Directory of Open Access Journals (Sweden)
Bruno Mantel
Full Text Available Body movement influences the structure of multiple forms of ambient energy, including optics and gravito-inertial force. Some researchers have argued that egocentric distance is derived from inferential integration of visual and non-visual stimulation. We suggest that accurate information about egocentric distance exists in perceptual stimulation as higher-order patterns that extend across optics and inertia. We formalize a pattern that specifies the egocentric distance of a stationary object across higher-order relations between optics and inertia. This higher-order parameter is created by self-generated movement of the perceiver in inertial space relative to the illuminated environment. For this reason, we placed minimal restrictions on the exploratory movements of our participants. We asked whether humans can detect and use the information available in this higher-order pattern. Participants judged whether a virtual object was within reach. We manipulated relations between body movement and the ambient structure of optics and inertia. Judgments were precise and accurate when the higher-order optical-inertial parameter was available. When only optic flow was available, judgments were poor. Our results reveal that participants perceived egocentric distance from the higher-order, optical-inertial consequences of their own exploratory activity. Analysis of participants' movement trajectories revealed that self-selected movements were complex, and tended to optimize availability of the optical-inertial pattern that specifies egocentric distance. We argue that accurate information about egocentric distance exists in higher-order patterns of ambient energy, that self-generated movement can generate these higher-order patterns, and that these patterns can be detected and used to support perception of egocentric distance that is precise and accurate.
Institute of Scientific and Technical Information of China (English)
Li Xi-Zeng; Su Bao-Xia; Chai Lu
2005-01-01
It is found that the field of the combined mode of the probe wave and the phase conjugate wave in the process of non-degenerate four-wave mixing exhibits higher-order squeezing to all even orders. The higher-order squeezed parameter and squeezed limit due to the modulation frequency are investigated. The smaller the modulation frequency is, the stronger the degree of higher-order squeezing becomes. Furthermore, the higher-order uncertainty relations in the process of non-degenerate four-wave mixing are presented for the first time. The product of higher-order noise moments is related to even order number N and the length L of the medium.
International Nuclear Information System (INIS)
The global safety of nuclear power plants is greatly affected by the resistance of internal and external plate and shell-type structures to dynamic loads caused by accidentally generated flying objects, such as parts of failed rotating equipment or ruptured piping, tornado missiles or impacting aircraft engines. This paper describes the development of a linear and nonlinear laminated plate dynamics computer program based on explicit time integration with a special mass matrix diagonalization scheme using a higher-order theory and Co finite elements. A Lagrangian approach is adopted for the geometric nonlinear analysis and the stress and strain descriptions used are those due to Piola-Kirchhoff and Green respectively
Propagation of femtosecond terawatt laser pulses in N2 gas including higher-order Kerr effects
Directory of Open Access Journals (Sweden)
T. W. Huang
2012-12-01
Full Text Available Propagation characteristic of femtosecond terawatt laser pulses in N2 gas with higher-order Kerr effect (HOKE is investigated. Theoretical analysis shows that HOKE acting as Hamiltonian perturbation can destroy the coherent structure of a laser field and result in the appearance of incoherent patterns. Numerical simulations show that in this case two different types of complex structures can appear. It is found that the high-order focusing terms in HOKE can cause continuous phase shift and off-axis evolution of the laser fields when irregular homoclinic orbit crossings of the field in phase space take place. As the laser propagates, small-scale spatial structures rapidly appear and the evolution of the laser field becomes chaotic. The two complex patterns can switch between each other quasi-periodically. Numerical results show that the two complex patterns are associated with the stochastic evolution of the energy contained in the higher-order shorter-wavelength Fourier modes. Such complex patterns, associated with small-scale filaments, may be typical for laser propagation in a HOKE medium.
Ma, Zhipeng; Park, Seongsu; Yamashita, Naoki; Kawai, Kentaro; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu
2016-06-01
DNA origami provides a versatile method for the construction of nanostructures with defined shape, size and other properties; such nanostructures may enable a hierarchical assembly of large scale architecture for the placement of other nanomaterials with atomic precision. However, the effective use of these higher order structures as functional components depends on knowledge of their assembly behavior and mechanical properties. This paper demonstrates construction of higher order DNA origami arrays with controlled orientations based on the formation of two types of DNA junctions: anti-parallel and parallel double crossovers. A two-step assembly process, in which preformed rectangular DNA origami monomer structures themselves undergo further self-assembly to form numerically unlimited arrays, was investigated to reveal the influences of assembly parameters. AFM observations showed that when parallel double crossover DNA junctions are used, the assembly of DNA origami arrays occurs with fewer monomers than for structures formed using anti-parallel double crossovers, given the same assembly parameters, indicating that the configuration of parallel double crossovers is not energetically preferred. However, the direct measurement by AFM force-controlled mapping shows that both DNA junctions of anti-parallel and parallel double crossovers have homogeneous mechanical stability with any part of DNA origami.
On the Identities of Symmetry for the -Euler Polynomials of Higher Order
Directory of Open Access Journals (Sweden)
Park KyoungHo
2009-01-01
Full Text Available The main purpose of this paper is to investigate several further interesting properties of symmetry for the multivariate -adic fermionic integral on . From these symmetries, we can derive some recurrence identities for the -Euler polynomials of higher order, which are closely related to the Frobenius-Euler polynomials of higher order. By using our identities of symmetry for the -Euler polynomials of higher order, we can obtain many identities related to the Frobenius-Euler polynomials of higher order.
Generation of higher order Gauss-Laguerre modes in single-pass 2nd harmonic generation
DEFF Research Database (Denmark)
Buchhave, Preben; Tidemand-Lichtenberg, Peter
2008-01-01
We present a realistic method for dynamic simulation of the development of higher order modes in second harmonic generation. The deformation of the wave fronts due to the nonlinear interaction is expressed by expansion in higher order Gauss-Laguerre modes.......We present a realistic method for dynamic simulation of the development of higher order modes in second harmonic generation. The deformation of the wave fronts due to the nonlinear interaction is expressed by expansion in higher order Gauss-Laguerre modes....
Analysis of Scattering by Inhomogeneous Dielectric Objects Using Higher-Order Hierarchical MoM
Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter; Breinbjerg, Olav
2003-01-01
An efficient technique for the analysis of electromagnetic scattering by arbitrary shaped inhomogeneous dielectric objects is presented. The technique is based on a higher-order method of moments (MoM) solution of the volume integral equation. This higher-order MoM solution comprises recently developed higher-order hierarchical Legendre basis functions for expansion of the electric flux density and higher-order geometry modeling. An unstructured mesh composed by trilinear (8-node) and/or curv...
Higher order hierarchical discretization scheme for surface integral equations for layered media
DEFF Research Database (Denmark)
Jørgensen, Erik; Kim, Oleksiy S.; Meincke, Peter;
2004-01-01
equation. This higher order MoM solution comprises higher order curved patches for the geometry modeling and higher order hierarchical basis functions for expansion of the electric surface current density. Due to the hierarchical property of the basis functions, the order of the expansion can be selected...
Energy Technology Data Exchange (ETDEWEB)
Aoki, Ryuta; Inui, Masafumi; Hayashi, Yohei; Sedohara, Ayako [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Okabayashi, Koji [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); ICORP Organ Regeneration Project, Japan Science and Technology Agency (JST), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Ohnuma, Kiyoshi, E-mail: kohnuma@vos.nagaokaut.ac.jp [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Murata, Masayuki [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Asashima, Makoto, E-mail: asashi@bio.c.u-tokyo.ac.jp [Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); ICORP Organ Regeneration Project, Japan Science and Technology Agency (JST), 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902 (Japan); Organ Development Research Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 4, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562 (Japan)
2010-09-17
Research highlights: {yields} An in vitro reconstitution system was established with isolated nuclei and cytoplasm. {yields} Chromatin fluidities were measured in the system using FRAP. {yields} Chromatin fluidities were higher in the cytoplasm of earlier-stage embryos. {yields} Chromatin fluidities were higher in the earlier-stage nuclei with egg-extract. {yields} Chromatin fluidity may decrease during embryonic development. -- Abstract: Chromatin fluidity, which is one of the indicators of higher-order structures in chromatin, is associated with cell differentiation. However, little is known about the relationships between chromatin fluidity and cell differentiation status in embryonic development. We established an in vitro reconstitution system that uses isolated nuclei and cytoplasmic extracts of Xenopus embryos and a fluorescence recovery after photobleaching assay to measure the fluidities of heterochromatin protein 1 (HP1) and histone H1 during development. The HP1 and H1 fluidities of nuclei isolated from the tailbuds of early tadpole stage (stage 32) embryos in the cytoplasmic extracts of eggs and of late blastula stage (stage 9) embryos were higher than those in the cytoplasmic extracts of mid-neurula stage (stage 15) embryos. The HP1 fluidities of nuclei isolated from animal cap cells of early gastrula stage (stage 10) embryos and from the neural plates of neural stage (stage 20) embryos were higher than those isolated from the tailbuds of stage 32 embryos in egg extracts, whereas the HP1 fluidities of these nuclei were the same in the cytoplasmic extracts of stage 15 embryos. These results suggest that chromatin fluidity is dependent upon both cytoplasmic and nuclear factors and decreases during development.
International Nuclear Information System (INIS)
Research highlights: → An in vitro reconstitution system was established with isolated nuclei and cytoplasm. → Chromatin fluidities were measured in the system using FRAP. → Chromatin fluidities were higher in the cytoplasm of earlier-stage embryos. → Chromatin fluidities were higher in the earlier-stage nuclei with egg-extract. → Chromatin fluidity may decrease during embryonic development. -- Abstract: Chromatin fluidity, which is one of the indicators of higher-order structures in chromatin, is associated with cell differentiation. However, little is known about the relationships between chromatin fluidity and cell differentiation status in embryonic development. We established an in vitro reconstitution system that uses isolated nuclei and cytoplasmic extracts of Xenopus embryos and a fluorescence recovery after photobleaching assay to measure the fluidities of heterochromatin protein 1 (HP1) and histone H1 during development. The HP1 and H1 fluidities of nuclei isolated from the tailbuds of early tadpole stage (stage 32) embryos in the cytoplasmic extracts of eggs and of late blastula stage (stage 9) embryos were higher than those in the cytoplasmic extracts of mid-neurula stage (stage 15) embryos. The HP1 fluidities of nuclei isolated from animal cap cells of early gastrula stage (stage 10) embryos and from the neural plates of neural stage (stage 20) embryos were higher than those isolated from the tailbuds of stage 32 embryos in egg extracts, whereas the HP1 fluidities of these nuclei were the same in the cytoplasmic extracts of stage 15 embryos. These results suggest that chromatin fluidity is dependent upon both cytoplasmic and nuclear factors and decreases during development.
Venkatesh, Priyanka; Panyutin, Irina V; Remeeva, Evgenia; Neumann, Ronald D; Panyutin, Igor G
2016-01-02
Chromatin structure affects the extent of DNA damage and repair. Thus, it has been shown that heterochromatin is more protective against DNA double strand breaks (DSB) formation by ionizing radiation (IR); and that DNA DSB repair may proceed differently in hetero- and euchromatin regions. Human embryonic stem cells (hESC) have a more open chromatin structure than differentiated cells. Here, we study the effect of chromatin structure in hESC on initial DSB formation and subsequent DSB repair. DSB were scored by comet assay; and DSB repair was assessed by repair foci formation via 53BP1 antibody staining. We found that in hESC, heterochromatin is confined to distinct regions, while in differentiated cells it is distributed more evenly within the nuclei. The same dose of ionizing radiation produced considerably more DSB in hESC than in differentiated derivatives, normal human fibroblasts; and one cancer cell line. At the same time, the number of DNA repair foci were not statistically different among these cells. We showed that in hESC, DNA repair foci localized almost exclusively outside the heterochromatin regions. We also noticed that exposure to ionizing radiation resulted in an increase in heterochromatin marker H3K9me3 in cancer HT1080 cells, and to a lesser extent in IMR90 normal fibroblasts, but not in hESCs. These results demonstrate the importance of chromatin conformation for DNA protection and DNA damage repair; and indicate the difference of these processes in hESC.
Higher-order Convergence Statistics for Three-dimensional Weak Gravitational Lensing
Munshi, Dipak; Coles, Peter
2010-01-01
Weak gravitational lensing on a cosmological scales can provide strong constraints both on the nature of dark matter and the dark energy equation of state. Most current weak lensing studies are restricted to (two-dimensional) projections, but tomographic studies with photometric redshifts have started, and future surveys offer the possibility of probing the evolution of structure with redshift. In future we will be able to probe the growth of structure in 3D and put tighter constraints on cosmological models than can be achieved by the use of galaxy redshift surveys alone. Earlier studies in this direction focused mainly on evolution of the 3D power spectrum, but extension to higher-order statistics can lift degeneracies as well as providing information on primordial non-gaussianity. We present analytical results for specific higher-order descriptors, the bispectrum and trispectrum, as well as collapsed multi-point statistics derived from them, i.e. cumulant correlators. We also compute quantities we call the...
Institute of Scientific and Technical Information of China (English)
张凯; 邓子辰; 王博
2013-01-01
A metallic cylindrical lattice tube under internal pressure was analyzed by using the HODF theory .The response of the structure was obtained and compared with that obtained by using the FEM analysis .By using the homogenization method , three cylindrical lattice tubs , whose lattice types were Triangle , Square, and Kagome re-spectively , under internal pressure were homogenized to be orthotropic material and calculated by HODF theory . The HODF theoretical results and the FEM results were respectively obtained and their comparisons show that the differences are very small .The radial displacement and axial displacement obtained with HODF theory are nearly the same as the respective displacements obtained with FEM .The errors in radial stress , hoop stress and radial strain are relatively small .The ratios of the displacements obtained respectively with HODF theory and FEM are calculated and the patterns of these respective ratios are nearly the same .The results of Triangle and Kagome are better than the results of Square .The comparison and analysis of calculated results confirm preliminarily that the higher-order displacement theory can be used to calculate the correct responses of the metallic cylindrical lattice tube under internal pressure .%基于高阶位移场理论研究了简支条件棱镜型圆柱壳体在内压力作用下的结构响应。首先，建立承受内压圆柱壳体的平衡方程，计算在该载荷作用下的各项同性材料的响应，与弹性力学理论解进行对比，验证所得平衡方程的正确性。采用均匀化方法，将正方形，三角形和Kagome 3种多孔金属圆柱壳体等效为正交各向异性的材料，计算了在内压下的结构响应，并与有限元计算结果进行对比，结果表明文中方法所得结果与有限元的结果非常接近，计算得到的径向位移和轴向应变与有限元的计算基本相同，径向应力，环向应力和径向应变等结
Chobanyan, E.; Ilić, M. M.; Notaroš, B. M.
2015-05-01
A novel double-higher-order entire-domain volume integral equation (VIE) technique for efficient analysis of electromagnetic structures with continuously inhomogeneous dielectric materials is presented. The technique takes advantage of large curved hexahedral discretization elements—enabled by double-higher-order modeling (higher-order modeling of both the geometry and the current)—in applications involving highly inhomogeneous dielectric bodies. Lagrange-type modeling of an arbitrary continuous variation of the equivalent complex permittivity of the dielectric throughout each VIE geometrical element is implemented, in place of piecewise homogeneous approximate models of the inhomogeneous structures. The technique combines the features of the previous double-higher-order piecewise homogeneous VIE method and continuously inhomogeneous finite element method (FEM). This appears to be the first implementation and demonstration of a VIE method with double-higher-order discretization elements and conformal modeling of inhomogeneous dielectric materials embedded within elements that are also higher (arbitrary) order (with arbitrary material-representation orders within each curved and large VIE element). The new technique is validated and evaluated by comparisons with a continuously inhomogeneous double-higher-order FEM technique, a piecewise homogeneous version of the double-higher-order VIE technique, and a commercial piecewise homogeneous FEM code. The examples include two real-world applications involving continuously inhomogeneous permittivity profiles: scattering from an egg-shaped melting hailstone and near-field analysis of a Luneburg lens, illuminated by a corrugated horn antenna. The results show that the new technique is more efficient and ensures considerable reductions in the number of unknowns and computational time when compared to the three alternative approaches.
Higher-Order Beta Matching with Solutions in Long Beta-Eta Normal Form
DEFF Research Database (Denmark)
Støvring, Kristian
2006-01-01
Higher-order matching is a special case of unification of simply-typed lambda-terms: in a matching equation, one of the two sides contains no unification variables. Loader has recently shown that higher-order matching up to beta equivalence is undecidable, but decidability of higher-order matching...... up to beta-eta equivalence is a long-standing open problem.We show that higher-order matching up to beta-eta equivalence is decidable if and only if a restricted form of higher-order matching up to beta equivalence is decidable: the restriction is that solutions must be in long beta-eta normal form....
Higher Order Moment Spectra Time-Frequency Analysis of the Geophysical Signal
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
On the basis of an introduction of the Wigner Higher-Order spectra(WHOS) and a general class of time-frequency higher-order moment spectra ,the geophysical signal was analyzed using the higher order time-frequency distributions(TFD). Simulation results obtained in this paper show that the higher-order TFD (Wigner Bispectrum,Wigner Trispectrum and Choi-Williams Trispectrum) have much better Time-Frequency Concentration than the second-order TFD ,and the reduced interference higher-order TFD such as CWT can effectively reduce the cross-term in multicomponent signals and simultaneously obtain high time-frequency concentration.
Brain Function and Chromatin Plasticity
Dulac, Catherine
2010-01-01
The characteristics of epigenetic control, including the potential for long-lasting, stable effects on gene expression that outlive an initial transient signal, could be of singular importance for post-mitotic neurons, which are subject to changes with short- to long-lasting influence on their activity and connectivity. Persistent changes in chromatin structure are thought to contribute to mechanisms of epigenetic inheritance. Recent advances in chromatin biology offer new avenues to investig...
Kim, Kihoon; Kim, AeRi
2010-09-01
Chromatin structure is modulated during transcriptional activation. The changes include the association of transcriptional activators, formation of hypersensitive sites and covalent modifications of histones. To understand the order of the various changes accompanying transcriptional activation, we analyzed the mouse beta globin gene, which is transcriptionally inducible in erythroid MEL cells over a time course of HMBA treatment. Transcription of the globin genes requires the locus control region (LCR) consisting of several hypersensitive sites (HSs). Erythroid specific transcriptional activators such as NF-E2, GATA-1, TAL1 and EKLF were associated with the LCR in the uninduced state before transcriptional activation. The HSs of the LCR were formed in this state as revealed by high sensitivity to DNase I and MNase attack. However the binding of transcriptional activators and the depletion of histones were observed in the promoter of the beta globin gene only after transcriptional activation. In addition, various covalent histone modifications were sequentially detected in lysine residues of histone H3 during the activation. Acetylation of K9, K36 and K27 was notable in both LCR HSs and gene after induction but before transcriptional initiation. Inactive histone marks such as K9me2, K36me2 and K27me2 were removed coincident with transcriptional initiation in the gene region. Taken together, these results indicate that LCR has a substantially active structure in the uninduced state while transcriptional activation serially adds active marks, including histone modifications, and removes inactive marks in the target gene of the LCR.
International Nuclear Information System (INIS)
In this study, we demonstrate analytically and experimentally the excitations of the higher order modes of vibrations in electrostatically actuated clamped–clamped microbeam resonators. The concept is based on using partial electrodes with shapes that induce strong excitation of the mode of interest. The devices are fabricated using polyimide as a structural layer coated with nickel from the top and chrome and gold layers from the bottom. Experimentally, frequency sweeps with different electro-dynamical loading conditions are shown to demonstrate the excitation of the higher order modes of vibration. Using a half electrode, the second mode is excited with high amplitude of vibration compared with almost zero response using the full electrode. Also, using a two-third electrode configuration is shown to amplify the third mode resonance amplitude compared with the full electrode under the same electrical loading conditions. An analytical model is developed based on the Euler–Bernollui beam model and the Galerkin method to simulate the device response. Good agreement between the simulation results and the experimental data is reported. (paper)
Higher-order exchange interactions leading to metamagnetism in FeRh
Barker, Joseph; Chantrell, Roy W.
2015-09-01
The origin of the metamagnetic antiferromagnetic-ferromagnetic phase transition of FeRh is a subject of debate. Competing explanations invoke magnetovolume effects or a purely thermodynamic transition within the spin system. It is experimentally difficult to observe the changes in the magnetic system and the lattice simultaneously, leading to conflicting evidence over which mechanism causes the phase transition. A noncollinear electronic structure study by Mryasov [Phase Transitions 78, 197 (2005), 10.1080/01411590412331316591] showed that nonlinear behavior of the Rh moment leads to higher-order exchange terms in FeRh. Using atomistic spin dynamics, we show that the phase transition can occur due to the competition between bilinear and the higher-order four spin exchange terms in an effective spin Hamiltonian. The phase transition we see is of first order and shows thermal hysteresis in agreement with experimental observations. Simulating subpicosecond laser heating, we show an agreement with pump-probe experiments with a ferromagnetic response on a picosecond time scale.
Improvements to local projective noise reduction through higher order and multiscale refinements
Moore, Jack Murdoch; Small, Michael; Karrech, Ali
2015-06-01
The broad spectrum characteristic of signals from nonlinear systems obstructs noise reduction techniques developed for linear systems. Local projection was developed to reduce noise while preserving nonlinear deterministic structures, and a second order refinement to local projection which was proposed ten years ago does so particularly effectively. It involves adjusting the origin of the projection subspace to better accommodate the geometry of the attractor. This paper describes an analytic motivation for the enhancement from which follows further higher order and multiple scale refinements. However, the established enhancement is frequently as or more effective than the new filters arising from solely geometric considerations. Investigation of the way that measurement errors reinforce or cancel throughout the refined local projection procedure explains the special efficacy of the existing enhancement, and leads to a new second order refinement offering widespread gains. Different local projective filters are found to be best suited to different noise levels. At low noise levels, the optimal order increases as noise increases. At intermediate levels second order tends to be optimal, while at high noise levels prototypical local projection is most effective. The new higher order filters perform better relative to established filters for longer signals or signals corresponding to higher dimensional attractors.
Cross-ratio Identities and Higher-order Poles of CHY-integrand
Cardona, Carlos; Gomez, Humberto; Huang, Rijun
2016-01-01
The evaluation of generic Cachazo-He-Yuan(CHY)-integrands is a big challenge and efficient computational methods are in demand for practical evaluation. In this paper, we propose a systematic decomposition algorithm by using cross-ratio identities, which provides an analytic and easy to implement method for the evaluation of any CHY-integrand. This algorithm aims to decompose a given CHY-integrand containing higher-order poles as a linear combination of CHY-integrands with only simple poles in a finite number of steps, which ultimately can be trivially evaluated by integration rules of simple poles. To make the method even more efficient for CHY-integrands with large number of particles and complicated higher-order pole structures, we combine the $\\Lambda$-algorithm and the cross-ratio identities, and as a by-product it provides us a way to deal with CHY-integrands where the $\\Lambda$-algorithm was not applicable in its original formulation.
Structural changes in single chromatin fibers induced by tension and torsion
Meng, He
2014-01-01
Since the discovery of the right-handed helical structure of DNA, 61 years have passed. The DNA molecule, which encodes genetic information, is also found twisted into coils. This extra twist of the helical structure, called supercoiling, plays important roles in both DNA compaction and gene regul
Two-photon or higher-order absorbing optical materials and methods of use
Marder, Seth (Inventor); Perry, Joseph (Inventor)
2012-01-01
Compositions capable of simultaneous two-photon absorption and higher order absorptivities are provided. Compounds having a donor-pi-donor or acceptor-pi-acceptor structure are of particular interest, where the donor is an electron donating group, acceptor is an electron accepting group, and pi is a pi bridge linking the donor and/or acceptor groups. The pi bridge may additionally be substituted with electron donating or withdrawing groups to alter the absorptive wavelength of the structure. Also disclosed are methods of generating an excited state of such compounds through optical stimulation with light using simultaneous absorption of photons of energies individually insufficient to achieve an excited state of the compound, but capable of doing so upon simultaneous absorption of two or more such photons. Applications employing such methods are also provided, including controlled polymerization achieved through focusing of the light source(s) used.
Higher order modes in superconducting radio frequency resonators for energy recovery linacs
International Nuclear Information System (INIS)
The main scope of this work is the automation of the extraction procedure of the external quality factors of Higher Order Modes (HOMs) in Superconducting Radio Frequency (SRF) cavities. The HOMs are generated by charged particle beams traveling through a SRF cavity at the speed of light. The HOMs decay very slowly, depending on localization inside the structure and cell-to-cell coupling, and may influence succeeding charged particle bunches. Thus it is important, at the SRF cavity design optimization stage, to calculate the external quality factors (Qext) of HOMs. Traveling Poles Elimination (TPE) scheme was used to automatically extract Qext from the transmission spectra and careful eigenmode analysis of the SC cavity was performed to confirm TPE results. The eigenmode analysis also delivers important information about band structure, cell-to-cell coupling of HOMs and allows rapid identification of modes that could interact with the charged particle bunches.
Kruithof, Maarten Christiaan
2009-01-01
Animals and plants are build from a large number of cells. These cells continuously respond to signals from outside and inside the cell by producing various kinds of proteins. The blueprints of these proteins are stored in genes. The genes, in cells with a nucleus, are carried in chromosomes: threadlike structures in the nucleus of a cell that become visible when the cell, upon dividing, condenses these structures. Chromosomes consist of roughly two parts: proteins, that take care of the cond...
Single Molecule Studies of Chromatin
Energy Technology Data Exchange (ETDEWEB)
Jeans, C; Thelen, M P; Noy, A
2006-02-06
In eukaryotic cells, DNA is packaged as chromatin, a highly ordered structure formed through the wrapping of the DNA around histone proteins, and further packed through interactions with a number of other proteins. In order for processes such as DNA replication, DNA repair, and transcription to occur, the structure of chromatin must be remodeled such that the necessary enzymes can access the DNA. A number of remodeling enzymes have been described, but our understanding of the remodeling process is hindered by a lack of knowledge of the fine structure of chromatin, and how this structure is modulated in the living cell. We have carried out single molecule experiments using atomic force microscopy (AFM) to study the packaging arrangements in chromatin from a variety of cell types. Comparison of the structures observed reveals differences which can be explained in terms of the cell type and its transcriptional activity. During the course of this project, sample preparation and AFM techniques were developed and optimized. Several opportunities for follow-up work are outlined which could provide further insight into the dynamic structural rearrangements of chromatin.
Chinone, N.; Yamasue, K.; Hiranaga, Y.; Honda, K.; Cho, Y.
2012-11-01
Scanning nonlinear dielectric microscopy (SNDM) can be used to visualize polarization distributions in ferroelectric materials and dopant profiles in semiconductor devices. Without using a special sharp tip, we achieved an improved lateral resolution in SNDM through the measurement of super-higher-order nonlinearity up to the fourth order. We observed a multidomain single crystal congruent LiTaO3 (CLT) sample, and a cross section of a metal-oxide-semiconductor (MOS) field-effect-transistor (FET). The imaged domain boundaries of the CLT were narrower in the super-higher-order images than in the conventional image. Compared to the conventional method, the super-higher-order method resolved the more detailed structure of the MOSFET.
DEFF Research Database (Denmark)
Ramsay, Jacob Søndergaard; Dupont, Sune Vestergaard Lund; Johansen, Mikkel Willum;
2013-01-01
Using femtosecond upconversion we investigate the time and wavelength structure of infrared supercontinuum generation. It is shown that radiation is scattered into higher order spatial modes (HOMs) when generating a supercontinuum using fibers that are not single-moded, such as a step-index ZBLAN...... not include scattering into HOMs, and including this provides an extra degree of freedom for tailoring supercontinuum sources....
Directory of Open Access Journals (Sweden)
Wang QL
2009-01-01
Full Text Available A new notion of higher-order weakly generalized adjacent epiderivative for a set-valued map is introduced. By virtue of the epiderivative and weak minimality, a higher-order Mond-Weir type dual problem and a higher-order Wolfe type dual problem are introduced for a constrained set-valued optimization problem, respectively. Then, corresponding weak duality, strong duality, and converse duality theorems are established.
Mathematics Teachers’ Interpretation of Higher-Order Thinking in Bloom’s Taxonomy
Tony Thompson
2008-01-01
This study investigated mathematics teachers’ interpretation of higher-order thinking in Bloom’s Taxonomy. Thirty-two high school mathematics teachers from the southeast U.S. were asked to (a) define lower- and higher-order thinking, (b) identify which thinking skills in Bloom’s Taxonomy represented lower- and higher-order thinking, and (c) create an Algebra I final exam item representative of each thinking skill. Results indicate that mathematics teachers have difficulty interpreting the thi...
Analysis of Buried Dielectric Objects Using Higher-Order MoM for Volume Integral Equations
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Meincke, Peter; Breinbjerg, Olav
2004-01-01
A higher-order method of moments (MoM) is applied to solve a volume integral equation for dielectric objects in layered media. In comparison to low-order methods, the higher-order MoM, which is based on higher-order hierarchical Legendre vector basis functions and curvilinear hexahedral elements......, requires considerably less number of unknowns and multilayer Green's function calculations for an accurate solution....
Mimasu, Ken; Sanz, Verónica; Williams, Ciaran
2016-08-01
We present predictions for the associated production of a Higgs boson at NLO+PS accuracy, including the effect of anomalous interactions between the Higgs and gauge bosons. We present our results in different frameworks, one in which the interaction vertex between the Higgs boson and Standard Model W and Z bosons is parameterized in terms of general Lorentz structures, and one in which Electroweak symmetry breaking is manifestly linear and the resulting operators arise through a six-dimensional effective field theory framework. We present analytic calculations of the Standard Model and Beyond the Standard Model contributions, and discuss the phenomenological impact of the higher order pieces. Our results are implemented in the NLO Monte Carlo program MCFM, and interfaced to shower Monte Carlos through the Powheg box framework.
Higher order Godunov methods for general systems of hyperbolic conservation laws
Energy Technology Data Exchange (ETDEWEB)
Bell, J. B.; Colella, P.; Trangenstein, J. A.
1989-06-01
We describe an extension of higher order Godunov methods to general systems of hyperbolic conservation laws. This extension allow the method to be applied to problems that are not strictly hyperbolic and exhibit local linear degeneracies in the wave fields. The method constructs an approximation of the Riemann problem from local wave information. A generalization of the Engquist--Osher flux for systems is then used to compute a numerical flux based on this approximation. This numerical flux replaces the Godunov numerical flux in the algorithm, thereby eliminating the need for a global Riemann problem solution. The additional modifications to the Godunov methodology that are needed to treat loss of strict hyperbolicity are described in detail. THe method is applied to some simple model problems for which the glocal analytic structure is known. The method is also applied to the black-oil model for multiphase flow in petroleum reservoirs. /copyright/ 1989 Academic Press, Inc.
Higher order Godunov methods for general systems of hyperbolic conservation laws
International Nuclear Information System (INIS)
We describe an extension of higher order Godunov methods to general systems of hyperbolic conservation laws. This extension allow the method to be applied to problems that are not strictly hyperbolic and exhibit local linear degeneracies in the wave fields. The method constructs an approximation of the Riemann problem from local wave information. A generalization of the Engquist--Osher flux for systems is then used to compute a numerical flux based on this approximation. This numerical flux replaces the Godunov numerical flux in the algorithm, thereby eliminating the need for a global Riemann problem solution. The additional modifications to the Godunov methodology that are needed to treat loss of strict hyperbolicity are described in detail. The method is applied to some simple model problems for which the glocal analytic structure is known. The method is also applied to the black-oil model for multiphase flow in petroleum reservoirs. copyright 1989 Academic Press, Inc
Double Quarter Wave Crab Cavity Field Profile Analysis and Higher Order Mode Characterization
Energy Technology Data Exchange (ETDEWEB)
Marques, Carlos [Brookhaven National Lab. (BNL), Upton, NY (United States). Accelerator R and D Div.; Stony Brook Univ., NY (United States). Physics and Astronomy Dept.; Xiao, B. P. [Brookhaven National Lab. (BNL), Upton, NY (United States). Accelerator R and D Div.; Belomestnykh, S. [Brookhaven National Lab. (BNL), Upton, NY (United States). Accelerator R and D Div.; Stony Brook Univ., NY (United States). Physics and Astronomy Dept.
2014-06-01
The Large Hadron Collider (LHC) is underway for a major upgrade to increase its luminosity by an order of magnitude beyond its original design specifications. This novel machine configuration known as the High Luminosity LHC (HL-LHC) will rely on various innovative technologies including very compact and ultra-precise superconducting crab cavities for beam rotation. A double quarter wave crab cavity (DQWCC) has been designed at Brookhaven National Laboratory for the HL-LHC. This cavity as well as the structural support components were fabricated and assembled at Niowave. The field profile of the crabbing mode for the DQWCC was investigated using a phase shift bead pulling technique and compared with simulated results to ensure proper operation or discover discrepancies from modeled results and/or variation in fabrication tolerances. Higher-Order Mode (HOM) characterization was also performed and correlated with simulations.
Chromatin remodelers and their roles in chromatin organization
Strålfors, Annelie
2012-01-01
The DNA in the eukaryotic nucleus is organized into a complex DNA-protein structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of 147 bp of DNA wrapped around a histone protein octamer. The nucleosomes form a “beads on a string” structure, which can be folded into higherorder structures that allow an extensive degree of DNA compaction. This compaction is so effective that 2 meters of DNA can fit into the human cell nucleus with a ...
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Meincke, Peter; Breinbjerg, Olav;
2007-01-01
applied to transform the VSIE into a system of linear equations. The higher-order MoM provides significant reduction in the number of unknowns in comparison with standard MoM formulations using low-order basis functions, such as RWG functions. Due to the orthogonal nature of the higher-order Legendre......The problem of electromagnetic scattering by composite metallic and dielectric objects is solved using the coupled volume-surface integral equation (VSIE). The method of moments (MoM) based on higher-order hierarchical Legendre basis functions and higher-order curvilinear geometrical elements is...
Gopalan, Sunita; Kasza, Aneta; Xu, Weili; Kiss, Daniel L.; Wilczynska, Katarzyna M.; Rydel, Russell E.; Kordula, Tomasz
2005-01-01
The distal serpin subcluster contains genes encoding α1-antichymotrypsin (ACT), protein C inhibitor (PCI), kallistatin (KAL), and the KAL-like protein that are expressed in hepatocytes but only the act gene is expressed in astrocytes. We show here that the tissue-specific expression of these genes associates with astrocyte- and hepatocyte-specific chromatin structures. In hepatocytes, we identified twelve DNase I-hypersenitive sites (DHS) that were distributed throughout the entire subcluster...
Indian Academy of Sciences (India)
Suman Guha; Sandeep Sangal; Sumit Basu
2015-06-01
In this paper we review developments in higher order strain gradient theories. Several variants of these theories have been proposed in order to explain the effects of size on plastic properties that are manifest in several experiments with micron sized metallic structures. It is generally appreciated that the size effect arises from the storage of geometrically necessary dislocations (GNDs) over and above the statistically stored dislocations (SSDs) required for homogeneous deformations. We review developments that show that the GNDs result from the non-homogeneous nature of the deformation field. Though the connection between GNDs and strain gradients are established in the framework of single crystal plasticity, generalisations to polycrystal plasticity has been made. Strain gradient plasticity inherently involves an intrinsic length scale. In our review, we show, through a few illustrative problems, that conventional plasticity solutions can always be reduced to a scale independent form. The same problems are solved with a simple higher order strain gradient formulation to capture the experimentally observed size effects. However, higher order theories need to be thermodynamically consistent. It has recently been shown that only a few of the existing theories pass this test. We review a few that do. Higher order theories require higher order boundary conditions that enable us to model effects of dislocation storage at impermeable boundaries. But these additional boundary conditions also lead to unique conceptual issues that are not encountered in conventional theories. We review attempts at resolving these issues pertaining to higher order boundary conditions. Finally, we review the future of such theories, their relevance and experimental validation.
Sondhiya, Deepak Kumar; Gwal, Ashok Kumar; Kumar, Sushil
2016-07-01
In recent years a number of scientists have reported correlations between observations of electromagnetic radiation and earthquakes. These observation of seismo-electromagnetic waves have been made both on the ground in the earthquake regions and by spacecraft over earthquake regions. In this work an attempt to develop a complex approach to the problem of searching for electromagnetic earthquake precursor signatures is made on the basis of DEMETER satellite observation.The main focus is concerned with the analysis of electric field data in Very Low Frequency (VLF) range using wavelet transform and higher order statistics. We observed electromagnetic turbulence in VLF range resulting from three earthquakes occurred at Keplulauan, Talud, Indonesia form 2009-2011.It is probably due to generation of electric field in a forthcoming earthquake's epicentral zone and penetrating in to the ionosphere. Large value of kurtosis shows the higher level of intermittence in the VLF signal before earthquake. It is possible to conjecture that the sources of this intermittence are the Coherent Structure (CS). For the better understanding of this behavior skewness parameter are used. The high energy at the large scales of the VLF turbulence due the earthquake preparation process contributes to creation of CS in the VLF signal. The results discussed were obtained during a very quiet time and therefore no ionospheric and magnetospheric sources of perturbation were expected. The statistical behavior of the signal (intermittent) and the shape of the spectra suggest that turbulence observed during this event is of the Kolmogorov type. Keywords: Turbulence, Higher order statistics and wave-wave interaction
Power Efficient Higher Order Sliding Mode Control of SR Motor for Speed Control Applications
Directory of Open Access Journals (Sweden)
Muhammad Rafiq
2011-05-01
Full Text Available This paper presents a novel scheme for speed regulation/tracking of Switched Reluctance (SR motors based on Higher-Order Sliding-Mode technique. In particular, a Second-Order Sliding-Mode Controller (SOSMC based on Super Twisting algorithm is devel-oped. Owing to the peculiar structural properties of SRM, torque produced by each motor phase is a function of phase current as well as rotor position. More importantly, unlike many other motors the polarity of the phase torque in SR motors is solely determined by the rotor position and is independent of the polarity of the applied voltage or phase current. The proposed controller takes advantage of this property and incorporates a commutation scheme which, at any time instant, selects only those motor phases for the computation of control law, which can contribute torque of the desired polarity at that instant. This feature helps in achieving the desired speed regulation/tracking objective in a power efficient manner as control efforts are applied through selective phases and counterproductive phases are left un-energized. This approach also minimizes the power loss in the motor windings thus reducing the heat generation within the motor. In order to highlight the advantages of Higher-Order Sliding-Mode controllers, a classical First-Order Sliding-Mode controller (FOSMC is also developed and applied to the same system. The comparison of the two schemes shows much reduced chattering in case of SOSMC. The performance of the proposed SOSMC controller for speed regulation is also compared with that of another sliding mode speed controller published in the literature.
From "Hello" to Higher-Order Thinking: The Effect of Coaching and Feedback on Online Chats
Stein, David S.; Wanstreet, Constance E.; Slagle, Paula; Trinko, Lynn A.; Lutz, Michelle
2013-01-01
This exploratory study examined the effect of a coaching and feedback intervention in teaching presence and social presence on higher-order thinking in an online community of inquiry. Coaching occurred before each chat, and feedback was provided immediately afterwards. The findings suggest that over time, the frequency of higher-order thinking…
Cauchy Problem for Quasilinear Hyperbolic Systems with Higher Order Dissipative Terms
Institute of Scientific and Technical Information of China (English)
Wei-guo Zhang
2003-01-01
In this paper, the author studies the global existence, singularities and life span of smooth solutions of the Cauchy problem for a class of quasilinear hyperbolic systems with higher order dissipative terms and gives their applications to nonlinear wave equations with higher order dissipative terms.
Analysis of Scattering by Inhomogeneous Dielectric Objects Using Higher-Order Hierarchical MoM
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter;
2003-01-01
developed higher-order hierarchical Legendre basis functions for expansion of the electric flux density and higher-order geometry modeling. An unstructured mesh composed by trilinear (8-node) and/or curved (27-node) hexahedral elements is used to represent the dielectric object accurately. It is shown...
Assessing Higher-Order Cognitive Constructs by Using an Information-Processing Framework
Dickison, Philip; Luo, Xiao; Kim, Doyoung; Woo, Ada; Muntean, William; Bergstrom, Betty
2016-01-01
Designing a theory-based assessment with sound psychometric qualities to measure a higher-order cognitive construct is a highly desired yet challenging task for many practitioners. This paper proposes a framework for designing a theory-based assessment to measure a higher-order cognitive construct. This framework results in a modularized yet…
A Study of Higher Order Need Strength and Job Satisfaction in Secondary Public School Teachers.
Pastor, Margaret C.; Erlandson, David A.
1982-01-01
Teacher motivation was explored through surveys determining the relationship between higher order needs (such as autonomy, variety) or lower order needs (such as high pay) and job satisfaction. Conclusions are that needs of the teachers studied are predominantly higher order and that job satisfaction is significantly related to teacher needs. (MJL)
Adaptive Integral Method for Higher-Order Hierarchical Method of Moments
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Meincke, Peter
2006-01-01
The Adaptive Integral Method (AIM) is applied to solve the volume integral equation in conjunction with the higher-order Method of Moments (MoM). The classical AIM is modified for larger discretization cells to take advantage of higher-order MoM. The technique combines the low computational...
Higher Order Thinking Skills among Secondary School Students in Science Learning
Saido, Gulistan Mohammed; Siraj, Saedah; Bin Nordin, Abu Bakar; Al Amedy, Omed Saadallah
2015-01-01
A central goal of science education is to help students to develop their higher order thinking skills to enable them to face the challenges of daily life. Enhancing students' higher order thinking skills is the main goal of the Kurdish Science Curriculum in the Iraqi-Kurdistan region. This study aimed at assessing 7th grade students' higher order…
Generalized q-Euler Numbers and Polynomials of Higher Order and Some Theoretic Identities
Directory of Open Access Journals (Sweden)
T. Kim
2010-01-01
Full Text Available We give a new construction of the q-Euler numbers and polynomials of higher order attached to Dirichlet's character χ. We derive some theoretic identities involving the generalized q-Euler numbers and polynomials of higher order.
Regularity of solutions to higher-order integrals of the calculus of variations
Ammi, Moulay Rchid Sidi
2007-01-01
We obtain new regularity conditions for problems of calculus of variations with higher-order derivatives. As a corollary, we get non-occurrence of the Lavrentiev phenomenon. Our main regularity result asserts that autonomous integral functionals with a Lagrangian having coercive partial derivatives with respect to the higher-order derivatives admit only minimizers with essentially bounded derivatives.
An Analysis of Higher-Order Thinking on Algebra I End-of-Course Tests
Thompson, Tony
2011-01-01
This research provides insight into one US state's effort to incorporate higher-order thinking on its Algebra I End-of-Course tests. To facilitate the inclusion of higher-order thinking, the state used "Dimensions of Thinking" (Marzano et al., 1988) and "Bloom's Taxonomy" (Bloom et al., 1956). An analysis of Algebra I test items found that the…
Higher-order blackhole solutions in N=2 supergravity and Calabi-Yau string backgrounds
Behrndt, K.; Cardoso, G.L.; de Wit, B.Q.P.J.; Lüst, D.; Mohaupt, T.; Sabra, W.A.
1998-01-01
Based on special geometry, we consider corrections to N=2 extremal black-hole solutions and their entropies originating from higher-order derivative terms in N=2 supergravity. These corrections are described by a holomorphic function, and the higher-order black-hole solutions can be expressed in ter
Teaching Higher Order Thinking in the Introductory MIS Course: A Model-Directed Approach
Wang, Shouhong; Wang, Hai
2011-01-01
One vision of education evolution is to change the modes of thinking of students. Critical thinking, design thinking, and system thinking are higher order thinking paradigms that are specifically pertinent to business education. A model-directed approach to teaching and learning higher order thinking is proposed. An example of application of the…
Schraw, Gregory, Ed.; Robinson, Daniel H., Ed.
2011-01-01
This volume examines the assessment of higher order thinking skills from the perspectives of applied cognitive psychology and measurement theory. The volume considers a variety of higher order thinking skills, including problem solving, critical thinking, argumentation, decision making, creativity, metacognition, and self-regulation. Fourteen…
Mathematics Teachers’ Interpretation of Higher-Order Thinking in Bloom’s Taxonomy
Directory of Open Access Journals (Sweden)
Tony Thompson
2008-07-01
Full Text Available This study investigated mathematics teachers’ interpretation of higher-order thinking in Bloom’s Taxonomy. Thirty-two high school mathematics teachers from the southeast U.S. were asked to (a define lower- and higher-order thinking, (b identify which thinking skills in Bloom’s Taxonomy represented lower- and higher-order thinking, and (c create an Algebra I final exam item representative of each thinking skill. Results indicate that mathematics teachers have difficulty interpreting the thinking skills in Bloom’s Taxonomy and creating test items for higher-order thinking. Alternatives to using Bloom’s Taxonomy to help mathematics teachers assess for higher-order thinking are discussed.
Even and Odd Charge Coherent States: Higher-Order Nonclassical Properties and Generation Scheme
Duc, Truong Minh; Dinh, Dang Huu; Dat, Tran Quang
2016-06-01
We examine the higher-order nonclassical properties of the even and odd charge coherent states as well as proposing a scheme to generate these states whose modes can freely travel in open space. We show that the even and odd charge coherent states exhibit both higher-order antibunching and higher-order squeezing. While the two-mode higher-order antibunching occurs in any order and essentially depends on the charge number, the two-mode higher-order squeezing appears only in the even orders. We also prove that these states are genuinely entangled, and they can be generated by means of cross-Kerr media, beam splitters, phase shifts and threshold detectors. We find that the fidelity and the corresponding success probability to generate these states are dependent on the correlative parameters.
Sabesan, Ramkumar; Jeong, Tae Moon; Carvalho, Luis; Cox, Ian G.; Williams, David R.; Yoon, Geunyoung
2007-04-01
Higher-order aberration correction in abnormal eyes can result in significant vision improvement, especially in eyes with abnormal corneas. Customized optics such as phase plates and customized contact lenses are one of the most practical, nonsurgical ways to correct these ocular higher-order aberrations. We demonstrate the feasibility of correcting higher-order aberrations and improving visual performance with customized soft contact lenses in keratoconic eyes while compensating for the static decentration and rotation of the lens. A reduction of higher-order aberrations by a factor of 3 on average was obtained in these eyes. The higher-order aberration correction resulted in an average improvement of 2.1 lines in visual acuity over the conventional correction of defocus and astigmatism alone.
Tunneling dynamics of Bose—Einstein condensates with higher-order interactions in optical lattice
International Nuclear Information System (INIS)
The nonlinear Landau—Zener tunneling and nonlinear Rabi oscillations of Bose—Einstein condensate (BEC) with higher-order atomic interaction between the Bloch bands in an accelerating optical lattice are discussed. Within the two-level model, the tunneling probability of BEC with higher-order atomic interaction between Bloch bands is obtained. We finds that the tunneling rate is closely related to the higher-order atomic interaction. Furthermore, the nonlinear Rabi oscillations of BEC with higher-order atomic interaction between the bands are discussed by imposing a periodic modulation on the level bias. Analytical expressions of the critical higher-order atomic interaction for suppressing/enhancing the Rabi oscillations are obtained. It is shown that the critical value strongly depends on the modulation parameters (i.e., the modulation amplitude and frequency) and the strength of periodic potential. (general)
Bose-Einstein Condensates in Optical Lattices with Higher-Order Interactions
Institute of Scientific and Technical Information of China (English)
张爱霞; 薛具奎
2012-01-01
The higher-order interactions of Bose-Einstein condensate in multi-dimensional optical lattices are discussed both analytically and numerically.It is demonstrated that the effects of the higher-order atomic interactions on the sound speed and the stabilities of Bloch waves strongly depend on the lattice strength.In the presence of higher-order effects,tighter and high-dimensional lattices are confirmed to be two positive factors for maintaining the system＇s energetic stability,and the dynamical instability of Bloch waves can take place simultaneously with the energetic instability.In addition,we find that the higher-order interactions exhibit a long-range behavior and the long-lived coherent Bloch oscillations in a tilted optical lattice exist.Our results provide an effective way to probe the higher-order interactions in optical lattices.
Tunneling dynamics of Bose-Einstein condensates with higher-order interactions in optical lattice
Institute of Scientific and Technical Information of China (English)
Tie Lu; Xue Ju-Kui
2011-01-01
The nonlinear Landau-Zener tunneling and nonlinear Rabi oscillations of Bose-Einstein condensate (BEC) with higher-order atomic interaction between the Bloch bands in an accelerating optical lattice are discussed.Within the two-level model,the tunneling probability of BEC with higher-order atomic interaction between Bloch bands is obtained.We finds that the tunneling rate is closely related to the higher-order atomic interaction.Furthermore,the nonlinear Rabi oscillations of BEC with higher-order atomic interaction between the bands are discussed by imposing a periodic modulation on the level bias.Analytical expressions of the critical higher-order atomic interaction for suppressing/enhancing the Rabi oscillations are obtained.It is shown that the critical value strongly depends on the modulation parameters (i.e.,the modulation amplitude and frequency) and the strength of periodic potential.
Tsai, Yu-Cheng; Cooke, Nancy E; Liebhaber, Stephen A
2016-06-01
The relationships of higher order chromatin organization to mammalian gene expression remain incompletely defined. The human Growth Hormone (hGH) multigene cluster contains five gene paralogs. These genes are selectively activated in either the pituitary or the placenta by distinct components of a remote locus control region (LCR). Prior studies have revealed that appropriate activation of the placental genes is dependent not only on the actions of the LCR, but also on the multigene composition of the cluster itself. Here, we demonstrate that the hGH LCR 'loops' over a distance of 28 kb in primary placental nuclei to make specific contacts with the promoters of the two GH genes in the cluster. This long-range interaction sequesters the GH genes from the three hCS genes which co-assemble into a tightly packed 'hCS chromatin hub'. Elimination of the long-range looping, via specific deletion of the placental LCR components, triggers a dramatic disruption of the hCS chromatin hub. These data reveal a higher-order structural pathway by which long-range looping from an LCR impacts on local chromatin architecture that is linked to tissue-specific gene regulation within a multigene cluster. PMID:26893355
Ocular higher-order aberrations features analysis after corneal refractive surgery
Institute of Scientific and Technical Information of China (English)
WANG Yan; ZHAO Kan-xing; HE Ji-chang; JIN Ying; ZUO Tong
2007-01-01
-3 in LASIK was higher and C5+1 and C5+3 were lower than those in the PRK group. C40 (spherical aberration) values were similar between PRK and LASIK, however, C3-1 and C31 (coma) in LASIK were higher than those in PRK, but these differences are of no statistical significance.Conclusions PRK and LASIK may increase ocular higher-order aberrations, but they both have their own features.The difference between the two types of surgery may be correlated with the change of the corneal shape, the conversion of biodynamics, the healing of the corneal cut, and re-structured corneal epithelium and/or the stroma.
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.
Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman
2016-08-01
During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called "superdomains," such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called "superloops." DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4 We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging. PMID:27432957
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
Darrow, Emily M.; Huntley, Miriam H.; Dudchenko, Olga; Stamenova, Elena K.; Durand, Neva C.; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L.; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P.; Lander, Eric S.; Chadwick, Brian P.; Aiden, Erez Lieberman
2016-01-01
During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called “superdomains,” such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called “superloops.” DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging. PMID:27432957
Shock waves with higher order effects in an electron depleted dusty Plasma
Ghai, Yashika; Singh Saini, Nareshpal; Singh, Manpreet
2016-07-01
Shock waves are characterized as a sudden change in properties of the medium that propagate faster than the speed of sound. A plasma system in which dissipation is dominant over dispersion of the medium, the balance between dissipation and nonlinearity leads to the formation of shock structures. A number of observations and in-situ measurements have confirmed the presence of excess superthermal populations in astrophysical and space plasmas. In fact, two temperature superthermal ion populations have been observed by Geotail spacecraft in earth's magnetotail. Moreover, charging of dust by accumulation of electrons in plasma leads to electron depleted plasma. In present investigation, shocks in an electron depleted dusty plasma with two temperature superthermal ions have been studied by using Burger's equation. Further, to incorporate higher order nonlinear effects, we have derived modified Burger's equation and studied its shock solution. The effects of various physical parameters such as superthermality of ions, kinematic viscosity and dust concentration have been observed on properties of shock structures. The results of present investigation may be useful in understanding the nonlinear structures formed in earth's atmosphere where dust and two temperature superthermal ions are observed.
Transcriptional networks and chromatin remodeling controlling adipogenesis
DEFF Research Database (Denmark)
Siersbæk, Rasmus; Nielsen, Ronni; Mandrup, Susanne
2012-01-01
Adipocyte differentiation is tightly controlled by a transcriptional cascade, which directs the extensive reprogramming of gene expression required to convert fibroblast-like precursor cells into mature lipid-laden adipocytes. Recent global analyses of transcription factor binding and chromatin...... remodeling have revealed 'snapshots' of this cascade and the chromatin landscape at specific time-points of differentiation. These studies demonstrate that multiple adipogenic transcription factors co-occupy hotspots characterized by an open chromatin structure and specific epigenetic modifications....... Such transcription factor hotspots are likely to represent key signaling nodes which integrate multiple adipogenic signals at specific chromatin sites, thereby facilitating coordinated action on gene expression....
R. van Driel
2007-01-01
Chromatin molecules have properties that set them aside from all other biomacromolecules in the cell. (i) Chromosomes, which are single chromatin molecules, are the largest macromolecules in eukaryotic cells. (ii) Chromatin molecules carry the cell's genetic and epigenetic information and all contro
Higher order modes impedance and damping study for the LHC capture cavity
Pan Wei Min
2002-01-01
To investigate the higher order mode (HOM) damping in the LHC 200 MHz capture cavity when using four HOM couplers, simulations have been carried out using both frequency domain and time domain methods. The impedance spectra of the higher order modes in the cavity before and after damping have been obtained. From this, detailed information about the HOM coupler's contribution to HOM damping can be obtained. The distribution and magnitude of some potentially dangerous higher order modes in the LHC capture cavity have been found. (5 refs).
On the Continuity Condition for the Higher-Order VSIE-MoM Formulation
DEFF Research Database (Denmark)
Kim, Oleksiy S.; Jørgensen, Erik; Meincke, Peter;
2004-01-01
A higher-order method of moments (MoM) solution of the volume-surface integral equation (VSIE) based on the higher-order hierarchical Legendre basis functions is presented. The technique is suitable for solving electromagnetic problems involving composite metallic-dielectric objects. Numerical...... examples for a finite FSS show that the explicit enforcement of the continuity condition at a metallic-dielectric interface significantly improves the solution if higher-order basis functions are defined on rather large domains with metallic edges present. This improvement manifests itself in reducing the...
Higher order capacity statistics of multi-hop transmission systems over Rayleigh fading channels
Yilmaz, Ferkan
2012-03-01
In this paper, we present an exact analytical expression to evaluate the higher order statistics of the channel capacity for amplify and forward (AF) multihop transmission systems operating over Rayleigh fading channels. Furthermore, we present simple and efficient closed-form expression to the higher order moments of the channel capacity of dual hop transmission system with Rayleigh fading channels. In order to analyze the behavior of the higher order capacity statistics and investigate the usefulness of the mathematical analysis, some selected numerical and simulation results are presented. Our results are found to be in perfect agreement. © 2012 IEEE.
Multi-domain, higher order level set scheme for 3D image segmentation on the GPU
DEFF Research Database (Denmark)
Sharma, Ojaswa; Zhang, Qin; Anton, François;
2010-01-01
to evaluate level set surfaces that are $C^2$ continuous, but are slow due to high computational burden. In this paper, we provide a higher order GPU based solver for fast and efficient segmentation of large volumetric images. We also extend the higher order method to multi-domain segmentation. Our streaming......Level set method based segmentation provides an efficient tool for topological and geometrical shape handling. Conventional level set surfaces are only $C^0$ continuous since the level set evolution involves linear interpolation to compute derivatives. Bajaj et al. present a higher order method...
Verifying object-oriented programs with higher-order separation logic in Coq
DEFF Research Database (Denmark)
Bengtson, Jesper; Jensen, Jonas Braband; Sieczkowski, Filip;
2011-01-01
We present a shallow Coq embedding of a higher-order separation logic with nested triples for an object-oriented programming language. Moreover, we develop novel specification and proof patterns for reasoning in higher-order separation logic with nested triples about programs that use interfaces...... and interface inheritance. In particular, we show how to use the higher-order features of the Coq formalisation to specify and reason modularly about programs that (1) depend on some unknown code satisfying a specification or that (2) return objects conforming to a certain specification. All of our results have...
Chromatin dynamics resolved with force spectroscopy
Chien, Fan-Tso
2011-01-01
In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases t
Existence Results for Higher-Order Boundary Value Problems on Time Scales
Sang Yanbin; Liu Jian
2009-01-01
By using the fixed-point index theorem, we consider the existence of positive solutions for the following nonlinear higher-order four-point singular boundary value problem on time scales , ; , ; , ; , , where , , , , , , , and is rd-continuous.
The geometry of higher-order Lagrange spaces applications to mechanics and physics
Miron, Radu
1997-01-01
This monograph is devoted to the problem of the geometrizing of Lagrangians which depend on higher-order accelerations It presents a construction of the geometry of the total space of the bundle of the accelerations of order k>=1 A geometrical study of the notion of the higher-order Lagrange space is conducted, and the old problem of prolongation of Riemannian spaces to k-osculator manifolds is solved Also, the geometrical ground for variational calculus on the integral of actions involving higher-order Lagrangians is dealt with Applications to higher-order analytical mechanics and theoretical physics are included as well Audience This volume will be of interest to scientists whose work involves differential geometry, mechanics of particles and systems, calculus of variation and optimal control, optimization, optics, electromagnetic theory, and biology
Directory of Open Access Journals (Sweden)
Caleb Chidozie Chinedu
2015-12-01
Full Text Available Higher order thinking skills (HOTS should be an integral part of teaching and learning especially at the higher education level. Thinking skills lessons should be part of the curriculum if students are to solve problems individually, cooperatively and creatively. Teachers on the other hand must be conversant with relevant techniques needed for teaching higher order thinking. An in-depth review of literature reveals that teachers are faced with the problem of how to prepare and teach higher order thinking skills in design and technology education. This paper is a library based work; and data were collected from textbooks, journal articles and internet search. The paper critically examined existing practices in the teaching of higher order thinking skills in design and technology education. Some of the key features mentioned were the use of concept, inferences, visualization, and schemas, among others. Recommendations for practice change were made regarding the development of HOTS.
The Need to Deliver Higher-Order Skills in the Context of Marketing in SMEs
Copley, Paul
2013-01-01
It is argued that the delivery of learning and the development of skills and competences are central to SME success; and there appears to be a requirement for higher-order education and training that can deliver a
Time-periodic Solution to a Nonlinear Parabolic Type Equation of Higher Order
Institute of Scientific and Technical Information of China (English)
Yan-ping Wang; You-lin Zhang
2008-01-01
In this paper, the existence and uniqueness of time-periodic generalized solutions and time-periodic classical solutions to a class of parabolic type equation of higher order are proved by Gaierkin method.
Higher-order mass defect analysis for mass spectra of complex organic mixtures.
Roach, Patrick J; Laskin, Julia; Laskin, Alexander
2011-06-15
Higher-order mass defect analysis is introduced as a unique formula assignment and visualization method for the analysis of complex mass spectra. This approach is an extension of the concepts of Kendrick mass transformation widely used for identification of homologous compounds differing only by a number of base units (e.g., CH(2), H(2), O, CH(2)O, etc.) in complex mixtures. We present an iterative renormalization routine for defining higher-order homologous series and multidimensional clustering of mass spectral features. This approach greatly simplifies visualization of complex mass spectra and increases the number of chemical formulas that can be confidently assigned for given mass accuracy. The potential for using higher-order mass defects for data reduction and visualization is shown. Higher-order mass defect analysis is described and demonstrated through third-order analysis of a deisotoped high-resolution mass spectrum of crude oil containing nearly 13,000 peaks. PMID:21526851
Energy Technology Data Exchange (ETDEWEB)
Burde, Georgy I, E-mail: georg@bgu.ac.i [Jacob Blaustein Institutes for Desert Research, Ben-Gurion University, Sede Boker Campus 84990 (Israel)
2010-02-26
New types of exact explicit solitary wave solutions of the higher order KdV equations are identified by applying a direct method designed specifically for constructing solitary wave solutions of evolution equations. The first type is the 'generalized Kaup-Kupershmidt' (GKK) solitary waves, which unify the structures of the sech{sup 2} KdV-like soliton and the Kaup-Kupershmidt soliton and also provide solutions of some other equations. One of those equations is found to possess the multi-soliton solutions which makes it a good candidate for being integrable in terms of the GKK solitons. Another type of solutions of the higher order KdV equations identified by applying the method represents the steady-state localized structures. The variety of equations possessing such solutions includes the integrable (in terms of the sech{sup 2} solitons) Sawada-Kotera equation which thus appears to provide the localized solutions of two types.
Hencken, Kai; Trautmann, Dirk; Baur, Gerhard
1998-01-01
We present a calculation of higher order effects for the impact parameter dependent probability for single and multiple electron-positron pairs in (peripheral) relativistic heavy ion collisions. Also total cross sections are given for SPS and RHIC energies. We make use of the expression derived recently by several groups where the summation of all higher orders can be done analytically in the high energy limit. An astonishing result is that the cross section, that is, integrating over all imp...
Lagrangian-Hamiltonian unified formalism for autonomous higher-order dynamical systems
Prieto Martínez, Pedro Daniel; Román Roy, Narciso
2011-01-01
The Lagrangian-Hamiltonian unified formalism of R. Skinner and R. Rusk was originally stated for autonomous dynamical systems in classical mechanics. It has been generalized for non-autonomous first-order mechanical systems, as well as for first-order and higher-order field theories. However, a complete generalization to higher-order mechanical systems has yet to be described. In this work, after reviewing the natural geometrical setting and the Lagrangian and Hamiltonian formalisms for highe...
On Prediction of 3d Stress State in Elastic Shell by Higher-order Shell Formulations
Brank, Boštjan; Ibrahimbegović, Adnan; Bohinc, Uroš
2008-01-01
In this work we study the accuracy of modem higher-order shell finite element formulations in computation of 3d stress state in elastic shells. In that sense we compare three higher-order shell models: (i) with seven dislacement-like kinematic parameters, and (ii, iii) with six displacement-like kinematic parameters plus one strain-like kinematic parameter introduced by two different versions of enhanced assumed strain (EAS) concept. The finite element approximations of all shell models are b...
TreatJS: Higher-Order Contracts for JavaScript (Artifact)
Keil, Matthias; Thiemann, Peter
2015-01-01
TreatJS is a language embedded, higher-order contract system for JavaScript which enforces contracts by run-time monitoring. Beyond providing the standard abstractions for building higher-order contracts (base, function, and object contracts), TreatJS's novel contributions are its guarantee of non-interfering contract execution, its systematic approach to blame assignment, its support for contracts in the style of union and intersection types, and its notion of a parameterized contract scope,...
Caleb Chidozie Chinedu; Oladiran Stephen Olabiyi; Yusri Bin Kamin
2015-01-01
Higher order thinking skills (HOTS) should be an integral part of teaching and learning especially at the higher education level. Thinking skills lessons should be part of the curriculum if students are to solve problems individually, cooperatively and creatively. Teachers on the other hand must be conversant with relevant techniques needed for teaching higher order thinking. An in-depth review of literature reveals that teachers are faced with the problem of how to prepare and teach higher o...
PRECONDITIONING HIGHER ORDER FINITE ELEMENT SYSTEMS BY ALGEBRAIC MULTIGRID METHOD OF LINEAR ELEMENTS
Institute of Scientific and Technical Information of China (English)
Yun-qing Huang; Shi Shu; Xi-jun Yu
2006-01-01
We present and analyze a robust preconditioned conjugate gradient method for the higher order Lagrangian finite element systems of a class of elliptic problems. An auxiliary linear element stiffness matrix is chosen to be the preconditioner for higher order finite elements. Then an algebraic multigrid method of linear finite element is applied for solving the preconditioner. The optimal condition number which is independent of the mesh size is obtained. Numerical experiments confirm the efficiency of the algorithm.
Higher-Order Income Risk and Social Insurance Policy Over the Business Cycle
Rocio Madera; Fatih Guvenen; David Domeij; Christopher Busch
2015-01-01
This paper studies how higher-order income risk varies over the business cycle as well as the extent to which such risks can be smoothed within households or with government social insurance policies. To provide a broad perspective on these questions, we study panel data on individuals and households from the United States, Germany, and Sweden, covering more than three decades of data for each country. We find that the underlying variation in higher-order risk is remarkably similar across the...
The contrasting role of higher order awareness in hypnosis and meditation
Semmens-Wheeler, Rebecca
2013-01-01
Two key questions underpin the research presented here. Firstly, how does altered higher order awareness contribute to hypnotic experience? Secondly, how do meditation and hypnosis differ in terms of the role of higher order awareness? These questions are addressed here in the form of four papers. In the first paper I review the literatures of hypnosis and meditation in order to consider the similarities and differences between meditation and hypnosis in terms of the role of attentional skill...
On higher order radiative corrections to elastic electron–proton scattering
Energy Technology Data Exchange (ETDEWEB)
Arbuzov, A. B., E-mail: arbuzov@theor.jinr.ru [Bogoliubov Laboratory of Theoretical Physics, JINR, 141980, Dubna (Russian Federation); Department of Higher Mathematics, Dubna State University, 141982, Dubna (Russian Federation); Kopylova, T. V. [Department of Higher Mathematics, Dubna State University, 141982, Dubna (Russian Federation)
2015-12-18
QED radiative corrections to elastic electron–proton scattering at low energies are discussed. Corrections to the electron line and effects due to vacuum polarization are computed. Higher order effects are estimated for the conditions of the experiment on the electric and magnetic proton form factors by the A1 Collaboration. Calculations are performed within the next-to-leading approximation. The inclusion of the higher order effects can affect the value of the proton charge radius extracted from the experimental data.
On higher order radiative corrections to elastic electron-proton scattering
Energy Technology Data Exchange (ETDEWEB)
Arbuzov, A.B. [Bogoliubov Laboratory of Theoretical Physics, Dubna (Russian Federation); Dubna State University, Department of Higher Mathematics, Dubna (Russian Federation); Kopylova, T.V. [Dubna State University, Department of Higher Mathematics, Dubna (Russian Federation)
2015-12-15
QED radiative corrections to elastic electron-proton scattering at low energies are discussed. Corrections to the electron line and effects due to vacuum polarization are computed. Higher order effects are estimated for the conditions of the experiment on the electric and magnetic proton form factors by the A1 Collaboration. Calculations are performed within the next-to-leading approximation. The inclusion of the higher order effects can affect the value of the proton charge radius extracted from the experimental data. (orig.)
International Nuclear Information System (INIS)
The supersymmetric version of the Stueckelberg Lagrangian of the massive vector superfield leads to an example of higher-order derivative model. The canonical quantization yields massive states which compose two irreducible representations, one physical supermultiplet and another spurious. The origin of the different spurious states are investigated, especially those originating from the higher-order derivative terms. The spurious superfield is found to be decoupled when the supercurrent satisfies some appropriate conditions. (orig.)
Higher order harmonic detection for exploring nonlinear interactions with nanoscale resolution
Vasudevan, R. K.; M. Baris Okatan; Rajapaksa, I.; Kim, Y.; Marincel, D.; Trolier-McKinstry, S.; Jesse, S.; Valanoor, N.; Kalinin, S. V.
2013-01-01
Nonlinear dynamics underpin a vast array of physical phenomena ranging from interfacial motion to jamming transitions. In many cases, insight into the nonlinear behavior can be gleaned through exploration of higher order harmonics. Here, a method using band excitation scanning probe microscopy (SPM) to investigate higher order harmonics of the electromechanical response, with nanometer scale spatial resolution is presented. The technique is demonstrated by probing the first three harmonics of...
Higher-order Schrödinger and Hartree–Fock equations
Energy Technology Data Exchange (ETDEWEB)
Carles, Rémi, E-mail: Remi.Carles@math.cnrs.fr [IMAG, UMR5149, CNRS and University Montpellier, CC051, 34095 Montpellier (France); Lucha, Wolfgang, E-mail: Wolfgang.Lucha@oeaw.ac.at [Institute for High Energy Physics, Austrian Academy of Sciences, Nikolsdorfergasse 18, A-1050 Vienna (Austria); Moulay, Emmanuel, E-mail: emmanuel.moulay@univ-poitiers.fr [XLIM (UMR-CNRS 7252), University Poitiers, 11 Blvd. Marie et Pierre Curie, BP 30179, 86962 Futuroscope Chasseneuil Cedex (France)
2015-12-15
The domain of validity of the higher-order Schrödinger equations is analyzed for harmonic-oscillator and Coulomb potentials as typical examples. Then, the Cauchy theory for higher-order Hartree–Fock equations with bounded and Coulomb potentials is developed. Finally, the existence of associated ground states for the odd-order equations is proved. This renders these quantum equations relevant for physics.
Glunčić, Matko; Rosandić, Marija; Jelovina, Denis; Dekanić, Krešimir; Vlahović, Ines; Paar, Vladimir
2012-01-01
Alpha satellites are tandemly repeated sequences found in all human centromeres. In addition to the functional and structural role within centromere they are also a suitable model for evolutionary stud-ies, because of being subject to concerted evolution. The Global Repeat Map (GRM) algorithm is a convenient computational tool to determine consensus repeat units and their exact size within a given genomic sequence, both of monomeric and higher-order (HOR) type. Using GRM, we identify in Build...
Higher-order weakly nonlinear theory for internal waves in three-layer fluid
Kurkina, O. E.; Kurkin, A. A.; Rouvinskaya, E. A.
2012-04-01
Three-layer stratifications are proved to be a proper approximation of sea water density profile in some basins in the World Ocean with specific hydrological conditions. Some shallow basins such as the Baltic Sea and some river estuaries have more or less continuous three-layer vertical structure caused by the interplay of fresh water discharge to the surface and salt water intrusion in the bottom layers. In order to describe the basic features of the internal wave field in such environments it is necessary to introduce a three-layer model. Such models are considerably more complex than the most popular two-layer systems; however, they represent new dynamical effects and allow for much more analytical progress in their studies compared to the fully stratified situation. In the present study two modes of long internal gravity waves in a three-layer fluid are investigated in the framework of higher-order nonlinear evolutionary equations derived with the use of asymptotic procedure from the governing Euler equations for inviscid incompressible layered medium with "rigid lid" and horizontal impermeable bottom. The equations are written upto the fifth order of the perturbation theory for both interfaces for the waves of both modes: first (fast mode) and second (slow mode, so-called double-humped or varicose). For each equation the coefficients of nonlinearity, dispersion and nonlinear dispersion are expressed explicitly in terms of parameters of this fluid configuration. The behavior and signs of the coefficients are analyzed. The necessary order of the equations is discussed and determined for each case. A few nonlinear asymptotic transformations are proposed to reduce higher-order equations to simpler lower-order or well-known integrable equations (Korteweg - de Vries, Gardner equations). Special attention is paid to the situations when the nonlinear terms of lower orders of perturbation theory can vanish. For such situations particular rescaling is performed in order
Functional independence in resting-state connectivity facilitates higher-order cognition.
James, G Andrew; Kearney-Ramos, Tonisha E; Young, Jonathan A; Kilts, Clinton D; Gess, Jennifer L; Fausett, Jennifer S
2016-06-01
Growing evidence suggests that intrinsic functional connectivity (i.e. highly structured patterns of communication between brain regions during wakeful rest) may encode cognitive ability. However, the generalizability of these findings is limited by between-study differences in statistical methodology and cognitive domains evaluated. To address this barrier, we evaluated resting-state neural representations of multiple cognitive domains within a relatively large normative adult sample. Forty-four participants (mean(sd) age=31(10) years; 18 male and 26 female) completed a resting-state functional MRI scan and neuropsychological assessments spanning motor, visuospatial, language, learning, memory, attention, working memory, and executive function performance. Robust linear regression related cognitive performance to resting-state connectivity among 200 a priori determined functional regions of interest (ROIs). Only higher-order cognitions (such as learning and executive function) demonstrated significant relationships between brain function and behavior. Additionally, all significant relationships were negative - characterized by moderately positive correlations among low performers and weak to moderately negative correlations among high performers. These findings suggest that functional independence among brain regions at rest facilitates cognitive performance. Our interpretation is consistent with graph theoretic analyses which represent the brain as independent functional nodes that undergo dynamic reorganization with task demand. Future work will build upon these findings by evaluating domain-specific variance in resting-state neural representations of cognitive impairment among patient populations. PMID:27105037
Magnitude and significance of the higher-order reduced density matrix cumulants
Herbert, John M.
Using full configuration interaction wave functions for Be and LiH, in both minimal and extended basis sets, we examine the absolute magnitude and energetic significance of various contributions to the three-electron reduced density matrix (3-RDM) and its connected (size-consistent) component, the 3-RDM cumulant (3-RDMC). Minimal basis sets are shown to suppress the magnitude of the 3-RDMC in an artificial manner, whereas in extended basis sets, 3-RDMC matrix elements are often comparable in magnitude to the corresponding 3-RDM elements, even in cases where this result is not required by spin angular momentum coupling. Formal considerations suggest that these observations should generalize to higher-order p-RDMs and p-RDMCs (p > 3). This result is discussed within the context of electronic structure methods based on the contracted Schrödinger equation (CSE), as solution of the CSE relies on 3- and 4-RDM ?reconstruction functionals? that neglect the 3-RDMC, the 4-RDMC, or both. Although the 3-RDMC is responsible for at most 0.2% of the total electronic energy in Be and LiH, it accounts for up to 70% of the correlation energy, raising questions regarding whether (and how) the CSE can offer a useful computational methodology.
Higher Order and Harmonic Corrections to the Quasi-de Sitter Inflation
Mohsenzadeh, M
2016-01-01
Since the trans-Planckian considerations can be associated with the re-definition of the initial vacuum, we investigate further the influence of trans-planckian physics on the spectra produced by initial quasi-de Sitter (dS) state during inflation. Recently, we have introduced asymptotic-dS mode to study the scale dependency of power spectrum during inflation. In this paper, we calculate the trans-Planckian corrections to the spectra resulted from that initial mode. As expected the modified spectra consisting of higher order corrections associated to the type of the geometry and harmonic terms sensitive to the fluctuations of space-time(or gravitational waves) during inflation. The corrections are tiny at far past time limit, but may have very important effects on the formation of large scale structure. Also, the results are always valid for any asymptotic dS space-time and particularly coincide the conventional results for the dS and flat space-time.
Triangular Alignment (TAME). A Tensor-based Approach for Higher-order Network Alignment
Energy Technology Data Exchange (ETDEWEB)
Mohammadi, Shahin [Purdue Univ., West Lafayette, IN (United States); Gleich, David F. [Purdue Univ., West Lafayette, IN (United States); Kolda, Tamara G. [Sandia National Laboratories (SNL-CA), Livermore, CA (United States); Grama, Ananth [Purdue Univ., West Lafayette, IN (United States)
2015-11-01
Network alignment is an important tool with extensive applications in comparative interactomics. Traditional approaches aim to simultaneously maximize the number of conserved edges and the underlying similarity of aligned entities. We propose a novel formulation of the network alignment problem that extends topological similarity to higher-order structures and provide a new objective function that maximizes the number of aligned substructures. This objective function corresponds to an integer programming problem, which is NP-hard. Consequently, we approximate this objective function as a surrogate function whose maximization results in a tensor eigenvalue problem. Based on this formulation, we present an algorithm called Triangular AlignMEnt (TAME), which attempts to maximize the number of aligned triangles across networks. We focus on alignment of triangles because of their enrichment in complex networks; however, our formulation and resulting algorithms can be applied to general motifs. Using a case study on the NAPABench dataset, we show that TAME is capable of producing alignments with up to 99% accuracy in terms of aligned nodes. We further evaluate our method by aligning yeast and human interactomes. Our results indicate that TAME outperforms the state-of-art alignment methods both in terms of biological and topological quality of the alignments.
Diffusion-driven looping provides a consistent framework for chromatin organization.
Directory of Open Access Journals (Sweden)
Manfred Bohn
Full Text Available Chromatin folding inside the interphase nucleus of eukaryotic cells is done on multiple scales of length and time. Despite recent progress in understanding the folding motifs of chromatin, the higher-order structure still remains elusive. Various experimental studies reveal a tight connection between genome folding and function. Chromosomes fold into a confined subspace of the nucleus and form distinct territories. Chromatin looping seems to play a dominant role both in transcriptional regulation as well as in chromatin organization and has been assumed to be mediated by long-range interactions in many polymer models. However, it remains a crucial question which mechanisms are necessary to make two chromatin regions become co-located, i.e. have them in spatial proximity. We demonstrate that the formation of loops can be accomplished solely on the basis of diffusional motion. The probabilistic nature of temporary contacts mimics the effects of proteins, e.g. transcription factors, in the solvent. We establish testable quantitative predictions by deriving scale-independent measures for comparison to experimental data. In this Dynamic Loop (DL model, the co-localization probability of distant elements is strongly increased compared to linear non-looping chains. The model correctly describes folding into a confined space as well as the experimentally observed cell-to-cell variation. Most importantly, at biological densities, model chromosomes occupy distinct territories showing less inter-chromosomal contacts than linear chains. Thus, dynamic diffusion-based looping, i.e. gene co-localization, provides a consistent framework for chromatin organization in eukaryotic interphase nuclei.
Chromatin domain boundaries: insulators and beyond
Institute of Scientific and Technical Information of China (English)
Gong Hong WEI; De Pei LIU; Chih Chuan LIANG
2005-01-01
The eukaryotic genome is organized into functionally and structurally distinct domains, representing regulatory units for gene expression and chromosome behavior. DNA sequences that mark the border between adjacent domains are the insulators or boundary elements, which are required in maintenance of the function of different domains. Some insulators need others enable to play insulation activity. Chromatin domains are defined by distinct sets of post-translationally modified histones. Recent studies show that these histone modifications are also involved in establishment of sharp chromatin boundaries in order to prevent the spreading of distinct domains. Additionally, in some loci, the high-order chromatin structures for long-range looping interactions also have boundary activities, suggesting a correlation between insulators and chromatin loop domains. In this review, we will discuss recent progress in the field of chromatin domain boundaries.
Siebenlist, U; Durand, D B; Bressler, P; Holbrook, N J; Norris, C A; Kamoun, M.; Kant, J A; Crabtree, G R
1986-01-01
The chromatin structure of the interleukin-2 (IL-2) gene was probed by DNase I treatment of isolated nuclei. The 5' region of the IL-2 gene contains three regions of hypersensitivity to DNase I. When peripheral blood T cells or Jurkat T cells are stimulated with mitogens, IL-2 message is induced, and the promoter region of the IL-2 gene develops an additional hypersensitive site. This suggests that a DNA sequence close to the transcriptional start site is involved in the transduction of the e...
Expression-dependent folding of interphase chromatin.
Directory of Open Access Journals (Sweden)
Hansjoerg Jerabek
Full Text Available Multiple studies suggest that chromatin looping might play a crucial role in organizing eukaryotic genomes. To investigate the interplay between the conformation of interphase chromatin and its transcriptional activity, we include information from gene expression profiles into a polymer model for chromatin that incorporates genomic loops. By relating loop formation to transcriptional activity, we are able to generate chromosome conformations whose structural and topological properties are consistent with experimental data. The model particularly allows to reproduce the conformational variations that are known to occur between highly and lowly expressed chromatin regions. As previously observed in experiments, lowly expressed regions of the simulated polymers are much more compact. Due to the changes in loop formation, the distributions of chromatin loops are also expression-dependent and exhibit a steeper decay in highly active regions. As a results of entropic interaction between differently looped parts of the chromosome, we observe topological alterations leading to a preferential positioning of highly transcribed loci closer to the surface of the chromosome territory. Considering the diffusional behavior of the chromatin fibre, the simulations furthermore show that the higher the expression level of specific parts of the chromatin fibre is, the more dynamic they are. The results exhibit that variations of loop formation along the chromatin fibre, and the entropic changes that come along with it, do not only influence the structural parameters on the local scale, but also effect the global chromosome conformation and topology.
Moldenhauer, Jacob; Thompson, John; Easson, Damien A
2010-01-01
We consider recently proposed higher order gravity models where the action is built from the Einstein-Hilbert action plus a function f(G) of the Gauss-Bonnet invariant. The models were previously shown to pass physical acceptability conditions as well as solar system tests. In this paper, we compare the models to combined data sets of supernovae, baryon acoustic oscillations, and constraints from the CMB surface of last scattering. We find that the models provide fits to the data that are close to those of the LCDM concordance model. The results provide a pool of higher order gravity models that pass these tests and need to be compared to constraints from large scale structure and full CMB analysis.
Amin, Muhammad Ruhul
2012-08-10
In this paper, a planar metallic nanostructure design, which supports two distinct Fano resonances in its extinction cross-section spectrum under normally incident and linearly polarized electromagnetic field, is proposed. The proposed design involves a circular disk embedding an elongated cavity; shifting and rotating the cavity break the symmetry of the structure with respect to the incident field and induce higher order plasmon modes. As a result, Fano resonances are generated in the visible spectrum due to the destructive interference between the sub-radiant higher order modes and super-radiant the dipolar mode. The Fano resonances can be tuned by varying the cavity\\'s width and the rotation angle. An RLC circuit, which is mathematically equivalent to a mass-spring oscillator, is proposed to model the optical response of the nanostructure design.
DEFF Research Database (Denmark)
Giesinger, Johannes M; Kieffer, Jacobien M; Fayers, Peter M;
2016-01-01
OBJECTIVE: To further evaluate the higher order measurement structure of the European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire Core 30 (QLQ-C30), with the aim of generating a summary score. STUDY DESIGN AND SETTING: Using pretreatment QLQ-C30 data (N...... = 3,282), we conducted confirmatory factor analyses to test seven previously evaluated higher order models. We compared the summary score(s) derived from the best performing higher order model with the original QLQ-C30 scale scores, using tumor stage, performance status, and change over time (N = 244...
Chromatin Dynamics of the mouse β-globin locus
M.P.C. van de Corput (Mariëtte); E. de Boer (Ernie); T.A. Knoch (Tobias); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)
2010-01-01
textabstractLately it has become more clear that (subtle) changes in 3D organization of chromatin can either trigger transcription or silence genes or gene clusters. It has also been postulated that due to changes in chromatin structure, a change in chromatin accessibility of transcription factors
An efficient higher-order PML in WLP-FDTD method for time reversed wave simulation
Wei, Xiao-Kun; Shao, Wei; Ou, Haiyan; Wang, Bing-Zhong
2016-09-01
Derived from a stretched coordinate formulation, a higher-order complex frequency shifted (CFS) perfectly matched layer (PML) is proposed for the unconditionally stable finite-difference time-domain (FDTD) method based on weighted Laguerre polynomials (WLPs). The higher-order PML is implemented with an auxiliary differential equation (ADE) approach. In order to further improve absorbing performance, the parameter values of stretching functions in the higher-order PML are optimized by the multi-objective genetic algorithm (MOGA). The optimal solutions can be chosen from the Pareto front for trading-off between two independent objectives. It is shown in a numerical test that the higher-order PML is efficient in terms of attenuating propagating waves and reducing late time reflections. Moreover, the higher-order PML can be placed very close to the wall when analyzing the channel characteristics of time reversal (TR) waves in a multipath indoor environment. Numerical examples of TR wave propagation demonstrate the availability of the proposed method.
Higher order aberrations in amblyopic children and their role in refractory amblyopia
Directory of Open Access Journals (Sweden)
Arnaldo Dias-Santos
2014-12-01
Full Text Available Objective: Some studies have hypothesized that an unfavourable higher order aberrometric profile could act as an amblyogenic mechanism and may be responsible for some amblyopic cases that are refractory to conventional treatment or cases of “idiopathic” amblyopia. This study compared the aberrometric profile in amblyopic children to that of children with normal visual development and compared the aberrometric profile in corrected amblyopic eyes and refractory amblyopic eyes with that of healthy eyes. Methods: Cross-sectional study with three groups of children – the CA group (22 eyes of 11 children with unilateral corrected amblyopia, the RA group (24 eyes of 13 children with unilateral refractory amblyopia and the C group (28 eyes of 14 children with normal visual development. Higher order aberrations were evaluated using an OPD-Scan III (NIDEK. Comparisons of the aberrometric profile were made between these groups as well as between the amblyopic and healthy eyes within the CA and RA groups. Results: Higher order aberrations with greater impact in visual quality were not significantly higher in the CA and RA groups when compared with the C group. Moreover, there were no statistically significant differences in the higher order aberrometric profile between the amblyopic and healthy eyes within the CA and RA groups. Conclusions: Contrary to lower order aberrations (e.g., myopia, hyperopia, primary astigmatism, higher order aberrations do not seem to be involved in the etiopathogenesis of amblyopia. Therefore, these are likely not the cause of most cases of refractory amblyopia.
Simplification of the Flux Function for a Higher-order Gas-kinetic Evolution Model
Zhou, Guangzhao; Liu, Feng
2016-01-01
The higher-order gas-kinetic scheme for solving the Navier-Stokes equations has been studied in recent years. In addition to the use of higher-order reconstruction techniques, many terms are used in the Taylor expansion of the gas distribution functions. Therefore, a large number of coefficients need to be determined in the calculation of the time evolution of the gas distribution function at cell interfaces. As a consequence, the higher-order flux function takes much more computational time than that of a second-order gas-kinetic scheme. This paper aims to simplify the evolution model by two steps. Firstly, the coefficients related to the higher-order spatial and temporal derivatives of a distribution function are redefined to reduce the computational cost. Secondly, based on the physical analysis, some terms can be removed without loss of accuracy. Through the simplifications, the computational efficiency of the higher-order scheme is increased significantly. In addition, a self-adaptive numerical viscosity...
Mozgová, Iva; Köhler, Claudia; Gaudin, Valérie; Hennig, Lars
2015-01-01
In June 2015, the fourth European Workshop on Plant Chromatin took place in Uppsala, Sweden, bringing together 80 researchers studying various aspects of plant chromatin and epigenetics. The intricate relationships between plant chromatin dynamics and gene expression change, chromatin organization within the plant cell nucleus, and the impact of chromatin structure on plant development were discussed. Among the main highlights of the meeting were an ever-growing list of newly identified players in chromatin structure establishment and the development of novel tools and approaches to foster our understanding of chromatin-mediated gene regulation, taking into account the context of the plant cell nucleus and its architecture. In this report, we summarize some of the main advances and prospects of plant chromatin research presented at this meeting. PMID:26646904
A finite deformation theory of higher-order gradient crystal plasticity
DEFF Research Database (Denmark)
Kuroda, Mitsutoshi; Tvergaard, Viggo
2008-01-01
For higher-order gradient crystal plasticity, a finite deformation formulation is presented. The theory does not deviate much from the conventional crystal plasticity theory. Only a back stress effect and additional differential equations for evolution of the geometrically necessary dislocation...... (GND) densities supplement the conventional theory within a non-work-conjugate framework in which there is no need to introduce higher-order microscopic stresses that would be work-conjugate to slip rate gradients. We discuss its connection to a work-conjugate type of finite deformation gradient...... crystal plasticity that is based on an assumption of the existence of higher-order stresses. Furthermore, a boundary-value problem for simple shear of a constrained thin strip is studied numerically, and some characteristic features of finite deformation are demonstrated through a comparison to a solution...
Higher-order effects on self-similar parabolic pulse in the microstructured fibre amplifier
Institute of Scientific and Technical Information of China (English)
Liu Wei-Ci; Xu Wen-Cheng; Feng Jie; Chen Wei-Cheng; Li Shu-Xian; Lin Song-Hao
2008-01-01
By considering higher-order effects, the properties of self-similar parabolic pulses propagating in the microstructured fibre amplifier with a normal group-velocity dispersion have been investigated. The numerical results indicate that the higher-order effects can badly distort self-similar parabolic pulse shape and optical spectrum, and at the same time the peak shift and oscillation appear, while the pulse still reveals highly linear chirp but grows into asymmetry. The influence of different higher-order effects on self-similar parabolic pulse propagation has been analysed. It shows thatthe self-steepening plays a more important role. We can manipulate the geometrical parameters of the microstructured fibre amplifier to gain a suitable dispersion and nonlinearity coefficient which will keep high-quality self-similar parabolic pulse propagation. These results are significant for the further study of self-similar parabolic pulse propagation.
Higher-order cumulants and spectral kurtosis for early detection of subterranean termites
de la Rosa, Juan José González; Moreno Muñoz, Antonio
2008-02-01
This paper deals with termite detection in non-favorable SNR scenarios via signal processing using higher-order statistics. The results could be extrapolated to all impulse-like insect emissions; the situation involves non-destructive termite detection. Fourth-order cumulants in time and frequency domains enhance the detection and complete the characterization of termite emissions, non-Gaussian in essence. Sliding higher-order cumulants offer distinctive time instances, as a complement to the sliding variance, which only reveal power excesses in the signal; even for low-amplitude impulses. The spectral kurtosis reveals non-Gaussian characteristics (the peakedness of the probability density function) associated to these non-stationary measurements, specially in the near ultrasound frequency band. Contrasted estimators have been used to compute the higher-order statistics. The inedited findings are shown via graphical examples.
Higher-order-statistics-based radial basis function networks for signal enhancement.
Lin, Bor-Shyh; Lin, Bor-Shing; Chong, Fok-Ching; Lai, Feipei
2007-05-01
In this paper, a higher-order-statistics (HOS)-based radial basis function (RBF) network for signal enhancement is introduced. In the proposed scheme, higher order cumulants of the reference signal were used as the input of HOS-based RBF. An HOS-based supervised learning algorithm, with mean square error obtained from higher order cumulants of the desired input and the system output as the learning criterion, was used to adapt weights. The motivation is that the HOS can effectively suppress Gaussian and symmetrically distributed non-Gaussian noise. The influence of a Gaussian noise on the input of HOS-based RBF and the HOS-based learning algorithm can be mitigated. Simulated results indicate that HOS-based RBF can provide better performance for signal enhancement under different noise levels, and its performance is insensitive to the selection of learning rates. Moreover, the efficiency of HOS-based RBF under the nonstationary Gaussian noise is stable.
Isomorphisms of types in the presence of higher-order references
Clairambault, Pierre
2011-01-01
We investigate the problem of type isomorphisms in a programming language with higher-order references. We first recall the game-theoretic model of higher-order references by Abramsky, Honda and McCusker. Solving an open problem by Laurent, we show that two finitely branching arenas are isomorphic if and only if they are geometrically the same, up to renaming of moves (Laurent's forest isomorphism). We deduce from this an equational theory characterizing isomorphisms of types in a finitary language with higher order references. We show however that Laurent's conjecture does not hold on infinitely branching arenas, yielding a non-trivial type isomorphism in the extension of this language with natural numbers.
Recurrent activity in higher order, modality non-specific brain regions
DEFF Research Database (Denmark)
Lou, Hans Olav Christensen; Joensson, Morten; Biermann-Ruben, Katja;
2011-01-01
It has been proposed that the workings of the brain are mainly intrinsically generated recurrent neuronal activity, with sensory inputs as modifiers of such activity in both sensory and higher order modality non-specific regions. This is supported by the demonstration of recurrent neuronal activity...... in the visual system as a response to visual stimulation. In contrast recurrent activity has never been demonstrated before in higher order modality non-specific regions. Using magneto-encephalography and Granger causality analysis, we tested in a paralimbic network the hypothesis that stimulation may enhance...... causal recurrent interaction between higher-order, modality non-specific regions. The network includes anterior cingulate/medial prefrontal and posterior cingulate/medial parietal cortices together with pulvinar thalami, a network known to be effective in autobiographic memory retrieval and self...
Automatic tracking of ground station antennas by means of higher order waveguide modes
Scheffer, H.
1980-02-01
Utilization of higher order waveguide modes, which are excited in the feed when the satellite is displaced from the boresight axis of the antenna is discussed. The physical relations involved in the excitation of higher order waveguide modes as a function of the antenna position are explained. The starting points of these considerations are the radiation patterns of the tracking modes excited by feeds with circular and square cross sections. Special mention is made of the derivation of the offset information in the cases of circular and linear polarization of the beacon signal. The principle of selective mode coupling by means of tracking mode couplers is described. A compilation of German ground station antennas is given, which apply tracking by higher order waveguide modes.
Application of Higher-Order Cumulant in Fault Diagnosis of Rolling Bearing
Shen, Yongjun; Yang, Shaopu; Wang, Junfeng
2013-07-01
In this paper a new method of pattern recognition based on higher-order cumulant and envelope analysis is presented. The core of this new method is to construct analytical signals from the given signals and obtain the envelope signals firstly, then compute and compare the higher-order cumulants of the envelope signals. The higher-order cumulants could be used as a characteristic quantity to distinguish these given signals. As an example, this method is applied in fault diagnosis for 197726 rolling bearing of freight locomotive. The comparisons of the second-order, third-order and fourth-order cumulants of the envelope signals from different vibration signals of rolling bearing show this new method could discriminate the normal and two fault signals distinctly.
Design and Application of Strategies/Tactics in Higher Order Logics
Archer, Myla (Editor); diVito, Ben (Editor); Munoz, Cesar (Editor)
2003-01-01
This Proceedings includes both a paper from the implementors of PVS providing guidance for PVS strategy writers and a tutorial on PVS strategy writing distilled from the experience of three PVS users who have written extensive sets of PVS user strategies. Following these are three full papers from the higher-order logic theorem proving community that discuss PVS strategies to enhance arithmetic and other interactive reasoning in PVS; implementing first-order tactics in higher-order provers; and a proposed technique for specifying small step semantics that can be used in multiple higher order logic theorem provers, with illustrations from both Coq and PVS. The Proceedings concludes with three position papers for a panel session that discuss three settings in which development of PVS strategies is worth while.
LENUS (Irish Health Repository)
Shieh, Grace S.
2011-12-22
Abstract Background The packaging of DNA into chromatin regulates transcription from initiation through 3\\' end processing. One aspect of transcription in which chromatin plays a poorly understood role is the co-transcriptional splicing of pre-mRNA. Results Here we provide evidence that H2B monoubiquitylation (H2BK123ub1) marks introns in Saccharomyces cerevisiae. A genome-wide map of H2BK123ub1 in this organism reveals that this modification is enriched in coding regions and that its levels peak at the transcribed regions of two characteristic subgroups of genes. First, long genes are more likely to have higher levels of H2BK123ub1, correlating with the postulated role of this modification in preventing cryptic transcription initiation in ORFs. Second, genes that are highly transcribed also have high levels of H2BK123ub1, including the ribosomal protein genes, which comprise the majority of intron-containing genes in yeast. H2BK123ub1 is also a feature of introns in the yeast genome, and the disruption of this modification alters the intragenic distribution of H3 trimethylation on lysine 36 (H3K36me3), which functionally correlates with alternative RNA splicing in humans. In addition, the deletion of genes encoding the U2 snRNP subunits, Lea1 or Msl1, in combination with an htb-K123R mutation, leads to synthetic lethality. Conclusion These data suggest that H2BK123ub1 facilitates cross talk between chromatin and pre-mRNA splicing by modulating the distribution of intronic and exonic histone modifications.
A maximum entropy test for evaluating higher-order correlations in spike counts.
Directory of Open Access Journals (Sweden)
Arno Onken
Full Text Available Evaluating the importance of higher-order correlations of neural spike counts has been notoriously hard. A large number of samples are typically required in order to estimate higher-order correlations and resulting information theoretic quantities. In typical electrophysiology data sets with many experimental conditions, however, the number of samples in each condition is rather small. Here we describe a method that allows to quantify evidence for higher-order correlations in exactly these cases. We construct a family of reference distributions: maximum entropy distributions, which are constrained only by marginals and by linear correlations as quantified by the Pearson correlation coefficient. We devise a Monte Carlo goodness-of-fit test, which tests--for a given divergence measure of interest--whether the experimental data lead to the rejection of the null hypothesis that it was generated by one of the reference distributions. Applying our test to artificial data shows that the effects of higher-order correlations on these divergence measures can be detected even when the number of samples is small. Subsequently, we apply our method to spike count data which were recorded with multielectrode arrays from the primary visual cortex of anesthetized cat during an adaptation experiment. Using mutual information as a divergence measure we find that there are spike count bin sizes at which the maximum entropy hypothesis can be rejected for a substantial number of neuronal pairs. These results demonstrate that higher-order correlations can matter when estimating information theoretic quantities in V1. They also show that our test is able to detect their presence in typical in-vivo data sets, where the number of samples is too small to estimate higher-order correlations directly.
A maximum entropy test for evaluating higher-order correlations in spike counts.
Onken, Arno; Dragoi, Valentin; Obermayer, Klaus
2012-01-01
Evaluating the importance of higher-order correlations of neural spike counts has been notoriously hard. A large number of samples are typically required in order to estimate higher-order correlations and resulting information theoretic quantities. In typical electrophysiology data sets with many experimental conditions, however, the number of samples in each condition is rather small. Here we describe a method that allows to quantify evidence for higher-order correlations in exactly these cases. We construct a family of reference distributions: maximum entropy distributions, which are constrained only by marginals and by linear correlations as quantified by the Pearson correlation coefficient. We devise a Monte Carlo goodness-of-fit test, which tests--for a given divergence measure of interest--whether the experimental data lead to the rejection of the null hypothesis that it was generated by one of the reference distributions. Applying our test to artificial data shows that the effects of higher-order correlations on these divergence measures can be detected even when the number of samples is small. Subsequently, we apply our method to spike count data which were recorded with multielectrode arrays from the primary visual cortex of anesthetized cat during an adaptation experiment. Using mutual information as a divergence measure we find that there are spike count bin sizes at which the maximum entropy hypothesis can be rejected for a substantial number of neuronal pairs. These results demonstrate that higher-order correlations can matter when estimating information theoretic quantities in V1. They also show that our test is able to detect their presence in typical in-vivo data sets, where the number of samples is too small to estimate higher-order correlations directly.
Where splicing joins chromatin
Hnilicová, Jarmila; Staněk, David
2011-01-01
There are numerous data suggesting that two key steps in gene expression—transcription and splicing influence each other closely. For a long time it was known that chromatin modifications regulate transcription, but only recently it was shown that chromatin and histone modifications play a significant role in pre-mRNA splicing. Here we summarize interactions between splicing machinery and chromatin and discuss their potential functional significance. We focus mainly on histone acetylation and...
Self-Deflection of Dark Screening Spatial Solitons Based on Higher-Order Space Charge Field
Institute of Scientific and Technical Information of China (English)
ZHANG Guang-Yong; LIU Jin-Song; LIU Shi-Xiong; WANG Cheng; ZHANG Hui-Lan
2007-01-01
The effects of higher-order space charge field on the self-deflection of dark screening spatial solitons in biased photorefractive crystals are numerically investigated under steady-state conditions. The expression for an induced space-charge electric field including higher-order space-charge field terms is obtained. Numerical results indicate that dark solitons possess a self-deflection process during propagation, and the solitons always bend in the direction of the c axis of the crystal The self-deflection of dark solitons can experience considerable increase especially in the regime of high bias field strengths.
Institute of Scientific and Technical Information of China (English)
Tan Xiaogang; Wei Ping; Li Liping
2009-01-01
To detect higher order polynomial phase signals (HOPPSs), the smoothed-pseudo polynomial Wigner-Ville distribution (SP-PWVD), an improved version of the polynomial Wigner-Ville distribution (PWVD), is pre-sented using a separable kernel. By adjusting the lengths of the functions in the kernel, the balance between resolution retaining and interference suppressing can be adjusted conveniently. The proposed method with merits of interference terms reduction and noise suppression can provide time frequency representation of better readability and more accurate instantaneous frequency (IF) estimation with higher order SP-PWVD. The performance of the SP-PWVD is verified by computer simulations.