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Sample records for chromatin higher-order structure

  1. Neutron scattering studies on chromatin higher-order structure

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

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

  2. Neutron scattering studies on chromatin higher-order structure

    International Nuclear Information System (INIS)

    Graziano, V.; Gerchman, S.E.; Schneider, D.K.; Ramakrishnan, V.

    1994-01-01

    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

  3. Higher-order structure of Saccharomyces cerevisiae chromatin

    International Nuclear Information System (INIS)

    Lowary, P.T.; Widom, J.

    1989-01-01

    We have developed a method for partially purifying chromatin from Saccharomyces cerevisiae (baker's yeast) to a level suitable for studies of its higher-order folding. This has required the use of yeast strains that are free of the ubiquitous yeast killer virus. Results from dynamic light scattering, electron microscopy, and x-ray diffraction show that the yeast chromatin undergoes a cation-dependent folding into 30-nm filaments that resemble those characteristic of higher-cell chromatin; moreover, the packing of nucleosomes within the yeast 30-nm filaments is similar to that of higher cells. These results imply that yeast has a protein or protein domain that serves the role of the histone H 1 found in higher cells; physical and genetic studies of the yeast activity could help elucidate the structure and function of H 1. Images of the yeast 30-nm filaments can be used to test crossed-linker models for 30-nm filament structure

  4. The effect of higher order chromatin structure on DNA damage and repair

    International Nuclear Information System (INIS)

    Yasui, L.S.; Warters, R.L.; Higashikubo, R.

    1985-01-01

    Alterations in chromatin structure are thought to play an important role in various radiobiological end points, i.e., DNA damage, DNA damage repair and cell survival. The authors use here the isoleucine deprivation technique to decondense higher order chromatin structure and asses X-ray induced DNA damage, DNA damage repair and cell survival on cells with decondensed chromatin as compared to controls. This chromatin decondensation manifests itself as a 30 fold decrease in nuclear area occupied by heterochromatin, an increased rate of Micrococcal nuclease digestion, 15% increased ethidium bromide intercalation and an altered binding capacity of Hl histone. These chromatin/nuclear changes do not affect X-ray induced DNA damage as measured by the alkaline elution technique or cell survival but slows DNA damage repair by 2 fold. Therefore, even though the chromatin appears more accessible to DNA damage and repair processes, these particular nuclear changes do not affect the DNA damaging effects of X-rays and in addition, repair is not enhanced by the ''relaxed'' state of chromatin. It is proposed that the altered metabolic state of isoleucine deprived cells provides a less efficient system for the repair of X-ray induced DNA damage

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

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Kozubek, Stanislav

    2010-01-01

    Roč. 704, 1-3 (2010), s. 88-100 ISSN 1383-5742 R&D Projects: GA MŠk ME 919; GA AV ČR(CZ) IAA500040802; GA AV ČR(CZ) 1QS500040508 Grant - others:GA MŠk(CZ) LC535 Program:LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : DNA double strand breaks * DSB repair * higher-order chromatin structure Subject RIV: BO - Biophysics Impact factor: 8.741, year: 2010

  6. Local changes of higher-order chromatin structure during DSB-repair

    International Nuclear Information System (INIS)

    Falk, M; Lukasova, E; Gabrielova, B; Ondrej, V; Kozubek, S

    2008-01-01

    We show that double-strand breaks (DSBs) induced in DNA of human cells by γ-radiation arise mainly in active, gene-rich, decondensed chromatin. We demonstrate that DSBs show limited movement in living cells, occasionally resulting in their permanent clustering, which poses a risk of incorrect DNA rejoining. In addition, some DSBs remain unrepaired for several days after irradiation, forming lesions repairable only with difficulty which are hazardous for genome stability. These 'late' DSBs colocalize with heterochromatin markers (dimethylated histone H3 at lysine 9, HP1 and CENP-A proteins), despite the low density of the surrounding chromatin. This indicates that there is epigenetic silencing of loci close to unrepaired DSBs and/or stabilization of damaged decondensed chromatin loops during repair and post-repair reconstitution of chromatin structure

  7. Higher-Order Chromatin Organisation in Cell Nuclei: Structure and Function

    Czech Academy of Sciences Publication Activity Database

    Kozubek, Stanislav; Lukášová, Emilie; Bártová, Eva; Kozubek, Michal; Skalníková, M.; Jirsová, Pavla; Koutná, I.

    2000-01-01

    Roč. 17, - (2000), s. 1145 ISSN 0739-1102. [Mendel - Brno 2000. DNA Structure and Interactions. Their Biological Roles and Implications in Biomedicine and Biotechnologies. 19.07.2000-23.07.2000, Brno] Institutional research plan: CEZ:A17/98:Z5-004-9-ii Subject RIV: BO - Biophysics

  8. Higher order chromatin organization in cancer

    Science.gov (United States)

    Reddy, Karen L.; Feinberg, Andrew P.

    2013-01-01

    In spite of our increased understanding of how genomes are dysregulated in cancer and a plethora of molecular diagnostic tools, the front line and ‘gold standard’ detection of cancer remains the pathologist’s detection of gross changes in cellular and tissue structure, most strikingly nuclear dis-organization. In fact, for over 140 years it has been noted that nuclear morphology is often disrupted in cancer. Even today, nuclear morphology measures include nuclear size, shape, DNA content (ploidy) and ‘chromatin organization’. Given the importance of nuclear shape to diagnoses of cancer phenotypes, it is surprising and frustrating that we currently lack a detailed understanding to explain these changes and how they might arise and relate to molecular events in the cell. It is an implicit hypothesis that perturbation of chromatin and epigenetic signatures may lead to alterations in nuclear structure (or vice versa) and that these perturbations lie at the heart of cancer genesis. In this review, we attempt to synthesize research leading to our current understanding on how chromatin interactions at the nuclear lamina, epigenetic modulation and gene regulation may intersect in cancer and offer a perspective on critical experiments that would help clarify how nuclear architecture may contribute to the cancerous phenotype. We also discuss the historical understanding of nuclear structure in normal cells and as a diagnostic in cancer. PMID:23266653

  9. A component of DNA double-strand break repair is dependent on the spatial orientation of the lesions within the higher-order structures of chromatin

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, P.J.; Bryant, P.E. (Saint Andrews Univ. (United Kingdom))

    1994-11-01

    By the use of a modified neutral filter elution procedure variations in the repair of DNA dsb have been observed between the ionising radiation sensitive mutant xrs-5 and the parent cell line CHO-K1. Conventional neutral filter elution requires harsh lysis conditions to remove higher-order chromatin structures which interfere with elution of DNA containing dsb. By lysing cells with non-ionic detergent in the presence of 2 mol dm[sup -3] salt, histone-depleted structures that retain the higher-order nuclear matrix organization, including chromatin loops, can be produced. Elution from these structures will only occur if two or more dsb lie within a single-looped domain delineated by points of attachment to the nuclear matrix. Repair experiments indicate that in CHO cells repair of dsb in loops containing multiple dsb are repaired with slow kinetics whilst dsb occurring in loops containing single dsb are repaired with fast kinetics. Xrs-5 cells are defective in the repair of multiply damaged loops. This work indicates that the spatial orientation of dsb in the higher-order structures of chromatin are a possible factor in the repair of these lesions. (Author).

  10. A component of DNA double-strand break repair is dependent on the spatial orientation of the lesions within the higher-order structures of chromatin

    International Nuclear Information System (INIS)

    Johnston, P.J.; Bryant, P.E.

    1994-01-01

    By the use of a modified neutral filter elution procedure variations in the repair of DNA dsb have been observed between the ionising radiation sensitive mutant xrs-5 and the parent cell line CHO-K1. Conventional neutral filter elution requires harsh lysis conditions to remove higher-order chromatin structures which interfere with elution of DNA containing dsb. By lysing cells with non-ionic detergent in the presence of 2 mol dm -3 salt, histone-depleted structures that retain the higher-order nuclear matrix organization, including chromatin loops, can be produced. Elution from these structures will only occur if two or more dsb lie within a single-looped domain delineated by points of attachment to the nuclear matrix. Repair experiments indicate that in CHO cells repair of dsb in loops containing multiple dsb are repaired with slow kinetics whilst dsb occurring in loops containing single dsb are repaired with fast kinetics. Xrs-5 cells are defective in the repair of multiply damaged loops. This work indicates that the spatial orientation of dsb in the higher-order structures of chromatin are a possible factor in the repair of these lesions. (Author)

  11. 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 decondensation....... Our data show that CHD4, the catalytic subunit of the NuRD complex, interacts with RNF8 and is essential for RNF8-mediated chromatin unfolding. The chromatin remodelling activity of CHD4 promotes efficient ubiquitin conjugation and assembly of RNF168 and BRCA1 at DNA double-strand breaks....... Interestingly, RNF8-mediated recruitment of CHD4 and subsequent chromatin remodelling were independent of the ubiquitin-ligase activity of RNF8, but involved a non-canonical interaction with the forkhead-associated (FHA) domain. Our study reveals a new mechanism of chromatin remodelling-assisted ubiquitylation...

  12. Heterochromatinization associated with cell differentiation as a model to study DNA double strand break induction and repair in the context of higher-order chromatin structure

    International Nuclear Information System (INIS)

    Falk, Martin; Lukášová, Emilie; Štefančíková, Lenka; Baranová, Elena; Falková, Iva; Ježková, Lucie; Davídková, Marie; Bačíková, Alena; Vachelová, Jana; Michaelidesová, Anna; Kozubek, Stanislav

    2014-01-01

    Cell differentiation is associated with extensive gene silencing, heterochromatinization and potentially decreasing need for repairing DNA double-strand breaks (DSBs). Differentiation stages of blood cells thus represent an excellent model to study DSB induction, repair and misrepair in the context of changing higher-order chromatin structure. We show that immature granulocytes form γH2AX and 53BP1 foci, contrary to the mature cells; however, these foci colocalize only rarely and DSB repair is inefficient. Moreover, specific chromatin structure of granulocytes probably influences DSB induction. - Highlights: ► DSB repair is absent in mature granulocytes with condensed chromatin. ► Repair proteins and γH2AX appear in immature stages but rarely colocalize. ► γH2AX persist long times in these cells and DSB repair is inefficient. ► Even though, γH2AX foci “move” out of the dense chromatin. ► 53BP1 enters HP1β domains only after their decondensation

  13. A model of photon cell killing based on the spatio-temporal clustering of DNA damage in higher order chromatin structures.

    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.

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

    DEFF Research Database (Denmark)

    Ebert, Grit; Steininger, Anne; Weißmann, Robert

    2014-01-01

    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......BACKGROUND: Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders...... chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome....

  15. H2O2-induced higher order chromatin degradation: A novel ...

    Indian Academy of Sciences (India)

    Unknown

    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 ... clease works through a single strand scission mechanism ... a great mutagenic risk to the surviving cells, because en-.

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

    Directory of Open Access Journals (Sweden)

    Ashwat Visvanathan

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

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

    Directory of Open Access Journals (Sweden)

    Cremer Thomas

    2005-12-01

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

  18. 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...... to the binding of systems in nature. It now appears that recent generalization to higher order Brunnian structures may potentially be realized as laboratory made or naturally occurring systems. With the binding energy as measure, we discuss possibilities of physical realization in nuclei, cold atoms...

  19. Chromatin Structure and Function

    CERN Document Server

    Wolffe, Alan P

    1999-01-01

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

  20. UV-induced structural changes in chromatin

    International Nuclear Information System (INIS)

    Lang, H.; Zimmer, C.; Vengerov, Yu.Yu.

    1985-01-01

    UV-induced structural alterations of chromatin were studied by means of CD, electron microscopic, and gel electrophoretic measurements. The results indicate that chromatin undergoes serious structural changes after irradiation even at very low fluences. In the low fluence range the structural transitions from the higher ordered chromatin structure to the unfolded state occur without detectable changes in the content of histone H1 and of the core histones. Histone H1 disappears only at fluences above 10 kJ/m 2 . Furthermore, DNA in chromatin is much more sensitive against UV-irradiation and shows a higher degree of strand scission relative to free DNA. While fragmentation in free DNA occurs at fluences above 15 kJ/m 2 , it occurs even at 5.5 kJ/m 2 in the case of chromatin. The biological meaning of the observed UV-induced structural alterations of chromatin is discussed. (author)

  1. The Higher Order Structure of Environmental Attitudes: A Cross-Cultural Examination

    Directory of Open Access Journals (Sweden)

    Taciano L. Milfont

    2010-01-01

    Full Text Available Past research has suggested that Preservation and Utilization are the two higher order dimensions forming the hierarchical structure of environmental attitudes. This means that these two higher order dimensions could group all kinds of perceptions or beliefs regarding the natural environment people have. A crosscultural study was conducted in Brazil, New Zealand, and South Africa to test this hierarchical structure of environmental attitudes. Results from single- and multi-group confirmatory factor analyses demonstrated that environmental attitudes are a multidimensional construct, and that their first-order factors associate to each other to form a vertical structure. However, the question whether the vertical structure comprise a single higher order factor or two higher order factors still remains unanswered. These results are discussed and directions for future research trying to demonstrate that Preservation and Utilization, taken as distinct second-order environmental attitudes factors, are more empirically meaningful than a single and generalised environmental attitudes higher order factor are presented.

  2. TADs are 3D structural units of higher-order chromosome organization in Drosophila

    Science.gov (United States)

    Szabo, Quentin; Jost, Daniel; Chang, Jia-Ming; Cattoni, Diego I.; Papadopoulos, Giorgio L.; Bonev, Boyan; Sexton, Tom; Gurgo, Julian; Jacquier, Caroline; Nollmann, Marcelo; Bantignies, Frédéric; Cavalli, Giacomo

    2018-01-01

    Deciphering the rules of genome folding in the cell nucleus is essential to understand its functions. Recent chromosome conformation capture (Hi-C) studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. Using a combination of Hi-C, three-dimensional (3D) fluorescent in situ hybridization, super-resolution microscopy, and polymer modeling, we provide an integrative view of chromatin folding in Drosophila. We observed that repressed TADs form a succession of discrete nanocompartments, interspersed by less condensed active regions. Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact events. These results indicate that TADs are fundamental 3D genome units that engage in dynamic higher-order inter-TAD connections. This domain-based architecture is likely to play a major role in regulatory transactions during DNA-dependent processes. PMID:29503869

  3. Higher order magnetic modulation structures in rare earth metal, alloys and compounds under extreme conditions

    International Nuclear Information System (INIS)

    Kawano, S.

    2003-01-01

    Magnetic materials consisting of rare earth ions form modulation structures such as a helical or sinusoidal structure caused by the oscillating magnetic interaction between rare earth ions due to RKKY magnetic interaction. These modulation structures, in some cases, develop further to higher order modulation structures by additional modulations caused by higher order crystalline electric field, magnetic interactions such as spin-lattice interaction, external magnetic field and pressure. The higher order modulation structures are observed in a spin-slip structure or a helifan structure in Ho, and a tilt helix structure in a TbEr alloy. Paramagnetic ions originated from frustration generate many magnetic phases under applied external magnetic field. KUR neutron diffraction groups have performed the development and adjustment of high-pressure instruments and external magnetic fields for neutron diffraction spectrometers. The studies of 'neutron diffraction under extreme conditions' by the seven groups are described in this report. (Y. Kazumata)

  4. Capturing Structural Heterogeneity in Chromatin Fibers.

    Science.gov (United States)

    Ekundayo, Babatunde; Richmond, Timothy J; Schalch, Thomas

    2017-10-13

    Chromatin fiber organization is implicated in processes such as transcription, DNA repair and chromosome segregation, but how nucleosomes interact to form higher-order structure remains poorly understood. We solved two crystal structures of tetranucleosomes with approximately 11-bp DNA linker length at 5.8 and 6.7 Å resolution. Minimal intramolecular nucleosome-nucleosome interactions result in a fiber model resembling a flat ribbon that is compatible with a two-start helical architecture, and that exposes histone and DNA surfaces to the environment. The differences in the two structures combined with electron microscopy reveal heterogeneous structural states, and we used site-specific chemical crosslinking to assess the diversity of nucleosome-nucleosome interactions through identification of structure-sensitive crosslink sites that provide a means to characterize fibers in solution. The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

    McGill, Ryan J.; Canivez, Gary L.

    2016-01-01

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

  7. Distribution of u.v.-induced repair events in higher-order chromatin loops in human and hamster fibroblasts

    International Nuclear Information System (INIS)

    Mullenders, L.H.F.; Zeeland, A.A. van; Natarajan, A.T.; Kesteren, A.C. van; Bussmann, C.J.M.

    1986-01-01

    The repair of u.v.-induced damage in human and rodent cells was investigated at the level of DNA loops attached to the nuclear matrix. After 2 h post-u.v. incubation, DNase I digestion studies revealed a 3- to 4-fold enrichment of repair-labeled DNA at the nuclear matrix in four xeroderma pigmentosum cell strains belonging to complementation group C. Two xeroderma pigmentosum cell strains of complementation group D and Syrian hamster embryonic cells, as well as in HeLa cells and normal human fibroblasts, no enrichment of repair-labeled DNA at the nuclear matrix was observed. Visualization of repair events in DNA loops by autoradiography of DNA halo - matrix structures confirmed the biochemical observations. The presence or absence of preferential repair of nuclear matrix-associated DNA paralleled the presence or absence of inhomogeneity in the distribution of T4 endonuclease-V-sensitive sites. In xeroderma pigmentosum cells of complementation group C showed that after 2 h post-u.v. incubation, repair events were found at both attachment sites in a limited number of loops and that large domains of loops were not subjected to repair. (author)

  8. Higher-Order Structure in Bacterial VapBC Toxin-Antitoxin Complexes

    DEFF Research Database (Denmark)

    Bendtsen, Kirstine L; Brodersen, Ditlev E

    2017-01-01

    Toxin-antitoxin systems are widespread in the bacterial kingdom, including in pathogenic species, where they allow rapid adaptation to changing environmental conditions through selective inhibition of key cellular processes, such as DNA replication or protein translation. Under normal growth...... that allow auto-regulation of transcription by direct binding to promoter DNA. In this chapter, we review our current understanding of the structural characteristics of type II toxin-antitoxin complexes in bacterial cells, with a special emphasis on the staggering variety of higher-order architecture...... conditions, type II toxins are inhibited through tight protein-protein interaction with a cognate antitoxin protein. This toxin-antitoxin complex associates into a higher-order macromolecular structure, typically heterotetrameric or heterooctameric, exposing two DNA binding domains on the antitoxin...

  9. Higher order Stark effect and transition probabilities on hyperfine structure components of hydrogen like atoms

    Energy Technology Data Exchange (ETDEWEB)

    Pal' chikov, V.G. [National Research Institute for Physical-Technical and Radiotechnical Measurements - VNIIFTRI (Russian Federation)], E-mail: vitpal@mail.ru

    2000-08-15

    A quantum-electrodynamical (QED) perturbation theory is developed for hydrogen and hydrogen-like atomic systems with interaction between bound electrons and radiative field being treated as the perturbation. The dependence of the perturbed energy of levels on hyperfine structure (hfs) effects and on the higher-order Stark effect is investigated. Numerical results have been obtained for the transition probability between the hfs components of hydrogen-like bismuth.

  10. 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)

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

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.

    2002-01-01

    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)

  12. ANOVA-HDMR structure of the higher order nodal diffusion solution

    International Nuclear Information System (INIS)

    Bokov, P. M.; Prinsloo, R. H.; Tomasevic, D. I.

    2013-01-01

    Nodal diffusion methods still represent a standard in global reactor calculations, but employ some ad-hoc approximations (such as the quadratic leakage approximation) which limit their accuracy in cases where reference quality solutions are sought. In this work we solve the nodal diffusion equations utilizing the so-called higher-order nodal methods to generate reference quality solutions and to decompose the obtained solutions via a technique known as High Dimensional Model Representation (HDMR). This representation and associated decomposition of the solution provides a new formulation of the transverse leakage term. The HDMR structure is investigated via the technique of Analysis of Variance (ANOVA), which indicates why the existing class of transversely-integrated nodal methods prove to be so successful. Furthermore, the analysis leads to a potential solution method for generating reference quality solutions at a much reduced calculational cost, by applying the ANOVA technique to the full higher order solution. (authors)

  13. A higher-order tensor vessel tractography for segmentation of vascular structures.

    Science.gov (United States)

    Cetin, Suheyla; Unal, Gozde

    2015-10-01

    A new vascular structure segmentation method, which is based on a cylindrical flux-based higher order tensor (HOT), is presented. On a vessel structure, the HOT naturally models branching points, which create challenges for vessel segmentation algorithms. In a general linear HOT model embedded in 3D, one has to work with an even order tensor due to an enforced antipodal-symmetry on the unit sphere. However, in scenarios such as in a bifurcation, the antipodally-symmetric tensor embedded in 3D will not be useful. In order to overcome that limitation, we embed the tensor in 4D and obtain a structure that can model asymmetric junction scenarios. During construction of a higher order tensor (e.g. third or fourth order) in 4D, the orientation vectors lie on the unit 3-sphere, in contrast to the unit 2-sphere in 3D tensor modeling. This 4D tensor is exploited in a seed-based vessel segmentation algorithm, where the principal directions of the 4D HOT is obtained by decomposition, and used in a HOT tractography approach. We demonstrate quantitative validation of the proposed algorithm on both synthetic complex tubular structures as well as real cerebral vasculature in Magnetic Resonance Angiography (MRA) datasets and coronary arteries from Computed Tomography Angiography (CTA) volumes.

  14. Analysis of Higher Order Modes in Large Superconducting Radio Frequency Accelerating Structures

    CERN Document Server

    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.

  15. Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture.

    Science.gov (United States)

    Moriyama, Kenji; Yoshizawa-Sugata, Naoko; Masai, Hisao

    2018-03-09

    Rap1-interacting protein 1 (Rif1) regulates telomere length in budding yeast. We previously reported that, in metazoans and fission yeast, Rif1 also plays pivotal roles in controlling genome-wide DNA replication timing. We proposed that Rif1 may assemble chromatin compartments that contain specific replication-timing domains by promoting chromatin loop formation. Rif1 also is involved in DNA lesion repair, restart after replication fork collapse, anti-apoptosis activities, replicative senescence, and transcriptional regulation. Although multiple physiological functions of Rif1 have been characterized, biochemical and structural information on mammalian Rif1 is limited, mainly because of difficulties in purifying the full-length protein. Here, we expressed and purified the 2418-amino-acid-long, full-length murine Rif1 as well as its partially truncated variants in human 293T cells. Hydrodynamic analyses indicated that Rif1 forms elongated or extended homo-oligomers in solution, consistent with the presence of a HEAT-type helical repeat segment known to adopt an elongated shape. We also observed that the purified murine Rif1 bound G-quadruplex (G4) DNA with high specificity and affinity, as was previously shown for Rif1 from fission yeast. Both the N-terminal (HEAT-repeat) and C-terminal segments were involved in oligomer formation and specifically bound G4 DNA, and the central intrinsically disordered polypeptide segment increased the affinity for G4. Of note, pulldown assays revealed that Rif1 simultaneously binds multiple G4 molecules. Our findings support a model in which Rif1 modulates chromatin loop structures through binding to multiple G4 assemblies and by holding chromatin fibers together. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-05-15

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

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

    International Nuclear Information System (INIS)

    Klein, Dionne C.G.; Latz, Eicke; Espevik, Terje; Stokke, Bjorn T.

    2010-01-01

    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.

  18. Measurements of higher order modes in a 30 cm long X-band structure

    International Nuclear Information System (INIS)

    Xiao, L.; Liang, Y.; Tong, D.; Zhang, H.

    2001-01-01

    The use of a cage of metallic wires as a bead is proposed to measure the higher order modes (HOMs) in an X-band accelerating structure. These long thin wires can isolate the longitudinal electric field component from other field components and produce sufficient frequency shift in bead-pull measurements. In the setup described in this paper, the bead is made by sputtering silver film onto a thin nylon line through a specially designed fixture. The cage has a size of approximately 0.5 mm in diameter, 2 mm in length and more than six metallic wires of less than 0.1 mm in width. The fabrication and calibration of the cage are described. The longitudinal electric fields of the lowest passband dipole mode TM 110 in a 30 cm long X-band structure are measured by bead-pull measurements. Results are compared with the calculated ones obtained from URMELT-code

  19. Study of higher order modes in superconducting accelerating structures for linac applications

    Energy Technology Data Exchange (ETDEWEB)

    Schuh, Marcel

    2011-06-22

    Higher Order Modes (HOMs) can severely limit the operation of superconducting cavities in a linear accelerator with high beam current, high duty factor and complex pulse structure. Therefore, the full HOM spectrum has to be analysed in detail to identify potentially dangerous modes already during the design phase and to define their damping requirements. For this purpose a dedicated beam dynamics simulation code, Simulation of higher order Mode Dynamics (SMD), focusing on beam-HOM interaction, has been developed in the frame of this project. SMD allows to analyse the beam behaviour under the presence of HOMs, taking into account many important effects, such as for example the HOM frequency spread, beam input jitter, different chopping patterns, as well as klystron and alignment errors. SMD is used to investigate in detail into the effects of HOMs in the Superconducting Proton Linac (SPL) at CERN and in particular their potential to drive beam instabilities in the longitudinal and transverse direction. Based on these results, HOM damping requirements for the HOM coupler design are then defined. In addition, the linear accelerators of the European Spallation Source (ESS) and the Spallation Neutron Source (SNS) are analysed with respect to HOM impact and the results are compared with the SPL simulations. (orig.)

  20. Assessment of higher order structure comparability in therapeutic proteins using nuclear magnetic resonance spectroscopy.

    Science.gov (United States)

    Amezcua, Carlos A; Szabo, Christina M

    2013-06-01

    In this work, we applied nuclear magnetic resonance (NMR) spectroscopy to rapidly assess higher order structure (HOS) comparability in protein samples. Using a variation of the NMR fingerprinting approach described by Panjwani et al. [2010. J Pharm Sci 99(8):3334-3342], three nonglycosylated proteins spanning a molecular weight range of 6.5-67 kDa were analyzed. A simple statistical method termed easy comparability of HOS by NMR (ECHOS-NMR) was developed. In this method, HOS similarity between two samples is measured via the correlation coefficient derived from linear regression analysis of binned NMR spectra. Applications of this method include HOS comparability assessment during new product development, manufacturing process changes, supplier changes, next-generation products, and the development of biosimilars to name just a few. We foresee ECHOS-NMR becoming a routine technique applied to comparability exercises used to complement data from other analytical techniques. Copyright © 2013 Wiley Periodicals, Inc.

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

    Science.gov (United States)

    Jin, Si

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

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

    Science.gov (United States)

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

    2001-01-01

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

  3. Localization of ultraviolet-induced excision repair in the nucleus and the distribution of repair events in higher order chromatin loops in mammalian cells

    Energy Technology Data Exchange (ETDEWEB)

    Mullenders, L.H.F.; Zeeland, A.A. van; Natarajan, A.T.

    1987-01-01

    Several lines of evidence indicate that eukaryotic DNA is arranged in highly supercoiled domains or loops, and that the repeating loops are constrained by attachment to a nuclear skeletal structure termed the nuclear matrix. We have investigated whether the repair of DNA damage occurs in the nuclear matrix compartment. Normal human fibroblasts, ultraviolet (u.v.)-irradiated with 30 J m/sup -2/ and post-u.v. incubated in the presence of hydroxyurea, did not show any evidence for the occurrence of repair synthesis at the nuclear matrix. 5 J m/sup -2/ repair synthesis seems to initiate at the nuclear matrix, although only part of the total repair could be localized there. In u.v.-irradiated (30 J m/sup -2/) normal human fibroblast post-u.v. incubated in the presence of hydroxyurea and arabinsosylcytosine for 2h, multiple single-stranded regions are generated in a DNA loop as a result of the inhibition of the excision repair process. Preferential repair of certain domains in the chromatin was shown to occur in xeroderma pigmentosum cells of complementation group C (XP-C) in contrast to XP-D cells and Syrian hamster embryonic cells.

  4. The localization of ultraviolet-induced excision repair in the nucleus and the distribution of repair events in higher order chromatin loops in mammalian cells

    International Nuclear Information System (INIS)

    Mullenders, L.H.F.; Zeeland, A.A. van; Natarajan, A.T.

    1987-01-01

    Several lines of evidence indicate that eukaryotic DNA is arranged in highly supercoiled domains or loops, and that the repeating loops are constrained by attachment to a nuclear skeletal structure termed the nuclear matrix. We have investigated whether the repair of DNA damage occurs in the nuclear matrix compartment. Normal human fibroblasts, ultraviolet (u.v.)-irradiated with 30 J m -2 and post-u.v. incubated in the presence of hydroxyurea, did not show any evidence for the occurrence of repair synthesis at the nuclear matrix. 5 J m -2 repair synthesis seems to initiate at the nuclear matrix, although only part of the total repair could be localized there. In u.v.-irradiated (30 J m -2 ) normal human fibroblast post-u.v. incubated in the presence of hydroxyurea and arabinsosylcytosine for 2h, multiple single-stranded regions are generated in a DNA loop as a result of the inhibition of the excision repair process. Preferential repair of certain domains in the chromatin was shown to occur in xeroderma pigmentosum cells of complementation group C (XP-C) in contrast to XP-D cells and Syrian hamster embryonic cells. (author)

  5. 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...... the experimentally observed micro-structural behavior, within a framework based on continuous field quantities, poses obvious challenges, since the evolution of dislocation structures is inherently a discrete and discontinuous process. This challenge, in particular, motivates the present study, and the aim...... 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...

  6. Getting in (and out of) the loop: regulating higher order telomere structures.

    Science.gov (United States)

    Luke-Glaser, Sarah; Poschke, Heiko; Luke, Brian

    2012-01-01

    The DNA at the ends of linear chromosomes (the telomere) folds back onto itself and forms an intramolecular lariat-like structure. Although the telomere loop has been implicated in the protection of chromosome ends from nuclease-mediated resection and unscheduled DNA repair activities, it potentially poses an obstacle to the DNA replication machinery during S-phase. Therefore, the coordinated regulation of telomere loop formation, maintenance, and resolution is required in order to establish a balance between protecting the chromosome ends and promoting their duplication prior to cell division. Until recently, the only factor known to influence telomere looping in human cells was TRF2, a component of the shelterin complex. Recent work in yeast and mouse cells has uncovered additional regulatory factors that affect the loop structure at telomeres. In the following "perspective" we outline what is known about telomere looping and highlight the latest results regarding the regulation of this chromosome end structure. We speculate about how the manipulation of the telomere loop may have therapeutic implications in terms of diseases associated with telomere dysfunction and uncontrolled proliferation.

  7. Getting in (and out of the loop: regulating higher order telomere structures

    Directory of Open Access Journals (Sweden)

    Sarah eLuke-Glaser

    2012-11-01

    Full Text Available The DNA at the ends of linear chromosomes (the telomere folds back onto itself and forms an intramolecular lariat-like structure. Although the telomere loop has been implicated in the protection of chromosome ends from nuclease-mediated resection and unscheduled DNA repair activities, it potentially poses an obstacle to the DNA replication machinery during S phase. Therefore, the coordinated regulation of telomere loop formation, maintenance and resolution is required in order to establish a balance between protecting the chromosome ends and promoting their duplication prior to cell division. Until recently, the only factor know to influence telomere looping in human cells was TRF2, a component of the shelterin complex. Recent work in yeast and mouse cells has uncovered additional regulatory factors that affect the loop structure at telomeres. In the following perspective we will outline what is known about telomere looping and highlight the latest results regarding the regulation of this chromosome end structure. We will speculate about how the manipulation of the telomere loop may have therapeutic implications in terms of diseases associated with telomere dysfunction and uncontrolled proliferation.

  8. Structural interactions in ionic liquids linked to higher-order Poisson-Boltzmann equations

    Science.gov (United States)

    Blossey, R.; Maggs, A. C.; Podgornik, R.

    2017-06-01

    We present a derivation of generalized Poisson-Boltzmann equations starting from classical theories of binary fluid mixtures, employing an approach based on the Legendre transform as recently applied to the case of local descriptions of the fluid free energy. Under specific symmetry assumptions, and in the linearized regime, the Poisson-Boltzmann equation reduces to a phenomenological equation introduced by Bazant et al. [Phys. Rev. Lett. 106, 046102 (2011)], 10.1103/PhysRevLett.106.046102, whereby the structuring near the surface is determined by bulk coefficients.

  9. Higher Order QED Contributions to the Atomic Structure at Strong Central Fields

    International Nuclear Information System (INIS)

    Mokler, P H

    2007-01-01

    An accurate determination of the precise structure of highly charged, very heavy ions is crucial for understanding QED at strong fields. The experimental advances in the spectroscopy of very heavy, highly charged ions-in particular H-, He- and Li-like species-are reviewed: Presently the ground state Lamb shift for H-like U ions is measured on a 1% level of accuracy; the screening terms in two-electron QED have just been touched by experiments for He-like U; and two-loop QED terms have been determined with ultimate accuracy for Li-like heavy species. The different approaches on QED measurements in strong fields will be discussed and the results compared to theory

  10. Functional requirements of AID's higher order structures and their interaction with RNA-binding proteins.

    Science.gov (United States)

    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.

  11. Higher-order Stark effect on magnetic fine structure of the helium atom

    Energy Technology Data Exchange (ETDEWEB)

    Magunov, A.; Pal' chikov, V.; Pivovarov, V. [National Research Inst. for Physical-Technical and Radiotechnical Measurements (VNIIFTRI), Mendeleevo, Moscow Region (Russian Federation); Ovsiannikov, V. [Dept. of Physics, Voronezh State Univ. (Russian Federation); Oppen, G. von [Inst. fuer Analytische und Atomare Physik at Technische Univ. Berlin (Germany)

    2001-07-01

    We have calculated the scalar and tensor dipole polarizabilities ({beta}) and hyperpolarizabilities ({gamma}) of excited 1s2p {sup 3}P{sub 0}, 1s2p {sup 3}P{sub 2}- states of helium. Our theory includes fine structure of triplet sublevels. Semiempirical and accurate electron-correlated wave functions have been used to determine the static values of {beta} and {gamma}. Numerical calculations are carried out using sums of oscillator strengths and, alternatively, with the Green function for the excited valence electron. Specifically, we present results for the integral over the continuum, for second- and fourth-order matrix elements. The corresponding estimations indicate that these corrections are of the order of 23% for the scalar part of polarizability and only of the order of 3% for the tensor part.

  12. Higher order structure analysis of nano-materials by spectral reflectance of laser-plasma soft x-ray

    International Nuclear Information System (INIS)

    Azuma, Hirozumi; Takeichi, Akihiro; Noda, Shoji

    1995-01-01

    We have proposed a new experimental arrangement to measure spectral reflectance of nano-materials for analyzing higher order structure with laser-plasma soft x-rays. Structure modification of annealed Mo/Si multilayers and a nylon-6/clay hybrid with poor periodicity was investigated. The measurement of the spectral reflectance of soft x-rays from laser-produced plasma was found to be a useful method for the structure analysis of nano-materials, especially those of rather poor periodicity

  13. Field profile and loading measurements on higher order modes in a two cell 500 MHz superconducting structure

    International Nuclear Information System (INIS)

    Barry, W.; Edighoffer, J.; Chattopadhyay, S.; Fornaco, S.

    1992-01-01

    The Infrared Free Electron Laser, being designed at LBL as part of the Chemical Dynamics Research Laboratory, is based on a 500 MHz superconducting linac driver that consists of five 4-cell structures of the CERN/DESY type. A 500 MHz, 2-cell version of this structure is being used in a joint Stanford/LBL/BNL program to study accelerator issues relevant to the FEL applications. As part of this study, field profile and loading measurements of higher order modes have been made on the prototype structure. (Author) 3 refs., 2 figs., tab

  14. Field profile and loading measurements on higher order modes in a two cell 500 MHz superconducting structure

    International Nuclear Information System (INIS)

    Barry, W.; Edighoffer, J.; Chattopadhyay, S.; Fornaca, S.

    1992-08-01

    The Infrared Free Electron Laser, being designed at LBL as part of the Chemical Dynamics Research Laboratory, is based on a 500 MHz superconducting linac driver that consists of five 4-cell structures of the CERN/DESY type. A 500 MHz, 2-cell version of this structure is being used in a joint Stanford/LBL/BNL program to study accelerator issues relevant to the FEL applications. As part of this study, field profile and loading measurements of higher order modes have been made on the prototype structure

  15. Structured illumination to spatially map chromatin motions.

    Science.gov (United States)

    Bonin, Keith; Smelser, Amanda; Moreno, Naike Salvador; Holzwarth, George; Wang, Kevin; Levy, Preston; Vidi, Pierre-Alexandre

    2018-05-01

    We describe a simple optical method that creates structured illumination of a photoactivatable probe and apply this method to characterize chromatin motions in nuclei of live cells. A laser beam coupled to a diffractive optical element at the back focal plane of an excitation objective generates an array of near diffraction-limited beamlets with FWHM of 340  ±  30  nm, which simultaneously photoactivate a 7  ×  7 matrix pattern of GFP-labeled histones, with spots 1.70  μm apart. From the movements of the photoactivated spots, we map chromatin diffusion coefficients at multiple microdomains of the cell nucleus. The results show correlated motions of nearest chromatin microdomain neighbors, whereas chromatin movements are uncorrelated at the global scale of the nucleus. The method also reveals a DNA damage-dependent decrease in chromatin diffusion. The diffractive optical element instrumentation can be easily and cheaply implemented on commercial inverted fluorescence microscopes to analyze adherent cell culture models. A protocol to measure chromatin motions in nonadherent human hematopoietic stem and progenitor cells is also described. We anticipate that the method will contribute to the identification of the mechanisms regulating chromatin mobility, which influences most genomic processes and may underlie the biogenesis of genomic translocations associated with hematologic malignancies. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

  16. 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

  17. Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats

    Science.gov (United States)

    Pierce, Sarah E.; Wang, Junmei; Jayawickramarajah, Janarthanan; Hamilton, Andrew D.; Brodbelt, Jennifer S.

    2010-01-01

    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. The guanine-containing strand (G9) consistently formed quadruplexes upon annealing, whereas the isoguanine strand (Ig9) formed both pentaplexes and quadruplexes depending on the annealing cation. Quadruplex formation with G9 showed some dependence on the identity of the cation present during annealing with high relative quadruplex formation detected with six of ten cations. Analogous annealing experiments with Ig9 resulted in complex formation with all ten cations, and the majority of the resulting complexes were pentaplexes. CD results indicated most of the original complexes survived the desalting process necessary for ESI-MS analysis. In addition, several complexes, especially the pentaplexes, were found to be capable of cation exchange with ammonium ions. Ab initio calculations were conducted for isoguanine tetrads and pentads coordinated with all ten cations to predict the most energetically stable structures of the complexes in the gas phase. The observed preference of forming quadruplexes versus pentaplexes as a function of the coordinated cation can be interpreted by the calculated reaction energies of both the tetrads and pentads in combination with the distortion energies of tetrads. PMID:19746468

  18. The application of the mesh-free method in the numerical simulations of the higher-order continuum structures

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Yuzhou, E-mail: yuzhousun@126.com; Chen, Gensheng; Li, Dongxia [School of Civil Engineering and Architecture, Zhongyuan University of Technology, Zhengzhou (China)

    2016-06-08

    This paper attempts to study the application of mesh-free method in the numerical simulations of the higher-order continuum structures. A high-order bending beam considers the effect of the third-order derivative of deflections, and can be viewed as a one-dimensional higher-order continuum structure. The moving least-squares method is used to construct the shape function with the high-order continuum property, the curvature and the third-order derivative of deflections are directly interpolated with nodal variables and the second- and third-order derivative of the shape function, and the mesh-free computational scheme is establish for beams. The coupled stress theory is introduced to describe the special constitutive response of the layered rock mass in which the bending effect of thin layer is considered. The strain and the curvature are directly interpolated with the nodal variables, and the mesh-free method is established for the layered rock mass. The good computational efficiency is achieved based on the developed mesh-free method, and some key issues are discussed.

  19. The global relationship between chromatin physical topology, fractal structure, and gene expression

    DEFF Research Database (Denmark)

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

    2017-01-01

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

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

    Science.gov (United States)

    Wolff, Hans-Georg; Preising, Katja

    2005-02-01

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

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

    DEFF Research Database (Denmark)

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

    1983-01-01

    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...

  2. Higher-Order Hierarchies

    DEFF Research Database (Denmark)

    Ernst, Erik

    2003-01-01

    This paper introduces the notion of higher-order inheritance hierarchies. They are useful because they provide well-known benefits of object-orientation at the level of entire hierarchies-benefits which are not available with current approaches. Three facets must be adressed: First, it must be po...

  3. Higher Order Mode Fibers

    DEFF Research Database (Denmark)

    Israelsen, Stine Møller

    This PhD thesis considers higher order modes (HOMs) in optical fibers. That includes their excitation and characteristics. Within the last decades, HOMs have been applied both for space multiplexing in optical communications, group velocity dispersion management and sensing among others......-radial polarization as opposed to the linear polarization of the LP0X modes. The effect is investigated numerically in a double cladding fiber with an outer aircladding using a full vectorial modesolver. Experimentally, the bowtie modes are excited using a long period grating and their free space characteristics...... and polarization state are investigated. For this fiber, the onset of the bowtie effect is shown numerically to be LP011. The characteristics usually associated with Bessel-likes modes such as long diffraction free length and selfhealing are shown to be conserved despite the lack of azimuthal symmetry...

  4. Nuclear and chromatin structures and their influence on the radiosensitivity of DNA

    International Nuclear Information System (INIS)

    Oleinick, N.L.; Chiu, S.-M.

    1994-01-01

    Among the factors contributing to the distribution of DNA damage within irradiated mammalian cell nuclei are the interactions of DNA with nuclear proteins and the formation of multi-molecular chromatin structures. Studies on the manipulation of chromatin structures of isolated nuclei are summarised. The majority of chromatin within the nucleus of living cells is tightly compacted into nucleosomal superhelices and other higher order structures which have a limited ability to be damaged by radiation. The treatment of isolated nuclei with hypotonic buffers causes a decondensation of these structures and markedly sensitises the DNA to radiation, while retaining the majority of the chromosomal proteins. On the other hand, treatment of nuclei with hypertonic buffers strips the DNA of specific classes of nuclear proteins, destroying chromatin structure, and this procedure also enhances the sensitivity of the DNA to radiation. The various expanded chromatin structures are models for the structure of the minor fraction of DNA which is decondensed in preparation for transcription or replication. The combined results indicate that the majority of nuclear DNA is protected by histones and other nuclear proteins from radiation damage, partially as a result of the limited accessibility of the condensed structures to hydroxyl radical and partially as a result of the scavenging of radicals by the proteins. (Author)

  5. Higher-order semantic structures in an African Grey parrot's vocalizations: evidence from the hyperspace analog to language (HAL) model.

    Science.gov (United States)

    Kaufman, Allison B; Colbert-White, Erin N; Burgess, Curt

    2013-09-01

    Previous research has described the significant role that social interaction plays in both the acquisition and use of speech by parrots. The current study analyzed the speech of one home-raised African Grey parrot (Psittacus erithacus erithacus) across three different social contexts: owner interacting with parrot in the same room, owner and parrot interacting out of view in adjacent rooms, and parrot home alone. The purpose was to determine the extent to which the subject's speech reflected an understanding of the contextual substitutability (e.g., the word street can be substituted in context for the word road) of the vocalizations that comprised the units in her repertoire (i.e., global co-occurrence of repertoire units; Burgess in Behav Res Methods Instrum Comput 30:188-198, 1998; Lund and Burgess in Behav Res Methods Instrum Comput 28:203-208, 1996). This was accomplished via the human language model hyperspace analog to language (HAL). HAL is contextually driven and bootstraps language "rules" from input without human intervention. Because HAL does not require human tutelage, it provided an objective measure to empirically examine the parrot's vocalizations. Results indicated that the subject's vocalization patterns did contain global co-occurrence. The presence of this quality in this nonhuman's speech may be strongly indicative of higher-order cognitive skills.

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

    DEFF Research Database (Denmark)

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

    1984-01-01

    An experimental approach was used to determine, and compare, the higher-order structure within domain VI of the 23 S ribosomal RNAs from Escherichia coli and Bacillus stearothermophilus. This domain, which encompasses approximately 300 nucleotides at the 3' end of the RNAs, consists of two large ...

  7. Implications of Self-Deception for Self-Reported Intrinsic and Extrinsic Motivational Dispositions and Actual Learning Performance: A Higher Order Structural Model

    Science.gov (United States)

    Hirschfeld, Robert R.; Thomas, Christopher H.; McNatt, D. Brian

    2008-01-01

    The authors explored implications of individuals' self-deception (a trait) for their self-reported intrinsic and extrinsic motivational dispositions and their actual learning performance. In doing so, a higher order structural model was developed and tested in which intrinsic and extrinsic motivational dispositions were underlying factors that…

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

    Energy Technology Data Exchange (ETDEWEB)

    Gee, Anthony; Shin, Young-Min

    2013-01-01

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

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

    KAUST Repository

    Chawla, Mohit

    2013-10-10

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

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

    DEFF Research Database (Denmark)

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

    2016-01-01

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

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

    International Nuclear Information System (INIS)

    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 2 cm long slow wave structure (SWS) has 1–5 dB insertion loss over the passband (TM 31 mode) with ∼28% cold bandwidth. Analytic gain calculation indicates that in the SWS, TM 31 -mode is amplified with 15–20 dB/beam at 64–84 GHz with three elliptical beams of 10 kV and 150 mA/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

  12. Nuclear visions enhanced: chromatin structure, organization and dynamics

    OpenAIRE

    Meshorer, Eran; Herrmann, Harald; Raška, Ivan

    2011-01-01

    The EMBO Workshop on ‘Chromatin Structure, Organization and Dynamics' took place in April 2011 in Prague, Czech Republic. Participants presented data on the generation of models of the genome, working to correlate changes in the organization of chromatin with the functional state of the genome.

  13. Decrease of H1 histone and changes in chromatin structure and transcription in pea seedlings after γ-irradiation

    International Nuclear Information System (INIS)

    Bagi, G.; Hidvegi, E.J.

    1983-01-01

    Seeds and seedlings of pea have been irradiated between zero to 300 Gy doses of 60 Co gamma-irradiation and examinations were carried out on the chromatin of shoots of 1-week-old etiolated seedlings. There was only a slight change in the gross composition of chromatin after irradiation (in the mass ratios of DNA:RNA:histone:non-histone proteins). Separation of histones, however, showed that after 300 Gy irradiation the quantity of H1 histones decreased by 33% after seed irradiation and 43% after seedling irradiation. The ratio of H1 subfractions also changed. Enzymes DNAase II and micrococcal nuclease digested the chromatin of the irradiated sample 30% faster than the unirradiated one. Transcription kinetics of chromatin showed a gradual decrease of Ksub(m) value on increasing doses of irradiation. There was, however, no difference in the rate of transcription of DNAs, isolated from the chromatin of the control and irradiated samples. Protease and RNAase activity of whole shoots showed enhancement after irradiation. These data suggest that irradiation of either seeds or seedlings results in loosening of the seedling chromatin structure, while there is no change in basic nucleosomal structure. The specific degradation or dissociation of histone H1, localized in the internucleosomal region may be responsible for these changes in the higher order structure of chromatin. This may explain the easier accessibility of chromatin to DNAase II after irradiation and the more tightly bound RNA polymerase, exhibited in decreasing Ksub(m) values. (Auth.)

  14. Chromosome aberration model combining radiation tracks, chromatin structure, DSB repair and chromatin mobility

    International Nuclear Information System (INIS)

    Friedland, W.; Kundrat, P.

    2015-01-01

    The module that simulates the kinetics and yields of radiation-induced chromosome aberrations within the biophysical code PARTRAC is described. Radiation track structures simulated by Monte Carlo methods are overlapped with multi-scale models of DNA and chromatin to assess the resulting DNA damage. Spatial mobility of individual DNA ends from double-strand breaks is modelled simultaneously with their processing by the non-homologous end-joining enzymes. To score diverse types of chromosome aberrations, the joined ends are classified regarding their original chromosomal location, orientation and the involvement of centromeres. A comparison with experimental data on dicentrics induced by gamma and alpha particles shows that their relative dose dependence is predicted correctly, although the absolute yields are overestimated. The critical model assumptions on chromatin mobility and on the initial damage recognition and chromatin remodelling steps and their future refinements to solve this issue are discussed. (authors)

  15. Real-time object recognition in multidimensional images based on joined extended structural tensor and higher-order tensor decomposition methods

    Science.gov (United States)

    Cyganek, Boguslaw; Smolka, Bogdan

    2015-02-01

    In this paper a system for real-time recognition of objects in multidimensional video signals is proposed. Object recognition is done by pattern projection into the tensor subspaces obtained from the factorization of the signal tensors representing the input signal. However, instead of taking only the intensity signal the novelty of this paper is first to build the Extended Structural Tensor representation from the intensity signal that conveys information on signal intensities, as well as on higher-order statistics of the input signals. This way the higher-order input pattern tensors are built from the training samples. Then, the tensor subspaces are built based on the Higher-Order Singular Value Decomposition of the prototype pattern tensors. Finally, recognition relies on measurements of the distance of a test pattern projected into the tensor subspaces obtained from the training tensors. Due to high-dimensionality of the input data, tensor based methods require high memory and computational resources. However, recent achievements in the technology of the multi-core microprocessors and graphic cards allows real-time operation of the multidimensional methods as is shown and analyzed in this paper based on real examples of object detection in digital images.

  16. Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes

    Science.gov (United States)

    Fournier, David; Redl, Stefan; Best, Gerrit; Borsos, Máté; Tiwari, Vijay K.; Tachibana-Konwalski, Kikuë; Ketting, René F.; Parekh, Sapun H.; Cremer, Christoph; Birk, Udo J.

    2015-01-01

    During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated. PMID:26561583

  17. Probing chromatin structure with nuclease sensitivity assays.

    Science.gov (United States)

    Gregory, R I; Khosla, S; Feil, R

    2001-01-01

    To further our understanding of genomic imprinting it will be essential to identify key control elements, and to investigate their regulation by both epigenetic modifications (such as DNA methylation) and trans-acting factors. So far, sequence elements that regulate parental allele-specific gene expression have been identified in a number of imprinted loci, either because of their differential DNA methylation or through functional studies in transgenic mice (1,2). A systematic search for allele-specific chromatin features constitutes an alternative strategy to identify elements that regulate imprinting. The validity of such an in vivo chromatin approach derives from the fact that in several known imprinting control-elements, a specialized organization of chromatin characterized by nuclease hypersensitivity is present on only one of the two parental chromosome (3). For example, the differentially methylated 5 -portion of the human SNRPN gene-a sequence element that controls imprinting in the Prader-Willi and Angelman syndromes' domain on chromosome 15q11- q13-has strong DNase-I hypersensitive sites on the unmethylated paternal chromosome (4). A differentially methylated region that regulates the imprinting of H19 and that of the neighboring insulin-like growth factor-2 gene on mouse chromosome 7 was also found to have parental chromosome-specific hypersensitive sites (5,6). The precise nature of the allelic nuclease hypersensitivity in these and other imprinted loci remains to be determined in more detail, for example, by applying complementary chromatin methodologies (7,8). However, it is commonly observed that a nuclease hypersensitive site corresponds to a small region where nucleosomes are absent or partially disrupted.

  18. Chromatin structure influences the sensitivity of DNA to gamma-radiation

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Kozubek, Stanislav

    2008-01-01

    Roč. 1783, č. 12 (2008), s. 2398-2414 ISSN 0167-4889 R&D Projects: GA ČR(CZ) GP204/06/P349; GA AV ČR(CZ) IAA500040802; GA AV ČR(CZ) 1QS500040508 Grant - others:GA MŠk(CZ) LC535 Program:LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : sensitivity to DNA double- strand breaks induction * DSB repair * higher-order chromatin structure Subject RIV: BO - Biophysics Impact factor: 4.893, year: 2008

  19. Structural domains and conformational changes in nuclear chromatin: a quantitative thermodynamic approach by differential scanning calorimetry.

    Science.gov (United States)

    Balbi, C; Abelmoschi, M L; Gogioso, L; Parodi, S; Barboro, P; Cavazza, B; Patrone, E

    1989-04-18

    A good deal of information on the thermodynamic properties of chromatin was derived in the last few years from optical melting experiments. The structural domains of the polynucleosomal chain, the linker, and the core particle denature as independent units. The differential scanning calorimetry profile of isolated chromatin is made up of three endotherms, at approximately 74, 90, and 107 degrees C, having an almost Gaussian shape. Previous work on this matter, however, was mainly concerned with the dependence of the transition enthalpy on external parameters, such as the ionic strength, or with the melting of nuclei from different sources. In this paper we report the structural assignment of the transitions of rat liver nuclei, observed at 58, 66, 75, 92, and 107 degrees C. They are representative of the quiescent state of the cell. The strategy adopted in this work builds on the method developed for the investigation of complex biological macromolecules. The heat absorption profile of the nucleus was related to the denaturation of isolated nuclear components; electron microscopy and electrophoretic techniques were used for their morphological and molecular characterization. The digestion of chromatin by endogenous nuclease mimics perfectly the decondensation of the higher order structure and represented the source of several misinterpretations. This point was carefully examined in order to define unambiguously the thermal profile of native nuclei. The low-temperature transitions, centered around 58 and 66 degrees C, arise from the melting of scaffolding structures and of the proteins associated with heterogeneous nuclear RNA.(ABSTRACT TRUNCATED AT 250 WORDS)

  20. Higher twist contributions to the structure functions Fp2(x,Q2) and Fd2(x,Q2) at large x at higher orders

    International Nuclear Information System (INIS)

    Bluemlein, J.; Boettcher, H.

    2008-02-01

    The higher twist contributions to the deeply inelastic structure functions F p 2 (x,Q 2 ) and F d 2 (x,Q 2 ) for larger values of the Bjorken variable x are extracted extrapolating the twist-2 contributions measured in the large W 2 region to the region 4 GeV 2 ≤W 2 ≤12.5 GeV 2 applying target mass corrections. We compare the results for the NLO, NNLO and N 3 LO analyzes and include also the large x at N 4 LO to the Wilson coefficients. A gradual lowering of the higher twist contributions going from NLO to N 4 LO is observed, which stresses the importance of higher order corrections. (orig.)

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

    Science.gov (United States)

    Canivez, Gary L; Watkins, Marley W

    2010-12-01

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

  2. RNA polymerase III transcription - regulated by chromatin structure and regulator of nuclear chromatin organization.

    Science.gov (United States)

    Pascali, Chiara; Teichmann, Martin

    2013-01-01

    RNA polymerase III (Pol III) transcription is regulated by modifications of the chromatin. DNA methylation and post-translational modifications of histones, such as acetylation, phosphorylation and methylation have been linked to Pol III transcriptional activity. In addition to being regulated by modifications of DNA and histones, Pol III genes and its transcription factors have been implicated in the organization of nuclear chromatin in several organisms. In yeast, the ability of the Pol III transcription system to contribute to nuclear organization seems to be dependent on direct interactions of Pol III genes and/or its transcription factors TFIIIC and TFIIIB with the structural maintenance of chromatin (SMC) protein-containing complexes cohesin and condensin. In human cells, Pol III genes and transcription factors have also been shown to colocalize with cohesin and the transcription regulator and genome organizer CCCTC-binding factor (CTCF). Furthermore, chromosomal sites have been identified in yeast and humans that are bound by partial Pol III machineries (extra TFIIIC sites - ETC; chromosome organizing clamps - COC). These ETCs/COC as well as Pol III genes possess the ability to act as boundary elements that restrict spreading of heterochromatin.

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

    Science.gov (United States)

    Lieberman, Paul M

    2015-01-01

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

  4. 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...... of the logic is examined by a case study in the domain of medicine. Thus we try to build a bridge between the HOL and MVL communities. A sequent calculus is proposed based on recent work by Muskens. Many non-classical logics are, at the propositional level, funny toys which work quite good, but when one wants...

  5. The influence of chromatin structure on the frequency of radiation-induced DNA strand breaks: a study using nuclear and nucleoid monolayers

    International Nuclear Information System (INIS)

    Ljungman, M.

    1991-01-01

    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

  6. On the Analytical Superiority of 1D NMR for Fingerprinting the Higher Order Structure of Protein Therapeutics Compared to Multidimensional NMR Methods.

    Science.gov (United States)

    Poppe, Leszek; Jordan, John B; Rogers, Gary; Schnier, Paul D

    2015-06-02

    An important aspect in the analytical characterization of protein therapeutics is the comprehensive characterization of higher order structure (HOS). Nuclear magnetic resonance (NMR) is arguably the most sensitive method for fingerprinting HOS of a protein in solution. Traditionally, (1)H-(15)N or (1)H-(13)C correlation spectra are used as a "structural fingerprint" of HOS. Here, we demonstrate that protein fingerprint by line shape enhancement (PROFILE), a 1D (1)H NMR spectroscopy fingerprinting approach, is superior to traditional two-dimensional methods using monoclonal antibody samples and a heavily glycosylated protein therapeutic (Epoetin Alfa). PROFILE generates a high resolution structural fingerprint of a therapeutic protein in a fraction of the time required for a 2D NMR experiment. The cross-correlation analysis of PROFILE spectra allows one to distinguish contributions from HOS vs protein heterogeneity, which is difficult to accomplish by 2D NMR. We demonstrate that the major analytical limitation of two-dimensional methods is poor selectivity, which renders these approaches problematic for the purpose of fingerprinting large biological macromolecules.

  7. Chromatin Structure in Cell Differentiation, Aging and Cancer

    NARCIS (Netherlands)

    S. Kheradmand Kia (Sima)

    2009-01-01

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

  8. Nonlocal higher order evolution equations

    KAUST Repository

    Rossi, Julio D.; Schö nlieb, Carola-Bibiane

    2010-01-01

    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

  9. Polymer physics predicts the effects of structural variants on chromatin architecture.

    Science.gov (United States)

    Bianco, Simona; Lupiáñez, Darío G; Chiariello, Andrea M; Annunziatella, Carlo; Kraft, Katerina; Schöpflin, Robert; Wittler, Lars; Andrey, Guillaume; Vingron, Martin; Pombo, Ana; Mundlos, Stefan; Nicodemi, Mario

    2018-05-01

    Structural variants (SVs) can result in changes in gene expression due to abnormal chromatin folding and cause disease. However, the prediction of such effects remains a challenge. Here we present a polymer-physics-based approach (PRISMR) to model 3D chromatin folding and to predict enhancer-promoter contacts. PRISMR predicts higher-order chromatin structure from genome-wide chromosome conformation capture (Hi-C) data. Using the EPHA4 locus as a model, the effects of pathogenic SVs are predicted in silico and compared to Hi-C data generated from mouse limb buds and patient-derived fibroblasts. PRISMR deconvolves the folding complexity of the EPHA4 locus and identifies SV-induced ectopic contacts and alterations of 3D genome organization in homozygous or heterozygous states. We show that SVs can reconfigure topologically associating domains, thereby producing extensive rewiring of regulatory interactions and causing disease by gene misexpression. PRISMR can be used to predict interactions in silico, thereby providing a tool for analyzing the disease-causing potential of SVs.

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

    Science.gov (United States)

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

    2017-01-15

    During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Relationship between chromatin structure and sensitivity to molecularly targeted auger electron radiation therapy.

    NARCIS (Netherlands)

    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

  12. Higher-Order Program Generation

    DEFF Research Database (Denmark)

    Rhiger, Morten

    for OCaml, a dialect of ML, that provides run-time code generation for OCaml programs. We apply these byte-code combinators in semantics-directed compilation for an imperative language and in run-time specialization using type-directed partial evaluation. Finally, we present an approach to compiling goal......This dissertation addresses the challenges of embedding programming languages, specializing generic programs to specific parameters, and generating specialized instances of programs directly as executable code. Our main tools are higher-order programming techniques and automatic program generation....... 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...

  13. Nonlocal higher order evolution equations

    KAUST Repository

    Rossi, Julio D.

    2010-06-01

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

  14. Forging the ring: from fungal septins' divergent roles in morphology, septation and virulence to factors contributing to their assembly into higher order structures.

    Science.gov (United States)

    Vargas-Muñiz, Jose M; Juvvadi, Praveen R; Steinbach, William J

    2016-09-01

    Septins are a conserved family of GTP-binding proteins that are distributed across different lineages of the eukaryotes, with the exception of plants. Septins perform a myriad of functions in fungal cells, ranging from controlling morphogenetic events to contributing to host tissue invasion and virulence. One key attribute of the septins is their ability to assemble into heterooligomeric complexes that organizse into higher order structures. In addition to the established role of septins in the model budding yeast, Saccharomyces cerevisiae, their importance in other fungi recently emerges. While newer roles for septins are being uncovered in these fungi, the mechanism of how septins assemble into a complex and their regulation is only beginning to be comprehended. In this review, we summarize recent findings on the role of septins in different fungi and focus on how the septin complexes of different fungi are organized in vitro and in vivo. Furthermore, we discuss on how phosphorylation/dephosphorylation can serve as an important mechanism of septin complex assembly and regulation.

  15. Approach to characterization of the higher order structure of disulfide-containing proteins using hydrogen/deuterium exchange and top-down mass spectrometry.

    Science.gov (United States)

    Wang, Guanbo; Kaltashov, Igor A

    2014-08-05

    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 factors. While the limitations imposed by the physical size of the proteins gradually become more relaxed as the sensitivity, resolution and dynamic range of modern MS instrumentation continue to improve at an ever accelerating pace, the presence of the disulfide linkages remains a much less forgiving limitation even for the proteins of relatively modest size. To circumvent this problem, we introduce an online chemical reduction step following completion and quenching of the HDX reactions and prior to the top-down MS measurements of deuterium occupancy of individual backbone amides. Application of the new methodology to the top-down HDX MS characterization of a small (99 residue long) disulfide-containing protein β2-microglobulin allowed the backbone amide protection to be probed with nearly a single-residue resolution across the entire sequence. The high-resolution backbone protection pattern deduced from the top-down HDX MS measurements carried out under native conditions is in excellent agreement with the crystal structure of the protein and high-resolution NMR data, suggesting that introduction of the chemical reduction step to the top-down routine does not trigger hydrogen scrambling either during the electrospray ionization process or in the gas phase prior to the protein ion dissociation.

  16. [Neutron scatter studies of chromatin structure related to function

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1990-01-01

    This study is concerned with the application of neutron scatter techniques to the different structural states of nucleosomes and chromatin with the long term objective of understanding how the enormous lengths of DNA are folded into chromosomes. Micrococcal nuclease digestion kinetics have defined two subnucleosome particles; the chromatosome with 168 bp DNA, the histone octamer and one H1 and the nucleosome core particle with 146 bp DNA and the histone octamer. As will be discussed, the structure of the 146 bp DNA core particle is known in solution at low resolution from neutron scatter studies and in crystals. Based on this structure, the authors have a working model for the chromatosome and the mode of binding of H1. In order to define the structure of the nucleosome and also the different orders of chromatin structures they need to know the paths of DNA that link nucleosomes and the factors associated with chromosome functions that act on those DNA paths. The major region for this situation is the inherent variabilities in nucleosome DNA sequences, in the histone subtypes and their states of chemical modification and in the precise locations of nucleosomes. Such variabilities obscure the underlying principles that govern the packaging of DNA into the different structural states of nucleosomes and chromatin. The only way to elucidate these principles is to study the structures of nucleosomes and oligonucleosomes that are fully defined. They have largely achieved these objectives

  17. 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.

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

    Directory of Open Access Journals (Sweden)

    Yolanda Stypula-Cyrus

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

  19. Classical higher-order processes

    DEFF Research Database (Denmark)

    Montesi, Fabrizio

    2017-01-01

    Classical Processes (CP) is a calculus where the proof theory of classical linear logic types processes à la Π-calculus, building on a Curry-Howard correspondence between session types and linear propositions. We contribute to this research line by extending CP with process mobility, inspired...... by the Higher-Order Π-calculus. The key to our calculus is that sequents are asymmetric: one side types sessions as in CP and the other types process variables, which can be instantiated with process values. The controlled interaction between the two sides ensures that process variables can be used at will......, but always respecting the linear usage of sessions expected by the environment....

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

    Science.gov (United States)

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

    1978-05-01

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

  1. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-01-01

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome

  2. Neutron scatter studies of chromatin structures related to functions

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1992-01-01

    Despite of setbacks in the lack of neutrons for the proposed We have made considerable progress in chromatin reconstitution with the VLR histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized an intrinsically bent DNA region flanking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interatctions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin

  3. Neutron scatter studies of chromatin structures related to functions

    International Nuclear Information System (INIS)

    Bradbury, E.M.

    1992-01-01

    We have made considerable progress in chromatin reconstitution with very lysine rich histone H1/H5 and in understanding the dynamics of nucleosomes. A ferromagnetic fluid was developed to align biological molecules for structural studies using small-angle-neutron-scattering. We have also identified and characterized in intrinsically bent DNA region flaking the RNA polymerase I binding site of the ribosomal RNA gene in Physarum Polycephalum. Finally projects in progress are in the areas of studying the interactions of histone H4 amino-terminus peptide 1-23 and acetylated 1-23 peptide with DNA using thermal denaturation; study of GGAAT repeats found in human centromeres using high resolution Nuclear Magnetic Resonance and nuclease sentivity assay; and the role of histones and other sperm specific proteins with sperm chromatin

  4. Poly(ADP-ribosyl)ation of Methyl CpG Binding Domain Protein 2 Regulates Chromatin Structure*

    Science.gov (United States)

    Becker, Annette; Zhang, Peng; Allmann, Lena; Meilinger, Daniela; Bertulat, Bianca; Eck, Daniel; Hofstaetter, Maria; Bartolomei, Giody; Hottiger, Michael O.; Schreiber, Valérie; Leonhardt, Heinrich; Cardoso, M. Cristina

    2016-01-01

    The epigenetic information encoded in the genomic DNA methylation pattern is translated by methylcytosine binding proteins like MeCP2 into chromatin topology and structure and gene activity states. We have shown previously that the MeCP2 level increases during differentiation and that it causes large-scale chromatin reorganization, which is disturbed by MeCP2 Rett syndrome mutations. Phosphorylation and other posttranslational modifications of MeCP2 have been described recently to modulate its function. Here we show poly(ADP-ribosyl)ation of endogenous MeCP2 in mouse brain tissue. Consequently, we found that MeCP2 induced aggregation of pericentric heterochromatin and that its chromatin accumulation was enhanced in poly(ADP-ribose) polymerase (PARP) 1−/− compared with wild-type cells. We mapped the poly(ADP-ribosyl)ation domains and engineered MeCP2 mutation constructs to further analyze potential effects on DNA binding affinity and large-scale chromatin remodeling. Single or double deletion of the poly(ADP-ribosyl)ated regions and PARP inhibition increased the heterochromatin clustering ability of MeCP2. Increased chromatin clustering may reflect increased binding affinity. In agreement with this hypothesis, we found that PARP-1 deficiency significantly increased the chromatin binding affinity of MeCP2 in vivo. These data provide novel mechanistic insights into the regulation of MeCP2-mediated, higher-order chromatin architecture and suggest therapeutic opportunities to manipulate MeCP2 function. PMID:26772194

  5. 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.

  6. Heterochromatinization associated with cell differentiation as a model to study DNA double strand break induction and repair in the context of higher-order chromatin structure

    Czech Academy of Sciences Publication Activity Database

    Falk, Martin; Lukášová, Emilie; Štefančíková, Lenka; Baranová, E.; Falková, Iva; Ježková, L.; Davídková, Marie; Bačíková, Alena; Vachelová, Jana; Michaelidesová, Anna; Kozubek, Stanislav

    2014-01-01

    Roč. 83, Jan (2014), s. 177-185 ISSN 0969-8043 R&D Projects: GA MŠk(CZ) LD12039 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : DNA double strand break (DSB) repair * Immature and terminally differentiated granulocytes * gamma H2AX/53BP1 repair foci Subject RIV: BO - Biophysics; BO - Biophysics (UJF-V) Impact factor: 1.231, year: 2014

  7. Analogy, higher order thinking, and education.

    Science.gov (United States)

    Richland, Lindsey Engle; Simms, Nina

    2015-01-01

    Analogical reasoning, the ability to understand phenomena as systems of structured relationships that can be aligned, compared, and mapped together, plays a fundamental role in the technology rich, increasingly globalized educational climate of the 21st century. Flexible, conceptual thinking is prioritized in this view of education, and schools are emphasizing 'higher order thinking', rather than memorization of a cannon of key topics. The lack of a cognitively grounded definition for higher order thinking, however, has led to a field of research and practice with little coherence across domains or connection to the large body of cognitive science research on thinking. We review literature on analogy and disciplinary higher order thinking to propose that relational reasoning can be productively considered the cognitive underpinning of higher order thinking. We highlight the utility of this framework for developing insights into practice through a review of mathematics, science, and history educational contexts. In these disciplines, analogy is essential to developing expert-like disciplinary knowledge in which concepts are understood to be systems of relationships that can be connected and flexibly manipulated. At the same time, analogies in education require explicit support to ensure that learners notice the relevance of relational thinking, have adequate processing resources available to mentally hold and manipulate relations, and are able to recognize both the similarities and differences when drawing analogies between systems of relationships. © 2015 John Wiley & Sons, Ltd.

  8. Higher-Order and Symbolic Computation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Mason, Ian

    2008-01-01

    a 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....

  9. Heterogeneous chromatin target model

    International Nuclear Information System (INIS)

    Watanabe, Makoto

    1996-01-01

    The higher order structure of the entangled chromatin fibers in a chromosome plays a key role in molecular control mechanism involved in chromosome mutation due to ionizing radiations or chemical mutagens. The condensed superstructure of chromatin is not so rigid and regular as has been postulated in general. We have proposed a rheological explanation for the flexible network system ('chromatin network') that consists of the fluctuating assembly of nucleosome clusters linked with supertwisting DNA in a chromatin fiber ('Supertwisting Particulate Model'). We have proposed a 'Heterosensitive Target Model' for cellular radiosensitivity that is a modification of 'Heterogeneous Target Model'. The heterogeneity of chromatin target is derived from the highly condensed organization of chromatin segments consist of unstable and fragile sites in the fluctuating assembly of nucleosome clusters, namely 'supranucleosomal particles' or 'superbeads'. The models have been principally supported by our electron microscopic experiments employing 'surface - spreading whole - mount technique' since 1967. However, some deformation and artifacts in the chromatin structure are inevitable with these electron microscopic procedures. On the contrary, the 'atomic force microscope (AFM)' can be operated in liquid as well as in the air. A living specimen can be examined without any preparative procedures. Micromanipulation of the isolated chromosome is also possible by the precise positional control of a cantilever on the nanometer scale. The living human chromosomes were submerged in a solution of culture medium and observed by AFM using a liquid immersion cell. The surface - spreading whole - mount technique was applicable for this observation. The particulate chromatin segments of nucleosome clusters were clearly observed within mitotic human chromosomes in a living hydrated condition. These findings support the heterogeneity of chromatin target in a living cell. (J.P.N.)

  10. 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.

  11. Chromatin Structure and Radiation-Induced Intrachromosome Exchange

    Science.gov (United States)

    Mangala; Zhang, Ye; Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

    2011-01-01

    We have recently investigated the location of breaks involved in intrachromosomal type exchange events, using the multicolor banding in situ hybridization (mBAND) technique for human chromosome 3. In human epithelial cells exposed to both low- and high-LET radiations in vitro, intrachromosome exchanges were found to occur preferentially between a break in the 3p21 and one in the 3q11. Exchanges were also observed between a break in 3p21 and one in 3q26, but few exchanges were observed between breaks in 3q11 and 3q26, even though the two regions were on the same arm of the chromosome. To explore the relationships between intrachromosome exchanges and chromatin structure, we used probes that hybridize the three regions of 3p21, 3q11 and 3q26, and measured the distance between two of the three regions in interphase cells. We further analyzed fragile sites on the chromosome that have been identified in various types of cancers. Our results demonstrated that the distribution of breaks involved in radiation-induced intrachromosome aberrations depends upon both the location of fragile sites and the folding of chromatins

  12. Replicating chromatin: a tale of histones

    DEFF Research Database (Denmark)

    Groth, Anja

    2009-01-01

    Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...

  13. Higher order modes of coupled optical fibres

    International Nuclear Information System (INIS)

    Alexeyev, C N; Yavorsky, M A; Boklag, N A

    2010-01-01

    The structure of hybrid higher order modes of two coupled weakly guiding identical optical fibres is studied. On the basis of perturbation theory with degeneracy for the vector wave equation expressions for modes with azimuthal angular number l ≥ 1 are obtained that allow for the spin–orbit interaction. The spectra of polarization corrections to the scalar propagation constants are calculated in a wide range of distances between the fibres. The limiting cases of widely and closely spaced fibres are studied. The obtained results can be used for studying the tunnelling of optical vortices in directional couplers and in matters concerned with information security

  14. 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....

  15. Challenges in higher order mode Raman amplifiers

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  16. Individual-level movement bias leads to the formation of higher-order social structure in a mobile group of baboons.

    Science.gov (United States)

    Bonnell, Tyler R; Clarke, Parry M; Henzi, S Peter; Barrett, Louise

    2017-07-01

    In mobile social groups, influence patterns driving group movement can vary between democratic and despotic. The arrival at any single pattern of influence is thought to be underpinned by both environmental factors and group composition. To identify the specific patterns of influence driving travel decision-making in a chacma baboon troop, we used spatially explicit data to extract patterns of individual movement bias. We scaled these estimates of individual-level bias to the level of the group by constructing an influence network and assessing its emergent structural properties. Our results indicate that there is heterogeneity in movement bias: individual animals respond consistently to particular group members, and higher-ranking animals are more likely to influence the movement of others. This heterogeneity resulted in a group-level network structure that consisted of a single core and two outer shells. Here, the presence of a core suggests that a set of highly interdependent animals drove routine group movements. These results suggest that heterogeneity at the individual level can lead to group-level influence structures, and that movement patterns in mobile social groups can add to the exploration of both how these structures develop (i.e. mechanistic aspects) and what consequences they have for individual- and group-level outcomes (i.e. functional aspects).

  17. Fast neutron irradiation effects on liver chromatin structure

    International Nuclear Information System (INIS)

    Constantinescu, B.; Radu, L.

    1996-01-01

    The growing interest in neutron therapy requires complex studies on the mechanisms of neutron action on biological systems, especially on chromatin. The chromatin was extracted from a normal tissue-livers of Wistar rats - and from a tumoral tissue - Walker tumour maintained on Wistar rats. Irradiation doses from 5 Gy to 100 Gy by fast neutron intense beams produced via d(13.5 MeV) +Be (thick target) reaction at Bucharest U-120 Classical Cyclotron were used. To study the post-irradiation effects, various methods were employed. So, the variation in the 260 nm absorbency in chromatin thermal transition was pursuit. The chromatin-ethidium bromide complexes fluorescence with λ ex =480 nm and λ em =600 nm was analyzed. To determine chromatin DNA strand breaks a fluorimetric method, with cells' suspensions as starting material was used. This method requires a partial treatment with alkali producing three components: T-estimating the total fluorescence of DNA double helix, P-assigning the untwisting rate and B-the blank, where DNA is completely unfolded The percentsge of DNA double strand,-D-, remaining after this treatment, is: %D=100x(P-B)/(T-B). The intrinsic chromatin fluorescence was determined for tyrosine (λ ex =280 nm, λ em =305 nm), specific for badic chromatin prooteins, and for tryptophane (λ ex =290 nm, λ em =345 nm) specific for acid chromatin proteins. Polyacrylamide gel electrophoresis was performed: The double fluorescent labelling of chromatin was realized with acridine orange for DNA and with dansyl chloride for chromatin proteins. Fluorescence intensity determinations were done with λ ex =505 nm, λ em =530 nm for acridine orange and with λ ex =323 nm, λ em =505 nm for dansyl chloride. A Pye Unicam SP 1800 spectrophotometer and a Aminco SPF 500 spectrofluorimeter were employed. (author)

  18. Higher order cumulants in colorless partonic plasma

    Energy Technology Data Exchange (ETDEWEB)

    Cherif, S. [Sciences and Technologies Department, University of Ghardaia, Ghardaia, Algiers (Algeria); Laboratoire de Physique et de Mathématiques Appliquées (LPMA), ENS-Kouba (Bachir El-Ibrahimi), Algiers (Algeria); Ahmed, M. A. A. [Department of Physics, College of Science, Taibah University Al-Madinah Al-Mounawwarah KSA (Saudi Arabia); Department of Physics, Taiz University in Turba, Taiz (Yemen); Laboratoire de Physique et de Mathématiques Appliquées (LPMA), ENS-Kouba (Bachir El-Ibrahimi), Algiers (Algeria); Ladrem, M., E-mail: mladrem@yahoo.fr [Department of Physics, College of Science, Taibah University Al-Madinah Al-Mounawwarah KSA (Saudi Arabia); Laboratoire de Physique et de Mathématiques Appliquées (LPMA), ENS-Kouba (Bachir El-Ibrahimi), Algiers (Algeria)

    2016-06-10

    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{sub 0}(V), a new approach based on the finite-size cumulant expansion of the order parameter and the ℒ{sub 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 transition point. In the context of our model, we have shown that the finite volume transition point is always associated to the appearance of a particular point in whole higher order cumulants under consideration.

  19. 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.

  20. Higher Order Expectations in Asset Pricing

    OpenAIRE

    Philippe BACCHETTA; Eric VAN WINCOOP

    2004-01-01

    We examine formally Keynes' idea that higher order beliefs can drive a wedge between an asset price and its fundamental value based on expected future payoffs. Higher order expectations add an additional term to a standard asset pricing equation. We call this the higher order wedge, which depends on the difference between higher and first order expectations of future payoffs. We analyze the determinants of this wedge and its impact on the equilibrium price. In the context of a dynamic noisy r...

  1. Higher order harmonics of reactor neutron equation

    International Nuclear Information System (INIS)

    Li Fu; Hu Yongming; Luo Zhengpei

    1996-01-01

    The flux mapping method using the higher order harmonics of the neutron equation is proposed. Based on the bi-orthogonality of the higher order harmonics, the process and formulas for higher order harmonics calculation are derived via the source iteration method with source correction. For the first time, not only any order harmonics for up-to-3-dimensional geometry are achieved, but also the preliminary verification to the capability for flux mapping have been carried out

  2. Adenovirus chromatin structure at different stages of infection

    Energy Technology Data Exchange (ETDEWEB)

    Daniell, E.; Groff, D.E.; Fedor, M.J.

    1981-12-01

    The authors investigated the structure of adenovirus deoxyribonecleic acid (DNA)-protein complexes in nuclei of infected cells by using micrococal nuclease. Parental (infecting) DNA was digested into multimers which had a unit fragment size that was indistinguishable from the size of the nucleosomal repeat of cellular chromatin. This pattern was maintained in parental DNA throughout infection. Similar repeating units were detected in hamster cells that were nonpermissive for human adenovirus and in cells pretreated with n-butyrate. Late in infection, the pattern of digestion of viral DNA was determined by two different experimental approaches. Nuclear DNA was electrophoresed, blotted, and hybridized with labeled viral sequences; in this procedure all virus-specific DNA was detected. This technique revealed a diffuse protected band of viral DNA that was smaller than 160 base pairs, but no discrete multimers. All regions of the genome were represented in the protected DNA. To examine the nuclease protection of newly replicated viral DNA, infected cells were labeled with (/sup 3/)thymidine after blocking of cellular DNA synthesis but not viral DNA synthesis. With this procedure they identified a repeating unit which was distinctly different from the cellular nucleosomal repeat. The authors found broad bands with midpoints at 200, 400, and 600 base pairs, as well as the limit digest material revealed by blotting. High-resolution acrylamide gel electrophoresis revealed that the viral species comprised a series of closely spaced bands ranging in size from less than 30 to 250 base pairs.

  3. Large-scale Comparative Study of Hi-C-based Chromatin 3D Structure Modeling Methods

    KAUST Repository

    Wang, Cheng

    2018-05-17

    Chromatin is a complex polymer molecule in eukaryotic cells, primarily consisting of DNA and histones. Many works have shown that the 3D folding of chromatin structure plays an important role in DNA expression. The recently proposed Chro- mosome Conformation Capture technologies, especially the Hi-C assays, provide us an opportunity to study how the 3D structures of the chromatin are organized. Based on the data from Hi-C experiments, many chromatin 3D structure modeling methods have been proposed. However, there is limited ground truth to validate these methods and no robust chromatin structure alignment algorithms to evaluate the performance of these methods. In our work, we first made a thorough literature review of 25 publicly available population Hi-C-based chromatin 3D structure modeling methods. Furthermore, to evaluate and to compare the performance of these methods, we proposed a novel data simulation method, which combined the population Hi-C data and single-cell Hi-C data without ad hoc parameters. Also, we designed a global and a local alignment algorithms to measure the similarity between the templates and the chromatin struc- tures predicted by different modeling methods. Finally, the results from large-scale comparative tests indicated that our alignment algorithms significantly outperform the algorithms in literature.

  4. Higher-order (non-)modularity

    DEFF Research Database (Denmark)

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

    2010-01-01

    We show that, contrary to the situation in first-order term rewriting, almost none of the usual properties of rewriting are modular for higher-order rewriting, irrespective of the higher-order rewriting format. We show that for the particular format of simply typed applicative term rewriting...... systems modularity of confluence, normalization, and termination can be recovered by imposing suitable linearity constraints....

  5. Difference equations in massive higher order calculations

    International Nuclear Information System (INIS)

    Bierenbaum, I.; Bluemlein, J.; Klein, S.; Schneider, C.

    2007-07-01

    The calculation of massive 2-loop operator matrix elements, required for the higher order Wilson coefficients for heavy flavor production in deeply inelastic scattering, leads to new types of multiple infinite sums over harmonic sums and related functions, which depend on the Mellin parameter N. We report on the solution of these sums through higher order difference equations using the summation package Sigma. (orig.)

  6. The Drosophila melanogaster CHD1 chromatin remodeling factor modulates global chromosome structure and counteracts HP1a and H3K9me2.

    Science.gov (United States)

    Bugga, Lakshmi; McDaniel, Ivy E; Engie, Liana; Armstrong, Jennifer A

    2013-01-01

    CHD1 is a conserved chromatin remodeling factor that localizes to active genes and functions in nucleosome assembly and positioning as well as histone turnover. Mouse CHD1 is required for the maintenance of stem cell pluripotency while human CHD1 may function as a tumor suppressor. To investigate the action of CHD1 on higher order chromatin structure in differentiated cells, we examined the consequences of loss of CHD1 and over-expression of CHD1 on polytene chromosomes from salivary glands of third instar Drosophila melanogaster larvae. We observed that chromosome structure is sensitive to the amount of this remodeler. Loss of CHD1 resulted in alterations of chromosome structure and an increase in the heterochromatin protein HP1a, while over-expression of CHD1 disrupted higher order chromatin structure and caused a decrease in levels of HP1a. Over-expression of an ATPase inactive form of CHD1 did not result in severe chromosomal defects, suggesting that the ATPase activity is required for this in vivo phenotype. Interestingly, changes in CHD1 protein levels did not correlate with changes in the levels of the euchromatin mark H3K4me3 or elongating RNA Polymerase II. Thus, while CHD1 is localized to transcriptionally active regions of the genome, it can function to alter the levels of HP1a, perhaps through changes in methylation of H3K9.

  7. The Drosophila melanogaster CHD1 chromatin remodeling factor modulates global chromosome structure and counteracts HP1a and H3K9me2.

    Directory of Open Access Journals (Sweden)

    Lakshmi Bugga

    Full Text Available CHD1 is a conserved chromatin remodeling factor that localizes to active genes and functions in nucleosome assembly and positioning as well as histone turnover. Mouse CHD1 is required for the maintenance of stem cell pluripotency while human CHD1 may function as a tumor suppressor. To investigate the action of CHD1 on higher order chromatin structure in differentiated cells, we examined the consequences of loss of CHD1 and over-expression of CHD1 on polytene chromosomes from salivary glands of third instar Drosophila melanogaster larvae. We observed that chromosome structure is sensitive to the amount of this remodeler. Loss of CHD1 resulted in alterations of chromosome structure and an increase in the heterochromatin protein HP1a, while over-expression of CHD1 disrupted higher order chromatin structure and caused a decrease in levels of HP1a. Over-expression of an ATPase inactive form of CHD1 did not result in severe chromosomal defects, suggesting that the ATPase activity is required for this in vivo phenotype. Interestingly, changes in CHD1 protein levels did not correlate with changes in the levels of the euchromatin mark H3K4me3 or elongating RNA Polymerase II. Thus, while CHD1 is localized to transcriptionally active regions of the genome, it can function to alter the levels of HP1a, perhaps through changes in methylation of H3K9.

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

    KAUST Repository

    Bigeard, Jean; Rayapuram, Naganand; Pflieger, Delphine; Hirt, Heribert

    2014-01-01

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

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

    KAUST Repository

    Bigeard, Jean

    2014-07-10

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

  10. Model for the structure of the active nucleolar chromatin

    International Nuclear Information System (INIS)

    Labhart, P.; Ness, P.; Banz, E.; Parish, R.; Koller, T.; Universitaet Zurich, Switzerland)

    1983-01-01

    Transcribed ribosomal genes of Xenopus laevis oocytes and of Dictyostelium discoideum were studied electron microscopically using step gradients at different ionic strengths. Under these conditions the fiber of the active chromatin appears smooth and is indistinguishable from free DNA. The accessibility of the coding region and of a nontranscribed spacer region to restriction enzymes and micrococcal nuclease were investigated. All of the results obtained are consistent with a model in which active nucleolar chromatin is mostly composed of free DNA and the components required for transcription. 50 references, 7 figures

  11. Chromatin Structure in Bands and Interbands of Polytene Chromosomes Imaged by Atomic Force Microscopy

    NARCIS (Netherlands)

    de Grauw, C.J.; de Grauw, C.J.; Avogadro, A.; van den Heuvel, D.J.; van den Heuvel, D.J.; van der Werf, Kees; Otto, Cornelis; Kraan, Yvonne M.; van Hulst, N.F.; Greve, Jan

    1998-01-01

    Polytene chromosomes from Drosophila melanogaster, observed from squash preparations, and chromosomes from Chironomus thummi thummi, investigated under physiological conditions, are imaged using an Atomic Force Microscope. Various chromatin fiber structures can be observed with high detail in fixed

  12. Structural chromatin organization as a factor determining the rate of chromatin endonucleolysis in irradiated and intact thymocytes

    International Nuclear Information System (INIS)

    Ryabchenko, N.I.; Ivannik, B.P.

    1987-01-01

    A study was made of chromatin endonucleolysis in hypotonized thymocytes incubating in digestive buffers containing different concentrations of potassium, magnesium, calcium, and mercaptoethanol. Inhibition of endonucleolysis by univalent cation during the first 20 min of incubation was followed by intensive chromatin degradation. A decrease in free potassium content retarded chromatin degradation and enhanced the inhibiting effect of the univalent cations. The regularities of changes in the rate of chromatin endonucleolysis in different digestive buffers were similar with both exposed and intact thymocytes

  13. Chromatin remodeling, development and disease

    International Nuclear Information System (INIS)

    Ko, Myunggon; Sohn, Dong H.; Chung, Heekyoung; Seong, Rho H.

    2008-01-01

    Development is a stepwise process in which multi-potent progenitor cells undergo lineage commitment, differentiation, proliferation and maturation to produce mature cells with restricted developmental potentials. This process is directed by spatiotemporally distinct gene expression programs that allow cells to stringently orchestrate intricate transcriptional activation or silencing events. In eukaryotes, chromatin structure contributes to developmental progression as a blueprint for coordinated gene expression by actively participating in the regulation of gene expression. Changes in higher order chromatin structure or covalent modification of its components are considered to be critical events in dictating lineage-specific gene expression during development. Mammalian cells utilize multi-subunit nuclear complexes to alter chromatin structure. Histone-modifying complex catalyzes covalent modifications of histone tails including acetylation, methylation, phosphorylation and ubiquitination. ATP-dependent chromatin remodeling complex, which disrupts histone-DNA contacts and induces nucleosome mobilization, requires energy from ATP hydrolysis for its catalytic activity. Here, we discuss the diverse functions of ATP-dependent chromatin remodeling complexes during mammalian development. In particular, the roles of these complexes during embryonic and hematopoietic development are reviewed in depth. In addition, pathological conditions such as tumor development that are induced by mutation of several key subunits of the chromatin remodeling complex are discussed, together with possible mechanisms that underlie tumor suppression by the complex

  14. Effects of blending poly(D,L-lactide) with poly(ethylene glycol) on the higher-order crystalline structures of poly(ethylene glycol) as revealed by small-angle X-ray scattering

    International Nuclear Information System (INIS)

    Tien, N D; Kimura, G; Yamashiro, Y; Fujiwara, H; Sasaki, S; Sakurai, S; Hoa, T P; Mochizuki, M

    2011-01-01

    Effects of blending poly(lactic acid) (PLA) with poly(ethylene glycol) (PEG) on higher-order crystalline structures of PEG were examined using small-angle X-ray scattering (SAXS). For this purpose, the fact that two polymers are both crystalline makes situtation much complicated. To simplify, non-crystalline PLA is suitable. Thus, we used poly(D,L-lactic acid) (DLPLA), which is random copolymer comprising D- and L-lactic acid moieties. Multiple scattering peaks arising from the regular crystalline lamellar structure were observed for the PEG homopolymer and the blends. Surprisingly, the structure is much more regular for the blend DLPLA/PEG at composition of 20/80 wt.% than for the PEG homopolymer. Also for this blend sample as well as for a PEG homopolymer, very peculiar SAXS profiles were observed just 1 deg. C below T m of PEG. This is found to be a particle scattering of plate-like objects, which has never been reported for polymer blends or crystalline polymers. Futhermore, it was found that there was strong hysteresis of the higher-order structure formation.

  15. Modulation of chromatin structure by the FACT histone chaperone complex regulates HIV-1 integration.

    Science.gov (United States)

    Matysiak, Julien; Lesbats, Paul; Mauro, Eric; Lapaillerie, Delphine; Dupuy, Jean-William; Lopez, Angelica P; Benleulmi, Mohamed Salah; Calmels, Christina; Andreola, Marie-Line; Ruff, Marc; Llano, Manuel; Delelis, Olivier; Lavigne, Marc; Parissi, Vincent

    2017-07-28

    Insertion of retroviral genome DNA occurs in the chromatin of the host cell. This step is modulated by chromatin structure as nucleosomes compaction was shown to prevent HIV-1 integration and chromatin remodeling has been reported to affect integration efficiency. LEDGF/p75-mediated targeting of the integration complex toward RNA polymerase II (polII) transcribed regions ensures optimal access to dynamic regions that are suitable for integration. Consequently, we have investigated the involvement of polII-associated factors in the regulation of HIV-1 integration. Using a pull down approach coupled with mass spectrometry, we have selected the FACT (FAcilitates Chromatin Transcription) complex as a new potential cofactor of HIV-1 integration. FACT is a histone chaperone complex associated with the polII transcription machinery and recently shown to bind LEDGF/p75. We report here that a tripartite complex can be formed between HIV-1 integrase, LEDGF/p75 and FACT in vitro and in cells. Biochemical analyzes show that FACT-dependent nucleosome disassembly promotes HIV-1 integration into chromatinized templates, and generates highly favored nucleosomal structures in vitro. This effect was found to be amplified by LEDGF/p75. Promotion of this FACT-mediated chromatin remodeling in cells both increases chromatin accessibility and stimulates HIV-1 infectivity and integration. Altogether, our data indicate that FACT regulates HIV-1 integration by inducing local nucleosomes dissociation that modulates the functional association between the incoming intasome and the targeted nucleosome.

  16. [Automated morphometric evaluation of the chromatin structure of liver cell nuclei after vagotomy].

    Science.gov (United States)

    Butusova, N N; Zhukotskiĭ, A V; Sherbo, I V; Gribkov, E N; Dubovaia, T K

    1989-05-01

    The morphometric analysis of the interphase chromatine structure of the hepatic cells nuclei was carried out on the automated TV installation for the quantitative analysis of images "IBAS-2" (by the OPTON firm, the FRG) according to 50 optical and geometric parameters during various periods (1.2 and 4 weeks) after the vagotomy operation. It is determined that upper-molecular organisation of chromatine undergoes the biggest changes one week after operation, and changes of granular component are more informative than changes of the nongranular component (with the difference 15-20%). It was also revealed that chromatine components differ in tinctorial properties, which are evidently dependent on physicochemical characteristics of the chromatine under various functional conditions of the cell. As a result of the correlation analysis the group of morphometric indices of chromatine structure was revealed, which are highly correlated with level of transcription activity of chromatine during various terms after denervation. The correlation quotient of these parameters is 0.85-0.97. The summing up: vagus denervation of the liver causes changes in the morphofunctional organisation of the chromatine.

  17. Chromatin structure and dynamics in hot environments: architectural proteins and DNA topoisomerases of thermophilic archaea.

    Science.gov (United States)

    Visone, Valeria; Vettone, Antonella; Serpe, Mario; Valenti, Anna; Perugino, Giuseppe; Rossi, Mosè; Ciaramella, Maria

    2014-09-25

    In all organisms of the three living domains (Bacteria, Archaea, Eucarya) chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair). Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C), chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  18. Chromatin Structure and Dynamics in Hot Environments: Architectural Proteins and DNA Topoisomerases of Thermophilic Archaea

    Directory of Open Access Journals (Sweden)

    Valeria Visone

    2014-09-01

    Full Text Available In all organisms of the three living domains (Bacteria, Archaea, Eucarya chromosome-associated proteins play a key role in genome functional organization. They not only compact and shape the genome structure, but also regulate its dynamics, which is essential to allow complex genome functions. Elucidation of chromatin composition and regulation is a critical issue in biology, because of the intimate connection of chromatin with all the essential information processes (transcription, replication, recombination, and repair. Chromatin proteins include architectural proteins and DNA topoisomerases, which regulate genome structure and remodelling at two hierarchical levels. This review is focussed on architectural proteins and topoisomerases from hyperthermophilic Archaea. In these organisms, which live at high environmental temperature (>80 °C <113 °C, chromatin proteins and modulation of the DNA secondary structure are concerned with the problem of DNA stabilization against heat denaturation while maintaining its metabolic activity.

  19. Higher-order techniques in computational electromagnetics

    CERN Document Server

    Graglia, Roberto D

    2016-01-01

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

  20. Higher-order rewriting and partial evaluation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Rose, Kristoffer H.

    1998-01-01

    We demonstrate the usefulness of higher-order rewriting techniques for specializing programs, i.e., for partial evaluation. More precisely, we demonstrate how casting program specializers as combinatory reduction systems (CRSs) makes it possible to formalize the corresponding program...

  1. Chromatin organisation during Arabidopsis root development

    NARCIS (Netherlands)

    Lorvellec, M.

    2007-01-01

    The genetic information is stored in a highly compact manner in every nucleus. About 150 bp of DNA is packed around a histone octamer constituting a nucleosome. Nucleosomes are linked together by histone H1 and further compaction of this "beads on a string" form higher-order chromatin structures.

  2. Function of chromatin structure and dynamics in DNA damage, repair and misrepair: gamma-rays and protons in action

    Czech Academy of Sciences Publication Activity Database

    Ježková, L.; Falk, Martin; Falková, Iva; Davídková, Marie; Bačíková, Alena; Štefančíková, Lenka; Vachelová, Jana; Michaelidesová, Anna; Lukášová, Emilie; Boreyko, A.; Krasavin, E.; Kozubek, Stanislav

    2014-01-01

    Roč. 83, SI (2014), s. 128-136 ISSN 0969-8043 R&D Projects: GA MŠk(CZ) EE2.3.30.0030; GA ČR(CZ) GBP302/12/G157; GA ČR(CZ) GAP302/10/1022; GA ČR(CZ) GBP108/12/G108; GA MŠk(CZ) LD12039; GA MŠk(CZ) LD12008 Institutional support: RVO:68081707 ; RVO:61389005 Keywords : DNA double-strand breaks * Higher-order chromatin structure and DSB repair * Formation of chromosomal translocations Subject RIV: BO - Biophysics; BO - Biophysics (UJF-V) Impact factor: 1.231, year: 2014

  3. The differential geometry of higher order jets and tangent bundles

    International Nuclear Information System (INIS)

    De Leon, M.; Rodrigues, P.R.

    1985-01-01

    This chapter is devoted to the study of basic geometrical notions required for the development of the main object of the text. Some facts about Jet theory are reviewed. A particular case of Jet manifolds is considered: the tangent bundle of higher order. It is shown that this jet bundle possesses in a canonical way a certain kind of geometric structure, the so called almost tangent structure of higher order, and which is a generalization of the almost tangent geometry of the tangent bundle. Another important fact examined is the extension of the notion of 'spray' to higher order tangent bundles. (Auth.)

  4. The Serenity of the Meditating Mind: A Cross-Cultural Psychometric Study on a Two-Factor Higher Order Structure of Mindfulness, Its Effects, and Mechanisms Related to Mental Health among Experienced Meditators

    Science.gov (United States)

    Tran, Ulrich S.; Cebolla, Ausiàs; Glück, Tobias M.; Soler, Joaquim; Garcia-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 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. PMID:25330072

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

    Directory of Open Access Journals (Sweden)

    Ulrich S Tran

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

  6. HIGHER ORDER THINKING IN TEACHING GRAMMAR

    Directory of Open Access Journals (Sweden)

    Citra Dewi

    2017-04-01

    Full Text Available The aim of this paper discussed about how to enhance students’ higher order thinking that should be done by teacher in teaching grammar. Usually teaching grammar was boring and has the same way to learn like change the pattern of sentence into positive, negative and introgative while the students’ need more various way to develop their thinking. The outcome of students’ competence in grammar sometimes not sufficient enough when the students’ occured some test international standart like Test of English Foreign Language, International English Language Testing. Whereas in TOEFL test it needed higher order thinking answer, so teacher should develop students’ higher order thingking in daily teaching grammar in order to make the students’ enhance their thinking are higher. The method was used in this paper by using field study based on the experience of teaching grammar. It can be shown by students’ toefl score was less in stucture and written expression. The result of this paper was after teacher gave some treatments to enhance students’ higher order thinking in teaching grammar, the students’ toefl scores are sufficient enough as a part of stucture and written expression. It can concluded that it needed some strategies to enhancce students higher order thinking by teaching grammar it can make students’ higher toefl score. Teachers should be creative and inovative to teach the students’ started from giving the students’ question or test in teaching grammar.

  7. Electromagnetic cloaking in higher order spherical cloaks

    Science.gov (United States)

    Sidhwa, H. H.; Aiyar, R. P. R. C.; Kulkarni, S. V.

    2017-06-01

    The inception of transformation optics has led to the realisation of the invisibility devices for various applications, one of which is spherical cloaking. In this paper, a formulation for a higher-order spherical cloak has been proposed to reduce its physical thickness significantly by introducing a nonlinear relation between the original and transformed coordinate systems and it has been verified using the ray tracing approach. Analysis has been carried out to observe the anomalies in the variation of refractive index for higher order cloaks indicating the presence of poles in the relevant equations. Furthermore, a higher-order spherical cloak with predefined values of the material characteristics on its inner and outer surfaces has been designed for practical application.

  8. Higher-order force gradient symplectic algorithms

    Science.gov (United States)

    Chin, Siu A.; Kidwell, Donald W.

    2000-12-01

    We show that a recently discovered fourth order symplectic algorithm, which requires one evaluation of force gradient in addition to three evaluations of the force, when iterated to higher order, yielded algorithms that are far superior to similarly iterated higher order algorithms based on the standard Forest-Ruth algorithm. We gauge the accuracy of each algorithm by comparing the step-size independent error functions associated with energy conservation and the rotation of the Laplace-Runge-Lenz vector when solving a highly eccentric Kepler problem. For orders 6, 8, 10, and 12, the new algorithms are approximately a factor of 103, 104, 104, and 105 better.

  9. Chromatin structure in the unicellular algae Olisthodiscus luteus, Crypthecodinium cohnii and Peridiniun balticum.

    Science.gov (United States)

    Rizzo, P J; Burghardt, R C

    1980-01-01

    Isolated nuclei of the unicellular alga Olisthodiscus luteus, the uninucleate dinoflagellate Crypthecodinium cohnii and the binucleate dinoflagellate Peridinium balticum were lysed and deposited on grids by the microcentrifugation technique. The ultrastructure of the released chromatin fibers was compared to that of mouse liver nuclei. Chromatin from nuclei of Olisthodiscus luteus and the "eukaryotic" nuclei of Peridinium balticum, appeared as linear arrays of regularly repeating subunits which were identical in size and morphology to mouse nucleosomes. In contrast, the chromatin fibers from Crypthecodinium cohnii nuclei appeared as smoothe threads with a diameter of about 6.5 nm. Nuclear preparations containing mixtures of "dinokaryotic" and "eukaryotic" nuclei of Peridinium balticum also contained smooth fibers which most likely originated from the dinokaryotic nuclei. These and other results demonstrating the presence of nucleosomes in lower eukaryotes suggest that the subunit structure of chromatin arose very early in the evolution of the eukaryotic cell.

  10. Chromatin structure and epigenetics of tumour cells: A review

    Czech Academy of Sciences Publication Activity Database

    Bártová, Eva; Krejčí, Jana; Hájek, R.; Harničarová, Andrea; Kozubek, Stanislav

    2009-01-01

    Roč. 9, č. 1 (2009), s. 51-61 ISSN 1871-529X R&D Projects: GA AV ČR(CZ) 1QS500040508; GA ČR(CZ) GA204/06/0978 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : tumour cells * chromatin * radiation Subject RIV: BO - Biophysics

  11. Frontiers of higher order fuzzy sets

    CERN Document Server

    Tahayori, Hooman

    2015-01-01

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

  12. Higher-order tensors in diffusion imaging

    NARCIS (Netherlands)

    Schultz, T.; Fuster, A.; Ghosh, A.; Deriche, R.; Florack, L.M.J.; Lim, L.H.; Westin, C.-F.; Vilanova, A.; Burgeth, B.

    2014-01-01

    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

  13. Higher-Order Components for Grid Programming

    CERN Document Server

    Dünnweber, Jan

    2009-01-01

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

  14. Higher order antibunching in intermediate states

    International Nuclear Information System (INIS)

    Verma, Amit; Sharma, Navneet K.; Pathak, Anirban

    2008-01-01

    Since the introduction of binomial state as an intermediate state, different intermediate states have been proposed. Different nonclassical effects have also been reported in these intermediate states. But till now higher order antibunching is predicted in only one type of intermediate state, which is known as shadowed negative binomial state. Recently we have shown that the higher order antibunching is not a rare phenomenon [P. Gupta, P. Pandey, A. Pathak, J. Phys. B 39 (2006) 1137]. To establish our earlier claim further, here we have shown that the higher order antibunching can be seen in different intermediate states, such as binomial state, reciprocal binomial state, hypergeometric state, generalized binomial state, negative binomial state and photon added coherent state. We have studied the possibility of observing the higher order subpoissonian photon statistics in different limits of intermediate states. The effects of different control parameters on the depth of non classicality have also been studied in this connection and it has been shown that the depth of nonclassicality can be tuned by controlling various physical parameters

  15. Certified higher-order recursive path ordering

    NARCIS (Netherlands)

    Koprowski, A.; Pfenning, F.

    2006-01-01

    The paper reports on a formalization of a proof of wellfoundedness of the higher-order recursive path ordering (HORPO) in the proof checker Coq. The development is axiom-free and fully constructive. Three substantive parts that could be used also in other developments are the formalizations of the

  16. 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...

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

    Science.gov (United States)

    Smith, Owen K.; Aladjem, Mirit I.

    2014-01-01

    The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

  18. Structural hierarchy of chromatin in chicken erythrocyte nuclei based on small-angle neutron scattering: Fractal nature of the large-scale chromatin organization

    International Nuclear Information System (INIS)

    Lebedev, D. V.; Filatov, M. V.; Kuklin, A. I.; Islamov, A. Kh.; Stellbrink, J.; Pantina, R. A.; Denisov, Yu. Yu.; Toperverg, B. P.; Isaev-Ivanov, V. V.

    2008-01-01

    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

  19. A Higher-Order Colon Translation

    DEFF Research Database (Denmark)

    Danvy, Olivier; Nielsen, Lasse Reichstein

    2001-01-01

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

  20. XY model with higher-order exchange.

    Science.gov (United States)

    Žukovič, Milan; Kalagov, Georgii

    2017-08-01

    An XY model, generalized by inclusion of up to an infinite number of higher-order pairwise interactions with an exponentially decreasing strength, is studied by spin-wave theory and Monte Carlo simulations. At low temperatures the model displays a quasi-long-range-order phase characterized by an algebraically decaying correlation function with the exponent η=T/[2πJ(p,α)], nonlinearly dependent on the parameters p and α that control the number of the higher-order terms and the decay rate of their intensity, respectively. At higher temperatures the system shows a crossover from the continuous Berezinskii-Kosterlitz-Thouless to the first-order transition for the parameter values corresponding to a highly nonlinear shape of the potential well. The role of topological excitations (vortices) in changing the nature of the transition is discussed.

  1. Lagrangian procedures for higher order field equations

    International Nuclear Information System (INIS)

    Bollini, C.G.

    1987-01-01

    A Lagrangian procedure for a pedagogical way is presented for the treatment of higher order field equations. The energy-momentum tensor and the conserved density current are built. In particular the case in which the derivatives appear only in the invariant D'Alembertian operator is discussed. Some examples are discussed. The fields are quantized and the corresponding Hamilonian which is shown not to be positive defructed. Rules are given to write the causal propagators. (author) [pt

  2. Lagrangian procedures for higher order field equations

    International Nuclear Information System (INIS)

    Bollini, C.G.; Giambiagi, J.J.

    1986-01-01

    We present in a pedagogical way a Lagrangian procedure for the treatment of higher order field equations. We build the energy-momentum tensor and the conserved density current. In particular we discuss the case in which the derivatives appear only in the invariant D'Alembertian operator. We discuss some examples. We quantize the fields and construct the corresponding Hamiltonian which is shown not to be positive definite. We give the rules for the causal propagators. (Author) [pt

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

    Directory of Open Access Journals (Sweden)

    Sha Ky

    2010-08-01

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

  4. Higher order correlations in computed particle distributions

    International Nuclear Information System (INIS)

    Hanerfeld, H.; Herrmannsfeldt, W.; Miller, R.H.

    1989-03-01

    The rms emittances calculated for beam distributions using computer simulations are frequently dominated by higher order aberrations. Thus there are substantial open areas in the phase space plots. It has long been observed that the rms emittance is not an invariant to beam manipulations. The usual emittance calculation removes the correlation between transverse displacement and transverse momentum. In this paper, we explore the possibility of defining higher order correlations that can be removed from the distribution to result in a lower limit to the realizable emittance. The intent is that by inserting the correct combinations of linear lenses at the proper position, the beam may recombine in a way that cancels the effects of some higher order forces. An example might be the non-linear transverse space charge forces which cause a beam to spread. If the beam is then refocused so that the same non-linear forces reverse the inward velocities, the resulting phase space distribution may reasonably approximate the original distribution. The approach to finding the location and strength of the proper lens to optimize the transported beam is based on work by Bruce Carlsten of Los Alamos National Laboratory. 11 refs., 4 figs

  5. Using local chromatin structure to improve CRISPR/Cas9 efficiency in zebrafish.

    Science.gov (United States)

    Chen, Yunru; Zeng, Shiyang; Hu, Ruikun; Wang, Xiangxiu; Huang, Weilai; Liu, Jiangfang; Wang, Luying; Liu, Guifen; Cao, Ying; Zhang, Yong

    2017-01-01

    Although the CRISPR/Cas9 has been successfully applied in zebrafish, considerable variations in efficiency have been observed for different gRNAs. The workload and cost of zebrafish mutant screening is largely dependent on the mutation rate of injected embryos; therefore, selecting more effective gRNAs is especially important for zebrafish mutant construction. Besides the sequence features, local chromatin structures may have effects on CRISPR/Cas9 efficiency, which remain largely unexplored. In the only related study in zebrafish, nucleosome organization was not found to have an effect on CRISPR/Cas9 efficiency, which is inconsistent with recent studies in vitro and in mammalian cell lines. To understand the effects of local chromatin structure on CRISPR/Cas9 efficiency in zebrafish, we first determined that CRISPR/Cas9 introduced genome editing mainly before the dome stage. Based on this observation, we reanalyzed our published nucleosome organization profiles and generated chromatin accessibility profiles in the 256-cell and dome stages using ATAC-seq technology. Our study demonstrated that chromatin accessibility showed positive correlation with CRISPR/Cas9 efficiency, but we did not observe a clear correlation between nucleosome organization and CRISPR/Cas9 efficiency. We constructed an online database for zebrafish gRNA selection based on local chromatin structure features that could prove beneficial to zebrafish homozygous mutant construction via CRISPR/Cas9.

  6. Effect of Polysorbate 20 and Polysorbate 80 on the Higher-Order Structure of a Monoclonal Antibody and Its Fab and Fc Fragments Probed Using 2D Nuclear Magnetic Resonance Spectroscopy.

    Science.gov (United States)

    Singh, Surinder M; Bandi, Swati; Jones, David N M; Mallela, Krishna M G

    2017-12-01

    We examined how polysorbate 20 (PS20; Tween 20) and polysorbate 80 (PS80; Tween 80) affect the higher-order structure of a monoclonal antibody (mAb) and its antigen-binding (Fab) and crystallizable (Fc) fragments, using near-UV circular dichroism and 2D nuclear magnetic resonance (NMR). Both polysorbates bind to the mAb with submillimolar affinity. Binding causes significant changes in the tertiary structure of mAb with no changes in its secondary structure. 2D 13 C- 1 H methyl NMR indicates that with increasing concentration of polysorbates, the Fab region showed a decrease in crosspeak volumes. In addition to volume changes, PS20 caused significant changes in the chemical shifts compared to no changes in the case of PS80. No such changes in crosspeak volumes or chemical shifts were observed in the case of Fc region, indicating that polysorbates predominantly affect the Fab region compared to the Fc region. This differential effect of polysorbates on the Fab and Fc regions was because of the lesser thermodynamic stability of the Fab compared to the Fc. These results further indicate that PS80 is the preferred polysorbate for this mAb formulation, because it offers higher protection against aggregation, causes lesser structural perturbation, and has weaker binding affinity with fewer binding sites compared to PS20. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Ana Paula Santos

    2017-01-01

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

  9. Ward identities of higher order Virasoro algebra

    International Nuclear Information System (INIS)

    Zha Chaozeng; Dolate, S.

    1994-11-01

    The general formulations of primary fields versus quasi-primary ones in the context of high order Virasoro algebra (HOVA) and the corresponding Ward identity are explored. The primary fields of conformal spins up to 8 are given in terms of quasi-primary fields, and the general features of the higher order expressions are also discussed. It is observed that the local fields, either primary of quasi-primary, carry the same numbers of central charges, and not all the primary fields contribute to the anomalies in the Ward identities. (author). 6 refs

  10. Theorem Proving In Higher Order Logics

    Science.gov (United States)

    Carreno, Victor A. (Editor); Munoz, Cesar A.; Tahar, Sofiene

    2002-01-01

    The TPHOLs International Conference serves as a venue for the presentation of work in theorem proving in higher-order logics and related areas in deduction, formal specification, software and hardware verification, and other applications. Fourteen papers were submitted to Track B (Work in Progress), which are included in this volume. Authors of Track B papers gave short introductory talks that were followed by an open poster session. The FCM 2002 Workshop aimed to bring together researchers working on the formalisation of continuous mathematics in theorem proving systems with those needing such libraries for their applications. Many of the major higher order theorem proving systems now have a formalisation of the real numbers and various levels of real analysis support. This work is of interest in a number of application areas, such as formal methods development for hardware and software application and computer supported mathematics. The FCM 2002 consisted of three papers, presented by their authors at the workshop venue, and one invited talk.

  11. Global chromatin fibre compaction in response to DNA damage

    International Nuclear Information System (INIS)

    Hamilton, Charlotte; Hayward, Richard L.; Gilbert, Nick

    2011-01-01

    Highlights: ► Robust KAP1 phosphorylation in response to DNA damage in HCT116 cells. ► DNA repair foci are found in soluble chromatin. ► Biophysical analysis reveals global chromatin fibre compaction after DNA damage. ► DNA damage is accompanied by rapid linker histone dephosphorylation. -- Abstract: DNA is protected by packaging it into higher order chromatin fibres, but this can impede nuclear processes like DNA repair. Despite considerable research into the factors required for signalling and repairing DNA damage, it is unclear if there are concomitant changes in global chromatin fibre structure. In human cells DNA double strand break (DSB) formation triggers a signalling cascade resulting in H2AX phosphorylation (γH2AX), the rapid recruitment of chromatin associated proteins and the subsequent repair of damaged sites. KAP1 is a transcriptional corepressor and in HCT116 cells we found that after DSB formation by chemicals or ionising radiation there was a wave of, predominantly ATM dependent, KAP1 phosphorylation. Both KAP1 and phosphorylated KAP1 were readily extracted from cells indicating they do not have a structural role and γH2AX was extracted in soluble chromatin indicating that sites of damage are not attached to an underlying structural matrix. After DSB formation we did not find a concomitant change in the sensitivity of chromatin fibres to micrococcal nuclease digestion. Therefore to directly investigate higher order chromatin fibre structures we used a biophysical sedimentation technique based on sucrose gradient centrifugation to compare the conformation of chromatin fibres isolated from cells before and after DNA DSB formation. After damage we found global chromatin fibre compaction, accompanied by rapid linker histone dephosphorylation, consistent with fibres being more regularly folded or fibre deformation being stabilized by linker histones. We suggest that following DSB formation, although there is localised chromatin unfolding to

  12. 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.

  13. Gibberellin-induced change in the structure of chromatin in wheat sprouts: decrease in the accessibility of DNA in preparations of soluble chromatin to the action of EcoRII methylase

    International Nuclear Information System (INIS)

    Noskov, V.A.; Kintsurashvili, L.N.; Smirnova, T.A.; Manamsh'yan, T.A.; Kir'yanov, G.I.; Vanyushin, B.F.

    1986-01-01

    A method has been perfected for producing soluble chromatin from whole wheat sprouts at low ionic strength. The chromatin preparations isolated possess a native structure: they have a nucleosome organization. Under identical conditions the soluble wheat chromatin undergoes more profound degradation by DNase I and staphylococcal nuclease than the chromatin from the rat liver. The DNA contained in the isolated chromatin is capable of accepting CHnumber groups from S-[methyl- 3 H]-adenosylmethionine during incubation with DNA methylase EcoRII; not all the CC A/T GG sequences in DNA are methylated in vivo. Chromatin from gibberellin A 3 -treated wheat sprout DNA accepts 40% fewer CH 3 groups than that from the control sprouts, which is probably due to the greater compactness of the chromatin. In the case of longer incubation, the level of methylation of the chromatin falls, which may be associated with the presence of DNA-demethylating activity

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

    Directory of Open Access Journals (Sweden)

    Ryosuke eOhsawa

    2013-07-01

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

  15. Finding Higher Order Differentials of MISTY1

    Science.gov (United States)

    Tsunoo, Yukiyasu; Saito, Teruo; Kawabata, Takeshi; Nakagawa, Hirokatsu

    MISTY1 is a 64-bit block cipher that has provable security against differential and linear cryptanalysis. MISTY1 is one of the algorithms selected in the European NESSIE project, and it is recommended for Japanese e-Government ciphers by the CRYPTREC project. In this paper, we report on 12th order differentials in 3-round MISTY1 with FL functions and 44th order differentials in 4-round MISTY1 with FL functions both previously unknown. We also report that both data complexity and computational complexity of higher order differential attacks on 6-round MISTY1 with FL functions and 7-round MISTY1 with FL functions using the 46th order differential can be reduced to as much as 1/22 of the previous values by using multiple 44th order differentials simultaneously.

  16. Three weights higher order Hardy type inequalities

    Directory of Open Access Journals (Sweden)

    Aigerim A. Kalybay

    2006-01-01

    Full Text Available We investigate the following three weights higher order Hardy type inequality (0.1 ‖g‖q,u≤  C‖Dρkg‖p,v where Dρi denotes the following weighted differential operator: {dig(tdti,i=0,1,...,m−1,di−mdti−m(p(tdmg(tdtm,i=m,m+1,...,k, for a weight function ρ(⋅. A complete description of the weights u, v and ρ so that (0.1 holds was given in [4] for the case 1

  17. Interactions, strings and isotopies in higher order anisotropic superspaces

    CERN Document Server

    Vacaru, Sergiu Ion

    2001-01-01

    The monograph summarizes the author's results on the geometry of anholonomic and locally anisotropic interactions, published in J. Math. Phys., Nucl. Phys. B, Ann. Phys. (NY), JHEP, Rep. Math. Phys., Int. J. Theor. Phys. and in some former Soviet Union and Romanian scientific journals. The main subjects are in the theory of field interactions, strings and diffusion processes on spaces, superspaces and isospaces with higher order anisotropy and inhomogeneity. The approach proceeds by developing the concept of higher order anisotropic (super)space which unifies the logical and manthematical aspects of modern Kaluza--Klein theories and generalized Lagrange and Finsler geometry and leads to modeling of physical processes on higher order fiber (super)bundles provided with nonlinear and distinguished connections and metric structures. This book can be also considered as a pedagogical survey on the mentioned subjects.

  18. DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes.

    Science.gov (United States)

    Guha, Mithu; Saare, Mario; Maslovskaja, Julia; Kisand, Kai; Liiv, Ingrid; Haljasorg, Uku; Tasa, Tõnis; Metspalu, Andres; Milani, Lili; Peterson, Pärt

    2017-04-21

    The autoimmune regulator (AIRE) protein is the key factor in thymic negative selection of autoreactive T cells by promoting the ectopic expression of tissue-specific genes in the thymic medullary epithelium. Mutations in AIRE cause a monogenic autoimmune disease called autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. AIRE has been shown to promote DNA breaks via its interaction with topoisomerase 2 (TOP2). In this study, we investigated topoisomerase-induced DNA breaks and chromatin structural alterations in conjunction with AIRE-dependent gene expression. Using RNA sequencing, we found that inhibition of TOP2 religation activity by etoposide in AIRE-expressing cells had a synergistic effect on genes with low expression levels. AIRE-mediated transcription was not only enhanced by TOP2 inhibition but also by the TOP1 inhibitor camptothecin. The transcriptional activation was associated with structural rearrangements in chromatin, notably the accumulation of γH2AX and the exchange of histone H1 with HMGB1 at AIRE target gene promoters. In addition, we found the transcriptional up-regulation to co-occur with the chromatin structural changes within the genomic cluster of carcinoembryonic antigen-like cellular adhesion molecule genes. Overall, our results suggest that the presence of AIRE can trigger molecular events leading to an altered chromatin landscape and the enhanced transcription of low-expressed genes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

    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-epidermal i......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......-epidermal immune complex deposits have similar molecular composition as glomerular deposits, (ii) whether chromatin fragments bind dermo-epidermal structures, and (iii) whether deposits in nephritic glomeruli predispose for accumulation of similar deposits in skin. Paired skin and kidney biopsies from nephritic...... (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...

  20. Local chromatin structure of heterochromatin regulates repeated DNA stability, nucleolus structure, and genome integrity

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Jamy C. [Univ. of California, Berkeley, CA (United States)

    2007-01-01

    Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project investigates how heterochromatin formation and function impact nuclear architecture, repeated DNA organization, and genome stability in Drosophila melanogaster. H3K9me-based chromatin reduces extrachromosomal DNA formation; most likely by restricting the access of repair machineries to repeated DNAs. Reducing extrachromosomal ribosomal DNA stabilizes rDNA repeats and the nucleolus structure. H3K9me-based chromatin also inhibits DNA damage in heterochromatin. Cells with compromised heterochromatin structure, due to Su(var)3-9 or dcr-2 (a component of the RNAi pathway) mutations, display severe DNA damage in heterochromatin compared to wild type. In these mutant cells, accumulated DNA damage leads to chromosomal defects such as translocations, defective DNA repair response, and activation of the G2-M DNA repair and mitotic checkpoints that ensure cellular and animal viability. My thesis research suggests that DNA replication, repair, and recombination mechanisms in heterochromatin differ from those in

  1. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea.

    Science.gov (United States)

    Guo, Li; Feng, Yingang; Zhang, Zhenfeng; Yao, Hongwei; Luo, Yuanming; Wang, Jinfeng; Huang, Li

    2008-03-01

    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 higher affinity for double-stranded DNA than for single-stranded DNA, constrains negative DNA supercoils and is associated with genomic DNA in vivo. The solution structure and DNA-binding surface of Cren7 from the hyperthermophilic crenarchaeon Sulfolobus solfataricus were determined by NMR. The protein adopts an SH3-like fold. It interacts with duplex DNA through a beta-sheet and a long flexible loop, presumably resulting in DNA distortions through intercalation of conserved hydrophobic residues into the DNA structure. These data suggest that the crenarchaeal kingdom in the Archaea shares a common strategy in chromatin organization.

  2. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure

    NARCIS (Netherlands)

    M. Rosa-Garrido (Manuel); Chapski, D.J. (Douglas J.); Schmitt, A.D. (Anthony D.); Kimball, T.H. (Todd H.); Karbassi, E. (Elaheh); Monte, E. (Emma); Balderas, E. (Enrique); Pellegrini, M. (Matteo); Shih, T.-T. (Tsai-Ting); Soehalim, E. (Elizabeth); D.A. Liem (David); Ping, P. (Peipei); N.J. Galjart (Niels); Ren, S. (Shuxun); Wang, Y. (Yibin); Ren, B. (Bing); Vondriska, T.M. (Thomas M.)

    2017-01-01

    textabstractBACKGROUND: Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined.METHODS: To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation

  3. High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure.

    Science.gov (United States)

    Rosa-Garrido, Manuel; Chapski, Douglas J; Schmitt, Anthony D; Kimball, Todd H; Karbassi, Elaheh; Monte, Emma; Balderas, Enrique; Pellegrini, Matteo; Shih, Tsai-Ting; Soehalim, Elizabeth; Liem, David; Ping, Peipei; Galjart, Niels J; Ren, Shuxun; Wang, Yibin; Ren, Bing; Vondriska, Thomas M

    2017-10-24

    Cardiovascular disease is associated with epigenomic changes in the heart; however, the endogenous structure of cardiac myocyte chromatin has never been determined. To investigate the mechanisms of epigenomic function in the heart, genome-wide chromatin conformation capture (Hi-C) and DNA sequencing were performed in adult cardiac myocytes following development of pressure overload-induced hypertrophy. Mice with cardiac-specific deletion of CTCF (a ubiquitous chromatin structural protein) were generated to explore the role of this protein in chromatin structure and cardiac phenotype. Transcriptome analyses by RNA-seq were conducted as a functional readout of the epigenomic structural changes. Depletion of CTCF was sufficient to induce heart failure in mice, and human patients with heart failure receiving mechanical unloading via left ventricular assist devices show increased CTCF abundance. Chromatin structural analyses revealed interactions within the cardiac myocyte genome at 5-kb resolution, enabling examination of intra- and interchromosomal events, and providing a resource for future cardiac epigenomic investigations. Pressure overload or CTCF depletion selectively altered boundary strength between topologically associating domains and A/B compartmentalization, measurements of genome accessibility. Heart failure involved decreased stability of chromatin interactions around disease-causing genes. In addition, pressure overload or CTCF depletion remodeled long-range interactions of cardiac enhancers, resulting in a significant decrease in local chromatin interactions around these functional elements. These findings provide a high-resolution chromatin architecture resource for cardiac epigenomic investigations and demonstrate that global structural remodeling of chromatin underpins heart failure. The newly identified principles of endogenous chromatin structure have key implications for epigenetic therapy. © 2017 The Authors.

  4. Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

    Science.gov (United States)

    Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude

    2013-01-01

    In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.

  5. Chromatin structure influence the sensitivity of DNA to ionizing radiation induced DNA damage

    International Nuclear Information System (INIS)

    Gupta, Sanjay

    2016-01-01

    Chromatin acts as a natural hindrance in DNA-damage recognition, repair and recovery. Histone and their variants undergo differential post-translational modification(s) and regulate chromatin structure to facilitate DNA damage response (DDR). During the presentation we will discuss the importance of chromatin organization and histone modification(s) during IR-induced DNA damage response in human liver cells. Our data shows G1-phase specific decrease of H3 serine10 phosphorylation in response to DNA damage is coupled with chromatin compaction in repair phase of DDR. The loss of H3Ser10P during DNA damage shows an inverse correlation with gain of γH2AX from a same mono-nucleosome in a dose-dependent manner. The loss of H3Ser10P is a universal phenomenon as it is independent of origin of cell lines and nature of genotoxic agents in G1 phase cells. The reversible reduction of H3Ser10P is mediated by opposing activities of phosphatase, MKP1 and kinase, MSK1 of the MAP kinase pathway. The present study suggests distinct reversible histone marks are associated with G1-phase of cell cycle and plays a critical role in chromatin organization which may facilitate differential sensitivity against radiation. Thus, the study raises the possibility of combinatorial modulation of H3Ser10P and histone acetylation with specific inhibitors to target the radio-resistant cancer cells in G1-phase and thus may serve as promising targets for cancer therapy. (author)

  6. DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure

    International Nuclear Information System (INIS)

    Revaud, D.

    2009-06-01

    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)

  7. FANCJ couples replication past natural fork barriers with maintenance of chromatin structure.

    Science.gov (United States)

    Schwab, Rebekka A; Nieminuszczy, Jadwiga; Shin-ya, Kazuo; Niedzwiedz, Wojciech

    2013-04-01

    Defective DNA repair causes Fanconi anemia (FA), a rare childhood cancer-predisposing syndrome. At least 15 genes are known to be mutated in FA; however, their role in DNA repair remains unclear. Here, we show that the FANCJ helicase promotes DNA replication in trans by counteracting fork stalling on replication barriers, such as G4 quadruplex structures. Accordingly, stabilization of G4 quadruplexes in ΔFANCJ cells restricts fork movements, uncouples leading- and lagging-strand synthesis and generates small single-stranded DNA gaps behind the fork. Unexpectedly, we also discovered that FANCJ suppresses heterochromatin spreading by coupling fork movement through replication barriers with maintenance of chromatin structure. We propose that FANCJ plays an essential role in counteracting chromatin compaction associated with unscheduled replication fork stalling and restart, and suppresses tumorigenesis, at least partially, in this replication-specific manner.

  8. Chromatin structure and ionizing-radiation-induced chromosome aberrations

    International Nuclear Information System (INIS)

    Muehlmann-Diaz, M.C.

    1993-01-01

    The possible influence of chromatic structure or activity on chromosomal radiosensitivity was studied. A cell line was isolated which contained some 10 5 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 G 0 , 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

  9. Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure.

    Directory of Open Access Journals (Sweden)

    Ana-Maria Florescu

    2016-06-01

    Full Text Available Characterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple biophysical model where interphase chromosomes are described in terms of the folding of chromatin sequences composed of alternating blocks of fibers with different thicknesses and flexibilities, and we use it to study the influence of sequence disorder on chromosome behaviors in space and time. By employing extensive computer simulations, we thus demonstrate that chromosomes undergo noticeable conformational changes only on length-scales smaller than 105 basepairs and time-scales shorter than a few seconds, and we suggest there might exist effective upper bounds to the detection of chromosome reorganization in eukaryotes. We prove the relevance of our framework by modeling recent experimental FISH data on murine chromosomes.

  10. Comparative study of cyanotoxins affecting cytoskeletal and chromatin structures in CHO-K1 cells.

    Science.gov (United States)

    Gácsi, Mariann; Antal, Otilia; Vasas, Gábor; Máthé, Csaba; Borbély, György; Saker, Martin L; Gyori, János; Farkas, Anna; Vehovszky, Agnes; Bánfalvi, Gáspár

    2009-06-01

    In this study we compared the effects of the two frequently occuring and most dangerous cyanobacterial toxins on the cellular organization of microfilaments, microtubules and on the chromatin structure in Chinese hamster ovary (CHO-K1) cells. These compounds are the widely known microcystin-LR (MC-LR) and cylindrospermopsin (CYN) classified as the highest-priority cyanotoxin. Toxic effects were tested in a concentration and time dependent manner. The hepatotoxic MC-LR did not cause significant cytotoxicity on CHO-K1 cells under 20 microM, but caused apoptotic changes at higher concentrations. Apoptotic shrinkage was associated with the shortening and loss of actin filaments and with a concentration dependent depolymerization of microtubules. No necrosis was observed over the concentration range (1-50 microM MC-LR) tested. Cylindrospermopsin did cause apoptosis at low concentrations (1-2 microM) and over short exposure periods (12h). Necrosis was observed at higher concentrations (5-10 microM) and following longer exposure periods (24 or 48h). Cyanotoxins also affected the chromatin structure. The condensation process was inhibited by MC-LR at a later stage and manifested as broken elongated prechromosomes. CYN inhibited chromatin condensation at the early fibrillary stage leading to blurred fluorescent images of apoptotic bodies and preventing the formation of metaphase chromosomes. Cylindrospermopsin exhibited a more pronounced toxic effect causing cytoskeletal and nuclear changes as well as apoptotic and necrotic alterations.

  11. Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells

    Directory of Open Access Journals (Sweden)

    Chang Pyo Hong

    2012-09-01

    Full Text Available Chromatin structure and dynamics that are influenced by epigenetic marks, such as histone modification and DNA methylation, play a crucial role in modulating gene transcription. To understand the relationship between histone modifications and regulatory elements in breast cancer cells, we compared our chromatin immunoprecipitation sequencing (ChIP-Seq histone modification patterns for histone H3K4me1, H3K4me3, H3K9/16ac, and H3K27me3 in MCF-7 cells with publicly available formaldehyde-assisted isolation of regulatory elements (FAIRE-chip signals in human chromosomes 8, 11, and 12, identified by a method called FAIRE. Active regulatory elements defined by FAIRE were highly associated with active histone modifications, like H3K4me3 and H3K9/16ac, especially near transcription start sites. The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. Our results might provide an insight into epigenetic regulatory mechanisms explaining the association of histone modifications with open chromatin structure in breast cancer cells.

  12. Reasoning About Higher-Order Relational Specifications

    OpenAIRE

    Wang , Yuting; Chaudhuri , Kaustuv; Gacek , Andrew; Nadathur , Gopalan

    2013-01-01

    International audience; The logic of hereditary Harrop formulas (HH) has proven useful for specifying a wide range of formal systems. This logic includes a form of hypothetical judgment that leads to dynamically changing sets of assumptions and that is key to encoding side conditions and contexts that occur frequently in structural operational semantics (SOS) style presentations. Specifications are often useful in reasoning about the systems they describe. The Abella theorem prover supports s...

  13. The Meaning of Higher-Order Factors in Reflective-Measurement Models

    Science.gov (United States)

    Eid, Michael; Koch, Tobias

    2014-01-01

    Higher-order factor analysis is a widely used approach for analyzing the structure of a multidimensional test. Whenever first-order factors are correlated researchers are tempted to apply a higher-order factor model. But is this reasonable? What do the higher-order factors measure? What is their meaning? Willoughby, Holochwost, Blanton, and Blair…

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

    Directory of Open Access Journals (Sweden)

    Anderly C Chueh

    2009-01-01

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

  15. Evidence for the distortion product frequency place as a source of distribution product otoacoustic emission (DPOAE) fine structure in humans : I. Fine structure and higher-order DPOAE as a function of the frequency ratio f2/f1

    NARCIS (Netherlands)

    Mauermann, M; Uppenkamp, S; van Hengel, P.W.J.; 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

  16. Higher order corrections in quantum electrodynamics

    International Nuclear Information System (INIS)

    Rafael, E.

    1977-01-01

    Theoretical contributions to high-order corrections in purely leptonic systems, such as electrons and muons, muonium (μ + e - ) and positronium (e + e - ), are reviewed to establish the validity of quantum electrodynamics (QED). Two types of QED contributions to the anomalous magnetic moments are considered, from diagrams with one fermion type lines and those witn two fermion type lines. The contributions up to eighth order are compared to the data available with a different accuracy. Good agreement is stated within the experimental errors. The experimental accuracy of the muonium hyperfine structure and of the radiative corrections to the decay of positronium are compared to the one attainable in theoretical calculations. The need for a higher precision in both experimental data and theoretical calculations is stated

  17. Developing Higher-Order Materials Knowledge Systems

    Science.gov (United States)

    Fast, Anthony Nathan

    2011-12-01

    Advances in computational materials science and novel characterization techniques have allowed scientists to probe deeply into a diverse range of materials phenomena. These activities are producing enormous amounts of information regarding the roles of various hierarchical material features in the overall performance characteristics displayed by the material. Connecting the hierarchical information over disparate domains is at the crux of multiscale modeling. The inherent challenge of performing multiscale simulations is developing scale bridging relationships to couple material information between well separated length scales. Much progress has been made in the development of homogenization relationships which replace heterogeneous material features with effective homogenous descriptions. These relationships facilitate the flow of information from lower length scales to higher length scales. Meanwhile, most localization relationships that link the information from a from a higher length scale to a lower length scale are plagued by computationally intensive techniques which are not readily integrated into multiscale simulations. The challenge of executing fully coupled multiscale simulations is augmented by the need to incorporate the evolution of the material structure that may occur under conditions such as material processing. To address these challenges with multiscale simulation, a novel framework called the Materials Knowledge System (MKS) has been developed. This methodology efficiently extracts, stores, and recalls microstructure-property-processing localization relationships. This approach is built on the statistical continuum theories developed by Kroner that express the localization of the response field at the microscale using a series of highly complex convolution integrals, which have historically been evaluated analytically. The MKS approach dramatically improves the accuracy of these expressions by calibrating the convolution kernels in these

  18. Concept Mapping for Higher Order Thinking

    Directory of Open Access Journals (Sweden)

    Susan Marie Zvacek

    2013-02-01

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

  19. [Changes in the chromatin structure of hepatocyte nuclei of rats trained to hypoxia].

    Science.gov (United States)

    Domkina, L K; Bresler, V M; Simanovskiĭ, L N

    1976-03-01

    Structure of chromatin in the nuclei of the isolated surviving hepatocytes and in the isolated nuclei of hepatocytes were studied by fluorochroming with acridine orange and by microfluorimetry of fluorescenc connected with the stain chromatin at 530 and 590 nm in intact rats and in the animals trained to hypoxia in a pressure chamber for 60 days. The nuclei of hepatocytes of intact rats were distributed by fluorescence at 530 nm into three classes with the intensity ratio of 1:2:4; as to the nuclei of hepatocytes of the rats trained to hypoxia - they formed a single class corresponding to the second class of control. In intact rats the ratio of the fluorescence intensity at 590 nm to such at 530 nm (alpha coefficient) formed normal distribution; in trained rats - a bimodal distribution with a shift of the maximum in the direction of reduction and increase of alpha in comparison with control. It is supposed that in hypoxia there is a repression of one and depression of other genes in the chromatine of the nuclei of the liver.

  20. Chromatin replication and epigenome maintenance

    DEFF Research Database (Denmark)

    Alabert, Constance; Groth, Anja

    2012-01-01

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

  1. Genome instability in the context of chromatin structure and fragile sites

    Czech Academy of Sciences Publication Activity Database

    Bártová, Eva; Galiová-Šustáčková, Gabriela; Legartová, Soňa; Stixová, Lenka; Jugová, Alžbeta; Kozubek, Stanislav

    2010-01-01

    Roč. 20, č. 3 (2010), s. 181-194 ISSN 1045-4403 R&D Projects: GA MŠk ME 919; GA ČR(CZ) GAP302/10/1022 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * fragile sites * chromatin structure Subject RIV: BO - Biophysics Impact factor: 4.111, year: 2010

  2. Relationship Between Chromatin Structure and Sensitivity to Molecularly Targeted Auger Electron Radiation Therapy

    International Nuclear Information System (INIS)

    Terry, Samantha Y.A.; Vallis, Katherine 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 altered in MDA-MB-468 and 231-H2N human breast cancer cells by suberoylanilide hydroxamic acid (SAHA), 5-aza-2-deoxycytidine, or hypertonic treatment. The extent and duration of chromatin structural changes were evaluated using the micrococcal nuclease assay. DNA damage (γH2AX assay) and clonogenic survival were evaluated after exposure to 111 In-DTPA-hEGF, an Auger electron-emitting radiopharmaceutical, or IR. The intracellular distribution of 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 γH2AX foci per cell was greater in MDA-MB-468 and 231-H2N cells after IR (0.5 Gy) plus SAHA (1 μM) compared with IR alone (16 ± 0.6 and 14 ± 0.3 vs. 12 ± 0.4 and 11 ± 0.2, respectively). More γH2AX foci were observed in MDA-MB-468 and 231-H2N cells exposed to 111 In-DTPA-hEGF (6 MBq/μg) plus SAHA vs. 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 111 In-DTPA-hEGF. Clonogenic survival was reduced in MDA-MB-468 and 231-H2N cells after IR (6 Gy) plus SAHA (1 μM) vs. IR alone (0.6% ± 0.01 and 0.3% ± 0.2 vs. 5.8% ± 0.2 and 2% ± 0.1, respectively) and after 111 In-DTPA-hEGF plus SAHA compared to 111 In-DTPA-hEGF alone (21% ± 0.4% and 19% ± 4.6 vs. 33% ± 2.3 and 32% ± 3.7). SAHA did not affect 111 In-DTPA-hEGF nuclear localization. Hypertonic treatment resulted in fewer γH2AX foci per cell after IR and 111 In-DTPA-hEGF compared to controls but did not significantly alter clonogenic

  3. Conceptualizing and Assessing Higher-Order Thinking in Reading

    Science.gov (United States)

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

    2015-01-01

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

  4. FoxA1 binding to the MMTV LTR modulates chromatin structure and transcription

    International Nuclear Information System (INIS)

    Holmqvist, Per-Henrik; Belikov, Sergey; Zaret, Kenneth S.; Wrange, Oerjan

    2005-01-01

    Novel binding sites for the forkhead transcription factor family member Forkhead box A (FoxA), previously referred to as Hepatocyte Nuclear Factor 3 (HNF3), were found within the mouse mammary tumor virus long terminal repeat (MMTV LTR). The effect of FoxA1 on MMTV LTR chromatin structure, and expression was evaluated in Xenopus laevis oocytes. Mutagenesis of either of the two main FoxA binding sites showed that the distal site, -232/-221, conferred FoxA1-dependent partial inhibition of glucocorticoid receptor (GR) driven MMTV transcription. The proximal FoxA binding segment consisted of two individual FoxA sites at -57/-46 and -45/-34, respectively, that mediated an increased basal MMTV transcription. FoxA1 binding altered the chromatin structure of both the inactive- and the hormone-activated MMTV LTR. Hydroxyl radical foot printing revealed FoxA1-mediated changes in the nucleosome arrangement. Micrococcal nuclease digestion showed the hormone-dependent sub-nucleosome complex, containing ∼120 bp of DNA, to be expanded by FoxA1 binding to the proximal segment into a larger complex containing ∼200 bp. The potential function of the FoxA1-mediated expression of the MMTV provirus for maintenance of expression in different tissues is discussed

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

    Directory of Open Access Journals (Sweden)

    David eRoquis

    2014-07-01

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

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

    KAUST Repository

    Bonito, Andrea

    2013-01-01

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

  7. Changes in chromatin structure during the aging of cell cultures as revealed by differential scanning calorimetry

    International Nuclear Information System (INIS)

    Almagor, M.; Cole, R.D.

    1989-01-01

    Nuclei from cultured human cells were examined by differential scanning calorimetry. Their melting profiles revealed four structural transitions at 60, 76, 88, and 105 degrees C (transitions I-IV, respectively). In immortalized (i.e., tumor) cell cultures and in normal cell cultures of low passage number, melting profiles were dominated by the 105 degrees C transition (transition IV), but in vitro aging of normal and Werner syndrome cells was associated with a marked decrease in transition IV followed by an increase in transition III at the expense of transition IV. At intermediate times in the aging process, much DNA melted at a temperature range (95-102 degrees C) intermediate between transitions III and IV, and this is consistent with the notion that aging of cell cultures is accompanied by an increase in single-strand character of the DNA. Calorimetric changes were observed in the melting profile of nuclei from UV-irradiated tumor cells that resembled the age-induced intermediate melting of chromatin. It is suggested that aging is accompanied by an increase in single-stranded character of the DNA in chromatin, which lowers its melting temperature, followed by strand breaks in the DNA that destroy its supercoiling potential

  8. Reprogramming chromatin

    DEFF Research Database (Denmark)

    Ehrensberger, Andreas Hasso; Svejstrup, Jesper Qualmann

    2012-01-01

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

  9. 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.

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

    Science.gov (United States)

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

    2012-07-01

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

  11. Nil Bohr-sets and almost automorphy of higher order

    CERN Document Server

    Huang, Wen; Ye, Xiangdong

    2016-01-01

    Two closely related topics, higher order Bohr sets and higher order almost automorphy, are investigated in this paper. Both of them are related to nilsystems. In the first part, the problem which can be viewed as the higher order version of an old question concerning Bohr sets is studied: for any d\\in \\mathbb{N} does the collection of \\{n\\in \\mathbb{Z}: S\\cap (S-n)\\cap\\ldots\\cap (S-dn)\

  12. Biochemical and structural characterization of Cren7, a novel chromatin protein conserved among Crenarchaea

    OpenAIRE

    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...

  13. Quantitative analysis of the chromatin of lymphocytes: an assay on comparative structuralism.

    Science.gov (United States)

    Meyer, F

    1980-01-01

    With 26 letters we can form all the words we use, and with a few words it is possible to form an infinite number of different meaningful sentences. In our case, the letters will be a few simple neighborhood image transformations and area measurements. The paper shows how, by iterating these transformations, it is possible to obtain a good quantitative description of the nuclear structure of Feulgen-stained lymphocytes (CLL and normal). The fact that we restricted ourselves to a small number of image transformations made it possible to construct an image analysis system (TAS) able to do these transformations very quickly. We will see, successively, how to segment the nucleus itself, the chromatin, and the interchromatinic channels, how openings and closings lead to size and spatial distribution curves, and how skeletons may be used for measuring the lengths of interchromatinic channels.

  14. Higher-order phase transitions on financial markets

    Science.gov (United States)

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

    2010-08-01

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

  15. Higher-Order Hybrid Gaussian Kernel in Meshsize Boosting Algorithm

    African Journals Online (AJOL)

    In this paper, we shall use higher-order hybrid Gaussian kernel in a meshsize boosting algorithm in kernel density estimation. Bias reduction is guaranteed in this scheme like other existing schemes but uses the higher-order hybrid Gaussian kernel instead of the regular fixed kernels. A numerical verification of this scheme ...

  16. Higher-order Jordan Osserman pseudo-Riemannian manifolds

    International Nuclear Information System (INIS)

    Gilkey, Peter B; Ivanova, Raina; Zhang Tan

    2002-01-01

    We study the higher-order Jacobi operator in pseudo-Riemannian geometry. We exhibit a family of manifolds so that this operator has constant Jordan normal form on the Grassmannian of subspaces of signature (r, s) for certain values of (r, s). These pseudo-Riemannian manifolds are new and non-trivial examples of higher-order Osserman manifolds

  17. Higher-order Jordan Osserman pseudo-Riemannian manifolds

    Energy Technology Data Exchange (ETDEWEB)

    Gilkey, Peter B [Mathematics Department, University of Oregon, Eugene, OR 97403 (United States); Ivanova, Raina [Mathematics Department, University of Hawaii - Hilo, 200 W Kawili St, Hilo, HI 96720 (United States); Zhang Tan [Department of Mathematics and Statistics, Murray State University, Murray, KY 42071 (United States)

    2002-09-07

    We study the higher-order Jacobi operator in pseudo-Riemannian geometry. We exhibit a family of manifolds so that this operator has constant Jordan normal form on the Grassmannian of subspaces of signature (r, s) for certain values of (r, s). These pseudo-Riemannian manifolds are new and non-trivial examples of higher-order Osserman manifolds.

  18. Exact solutions to two higher order nonlinear Schroedinger equations

    International Nuclear Information System (INIS)

    Xu Liping; Zhang Jinliang

    2007-01-01

    Using the homogeneous balance principle and F-expansion method, the exact solutions to two higher order nonlinear Schroedinger equations which describe the propagation of femtosecond pulses in nonlinear fibres are obtained with the aid of a set of subsidiary higher order ordinary differential equations (sub-equations for short)

  19. Neural classifiers for learning higher-order correlations

    International Nuclear Information System (INIS)

    Gueler, M.

    1999-01-01

    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

  20. Neural Classifiers for Learning Higher-Order Correlations

    Science.gov (United States)

    Güler, Marifi

    1999-01-01

    Studies by various authors suggest that higher-order networks can be more powerful and are biologically more plausible with respect to the more traditional multilayer networks. These architectures 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 pattern 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.

  1. Higher order mode analysis of the SNS superconducting linac

    CERN Document Server

    Sang Ho Kim; Dong Jeon; Sundelin, R

    2001-01-01

    Higher order modes (HOM's) of monopoles, dipoles, quadrupoles and sextupoles in beta =0.61 and beta =0.81 6-cell superconducting (SC) cavities for the Spallation Neutron Source (SNS) project, have been found up to about 3 GHz and their properties such as R/Q, trapping possibility, etc have been figured out concerning manufacturing imperfection. The main issues of HOM's are beam instabilities (published separately) and HOM induced power especially from TM monopoles. The time structure of SNS beam has three different time scales of pulses, which are micro-pulse, midi-pulse and macropulse. Each time structure will generate resonances. When a mode is near these resonance frequencies, the induced voltage could be large and accordingly the resulting HOM power. In order to understand the effects from such a complex beam time structure on the mode excitation and resulting HOM power, analytic expressions are developed. With these analytic expressions, the induced HOM voltage and HOM power were calculated by assuming e...

  2. Higher order Lie-Baecklund symmetries of evolution equations

    International Nuclear Information System (INIS)

    Roy Chowdhury, A.; Roy Chowdhury, K.; Paul, S.

    1983-10-01

    We have considered in detail the analysis of higher order Lie-Baecklund symmetries for some representative nonlinear evolution equations. Until now all such symmetry analyses have been restricted only to the first order of the infinitesimal parameter. But the existence of Baecklund transformation (which can be shown to be an overall sum of higher order Lie-Baecklund symmetries) makes it necessary to search for such higher order Lie-Baecklund symmetries directly without taking recourse to the Baecklund transformation or inverse scattering technique. (author)

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

    International Nuclear Information System (INIS)

    Ding De-Sheng; Huang Jin-Huang

    2016-01-01

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

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

    Science.gov (United States)

    Ding, De-Sheng; Huang, Jin-Huang

    2016-12-01

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

  5. Protein scaffolds and higher-order complexes in synthetic biology

    NARCIS (Netherlands)

    den Hamer, A.; Rosier, B.J.H.M.; Brunsveld, L.; de Greef, T.F.A.; Ryadnov, M.; Brunsveld, L.; Suga, H.

    2017-01-01

    Interactions between proteins control molecular functions such as signalling or metabolic activity. Assembly of proteins via scaffold proteins or in higher-order complexes is a key regulatory mechanism. Understanding and functionally applying this concept requires the construction, study, and

  6. Generating superpositions of higher order bessel beams [Conference paper

    CSIR Research Space (South Africa)

    Vasilyeu, R

    2009-10-01

    Full Text Available An experimental setup to generate a superposition of higher-order Bessel beams by means of a spatial light modulator and ring aperture is presented. The experimentally produced fields are in good agreement with those calculated theoretically....

  7. Higher-order curvature terms and extended inflation

    International Nuclear Information System (INIS)

    Wang Yun

    1990-01-01

    We consider higher-order curvature terms in context of the Brans-Dicke theory of gravity, and investigate the effects of these terms on extended inflationary theories. We find that the higher-order curvature terms tend to speed up inflation, although the original extended-inflation solutions are stable when these terms are small. Analytical solutions are found for two extreme cases: when the higher-order curvature terms are small, and when they dominate. A conformal transformation is employed in solving the latter case, and some of the subtleties in this technique are discussed. We note that percolation is less likely to occur when the higher-order curvature terms are present. An upper bound on α is expected if we are to avoid excessive and inadequate percolation of true-vacuum bubbles

  8. Unambiguous formalism for higher order Lagrangian field theories

    International Nuclear Information System (INIS)

    Campos, Cedric M; De Leon, Manuel; De Diego, David MartIn; Vankerschaver, Joris

    2009-01-01

    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.

  9. Higher-order RANS turbulence models for separated flows

    Data.gov (United States)

    National Aeronautics and Space Administration — Higher-order Reynolds-averaged Navier-Stokes (RANS) models are developed to overcome the shortcomings of second-moment RANS models in predicting separated flows....

  10. A simplified parsimonious higher order multivariate Markov chain model

    Science.gov (United States)

    Wang, Chao; Yang, Chuan-sheng

    2017-09-01

    In this paper, a simplified parsimonious higher-order multivariate Markov chain model (SPHOMMCM) is presented. Moreover, parameter estimation method of TPHOMMCM is give. Numerical experiments shows the effectiveness of TPHOMMCM.

  11. A tridiagonal parsimonious higher order multivariate Markov chain model

    Science.gov (United States)

    Wang, Chao; Yang, Chuan-sheng

    2017-09-01

    In this paper, we present a tridiagonal parsimonious higher-order multivariate Markov chain model (TPHOMMCM). Moreover, estimation method of the parameters in TPHOMMCM is give. Numerical experiments illustrate the effectiveness of TPHOMMCM.

  12. Application of Mass Lumped Higher Order Finite Elements

    International Nuclear Information System (INIS)

    J. Chen, H.R. Strauss, S.C. Jardin, W. Park, L.E. Sugiyama, G. Fu, J. Breslau

    2005-01-01

    There are many interesting phenomena in extended-MHD such as anisotropic transport, mhd, 2-fluid effects stellarator and hot particles. Any one of them challenges numerical analysts, and researchers are seeking for higher order methods, such as higher order finite difference, higher order finite elements and hp/spectral elements. It is true that these methods give more accurate solution than their linear counterparts. However, numerically they are prohibitively expensive. Here we give a successful solution of this conflict by applying mass lumped higher order finite elements. This type of elements not only keep second/third order accuracy but also scale closely to linear elements by doing mass lumping. This is especially true for second order lump elements. Full M3D and anisotropic transport models are studied

  13. The role of formative feedback in promoting higher order thinking ...

    African Journals Online (AJOL)

    The role of formative feedback in promoting higher order thinking skills in ... activities, task characteristics, validating students' thinking, and providing feedback. ... Keywords: classroom environment, formative assessment, formative feedback, ...

  14. Asymptotic Expansions for Higher-Order Scalar Difference Equations

    Directory of Open Access Journals (Sweden)

    Ravi P. Agarwal

    2007-04-01

    Full Text Available We give an asymptotic expansion of the solutions of higher-order Poincaré difference equation in terms of the characteristic solutions of the limiting equation. As a consequence, we obtain an asymptotic description of the solutions approaching a hyperbolic equilibrium of a higher-order nonlinear difference equation with sufficiently smooth nonlinearity. The proof is based on the inversion formula for the z -transform and the residue theorem.

  15. Asymptotic Expansions for Higher-Order Scalar Difference Equations

    Directory of Open Access Journals (Sweden)

    Pituk Mihály

    2007-01-01

    Full Text Available We give an asymptotic expansion of the solutions of higher-order Poincaré difference equation in terms of the characteristic solutions of the limiting equation. As a consequence, we obtain an asymptotic description of the solutions approaching a hyperbolic equilibrium of a higher-order nonlinear difference equation with sufficiently smooth nonlinearity. The proof is based on the inversion formula for the z -transform and the residue theorem.

  16. Higher order aberrations of the eye: Part one

    Directory of Open Access Journals (Sweden)

    Marsha Oberholzer

    2016-06-01

    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

  17. 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....

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

    Directory of Open Access Journals (Sweden)

    Mustapha Rachidi

    2008-07-01

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

  19. Higher-order scalar interactions and SM vacuum stability

    Energy Technology Data Exchange (ETDEWEB)

    Lalak, Zygmunt; Lewicki, Marek; Olszewski, Paweł [Institute of Theoretical Physics, Faculty of Physics, University of Warsawul. Hoża 69, Warsaw (Poland)

    2014-05-26

    Investigation of the structure of the Standard Model effective potential at very large field strengths opens a window towards new phenomena and can reveal properties of the UV completion of the SM. The map of the lifetimes of the vacua of the SM enhanced by nonrenormalizable scalar couplings has been compiled to show how new interactions modify stability of the electroweak vacuum. Whereas it is possible to stabilize the SM by adding Planck scale suppressed interactions and taking into account running of the new couplings, the generic effect is shortening the lifetime and hence further destabilisation of the SM electroweak vacuum. These findings have been illustrated with phase diagrams of modified SM-like models. It has been demonstrated that stabilisation can be achieved by lowering the suppression scale of higher order operators while picking up such combinations of new couplings, which do not deepen the new minima of the potential. Our results show the dependence of the lifetime of the electroweak minimum on the magnitude of the new couplings, including cases with very small couplings (which means very large effective suppression scale) and couplings vastly different in magnitude (which corresponds to two different suppression scales)

  20. General relativity and gauge gravity theories of higher order

    International Nuclear Information System (INIS)

    Konopleva, N.P.

    1998-01-01

    It is a short review of today's gauge gravity theories and their relations with Einstein General Relativity. The conceptions of construction of the gauge gravity theories with higher derivatives are analyzed. GR is regarded as the gauge gravity theory corresponding to the choice of G ∞4 as the local gauge symmetry group and the symmetrical tensor of rank two g μν as the field variable. Using the mathematical technique, single for all fundamental interactions (namely variational formalism for infinite Lie groups), we can obtain Einstein's theory as the gauge theory without any changes. All other gauge approaches lead to non-Einstein theories of gravity. But above-mentioned mathematical technique permits us to construct the gauge gravity theory of higher order (for instance SO (3,1)-gravity) so that all vacuum solutions of Einstein equations are the solutions of the SO (3,1)-gravity theory. The structure of equations of SO(3,1)-gravity becomes analogous to Weeler-Misner geometrodynamics one

  1. Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks.

    Directory of Open Access Journals (Sweden)

    Brendan Chambers

    2016-08-01

    Full Text Available 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.

  2. Higher-order relativistic periastron advances and binary pulsars

    International Nuclear Information System (INIS)

    Damour, T.; Schafer, G.

    1988-01-01

    The contributions to the periastron advance of a system of two condensed bodies coming from relativistic dynamical effects of order higher than the usual first post-Newtonian (1PN) equations of motion are investigated. The structure of the solution of the orbital second post-Newtonian (2PN) equations of motion is given in a simple parametrized form. The contributions to the secular pariastron advance, and the period, of orbital 2PN effects are then explicitly worked out by using the Hamilton-Jacobi method. The spin-orbit contribution to the secular precession of the orbit in space is rederived in a streamlined way by making full use of Hamiltonian methods. These results are then applied to the theoretical interpretation of the observational data of pulsars in close eccentric binary systems. It is shown that the higher-order relativistic contributions are already of theoretical and astophysical significance for interpreting the high-precision measurement of the secular periastron advance of PSR 1913+16 achived by Taylor and coworkers. The case of extremely fast spinning (millisecond) binary pulsars is also discussed, and shown to offer an easier ground for getting new tests of general relativity, and/or, a direct measurement of the moment of inertia of a neutron star

  3. The Correlation of Interphase Chromatin Structure with the Radiation-Induced Inter- and Intrachromosome Exchange Hotspots

    Science.gov (United States)

    Zhang, Ye; Mangala, Lingegowda S.; Purgason, Ashley M.; Hada, Megumi; Cucinotta, Francis A.; Wu, Honglu

    2011-01-01

    To investigate the relationship between chromosome aberrations induced by radiation and chromatin folding, we reconstructed three dimensional structure of chromosome 3 and measured the physical distances between different regions of the chromosome. Previously, we have investigated the location of breaks involved in inter- and intrachromosomal type exchange events in human chromosome 3, using the multicolor banding in situ hybridization (mBAND) technique. In human epithelial cells exposed to both low- and high-LET radiations in vitro, we reported that intra-chromosome exchanges occurred preferentially between a break in the 3p21 and one in the 3q11 regions, and the breaks involving in inter-chromosome exchanges occurred in two regions towards the telomeres of the chromosome. Exchanges were also observed between a break in 3p21 and one in 3q26, but few exchanges were observed between breaks in 3q11 and 3q26, even though the two regions are located on the same arm of the chromosome. In this study, human epithelial cells were fixed at G1 phase and the interphase cells were hybridized using the XCyte3 mBAND kit from MetaSystems. The z-section images of chromosome 3 were captured with a Leica and an LSM 510 Meta laser scanning confocal microscopes. A total of 100 chromosomes were analyzed. The reconstruction of three dimensional structure of interphase chromosome 3 with six different colored regions was achieved using the Imaris software. The relative distance between different regions was measured as well. We further analyzed fragile sites on the chromosome that have been identified in various types of cancers. The data showed that, in majority of the cells, the regions containing 3p21 and 3q11 are colocalized in the center of the chromosome, whereas, the regions towards the telomeres of the chromosome are either physically wrapping outside the chromosome center or with arms sticking out. Our results demonstrated that the distribution of breaks involved in radiation

  4. Applications of high-throughput sequencing to chromatin structure and function in mammals

    OpenAIRE

    Dunham, Ian

    2009-01-01

    High-throughput DNA sequencing approaches have enabled direct interrogation of chromatin samples from mammalian cells. We are beginning to develop a genome-wide description of nuclear function during development, but further data collection, refinement, and integration are needed.

  5. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis

    DEFF Research Database (Denmark)

    Sarusi Portuguez, Avital; Schwartz, Michal; Siersbaek, Rasmus

    2017-01-01

    The three dimensional folding of mammalian genomes is cell type specific and difficult to alter suggesting that it is an important component of gene regulation. However, given the multitude of chromatin-associating factors, the mechanisms driving the colocalization of active chromosomal domains...... by PPARγ and Lpin1, undergoes orchestrated reorganization during adipogenesis. Coupling the dynamics of genome architecture with multiple chromatin datasets indicated that among all the transcription factors (TFs) tested, RXR is central to genome reorganization at the beginning of adipogenesis...

  6. Additive scaling law for structural organization of chromatin in chicken erythrocyte nuclei

    Science.gov (United States)

    Iashina, E. G.; Velichko, E. V.; Filatov, M. V.; Bouwman, W. G.; Duif, C. P.; Brulet, A.; Grigoriev, S. V.

    2017-07-01

    Small-angle neutron scattering (SANS) on nuclei of chicken erythrocytes demonstrates the cubic dependence of the scattering intensity Q-3 in the range of momentum transfer Q ∈10-3-10-2nm-1 . Independent spin-echo SANS measurements give the spin-echo function, which is well described by the exponential law in a range of sizes (3 ×102) -(3 ×104) nm. Both experimental dependences reflect the nature of the structural organization of chromatin in the nucleus of a living cell, which corresponds to the correlation function γ (r )=ln(ξ /r ) for r <ξ , where ξ =(3.69 ±0.07 ) ×103 nm, the size of the nucleus. It has the specific scaling property of the logarithmic fractal γ (r /a )=γ (r )+ln(a ), i.e., the scaling down by a gives an additive constant to the correlation function, which distinguishes it from the mass fractal, which is characterized by multiplicative constant.

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

    NARCIS (Netherlands)

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

    2003-01-01

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

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

    Science.gov (United States)

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

    2011-12-16

    We report theoretical, numerical, and experimental studies of higher-order modulation instability in the focusing nonlinear Schrödinger equation. This higher-order instability arises from the nonlinear superposition of elementary instabilities, associated with initial single breather evolution followed by a regime of complex, yet deterministic, pulse splitting. We analytically describe the process using the Darboux transformation and compare with experiments in optical fiber. We show how a suitably low frequency modulation on a continuous wave field induces higher-order modulation instability splitting with the pulse characteristics at different phases of evolution related by a simple scaling relationship. We anticipate that similar processes are likely to be observed in many other systems including plasmas, Bose-Einstein condensates, and deep water waves. © 2011 American Physical Society

  9. Higher Order Lagrange Finite Elements In M3D

    International Nuclear Information System (INIS)

    Chen, J.; Strauss, H.R.; Jardin, S.C.; Park, W.; Sugiyama, L.E.; Fu, G.; Breslau, J.

    2004-01-01

    The M3D code has been using linear finite elements to represent multilevel MHD on 2-D poloidal planes. Triangular higher order elements, up to third order, are constructed here in order to provide M3D the capability to solve highly anisotropic transport problems. It is found that higher order elements are essential to resolve the thin transition layer characteristic of the anisotropic transport equation, particularly when the strong anisotropic direction is not aligned with one of the Cartesian coordinates. The transition layer is measured by the profile width, which is zero for infinite anisotropy. It is shown that only higher order schemes have the ability to make this layer converge towards zero when the anisotropy gets stronger and stronger. Two cases are considered. One has the strong transport direction partially aligned with one of the element edges, the other doesn't have any alignment. Both cases have the strong transport direction misaligned with the grid line by some angles

  10. Practical implementation of a higher order transverse leakage approximation

    International Nuclear Information System (INIS)

    Prinsloo, Rian H.; Tomašević

    2011-01-01

    Transverse integrated nodal diffusion methods currently represent the standard in full core neutronic simulation. The primary shortcoming in this approach, be it via the Analytic Nodal Method or Nodal Expansion Method, is the utilization of the quadratic transverse leakage approximation. This approach, although proven to work well for typical LWR problems, is not consistent with the formulation of nodal methods and can cause accuracy and convergence problems. In this work an improved, consistent quadratic leakage approximation is formulated, which derives from the class of higher order nodal methods developed some years ago. In this new approach, only information relevant to describing the transverse leak- age terms in the zero-order nodal equations are obtained from the higher order formalism. The method yields accuracy comparable to full higher order methods, but does not suffer from the same computational burden which these methods typically incur. (author)

  11. Threshold resummation and higher order effects in QCD

    International Nuclear Information System (INIS)

    Ringer, Felix Maximilian

    2015-01-01

    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.

  12. Higher order energy transfer. Quantum electrodynamical calculations and graphical representation

    International Nuclear Information System (INIS)

    Jenkins, R.D.

    2000-01-01

    In Chapter 1, a novel method of calculating quantum electrodynamic amplitudes is formulated using combinatorial theory. This technique is used throughout instead of conventional time-ordered methods. A variety of hyperspaces are discussed to highlight isomorphism between a number of A generalisation of Pascal's triangle is shown to be beneficial in determining the form of hyperspace graphs. Chapter 2 describes laser assisted resonance energy transfer (LARET), a higher order perturbative contribution to the well-known process resonance energy transfer, accommodating an off resonance auxiliary laser field to stimulate the migration. Interest focuses on energy exchanges between two uncorrelated molecular species, as in a system where molecules are randomly oriented. Both phase-weighted and standard isotropic averaging are required for the calculations. Results are discussed in terms of a laser intensity-dependent mechanism. Identifying the applied field regime where LARET should prove experimentally significant, transfer rate increases of up to 30% are predicted. General results for three-center energy transfer are elucidated in chapter 3. Cooperative and accretive mechanistic pathways are identified with theory formulated to elicit their role in a variety of energy transfer phenomena and their relative dominance. In multichromophoric the interplay of such factors is analysed with regard to molecular architectures. The alignments and magnitudes of donor and acceptor transition moments and polarisabilities prove to have profound effects on achievable pooling efficiency for linear configurations. Also optimum configurations are offered. In ionic lattices, although both mechanisms play significant roles in pooling and cutting processes, only the accretive is responsible for sensitisation. The local, microscopic level results are used to gauge the lattice response, encompassing concentration and structural effects. (author)

  13. Higher order multipoles and splines in plasma simulations

    International Nuclear Information System (INIS)

    Okuda, H.; Cheng, C.Z.

    1978-01-01

    The reduction of spatial grid effects in plasma simulations has been studied numerically using higher order multipole expansions and the spline method in one dimension. It is found that, while keeping the higher order moments such as quadrupole and octopole moments substantially reduces the grid effects, quadratic and cubic splines in general have better stability properties for numerical plasma simulations when the Debye length is much smaller than the grid size. In particular the spline method may be useful in three-dimensional simulations for plasma confinement where the grid size in the axial direction is much greater than the Debye length. (Auth.)

  14. Higher-order multipoles and splines in plasma simulations

    International Nuclear Information System (INIS)

    Okuda, H.; Cheng, C.Z.

    1977-12-01

    Reduction of spatial grid effects in plasma simulations has been studied numerically using higher order multipole expansions and spline method in one dimension. It is found that, while keeping the higher order moments such as quadrupole and octopole moments substantially reduces the grid effects, quadratic and cubic splines in general have better stability properties for numerical plasma simulations when the Debye length is much smaller than the grid size. In particular, spline method may be useful in three dimensional simulations for plasma confinement where the grid size in the axial direction is much greater than the Debye length

  15. 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...... order and higher order discretizations, results from a low-memory, high-speed MLFMM implementation of a HO hierarchical discretization are shown. These results challenge the general view that the benefits of HO and HF-MLFMM cannot be combined....

  16. The Cauchy problem for higher order abstract differential equations

    CERN Document Server

    Xiao, Ti-Jun

    1998-01-01

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

  17. Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures.

    Science.gov (United States)

    Liang, Ying; Yang, Gen; Liu, Feng; Wang, Yugang

    2016-01-07

    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 (60)Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with (60)Co 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.

  18. Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures

    International Nuclear Information System (INIS)

    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 60 Co γ irradiation and α particle irradiation are compared with the measurements accordingly. The excellent agreement with 60 Co 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. (paper)

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-15

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

  20. The Role of Formative Feedback in Promoting Higher Order ...

    African Journals Online (AJOL)

    DrNneka

    An International Multi-disciplinary Journal, Ethiopia. AFRREV ... make contribution to this research gap by proposing a theoretical feedback model that can promote higher order thinking skills in the classroom. The proposed ..... process; students provided with tasks that are novel, complex, creative, and non- algorithmic ...

  1. Developing Higher-Order Thinking Skills through WebQuests

    Science.gov (United States)

    Polly, Drew; Ausband, Leigh

    2009-01-01

    In this study, 32 teachers participated in a year-long professional development project related to technology integration in which they designed and implemented a WebQuest. This paper describes the extent to which higher-order thinking skills (HOTS) and levels of technology implementation (LoTI) occur in the WebQuests that participants designed.…

  2. Hamiltonian formulation of theory with higher order derivatives

    International Nuclear Information System (INIS)

    Gitman, D.M.; Lyakhovich, S.L.; Tyutin, I.V.

    1983-01-01

    A method of ''hamiltonization'' of a special theory with higher order derivatives is described. In a nonspecial case the result coincides with the known Ostrogradsky formulation. It is shown that in the nonspecial theory the lagrange equations of motion are reduced to the normal form

  3. Numerical methods of higher order of accuracy for incompressible flows

    Czech Academy of Sciences Publication Activity Database

    Kozel, K.; Louda, Petr; Příhoda, Jaromír

    2010-01-01

    Roč. 80, č. 8 (2010), s. 1734-1745 ISSN 0378-4754 Institutional research plan: CEZ:AV0Z20760514 Keywords : higher order methods * upwind methods * backward-facing step Subject RIV: BK - Fluid Dynamics Impact factor: 0.812, year: 2010

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

    CERN Document Server

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

    2011-01-01

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

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

    KAUST Repository

    Bonito, Andrea; Kyza, Irene; Nochetto, Ricardo H.

    2013-01-01

    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

  6. 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...

  7. Decidable Fragments of a Higher Order Calculus with Locations

    DEFF Research Database (Denmark)

    Bundgaard, Mikkel; Godskesen, Jens Christian; Huttel, Hans

    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...

  8. Computer-Mediated Assessment of Higher-Order Thinking Development

    Science.gov (United States)

    Tilchin, Oleg; Raiyn, Jamal

    2015-01-01

    Solving complicated problems in a contemporary knowledge-based society requires higher-order thinking (HOT). The most productive way to encourage development of HOT in students is through use of the Problem-based Learning (PBL) model. This model organizes learning by solving corresponding problems relative to study courses. Students are directed…

  9. 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...

  10. Constrained variational calculus for higher order classical field theories

    Energy Technology Data Exchange (ETDEWEB)

    Campos, Cedric M; De Leon, Manuel; De Diego, David MartIn, E-mail: cedricmc@icmat.e, E-mail: mdeleon@icmat.e, E-mail: david.martin@icmat.e [Instituto de Ciencias Matematicas, CSIC-UAM-UC3M-UCM, Serrano 123, 28006 Madrid (Spain)

    2010-11-12

    We develop an intrinsic geometrical setting for higher order constrained field theories. As a main tool we use an appropriate generalization of the classical Skinner-Rusk formalism. Some examples of applications are studied, in particular to the geometrical description of optimal control theory for partial differential equations.

  11. Constrained variational calculus for higher order classical field theories

    International Nuclear Information System (INIS)

    Campos, Cedric M; De Leon, Manuel; De Diego, David MartIn

    2010-01-01

    We develop an intrinsic geometrical setting for higher order constrained field theories. As a main tool we use an appropriate generalization of the classical Skinner-Rusk formalism. Some examples of applications are studied, in particular to the geometrical description of optimal control theory for partial differential equations.

  12. Higher-Order Integral Equation Methods in Computational Electromagnetics

    DEFF Research Database (Denmark)

    Jørgensen, Erik; Meincke, Peter

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

  13. Higher-Order Separation Logic in Isabelle/HOLCF

    DEFF Research Database (Denmark)

    Varming, Carsten; Birkedal, Lars

    2008-01-01

    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 o...

  14. 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...

  15. Enhancing Higher Order Thinking Skills through Clinical Simulation

    Science.gov (United States)

    Varutharaju, Elengovan; Ratnavadivel, Nagendralingan

    2014-01-01

    Purpose: The study aimed to explore, describe and analyse the design and implementation of clinical simulation as a pedagogical tool in bridging the deficiency of higher order thinking skills among para-medical students, and to make recommendations on incorporating clinical simulation as a pedagogical tool to enhance thinking skills and align the…

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  17. Higher-Order Hierarchical Legendre Basis Functions in Applications

    DEFF Research Database (Denmark)

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

    2007-01-01

    The higher-order hierarchical Legendre basis functions have been developed for effective solution of integral equations with the method of moments. They are derived from orthogonal Legendre polynomials modified to enforce normal continuity between neighboring mesh elements, while preserving a high...

  18. Chromatin Hydrodynamics

    Science.gov (United States)

    Bruinsma, Robijn; Grosberg, Alexander Y.; Rabin, Yitzhak; Zidovska, Alexandra

    2014-01-01

    Following recent observations of large scale correlated motion of chromatin inside the nuclei of live differentiated cells, we present a hydrodynamic theory—the two-fluid model—in which the content of a nucleus is described as a chromatin solution with the nucleoplasm playing the role of the solvent and the chromatin fiber that of a solute. This system is subject to both passive thermal fluctuations and active scalar and vector events that are associated with free energy consumption, such as ATP hydrolysis. Scalar events drive the longitudinal viscoelastic modes (where the chromatin fiber moves relative to the solvent) while vector events generate the transverse modes (where the chromatin fiber moves together with the solvent). Using linear response methods, we derive explicit expressions for the response functions that connect the chromatin density and velocity correlation functions to the corresponding correlation functions of the active sources and the complex viscoelastic moduli of the chromatin solution. We then derive general expressions for the flow spectral density of the chromatin velocity field. We use the theory to analyze experimental results recently obtained by one of the present authors and her co-workers. We find that the time dependence of the experimental data for both native and ATP-depleted chromatin can be well-fitted using a simple model—the Maxwell fluid—for the complex modulus, although there is some discrepancy in terms of the wavevector dependence. Thermal fluctuations of ATP-depleted cells are predominantly longitudinal. ATP-active cells exhibit intense transverse long wavelength velocity fluctuations driven by force dipoles. Fluctuations with wavenumbers larger than a few inverse microns are dominated by concentration fluctuations with the same spectrum as thermal fluctuations but with increased intensity. PMID:24806919

  19. Higher order QCD corrections in small x physics

    International Nuclear Information System (INIS)

    Chachamis, G.

    2006-11-01

    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.)

  20. 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.)

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

    CERN Document Server

    Schultz, Thomas

    2015-01-01

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

  2. [Correcting influence of vitamin E short chain derivatives on lipid peroxidation, liver cell membrane, and chromatin structure when rats are exposed to embichin].

    Science.gov (United States)

    Kovalenko, V M; Byshovets', T F; Hubs'kyĭ, Iu I; Levyts'kyĭ, Ie L; Shaiakhmetova, H M; Marchenko, O M; Voloshyna, O S; Saĭfetdinova, H A; Okhrimenko, V O; Donchenko, H V

    2000-01-01

    Embikhin causes activation of LPO processes in endoplasmic reticulum and in nuclear chromatine fractions of rat liver cells. The latter is accompanied by the impairment of repressive and active nuclear chromatine fractions structure. Derivate of vitamin E in these conditions renders correcting action on parameters of lipid peroxidation in the investigated subcellular structures, testifying its positive influence on the cell heredity apparatus state. The normalizing action of tocopherol derivative on cytochromes P450 and b5 levels is shown.

  3. Self-similarity of higher-order moving averages

    Science.gov (United States)

    Arianos, Sergio; Carbone, Anna; Türk, Christian

    2011-10-01

    In this work, higher-order moving average polynomials are defined by straightforward generalization of the standard moving average. The self-similarity of the polynomials is analyzed for fractional Brownian series and quantified in terms of the Hurst exponent H by using the detrending moving average method. We prove that the exponent H of the fractional Brownian series and of the detrending moving average variance asymptotically agree for the first-order polynomial. Such asymptotic values are compared with the results obtained by the simulations. The higher-order polynomials correspond to trend estimates at shorter time scales as the degree of the polynomial increases. Importantly, the increase of polynomial degree does not require to change the moving average window. Thus trends at different time scales can be obtained on data sets with the same size. These polynomials could be interesting for those applications relying on trend estimates over different time horizons (financial markets) or on filtering at different frequencies (image analysis).

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

    Directory of Open Access Journals (Sweden)

    Taher S. Hassan

    2016-01-01

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

  5. Higher order mode damping in Kaon factory RF cavities

    International Nuclear Information System (INIS)

    Enegren, T.; Poirier, R.; Griffin, J.; Walling, L.; Thiessen, H.A.; Smythe, W.R.

    1989-05-01

    Proposed designs for Kaon factory accelerators require that the rf cavities support beam currents on the order of several amperes. The beam current has Fourier components at all multiples of the rf frequency. Empty rf buckets produce additional components at all multiples of the revolution frequency. If a Fourier component of the beam coincides with the resonant frequency of a higher order mode of the cavity, which is inevitable if the cavity has a large frequency swing, significant excitation of this mode can occur. The induced voltage may then excite coupled bunch mode instabilities. Effective means are required to damp higher order modes without significantly affecting the fundamental mode. A mode damping scheme based on coupled transmission lines has been investigated and is report

  6. Higher Order Differential Attack on 6-Round MISTY1

    Science.gov (United States)

    Tsunoo, Yukiyasu; Saito, Teruo; Nakashima, Hiroki; Shigeri, Maki

    MISTY1 is a 64-bit block cipher that has provable security against differential and linear cryptanalysis. MISTY1 is one of the algorithms selected in the European NESSIE project, and it has been recommended for Japanese e-Government ciphers by the CRYPTREC project. This paper reports a previously unknown higher order differential characteristic of 4-round MISTY1 with the FL functions. It also shows that a higher order differential attack that utilizes this newly discovered characteristic is successful against 6-round MISTY1 with the FL functions. This attack can recover a partial subkey with a data complexity of 253.7 and a computational complexity of 264.4, which is better than any previous cryptanalysis of MISTY1.

  7. Higher-order risk preferences in social settings.

    Science.gov (United States)

    Heinrich, Timo; Mayrhofer, Thomas

    2018-01-01

    We study prudence and temperance (next to risk aversion) in social settings. Previous experimental studies have shown that these higher-order risk preferences affect the choices of individuals deciding privately on lotteries that only affect their own payoff. Yet, many risky and financially relevant decisions are made in the social settings of households or organizations. We elicit higher-order risk preferences of individuals and systematically vary how an individual's decision is made (alone or while communicating with a partner) and who is affected by the decision (only the individual or the partner as well). In doing so, we can isolate the effects of other-regarding concerns and communication on choices. Our results reveal that the majority of choices are risk averse, prudent, and temperate across social settings. We also observe that individuals are influenced significantly by the preferences of a partner when they are able to communicate and choices are payoff-relevant for both of them.

  8. Higher-order geodesic deviations applied to the Kerr metric

    CERN Document Server

    Colistete, R J; Kerner, R

    2002-01-01

    Starting with an exact and simple geodesic, we generate approximate geodesics by summing up higher-order geodesic deviations within a general relativistic setting, without using Newtonian and post-Newtonian approximations. We apply this method to the problem of closed orbital motion of test particles in the Kerr metric spacetime. With a simple circular orbit in the equatorial plane taken as the initial geodesic, we obtain finite eccentricity orbits in the form of Taylor series with the eccentricity playing the role of a small parameter. The explicit expressions of these higher-order geodesic deviations are derived using successive systems of linear equations with constant coefficients, whose solutions are of harmonic oscillator type. This scheme gives best results when applied to orbits with low eccentricities, but with arbitrary possible values of (GM/Rc sup 2).

  9. An Algorithm for Higher Order Hopf Normal Forms

    Directory of Open Access Journals (Sweden)

    A.Y.T. Leung

    1995-01-01

    Full Text Available Normal form theory is important for studying the qualitative behavior of nonlinear oscillators. In some cases, higher order normal forms are required to understand the dynamic behavior near an equilibrium or a periodic orbit. However, the computation of high-order normal forms is usually quite complicated. This article provides an explicit formula for the normalization of nonlinear differential equations. The higher order normal form is given explicitly. Illustrative examples include a cubic system, a quadratic system and a Duffing–Van der Pol system. We use exact arithmetic and find that the undamped Duffing equation can be represented by an exact polynomial differential amplitude equation in a finite number of terms.

  10. The higher order flux mapping method in large size PHWRs

    International Nuclear Information System (INIS)

    Kulkarni, A.K.; Balaraman, V.; Purandare, H.D.

    1997-01-01

    A new higher order method is proposed for obtaining flux map using single set of expansion mode. In this procedure, one can make use of the difference between predicted value of detector reading and their actual values for determining the strength of local fluxes around detector site. The local fluxes are arising due to constant perturbation changes (both extrinsic and intrinsic) taking place in the reactor. (author)

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

    DEFF Research Database (Denmark)

    Poswolsky, Adam; Schürmann, Carsten

    2008-01-01

    , tedious, and error-prone. In this paper, we describe the underlying calculus of Delphin. Delphin is a fully implemented functional-programming language supporting reasoning over higher-order encodings and dependent types, while maintaining the benefits of HOAS. More specifically, just as representations...... for instantiation from those that will remain uninstantiated, utilizing a variation of Miller and Tiu’s ∇-quantifier [1]....

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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......, its context within an organisation and the effects on security as outcomes of a theorem proving analysis....

  13. Higher order Bose-Einstein correlations in identical particle production

    International Nuclear Information System (INIS)

    Biyajima, M.

    1990-01-01

    A diagram technique to calculate the higher order Bose-Einstein correlations is formulated. This technique is applied to derive explicit expressions for the n-pion correlation functions for n = 2, 3, 4, and 5, and numerical predictions are given. In a comparison with the AFS and NA23 data on two-pion and three-pion Bose-Einstein correlations good agreement is obtained. 21 refs., 5 figs. (Authors)

  14. Diazinon alters sperm chromatin structure in mice by phosphorylating nuclear protamines

    International Nuclear Information System (INIS)

    Pina-Guzman, B.; Solis-Heredia, M.J.; Quintanilla-Vega, B.

    2005-01-01

    Organophosphorus (OP) pesticides, widely used in agriculture and pest control, are associated with male reproductive effects, including sperm chromatin alterations, but the mechanisms underlying these effects are unknown. The main toxic action of OP is related to phosphorylation of proteins. Chemical alterations in sperm nuclear proteins (protamines), which pack DNA during the last steps of spermatogenesis, contribute to male reproductive toxicity. Therefore, in the present study, we tested the ability of diazinon (DZN), an OP compound, to alter sperm chromatin by phosphorylating nuclear protamines. Mice were injected with a single dose of DZN (8.12 mg/kg, i.p.), and killed 8 and 15 days after treatment. Quality of sperm from epididymis and vas deferens was evaluated through standard methods and chromatin condensation by flow cytometry (DNA Fragmented Index parameters: DFI and DFI%) and fluorescence microscopy using chromomycin-A 3 (CMA 3 ). Increases in DFI (15%), DFI% (4.5-fold), and CMA 3 (2-fold) were observed only at 8 days post-treatment, indicating an alteration in sperm chromatin condensation and DNA damage during late spermatid differentiation. In addition, an increase of phosphorous content (approximately 50%) in protamines, especially in the phosphoserine content (approximately 73%), was found at 8 days post-treatment. Sperm viability, motility, and morphology showed significant alterations at this time. These data strongly suggest that spermatozoa exposed during the late steps of maturation were the targets of DZN exposure. The correlation observed between the phosphorous content in nuclear protamines with DFI%, DFI, and CMA 3 provides evidence that phosphorylation of nuclear protamines is involved in the OP effects on sperm chromatin

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

    Science.gov (United States)

    Aguilar, Carlos A.; Craighead, Harold G.

    2013-10-01

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

  16. APPLICATION OF THE SPERM CHROMATIN STRUCTURE ASSAY TO THE TEPLICE PROGRAM SEMEN STUDIES: A NEW METHOD FOR EVALUATING SPERM NUCLEAR CHROMATIN DAMAGE

    Science.gov (United States)

    ABSTRACTA measure of sperm chromatin integrity was added to the routine semen end points evaluated in the Teplice Program male reproductive health studies. To address the hypothesis that exposure to periods of elevated air pollution may be associated with abnormalities in sp...

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

    Directory of Open Access Journals (Sweden)

    Nishal S Patel

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

  18. Saccharomyces cerevisiae Linker Histone—Hho1p Maintains Chromatin Loop Organization during Ageing

    Directory of Open Access Journals (Sweden)

    Katya Uzunova

    2013-01-01

    Full Text Available Intricate, dynamic, and absolutely unavoidable ageing affects cells and organisms through their entire lifetime. Driven by diverse mechanisms all leading to compromised cellular functions and finally to death, this process is a challenge for researchers. The molecular mechanisms, the general rules that it follows, and the complex interplay at a molecular and cellular level are yet little understood. Here, we present our results showing a connection between the linker histones, the higher-order chromatin structures, and the process of chronological lifespan of yeast cells. By deleting the gene for the linker histone in Saccharomyces cerevisiae we have created a model for studying the role of chromatin structures mainly at its most elusive and so far barely understood higher-order levels of compaction in the processes of yeast chronological lifespan. The mutant cells demonstrated controversial features showing slower growth than the wild type combined with better survival during the whole process. The analysis of the global chromatin organization during different time points demonstrated certain loss of the upper levels of chromatin compaction in the cells without linker histone. The results underlay the importance of this histone for the maintenance of the chromatin loop structures during ageing.

  19. Higher-Order Finite Element Solutions of Option Prices

    DEFF Research Database (Denmark)

    Raahauge, Peter

    2004-01-01

    Kinks and jumps in the payoff function of option contracts prevent an effectiveimplementation of higher-order numerical approximation methods. Moreover, thederivatives (the greeks) are not easily determined around such singularities, even withstandard lower-order methods. This paper suggests...... for prices as well as for first and second order derivatives(delta and gamma). Unlike similar studies, numerical approximation errors aremeasured both as weighted averages and in the supnorm over a state space includingtime-to-maturities down to a split second.KEYWORDS: Numerical option pricing, Transformed...

  20. Development of higher order mode couplers at Cornell

    International Nuclear Information System (INIS)

    Amato, J.C.

    1988-01-01

    Higher order mode (HOM) couplers are integral parts of a superconducting accelerator cavity. The damping which the couplers must provide is dictated by the frequency and shunt impedance of the cavity modes as well as by the stability requirements of the accelerator incorporating the cavities. Cornell's 5-cell 1500 MHz elliptical cavity was designed for use in a 50 x 50 GeV electron-positron storage ring with a total beam current of 3.5 mA (CESR-II). HOM couplers for the Cornell cavity were designed and evaluated with this machine in mind. The development of these couplers is described in this paper. 8 references, 8 figures

  1. Theory of a higher-order Sturm-Liouville equation

    CERN Document Server

    Kozlov, Vladimir

    1997-01-01

    This book develops a detailed theory of a generalized Sturm-Liouville Equation, which includes conditions of solvability, classes of uniqueness, positivity properties of solutions and Green's functions, asymptotic properties of solutions at infinity. Of independent interest, the higher-order Sturm-Liouville equation also proved to have important applications to differential equations with operator coefficients and elliptic boundary value problems for domains with non-smooth boundaries. The book addresses graduate students and researchers in ordinary and partial differential equations, and is accessible with a standard undergraduate course in real analysis.

  2. Integrable higher order deformations of Heisenberg supermagnetic model

    International Nuclear Information System (INIS)

    Guo Jiafeng; Yan Zhaowen; Wang Shikun; Wu Ke; Zhao Weizhong

    2009-01-01

    The Heisenberg supermagnet model is an integrable supersymmetric system and has a close relationship with the strong electron correlated Hubbard model. In this paper, we investigate the integrable higher order deformations of Heisenberg supermagnet models with two different constraints: (i) S 2 =3S-2I for S is an element of USPL(2/1)/S(U(2)xU(1)) and (ii) S 2 =S for S is an element of USPL(2/1)/S(L(1/1)xU(1)). In terms of the gauge transformation, their corresponding gauge equivalent counterparts are derived.

  3. Oscillation of solutions of some higher order linear differential equations

    Directory of Open Access Journals (Sweden)

    Hong-Yan Xu

    2009-11-01

    Full Text Available In this paper, we deal with the order of growth and the hyper order of solutions of higher order linear differential equations $$f^{(k}+B_{k-1}f^{(k-1}+\\cdots+B_1f'+B_0f=F$$ where $B_j(z (j=0,1,\\ldots,k-1$ and $F$ are entire functions or polynomials. Some results are obtained which improve and extend previous results given by Z.-X. Chen, J. Wang, T.-B. Cao and C.-H. Li.

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

    Science.gov (United States)

    Kim, Jinkyu

    2014-01-01

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

  5. Programming real-time executives in higher order language

    Science.gov (United States)

    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.

  6. 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...

  7. Higher-order dynamical effects in Coulomb dissociation

    International Nuclear Information System (INIS)

    Esbensen, H.

    1994-06-01

    We study the effect of higher-order processes in Coulomb dissociation of 11 Li by numerically solving the three-dimensional time-dependent Schroedinger equation for the relative motion of a di-neutron and the 9 Li core. Comparisons are made to first-order perturbation theory and to measurements. The calculated Coulomb reacceleration effects improve the agreement with experiment, but some discrepancy remains. The effects are much smaller in the dissociation of 11 Be, and they decrease with increasing beam energy. (orig.)

  8. Inseparability inequalities for higher order moments for bipartite systems

    International Nuclear Information System (INIS)

    Agarwal, G S; Biswas, Asoka

    2005-01-01

    There are several examples of bipartite entangled states of continuous variables for which the existing criteria for entanglement using the inequalities involving the second-order moments are insufficient. We derive new inequalities involving higher order correlation, for testing entanglement in non-Gaussian states. In this context, we study an example of a non-Gaussian state, which is a bipartite entangled state of the form Ψ(x a , x b ) ∝ (αx a + βx b ) e -(x a 2 +x b 2 )/2 . Our results open up an avenue to search for new inequalities to test entanglement in non-Gaussian states

  9. Higher-order thinking in foreign language learning

    OpenAIRE

    Bastos, Ascensão; Ramos, Altina

    2017-01-01

    A project is being conducted in English as a foreign language (EFL), involving eleventh graders in formal and non-formal learning contexts, in a Portuguese high school. The goal of this study is to examine the impact of cognitive tools and higher-order thinking processes on the learning of EFL and achievement of larger processes oriented to action, involving problem solving, decision-making and creation of new products. YouTube videos emerge as cognitive tools in the process. Final results sh...

  10. Impact of nuclear organization and chromatin structure on DNA repair and genome stability

    International Nuclear Information System (INIS)

    Batte, Amandine

    2016-01-01

    The non-random organization of the eukaryotic cell nucleus and the folding of genome in chromatin more or less condensed can influence many functions related to DNA metabolism, including genome stability. Double-strand breaks (DSBs) are the most deleterious DNA damages for the cells. To preserve genome integrity, eukaryotic cells thus developed DSB repair mechanisms conserved from yeast to human, among which homologous recombination (HR) that uses an intact homologous sequence to repair a broken chromosome. HR can be separated in two sub-pathways: Gene Conversion (GC) transfers genetic information from one molecule to its homologous and Break Induced Replication (BIR) establishes a replication fork than can proceed until the chromosome end. My doctorate work was focused on the contribution of the chromatin context and 3D genome organization on DSB repair. In S. cerevisiae, nuclear organization and heterochromatin spreading at sub-telomeres can be modified through the overexpression of the Sir3 or sir3A2Q mutant proteins. We demonstrated that reducing the physical distance between homologous sequences increased GC rates, reinforcing the notion that homology search is a limiting step for recombination. We also showed that hetero-chromatinization of DSB site fine-tunes DSB resection, limiting the loss of the DSB ends required to perform homology search and complete HR. Finally, we noticed that the presence of heterochromatin at the donor locus decreased both GC and BIR efficiencies, probably by affecting strand invasion. This work highlights new regulatory pathways of DNA repair. (author) [fr

  11. Compiler-Directed Transformation for Higher-Order Stencils

    Energy Technology Data Exchange (ETDEWEB)

    Basu, Protonu [Univ. of Utah, Salt Lake City, UT (United States); Hall, Mary [Univ. of Utah, Salt Lake City, UT (United States); Williams, Samuel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Straalen, Brian Van [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Oliker, Leonid [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Colella, Phillip [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-07-20

    As the cost of data movement increasingly dominates performance, developers of finite-volume and finite-difference solutions for partial differential equations (PDEs) are exploring novel higher-order stencils that increase numerical accuracy and computational intensity. This paper describes a new compiler reordering transformation applied to stencil operators that performs partial sums in buffers, and reuses the partial sums in computing multiple results. This optimization has multiple effect son improving stencil performance that are particularly important to higher-order stencils: exploits data reuse, reduces floating-point operations, and exposes efficient SIMD parallelism to backend compilers. We study the benefit of this optimization in the context of Geometric Multigrid (GMG), a widely used method to solvePDEs, using four different Jacobi smoothers built from 7-, 13-, 27-and 125-point stencils. We quantify performance, speedup, andnumerical accuracy, and use the Roofline model to qualify our results. Ultimately, we obtain over 4× speedup on the smoothers themselves and up to a 3× speedup on the multigrid solver. Finally, we demonstrate that high-order multigrid solvers have the potential of reducing total data movement and energy by several orders of magnitude.

  12. Higher-Order Cyclostationarity Detection for Spectrum Sensing

    Directory of Open Access Journals (Sweden)

    Julien Renard

    2010-01-01

    Full Text Available Recent years have shown a growing interest in the concept of Cognitive Radios (CRs, able to access portions of the electromagnetic spectrum in an opportunistic operating way. Such systems require efficient detectors able to work in low Signal-to-Noise Ratio (SNR environments, with little or no information about the signals they are trying to detect. Energy detectors are widely used to perform such blind detection tasks, but quickly reach the so-called SNR wall below which detection becomes impossible Tandra (2005. Cyclostationarity detectors are an interesting alternative to energy detectors, as they exploit hidden periodicities present in man-made signals, but absent in noise. Such detectors use quadratic transformations of the signals to extract the hidden sine-waves. While most of the literature focuses on the second-order transformations of the signals, we investigate the potential of higher-order transformations of the signals. Using the theory of Higher-Order Cyclostationarity (HOCS, we derive a fourth-order detector that performs similarly to the second-order ones to detect linearly modulated signals, at SNR around 0 dB, which may be used if the signals of interest do not exhibit second-order cyclostationarity. More generally this paper reviews the relevant aspects of the cyclostationary and HOCS theory, and shows their potential for spectrum sensing.

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

    Directory of Open Access Journals (Sweden)

    Cauchy Pradhan

    2012-01-01

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

  14. Chromatin replication and histone dynamics

    DEFF Research Database (Denmark)

    Alabert, Constance; Jasencakova, Zuzana; Groth, Anja

    2017-01-01

    Inheritance of the DNA sequence and its proper organization into chromatin is fundamental for genome stability and function. Therefore, how specific chromatin structures are restored on newly synthesized DNA and transmitted through cell division remains a central question to understand cell fate...... choices and self-renewal. Propagation of genetic information and chromatin-based information in cycling cells entails genome-wide disruption and restoration of chromatin, coupled with faithful replication of DNA. In this chapter, we describe how cells duplicate the genome while maintaining its proper...... organization into chromatin. We reveal how specialized replication-coupled mechanisms rapidly assemble newly synthesized DNA into nucleosomes, while the complete restoration of chromatin organization including histone marks is a continuous process taking place throughout the cell cycle. Because failure...

  15. Chromatin dynamics in genome stability

    DEFF Research Database (Denmark)

    Nair, Nidhi; Shoaib, Muhammad; Sørensen, Claus Storgaard

    2017-01-01

    Genomic DNA is compacted into chromatin through packaging with histone and non-histone proteins. Importantly, DNA accessibility is dynamically regulated to ensure genome stability. This is exemplified in the response to DNA damage where chromatin relaxation near genomic lesions serves to promote...... access of relevant enzymes to specific DNA regions for signaling and repair. Furthermore, recent data highlight genome maintenance roles of chromatin through the regulation of endogenous DNA-templated processes including transcription and replication. Here, we review research that shows the importance...... of chromatin structure regulation in maintaining genome integrity by multiple mechanisms including facilitating DNA repair and directly suppressing endogenous DNA damage....

  16. 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

  17. Higher order perturbation theory - An example for discussion

    International Nuclear Information System (INIS)

    Lewins, J.D.; Parks, G.; Babb, A.L.

    1986-01-01

    Higher order perturbation theory is developed in the form of a Taylor series expansion to third order to calculate the thermal utilization of a nonuniform cell. The development takes advantage of the self-adjoint property of the diffusion operator to provide a simple development of this illustration of generalized perturbation theory employing scalar perturbation parameters. The results show how a designer might employ a second-order theory to quantify proposed design improvements, together with the limitations of second- and third-order theory. The chosen example has an exact optimization solution and thus provides a clear understanding of the role of perturbation theory at its various orders. Convergence and the computational advantages and disadvantages of the method are discussed

  18. Higher-order force moments of active particles

    Science.gov (United States)

    Nasouri, Babak; Elfring, Gwynn J.

    2018-04-01

    Active particles moving through fluids generate disturbance flows due to their activity. For simplicity, the induced flow field is often modeled by the leading terms in a far-field approximation of the Stokes equations, whose coefficients are the force, torque, and stresslet (zeroth- and first-order force moments) of the active particle. This level of approximation is quite useful, but may also fail to predict more complex behaviors that are observed experimentally. In this study, to provide a better approximation, we evaluate the contribution of the second-order force moments to the flow field and, by reciprocal theorem, present explicit formulas for the stresslet dipole, rotlet dipole, and potential dipole for an arbitrarily shaped active particle. As examples of this method, we derive modified Faxén laws for active spherical particles and resolve higher-order moments for active rod-like particles.

  19. Higher-order automatic differentiation of mathematical functions

    Science.gov (United States)

    Charpentier, Isabelle; Dal Cappello, Claude

    2015-04-01

    Functions of mathematical physics such as the Bessel functions, the Chebyshev polynomials, the Gauss hypergeometric function and so forth, have practical applications in many scientific domains. On the one hand, differentiation formulas provided in reference books apply to real or complex variables. These do not account for the chain rule. On the other hand, based on the chain rule, the automatic differentiation has become a natural tool in numerical modeling. Nevertheless automatic differentiation tools do not deal with the numerous mathematical functions. This paper describes formulas and provides codes for the higher-order automatic differentiation of mathematical functions. The first method is based on Faà di Bruno's formula that generalizes the chain rule. The second one makes use of the second order differential equation they satisfy. Both methods are exemplified with the aforementioned functions.

  20. Influence of higher order modes on angled-facet amplifiers

    DEFF Research Database (Denmark)

    Wang, Z.; Mikkelsen, B.; Stubkjær, Kristian

    1991-01-01

    The influence of the first-order mode on the residual reflectivity of angled-facet amplifiers is analyzed. For a 7 degrees angled-facet ridge waveguide amplifier with a single-layer antireflective (AR) coating, a gain ripple lower than 1-dB at 25-dB gain can be obtained independent...... of the polarization, even in the presence of a first-order mode with a 15-dB gain. The tolerances for the thickness and refractive index of the AR coating are reduced by a factor of three compared to operation in the fundamental mode only. The influence of the higher order mode can virtually be suppressed...

  1. Higher order branching of periodic orbits from polynomial isochrones

    Directory of Open Access Journals (Sweden)

    B. Toni

    1999-09-01

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

  2. Minimization of heat slab nodes with higher order boundary conditions

    International Nuclear Information System (INIS)

    Solbrig, C.W.

    1992-01-01

    The accuracy of a numerical solution can be limited by the numerical approximation to the boundary conditions rather than the accuracy of the equations which describe the interior. The study presented in this paper compares the results from two different numerical formulations of the convective boundary condition on the face of a heat transfer slab. The standard representation of the boundary condition in a test problem yielded an unacceptable error even when the heat transfer slab was partitioned into over 300 nodes. A higher order boundary condition representation was obtained by using a second order approximation for the first derivative at the boundary and combining it with the general equation used for inner nodes. This latter formulation produced reasonable results when as few as ten nodes were used

  3. Mixed Higher Order Variational Model for Image Recovery

    Directory of Open Access Journals (Sweden)

    Pengfei Liu

    2014-01-01

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

  4. MHD stability analysis using higher order spline functions

    Energy Technology Data Exchange (ETDEWEB)

    Ida, Akihiro [Department of Energy Engineering and Science, Graduate School of Engineering, Nagoya University, Nagoya, Aichi (Japan); Todoroki, Jiro; Sanuki, Heiji

    1999-04-01

    The eigenvalue problem of the linearized magnetohydrodynamic (MHD) equation is formulated by using higher order spline functions as the base functions of Ritz-Galerkin approximation. When the displacement vector normal to the magnetic surface (in the magnetic surface) is interpolated by B-spline functions of degree p{sub 1} (degree p{sub 2}), which is continuously c{sub 1}-th (c{sub 2}-th) differentiable on neighboring finite elements, the sufficient conditions for the good approximation is given by p{sub 1}{>=}p{sub 2}+1, c{sub 1}{<=}c{sub 2}+1, (c{sub 1}{>=}1, p{sub 2}{>=}c{sub 2}{>=}0). The influence of the numerical integration upon the convergence of calculated eigenvalues is discussed. (author)

  5. 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......To achieve sparse parametrizations that allow 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. To accomplish this, we introduce in this paper...... higher-order momentum distributions in the large deformation diffeomorphic metric mapping (LDDMM) registration framework. While the zeroth-order moments previously used in LDDMM only describe local displacement, the first-order momenta that are proposed here represent a basis that allows local...

  6. Higher order corrections to asymptotic-de Sitter inflation

    Science.gov (United States)

    Mohsenzadeh, M.; Yusofi, E.

    2017-08-01

    Since 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 the initial quasi-de Sitter (dS) state during inflation. We use the asymptotic-dS mode to study the trans-Planckian correction of the power spectrum to the quasi-dS inflation. The obtained spectra consist of higher order corrections associated with the type of geometry and harmonic terms sensitive to the fluctuations of space-time (or gravitational waves) during inflation. As an important result, the amplitude of the power spectrum is dependent on the choice of c, i.e. the type of space-time in the period of inflation. Also, the results are always valid for any asymptotic dS space-time and particularly coincide with the conventional results for dS and flat space-time.

  7. 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.

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

    Science.gov (United States)

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

    2016-10-01

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

  9. 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.

  10. Predictors of third and Higher order births in India

    Directory of Open Access Journals (Sweden)

    Payal Singh

    2015-12-01

    Full Text Available Background: Total fertility rate (TFR reflecting population growth is closely related to higher order parity progression. Many Indian states reached replacement level of TFR, but still states constituting nearly 40% population are with TFR ≥ 3. The predictors are the desire of son’s, poor contraceptives practices, younger age at marriage, child loss and shorter birth spacing. Objective: This analysis assessed the degree of relation of 3rd and higher order parity progression with the above mentioned predictors. Material and Methods: State/Union Territories wise proportions of women: progressing to ≥3 births, more sons desire, birth spacing <24 months, adopting modern contraception and median marriage age <18 years along with infant mortality rate (IMR were taken from NFHS-III report. Correlation matrix and stepwise forward multiple regression carried. Significance was seen at 5%. Results: Hindi speaking states constituting 38.92% nation population recorded TFR ≥3. Positive correlation of mothers progressing ≥ 3 births was highest (0.746 with those desiring more sons followed by IMR (0.445; while maximum negative correlation with those practicing modern contraceptives (-0.565 followed by median age at marriage (-0.391. Multiple regression analysis in order identified desire of more sons, practicing modern contraception and shorter birth spacing as the significant predictors and jointly explained 77.9% of the total variation with gain of 15.5% by adding modern contraceptive practice and 8.3% by adding shorter birth spacing. Conclusions: Desire of more sons appeared the most important predictor to progress ≥3 births that is governed by society culture and educational attainment, require attitudinal change. Further, mothers need motivation to practice both spacing and terminal methods once family is complete.

  11. Higher-order conditioning is impaired by hippocampal lesions.

    Science.gov (United States)

    Gilboa, Asaf; Sekeres, Melanie; Moscovitch, Morris; Winocur, Gordon

    2014-09-22

    Behavior in the real world is rarely motivated by primary conditioned stimuli that have been directly associated with potent unconditioned reinforcers. Instead, motivation and choice behavior are driven by complex chains of higher-order associations that are only indirectly linked to intrinsic reward and often exert their influence outside awareness. Second-order conditioning (SOC) [1] is a basic associative-learning mechanism whereby stimuli acquire motivational salience by proxy, in the absence of primary incentives [2, 3]. Memory-systems theories consider first-order conditioning (FOC) and SOC to be prime examples of hippocampal-independent nondeclarative memory [4, 5]. Accordingly, neurobiological models of SOC focus almost exclusively on nondeclarative neural systems that support motivational salience and reward value. Transfer of value from a conditioned stimulus to a neutral stimulus is thought to require the basolateral amygdala [6, 7] and the ventral striatum [2, 3], but not the hippocampus. We developed a new paradigm to measure appetitive SOC of tones in rats. Hippocampal lesions severely impaired both acquisition and expression of SOC despite normal FOC. Unlike controls, rats with hippocampal lesions could not discriminate between positive and negative secondary conditioned tones, although they exhibited general familiarity with previously presented tones compared with new tones. Importantly, normal rats' behavior, in contrast to that of hippocampal groups, also revealed different confidence levels as indexed by effort, a central characteristic of hippocampal relational memory. The results indicate, contrary to current systems models, that representations of intrinsic relationships between reward value, stimulus identity, and motivation require hippocampal mediation when these relationships are of a higher order. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Chromatin structure with respect to histone signature changes during cell differentiation

    Czech Academy of Sciences Publication Activity Database

    Harničarová, Andrea; Bártová, Eva; Kozubek, Stanislav

    2010-01-01

    Roč. 35, č. 1 (2010), s. 31-44 ISSN 0386-7196 R&D Projects: GA MŠk ME 919; GA ČR(CZ) GAP302/10/1022 Grant - others:GA MŠk(CZ) LC06027; GA MŠk(CZ) LC535 Program:LC; LC Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : chromatin * gene expression * differentiation Subject RIV: BO - Biophysics Impact factor: 3.265, year: 2010

  13. Higher-order geodesic deviation for charged particles and resonance induced by gravitational waves

    Science.gov (United States)

    Heydari-Fard, M.; Hasani, S. N.

    We generalize the higher-order geodesic deviation for the structure-less test particles to the higher-order geodesic deviation equations of the charged particles [R. Kerner, J. W. van Holten and R. Colistete Jr., Class. Quantum Grav. 18 (2001) 4725]. By solving these equations for charged particles moving in a constant magnetic field in the spacetime of a gravitational wave, we show for both cases when the gravitational wave is parallel and perpendicular to the constant magnetic field, a magnetic resonance appears at wg = Ω. This feature might be useful to detect the gravitational wave with high frequencies.

  14. Higher-order resonant electronic recombination as a manifestation of configuration interaction

    International Nuclear Information System (INIS)

    Beilmann, C; Amaro, P; Tashenov, S; Bekker, H; Harman, Z; Crespo López-Urrutia, J R

    2013-01-01

    Theoretical and experimental investigations of higher-order electron–ion recombination resonances including inter-shell excitations are presented for L-shell ions of Kr with the aim of examining details of atomic structure calculations. The particular importance of electron–electron interaction and configuration mixing effects for these recombination processes enables their use for detailed tests of electron correlation effects. A test of the required level of considered mixing configurations is presented and further experiments involving higher-order recombination channels are motivated. (paper)

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

    Science.gov (United States)

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

    2017-01-01

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

  16. Chromatin structure of ribosomal RNA genes in dipterans and its relationship to the location of nucleolar organizers.

    Science.gov (United States)

    Madalena, Christiane Rodriguez Gutierrez; Díez, José Luís; Gorab, Eduardo

    2012-01-01

    Nucleoli, nuclear organelles in which ribosomal RNA is synthesized and processed, emerge from nucleolar organizers (NORs) located in distinct chromosomal regions. In polytene nuclei of dipterans, nucleoli of some species can be observed under light microscopy exhibiting distinctive morphology: Drosophila and chironomid species display well-formed nucleoli in contrast to the fragmented and dispersed nucleoli seen in sciarid flies. The available data show no apparent relationship between nucleolar morphology and location of NORs in Diptera. The regulation of rRNA transcription involves controlling both the transcription rate per gene as well as the proportion of rRNA genes adopting a proper chromatin structure for transcription, since active and inactive rRNA gene copies coexist in NORs. Transcription units organized in nucleosomes and those lacking canonical nucleosomes can be analyzed by the method termed psoralen gel retarding assay (PGRA), allowing inferences on the ratio of active to inactive rRNA gene copies. In this work, possible connections between chromosomal location of NORs and proportion of active rRNA genes were studied in Drosophila melanogaster, and in chironomid and sciarid species. The data suggested a link between location of NORs and proportion of active rRNA genes since the copy number showing nucleosomal organization predominates when NORs are located in the pericentric heterochromatin. The results presented in this work are in agreement with previous data on the chromatin structure of rRNA genes from distantly related eukaryotes, as assessed by the PGRA.

  17. Chromatin structure of ribosomal RNA genes in dipterans and its relationship to the location of nucleolar organizers.

    Directory of Open Access Journals (Sweden)

    Christiane Rodriguez Gutierrez Madalena

    Full Text Available Nucleoli, nuclear organelles in which ribosomal RNA is synthesized and processed, emerge from nucleolar organizers (NORs located in distinct chromosomal regions. In polytene nuclei of dipterans, nucleoli of some species can be observed under light microscopy exhibiting distinctive morphology: Drosophila and chironomid species display well-formed nucleoli in contrast to the fragmented and dispersed nucleoli seen in sciarid flies. The available data show no apparent relationship between nucleolar morphology and location of NORs in Diptera. The regulation of rRNA transcription involves controlling both the transcription rate per gene as well as the proportion of rRNA genes adopting a proper chromatin structure for transcription, since active and inactive rRNA gene copies coexist in NORs. Transcription units organized in nucleosomes and those lacking canonical nucleosomes can be analyzed by the method termed psoralen gel retarding assay (PGRA, allowing inferences on the ratio of active to inactive rRNA gene copies. In this work, possible connections between chromosomal location of NORs and proportion of active rRNA genes were studied in Drosophila melanogaster, and in chironomid and sciarid species. The data suggested a link between location of NORs and proportion of active rRNA genes since the copy number showing nucleosomal organization predominates when NORs are located in the pericentric heterochromatin. The results presented in this work are in agreement with previous data on the chromatin structure of rRNA genes from distantly related eukaryotes, as assessed by the PGRA.

  18. Chromatin challenges during DNA replication and repair

    DEFF Research Database (Denmark)

    Groth, Anja; Rocha, Walter; Verreault, Alain

    2007-01-01

    Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet...... the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic...... landscape may be stably maintained even in the face of dramatic changes in chromatin structure....

  19. Higher order effects in electroweak theory 1981-12 (KEK)

    International Nuclear Information System (INIS)

    Aoki, Ken-ichi

    1982-01-01

    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(m 2 q 2 /M 2 ) 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) (q 2 ) O(i), where C(i)(q 2 ) 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 sin 2 (theta) from the νN reaction are presented. (Kato, T.)

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

    Science.gov (United States)

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

    2016-01-01

    Visual perceptual learning has been shown to be highly specific to the retinotopic location and attributes of the trained stimulus. Recent psychophysical studies suggest that these specificities, which have been associated with early retinotopic visual cortex, may in fact not be inherent in perceptual learning and could be related to higher-order brain functions. Here we provide direct electrophysiological evidence in support of this proposition. In a series of event-related potential (ERP) experiments, we recorded high-density electroencephalography (EEG) from human adults over the course of learning in a texture discrimination task (TDT). The results consistently showed that the earliest C1 component (68-84ms), known to reflect V1 activity driven by feedforward inputs, was not modulated by learning regardless of whether the behavioral improvement is location specific or not. In contrast, two later posterior ERP components (posterior P1 and P160-350) over the occipital cortex and one anterior ERP component (anterior P160-350) over the prefrontal cortex were progressively modified day by day. Moreover, the change of the anterior component was closely correlated with improved behavioral performance on a daily basis. Consistent with recent psychophysical and imaging observations, our results indicate that perceptual learning can mainly involve changes in higher-level visual cortex as well as in the neural networks responsible for cognitive functions such as attention and decision making. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Estimation of uncertainties from missing higher orders in perturbative calculations

    International Nuclear Information System (INIS)

    Bagnaschi, E.

    2015-05-01

    In this proceeding we present the results of our recent study (hep-ph/1409.5036) of the statistical performances of two different approaches, Scale Variation (SV) and the Bayesian model of Cacciari and Houdeau (CH)(hep-ph/1105.5152) (which we also extend to observables with initial state hadrons), to the estimation of Missing Higher-Order Uncertainties (MHOUs)(hep-ph/1307.1843) in perturbation theory. The behavior of the models is determined by analyzing, on a wide set of observables, how the MHOU intervals they produce are successful in predicting the next orders. We observe that the Bayesian model behaves consistently, producing intervals at 68% Degree of Belief (DoB) comparable with the scale variation intervals with a rescaling factor r larger than 2 and closer to 4. Concerning SV, our analysis allows the derivation of a heuristic Confidence Level (CL) for the intervals. We find that assigning a CL of 68% to the intervals obtained with the conventional choice of varying the scales within a factor of two with respect to the central scale could potentially lead to an underestimation of the uncertainties in the case of observables with initial state hadrons.

  2. Effective description of higher-order scalar-tensor theories

    Energy Technology Data Exchange (ETDEWEB)

    Langlois, David [APC—Astroparticule et Cosmologie, Université Paris Diderot Paris 7, 75013 Paris (France); Mancarella, Michele; Vernizzi, Filippo [Institut de physique théorique, Université Paris Saclay, CEA, CNRS, 91191 Gif-sur-Yvette (France); Noui, Karim, E-mail: langlois@apc.univ-paris7.fr, E-mail: michele.mancarella@cea.fr, E-mail: karim.noui@lmpt.univ-tours.fr, E-mail: filippo.vernizzi@cea.fr [Laboratoire de Mathématiques et Physique Théorique, Université François Rabelais, Parc de Grandmont, 37200 Tours (France)

    2017-05-01

    Most existing theories of dark energy and/or modified gravity, involving a scalar degree of freedom, can be conveniently described within the framework of the Effective Theory of Dark Energy, based on the unitary gauge where the scalar field is uniform. We extend this effective approach by allowing the Lagrangian in unitary gauge to depend on the time derivative of the lapse function. Although this dependence generically signals the presence of an extra scalar degree of freedom, theories that contain only one propagating scalar degree of freedom, in addition to the usual tensor modes, can be constructed by requiring the initial Lagrangian to be degenerate. Starting from a general quadratic action, we derive the dispersion relations for the linear perturbations around Minkowski and a cosmological background. Our analysis directly applies to the recently introduced Degenerate Higher-Order Scalar-Tensor (DHOST) theories. For these theories, we find that one cannot recover a Poisson-like equation in the static linear regime except for the subclass that includes the Horndeski and so-called 'beyond Horndeski' theories. We also discuss Lorentz-breaking models inspired by Horava gravity.

  3. Scalar brane backgrounds in higher order curvature gravity

    International Nuclear Information System (INIS)

    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 particularly 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. Generically, 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 but infinite volume element. (author)

  4. Analysis of higher order harmonics with holographic reflection gratings

    Science.gov (United States)

    Mas-Abellan, P.; Madrigal, R.; Fimia, A.

    2017-05-01

    Silver halide emulsions have been considered one of the most energetic sensitive materials for holographic applications. Nonlinear recording effects on holographic reflection gratings recorded on silver halide emulsions have been studied by different authors obtaining excellent experimental results. In this communication specifically we focused our investigation on the effects of refractive index modulation, trying to get high levels of overmodulation that will produce high order harmonics. We studied the influence of the overmodulation and its effects on the transmission spectra for a wide exposure range by use of 9 μm thickness films of ultrafine grain emulsion BB640, exposed to single collimated beams using a red He-Ne laser (wavelength 632.8 nm) with Denisyuk configuration obtaining a spatial frequency of 4990 l/mm recorded on the emulsion. The experimental results show that high overmodulation levels of refractive index produce second order harmonics with high diffraction efficiency (higher than 75%) and a narrow grating bandwidth (12.5 nm). Results also show that overmodulation produce diffraction spectra deformation of the second order harmonic, transforming the spectrum from sinusoidal to approximation of square shape due to very high overmodulation. Increasing the levels of overmodulation of refractive index, we have obtained higher order harmonics, obtaining third order harmonic with diffraction efficiency (up to 23%) and narrowing grating bandwidth (5 nm). This study is the first step to develop a new easy technique to obtain narrow spectral filters based on the use of high index modulation reflection gratings.

  5. Correlated stopping, proton clusters and higher order proton cumulants

    Energy Technology Data Exchange (ETDEWEB)

    Bzdak, Adam [AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, Krakow (Poland); Koch, Volker [Lawrence Berkeley National Laboratory, Nuclear Science Division, Berkeley, CA (United States); Skokov, Vladimir [RIKEN/BNL, Brookhaven National Laboratory, Upton, NY (United States)

    2017-05-15

    We investigate possible effects of correlations between stopped nucleons on higher order proton cumulants at low energy heavy-ion collisions. We find that fluctuations of the number of wounded nucleons N{sub part} lead to rather nontrivial dependence of the correlations on the centrality; however, this effect is too small to explain the large and positive four-proton correlations found in the preliminary data collected by the STAR collaboration at √(s) = 7.7 GeV. We further demonstrate that, by taking into account additional proton clustering, we are able to qualitatively reproduce the preliminary experimental data. We speculate that this clustering may originate either from collective/multi-collision stopping which is expected to be effective at lower energies or from a possible first-order phase transition, or from (attractive) final state interactions. To test these ideas we propose to measure a mixed multi-particle correlation between stopped protons and a produced particle (e.g. pion, antiproton). (orig.)

  6. Near integrability of kink lattice with higher order interactions

    Science.gov (United States)

    Jiang, Yun-Guo; Liu, Jia-Zhen; He, Song

    2017-11-01

    We make use of Manton’s analytical method to investigate the force between kinks and anti-kinks at large distances in 1+1 dimensional field theory. The related potential has infinite order corrections of exponential pattern, and the coefficients for each order are determined. These coefficients can also be obtained by solving the equation of the fluctuations 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 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 is a near integrable system. We make use of Flaschka’s variables to study the Lax pair of the kink lattice. These Flaschka’s variables have interesting algebraic relations and non-integrability can be manifested. We also discuss the higher Hamiltonians for the deformed open Toda lattice, which has a similar result to the ordinary deformed Toda. Supported by Shandong Provincial Natural Science Foundation (ZR2014AQ007), National Natural Science Foundation of China (11403015, U1531105), S. He is supported by Max-Planck fellowship in Germany and National Natural Science Foundation of China (11305235)

  7. Higher order corrections to energy levels of muonic atoms

    International Nuclear Information System (INIS)

    Rinker, G.A. Jr.; Steffen, R.M.

    1975-08-01

    In order to facilitate the analysis of muonic x-ray spectra, the results of numerical computations of all higher order quantum electrodynamical corrections to the energy levels of muonic atoms are presented in tabular and graphical form. These corrections include the vacuum polarization corrections caused by emission and reabsorption of virtual electron pairs to all orders, including ''double-bubble'' and ''cracked-egg'' diagrams. An estimate of the Delbruecke scattering-type correction is presented. The Lamb-shift (second- and fourth-order vertex) corrections have been calculated including the correction for the anomalous magnetic moment of the muon. The relativistic nuclear motion (or recoil) correction as well as the correction caused by the screening of the atomic electrons is presented in graphs. For the sake of completeness a graph of the nuclear polarization as computed on the basis of Chen's approach has been included. All calculations were made with a two-parameter Fermi distribution of the nuclear charge density. 7 figures, 23 references

  8. Higher Order Modes Excitation of Micro Cantilever Beams

    KAUST Repository

    Jaber, Nizar

    2014-05-01

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

  9. Holographic conductivity of holographic superconductors with higher-order corrections

    Energy Technology Data Exchange (ETDEWEB)

    Sheykhi, Ahmad [Shiraz University, Physics Department and Biruni Observatory, College of Sciences, Shiraz (Iran, Islamic Republic of); Research Institute for Astronomy and Astrophysics of Maragha (RIAAM), Maragha (Iran, Islamic Republic of); Ghazanfari, Afsoon; Dehyadegari, Amin [Shiraz University, Physics Department and Biruni Observatory, College of Sciences, Shiraz (Iran, Islamic Republic of)

    2018-02-15

    We analytically and numerically disclose the effects of the higher-order correction terms in the gravity and in the gauge field on the properties of s-wave holographic superconductors. On the gravity side, we consider the higher curvature Gauss-Bonnet corrections and on the gauge field side, we add a quadratic correction term to the Maxwell Lagrangian. We show that, for this system, one can still obtain an analytical relation between the critical temperature and the charge density. We also calculate the critical exponent and the condensation value both analytically and numerically. We use a variational method, based on the Sturm-Liouville eigenvalue problem for our analytical study, as well as a numerical shooting method in order to compare with our analytical results. For a fixed value of the Gauss-Bonnet parameter, we observe that the critical temperature decreases with increasing the nonlinearity of the gauge field. This implies that the nonlinear correction term to the Maxwell electrodynamics makes the condensation harder. We also study the holographic conductivity of the system and disclose the effects of the Gauss-Bonnet and nonlinear parameters α and b on the superconducting gap. We observe that, for various values of α and b, the real part of the conductivity is proportional to the frequency per temperature, ω/T, as the frequency is large enough. Besides, the conductivity has a minimum in the imaginary part which is shifted toward greater frequency with decreasing temperature. (orig.)

  10. Higher-order scene statistics of breast images

    Science.gov (United States)

    Abbey, Craig K.; Sohl-Dickstein, Jascha N.; Olshausen, Bruno A.; Eckstein, Miguel P.; Boone, John M.

    2009-02-01

    Researchers studying human and computer vision have found description and construction of these systems greatly aided by analysis of the statistical properties of naturally occurring scenes. More specifically, it has been found that receptive fields with directional selectivity and bandwidth properties similar to mammalian visual systems are more closely matched to the statistics of natural scenes. It is argued that this allows for sparse representation of the independent components of natural images [Olshausen and Field, Nature, 1996]. These theories have important implications for medical image perception. For example, will a system that is designed to represent the independent components of natural scenes, where objects occlude one another and illumination is typically reflected, be appropriate for X-ray imaging, where features superimpose on one another and illumination is transmissive? In this research we begin to examine these issues by evaluating higher-order statistical properties of breast images from X-ray projection mammography (PM) and dedicated breast computed tomography (bCT). We evaluate kurtosis in responses of octave bandwidth Gabor filters applied to PM and to coronal slices of bCT scans. We find that kurtosis in PM rises and quickly saturates for filter center frequencies with an average value above 0.95. By contrast, kurtosis in bCT peaks near 0.20 cyc/mm with kurtosis of approximately 2. Our findings suggest that the human visual system may be tuned to represent breast tissue more effectively in bCT over a specific range of spatial frequencies.

  11. Higher-order Skyrme hair of black holes

    Science.gov (United States)

    Gudnason, Sven Bjarke; Nitta, Muneto

    2018-05-01

    Higher-order derivative terms are considered as replacement for the Skyrme term in an Einstein-Skyrme-like model in order to pinpoint which properties are necessary for a black hole to possess stable static scalar hair. We find two new models able to support stable black hole hair in the limit of the Skyrme term being turned off. They contain 8 and 12 derivatives, respectively, and are roughly the Skyrme-term squared and the so-called BPS-Skyrme-term squared. In the twelfth-order model we find that the lower branches, which are normally unstable, become stable in the limit where the Skyrme term is turned off. We check this claim with a linear stability analysis. Finally, we find for a certain range of the gravitational coupling and horizon radius, that the twelfth-order model contains 4 solutions as opposed to 2. More surprisingly, the lowest part of the would-be unstable branch turns out to be the stable one of the 4 solutions.

  12. Higher order total variation regularization for EIT reconstruction.

    Science.gov (United States)

    Gong, Bo; Schullcke, Benjamin; Krueger-Ziolek, Sabine; Zhang, Fan; Mueller-Lisse, Ullrich; Moeller, Knut

    2018-01-08

    Electrical impedance tomography (EIT) attempts to reveal the conductivity distribution of a domain based on the electrical boundary condition. This is an ill-posed inverse problem; its solution is very unstable. Total variation (TV) regularization is one of the techniques commonly employed to stabilize reconstructions. However, it is well known that TV regularization induces staircase effects, which are not realistic in clinical applications. To reduce such artifacts, modified TV regularization terms considering a higher order differential operator were developed in several previous studies. One of them is called total generalized variation (TGV) regularization. TGV regularization has been successively applied in image processing in a regular grid context. In this study, we adapted TGV regularization to the finite element model (FEM) framework for EIT reconstruction. Reconstructions using simulation and clinical data were performed. First results indicate that, in comparison to TV regularization, TGV regularization promotes more realistic images. Graphical abstract Reconstructed conductivity changes located on selected vertical lines. For each of the reconstructed images as well as the ground truth image, conductivity changes located along the selected left and right vertical lines are plotted. In these plots, the notation GT in the legend stands for ground truth, TV stands for total variation method, and TGV stands for total generalized variation method. Reconstructed conductivity distributions from the GREIT algorithm are also demonstrated.

  13. Higher-order gravity and the classical equivalence principle

    Science.gov (United States)

    Accioly, Antonio; Herdy, Wallace

    2017-11-01

    As is well known, the deflection of any particle by a gravitational field within the context of Einstein’s general relativity — which is a geometrical theory — is, of course, nondispersive. Nevertheless, as we shall show in this paper, the mentioned result will change totally if the bending is analyzed — at the tree level — in the framework of higher-order gravity. Indeed, to first order, the deflection angle corresponding to the scattering of different quantum particles by the gravitational field mentioned above is not only spin dependent, it is also dispersive (energy-dependent). Consequently, it violates the classical equivalence principle (universality of free fall, or equality of inertial and gravitational masses) which is a nonlocal principle. However, contrary to popular belief, it is in agreement with the weak equivalence principle which is nothing but a statement about purely local effects. It is worthy of note that the weak equivalence principle encompasses the classical equivalence principle locally. We also show that the claim that there exists an incompatibility between quantum mechanics and the weak equivalence principle, is incorrect.

  14. Modulating chromatin structure and DNA accessibility by deacetylase inhibition enhances the anti-cancer activity of silver nanoparticles.

    Science.gov (United States)

    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. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    David Llères

    2017-02-01

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

  16. On higher-order corrections in M theory

    International Nuclear Information System (INIS)

    Howe, P.S.; Tsimpis, D.

    2003-01-01

    A theoretical analysis of higher-order corrections to D=11 supergravity is given in a superspace framework. It is shown that any deformation of D=11 supergravity for which the lowest-dimensional component of the four-form G 4 vanishes is trivial. This implies that the equations of motion of D=11 supergravity are specified by an element of a certain spinorial cohomology group and generalises previous results obtained using spinorial or pure spinor cohomology to the fully non-linear theory. The first deformation of the theory is given by an element of a different spinorial cohomology group with coefficients which are local tensorial functions of the massless supergravity fields. The four-form Bianchi Identities are solved, to first order and at dimension -{1/2}, in the case that the lowest-dimensional component of G 4 is non-zero. Moreover, it is shown how one can calculate the first-order correction to the dimension-zero torsion and thus to the supergravity equations of motion given an explicit expression for this object in terms of the supergravity fields. The version of the theory with both a four-form and a seven-form is discussed in the presence of the five-brane anomaly-cancelling term. It is shown that the supersymmetric completion of this term exists and it is argued that it is the unique anomaly-cancelling invariant at this dimension which is at least quartic in the fields. This implies that the first deformation of the theory is completely determined by the anomaly term from which one can, in principle, read off the corrections to all of the superspace field strength tensors. (author)

  17. 1957-2007: 50 Years of Higher Order Programming Languages

    Directory of Open Access Journals (Sweden)

    Alen Lovrenčić

    2009-06-01

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

  18. Preparation and characterization of stable aqueous higher-order fullerenes

    International Nuclear Information System (INIS)

    Aich, Nirupam; Flora, Joseph R V; Saleh, Navid B

    2012-01-01

    Stable aqueous suspensions of nC 60 and individual higher fullerenes, i.e. C 70 , C 76 and C 84 , are prepared by a calorimetric modification of a commonly used liquid–liquid extraction technique. The energy requirement for synthesis of higher fullerenes has been guided by molecular-scale interaction energy calculations. Solubilized fullerenes show crystalline behavior by exhibiting lattice fringes in high resolution transmission electron microscopy images. The fullerene colloidal suspensions thus prepared are stable with a narrow distribution of cluster radii (42.7 ± 0.8 nm, 46.0 ± 14.0 nm, 60 ± 3.2 nm and 56.3 ± 1.1 nm for nC 60 , nC 70 , nC 76 and nC 84 , respectively) as measured by time-resolved dynamic light scattering. The ζ-potential values for all fullerene samples showed negative surface potentials with similar magnitude ( − 38.6 ± 5.8 mV, − 39.1 ± 4.2 mV, − 38.9 ± 5.8 mV and − 41.7 ± 5.1 mV for nC 60 , nC 70 , nC 76 and nC 84 , respectively), which provide electrostatic stability to the colloidal clusters. This energy-based modified solubilization technique to produce stable aqueous fullerenes will likely aid in future studies focusing on better applicability, determination of colloidal properties, and understanding of environmental fate, transport and toxicity of higher-order fullerenes. (paper)

  19. Keeping it quiet: chromatin control of gammaherpesvirus latency.

    Science.gov (United States)

    Lieberman, Paul M

    2013-12-01

    The human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi's sarcoma-associated herpesvirus (KSHV) establish long-term latent infections associated with diverse human cancers. Viral oncogenesis depends on the ability of the latent viral genome to persist in host nuclei as episomes that express a restricted yet dynamic pattern of viral genes. Multiple epigenetic events control viral episome generation and maintenance. This Review highlights some of the recent findings on the role of chromatin assembly, histone and DNA modifications, and higher-order chromosome structures that enable gammaherpesviruses to establish stable latent infections that mediate viral pathogenesis.

  20. Analysis of wheezes using wavelet higher order spectral features.

    Science.gov (United States)

    Taplidou, Styliani A; Hadjileontiadis, Leontios J

    2010-07-01

    . This paves the way for the use of the wavelet higher order spectral features as an input vector to an efficient classifier. Apparently, this would integrate the intrinsic characteristics of wheezes within computerized diagnostic tools toward their more efficient evaluation.

  1. Higher-order aberrations and visual acuity after LASEK.

    Science.gov (United States)

    Urgancioglu, Berrak; Bilgihan, Kamil; Ozturk, Sertac

    2008-08-01

    To determine ocular higher-order aberrations (HOAs) in eyes with supernormal vision after myopic astigmatic laser subepithelial keratomileusis (LASEK) and to compare the findings with those in eyes with natural supernormal vision. Ocular HOAs were measured after LASEK in 20 eyes of 12 myopic astigmatic patients with postoperative uncorrected visual acuity (UCVA) of >20/16 (group 1). Patients who were included in the study had no visual symptoms like glare, halo or double vision. The measurements were taken 8.3 +/- 3 months after LASEK surgery. In group 2 ocular HOAs were examined in 20 eyes of 10 subjects with natural UCVA of >20/16 as a control. Measurements were taken across a pupil with a diameter of 4.0 mm and 6.0 mm. Root-mean-square (RMS) values of HOAs, Z(3)-1, Z(3)1, Z(4)0, Z(5)-1, Z(5)1 and Z(6)0 were analyzed. The mean RMS values for each order were higher in group 1 when compared with group 2 at 4.0 mm and 6.0 mm pupil diameters. There was no statistically significant difference between groups in spherical and coma aberrations (P > 0.05). Mean RMS values for total HOAs were 0.187 +/- 0.09 microm at 4.0 mm and 0.438 +/- 0.178 microm at 6.0 mm pupil in group 1 and 0.120 +/- 0.049 microm at 4.0 mm and 0.344 +/- 0.083 microm at 6.0 mm pupil in group 2. The difference between groups in total HOAs was statistically significant at 4.0 mm and 6.0 mm pupil diameters (P < 0.05). Ocular HOAs exist in eyes with supernormal vision. After LASEK, the amount of HOAs of the eye increases under both mesopic and photopic conditions. However the amount of HOA increase does not seem to be consistent with visual symptoms.

  2. Dynamics and phenomenology of higher order gravity cosmological models

    Science.gov (United States)

    Moldenhauer, Jacob Andrew

    2010-10-01

    I present here some new results about a systematic approach to higher-order gravity (HOG) cosmological models. The HOG models are derived from curvature invariants that are more general than the Einstein-Hilbert action. Some of the models exhibit late-time cosmic acceleration without the need for dark energy and fit some current observations. The open question is that there are an infinite number of invariants that one could select, and many of the published papers have stressed the need to find a systematic approach that will allow one to study methodically the various possibilities. We explore a new connection that we made between theorems from the theory of invariants in general relativity and these cosmological models. In summary, the theorems demonstrate that curvature invariants are not all independent from each other and that for a given Ricci Segre type and Petrov type (symmetry classification) of the space-time, there exists a complete minimal set of independent invariants (a basis) in terms of which all the other invariants can be expressed. As an immediate consequence of the proposed approach, the number of invariants to consider is dramatically reduced from infinity to four invariants in the worst case and to only two invariants in the cases of interest, including all Friedmann-Lemaitre-Robertson-Walker metrics. We derive models that pass stability and physical acceptability conditions. We derive dynamical equations and phase portrait analyses that show the promise of the systematic approach. We consider observational constraints from magnitude-redshift Supernovae Type Ia data, distance to the last scattering surface of the Cosmic Microwave Background radiation, and Baryon Acoustic Oscillations. We put observational constraints on general HOG models. We constrain different forms of the Gauss-Bonnet, f(G), modified gravity models with these observations. We show some of these models pass solar system tests. We seek to find models that pass physical and

  3. Electron microscopic study on the initial effect of gamma-irradiation on the chromatin structure of L cells

    International Nuclear Information System (INIS)

    Kondo, Takashi; Nakanishi, Y.H.; Yoshii, Giichi

    1979-01-01

    Mouse L cells are gamma-irradiated at a dose of 1 Mrad, and ultrathin sections of the cells are examined by electron microscopy. The distance between chromatin fibers in diffused chromatin regions in the irradiated nuclei is essentially identical with the nonirradiated control. In contrast, an increase of the distance between the chromatin fibers is observed in the excess of Ca ions in irradiation. (author)

  4. Disconnect between alcohol-induced alterations in chromatin structure and gene transcription in a mouse embryonic stem cell model of exposure.

    Science.gov (United States)

    Veazey, Kylee J; Wang, Haiqing; Bedi, Yudhishtar S; Skiles, William M; Chang, Richard Cheng-An; Golding, Michael C

    2017-05-01

    Alterations to chromatin structure induced by environmental insults have become an attractive explanation for the persistence of exposure effects into subsequent life stages. However, a growing body of work examining the epigenetic impact that alcohol and other drugs of abuse exert consistently notes a disconnection between induced changes in chromatin structure and patterns of gene transcription. Thus, an important question is whether perturbations in the 'histone code' induced by prenatal exposures to alcohol implicitly subvert gene expression, or whether the hierarchy of cellular signaling networks driving development is such that they retain control over the transcriptional program. To address this question, we examined the impact of ethanol exposure in mouse embryonic stem cells cultured under 2i conditions, where the transcriptional program is rigidly enforced through the use of small molecule inhibitors. We find that ethanol-induced changes in post-translational histone modifications are dose-dependent, unique to the chromatin modification under investigation, and that the extent and direction of the change differ between the period of exposure and the recovery phase. Similar to in vivo models, we find post-translational modifications affecting histone 3 lysine 9 are the most profoundly impacted, with the signature of exposure persisting long after alcohol has been removed. These changes in chromatin structure associate with dose-dependent alterations in the levels of transcripts encoding Dnmt1, Uhrf1, Tet1, Tet2, Tet3, and Polycomb complex members Eed and Ezh2. However, in this model, ethanol-induced changes to the chromatin template do not consistently associate with changes in gene transcription, impede the process of differentiation, or affect the acquisition of monoallelic patterns of expression for the imprinted gene Igf2R. These findings question the inferred universal relevance of epigenetic changes induced by drugs of abuse and suggest that changes

  5. The alteration of chromatin domains during damage repair induced by ionizing radiation

    International Nuclear Information System (INIS)

    Cress, A.E.; Olson, K.M.; Olson, G.B.

    1995-01-01

    Several groups previously have reported the ability of chromatin structure to influence the production of damage induced by ionizing radiation. The authors' interest has been to determine whether chromatin structural alterations exist after ionizing radiation during a repair interval. The earlier work investigated this question using biochemical techniques. The crosslinking of nuclear structural proteins to DNA after ionizing radiation was observed. In addition, they found that the chromatin structure in vitro as measured by sucrose density gradient sedimentation, was altered after ionizing radiation. These observations added to earlier studies in which digital imaging techniques showed an alteration in feulgen-positive DNA after irradiation prompted the present study. The object of this study was to detect whether the higher order structure of DNA into chromatin domains within interphase human cells was altered in interphase cells in response to a radiation induced damage. The present study takes advantage of the advances in the detection of chromatin domains in situ using DNA specific dyes and digital image processing of established human T and B cell lines

  6. Sperm DNA quality evaluated by comet assay and sperm chromatin structure assay in stallions after unilateral orchiectomy.

    Science.gov (United States)

    Serafini, R; Varner, D D; Bissett, W; Blanchard, T L; Teague, S R; Love, C C

    2015-09-15

    Unilateral orchiectomy (UO) may interfere with thermoregulation of the remaining testis caused by inflammation surrounding the incision site, thus altering normal spermatogenesis and consequently sperm quality. Two measures of sperm DNA quality (neutral comet assay and the sperm chromatin structure assay [SCSA]) were compared before UO (0 days) and at 14, 30, and 60 days after UO to determine whether sperm DNA changed after a mild testis stress (i.e., UO). The percent DNA in the comet tail was higher at 14 and 60 days compared to 0 days (P comet tail measures (i.e., length, moment, migration) were higher at all time periods after UO compared to 0 days (P comet assay and the SCSA, which was not identified using traditional measures of sperm quality. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

    Science.gov (United States)

    Tsai, Zing Tsung-Yeh; Shiu, Shin-Han; Tsai, Huai-Kuang

    2015-08-01

    Transcription factor (TF) binding is determined by the presence of specific sequence motifs (SM) and chromatin accessibility, where the latter is influenced by both chromatin state (CS) and DNA structure (DS) properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy) that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.

  8. Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

    Directory of Open Access Journals (Sweden)

    Zing Tsung-Yeh Tsai

    2015-08-01

    Full Text Available Transcription factor (TF binding is determined by the presence of specific sequence motifs (SM and chromatin accessibility, where the latter is influenced by both chromatin state (CS and DNA structure (DS properties. Although SM, CS, and DS have been used to predict TF binding sites, a predictive model that jointly considers CS and DS has not been developed to predict either TF-specific binding or general binding properties of TFs. Using budding yeast as model, we found that machine learning classifiers trained with either CS or DS features alone perform better in predicting TF-specific binding compared to SM-based classifiers. In addition, simultaneously considering CS and DS further improves the accuracy of the TF binding predictions, indicating the highly complementary nature of these two properties. The contributions of SM, CS, and DS features to binding site predictions differ greatly between TFs, allowing TF-specific predictions and potentially reflecting different TF binding mechanisms. In addition, a "TF-agnostic" predictive model based on three DNA "intrinsic properties" (in silico predicted nucleosome occupancy, major groove geometry, and dinucleotide free energy that can be calculated from genomic sequences alone has performance that rivals the model incorporating experiment-derived data. This intrinsic property model allows prediction of binding regions not only across TFs, but also across DNA-binding domain families with distinct structural folds. Furthermore, these predicted binding regions can help identify TF binding sites that have a significant impact on target gene expression. Because the intrinsic property model allows prediction of binding regions across DNA-binding domain families, it is TF agnostic and likely describes general binding potential of TFs. Thus, our findings suggest that it is feasible to establish a TF agnostic model for identifying functional regulatory regions in potentially any sequenced genome.

  9. Arrangement of nuclear structures is not transmitted through mitosis but is identical in sister cells

    NARCIS (Netherlands)

    Orlova, Darya Yu; Stixová, Lenka; Kozubek, Stanislav; Gierman, Hinco J.; Šustáčková, Gabriela; Chernyshev, Andrei V.; Medvedev, Ruslan N.; Legartová, Soňa; Versteeg, Rogier; Matula, Pavel; Stoklasa, Roman; Bártová, Eva

    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

  10. Integrated Software Development System/Higher Order Software Conceptual Description (ISDS/HOS)

    Science.gov (United States)

    1976-11-01

    Structured Flowchart Conventions 270 6.3.5.3 Design Diagram Notation 273 xii HIGHER ORDER SOFTWARE, INC. 843 MASSACHUSETTS AVENUE. CAMBRIDGE, MASSACHUSETTS...associated with the process steps. They also reference other HIPO diagrams as well an non-HIPO documentation such as flowcharts or decision tables of...syntax that is easy to learn and must provide the novice with some prompting to help him avoid classic beginner errors. Desirable editing capabilities

  11. Multilevel Higher-Order Item Response Theory Models

    Science.gov (United States)

    Huang, Hung-Yu; Wang, Wen-Chung

    2014-01-01

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

  12. Higher-order probabilistic perceptrons as Bayesian inference engines

    International Nuclear Information System (INIS)

    Clark, J.W.; Ristig, M.L.

    1994-08-01

    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

  13. INARCH(1) processes: Higher-order moments and jumps

    OpenAIRE

    Weiß , Christian H.

    2010-01-01

    Abstract The INARCH(1) model is a simple but practically relevant, two-parameter model for processes of overdispersed counts with an autoregressive serial dependence structure. We derive closed-form expressions for the joint (central) moments and cumulants of the INARCH(1) model up to order 4. These expressions are applied to derive moments of jumps in INARCH(1) processes. We illustrate this kind of application with a real-data example, and outline further potential applications. ...

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

    International Nuclear Information System (INIS)

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

    2014-01-01

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

  15. Higher-order predictions for splitting functions and coefficient functions from physical evolution kernels

    International Nuclear Information System (INIS)

    Vogt, A; Soar, G.; Vermaseren, J.A.M.

    2010-01-01

    We have studied the physical evolution kernels for nine non-singlet observables in deep-inelastic scattering (DIS), semi-inclusive e + e - annihilation and the Drell-Yan (DY) process, and for the flavour-singlet case of the photon- and heavy-top Higgs-exchange structure functions (F 2 , F φ ) in DIS. All known contributions to these kernels show an only single-logarithmic large-x enhancement at all powers of (1-x). Conjecturing that this behaviour persists to (all) higher orders, we have predicted the highest three (DY: two) double logarithms of the higher-order non-singlet coefficient functions and of the four-loop singlet splitting functions. The coefficient-function predictions can be written as exponentiations of 1/N-suppressed contributions in Mellin-N space which, however, are less predictive than the well-known exponentiation of the ln k N terms. (orig.)

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

    KAUST Repository

    Li, Er

    2015-08-01

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

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

    Science.gov (United States)

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

    2016-01-02

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

  18. Chromatin in embryonic stem cell neuronal differentiation.

    Science.gov (United States)

    Meshorer, E

    2007-03-01

    Chromatin, the basic regulatory unit of the eukaryotic genetic material, is controlled by epigenetic mechanisms including histone modifications, histone variants, DNA methylation and chromatin remodeling. Cellular differentiation involves large changes in gene expression concomitant with alterations in genome organization and chromatin structure. Such changes are particularly evident in self-renewing pluripotent embryonic stem cells, which begin, in terms of cell fate, as a tabula rasa, and through the process of differentiation, acquire distinct identities. Here I describe the changes in chromatin that accompany neuronal differentiation, particularly of embryonic stem cells, and discuss how chromatin serves as the master regulator of cellular destiny.

  19. Radiation response and chromatin dynamics

    International Nuclear Information System (INIS)

    Ikura, Tsuyoshi

    2009-01-01

    Described is a recent progress in studies of chromatin structural alterations induced by DNA damage by radiation. DNA in eukaryotes exists in the chromatin structure and different mechanisms of response to damage and repair of DNA from those in prokaryotes have been recognized. Chromatin is composed from its unit structure of mono-nucleosome, which is formed from DNA and an octamer of core histones of H2A, H2B, H3 and H4. When DNA is damaged, histone structural alterations are required for repair factors and checkpoint proteins to access the damaged site. At the actual genome damage, chemical modification of histone to work as a code occurs dependently on the damage where chromatin remodeling factors and histone chaperone participate for structural alteration and remodeling. As well, the exchange of histone variants and fluidization of histones are recently reported. Known chemical modification involves phosphorylation, acetylation and ubiquitination of H2AX (a variant of H2A), and acetylation and methylation of H3. Each complex of TIP60, NuA4 and INO80 is known to be included in the regulation of chromatin with damaged/repaired DNA for remodeling, but little is known about recruitment of the factors concerned at the damage site. Regulatory mechanisms in above chromatin dynamics with consideration of quality and timing of radiation should be further elucidated for understanding the precise response to DNA damage. (K.T.)

  20. Higher-Order Hamiltonian Model for Unidirectional Water Waves

    Science.gov (United States)

    Bona, J. L.; Carvajal, X.; Panthee, M.; Scialom, M.

    2018-04-01

    Formally second-order correct, mathematical descriptions of long-crested water waves propagating mainly in one direction are derived. These equations are analogous to the first-order approximations of KdV- or BBM-type. The advantage of these more complex equations is that their solutions corresponding to physically relevant initial perturbations of the rest state may be accurate on a much longer timescale. The initial value problem for the class of equations that emerges from our derivation is then considered. A local well-posedness theory is straightforwardly established by a contraction mapping argument. A subclass of these equations possess a special Hamiltonian structure that implies the local theory can be continued indefinitely.

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

    Science.gov (United States)

    Housman, Jeffrey A.; Kiris, Cetin

    2016-01-01

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

  2. Wigner higher-order spectra: definition, properties, computation and application to transient signal analysis

    OpenAIRE

    Rodríguez Fonollosa, Javier; Nikias, Chrysostomos L.

    1993-01-01

    The Wigner higher order moment spectra (WHOS) are defined as extensions of the Wigner-Ville distribution (WD) to higher order moment spectra domains. A general class of time-frequency higher order moment spectra is also defined in terms of arbitrary higher order moments of the signal as generalizations of the Cohen’s general class of time-frequency representations. The properties of the general class of time-frequency higher order moment spectra can be related to the properties...

  3. Transverse vibrations of shear-deformable beams using a general higher order theory

    Science.gov (United States)

    Kosmatka, J. B.

    1993-01-01

    A general higher order theory is developed to study the static and vibrational behavior of beam structures having an arbitrary cross section that utilizes both out-of-plane shear-dependent warping and in-plane (anticlastic) deformations. The equations of motion are derived via Hamilton's principle, where the full 3D constitutive relations are used. A simplified version of the general higher-order theory is also presented for beams having an arbitrary cross section that includes out-of-plane shear deformation but assumes that stresses within the cross section and in-plane deformations are negligible. This simplified model, which is accurate for long to moderately short wavelengths, offers substantial improvements over existing higher order theories that are limited to beams with thin rectangular cross sections. The current approach will be very useful in the study of thin-wall closed-cell beams such as airfoil-type sections where the magnitude of shear-related cross-sectional warping is significant.

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

    Energy Technology Data Exchange (ETDEWEB)

    Peschke, C.

    2006-03-15

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

  5. Alpha radiation-induced alterations of the proliferation kinetics, chromatin structure and gene expression in mammalian cells

    International Nuclear Information System (INIS)

    Hieber, L.

    1983-01-01

    Exponentially growing mammalian cells were exposed to 3.4 MeV alpha particles. The chromatin of cells arrested in G2 by alpha irradiation was severely damaged, though all cells were still capable to condensate their chromatin after fusion with mitotic cells. In addition to the common types of aberrations (breaks, gaps, dicentrics and exchanges) cells were found possessing one or more chromosomes with long stretches of undercondensed chromatin. Repair of these lesions was indicated by site specific unscheduled DNA synthesis and by the observation that condensation of these regions improved during G2 arrest. Furthermore, during G2 arrest the synthesis of two cellular proteins was stimulated. This was studied by two-dimensional gel electrophoresis of 35 S-methionine labeled cellular proteins. All these findings provided evidence that radiation-induced G2 arrest is caused by chromatin damage, which prevents regular chromosome condensation for mitosis. (orig./MG) [de

  6. Structural changes in single chromatin fibers induced by tension and torsion

    NARCIS (Netherlands)

    Meng, He

    2014-01-01

    Since the discovery of the right-handed helical structure of DNA, 61 years have passed. The DNA molecule, which encodes genetic information, is also found twisted into coils. This extra twist of the helical structure, called supercoiling, plays important roles in both DNA compaction and gene

  7. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain.

    Directory of Open Access Journals (Sweden)

    Nicole C Riddle

    2012-09-01

    Full Text Available Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in euchromatin or pericentric heterochromatin: while there is a depletion of silencing marks at the transcription start sites (TSSs, HP1a and H3K9me3, but not H3K9me2, are enriched strongly over gene bodies. Intriguingly, genes on chromosome 4 are less frequently associated with paused polymerase. However, when the chromatin is altered by depleting HP1a or POF, the RNA pol II enrichment patterns of many chromosome 4 genes shift, showing a significant decrease over gene bodies but not at TSSs, accompanied by lower expression of those genes. Chromosome 4 genes have a low incidence of TRL/GAGA factor binding sites and a low T(m downstream of the TSS, characteristics that could contribute to a low incidence of RNA polymerase pausing. Our data also indicate that EGG and POF jointly regulate H3K9 methylation and promote HP1a binding over gene bodies, while HP1a targeting and H3K9 methylation are maintained at the repeats by an independent mechanism. The HP1a-enriched, POF-associated chromatin structure over the gene bodies may represent one type of adaptation for genes embedded in repetitive DNA.

  8. Electrodynamic characterisitcs measurements of higher order modes in S-band cavity

    Science.gov (United States)

    Donetsky, R.; Lalayan, M.; Sobenin, N. P.; Orlov, A.; Bulygin, A.

    2017-12-01

    The 800 MHz superconducting cavities with grooved beam pipes were suggested as one of the harmonic cavities design options for High Luminosity LHC project. Cavity simulations were carried out and scaled aluminium prototype having operational mode frequency of 2400 MHz was manufactured for testing the results of simulations. The experimental measurements of transverse shunt impedance with error estimation for higher order modes TM 110 and TE 111 for S-band elliptical cavity were done. The experiments using dielectric and metallic spherical beads and with ring probe were carried out. The Q-factor measurements for two-cell structure and array of two cells were carried out.

  9. Exploratory Movement Generates Higher-Order Information That Is Sufficient for Accurate Perception of Scaled Egocentric Distance

    Science.gov (United States)

    Mantel, Bruno; Stoffregen, Thomas A.; Campbell, Alain; Bardy, Benoît G.

    2015-01-01

    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. PMID:25856410

  10. The 3D chromatin structure of the mouse β-haemoglobin gene cluster

    NARCIS (Netherlands)

    M.P.C. van de Corput (Mariëtte); T.A. Knoch (Tobias); E. de Boer (Ernie); W.A. van Cappellen (Gert); M. Lesnussa (Michael); H.J.F.M.M. Eussen (Bert)

    2010-01-01

    textabstractHere we show a 3D DNA-FISH method to visualizes the 3D structure of the β-globin locus. Geometric size and shape measurements of the 3D rendered signals (128Kb) show that the volume of the β-globin locus decreases almost two fold upon gene activation. A decrease in length and a

  11. Important hydrodynamic and spectroscopic techniques in the field of chromatin structure

    Energy Technology Data Exchange (ETDEWEB)

    Olins, D. E.

    1978-01-01

    Combining hydrodynamic and spectroscopic techniques in the study of conformational states of ..nu../sub 1/ induced by a variety of perturbants has led us to a general coneption: the two structural domains of ..nu../sub 1/ (i.e., the DNA-rich outer shell and the ..cap alpha..-helix-rich apolar histone core) exhibit differential responsiveness. In general, the ..cap alpha..-helical regions are more resistant, than DNA conformation or ..nu../sub 1/ size and shape, to the perturbing effects of urea, decreased ionic strength and pH, trypsin treatment, or a variety of water-miscible organic solvents. There are a number of reasonable conceptual models to explain this differential responsiveness of the structural domains of ..nu../sub 1/.

  12. 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

    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...

  13. Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

    Czech Academy of Sciences Publication Activity Database

    Fišerová, Jindřiška; Efenberková, Michaela; Sieger, T.; Maninová, Miloslava; Uhlířová, Jana; Hozák, Pavel

    2017-01-01

    Roč. 130, č. 12 (2017), s. 2066-2077 ISSN 0021-9533 R&D Projects: GA ČR GJ15-08835Y; GA MŠk(CZ) LM2015062 Institutional support: RVO:68378050 Keywords : Structured illumination * Image analysis * Chromation * Nucleus * Histone modification * Nuclear pore complexes Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Cell biology Impact factor: 4.431, year: 2016

  14. Not just gene expression: 3D implications of chromatin modifications during sexual plant reproduction.

    Science.gov (United States)

    Dukowic-Schulze, Stefanie; Liu, Chang; Chen, Changbin

    2018-01-01

    DNA methylation and histone modifications are epigenetic changes on a DNA molecule that alter the three-dimensional (3D) structure locally as well as globally, impacting chromatin looping and packaging on a larger scale. Epigenetic marks thus inform higher-order chromosome organization and placement in the nucleus. Conventional epigenetic marks are joined by chromatin modifiers like cohesins, condensins and membrane-anchoring complexes to support particularly 3D chromosome organization. The most popular consequences of epigenetic modifications are gene expression changes, but chromatin modifications have implications beyond this, particularly in actively dividing cells and during sexual reproduction. In this opinion paper, we will focus on epigenetic mechanisms and chromatin modifications during meiosis as part of plant sexual reproduction where 3D management of chromosomes and re-organization of chromatin are defining features and prime tasks in reproductive cells, not limited to modulating gene expression. Meiotic chromosome organization, pairing and synapsis of homologous chromosomes as well as distribution of meiotic double-strand breaks and resulting crossovers are presumably highly influenced by epigenetic mechanisms. Special mobile small RNAs have been described in anthers, where these so-called phasiRNAs seem to direct DNA methylation in meiotic cells. Intriguingly, many of the mentioned developmental processes make use of epigenetic changes and small RNAs in a manner other than gene expression changes. Widening our approaches and opening our mind to thinking three-dimensionally regarding epigenetics in plant development holds high promise for new discoveries and could give us a boost for further knowledge.

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

    NARCIS (Netherlands)

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

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

  16. 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,...

  17. Higher-order-mode (HOM) power in elliptical superconducting cavities for intense pulsed proton accelerators

    CERN Document Server

    Sang Ho Kim; Dong O Jeon; Sundeli, R

    2002-01-01

    In linacs for intense pulsed proton accelerators, the beam has a multiple time-structure, and each beam time-structure generates resonance. When a higher-order mode (HOM) is near these resonance frequencies, the induced voltage could be large and accordingly the resulting HOM power, too. In order to understand the effects of a complex beam time-structure on the mode excitations and the resulting HOM powers in elliptical superconducting cavities, analytic expressions are developed, with which the beam-induced voltage and corresponding power are explored, taking into account the properties of HOM frequency behavior in elliptical superconducting cavities. The results and understandings from this analysis are presented with the beam parameters of the Spallation Neutron Source (SNS) superconducting linac.

  18. Chromatin structure influence of DNA damage measurements by four assays: pulsed- and constant-field gel electrophoresis, DNA precipitation and non-denaturing filter elution

    International Nuclear Information System (INIS)

    Wlodek, D.; Olive, P.L.

    1996-01-01

    The of elution of DNA during non-denaturing filter elution (NFE) often correlates with cell sensitivity to radiation. The elution rate is influenced by two cellular factors: chromatin structure and the number of DNA-strand breaks (DSBs) produced in an intact cell by ionizing radiation. To determine which of the above factors is relevant to cell radiosensitivity, four assays were used to measure induction of DNA damage in three cell lines varying in radiosensitivity (V79, CHO, and L5178Y-R). Each of the assays, neutral filter elution (NFE), DNA precipitation, constant (CFGE) and pulsed field gel electrophoresis (PFGE) have different physical basis for DNA damage measurement and might be differently affected by chromatin structure. Three of the methods used to measure DNA double-strand breaks gave different results: NFE was dependent on cell type and location of DNA relative to the replication fork, gel electrophoresis was independent of cell type but was affected by proximity to the replication fork, and the precipitation assay was independent of both cell type and replication status. Pulsed field gel electrophoresis produced the same results and constant field gel electrophoresis for 3 cell lines examined. Only NFE showed differences in sensitivity which correlated with cell survival following irradiation. The results suggest that three is the same initial amount of DSBs in cells from all three lines and that the sensitivity to radiation is determined by some additional factors, probably chromatin structure. (author). 18 refs, 5 figs

  19. In-service teacher education: asking questions for higher order thinking in visual literacy

    Directory of Open Access Journals (Sweden)

    Visvaganthie Moodley

    2013-01-01

    Full Text Available The kinds of questions teachers ask may thwart or promote learner high-order thinking; teachers themselves must have expertise in questioning skills to promote higher order cognition among learners. Drawing on experiential knowledge of assessment, and as an English-teaching professional development programme (PDP facilitator, I demonstrate that within the framework of a carefully structured subject-specific PDP, teachers can be taught how to enhance thinking skills in the English visual literacy (VL learning classroom. Guided by an earlier taxonomy of cognition, and using qualitative methodology, the paper analyses data obtained from: (i observation notes and examination equivalents of 40 teachers from various public schools in Gauteng who were engaged in the Advanced Certificate in Education (ACE, English specialization programme; and (ii a case study of three teachers by means of semi-structured interviews, and a study of their lesson plans and worksheets.The paper examines, specifically, teachers' choice of texts and questions asked, for English second-language learners for the teaching of VL. It concludes by suggesting that if teachers themselves are first engaged in the cognitive processes they wish learners to acquire, they are better positioned to promote higher order among their learners.

  20. Molecular basis for the redox control of nuclear transport of the structural chromatin protein Hmgb1

    International Nuclear Information System (INIS)

    Hoppe, George; Talcott, Katherine E.; Bhattacharya, Sanjoy K.; Crabb, John W.; Sears, Jonathan E.

    2006-01-01

    Oxidative stress can induce a covalent disulfide bond between protein and peptide thiols that is reversible through enzymatic catalysis. This process provides a post-translational mechanism for control of protein function and may also protect thiol groups from irreversible oxidation. High mobility group protein B1 (Hmgb1), a DNA-binding structural chromosomal protein and transcriptional co-activator was identified as a substrate of glutaredoxin. Hmgb1 contains 3 cysteines, Cys23, 45, and 106. In mild oxidative conditions, Cys23 and Cys45 readily form an intramolecular disulfide bridge, whereas Cys106 remains in the reduced form. The disulfide bond between Cys23 and Cys45 is a target of glutathione-dependent reduction by glutaredoxin. Endogenous Hmgb1 as well as GFP-tagged wild-type Hmgb1 co-localize in the nucleus of CHO cells. While replacement of Hmgb1 Cys23 and/or 45 with serines did not affect the nuclear distribution of the mutant proteins, Cys106-to-Ser and triple cysteine mutations impaired nuclear localization of Hmgb1. Our cysteine targeted mutational analysis suggests that Cys23 and 45 induce conformational changes in response to oxidative stress, whereas Cys106 appears to be critical for the nucleocytoplasmic shuttling of Hmgb1

  1. A hierarchical generalization of the acoustic reciprocity theorem involving higher-order derivatives and interaction quantities.

    Science.gov (United States)

    Lin, Ju; Li, Jie; Li, Xiaolei; Wang, Ning

    2016-10-01

    An acoustic reciprocity theorem is generalized, for a smoothly varying perturbed medium, to a hierarchy of reciprocity theorems including higher-order derivatives of acoustic fields. The standard reciprocity theorem is the first member of the hierarchy. It is shown that the conservation of higher-order interaction quantities is related closely to higher-order derivative distributions of perturbed media. Then integral reciprocity theorems are obtained by applying Gauss's divergence theorem, which give explicit integral representations connecting higher-order interactions and higher-order derivative distributions of perturbed media. Some possible applications to an inverse problem are also discussed.

  2. Method of moments solution of volume integral equations using higher-order hierarchical Legendre basis functions

    DEFF Research Database (Denmark)

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

    2004-01-01

    An efficient higher-order method of moments (MoM) solution of volume integral equations is presented. The higher-order MoM solution is based on higher-order hierarchical Legendre basis functions and higher-order geometry modeling. An unstructured mesh composed of 8-node trilinear and/or curved 27...... of magnitude in comparison to existing higher-order hierarchical basis functions. Consequently, an iterative solver can be applied even for high expansion orders. Numerical results demonstrate excellent agreement with the analytical Mie series solution for a dielectric sphere as well as with results obtained...

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

    Science.gov (United States)

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

    2013-01-01

    This study examines the relations of higher order (i.e., abstract) thinking (HOT) skills to specific domains of social competence in Black boys (n = 108) attending publicly sponsored prekindergarten (pre-K) programs. Data for the study were collected as part of the National Center for Early Development and Learning (NCEDL) Multi-State Study, a national, longitudinal study examining the quality and outcomes in a representative sample of publicly sponsored pre-K programs in six states (N = 240). Pre-K and kindergarten teachers rated randomly selected children on measures of abstract thinking, self-regulation, and social functioning at the beginning and end of each school year. Applying structural equation modeling, compared with earlier time points, HOT measured in the fall of kindergarten significantly predicted each of the domains of social competence in the spring of kindergarten, with the exception of peer social skills, while controlling for general cognitive ability. Results suggest that early intervention to improve HOT may be an effective and more focused approach to address concerns about Black boys' early social competencies in specific domains and potentially reduce the risk of later social difficulties. © 2013 American Orthopsychiatric Association.

  4. Substance and Artifact in the Higher-Order Factors of the Big Five

    Science.gov (United States)

    McCrae, Robert R.; Jang, Kerry L.; Ando, Juko; Ono, Yutaka; Yamagata, Shinji; Riemann, Rainer; Angleitner, Alois; Spinath, Frank M.

    2018-01-01

    J. M. Digman (1997) proposed that the Big Five personality traits showed a higher-order structure with 2 factors he labeled α and β. These factors have been alternatively interpreted as heritable components of personality or as artifacts of evaluative bias. Using structural equation modeling, the authors reanalyzed data from a cross-national twin study and from American cross-observer studies and analyzed new multimethod data from a German twin study. In all analyses, artifact models outperformed substance models by root-mean-square error of approximation criteria, but models combining both artifact and substance were slightly better. These findings suggest that the search for the biological basis of personality traits may be more profitably focused on the 5 factors themselves and their specific facets, especially in monomethod studies. PMID:18665712

  5. Two-photon or higher-order absorbing optical materials and methods of use

    Science.gov (United States)

    Marder, Seth (Inventor); Perry, Joseph (Inventor)

    2012-01-01

    Compositions capable of simultaneous two-photon absorption and higher order absorptivities are provided. Compounds having a donor-pi-donor or acceptor-pi-acceptor structure are of particular interest, where the donor is an electron donating group, acceptor is an electron accepting group, and pi is a pi bridge linking the donor and/or acceptor groups. The pi bridge may additionally be substituted with electron donating or withdrawing groups to alter the absorptive wavelength of the structure. Also disclosed are methods of generating an excited state of such compounds through optical stimulation with light using simultaneous absorption of photons of energies individually insufficient to achieve an excited state of the compound, but capable of doing so upon simultaneous absorption of two or more such photons. Applications employing such methods are also provided, including controlled polymerization achieved through focusing of the light source(s) used.

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

    KAUST Repository

    Jaber, Nizar

    2016-01-06

    © 2016 IOP Publishing Ltd. In this study, we demonstrate analytically and experimentally the excitations of the higher order modes of vibrations in electrostatically actuated clamped-clamped microbeam resonators. The concept is based on using partial electrodes with shapes that induce strong excitation of the mode of interest. The devices are fabricated using polyimide as a structural layer coated with nickel from the top and chrome and gold layers from the bottom. Experimentally, frequency sweeps with different electro-dynamical loading conditions are shown to demonstrate the excitation of the higher order modes of vibration. Using a half electrode, the second mode is excited with high amplitude of vibration compared with almost zero response using the full electrode. Also, using a two-third electrode configuration is shown to amplify the third mode resonance amplitude compared with the full electrode under the same electrical loading conditions. An analytical model is developed based on the Euler-Bernollui beam model and the Galerkin method to simulate the device response. Good agreement between the simulation results and the experimental data is reported.

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

    Science.gov (United States)

    Gutmann, Michael U; Laparra, Valero; Hyvärinen, Aapo; Malo, Jesús

    2014-01-01

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

  8. Multipacting and higher order mode analysis of 325 MHz single spoke resonators

    International Nuclear Information System (INIS)

    Pal, Mukesh Kumar; Gaur, Rahul; Kumar, Vinit

    2015-01-01

    Superconducting Single Spoke Resonators (SSRs) will be used to accelerate the H - ions from 3 MeV to 160 MeV in the injector linac for the proposed Indian Spallation Neutron Source (ISNS) at RRCAT. Electromagnetic design studies of 325 MHz SSRs have been performed for βg = 0.11, 0.22 and 0.42. Performance of SSRs are typically limited by multipacting phenomenon and higher order modes. In our design, we have performed detailed studies of electron multipacting phenomenon, which is a resonant process, using a computer code CST-PS. Based on this analysis, refinements in the geometry of the SSRs have been made, in order to reduce the growth rate of multipacting. We have also carried out extensive analysis of Higher Order Mode (HOM) for the SSR structure, using the computer code CST-MWS, where the R/Q parameter has been calculated for monopole, dipole and quadrupole HaMs. Details of these calculations will be presented in this paper. (author)

  9. 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....

  10. Chromatin is wonderful stuff.

    NARCIS (Netherlands)

    van Driel, R.

    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

  11. Studies on sex-organ development. Changes in chromatin structure during spermatogenesis in maturing rooster testis as demonstrated by the initiation pattern of ribonucleic acid synthesis in vitro.

    Science.gov (United States)

    Mezquita, C; Teng, C S

    1978-01-01

    To probe the structural change in the genome of the differentiating germ cell of the maturing rooster testis, the chromatin from nuclei at various stages of differentiation were transcribed with prokaryotic RNA polymerase from Escherichia coli or with eukaryotic RNA polymerase II from wheat germ. The transcription was performed under conditions of blockage of RNA chain reinitiation in vitro with rifampicin or rifampicin AF/013. With the E. coli enzyme, the changes in (1) the titration curve for the enzyme-chromatin interaction, (2) the number of initiation sites, (3) the rate of elongation of RNA chains, and (4) the kinetics of the formation of stable initiation complexes revealed the unmasking of DNA in elongated spermatids and the masking of DNA in spermatozoa. In both cases the stability of the DNA duplex in the initiation region for RNA synthesis greatly increased. In contrast with the E. coli enzyme, the wheat-germ RNA polymerase II was relatively inefficient at transcribing chromatin of elongated spermatids. Such behaviour can be predicted if unmasked double-stranded DNA is present in elongated spermatids. PMID:346018

  12. Chromatin dynamics resolved with force spectroscopy

    NARCIS (Netherlands)

    Chien, Fan-Tso

    2011-01-01

    In eukaryotic cells, genomic DNA is organized in chromatin fibers composed of nucleosomes as structural units. A nucleosome contains 1.7 turns of DNA wrapped around a histone octamer and is connected to the adjacent nucleosomes with linker DNA. The folding of chromatin fibers effectively increases

  13. Transcription Through Chromatin - Dynamic Organization of Genes

    Indian Academy of Sciences (India)

    different proteins involved in the synthesis of mRNA from the. DNA template. ... CBP - CREB Binding Protein. CHRAC. Chromatin .... nucleosomal interactions, and thereby change the chromatin structure, as per the ..... methyltransferases in gene regulation is yet to be elucidated. .... Molecular Biology and. Genetics Unit.

  14. A comparison of different methods to implement higher order derivatives of density functionals

    Energy Technology Data Exchange (ETDEWEB)

    van Dam, Hubertus J.J. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-05-18

    Density functional theory is the dominant approach in electronic structure methods today. To calculate properties higher order derivatives of the density functionals are required. These derivatives might be implemented manually,by automatic differentiation, or by symbolic algebra programs. Different authors have cited different reasons for using the particular method of their choice. This paper presents work where all three approaches were used and the strengths and weaknesses of each approach are considered. It is found that all three methods produce code that is suffficiently performanted for practical applications, despite the fact that our symbolic algebra generated code and our automatic differentiation code still have scope for significant optimization. The automatic differentiation approach is the best option for producing readable and maintainable code.

  15. Phase-plane analysis to an “anisotropic” higher-order traffic flow model

    Science.gov (United States)

    Wu, Chun-Xiu

    2018-04-01

    The qualitative theory of differential equations is applied to investigate the traveling wave solution to an “anisotropic” higher-order viscous traffic flow model under the Lagrange coordinate system. The types and stabilities of the equilibrium points are discussed in the phase plane. Through the numerical simulation, the overall distribution structures of trajectories are drawn to analyze the relation between the phase diagram and the selected conservative solution variables, and the influences of the parameters on the system are studied. The limit-circle, limit circle-spiral point, saddle-spiral point and saddle-nodal point solutions are obtained. These steady-state solutions provide good explanation for the phenomena of the oscillatory and homogeneous congestions in real-world traffic.

  16. Relativistic stars in degenerate higher-order scalar-tensor theories after GW170817

    Science.gov (United States)

    Kobayashi, Tsutomu; Hiramatsu, Takashi

    2018-05-01

    We study relativistic stars in degenerate higher-order scalar-tensor theories that evade the constraint on the speed of gravitational waves imposed by GW170817. It is shown that the exterior metric is given by the usual Schwarzschild solution if the lower order Horndeski terms are ignored in the Lagrangian and a shift symmetry is assumed. However, this class of theories exhibits partial breaking of Vainshtein screening in the stellar interior and thus modifies the structure of a star. Employing a simple concrete model, we show that for high-density stars the mass-radius relation is altered significantly even if the parameters are chosen so that only a tiny correction is expected in the Newtonian regime. We also find that, depending on the parameters, there is a maximum central density above which solutions cease to exist.

  17. Higher order Godunov methods for general systems of hyperbolic conservation laws

    International Nuclear Information System (INIS)

    Bell, J.B.; Colella, P.; Trangenstein, J.A.

    1989-01-01

    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

  18. Suppression of Higher Order Modes in an Array of Cavities Using Waveguides

    Science.gov (United States)

    Shashkov, Ya. V.; Sobenin, N. P.; Bazyl, D. S.; Kaminskiy, V. I.; Mitrofanov, A. A.; Zobov, M. M.

    An application of additional harmonic cavities operating at multiplies of the main RF system frequency of 400 MHz is currently under discussionin the framework of the High Luminosity LHC upgrade program [1,2]. A structure consisting of two 800 MHz single cell superconducting cavities with grooved beam pipes coupled by drift tubes has been suggested for implementation. However, it is desirable to increase the number of single cells installed in one cryomodule in order to decrease the number of transitions between "warm" and "cold" parts of the collider vacuum chamber. Unfortunately, it can lead to the appearance of higher order modes (HOM) trapped between the cavities. In order to solve this problem the methods of HOM damping with rectangular waveguides connected to the drift tubes were investigated and compared. We describe the results obtained for arrays of 2, 4 and 8 cavitiesin this paper.

  19. Higher-order threshold resummation for semi-inclusive e+e- annihilation

    International Nuclear Information System (INIS)

    Moch, S.; Vogt, A.

    2009-08-01

    The complete soft-enhanced and virtual-gluon contributions are derived for the quark coefficient functions in semi-inclusive e + e - annihilation to the third order in massless perturbative QCD. These terms enable us to extend the soft-gluon resummation for the fragmentation functions by two orders to the next-to-next-to-next-to-leading logarithmic (N 3 LL) accuracy. The resummation exponent is found to be the same as for the structure functions in inclusive deep-inelastic scattering. This finding, together with known results on the higher-order quark form factor, facilitates the determination of all soft and virtual contributions of the fourth-order difference of the coefficient functions for these two processes. Unlike the previous (N 2 LL) order in the exponentiation, the numerical effect of the N 3 LL contributions turns out to be negligible at LEP energies. (orig.)

  20. Recurrence approach and higher order polynomial algebras for superintegrable monopole systems

    Science.gov (United States)

    Hoque, Md Fazlul; Marquette, Ian; Zhang, Yao-Zhong

    2018-05-01

    We revisit the MIC-harmonic oscillator in flat space with monopole interaction and derive the polynomial algebra satisfied by the integrals of motion and its energy spectrum using the ad hoc recurrence approach. We introduce a superintegrable monopole system in a generalized Taub-Newman-Unti-Tamburino (NUT) space. The Schrödinger equation of this model is solved in spherical coordinates in the framework of Stäckel transformation. It is shown that wave functions of the quantum system can be expressed in terms of the product of Laguerre and Jacobi polynomials. We construct ladder and shift operators based on the corresponding wave functions and obtain the recurrence formulas. By applying these recurrence relations, we construct higher order algebraically independent integrals of motion. We show that the integrals form a polynomial algebra. We construct the structure functions of the polynomial algebra and obtain the degenerate energy spectra of the model.

  1. Mathematics Teachers’ Interpretation of Higher-Order Thinking in Bloom’s Taxonomy

    OpenAIRE

    Tony Thompson

    2008-01-01

    This study investigated mathematics teachers’ interpretation of higher-order thinking in Bloom’s Taxonomy. Thirty-two high school mathematics teachers from the southeast U.S. were asked to (a) define lower- and higher-order thinking, (b) identify which thinking skills in Bloom’s Taxonomy represented lower- and higher-order thinking, and (c) create an Algebra I final exam item representative of each thinking skill. Results indicate that mathematics teachers have difficulty interpreting the thi...

  2. Generation of infrared supercontinuum radiation: spatial mode dispersion and higher-order mode propagation in ZBLAN step-index fibers

    DEFF Research Database (Denmark)

    Ramsay, Jacob Søndergaard; Dupont, Sune Vestergaard Lund; Johansen, Mikkel Willum

    2013-01-01

    Using femtosecond upconversion we investigate the time and wavelength structure of infrared supercontinuum generation. It is shown that radiation is scattered into higher order spatial modes (HOMs) when generating a supercontinuum using fibers that are not single-moded, such as a step-index ZBLAN...... not include scattering into HOMs, and including this provides an extra degree of freedom for tailoring supercontinuum sources....

  3. Environmental toxicants cause sperm DNA fragmentation as detected by the Sperm Chromatin Structure Assay (SCSA[reg])

    International Nuclear Information System (INIS)

    Evenson, Donald P.; Wixon, Regina

    2005-01-01

    Studies over the past two decades have clearly shown that reproductive toxicants cause sperm DNA fragmentation. This DNA fragmentation can usually be detected prior to observing alterations of metaphase chromosomes in embryos. Thus, Sperm Chromatin Structure Assay (SCSA)-detected DNA damage is viewed as the molecular precursor to later gross chromosome damage observed under the light microscope. SCSA measurements of animal or human sperm consist of first obtaining a fresh or flash frozen neat semen sample in LN2 or dry ice. Samples are then sent to a SCSA diagnostic laboratory where the samples are thawed, diluted to ∼1-2 x 106 sperm/ml, treated for 30 s with a pH 1.2 detergent buffer and then stained with acridine orange (AO). The low pH partially denatures DNA at the sites of DNA strand breaks and the AO-ssDNA fluoresces red while the AO-dsDNA fluoresces green. Flow cytometry measurements of 5000 sperm/sample provide statistically robust data on the ratio of red to green sperm, the extent of the DNA fragmentation and the standard deviations of measures. Numerous experiments on rodents treated with reproductive toxicants clearly showed that SCSA measures are highly dose responsive and have a very low CV. Different agents that act on germ cells at various stages of development usually showed sperm DNA fragmentation when that germ cell fraction arrived in the epididymis or ejaculate. Some of these treated samples were capable of successful in vitro fertilization but with frequent embryo failure. A 2-year longitudinal study of men living a valley town with a reported abnormal level of infertility and spontaneous miscarriages and also a seasonal atmospheric smog pollution, showed, for the first time, that SCSA measurements of human sperm DNA fragmentation were detectable and correlated with dosage of air pollution while the classical semen measures were not correlated. Also, young men spraying pesticides without protective gear are at an increased risk for elevated

  4. Map of open and closed chromatin domains in Drosophila genome.

    Science.gov (United States)

    Milon, Beatrice; Sun, Yezhou; Chang, Weizhong; Creasy, Todd; Mahurkar, Anup; Shetty, Amol; Nurminsky, Dmitry; Nurminskaya, Maria

    2014-11-18

    Chromatin compactness has been considered a major determinant of gene activity and has been associated with specific chromatin modifications in studies on a few individual genetic loci. At the same time, genome-wide patterns of open and closed chromatin have been understudied, and are at present largely predicted from chromatin modification and gene expression data. However the universal applicability of such predictions is not self-evident, and requires experimental verification. We developed and implemented a high-throughput analysis for general chromatin sensitivity to DNase I which provides a comprehensive epigenomic assessment in a single assay. Contiguous domains of open and closed chromatin were identified by computational analysis of the data, and correlated to other genome annotations including predicted chromatin "states", individual chromatin modifications, nuclear lamina interactions, and gene expression. While showing that the widely trusted predictions of chromatin structure are correct in the majority of cases, we detected diverse "exceptions" from the conventional rules. We found a profound paucity of chromatin modifications in a major fraction of closed chromatin, and identified a number of loci where chromatin configuration is opposite to that expected from modification and gene expression patterns. Further, we observed that chromatin of large introns tends to be closed even when the genes are expressed, and that a significant proportion of active genes including their promoters are located in closed chromatin. These findings reveal limitations of the existing predictive models, indicate novel mechanisms of epigenetic regulation, and provide important insights into genome organization and function.

  5. PRE-SERVICE MATHEMATICS TEACHERS’ CONCEPTION OF HIGHER-ORDER THINKING LEVEL IN BLOOM'S TAXONOMY

    OpenAIRE

    Damianus D Samo

    2017-01-01

    The purpose of this study is to explore pre-service mathematics teachers' conception of higher-order thinking in Bloom's Taxonomy, to explore pre-service mathematics teachers' ability in categorizing six cognitive levels of Bloom's Taxonomy as lower-order thinking and higher-order thinking, and pre-service mathematics teachers' ability in identifying some questionable items as lower-order and higher-order thinking. The higher-order thinking is the type of non-algorithm thinking which include ...

  6. Analysis and Improvement of the Generic Higher-Order Masking Scheme of FSE 2012

    OpenAIRE

    Roy, Arnab; Venkatesh, Srinivas Vivek

    2013-01-01

    Masking is a well-known technique used to prevent block cipher implementations from side-channel attacks. Higher-order side channel attacks (e.g. higher-order DPA attack) on widely used block cipher like AES have motivated the design of efficient higher-order masking schemes. Indeed, it is known that as the masking order increases, the difficulty of side-channel attack increases exponentially. However, the main problem in higher-order masking is to design an efficient and secure technique for...

  7. [The effect of structure of benzimidazoles on the character of forming intramolecular cross-links in DNA and chromatin].

    Science.gov (United States)

    Mil', E M; Zhil'tsova, V M; Biniukov, V I; Zhizhina, G P; Stoliarova, L G; Kuznetsov, Iu P

    1994-01-01

    An investigation of a number of benzimidazole class preparations, being distinguished by a position of aminomethyl substitutes, has been carried out. It has been shown, that the non-substituted preparation BIO-10 does not form UV-cross-links in DNA and chromatine; BIO-40, having one substitute in the position 2, causes the formation of inter-molecular cross-links DNA-DNA. The preparation BIO-50, having 2 aminomethyl groups in the imidazole nucleus positions 2 and 6, forms cross-links DNA-DNA and DNA-protein in chromatine. The generation of radicals by the preparations BIO-10 and BIO-50 has been studied by the EPR-method by use of spin trap. It has been demonstrated, that BIO-10, unlike BIO-50, actively generates superoxide. A supposition has been made, that an UV-formation of superoxide-radical in the presence of BIO-10 might be a reason of DNA-macromolecule destruction.

  8. Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture.

    Science.gov (United States)

    Darrow, Emily M; Huntley, Miriam H; Dudchenko, Olga; Stamenova, Elena K; Durand, Neva C; Sun, Zhuo; Huang, Su-Chen; Sanborn, Adrian L; Machol, Ido; Shamim, Muhammad; Seberg, Andrew P; Lander, Eric S; Chadwick, Brian P; Aiden, Erez Lieberman

    2016-08-02

    During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the "Barr body." Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called "superdomains," such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called "superloops." DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4 We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.

  9. Interaction of a common painkiller piroxicam and copper-piroxicam with chromatin causes structural alterations accompanied by modulation at the epigenomic/genomic level.

    Science.gov (United States)

    Goswami, Sathi; Sanyal, Sulagna; Chakraborty, Payal; Das, Chandrima; Sarkar, Munna

    2017-08-01

    NSAIDs are the most common class of painkillers and anti-inflammatory agents. They also show other functions like chemoprevention and chemosuppression for which they act at the protein but not at the genome level since they are mostly anions at physiological pH, which prohibit their approach to the poly-anionic DNA. Complexing the drugs with bioactive metal obliterate their negative charge and allow them to bind to the DNA, thereby, opening the possibility of genome level interaction. To test this hypothesis, we present the interaction of a traditional NSAID, Piroxicam and its copper complex with core histone and chromatin. Spectroscopy, DLS, and SEM studies were applied to see the effect of the interaction on the structure of histone/chromatin. This was coupled with MTT assay, immunoblot analysis, confocal microscopy, micro array analysis and qRT-PCR. The interaction of Piroxicam and its copper complex with histone/chromatin results in structural alterations. Such structural alterations can have different biological manifestations, but to test our hypothesis, we have focused only on the accompanied modulations at the epigenomic/genomic level. The complex, showed alteration of key epigenetic signatures implicated in transcription in the global context, although Piroxicam caused no significant changes. We have correlated such alterations caused by the complex with the changes in global gene expression and validated the candidate gene expression alterations. Our results provide the proof of concept that DNA binding ability of the copper complexes of a traditional NSAID, opens up the possibility of modulations at the epigenomic/genomic level. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Authentic Instruction for 21st Century Learning: Higher Order Thinking in an Inclusive School

    Science.gov (United States)

    Preus, Betty

    2012-01-01

    The author studied a public junior high school identified as successfully implementing authentic instruction. Such instruction emphasizes higher order thinking, deep knowledge, substantive conversation, and value beyond school. To determine in what ways higher order thinking was fostered both for students with and without disabilities, the author…

  11. An Investigation of Higher-Order Thinking Skills in Smaller Learning Community Social Studies Classrooms

    Science.gov (United States)

    Fischer, Christopher; Bol, Linda; Pribesh, Shana

    2011-01-01

    This study investigated the extent to which higher-order thinking skills are promoted in social studies classes in high schools that are implementing smaller learning communities (SLCs). Data collection in this mixed-methods study included classroom observations and in-depth interviews. Findings indicated that higher-order thinking was rarely…

  12. From "Hello" to Higher-Order Thinking: The Effect of Coaching and Feedback on Online Chats

    Science.gov (United States)

    Stein, David S.; Wanstreet, Constance E.; Slagle, Paula; Trinko, Lynn A.; Lutz, Michelle

    2013-01-01

    This exploratory study examined the effect of a coaching and feedback intervention in teaching presence and social presence on higher-order thinking in an online community of inquiry. Coaching occurred before each chat, and feedback was provided immediately afterwards. The findings suggest that over time, the frequency of higher-order thinking…

  13. Comparing higher order models for the EORTC QLQ-C30

    DEFF Research Database (Denmark)

    Gundy, Chad M; Fayers, Peter M; Grønvold, Mogens

    2012-01-01

    To investigate the statistical fit of alternative higher order models for summarizing the health-related quality of life profile generated by the EORTC QLQ-C30 questionnaire.......To investigate the statistical fit of alternative higher order models for summarizing the health-related quality of life profile generated by the EORTC QLQ-C30 questionnaire....

  14. Teaching Higher Order Thinking in the Introductory MIS Course: A Model-Directed Approach

    Science.gov (United States)

    Wang, Shouhong; Wang, Hai

    2011-01-01

    One vision of education evolution is to change the modes of thinking of students. Critical thinking, design thinking, and system thinking are higher order thinking paradigms that are specifically pertinent to business education. A model-directed approach to teaching and learning higher order thinking is proposed. An example of application of the…

  15. Exact Solutions to Nonlinear Schroedinger Equation and Higher-Order Nonlinear Schroedinger Equation

    International Nuclear Information System (INIS)

    Ren Ji; Ruan Hangyu

    2008-01-01

    We study solutions of the nonlinear Schroedinger equation (NLSE) and higher-order nonlinear Schroedinger equation (HONLSE) with variable coefficients. By considering all the higher-order effect of HONLSE as a new dependent variable, the NLSE and HONLSE can be changed into one equation. Using the generalized Lie group reduction method (GLGRM), the abundant solutions of NLSE and HONLSE are obtained

  16. Higher Order Thinking Skills among Secondary School Students in Science Learning

    Science.gov (United States)

    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…

  17. The Relationship between Higher Order Thinking Skills and Academic Performance of Student in Mathematics Instruction

    Science.gov (United States)

    Tanujaya, Benidiktus; Mumu, Jeinne; Margono, Gaguk

    2017-01-01

    Higher order thinking skills (HOTS) is one of important aspects in education. Students with high level of higher order thinking skills tend to be more successful. However, do this phenomenon also happen in the learning of Mathematics? To answer this question, this research aims to study the relationship between HOTS and students' academic…

  18. 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...

  19. Higher-order blackhole solutions in N=2 supergravity and Calabi-Yau string backgrounds

    NARCIS (Netherlands)

    Behrndt, K.; Cardoso, G.L.; de Wit, B.Q.P.J.; Lüst, D.; Mohaupt, T.; Sabra, W.A.

    1998-01-01

    Based on special geometry, we consider corrections to N=2 extremal black-hole solutions and their entropies originating from higher-order derivative terms in N=2 supergravity. These corrections are described by a holomorphic function, and the higher-order black-hole solutions can be expressed in

  20. Chromatin organization and cellular sensitivity to ionizing radiation

    International Nuclear Information System (INIS)

    Szumiel, I.; Walicka, M.

    1987-01-01

    The paper briefly describes chromatin organization in mammalian cells and reviews experimental work concerning relations between chromatin structure and accesibility of damaged DNA to repair enzymes. The ''contact effect'', the size of super-coiled DNA domains and ADP-ribosylation of chromatin proteins are discussed in relation to cellular radiosensitivity. 88 refs. (author)

  1. Chromatin Dynamics of the mouse β-globin locus

    NARCIS (Netherlands)

    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

  2. Construction of special eye models for investigation of chromatic and higher-order aberrations of eyes.

    Science.gov (United States)

    Zhai, Yi; Wang, Yan; Wang, Zhaoqi; Liu, Yongji; Zhang, Lin; He, Yuanqing; Chang, Shengjiang

    2014-01-01

    An achromatic element eliminating only longitudinal chromatic aberration (LCA) while maintaining transverse chromatic aberration (TCA) is established for the eye model, which involves the angle formed by the visual and optical axis. To investigate the impacts of higher-order aberrations on vision, the actual data of higher-order aberrations of human eyes with three typical levels are introduced into the eye model along visual axis. Moreover, three kinds of individual eye models are established to investigate the impacts of higher-order aberrations, chromatic aberration (LCA+TCA), LCA and TCA on vision under the photopic condition, respectively. Results show that for most human eyes, the impact of chromatic aberration on vision is much stronger than that of higher-order aberrations, and the impact of LCA in chromatic aberration dominates. The impact of TCA is approximately equal to that of normal level higher-order aberrations and it can be ignored when LCA exists.

  3. Higher-order human telomeric G-quadruplex DNA metalloenzymes enhance enantioselectivity in the Diels-Alder reaction.

    Science.gov (United States)

    Li, Yinghao; Jia, Guoqing; Wang, Changhao; Cheng, Mingpan; Li, Can

    2015-03-02

    Short human telomeric (HT) DNA sequences form single G-quadruplex (G4 ) units and exhibit structure-based stereocontrol for a series of reactions. However, for more biologically relevant higher-order HT G4 -DNAs (beyond a single G4 unit), the catalytic performances are unknown. Here, we found that higher-order HT G4 -DNA copper metalloenzymes (two or three G4 units) afford remarkably higher enantioselectivity (>90 % ee) and a five- to sixfold rate increase, compared to a single G4 unit, for the Diels-Alder reaction. Electron paramagnetic resonance (EPR) and enzymatic kinetic studies revealed that the distinct catalytic function between single and higher-order G4 -DNA copper metalloenzymes can be attributed to different Cu(II) coordination environments and substrate specificity. Our finding suggests that, like protein enzymes and ribozymes, higher-order structural organization is crucial for G4 -DNA-based catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

    Directory of Open Access Journals (Sweden)

    Shieh Grace S

    2011-12-01

    Full Text Available 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.

  5. H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast

    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.

  6. Effect of hyperthermia on replicating chromatin

    International Nuclear Information System (INIS)

    Warters, R.L.; Roti Roti, J.L.

    1981-01-01

    The extent of heat-induced structural alterations in chromatin containing nascent (pulse-labeled) DNA was assayed using the enzyme micrococcal nuclease. The basic nucleosome structure in nascent and mature chromatin of S-phase cells appeared unaltered for up to 16 hr after exposure to hyperthermic temperatures as high as 48 0 C for 15 min. However, the rate of nuclease digestion of DNA in both nascent and mature chromatin is inhibited following exposure to hyperthermic temperatures. In unheated cells, pulse-labeled nascent DNA matured into mature chromatin structure with a half-time of 2.5 min. The half-time for the maturation of pulse-labeled DNA from nascent into mature chromatin increased in a linear manner as a function of increasing temperature of exposure with constant heating time at temperatures above 43 0 C. Both the reduced nuclease digestibility of nascent DNA and the increased time for chromatin structural changes could be due to the increased protein mass of chromatin following hyperthermia

  7. Chromatin Remodelers: From Function to Dysfunction

    Directory of Open Access Journals (Sweden)

    Gernot Längst

    2015-06-01

    Full Text Available Chromatin remodelers are key players in the regulation of chromatin accessibility and nucleosome positioning on the eukaryotic DNA, thereby essential for all DNA dependent biological processes. Thus, it is not surprising that upon of deregulation of those molecular machines healthy cells can turn into cancerous cells. Even though the remodeling enzymes are very abundant and a multitude of different enzymes and chromatin remodeling complexes exist in the cell, the particular remodeling complex with its specific nucleosome positioning features must be at the right place at the right time in order to ensure the proper regulation of the DNA dependent processes. To achieve this, chromatin remodeling complexes harbor protein domains that specifically read chromatin targeting signals, such as histone modifications, DNA sequence/structure, non-coding RNAs, histone variants or DNA bound interacting proteins. Recent studies reveal the interaction between non-coding RNAs and chromatin remodeling complexes showing importance of RNA in remodeling enzyme targeting, scaffolding and regulation. In this review, we summarize current understanding of chromatin remodeling enzyme targeting to chromatin and their role in cancer development.

  8. Chromatin damage induced by fast neutrons or UV laser radiation

    Energy Technology Data Exchange (ETDEWEB)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I

    2002-07-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m{sup -2}. The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  9. Chromatin damage induced by fast neutrons or UV laser radiation

    International Nuclear Information System (INIS)

    Radu, L.; Constantinescu, B.; Gazdaru, D.; Mihailescu, I.

    2002-01-01

    Chromatin samples from livers of Wistar rats were subjected to fast neutron irradiation in doses of 10-100 Gy or to a 248 nm excimer laser radiation, in doses of 0.5-3 MJ.m -2 . The action of the radiation on chromatin was monitored by chromatin intrinsic fluorescence and fluorescence lifetimes (of bound ethidium bromide to chromatin) and by analysing fluorescence resonance energy transfer between dansyl chloride and acridine orange coupled to chromatin. For the mentioned doses of UV excimer laser radiation, the action on chromatin was more intense than in the case of fast neutrons. The same types of damage are produced by the two radiations: acidic and basic destruction of chromatin protein structure, DNA strand breaking and the increase of the distance between DNA and proteins in chromatin. (author)

  10. Higher Order Analysis of Turbulent Changes Found in the ELF Range Electric Field Plasma Before Major Earthquakes

    Science.gov (United States)

    Kosciesza, M.; Blecki, J. S.; Parrot, M.

    2014-12-01

    We report the structure function analysis of changes found in electric field in the ELF range plasma turbulence registered in the ionosphere over epicenter region of major earthquakes with depth less than 40 km that took place during 6.5 years of the scientific mission of the DEMETER satellite. We compare the data for the earthquakes for which we found turbulence with events without any turbulent changes. The structure functions were calculated also for the Polar CUSP region and equatorial spread F region. Basic studies of the turbulent processes were conducted with use of higher order spectra and higher order statistics. The structure function analysis was performed to locate and check if there are intermittent behaviors in the ionospheres plasma over epicenter region of the earthquakes. These registrations are correlated with the plasma parameters measured onboard DEMETER satellite and with geomagnetic indices.

  11. Probing white-matter microstructure with higher-order diffusion tensors and susceptibility tensor MRI

    Science.gov (United States)

    Liu, Chunlei; Murphy, Nicole E.; Li, Wei

    2012-01-01

    Diffusion MRI has become an invaluable tool for studying white matter microstructure and brain connectivity. The emergence of quantitative susceptibility mapping and susceptibility tensor imaging (STI) has provided another unique tool for assessing the structure of white matter. In the highly ordered white matter structure, diffusion MRI measures hindered water mobility induced by various tissue and cell membranes, while susceptibility sensitizes to the molecular composition and axonal arrangement. Integrating these two methods may produce new insights into the complex physiology of white matter. In this study, we investigated the relationship between diffusion and magnetic susceptibility in the white matter. Experiments were conducted on phantoms and human brains in vivo. Diffusion properties were quantified with the diffusion tensor model and also with the higher order tensor model based on the cumulant expansion. Frequency shift and susceptibility tensor were measured with quantitative susceptibility mapping and susceptibility tensor imaging. These diffusion and susceptibility quantities were compared and correlated in regions of single fiber bundles and regions of multiple fiber orientations. Relationships were established with similarities and differences identified. It is believed that diffusion MRI and susceptibility MRI provide complementary information of the microstructure of white matter. Together, they allow a more complete assessment of healthy and diseased brains. PMID:23507987

  12. Higher order visual input to the mushroom bodies in the bee, Bombus impatiens.

    Science.gov (United States)

    Paulk, Angelique C; Gronenberg, Wulfila

    2008-11-01

    To produce appropriate behaviors based on biologically relevant associations, sensory pathways conveying different modalities are integrated by higher-order central brain structures, such as insect mushroom bodies. To address this function of sensory integration, we characterized the structure and response of optic lobe (OL) neurons projecting to the calyces of the mushroom bodies in bees. Bees are well known for their visual learning and memory capabilities and their brains possess major direct visual input from the optic lobes to the mushroom bodies. To functionally characterize these visual inputs to the mushroom bodies, we recorded intracellularly from neurons in bumblebees (Apidae: Bombus impatiens) and a single neuron in a honeybee (Apidae: Apis mellifera) while presenting color and motion stimuli. All of the mushroom body input neurons were color sensitive while a subset was motion sensitive. Additionally, most of the mushroom body input neurons would respond to the first, but not to subsequent, presentations of repeated stimuli. In general, the medulla or lobula neurons projecting to the calyx signaled specific chromatic, temporal, and motion features of the visual world to the mushroom bodies, which included sensory information required for the biologically relevant associations bees form during foraging tasks.

  13. 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...

  14. Lagrangian-Hamiltonian unified formalism for autonomous higher order dynamical systems

    International Nuclear Information System (INIS)

    Prieto-Martinez, Pedro Daniel; Roman-Roy, Narciso

    2011-01-01

    The Lagrangian-Hamiltonian unified formalism of Skinner and 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 is yet to be described. In this work, after reviewing the natural geometrical setting and the Lagrangian and Hamiltonian formalisms for higher order autonomous mechanical systems, we develop a complete generalization of the Lagrangian-Hamiltonian unified formalism for these kinds of systems, and we use it to analyze some physical models from this new point of view. (paper)

  15. Higher order capacity statistics of multi-hop transmission systems over Rayleigh fading channels

    KAUST Repository

    Yilmaz, Ferkan

    2012-03-01

    In this paper, we present an exact analytical expression to evaluate the higher order statistics of the channel capacity for amplify and forward (AF) multihop transmission systems operating over Rayleigh fading channels. Furthermore, we present simple and efficient closed-form expression to the higher order moments of the channel capacity of dual hop transmission system with Rayleigh fading channels. In order to analyze the behavior of the higher order capacity statistics and investigate the usefulness of the mathematical analysis, some selected numerical and simulation results are presented. Our results are found to be in perfect agreement. © 2012 IEEE.

  16. 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....... The third chapter of the thesis is a case study of the C# joins library. What makes this library interesting as a case study is that it combines a lot of advanced features (higher-order code with effects, concurrency, recursion through the store, shared mutable state, and fine-grained synchronization...

  17. Analysis of Scattering by Inhomogeneous Dielectric Objects Using Higher-Order Hierarchical MoM

    DEFF Research Database (Denmark)

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

    2003-01-01

    An efficient technique for the analysis of electromagnetic scattering by arbitrary shaped inhomogeneous dielectric objects is presented. The technique is based on a higher-order method of moments (MoM) solution of the volume integral equation. This higher-order MoM solution comprises recently...... that the condition number of the resulting MoM matrix is reduced by several orders of magnitude in comparison to existing higher-order hierarchical basis functions and, consequently, an iterative solver can be applied even for high expansion orders. Numerical results demonstrate excellent agreement...

  18. Generating higher-order Lie algebras by expanding Maurer-Cartan forms

    International Nuclear Information System (INIS)

    Caroca, R.; Merino, N.; Salgado, P.; Perez, A.

    2009-01-01

    By means of a generalization of the Maurer-Cartan expansion method, we construct a procedure to obtain expanded higher-order Lie algebras. The expanded higher-order Maurer-Cartan equations for the case G=V 0 +V 1 are found. A dual formulation for the S-expansion multialgebra procedure is also considered. The expanded higher-order Maurer-Cartan equations are recovered from S-expansion formalism by choosing a special semigroup. This dual method could be useful in finding a generalization to the case of a generalized free differential algebra, which may be relevant for physical applications in, e.g., higher-spin gauge theories.

  19. Modeling 3D PCMI using the Extended Finite Element Method with higher order elements

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, W. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Spencer, Benjamin W. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2017-03-31

    This report documents the recent development to enable XFEM to work with higher order elements. It also demonstrates the application of higher order (quadratic) elements to both 2D and 3D models of PCMI problems, where discrete fractures in the fuel are represented using XFEM. The modeling results demonstrate the ability of the higher order XFEM to accurately capture the effects of a crack on the response in the vicinity of the intersecting surfaces of cracked fuel and cladding, as well as represent smooth responses in the regions away from the crack.

  20. Higher-Order Blind Signal Feature Separation: An Enabling Technology for Battlefield Awareness

    National Research Council Canada - National Science Library

    Su, Wei; Kosinski, John A

    2006-01-01

    Higher-order transform blind signal feature classification is discussed for separating bar-shaped, circular, squared, circular-squared, and offset-diamonded constellation patterns of digital linear signals...

  1. Higher-Order Wavefront Aberrations for Populations of Young Emmetropes and Myopes

    Directory of Open Access Journals (Sweden)

    Jinhua Bao

    2009-01-01

    Conclusions: Human eyes have systematical higher order aberrations in population, and factors that cause bilateral symmetry of wavefront aberrations between the right and left eyes made important contribution to the systematical aberrations.

  2. A Content Analysis of General Chemistry Laboratory Manuals for Evidence of Higher-Order Cognitive Tasks

    Science.gov (United States)

    Domin, Daniel S.

    1999-01-01

    The science laboratory instructional environment is ideal for fostering the development of problem-solving, manipulative, and higher-order thinking skills: the skills needed by today's learner to compete in an ever increasing technology-based society. This paper reports the results of a content analysis of ten general chemistry laboratory manuals. Three experiments from each manual were examined for evidence of higher-order cognitive activities. Analysis was based upon the six major cognitive categories of Bloom's Taxonomy of Educational Objectives: knowledge, comprehension, application, analysis, synthesis, and evaluation. The results of this study show that the overwhelming majority of general chemistry laboratory manuals provide tasks that require the use of only the lower-order cognitive skills: knowledge, comprehension, and application. Two of the laboratory manuals were disparate in having activities that utilized higher-order cognition. I describe the instructional strategies used within these manuals to foster higher-order cognitive development.

  3. The Need to Deliver Higher-Order Skills in the Context of Marketing in SMEs

    Science.gov (United States)

    Copley, Paul

    2013-01-01

    It is argued that the delivery of learning and the development of skills and competences are central to SME success; and there appears to be a requirement for higher-order education and training that can deliver a

  4. Covariant quantization of infinite spin particle models, and higher order gauge theories

    International Nuclear Information System (INIS)

    Edgren, Ludde; Marnelius, Robert

    2006-01-01

    Further properties of a recently proposed higher order infinite spin particle model are derived. Infinitely many classically equivalent but different Hamiltonian formulations are shown to exist. This leads to a condition of uniqueness in the quantization process. A consistent covariant quantization is shown to exist. Also a recently proposed supersymmetric version for half-odd integer spins is quantized. A general algorithm to derive gauge invariances of higher order Lagrangians is given and applied to the infinite spin particle model, and to a new higher order model for a spinning particle which is proposed here, as well as to a previously given higher order rigid particle model. The latter two models are also covariantly quantized

  5. Higher-order asymptotic homogenization of periodic materials with low scale separation

    NARCIS (Netherlands)

    Ameen, M.M.; Peerlings, R.H.J.; Geers, M.G.D

    2016-01-01

    In this work, we investigate the limits of classical homogenization theories pertaining to homogenization of periodic linear elastic composite materials at low scale separations and demonstrate the effectiveness of higher-order periodic homogenization in alleviating this limitation. Classical

  6. Higher Order Thinking in the Australian Army Suite of Logistic Officer Courses

    National Research Council Canada - National Science Library

    Bradford, Scott R

    2006-01-01

    .... The current Suite of Logistic Officer Courses (SOLOC) has been recently criticized for failing to meet this requirement, with the general perception that there is a distinct lack of higher-order thinking competencies within this continuum...

  7. Non-Poisson Dichotomous Noise: Higher-Order Correlation Functions and Aging

    National Research Council Canada - National Science Library

    Allegrini, Paolo; Grigolini, Paolo; Palatella, Luigi; West, Bruce J

    2004-01-01

    .... The transition of psi(tau) from the exponential to the nonexponential condition yields the breakdown of the usual factorization condition of higher-order correlation functions, as well as the birth of aging effects...

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

    KAUST Repository

    Jaber, Nizar; Ramini, Abdallah; Carreno, Armando Arpys Arevalo; Younis, Mohammad I.

    2016-01-01

    © 2016 IOP Publishing Ltd. In this study, we demonstrate analytically and experimentally the excitations of the higher order modes of vibrations in electrostatically actuated clamped-clamped microbeam resonators. The concept is based on using

  9. A stable higher order space time Galerkin marching-on-in-time scheme

    KAUST Repository

    Pray, Andrew J.; Shanker, Balasubramaniam; Bagci, Hakan

    2013-01-01

    We present a method for the stable solution of time-domain integral equations. The method uses a technique developed in [1] to accurately evaluate matrix elements. As opposed to existing stabilization schemes, the method presented uses higher order

  10. Connection between weighted LPC and higher-order statistics for AR model estimation

    NARCIS (Netherlands)

    Kamp, Y.; Ma, C.

    1993-01-01

    This paper establishes the relationship between a weighted linear prediction method used for robust analysis of voiced speech and the autoregressive modelling based on higher-order statistics, known as cumulants

  11. Deformation from symmetry for Schrodinger equations of higher order on unbounded domains

    Directory of Open Access Journals (Sweden)

    Addolorata Salvatore

    2003-06-01

    Full Text Available By means of a perturbation method recently introduced by Bolle, we discuss the existence of infinitely many solutions for a class of perturbed symmetric higher order Schrodinger equations with non-homogeneous boundary data on unbounded domains.

  12. Exact solutions for the higher-order nonlinear Schoerdinger equation in nonlinear optical fibres

    International Nuclear Information System (INIS)

    Liu Chunping

    2005-01-01

    First, by using the generally projective Riccati equation method, many kinds of exact solutions for the higher-order nonlinear Schoerdinger equation in nonlinear optical fibres are obtained in a unified way. Then, some relations among these solutions are revealed

  13. The geometry of higher-order Lagrange spaces applications to mechanics and physics

    CERN Document Server

    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

  14. Higher order capacity statistics of multi-hop transmission systems over Rayleigh fading channels

    KAUST Repository

    Yilmaz, Ferkan; Tabassum, Hina; Alouini, Mohamed-Slim

    2012-01-01

    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

  15. Solution of volume-surface integral equations using higher-order hierarchical Legendre basis functions

    DEFF Research Database (Denmark)

    Kim, Oleksiy S.; Meincke, Peter; Breinbjerg, Olav

    2007-01-01

    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...... with the analytical Mie series solution. Scattering by more complex metal-dielectric objects are also considered to compare the presented technique with other numerical methods....

  16. Ultra-compact Higher-Order-Mode Pass Filter in a Silicon Waveguide

    DEFF Research Database (Denmark)

    Guan, Xiaowei; Frandsen, Lars Hagedorn; Ding, Yunhong

    2015-01-01

    An 3.7 μm long higher-order-mode pass filter with an extinction ratio larger than 20 dB is demonstrated in a 1D corrugated silicon multimode waveguide......An 3.7 μm long higher-order-mode pass filter with an extinction ratio larger than 20 dB is demonstrated in a 1D corrugated silicon multimode waveguide...

  17. Higher order mode of a microstripline fed cylindrical dielectric resonator antenna

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, A. V. Praveen, E-mail: praveen.kumar@pilani.bits-pilani.ac.in [Department of Electrical and Electronics Engineering, BITS Pilani, Pilani, Rajasthan-333 031 (India)

    2016-03-09

    A microstrip transmission line can be used to excite the broadside radiating mode of a cylindrical dielectric resonator antenna (CDRA). The same is found to excite considerably well a higher order mode (HOM) as well. However unlike the broadside mode, the higher order mode gives distorted radiation pattern which makes this mode less useful for practical applications. The cause of distortion in the HOM radiation and the dependence of HOM coupling on the microstrip feed line are explored using HFSS simulations.

  18. Consensus Algorithms for Networks of Systems with Second- and Higher-Order Dynamics

    Science.gov (United States)

    Fruhnert, Michael

    This thesis considers homogeneous networks of linear systems. We consider linear feedback controllers and require that the directed graph associated with the network contains a spanning tree and systems are stabilizable. We show that, in continuous-time, consensus with a guaranteed rate of convergence can always be achieved using linear state feedback. For networks of continuous-time second-order systems, we provide a new and simple derivation of the conditions for a second-order polynomials with complex coefficients to be Hurwitz. We apply this result to obtain necessary and sufficient conditions to achieve consensus with networks whose graph Laplacian matrix may have complex eigenvalues. Based on the conditions found, methods to compute feedback gains are proposed. We show that gains can be chosen such that consensus is achieved robustly over a variety of communication structures and system dynamics. We also consider the use of static output feedback. For networks of discrete-time second-order systems, we provide a new and simple derivation of the conditions for a second-order polynomials with complex coefficients to be Schur. We apply this result to obtain necessary and sufficient conditions to achieve consensus with networks whose graph Laplacian matrix may have complex eigenvalues. We show that consensus can always be achieved for marginally stable systems and discretized systems. Simple conditions for consensus achieving controllers are obtained when the Laplacian eigenvalues are all real. For networks of continuous-time time-variant higher-order systems, we show that uniform consensus can always be achieved if systems are quadratically stabilizable. In this case, we provide a simple condition to obtain a linear feedback control. For networks of discrete-time higher-order systems, we show that constant gains can be chosen such that consensus is achieved for a variety of network topologies. First, we develop simple results for networks of time

  19. Defining Higher-Order Turbulent Moment Closures with an Artificial Neural Network and Random Forest

    Science.gov (United States)

    McGibbon, J.; Bretherton, C. S.

    2017-12-01

    Unresolved turbulent advection and clouds must be parameterized in atmospheric models. Modern higher-order closure schemes depend on analytic moment closure assumptions that diagnose higher-order moments in terms of lower-order ones. These are then tested against Large-Eddy Simulation (LES) higher-order moment relations. However, these relations may not be neatly analytic in nature. Rather than rely on an analytic higher-order moment closure, can we use machine learning on LES data itself to define a higher-order moment closure?We assess the ability of a deep artificial neural network (NN) and random forest (RF) to perform this task using a set of observationally-based LES runs from the MAGIC field campaign. By training on a subset of 12 simulations and testing on remaining simulations, we avoid over-fitting the training data.Performance of the NN and RF will be assessed and compared to the Analytic Double Gaussian 1 (ADG1) closure assumed by Cloudy Layers Unified By Binormals (CLUBB), a higher-order turbulence closure currently used in the Community Atmosphere Model (CAM). We will show that the RF outperforms the NN and the ADG1 closure for the MAGIC cases within this diagnostic framework. Progress and challenges in using a diagnostic machine learning closure within a prognostic cloud and turbulence parameterization will also be discussed.

  20. Higher-order neural processing tunes motion neurons to visual ecology in three species of hawkmoths.

    Science.gov (United States)

    Stöckl, A L; O'Carroll, D; Warrant, E J

    2017-06-28

    To sample information optimally, sensory systems must adapt to the ecological demands of each animal species. These adaptations can occur peripherally, in the anatomical structures of sensory organs and their receptors; and centrally, as higher-order neural processing in the brain. While a rich body of investigations has focused on peripheral adaptations, our understanding is sparse when it comes to central mechanisms. We quantified how peripheral adaptations in the eyes, and central adaptations in the wide-field motion vision system, set the trade-off between resolution and sensitivity in three species of hawkmoths active at very different light levels: nocturnal Deilephila elpenor, crepuscular Manduca sexta , and diurnal Macroglossum stellatarum. Using optical measurements and physiological recordings from the photoreceptors and wide-field motion neurons in the lobula complex, we demonstrate that all three species use spatial and temporal summation to improve visual performance in dim light. The diurnal Macroglossum relies least on summation, but can only see at brighter intensities. Manduca, with large sensitive eyes, relies less on neural summation than the smaller eyed Deilephila , but both species attain similar visual performance at nocturnal light levels. Our results reveal how the visual systems of these three hawkmoth species are intimately matched to their visual ecologies. © 2017 The Author(s).

  1. Multi-linear sparse reconstruction for SAR imaging based on higher-order SVD

    Science.gov (United States)

    Gao, Yu-Fei; Gui, Guan; Cong, Xun-Chao; Yang, Yue; Zou, Yan-Bin; Wan, Qun

    2017-12-01

    This paper focuses on the spotlight synthetic aperture radar (SAR) imaging for point scattering targets based on tensor modeling. In a real-world scenario, scatterers usually distribute in the block sparse pattern. Such a distribution feature has been scarcely utilized by the previous studies of SAR imaging. Our work takes advantage of this structure property of the target scene, constructing a multi-linear sparse reconstruction algorithm for SAR imaging. The multi-linear block sparsity is introduced into higher-order singular value decomposition (SVD) with a dictionary constructing procedure by this research. The simulation experiments for ideal point targets show the robustness of the proposed algorithm to the noise and sidelobe disturbance which always influence the imaging quality of the conventional methods. The computational resources requirement is further investigated in this paper. As a consequence of the algorithm complexity analysis, the present method possesses the superiority on resource consumption compared with the classic matching pursuit method. The imaging implementations for practical measured data also demonstrate the effectiveness of the algorithm developed in this paper.

  2. 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.

  3. Chromatin meets its organizers.

    Science.gov (United States)

    Bodnar, Megan S; Spector, David L

    2013-06-06

    Chromatin organization and gene-gene interactions are critical components of carrying out developmental programs. Phillips-Cremins et al. identify a series of unexpected architectural proteins that work in a combinatorial manner to functionally organize chromatin in a cell-type-specific manner at the submegabase-length scale. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Extracellular Matrix, Nuclear and Chromatin Structure and GeneExpression in Normal Tissues and Malignant Tumors: A Work inProgress

    Energy Technology Data Exchange (ETDEWEB)

    Spencer, Virginia A.; Xu, Ren; Bissell, Mina J.

    2006-08-01

    Almost three decades ago, we presented a model where theextracellular matrix (ECM) was postulated to influence gene expressionand tissue-specificity through the action of ECM receptors and thecytoskeleton. This hypothesis implied that ECM molecules could signal tothe nucleus and that the unit of function in higher organisms was not thecell alone, but the cell plus its microenvironment. We now know that ECMinvokes changes in tissue and organ architecture and that tissue, cell,nuclear, and chromatin structure are changed profoundly as a result ofand during malignant progression. Whereas some evidence has beengenerated for a link between ECM-induced alterations in tissuearchitecture and changes in both nuclear and chromatin organization, themanner by which these changes actively induce or repress gene expressionin normal and malignant cells is a topic in need of further attention.Here, we will discuss some key findings that may provide insights intomechanisms through which ECM could influence gene transcription and howtumor cells acquire the ability to overcome these levels ofcontrol.

  5. In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory.

    Science.gov (United States)

    Watson, L Ashley; Tsai, Li-Huei

    2017-04-01

    Different aspects of learning, memory, and cognition are regulated by epigenetic mechanisms such as covalent DNA modifications and histone post-translational modifications. More recently, the modulation of chromatin architecture and nuclear organization is emerging as a key factor in dynamic transcriptional regulation of the post-mitotic neuron. For instance, neuronal activity induces relocalization of gene loci to 'transcription factories', and specific enhancer-promoter looping contacts allow for precise transcriptional regulation. Moreover, neuronal activity-dependent DNA double-strand break formation in the promoter of immediate early genes appears to overcome topological constraints on transcription. Together, these findings point to a critical role for genome topology in integrating dynamic environmental signals to define precise spatiotemporal gene expression programs supporting cognitive processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. DNA breaks and repair in interstitial telomere sequences: Influence of chromatin structure; Etude des cassures de l'ADN et des mecanismes de reparation dans les sequences telomeriques interstitielles: Influence de la structure chromatinienne

    Energy Technology Data Exchange (ETDEWEB)

    Revaud, D.

    2009-06-15

    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)

  7. Fiscal 2000 achievement report on the important regional technology research and development. Research and development of eco-tailored tribo-material creation process technology (Higher order composite structure material creation process); 2000 nendo juyo chiiki gijutsu kenkyu kaihatsu seika hokokusho. Eco tailored tribo material sosei process gijutsu (koji fukugo kozo material sosei process gijutsu)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    Efforts are made to develop novel tribo-material creation processes through the application of an inclined constitution/structure control, a nonstoichiometric constitution control, or the like, to the manufacture of materials having excellent tribological characteristics for the purpose of improving on the performance of tribology related parts. In fiscal 2000, activities are conducted in the four fields of (1) the experimental manufacture of tribo-materials by powder sintering and the review of the process, (2) the experimental manufacture of tribo-materials by melting and the review of the process, (3) the experimental manufacture of brake disk materials and the review of the process, and (4) the experimental manufacture of bearing materials and the review of the process. In field (1), the preparation of an Fe{sub 3}Al/FeAl intermetallic compound powder by mechanical alloying and gas atomization and the conditions of pressure sintering by HIP (hot isostatic press) or the like are established. Concerning the melting method, basic techniques are established and an experimentally built rotor is evaluated for braking characteristics. In field (3), efforts are made to develop Cu/Sb free brake linings that will match TiAl-made rotors and then an MgO/C system is discovered, which is found to be on the same level as the conventional materials. (NEDO)

  8. 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.

  9. Investigation of Fano resonances induced by higher order plasmon modes on a circular nano-disk with an elongated cavity

    KAUST Repository

    Amin, Muhammad Ruhul

    2012-08-10

    In this paper, a planar metallic nanostructure design, which supports two distinct Fano resonances in its extinction cross-section spectrum under normally incident and linearly polarized electromagnetic field, is proposed. The proposed design involves a circular disk embedding an elongated cavity; shifting and rotating the cavity break the symmetry of the structure with respect to the incident field and induce higher order plasmon modes. As a result, Fano resonances are generated in the visible spectrum due to the destructive interference between the sub-radiant higher order modes and super-radiant the dipolar mode. The Fano resonances can be tuned by varying the cavity\\'s width and the rotation angle. An RLC circuit, which is mathematically equivalent to a mass-spring oscillator, is proposed to model the optical response of the nanostructure design.

  10. Higher-order rogue wave solutions of the three-wave resonant interaction equation via the generalized Darboux transformation

    International Nuclear Information System (INIS)

    Wang, Xin; Chen, Yong; Cao, Jianli

    2015-01-01

    In this paper, we utilize generalized Darboux transformation to study higher-order rogue wave solutions of the three-wave resonant interaction equation, which describes the propagation and mixing of waves with different frequencies in weakly nonlinear dispersive media. A general Nth-order rogue wave solution with two characteristic velocities structural parameters and 3N independent parameters under a determined plane-wave background and a specific parameter condition is derived. As an application, we show that four fundamental rogue waves with fundamental, two kinds of line and quadrilateral patterns, or six fundamental rogue waves with fundamental, triangular, two kinds of quadrilateral and circular patterns can emerge in the second-order rogue waves. Moreover, several important wave characteristics including the maximum values, the corresponding coordinate positions of the humps, and the stability problem for some special higher-order rogue wave solutions such as the fundamental and quadrilateral cases are discussed. (paper)

  11. Competition of Dzyaloshinskii-Moriya and Higher-Order Exchange Interactions in Rh /Fe Atomic Bilayers on Ir(111)

    Science.gov (United States)

    Romming, Niklas; Pralow, Henning; Kubetzka, André; Hoffmann, Markus; von Malottki, Stephan; Meyer, Sebastian; Dupé, Bertrand; Wiesendanger, Roland; von Bergmann, Kirsten; Heinze, Stefan

    2018-05-01

    Using spin-polarized scanning tunneling microscopy and density functional theory we demonstrate the occurrence of a novel type of noncollinear spin structure in Rh /Fe atomic bilayers on Ir(111). We find that higher-order exchange interactions depend sensitively on the stacking sequence. For fcc-Rh /Fe /Ir (111 ) , frustrated exchange interactions are dominant and lead to the formation of a spin spiral ground state with a period of about 1.5 nm. For hcp-Rh /Fe /Ir (111 ) , higher-order exchange interactions favor an up-up-down-down (↑↑↓↓) state. However, the Dzyaloshinskii-Moriya interaction at the Fe /Ir interface leads to a small angle of about 4° between adjacent magnetic moments resulting in a canted ↑↑↓↓ ground state.

  12. Higher-order Peregrine combs and Peregrine walls for the variable-coefficient Lenells-Fokas equation

    Science.gov (United States)

    Wang, Zi-Qi; Wang, Xin; Wang, Lei; Sun, Wen-Rong; Qi, Feng-Hua

    2017-02-01

    In this paper, we study the variable-coefficient Lenells-Fokas (LF) model. Under large periodic modulations in the variable coefficients of the LF model, the generalized Akhmediev breathers develop into the breather multiple births (BMBs) from which we obtain the Peregrine combs (PCs). The PCs can be considered as the limiting case of the BMBs and be transformed into the Peregrine walls (PWs) with a specific amplitude of periodic modulation. We further investigate the spatiotemporal characteristics of the PCs and PWs analytically. Based on the second-order breather and rogue-wave solutions, we derive the corresponding higher-order structures (higher-order PCs and PWs) under proper periodic modulations. What is particularly noteworthy is that the second-order PC can be converted into the Peregrine pyramid which exhibits the higher amplitude and thickness. Our results could be helpful for the design of experiments in the optical fiber communications.

  13. MIMO processing based on higher-order Poincaré spheres

    Science.gov (United States)

    Fernandes, Gil M.; Muga, Nelson J.; Pinto, Armando N.

    2017-08-01

    A multi-input multi-output (MIMO) algorithm based on higher-order Poincaré spheres is demonstrated for space-division multiplexing (SDM) systems. The MIMO algorithm is modulation format agnostic, robust to frequency offset and does not require training sequences. In this approach, the space-multiplexed signal is decomposed in sets of two tributary signals, with each set represented in a higher-order Poincaré sphere. For any arbitrary complex modulation format, the samples of two tributaries can be represented in a given higher-order Poincaré sphere with a symmetry plane. The crosstalk along propagation changes the spatial orientation of this plane and, therefore, it can be compensated by computing and realigning the best fit plane. We show how the transmitted signal can be successfully recovered using this procedure for all possible combinations of tributaries. Moreover, we analyze the convergence speed for the MIMO technique considering several optical-to-noise ratios.

  14. 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...

  15. Higher order polynomial expansion nodal method for hexagonal core neutronics analysis

    International Nuclear Information System (INIS)

    Jin, Young Cho; Chang, Hyo Kim

    1998-01-01

    A higher-order polynomial expansion nodal(PEN) method is newly formulated as a means to improve the accuracy of the conventional PEN method solutions to multi-group diffusion equations in hexagonal core geometry. The new method is applied to solving various hexagonal core neutronics benchmark problems. The computational accuracy of the higher order PEN method is then compared with that of the conventional PEN method, the analytic function expansion nodal (AFEN) method, and the ANC-H method. It is demonstrated that the higher order PEN method improves the accuracy of the conventional PEN method and that it compares very well with the other nodal methods like the AFEN and ANC-H methods in accuracy

  16. Alignment of learning objectives and assessments in therapeutics courses to foster higher-order thinking.

    Science.gov (United States)

    FitzPatrick, Beverly; Hawboldt, John; Doyle, Daniel; Genge, Terri

    2015-02-17

    To determine whether national educational outcomes, course objectives, and classroom assessments for 2 therapeutics courses were aligned for curricular content and cognitive processes, and if they included higher-order thinking. Document analysis and student focus groups were used. Outcomes, objectives, and assessment tasks were matched for specific therapeutics content and cognitive processes. Anderson and Krathwohl's Taxonomy was used to define higher-order thinking. Students discussed whether assessments tested objectives and described their thinking when responding to assessments. There were 7 outcomes, 31 objectives, and 412 assessment tasks. The alignment for content and cognitive processes was not satisfactory. Twelve students participated in the focus groups. Students thought more short-answer questions than multiple choice questions matched the objectives for content and required higher-order thinking. The alignment analysis provided data that could be used to reveal and strengthen the enacted curriculum and improve student learning.

  17. A Linear-Elasticity Solver for Higher-Order Space-Time Mesh Deformation

    Science.gov (United States)

    Diosady, Laslo T.; Murman, Scott M.

    2018-01-01

    A linear-elasticity approach is presented for the generation of meshes appropriate for a higher-order space-time discontinuous finite-element method. The equations of linear-elasticity are discretized using a higher-order, spatially-continuous, finite-element method. Given an initial finite-element mesh, and a specified boundary displacement, we solve for the mesh displacements to obtain a higher-order curvilinear mesh. Alternatively, for moving-domain problems we use the linear-elasticity approach to solve for a temporally discontinuous mesh velocity on each time-slab and recover a continuous mesh deformation by integrating the velocity. The applicability of this methodology is presented for several benchmark test cases.

  18. Collocated electrodynamic FDTD schemes using overlapping Yee grids and higher-order Hodge duals

    Science.gov (United States)

    Deimert, C.; Potter, M. E.; Okoniewski, M.

    2016-12-01

    The collocated Lebedev grid has previously been proposed as an alternative to the Yee grid for electromagnetic finite-difference time-domain (FDTD) simulations. While it performs better in anisotropic media, it performs poorly in isotropic media because it is equivalent to four overlapping, uncoupled Yee grids. We propose to couple the four Yee grids and fix the Lebedev method using discrete exterior calculus (DEC) with higher-order Hodge duals. We find that higher-order Hodge duals do improve the performance of the Lebedev grid, but they also improve the Yee grid by a similar amount. The effectiveness of coupling overlapping Yee grids with a higher-order Hodge dual is thus questionable. However, the theoretical foundations developed to derive these methods may be of interest in other problems.

  19. Development of a Higher Order Laminate Theory for Modeling Composites with Induced Strain Actuators

    Science.gov (United States)

    Chattopadhyay, Aditi; Seeley, Charles E.

    1996-01-01

    A refined higher order plate theory is developed to investigate the actuation mechanism of piezoelectric materials surface bonded or embedded in composite laminates. The current analysis uses a displacement field which accurately accounts for transverse shear stresses. Some higher order terms are identified by using the conditions that shear stresses vanish at all free surfaces. Therefore, all boundary conditions for displacements and stresses are satisfied in the present theory. The analysis is implemented using the finite element method which provides a convenient means to construct a numerical solution due to the discrete nature of the actuators. The higher order theory is computationally less expensive than a full three dimensional analysis. The theory is also shown to agree well with published experimental results. Numerical examples are presented for composite plates with thicknesses ranging from thin to very thick.

  20. Application of Higher-Order Cumulant in Fault Diagnosis of Rolling Bearing

    International Nuclear Information System (INIS)

    Shen, Yongjun; Yang, Shaopu; Wang, Junfeng

    2013-01-01

    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