Science.gov

Sample records for higher order structures

  1. Generalized structure of higher order nonclassicality

    NASA Astrophysics Data System (ADS)

    Verma, Amit; Pathak, Anirban

    2010-02-01

    A generalized notion of higher order nonclassicality (in terms of higher order moments) is introduced. Under this generalized framework of higher order nonclassicality, conditions of higher order squeezing and higher order subpoissonian photon statistics are derived. A simpler form of the Hong-Mandel higher order squeezing criterion is derived under this framework by using an operator ordering theorem introduced by us in [A. Pathak, J. Phys. A 33 (2000) 5607]. It is also generalized for multi-photon Bose operators of Brandt and Greenberg. Similarly, condition for higher order subpoissonian photon statistics is derived by normal ordering of higher powers of number operator. Further, with the help of simple density matrices, it is shown that the higher order antibunching (HOA) and higher order subpoissonian photon statistics (HOSPS) are not the manifestation of the same phenomenon and consequently it is incorrect to use the condition of HOA as a test of HOSPS. It is also shown that the HOA and HOSPS may exist even in absence of the corresponding lower order phenomenon. Binomial state, nonlinear first order excited squeezed state (NLESS) and nonlinear vacuum squeezed state (NLVSS) are used as examples of quantum state and it is shown that these states may show higher order nonclassical characteristics. It is observed that the Binomial state which is always antibunched, is not always higher order squeezed and NLVSS which shows higher order squeezing does not show HOSPS and HOA. The opposite is observed in NLESS and consequently it is established that the HOSPS and HOS are two independent signatures of higher order nonclassicality.

  2. Chromatin Higher-order Structure and Dynamics

    PubMed Central

    Woodcock, Christopher L.; Ghosh, Rajarshi P.

    2010-01-01

    The primary role of the nucleus as an information storage, retrieval, and replication site requires the physical organization and compaction of meters of DNA. Although it has been clear for many years that nucleosomes constitute the first level of chromatin compaction, this contributes a relatively small fraction of the condensation needed to fit the typical genome into an interphase nucleus or set of metaphase chromosomes, indicating that there are additional “higher order” levels of chromatin condensation. Identifying these levels, their interrelationships, and the principles that govern their occurrence has been a challenging and much discussed problem. In this article, we focus on recent experimental advances and the emerging evidence indicating that structural plasticity and chromatin dynamics play dominant roles in genome organization. We also discuss novel approaches likely to yield important insights in the near future, and suggest research areas that merit further study. PMID:20452954

  3. Chromatin higher-order structures and gene regulation

    PubMed Central

    Li, Guohong

    2011-01-01

    Genomic DNA in the eukaryotic nucleus is hierarchically packaged by histones into chromatin to fit inside the nucleus. The dynamics of higher-order chromatin compaction play a critical role in transcription and other biological processes inherent to DNA. Many factors, including histone variants, histone modifications, DNA methylation and the binding of non-histone architectural proteins regulate the structure of chromatin. Although the structure of nucleosomes, the fundamental repeating unit of chromatin, is clear, there is still much discussion on the higher-order levels of chromatin structure. In this review, we focus on the recent progress in elucidating the structure of the 30-nm chromatin fiber. We also discuss the structural plasticity/dynamics and epigenetic inheritance of higher-order chromatin and the roles of chromatin higher-order organization in eukaryotic gene regulation. PMID:21342762

  4. Symplectic structures related with higher order variational problems

    NASA Astrophysics Data System (ADS)

    Kijowski, Jerzy; Moreno, Giovanni

    2015-06-01

    In this paper, we derive the symplectic framework for field theories defined by higher order Lagrangians. The construction is based on the symplectic reduction of suitable spaces of iterated jets. The possibility of reducing a higher order system of partial differential equations to a constrained first-order one, the symplectic structures naturally arising in the dynamics of a first-order Lagrangian theory, and the importance of the Poincaré-Cartan form for variational problems, are all well-established facts. However, their adequate combination corresponding to higher order theories is missing in the literature. Here we obtain a consistent and truly finite-dimensional canonical formalism, as well as a higher order version of the Poincaré-Cartan form. In our exposition, the rigorous global proofs of the main results are always accompanied by their local coordinate descriptions, indispensable to work out practical examples.

  5. Higher-order structure of rRNA

    NASA Technical Reports Server (NTRS)

    Gutell, R. R.; Woese, C. R.

    1986-01-01

    A comparative search for phylogenetically covarying basepair replacements within potential helices has been the only reliable method to determine the correct secondary structure of the 3 rRNAs, 5S, 16S, and 23S. The analysis of 16S from a wide phylogenetic spectrum, that includes various branches of the eubacteria, archaebacteria, eucaryotes, in addition to the mitochondria and chloroplast, is beginning to reveal the constraints on the secondary structures of these rRNAs. Based on the success of this analysis, and the assumption that higher order structure will also be phylogenetically conserved, a comparative search was initiated for positions that show co-variation not involved in secondary structure helices. From a list of potential higher order interactions within 16S rRNA, two higher-order interactions are presented. The first of these interactions involves positions 570 and 866. Based on the extent of phylogenetic covariation between these positions while maintaining Watson-Crick pairing, this higher-order interaction is considered proven. The other interaction involves a minimum of six positions between the 1400 and 1500 regions of the 16S rRNA. Although these patterns of covariation are not as striking as the 570/866 interaction, the fact that they all exist in an anti-parallel fashion and that experimental methods previously implicated these two regions of the molecule in tRNA function suggests that these interactions be given serious consideration.

  6. Stable static structures in models with higher-order derivatives

    SciTech Connect

    Bazeia, D.; Lobão, A.S.; Menezes, R.

    2015-09-15

    We investigate the presence of static solutions in generalized models described by a real scalar field in four-dimensional space–time. We study models in which the scalar field engenders higher-order derivatives and spontaneous symmetry breaking, inducing the presence of domain walls. Despite the presence of higher-order derivatives, the models keep to equations of motion second-order differential equations, so we focus on the presence of first-order equations that help us to obtain analytical solutions and investigate linear stability on general grounds. We then illustrate the general results with some specific examples, showing that the domain wall may become compact and that the zero mode may split. Moreover, if the model is further generalized to include k-field behavior, it may contribute to split the static structure itself.

  7. Higher-order structure of Saccharomyces cerevisiae chromatin

    SciTech Connect

    Lowary, P.T.; Widom, J. )

    1989-11-01

    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.

  8. Revealing Higher Order Protein Structure Using Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chait, Brian T.; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P.; Shi, Yi

    2016-06-01

    The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope.

  9. Revealing Higher Order Protein Structure Using Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Chait, Brian T.; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P.; Shi, Yi

    2016-04-01

    The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope.

  10. Revealing Higher Order Protein Structure Using Mass Spectrometry.

    PubMed

    Chait, Brian T; Cadene, Martine; Olinares, Paul Dominic; Rout, Michael P; Shi, Yi

    2016-06-01

    The development of rapid, sensitive, and accurate mass spectrometric methods for measuring peptides, proteins, and even intact protein assemblies has made mass spectrometry (MS) an extraordinarily enabling tool for structural biology. Here, we provide a personal perspective of the increasingly useful role that mass spectrometric techniques are exerting during the elucidation of higher order protein structures. Areas covered in this brief perspective include MS as an enabling tool for the high resolution structural biologist, for compositional analysis of endogenous protein complexes, for stoichiometry determination, as well as for integrated approaches for the structural elucidation of protein complexes. We conclude with a vision for the future role of MS-based techniques in the development of a multi-scale molecular microscope. Graphical Abstract ᅟ. PMID:27080007

  11. Neutron scattering studies on chromatin higher-order structure

    SciTech Connect

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

    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.

  12. Technical decision making with higher order structure data: higher order structure characterization during protein therapeutic candidate screening.

    PubMed

    Jiang, Yijia; Li, Cynthia; Li, Jenny; Gabrielson, John P; Wen, Jie

    2015-04-01

    Protein therapeutics differ considerably from small molecule drugs because of the presence of higher order structure (HOS), post-translational modifications, inherent molecular heterogeneity, and unique stability profiles. At early stages of development, multiple molecular candidates are often produced for the same biological target. In order to select the most promising molecule for further development, studies are carried out to compare and rank order the candidates in terms of their manufacturability, purity, and stability profiles. This note reports a case study on the use of selected HOS characterization methods for candidate selection and the role of HOS data in identifying potential challenges that may be avoided by selecting the optimal molecular entity for continued development. PMID:25716705

  13. Higher order structure of proteins solubilized in AOT reverse micelles.

    PubMed

    Naoe, Kazumitsu; Noda, Kazuki; Kawagoe, Mikio; Imai, Masanao

    2004-11-15

    The higher order structure of proteins solubilized in an bis(2-ethylhexyl) sulfosuccinate sodium (AOT) reverse micellar system was investigated. From circular dichroic (CD) measurement, CD spectra of cytochrome c, which is solubilized at the interface of reverse micelles, markedly changed on going from buffer solution to the reverse micellar solution, and the ellipticity values in the far- and near-UV regions decreased with decreasing the water content (W0: molar ratio of water to AOT), indicating that the secondary and tertiary structures of cytochrome c changed with the water content. The ellipticity of ribonuclease A, which is solubilized in the center of micellar water pool, in the near-UV region was dependent on W0 and became minimum when W0 of ca. 8 while the ellipticity in the far-UV region was almost constant, indicating that the tertiary structure of ribonuclease A was affected by the water content, but the secondary structure was conserved. The degree of curvature of the micellar interface appears to influence the protein structure because the reverse micelle size is linearly proportional to the W0 value. As evidence of this, when the micelle size was comparable to the protein's dimensions, the structures were more affected by the water content. Judging from the dependence of the factor influencing the protein structure on the protein species, the location of solubilized protein in reverse micelles is significantly related to whether the protein structure in the system is affected by the micellar interface. In the cases of cytochrome c and lysozyme, the ellipticity against W0 was dependent on the AOT concentration. In contrast, ribonuclease A gave very similar ellipticity values whatever the AOT concentration. In the n-hexane micellar system, cytochrome c exhibited lower ellipticity values and ribonuclease A in the lower W0 range (W0higher ellipticity values. These results indicated that the interaction between the protein and the micellar

  14. MJO structure associated with the higher-order CEOF modes

    NASA Astrophysics Data System (ADS)

    Liu, Ping

    2014-10-01

    the total 432 CEOF modes retain all variance of the baseline MJO, while those higher than 10 contain less information and more noise and can be discarded. Furthermore, this study indicated that the longitudinal STD of the reconstructed anomalies detects the MJO phases and magnitudes in the western Pacific with more physical meaning and in better agreement with the Hovmöller diagrams than the RMM-like amplitude. The results provide an integral figure of the MJO structure from the CEOF analysis and a more robust RMM framework for monitoring the MJO's evolution in real time and for validating its numerical forecast and simulations.

  15. Higher order structures of the caseins: a paradox?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This book chapter deals with the molecular architecture of the major milk proteins, the caseins. Earlier theories of casein structure classified them as random coils; i.e., flexible without definite structural elements. Recent advances in the field of protein chemistry have significantly enhanced ...

  16. The Structure of Higher Education: Order in the Academy

    ERIC Educational Resources Information Center

    Smith, Clair A.

    2009-01-01

    Higher education in the U.S. is provided by an interesting mix of public, private non-profit, and for-profit institutions. The for-profit educational firm serves the residual claimant owners and has the greatest incentive for efficient operation. The public and private non-profit schools have less efficient incentives, but benefit from charitable…

  17. Higher order chromatin structure: bridging physics and biology

    PubMed Central

    Fudenberg, Geoffrey; Mirny, Leonid A.

    2012-01-01

    Recent advances in microscopy and genomic techniques have provided new insight into spatial chromatin organization inside of the nucleus. In particular, chromosome conformation capture data has highlighted the relevance of polymer physics for high-order chromatin organization. In this context, we review basic polymer states, discuss how an appropriate polymer model can be determined from experimental data, and examine the success and limitations of various polymer models of high-order interphase chromatin organization. By taking into account topological constraints acting on the chromatin fiber, recently-developed polymer models of interphase chromatin can reproduce the observed scaling of distances between genomic loci, chromosomal territories, and probabilities of contacts between loci measured by chromosome conformation capture methods. Polymer models provide a framework for the interpretation of experimental data as ensembles of conformations rather than collections of loops, and will be crucial for untangling functional implications of chromosomal organization. PMID:22360992

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

    PubMed

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

    2016-09-01

    Monoclonal antibody (mAb) drugs constitute the largest class of protein therapeutics currently on the market. Correctly folded protein higher order structure (HOS), including quinary structure, is crucial for mAb drug quality. The quinary structure is defined as the association of quaternary structures (e.g., oligomerized mAb). Here, several commonly available analytical methods, i.e., size-exclusion-chromatography (SEC) FPLC, multi-angle light scattering (MALS), circular dichroism (CD), NMR and multivariate analysis, were combined and modified to yield a complete profile of HOS and comparable metrics. Rituximab and infliximab were chosen for method evaluation because both IgG1 molecules are known to be homologous in sequence, superimposable in Fab crystal structure and identical in Fc structure. However, herein the two are identified to be significantly different in quinary structure in addition to minor secondary structure differences. All data collectively showed rituximab was mostly monomeric while infliximab was in mono-oligomer equilibrium driven by its Fab fragment. The quinary structure differences were qualitatively inferred from the less used but more reproducible dilution-injection-SEC-FPLC curve method. Quantitative principal component analysis (PCA) was performed on NMR spectra of either the intact or the in-situ enzymatic-digested mAb samples. The cleavage reactions happened directly in NMR tubes without further separation, which greatly enhanced NMR spectra quality and resulted in larger inter- and intra-lot variations based on PCA. The new in-situ enzymatic digestion method holds potential in identifying structural differences on larger therapeutic molecules using NMR. PMID:27344629

  19. The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules.

    PubMed

    Wu, Hao; Fuxreiter, Monika

    2016-05-19

    We here attempt to achieve an integrated understanding of the structure and dynamics of a number of higher-order assemblies, including amyloids, various kinds of signalosomes, and cellular granules. We propose that the synergy between folded domains, linear motifs, and intrinsically disordered regions regulates the formation and intrinsic fuzziness of all higher-order assemblies, creating a structural and dynamic continuum. We describe how such regulatory mechanisms could be influenced under pathological conditions. PMID:27203110

  20. Development of higher-order modal methods for transient thermal and structural analysis

    NASA Technical Reports Server (NTRS)

    Camarda, Charles J.; Haftka, Raphael T.

    1989-01-01

    A force-derivative method which produces higher-order modal solutions to transient problems is evaluated. These higher-order solutions converge to an accurate response using fewer degrees-of-freedom (eigenmodes) than lower-order methods such as the mode-displacement or mode-acceleration methods. Results are presented for non-proportionally damped structural problems as well as thermal problems modeled by finite elements.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  2. Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

    PubMed Central

    Chambers, Emily V.; Bickmore, Wendy A.; Semple, Colin A.

    2013-01-01

    Several recent studies have examined different aspects of mammalian higher order chromatin structure – replication timing, lamina association and Hi-C inter-locus interactions — and have suggested that most of these features of genome organisation are conserved over evolution. However, the extent of evolutionary divergence in higher order structure has not been rigorously measured across the mammalian genome, and until now little has been known about the characteristics of any divergent loci present. Here, we generate a dataset combining multiple measurements of chromatin structure and organisation over many embryonic cell types for both human and mouse that, for the first time, allows a comprehensive assessment of the extent of structural divergence between mammalian genomes. Comparison of orthologous regions confirms that all measurable facets of higher order structure are conserved between human and mouse, across the vast majority of the detectably orthologous genome. This broad similarity is observed in spite of many loci possessing cell type specific structures. However, we also identify hundreds of regions (from 100 Kb to 2.7 Mb in size) showing consistent evidence of divergence between these species, constituting at least 10% of the orthologous mammalian genome and encompassing many hundreds of human and mouse genes. These regions show unusual shifts in human GC content, are unevenly distributed across both genomes, and are enriched in human subtelomeric regions. Divergent regions are also relatively enriched for genes showing divergent expression patterns between human and mouse ES cells, implying these regions cause divergent regulation. Particular divergent loci are strikingly enriched in genes implicated in vertebrate development, suggesting important roles for structural divergence in the evolution of mammalian developmental programmes. These data suggest that, though relatively rare in the mammalian genome, divergence in higher order chromatin

  3. HIGHER ORDER FACTOR STRUCTURE OF THE WISC-IV IN A CLINICAL NEUROPSYCHOLOGICAL SAMPLE

    PubMed Central

    Bodin, Doug; Pardini, Dustin A.; Burns, Thomas G.; Stevens, Abigail B.

    2010-01-01

    A confirmatory factor analysis was conducted examining the higher order factor structure of the WISC-IV scores for 344 children who participated in neuropsychological evaluations at a large children’s hospital. The WISC-IV factor structure mirrored that of the standardization sample. The second order general intelligence factor (g) accounted for the largest proportion of variance in the first-order latent factors and in the individual subtests, especially for the working memory index. The first-order processing speed factor exhibited the most unique variance beyond the influence of g. The results suggest that clinicians should not ignore the contribution of g when interpreting the first-order factors. PMID:19132580

  4. The post-mitotic state in neurons correlates with a stable nuclear higher-order structure.

    PubMed

    Aranda-Anzaldo, Armando

    2012-03-01

    Neurons become terminally differentiated (TD) post-mitotic cells very early during development yet they may remain alive and functional for decades. TD neurons preserve the molecular machinery necessary for DNA synthesis that may be reactivated by different stimuli but they never complete a successful mitosis. The non-reversible nature of the post-mitotic state in neurons suggests a non-genetic basis for it since no set of mutations has been able to revert it. Comparative studies of the nuclear higher-order structure in neurons and cells with proliferating potential suggest that the non-reversible nature of the post-mitotic state in neurons has a structural basis in the stability of the nuclear higher-order structure. PMID:22808316

  5. Technical decision-making with higher order structure data: specific binding of a nonionic detergent perturbs higher order structure of a therapeutic monoclonal antibody.

    PubMed

    Budyak, Ivan L; Doyle, Brandon L; Weiss, William F

    2015-04-01

    Robust higher order structure (HOS) characterization capability and strategy are critical throughout biopharmaceutical development from initial candidate selection and formulation screening to process optimization and manufacturing. This case study describes the utility of several orthogonal HOS methods as investigational tools during purification process development. An atypically high level of residual detergent in a development drug substance batch of a therapeutic monoclonal antibody triggered a root cause investigation. Several orthogonal biophysical techniques were used to uncover and characterize a specific interaction between the detergent and the antibody. Isothermal titration calorimetry (ITC) was used to quantify the molar ratio and affinity of the binding event, and circular dichroism (CD) spectroscopy and differential scanning calorimetry (DSC) were used to evaluate corresponding impacts on secondary/tertiary structure and thermal stability, respectively. As detergents are used routinely in biopharmaceutical processing, this case study highlights the value and power of HOS data in informing technical investigations and underlines the importance of HOS characterization as a component of overall biopharmaceutical analytical control strategy. PMID:25545760

  6. The role of Bni5 in the regulation of septin higher-order structure formation.

    PubMed

    Patasi, Csilla; Godočíková, Jana; Michlíková, Soňa; Nie, Yan; Káčeriková, Radka; Kválová, Katarína; Raunser, Stefan; Farkašovský, Marian

    2015-12-01

    Septins are a family of conserved cytoskeletal proteins playing an essential role in cytokinesis and in many other cellular processes in fungi and animals. In budding yeast Saccharomyces cerevisiae, septins form filaments and higher-order structures at the mother-bud neck depending on the particular stage of the cell cycle. Septin structures at the division plane serve as a scaffold to recruit the proteins required for particular cellular processes. The formation and localization of septin structures at particular stages of the cell cycle also determine functionality of these proteins. Many different proteins participate in regulating septin assembly. Despite recent developments, we are only beginning to understand how specific protein-protein interactions lead to changes in the polymerization of septin filaments or assembly of higher-order structures. Here, using fluorescence and electron microscopy, we found that Bni5 crosslinks septin filaments into networks by bridging pairs or multiple filaments, forming structures that resemble railways. Furthermore, Bni5 appears to be a substrate of the Elm1 protein kinase in vitro. Moreover, Elm1 induces in the presence of Bni5 disassembly of long septin filaments, suggesting that these proteins may participate in the hourglass to double ring transition. This work gives new insight into the regulatory role of Bni5 in the structural changes of septins. PMID:26351911

  7. Structure-Specific Ribonucleases for MS-Based Elucidation of Higher-Order RNA Structure

    NASA Astrophysics Data System (ADS)

    Scalabrin, Matteo; Siu, Yik; Asare-Okai, Papa Nii; Fabris, Daniele

    2014-07-01

    Supported by high-throughput sequencing technologies, structure-specific nucleases are experiencing a renaissance as biochemical probes for genome-wide mapping of nucleic acid structure. This report explores the benefits and pitfalls of the application of Mung bean (Mb) and V1 nuclease, which attack specifically single- and double-stranded regions of nucleic acids, as possible structural probes to be employed in combination with MS detection. Both enzymes were found capable of operating in ammonium-based solutions that are preferred for high-resolution analysis by direct infusion electrospray ionization (ESI). Sequence analysis by tandem mass spectrometry (MS/MS) was performed to confirm mapping assignments and to resolve possible ambiguities arising from the concomitant formation of isobaric products with identical base composition and different sequences. The observed products grouped together into ladder-type series that facilitated their assignment to unique regions of the substrate, but revealed also a certain level of uncertainty in identifying the boundaries between paired and unpaired regions. Various experimental factors that are known to stabilize nucleic acid structure, such as higher ionic strength, presence of Mg(II), etc., increased the accuracy of cleavage information, but did not completely eliminate deviations from expected results. These observations suggest extreme caution in interpreting the results afforded by these types of reagents. Regardless of the analytical platform of choice, the results highlighted the need to repeat probing experiments under the most diverse possible conditions to recognize potential artifacts and to increase the level of confidence in the observed structural information.

  8. RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

    PubMed

    Lu, Zhipeng; Zhang, Qiangfeng Cliff; Lee, Byron; Flynn, Ryan A; Smith, Martin A; Robinson, James T; Davidovich, Chen; Gooding, Anne R; Goodrich, Karen J; Mattick, John S; Mesirov, Jill P; Cech, Thomas R; Chang, Howard Y

    2016-05-19

    RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT. PMID:27180905

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

    SciTech Connect

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

    2013-07-01

    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)

  10. Simultaneous silence organizes structured higher-order interactions in neural populations

    PubMed Central

    Shimazaki, Hideaki; Sadeghi, Kolia; Ishikawa, Tomoe; Ikegaya, Yuji; Toyoizumi, Taro

    2015-01-01

    Activity patterns of neural population are constrained by underlying biological mechanisms. These patterns are characterized not only by individual activity rates and pairwise correlations but also by statistical dependencies among groups of neurons larger than two, known as higher-order interactions (HOIs). While HOIs are ubiquitous in neural activity, primary characteristics of HOIs remain unknown. Here, we report that simultaneous silence (SS) of neurons concisely summarizes neural HOIs. Spontaneously active neurons in cultured hippocampal slices express SS that is more frequent than predicted by their individual activity rates and pairwise correlations. The SS explains structured HOIs seen in the data, namely, alternating signs at successive interaction orders. Inhibitory neurons are necessary to maintain significant SS. The structured HOIs predicted by SS were observed in a simple neural population model characterized by spiking nonlinearity and correlated input. These results suggest that SS is a ubiquitous feature of HOIs that constrain neural activity patterns and can influence information processing. PMID:25919985

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

    PubMed

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

    2014-06-25

    The design and construction of higher-order structure and function in proteinosome microcompartments enclosed by a cross-linked membrane of amphiphilic bovine serum albumin/poly(N-isopropylacrylamide) (BSA-NH2/PNIPAAm) nanoconjugates is described. Three structure/function relationships are investigated: (i) differential chemical cross-linking for the control of membrane disassembly and regulated release of encapsulated genetic polymers; (ii) enzyme-mediated hydrogel structuring of the internal microenvironment to increase mechanical robustness and generate a molecularly crowded reaction environment; and (iii) self-production of a membrane-enclosing outer hydrogel wall for generating protease-resistant forms of the protein-polymer protocells. Our results highlight the potential of integrating aspects of supramolecular and polymer chemistry into the design and construction of novel bioinspired microcompartments as a step toward small-scale materials systems based on synthetic cellularity. PMID:24905973

  12. Higher-order structure in the trajectories of depression and anxiety following sudden involuntary unemployment.

    PubMed

    Howe, George W; Hornberger, Anna P; Weihs, Karen; Moreno, Francisco; Neiderhiser, Jenae M

    2012-05-01

    Recent work on comorbidity finds evidence for hierarchical structure of mood and anxiety disorders and symptoms. This study tests whether a higher-order internalizing factor accounts for variation in depression and anxiety symptom severity and change over time in a sample experiencing a period of major life stress. Data on symptoms of depression, chronic worry, and social anxiety were collected five times across seven months from 426 individuals who had recently lost jobs. Growth models for each type of symptom found significant variation in individual trajectories. Slopes were highly correlated across symptom type, as were intercepts. Multilevel confirmatory factor analyses found evidence for a higher-order internalizing factor for both slopes and intercepts, reflective of comorbidity of depression and anxiety, with the internalizing factor accounting for 54% to 91% of the variance in slopes and intercepts of specific symptom sets, providing evidence for both a general common factor and domain-specific factors characterizing level and change in symptoms. Loadings on the higher order factors differed modestly for men and women, and when comparing African American and White participants, but did not differ by age, education, or history of depression. More distal factors including gender and history of depression were strongly associated with internalizing in the early weeks after job loss, but rates of change in internalizing were associated most strongly with reemployment. Findings suggest that stressors may contribute in different ways to the common internalizing factor as compared to variance in anxiety and depression that is independent of that factor. PMID:22103803

  13. SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells.

    PubMed

    Barutcu, A Rasim; Lajoie, Bryan R; Fritz, Andrew J; McCord, Rachel P; Nickerson, Jeffrey A; van Wijnen, Andre J; Lian, Jane B; Stein, Janet L; Dekker, Job; Stein, Gary S; Imbalzano, Anthony N

    2016-09-01

    The packaging of DNA into chromatin plays an important role in transcriptional regulation and nuclear processes. Brahma-related gene-1 SMARCA4 (also known as BRG1), the essential ATPase subunit of the mammalian SWI/SNF chromatin remodeling complex, uses the energy from ATP hydrolysis to disrupt nucleosomes at target regions. Although the transcriptional role of SMARCA4 at gene promoters is well-studied, less is known about its role in higher-order genome organization. SMARCA4 knockdown in human mammary epithelial MCF-10A cells resulted in 176 up-regulated genes, including many related to lipid and calcium metabolism, and 1292 down-regulated genes, some of which encode extracellular matrix (ECM) components that can exert mechanical forces and affect nuclear structure. ChIP-seq analysis of SMARCA4 localization and SMARCA4-bound super-enhancers demonstrated extensive binding at intergenic regions. Furthermore, Hi-C analysis showed extensive SMARCA4-mediated alterations in higher-order genome organization at multiple resolutions. First, SMARCA4 knockdown resulted in clustering of intra- and inter-subtelomeric regions, demonstrating a novel role for SMARCA4 in telomere organization. SMARCA4 binding was enriched at topologically associating domain (TAD) boundaries, and SMARCA4 knockdown resulted in weakening of TAD boundary strength. Taken together, these findings provide a dynamic view of SMARCA4-dependent changes in higher-order chromatin organization and gene expression, identifying SMARCA4 as a novel component of chromatin organization. PMID:27435934

  14. A family of higher-order integration methods for structural dynamics

    SciTech Connect

    Chang, S.Y.

    1996-12-01

    A new family of higher-order implicit, one-step integration algorithms has been developed by Chang (1994). These algorithms have minimum order of accuracy two, and maximum order of accuracy four. In general, they have order of accuracy three. All the algorithms are unconditionally stable, do not overshoot in displacements or in velocities and possess desirable numerical dissipation which can be continuously controlled. In particular, these schemes possess better dissipative and dispersive characteristics than the commonly used second-order methods. It has been found that one of these algorithms can provide an appropriate amplitude compensation effect for nonlinear systems. This amplitude compensation effect can effectively suppress the linearization errors which are introduced by the assumption that the structural properties remain constant during each time step. Because of the excellent properties possessed by the algorithm, especially the amplitude compensation effect and no growth of high-frequency response, a time step as large as two orders of magnitude greater than what is needed for the average acceleration method can be used, leading to a very significant saving of computational effort.

  15. Higher-Order Structure of the Rous Sarcoma Virus SP Assembly Domain

    PubMed Central

    Bush, Di L.; Monroe, Eric B.; Bedwell, Gregory J.; Phillips, Judith M.

    2014-01-01

    ABSTRACT Purified retroviral Gag proteins can assemble in vitro to form immature virus-like particles (VLPs). By cryoelectron tomography, Rous sarcoma virus VLPs show an organized hexameric lattice consisting chiefly of the capsid (CA) domain, with periodic stalk-like densities below the lattice. We hypothesize that the structure represented by these densities is formed by amino acid residues immediately downstream of the folded CA, namely, the short spacer peptide SP, along with a dozen flanking residues. These 24 residues comprise the SP assembly (SPA) domain, and we propose that neighboring SPA units in a Gag hexamer coalesce to form a six-helix bundle. Using in vitro assembly, alanine scanning mutagenesis, and biophysical analyses, we have further characterized the structure and function of SPA. Most of the amino acid residues in SPA could not be mutated individually without abrogating assembly, with the exception of a few residues near the N and C termini, as well as three hydrophilic residues within SPA. We interpret these results to mean that the amino acids that do not tolerate mutations contribute to higher-order structures in VLPs. Hydrogen-deuterium exchange analyses of unassembled Gag compared that of assembled VLPs showed strong protection at the SPA region, consistent with a higher-order structure. Circular dichroism revealed that a 29mer SPA peptide shifts from a random coil to a helix in a concentration-dependent manner. Analytical ultracentrifugation showed concentration-dependent self-association of the peptide into a hexamer. Taken together, these results provide strong evidence for the formation of a critical six-helix bundle in Gag assembly. IMPORTANCE The structure of a retrovirus like HIV is created by several thousand molecules of the viral Gag protein, which assemble to form the known hexagonal protein lattice in the virus particle. How the Gag proteins pack together in the lattice is incompletely understood. A short segment of Gag known to

  16. Variational-method-based higher order mode analysis extendible to realistic tapered disk-loaded structures

    NASA Astrophysics Data System (ADS)

    Wang, L. F.; Lin, Y. Z.; Higo, T.

    2002-04-01

    In order to obtain high luminosity and energy efficiency in future linear colliders, most designs for e + and e - collisions in the TeV range will use multi-bunch operation. Therefore, the study of higher order modes excited by previous bunches in the train becomes very important for the optimal design of the accelerator components. Many designs have used tapered disk-loaded waveguides for acceleration. Various numerical methods have been used for the modal analysis of the structure. In this paper, a high-precision eigenmode-computation analysis based on a variational method will be discussed. It allows for rounding the edge of a disk hole without any approximation in shape treatment and calculates the exactly synchronous modes. It converges much faster than the mesh-based computer code SUPERFISH. Good agreement was observed between the results of the variational method and those of other methods.

  17. Representation of higher-order statistical structures in natural scenes via spatial phase distributions.

    PubMed

    MaBouDi, HaDi; Shimazaki, Hideaki; Amari, Shun-Ichi; Soltanian-Zadeh, Hamid

    2016-03-01

    Natural scenes contain richer perceptual information in their spatial phase structure than their amplitudes. Modeling phase structure of natural scenes may explain higher-order structure inherent to the natural scenes, which is neglected in most classical models of redundancy reduction. Only recently, a few models have represented images using a complex form of receptive fields (RFs) and analyze their complex responses in terms of amplitude and phase. However, these complex representation models often tacitly assume a uniform phase distribution without empirical support. The structure of spatial phase distributions of natural scenes in the form of relative contributions of paired responses of RFs in quadrature has not been explored statistically until now. Here, we investigate the spatial phase structure of natural scenes using complex forms of various Gabor-like RFs. To analyze distributions of the spatial phase responses, we constructed a mixture model that accounts for multi-modal circular distributions, and the EM algorithm for estimation of the model parameters. Based on the likelihood, we report presence of both uniform and structured bimodal phase distributions in natural scenes. The latter bimodal distributions were symmetric with two peaks separated by about 180°. Thus, the redundancy in the natural scenes can be further removed by using the bimodal phase distributions obtained from these RFs in the complex representation models. These results predict that both phase invariant and phase sensitive complex cells are required to represent the regularities of natural scenes in visual systems. PMID:26278166

  18. Protein-protein interactions in a higher-order structure direct lambda site-specific recombination.

    PubMed

    Thompson, J F; de Vargas, L M; Skinner, S E; Landy, A

    1987-06-01

    The highly directional site-specific recombination of bacteriophage lambda is tightly regulated by the binding of three different proteins to a complex array of sites. The manner in which these reactions are both stimulated and inhibited by co-operative binding of proteins to specific sites on the P arm of attP and AttR has been elucidated by correlation of nuclease protection with recombination studies of both wild-type and mutant DNAs. In addition to co-operative forces, there is a specific competitive interaction that allows the protein-DNA complex to serve as a "biological switch". This switch does not depend upon the simple occlusion of DNA binding sites by neighboring proteins; but, rather, the outcome of this competition is dependent on long-range interactions that vary between the higher-order structures of attP and attR. These higher-order structures are dependent on cooperative interactions involving three proteins binding to five or more sites. PMID:2958633

  19. An evaluation of higher-order model methods for calculating transient structural response

    NASA Technical Reports Server (NTRS)

    Camarda, Charles J.; Haftka, Raphael T.; Riley, Michael F.

    1987-01-01

    A higher-order modal method proposed by Leung for transient structural analysis entitled the force-derivative method is evaluated. This method repeatedly integrates by parts with respect to time the convolution-integral form of the structural response to produce successively better approximations to the contribution of the higher modes which are neglected in the modal summation. Comparisons are made of the force-derivative, the mode-displacement, and the mode-acceleration methods for several numerical example problems for various times, levels of damping, and forcing functions. The example problems include a tip-loaded cantilevered beam and a simply-supported multispan beam. The force-derivative method is shown to converge to an accurate solution in fewer modes than either the mode-displacement or the mode-acceleration methods. In addition, for problems in which there are a large number of closely-spaced frequencies whose mode shapes have a negligible contribution to the response, the force-derivative method is very effective in representing the effect of the important, but otherwise neglected, higher modes.

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

    NASA Astrophysics Data System (ADS)

    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

  1. Higher Order Amyloid Fibril Structure by MAS NMR and DNP Spectroscopy

    PubMed Central

    Debelouchina, Galia T.; Bayro, Marvin J.; Fitzpatrick, Anthony W.; Ladizhansky, Vladimir; Colvin, Michael T.; Caporini, Marc A.; Jaroniec, Christopher P.; Bajaj, Vikram S.; Rosay, Melanie; MacPhee, Cait E.; Vendruscolo, Michele; Maas, Werner E.; Dobson, Christopher M.; Griffin, Robert G.

    2014-01-01

    Protein magic angle spinning (MAS) NMR spectroscopy has generated structural models of several amyloid fibril systems, thus providing valuable information regarding the forces and interactions that confer the extraordinary stability of the amyloid architecture. Despite these advances, however, obtaining atomic resolution information describing the higher levels of structural organization within the fibrils remains a significant challenge. Here, we detail MAS NMR experiments and sample labeling schemes designed specifically to probe such higher order amyloid structure and we have applied them to the fibrils formed by an eleven-residue segment of the amyloidogenic protein transthyretin (TTR(105-115)). These experiments have allowed us to define unambiguously not only the arrangement of the peptide β-strands into β-sheets but also the β-sheet interfaces within each protofilament, and in addition to identify the nature of the protofilament-to-protofilament contacts that lead to the formation of the complete fibril. Our efforts have resulted in 111 quantitative distance and torsion angle restraints (10 per residue) that describe the various levels of structure organization. The experiments benefited extensively from the use of dynamic nuclear polarization (DNP), which in some cases allowed us to shorten the data acquisition time from days to hours and to improve significantly the signal-to-noise ratios of the spectra. The β-sheet interface and protofilament interactions identified here revealed local variations in the structure that result in multiple peaks for the exposed N- and C-termini of the peptide and in inhomogeneous line-broadening for the side-chains buried within the interior of the fibrils. PMID:24304221

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

    PubMed Central

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

    2009-01-01

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

  3. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes.

    PubMed

    Lermyte, Frederik; Sobott, Frank

    2015-08-01

    Top-down sequencing approaches are becoming ever more popular for protein characterization, due to the ability to distinguish and characterize different protein isoforms. Under non-denaturing conditions, electron transfer dissociation (ETD) can furthermore provide important information on the exposed surface of proteins or complexes, thereby contributing to the characterization of their higher-order structure. Here, we investigate this approach using top-down ETD of tetrameric hemoglobin, concanavalin A, and alcohol dehydrogenase combined with ion mobility (IM) on a commercially available quadrupole/ion mobility/time-of-flight instrument (Waters Synapt G2). By applying supplemental activation in the transfer cell (post-IM), we release ETD fragments and attain good sequence coverage in the exposed terminal regions of the protein. We investigate the correlation between observed sites of fragmentation with regions of solvent accessibility, as derived from the crystal structure. Ion acceleration prior to ETD is also used to cause collision-induced unfolding (CIU) of the complexes without monomer ejection, as evidenced by the IM profiles. These partially unfolded tetramers show efficient fragmentation in some regions which are not sequenced under more gentle MS conditions. We show that by increasing CIU in small increments and monitoring the changes in the fragmentation pattern, it is possible to follow the initial steps of gas-phase protein unfolding. Fragments from partially unfolded protein complexes are released immediately after electron transfer, prior to IM (they do not share the drift time of their precursor), and observed without the need for supplemental activation. This is further evidence that the higher-order structure in these protein regions has been disrupted. PMID:26081219

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

    NASA Technical Reports Server (NTRS)

    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.

  5. RF-Thermal-Structural Analysis of a Waveguide Higher Order Mode Absorber

    SciTech Connect

    G. Cheng; E. F. Daly; R. A. Rimmer; M. Stirbet; L. Vogel; H. Wang; K. M. Wilson

    2007-07-03

    For an ongoing high current cryomodule project, a total of 5 higher order mode (HOM) absorbers are required per cavity. The load is designed to absorb Radio Frequency (RF) heat induced by HOMs in a 748.5MHz cavity. Each load is targeted at a 4 kW dissipation capability. Water cooling is employed to remove the heat generated in ceramic tiles and by surface losses on the waveguide walls. A sequentially coupled RF-thermal-structural analysis was developed in ANSYS to optimize the HOM load design. Frequency-dependent dielectric material properties measured from samples and RF power spectrum calculated by the beam-cavity interaction codes were considered. The coupled field analysis capability of ANSYS avoided mapping of results between separate RF and thermal/structural simulation codes. For verification purposes, RF results obtained from ANSYS were compared to those from MAFIA, HFSS, and Microwave Studio. Good agreement was reached and this confirms that multiple-field coupled analysis is a desirable choice in analysis of HOM loads. Similar analysis could be performed on other particle accelerator components where distributed RF heating and surface current induced losses are inevitable.

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

    PubMed Central

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

    2011-01-01

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

  7. Development of antibody arrays for monoclonal antibody Higher Order Structure analysis

    PubMed Central

    Wang, Xing; Li, Qing; Davies, Michael

    2013-01-01

    Antibody arrays were developed to probe a monoclonal antibody's three-dimensional structure (3-D structure). Peptides with overlapping regions were designed to cover the whole mAb light chain and heavy chain, respectively, and used to generate polyclonal antibodies after the conjugation of the peptides to a carrier protein, KLH. It was shown that good peptide specificity was achieved from the antibodies generated. Using more than 30 different polyclonal antibodies to measure the surface epitope distribution, it was shown that the mAb antibody array can detect epitope exposure as low as 0.1% of defined mAb populations. This ELISA-based analysis of mAb epitope exposure can be considered as a measurement of “conformational impurity” in biologics development, similar to the analysis of other product-related impurities such as different forms of glycosylation, deamidation, and oxidation. This analysis of “conformational impurity” could provide valuable information on the mAb conformational comparability for biosimilar mAbs as well as novel mAbs, especially in the area of protein immunogenicity. Furthermore, stability studies indicated that there are several conformational “hot spots” in many mAbs tested, especially in the hinge region. This antibody array technology can be used for novel mAb Higher Order Structure (HOS) analysis during process and formulation development. Another important area of application is for biosimilar mAb development where the innovator molecule and biosimilar molecule could be compared based on their systemic “fingerprint” from the 30 plus antibodies. PMID:23970865

  8. Higher-Order Theory: Structural/MicroAnalysis Code (HOTSMAC) Developed

    NASA Technical Reports Server (NTRS)

    Arnold, Steven M.

    2002-01-01

    The full utilization of advanced materials (be they composite or functionally graded materials) in lightweight aerospace components requires the availability of accurate analysis, design, and life-prediction tools that enable the assessment of component and material performance and reliability. Recently, a new commercially available software product called HOTSMAC (Higher-Order Theory--Structural/MicroAnalysis Code) was jointly developed by Collier Research Corporation, Engineered Materials Concepts LLC, and the NASA Glenn Research Center under funding provided by Glenn's Commercial Technology Office. The analytical framework for HOTSMAC is based on almost a decade of research into the coupled micromacrostructural analysis of heterogeneous materials. Consequently, HOTSMAC offers a comprehensive approach for analyzing/designing the response of components with various microstructural details, including certain advantages not always available in standard displacement-based finite element analysis techniques. The capabilities of HOTSMAC include combined thermal and mechanical analysis, time-independent and time-dependent material behavior, and internal boundary cells (e.g., those that can be used to represent internal cooling passages, see the preceding figure) to name a few. In HOTSMAC problems, materials can be randomly distributed and/or functionally graded (as shown in the figure, wherein the inclusions are distributed linearly), or broken down by strata, such as in the case of thermal barrier coatings or composite laminates.

  9. Solvent-Dependent Properties and Higher-Order Structures of Aryl Alcohol + Surfactant Molecular Gels.

    PubMed

    Katsube, Shotaro; Kinoshita, Masaru; Amano, Kenshi; Sato, Takaaki; Katsumoto, Yukiteru; Umecky, Tatsuya; Takamuku, Toshiyuki; Kaji, Toshihiko; Hiramoto, Masahiro; Tsurunaga, Yoko; Nishiyama, Katsura

    2016-05-01

    Molecular organogels, comprising small organic gelators in solvents, can be applied for dispersal of optical devices, such as emitters. Phenolic compounds and the surfactant bis(2-ethylhexyl) sulfosuccinate (AOT) are known examples of self-assembly organogels. However, conventional phenol + AOT gels in aromatic and acyclic alkane solvents are optically turbid, which is an obstacle for use as host materials in optical devices. In this study, a variety of aryl alcohol-AOT-solvent sets have been investigated systematically, and the correlation between the molecular architecture and optical transparency of the gels was considered. Accordingly, p-chlorophenol + AOT gels in cyclic alkane solvents were shown to form optically transparent gels. In contrast, aromatic and acyclic alkane solvents gave rise to turbid or opaque gels, even when utilizing the same gelators. AFM, NMR, SAXS, and FTIR were employed to determine the organogel structures. Consequently, we found that the gel transparency strongly depends on the size of the fibrous network of the gel, the structure of which is attributed to higher-order aggregates of the gelators. The average contour length and diameter of the fibrous network, lav and dav, respectively, were determined from AFM images. The transparent gels were shown to have lav = 4-9 μm and dav ≤ 0.3 μm, whereas the turbid gels had lav = 15 μm and dav = 0.4-0.6 μm. Such differences in the size of the fibrous network significantly affected the mechanical response of the gels, as shown by stress-strain measurements. PMID:27064848

  10. An Examination of the Higher-Order Structure of Psychopathology and Its Relationship to Personality.

    PubMed

    Uliaszek, Amanda A; Zinbarg, Richard E

    2016-04-01

    This study compared a series of higher-order models encompassing symptoms of both clinical and personality disorders. The final model was then correlated with a latent variable model of normal personality traits. A total of 420 undergraduates completed a battery of self-report symptom and personality questionnaires, with informant-reports and diagnostic interviews provided by overlapping subsamples. A three-level model with two factors at the highest level and four factors at the second level was the best fitting model. The higher-order internalizing and externalizing factors were then correlated with 30 latent personality facets. Results demonstrate an elevation on the neuroticism facets for the higher-order internalizing factor, along with low positive emotions, low actions, and low competence. The higher-order externalizing factor was negatively associated with most conscientiousness and agreeableness factors, while showing an elevation on excitement-seeking, impulsivity, and angry hostility. Future studies should replicate these models with the inclusion of more low base-rate disorders (i.e., psychosis). PMID:25893555

  11. The higher-order structure in the cells nucleus as the structural basis of the post-mitotic state.

    PubMed

    Aranda-Anzaldo, Armando; Dent, Myrna A R; Martínez-Gómez, Alejandro

    2014-05-01

    In metazoan cells during the interphase nuclear DNA is organized in supercoiled, topologically constrained loops anchored to a proteinaceous compartment or substructure commonly known as the nuclear matrix (NM). The DNA-NM interactions result from a thermodynamically-driven process leading to the necessary dissipation of structural stress along chromosomal DNA, otherwise the chromosomes would break into pieces. Such DNA-NM interactions define a nuclear higher-order structure that is independent of chromatin proteins. On the other hand, a metazoan cell no longer able to undergo mitosis is defined as post-mitotic and this condition indicates a terminally differentiated cell that may survive in such a state for indefinite time. The non-reversible nature of the post-mitotic state suggests a non-genetic basis for it since no spontaneous or induced mutations can revert it. Yet in individual cells the loss of proliferative potential has both a developmental and a stochastic component. Here we discuss evidence suggesting that the stability of the nuclear higher-order structure is the factor that links the stochastic and developmental components leading to the post-mitotic state. PMID:24556025

  12. Higher-order aggregate networks in the analysis of temporal networks: path structures and centralities

    NASA Astrophysics Data System (ADS)

    Scholtes, Ingo; Wider, Nicolas; Garas, Antonios

    2016-03-01

    Despite recent advances in the study of temporal networks, the analysis of time-stamped network data is still a fundamental challenge. In particular, recent studies have shown that correlations in the ordering of links crucially alter causal topologies of temporal networks, thus invalidating analyses based on static, time-aggregated representations of time-stamped data. These findings not only highlight an important dimension of complexity in temporal networks, but also call for new network-analytic methods suitable to analyze complex systems with time-varying topologies. Addressing this open challenge, here we introduce a novel framework for the study of path-based centralities in temporal networks. Studying betweenness, closeness and reach centrality, we first show than an application of these measures to time-aggregated, static representations of temporal networks yields misleading results about the actual importance of nodes. To overcome this problem, we define path-based centralities in higher-order aggregate networks, a recently proposed generalization of the commonly used static representation of time-stamped data. Using data on six empirical temporal networks, we show that the resulting higher-order measures better capture the true, temporal centralities of nodes. Our results demonstrate that higher-order aggregate networks constitute a powerful abstraction, with broad perspectives for the design of new, computationally efficient data mining techniques for time-stamped relational data.

  13. Maintenance of a functional higher order chromatin structure: The role of the nuclear matrix in normal and disease states

    PubMed Central

    Linnemann, Amelia K.; Krawetz, Stephen A.

    2010-01-01

    Summary The ordered packaging of DNA within the nucleus of somatic cells reflects a dynamic supportive structure that facilitates stable transcription interrupted by intermittent cycles of extreme condensation. This dynamic mode of packing and unpacking chromatin is intimately linked to the ability of the genome to specifically complex with both histones and non-histone proteins. Understanding the underlying mechanism that governs the formation of higher order chromatin structures is a key to understanding how local architecture modulates transcription. In part, the formation of these structures appears to be regulated through genomic looping that is dynamically mediated by attachment to the nuclear scaffold/matrix at S/MARs, i.e., Scaffold/Matrix Attachment Regions. Although the mechanism guiding the formation and use of these higher-ordered structures remains unknown, S/MARs continue to reveal a multitude of roles in development and the pathogenesis of disease. PMID:20948980

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

    PubMed Central

    Trousdale, James; Hu, Yu; Shea-Brown, Eric; Josić, Krešimir

    2013-01-01

    Emerging technologies are revealing the spiking activity in ever larger neural ensembles. Frequently, this spiking is far from independent, with correlations in the spike times of different cells. Understanding how such correlations impact the dynamics and function of neural ensembles remains an important open problem. Here we describe a new, generative model for correlated spike trains that can exhibit many of the features observed in data. Extending prior work in mathematical finance, this generalized thinning and shift (GTaS) model creates marginally Poisson spike trains with diverse temporal correlation structures. We give several examples which highlight the model's flexibility and utility. For instance, we use it to examine how a neural network responds to highly structured patterns of inputs. We then show that the GTaS model is analytically tractable, and derive cumulant densities of all orders in terms of model parameters. The GTaS framework can therefore be an important tool in the experimental and theoretical exploration of neural dynamics. PMID:23908626

  15. Higher Order Factor Structure of a Self-Control Test: Evidence from Confirmatory Factor Analysis with Polychoric Correlations.

    ERIC Educational Resources Information Center

    Flora, David B.; Finkel, Eli J.; Foshee, Vangie A.

    2003-01-01

    Studied the higher order factor structure of a self-control test developed by H. Grasmick and others (1993). Results for 1,966 eighth and ninth graders show that the self-control test may provide more valid measurement of the constructs it was designed to measure than previous research suggested. (SLD)

  16. The Effect of a Structured Story Reading Intervention, Story Retelling and Higher Order Thinking for English Language and Literacy Acquisition

    ERIC Educational Resources Information Center

    Cruz de Quiros, Ana M.; Lara-Alecio, Rafael; Tong, Fuhui; Irby, Beverly J.

    2012-01-01

    The purpose of this study was to investigate the effectiveness of structured story reading intervention, "S"tory re"T"elling and higher order thinking for "E"nglish "L"anguage and "L"iteracy "A"cquisition (STELLA), delivered to 38 Hispanic English language learners (ELL) placed in an enhanced transitional bilingual programme over 2 years from…

  17. Orthogonal Higher Order Factor Structure of the Stanford-Binet Intelligence Scales--Fifth Edition for Children and Adolescents

    ERIC Educational Resources Information Center

    Canivez, Gary L.

    2008-01-01

    Orthogonal higher-order factor structure of the Stanford-Binet Intelligence Scales-Fifth Edition (SB-5; Roid, 2003a) for child and adolescent samples is reported. Multiple criteria for factor extraction unanimously supported extraction of only one dimension and a unidimensional model. However, following results from DiStefano and Dombrowski (2006)…

  18. A symmetric modal formulation of fluid-structure interaction, including a static approximation to higher order fluid modes

    NASA Technical Reports Server (NTRS)

    Macneal, R. H.; Citerley, R.; Chargin, M.

    1980-01-01

    A method of fluid-structure coupling which provides symmetrical matrix equations of standard form solved by existing finite element computer programs is presented. The method postulates that the uncoupled vibration modes of the fluid or the structure be calculated before the coupled analysis. A numerical solution of vibration modes in an axisymmetric container demonstrated that a static approximation to higher order fluid modes can improve the accuracy of dynamic response computations using modal methods.

  19. Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures.

    PubMed

    Li, Rui; Zhu, Hongliang; Luo, Yunbo

    2016-01-01

    Although thousands of long non-coding RNAs (lncRNAs) have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure-function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq), selective 2'-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq), parallel analysis of RNA structure (PARS), and fragmentation sequencing (FragSeq). The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level. PMID:27196897

  20. Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures

    PubMed Central

    Li, Rui; Zhu, Hongliang; Luo, Yunbo

    2016-01-01

    Although thousands of long non-coding RNAs (lncRNAs) have been discovered in eukaryotes, very few molecular mechanisms have been characterized due to an insufficient understanding of lncRNA structure. Therefore, investigations of lncRNA structure and subsequent elucidation of the regulatory mechanisms are urgently needed. However, since lncRNA are high molecular weight molecules, which makes their crystallization difficult, obtaining information about their structure is extremely challenging, and the structures of only several lncRNAs have been determined so far. Here, we review the structure–function relationships of the widely studied lncRNAs found in the animal and plant kingdoms, focusing on the principles and applications of both in vitro and in vivo technologies for the study of RNA structures, including dimethyl sulfate-sequencing (DMS-seq), selective 2′-hydroxyl acylation analyzed by primer extension-sequencing (SHAPE-seq), parallel analysis of RNA structure (PARS), and fragmentation sequencing (FragSeq). The aim of this review is to provide a better understanding of lncRNA biological functions by studying them at the structural level. PMID:27196897

  1. Vibration suppression of laminated shell structures investigated using higher order shear deformation theory

    NASA Astrophysics Data System (ADS)

    Lee, S. J.; Reddy, J. N.

    2004-10-01

    Third-order shear deformation theories of laminated composite shells are developed using the strain-displacement relations of Donnell and Sanders theories. These theories also account for geometric nonlinearity in the von Kármán sense. Analytical (Navier) solutions for vibration suppression in cross-ply laminated composite shells with surface mounted smart material layers are developed using the linear versions of the two shell theories and for simply supported boundary conditions. Numerical results are presented to bring out the parametric effects of shell types (cylindrical, spherical, and doubly curved shells) and material properties on vibration suppression. A simple negative velocity feedback control in a closed loop is used.

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

    SciTech Connect

    Carlson, Carl E.; Vanderhaeghen, Marc

    2011-08-15

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

  3. Orthogonal higher order structure and confirmatory factor analysis of the French Wechsler Adult Intelligence Scale (WAIS-III).

    PubMed

    Golay, Philippe; Lecerf, Thierry

    2011-03-01

    According to the most widely accepted Cattell-Horn-Carroll (CHC) model of intelligence measurement, each subtest score of the Wechsler Intelligence Scale for Adults (3rd ed.; WAIS-III) should reflect both 1st- and 2nd-order factors (i.e., 4 or 5 broad abilities and 1 general factor). To disentangle the contribution of each factor, we applied a Schmid-Leiman orthogonalization transformation (SLT) to the standardization data published in the French technical manual for the WAIS-III. Results showed that the general factor accounted for 63% of the common variance and that the specific contributions of the 1st-order factors were weak (4.7%-15.9%). We also addressed this issue by using confirmatory factor analysis. Results indicated that the bifactor model (with 1st-order group and general factors) better fit the data than did the traditional higher order structure. Models based on the CHC framework were also tested. Results indicated that a higher order CHC model showed a better fit than did the classical 4-factor model; however, the WAIS bifactor structure was the most adequate. We recommend that users do not discount the Full Scale IQ when interpreting the index scores of the WAIS-III because the general factor accounts for the bulk of the common variance in the French WAIS-III. The 4 index scores cannot be considered to reflect only broad ability because they include a strong contribution of the general factor. PMID:21171782

  4. Higher order stationary subspace analysis

    NASA Astrophysics Data System (ADS)

    Panknin, Danny; von Bünau, Paul; Kawanabe, Motoaki; Meinecke, Frank C.; Müller, Klaus-Robert

    2016-03-01

    Non-stationarity in data is an ubiquitous problem in signal processing. The recent stationary subspace analysis procedure (SSA) has enabled to decompose such data into a stationary subspace and a non-stationary part respectively. Algorithmically only weak non- stationarities could be tackled by SSA. The present paper takes the conceptual step generalizing from the use of first and second moments as in SSA to higher order moments, thus defining the proposed higher order stationary subspace analysis procedure (HOSSA). The paper derives the novel procedure and shows simulations. An obvious trade-off between the necessity of estimating higher moments and the accuracy and robustness with which they can be estimated is observed. In an ideal setting of plenty of data where higher moment information is dominating our novel approach can win against standard SSA. However, with limited data, even though higher moments actually dominate the underlying data, still SSA may arrive on par.

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

    PubMed

    Mondal, Samiran; Begum, Nasim A; Hu, Wenjun; Honjo, Tasuku

    2016-03-15

    Activation-induced cytidine deaminase (AID) is essential for the somatic hypermutation (SHM) and class-switch recombination (CSR) of Ig genes. Although both the N and C termini of AID have unique functions in DNA cleavage and recombination, respectively, during SHM and CSR, their molecular mechanisms are poorly understood. Using a bimolecular fluorescence complementation (BiFC) assay combined with glycerol gradient fractionation, we revealed that the AID C terminus is required for a stable dimer formation. Furthermore, AID monomers and dimers form complexes with distinct heterogeneous nuclear ribonucleoproteins (hnRNPs). AID monomers associate with DNA cleavage cofactor hnRNP K whereas AID dimers associate with recombination cofactors hnRNP L, hnRNP U, and Serpine mRNA-binding protein 1. All of these AID/ribonucleoprotein associations are RNA-dependent. We propose that AID's structure-specific cofactor complex formations differentially contribute to its DNA-cleavage and recombination functions. PMID:26929374

  6. Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions

    PubMed Central

    Fabris, D.; Kellersberger, K.A.; Wilhide, J.A.

    2012-01-01

    Non-ergodic as well as ergodic activation methods are capable of maintaining the integrity of base pairs during the top-down analysis of nucleic acids. Here, we investigate the significance of this characteristic in the investigation of higher-order structures of increasing complexity. We show that cognate fragments produced by typical backbone cleavages may not be always detected as separate sequence ions, but rather as individual products that remain associated through mutual pairing contacts. This effect translates into unintended masking of cleavage events that take place in double-stranded regions, thus leading to the preferential detection of fragments originating from unpaired regions. Such effect is determined by the stability of the weak non-covalent association between complementary stretches, which is affected by base composition, length of the double-stranded structure, and charge of the precursor ion selected for analysis. Although such effect may prevent the achievement of full sequence coverage for primary structure determination, it may provide the key to correctly differentiate double- versus single-stranded regions, in what could be defined as gas-phase footprinting experiments. In light of the critical role played by base pairs in defining the higher-order structure of nucleic acids, these approaches will be expected to support an increased utilization of mass spectrometry for the investigation of nucleic acid structure and dynamics. PMID:24027423

  7. Rapid separable analysis of higher order correlators in large-scale structure

    NASA Astrophysics Data System (ADS)

    Fergusson, J. R.; Regan, D. M.; Shellard, E. P. S.

    2012-09-01

    We present an efficient separable approach to the estimation and reconstruction of the bispectrum and the trispectrum from observational (or simulated) large-scale structure data. This is developed from general cosmic microwave background (poly)spectra methods that exploit the fact that the bispectrum and trispectrum in the literature can be represented by a separable mode expansion that converges rapidly (with nmax⁡=O(30) terms). The underlying methodology can encompass a wide variety of modal types, including polynomials, trigonometric functions, wavelets, and bins. With an effective grid resolution lmax⁡ (number of particles/grid points N=lmax⁡3), we present a bispectrum estimator that requires only O(nmax⁡×lmax⁡3) operations, along with a corresponding method for direct bispectrum reconstruction. This method is extended to the trispectrum revealing an estimator that requires only O(nmax⁡4/3×lmax⁡3) operations. The complexity in calculating the trispectrum in this method is now involved in the original decomposition and orthogonalization process that need only be performed once for each model. However, for nondiagonal trispectra these processes present little extra difficulty and may be performed in O(lmax⁡4) operations. A discussion of how the methodology may be applied to the quadspectrum is also given. An efficient algorithm for the generation of arbitrary non-Gaussian initial conditions for use in N-body codes using this separable approach is described. This prescription allows for the production of non-Gaussian initial conditions for arbitrary bispectra and trispectra. A brief outline of the key issues involved in parameter estimation, particularly in the nonlinear regime, is also given.

  8. Higher order turbulence closure models

    NASA Technical Reports Server (NTRS)

    Amano, Ryoichi S.; Chai, John C.; Chen, Jau-Der

    1988-01-01

    Theoretical models are developed and numerical studies conducted on various types of flows including both elliptic and parabolic. The purpose of this study is to find better higher order closure models for the computations of complex flows. This report summarizes three new achievements: (1) completion of the Reynolds-stress closure by developing a new pressure-strain correlation; (2) development of a parabolic code to compute jets and wakes; and, (3) application to a flow through a 180 deg turnaround duct by adopting a boundary fitted coordinate system. In the above mentioned models near-wall models are developed for pressure-strain correlation and third-moment, and incorporated into the transport equations. This addition improved the results considerably and is recommended for future computations. A new parabolic code to solve shear flows without coordinate tranformations is developed and incorporated in this study. This code uses the structure of the finite volume method to solve the governing equations implicitly. The code was validated with the experimental results available in the literature.

  9. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus.

    PubMed

    Yang, Rui; Kerschner, Jenny L; Gosalia, Nehal; Neems, Daniel; Gorsic, Lidija K; Safi, Alexias; Crawford, Gregory E; Kosak, Steven T; Leir, Shih-Hsing; Harris, Ann

    2016-04-20

    Higher order chromatin structure establishes domains that organize the genome and coordinate gene expression. However, the molecular mechanisms controlling transcription of individual loci within a topological domain (TAD) are not fully understood. The cystic fibrosis transmembrane conductance regulator (CFTR) gene provides a paradigm for investigating these mechanisms.CFTR occupies a TAD bordered by CTCF/cohesin binding sites within which are cell-type-selective cis-regulatory elements for the locus. We showed previously that intronic and extragenic enhancers, when occupied by specific transcription factors, are recruited to the CFTR promoter by a looping mechanism to drive gene expression. Here we use a combination of CRISPR/Cas9 editing of cis-regulatory elements and siRNA-mediated depletion of architectural proteins to determine the relative contribution of structural elements and enhancers to the higher order structure and expression of the CFTR locus. We found the boundaries of the CFTRTAD are conserved among diverse cell types and are dependent on CTCF and cohesin complex. Removal of an upstream CTCF-binding insulator alters the interaction profile, but has little effect on CFTR expression. Within the TAD, intronic enhancers recruit cell-type selective transcription factors and deletion of a pivotal enhancer element dramatically decreases CFTR expression, but has minor effect on its 3D structure. PMID:26673704

  10. Higher-order organization of complex networks.

    PubMed

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

    2016-07-01

    Networks are a fundamental tool for understanding and modeling complex systems in physics, biology, neuroscience, engineering, and social science. Many networks are known to exhibit rich, lower-order connectivity patterns that can be captured at the level of individual nodes and edges. However, higher-order organization of complex networks--at the level of small network subgraphs--remains largely unknown. Here, we develop a generalized framework for clustering networks on the basis of higher-order connectivity patterns. This framework provides mathematical guarantees on the optimality of obtained clusters and scales to networks with billions of edges. The framework reveals higher-order organization in a number of networks, including information propagation units in neuronal networks and hub structure in transportation networks. Results show that networks exhibit rich higher-order organizational structures that are exposed by clustering based on higher-order connectivity patterns. PMID:27387949

  11. A Role for LHC1 in Higher Order Structure and Complement Binding of the Cryptococcus neoformans Capsule

    PubMed Central

    Park, Yoon-Dong; Shin, Soowan; Panepinto, John; Ramos, Jeanie; Qiu, Jin; Frases, Susana; Albuquerque, Patricia; Cordero, Radames J. B.; Zhang, Nannan; Himmelreich, Uwe; Beenhouwer, David; Bennett, John E.; Casadevall, Arturo; Williamson, Peter R.

    2014-01-01

    Polysaccharide capsules are important virulence factors for many microbial pathogens including the opportunistic fungus Cryptococcus neoformans. In the present study, we demonstrate an unusual role for a secreted lactonohydrolase of C. neoformans, LHC1 in capsular higher order structure. Analysis of extracted capsular polysaccharide from wild-type and lhc1Δ strains by dynamic and static light scattering suggested a role for the LHC1 locus in altering the capsular polysaccharide, both reducing dimensions and altering its branching, density and solvation. These changes in the capsular structure resulted in LHC1-dependent alterations of antibody binding patterns, reductions in human and mouse complement binding and phagocytosis by the macrophage-like cell line J774, as well as increased virulence in mice. These findings identify a unique molecular mechanism for tertiary structural changes in a microbial capsule, facilitating immune evasion and virulence of a fungal pathogen. PMID:24789368

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

    PubMed Central

    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

  13. Higher-order mode absorption measurement of X-band choke-mode cavities in a radial line structure

    NASA Astrophysics Data System (ADS)

    Zha, Hao; Shi, Jiaru; Wu, Xiaowei; Chen, Huaibi

    2016-04-01

    An experiment is presented to study the higher-order mode (HOM) suppression of X-band choke-mode structures with a vector network analyzer (VNA). Specific radial line disks were built to test the reflection from the corresponding damping load and different choke geometries. The mismatch between the radial lines and the VNA was calibrated through a special multi-short-load calibration method. The measured reflections of different choke geometries showed good agreement with the theoretical calculations and verified the HOM absorption feature of each geometric design.

  14. Higher-order derivative correlations and the alignment of small-scale structures in isotropic numerical turbulence

    NASA Technical Reports Server (NTRS)

    Kerr, R. A.

    1983-01-01

    In a three dimensional simulation higher order derivative correlations, including skewness and flatness factors, are calculated for velocity and passive scalar fields and are compared with structures in the flow. The equations are forced to maintain steady state turbulence and collect statistics. It is found that the scalar derivative flatness increases much faster with Reynolds number than the velocity derivative flatness, and the velocity and mixed derivative skewness do not increase with Reynolds number. Separate exponents are found for the various fourth order velocity derivative correlations, with the vorticity flatness exponent the largest. Three dimensional graphics show strong alignment between the vorticity, rate of strain, and scalar-gradient fields. The vorticity is concentrated in tubes with the scalar gradient and the largest principal rate of strain aligned perpendicular to the tubes. Velocity spectra, in Kolmogorov variables, collapse to a single curve and a short minus 5/3 spectral regime is observed.

  15. Higher order differential-integral microphone arrays.

    PubMed

    Abhayapala, Thushara D; Gupta, Aastha

    2010-05-01

    This paper develops theory to design higher order directional microphone arrays. The proposed higher order designs have similar inter sensor spacings as traditional first and second order differential arrays. The Jacobi-Anger expansion is used to exploit the underlying structure of microphone signals from pairs of closely spaced sensors. Specifically, the difference and sum of these microphone signals are processed to design the novel directional array. PMID:21117719

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

    NASA Technical Reports Server (NTRS)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    1998-01-01

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

  17. Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures.

    PubMed

    Zarudnaya, Margarita I; Kolomiets, Iryna M; Potyahaylo, Andriy L; Hovorun, Dmytro M

    2003-03-01

    Primary, secondary and higher-order structures of downstream elements of mammalian pre-mRNA polyadenylation signals [poly(A) signals] are re viewed. We have carried out a detailed analysis on our database of 244 human pre-mRNA poly(A) signals in order to characterize elements in their downstream regions. We suggest that the downstream region of the mammalian pre-mRNA poly(A) signal consists of various simple elements located at different distances from each other. Thus, the downstream region is not described by any precise consensus. Searching our database, we found that approximately 80% of pre-mRNAs with the AAUAAA or AUUAAA core upstream elements contain simple downstream elements, consisting of U-rich and/or 2GU/U tracts, the former occurring approximately 2-fold more often than the latter. Approximately one-third of the pre-mRNAs analyzed here contain sequences that may form G-quadruplexes. A substantial number of these sequences are located immediately downstream of the poly(A) signal. A possible role of G-rich sequences in the polyadenylation process is discussed. A model of the secondary structure of the SV40 late pre-mRNA poly(A) signal downstream region is presented. PMID:12595544

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

    PubMed Central

    Fabris, Daniele; Yu, Eizadora T.

    2010-01-01

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

  19. DGCR8 recognizes primary transcripts of microRNAs through highly cooperative binding and formation of higher-order structures

    PubMed Central

    Faller, Michael; Toso, Daniel; Matsunaga, Michio; Atanasov, Ivo; Senturia, Rachel; Chen, Yanqiu; Zhou, Z. Hong; Guo, Feng

    2010-01-01

    DiGeorge critical region 8 (DGCR8) is essential for maturation of microRNAs (miRNAs) in animals. In the cleavage of primary transcripts of miRNAs (pri-miRNAs) by the Drosha nuclease, the DGCR8 protein directly binds and recognizes pri-miRNAs through a mechanism currently controversial. Our previous data suggest that DGCR8 trimerizes upon cooperative binding to pri-mir-30a. However, a separate study proposed a model in which a DGCR8 molecule contacts one or two pri-miRNA molecules using its two double-stranded RNA binding domains. Here, we extensively characterized the interaction between DGCR8 and pri-miRNAs using biochemical and structural methods. First, a strong correlation was observed between the association of DGCR8 with pri-mir-30a and the rate of pri-miRNA processing in vitro. Second, we show that the high binding cooperativity allows DGCR8 to distinguish pri-miRNAs from a nonspecific competitor with subtle differences in dissociation constants. The highly cooperative binding of DGCR8 to a pri-miRNA is mediated by the formation of higher-order structures, most likely a trimer of DGCR8 dimers, on the pri-miRNA. These properties are not limited to its interaction with pri-mir-30a. Furthermore, the amphipathic C-terminal helix of DGCR8 is important both for trimerization of DGCR8 on pri-miRNAs and for the cleavage of pri-miRNAs by Drosha. Finally, our three-dimensional model from electron tomography analysis of the negatively stained DGCR8–pri-mir-30a complex directly supports the trimerization model. Our study provides a molecular basis for recognition of pri-miRNAs by DGCR8. We further propose that the higher-order structures of the DGCR8–pri-miRNA complexes trigger the cleavage of pri-miRNAs by Drosha. PMID:20558544

  20. Quantitative assessment of higher-order chromatin structure of the INK4/ARF locus in human senescent cells.

    PubMed

    Hirosue, Akiyuki; Ishihara, Ko; Tokunaga, Kazuaki; Watanabe, Takehisa; Saitoh, Noriko; Nakamoto, Masafumi; Chandra, Tamir; Narita, Masashi; Shinohara, Masanori; Nakao, Mitsuyoshi

    2012-06-01

    Somatic cells can be reset to oncogene-induced senescent (OIS) cells or induced pluripotent stem (iPS) cells by expressing specified factors. The INK4/ARF locus encodes p15(INK4b) , ARF, and p16(INK4a) genes in human chromosome 9p21, the products of which are known as common key reprogramming regulators. Compared with growing fibroblasts, the CCCTC-binding factor CTCF is remarkably up-regulated in iPS cells with silencing of the three genes in the locus and is reversely down-regulated in OIS cells with high expression of p15(INK4b) and p16(INK4a) genes. There are at least three CTCF-enriched sites in the INK4/ARF locus, which possess chromatin loop-forming activities. These CTCF-enriched sites and the p16(INK4a) promoter associate to form compact chromatin loops in growing fibroblasts, while CTCF depletion disrupts the loop structure. Interestingly, the loose chromatin structure is found in OIS cells. In addition, the INK4/ARF locus has an intermediate type of chromatin compaction in iPS cells. These results suggest that senescent cells have distinct higher-order chromatin signature in the INK4/ARF locus. PMID:22340434

  1. Comparability of higher order structure in proteins: chemometric analysis of second-derivative amide I Fourier transform infrared spectra.

    PubMed

    Stockdale, Gregory; Murphy, Brian M; D'Antonio, Jennifer; Manning, Mark Cornell; Al-Azzam, Wasfi

    2015-01-01

    Comparing higher order structure (HOS) in therapeutic proteins is a significant challenge. Previously, we showed that changes in solution conditions produced detectable changes in the second-derivative amide I Fourier transform infrared (FTIR) spectra for a variety of model proteins. Those comparisons utilized vector-based approaches, such as spectral overlap and spectral correlation coefficients to quantify differences between spectra. In this study, chemometric analyses of the same data were performed, to classify samples into different groups based on the solution conditions received. The solution conditions were composed of various combinations of temperature, pH, and salt types. At first, principal component analysis (PCA) was used to visually demonstrate that FTIR spectra respond to changes in solution conditions, which, presumably indicates variations in HOS. This observed when samples from the same solution condition form clusters within a PCA score plot. The second approach, called soft independent modeling of class analogy (SIMCA), was conducted to account for the within-class experimental error for the lysozyme spectra. The DModX values, indicative of the distance of each spectra to their respective class models, was found to be a more sensitive quantitative indicator of changes in HOS, when compared with the modified area of overlap algorithm. The SIMCA approach provides a metric to determine whether new observations do, or do not belong to a particular class or group. Thus, SIMCA is the recommended approach when multiple samples from each condition are available. PMID:25382804

  2. Higher order nonlinear effects on wave structures in a four-component dusty plasma with nonisothermal electrons

    SciTech Connect

    Singh Gill, Tarsem; Bedi, Chanchal; Saini, Nareshpal Singh

    2011-04-15

    The higher order solutions of dust acoustic wave in dusty plasma consisting of positively charged warm adiabatic dust, negatively charged cold dust, and nonisothermally distributed electrons are studied. The Schamel-KdV equation is derived using reductive perturbation method (RPM). RPM is further extended to include the contributions of higher order terms and a generalized KdV equation is derived to observe the deviation from isothermality. Effects of nonisothermal parameter, mass and charge ratio, ratio of ion to electron temperatures, and ratio of dust to ion temperatures have been thoroughly studied. By using the renormalization method of Kodama and Taniuti [J. Phys. Soc. Jpn. 45, 298 (1978)], authors have also discussed characteristics of the dressed solitons.

  3. Exploded view of higher order G-quadruplex structures through click-chemistry assisted single-molecule mechanical unfolding.

    PubMed

    Selvam, Sangeetha; Yu, Zhongbo; Mao, Hanbin

    2016-01-01

    Due to the long-range nature of high-order interactions between distal components in a biomolecule, transition dynamics of tertiary structures is often too complex to profile using conventional methods. Inspired by the exploded view in mechanical drawing, here, we used laser tweezers to mechanically dissect high-order DNA structures into two constituting G-quadruplexes in the promoter of the human telomerase reverse transcriptase (hTERT) gene. Assisted with click-chemistry coupling, we sandwiched one G-quadruplex with two dsDNA handles while leaving the other unit free. Mechanical unfolding through these handles revealed transition dynamics of the targeted quadruplex in a native environment, which is named as native mechanical segmentation (NMS). Comparison between unfolding of an NMS construct and that of truncated G-quadruplex constructs revealed a quadruplex-quadruplex interaction with 2 kcal/mol stabilization energy. After mechanically targeting the two G-quadruplexes together, the same interaction was observed during the first unfolding step. The unfolding then proceeded through disrupting the weaker G-quadruplex at the 5'-end, followed by the stronger G-quadruplex at the 3'-end via various intermediates. Such a pecking order in unfolding well reflects the hierarchical nature of nucleic acid structures. With surgery-like precisions, we anticipate this NMS approach offers unprecedented perspective to decipher dynamic transitions in complex biomacromolecules. PMID:26626151

  4. Exploded view of higher order G-quadruplex structures through click-chemistry assisted single-molecule mechanical unfolding

    PubMed Central

    Selvam, Sangeetha; Yu, Zhongbo; Mao, Hanbin

    2016-01-01

    Due to the long-range nature of high-order interactions between distal components in a biomolecule, transition dynamics of tertiary structures is often too complex to profile using conventional methods. Inspired by the exploded view in mechanical drawing, here, we used laser tweezers to mechanically dissect high-order DNA structures into two constituting G-quadruplexes in the promoter of the human telomerase reverse transcriptase (hTERT) gene. Assisted with click-chemistry coupling, we sandwiched one G-quadruplex with two dsDNA handles while leaving the other unit free. Mechanical unfolding through these handles revealed transition dynamics of the targeted quadruplex in a native environment, which is named as native mechanical segmentation (NMS). Comparison between unfolding of an NMS construct and that of truncated G-quadruplex constructs revealed a quadruplex–quadruplex interaction with 2 kcal/mol stabilization energy. After mechanically targeting the two G-quadruplexes together, the same interaction was observed during the first unfolding step. The unfolding then proceeded through disrupting the weaker G-quadruplex at the 5′-end, followed by the stronger G-quadruplex at the 3′-end via various intermediates. Such a pecking order in unfolding well reflects the hierarchical nature of nucleic acid structures. With surgery-like precisions, we anticipate this NMS approach offers unprecedented perspective to decipher dynamic transitions in complex biomacromolecules. PMID:26626151

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

    SciTech Connect

    Gee, Anthony; Shin, Young-Min; Accelerator Physics Center , Fermi National Accelerator Laboratory , Batavia, Illinois 60510

    2013-07-15

    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{sub 31} mode) with ∼28% cold bandwidth. Analytic gain calculation indicates that in the SWS, TM{sub 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.

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

    SciTech Connect

    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.

  7. Analogy, higher order thinking, and education.

    PubMed

    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. PMID:26263071

  8. Higher-order dielectrophoresis of nonspherical particles

    NASA Astrophysics Data System (ADS)

    Nili, Hossein; Green, Nicolas G.

    2014-06-01

    Higher-order terms of dielectrophoretic (DEP) force are commonly ignored by invoking the simplifying dipole approximation. Concurrently, the trend towards micro- and nano-electrode structures in DEP design is bringing about an increasing number of instances where the approximation is expected to lose reliability. The case is severe for nonspherical particles (the shape of many biological particles) due to the shape-dependent nature of dielectric polarization. However, there is a lack of analytical means to determine multipole moments of nonspherical particles, numerical calculations of the same are regarded as unreliable, and there is a prevalence for higher-order force considerations to be ignored. As a result, the dipole approximation is used and/or nonspherical particles are approximated as spheres. This work proves the inefficacy of current qualitative criteria for the reliability of the dipole approximation and presents a quantitative substitute, with verified accuracy, that enables precise determination of the extent to which the dipole approximation would be reliable, and if found unreliable, corrects the approximation by adding second- and third-order terms of the DEP force. The effects of field nonuniformity, electrode design, and particle shape and aspect ratio on the significance of higher-order DEP forces is quantitatively analyzed. The results show that higher-order DEP forces are indeed of substantially increased significance for nonspherical particles; in the cases examined in this work, multipolar terms are seen to constitute more than 40% of the total force on ellipsoidal and cylindrical particles. It is further shown that approximating nonspherical particles as spheres of similar dimensions is subject to substantial error. Last, the substantial importance of the electrode design in influencing higher-order forces is shown.

  9. Higher order architecture of collections of objects

    NASA Astrophysics Data System (ADS)

    Baas, Nils A.

    2015-01-01

    We show that on an arbitrary collection of objects there is a wide variety of higher order architectures governed by hyperstructures. Higher order gluing, local to global processes, fusion of collections, bridges and higher order types are discussed. We think that these types of architectures may have interesting applications in many areas of science.

  10. Higher-Order Factors in Structure-of-Intellect (SOI) Aptitude Tests Hypothesized to Portray Constructs of Military Leadership: A Re-analysis of an SOI Data Base.

    ERIC Educational Resources Information Center

    Ulosevich, Steven N.; And Others

    1991-01-01

    A correlation matrix of 21 structure-of-intellect (SOI) tests taken by 204 Marine officers at a military base in Southern California, which was intended to reflect aptitudes for military leadership, was reanalyzed through exploratory factor analysis and confirmatory maximum likelihood factor analysis. Higher order factors appeared to have…

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

    ERIC Educational Resources Information Center

    Canivez, Gary L.; Watkins, Marley W.

    2010-01-01

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

  12. Crystallographic Studies on the Mechanisms of the Cluster Formation and the Higher Order Structure Evolution of Mixed-valence Polyoxometalates

    NASA Astrophysics Data System (ADS)

    Ozeki, Tomoji

    The advantages of the use of synchrotron radiation for single crystal X-ray diffraction experiments were exploited to obtain a deeper understanding of the chemistry of polyoxometalates through structural investigations. The pH dependence of the structures of {Mo154-x} mixed-valence oxomolybdate clusters were investigated by analyzing the structures of systematically prepared compounds containing wheel-shaped mixed-valence polyoxometalates with 138, 142, 148, 150, or 152 molybdenum atoms. Direct correlation was observed between the nuclearity of the clusters with the pH of the mother liquor. On the other hand, the geometries of extended structures do not show apparent correlation with the pH. They turned out to be determined by the structures of the constituent polyoxometalate. The pH of the mother liquor exerts influence on the extended structure through the structures of the constituent clusters. Such systematic preparation—structure determination study was enabled by the use of synchrotron radiation.

  13. Resonant radiation from oscillating higher order solitons.

    PubMed

    Driben, R; Yulin, A V; Efimov, A

    2015-07-27

    We present radiation mechanism exhibited by a higher order soliton. In a course of its evolution the higher-order soliton emits polychromatic radiation resulting in formation of multipeak frequency comb-like spectral band. The shape and spectral position of this band can be effectively controlled by the relative strength of the third order dispersion. An analytical description is corroborated by numerical simulations. It is shown that for longer pulses the described effect persists also under the action of higher order perturbations such as Raman and self-steepening. PMID:26367574

  14. Resonant radiation from oscillating higher order solitons

    SciTech Connect

    Driben, R.; Yulin, A. V.; Efimov, A.

    2015-07-15

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

  15. Higher order Godunov schemes for isothermal hydrodynamics

    NASA Technical Reports Server (NTRS)

    Balsara, Dinshaw S.

    1994-01-01

    In this paper we construct higher order Godunov schemes for isothermal flow. Isothermal hydrodynamics serves as a good representation for several systems of astrophysical interest. The schemes designed here have second-order accuracy in space and time and some are third-order accurate for advection. Moreover, several ingredients of these schemes are essential components of even higher order. The methods designed here have excellent ability to represent smooth flow yet capture shocks with high resolution. Several test problems are presented. The algorithms presented here are compared with other algorithms having a comparable formal order of accuracy.

  16. Orthogonal Higher Order Structure and Confirmatory Factor Analysis of the French Wechsler Adult Intelligence Scale (WAIS-III)

    ERIC Educational Resources Information Center

    Golay, Philippe; Lecerf, Thierry

    2011-01-01

    According to the most widely accepted Cattell-Horn-Carroll (CHC) model of intelligence measurement, each subtest score of the Wechsler Intelligence Scale for Adults (3rd ed.; WAIS-III) should reflect both 1st- and 2nd-order factors (i.e., 4 or 5 broad abilities and 1 general factor). To disentangle the contribution of each factor, we applied a…

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

    PubMed

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

    2009-04-01

    Most studies about the higher-order dimensions to be considered in order to parsimoniously describe Personality Disorders (PDs) have identified between two and four factors but there is still no consensus about their exact number. In this context, the cultural stability of these structures might be a criterion to be considered. The aim of this study was to identify stable higher-order structures of PD traits in a French-speaking African and Swiss sample (N = 2,711). All subjects completed the IPDE screening questionnaire. Using Everett's criterion and conducting a series of principal component analyses, a cross-culturally stable two- and four-factor structure were identified, associated with a total congruence coefficient of .98 and .94, respectively, after Procrustes rotation. Moreover, these two structures were also highly replicable across the four African regions considered, North Africa, West Africa, Central Africa, and Mauritius, with a mean total congruence coefficient of .97 and .87, respectively. The four-factor structure presented the advantage of being similar to Livesely's four components and of describing the ten PDs more accurately. PMID:19379094

  18. Factor Structure and Validity of Paper-and-Pencil Measures of Mental Speed: Evidence for a Higher-Order Model?

    ERIC Educational Resources Information Center

    Danthiir, Vanessa; Wilhelm, Oliver; Schulze, Ralf; Roberts, Richard D.

    2005-01-01

    This study explored the structure of elementary cognitive tasks (ECTs) and relations between the corresponding construct(s) with processing speed (Gs) and fluid intelligence (Gf). Participants (N=321) completed 14 ECTs, 3 Gs, and 6 Gf marker tests, all administered in paper-and-pencil format to reduce potential confounds evident when tasks are…

  19. Higher-Order Factor Structure of the Differential Ability Scales-II: Consistency across Ages 4 to 17

    ERIC Educational Resources Information Center

    Keith, Timothy Z.; Low, Justin A.; Reynolds, Matthew R.; Patel, Puja G.; Ridley, Kristen P.

    2010-01-01

    The recently published second edition of the Differential Abilities Scale (DAS-II) is designed to measure multiple broad and general abilities from Cattell-Horn-Carroll (CHC) theory. Although the technical manual presents information supporting the test's structure, additional research is needed to determine the constructs measured by the test and…

  20. Applicability/evaluation of flux based representations for linear/higher order elements for heat transfer in structures - Generalized gamma(T)-family

    NASA Technical Reports Server (NTRS)

    Namburu, R. R.; Tamma, K. K.

    1991-01-01

    The applicability and evaluation of a generalized gamma(T) family of flux-based representations are examined for two different thermal analysis formulations for structures and materials which exhibit no phase change effects. The so-called H-theta and theta forms are demonstrated for numerous test models and linear and higher-order elements. The results show that the theta form with flux-based representations is generally superior to traditional approaches.

  1. Extreme brain events: Higher-order statistics of brain resting activity and its relation with structural connectivity

    NASA Astrophysics Data System (ADS)

    Amor, T. A.; Russo, R.; Diez, I.; Bharath, P.; Zirovich, M.; Stramaglia, S.; Cortes, J. M.; de Arcangelis, L.; Chialvo, D. R.

    2015-09-01

    The brain exhibits a wide variety of spatiotemporal patterns of neuronal activity recorded using functional magnetic resonance imaging as the so-called blood-oxygenated-level-dependent (BOLD) signal. An active area of work includes efforts to best describe the plethora of these patterns evolving continuously in the brain. Here we explore the third-moment statistics of the brain BOLD signals in the resting state as a proxy to capture extreme BOLD events. We find that the brain signal exhibits typically nonzero skewness, with positive values for cortical regions and negative values for subcortical regions. Furthermore, the combined analysis of structural and functional connectivity demonstrates that relatively more connected regions exhibit activity with high negative skewness. Overall, these results highlight the relevance of recent results emphasizing that the spatiotemporal location of the relatively large-amplitude events in the BOLD time series contains relevant information to reproduce a number of features of the brain dynamics during resting state in health and disease.

  2. Higher-Order Neural Networks Recognize Patterns

    NASA Technical Reports Server (NTRS)

    Reid, Max B.; Spirkovska, Lilly; Ochoa, Ellen

    1996-01-01

    Networks of higher order have enhanced capabilities to distinguish between different two-dimensional patterns and to recognize those patterns. Also enhanced capabilities to "learn" patterns to be recognized: "trained" with far fewer examples and, therefore, in less time than necessary to train comparable first-order neural networks.

  3. Using Reflection to Develop Higher Order Processes

    ERIC Educational Resources Information Center

    Lerch, Carol; Bilics, Andrea; Colley, Binta

    2006-01-01

    The main purpose of this study was to look at how we used specific writing assignments in our courses to encourage metacognitive reflection in order to increase the learning that takes place. The study also aimed to aid in the development of higher order processing skills through the development of student reflection. The students involved in the…

  4. Human motion perception: Higher-order organization

    NASA Technical Reports Server (NTRS)

    Kaiser, Mary K.; Proffitt, Dennis R.

    1990-01-01

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

  5. Higher-order awareness, misrepresentation and function.

    PubMed

    Rosenthal, David

    2012-05-19

    Conscious mental states are states we are in some way aware of. I compare higher-order theories of consciousness, which explain consciousness by appeal to such higher-order awareness (HOA), and first-order theories, which do not, and I argue that higher-order theories have substantial explanatory advantages. The higher-order nature of our awareness of our conscious states suggests an analogy with the metacognition that figures in the regulation of psychological processes and behaviour. I argue that, although both consciousness and metacognition involve higher-order psychological states, they have little more in common. One thing they do share is the possibility of misrepresentation; just as metacognitive processing can misrepresent one's cognitive states and abilities, so the HOA in virtue of which one's mental states are conscious can, and sometimes does, misdescribe those states. A striking difference between the two, however, has to do with utility for psychological processing. Metacognition has considerable benefit for psychological processing; in contrast, it is unlikely that there is much, if any, utility to mental states' being conscious over and above the utility those states have when they are not conscious. PMID:22492758

  6. Higher-order awareness, misrepresentation and function

    PubMed Central

    Rosenthal, David

    2012-01-01

    Conscious mental states are states we are in some way aware of. I compare higher-order theories of consciousness, which explain consciousness by appeal to such higher-order awareness (HOA), and first-order theories, which do not, and I argue that higher-order theories have substantial explanatory advantages. The higher-order nature of our awareness of our conscious states suggests an analogy with the metacognition that figures in the regulation of psychological processes and behaviour. I argue that, although both consciousness and metacognition involve higher-order psychological states, they have little more in common. One thing they do share is the possibility of misrepresentation; just as metacognitive processing can misrepresent one's cognitive states and abilities, so the HOA in virtue of which one's mental states are conscious can, and sometimes does, misdescribe those states. A striking difference between the two, however, has to do with utility for psychological processing. Metacognition has considerable benefit for psychological processing; in contrast, it is unlikely that there is much, if any, utility to mental states' being conscious over and above the utility those states have when they are not conscious. PMID:22492758

  7. The exception that confirms the rule: a higher-order telomeric G-quadruplex structure more stable in sodium than in potassium

    PubMed Central

    Saintomé, Carole; Amrane, Samir; Mergny, Jean-Louis; Alberti, Patrizia

    2016-01-01

    DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and protein-binding assays), we show that the (GGGTTA)7GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45°C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higher-order structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium. PMID:26762980

  8. The exception that confirms the rule: a higher-order telomeric G-quadruplex structure more stable in sodium than in potassium.

    PubMed

    Saintomé, Carole; Amrane, Samir; Mergny, Jean-Louis; Alberti, Patrizia

    2016-04-01

    DNA and RNA guanine-quadruplexes (G4s) are stabilized by several cations, in particular by potassium and sodium ions. Generally, potassium stabilizes guanine-quartet assemblies to a larger extent than sodium; in this article we report about a higher-order G4 structure more stable in sodium than in potassium. Repeats of the DNA GGGTTA telomeric motif fold into contiguous G4 units. Using three independent approaches (thermal denaturation experiments, isothermal molecular-beacon and protein-binding assays), we show that the (GGGTTA)7GGG sequence, folding into two contiguous G4 units, exhibits an unusual feature among G4 motifs: despite a lower thermal stability, its sodium conformation is more stable than its potassium counterpart at physiological temperature. Using differential scanning calorimetry and mutated sequences, we show that this switch in the relative stability of the sodium and potassium conformations (occurring around 45 °C in 100 mM cation concentration) is the result of a more favorable enthalpy change upon folding in sodium, generated by stabilizing interactions between the two G4 units in the sodium conformation. Our work demonstrates that interactions between G4 structural domains can make a higher-order structure more stable in sodium than in potassium, even though its G4 structural domains are individually more stable in potassium than in sodium. PMID:26762980

  9. Interaction of chromatin with NaCl and MgCl2. Solubility and binding studies, transition to and characterization of the higher-order structure.

    PubMed

    Ausio, J; Borochov, N; Seger, D; Eisenberg, H

    1984-08-15

    Chicken erythrocyte chromatin containing histones H1 and H5 was carefully separated into a number of well-characterized fractions. A distinction could be made between chromatin insoluble in NaCl above about 80 mM, and chromatin soluble at all NaCl concentrations. Both chromatin forms were indistinguishable electrophoretically and both underwent the transition from the low salt "10 nm" coil to the "30 nm" higher-order structure solenoid by either raising the MgCl2 concentration to about 0.3 mM or the NaCl concentration to about 75 mM. The transitions were examined in detail by elastic light-scattering procedures. It could be shown that the 10 nm form is a flexible coil. For the 30 nm solenoid, the assumption of a rigid cylindrical structure was in good agreement with 5.7 nucleosomes per helical turn. However, disagreement of calculated frictional parameters with values derived from quasielastic light-scattering and sedimentation introduced the possibility that the higher-order structure, under these conditions, is more extended, flexible, or perhaps a mixture of structures. Values for density and refractive index increments of chromatin are also given. To understand the interaction of chromatin with NaCl and with MgCl2, a number of experiments were undertaken to study solubility, precipitation, conformational transitions and binding of ions over a wide range of experimental conditions, including chromatin concentration. PMID:6471101

  10. Second- and higher-order structural changes of DNA induced by antitumor-active tetrazolato-bridged dinuclear platinum(II) complexes with different types of 5-substituent.

    PubMed

    Uemura, Masako; Yoshikawa, Yuko; Yoshikawa, Kenichi; Sato, Takaji; Mino, Yoshiki; Chikuma, Masahiko; Komeda, Seiji

    2013-10-01

    Here, we used circular dichroism (CD) and fluorescence microscopy (FM) to examine the interactions of a series of antitumor-active tetrazolato-bridged dinuclear platinum(II) complexes, [{cis-Pt(NH3)2}2(μ-OH)(μ-5-R-tetrazolato-N2,N3)](n+) (R=CH3 (1), C6H5 (2), CH2COOCH2CH3 (3), CH2COO(-) (4), n=2 (1-3) or 1 (4)), which are derivatives of [{cis-Pt(NH3)2}2(μ-OH)(μ-tetrazolato-N2,N3)](2+) (5-H-Y), with DNA to elucidate the influence of these interactions on the secondary or higher-order structure of DNA and reveal the mechanism of action. The CD study showed that three derivatives, 1-3, with a double-positive charge altered the secondary structures of calf thymus DNA but that 4, the only complex with a single positive charge, induced almost no change, implying that the B- to C-form conformational change is influenced by ionic attraction. Unexpectedly, single-molecule observations with FM revealed that 4 changed the higher-order structure of T4 DNA into the compact-globule state most efficiently, at the lowest concentration, which was nearly equal to that of 5-H-Y. These contradictory results suggest that secondary structural changes are not necessarily linked to higher-order ones, and that the non-coordinative interaction could be divided into two distinct interactions: (1) ionic attraction and (2) hydrogen bonding and/or van der Waals contact. The relationship between diffusion-controlled non-coordinative DNA interactions and cytotoxicities is also discussed. PMID:23725767

  11. Higher Order Thermal Lattice Boltzmann Model

    NASA Astrophysics Data System (ADS)

    Sorathiya, Shahajhan; Ansumali, Santosh

    2013-03-01

    Lattice Boltzmann method (LBM) modelling of thermal flows, compressible and micro flows requires an accurate velocity space discretization. The sub optimality of Gauss-Hermite quadrature in this regard is well known. Most of the thermal LBM in the past have suffered from instability due to lack of proper H-theorem and accuracy. Motivated from these issues, the present work develops along the two works and and imposes an eighth higher order moment to get correct thermal physics. We show that this can be done by adding just 6 more velocities to D3Q27 model and obtain a ``multi-speed on lattice thermal LBM'' with 33 velocities in 3D and calO (u4) and calO (T4) accurate fieq with a consistent H-theorem and inherent numerical stability. Simulations for Rayleigh-Bernard as well as velocity and temperature slip in micro flows matches with analytical results. Lid driven cavity set up for grid convergence is studied. Finally, a novel data structure is developed for HPC. The authors express their gratitude for computational resources and financial support provide by Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, India.

  12. Breastfeeding twins and higher-order multiples.

    PubMed

    Gromada, K K; Spangler, A K

    1998-01-01

    The benefits of breastfeeding for pre-term and full-term infants are well documented. Breastfeeding facilitates maternal-infant attachment, provides optimal infant nutrition and immunologic protection, and minimizes economic impact. These benefits are multiplied with twins and higher-order multiples, who often are born at risk. Supporting a mother as she initiates and continues to breastfeed one infant requires specific knowledge and skills. Health professionals need additional knowledge and skills if they are to provide appropriate assessment, intervention, and support when a mother breastfeeds twins or higher-order multiples. PMID:9684207

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

    NASA Astrophysics Data System (ADS)

    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.

  14. Higher-order structure of bovine mitochondrial tRNA(Phe) lacking the 'conserved' GG and T psi CG sequences as inferred by enzymatic and chemical probing.

    PubMed Central

    Wakita, K; Watanabe, Y; Yokogawa, T; Kumazawa, Y; Nakamura, S; Ueda, T; Watanabe, K; Nishikawa, K

    1994-01-01

    Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order structure was investigated using RNaseT2 and chemical reagents as structural probes. The D and T loop regions as well as the anticodon loop region were accessible to RNaseT2, and the N-3 positions of cytidines present in the D and T loops were easily modified under the native conditions in the presence of 10mM Mg2+. On the other hand, the nucleotides present in the extra loop were protected from the chemical modification under the native conditions. From the results of these probing analyses and a comparison of the sequences of mitochondrial tRNA(Phe) genes from various organisms, it was inferred that bovine mt tRNA(Phe) lacks the D loop/T loop tertiary interactions, but does have the canonical extra loop/D stem interactions, which seem to be the main factor for bovine mt tRNA(Phe) to preserve its L-shaped higher-order structure. Images PMID:7510390

  15. Subzero temperature chromatography and top-down mass spectrometry for protein higher-order structure characterization: method validation and application to therapeutic antibodies.

    PubMed

    Pan, Jingxi; Zhang, Suping; Parker, Carol E; Borchers, Christoph H

    2014-09-17

    Characterization of the higher-order structure and structural dynamics of proteins is crucial for in-depth understanding of their functions. Amide hydrogen/deuterium exchange (HDX), monitored by mass spectrometry (MS), is now a popular technique for measuring protein higher-order structural changes. Although the proteolysis-based HDX-MS approach is most commonly used, the "top-down" approach, which fragments intact proteins directly using electron-based dissociation, is becoming an important alternative and has several advantages. However, the commonly used top-down strategies are direct-infusion based and thus can only be used with volatile buffers. This has meant that the "top-down" approach could not be used for studying proteins under physiological conditions-the very conditions which are often very important for preserving a protein's native structure and function. More complex proteins such as those with disulfide bonds present another challenge. Therefore, there is significant interest in developing novel top-down HDX methods that are applicable to all types of protein samples. In this paper, we show how top-down electron capture dissociation and subzero temperature HPLC can be combined and used for this purpose. This method keeps the back-exchange level as low as 2% and has no limitations in terms of protein type and sample solution conditions. Close to single-residue level protein structural information can be generated. The new method is validated through comparison with NMR data using calmodulin as a model protein. Its capability of determining structural changes in therapeutic antibodies (Herceptin) is also demonstrated. PMID:25152011

  16. Modulational instability, higher-order localized wave structures, and nonlinear wave interactions for a nonautonomous Lenells-Fokas equation in inhomogeneous fibers.

    PubMed

    Wang, Lei; Zhu, Yu-Jie; Qi, Feng-Hua; Li, Min; Guo, Rui

    2015-06-01

    In this paper, the nonautonomous Lenells-Fokas (LF) model is investigated. The modulational instability analysis of the solutions with variable coefficients in the presence of a small perturbation is studied. Higher-order soliton, breather, earthwormon, and rogue wave solutions of the nonautonomous LF model are derived via the n-fold variable-coefficient Darboux transformation. The solitons and earthwormons display the elastic collisions. It is found that the nonautonomous LF model admits the higher-order periodic rogue waves, composite rogue waves (rogue wave pair), and oscillating rogue waves, whose dynamics can be controlled by the inhomogeneous nonlinear parameters. Based on the second-order rogue wave, a diamond structure consisting of four first-order rogue waves is observed. In addition, the semirational solutions (the mixed rational-exponential solutions) of the nonautonomous LF model are obtained, which can be used to describe the interactions between the rogue waves and breathers. Our results could be helpful for the design of experiments in the optical fiber communications. PMID:26117105

  17. Assessing Higher Order Thinking in Mathematics.

    ERIC Educational Resources Information Center

    Kulm, Gerald, Ed.

    This book explores current theory, research, practice, and policy in the assessment of higher order thinking in mathematics, focusing on the elementary and secondary grades. Current knowledge and research on mathematics learning and testing is synthesized. Examples of innovative test items for classroom use and state assessment programs are…

  18. Higher Order Thinking in the Dance Studio

    ERIC Educational Resources Information Center

    Moffett, Ann-Thomas

    2012-01-01

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

  19. Enhanced higher order parametric x radiation production

    NASA Astrophysics Data System (ADS)

    Dinova, Kay L.

    1992-12-01

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

  20. Simulation Higher Order Language Requirements Study.

    ERIC Educational Resources Information Center

    Goodenough, John B.; Braun, Christine L.

    The definitions provided for high order language (HOL) requirements for programming flight training simulators are based on the analysis of programs written for a variety of simulators. Examples drawn from these programs are used to justify the need for certain HOL capabilities. A description of the general structure and organization of the…

  1. The regular state in higher order gravity

    NASA Astrophysics Data System (ADS)

    Cotsakis, Spiros; Kadry, Seifedine; Trachilis, Dimitrios

    2016-08-01

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

  2. Performance assessment of higher order thinking.

    PubMed

    Griffin, Patrick

    2014-01-01

    This article describes a study investigating the effect of intervention on student problem solving and higher order competency development using a series of complex numeracy performance tasks (Airasian and Russell, 2008). The tasks were sequenced to promote and monitor student development towards hypothetico-deductive reasoning. Using Rasch partial credit analysis (Wright and Masters, 1982) to calibrate the tasks and analysis of residual gain scores to examine the effect of class and school membership, the study illustrates how directed intervention can improve students' higher order competency skills. This paper demonstrates how the segmentation defined by Wright and Masters can offer a basis for interpreting the construct underlying a test and how segment definitions can deliver targeted interventions. Implications for teacher intervention and teaching mentor schemes are considered. The article also discusses multilevel regression models that differentiate class and school effects, and describes a process for generating, testing and using value added models. PMID:24518581

  3. Higher-Order Mentalising and Executive Functioning

    PubMed Central

    2015-01-01

    Higher-order mentalising is the ability to represent the beliefs and desires of other people at multiple, iterated levels – a capacity that sets humans apart from other species. However, there has not yet been a systematic attempt to determine what cognitive processes underlie this ability. Here we present three correlational studies assessing the extent to which performance on higher-order mentalising tasks relates to emotion recognition, self-reported empathy and self-inhibition. In Study 1a and 1b, examining emotion recognition and empathy, a relationship was identified between individual differences in the ability to mentalise and an emotion recognition task (the Reading the Mind in the Eyes task), but no correlation was found with the Empathy Quotient, a self-report scale of empathy. Study 2 investigated whether a relationship exists between individual mentalising abilities and four different forms of self-inhibition: motor inhibition, executive inhibition, automatic imitation and temporal discounting. Results demonstrate that only temporal discounting performance relates to mentalising ability; suggesting that cognitive skills relevant to representation of the minds of others’ are not influenced by the ability to perform more basic inhibition. Higher-order mentalising appears to rely on the cognitive architecture that serves both low-level social cognition (emotion recognition), and complex forms of inhibition. PMID:26543298

  4. Nonlinearity, structure, and the role of higher order statistics: What kind of universality can be expected in MHD and plasma turbulence? (Invited)

    NASA Astrophysics Data System (ADS)

    Matthaeus, W. H.; Wan, M.; Osman, K.; Servidio, S.; Oughton, S.; Dmitruk, P.; Greco, A.

    2010-12-01

    “Universality” in hydrodynamic turbulence usually refers to the existence of unique statistical distributions that are obtained as the Reynolds number tends to infinity. In such cases the hierarchy of structure functions would approach particular functional forms, implying for example a standard form of the energy spectrum. Magnetohydrodynamics (MHD) is more complex for several reasons. First, there are several spectral fluxes and several types of cascades, including inverse and direct cascades. Second, there are several additional dimensionless parameters, including the ratio of magnetic Reynolds number to Reynolds number, the ratio of kinetic to magnetic energy, and when cross helicity is nonzero, the ratio of two fundamental lengths scales - one for each Elsasser field. For these reasons it is doubtful that there are universal MHD turbulence statistics, in the usual sense. Recent simulation work supports this conclusion, as very similar initial energy spectra can lead to very different time evolution depending on details of initial conditions. We suggest here another approach to finding unifying principles for MHD turbulence. We begin with discussion of spontaneous generation of distinctive local correlations, including those corresponding to Beltrami, Alfvenic and force-free states. An argument is outlined as to how these correlations require certain higher order correlations to be generated. In real space these correspond to generation of region of reduced nonlinearity. Spatial patches of correlation may be separated by quasi-discontinuous jumps in the local parameters. This gives rise, e.g., to frequent appearance of “tangential discontinuities” due to formation of current sheets (and the possibility of reconnection) between adjacent quasi-relaxed flux tubes. Recent evidence supports the view that (1) the generation of high wavenumber nonGaussian statistics is a signature of these local rapid relaxation processes, (2) distinctive correlations form in

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

    NASA Technical Reports Server (NTRS)

    Pindera, Marek-Jerzy; Aboudi, Jacob

    2000-01-01

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

  6. Visualizing higher order finite elements. Final report

    SciTech Connect

    Thompson, David C; Pebay, Philippe Pierre

    2005-11-01

    This report contains an algorithm for decomposing higher-order finite elements into regions appropriate for isosurfacing and proves the conditions under which the algorithm will terminate. Finite elements are used to create piecewise polynomial approximants to the solution of partial differential equations for which no analytical solution exists. These polynomials represent fields such as pressure, stress, and momentum. In the past, these polynomials have been linear in each parametric coordinate. Each polynomial coefficient must be uniquely determined by a simulation, and these coefficients are called degrees of freedom. When there are not enough degrees of freedom, simulations will typically fail to produce a valid approximation to the solution. Recent work has shown that increasing the number of degrees of freedom by increasing the order of the polynomial approximation (instead of increasing the number of finite elements, each of which has its own set of coefficients) can allow some types of simulations to produce a valid approximation with many fewer degrees of freedom than increasing the number of finite elements alone. However, once the simulation has determined the values of all the coefficients in a higher-order approximant, tools do not exist for visual inspection of the solution. This report focuses on a technique for the visual inspection of higher-order finite element simulation results based on decomposing each finite element into simplicial regions where existing visualization algorithms such as isosurfacing will work. The requirements of the isosurfacing algorithm are enumerated and related to the places where the partial derivatives of the polynomial become zero. The original isosurfacing algorithm is then applied to each of these regions in turn.

  7. Representing higher-order dependencies in networks

    PubMed Central

    Xu, Jian; Wickramarathne, Thanuka L.; Chawla, Nitesh V.

    2016-01-01

    To ensure the correctness of network analysis methods, the network (as the input) has to be a sufficiently accurate representation of the underlying data. However, when representing sequential data from complex systems, such as global shipping traffic or Web clickstream traffic as networks, conventional network representations that implicitly assume the Markov property (first-order dependency) can quickly become limiting. This assumption holds that, when movements are simulated on the network, the next movement depends only on the current node, discounting the fact that the movement may depend on several previous steps. However, we show that data derived from many complex systems can show up to fifth-order dependencies. In these cases, the oversimplifying assumption of the first-order network representation can lead to inaccurate network analysis results. To address this problem, we propose the higher-order network (HON) representation that can discover and embed variable orders of dependencies in a network representation. Through a comprehensive empirical evaluation and analysis, we establish several desirable characteristics of HON, including accuracy, scalability, and direct compatibility with the existing suite of network analysis methods. We illustrate how HON can be applied to a broad variety of tasks, such as random walking, clustering, and ranking, and we demonstrate that, by using it as input, HON yields more accurate results without any modification to these tasks. PMID:27386539

  8. Quantifying higher-order correlations in a neuronal pool

    NASA Astrophysics Data System (ADS)

    Montangie, Lisandro; Montani, Fernando

    2015-03-01

    Recent experiments involving a relatively large population of neurons have shown a very significant amount of higher-order correlations. However, little is known of how these affect the integration and firing behavior of a population of neurons beyond the second order statistics. To investigate how higher-order inputs statistics can shape beyond pairwise spike correlations and affect information coding in the brain, we consider a neuronal pool where each neuron fires stochastically. We develop a simple mathematically tractable model that makes it feasible to account for higher-order spike correlations in a neuronal pool with highly interconnected common inputs beyond second order statistics. In our model, correlations between neurons appear from q-Gaussian inputs into threshold neurons. The approach constitutes the natural extension of the Dichotomized Gaussian model, where the inputs to the model are just Gaussian distributed and therefore have no input interactions beyond second order. We obtain an exact analytical expression for the joint distribution of firing, quantifying the degree of higher-order spike correlations, truly emphasizing the functional aspects of higher-order statistics, as we account for beyond second order inputs correlations seen by each neuron within the pool. We determine how higher-order correlations depend on the interaction structure of the input, showing that the joint distribution of firing is skewed as the parameter q increases inducing larger excursions of synchronized spikes. We show how input nonlinearities can shape higher-order correlations and enhance coding performance by neural populations.

  9. A Novel Higher Order Artificial Neural Networks

    NASA Astrophysics Data System (ADS)

    Xu, Shuxiang

    2010-05-01

    In this paper a new Higher Order Neural Network (HONN) model is introduced and applied in several data mining tasks. Data Mining extracts hidden patterns and valuable information from large databases. A hyperbolic tangent function is used as the neuron activation function for the new HONN model. Experiments are conducted to demonstrate the advantages and disadvantages of the new HONN model, when compared with several conventional Artificial Neural Network (ANN) models: Feedforward ANN with the sigmoid activation function; Feedforward ANN with the hyperbolic tangent activation function; and Radial Basis Function (RBF) ANN with the Gaussian activation function. The experimental results seem to suggest that the new HONN holds higher generalization capability as well as abilities in handling missing data.

  10. Finesky -- removing higher order sky residuals

    NASA Astrophysics Data System (ADS)

    Dahlen, Tomas; Grumm, David

    2010-07-01

    We report on a new IRAF task called finesky that removes higher order sky residuals in NICMOS images by creating a masked median image of the observed sky. This median sky image is thereafter subtracted from the science images. A residual signal after image processing using the calibration software calnica may be present due to reference files that do not sufficiently match the conditions of the observations. This includes a slight mismatch in the dark current or the flat-field corrections. The task described here can also used to create sky flat-field images.

  11. Higher-order brane gravity models

    SciTech Connect

    Dabrowski, Mariusz P.; Balcerzak, Adam

    2010-06-23

    We discuss a very general theory of gravity, of which Lagrangian is an arbitrary function of the curvature invariants, on the brane. In general, the formulation of the junction conditions (except for Euler characteristics such as Gauss-Bonnet term) leads to the powers of the delta function and requires regularization. We suggest the way to avoid such a problem by imposing the metric and its first derivative to be regular at the brane, the second derivative to have a kink, the third derivative of the metric to have a step function discontinuity, and no sooner as the fourth derivative of the metric to give the delta function contribution to the field equations. Alternatively, we discuss the reduction of the fourth-order gravity to the second order theory by introducing extra scalar and tensor fields: the scalaron and the tensoron. In order to obtain junction conditions we apply two methods: the application of the Gauss-Codazzi formalism and the application of the generalized Gibbons-Hawking boundary terms which are appended to the appropriate actions. In the most general case we derive junction conditions without assuming the continuity of the scalaron and the tensoron on the brane. The derived junction conditions can serve studying the cosmological implications of the higher-order brane gravity models.

  12. On higher structures

    NASA Astrophysics Data System (ADS)

    Baas, Nils A.

    2016-08-01

    In this paper, we discuss various philosophical aspects of the hyperstructure concept extending networks and higher categories. By this discussion, we hope to pave the way for applications and further developments of the mathematical theory of hyperstructures.

  13. Theorem Proving In Higher Order Logics

    NASA Technical Reports Server (NTRS)

    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.

  14. Higher Order Macro Coefficients in Periodic Homogenization

    NASA Astrophysics Data System (ADS)

    Conca, Carlos; San Martin, Jorge; Smaranda, Loredana; Vanninathan, Muthusamy

    2011-09-01

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

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

    PubMed

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

    2016-07-15

    The IM30 (inner membrane-associated protein of 30 kDa), also known as the Vipp1 (vesicle-inducing protein in plastids 1), has a crucial role in thylakoid membrane biogenesis and maintenance. Recent results suggest that the protein binds peripherally to membranes containing negatively charged lipids. However, although IM30 monomers interact and assemble into large oligomeric ring complexes with different numbers of monomers, it is still an open question whether ring formation is crucial for membrane interaction. Here we show that binding of IM30 rings to negatively charged phosphatidylglycerol membrane surfaces results in a higher ordered membrane state, both in the head group and in the inner core region of the lipid bilayer. Furthermore, by using gold nanorods covered with phosphatidylglycerol layers and single particle spectroscopy, we show that not only IM30 rings but also lower oligomeric IM30 structures interact with membranes, although with higher affinity. Thus, ring formation is not crucial for, and even counteracts, membrane interaction of IM30. PMID:27226585

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

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  17. Higher-order Genome Organization in Human Disease

    PubMed Central

    Misteli, Tom

    2010-01-01

    Genomes are organized into complex higher-order structures by folding of the DNA into chromatin fibers, chromosome domains, and ultimately chromosomes. The higher-order organization of genomes is functionally important for gene regulation and control of gene expression programs. Defects in how chromatin is globally organized are relevant for physiological and pathological processes. Mutations and transcriptional misregulation of several global genome organizers are linked to human diseases and global alterations in chromatin structure are emerging as key players in maintenance of genome stability, aging, and the formation of cancer translocations. PMID:20591991

  18. Higher-Order Abilities Conceptualized within Guilford's Structure-of-Intellect (SOI) Model for a Sample of United States Coast Guard Academy Cadets: A Reanalysis of an SOI Data Base.

    ERIC Educational Resources Information Center

    Chen, Chin-Yi; Michael, William B.

    1993-01-01

    Empirical validation of the first-order and higher-order factor structures of the structure-of-intellect (SOI) model was provided by reanalysis of a database of 39 measures administered to 178 Coast Guard Cadets. Results suggest that SOI could be reconceptualized as a pyramid-like hierarchical theory of intelligence. (SLD)

  19. Applications of circular dichroism (CD) for structural analysis of proteins: qualification of near- and far-UV CD for protein higher order structural analysis.

    PubMed

    Li, Cynthia H; Nguyen, Xichdao; Narhi, Linda; Chemmalil, Letha; Towers, Edward; Muzammil, Salman; Gabrielson, John; Jiang, Yijia

    2011-11-01

    Circular dichroism (CD) spectroscopy is routinely used in the biopharmaceutical industry to study the effects of manufacturing, formulation, and storage conditions on protein conformation and stability, and these results are often included in regulatory filings. In this context, the purpose of CD spectroscopy is often to verify that a change in the formulation or manufacturing process of a product has not produced a change in the conformation of a protein. A comparison of two or more spectra is often required to confirm that the protein's structure has been maintained. Traditionally, such comparisons have been qualitative in nature, based on visually inspecting the overlaid spectra. However, visual assessment is inherently subjective and therefore prone to error. Furthermore, recent requests from regulatory agencies to demonstrate the suitability of the CD spectroscopic method for the purpose of comparing spectra have highlighted the need to appropriately qualify CD spectroscopy for characterization of biopharmaceutical protein products. In this study, we use a numerical spectral comparison approach to establish the precision of the CD spectroscopic method and to demonstrate that it is suitable for protein structural characterization in numerous biopharmaceutical applications. PMID:21732370

  20. Higher Education Guidelines for Executive Order 11246.

    ERIC Educational Resources Information Center

    Office for Civil Rights (DHEW), Washington, DC.

    This document presents and explains Executive Order 11246, the order prohibiting discrimination under federal contracts in colleges and universities. Part one of the document describes the legal provisions of the order; part two deals with personnel policies and practices including recruitment, hiring, anti-nepotism policies, training, promotion,…

  1. Symplectic representation of higher-order guiding-center theory

    NASA Astrophysics Data System (ADS)

    Brizard, Alain; Tronko, Natalia

    2012-03-01

    Two representations of guiding-center theory are possible depending on whether the guiding-center Poisson bracket (i.e., the symplectic structure) or the Hamiltonian contains higher-order corrections due to the nonuniformity of the magnetic field. By combining the guiding-center parallel hierarchy with the symplectic representation, the guiding-center equations of motion are derived with second-order corrections included in the symplectic structure without the need of carrying out the guiding-center transformation to second order. Guiding-center polarization and magnetization are thus shown to arise naturally from higher-order guiding-center theory within the context of a two-step derivation of nonlinear gyrokinetic theory.footnotetextA. J. Brizard and T. S. Hahm, Rev. Mod. Phys. 79, 421 (2007).

  2. Hydrogen peroxide mediates higher order chromatin degradation.

    PubMed

    Bai, H; Konat, G W

    2003-01-01

    Although a large body of evidence supports a causative link between oxidative stress and neurodegeneration, the mechanisms are still elusive. We have recently demonstrated that hydrogen peroxide (H(2)O(2)), the major mediator of oxidative stress triggers higher order chromatin degradation (HOCD), i.e. excision of chromatin loops at the matrix attachment regions (MARs). The present study was designed to determine the specificity of H(2)O(2) in respect to HOCD induction. Rat glioma C6 cells were exposed to H(2)O(2) and other oxidants, and the fragmentation of genomic DNA was assessed by field inversion gel electrophoresis (FIGE). S1 digestion before FIGE was used to detect single strand fragmentation. The exposure of C6 cells to H(2)O(2) induced a rapid and extensive HOCD. Thus, within 30 min, total chromatin was single strandedly digested into 50 kb fragments. Evident HOCD was elicited by H(2)O(2) at concentrations as low as 5 micro M. HOCD was mostly reversible during 4-8h following the removal of H(2)O(2) from the medium indicating an efficient relegation of the chromatin fragments. No HOCD was induced by H(2)O(2) in isolated nuclei indicating that HOCD-endonuclease is activated indirectly by cytoplasmic signal pathways triggered by H(2)O(2). The exposure of cells to a synthetic peroxide, i.e. tert-butyrylhydroperoxide (tBH) also induced HOCD, but to a lesser extent than H(2)O(2). Contrary to the peroxides, the exposure of cells to equitoxic concentration of hypochlorite and spermine NONOate, a nitric oxide generator, failed to induce rapid HOCD. These results indicate that rapid HOCD is not a result of oxidative stress per se, but is rather triggered by signaling cascades initiated specifically by H(2)O(2). Furthermore, the rapid and extensive HOCD was observed in several rat and human cell lines challenged with H(2)O(2), indicating that the process is not restricted to glial cells, but rather represents a general response of cells to H(2)O(2). PMID:12421592

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

    PubMed

    Herr, Lisa; Friedrich, Thomas; Durante, Marco; Scholz, Michael

    2014-01-01

    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. PMID:24392100

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

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  5. Fostering Higher-Order Thinking in Science Class: Teachers' Reflections

    ERIC Educational Resources Information Center

    Barak, Moshe; Shakhman, Larisa

    2008-01-01

    The study reported in this article aimed at exploring what teachers know and do about fostering higher-order thinking skills in teaching science, and how they see themselves involved in achieving this end. Data were collected through semi-structured interviews with 11 teachers experienced in teaching high school physics, which is considered a…

  6. On the higher orders of hyperspherical harmonics

    NASA Astrophysics Data System (ADS)

    Arribas, E.; Navarro, J.; Fabre de la Ripelle, M.

    1983-08-01

    We suggest a procedure to evaluate matrix elements between hyperspherical harmonics of any order. The method is based on the hyperspherical expansion of a Slater determinant constructed with oscillator wavefunctions. Explicit formulas are given for all matrix elements up to order Lm+2.

  7. Higher-order corrections in threshold resummation

    NASA Astrophysics Data System (ADS)

    Moch, S.; Vermaseren, J. A. M.; Vogt, A.

    2005-10-01

    We extend the threshold resummation exponents G in Mellin- N space to the fourth logarithmic (N 3LL) order collecting the terms αs2( to all orders in the strong coupling constant α. Comparing the results to our previous three-loop calculations for deep-inelastic scattering (DIS), we derive the universal coefficients B and B governing the final-state jet functions to order αs3, extending the previous quark and gluon results by one and two orders. A curious relation is found at second order between these quantities, the splitting functions and the large-angle soft emissions in Drell-Yan type processes. We study the numerical effect of the N 3LL corrections using both the fully exponentiated form and the expansion of the coefficient function in towers of logarithms.

  8. Constructing higher-order hydrodynamics: The third order

    NASA Astrophysics Data System (ADS)

    Grozdanov, Sašo; Kaplis, Nikolaos

    2016-03-01

    Hydrodynamics can be formulated as the gradient expansion of conserved currents in terms of the fundamental fields describing the near-equilibrium fluid flow. In the relativistic case, the Navier-Stokes equations follow from the conservation of the stress-energy tensor to first order in derivatives. In this paper, we go beyond the presently understood second-order hydrodynamics and discuss the systematization of obtaining the hydrodynamic expansion to an arbitrarily high order. As an example of the algorithm that we present, we fully classify the gradient expansion at third order for neutral fluids in four dimensions, thus finding the most general next-to-leading-order corrections to the relativistic Navier-Stokes equations in curved space-time. In doing so, we list 20 new transport coefficient candidates in the conformal case and 68 in the nonconformal case. As we do not consider any constraints that could potentially arise from the local entropy current analysis, this is the maximal possible set of neutral third-order transport coefficients. To investigate the physical implications of these new transport coefficients, we obtain the third-order corrections to the linear dispersion relations that describe the propagation of diffusion and sound waves in relativistic fluids. We also compute the corrections to the scalar (spin-2) two-point correlation function of the third-order stress-energy tensor. Furthermore, as an example of a nonlinear hydrodynamic flow, we calculate the third-order corrections to the energy density of a boost-invariant Bjorken flow. Finally, we apply our field theoretic results to the N =4 supersymmetric Yang-Mills fluid at infinite 't Hooft coupling and an infinite number of colors to find the values of five new linear combinations of the conformal transport coefficients.

  9. Modeling Higher-Order Correlations within Cortical Microcolumns

    PubMed Central

    Köster, Urs; Sohl-Dickstein, Jascha; Gray, Charles M.; Olshausen, Bruno A.

    2014-01-01

    We statistically characterize the population spiking activity obtained from simultaneous recordings of neurons across all layers of a cortical microcolumn. Three types of models are compared: an Ising model which captures pairwise correlations between units, a Restricted Boltzmann Machine (RBM) which allows for modeling of higher-order correlations, and a semi-Restricted Boltzmann Machine which is a combination of Ising and RBM models. Model parameters were estimated in a fast and efficient manner using minimum probability flow, and log likelihoods were compared using annealed importance sampling. The higher-order models reveal localized activity patterns which reflect the laminar organization of neurons within a cortical column. The higher-order models also outperformed the Ising model in log-likelihood: On populations of 20 cells, the RBM had 10% higher log-likelihood (relative to an independent model) than a pairwise model, increasing to 45% gain in a larger network with 100 spatiotemporal elements, consisting of 10 neurons over 10 time steps. We further removed the need to model stimulus-induced correlations by incorporating a peri-stimulus time histogram term, in which case the higher order models continued to perform best. These results demonstrate the importance of higher-order interactions to describe the structure of correlated activity in cortical networks. Boltzmann Machines with hidden units provide a succinct and effective way to capture these dependencies without increasing the difficulty of model estimation and evaluation. PMID:24991969

  10. HIGHER ORDER HARD EDGE END FIELD EFFECTS.

    SciTech Connect

    BERG,J.S.

    2004-09-14

    In most cases, nonlinearities from magnets must be properly included in tracking and analysis to properly compute quantities of interest, in particular chromatic properties and dynamic aperture. One source of nonlinearities in magnets that is often important and cannot be avoided is the nonlinearity arising at the end of a magnet due to the longitudinal variation of the field at the end of the magnet. Part of this effect is independent of the longitudinal of the end. It is lowest order in the body field of the magnet, and is the result of taking a limit as the length over which the field at the end varies approaches zero. This is referred to as a ''hard edge'' end field. This effect has been computed previously to lowest order in the transverse variables. This paper describes a method to compute this effect to arbitrary order in the transverse variables, under certain constraints.

  11. Discrimination of higher-order textures.

    PubMed

    Nothdurft, H C

    1985-01-01

    Arrays of figural elements differing in certain features ('textons') may be visually segregated to yield the impression of a global figure of different texture. This fact was used to construct texture patterns of a higher level of complexity. In microstructure, these patterns reveal regular arrays of distinguishable figural elements, the segregation of which can be predicted from previous studies of human texture sensitivity. In macrostructure, clusters of such elements form new figural elements which, when repeated over space, themselves give the impression of texture at a perceptually higher level. Discrimination of such macrostructure textures was found to place similar restrictions on the form of figural elements as those of texture discrimination at the microstructure level. PMID:3836385

  12. LOCAL ANISOTROPY, HIGHER ORDER STATISTICS, AND TURBULENCE SPECTRA

    SciTech Connect

    Matthaeus, W. H.; Wan, M.; Osman, K. T.; Servidio, S.; Carbone, V.; Dmitruk, P.; Oughton, S.

    2012-05-10

    Correlation anisotropy emerges dynamically in magnetohydrodynamics (MHD), producing stronger gradients across the large-scale mean magnetic field than along it. This occurs both globally and locally, and has significant implications in space and astrophysical plasmas, including particle scattering and transport, and theories of turbulence. Properties of local correlation anisotropy are further documented here by showing through numerical experiments that the effect is intensified in more localized estimates of the mean field. The mathematical formulation of this property shows that local anisotropy mixes second-order with higher order correlations. Sensitivity of local statistical estimates to higher order correlations can be understood in connection with the stochastic coordinate system inherent in such formulations. We demonstrate this in specific cases, and illustrate the connection to higher order statistics by showing the sensitivity of local anisotropy to phase randomization, after which the global measure of anisotropy is recovered at all scales of averaging. This establishes that anisotropy of the local structure function is not a measure of anisotropy of the energy spectrum. Evidently, the local enhancement of correlation anisotropy is of substantial fundamental interest and must be understood in terms of higher order correlations, specifically fourth-order and above.

  13. Invariant Higher-Order Variational Problems II

    NASA Astrophysics Data System (ADS)

    Gay-Balmaz, François; Holm, Darryl D.; Meier, David M.; Ratiu, Tudor S.; Vialard, François-Xavier

    2012-08-01

    Motivated by applications in computational anatomy, we consider a second-order problem in the calculus of variations on object manifolds that are acted upon by Lie groups of smooth invertible transformations. This problem leads to solution curves known as Riemannian cubics on object manifolds that are endowed with normal metrics. The prime examples of such object manifolds are the symmetric spaces. We characterize the class of cubics on object manifolds that can be lifted horizontally to cubics on the group of transformations. Conversely, we show that certain types of non-horizontal geodesic on the group of transformations project to cubics. Finally, we apply second-order Lagrange-Poincaré reduction to the problem of Riemannian cubics on the group of transformations. This leads to a reduced form of the equations that reveals the obstruction for the projection of a cubic on a transformation group to again be a cubic on its object manifold.

  14. Higher order diffractions from a circular disk

    NASA Technical Reports Server (NTRS)

    Marsland, Diane P.; Balanis, Constantine A.; Brumley, Stephen A.

    1987-01-01

    The backscattering from a circular disk is analyzed using the geometrical theory of diffraction. First-, second-, and third-order diffractions are included in the hard polarization analysis, while first-, second-, and third-order slope diffractions are included for soft polarization. Improvements in the prediction of the monostatic radar cross section over previous works are noted. For hard polarization, an excellent agreement is exhibited between experimental and theoretical results, while a very good agreement is noted for soft polarization. To further improve the soft polarization results for wide angles, a model for the creeping wave or circulating current on the edge of the disk is obtained and used to find an additional component of the backscattered field. The addition of this component significantly improves the results for wide angles, leading to excellent agreement for soft polarization also. An axial-caustic correction method using equivalent currents is also included in the analysis.

  15. Higher-order terms in mode conversion

    NASA Astrophysics Data System (ADS)

    Swanson, D. G.

    1998-07-01

    The development of model equations to describe mode conversion and tunneling in an inhomogeneous plasma usually uses expansions of the Modified Bessel functions in the parameter λ=1/2k⊥2ρL2, keeping only the lowest possible order to demonstrate tunneling. With the high temperatures of fusion parameters, especially for fusion alpha particles, this parameter may not be small. It is shown here that the effective expansion parameter is really βj=2μ0njkTj/B02, the ratio of plasma pressure to the magnetic pressure.

  16. Systems with Higher-Order Modulation

    NASA Astrophysics Data System (ADS)

    Seimetz, Matthias

    With the objective of reducing costs per information bit in optical communication networks, per fibre capacities and optical transparent transmission lengths have been stepped up by the introduction of new technology in recent years. The innovation of the erbium-doped fibre amplifier (EDFA) at the beginning of the nineties facilitated long distances to be bridged without electro-optical conversion. Wavelength division multiplexing (WDM) technology allowed a lot of wavelength channels to be simultaneously transmitted over one fibre and to be amplified by one EDFA with high bandwidth, offering a huge network capacity. At this time, the modulation format of choice was the simple "on-off keying" (OOK), and there was no need for increasing spectral efficiency. The internet traffic growth during the nineties required increasing transmission rates. In that context, the transmission impairments of the optical fibre had to be counteracted and the application of differential binary phased shift keying (DBPSK) became an issue, providing for a higher robustness against nonlinear effects [1]. Moreover, the transmission behaviour of binary intensity modulation was optimized by using alternative optical pulse shapes such as return to zero (RZ) and by employing schemes with auxiliary phase coding, such as optical duobinary, which exhibits a higher tolerance against chromatic dispersion (CD). The capacity-distance product was further enhanced by applying optical dispersion compensation, Raman amplification and advanced optical fibres, as well as through electronic means, such as forward error correction (FEC) and the adaptive compensation of CD and polarization mode dispersion (PMD).

  17. Evaluation of expressions involving higher order derivations

    NASA Technical Reports Server (NTRS)

    Grossman, Robert

    1990-01-01

    The local geometric properties of a nonlinear control system defined by vector fields E(sub 1),..., E(sub M) are determined by the algebraic properties of the iterated Lie brackets of the E(sub j)'s. The problem of rewriting expressions is examined involving the E(sub j)'s in terms of the D(sub mu)'s in such a way as to handle effectively any cancellation occurring due to commuting of the D(sub mu)'s. A data structure is introduced which allows us to organize the computation to take advantage of the symmetries in the expression and reduce the operation count.

  18. Higher Order Chromaticity Correction for ELIC

    NASA Astrophysics Data System (ADS)

    Sayed, Hisham; Bogacz, Alex

    2010-02-01

    The proposed electron collider lattice design with extremely low betas at the interaction Point IP (β*˜ 0.5cm) and the precedently large longitudinal acceptance of the collider ring (δp/p = 0.005) [1], makes the chromatic corrections of paramount importance. Here the chromatic effects of the final focus quadruples are corrected with two families of sextuples in a dispersive region; one family per plane. Each family consists of two pairs of sextuples located symmetrically around the interaction point IP. A confined dispersion wave around the IP is generated by two bending magnets (one at each side of the IP with mirror reflected Polarities) which also develop the vertical staking design. The resulting spherical aberrations induced by the sextuples are mitigated by design; the matching section optics features an inverse identity transformation between sextuples in each pair. A dedicated optics is placed in the matching region to implement sextuple orthogonality in both planes, which in turns minimizes the required sextuple strength and eventually leads to larger dynamic aperture of the collider. The betatron phase advances from the IP to the sextuples are chosen to eliminate the second order chromatic aberration. )

  19. Higher order intercommutations in cosmic string collisions.

    PubMed

    Achúcarro, A; Verbiest, G J

    2010-07-01

    We report the first observation of multiple intercommutation (more than two successive reconnections) of Abelian Higgs cosmic strings at ultrahigh collision speeds, and the formation of "kink trains" with up to four closely spaced left- or right-moving kinks, in the deep type-II regime 16 ≤ β ≤ 64 (where β=m(scalar)2/m(gauge)2). The minimum critical speed for double reconnection goes down from ∼0.98c at β = 1 to ∼0.86c for β = 64. The process leading to the second intercommutation changes with β: it involves an expanding loop if β ≥ 16, but only a radiation blob if 1 < β ≤ 8. Triple reconnections are generic in the loop-mediated regime for collision parameters on the boundary between single and double reconnection. For β = 16 we observe quadruple events. We comment on the effect of strongly repulsive core interactions on the small scale structure on the strings and their gravitational wave emission. PMID:20867697

  20. Higher Order Intercommutations in Cosmic String Collisions

    SciTech Connect

    Achucarro, A.; Verbiest, G. J.

    2010-07-09

    We report the first observation of multiple intercommutation (more than two successive reconnections) of Abelian Higgs cosmic strings at ultrahigh collision speeds, and the formation of ''kink trains'' with up to four closely spaced left- or right-moving kinks, in the deep type-II regime 16{<=}{beta}{<=}64 (where {beta}=m{sub scalar}{sup 2}/m{sub gauge}{sup 2}). The minimum critical speed for double reconnection goes down from {approx}0.98c at {beta}=1 to {approx}0.86c for {beta}=64. The process leading to the second intercommutation changes with {beta}: it involves an expanding loop if {beta}{>=}16, but only a radiation blob if 1<{beta}{<=}8. Triple reconnections are generic in the loop-mediated regime for collision parameters on the boundary between single and double reconnection. For {beta}=16 we observe quadruple events. We comment on the effect of strongly repulsive core interactions on the small scale structure on the strings and their gravitational wave emission.

  1. Higher-order polarization singularitites in tailored vector beams

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  2. Structural order in glassy water.

    PubMed

    Giovambattista, Nicolas; Debenedetti, Pablo G; Sciortino, Francesco; Stanley, H Eugene

    2005-06-01

    We investigate structural order in glassy water by performing classical molecular dynamics simulations using the extended simple point charge (SPC/E) model of water. We perform isochoric cooling simulations across the glass transition temperature at different cooling rates and densities. We quantify structural order by orientational and translational order metrics. Upon cooling the liquid into the glassy state, both the orientational order parameter Q and translational order parameter tau increase. At T=0 K, the glasses fall on a line in the Q-tau plane or order map. The position of this line depends only on density and coincides with the location in the order map of the inherent structures (IS) sampled upon cooling. We evaluate the energy of the IS, eIS(T), and find that both order parameters for the IS are proportional to eIS. We also study the structural order during the transformation of low-density amorphous ice (LDA) to high-density amorphous ice (HDA) upon isothermal compression and are able to identify distinct regions in the order map corresponding to these glasses. Comparison of the order parameters for LDA and HDA with those obtained upon isochoric cooling indicates major structural differences between glasses obtained by cooling and glasses obtained by compression. These structural differences are only weakly reflected in the pair correlation function. We also characterize the evolution of structural order upon isobaric annealing, leading at high pressure to very-high density amorphous ice (VHDA). PMID:16089741

  3. Conceptualizing and Assessing Higher-Order Thinking in Reading

    ERIC Educational Resources Information Center

    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. Skinner-Rusk unified formalism for higher-order systems

    NASA Astrophysics Data System (ADS)

    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.

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

    ERIC Educational Resources Information Center

    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…

  6. Higher-order Dirac solitons in binary waveguide arrays

    SciTech Connect

    Tran, Truong X.; Duong, Dũng C.

    2015-10-15

    We study optical analogues of higher-order Dirac solitons (HODSs) in binary waveguide arrays. Like higher-order solitons obtained from the well-known nonlinear Schrödinger equation governing the pulse propagation in an optical fiber, these HODSs have amplitude profiles which are numerically shown to be periodic over large propagation distances. At the same time, HODSs possess some unique features. Firstly, the period of a HODS depends on its order parameter. Secondly, the discrete nature in binary waveguide arrays imposes the upper limit on the order parameter of HODSs. Thirdly, the order parameter of HODSs can vary continuously in a certain range. - Highlights: • Higher-order Dirac solitons in nonlinear binary waveguide arrays are numerically demonstrated. • Amplitude profiles of higher-order Dirac solitons are periodic during propagation. • The period of higher-order Dirac solitons decreases when the soliton order increases.

  7. Introduction to Higher Order Spatial Statistics in Cosmology

    NASA Astrophysics Data System (ADS)

    Szapudi, I.

    Higher order spatial statistics characterize non-Gaussian aspects of random fields, which are ubiquitous in cosmology: from the cosmic microwave background (CMB) to the large-scale structure (LSS) of the universe. These random fields are rich in their properties; they can be continuous or discrete; can have one through three, or even more dimensions; their degree of non- Gaussianity ranges from tiny to significant. Yet, there are several techniques and ideas, which are applicable to virtually all cosmological random fields, be it Lyman-a forests, LSS, or CMB.

  8. Higher Education's New Global Order: How and Why Governments Are Creating Structured Opportunity Markets. Research & Occasional Paper Series: CSHE.10.09

    ERIC Educational Resources Information Center

    Douglass, John Aubrey

    2009-01-01

    In the United States, developing "human capital" for both economic and social benefit is an idea as old as the nation itself and led to the emergence of world's first mass higher education system. Now most other nations are racing to expand access to universities and colleges and to expand their role in society. Higher education is growing…

  9. A Recurrence Relation Approach to Higher Order Quantum Superintegrability

    NASA Astrophysics Data System (ADS)

    Kalnins, Ernie G.; Kress, Jonathan M.; Miller, Willard

    2011-03-01

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

  10. Promoting Higher Order Thinking Skills Using Inquiry-Based Learning

    ERIC Educational Resources Information Center

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

    2012-01-01

    Active learning pedagogies play an important role in enhancing higher order cognitive skills among the student community. In this work, a laboratory course for first year engineering chemistry is designed and executed using an inquiry-based learning pedagogical approach. The goal of this module is to promote higher order thinking skills in…

  11. Higher-Order Theory for Functionally Graded Materials

    NASA Technical Reports Server (NTRS)

    Aboudi, Jacob; Pindera, Marek-Jerzy; Arnold, Steven M.

    1999-01-01

    This paper presents the full generalization of the Cartesian coordinate-based higher-order theory for functionally graded materials developed by the authors during the past several years. This theory circumvents the problematic use of the standard micromechanical approach, based on the concept of a representative volume element, commonly employed in the analysis of functionally graded composites by explicitly coupling the local (microstructural) and global (macrostructural) responses. The theoretical framework is based on volumetric averaging of the various field quantities, together with imposition of boundary and interfacial conditions in an average sense between the subvolumes used to characterize the composite's functionally graded microstructure. The generalization outlined herein involves extension of the theoretical framework to enable the analysis of materials characterized by spatially variable microstructures in three directions. Specialization of the generalized theoretical framework to previously published versions of the higher-order theory for materials functionally graded in one and two directions is demonstrated. In the applications part of the paper we summarize the major findings obtained with the one-directional and two-directional versions of the higher-order theory. The results illustrate both the fundamental issues related to the influence of microstructure on microscopic and macroscopic quantities governing the response of composites and the technologically important applications. A major issue addressed herein is the applicability of the classical homogenization schemes in the analysis of functionally graded materials. The technologically important applications illustrate the utility of functionally graded microstructures in tailoring the response of structural components in a variety of applications involving uniform and gradient thermomechanical loading.

  12. First and Higher Order Effects on Zero Order Radiative Transfer Model

    NASA Astrophysics Data System (ADS)

    Neelam, M.; Mohanty, B.

    2014-12-01

    Microwave radiative transfer model are valuable tool in understanding the complex land surface interactions. Past literature has largely focused on local sensitivity analysis for factor priotization and ignoring the interactions between the variables and uncertainties around them. Since land surface interactions are largely nonlinear, there always exist uncertainties, heterogeneities and interactions thus it is important to quantify them to draw accurate conclusions. In this effort, we used global sensitivity analysis to address the issues of variable uncertainty, higher order interactions, factor priotization and factor fixing for zero-order radiative transfer (ZRT) model. With the to-be-launched Soil Moisture Active Passive (SMAP) mission of NASA, it is very important to have a complete understanding of ZRT for soil moisture retrieval to direct future research and cal/val field campaigns. This is a first attempt to use GSA technique to quantify first order and higher order effects on brightness temperature from ZRT model. Our analyses reflect conditions observed during the growing agricultural season for corn and soybeans in two different regions in - Iowa, U.S.A and Winnipeg, Canada. We found that for corn fields in Iowa, there exist significant second order interactions between soil moisture, surface roughness parameters (RMS height and correlation length) and vegetation parameters (vegetation water content, structure and scattering albedo), whereas in Winnipeg, second order interactions are mainly due to soil moisture and vegetation parameters. But for soybean fields in both Iowa and Winnipeg, we found significant interactions only to exist between soil moisture and surface roughness parameters.

  13. Higher Order Mode Excitations in Gyro-amplifiers

    NASA Astrophysics Data System (ADS)

    Nguyen, Khanh

    2000-10-01

    A key element in the design of gyro-amplifier RF structures is the minimization of unwanted modes. For example, a nonlinear output taper is often employed in the transition from the near cutoff radius of the interacting circuit to a much larger output waveguide, which also serves as the collector. The taper designs are usually done without considering the effect of a bunched beam. However, recent simulations [1] with the self-consistent MAGY code [2] reveal that higher order mode interactions with the bunched electron beam can substantially compromise the mode purity of the RF output. The interaction in the taper region is that of a travelling-wave type and is strongly dependent on the beam bunching characteristics resulting from previous interaction with the operating mode in the interacting circuit. Subsequent to this prediction, an experiment was performed to measure the RF output mode content from a Ka-band gyro-klystron at the Naval Research Laboratory. The agreement between salient theoretical and measured RF output characteristics confirms the existence higher order mode excitation in output tapers as predicted by theory. Another example of the need to employ self-consistent theoretical model in the design of gyro-amplifier RF structures is the phenomenon of beam-induced RF excitation in drift sections, which are cutoff to the operating mode and are used to separate cavities in gyroklystron amplifiers. This non-resonant RF excitation is at the drive frequency and the RF field structure is that of the operating mode. The RF amplitude is found to scale linearly with the bunched beam current. The presence of RF in the drift section has important thermal implications in the design and use of lossy dielectrics in drift-sections, especially for high-average power devices. [1] K. Nguyen, et al., IEEE Trans. Plasma Science, in press 2000. [2] M. Botton, et al., IEEE Trans. Plasma Science, V.26, p.882, June 1998.

  14. Higher-order theories from the minimal length

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  15. Higher Order Modeling In the BEM/FEM Hybrid Formulation

    NASA Technical Reports Server (NTRS)

    Fink, Patrick W.; Wilton, Don R.

    2000-01-01

    Hybrid formulations using low order curl-conforming bases to represent the total electric field within a finite element region and low order divergence-conforming bases to represent equivalent electric and magnetic currents on the boundary are well known. However, higher-order divergence and curl-conforming bases have been shown to provide significant benefits in convergence rates and accuracy when employed in strictly integral equation and strictly finite element formulations. In this paper, a hybrid electric field formulation employing higher order bases is presented. The paper addresses benefits and issues associated with using higher order divergence-and curl-conforming bases in the hybrid finite element/boundary element electric field formulation. The method of singularity subtraction may be used to compute the self terms of the boundary integral when the bases are of low order. But this method becomes laborious and requires great care when the divergence conforming bases are of higher order. In order to handle these singularities simply and accurately, a generalized Gaussian quadrature method is employed in which the expansion functions account for the singularity. In preliminary tests of the higher order hybrid formulation, the equivalent electric current induced by scattering of a plane wave from a square dielectric cylinder is examined. Accurate results are obtained using only a two-triangle mesh when the current basis is of order 4 or 5. Additional results are presented comparing the error obtained using higher order bases to that obtained using lower order bases when the number of unknowns is approximately equal. Also, convergence rates obtained with higher order bases are compared to those obtained with lower order bases for selected sample problems.

  16. Application of Mass Lumped Higher Order Finite Elements

    SciTech Connect

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

    2005-11-01

    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.

  17. Purification and characterization of Ara h1 and Ara h3 from four peanut market types revealed higher order oligomeric structures.

    PubMed

    Yusnawan, Eriyanto; Marquis, Christopher P; Lee, N Alice

    2012-10-17

    This study aimed to purify and characterize the peanut allergens Ara h1 and Ara h3 from four cultivars that represent the four major market types to provide better understanding of the molecular organization of oligomers in different market types. The chromatographic profiles of Ara h1 and Ara h3 from the four cultivars obtained from anion exchange chromatography were similar. However, they differed in the distribution of trimeric and hexameric structures of Ara h3 isolated by size exclusion chromatography. The Menzies (Runner market type) and Walter (Spanish market type) cultivars, wherein Ara h3 proteins consist of two acidic subunits, exhibited trimeric and hexameric conformations proportionally. However, the Middleton (Virginia market type) and Kelinci (Valencia market type) cultivars, wherein Ara h3 proteins consist of three acidic subunits, showed predominantly a hexameric structure. The oligomeric structures of the purified Ara h1 demonstrated strong IgE binding properties, whereas the allergenic property of the oligomeric Ara h3 could not be performed due to lack of availability of specific IgE. In addition, the polyclonal antibodies raised against the purified Ara h1 and Ara h3 showed highly specific binding to their respective antigens. PMID:22998620

  18. Insights into Higher-Order Organization of the Cellulosome Revealed by a Dissect-and build Approach: Crystal Structure of Interacting Clostridium thermocellum Multimodular components

    SciTech Connect

    J Adams; M Currie; S Ali; E Bayer; Z Jia; S Smith

    2011-12-31

    Cellulosomes are large, multienzyme, plant cell wall-degrading protein complexes found affixed to the surface of a variety of anaerobic microbes. The core of the cellulosome is a noncatalytic scaffoldin protein, which contains several type-I cohesin modules that bind type-I dockerin-containing enzymatic subunits, a cellulose-binding module, an X module, and a type-II dockerin that interacts with type-II cohesin-containing cell surface proteins. The unique arrangement of the enzymatic subunits in the cellulosome complex, made possible by the scaffoldin subunit, promotes enhanced substrate degradation relative to the enzymes free in solution. Despite representative high-resolution structures of all of the individual modules of the cellulosome, this mechanism of enzymatic synergy remains poorly understood. Consequently, a model of the entire cellulosome and a detailed picture of intermodular contacts will provide more detailed insight into cellulosome activity. Toward this goal, we have solved the structure of a multimodular heterodimeric complex from Clostridium thermocellum composed of the type-II cohesin module of the cell surface protein SdbA bound to a trimodular C-terminal fragment of the scaffoldin subunit CipA to a resolution of 1.95 {angstrom}. The linker that connects the ninth type-I cohesin module and the X module has elevated temperature factors, reflecting an inherent flexibility within this region. Interestingly, a novel dimer interface was observed between CipA and a second, symmetry-related CipA molecule within the crystal structure, mediated by contacts between a type-I cohesin and an X module of a symmetry mate, resulting in two intertwined scaffoldins. Sedimentation velocity experiments confirmed that dimerization also occurs in solution. These observations support the intriguing possibility that individual cellulosomes can associate with one another via inter-scaffoldin interactions, which may play a role in the mechanism of action of the complex.

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

    PubMed

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

    2016-08-01

    The language of graph theory, or network science, has proven to be an exceptional tool for addressing myriad problems in neuroscience. Yet, the use of networks is predicated on a critical simplifying assumption: that the quintessential unit of interest in a brain is a dyad - two nodes (neurons or brain regions) connected by an edge. While rarely mentioned, this fundamental assumption inherently limits the types of neural structure and function that graphs can be used to model. Here, we describe a generalization of graphs that overcomes these limitations, thereby offering a broad range of new possibilities in terms of modeling and measuring neural phenomena. Specifically, we explore the use of simplicial complexes: a structure developed in the field of mathematics known as algebraic topology, of increasing applicability to real data due to a rapidly growing computational toolset. We review the underlying mathematical formalism as well as the budding literature applying simplicial complexes to neural data, from electrophysiological recordings in animal models to hemodynamic fluctuations in humans. Based on the exceptional flexibility of the tools and recent ground-breaking insights into neural function, we posit that this framework has the potential to eclipse graph theory in unraveling the fundamental mysteries of cognition. PMID:27287487

  20. Technical Decision-Making with Higher Order Structure Data: Detecting Reversible Concentration-Dependent Self-Association in a Monoclonal Antibody and a Preliminary Investigation to Eliminate It.

    PubMed

    Wei, Julie Y; Bou-Assaf, George M; Houde, Damian; Weiskopf, Andrew

    2015-11-01

    Protein self-association or aggregation is a property of significant concern for biopharmaceutical products due to the potential ability of aggregates to cause adverse toxicological and immunological effects. Thus, during the development of a protein biopharmaceutical, it is important to detect and quantify the level and nature of aggregate species as early as possible in order to make well-informed decisions and to mitigate and control potential risks. Although a deeper understanding of the mechanism of aggregation (i.e., protein-protein interactions) is desirable, such detailed assessment is not always necessary from a biopharmaceutical process development point of view. In fact, the scope of characterization efforts is often focused on achieving a well-controlled process, which generates a product that reliably meets established acceptance criteria for safety and efficacy. In this brief note, we evaluated the utility of size-exclusion chromatography, dynamic light scattering, and analytical ultracentrifugation in their simplest forms, to effectively reveal and confirm the presence of concentration-dependent reversible self-association (RSA) in a monoclonal antibody in the early stages of formulation development. Using these techniques, we also initiated preliminary work aimed at reducing the occurrence of this RSA behavior by varying the pH of the formulation buffer. PMID:26308556

  1. On higher order geometric and renormalization group flows

    NASA Astrophysics Data System (ADS)

    Prabhu, Kartik; Das, Sanjit; Kar, Sayan

    2011-10-01

    Renormalization group (RG) flows of the bosonic nonlinear σ-model are governed, perturbatively, at different orders of α', by perturbatively evaluated β-functions. In regions where {α'}/{Rc2}≪1 ( {1}/{Rc2} represents the curvature scale), the flow equations at various orders in α' can be thought of as approximating the full, non-perturbative RG flow. On the other hand, taking a different viewpoint, we may consider the above-mentioned RG flow equations as viable geometric flows in their own right, without any reference to the RG aspect. Looked at as purely geometric flows where higher order terms appear, we no longer have the perturbative restrictions (small curvatures). In this paper, we perform our analysis from both these perspectives using specific target manifolds such as S2, H2, unwarped S2×H2 and simple warped products. We analyse and solve the higher order RG flow equations within the appropriate perturbative domains and find the corrections arising due to the inclusion of higher order terms. Such corrections, within the perturbative regime, are shown to be small and they provide an estimate of the error that arises when higher orders are ignored. We also investigate higher order geometric flows on the same manifolds and figure out generic features of geometric evolution, the appearance of singularities and solitons. The aim, in this context, is to demonstrate the role of higher order terms in modifying the flow. One interesting aspect of our analysis is that, separable solutions of the higher order flow equations for simple warped spacetimes (of the kind used in bulk-brane models with a single extra dimension), correspond to constant curvature anti de Sitter (AdS) spacetimes, modulo an overall flow parameter dependent scale factor. The functional form of this scale factor (that we obtain) changes on the inclusion of successive higher order terms in the flow.

  2. Higher-order phase transitions on financial markets

    NASA Astrophysics Data System (ADS)

    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

  3. Chromatin higher-order structure: two-start double superhelix formed by zig-zag shaped nucleosome chain with folded linker DNA.

    PubMed

    Osipova, T N; Karpova, E V; Vorob'ev, V I

    1990-08-01

    Hydrodynamic properties of chromatins differing in linker DNA length and in transcriptional activity have been studied by the method of sedimentation velocity. Oligonucleosomes of different chain length were isolated from chromatins of pigeon brain cortical neurones, rat thymus and sea urchin sperm characterized by nucleosome DNA repeat length of 165, 198 and 248 base pairs respectively. The hydrodynamic behaviour of oligonucleosomes in the dependence on the number of nucleosomes in the chain and on the ionic strength has been analysed on the basis of cylinder model. The data obtained allows one to calculate the main structural parameters of the oligonucleosomal chain: its mass per unit length, the hydrodynamic diameter of the chain, the length of the chain per nucleosome and DNA packing ratio. It is shown that hydrodynamic behaviour of nucleosome oligomers from all types of chromatins investigated at low ionic strength can be well described by the model of three-dimensional zig-zag chain with similar diameter and length of the chain per nucleosome, DNA packing ratio growing with the increase of linker DNA length. It can be achieved by unfolding the short linker DNA in neurone chromatin and by coiling the long linker DNA of sea urchin sperm chromatin into a loop. With the increase of ionic strength zig-zag shaped nucleosomal chain is condensed into a two-start double superhelix with closely arranged nucleosomes and linker DNA loops packed inside the superhelix. The suggested model is in good agreement with available experimental data and overcomes a number of difficulties which arise for the solenoid model and other models of the 30-nm chromatin fibril. PMID:2275789

  4. A Testing Theory for a Higher-Order Cryptographic Language

    NASA Astrophysics Data System (ADS)

    Koutavas, Vasileios; Hennessy, Matthew

    We study a higher-order concurrent language with cryptographic primitives, for which we develop a sound and complete, first-order testing theory for the preservation of safety properties. Our theory is based on co-inductive set simulations over transitions in a first-order Labelled Transition System. This keeps track of the knowledge of the observer, and treats transmitted higher-order values in a symbolic manner, thus obviating the quantification over functional contexts. Our characterisation provides an attractive proof technique, and we illustrate its usefulness in proofs of equivalence, including cases where bisimulation theory does not apply.

  5. Superposition rules for higher order systems and their applications

    NASA Astrophysics Data System (ADS)

    Cariñena, J. F.; Grabowski, J.; de Lucas, J.

    2012-05-01

    Superposition rules form a class of functions that describe general solutions of systems of first-order ordinary differential equations in terms of generic families of particular solutions and certain constants. In this work, we extend this notion and other related ones to systems of higher order differential equations and analyse their properties. Several results concerning the existence of various types of superposition rules for higher order systems are proved and illustrated with examples extracted from the physics and mathematics literature. In particular, two new superposition rules for the second- and third-order Kummer-Schwarz equations are derived.

  6. Unambiguous formalism for higher order Lagrangian field theories

    NASA Astrophysics Data System (ADS)

    Campos, Cédric M.; de León, Manuel; Martín de Diego, David; Vankerschaver, Joris

    2009-11-01

    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.

  7. On the Evaluation of Higher-Order Science Instructional Objectives

    ERIC Educational Resources Information Center

    Hambleton, Ronald K.; Sheehan, Daniel S.

    1977-01-01

    Advocates the use of a free-sort categorization technique for evaluation of higher-order science instructional objectives. An explanation and demonstration of the use of the evaluation technique with 284 ninth-grade science students is provided. (CP)

  8. Higher order derivatives of R-Jacobi polynomials

    NASA Astrophysics Data System (ADS)

    Das, Sourav; Swaminathan, A.

    2016-06-01

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

  9. The Lagrangian-Hamiltonian formalism for higher order field theories

    NASA Astrophysics Data System (ADS)

    Vitagliano, Luca

    2010-06-01

    We generalize the Lagrangian-Hamiltonian formalism of Skinner and Rusk to higher order field theories on fiber bundles. As a byproduct we solve the long standing problem of defining, in a coordinate free manner, a Hamiltonian formalism for higher order Lagrangian field theories. Namely, our formalism does only depend on the action functional and, therefore, unlike previously proposed ones, is free from any relevant ambiguity.

  10. Higher Order Lagrange Finite Elements In M3D

    SciTech Connect

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

    2004-12-17

    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.

  11. Higher-order Fourier analysis over finite fields and applications

    NASA Astrophysics Data System (ADS)

    Hatami, Pooya

    Higher-order Fourier analysis is a powerful tool in the study of problems in additive and extremal combinatorics, for instance the study of arithmetic progressions in primes, where the traditional Fourier analysis comes short. In recent years, higher-order Fourier analysis has found multiple applications in computer science in fields such as property testing and coding theory. In this thesis, we develop new tools within this theory with several new applications such as a characterization theorem in algebraic property testing. One of our main contributions is a strong near-equidistribution result for regular collections of polynomials. The densities of small linear structures in subsets of Abelian groups can be expressed as certain analytic averages involving linear forms. Higher-order Fourier analysis examines such averages by approximating the indicator function of a subset by a function of bounded number of polynomials. Then, to approximate the average, it suffices to know the joint distribution of the polynomials applied to the linear forms. We prove a near-equidistribution theorem that describes these distributions for the group F(n/p) when p is a fixed prime. This fundamental fact was previously known only under various extra assumptions about the linear forms or the field size. We use this near-equidistribution theorem to settle a conjecture of Gowers and Wolf on the true complexity of systems of linear forms. Our next application is towards a characterization of testable algebraic properties. We prove that every locally characterized affine-invariant property of functions f : F(n/p) → R with n∈ N, is testable. In fact, we prove that any such property P is proximity-obliviously testable. More generally, we show that any affine-invariant property that is closed under subspace restrictions and has "bounded complexity" is testable. We also prove that any property that can be described as the property of decomposing into a known structure of low

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

    NASA Astrophysics Data System (ADS)

    Kotzagiannidis, Madeleine S.; Dragotti, Pier Luigi

    2015-08-01

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

  13. Image Segmentation Using Higher-Order Correlation Clustering.

    PubMed

    Kim, Sungwoong; Yoo, Chang D; Nowozin, Sebastian; Kohli, Pushmeet

    2014-09-01

    In this paper, a hypergraph-based image segmentation framework is formulated in a supervised manner for many high-level computer vision tasks. To consider short- and long-range dependency among various regions of an image and also to incorporate wider selection of features, a higher-order correlation clustering (HO-CC) is incorporated in the framework. Correlation clustering (CC), which is a graph-partitioning algorithm, was recently shown to be effective in a number of applications such as natural language processing, document clustering, and image segmentation. It derives its partitioning result from a pairwise graph by optimizing a global objective function such that it simultaneously maximizes both intra-cluster similarity and inter-cluster dissimilarity. In the HO-CC, the pairwise graph which is used in the CC is generalized to a hypergraph which can alleviate local boundary ambiguities that can occur in the CC. Fast inference is possible by linear programming relaxation, and effective parameter learning by structured support vector machine is also possible by incorporating a decomposable structured loss function. Experimental results on various data sets show that the proposed HO-CC outperforms other state-of-the-art image segmentation algorithms. The HO-CC framework is therefore an efficient and flexible image segmentation framework. PMID:26352230

  14. Unified formalism for higher order non-autonomous dynamical systems

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

    This work is devoted to giving a geometric framework for describing higher order non-autonomous mechanical systems. The starting point is to extend the Lagrangian-Hamiltonian unified formalism of Skinner and Rusk for these kinds of systems, generalizing previous developments for higher order autonomous mechanical systems and first-order non-autonomous mechanical systems. Then, we use this unified formulation to derive the standard Lagrangian and Hamiltonian formalisms, including the Legendre-Ostrogradsky map and the Euler-Lagrange and the Hamilton equations, both for regular and singular systems. As applications of our model, two examples of regular and singular physical systems are studied.

  15. Higher-order conditioning and the retrosplenial cortex.

    PubMed

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

    2016-09-01

    The retrosplenial cortex (RSC) is known to contribute to contextual and spatial learning and memory. This is consistent with its well-established connectivity; the RSC is located at the interface of visuo-spatial association areas and the parahippocampal-hippocampal memory system. However, the RSC also contributes to learning and memory for discrete cues. For example, both permanent lesions and temporary inactivation of the RSC have been shown to impair sensory preconditioning, a form of higher-order conditioning. The purpose of the present experiment was to examine the role of the RSC in a closely related higher-order conditioning paradigm: second-order conditioning. Sham and RSC lesioned rats received first-order conditioning in which one visual stimulus (V1) was paired with footshock and one visual stimulus (V2) was not. Following first-order conditioning, one auditory stimulus (A1) was then paired with V1 and a second auditory stimulus (A2) was paired with V2. Although lesions of the RSC impaired the first-order discrimination, they had no impact on the acquisition of second-order conditioning. Thus, the RSC does not appear necessary for acquisition/expression of second-order fear conditioning. The role of the RSC in higher-order conditioning, as well as a possible dissociation from the hippocampus, is discussed. PMID:27208598

  16. Optimized higher-order automatic differentiation for the Faddeeva function

    NASA Astrophysics Data System (ADS)

    Charpentier, Isabelle

    2016-08-01

    Considerable research efforts have been directed at implementing the Faddeeva function w(z) and its derivatives with respect to z, but these did not consider the key computing issue of a possible dependence of z on some variable t. The general case is to differentiate the compound function w(z(t)) = w ∘ z(t) with respect to t by applying the chain rule for a first order derivative, or Faà di Bruno's formula for higher-order ones. Higher-order automatic differentiation (HOAD) is an efficient and accurate technique for derivative calculation along scientific computing codes. Although codes are available for w(z) , a special symbolic HOAD is required to compute accurate higher-order derivatives for w ∘ z(t) in an efficient manner. A thorough evaluation is carried out considering a nontrivial case study in optics to support this assertion.

  17. Ordered chlorinated monolayer silicene structures

    NASA Astrophysics Data System (ADS)

    Li, Wenbin; Sheng, Shaoxiang; Chen, Jian; Cheng, Peng; Chen, Lan; Wu, Kehui

    2016-04-01

    We report on a systematic experimental study on the chlorination of monatomic silicene layer on Ag(111) by scanning tunneling microscopy. Monolayer silicene on Ag(111) can form 4×4, (√13×√13)R ± 13.9°, and (2√3×2√3)R30° reconstructions due to their different buckling configurations. We found that at low dosage, Cl atoms attach to the upper buckled Si atoms without changing the buckling configuration of the silicene monolayer. However, at high coverage, the global buckling configuration will be significantly changed, resulting in new ordered structures. Interestingly, all monolayer silicene structures, regardless of their initial reconstructions, tend to form a local silicene 1×1 structure at the saturation coverage. The mechanism for chlorination of monolayer silicene is explained.

  18. Evidence for higher-order structure formation by the c-myb 18-mer phosphorothioate antisense (codons 2-7) oligodeoxynucleotide: potential relationship to antisense c-myb inhibition.

    PubMed

    Vilenchik, M; Benimetsky, L; Kolbanovsky, A; Miller, P; Stein, C A

    2001-04-01

    We have demonstrated the formation of higher-order structures (presumably tetraplexes) by an 18-mer phosphorothioate antisense c-myb oligodeoxyribonucleotide that has been shown to have activity in the treatment of leukemia xenograft models. Although not observable by conventionally employed techniques, such as PAGE and dimethyl sulfate (DMS) protection, the formation of such higher-order structures by this oligonucleotide was revealed by several techniques. These included capillary gel electrophoresis (CGE), which demonstrated the presence of molecules with greatly increased retention time compared with the monomer; magnetic circular dichroism spectroscopy, which demonstrated a band at 290 nm, a characteristic of antiparallel tetraplexes; and fluorescence energy transfer measurements. For the last, the 18-mer phosphorothioate oligonucleotide was synthesized with a 5'-fluorescein group. Similar to the molecular beacon model, its fluorescence was quenched when combined in solution with tetraplex-forming oligomers that contained a 3'-Dabcyl moiety. 7-Deazaguanosine inhibits the formation of tetraplexes by eliminated Hoogsteen base pair interactions. The wild-type and 7-deazaguanosine-substituted antisense c-myb oligomers differentially downregulated the expression of the c-myb proto-oncogene in K562 and HL60 cells, with the wild-type oligomer being the least active. The 18-mer c-myb molecule can, therefore, form highly complex structures, whose analysis in solution cannot be limited to examination of slab gel electrophoresis results alone. PMID:11334144

  19. 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

    PubMed Central

    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

  20. Higher-order motion sensitivity in fly visual circuits.

    PubMed

    Lee, Yu-Jen; Nordström, Karin

    2012-05-29

    In higher-order motion stimuli, the direction of object motion does not follow the direction of luminance change. Such stimuli could be generated by the wing movements of a flying butterfly and further complicated by its motion in and out of shadows. Human subjects readily perceive the direction of higher-order motion, although this stands in stark contrast to prevailing motion vision models. Flies and humans compute motion in similar ways, and because flies behaviorally track bars containing higher-order motion cues, they become an attractive model system for investigating the neurophysiology underlying higher-order motion sensitivity. We here use intracellular electrophysiology of motion-vision-sensitive neurons in the hoverfly lobula plate to quantify responses to stimuli containing higher-order motion. We show that motion sensitivity can be broken down into two separate streams, directionally coding for elementary motion and figure motion, respectively, and that responses to Fourier and theta motion can be predicted from these. The sensitivity is affected both by the stimulus' time course and by the neuron's underlying receptive field. Responses to preferred-direction theta motion are sexually dimorphic and particularly robust along the visual midline. PMID:22586123

  1. Higher-order motion sensitivity in fly visual circuits

    PubMed Central

    Lee, Yu-Jen; Nordström, Karin

    2012-01-01

    In higher-order motion stimuli, the direction of object motion does not follow the direction of luminance change. Such stimuli could be generated by the wing movements of a flying butterfly and further complicated by its motion in and out of shadows. Human subjects readily perceive the direction of higher-order motion, although this stands in stark contrast to prevailing motion vision models. Flies and humans compute motion in similar ways, and because flies behaviorally track bars containing higher-order motion cues, they become an attractive model system for investigating the neurophysiology underlying higher-order motion sensitivity. We here use intracellular electrophysiology of motion-vision–sensitive neurons in the hoverfly lobula plate to quantify responses to stimuli containing higher-order motion. We show that motion sensitivity can be broken down into two separate streams, directionally coding for elementary motion and figure motion, respectively, and that responses to Fourier and theta motion can be predicted from these. The sensitivity is affected both by the stimulus’ time course and by the neuron’s underlying receptive field. Responses to preferred-direction theta motion are sexually dimorphic and particularly robust along the visual midline. PMID:22586123

  2. Dynamics and control of higher-order nonholonomic systems

    NASA Astrophysics Data System (ADS)

    Rubio Hervas, Jaime

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

  3. Ordered structures and jet noise

    NASA Technical Reports Server (NTRS)

    Petersen, R. A.; Kaplan, R. E.; Laufer, J.

    1974-01-01

    A series of measurements of near field pressures and turbulent velocity fluctuations were made in a jet having a Reynolds number of about 50,000 in order to investigate more quantitatively the character and behavior of the large scale structures, and to ascertain their importance to the jet noise problem. It was found that the process of interaction between vortices can be inhibited by artificially exciting the shear layers with periodic disturbances of certain frequency. The turbulent fluctuation amplitudes measured at four diameters downstream decreased considerably. Finally, it was observed that the passage frequency of the structures decreased with x in a similar manner as the frequency corresponding to the maximum intensity radiation emanating from the same value of x.

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

    SciTech Connect

    Kenny, Joseph P.; Bader, Brett William; Kolda, Tamara Gibson

    2005-07-01

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

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

    PubMed Central

    Chambers, Brendan; MacLean, Jason N.

    2016-01-01

    Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex. Circuit dynamics emerge from complex interactions of interconnected neurons, necessitating that links between connectivity and dynamics be evaluated at the network level. Here we map propagating activity in large neuronal ensembles from mouse neocortex and compare it to a recurrent network model, where connectivity can be precisely measured and manipulated. We find that a dynamical feature dominates statistical descriptions of propagating activity for both neocortex and the model: convergent clusters comprised of fan-in triangle motifs, where two input neurons are themselves connected. Fan-in triangles coordinate the timing of presynaptic inputs during ongoing activity to effectively generate postsynaptic spiking. As a result, paradoxically, fan-in triangles dominate the statistics of spike propagation even in randomly connected recurrent networks. Interplay between higher-order synaptic connectivity and the integrative properties of neurons constrains the structure of network dynamics and shapes the routing of information in neocortex. PMID:27542093

  6. Spectral imaging to visualize higher-order genomic organization.

    PubMed

    Sawyer, Iain A; Shevtsov, Sergei P; Dundr, Miroslav

    2016-05-01

    A concern in the field of genomics is the proper interpretation of large, high-throughput sequencing datasets. The use of DNA FISH followed by high-content microscopy is a valuable tool for validation and contextualization of frequently occurring gene pairing events at the single-cell level identified by deep sequencing. However, these techniques possess certain limitations. Firstly, they do not permit the study of colocalization of many gene loci simultaneously. Secondly, the direct assessment of the relative position of many clustered gene loci within their respective chromosome territories is impossible. Thus, methods are required to advance the study of higher-order nuclear and cellular organization. Here, we describe a multiplexed DNA FISH technique combined with indirect immunofluorescence to study the relative position of 6 distinct genomic or cellular structures. This can be achieved in a single hybridization step using spectral imaging during image acquisition and linear unmixing. Here, we detail the use of this method to quantify gene pairing between highly expressed spliceosomal genes and compare these data to randomly positioned in silico simulated gene clusters. This is a potentially universally applicable approach for the validation of 3C-based technologies, deep imaging of spatial organization within the nucleus and global cellular organization. PMID:27167405

  7. Generation of Higher Order Modes in a Rectangular Duct

    NASA Technical Reports Server (NTRS)

    Gerhold, Carl H.; Cabell, Randolph H.; Brown, Donald E.

    2004-01-01

    Advanced noise control methodologies to reduce sound emission from aircraft engines take advantage of the modal structure of the noise in the duct. This noise is caused by the interaction of rotor wakes with downstream obstructions such as exit guide vanes. Mode synthesis has been accomplished in circular ducts and current active noise control work has made use of this capability to cancel fan noise. The goal of the current effort is to examine the fundamental process of higher order mode propagation through an acoustically treated, curved duct. The duct cross-section is rectangular to permit greater flexibility in representation of a range of duct curvatures. The work presented is the development of a feedforward control system to generate a user-specified modal pattern in the duct. The multiple-error, filtered-x LMS algorithm is used to determine the magnitude and phase of signal input to the loudspeakers to produce a desired modal pattern at a set of error microphones. Implementation issues, including loudspeaker placement and error microphone placement, are discussed. Preliminary results from a 9-3/8 inch by 21 inch duct, using 12 loudspeakers and 24 microphones, are presented. These results demonstrate the ability of the control system to generate a user-specified mode while suppressing undesired modes.

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

    PubMed

    Chambers, Brendan; MacLean, Jason N

    2016-08-01

    Linking synaptic connectivity to dynamics is key to understanding information processing in neocortex. Circuit dynamics emerge from complex interactions of interconnected neurons, necessitating that links between connectivity and dynamics be evaluated at the network level. Here we map propagating activity in large neuronal ensembles from mouse neocortex and compare it to a recurrent network model, where connectivity can be precisely measured and manipulated. We find that a dynamical feature dominates statistical descriptions of propagating activity for both neocortex and the model: convergent clusters comprised of fan-in triangle motifs, where two input neurons are themselves connected. Fan-in triangles coordinate the timing of presynaptic inputs during ongoing activity to effectively generate postsynaptic spiking. As a result, paradoxically, fan-in triangles dominate the statistics of spike propagation even in randomly connected recurrent networks. Interplay between higher-order synaptic connectivity and the integrative properties of neurons constrains the structure of network dynamics and shapes the routing of information in neocortex. PMID:27542093

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

    SciTech Connect

    Chiravalle, Vincent P

    2011-01-05

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

  10. Breaking the symmetry for enhanced higher-order mode delocalization

    NASA Astrophysics Data System (ADS)

    Stutzki, Fabian; Jansen, Florian; Jauregui, Cesar; Limpert, Jens; Tünnermann, Andreas

    2014-03-01

    Large-pitch fibers (LPFs) have enabled the current records for average power, pulse energy and pulse peak power in ultra-fast fiber laser systems. In this paper the working principle of LPFs, which is based on higher-order mode delocalization, is numerically analyzed paying special attention to thermal effects and index mismatch. An enhanced design concept is proposed with a reduced symmetry to improve the delocalization of higher-order modes. This enhanced design has been obtained by transferring the most important characteristics of spiral geometries to a common hexagonal lattice.

  11. Higher order mode laser beam scintillations in oceanic medium

    NASA Astrophysics Data System (ADS)

    Baykal, Yahya

    2016-01-01

    In a horizontal oceanic optical wireless communication link, the scintillation index (the measure for the intensity fluctuations) of the received intensity caused by the oceanic turbulence is formulated and evaluated when the source is a higher order mode laser. Variations in the scintillation index vs. the underwater turbulence parameters, size of the higher order mode laser source, link length, and the wavelength are examined. Underwater turbulence parameters are the ratio that determines the relative strength of temperature and salinity in driving the index fluctuations, the rate of dissipation of the mean squared temperature, the rate of dissipation of the turbulent kinetic energy, and the Kolmogorov microscale length.

  12. Vakonomic Constraints in Higher-Order Classical Field Theory

    NASA Astrophysics Data System (ADS)

    Campos, Cédric M.

    2010-07-01

    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. The result is that we obtain a unique and global intrinsic description of the dynamics. The case of vakonomic constraints is also studied within this formalism.

  13. Higher Order Mode Coupler Heating in Continuous Wave Operation

    NASA Astrophysics Data System (ADS)

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

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

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

    USGS Publications Warehouse

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

    2008-01-01

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

  15. Higher order matrix differential equations with singular coefficient matrices

    SciTech Connect

    Fragkoulis, V. C.; Kougioumtzoglou, I. A.; Pantelous, A. A.; Pirrotta, A.

    2015-03-10

    In this article, the class of higher order linear matrix differential equations with constant coefficient matrices and stochastic process terms is studied. The coefficient of the highest order is considered to be singular; thus, rendering the response determination of such systems in a straightforward manner a difficult task. In this regard, the notion of the generalized inverse of a singular matrix is used for determining response statistics. Further, an application relevant to engineering dynamics problems is included.

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

    PubMed

    Mauermann, M; Uppenkamp, S; van Hengel, P W; Kollmeier, B

    1999-12-01

    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 dependence of fine-structure patterns on the frequency ratio f2/f1 was investigated by changing f1 or f2 only (fixed f2 or fixed f1 paradigm, respectively), and by changing both primaries at a fixed ratio and looking at different order DPOAE. When f2/f1 is varied in the fixed ratio paradigm, the patterns of 2 f1-f2 fine structure vary considerably more if plotted as a function of f2 than as a function of fDP. Different order distortion products located at the same characteristic place on the basilar membrane (BM) show similar patterns for both, the fixed-f2 and fDP paradigms. Fluctuations in DPOAE level up to 20 dB can be observed. In contrast, the results from a fixed-fDP paradigm do not show any fine structure but only an overall dependence of DP level on the frequency ratio, with a maximum for 2f1-f2 at f2/f1 close to 1.2. Similar stimulus configurations used in the experiments have also been used for computer simulations of DPOAE in a nonlinear and active model of the cochlea. Experimental results and model simulations give strong evidence for a two-source model of DPOAE generation: The first source is the initial nonlinear interaction of the primaries close to the f2 place. The second source is caused by coherent reflection from a re-emission site at the characteristic place of the distortion product frequency. The spectral fine structure of DPOAE observed in the ear canal reflects the interaction of both these sources. PMID:10615687

  17. Prominent Higher-Order Contributions to Electronic Recombination

    SciTech Connect

    Beilmann, C.; Mokler, P. H.; Bernitt, S.; Keitel, C. H.; Ullrich, J.; Lopez-Urrutia, J. R. Crespo; Harman, Z.

    2011-09-30

    Intershell higher-order (HO) electronic recombination is reported for highly charged Ar, Fe, and Kr ions, where simultaneous excitation of one K-shell electron and one or two additional L-shell electrons occurs upon resonant capture of a free electron. For the mid-Z region, HO resonance strengths grow unexpectedly strong with decreasing atomic number Z ({proportional_to}Z{sup -4}), such that, for Ar ions the 2nd-order overwhelms the 1st-order resonant recombination considerably. The experimental findings are confirmed by multiconfiguration Dirac-Fock calculations including hitherto neglected excitation pathways.

  18. Higher-order dynamical effects in Coulomb dissociation

    SciTech Connect

    Esbensen, H.; Bertsch, G.F.; Bertulani, C.A.

    1995-08-01

    Coulomb dissociation is a technique commonly used to extract the dipole response of nuclei far from stability. This technique is applicable if the dissociation is dominated by dipole transitions and if first-order perturbation theory is valid. In order to assess the significance of higher-order processes we solve numerically the time evolution of the wave function for a two-body breakup in the Coulomb field from a high Z target. We applied this method to the breakup reactions: {sup 11}Be {yields} {sup 10}Be + n and {sup 11}Li {yields} +2n. The latter is treated as a two-body breakup, using a di-neutron model.

  19. Higher Order Language Competence and Adolescent Mental Health

    ERIC Educational Resources Information Center

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

    2013-01-01

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

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

    ERIC Educational Resources Information Center

    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…

  1. Using Higher Order Computer Tasks with Disadvantaged Students.

    ERIC Educational Resources Information Center

    Anderson, Neil

    A pilot program initially designed for a 12-year-old girl with mild to moderate intellectual disabilities in higher order computer tasks was developed for a larger group of students with similar disabilities enrolled in fifth and sixth grades (ages 9-12) at three different schools. An examination of the original pilot study was undertaken to…

  2. Higher-Order Latent Trait Models for Cognitive Diagnosis

    ERIC Educational Resources Information Center

    de la Torre, Jimmy; Douglas, Jeffrey A.

    2004-01-01

    Higher-order latent traits are proposed for specifying the joint distribution of binary attributes in models for cognitive diagnosis. This approach results in a parsimonious model for the joint distribution of a high-dimensional attribute vector that is natural in many situations when specific cognitive information is sought but a less informative…

  3. Constrained variational calculus for higher order classical field theories

    NASA Astrophysics Data System (ADS)

    Campos, Cédric M.; de León, Manuel; Martín de Diego, David

    2010-11-01

    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.

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

    PubMed

    Maimaiti, Aili; Truong, Viet Giang; Sergides, Marios; Gusachenko, Ivan; Nic Chormaic, Síle

    2015-01-01

    Optical manipulation in the vicinity of optical micro- and nanofibres has shown potential across several fields in recent years, including microparticle control, and cold atom probing and trapping. To date, most work has focussed on the propagation of the fundamental mode through the fibre. However, along the maximum mode intensity axis, higher order modes have a longer evanescent field extension and larger field amplitude at the fibre waist compared to the fundamental mode, opening up new possibilities for optical manipulation and particle trapping. We demonstrate a microfibre/optical tweezers compact system for trapping and propelling dielectric particles based on the excitation of the first group of higher order modes at the fibre waist. Speed enhancement of polystyrene particle propulsion was observed for the higher order modes compared to the fundamental mode for particles ranging from 1 μm to 5 μm in diameter. The optical propelling velocity of a single, 3 μm polystyrene particle was found to be 8 times faster under the higher order mode than the fundamental mode field for a waist power of 25 mW. Experimental data are supported by theoretical calculations. This work can be extended to trapping and manipulation of laser-cooled atoms with potential for quantum networks. PMID:25766925

  5. Building Higher-Order Markov Chain Models with EXCEL

    ERIC Educational Resources Information Center

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

    2004-01-01

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

  6. Using Database Projects To Promote Higher-Order Thinking Skills.

    ERIC Educational Resources Information Center

    Lytle, Cora

    1999-01-01

    Explains how the process of creating a database provides opportunities for business instructors to use teaching strategies that promote higher-order thinking skills. Describes a project at a school of business in which each student must build an original database and apply functions of tables, queries, forms, and reports. (JOW)

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

    PubMed Central

    Maimaiti, Aili; Truong, Viet Giang; Sergides, Marios; Gusachenko, Ivan; Nic Chormaic, Síle

    2015-01-01

    Optical manipulation in the vicinity of optical micro- and nanofibres has shown potential across several fields in recent years, including microparticle control, and cold atom probing and trapping. To date, most work has focussed on the propagation of the fundamental mode through the fibre. However, along the maximum mode intensity axis, higher order modes have a longer evanescent field extension and larger field amplitude at the fibre waist compared to the fundamental mode, opening up new possibilities for optical manipulation and particle trapping. We demonstrate a microfibre/optical tweezers compact system for trapping and propelling dielectric particles based on the excitation of the first group of higher order modes at the fibre waist. Speed enhancement of polystyrene particle propulsion was observed for the higher order modes compared to the fundamental mode for particles ranging from 1 μm to 5 μm in diameter. The optical propelling velocity of a single, 3 μm polystyrene particle was found to be 8 times faster under the higher order mode than the fundamental mode field for a waist power of 25 mW. Experimental data are supported by theoretical calculations. This work can be extended to trapping and manipulation of laser-cooled atoms with potential for quantum networks. PMID:25766925

  8. Assessing the Influence of Portfolios on Higher Order Thinking Skills.

    ERIC Educational Resources Information Center

    Seiter, David M.

    How the use of portfolios in the classroom will influence the higher order thinking skills is the main focus of this project. The introduction of portfolios as assessment tools is rather new to educational research, but does offer a legitimate area for serious study. Portfolios when used by students can offer them not only a way to showcase their…

  9. Multiple-Try Feedback and Higher-Order Learning Outcomes

    ERIC Educational Resources Information Center

    Clariana, Roy B.; Koul, Ravinder

    2005-01-01

    Although feedback is an important component of computer-based instruction (CBI), the effects of feedback on higher-order learning outcomes are not well understood. Several meta-analyses provide two rules of thumb: any feedback is better than no feedback and feedback with more information is better than feedback with less information. …

  10. Developing Higher-Order Thinking Skills through WebQuests

    ERIC Educational Resources Information Center

    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.…

  11. Using Higher-Order Skills in American History.

    ERIC Educational Resources Information Center

    Litogot, Sandra A.

    1991-01-01

    Provides a six-part lesson plan for use in secondary U.S. history classes. Illustrates the development of higher-order reading, writing, and thinking skills in assignments and projects dealing with the history of westward expansion. Specific skills addressed are comparison, contrast, prediction, and evaluation. Recommends cooperative learning…

  12. Higher-order ionospheric error at Arecibo, Millstone, and Jicamarca

    NASA Astrophysics Data System (ADS)

    Matteo, N. A.; Morton, Y. T.

    2010-12-01

    The ionosphere is a dominant source of Global Positioning System receiver range measurement error. Although dual-frequency receivers can eliminate the first-order ionospheric error, most second- and third-order errors remain in the range measurements. Higher-order ionospheric error is a function of both electron density distribution and the magnetic field vector along the GPS signal propagation path. This paper expands previous efforts by combining incoherent scatter radar (ISR) electron density measurements, the International Reference Ionosphere model, exponential decay extensions of electron densities, the International Geomagnetic Reference Field, and total electron content maps to compute higher-order error at ISRs in Arecibo, Puerto Rico; Jicamarca, Peru; and Millstone Hill, Massachusetts. Diurnal patterns, dependency on signal direction, seasonal variation, and geomagnetic activity dependency are analyzed. Higher-order error is largest at Arecibo with code phase maxima circa 7 cm for low-elevation southern signals. The maximum variation of the error over all angles of arrival is circa 8 cm.

  13. Speckle reduction via higher order total variation approach.

    PubMed

    Wensen Feng; Hong Lei; Yang Gao

    2014-04-01

    Multiplicative noise (also known as speckle) reduction is a prerequisite for many image-processing tasks in coherent imaging systems, such as the synthetic aperture radar. One approach extensively used in this area is based on total variation (TV) regularization, which can recover significantly sharp edges of an image, but suffers from the staircase-like artifacts. In order to overcome the undesirable deficiency, we propose two novel models for removing multiplicative noise based on total generalized variation (TGV) penalty. The TGV regularization has been mathematically proven to be able to eliminate the staircasing artifacts by being aware of higher order smoothness. Furthermore, an efficient algorithm is developed for solving the TGV-based optimization problems. Numerical experiments demonstrate that our proposed methods achieve state-of-the-art results, both visually and quantitatively. In particular, when the image has some higher order smoothness, our methods outperform the TV-based algorithms. PMID:24808350

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

    PubMed Central

    Pradhan, Cauchy; Jena, Susant K.; Nadar, Sreenivasan R.; Pradhan, N.

    2012-01-01

    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. PMID:22400046

  15. Higher order corrections in minimal supergravity models of inflation

    SciTech Connect

    Ferrara, Sergio; Kallosh, Renata; Linde, Andrei; Porrati, Massimo E-mail: kallosh@stanford.edu E-mail: massimo.porrati@nyu.edu

    2013-11-01

    We study higher order corrections in new minimal supergravity models of a single scalar field inflation. The gauging in these models leads to a massive vector multiplet and the D-term potential for the inflaton field with a coupling g{sup 2} ∼ 10{sup −10}. In the de-Higgsed phase with vanishing g{sup 2}, the chiral and vector multiplets are non-interacting, and the potential vanishes. We present generic manifestly supersymmetric higher order corrections for these models. In particular, for a supersymmetric gravity model −R+R{sup 2} we derive manifestly supersymmetric corrections corresponding to R{sup n}. The dual version corresponds to a standard supergravity model with a single scalar and a massive vector. It includes, in addition, higher Maxwell curvature/scalar interaction terms of the Born-Infeld type and a modified D-term scalar field potential. We use the dual version of the model to argue that higher order corrections do not affect the last 60 e-foldings of inflation; for example the ξR{sup 4} correction is irrelevant as long as ξ < 10{sup 24}.

  16. Synchronous firing and higher-order interactions in neuron pool.

    PubMed

    Amari, Shun-Ichi; Nakahara, Hiroyuki; Wu, Si; Sakai, Yutaka

    2003-01-01

    The stochastic mechanism of synchronous firing in a population of neurons is studied from the point of view of information geometry. Higher-order interactions of neurons, which cannot be reduced to pairwise correlations, are proved to exist in synchronous firing. In a neuron pool where each neuron fires stochastically, the probability distribution q(r) of the activity r, which is the fraction of firing neurons in the pool, is studied. When q(r) has a widespread distribution, in particular, when q(r) has two peaks, the neurons fire synchronously at one time and are quiescent at other times. The mechanism of generating such a probability distribution is interesting because the activity r is concentrated on its mean value when each neuron fires independently, because of the law of large numbers. Even when pairwise interactions, or third-order interactions, exist, the concentration is not resolved. This shows that higher-order interactions are necessary to generate widespread activity distributions. We analyze a simple model in which neurons receive common overlapping inputs and prove that such a model can have a widespread distribution of activity, generating higher-order stochastic interactions. PMID:12590822

  17. Higher order correlation beams in atmosphere under strong turbulence conditions.

    PubMed

    Avetisyan, H; Monken, C H

    2016-02-01

    Higher order correlation beams, that is, two-photon beams obtained from the process of spontaneous parametric down-conversion pumped by Hermite-Gauss or Laguerre-Gauss beams of any order, can be used to encode information in many modes, opening the possibility of quantum communication with large alphabets. In this paper we calculate, analytically, the fourth-order correlation function for the Hermite-Gauss and Laguerre-Gauss coherent and partially coherent correlation beams propagating through a strong turbulent medium. We show that fourth-order correlation functions for correlation beams have, under certain conditions, expressions similar to those of intensities of classical beams and are degraded by turbulence in a similar way as the classical beams. Our results can be useful in establishing limits for the use of two-photon beams in quantum communications with larger alphabets under atmospheric turbulence. PMID:26906808

  18. Lipkin method of particle-number restoration to higher orders

    NASA Astrophysics Data System (ADS)

    Wang, X. B.; Dobaczewski, J.; Kortelainen, M.; Yu, L. F.; Stoitsov, M. V.

    2014-07-01

    Background: On the mean-field level, pairing correlations are incorporated through the Bogoliubov-Valatin transformation, whereby the particle degrees of freedom are replaced by quasiparticles. This approach leads to a spontaneous breaking of the particle-number symmetry and mixing of states with different particle numbers. In order to restore the particle number, various methods have been employed, which are based on projection approaches before or after variation. Approximate variation-after-projection (VAP) schemes, utilizing the Lipkin method, have mostly been used within the Lipkin-Nogami prescription. Purpose: Without employing the Lipkin-Nogami prescription, and using, instead, states rotated in the gauge space, we derive the Lipkin method of particle-number restoration up to sixth order and we test the convergence and accuracy of the obtained expansion. Methods: We perform self-consistent calculations using the higher-order Lipkin method to restore the particle-number symmetry in the framework of superfluid nuclear energy-density functional theory. We also apply the Lipkin method to a schematic exactly solvable two-level pairing model. Results: Calculations performed in open-shell tin and lead isotopes show that the Lipkin method converges at fourth order and satisfactorily reproduces the VAP ground-state energies and energy kernels. Near closed shells, the higher-order Lipkin method cannot be applied because of a nonanalytic kink in the ground-state energies as a function of the particle number. Conclusions: In open-shell nuclei, the higher-order Lipkin method provides a good approximation to the exact VAP energies. The method is computationally inexpensive, making it particularly suitable, for example, for future optimizations of the nuclear energy density functionals and simultaneous restoration of different symmetries.

  19. A Short Note on Rules and Higher Order Rules.

    ERIC Educational Resources Information Center

    Scandura, Joseph M.

    This brief paper argues that structural analysis--an extended form of cognitive task analysis--demonstrates that both domain dependent and domain independent knowledge can be derived from specific content domains. It is noted that the major difference between the two is that lower order rules (specific knowledge) are derived directly from specific…

  20. A higher order theory of laminated composite cylindrical shells

    NASA Technical Reports Server (NTRS)

    Krishna Murthy, A. V.; Reddy, T. S. R.

    1986-01-01

    A new higher order theory has been proposed for the analysis of composite cylindrical shells. The formulation allows for arbitrary variation of inplane displacements. Governing equations are presented in the form of a hierarchy of sets of partial differential equations. Each set describes the shell behavior to a certain degree of approximation. The natural frequencies of simply-supported isotropic and laminated shells and stresses in a ring loaded composite shell have been determined to various orders of approximation and compared with three dimensional solutions. These numerical studies indicate the improvements achievable in estimating the natural frequencies and the interlaminar shear stresses in laminated composite cylinders.

  1. Algorithmic and Experimental Computation of Higher-Order Safe Primes

    NASA Astrophysics Data System (ADS)

    Díaz, R. Durán; Masqué, J. Muñoz

    2008-09-01

    This paper deals with a class of special primes called safe primes. In the regular definition, an odd prime p is safe if, at least, one of (p±1)/2 is prime. Safe primes have been recommended as factors of RSA moduli. In this paper, the concept of safe primes is extended to higher-order safe primes, and an explicit formula to compute the density of this class of primes in the set of the integers is supplied. Finally, explicit conditions are provided permitting the algorithmic computation of safe primes of arbitrary order. Some experimental results are provided as well.

  2. Sandia Higher Order Elements (SHOE) v 0.5 alpha

    SciTech Connect

    2013-09-24

    SHOE is research code for characterizing and visualizing higher-order finite elements; it contains a framework for defining classes of interpolation techniques and element shapes; methods for interpolating triangular, quadrilateral, tetrahedral, and hexahedral cells using Lagrange and Legendre polynomial bases of arbitrary order; methods to decompose each element into domains of constant gradient flow (using a polynomial solver to identify critical points); and an isocontouring technique that uses this decomposition to guarantee topological correctness. Please note that this is an alpha release of research software and that some time has passed since it was actively developed; build- and run-time issues likely exist.

  3. Sandia Higher Order Elements (SHOE) v 0.5 alpha

    Energy Science and Technology Software Center (ESTSC)

    2013-09-24

    SHOE is research code for characterizing and visualizing higher-order finite elements; it contains a framework for defining classes of interpolation techniques and element shapes; methods for interpolating triangular, quadrilateral, tetrahedral, and hexahedral cells using Lagrange and Legendre polynomial bases of arbitrary order; methods to decompose each element into domains of constant gradient flow (using a polynomial solver to identify critical points); and an isocontouring technique that uses this decomposition to guarantee topological correctness. Please notemore » that this is an alpha release of research software and that some time has passed since it was actively developed; build- and run-time issues likely exist.« less

  4. Analytical formulas for gravitational lensing: Higher order calculation

    SciTech Connect

    Amore, Paolo; Arceo, Santiago; Fernandez, Francisco M.

    2006-10-15

    We extend to higher order a recently published method for calculating the deflection angle of light in a general static and spherically symmetric metric. We have tested our method on the metric of Schwarzschild and Reissner-Nordstroem black holes, on the metric of a charged black hole coupled to Born-Infeld electrodynamics and on the metric of Weyl gravity. Since our method is geometrically convergent, as proved in our previous work, our analytical formulas obtained working to fourth order are sufficient to reach errors of few percents even in proximity of the photon sphere.

  5. Stabilization with target oriented control for higher order difference equations

    NASA Astrophysics Data System (ADS)

    Braverman, Elena; Franco, Daniel

    2015-06-01

    For a physical or biological model whose dynamics is described by a higher order difference equation un+1 = f (un ,un-1 , … ,u n - k + 1), we propose a version of a target oriented control un+1 = cT + (1 - c) f (un ,un-1 , … ,u n - k + 1), with T ≥ 0, c ∈ [ 0 , 1). In ecological systems, the method incorporates harvesting and recruitment and for a wide class of f, allows to stabilize (locally or globally) a fixed point of f. If a point which is not a fixed point of f has to be stabilized, the target oriented control is an appropriate method for achieving this goal. As a particular case, we consider pest control applied to pest populations with delayed density-dependence. This corresponds to a proportional feedback method, which includes harvesting only, for higher order equations.

  6. Spatial complexity of solutions of higher order partial differential equations

    NASA Astrophysics Data System (ADS)

    Kukavica, Igor

    2004-03-01

    We address spatial oscillation properties of solutions of higher order parabolic partial differential equations. In the case of the Kuramoto-Sivashinsky equation ut + uxxxx + uxx + u ux = 0, we prove that for solutions u on the global attractor, the quantity card {x epsi [0, L]:u(x, t) = lgr}, where L > 0 is the spatial period, can be bounded by a polynomial function of L for all \\lambda\\in{\\Bbb R} . A similar property is proven for a general higher order partial differential equation u_t+(-1)^{s}\\partial_x^{2s}u+ \\sum_{k=0}^{2s-1}v_k(x,t)\\partial_x^k u =0 .

  7. High Precision Superconducting Cavity Diagnostics With Higher Order Mode Measurements

    SciTech Connect

    Molloy, S.; Frisch, J.; McCormick, D.; May, J.; Ross, M.; Smith, T.; Baboi, N.; Hensler, O.; Petrosian, L.; Napoly, O.; Paparella, R.C.; Simon, C.; Eddy, N.; Nagaitsev, S.; Wendt, M.; /Fermilab

    2007-02-12

    Experiments at the FLASH facility at DESY have demonstrated that the higher order modes induced in superconducting cavities can be used to provide a variety of beam and cavity diagnostics. The axes of the modes can be determined from the beam orbit that produces minimum power in the dipole HOM modes. The phase and amplitude of the dipole modes can be used to obtain high resolution beam position information, and the phase of the monopole modes to measure the beam phase relative to the accelerator rf. For most superconducting accelerators, the existing higher order mode couplers provide the necessary signals, and the downmix and digitizing electronics are straightforward, similar to those for a conventional beam position monitor.

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  9. Higher order mode excitations in gyro-amplifiers

    NASA Astrophysics Data System (ADS)

    Nguyen, K. T.; Calame, J. P.; Danly, B. G.; Levush, B.; Garven, M.; Antonsen, T.

    2001-05-01

    In gyro-devices, a nonlinear output taper is often employed as the transition from the near cutoff radius of the interaction circuit to a much larger output waveguide. The tapers are usually designed to avoid passive mode conversion, and thus do not consider the effect of a bunched beam. However, recent simulations with the self-consistent MAGY code [Botton et al., IEEE Trans. Plasma Sci. 26, 882 (1998)] indicate that higher order mode interactions with the bunched electron beam can substantially compromise the mode purity of the rf output. The interaction in the taper region is traveling wave in nature, and is strongly dependent on the residual beam bunching characteristics resulting from the upstream operating mode interaction. An experiment has been performed to quantify the rf output mode content from a Ka-band gyroklystron. The agreement between salient theoretical and measured rf output characteristics confirms the existence of higher order mode excitation in output tapers as predicted by theory.

  10. Validating variational principle for higher order theory of gravity

    NASA Astrophysics Data System (ADS)

    Ruz, Soumendranath; Sarkar, Kaushik; Sk, Nayem; Sanyal, Abhik Kumar

    2015-06-01

    Metric variation of higher order theory of gravity requires fixing of the Ricci scalar in addition to the metric tensor at the boundary. Fixing Ricci scalar at the boundary implies that the classical solutions are fixed once and forever to the de Sitter or anti-de Sitter (dS/AdS) solutions. Here, we justify such requirement from the standpoint of Noether symmetry.