New ARCH: Future Generation Internet Architecture

DTIC Science & Technology

2004-08-01

a vocabulary to talk about a system . This provides a framework ( a “reference model ...layered model Modularity and abstraction are central tenets of Computer Science thinking. Modularity breaks a system into parts, normally to permit...this complexity is hidden. Abstraction suggests a structure for the system . A popular and simple structure is a layered model : lower layer

Structural Relations of Personal and Collective Self-Esteem to Subjective Well-Being: Attachment as Moderator

ERIC Educational Resources Information Center

Simsek, Omer Faruk

2013-01-01

A model indicating that the relationship between collective self-esteem and indicators of subjective well-being, happiness and life satisfaction, was mediated by personal self-esteem was tested by structural equation modeling. The model, including all participants, fitted well to the data. The results suggested that the relationship of collective…

On the temporal evolution of long-wavelength mantle structure of the Earth since the early Paleozoic

NASA Astrophysics Data System (ADS)

Zhong, Shijie; Rudolph, Maxwell L.

2015-05-01

The seismic structure of the Earth's lower mantle is characterized by a dominantly degree-2 pattern with the African and Pacific large low shear velocity provinces (i.e., LLSVP) that are separated by circum-Pacific seismically fast anomalies. It is important to understand the origin of such a degree-2 mantle structure and its temporal evolution. In this study, we investigated the effects of plate motion history and mantle viscosity on the temporal evolution of the lower mantle structure since the early Paleozoic by formulating 3-D spherical shell models of thermochemical convection. For convection models with realistic mantle viscosity and no initial structure, it takes about ˜50 Myr to develop dominantly degree-2 lower mantle structure using the published plate motion models for the last either 120 Ma or 250 Ma. However, it takes longer time to develop the mantle structure for more viscous mantle. While the circum-Pangea subduction in plate motion history models promotes the formation of degree-2 mantle structure, the published pre-Pangea plate motions before 330 Ma produce relatively cold lower mantle in the African hemisphere and significant degree-1 structure in the early Pangea (˜300 Ma) or later times, even if the lower mantle has an initially degree-2 structure and a viscosity as high as 1023 Pas. This suggests that the African LLSVP may not be stationary since the early Paleozoic. With the published plate motion models and lower mantle viscosity of 1022 Pas, our mantle convection models suggest that the present-day degree-2 mantle structure may have largely been formed by ˜200 Ma.

Hubble space telescope observations and geometric models of compact multipolar planetary nebulae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsia, Chih-Hao; Chau, Wayne; Zhang, Yong

2014-05-20

We report high angular resolution Hubble Space Telescope observations of 10 compact planetary nebulae (PNs). Many interesting internal structures, including multipolar lobes, arcs, two-dimensional rings, tori, and halos, are revealed for the first time. These results suggest that multipolar structures are common among PNs, and these structures develop early in their evolution. From three-dimensional geometric models, we have determined the intrinsic dimensions of the lobes. Assuming the lobes are the result of interactions between later-developed fast winds and previously ejected asymptotic giant branch winds, the geometric structures of these PNs suggest that there are multiple phases of fast winds separatedmore » by temporal variations and/or directional changes. A scenario of evolution from lobe-dominated to cavity-dominated stages is presented. The results reported here will provide serious constraints on any dynamical models of PNs.« less

Froissart bound and self-similarity based models of proton structure functions

NASA Astrophysics Data System (ADS)

Choudhury, D. K.; Saikia, Baishali

2018-03-01

Froissart bound implies that the total proton-proton cross-section (or equivalently proton structure function) cannot rise faster than log2s ˜log2 1 x. Compatibility of such behavior with the notion of self-similarity in proton structure function was suggested by us sometime back. In the present work, we generalize and improve it further by considering more recent self-similarity based models of proton structure functions and compare with recent data as well as with the model of Block, Durand, Ha and McKay.

Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure.

PubMed

Lemieux, M Joanne

2007-01-01

The major facilitator superfamily (MFS) of transporters represents the largest family of secondary active transporters and has a diverse range of substrates. With structural information for four MFS transporters, we can see a strong structural commonality suggesting, as predicted, a common architecture for MFS transporters. The rate for crystal structure determination of MFS transporters is slow, making modeling of both prokaryotic and eukaryotic transporters more enticing. In this review, models of eukaryotic transporters Glut1, G6PT, OCT1, OCT2 and Pho84, based on the crystal structures of the prokaryotic GlpT, based on the crystal structure of LacY are discussed. The techniques used to generate the different models are compared. In addition, the validity of these models and the strategy of using prokaryotic crystal structures to model eukaryotic proteins are discussed. For comparison, E. coli GlpT was modeled based on the E. coli LacY structure and compared to the crystal structure of GlpT demonstrating that experimental evidence is essential for accurate modeling of membrane proteins.

A Maslovian Counseling Method.

ERIC Educational Resources Information Center

Kirkpatrick, J. Stephen

1979-01-01

With Maslow's hierarchy as a basis, the model provides structure for setting goals in counseling cases and overall programs. Different kinds of client concerns are identified, and suggestions are made for using these 14 categories. The article includes specific suggestions for using the model in diagnosis, evaluation, counselor education, and…

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

DOE PAGES

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy; ...

2014-10-10

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

Evidence for the Continuous Latent Structure of Mania in the Epidemiologic Catchment Area from Multiple Latent Structure and Construct Validation Methodologies

PubMed Central

Prisciandaro, James J.; Roberts, John E.

2011-01-01

Background Although psychiatric diagnostic systems have conceptualized mania as a discrete phenomenon, appropriate latent structure investigations testing this conceptualization are lacking. In contrast to these diagnostic systems, several influential theories of mania have suggested a continuous conceptualization. The present study examined whether mania has a continuous or discrete latent structure using a comprehensive approach including taxometric, information-theoretic latent distribution modeling (ITLDM), and predictive validity methodologies in the Epidemiologic Catchment Area (ECA) study. Methods Eight dichotomous manic symptom items were submitted to a variety of latent structural analyses; including factor analyses, taxometric procedures, and ITLDM; in 10,105 ECA community participants. Additionally, a variety of continuous and discrete models of mania were compared in terms of their relative abilities to predict outcomes (i.e., health service utilization, internalizing and externalizing disorders, and suicidal behavior). Results Taxometric and ITLDM analyses consistently supported a continuous conceptualization of mania. In ITLDM analyses, a continuous model of mania demonstrated 6:52:1 odds over the best fitting latent class model of mania. Factor analyses suggested that the continuous structure of mania was best represented by a single latent factor. Predictive validity analyses demonstrated a consistent superior ability of continuous models of mania relative to discrete models. Conclusions The present study provided three independent lines of support for a continuous conceptualization of mania. The implications of a continuous model of mania are discussed. PMID:20507671

Models of determining deformations

NASA Astrophysics Data System (ADS)

Gladilin, V. N.

2016-12-01

In recent years, a lot of functions designed to determine deformation values that occur mostly as a result of settlement of structures and industrial equipment. Some authors suggest such advanced mathematical functions approximating deformations as general methods for the determination of deformations. The article describes models of deformations as physical processes. When comparing static, cinematic and dynamic models, it was found that the dynamic model reflects the deformation of structures and industrial equipment most reliably.

Structure and thermodynamics of core-softened models for alcohols

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munaò, Gianmarco, E-mail: gmunao@unime.it; Urbic, Tomaz

The phase behavior and the fluid structure of coarse-grain models for alcohols are studied by means of reference interaction site model (RISM) theory and Monte Carlo simulations. Specifically, we model ethanol and 1-propanol as linear rigid chains constituted by three (trimers) and four (tetramers) partially fused spheres, respectively. Thermodynamic properties of these models are examined in the RISM context, by employing closed formulæ for the calculation of free energy and pressure. Gas-liquid coexistence curves for trimers and tetramers are reported and compared with already existing data for a dimer model of methanol. Critical temperatures slightly increase with the number ofmore » CH{sub 2} groups in the chain, while critical pressures and densities decrease. Such a behavior qualitatively reproduces the trend observed in experiments on methanol, ethanol, and 1-propanol and suggests that our coarse-grain models, despite their simplicity, can reproduce the essential features of the phase behavior of such alcohols. The fluid structure of these models is investigated by computing radial distribution function g{sub ij}(r) and static structure factor S{sub ij}(k); the latter shows the presence of a low−k peak at intermediate-high packing fractions and low temperatures, suggesting the presence of aggregates for both trimers and tetramers.« less

Diagnosing the influence of model structure on the simulation of water, energy and carbon fluxes on bark beetle infested forests

NASA Astrophysics Data System (ADS)

Gochis, D. J.; Gutmann, E. D.; Brooks, P. D.; Reed, D. E.; Ewers, B. E.; Pendall, E.; Biederman, J. A.; Harpold, A. A.; Barnard, H. R.; Hu, J.

2011-12-01

Forest dynamics induced by insect infestation can have a significant, local impact on plant physiological regulation of water, energy and carbon fluxes. Rapid mortality succeeded by more gradually varying land cover changes are presently thought to initiate a cascade of changes to water, energy and carbon budgets at the forest stand scale. Initial model sensitivity results have suggested very strong changes in land-atmosphere exchanges of these variables. Specifically, model results from the Noah land surface model, a relatively simple model, have suggested that loss of transpiration function may result in a nearly 50% increase in seasonal soil moisture values and similar increases in runoff production for locations in the central Rocky Mountains. However, differing model structures, such as the representation of plant canopy architecture, snowpack dynamics, dynamic vegetation and hillslope hydrologic processes, may significantly confound the synthesis of results from different modeling systems. We assess the performance of new suite of model simulations from three different land surface models of differing model structures and complexity levels against a comprehensive set of field observations of land surface flux and state variables. The focus of the analysis is in diagnosing how model structure influences changes in energy, water and carbon budget partitioning prior to and following insect infestation. Specific emphasis in this presentation is placed on verifying variables that characterize top of canopy and within canopy energy and water fluxes. We conclude the presentation with a set of recommendations about the advantages and disadvantages of various model structures in their simulation of insect driven forest dynamics.

Toward a Model-Based Approach to the Clinical Assessment of Personality Psychopathology

PubMed Central

Eaton, Nicholas R.; Krueger, Robert F.; Docherty, Anna R.; Sponheim, Scott R.

2015-01-01

Recent years have witnessed tremendous growth in the scope and sophistication of statistical methods available to explore the latent structure of psychopathology, involving continuous, discrete, and hybrid latent variables. The availability of such methods has fostered optimism that they can facilitate movement from classification primarily crafted through expert consensus to classification derived from empirically-based models of psychopathological variation. The explication of diagnostic constructs with empirically supported structures can then facilitate the development of assessment tools that appropriately characterize these constructs. Our goal in this paper is to illustrate how new statistical methods can inform conceptualization of personality psychopathology and therefore its assessment. We use magical thinking as example, because both theory and earlier empirical work suggested the possibility of discrete aspects to the latent structure of personality psychopathology, particularly forms of psychopathology involving distortions of reality testing, yet other data suggest that personality psychopathology is generally continuous in nature. We directly compared the fit of a variety of latent variable models to magical thinking data from a sample enriched with clinically significant variation in psychotic symptomatology for explanatory purposes. Findings generally suggested a continuous latent variable model best represented magical thinking, but results varied somewhat depending on different indices of model fit. We discuss the implications of the findings for classification and applied personality assessment. We also highlight some limitations of this type of approach that are illustrated by these data, including the importance of substantive interpretation, in addition to use of model fit indices, when evaluating competing structural models. PMID:24007309

The Presence of Turbulent and Ordered Local Structure within the ICME Shock-sheath and Its Contribution to Forbush Decrease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaikh, Zubair; Bhaskar, Ankush; Raghav, Anil, E-mail: raghavanil1984@gmail.com

The transient interplanetary disturbances evoke short-time cosmic-ray flux decrease, which is known as Forbush decrease. The traditional model and understanding of Forbush decrease suggest that the sub-structure of an interplanetary counterpart of coronal mass ejection (ICME) independently contributes to cosmic-ray flux decrease. These sub-structures, shock-sheath, and magnetic cloud (MC) manifest as classical two-step Forbush decrease. The recent work by Raghav et al. has shown multi-step decreases and recoveries within the shock-sheath. However, this cannot be explained by the ideal shock-sheath barrier model. Furthermore, they suggested that local structures within the ICME’s sub-structure (MC and shock-sheath) could explain this deviation ofmore » the FD profile from the classical FD. Therefore, the present study attempts to investigate the cause of multi-step cosmic-ray flux decrease and respective recovery within the shock-sheath in detail. A 3D-hodogram method is utilized to obtain more details regarding the local structures within the shock-sheath. This method unambiguously suggests the formation of small-scale local structures within the ICME (shock-sheath and even in MC). Moreover, the method could differentiate the turbulent and ordered interplanetary magnetic field (IMF) regions within the sub-structures of ICME. The study explicitly suggests that the turbulent and ordered IMF regions within the shock-sheath do influence cosmic-ray variations differently.« less

Some guidelines for structural equation modelling in cognitive neuroscience: the case of Charlton et al.'s study on white matter integrity and cognitive ageing.

PubMed

Penke, Lars; Deary, Ian J

2010-09-01

Charlton et al. (2008) (Charlton, R.A., Landua, S., Schiavone, F., Barrick, T.R., Clark, C.A., Markus, H.S., Morris, R.G.A., 2008. Structural equation modelling investigation of age-related variance in executive function and DTI-measured white matter change. Neurobiol. Aging 29, 1547-1555) presented a model that suggests a specific age-related effect of white matter integrity on working memory. We illustrate potential pitfalls of structural equation modelling by criticizing their model for (a) its neglect of latent variables, (b) its complexity, (c) its questionable causal assumptions, (d) the use of empirical model reduction, (e) the mix-up of theoretical perspectives, and (f) the failure to compare alternative models. We show that a more parsimonious model, based solely on the well-established general factor of cognitive ability, fits their data at least as well. Importantly, when modelled this way there is no support for a role of white matter integrity in cognitive aging in this sample, indicating that their conclusion is strongly dependent on how the data are analysed. We suggest that evidence from more conclusive study designs is needed. Copyright 2009 Elsevier Inc. All rights reserved.

Using Structural Equation Models with Latent Variables to Study Student Growth and Development.

ERIC Educational Resources Information Center

Pike, Gary R.

1991-01-01

Analysis of data on freshman-to-senior developmental gains in 722 University of Tennessee-Knoxville students provides evidence of the advantages of structural equation modeling with latent variables and suggests that the group differences identified by traditional analysis of variance and covariance techniques may be an artifact of measurement…

Modeling socio-demography to capture tuberculosis transmission dynamics in a low burden setting

PubMed Central

Ajelli, Marco; Yang, Zhenhua; Merler, Stefano; Furlanello, Cesare; Kirschner, Denise

2011-01-01

Evidence of preferential mixing through selected social routes has been suggested for the transmission of tuberculosis (TB) infection in low burden settings. A realistic modelization of these contact routes is needed to appropriately assess the impact of individually targeted control strategies, such as contact network investigation of index cases and treatment of latent TB infection (LTBI). We propose an age-structured, socio-demographic individual based model (IBM) with a realistic, time-evolving structure of preferential contacts in a population. In particular, transmission within households, schools and work-places, together with a component of casual, distance-dependent contacts are considered. We also compared the model against two other formulations having no social structure of contacts (homogeneous mixing transmission): a baseline deterministic model without age structure and an age-structured IBM. The socio-demographic IBM better fitted recent longitudinal data on TB epidemiology in Arkansas, USA, which serves as an example of a low burden setting. Inclusion of age structure in the model proved fundamental to capturing actual proportions of reactivated TB cases (as opposed to recently transmitted) as well as profiling age-group specific incidence. The socio-demographic structure additionally provides a prediction of TB transmission rates (the rate of infection in household contacts and the rate of secondary cases in household and workplace contacts). These results suggest that the socio-demographic IBM is an optimal choice for evaluating current control strategies, including contact network investigation of index cases, and the simulation of alternative scenarios, particularly for TB eradication targets. PMID:21906603

Framework for Understanding Structural Errors (FUSE): A modular framework to diagnose differences between hydrological models

USGS Publications Warehouse

Clark, Martyn P.; Slater, Andrew G.; Rupp, David E.; Woods, Ross A.; Vrugt, Jasper A.; Gupta, Hoshin V.; Wagener, Thorsten; Hay, Lauren E.

2008-01-01

The problems of identifying the most appropriate model structure for a given problem and quantifying the uncertainty in model structure remain outstanding research challenges for the discipline of hydrology. Progress on these problems requires understanding of the nature of differences between models. This paper presents a methodology to diagnose differences in hydrological model structures: the Framework for Understanding Structural Errors (FUSE). FUSE was used to construct 79 unique model structures by combining components of 4 existing hydrological models. These new models were used to simulate streamflow in two of the basins used in the Model Parameter Estimation Experiment (MOPEX): the Guadalupe River (Texas) and the French Broad River (North Carolina). Results show that the new models produced simulations of streamflow that were at least as good as the simulations produced by the models that participated in the MOPEX experiment. Our initial application of the FUSE method for the Guadalupe River exposed relationships between model structure and model performance, suggesting that the choice of model structure is just as important as the choice of model parameters. However, further work is needed to evaluate model simulations using multiple criteria to diagnose the relative importance of model structural differences in various climate regimes and to assess the amount of independent information in each of the models. This work will be crucial to both identifying the most appropriate model structure for a given problem and quantifying the uncertainty in model structure. To facilitate research on these problems, the FORTRAN‐90 source code for FUSE is available upon request from the lead author.

A structural model for surface-enhanced stabilization in some metallic glass formers

NASA Astrophysics Data System (ADS)

Levchenko, Elena V.; Evteev, Alexander V.; Yavari, Alain R.; Louzguine-Luzgin, Dmitri V.; Belova, Irina V.; Murch, Graeme E.

2013-01-01

A structural model for surface-enhanced stabilization in some metallic glass formers is proposed. In this model, the alloy surface structure is represented by five-layer Kagomé-net-based lateral ordering. Such surface structure has intrinsic abilities to stabilize icosahedral-like short-range order in the bulk, acting as 'a cloak of liquidity'. In particular, recent experimental observations of surface-induced lateral ordering and a very high glass forming ability of the liquid alloy Au49Ag5.5Pd2.3Cu26.9Si16.3 can be united using this structural model. This model may be useful for the interpretation of surface structure of other liquid alloys with a high glass forming ability. In addition, it suggests the possibility of guiding the design of the surface coating of solid containers for the stabilization of undercooled liquids.

Revised Atomistic Models of the Crystal Structure of C-S-H with high C/S Ratio

NASA Astrophysics Data System (ADS)

Kovačević, Goran; Nicoleau, Luc; Nonat, André; Veryazov, Valera

2016-09-01

The atomic structure of calcium-silicate-hydrate (C1.67-S-Hx) has been studied. Atomistic C-S-H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C-S-H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C-S-H. The new geometries of C-S-H, reported in this paper, show lower relative energy with respect to the geometries from the original definition of C-S-H models. Model that corresponds to calcium enriched tobermorite structure has the lowest relative energy and the density closest to the experimental values.

Molecular Modeling in Drug Design for the Development of Organophosphorus Antidotes/Prophylactics.

DTIC Science & Technology

1986-06-01

multidimensional statistical QSAR analysis techniques to suggest new structures for synthesis and evaluation. C. Application of quantum chemical techniques to...compounds for synthesis and testing for antidotal potency. E. Use of computer-assisted methods to determine the steric constraints at the active site...modeling techniques to model the enzyme acetylcholinester-se. H. Suggestion of some novel compounds for synthesis and testing for reactivating

Student perception and conceptual development as represented by student mental models of atomic structure

NASA Astrophysics Data System (ADS)

Park, Eun Jung

The nature of matter based upon atomic theory is a principal concept in science; hence, how to teach and how to learn about atoms is an important subject for science education. To this end, this study explored student perceptions of atomic structure and how students learn about this concept by analyzing student mental models of atomic structure. Changes in student mental models serve as a valuable resource for comprehending student conceptual development. Data was collected from students who were taking the introductory chemistry course. Responses to course examinations, pre- and post-questionnaires, and pre- and post-interviews were used to analyze student mental models of atomic structure. First, this study reveals that conceptual development can be achieved, either by elevating mental models toward higher levels of understanding or by developing a single mental model. This study reinforces the importance of higher-order thinking skills to enable students to relate concepts in order to construct a target model of atomic structure. Second, Bohr's orbital structure seems to have had a strong influence on student perceptions of atomic structure. With regard to this finding, this study suggests that it is instructionally important to teach the concept of "orbitals" related to "quantum theory." Third, there were relatively few students who had developed understanding at the level of the target model, which required student understanding of the basic ideas of quantum theory. This study suggests that the understanding of atomic structure based on the idea of quantum theory is both important and difficult. Fourth, this study included different student assessments comprised of course examinations, questionnaires, and interviews. Each assessment can be used to gather information to map out student mental models. Fifth, in the comparison of the pre- and post-interview responses, this study showed that high achieving students moved toward more improved models or to advanced levels of understanding. The analysis of mental models in this study has provided information describing student understanding of the nature and structure of an atom. In addition to an assessment of student cognition, information produced from this study can serve as an important resource for curriculum development, teacher education, and instruction.

Identity related to living situation in six individuals with congenital quadriplegia.

PubMed

Robey, Kenneth L

2008-01-01

This study was a preliminary examination of structural aspects of identity, particularly identity associated with living situation, in individuals who have quadriplegia due to cerebral palsy. A hierarchical classes algorithm (HICLAS) was used to construct idiographic 'identity structure' models for three individuals who are living in an inpatient hospital setting and for three individuals living in community-based group residences. Indices derived from the models indicate that the identity 'myself as one who has a disability' was structurally superordinate (i.e., resided at a high hierarchical level) for all six participants, suggesting a high level of importance of this identity in participants' sense of self. The models also indicate that while identity associated with one's particular living situation was superordinate for persons living in the hospital, it was not for persons living in community residences. While conclusions based on this small sample are necessarily limited, the data suggest that identity associated with living situation might differ in structural centrality, and presumably subjective importance, for persons living in inpatient versus community-based settings.

Modelling Students' Visualisation of Chemical Reaction

ERIC Educational Resources Information Center

Cheng, Maurice M. W.; Gilbert, John K.

2017-01-01

This paper proposes a model-based notion of "submicro representations of chemical reactions". Based on three structural models of matter (the simple particle model, the atomic model and the free electron model of metals), we suggest there are two major models of reaction in school chemistry curricula: (a) reactions that are simple…

Structure and dynamics of complex liquid water: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

S, Indrajith V.; Natesan, Baskaran

2015-06-01

We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

Quantitative structure-retention relationships for gas chromatographic retention indices of alkylbenzenes with molecular graph descriptors.

PubMed

Ivanciuc, O; Ivanciuc, T; Klein, D J; Seitz, W A; Balaban, A T

2001-02-01

Quantitative structure-retention relationships (QSRR) represent statistical models that quantify the connection between the molecular structure and the chromatographic retention indices of organic compounds, allowing the prediction of retention indices of novel, not yet synthesized compounds, solely from their structural descriptors. Using multiple linear regression, QSRR models for the gas chromatographic Kováts retention indices of 129 alkylbenzenes are generated using molecular graph descriptors. The correlational ability of structural descriptors computed from 10 molecular matrices is investigated, showing that the novel reciprocal matrices give numerical indices with improved correlational ability. A QSRR equation with 5 graph descriptors gives the best calibration and prediction results, demonstrating the usefulness of the molecular graph descriptors in modeling chromatographic retention parameters. The sequential orthogonalization of descriptors suggests simpler QSRR models by eliminating redundant structural information.

What Quasars Really Look Like: Unification of the Emission and Absorption Line Regions

NASA Technical Reports Server (NTRS)

Elvis, Martin

2000-01-01

We propose a simple unifying structure for the inner regions of quasars and AGN. This empirically derived model links together the broad absorption line (BALS), the narrow UV/X-ray ionized absorbers, the BELR, and the 5 Compton scattering/fluorescing regions into a single structure. The model also suggests an alternative origin for the large-scale bi-conical outflows. Some other potential implications of this structure are discussed.

Chemokines and their receptors: insights from molecular modeling and crystallography.

PubMed

Kufareva, Irina

2016-10-01

Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of Leadership and Pictures of the Power Structure.

ERIC Educational Resources Information Center

Cook, James B.

Presenting models describing a monolithic power structure, a pluralist power structure, and variations of these, this paper asserts that the monolithic power structure traditionally associated with rural areas is no longer valid for rural development. It is suggested that the following decision making mandate would serve as a better touch stone…

The factor structure of posttraumatic stress disorder: a literature update, critique of methodology, and agenda for future research.

PubMed

Elhai, Jon D; Palmieri, Patrick A

2011-08-01

We present an update of recent literature (since 2007) exploring the factor structure of posttraumatic stress disorder (PTSD) symptom measures. Research supporting a four-factor emotional numbing model and a four-factor dysphoria model is presented, with these models fitting better than all other models examined. Variables accounting for factor structure differences are reviewed, including PTSD query instructions, type of PTSD measure, extent of trauma exposure, ethnicity, and timing of administration. Methodological and statistical limitations with recent studies are presented. Finally, a research agenda and recommendations are offered to push this research area forward, including suggestions to validate PTSD’s factors against external measures of psychopathology, test moderators of factor structure, and examine heterogeneity of symptom presentations based on factor structure examination.

Scottish Schools Science Equipment Research Centre, Bulletin No. 56, June 1972.

ERIC Educational Resources Information Center

1972

A model demonstrating the relationship between the structure of blood vessels and the flow of blood is described and illustrated in the biology section of the newsletter. The apparatus also contains a functional (but not structural) model of the heart. Suggestions for the preparation of a relatively permanent dialysis bag from visking tubing are…

Two Models of Raters in a Structured Oral Examination: Does It Make a Difference?

ERIC Educational Resources Information Center

Touchie, Claire; Humphrey-Murto, Susan; Ainslie, Martha; Myers, Kathryn; Wood, Timothy J.

2010-01-01

Oral examinations have become more standardized over recent years. Traditionally a small number of raters were used for this type of examination. Past studies suggested that more raters should improve reliability. We compared the results of a multi-station structured oral examination using two different rater models, those based in a station,…

Socioeconomic Status and Asian American and Pacific Islander Students' Transition to College: A Structural Equation Modeling Analysis

ERIC Educational Resources Information Center

Museus, Samuel D.; Vue, Rican

2013-01-01

The purpose of this study is to examine socioeconomic differences in the interpersonal factors that influence college access among Asian Americans and Pacific Islanders (AAPIs). Data on 1,460 AAPIs from the Education Longitudinal Study (ELS: 02/06) were analyzed using structural equation modeling techniques. Findings suggest that parental…

Mixture IRT Model with a Higher-Order Structure for Latent Traits

ERIC Educational Resources Information Center

Huang, Hung-Yu

2017-01-01

Mixture item response theory (IRT) models have been suggested as an efficient method of detecting the different response patterns derived from latent classes when developing a test. In testing situations, multiple latent traits measured by a battery of tests can exhibit a higher-order structure, and mixtures of latent classes may occur on…

Control-structure interaction study for the Space Station solar dynamic power module

NASA Technical Reports Server (NTRS)

Cheng, J.; Ianculescu, G.; Ly, J.; Kim, M.

1991-01-01

The authors investigate the feasibility of using a conventional PID (proportional plus integral plus derivative) controller design to perform the pointing and tracking functions for the Space Station Freedom solar dynamic power module. Using this simple controller design, the control/structure interaction effects were also studied without assuming frequency bandwidth separation. From the results, the feasibility of a simple solar dynamic control solution with a reduced-order model, which satisfies the basic system pointing and stability requirements, is suggested. However, the conventional control design approach is shown to be very much influenced by the order of reduction of the plant model, i.e., the number of the retained elastic modes from the full-order model. This suggests that, for complex large space structures, such as the Space Station Freedom solar dynamic, the conventional control system design methods may not be adequate.

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

PubMed

Hurst, Travis; Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2018-05-10

The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.

From intuition to statistics in building subsurface structural models

USGS Publications Warehouse

Brandenburg, J.P.; Alpak, F.O.; Naruk, S.; Solum, J.

2011-01-01

Experts associated with the oil and gas exploration industry suggest that combining forward trishear models with stochastic global optimization algorithms allows a quantitative assessment of the uncertainty associated with a given structural model. The methodology is applied to incompletely imaged structures related to deepwater hydrocarbon reservoirs and results are compared to prior manual palinspastic restorations and borehole data. This methodology is also useful for extending structural interpretations into other areas of limited resolution, such as subsalt in addition to extrapolating existing data into seismic data gaps. This technique can be used for rapid reservoir appraisal and potentially have other applications for seismic processing, well planning, and borehole stability analysis.

Structural and Practical Identifiability Issues of Immuno-Epidemiological Vector-Host Models with Application to Rift Valley Fever.

PubMed

Tuncer, Necibe; Gulbudak, Hayriye; Cannataro, Vincent L; Martcheva, Maia

2016-09-01

In this article, we discuss the structural and practical identifiability of a nested immuno-epidemiological model of arbovirus diseases, where host-vector transmission rate, host recovery, and disease-induced death rates are governed by the within-host immune system. We incorporate the newest ideas and the most up-to-date features of numerical methods to fit multi-scale models to multi-scale data. For an immunological model, we use Rift Valley Fever Virus (RVFV) time-series data obtained from livestock under laboratory experiments, and for an epidemiological model we incorporate a human compartment to the nested model and use the number of human RVFV cases reported by the CDC during the 2006-2007 Kenya outbreak. We show that the immunological model is not structurally identifiable for the measurements of time-series viremia concentrations in the host. Thus, we study the non-dimensionalized and scaled versions of the immunological model and prove that both are structurally globally identifiable. After fixing estimated parameter values for the immunological model derived from the scaled model, we develop a numerical method to fit observable RVFV epidemiological data to the nested model for the remaining parameter values of the multi-scale system. For the given (CDC) data set, Monte Carlo simulations indicate that only three parameters of the epidemiological model are practically identifiable when the immune model parameters are fixed. Alternatively, we fit the multi-scale data to the multi-scale model simultaneously. Monte Carlo simulations for the simultaneous fitting suggest that the parameters of the immunological model and the parameters of the immuno-epidemiological model are practically identifiable. We suggest that analytic approaches for studying the structural identifiability of nested models are a necessity, so that identifiable parameter combinations can be derived to reparameterize the nested model to obtain an identifiable one. This is a crucial step in developing multi-scale models which explain multi-scale data.

Minimum stiffness criteria for ring frame stiffeners of space launch vehicles

NASA Astrophysics Data System (ADS)

Friedrich, Linus; Schröder, Kai-Uwe

2016-12-01

Frame stringer-stiffened shell structures show high load carrying capacity in conjunction with low structural mass and are for this reason frequently used as primary structures of aerospace applications. Due to the great number of design variables, deriving suitable stiffening configurations is a demanding task and needs to be realized using efficient analysis methods. The structural design of ring frame stringer-stiffened shells can be subdivided into two steps. One, the design of a shell section between two ring frames. Two, the structural design of the ring frames such that a general instability mode is avoided. For sizing stringer-stiffened shell sections, several methods were recently developed, but existing ring frame sizing methods are mainly based on empirical relations or on smeared models. These methods do not mandatorily lead to reliable designs and in some cases the lightweight design potential of stiffened shell structures can thus not be exploited. In this paper, the explicit physical behaviour of ring frame stiffeners of space launch vehicles at the onset of panel instability is described using mechanical substitute models. Ring frame stiffeners of a stiffened shell structure are sized applying existing methods and the method suggested in this paper. To verify the suggested method and to demonstrate its potential, geometrically non-linear finite element analyses are performed using detailed finite element models.

Ask Questions to Encourage Questions Asked

ERIC Educational Resources Information Center

belcastro, sarah-marie

2017-01-01

We delineate some types of structured practice (modeling, requests, feedback, and space-making) that help students learn to pose appropriate questions and to initiate exploration of those questions. Developing skills requires practice, so we suggest ways to embed structured practice into existing class sessions. Including structured practice is…

Modelling the effect of temperament on BMI through appetite reactivity and self-regulation in eating: a Structural Equation Modelling approach in young adolescents.

PubMed

Godefroy, V; Trinchera, L; Romo, L; Rigal, N

2016-04-01

Appetitive traits and general temperament traits have both been correlated with adiposity and obesity in children. However, very few studies have tested structural models to identify the links between temperament, appetitive traits and adiposity in children. A validated structural model would help suggesting mechanisms to explain the impact of temperament on body mass index (BMI). In this study, we used Rothbart's heuristic definition of temperament as a starting point to define four appetitive traits, including two appetite reactivity dimensions (Appetite Arousal and Appetite Persistence) and two dimensions of self-regulation in eating (Self-regulation In Eating Without Hunger and Self-regulation in Eating Speed). We conducted a cross-sectional study in young adolescents to validate a structural model including these four appetitive traits, Effortful Control (a general temperament trait) and adiposity. A questionnaire assessing the four appetitive trait dimensions and Effortful Control was completed by adolescents from 10 to 14 years old (n=475), and their BMI-for-age was calculated (n=441). In total, 74% of the study participants were normal weight, 26% were overweight and 8% were obese. We then used structural equation modelling to test the structural model. We identified a well-fitting structural model (Comparative Fit Index=0.91; Root Mean Square Error of Approximation=0.04) that supports the hypothesis that Effortful Control impacts both dimensions of self-regulation in eating, which in turn are linked with both appetite reactivity dimensions. Moreover, Appetite Persistence is the only appetitive trait that was significantly related to adiposity (B=0.12; P<0.05). Our model shows that Effortful Control is related to adiposity through the mediation of an individual's 'eating temperament' (appetite reactivity and self-regulation in eating). Results suggest that young adolescents who exhibit high appetite reactivity but a low level of self-regulation in eating are at higher risk for excess adiposity.

Information and the Ecology of Scholars

ERIC Educational Resources Information Center

Blackburn, Thomas R.

1973-01-01

Suggests a logical basis for the use of ecological concepts in modeling a special subculture; that of scholars (and in particular scientists), who produce, barter, and structure information as an ecosystem produces, exchanges, and structures biomass. (JR)

Rainfall runoff modelling of the Upper Ganga and Brahmaputra basins using PERSiST.

PubMed

Futter, M N; Whitehead, P G; Sarkar, S; Rodda, H; Crossman, J

2015-06-01

There are ongoing discussions about the appropriate level of complexity and sources of uncertainty in rainfall runoff models. Simulations for operational hydrology, flood forecasting or nutrient transport all warrant different levels of complexity in the modelling approach. More complex model structures are appropriate for simulations of land-cover dependent nutrient transport while more parsimonious model structures may be adequate for runoff simulation. The appropriate level of complexity is also dependent on data availability. Here, we use PERSiST; a simple, semi-distributed dynamic rainfall-runoff modelling toolkit to simulate flows in the Upper Ganges and Brahmaputra rivers. We present two sets of simulations driven by single time series of daily precipitation and temperature using simple (A) and complex (B) model structures based on uniform and hydrochemically relevant land covers respectively. Models were compared based on ensembles of Bayesian Information Criterion (BIC) statistics. Equifinality was observed for parameters but not for model structures. Model performance was better for the more complex (B) structural representations than for parsimonious model structures. The results show that structural uncertainty is more important than parameter uncertainty. The ensembles of BIC statistics suggested that neither structural representation was preferable in a statistical sense. Simulations presented here confirm that relatively simple models with limited data requirements can be used to credibly simulate flows and water balance components needed for nutrient flux modelling in large, data-poor basins.

Northeastern Brazilian margin: Regional tectonic evolution based on integrated analysis of seismic reflection and potential field data and modelling

NASA Astrophysics Data System (ADS)

Blaich, Olav A.; Tsikalas, Filippos; Faleide, Jan Inge

2008-10-01

Integration of regional seismic reflection and potential field data along the northeastern Brazilian margin, complemented by crustal-scale gravity modelling, is used to reveal and illustrate onshore-offshore crustal structure correlation, the character of the continent-ocean boundary, and the relationship of crustal structure to regional variation of potential field anomalies. The study reveals distinct along-margin structural and magmatic changes that are spatially related to a number of conjugate Brazil-West Africa transfer systems, governing the margin segmentation and evolution. Several conceptual tectonic models are invoked to explain the structural evolution of the different margin segments in a conjugate margin context. Furthermore, the constructed transects, the observed and modelled Moho relief, and the potential field anomalies indicate that the Recôncavo, Tucano and Jatobá rift system may reflect a polyphase deformation rifting-mode associated with a complex time-dependent thermal structure of the lithosphere. The constructed transects and available seismic reflection profiles, indicate that the northern part of the study area lacks major breakup-related magmatic activity, suggesting a rifted non-volcanic margin affinity. In contrast, the southern part of the study area is characterized by abrupt crustal thinning and evidence for breakup magmatic activity, suggesting that this region evolved, partially, with a rifted volcanic margin affinity and character.

Two Growth Modes of Graphitic Carbon Nanofibers with Herring-Bone Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merkulov, Igor A; Melechko, Anatoli Vasilievich; Wells, Jack C

2005-01-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Two growth modes of graphitic carbon nanofibers with herring-bone structure

NASA Astrophysics Data System (ADS)

Merkulov, I. A.; Meleshko, A. V.; Wells, J. C.; Cui, H.; Merkulov, V. I.; Simpson, M. L.; Lowndes, D. H.

2005-07-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Applying ethnic equivalence and cultural values models to African-American teens' perceptions of parents.

PubMed

Lamborn, Susie D; Felbab, Amanda J

2003-10-01

This study evaluated both the parenting styles and family ecologies models with interview responses from 93 14- and 15-year-old African-American adolescents. The parenting styles model was more strongly represented in both open-ended and structured interview responses. Using variables from the structured interview as independent variables, regression analyses contrasted each model with a joint model for predicting self-esteem, self-reliance, work orientation, and ethnic identity. Overall, the findings suggest that a joint model that combines elements from both models provides a richer understanding of African-American families.

A multi-frequency receiver function inversion approach for crustal velocity structure

NASA Astrophysics Data System (ADS)

Li, Xuelei; Li, Zhiwei; Hao, Tianyao; Wang, Sheng; Xing, Jian

2017-05-01

In order to constrain the crustal velocity structures better, we developed a new nonlinear inversion approach based on multi-frequency receiver function waveforms. With the global optimizing algorithm of Differential Evolution (DE), low-frequency receiver function waveforms can primarily constrain large-scale velocity structures, while high-frequency receiver function waveforms show the advantages in recovering small-scale velocity structures. Based on the synthetic tests with multi-frequency receiver function waveforms, the proposed approach can constrain both long- and short-wavelength characteristics of the crustal velocity structures simultaneously. Inversions with real data are also conducted for the seismic stations of KMNB in southeast China and HYB in Indian continent, where crustal structures have been well studied by former researchers. Comparisons of inverted velocity models from previous and our studies suggest good consistency, but better waveform fitness with fewer model parameters are achieved by our proposed approach. Comprehensive tests with synthetic and real data suggest that the proposed inversion approach with multi-frequency receiver function is effective and robust in inverting the crustal velocity structures.

Connections between Concepts Revealed by the Electronic Structure of Carbon Monoxide

ERIC Educational Resources Information Center

Liu, Ying; Liu, Bihui; Liu, Yue; Drew, Michael G. B.

2012-01-01

Different models for the electronic structure of carbon monoxide are suggested in influential textbooks. Therefore, this electronic structure offers an interesting subject in teaching because it can be used as an example to relate seemingly conflicting concepts. Understanding the connections between ostensibly different methods and between…

Attitude Change and Simulation Games: The Ability of a Simulation Game to Change Attitudes when Structured in Accordance with Either the Cognitive Dissonance or Incentive Models of Attitude Change.

ERIC Educational Resources Information Center

Williams, Robert H.

1980-01-01

Three groups of 109 undergraduates evidenced attitude shifts from participation to simulation games which were structured in accordance with either the cognitive dissonance or incentive models of attitude change. Identification was suggested as an extra factor influencing attitude change. (CMV)

Taking a systems approach to ecological systems

USGS Publications Warehouse

Grace, James B.

2015-01-01

Increasingly, there is interest in a systems-level understanding of ecological problems, which requires the evaluation of more complex, causal hypotheses. In this issue of the Journal of Vegetation Science, Soliveres et al. use structural equation modeling to test a causal network hypothesis about how tree canopies affect understorey communities. Historical analysis suggests structural equation modeling has been under-utilized in ecology.

Bayesian Network Webserver: a comprehensive tool for biological network modeling.

PubMed

Ziebarth, Jesse D; Bhattacharya, Anindya; Cui, Yan

2013-11-01

The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW. (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). ycui2@uthsc.edu. Supplementary data are available at Bioinformatics online.

The latent structure of personality functioning: Investigating criterion a from the alternative model for personality disorders in DSM-5.

PubMed

Zimmermann, Johannes; Böhnke, Jan R; Eschstruth, Rhea; Mathews, Alessa; Wenzel, Kristin; Leising, Daniel

2015-08-01

The alternative model for the classification of personality disorders (PD) in the Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5) Section III comprises 2 major components: impairments in personality functioning (Criterion A) and maladaptive personality traits (Criterion B). In this study, we investigated the latent structure of Criterion A (a) within subdomains, (b) across subdomains, and (c) in conjunction with the Criterion B trait facets. Data were gathered as part of an online study that collected other-ratings by 515 laypersons and 145 therapists. Laypersons were asked to assess 1 of their personal acquaintances, whereas therapists were asked to assess 1 of their patients, using 135 items that captured features of Criteria A and B. We were able to show that (a) the structure within the Criterion A subdomains can be appropriately modeled using generalized graded unfolding models, with results suggesting that the items are indeed related to common underlying constructs but often deviate from their theoretically expected severity level; (b) the structure across subdomains is broadly in line with a model comprising 2 strongly correlated factors of self- and interpersonal functioning, with some notable deviations from the theoretical model; and (c) the joint structure of the Criterion A subdomains and the Criterion B facets broadly resembles the expected model of 2 plus 5 factors, albeit the loading pattern suggests that the distinction between Criteria A and B is somewhat blurry. Our findings provide support for several major assumptions of the alternative DSM-5 model for PD but also highlight aspects of the model that need to be further refined. (c) 2015 APA, all rights reserved).

Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

PubMed Central

Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

2015-01-01

The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

The Communication Model Perspective of Oral Interpretation.

ERIC Educational Resources Information Center

Peterson, Eric E.

Communication models suggest that oral interpretation is a communicative process, that this process may be represented by specification of implicit and explicit content and structure, and that the models themselves are useful. This paper examines these assumptions through a comparative analysis of communication models employed by oral…

Mendelian Genetics: Paradigm, Conjecture, or Research Program.

ERIC Educational Resources Information Center

Oldham, V.; Brouwer, W.

1984-01-01

Applies Kuhn's model of the structure of scientific revolutions, Popper's hypothetic-deductive model of science, and Lakatos' methodology of competing research programs to a historical biological episode. Suggests using Kuhn's model (emphasizing the nonrational basis of science) and Popper's model (emphasizing the rational basis of science) in…

Emergent structure-function relations in emphysema and asthma.

PubMed

Winkler, Tilo; Suki, Béla

2011-01-01

Structure-function relationships in the respiratory system are often a result of the emergence of self-organized patterns or behaviors that are characteristic of certain respiratory diseases. Proper description of such self-organized behavior requires network models that include nonlinear interactions among different parts of the system. This review focuses on 2 models that exhibit self-organized behavior: a network model of the lung parenchyma during the progression of emphysema that is driven by mechanical force-induced breakdown, and an integrative model of bronchoconstriction in asthma that describes interactions among airways within the bronchial tree. Both models suggest that the transition from normal to pathologic states is a nonlinear process that includes a tipping point beyond which interactions among the system components are reinforced by positive feedback, further promoting the progression of pathologic changes. In emphysema, the progressive destruction of tissue is irreversible, while in asthma, it is possible to recover from a severe bronchoconstriction. These concepts may have implications for pulmonary medicine. Specifically, we suggest that structure-function relationships emerging from network behavior across multiple scales should be taken into account when the efficacy of novel treatments or drug therapy is evaluated. Multiscale, computational, network models will play a major role in this endeavor.

Latent structures of female sexual functioning.

PubMed

Carvalho, Joana; Vieira, Armando Luís; Nobre, Pedro

2012-08-01

For the last three decades, male and female sexual responses have been conceptualized as similar, based on separated and sequential phases as proposed by the models of Masters and Johnson (1966) and Kaplan (1979) model. However, there is a growing debate around the need to conceptualize female sexual response and the classification of sexual dysfunction in women, in view of the upcoming editions of the DSM and ICD. The aim of this study was to test, using structural equation modeling, five conceptual, alternative models of female sexual function, using a sample of women with sexual difficulties and a sample of women without sexual problems. A total of 1993 Portuguese women participated in the study and completed a modified version of the Female Sexual Function Index. Findings suggested a four-factor solution as the model that best fit the data regarding women presenting sexual difficulties: (1) desire/arousal; (2) lubrication; (3) orgasm; (4) pain/vaginismus. In relation to sexually healthy women, the best model was a five-factor solution comprising of (1) desire; (2) arousal; (3) lubrication; (4) orgasm; and (5) pain/vaginismus. Discriminant validity between factors was supported, suggesting that these dimensions measure distinct phenomena. Model fit to the data significantly decreased in both samples, as models began to successively consider greater levels of overlap among phases of sexual function, towards a single-factor solution. By suggesting the overlap between pain and vaginismus, results partially support the new classification that is currently being discussed regarding DSM-5. Additionally, results on the relationship between sexual desire and arousal were inconclusive as sexually healthy women were better characterized by a five-factor model that considered the structural independence among these factors, whereas women with sexual difficulties better fit with a four-factor model merging sexual desire and subjective sexual arousal.

Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization

NASA Astrophysics Data System (ADS)

di Stefano, Marco; Paulsen, Jonas; Lien, Tonje G.; Hovig, Eivind; Micheletti, Cristian

2016-10-01

Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based constraints for large-scale three-dimensional models of the human diploid genome. The resulting models remain minimally entangled and acquire several functional features that are observed in vivo and that were never used as input for the model. We find, for instance, that gene-rich, active regions are drawn towards the nuclear center, while gene poor and lamina associated domains are pushed to the periphery. These and other properties persist upon adding local contact constraints, suggesting their compatibility with non-local constraints for the genome organization. The results show that suitable combinations of data analysis and physical modelling can expose the unexpectedly rich functionally-related properties implicit in chromosome-chromosome contact data. Specific directions are suggested for further developments based on combining experimental data analysis and genomic structural modelling.

Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization.

PubMed

Di Stefano, Marco; Paulsen, Jonas; Lien, Tonje G; Hovig, Eivind; Micheletti, Cristian

2016-10-27

Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based constraints for large-scale three-dimensional models of the human diploid genome. The resulting models remain minimally entangled and acquire several functional features that are observed in vivo and that were never used as input for the model. We find, for instance, that gene-rich, active regions are drawn towards the nuclear center, while gene poor and lamina associated domains are pushed to the periphery. These and other properties persist upon adding local contact constraints, suggesting their compatibility with non-local constraints for the genome organization. The results show that suitable combinations of data analysis and physical modelling can expose the unexpectedly rich functionally-related properties implicit in chromosome-chromosome contact data. Specific directions are suggested for further developments based on combining experimental data analysis and genomic structural modelling.

Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-random Features of Cortical Synaptic Wiring

PubMed Central

Miner, Daniel; Triesch, Jochen

2016-01-01

Understanding the structure and dynamics of cortical connectivity is vital to understanding cortical function. Experimental data strongly suggest that local recurrent connectivity in the cortex is significantly non-random, exhibiting, for example, above-chance bidirectionality and an overrepresentation of certain triangular motifs. Additional evidence suggests a significant distance dependency to connectivity over a local scale of a few hundred microns, and particular patterns of synaptic turnover dynamics, including a heavy-tailed distribution of synaptic efficacies, a power law distribution of synaptic lifetimes, and a tendency for stronger synapses to be more stable over time. Understanding how many of these non-random features simultaneously arise would provide valuable insights into the development and function of the cortex. While previous work has modeled some of the individual features of local cortical wiring, there is no model that begins to comprehensively account for all of them. We present a spiking network model of a rodent Layer 5 cortical slice which, via the interactions of a few simple biologically motivated intrinsic, synaptic, and structural plasticity mechanisms, qualitatively reproduces these non-random effects when combined with simple topological constraints. Our model suggests that mechanisms of self-organization arising from a small number of plasticity rules provide a parsimonious explanation for numerous experimentally observed non-random features of recurrent cortical wiring. Interestingly, similar mechanisms have been shown to endow recurrent networks with powerful learning abilities, suggesting that these mechanism are central to understanding both structure and function of cortical synaptic wiring. PMID:26866369

Reconceptualizing the classification of PNAS articles

PubMed Central

Airoldi, Edoardo M.; Erosheva, Elena A.; Fienberg, Stephen E.; Joutard, Cyrille; Love, Tanzy; Shringarpure, Suyash

2010-01-01

PNAS article classification is rooted in long-standing disciplinary divisions that do not necessarily reflect the structure of modern scientific research. We reevaluate that structure using latent pattern models from statistical machine learning, also known as mixed-membership models, that identify semantic structure in co-occurrence of words in the abstracts and references. Our findings suggest that the latent dimensionality of patterns underlying PNAS research articles in the Biological Sciences is only slightly larger than the number of categories currently in use, but it differs substantially in the content of the categories. Further, the number of articles that are listed under multiple categories is only a small fraction of what it should be. These findings together with the sensitivity analyses suggest ways to reconceptualize the organization of papers published in PNAS. PMID:21078953

Crystal structures of η''-Cu3+xSi and η'''-Cu3+xSi.

PubMed

Corrêa, Cinthia Antunes; Perez, Olivier; Kopeček, Jaromír; Brázda, Petr; Klementová, Mariana; Palatinus, Lukáš

2017-08-01

The binary phase diagram of Cu-Si is unexpectedly complex in the vicinity of Cu 3+x Si. The low-temperature region contains three closely related incommensurately modulated phases denoted, in order of increasing temperature of stability, η''', η'' and η'. The structure analysis of η' has been reported previously [Palatinus et al. (2011). Inorg. Chem. 50, 3743]. Here the structure model for the phases η'' and η''' is reported. The structures could be solved in superspace, but no superspace structure model could be constructed due to the complexity of the modulation functions. Therefore, the structures were described in a supercell approximation, which involved a 4 × 4 × 3 supercell for the η'' phase and a 14 × 14 × 3 supercell for the η''' phase. Both structures are very similar and differ only by a subtle symmetry lowering from η'' to η'''. A comparison of the structure models of η'' and η''' with the reported structure of η' suggests that the reported structure model of η' contains an incorrect assignment of atomic types.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Application of geologic-mathematical 3D modeling for complex structure deposits by the example of Lower- Cretaceous period depositions in Western Ust - Balykh oil field (Khanty-Mansiysk Autonomous District)

NASA Astrophysics Data System (ADS)

Perevertailo, T.; Nedolivko, N.; Prisyazhnyuk, O.; Dolgaya, T.

2015-11-01

The complex structure of the Lower-Cretaceous formation by the example of the reservoir BC101 in Western Ust - Balykh Oil Field (Khanty-Mansiysk Autonomous District) has been studied. Reservoir range relationships have been identified. 3D geologic- mathematical modeling technique considering the heterogeneity and variability of a natural reservoir structure has been suggested. To improve the deposit geological structure integrity methods of mathematical statistics were applied, which, in its turn, made it possible to obtain equal probability models with similar input data and to consider the formation conditions of reservoir rocks and cap rocks.

The Importance of Model Structure in the Cost-Effectiveness Analysis of Primary Care Interventions for the Management of Hypertension.

PubMed

Peñaloza-Ramos, Maria Cristina; Jowett, Sue; Sutton, Andrew John; McManus, Richard J; Barton, Pelham

2018-03-01

Management of hypertension can lead to significant reductions in blood pressure, thereby reducing the risk of cardiovascular disease. Modeling the course of cardiovascular disease is not without complications, and uncertainty surrounding the structure of a model will almost always arise once a choice of a model structure is defined. To provide a practical illustration of the impact on the results of cost-effectiveness of changing or adapting model structures in a previously published cost-utility analysis of a primary care intervention for the management of hypertension Targets and Self-Management for the Control of Blood Pressure in Stroke and at Risk Groups (TASMIN-SR). The case study assessed the structural uncertainty arising from model structure and from the exclusion of secondary events. Four alternative model structures were implemented. Long-term cost-effectiveness was estimated and the results compared with those from the TASMIN-SR model. The main cost-effectiveness results obtained in the TASMIN-SR study did not change with the implementation of alternative model structures. Choice of model type was limited to a cohort Markov model, and because of the lack of epidemiological data, only model 4 captured structural uncertainty arising from the exclusion of secondary events in the case study model. The results of this study indicate that the main conclusions drawn from the TASMIN-SR model of cost-effectiveness were robust to changes in model structure and the inclusion of secondary events. Even though one of the models produced results that were different to those of TASMIN-SR, the fact that the main conclusions were identical suggests that a more parsimonious model may have sufficed. Copyright © 2018 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Identifying determinants of nations' wetland management programs using structural equation modeling: An exploratory analysis

USGS Publications Warehouse

La Peyre, M.K.; Mendelssohn, I.A.; Reams, M.A.; Templet, P.H.; Grace, J.B.

2001-01-01

Integrated management and policy models suggest that solutions to environmental issues may be linked to the socioeconomic and political Characteristics of a nation. In this study, we empirically explore these suggestions by applying them to the wetland management activities of nations. Structural equation modeling was used to evaluate a model of national wetland management effort and one of national wetland protection. Using five predictor variables of social capital, economic capital, environmental and political characteristics, and land-use pressure, the multivariate models were able to explain 60% of the variation in nations' wetland protection efforts based on data from 90 nations, as defined by level of participation, in the international wetland convention. Social capital had the largest direct effect on wetland protection efforts, suggesting that increased social development may eventually lead to better wetland protection. In contrast, increasing economic development had a negative linear relationship with wetland protection efforts, suggesting the need for explicit wetland protection programs as nations continue to focus on economic development. Government, environmental characteristics, and land-use pressure also had a positive direct effect on wetland protection, and mediated the effect of social capital on wetland protection. Explicit wetland protection policies, combined with a focus on social development, would lead to better wetland protection at the national level.

Development Of Educational Programs In Renewable And Alternative Energy Processing: The Case Of Russia

NASA Astrophysics Data System (ADS)

Svirina, Anna; Shindor, Olga; Tatmyshevsky, Konstantin

2014-12-01

The paper deals with the main problems of Russian energy system development that proves necessary to provide educational programs in the field of renewable and alternative energy. In the paper the process of curricula development and defining teaching techniques on the basis of expert opinion evaluation is defined, and the competence model for renewable and alternative energy processing master students is suggested. On the basis of a distributed questionnaire and in-depth interviews, the data for statistical analysis was obtained. On the basis of this data, an optimization of curricula structure was performed, and three models of a structure for optimizing teaching techniques were developed. The suggested educational program structure which was adopted by employers is presented in the paper. The findings include quantitatively estimated importance of systemic thinking and professional skills and knowledge as basic competences of a masters' program graduate; statistically estimated necessity of practice-based learning approach; and optimization models for structuring curricula in renewable and alternative energy processing. These findings allow the establishment of a platform for the development of educational programs.

Disorders without borders: current and future directions in the meta-structure of mental disorders.

PubMed

Carragher, Natacha; Krueger, Robert F; Eaton, Nicholas R; Slade, Tim

2015-03-01

Classification is the cornerstone of clinical diagnostic practice and research. However, the extant psychiatric classification systems are not well supported by research evidence. In particular, extensive comorbidity among putatively distinct disorders flags an urgent need for fundamental changes in how we conceptualize psychopathology. Over the past decade, research has coalesced on an empirically based model that suggests many common mental disorders are structured according to two correlated latent dimensions: internalizing and externalizing. We review and discuss the development of a dimensional-spectrum model which organizes mental disorders in an empirically based manner. We also touch upon changes in the DSM-5 and put forward recommendations for future research endeavors. Our review highlights substantial empirical support for the empirically based internalizing-externalizing model of psychopathology, which provides a parsimonious means of addressing comorbidity. As future research goals, we suggest that the field would benefit from: expanding the meta-structure of psychopathology to include additional disorders, development of empirically based thresholds, inclusion of a developmental perspective, and intertwining genomic and neuroscience dimensions with the empirical structure of psychopathology.

Sculpting Cells with Play Doh.

ERIC Educational Resources Information Center

Way, Virginia A.

1982-01-01

Suggests using Play Doh to mold models of the nucleus, mitochondria, and inner cellular structures. Students can conceptualize the cell's structures as three-dimensional even though they appear two-dimensional under a microscope. Includes instructions for preparing homemade dough. (Author/JN)

Common quandaries and their practical solutions in Bayesian network modeling

Treesearch

Bruce G. Marcot

2017-01-01

Use and popularity of Bayesian network (BN) modeling has greatly expanded in recent years, but many common problems remain. Here, I summarize key problems in BN model construction and interpretation,along with suggested practical solutions. Problems in BN model construction include parameterizing probability values, variable definition, complex network structures,...

Spatially explicit measurements of forest structure and fire behavior following restoration treatments in dry forests

Treesearch

Justin Paul Ziegler; Chad Hoffman; Michael Battaglia; William Mell

2017-01-01

Restoration treatments in dry forests of the western US often attempt silvicultural practices to restore the historical characteristics of forest structure and fire behavior. However, it is suggested that a reliance on non-spatial metrics of forest stand structure, along with the use of wildland fire behavior models that lack the ability to handle complex structures,...

Models of metal binding structures in fulvic acid from the Suwannee River, Georgia

USGS Publications Warehouse

Leenheer, J.A.; Brown, G.K.; MacCarthy, P.; Cabaniss, S.E.

1998-01-01

Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The 'metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-1R spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short- chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca2+, Cd2+, Cu2+, Ni2+, and Zn2+ ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca2+ ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The `metal binding' fraction was characterized by quantitative 13C NMR, 1H NMR, and FT-IR spectrometry and elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca2+ binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.

Factor Structure of a Multidimensional Gender Identity Scale in a Sample of Chinese Elementary School Children

PubMed Central

Yu, Lu; Xie, Dong; Shek, Daniel T. L.

2012-01-01

This study examined the factor structure of a scale based on the four-dimensional gender identity model (Egan and Perry, 2001) in 726 Chinese elementary school students. Exploratory factor analyses suggested a three-factor model, two of which corresponded to “Felt Pressure” and “Intergroup Bias” in the original model. The third factor “Gender Compatibility” appeared to be a combination of “Gender Typicality” and “Gender Contentment” in the original model. Follow-up confirmatory factor analysis (CFA) indicated that, relative to the initial four-factor structure, the three-factor model fits the current Chinese sample better. These results are discussed in light of cross-cultural similarities and differences in development of gender identity. PMID:22701363

Profile-Likelihood Approach for Estimating Generalized Linear Mixed Models with Factor Structures

ERIC Educational Resources Information Center

Jeon, Minjeong; Rabe-Hesketh, Sophia

2012-01-01

In this article, the authors suggest a profile-likelihood approach for estimating complex models by maximum likelihood (ML) using standard software and minimal programming. The method works whenever setting some of the parameters of the model to known constants turns the model into a standard model. An important class of models that can be…

Entropy model of dissipative structure on corporate social responsibility

NASA Astrophysics Data System (ADS)

Li, Zuozhi; Jiang, Jie

2017-06-01

Enterprise is prompted to fulfill the social responsibility requirement by the internal and external environment. In this complex system, some studies suggest that firms have an orderly or chaotic entropy exchange behavior. Based on the theory of dissipative structure, this paper constructs the entropy index system of corporate social responsibility(CSR) and explores the dissipative structure of CSR through Brusselator model criterion. Picking up listed companies of the equipment manufacturing, the research shows that CSR has positive incentive to negative entropy and promotes the stability of dissipative structure. In short, the dissipative structure of CSR has a positive impact on the interests of stakeholders and corporate social images.

Quantification of loading in biomechanical testing: the influence of dissection sequence.

PubMed

Funabashi, Martha; El-Rich, Marwan; Prasad, Narasimha; Kawchuk, Gregory N

2015-09-18

Sequential dissection is a technique used to investigate loads experienced by articular tissues. When the joint of interest is tested in an unconstrained manner, its kinematics change with each tissue removal. To address this limitation, sufficiently rigid robots are used to constrain joint kinematics. While this approach can quantify loads experienced by each tissue, it does not assure similar results when removal order is changed. Specifically, structure loading is assumed to be independent of removal order if the structure behaves linearly (i.e. principle of superposition applies), but dependent on removal order when response is affected by material and/or geometry nonlinearities and/or viscoelasticiy (e.g. biological tissues). Therefore, this experiment was conducted to evaluate if structure loading created through robotic testing is dependent on the order in which connectors are removed. Six identical models were 3D printed. Each model was composed of 2 rigid bodies and 3 connecting structures with nonlinear time-dependent behavior. To these models, pure rotations were applied about a predefined static center of rotation using a parallel robot. A unique dissection sequence was used for each of the six models and the same movements applied robotically after each dissection. When comparing the moments experienced by each structure between different removal sequences, a statistically significant difference (p<0.05) was observed. These results suggest that even in an optimized environment, the sequence in which nonlinear viscoelastic structures are removed influence model loading. These findings support prior work suggesting that tissue loads obtained from robotic testing are specific to removal order. Copyright © 2015 Elsevier Ltd. All rights reserved.

Revisiting the structures of several antibiotics bound to the bacterial ribosome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bulkley, David; Innis, C. Axel; Blaha, Gregor

2010-10-08

The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model.more » Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.« less

Revisiting the Structures of Several Antibiotics Bound to the Bacterial Ribosome

DOE Office of Scientific and Technical Information (OSTI.GOV)

D Bulkley; C Innis; G Blaha

2011-12-31

The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model.more » Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.« less

The structure of PTSD symptoms according to DSM-5 and IDC-11 proposal: A multi-sample analysis.

PubMed

Cyniak-Cieciura, M; Staniaszek, K; Popiel, A; Pragłowska, E; Zawadzki, B

2017-07-01

Posttraumatic stress disorder (PTSD) symptoms structure is a subject of ongoing debate since its inclusion in DSM-III classification in 1980. Different research on PTSD symptoms structure proved the better fit of four-factor and five-factor models comparing to the one proposed by DSM-IV. With the publication of DSM-5 classification, which introduced significant changes to PTSD diagnosis, the question arises about the adequacy of the proposed criteria to the real structure of disorder symptoms. Recent analyses suggest that seven-factor hybrid model is the best reflection of symptoms structure proposed to date. At the same time, some researchers and ICD-11 classification postulate a simplification of PTSD diagnosis restricting it to only three core criteria and adding additional diagnostic unit of complex-PTSD. This research aimed at checking symptoms' structure according to well-known and supported four-, five-, six- and seven-factor models based on DSM-5 symptoms and the conceptualization proposed by the ICD-11 as well as examining the relation between PTSD symptoms categories with borderline personality disorder. Four different trauma populations were examined with self-reported Posttraumatic Diagnostic Scale for DSM-5 (PDS-5) measure. The results suggest that six- and seven-factor hybrid model as well as three-factor ICD-11 concept fits the data better than other models. The core PTSD symptoms were less related to borderline personality disorder than other, broader, symptoms categories only in one sample. Combination of ICD-11 simplified PTSD diagnosis with the more complex approach (e.g. basing on a seven-factor model) may be an attractive proposal for both scientists and practitioners, however does not necessarily lower its comorbidity with borderline personality disorder. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning.

PubMed

Li, Haiou; Lyu, Qiang; Cheng, Jianlin

2016-12-01

Protein structure prediction is an important problem in computational biology, and is widely applied to various biomedical problems such as protein function study, protein design, and drug design. In this work, we developed a novel deep learning approach based on a deeply stacked denoising autoencoder for protein structure reconstruction. We applied our approach to a template-based protein structure prediction using only the 3D structural coordinates of homologous template proteins as input. The templates were identified for a target protein by a PSI-BLAST search. 3DRobot (a program that automatically generates diverse and well-packed protein structure decoys) was used to generate initial decoy models for the target from the templates. A stacked denoising autoencoder was trained on the decoys to obtain a deep learning model for the target protein. The trained deep model was then used to reconstruct the final structural model for the target sequence. With target proteins that have highly similar template proteins as benchmarks, the GDT-TS score of the predicted structures is greater than 0.7, suggesting that the deep autoencoder is a promising method for protein structure reconstruction.

A random-walk/giant-loop model for interphase chromosomes.

PubMed Central

Sachs, R K; van den Engh, G; Trask, B; Yokota, H; Hearst, J E

1995-01-01

Fluorescence in situ hybridization data on distances between defined genomic sequences are used to construct a quantitative model for the overall geometric structure of a human chromosome. We suggest that the large-scale geometry during the G0/G1 part of the cell cycle may consist of flexible chromatin loops, averaging approximately 3 million bp, with a random-walk backbone. A fully explicit, three-parametric polymer model of this random-walk/giant-loop structure can account well for the data. More general models consistent with the data are briefly discussed. PMID:7708711

Structural and spectroscopic studies of a commercial glassy carbon

NASA Astrophysics Data System (ADS)

Parker, Stewart F.; Imberti, Silvia; Callear, Samantha K.; Albers, Peter W.

2013-12-01

Glassy carbon is a form of carbon made by heating a phenolic resin to high temperature in an inert atmosphere. It has been suggested that it is composed of fullerene-like structures. The aim of the present work was to characterize the material using both structural (neutron diffraction and transmission electron microscopy) and spectroscopic (inelastic neutron scattering, Raman and X-ray photoelectron spectroscopies) methods. We find no evidence to support the suggestion of fullerene-like material being present to a significant extent, rather the model that emerges from all of the techniques is that the material is very like amorphous carbon, consisting of regions of small graphite-like basic structural units of partly stacked but mismatched structure with the edges terminated by hydrogen or hydroxyls. We do find evidence for the presence of a small quantity of water trapped in the network and suggest that this may account for batch-to-batch variation in properties that may occur.

Hydrologic consistency as a basis for assessing complexity of monthly water balance models for the continental United States

NASA Astrophysics Data System (ADS)

Martinez, Guillermo F.; Gupta, Hoshin V.

2011-12-01

Methods to select parsimonious and hydrologically consistent model structures are useful for evaluating dominance of hydrologic processes and representativeness of data. While information criteria (appropriately constrained to obey underlying statistical assumptions) can provide a basis for evaluating appropriate model complexity, it is not sufficient to rely upon the principle of maximum likelihood (ML) alone. We suggest that one must also call upon a "principle of hydrologic consistency," meaning that selected ML structures and parameter estimates must be constrained (as well as possible) to reproduce desired hydrological characteristics of the processes under investigation. This argument is demonstrated in the context of evaluating the suitability of candidate model structures for lumped water balance modeling across the continental United States, using data from 307 snow-free catchments. The models are constrained to satisfy several tests of hydrologic consistency, a flow space transformation is used to ensure better consistency with underlying statistical assumptions, and information criteria are used to evaluate model complexity relative to the data. The results clearly demonstrate that the principle of consistency provides a sensible basis for guiding selection of model structures and indicate strong spatial persistence of certain model structures across the continental United States. Further work to untangle reasons for model structure predominance can help to relate conceptual model structures to physical characteristics of the catchments, facilitating the task of prediction in ungaged basins.

Structural damping studies at cryogenic temperatures

NASA Technical Reports Server (NTRS)

Young, Clarence P., Jr.; Buehrle, Ralph D.

1994-01-01

Results of an engineering study to measure changes in structural damping properties of two cryogenic wind tunnel model systems and two metallic test specimens at cryogenic temperatures are presented. Data are presented which indicate overall, a trend toward reduced structural damping at cryogenic temperatures (-250 degrees F) when compared with room temperature damping properties. The study was focused on structures and materials used for model systems tested in the National Transonic Facility (NTF). The study suggests that the significant reductions in damping at extremely cold temperatures are most likely associated with changes in mechanical joint compliance damping rather than changes in material (solid) damping.

Matrix Management: An Organizational Alternative for Libraries.

ERIC Educational Resources Information Center

Johnson, Peggy

1990-01-01

Describes various organizational structures and models, presents matrix management as an alternative to traditional hierarchical structures, and suggests matrix management as an appropriate organizational alternative for academic libraries. Benefits that are discussed include increased flexibility, a higher level of professional independence, and…

Multistable binary decision making on networks

NASA Astrophysics Data System (ADS)

Lucas, Andrew; Lee, Ching Hua

2013-03-01

We propose a simple model for a binary decision making process on a graph, motivated by modeling social decision making with cooperative individuals. The model is similar to a random field Ising model or fiber bundle model, but with key differences in behavior on heterogeneous networks. For many types of disorder and interactions between the nodes, we predict with mean field theory discontinuous phase transitions that are largely independent of network structure. We show how these phase transitions can also be understood by studying microscopic avalanches and describe how network structure enhances fluctuations in the distribution of avalanches. We suggest theoretically the existence of a “glassy” spectrum of equilibria associated with a typical phase, even on infinite graphs, so long as the first moment of the degree distribution is finite. This behavior implies that the model is robust against noise below a certain scale and also that phase transitions can switch from discontinuous to continuous on networks with too few edges. Numerical simulations suggest that our theory is accurate.

Wasp waist or beer belly? Modeling food web structure and energetic control in Alaskan marine ecosystems, with implications for fishing and environmental forcing

NASA Astrophysics Data System (ADS)

Gaichas, Sarah; Aydin, Kerim; Francis, Robert C.

2015-11-01

The Eastern Bering Sea (EBS) and Gulf of Alaska (GOA) continental shelf ecosystems show some similar and some distinctive groundfish biomass dynamics. Given that similar species occupy these regions and fisheries management is also comparable, similarities might be expected, but to what can we attribute the differences? Different types of ecosystem structure and control (e.g. top-down, bottom-up, mixed) can imply different ecosystem dynamics and climate interactions. Further, the structural type identified for a given ecosystem may suggest optimal management for sustainable fishing. Here, we use information on the current system state derived from food web models of both the EBS and the GOA combined with dynamic ecosystem models incorporating uncertainty to classify each ecosystem by its structural type. We then suggest how this structure might be generally related to dynamics and predictability. We find that the EBS and GOA have fundamentally different food web structures both overall, and when viewed from the perspective of the same commercially and ecologically important species in each system, walleye pollock (Gadus chalcogrammus). EBS food web structure centers on a large mass of pollock, which appears to contribute to relative system stability and predictability. In contrast, GOA food web structure features high predator biomass, which contributes to a more dynamic, less predictable ecosystem. Mechanisms for climate influence on pollock production in the EBS are increasingly understood, while climate forcing mechanisms contributing to the potentially destabilizing high predator biomass in the GOA remain enigmatic. We present results of identical pollock fishing and climate-driven pollock recruitment simulations in the EBS and GOA which show different system responses, again with less predictable response in the GOA. Overall, our results suggest that identifying structural properties of fished food webs is as important for sustainable fisheries management as attempting to predict climate and fisheries effects within each ecosystem.

Structural analysis of two different stent configurations.

PubMed

Simão, M; Ferreira, J M; Mora-Rodriguez, J; Ramos, H M

2017-06-01

Two different stent configurations (i.e. the well known Palmaz-Schatz (PS) and a new stent configuration) are mechanically investigated. A finite element model was used to study the two geometries under combining loads and a computational fluid dynamic model based on fluid structure interaction was developed investigating the plaque and the artery wall reactions in a stented arterial segment. These models determine the stress and displacement fields of the two stents under internal pressure conditions. Results suggested that stent designs cause alterations in vascular anatomy that adversely affect arterial stress distributions within the wall, which have impact in the vessel responses such as the restenosis. The hemodynamic analysis shows the use of new stent geometry suggests better biofluid mechanical response such as the deformation and the progressive amount of plaque growth.

Simulation modeling to understand how selective foraging by beaver can drive the structure and function of a willow community

USGS Publications Warehouse

Peinetti, H.R.; Baker, B.W.; Coughenour, M.B.

2009-01-01

Beaver-willow (Castor-Salix) communities are a unique and vital component of healthy wetlands throughout the Holarctic region. Beaver selectively forage willow to provide fresh food, stored winter food, and construction material. The effects of this complex foraging behavior on the structure and function of willow communities is poorly understood. Simulation modeling may help ecologists understand these complex interactions. In this study, a modified version of the SAVANNA ecosystem model was developed to better understand how beaver foraging affects the structure and function of a willow community in a simulated riparian ecosystem in Rocky Mountain National Park, Colorado (RMNP). The model represents willow in terms of plant and stem dynamics and beaver foraging in terms of the quantity and quality of stems cut to meet the energetic and life history requirements of beaver. Given a site where all stems were equally available, the model suggested a simulated beaver family of 2 adults, 2 yearlings, and 2 kits required a minimum of 4 ha of willow (containing about10 stems m-2) to persist in a steady-state condition. Beaver created a willow community where the annual net primary productivity (ANPP) was 2 times higher and plant architecture was more diverse than the willow community without beaver. Beaver foraging created a plant architecture dominated by medium size willow plants, which likely explains how beaver can increase ANPP. Long-term simulations suggested that woody biomass stabilized at similar values even though availability differed greatly at initial condition. Simulations also suggested that willow ANPP increased across a range of beaver densities until beaver became food limited. Thus, selective foraging by beaver increased productivity, decreased biomass, and increased structural heterogeneity in a simulated willow community.

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

PubMed

Liang, Cong; Forrest, Alistair R R; Wagner, Günter P

2015-01-14

In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination.

Dependence of credit spread and macro-conditions based on an alterable structure model.

PubMed

Xie, Yun; Tian, Yixiang; Xiao, Zhuang; Zhou, Xiangyun

2018-01-01

The fat-tail financial data and cyclical financial market makes it difficult for the fixed structure model based on Gaussian distribution to characterize the dynamics of corporate bonds spreads. Using a flexible structure model based on generalized error distribution, this paper focuses on the impact of macro-level factors on the spreads of corporate bonds in China. It is found that in China's corporate bonds market, macroeconomic conditions have obvious structural transformational effects on bonds spreads, and their structural features remain stable with the downgrade of bonds ratings. The impact of macroeconomic conditions on spreads is significant for different structures, and the differences between the structures increase as ratings decline. For different structures, the persistent characteristics of bonds spreads are obviously stronger than those of recursive ones, which suggest an obvious speculation in bonds market. It is also found that the structure switching of bonds with different ratings is not synchronous, which indicates the shift of investment between different grades of bonds.

Dependence of credit spread and macro-conditions based on an alterable structure model

PubMed Central

2018-01-01

The fat-tail financial data and cyclical financial market makes it difficult for the fixed structure model based on Gaussian distribution to characterize the dynamics of corporate bonds spreads. Using a flexible structure model based on generalized error distribution, this paper focuses on the impact of macro-level factors on the spreads of corporate bonds in China. It is found that in China's corporate bonds market, macroeconomic conditions have obvious structural transformational effects on bonds spreads, and their structural features remain stable with the downgrade of bonds ratings. The impact of macroeconomic conditions on spreads is significant for different structures, and the differences between the structures increase as ratings decline. For different structures, the persistent characteristics of bonds spreads are obviously stronger than those of recursive ones, which suggest an obvious speculation in bonds market. It is also found that the structure switching of bonds with different ratings is not synchronous, which indicates the shift of investment between different grades of bonds. PMID:29723295

Structural controls on geothermal circulation in Surprise Valley, California: A re-evaluation of the Lake City fault zone

USGS Publications Warehouse

Anne E. Egger,; Glen, Jonathan; McPhee, Darcy K.

2014-01-01

Faults and fractures play an important role in the circulation of geothermal fluids in the crust, and the nature of that role varies according to structural setting and state of stress. As a result, detailed geologic and geophysical mapping that relates thermal springs to known structural features is essential to modeling geothermal systems. Published maps of Surprise Valley in northeastern California suggest that the “Lake City fault” or “Lake City fault zone” is a significant structural feature, cutting obliquely across the basin and connecting thermal springs across the valley. Newly acquired geophysical data (audio-magnetotelluric, gravity, and magnetic), combined with existing geochemical and geological data, suggest otherwise. We examine potential field profiles and resistivity models that cross the mapped Lake City fault zone. While there are numerous geophysical anomalies that suggest subsurface structures, they mostly do not coincide with the mapped traces of the Lake City fault zone, nor do they show a consistent signature in gravity, magnetics, or resistivities that would suggest a through-going fault that would promote connectivity through lateral fluid flow. Instead of a single, continuous fault, we propose the presence of a deformation zone associated with the growth of the range-front Surprise Valley fault. The implication for geothermal circulation is that this is a zone of enhanced porosity but lacks length-wise connectivity that could conduct fluids across the valley. Thermal fluid circulation is most likely controlled primarily by interactions between N-S–trending normal faults.

Evaluation of optimal control type models for the human gunner in an Anti-Aircraft Artillery (AAA) system

NASA Technical Reports Server (NTRS)

Phatak, A. V.; Kessler, K. M.

1975-01-01

The selection of the structure of optimal control type models for the human gunner in an anti aircraft artillery system is considered. Several structures within the LQG framework may be formulated. Two basic types are considered: (1) kth derivative controllers; and (2) proportional integral derivative (P-I-D) controllers. It is shown that a suitable criterion for model structure determination can be based on the ensemble statistics of the tracking error. In the case when the ensemble tracking steady state error is zero, it is suggested that a P-I-D controller formulation be used in preference to the kth derivative controller.

Bond graph modelling of multibody dynamics and its symbolic scheme

NASA Astrophysics Data System (ADS)

Kawase, Takehiko; Yoshimura, Hiroaki

A bond graph method of modeling multibody dynamics is demonstrated. Specifically, a symbolic generation scheme which fully utilizes the bond graph information is presented. It is also demonstrated that structural understanding and representation in bond graph theory is quite powerful for the modeling of such large scale systems, and that the nonenergic multiport of junction structure, which is a multiport expression of the system structure, plays an important role, as first suggested by Paynter. The principal part of the proposed symbolic scheme, that is, the elimination of excess variables, is done through tearing and interconnection in the sense of Kron using newly defined causal and causal coefficient arrays.

Seismic Attenuation Structure and Intraplate Deformation

NASA Astrophysics Data System (ADS)

Bezada, M.; Kowalke, S.; Smale, J.

2017-12-01

It has been suggested that intraplate deformation and seismicity is localized at weak zones in the lithosphere and at rheological boundaries. Comparisons of intraplate deformation regions with mantle seismic velocity structure suggest a correlation, but are not universally accepted as compelling evidence. We present P-wave attenuation models built from records of teleseismic deep-focus earthquakes in three different regions that show significant correlation between attenuation structure and intraplate seismicity and deformation. In the eastern United States, the New Madrid, Wabash Valley, Eastern Tennessee, Central Virginia, and Carolina seismic zones all occur at or near the edges of high-Q (low attenuation) regions. In Spain, intraplate seismicity is absent from high-Q regions but relatively abundant in surrounding low-Q regions where intraplate orogeny is also observed. In Australia, where our model resolution is relatively poor owing to sparse and uneven station coverage, the Petermann and Alice Springs intraplate orogens occur near the edge of a high-Q feature roughly coinciding with the undeformed Amadeus basin. Our results suggest that lithospheric structure exerts important controls on the localization of intraplate deformation and seismicity and that seismic attenuation is a useful proxy for lithospheric strength.

Perspectives for computational modeling of cell replacement for neurological disorders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aimone, James B.; Weick, Jason P.

In mathematical modeling of anatomically-constrained neural networks we provide significant insights regarding the response of networks to neurological disorders or injury. Furthermore, a logical extension of these models is to incorporate treatment regimens to investigate network responses to intervention. The addition of nascent neurons from stem cell precursors into damaged or diseased tissue has been used as a successful therapeutic tool in recent decades. Interestingly, models have been developed to examine the incorporation of new neurons into intact adult structures, particularly the dentate granule neurons of the hippocampus. These studies suggest that the unique properties of maturing neurons, can impactmore » circuit behavior in unanticipated ways. In this perspective, we review the current status of models used to examine damaged CNS structures with particular focus on cortical damage due to stroke. Secondly, we suggest that computational modeling of cell replacement therapies can be made feasible by implementing approaches taken by current models of adult neurogenesis. The development of these models is critical for generating hypotheses regarding transplant therapies and improving outcomes by tailoring transplants to desired effects.« less

Perspectives for computational modeling of cell replacement for neurological disorders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aimone, James B.; Weick, Jason P.

Mathematical modeling of anatomically-constrained neural networks has provided significant insights regarding the response of networks to neurological disorders or injury. A logical extension of these models is to incorporate treatment regimens to investigate network responses to intervention. The addition of nascent neurons from stem cell precursors into damaged or diseased tissue has been used as a successful therapeutic tool in recent decades. Interestingly, models have been developed to examine the incorporation of new neurons into intact adult structures, particularly the dentate granule neurons of the hippocampus. These studies suggest that the unique properties of maturing neurons, can impact circuit behaviormore » in unanticipated ways. In this perspective, we review the current status of models used to examine damaged CNS structures with particular focus on cortical damage due to stroke. Secondly, we suggest that computational modeling of cell replacement therapies can be made feasible by implementing approaches taken by current models of adult neurogenesis. The development of these models is critical for generating hypotheses regarding transplant therapies and improving outcomes by tailoring transplants to desired effects.« less

The Problems of Contemporary Education

ERIC Educational Resources Information Center

Akar, Hüseyin; Dogan, Yildiz Burcu; Üstüner, Mehmet

2018-01-01

This research aimed to investigate the relationships between positive and negative perfectionisms, self-handicapping, self-efficacy and academic achievement. For this purpose, an extensive literature review was conducted and a model was suggested. Structural equation model was employed to test the model. The study group of the research consisted…

Development of an earth pressure model for design of earth retaining structures in piedmont soil.

DOT National Transportation Integrated Search

2008-10-01

Anecdotal evidence suggests that earth pressure in Piedmont residual soils is typically over estimated. Such estimates of earth pressure impact the design of earth retaining structures used on highway projects. Thus, the development of an appropriate...

Using structure to explore the sequence alignment space of remote homologs.

PubMed

Kuziemko, Andrew; Honig, Barry; Petrey, Donald

2011-10-01

Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template. However, sequence alignment methods based on dynamic programming (DP) are typically unable to generate accurate alignments for remote sequence homologs, thus limiting the applicability of modeling methods. A central problem is that the alignment that is "optimal" in terms of the DP score does not necessarily correspond to the alignment that produces the most accurate structural model. That is, the correct alignment based on structural superposition will generally have a lower score than the optimal alignment obtained from sequence. Variations of the DP algorithm have been developed that generate alternative alignments that are "suboptimal" in terms of the DP score, but these still encounter difficulties in detecting the correct structural alignment. We present here a new alternative sequence alignment method that relies heavily on the structure of the template. By initially aligning the query sequence to individual fragments in secondary structure elements and combining high-scoring fragments that pass basic tests for "modelability", we can generate accurate alignments within a small ensemble. Our results suggest that the set of sequences that can currently be modeled by homology can be greatly extended.

ARE TORNADO-LIKE MAGNETIC STRUCTURES ABLE TO SUPPORT SOLAR PROMINENCE PLASMA?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luna, M.; Moreno-Insertis, F.; Priest, E.

Recent high-resolution and high-cadence observations have surprisingly suggested that prominence barbs exhibit apparent rotating motions suggestive of a tornado-like structure. Additional evidence has been provided by Doppler measurements. The observations reveal opposite velocities for both hot and cool plasma on the two sides of a prominence barb. This motion is persistent for several hours and has been interpreted in terms of rotational motion of prominence feet. Several authors suggest that such barb motions are rotating helical structures around a vertical axis similar to tornadoes on Earth. One of the difficulties of such a proposal is how to support cool prominencemore » plasma in almost-vertical structures against gravity. In this work we model analytically a tornado-like structure and try to determine possible mechanisms to support the prominence plasma. We have found that the Lorentz force can indeed support the barb plasma provided the magnetic structure is sufficiently twisted and/or significant poloidal flows are present.« less

Factors influencing protein tyrosine nitration – structure-based predictive models

PubMed Central

Bayden, Alexander S.; Yakovlev, Vasily A.; Graves, Paul R.; Mikkelsen, Ross B.; Kellogg, Glen E.

2010-01-01

Models for exploring tyrosine nitration in proteins have been created based on 3D structural features of 20 proteins for which high resolution X-ray crystallographic or NMR data are available and for which nitration of 35 total tyrosines has been experimentally proven under oxidative stress. Factors suggested in previous work to enhance nitration were examined with quantitative structural descriptors. The role of neighboring acidic and basic residues is complex: for the majority of tyrosines that are nitrated the distance to the heteroatom of the closest charged sidechain corresponds to the distance needed for suspected nitrating species to form hydrogen bond bridges between the tyrosine and that charged amino acid. This suggests that such bridges play a very important role in tyrosine nitration. Nitration is generally hindered for tyrosines that are buried and for those tyrosines where there is insufficient space for the nitro group. For in vitro nitration, closed environments with nearby heteroatoms or unsaturated centers that can stabilize radicals are somewhat favored. Four quantitative structure-based models, depending on the conditions of nitration, have been developed for predicting site-specific tyrosine nitration. The best model, relevant for both in vitro and in vivo cases predicts 30 of 35 tyrosine nitrations (positive predictive value) and has a sensitivity of 60/71 (11 false positives). PMID:21172423

The Effects of Family Structure on African American Adolescents' Marijuana Use

ERIC Educational Resources Information Center

Mandara, Jelani; Rogers, Sheba Y.; Zinbarg, Richard E.

2011-01-01

The relationship between family structure and marijuana use throughout adolescence was assessed among 1,069 African Americans from the NLSY. A model was also tested suggesting that the effects of family structure on marijuana use would be mediated by poverty, neighborhood quality, and adolescents' self-control. As most prior studies have found,…

Physical constraints in the condensation of eukaryotic chromosomes. Local concentration of DNA versus linear packing ratio in higher order chromatin structures.

PubMed

Daban, J R

2000-04-11

The local concentration of DNA in metaphase chromosomes of different organisms has been determined in several laboratories. The average of these measurements is 0.17 g/mL. In the first level of chromosome condensation, DNA is wrapped around histones forming nucleosomes. This organization limits the DNA concentration in nucleosomes to 0. 3-0.4 g/mL. Furthermore, in the structural models suggested in different laboratories for the 30-40 nm chromatin fiber, the estimated DNA concentration is significantly reduced; it ranges from 0.04 to 0.27 g/mL. The DNA concentration is further reduced when the fiber is folded into the successive higher order structures suggested in different models for metaphase chromosomes; the estimated minimum decrease of DNA concentration represents an additional 40%. These observations suggest that most of the models proposed for the 30-40 nm chromatin fiber are not dense enough for the construction of metaphase chromosomes. In contrast, it is well-known that the linear packing ratio increases dramatically in each level of DNA folding in chromosomes. Thus, the consideration of the linear packing ratio is not enough for the study of chromatin condensation; the constraint resulting from the actual DNA concentration in metaphase chromosomes must be considered for the construction of models for condensed chromatin.

Dynamic and Structural Gas Turbine Engine Modeling

NASA Technical Reports Server (NTRS)

Turso, James A.

2003-01-01

Model the interactions between the structural dynamics and the performance dynamics of a gas turbine engine. Generally these two aspects are considered separate, unrelated phenomena and are studied independently. For diagnostic purposes, it is desirable to bring together as much information as possible, and that involves understanding how performance is affected by structural dynamics (if it is) and vice versa. This can involve the relationship between thrust response and the excitation of structural modes, for instance. The job will involve investigating and characterizing these dynamical relationships, generating a model that incorporates them, and suggesting and/or developing diagnostic and prognostic techniques that can be incorporated in a data fusion system. If no coupling is found, at the least a vibration model should be generated that can be used for diagnostics and prognostics related to blade loss, for instance.

Multi-wavelength Observations and Modeling of Solar Flares: Magnetic Structures

NASA Astrophysics Data System (ADS)

Su, Y.

2017-12-01

We present a review of our recent investigations on multi-wavelength observations and magnetic field modeling of solar flares. High-resolution observations taken by NVST and BBSO/NST reveal unprecedented fine structures of the flaring regions. Observations by SDO, IRIS, and GOES provide the complementary information. The magnetic field models are constructed using either non-linear force free field extrapolations or flux rope insertion method. Our studies have shown that the flaring regions often consist of double or multiple flux ropes, which often exist at different heights. The fine flare ribbon structures may be due to the magnetic reconnection in the complex quasi separatrix layers. The magnetic field modeling of several large flares suggests that the so called hot-channel structure is corresponding to the erupting flux rope above the X-point in a magnetic configuration with Hyperbolic Flux Tube.

Point process models for localization and interdependence of punctate cellular structures.

PubMed

Li, Ying; Majarian, Timothy D; Naik, Armaghan W; Johnson, Gregory R; Murphy, Robert F

2016-07-01

Accurate representations of cellular organization for multiple eukaryotic cell types are required for creating predictive models of dynamic cellular function. To this end, we have previously developed the CellOrganizer platform, an open source system for generative modeling of cellular components from microscopy images. CellOrganizer models capture the inherent heterogeneity in the spatial distribution, size, and quantity of different components among a cell population. Furthermore, CellOrganizer can generate quantitatively realistic synthetic images that reflect the underlying cell population. A current focus of the project is to model the complex, interdependent nature of organelle localization. We built upon previous work on developing multiple non-parametric models of organelles or structures that show punctate patterns. The previous models described the relationships between the subcellular localization of puncta and the positions of cell and nuclear membranes and microtubules. We extend these models to consider the relationship to the endoplasmic reticulum (ER), and to consider the relationship between the positions of different puncta of the same type. Our results do not suggest that the punctate patterns we examined are dependent on ER position or inter- and intra-class proximity. With these results, we built classifiers to update previous assignments of proteins to one of 11 patterns in three distinct cell lines. Our generative models demonstrate the ability to construct statistically accurate representations of puncta localization from simple cellular markers in distinct cell types, capturing the complex phenomena of cellular structure interaction with little human input. This protocol represents a novel approach to vesicular protein annotation, a field that is often neglected in high-throughput microscopy. These results suggest that spatial point process models provide useful insight with respect to the spatial dependence between cellular structures. © 2016 International Society for Advancement of Cytometry. © 2016 International Society for Advancement of Cytometry.

Pahranagat Shear System, Lincoln County, Nevada

NASA Technical Reports Server (NTRS)

Liggett, M. A. (Principal Investigator); Ehrenspreck, H. E.

1974-01-01

The author has identified the following significant results. A structural model which relates strike-slip deformation to Basin Range extensional tectonics was formulated on the basis of analysis and interpreatation of ERTS-1 MSS imagery over southern Lincoln County, Nevada. Study of published geologic data and field reconnaissance of key areas has been conducted to support the ERTS-1 data interpretation. The structural model suggests that a left-lateral strike-slip fault zone, called the Pahranagat Shear System, formed as a transform fault separating two areas of east-west structural extension.

Integrating data from multiple sources for insights into demographic processes: Simulation studies and proof of concept for hierarchical change-in-ratio models.

PubMed

Nilsen, Erlend B; Strand, Olav

2018-01-01

We developed a model for estimating demographic rates and population abundance based on multiple data sets revealing information about population age- and sex structure. Such models have previously been described in the literature as change-in-ratio models, but we extend the applicability of the models by i) using time series data allowing the full temporal dynamics to be modelled, by ii) casting the model in an explicit hierarchical modelling framework, and by iii) estimating parameters based on Bayesian inference. Based on sensitivity analyses we conclude that the approach developed here is able to obtain estimates of demographic rate with high precision whenever unbiased data of population structure are available. Our simulations revealed that this was true also when data on population abundance are not available or not included in the modelling framework. Nevertheless, when data on population structure are biased due to different observability of different age- and sex categories this will affect estimates of all demographic rates. Estimates of population size is particularly sensitive to such biases, whereas demographic rates can be relatively precisely estimated even with biased observation data as long as the bias is not severe. We then use the models to estimate demographic rates and population abundance for two Norwegian reindeer (Rangifer tarandus) populations where age-sex data were available for all harvested animals, and where population structure surveys were carried out in early summer (after calving) and late fall (after hunting season), and population size is counted in winter. We found that demographic rates were similar regardless whether we include population count data in the modelling, but that the estimated population size is affected by this decision. This suggest that monitoring programs that focus on population age- and sex structure will benefit from collecting additional data that allow estimation of observability for different age- and sex classes. In addition, our sensitivity analysis suggests that focusing monitoring towards changes in demographic rates might be more feasible than monitoring abundance in many situations where data on population age- and sex structure can be collected.

Identification of walking human model using agent-based modelling

NASA Astrophysics Data System (ADS)

Shahabpoor, Erfan; Pavic, Aleksandar; Racic, Vitomir

2018-03-01

The interaction of walking people with large vibrating structures, such as footbridges and floors, in the vertical direction is an important yet challenging phenomenon to describe mathematically. Several different models have been proposed in the literature to simulate interaction of stationary people with vibrating structures. However, the research on moving (walking) human models, explicitly identified for vibration serviceability assessment of civil structures, is still sparse. In this study, the results of a comprehensive set of FRF-based modal tests were used, in which, over a hundred test subjects walked in different group sizes and walking patterns on a test structure. An agent-based model was used to simulate discrete traffic-structure interactions. The occupied structure modal parameters found in tests were used to identify the parameters of the walking individual's single-degree-of-freedom (SDOF) mass-spring-damper model using 'reverse engineering' methodology. The analysis of the results suggested that the normal distribution with the average of μ = 2.85Hz and standard deviation of σ = 0.34Hz can describe human SDOF model natural frequency. Similarly, the normal distribution with μ = 0.295 and σ = 0.047 can describe the human model damping ratio. Compared to the previous studies, the agent-based modelling methodology proposed in this paper offers significant flexibility in simulating multi-pedestrian walking traffics, external forces and simulating different mechanisms of human-structure and human-environment interaction at the same time.

Occupational/Career Decision-Making Thought Processes of Adolescents of High Intellectual Ability

ERIC Educational Resources Information Center

Jung, Jae Yup

2017-01-01

Three competing models of the career decision-making thought processes of adolescents of high intellectual ability were tested in this study. Survey data were collected from 664 intellectually gifted Australian adolescents and analyzed using structural equation modeling procedures. The finally accepted, optimal model suggested that, regardless of…

Research on homeopathy: state of the art.

PubMed

Walach, Harald; Jonas, Wayne B; Ives, John; van Wijk, Roel; Weingärtner, Otto

2005-10-01

In this paper, we review research on homeopathy from four perspectives, focusing on reviews and some landmark studies. These perspectives are laboratory studies, clinical trials, observational studies, and theoretical work. In laboratory models, numerous effects and anomalies have been reported. However, no single model has been sufficiently widely replicated. Instead, researchers have focused on ever-new models and experiments, leaving the picture of scattered anomalies without coherence. Basic research, trying to elucidate a purported difference between homeopathic remedies and control solutions has also produced some encouraging results, but again, series of independent replications are missing. While there are nearly 200 reports on clinical trials, few series have been conducted for single conditions. Some of these series document clinically useful effects and differences against placebo and some series do not. Observational research into uncontrolled homeopathic practice documents consistently strong therapeutic effects and sustained satisfaction in patients. We suggest that this scattered picture has to do with the fourth line of research: lack of a good theory. Some of the extant theoretical models are reviewed, including placebo, water structure, silica contamination, energy models, and entanglement models. It emerges that local models, suggesting some change in structure in the solvent, are far from convincing. The nonlocal models proposed would predict that it is impossible to nail down homeopathic effects with direct experimental testing and this places homeopathy in a scientific dilemma. We close with some suggestions for potentially fruitful research.

Structural Dynamics of the Magnesium-bound Conformation of CorA in a lipid bilayer

PubMed Central

Dalmas, Olivier; Cuello, Luis G.; Jogini, Vishwanath; Cortes, D. Marien; Roux, Benoit; Perozo, Eduardo

2010-01-01

Summary The transmembrane conformation of Thermotoga maritima CorA, a Magnesium transport system, has been studied in it’s Mg2+-bound form by site-directed spin labeling and electron paramagnetic resonance spectroscopy. Probe mobility together with accessibility data were used to evaluate the overall dynamics and relative arrangement of individual transmembrane segments TM1 and TM2. TM1 extends toward the cytoplasmic side creating a water filled cavity, while TM2 is located in the periphery of the oligomer, contacting the lipid bilayer. A structural model for the conserved extracellular loop was generated based on EPR data and MD simulations, in which residue E316 is located towards the fivefold symmetry axis in position to electrostatically influence divalent ion translocation. Electrostatic analyses of our model suggest that, in agreement with the crystal structure, Mg2+ -bound CorA is in a close conformation. The present results suggest that long-range structural rearrangements are necessary to allow Mg2+ translocation. PMID:20637423

Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

PubMed

Brunger, Axel T; Adams, Paul D; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F

2012-06-06

In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

On the dimensionality of the stress-related growth scale: one, three, or seven factors?

PubMed

Roesch, Scott C; Rowley, Anthony A; Vaughn, Allison A

2004-06-01

We examined the factorial validity and dimensionality of the Stress-Related Growth Scale (SRGS; Park, Cohen, & Murch, 1996) using a large multiethnic sample (n = 1,070). Exploratory and confirmatory factor analyses suggested that a multidimensional representation of the SRGS fit better than a unidimensional representation. Specifically, we cross-validated both a 3-factor model and a 7-factor model using confirmatory factor analysis and were shown to be invariant across gender and ethnic groups. The 3-factor model was represented by global dimensions of growth that included rational/mature thinking, affective/emotional growth, and religious/spiritual growth. We replicated the 7-factor model of Armeli, Gunthert, and Cohen (2001) and it represented more specific components of growth such as Self-Understanding and Treatment of Others. However, some factors of the 7-factor model had questionable internal consistency and were strongly intercorrelated, suggesting redundancy. The findings support the notion that the factor structure of both the original 1-factor and revised 7-factor models are unstable and that the 3-factor model developed in this research has more reliable psychometric properties and structure.

Along-axis segmentation and isostasy in the Western rift, East Africa

NASA Astrophysics Data System (ADS)

Upcott, N. M.; Mukasa, R. K.; Ebinger, C. J.; Karner, G. D.

1996-02-01

Structural variations along the southern sectors of the Western rift, East Africa, have previously been described, but subsurface structures in the northern sector (Uganda, Zaire) are virtually unknown. Our aims are to investigate the along-axis segmentation of the northern sector, thereby adding to the structural picture of the Western rift, and to study the isostatic compensation of the varying rift morphology along the sector's length. This study describes the first gravity survey to be carried out on the shallow Lake Albert, forward models of these and existing gravity data, and the results from inverse modeling of existing aeromagnetic data designed to delimit border and transfer fault systems. Our tectonic model shows that the northern rift sector is segmented along-axis into five 25 to 65-km-wide, 80 to 100-km-long rift segments, characterized by closed-contour Bouguer anomaly lows, and bounded by steep gravity, aeromagnetic, and topographic/bathymetric gradients. Werner and Euler deconvolution results and gravity anomaly data reveal that some faulted basins are separated by structural highs and cross-rift ramps or faults and suggest sedimentary basin depths of 4-6 km. Forward modeling of structural and free-air gravity profiles across individual basins and flanks using a model that assumes flexural compensation also suggests sediment thicknesses of up to 5.5 km, similar to the estimates from magnetic data. The basin and flank morphology can be explained by 6-9 km of extension of a lithosphere with an effective elastic thickness (Te) of 25 km (equivalent to a flexural rigidity of 1.4 × 1023 N m), similar to results in other Western rift basins. Potential field data and lithospheric strength estimates in the Western rift system show small along-axis variations in lithospheric structure, regardless of the presence or absence of Cenozoic magmatism.

Fractal model of polarization switching kinetics in ferroelectrics under nonequilibrium conditions of electron irradiation

NASA Astrophysics Data System (ADS)

Maslovskaya, A. G.; Barabash, T. K.

2018-03-01

The paper presents the results of the fractal and multifractal analysis of polarization switching current in ferroelectrics under electron irradiation, which allows statistical memory effects to be estimated at dynamics of domain structure. The mathematical model of formation of electron beam-induced polarization current in ferroelectrics was suggested taking into account the fractal nature of domain structure dynamics. In order to realize the model the computational scheme was constructed using the numerical solution approximation of fractional differential equation. Evidences of electron beam-induced polarization switching process in ferroelectrics were specified at a variation of control model parameters.

Composite Stress Rupture: A New Reliability Model Based on Strength Decay

NASA Technical Reports Server (NTRS)

Reeder, James R.

2012-01-01

A model is proposed to estimate reliability for stress rupture of composite overwrap pressure vessels (COPVs) and similar composite structures. This new reliability model is generated by assuming a strength degradation (or decay) over time. The model suggests that most of the strength decay occurs late in life. The strength decay model will be shown to predict a response similar to that predicted by a traditional reliability model for stress rupture based on tests at a single stress level. In addition, the model predicts that even though there is strength decay due to proof loading, a significant overall increase in reliability is gained by eliminating any weak vessels, which would fail early. The model predicts that there should be significant periods of safe life following proof loading, because time is required for the strength to decay from the proof stress level to the subsequent loading level. Suggestions for testing the strength decay reliability model have been made. If the strength decay reliability model predictions are shown through testing to be accurate, COPVs may be designed to carry a higher level of stress than is currently allowed, which will enable the production of lighter structures

Study of Near-Surface Models in Large-Eddy Simulations of a Neutrally Stratified Atmospheric Boundary Layer

NASA Technical Reports Server (NTRS)

Senocak, I.; Ackerman, A. S.; Kirkpatrick, M. P.; Stevens, D. E.; Mansour, N. N.

2004-01-01

Large-eddy simulation (LES) is a widely used technique in armospheric modeling research. In LES, large, unsteady, three dimensional structures are resolved and small structures that are not resolved on the computational grid are modeled. A filtering operation is applied to distinguish between resolved and unresolved scales. We present two near-surface models that have found use in atmospheric modeling. We also suggest a simpler eddy viscosity model that adopts Prandtl's mixing length model (Prandtl 1925) in the vicinity of the surface and blends with the dynamic Smagotinsky model (Germano et al, 1991) away from the surface. We evaluate the performance of these surface models by simulating a neutraly stratified atmospheric boundary layer.

Automatically updating predictive modeling workflows support decision-making in drug design.

PubMed

Muegge, Ingo; Bentzien, Jörg; Mukherjee, Prasenjit; Hughes, Robert O

2016-09-01

Using predictive models for early decision-making in drug discovery has become standard practice. We suggest that model building needs to be automated with minimum input and low technical maintenance requirements. Models perform best when tailored to answering specific compound optimization related questions. If qualitative answers are required, 2-bin classification models are preferred. Integrating predictive modeling results with structural information stimulates better decision making. For in silico models supporting rapid structure-activity relationship cycles the performance deteriorates within weeks. Frequent automated updates of predictive models ensure best predictions. Consensus between multiple modeling approaches increases the prediction confidence. Combining qualified and nonqualified data optimally uses all available information. Dose predictions provide a holistic alternative to multiple individual property predictions for reaching complex decisions.

The African and Pacific Superplume Structures Constrained by Assembly and Breakup of Pangea

NASA Astrophysics Data System (ADS)

Zhang, N.; Zhong, S.; Leng, W.; Li, Z.

2009-12-01

Seismic tomography studies indicate that the Earth’s mantle structure is characterized by African and Pacific seismically slow velocity anomalies (i.e., superplumes) and circum-Pacific seismically fast anomalies (i.e., a globally spherical harmonic degree-2 structure). McNamara and Zhong (2005) have demonstrated that the African and Pacific superplume structures result from dynamic interaction between mantle convection and surface plate motion history in the last 120 Ma. However, their models produce slightly stronger degree 3 structure than degree 2 near the CMB. Here, we construct a proxy model of plate motions for the African hemisphere for the last 450 Ma since the Early Paleozoic using the paleogeographic reconstruction of continents constrained by paleomagnetic and geological observations. Using this proxy model for plate motion history as the time-dependent surface boundary conditions for a 3-dimensional spherical model of thermochemical mantle convection, we calculate the present-day mantle structure and explore the evolution of mantle structures since the Early Paleozoic. Our model calculations reproduce well the present-day mantle structure including the African and Pacific superplumes. The power spectra of our calculated present-day temperature field shows that the strongest power occurs at degree 2 in the lower mantle while in the upper mantle the strongest power is at degree 3. The degree correlation between tomography model S20RTS and our calculated temperature field shows a high correlation at the degree 1 and degree 2 in the lower mantle while the upper mantle and the short wavelength structures do not correlate well. The summed degree correlation for the lower mantle shows a relatively good correlation for the bottom 300 km of the mantle but the correlation is significantly reduced at depth 600 km above the CMB. For the evolution of mantle structures, we focus on the evolution of the African superplume. Our results suggest that the mantle in the African hemisphere before the assembly of Pangea is predominated by the cold downwelling structure resulting from plate convergence between Gondwana and Laurussia and the cold Africa hemisphere changes to hot due to the return flows from the circum-Pangea subduction after Pangea formation. Based on our results, we suggest that the African superplume structure may be formed no earlier than ~230 Ma ago (i.e., ~100 Ma after the assembly of Pangea).

Archaeogeophysical investigations of early Caddo settlement patterning at the Crenshaw site (3MI6)

NASA Astrophysics Data System (ADS)

Samuelsen, John R.

The Teran map, made during Don Domingo Teran de los Rios' expedition for New Spain, shows a Caddo settlement in 1691 with a vacant mound center and many small farmsteads dispersed across the countryside along both banks of the Red River. This map, combined with the 19th Century photographs taken by William Soule, provides a testable model for the settlement pattern of the Caddo people called the Teran-Soule model. This model states that large numbers of people besides a small caretaker population did not inhabit the mound centers, supporting a vacant mound center hypothesis. Recent studies have begun to challenge this hypothesis, using archaeogeophysical techniques to find structures near Middle to Late Caddo mounds. An archaeogeophysical survey of the Crenshaw site along the Great Bend of the Red River was conducted to determine if structures could be found there. Is the settlement pattern at this early Caddo site, occupied between A.D. 700 and 1400, consistent with the late historic model of a vacant mound center? Is there evidence that both Caddo and Fourche Maline occupations existed in horizontally distinct components? The 3.2 hectare survey identified more than 100 possible structures, of which more than 50 are probably structures associated with the Fourche Maline or early Caddo occupations of the site. Several structures were found in linear patterns, including an oval series of possible structures measuring 90 x 85 m in diameter. While cultural affiliation was not determined for most of these features, some can be attributed to Caddo origin based on architectural attributes, such as extended entranceways. This suggests that Crenshaw was not literally vacant, but the presence of extended entranceways suggests that some of the identified features were special use structures, which does not conflict with the vacant mound center hypothesis. However, the large number of possible structures present with unknown cultural affiliations provides ample opportunities for testing the model.

Linking the Pilot Structural Model and Pilot Workload

NASA Technical Reports Server (NTRS)

Bachelder, Edward; Hess, Ronald; Aponso, Bimal; Godfroy-Cooper, Martine

2018-01-01

Behavioral models are developed that closely reproduced pulsive control response of two pilots using markedly different control techniques while conducting a tracking task. An intriguing find was that the pilots appeared to: 1) produce a continuous, internally-generated stick signal that they integrated in time; 2) integrate the actual stick position; and 3) compare the two integrations to either issue or cease a pulse command. This suggests that the pilots utilized kinesthetic feedback in order to sense and integrate stick position, supporting the hypothesis that pilots can access and employ the proprioceptive inner feedback loop proposed by Hess's pilot Structural Model. A Pilot Cost Index was developed, whose elements include estimated workload, performance, and the degree to which the pilot employs kinesthetic feedback. Preliminary results suggest that a pilot's operating point (parameter values) may be based on control style and index minimization.

Assessing Spurious Interaction Effects in Structural Equation Modeling

ERIC Educational Resources Information Center

Harring, Jeffrey R.; Weiss, Brandi A.; Li, Ming

2015-01-01

Several studies have stressed the importance of simultaneously estimating interaction and quadratic effects in multiple regression analyses, even if theory only suggests an interaction effect should be present. Specifically, past studies suggested that failing to simultaneously include quadratic effects when testing for interaction effects could…

Insilico modeling and molecular dynamic simulation of claudin-1 point mutations in HCV infection.

PubMed

Vipperla, Bhavaniprasad; Dass, J Febin Prabhu; Jayanthi, S

2014-01-01

Claudin-1 (CLDN1) in association with envelope glycoprotein (CD81) mediates the fusion of HCV into the cytosol. Recent studies have indicated that point mutations in CLDN1 are important for the entry of hepatitis C virus (HCV). To validate these findings, we employed a computational platform to investigate the structural effect of two point mutations (I32M and E48K). Initially, three-dimensional co-ordinates for CLDN1 receptor sequence were generated. Then, three mutant models were built using the point mutation including a double mutant (I32M/E48K) model from the native model structure. Finally, all the four model structures including the native and three mutant models were subjected to molecular dynamics (MD) simulation for a period of 25 ns to appreciate their dynamic behavior. The MD trajectory files were analyzed using cluster and principal component method. The analysis suggested that either of the single mutation has negligible effect on the overall structure of CLDN1 compared to the double mutant form. However, the double mutant model of CLDN1 shows significant negative impact through the impairment of H-bonds and the simultaneous increase in solvent accessible surface area. Our simulation results are visibly consistent with the experimental report suggesting that the CLDN1 receptor distortion is prominent due to the double mutation with large surface accessibility. This increase in accessible surface area due to the coexistence of double mutation may be presumed as one of the key factor that results in permissive action of HCV attachment and infection.

Performance of Bootstrapping Approaches To Model Test Statistics and Parameter Standard Error Estimation in Structural Equation Modeling.

ERIC Educational Resources Information Center

Nevitt, Jonathan; Hancock, Gregory R.

2001-01-01

Evaluated the bootstrap method under varying conditions of nonnormality, sample size, model specification, and number of bootstrap samples drawn from the resampling space. Results for the bootstrap suggest the resampling-based method may be conservative in its control over model rejections, thus having an impact on the statistical power associated…

Ecumenical Worldview Development by Gender, Race, and Worldview: A Multiple-Group Analysis of Model Invariance

ERIC Educational Resources Information Center

Bryant, Alyssa N.

2011-01-01

Based upon a national longitudinal dataset of 14,527 college students generated by the UCLA Spirituality in Higher Education Project, this study used structural equation modeling to test the applicability of a model of ecumenical worldview development for students of diverse genders, races, and worldviews. The model suggests that challenging…

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langkilde, Annette E., E-mail: annette.langkilde@sund.ku.dk; Morris, Kyle L.; Serpell, Louise C.

The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-raymore » crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.« less

Ultimate strength performance of tankers associated with industry corrosion addition practices

NASA Astrophysics Data System (ADS)

Kim, Do Kyun; Kim, Han Byul; Zhang, Xiaoming; Li, Chen Guang; Paik, Jeom Kee

2014-09-01

In the ship and offshore structure design, age-related problems such as corrosion damage, local denting, and fatigue damage are important factors to be considered in building a reliable structure as they have a significant influence on the residual structural capacity. In shipping, corrosion addition methods are widely adopted in structural design to prevent structural capacity degradation. The present study focuses on the historical trend of corrosion addition rules for ship structural design and investigates their effects on the ultimate strength performance such as hull girder and stiffened panel of double hull oil tankers. Three types of rules based on corrosion addition models, namely historic corrosion rules (pre-CSR), Common Structural Rules (CSR), and harmonised Common Structural Rules (CSRH) are considered and compared with two other corrosion models namely UGS model, suggested by the Union of Greek Shipowners (UGS), and Time-Dependent Corrosion Wastage Model (TDCWM). To identify the general trend in the effects of corrosion damage on the ultimate longitudinal strength performance, the corrosion addition rules are applied to four representative sizes of double hull oil tankers namely Panamax, Aframax, Suezmax, and VLCC. The results are helpful in understanding the trend of corrosion additions for tanker structures

A comparative study of theoretical graph models for characterizing structural networks of human brain.

PubMed

Li, Xiaojin; Hu, Xintao; Jin, Changfeng; Han, Junwei; Liu, Tianming; Guo, Lei; Hao, Wei; Li, Lingjiang

2013-01-01

Previous studies have investigated both structural and functional brain networks via graph-theoretical methods. However, there is an important issue that has not been adequately discussed before: what is the optimal theoretical graph model for describing the structural networks of human brain? In this paper, we perform a comparative study to address this problem. Firstly, large-scale cortical regions of interest (ROIs) are localized by recently developed and validated brain reference system named Dense Individualized Common Connectivity-based Cortical Landmarks (DICCCOL) to address the limitations in the identification of the brain network ROIs in previous studies. Then, we construct structural brain networks based on diffusion tensor imaging (DTI) data. Afterwards, the global and local graph properties of the constructed structural brain networks are measured using the state-of-the-art graph analysis algorithms and tools and are further compared with seven popular theoretical graph models. In addition, we compare the topological properties between two graph models, namely, stickiness-index-based model (STICKY) and scale-free gene duplication model (SF-GD), that have higher similarity with the real structural brain networks in terms of global and local graph properties. Our experimental results suggest that among the seven theoretical graph models compared in this study, STICKY and SF-GD models have better performances in characterizing the structural human brain network.

Do priority effects outweigh environmental filtering in a guild of dominant freshwater macroinvertebrates?

PubMed

Little, Chelsea J; Altermatt, Florian

2018-04-11

Abiotic conditions have long been considered essential in structuring freshwater macroinvertebrate communities. Ecological drift, dispersal and biotic interactions also structure communities, and although these mechanisms are more difficult to detect, they may be of equal importance in natural communities. Here, we hypothesized that in 10 naturally replicated headwater streams in eastern Switzerland, locally dominant amphipod species would be associated with differences in environmental conditions. We conducted repeated surveys of amphipods and used a hierarchical joint species distribution model to assess the influence of different drivers on species co-occurrences. The species had unique environmental requirements, but a distinct spatial structure in their distributions was unrelated to habitat. Species co-occurred much less frequently than predicted by the model, which was surprising because laboratory and field evidence suggests they are capable of coexisting in equal densities. We suggest that niche preemption may limit their distribution and that a blocking effect related to the specific linear configuration of streams determines which species colonizes and dominates a given stream catchment, thus suggesting a new solution a long-standing conundrum in freshwater ecology. © 2018 The Author(s).

Unifying error structures in commonly used biotracer mixing models.

PubMed

Stock, Brian C; Semmens, Brice X

2016-10-01

Mixing models are statistical tools that use biotracers to probabilistically estimate the contribution of multiple sources to a mixture. These biotracers may include contaminants, fatty acids, or stable isotopes, the latter of which are widely used in trophic ecology to estimate the mixed diet of consumers. Bayesian implementations of mixing models using stable isotopes (e.g., MixSIR, SIAR) are regularly used by ecologists for this purpose, but basic questions remain about when each is most appropriate. In this study, we describe the structural differences between common mixing model error formulations in terms of their assumptions about the predation process. We then introduce a new parameterization that unifies these mixing model error structures, as well as implicitly estimates the rate at which consumers sample from source populations (i.e., consumption rate). Using simulations and previously published mixing model datasets, we demonstrate that the new error parameterization outperforms existing models and provides an estimate of consumption. Our results suggest that the error structure introduced here will improve future mixing model estimates of animal diet. © 2016 by the Ecological Society of America.

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

In this study, microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of processmore » rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.« less

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

State Effect of Traumatic Experience on Personality Structure

PubMed Central

Lee, Hong-seock; Lee, Sang-Kyu; Lee, Heung-Pyo

2012-01-01

Objective Personality is defined as the trait-like qualities of a person. However, it has been recently suggested that the state effect of a situation leads to changes in scores on personality assessments. We predicted that traumatic experiences would induce changes not only in personality scores but also in the factor structures of personality assessments. Methods MethodsaaWe conducted a cross-sectional, case-controlled study using two data sets: a traumatized adolescent sample (n=71) and a non-traumatized adolescent sample (n=296). Personality factor structures were compared between the two samples using exploratory factor analyses for 25 lower-ordered subscales of the Temperament and Character Inventory (TCI). In the non-traumatized sample, evaluation of the scree plot suggested a five-factor solution supporting TCI's original seven-factor model. Results The traumatized sample showed a three-factor structure representing a biological factor, a social factor and an existential factor. This decrease in number of personality factors was caused by strengthened correlations among personality subscales related to coping with traumatic situations. Cloninger's psychobiological model of personality (i.e., temperament-character) was adequate in capturing personality traits of non-traumatized adolescents, but the tripartite view of existential psychology (i.e., body-mind-spirit) clearly corresponded to the factor structure of the traumatized adolescents. Conclusion The three-factor solution of the present traumatized group is consistent with the tripartite model of personality (i.e., body-mind-spirit), while the five-factor solution of the non-traumatized group corresponds to Cloninger's seven-factor model. This is the first study to describe the state effects of traumatic experiences on personality structure. PMID:23251200

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

Microorganisms are vital in mediating the earth's biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: 'When do we need to understand microbial community structure to accurately predict function?' We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.

Structural equation models to estimate risk of infection and tolerance to bovine mastitis.

PubMed

Detilleux, Johann; Theron, Léonard; Duprez, Jean-Noël; Reding, Edouard; Humblet, Marie-France; Planchon, Viviane; Delfosse, Camille; Bertozzi, Carlo; Mainil, Jacques; Hanzen, Christian

2013-03-06

One method to improve durably animal welfare is to select, as reproducers, animals with the highest ability to resist or tolerate infection. To do so, it is necessary to distinguish direct and indirect mechanisms of resistance and tolerance because selection on these traits is believed to have different epidemiological and evolutionary consequences. We propose structural equation models with latent variables (1) to quantify the latent risk of infection and to identify, among the many potential mediators of infection, the few ones that influence it significantly and (2) to estimate direct and indirect levels of tolerance of animals infected naturally with pathogens. We applied the method to two surveys of bovine mastitis in the Walloon region of Belgium, in which we recorded herd management practices, mastitis frequency, and results of bacteriological analyses of milk samples. Structural equation models suggested that, among more than 35 surveyed herd characteristics, only nine (age, addition of urea in the rations, treatment of subclinical mastitis, presence of dirty liner, cows with hyperkeratotic teats, machine stripping, pre- and post-milking teat disinfection, and housing of milking cows in cubicles) were directly and significantly related to a latent measure of bovine mastitis, and that treatment of subclinical mastitis was involved in the pathway between post-milking teat disinfection and latent mastitis. These models also allowed the separation of direct and indirect effects of bacterial infection on milk productivity. Results suggested that infected cows were tolerant but not resistant to mastitis pathogens. We revealed the advantages of structural equation models, compared to classical models, for dissecting measurements of resistance and tolerance to infectious diseases, here bovine mastitis. Using our method, we identified nine major risk factors that were directly associated with an increased risk of mastitis and suggested that cows were tolerant but not resistant to mastitis. Selection should aim at improved resistance to infection by mastitis pathogens, although further investigations are needed due to the limitations of the data used in this study.

Overarching framework for data-based modelling

NASA Astrophysics Data System (ADS)

Schelter, Björn; Mader, Malenka; Mader, Wolfgang; Sommerlade, Linda; Platt, Bettina; Lai, Ying-Cheng; Grebogi, Celso; Thiel, Marco

2014-02-01

One of the main modelling paradigms for complex physical systems are networks. When estimating the network structure from measured signals, typically several assumptions such as stationarity are made in the estimation process. Violating these assumptions renders standard analysis techniques fruitless. We here propose a framework to estimate the network structure from measurements of arbitrary non-linear, non-stationary, stochastic processes. To this end, we propose a rigorous mathematical theory that underlies this framework. Based on this theory, we present a highly efficient algorithm and the corresponding statistics that are immediately sensibly applicable to measured signals. We demonstrate its performance in a simulation study. In experiments of transitions between vigilance stages in rodents, we infer small network structures with complex, time-dependent interactions; this suggests biomarkers for such transitions, the key to understand and diagnose numerous diseases such as dementia. We argue that the suggested framework combines features that other approaches followed so far lack.

Recursive formulae and performance comparisons for first mode dynamics of periodic structures

NASA Astrophysics Data System (ADS)

Hobeck, Jared D.; Inman, Daniel J.

2017-05-01

Periodic structures are growing in popularity especially in the energy harvesting and metastructures communities. Common types of these unique structures are referred to in the literature as zigzag, orthogonal spiral, fan-folded, and longitudinal zigzag structures. Many of these studies on periodic structures have two competing goals in common: (a) minimizing natural frequency, and (b) minimizing mass or volume. These goals suggest that no single design is best for all applications; therefore, there is a need for design optimization and comparison tools which first require efficient easy-to-implement models. All available structural dynamics models for these types of structures do provide exact analytical solutions; however, they are complex requiring tedious implementation and providing more information than necessary for practical applications making them computationally inefficient. This paper presents experimentally validated recursive models that are able to very accurately and efficiently predict the dynamics of the four most common types of periodic structures. The proposed modeling technique employs a combination of static deflection formulae and Rayleigh’s Quotient to estimate the first mode shape and natural frequency of periodic structures having any number of beams. Also included in this paper are the results of an extensive experimental validation study which show excellent agreement between model prediction and measurement. Lastly, the proposed models are used to evaluate the performance of each type of structure. Results of this performance evaluation reveal key advantages and disadvantages associated with each type of structure.

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

2011-01-01

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott

2012-02-13

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF)more » CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.« less

Psychometric Properties of the “Sport Motivation Scale (SMS)” Adapted to Physical Education

PubMed Central

Granero-Gallegos, Antonio; Baena-Extremera, Antonio; Gómez-López, Manuel; Sánchez-Fuentes, José Antonio; Abraldes, J. Arturo

2014-01-01

The aim of this study was to investigate the factor structure of a Spanish version of the Sport Motivation Scale adapted to physical education. A second aim was to test which one of three hypothesized models (three, five and seven-factor) provided best model fit. 758 Spanish high school students completed the Sport Motivation Scale adapted for Physical Education and also completed the Learning and Performance Orientation in Physical Education Classes Questionnaire. We examined the factor structure of each model using confirmatory factor analysis and also assessed internal consistency and convergent validity. The results showed that all three models in Spanish produce good indicators of fitness, but we suggest using the seven-factor model (χ2/gl = 2.73; ECVI = 1.38) as it produces better values when adapted to physical education, that five-factor model (χ2/gl = 2.82; ECVI = 1.44) and three-factor model (χ2/gl = 3.02; ECVI = 1.53). Key Points Physical education research conducted in Spain has used the version of SMS designed to assess motivation in sport, but validity reliability and validity results in physical education have not been reported. Results of the present study lend support to the factorial validity and internal reliability of three alternative factor structures (3, 5, and 7 factors) of SMS adapted to Physical Education in Spanish. Although all three models in Spanish produce good indicators of fitness, but we suggest using the seven-factor model. PMID:25435772

QSAR, docking and ADMET studies of artemisinin derivatives for antimalarial activity targeting plasmepsin II, a hemoglobin-degrading enzyme from P. falciparum.

PubMed

Qidwai, Tabish; Yadav, Dharmendra K; Khan, Feroz; Dhawan, Sangeeta; Bhakuni, R S

2012-01-01

This work presents the development of quantitative structure activity relationship (QSAR) model to predict the antimalarial activity of artemisinin derivatives. The structures of the molecules are represented by chemical descriptors that encode topological, geometric, and electronic structure features. Screening through QSAR model suggested that compounds A24, A24a, A53, A54, A62 and A64 possess significant antimalarial activity. Linear model is developed by the multiple linear regression method to link structures to their reported antimalarial activity. The correlation in terms of regression coefficient (r(2)) was 0.90 and prediction accuracy of model in terms of cross validation regression coefficient (rCV(2)) was 0.82. This study indicates that chemical properties viz., atom count (all atoms), connectivity index (order 1, standard), ring count (all rings), shape index (basic kappa, order 2), and solvent accessibility surface area are well correlated with antimalarial activity. The docking study showed high binding affinity of predicted active compounds against antimalarial target Plasmepsins (Plm-II). Further studies for oral bioavailability, ADMET and toxicity risk assessment suggest that compound A24, A24a, A53, A54, A62 and A64 exhibits marked antimalarial activity comparable to standard antimalarial drugs. Later one of the predicted active compound A64 was chemically synthesized, structure elucidated by NMR and in vivo tested in multidrug resistant strain of Plasmodium yoelii nigeriensis infected mice. The experimental results obtained agreed well with the predicted values.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Unal, B.; Jenks, C.J.; Thiel, P.A.

From other work, two preferred sites have been suggested for metals and semimetals adsorbed on the fivefold surfaces of icosahedral, Al-based quasicrystals. Because of their appearance in scanning tunneling microscopy (STM) images, these sites are known as dark stars and white flowers. In this paper, we analyze four bulk structural models in physical space to determine the types, chemical decorations, and densities of the dark star - and, to a lesser extent, the white flower - adsorption sites for the fivefold planes of icosahedral Al-Pd-Mn. We find that the chemical decorations of these sites are heterogeneous, even within a singlemore » model. Both features are also structurally heterogeneous, according to STM measurements, and the structural variation is consistent with the bulk structure models. Finally, from the models, the density of dark stars in the planes correlates with the step height. This may explain previous experimental observations of different properties for different terraces.« less

An Extended Structure of the APOBEC3G Catalytic Domain Suggests a Unique Holoenzyme Model

PubMed Central

Harjes, Elena; Gross, Phillip J.; Chen, Kuan-Ming; Lu, Yongjian; Shindo, Keisuke; Nowarski, Roni; Gross, John D.; Kotler, Moshe; Harris, Reuben S.; Matsuo, Hiroshi

2009-01-01

Summary Human APOBEC3G (A3G) belongs to a family of polynucleotide cytidine deaminases. This family includes APOBEC1 and AID, which edit APOB mRNA and antibody gene DNA, respectively. A3G deaminates cytidines to uridines in single-strand DNA and inhibits the replication of HIV-1, other retroviruses and retrotransposons. Although the mechanism of A3G-catalyzed DNA deamination has been investigated genetically and biochemically, atomic details are just starting to emerge. Here, we compare the DNA cytidine deaminase activities and NMR structures of two A3G catalytic domain constructs. The longer A3G191-384 protein is considerably more active than the shorter A3G198-384 variant. The longer structure has an α1 helix (residues 201–206) that was not apparent in the shorter protein and it contributes to catalytic activity through interactions with hydrophobic core structures (β1, β3, α5 and α6). Both A3G catalytic domain solution structures have a discontinuous β2 region that is clearly different than the continuous β2 strand of another family member APOBEC2. In addition, the longer A3G191-384 structure revealed part of the N-terminal pseudo-catalytic domain including the inter-domain linker and some of the last α-helix. These structured residues (191–196) enabled a novel full-length A3G model by providing physical overlap between the N-terminal pseudo-catalytic domain and the new C-terminal catalytic domain structure. Contrary to predictions, this structurally constrained model suggested that the two domains are tethered by structured residues and that the N- and C-terminal β2 regions are too distant from one another to participate in this interaction. PMID:19389408

Modeling and molecular dynamics simulations of the V33 variant of the integrin subunit β3: Structural comparison with the L33 (HPA-1a) and P33 (HPA-1b) variants.

PubMed

Jallu, Vincent; Poulain, Pierre; Fuchs, Patrick F J; Kaplan, Cecile; de Brevern, Alexandre G

2014-10-01

The human platelet alloantigen (HPA)-1 system, the first cause of alloimmune thrombocytopenia in Caucasians, results from leucine-to-proline substitution (alleles 1a and 1b) of residue 33 in β3 subunit of the integrin αIIbβ3. A third variant with a valine (V33) has been described. Although leucine and valine share similar physicochemical properties, sera containing alloantibodies to the HPA-1a antigen variably reacted with V33-β3, suggesting structural alterations of β3. To analyze the effect of the L33V transition, molecular dynamics simulations were performed on a 3D structural model of the V33 form of the whole β3 extracellular domain (690 residues). Dynamics of the PSI (carrying residue 33), I-EGF-1, and I-EGF-2 domains of β3 were compared to previously obtained dynamics of HPA-1a structure and HPA-1b structural model using classical and innovative developments (a structural alphabet). Clustering approach and local structure analysis showed that L33-β3 and V33-β3 mostly share common structures co-existing in different dynamic equilibria. The L33V substitution mainly displaces the equilibrium between common structures. These observations can explain the variable reactivity of anti-HPA-1a alloantibodies suggesting that molecular dynamic plays a key role in the binding of these alloantibodies. Unlike the L33P substitution, the L33V transition would not affect the structure flexibility of the β3 knee, and consequently the functions of αIIbβ3. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Computational Prediction of the Heterodimeric and Higher-Order Structure of gpE1/gpE2 Envelope Glycoproteins Encoded by Hepatitis C Virus.

PubMed

Freedman, Holly; Logan, Michael R; Hockman, Darren; Koehler Leman, Julia; Law, John Lok Man; Houghton, Michael

2017-04-15

Despite the recent success of newly developed direct-acting antivirals against hepatitis C, the disease continues to be a global health threat due to the lack of diagnosis of most carriers and the high cost of treatment. The heterodimer formed by glycoproteins E1 and E2 within the hepatitis C virus (HCV) lipid envelope is a potential vaccine candidate and antiviral target. While the structure of E1/E2 has not yet been resolved, partial crystal structures of the E1 and E2 ectodomains have been determined. The unresolved parts of the structure are within the realm of what can be modeled with current computational modeling tools. Furthermore, a variety of additional experimental data is available to support computational predictions of E1/E2 structure, such as data from antibody binding studies, cryo-electron microscopy (cryo-EM), mutational analyses, peptide binding analysis, linker-scanning mutagenesis, and nuclear magnetic resonance (NMR) studies. In accordance with these rich experimental data, we have built an in silico model of the full-length E1/E2 heterodimer. Our model supports that E1/E2 assembles into a trimer, which was previously suggested from a study by Falson and coworkers (P. Falson, B. Bartosch, K. Alsaleh, B. A. Tews, A. Loquet, Y. Ciczora, L. Riva, C. Montigny, C. Montpellier, G. Duverlie, E. I. Pecheur, M. le Maire, F. L. Cosset, J. Dubuisson, and F. Penin, J. Virol. 89:10333-10346, 2015, https://doi.org/10.1128/JVI.00991-15). Size exclusion chromatography and Western blotting data obtained by using purified recombinant E1/E2 support our hypothesis. Our model suggests that during virus assembly, the trimer of E1/E2 may be further assembled into a pentamer, with 12 pentamers comprising a single HCV virion. We anticipate that this new model will provide a useful framework for HCV envelope structure and the development of antiviral strategies. IMPORTANCE One hundred fifty million people have been estimated to be infected with hepatitis C virus, and many more are at risk for infection. A better understanding of the structure of the HCV envelope, which is responsible for attachment and fusion, could aid in the development of a vaccine and/or new treatments for this disease. We draw upon computational techniques to predict a full-length model of the E1/E2 heterodimer based on the partial crystal structures of the envelope glycoproteins E1 and E2. E1/E2 has been widely studied experimentally, and this provides valuable data, which has assisted us in our modeling. Our proposed structure is used to suggest the organization of the HCV envelope. We also present new experimental data from size exclusion chromatography that support our computational prediction of a trimeric oligomeric state of E1/E2. Copyright © 2017 American Society for Microbiology.

Computational Prediction of the Heterodimeric and Higher-Order Structure of gpE1/gpE2 Envelope Glycoproteins Encoded by Hepatitis C Virus

PubMed Central

Logan, Michael R.; Hockman, Darren; Koehler Leman, Julia; Law, John Lok Man

2017-01-01

ABSTRACT Despite the recent success of newly developed direct-acting antivirals against hepatitis C, the disease continues to be a global health threat due to the lack of diagnosis of most carriers and the high cost of treatment. The heterodimer formed by glycoproteins E1 and E2 within the hepatitis C virus (HCV) lipid envelope is a potential vaccine candidate and antiviral target. While the structure of E1/E2 has not yet been resolved, partial crystal structures of the E1 and E2 ectodomains have been determined. The unresolved parts of the structure are within the realm of what can be modeled with current computational modeling tools. Furthermore, a variety of additional experimental data is available to support computational predictions of E1/E2 structure, such as data from antibody binding studies, cryo-electron microscopy (cryo-EM), mutational analyses, peptide binding analysis, linker-scanning mutagenesis, and nuclear magnetic resonance (NMR) studies. In accordance with these rich experimental data, we have built an in silico model of the full-length E1/E2 heterodimer. Our model supports that E1/E2 assembles into a trimer, which was previously suggested from a study by Falson and coworkers (P. Falson, B. Bartosch, K. Alsaleh, B. A. Tews, A. Loquet, Y. Ciczora, L. Riva, C. Montigny, C. Montpellier, G. Duverlie, E. I. Pecheur, M. le Maire, F. L. Cosset, J. Dubuisson, and F. Penin, J. Virol. 89:10333–10346, 2015, https://doi.org/10.1128/JVI.00991-15). Size exclusion chromatography and Western blotting data obtained by using purified recombinant E1/E2 support our hypothesis. Our model suggests that during virus assembly, the trimer of E1/E2 may be further assembled into a pentamer, with 12 pentamers comprising a single HCV virion. We anticipate that this new model will provide a useful framework for HCV envelope structure and the development of antiviral strategies. IMPORTANCE One hundred fifty million people have been estimated to be infected with hepatitis C virus, and many more are at risk for infection. A better understanding of the structure of the HCV envelope, which is responsible for attachment and fusion, could aid in the development of a vaccine and/or new treatments for this disease. We draw upon computational techniques to predict a full-length model of the E1/E2 heterodimer based on the partial crystal structures of the envelope glycoproteins E1 and E2. E1/E2 has been widely studied experimentally, and this provides valuable data, which has assisted us in our modeling. Our proposed structure is used to suggest the organization of the HCV envelope. We also present new experimental data from size exclusion chromatography that support our computational prediction of a trimeric oligomeric state of E1/E2. PMID:28148799

Nanoscale structure in AgSbTe2 determined by diffuse elastic neutron scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Specht, Eliot D; Ma, Jie; Delaire, Olivier A

2015-01-01

Diffuse elastic neutron scattering measurements confirm that AgSbTe2 has a hierarchical structure, with defects on length scales from nanometers to microns. While scattering from mesoscale structure is consistent with previously-proposed structures in which Ag and Sb order on a NaCl lattice, more diffuse scattering from nanoscale structure suggests a structural rearrangement in which hexagonal layers form a combination of (ABC), (ABA), and (AAB) stacking sequences. The AgCrSe2 structure is the best-fitting model for the local atomic arrangements.

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.

PubMed Central

Jeruzalmi, D; Steitz, T A

1998-01-01

The T7 RNA polymerase-T7 lysozyme complex regulates phage gene expression during infection of Escherichia coli. The 2.8 A crystal structure of the complex reveals that lysozyme binds at a site remote from the polymerase active site, suggesting an indirect mechanism of inhibition. Comparison of the T7 RNA polymerase structure with that of the homologous pol I family of DNA polymerases reveals identities in the catalytic site but also differences specific to RNA polymerase function. The structure of T7 RNA polymerase presented here differs significantly from a previously published structure. Sequence similarities between phage RNA polymerases and those from mitochondria and chloroplasts, when interpreted in the context of our revised model of T7 RNA polymerase, suggest a conserved fold. PMID:9670025

Accommodating Missing Data in Mixture Models for Classification by Opinion-Changing Behavior.

ERIC Educational Resources Information Center

Hill, Jennifer L.

2001-01-01

Explored the assumptions implicit in models reflecting three different approaches to missing survey response data using opinion data collected from Swiss citizens at four time points over nearly 2 years. Results suggest that the latently ignorable model has the least restrictive structural assumptions. Discusses the idea of "durable…

Pregnant Low-Income Teenagers: A Social Structural Model of the Determinants of Abortion-Seeking Behavior.

ERIC Educational Resources Information Center

Dworkin, Rosalind J.; Poindexter, Alfred N.

1980-01-01

Reviews literature on teenage abortion seekers. Suggests and tests a theoretical model designed to predict whether a low-income pregnant teenager will decide to abort or to deliver her baby. Concludes that age and socioemotional variables are the strongest predictive elements in the model. (GC)

Proportional Reasoning of Preservice Elementary Education Majors: An Epistemic Model of the Proportional Reasoning Construct.

ERIC Educational Resources Information Center

Fleener, M. Jayne

Current research and learning theory suggest that a hierarchy of proportional reasoning exists that can be tested. Using G. Vergnaud's four complexity variables (structure, content, numerical characteristics, and presentation) and T. E. Kieren's model of rational number knowledge building, an epistemic model of proportional reasoning was…

Damage evaluation of reinforced concrete frame based on a combined fiber beam model

NASA Astrophysics Data System (ADS)

Shang, Bing; Liu, ZhanLi; Zhuang, Zhuo

2014-04-01

In order to analyze and simulate the impact collapse or seismic response of the reinforced concrete (RC) structures, a combined fiber beam model is proposed by dividing the cross section of RC beam into concrete fiber and steel fiber. The stress-strain relationship of concrete fiber is based on a model proposed by concrete codes for concrete structures. The stress-strain behavior of steel fiber is based on a model suggested by others. These constitutive models are implemented into a general finite element program ABAQUS through the user defined subroutines to provide effective computational tools for the inelastic analysis of RC frame structures. The fiber model proposed in this paper is validated by comparing with experiment data of the RC column under cyclical lateral loading. The damage evolution of a three-dimension frame subjected to impact loading is also investigated.

Model selection and parameter estimation in structural dynamics using approximate Bayesian computation

NASA Astrophysics Data System (ADS)

Ben Abdessalem, Anis; Dervilis, Nikolaos; Wagg, David; Worden, Keith

2018-01-01

This paper will introduce the use of the approximate Bayesian computation (ABC) algorithm for model selection and parameter estimation in structural dynamics. ABC is a likelihood-free method typically used when the likelihood function is either intractable or cannot be approached in a closed form. To circumvent the evaluation of the likelihood function, simulation from a forward model is at the core of the ABC algorithm. The algorithm offers the possibility to use different metrics and summary statistics representative of the data to carry out Bayesian inference. The efficacy of the algorithm in structural dynamics is demonstrated through three different illustrative examples of nonlinear system identification: cubic and cubic-quintic models, the Bouc-Wen model and the Duffing oscillator. The obtained results suggest that ABC is a promising alternative to deal with model selection and parameter estimation issues, specifically for systems with complex behaviours.

Psychometric properties of the Intrinsic Motivation Inventory in a competitive sport setting: a confirmatory factor analysis.

PubMed

McAuley, E; Duncan, T; Tammen, V V

1989-03-01

The present study was designed to assess selected psychometric properties of the Intrinsic Motivation Inventory (IMI) (Ryan, 1982), a multidimensional measure of subjects' experience with regard to experimental tasks. Subjects (N = 116) competed in a basketball free-throw shooting game, following which they completed the IMI. The LISREL VI computer program was employed to conduct a confirmatory factor analysis to assess the tenability of a five factor hierarchical model representing four first-order factors or dimensions and a second-order general factor representing intrinsic motivation. Indices of model acceptability tentatively suggest that the sport data adequately fit the hypothesized five factor hierarchical model. Alternative models were tested but did not result in significant improvements in the goodness-of-fit indices, suggesting the proposed model to be the most accurate of the models tested. Coefficient alphas for the four dimensions and the overall scale indicated adequate reliability. The results are discussed with regard to the importance of accurate assessment of psychological constructs and the use of linear structural equations in confirming the factor structures of measures.

Factor Structure of the Psychopathic Personality Inventory (PPI): Findings from a Large Incarcerated Sample

PubMed Central

Neumann, Craig S.; Malterer, Melanie B.; Newman, Joseph P.

2010-01-01

Recent exploratory factor analysis (EFA) of the Psychopathic Personality Inventory (PPI; Lilienfeld, 1990) with a community sample suggested that the PPI subscales may be comprised of two higher-order factors (Benning et al., 2003). However, little research has examined the PPI structure in offenders. The current study attempted to replicate the Benning et al. two-factor solution using a large (N=1224) incarcerated male sample. Confirmatory factor analysis (CFA) of this model with the full sample resulted in poor model fit. Next, to identify a factor solution that would summarize the offender data, EFA was conducted using a split-half of the total sample, followed by an attempt to replicate the EFA solution via CFA with the other split-half sample. Using the recommendations of Prooijen and van der Kloot (2001) for recovering EFA solutions, model fit results provided some evidence that the EFA solution could be recovered via CFA. However, this model involved extensive cross-loadings of the subscales across three factors, suggesting item overlap across PPI subscales. In sum, the two-factor solution reported by Benning et al. (2003) was not a viable model for the current sample of offenders, and additional research is needed to elucidate the latent structure of the PPI. PMID:18557694

Evaluation of a model of violence risk assessment among forensic psychiatric patients.

PubMed

Douglas, Kevin S; Ogloff, James R P; Hart, Stephen D

2003-10-01

This study tested the interrater reliability and criterion-related validity of structured violence risk judgments made by using one application of the structured professional judgment model of violence risk assessment, the HCR-20 violence risk assessment scheme, which assesses 20 key risk factors in three domains: historical, clinical, and risk management. The HCR-20 was completed for a sample of 100 forensic psychiatric patients who had been found not guilty by reason of a mental disorder and were subsequently released to the community. Violence in the community was determined from multiple file-based sources. Interrater reliability of structured final risk judgments of low, moderate, or high violence risk made on the basis of the structured professional judgment model was acceptable (weighted kappa=.61). Structured final risk judgments were significantly predictive of postrelease community violence, yielding moderate to large effect sizes. Event history analyses showed that final risk judgments made with the structured professional judgment model added incremental validity to the HCR-20 used in an actuarial (numerical) sense. The findings support the structured professional judgment model of risk assessment as well as the HCR-20 specifically and suggest that clinical judgment, if made within a structured context, can contribute in meaningful ways to the assessment of violence risk.

Is Small Still Beautiful for the Strengths and Difficulties Questionnaire? Novel Findings Using Exploratory Structural Equation Modeling.

PubMed

Garrido, Luis Eduardo; Barrada, Juan Ramón; Aguasvivas, José Armando; Martínez-Molina, Agustín; Arias, Víctor B; Golino, Hudson F; Legaz, Eva; Ferrís, Gloria; Rojo-Moreno, Luis

2018-06-01

During the present decade a large body of research has employed confirmatory factor analysis (CFA) to evaluate the factor structure of the Strengths and Difficulties Questionnaire (SDQ) across multiple languages and cultures. However, because CFA can produce strongly biased estimations when the population cross-loadings differ meaningfully from zero, it may not be the most appropriate framework to model the SDQ responses. With this in mind, the current study sought to assess the factorial structure of the SDQ using the more flexible exploratory structural equation modeling approach. Using a large-scale Spanish sample composed of 67,253 youths aged between 10 and 18 years ( M = 14.16, SD = 1.07), the results showed that CFA provided a severely biased and overly optimistic assessment of the underlying structure of the SDQ. In contrast, exploratory structural equation modeling revealed a generally weak factorial structure, including questionable indicators with large cross-loadings, multiple error correlations, and significant wording variance. A subsequent Monte Carlo study showed that sample sizes greater than 4,000 would be needed to adequately recover the SDQ loading structure. The findings from this study prevent recommending the SDQ as a screening tool and suggest caution when interpreting previous results in the literature based on CFA modeling.

A Structural Model Proposal for Turkish Faculties of Education Regarding ICT Integration Indicators

ERIC Educational Resources Information Center

Akbulut, Yavuz

2010-01-01

A recent survey study with 2515 pre-service teachers suggested an underlying structure to shelter ICT integration indicators. Eleven indicators were extracted, which were Teaching-Learning Methods, E-learning, E-interaction, Learning Communities, Infrastructure, Access, Ease of Use, Technical Assistance, Policy, Special Education and Health. In…

Using iMCFA to Perform the CFA, Multilevel CFA, and Maximum Model for Analyzing Complex Survey Data.

PubMed

Wu, Jiun-Yu; Lee, Yuan-Hsuan; Lin, John J H

2018-01-01

To construct CFA, MCFA, and maximum MCFA with LISREL v.8 and below, we provide iMCFA (integrated Multilevel Confirmatory Analysis) to examine the potential multilevel factorial structure in the complex survey data. Modeling multilevel structure for complex survey data is complicated because building a multilevel model is not an infallible statistical strategy unless the hypothesized model is close to the real data structure. Methodologists have suggested using different modeling techniques to investigate potential multilevel structure of survey data. Using iMCFA, researchers can visually set the between- and within-level factorial structure to fit MCFA, CFA and/or MAX MCFA models for complex survey data. iMCFA can then yield between- and within-level variance-covariance matrices, calculate intraclass correlations, perform the analyses and generate the outputs for respective models. The summary of the analytical outputs from LISREL is gathered and tabulated for further model comparison and interpretation. iMCFA also provides LISREL syntax of different models for researchers' future use. An empirical and a simulated multilevel dataset with complex and simple structures in the within or between level was used to illustrate the usability and the effectiveness of the iMCFA procedure on analyzing complex survey data. The analytic results of iMCFA using Muthen's limited information estimator were compared with those of Mplus using Full Information Maximum Likelihood regarding the effectiveness of different estimation methods.

Irreducible Uncertainty in Terrestrial Carbon Projections

NASA Astrophysics Data System (ADS)

Lovenduski, N. S.; Bonan, G. B.

2016-12-01

We quantify and isolate the sources of uncertainty in projections of carbon accumulation by the ocean and terrestrial biosphere over 2006-2100 using output from Earth System Models participating in the 5th Coupled Model Intercomparison Project. We consider three independent sources of uncertainty in our analysis of variance: (1) internal variability, driven by random, internal variations in the climate system, (2) emission scenario, driven by uncertainty in future radiative forcing, and (3) model structure, wherein different models produce different projections given the same emission scenario. Whereas uncertainty in projections of ocean carbon accumulation by 2100 is 100 Pg C and driven primarily by emission scenario, uncertainty in projections of terrestrial carbon accumulation by 2100 is 50% larger than that of the ocean, and driven primarily by model structure. This structural uncertainty is correlated with emission scenario: the variance associated with model structure is an order of magnitude larger under a business-as-usual scenario (RCP8.5) than a mitigation scenario (RCP2.6). In an effort to reduce this structural uncertainty, we apply various model weighting schemes to our analysis of variance in terrestrial carbon accumulation projections. The largest reductions in uncertainty are achieved when giving all the weight to a single model; here the uncertainty is of a similar magnitude to the ocean projections. Such an analysis suggests that this structural uncertainty is irreducible given current terrestrial model development efforts.

Structural basis of respiratory syncytial virus neutralization by motavizumab

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLellan, Jason S.; Chen, Man; Kim, Albert

2010-04-13

Motavizumab is {approx}tenfold more potent than its predecessor, palivizumab (Synagis), the FDA-approved monoclonal antibody used to prevent respiratory syncytial virus (RSV) infection. The structure of motavizumab in complex with a 24-residue peptide corresponding to its epitope on the RSV fusion (F) glycoprotein reveals the structural basis for this greater potency. Modeling suggests that motavizumab recognizes a different quaternary configuration of the F glycoprotein than that observed in a homologous structure.

Performance Evaluation and Improvement of Ferroelectric Field-Effect Transistor Memory

NASA Astrophysics Data System (ADS)

Yu, Hyung Suk

Flash memory is reaching scaling limitations rapidly due to reduction of charge in floating gates, charge leakage and capacitive coupling between cells which cause threshold voltage fluctuations, short retention times, and interference. Many new memory technologies are being considered as alternatives to flash memory in an effort to overcome these limitations. Ferroelectric Field-Effect Transistor (FeFET) is one of the main emerging candidates because of its structural similarity to conventional FETs and fast switching speed. Nevertheless, the performance of FeFETs have not been systematically compared and analyzed against other competing technologies. In this work, we first benchmark the intrinsic performance of FeFETs and other memories by simulations in order to identify the strengths and weaknesses of FeFETs. To simulate realistic memory applications, we compare memories on an array structure. For the comparisons, we construct an accurate delay model and verify it by benchmarking against exact HSPICE simulations. Second, we propose an accurate model for FeFET memory window since the existing model has limitations. The existing model assumes symmetric operation voltages but it is not valid for the practical asymmetric operation voltages. In this modeling, we consider practical operation voltages and device dimensions. Also, we investigate realistic changes of memory window over time and retention time of FeFETs. Last, to improve memory window and subthreshold swing, we suggest nonplanar junctionless structures for FeFETs. Using the suggested structures, we study the dimensional dependences of crucial parameters like memory window and subthreshold swing and also analyze key interference mechanisms.

Packaging double-helical DNA into viral capsids.

PubMed

LaMarque, Jaclyn C; Le, Thuc-Vy L; Harvey, Stephen C

2004-02-15

DNA packaging in bacteriophage P4 has been examined using a molecular mechanics model with a reduced representation containing one pseudoatom per turn of the double helix. The model is a discretized version of an elastic continuum model. The DNA is inserted piecewise into the model capsid, with the structure being reoptimized after each piece is inserted. Various optimization protocols were investigated, and it was found that molecular dynamics at a very low temperature (0.3 K) produces the optimal packaged structure. This structure is a concentric spool, rather than the coaxial spool that has been commonly accepted for so many years. This geometry, which was originally suggested by Hall and Schellman in 1982 (Biopolymers Vol. 21, pp. 2011-2031), produces a lower overall elastic energy than coaxial spooling. Copyright 2003 Wiley Periodicals, Inc.

Linking Structural Equation Modelling with Bayesian Network and Coastal Phytoplankton Dynamics in Bohai Bay

NASA Astrophysics Data System (ADS)

Chu, Jiangtao; Yang, Yue

2018-06-01

Bayesian networks (BN) have many advantages over other methods in ecological modelling and have become an increasingly popular modelling tool. However, BN are flawed in regard to building models based on inadequate existing knowledge. To overcome this limitation, we propose a new method that links BN with structural equation modelling (SEM). In this method, SEM is used to improve the model structure for BN. This method was used to simulate coastal phytoplankton dynamics in Bohai Bay. We demonstrate that this hybrid approach minimizes the need for expert elicitation, generates more reasonable structures for BN models and increases the BN model's accuracy and reliability. These results suggest that the inclusion of SEM for testing and verifying the theoretical structure during the initial construction stage improves the effectiveness of BN models, especially for complex eco-environment systems. The results also demonstrate that in Bohai Bay, while phytoplankton biomass has the greatest influence on phytoplankton dynamics, the impact of nutrients on phytoplankton dynamics is larger than the influence of the physical environment in summer. Furthermore, despite the Redfield ratio indicating that phosphorus should be the primary nutrient limiting factor, our results indicate that silicate plays the most important role in regulating phytoplankton dynamics in Bohai Bay.

Refinement of protein termini in template-based modeling using conformational space annealing.

PubMed

Park, Hahnbeom; Ko, Junsu; Joo, Keehyoung; Lee, Julian; Seok, Chaok; Lee, Jooyoung

2011-09-01

The rapid increase in the number of experimentally determined protein structures in recent years enables us to obtain more reliable protein tertiary structure models than ever by template-based modeling. However, refinement of template-based models beyond the limit available from the best templates is still needed for understanding protein function in atomic detail. In this work, we develop a new method for protein terminus modeling that can be applied to refinement of models with unreliable terminus structures. The energy function for terminus modeling consists of both physics-based and knowledge-based potential terms with carefully optimized relative weights. Effective sampling of both the framework and terminus is performed using the conformational space annealing technique. This method has been tested on a set of termini derived from a nonredundant structure database and two sets of termini from the CASP8 targets. The performance of the terminus modeling method is significantly improved over our previous method that does not employ terminus refinement. It is also comparable or superior to the best server methods tested in CASP8. The success of the current approach suggests that similar strategy may be applied to other types of refinement problems such as loop modeling or secondary structure rearrangement. Copyright © 2011 Wiley-Liss, Inc.

Biophysical and structural considerations for protein sequence evolution

PubMed Central

2011-01-01

Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550

A systematic literature review of PTSD's latent structure in the Diagnostic and Statistical Manual of Mental Disorders: DSM-IV to DSM-5.

PubMed

Armour, Cherie; Műllerová, Jana; Elhai, Jon D

2016-03-01

The factor structure of posttraumatic stress disorder (PTSD) has been widely researched, but consensus regarding the exact number and nature of factors is yet to be reached. The aim of the current study was to systematically review the extant literature on PTSD's latent structure in the Diagnostic and Statistical Manual of Mental Disorders (DSM) in order to identify the best-fitting model. One hundred and twelve research papers published after 1994 using confirmatory factor analysis and DSM-based measures of PTSD were included in the review. In the DSM-IV literature, four-factor models received substantial support, but the five-factor Dysphoric arousal model demonstrated the best fit, regardless of gender, measurement instrument or trauma type. The recently proposed DSM-5 PTSD model was found to be a good representation of PTSD's latent structure, but studies analysing the six- and seven-factor models suggest that the DSM-5 PTSD factor structure may need further alterations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structure of AA5056 after friction drilling

NASA Astrophysics Data System (ADS)

Eliseev, A. A.; Kalashnikova, T. A.; Fortuna, S. V.

2017-12-01

Here we present data on the structure of AA5056 alloy after friction drilling to unveil potentials of the process for use in model experiments on friction stir welding. Our analysis of the average size and volume content of precipitates shows that their content decreases immediately beneath the friction surface and that the structure of this zone is the same as the structure of stirring zones formed in friction stir welding. The data suggest that both processes provide similar metal structures.

Modeling the Elastic and Damping Properties of the Multilayered Torsion Bar-Blade Structure of Rotors of Light Helicopters of the New Generation. 1. Finite-Element Approximation of the Torsion Bar

NASA Astrophysics Data System (ADS)

Paimushin, V. N.; Shishkin, V. M.

2015-11-01

A prismatic semiquadratic element with a nonclassical approximation of its displacements is suggested for modeling the composite and soft layers of a torsion bar and multilayered plate-rod structures. The stiffness, weight, damping, and geometric stiffness matrices of the above-mentioned element are obtained. Expressions for computing stresses in the finite element under the action of static loads and vibrations in the resonance zone are presented. Test examples confirming the validity of the element suggested are given. An example of finite element determination of the dynamic response of a multilayered torsion bar in the resonant mode is considered.

Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II.

PubMed

Sproviero, Eduardo M; Gascón, José A; McEvoy, James P; Brudvig, Gary W; Batista, Victor S

2007-04-01

The annual production of 260 Gtonnes of oxygen, during the process of photosynthesis, sustains life on earth. Oxygen is produced in the thylakoid membranes of green-plant chloroplasts and the internal membranes of cyanobacteria by photocatalytic water oxidation at the oxygen-evolving complex (OEC) of photosystem II (PSII). Recent breakthroughs in X-ray crystallography and advances in quantum mechanics/molecular mechanics (QM/MM) hybrid methods have enabled the construction of chemically sensible models of the OEC of PSII. The resulting computational structural models suggest the complete ligation of the catalytic center by amino acid residues, water, hydroxide and chloride, as determined from the intrinsic electronic properties of the oxomanganese core and the perturbational influence of the surrounding protein environment. These structures are found to be consistent with available mechanistic data, and are also compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements. It is therefore conjectured that these OEC models are particularly relevant for the elucidation of the catalytic mechanism of water oxidation.

Discrete particle model for cement infiltration within open-cell structures: Prevention of osteoporotic fracture.

PubMed

Ramos-Infante, Samuel Jesús; Ten-Esteve, Amadeo; Alberich-Bayarri, Angel; Pérez, María Angeles

2018-01-01

This paper proposes a discrete particle model based on the random-walk theory for simulating cement infiltration within open-cell structures to prevent osteoporotic proximal femur fractures. Model parameters consider the cement viscosity (high and low) and the desired direction of injection (vertical and diagonal). In vitro and in silico characterizations of augmented open-cell structures validated the computational model and quantified the improved mechanical properties (Young's modulus) of the augmented specimens. The cement injection pattern was successfully predicted in all the simulated cases. All the augmented specimens exhibited enhanced mechanical properties computationally and experimentally (maximum improvements of 237.95 ± 12.91% and 246.85 ± 35.57%, respectively). The open-cell structures with high porosity fraction showed a considerable increase in mechanical properties. Cement augmentation in low porosity fraction specimens resulted in a lesser increase in mechanical properties. The results suggest that the proposed discrete particle model is adequate for use as a femoroplasty planning framework.

Variability in Rock Thermal Properties in the Late Archean Crust of the Kapuskasing Structural Zone and Implications for its Thermal Structure and Metamorphic History.

NASA Astrophysics Data System (ADS)

Merriman, J. D.; Whittington, A. G.; Hofmeister, A. M.

2017-12-01

The thermal properties of rocks such as internal heat production and thermal diffusivity (α) play a key role in determining the thermal structure of the lithosphere, and consequently, the rates and styles of metamorphism within the crust. Over the last decade, measurements of α using the method laser flash analysis have shown the ability of a rock to conduct heat can vary by as much as a factor of 5 between common rock types, and decrease by up to a factor of 10 for the same rock between 25-1000°C. Here we present a preliminary model for the variability in rock throughout the crust based on measurements of the α of a suite of 100 samples from late Archean crust exposed in and around the Kapuskasing Structural Zone in Ontario, Canada. Preliminary results suggest that α is controlled primarily by mineralogy, and can vary not only between different rock types as described above, but also within the same rock by a factor of 1.5 (or more). Thermal diffusivity results were combined with heat producing element concentrations measured with ICP-MS to create a thermal model of the Kapuskasing Structural Zone prior its uplift and exposure. To provide additional constraints for P-T conditions within the pre-uplift KSZ crust, a combination of trace-element and pseudosection thermobarometry was used to estimate metamorphic temperatures during an extended period of crustal stability at the end of the Archean. Preliminary results were compared to finite-difference numerical models of the steady-state geothermal gradient using heat production back-calculated to 2.6 Ga. Results suggest a minimum thickness of the continental lithosphere during the late Archean of at least 150 km. To test the response of the crust to the effects of large thermal events such as pluton emplacement, we also performed time-dependent models of the thermal structure of the pre-uplift KSZ crust. These models suggest that heat from thermal events in the upper and middle crust result in a more insulating crust, which causes heat to be retained in the lower crust for 10s of millions of years after the thermal event has ceased. Thus, metamorphic temperatures preserved in granulites are likely higher than steady-state, suggesting that lithospheric thickness at the end of the Archean for this region was considerably more than 150 km.

Factors influencing protein tyrosine nitration--structure-based predictive models.

PubMed

Bayden, Alexander S; Yakovlev, Vasily A; Graves, Paul R; Mikkelsen, Ross B; Kellogg, Glen E

2011-03-15

Models for exploring tyrosine nitration in proteins have been created based on 3D structural features of 20 proteins for which high-resolution X-ray crystallographic or NMR data are available and for which nitration of 35 total tyrosines has been experimentally proven under oxidative stress. Factors suggested in previous work to enhance nitration were examined with quantitative structural descriptors. The role of neighboring acidic and basic residues is complex: for the majority of tyrosines that are nitrated the distance to the heteroatom of the closest charged side chain corresponds to the distance needed for suspected nitrating species to form hydrogen bond bridges between the tyrosine and that charged amino acid. This suggests that such bridges play a very important role in tyrosine nitration. Nitration is generally hindered for tyrosines that are buried and for those tyrosines for which there is insufficient space for the nitro group. For in vitro nitration, closed environments with nearby heteroatoms or unsaturated centers that can stabilize radicals are somewhat favored. Four quantitative structure-based models, depending on the conditions of nitration, have been developed for predicting site-specific tyrosine nitration. The best model, relevant for both in vitro and in vivo cases, predicts 30 of 35 tyrosine nitrations (positive predictive value) and has a sensitivity of 60/71 (11 false positives). Copyright © 2010 Elsevier Inc. All rights reserved.

Investigation of secondary school, undergraduate, and graduate learners' mental models of ionic bonding

NASA Astrophysics Data System (ADS)

Coll, Richard K.; Treagust, David F.

2003-05-01

Secondary school, undergraduate, and graduate level learners' mental models of bonding in ionic substances were explored using an interview protocol that involved the use of physical substances and a focus card containing depictions of ionic bonding and structure. Teachers and faculty from the teaching institutions were interviewed to contextualize teaching models within the educational setting for the inquiry. These data resulted in two socially negotiated consensus teaching models and a series of criterial attributes for these models: the essential qualities, all of which must be negotiated, if the model is used in a way that is acceptable to scientists. The secondary school learners see ionic bonding as consisting of attraction of oppositely charged species that arise from the transfer of electrons driven by the desire of atoms to obtain an octet of electrons. The undergraduates see the lattice structure as a key component of ionic substances and quickly identified specific ionic lattices for the physical prompts used as probes. The graduates also identified strongly with ionic lattices, were less likely to focus on particular ionic structures, and had a stronger appreciation for the notion of the ionic-covalent continuum. The research findings suggest that learners at all educational levels harbor a number of alternative conceptions and prefer to use simple mental models. These findings suggest that teachers and university faculty need to provide stronger links between the detailed nature of a model and its intended purpose.

[Dimensional structure of the Brazilian version of the Scale of Satisfaction with Interpersonal Processes of General Medical Care].

PubMed

Nascimento, Maria Isabel do; Reichenheim, Michael Eduardo; Monteiro, Gina Torres Rego

2011-12-01

The objective of this study was to reassess the dimensional structure of a Brazilian version of the Scale of Satisfaction with Interpersonal Processes of General Medical Care, proposed originally as a one-dimensional instrument. Strict confirmatory factor analysis (CFA) and exploratory factor analysis modeled within a CFA framework (E/CFA) were used to identify the best model. An initial CFA rejected the one-dimensional structure, while an E/CFA suggested a two-dimensional structure. The latter structure was followed by a new CFA, which showed that the model without cross-loading was the most parsimonious, with adequate fit indices (CFI = 0.982 and TLI = 0.988), except for RMSEA (0.062). Although the model achieved convergent validity, discriminant validity was questionable, with the square-root of the mean variance extracted from dimension 1 estimates falling below the respective factor correlation. According to these results, there is not sufficient evidence to recommend the immediate use of the instrument, and further studies are needed for a more in-depth analysis of the postulated structures.

The introspective may achieve more: Enhancing existing Geoscientific models with native-language emulated structural reflection

NASA Astrophysics Data System (ADS)

Ji, Xinye; Shen, Chaopeng

2018-01-01

Geoscientific models manage myriad and increasingly complex data structures as trans-disciplinary models are integrated. They often incur significant redundancy with cross-cutting tasks. Reflection, the ability of a program to inspect and modify its structure and behavior at runtime, is known as a powerful tool to improve code reusability, abstraction, and separation of concerns. Reflection is rarely adopted in high-performance Geoscientific models, especially with Fortran, where it was previously deemed implausible. Practical constraints of language and legacy often limit us to feather-weight, native-language solutions. We demonstrate the usefulness of a structural-reflection-emulating, dynamically-linked metaObjects, gd. We show real-world examples including data structure self-assembly, effortless input/output (IO) and upgrade to parallel I/O, recursive actions and batch operations. We share gd and a derived module that reproduces MATLAB-like structure in Fortran and C++. We suggest that both a gd representation and a Fortran-native representation are maintained to access the data, each for separate purposes. Embracing emulated reflection allows generically-written codes that are highly re-usable across projects.

Independent and cooperative motions of the Kv1.2 channel: voltage sensing and gating.

PubMed

Yeheskel, Adva; Haliloglu, Turkan; Ben-Tal, Nir

2010-05-19

Voltage-gated potassium (Kv) channels, such as Kv1.2, are involved in the generation and propagation of action potentials. The Kv channel is a homotetramer, and each monomer is composed of a voltage-sensing domain (VSD) and a pore domain (PD). We analyzed the fluctuations of a model structure of Kv1.2 using elastic network models. The analysis suggested a network of coupled fluctuations of eight rigid structural units and seven hinges that may control the transition between the active and inactive states of the channel. For the most part, the network is composed of amino acids that are known to affect channel activity. The results suggested allosteric interactions and cooperativity between the subunits in the coupling between the motion of the VSD and the selectivity filter of the PD, in accordance with recent empirical data. There are no direct contacts between the VSDs of the four subunits, and the contacts between these and the PDs are loose, suggesting that the VSDs are capable of functioning independently. Indeed, they manifest many inherent fluctuations that are decoupled from the rest of the structure. In general, the analysis suggests that the two domains contribute to the channel function both individually and cooperatively. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Investigating melting induced mantle heterogeneities in plate driven mantle convection models

NASA Astrophysics Data System (ADS)

Price, M.; Davies, H.; Panton, J.

2017-12-01

Observations from geochemistry and seismology continue to suggest a range of complex heterogeneity in Earth's mantle. In the deep mantle, two large low velocity provinces (LLVPs) have been regularly observed in seismic studies, with their longevity, composition and density compared to the surrounding mantle debated. The cause of these observed LLVPs is equally uncertain, with previous studies advocating either thermal or thermo-chemical causes. There is also evidence that these structures could provide chemically distinct reservoirs within the mantle, with recent studies also suggesting there may be additional reservoirs in the mantle, such as bridgmanite-enriched ancient mantle structures (BEAMS). One way to test these hypotheses is using computational models of the mantle, with models that capture the full 3D system being both complex and computationally expensive. Here we present results from our global mantle model TERRA. Using our model, we can track compositional variations in the convecting mantle that are generated by self-consistent, evolving melting zones. Alongside the melting, we track trace elements and other volatiles which can be partitioned during melting events, and expelled and recycled at the surface. Utilising plate reconstruction models as a boundary condition, the models generate the tectonic features observed at Earth's surface, while also organising the lower mantle into recognisable degree-two structures. This results in our models generating basaltic `oceanic' crusts which are then brought into the mantle at tectonic boundaries, providing additional chemical heterogeneity in the mantle volume. Finally, by utilising thermodynamic lookup tables to convert the final outputs from the model to seismic structures, together with resolution filters for global tomography models, we are able to make direct comparisons between our results and observations. By varying the parameters of the model, we investigate a range of current hypotheses for heterogeneity in the mantle. Our work attempts to reconcile the many proposed current ideas for the deep mantle, giving additional insight from modelling on the latest observations from other Deep Earth disciplines.

Ultra-structural time-course study in the C. elegans model for Duchenne muscular dystrophy highlights a crucial role for sarcomere-anchoring structures and sarcolemma integrity in the earliest steps of the muscle degeneration process.

PubMed

Brouilly, Nicolas; Lecroisey, Claire; Martin, Edwige; Pierson, Laura; Mariol, Marie-Christine; Qadota, Hiroshi; Labouesse, Michel; Streichenberger, Nathalie; Mounier, Nicole; Gieseler, Kathrin

2015-11-15

Duchenne muscular dystrophy (DMD) is a genetic disease characterized by progressive muscle degeneration due to mutations in the dystrophin gene. In spite of great advances in the design of curative treatments, most patients currently receive palliative therapies with steroid molecules such as prednisone or deflazacort thought to act through their immunosuppressive properties. These molecules only slightly slow down the progression of the disease and lead to severe side effects. Fundamental research is still needed to reveal the mechanisms involved in the disease that could be exploited as therapeutic targets. By studying a Caenorhabditis elegans model for DMD, we show here that dystrophin-dependent muscle degeneration is likely to be cell autonomous and affects the muscle cells the most involved in locomotion. We demonstrate that muscle degeneration is dependent on exercise and force production. Exhaustive studies by electron microscopy allowed establishing for the first time the chronology of subcellular events occurring during the entire process of muscle degeneration. This chronology highlighted the crucial role for dystrophin in stabilizing sarcomeric anchoring structures and the sarcolemma. Our results suggest that the disruption of sarcomeric anchoring structures and sarcolemma integrity, observed at the onset of the muscle degeneration process, triggers subcellular consequences that lead to muscle cell death. An ultra-structural analysis of muscle biopsies from DMD patients suggested that the chronology of subcellular events established in C. elegans models the pathogenesis in human. Finally, we found that the loss of sarcolemma integrity was greatly reduced after prednisone treatment suggesting a role for this molecule in plasma membrane stabilization. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Structural model of dodecameric heat-shock protein Hsp21: Flexible N-terminal arms interact with client proteins while C-terminal tails maintain the dodecamer and chaperone activity.

PubMed

Rutsdottir, Gudrun; Härmark, Johan; Weide, Yoran; Hebert, Hans; Rasmussen, Morten I; Wernersson, Sven; Respondek, Michal; Akke, Mikael; Højrup, Peter; Koeck, Philip J B; Söderberg, Christopher A G; Emanuelsson, Cecilia

2017-05-12

Small heat-shock proteins (sHsps) prevent aggregation of thermosensitive client proteins in a first line of defense against cellular stress. The mechanisms by which they perform this function have been hard to define due to limited structural information; currently, there is only one high-resolution structure of a plant sHsp published, that of the cytosolic Hsp16.9. We took interest in Hsp21, a chloroplast-localized sHsp crucial for plant stress resistance, which has even longer N-terminal arms than Hsp16.9, with a functionally important and conserved methionine-rich motif. To provide a framework for investigating structure-function relationships of Hsp21 and understanding these sequence variations, we developed a structural model of Hsp21 based on homology modeling, cryo-EM, cross-linking mass spectrometry, NMR, and small-angle X-ray scattering. Our data suggest a dodecameric arrangement of two trimer-of-dimer discs stabilized by the C-terminal tails, possibly through tail-to-tail interactions between the discs, mediated through extended I X V X I motifs. Our model further suggests that six N-terminal arms are located on the outside of the dodecamer, accessible for interaction with client proteins, and distinct from previous undefined or inwardly facing arms. To test the importance of the I X V X I motif, we created the point mutant V181A, which, as expected, disrupts the Hsp21 dodecamer and decreases chaperone activity. Finally, our data emphasize that sHsp chaperone efficiency depends on oligomerization and that client interactions can occur both with and without oligomer dissociation. These results provide a generalizable workflow to explore sHsps, expand our understanding of sHsp structural motifs, and provide a testable Hsp21 structure model to inform future investigations. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Preliminary results on the dynamics of large and flexible space structures in Halo orbits

NASA Astrophysics Data System (ADS)

Colagrossi, Andrea; Lavagna, Michèle

2017-05-01

The global exploration roadmap suggests, among other ambitious future space programmes, a possible manned outpost in lunar vicinity, to support surface operations and further astronaut training for longer and deeper space missions and transfers. In particular, a Lagrangian point orbit location - in the Earth- Moon system - is suggested for a manned cis-lunar infrastructure; proposal which opens an interesting field of study from the astrodynamics perspective. Literature offers a wide set of scientific research done on orbital dynamics under the Three-Body Problem modelling approach, while less of it includes the attitude dynamics modelling as well. However, whenever a large space structure (ISS-like) is considered, not only the coupled orbit-attitude dynamics should be modelled to run more accurate analyses, but the structural flexibility should be included too. The paper, starting from the well-known Circular Restricted Three-Body Problem formulation, presents some preliminary results obtained by adding a coupled orbit-attitude dynamical model and the effects due to the large structure flexibility. In addition, the most relevant perturbing phenomena, such as the Solar Radiation Pressure (SRP) and the fourth-body (Sun) gravity, are included in the model as well. A multi-body approach has been preferred to represent possible configurations of the large cis-lunar infrastructure: interconnected simple structural elements - such as beams, rods or lumped masses linked by springs - build up the space segment. To better investigate the relevance of the flexibility effects, the lumped parameters approach is compared with a distributed parameters semi-analytical technique. A sensitivity analysis of system dynamics, with respect to different configurations and mechanical properties of the extended structure, is also presented, in order to highlight drivers for the lunar outpost design. Furthermore, a case study for a large and flexible space structure in Halo orbits around one of the Earth-Moon collinear Lagrangian points, L1 or L2, is discussed to point out some relevant outcomes for the potential implementation of such a mission.

The relationship between leadership, teamworking, structure, burnout and attitude to patients on acute psychiatric wards

PubMed Central

Nijman, Henk; Simpson, Alan; Jones, Julia

2010-01-01

Background Conflict (aggression, substance use, absconding, etc.) and containment (coerced medication, manual restraint, etc.) threaten the safety of patients and staff on psychiatric wards. Previous work has suggested that staff variables may be significant in explaining differences between wards in their rates of these behaviours, and that structure (ward organisation, rules and daily routines) might be the most critical of these. This paper describes the exploration of a large dataset to assess the relationship between structure and other staff variables. Methods A multivariate cross-sectional design was utilised. Data were collected from staff on 136 acute psychiatric wards in 26 NHS Trusts in England, measuring leadership, teamwork, structure, burnout and attitudes towards difficult patients. Relationships between these variables were explored through principal components analysis (PCA), structural equation modelling and cluster analysis. Results Principal components analysis resulted in the identification of each questionnaire as a separate factor, indicating that the selected instruments assessed a number of non-overlapping items relevant for ward functioning. Structural equation modelling suggested a linear model in which leadership influenced teamwork, teamwork structure; structure burnout; and burnout feelings about difficult patients. Finally, cluster analysis identified two significantly distinct groups of wards: the larger of which had particularly good leadership, teamwork, structure, attitudes towards patients and low burnout; and the second smaller proportion which was poor on all variables and high on burnout. The better functioning cluster of wards had significantly lower rates of containment events. Conclusion The overall performance of staff teams is associated with differing rates of containment on wards. Interventions to reduce rates of containment on wards may need to address staff issues at every level, from leadership through to staff attitudes. PMID:20082064

Why the Major Field Test in Business Does Not Report Subscores: Reliability and Construct Validity Evidence. Research Report. ETS RR-12-11

ERIC Educational Resources Information Center

Ling, Guangming

2012-01-01

To assess the value of individual students' subscores on the Major Field Test in Business (MFT Business), I examined the test's internal structure with factor analysis and structural equation model methods, and analyzed the subscore reliabilities using the augmented scores method. Analyses of the internal structure suggested that the MFT Business…

REVIEWS OF TOPICAL PROBLEMS: Nonlinear dynamics of the brain: emotion and cognition

NASA Astrophysics Data System (ADS)

Rabinovich, Mikhail I.; Muezzinoglu, M. K.

2010-07-01

Experimental investigations of neural system functioning and brain activity are standardly based on the assumption that perceptions, emotions, and cognitive functions can be understood by analyzing steady-state neural processes and static tomographic snapshots. The new approaches discussed in this review are based on the analysis of transient processes and metastable states. Transient dynamics is characterized by two basic properties, structural stability and information sensitivity. The ideas and methods that we discuss provide an explanation for the occurrence of and successive transitions between metastable states observed in experiments, and offer new approaches to behavior analysis. Models of the emotional and cognitive functions of the brain are suggested. The mathematical object that represents the observed transient brain processes in the phase space of the model is a structurally stable heteroclinic channel. The possibility of using the suggested models to construct a quantitative theory of some emotional and cognitive functions is illustrated.

Diel habitat selection of largemouth bass following woody structure installation in Table Rock Lake, Missouri

USGS Publications Warehouse

Harris, J.M.; Paukert, Craig P.; Bush, S.C.; Allen, M.J.; Siepker, Michael

2018-01-01

Largemouth bass Micropterus salmoides (Lacepède) use of installed habitat structure was evaluated in a large Midwestern USA reservoir to determine whether or not these structures were used in similar proportion to natural habitats. Seventy largemouth bass (>380 mm total length) were surgically implanted with radio transmitters and a subset was relocated monthly during day and night for one year. The top habitat selection models (based on Akaike's information criterion) suggest largemouth bass select 2–4 m depths during night and 4–7 m during day, whereas littoral structure selection was similar across diel periods. Largemouth bass selected boat docks at twice the rate of other structures. Installed woody structure was selected at similar rates to naturally occurring complex woody structure, whereas both were selected at a higher rate than simple woody structure. The results suggest the addition of woody structure may concentrate largemouth bass and mitigate the loss of woody habitat in a large reservoir.

Complex networks untangle competitive advantage in Australian football

NASA Astrophysics Data System (ADS)

Braham, Calum; Small, Michael

2018-05-01

We construct player-based complex network models of Australian football teams for the 2014 Australian Football League season; modelling the passes between players as weighted, directed edges. We show that analysis of these measures can give an insight into the underlying structure and strategy of Australian football teams, quantitatively distinguishing different playing styles. The relationships observed between network properties and match outcomes suggest that successful teams exhibit well-connected passing networks with the passes distributed between all 22 players as evenly as possible. Linear regression models of team scores and match margins show significant improvements in R2 and Bayesian information criterion when network measures are added to models that use conventional measures, demonstrating that network analysis measures contain useful, extra information. Several measures, particularly the mean betweenness centrality, are shown to be useful in predicting the outcomes of future matches, suggesting they measure some aspect of the intrinsic strength of teams. In addition, several local centrality measures are shown to be useful in analysing individual players' differing contributions to the team's structure.

Complex networks untangle competitive advantage in Australian football.

PubMed

Braham, Calum; Small, Michael

2018-05-01

We construct player-based complex network models of Australian football teams for the 2014 Australian Football League season; modelling the passes between players as weighted, directed edges. We show that analysis of these measures can give an insight into the underlying structure and strategy of Australian football teams, quantitatively distinguishing different playing styles. The relationships observed between network properties and match outcomes suggest that successful teams exhibit well-connected passing networks with the passes distributed between all 22 players as evenly as possible. Linear regression models of team scores and match margins show significant improvements in R 2 and Bayesian information criterion when network measures are added to models that use conventional measures, demonstrating that network analysis measures contain useful, extra information. Several measures, particularly the mean betweenness centrality, are shown to be useful in predicting the outcomes of future matches, suggesting they measure some aspect of the intrinsic strength of teams. In addition, several local centrality measures are shown to be useful in analysing individual players' differing contributions to the team's structure.

Inner Structure in the TW Hya Circumstellar Disk

NASA Astrophysics Data System (ADS)

Akeson, Rachel L.; Millan-Gabet, R.; Ciardi, D.; Boden, A.; Sargent, A.; Monnier, J.; McAlister, H.; ten Brummelaar, T.; Sturmann, J.; Sturmann, L.; Turner, N.

2011-05-01

TW Hya is a nearby (50 pc) young stellar object with an estimated age of 10 Myr and signs of active accretion. Previous modeling of the circumstellar disk has shown that the inner disk contains optically thin material, placing this object in the class of "transition disks". We present new near-infrared interferometric observations of the disk material and use these data, as well as previously published, spatially resolved data at 10 microns and 7 mm, to constrain disk models based on a standard flared disk structure. Our model demonstrates that the constraints imposed by the spatially resolved data can be met with a physically plausible disk but this requires a disk containing not only an inner gap in the optically thick disk as previously suggested, but also some optically thick material within this gap. Our model is consistent with the suggestion by previous authors of a planet with an orbital radius of a few AU. This work was conducted at the NASA Exoplanet Science Institute, California Institute of Technology.

[A Methodological Quality Assessment of South Korean Nursing Research using Structural Equation Modeling in South Korea].

PubMed

Kim, Jung-Hee; Shin, Sujin; Park, Jin-Hwa

2015-04-01

The purpose of this study was to evaluate the methodological quality of nursing studies using structural equation modeling in Korea. Databases of KISS, DBPIA, and National Assembly Library up to March 2014 were searched using the MeSH terms 'nursing', 'structure', 'model'. A total of 152 studies were screened. After removal of duplicates and non-relevant titles, 61 papers were read in full. Of the sixty-one articles retrieved, 14 studies were published between 1992 and 2000, 27, between 2001 and 2010, and 20, between 2011 and March 2014. The methodological quality of the review examined varied considerably. The findings of this study suggest that more rigorous research is necessary to address theoretical identification, two indicator rule, distribution of sample, treatment of missing values, mediator effect, discriminant validity, convergent validity, post hoc model modification, equivalent models issues, and alternative models issues should be undergone. Further research with robust consistent methodological study designs from model identification to model respecification is needed to improve the validity of the research.

What determines the spectrum of protein native state structures?

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Lesk, Arthur M; Maritan, Amos

2006-05-01

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focuses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu. 2006 Wiley-Liss, Inc.

Structure of turbulent non-premixed flames modeled with two-step chemistry

NASA Technical Reports Server (NTRS)

Chen, J. H.; Mahalingam, S.; Puri, I. K.; Vervisch, L.

1992-01-01

Direct numerical simulations of turbulent diffusion flames modeled with finite-rate, two-step chemistry, A + B yields I, A + I yields P, were carried out. A detailed analysis of the turbulent flame structure reveals the complex nature of the penetration of various reactive species across two reaction zones in mixture fraction space. Due to this two zone structure, these flames were found to be robust, resisting extinction over the parameter ranges investigated. As in single-step computations, mixture fraction dissipation rate and the mixture fraction were found to be statistically correlated. Simulations involving unequal molecular diffusivities suggest that the small scale mixing process and, hence, the turbulent flame structure is sensitive to the Schmidt number.

A Model for Earth's Mantle Dynamic History for The Last 500 Ma and Its Implications for Continental Vertical Motions and Geomagnetism

NASA Astrophysics Data System (ADS)

Zhong, S.; Olson, P.; Zhang, N.

2012-12-01

Seismic tomography studies indicate that the Earth's mantle structure is characterized by African and Pacific seismically slow velocity anomalies (i.e., thermochemical piles) and circum Pacific seismically fast anomalies (i.e., degree 2) in the lower mantle. Mantle convection calculations including plate motion history for the last 120 Ma suggest that these degree 2 thermochemical structures result from plate subduction history (e.g., McNamara and Zhong, 2005). Given the important controls of mantle structure and dynamics on surface tectonics and volcanism and geodynamo in the core, an important question is the long-term evolution of mantle structures, for example, was the mantle structure in the past similar to the present-day's degree 2 structure, or significantly different from the present day? To address this question, we constructed a proxy model of plate motions for the African hemisphere for the last 450 Ma using the paleogeographic reconstruction of continents constrained by paleomagnetic and geological observations (e.g., Pangea assembly and breakup). Coupled with assumed oceanic plate motions for the Pacific hemisphere before 120 Ma, this proxy model for the plate motion history is used in three dimensional spherical models of mantle convection to study the evolution of mantle structure since the Early Paleozoic. Our model calculations reproduce well the present day degree 2 mantle structure including the African and Pacific thermochemical piles, and present-day surface heat flux, bathymetry and dynamic topography. Our results suggest that while the mantle in the African hemisphere before the assembly of Pangea is dominated by the cold downwelling structure resulting from plate convergence between Gondwana and Laurussia, it is unlikely that the bulk of the African superplume structure can be formed before ˜230 Ma. Particularly, the last 120 Ma plate motion plays an important role in generating the African thermochemical pile. We reconstruct temporal evolution of the surface and CMB heat fluxes and continental vertical motions since the Paleozoic. The predicted vertical motion histories for the Slave and Kaapvaal cratons are consistent with those inferred from thermochronology studies. The predicted CMB heat fluxes were used as time-dependent boundary conditions for geodynamo simulations. And the geodynamo modelling shows that the time-dependent CMB heat fluxes may explain to the first order the frequencies of geomagnetic polarity reversals (e.g., superchrons).

Quantum structure in economics: The Ellsberg paradox

NASA Astrophysics Data System (ADS)

Aerts, Diederik; Sozzo, Sandro

2012-03-01

The expected utility hypothesis and Savage's Sure-Thing Principle are violated in real life decisions, as shown by the Allais and Ellsberg paradoxes. The popular explanation in terms of ambiguity aversion is not completely accepted. As a consequence, uncertainty is still problematical in economics. To overcome these difficulties a distinction between risk and ambiguity has been introduced which depends on the existence of a Kolmogorovian probabilistic structure modeling these uncertainties. On the other hand, evidence of everyday life suggests that context plays a fundamental role in human decisions under uncertainty. Moreover, it is well known from physics that any probabilistic structure modeling contextual interactions between entities structurally needs a non-Kolmogorovian framework admitting a quantum-like representation. For this reason, we have recently introduced a notion of contextual risk to mathematically capture situations in which ambiguity occurs. We prove in this paper that the contextual risk approach can be applied to the Ellsberg paradox, and elaborate a sphere model within our hidden measurement formalism which reveals that it is the overall conceptual landscape that is responsible of the disagreement between actual human decisions and the predictions of expected utility theory, which generates the paradox. This result points to the presence of a quantum conceptual layer in human thought which is superposed to the usually assumed classical logical layer, and conceptually supports the thesis of several authors suggesting the presence of quantum structure in economics and decision theory.

ITS2 sequence-structure phylogeny reveals diverse endophytic Pseudocercospora fungi on poplars.

PubMed

Yan, Dong-Hui; Gao, Qian; Sun, Xiaoming; Song, Xiaoyu; Li, Hongchang

2018-04-01

For matching the new fungal nomenclature to abolish pleomorphic names for a fungus, a genus Pseudocercospora s. str. was suggested to host holomorphic Pseudocercosproa fungi. But the Pseudocercosproa fungi need extra phylogenetic loci to clarify their taxonomy and diversity for their existing and coming species. Internal transcribed spacer 2 (ITS2) secondary structures have been promising in charactering species phylogeny in plants, animals and fungi. In present study, a conserved model of ITS2 secondary structures was confirmed on fungi in Pseudocercospora s. str. genus using RNAshape program. The model has a typical eukaryotic four-helix ITS2 secondary structure. But a single U base occurred in conserved motif of U-U mismatch in Helix 2, and a UG emerged in UGGU motif in Helix 3 to Pseudocercospora fungi. The phylogeny analyses based on the ITS2 sequence-secondary structures with compensatory base change characterizations are able to delimit more species for Pseudocercospora s. str. than phylogenic inferences of traditional multi-loci alignments do. The model was employed to explore the diversity of endophytic Pseudocercospora fungi in poplar trees. The analysis results also showed that endophytic Pseudocercospora fungi were diverse in species and evolved a specific lineage in poplar trees. This work suggested that ITS2 sequence-structures could become as additionally significant loci for species phylogenetic and taxonomic studies on Pseudocerospora fungi, and that Pseudocercospora endophytes could be important roles to Pseudocercospora fungi's evolution and function in ecology.

Using Instrumental Variable (IV) Tests to Evaluate Model Specification in Latent Variable Structural Equation Models*

PubMed Central

Kirby, James B.; Bollen, Kenneth A.

2009-01-01

Structural Equation Modeling with latent variables (SEM) is a powerful tool for social and behavioral scientists, combining many of the strengths of psychometrics and econometrics into a single framework. The most common estimator for SEM is the full-information maximum likelihood estimator (ML), but there is continuing interest in limited information estimators because of their distributional robustness and their greater resistance to structural specification errors. However, the literature discussing model fit for limited information estimators for latent variable models is sparse compared to that for full information estimators. We address this shortcoming by providing several specification tests based on the 2SLS estimator for latent variable structural equation models developed by Bollen (1996). We explain how these tests can be used to not only identify a misspecified model, but to help diagnose the source of misspecification within a model. We present and discuss results from a Monte Carlo experiment designed to evaluate the finite sample properties of these tests. Our findings suggest that the 2SLS tests successfully identify most misspecified models, even those with modest misspecification, and that they provide researchers with information that can help diagnose the source of misspecification. PMID:20419054

Facial first impressions and partner preference models: Comparable or distinct underlying structures?

PubMed

South Palomares, Jennifer K; Sutherland, Clare A M; Young, Andrew W

2017-12-17

Given the frequency of relationships nowadays initiated online, where impressions from face photographs may influence relationship initiation, it is important to understand how facial first impressions might be used in such contexts. We therefore examined the applicability of a leading model of verbally expressed partner preferences to impressions derived from real face images and investigated how the factor structure of first impressions based on potential partner preference-related traits might relate to a more general model of facial first impressions. Participants rated 1,000 everyday face photographs on 12 traits selected to represent (Fletcher, et al. 1999, Journal of Personality and Social Psychology, 76, 72) verbal model of partner preferences. Facial trait judgements showed an underlying structure that largely paralleled the tripartite structure of Fletcher et al.'s verbal preference model, regardless of either face gender or participant gender. Furthermore, there was close correspondence between the verbal partner preference model and a more general tripartite model of facial first impressions derived from a different literature (Sutherland et al., 2013, Cognition, 127, 105), suggesting an underlying correspondence between verbal conceptual models of romantic preferences and more general models of facial first impressions. © 2017 The British Psychological Society.

Solution Structures of Mycobacterium tuberculosis Thioredoxin C and Models of the Intact Thioredoxin System Suggest New Approaches to Inhibitor and Drug Design

PubMed Central

Olson, Andrew L.; Neumann, Terrence S.; Cai, Sheng; Sem, Daniel S.

2012-01-01

Here we report the NMR solution structures of Mycobacterium tuberculosis (M. tuberculosis) thioredoxin C in both oxidized and reduced states, with discussion of structural changes that occur in going between redox states. The NMR solution structure of the oxidized TrxC corresponds closely to that of the crystal structure, except in the C-terminal region. It appears that crystal packing effects have caused an artifactual shift in the α4 helix in the previously reported crystal structure, compared to the solution structure. Based on these TrxC structures, chemical shift mapping, a previously reported crystal structure of the M. tuberculosis thioredoxin reductase (not bound to a Trx) and structures for intermediates in the E. coli thioredoxin catalytic cycle, we have modeled the complete M. tuberculosis thioredoxin system for the various steps in the catalytic cycle. These structures and models reveal pockets at the TrxR/TrxC interface in various steps in the catalytic cycle, which can be targeted in the design of uncompetitive inhibitors as potential anti-mycobacterial agents, or as chemical genetic probes of function. PMID:23229911

Structure of an XPF endonuclease with and without DNA suggests a model for substrate recognition

PubMed Central

Newman, Matthew; Murray-Rust, Judith; Lally, John; Rudolf, Jana; Fadden, Andrew; Knowles, Philip P; White, Malcolm F; McDonald, Neil Q

2005-01-01

The XPF/Mus81 structure-specific endonucleases cleave double-stranded DNA (dsDNA) within asymmetric branched DNA substrates and play an essential role in nucleotide excision repair, recombination and genome integrity. We report the structure of an archaeal XPF homodimer alone and bound to dsDNA. Superposition of these structures reveals a large domain movement upon binding DNA, indicating how the (HhH)2 domain and the nuclease domain are coupled to allow the recognition of double-stranded/single-stranded DNA junctions. We identify two nonequivalent DNA-binding sites and propose a model in which XPF distorts the 3′ flap substrate in order to engage both binding sites and promote strand cleavage. The model rationalises published biochemical data and implies a novel role for the ERCC1 subunit of eukaryotic XPF complexes. PMID:15719018

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Rekha R.; Celina, Mathias C.; Giron, Nicholas Henry

We are developing computational models to help understand manufacturing processes, final properties and aging of structural foam, polyurethane PMDI. Th e resulting model predictions of density and cure gradients from the manufacturing process will be used as input to foam heat transfer and mechanical models. BKC 44306 PMDI-10 and BKC 44307 PMDI-18 are the most prevalent foams used in structural parts. Experiments needed to parameterize models of the reaction kinetics and the equations of motion during the foam blowing stages were described for BKC 44306 PMDI-10 in the first of this report series (Mondy et al. 2014). BKC 44307 PMDI-18more » is a new foam that will be used to make relatively dense structural supports via over packing. It uses a different catalyst than those in the BKC 44306 family of foams; hence, we expect that the reaction kineti cs models must be modified. Here we detail the experiments needed to characteriz e the reaction kinetics of BKC 44307 PMDI-18 and suggest parameters for the model based on these experiments. In additi on, the second part of this report describes data taken to provide input to the preliminary nonlinear visco elastic structural response model developed for BKC 44306 PMDI-10 foam. We show that the standard cu re schedule used by KCP does not fully cure the material, and, upon temperature elevation above 150°C, oxidation or decomposition reactions occur that alter the composition of the foam. These findings suggest that achieving a fully cured foam part with this formulation may be not be possible through therma l curing. As such, visco elastic characterization procedures developed for curing thermosets can provide only approximate material properties, since the state of the material continuously evolves during tests.« less

Structural Basis for Metallic-Like Conductivity in Microbial Nanowires

DOE PAGES

Malvankar, Nikhil S.; Vargas, Madeline; Nevin, Kelly; ...

2015-03-03

Direct measurement of multiple physical properties of Geobacter sulfurreducens pili have demonstrated that they possess metallic-like conductivity, but several studies have suggested that metallic-like conductivity is unlikely based on the structures of the G. sulfurreducens pilus predicted from homology models. In order to further evaluate this discrepancy, pili were examined with synchrotron X-ray microdiffraction and rocking-curve X-ray diffraction. Both techniques revealed a periodic 3.2-Å spacing in conductive, wild-type G. sulfurreducens pili that was missing in the nonconductive pili of strain Aro5, which lack key aromatic acids required for conductivity. The intensity of the 3.2-Å peak increased 100-fold when the pHmore » was shifted from 10.5 to 2, corresponding with a previously reported 100-fold increase in pilus conductivity with this pH change. These results suggest a clear structure-function correlation for metallic-like conductivity that can be attributed to overlapping π-orbitals of aromatic amino acids. A homology model of the G. sulfurreducens pilus was constructed with a Pseudomonas aeruginosa pilus model as a template as an alternative to previous models, which were based on a Neisseria gonorrhoeae pilus structure. This alternative model predicted that aromatic amino acids in G. sulfurreducens pili are packed within 3 to 4 Å, consistent with the experimental results. Thus, the predictions of homology modeling are highly sensitive to assumptions inherent in the model construction. Finally, the experimental results reported here further support the concept that the pili of G. sulfurreducens represent a novel class of electronically functional proteins in which aromatic amino acids promote long-distance electron transport.« less

Twilight reloaded: the peptide experience

PubMed Central

Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard

2017-01-01

The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallo­graphic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein–peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided. PMID:28291756

Twilight reloaded: the peptide experience.

PubMed

Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

2017-03-01

The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.

Electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clays. Role in U and Hg(II) transformations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scherer, Michelle

2016-08-31

During this project, we investigated Fe electron transfer and atom exchange between aqueous Fe(II) and structural Fe(III) in clay minerals. We used selective chemical extractions, enriched Fe isotope tracer experiments, computational molecular modeling, and Mössbauer spectroscopy. Our findings indicate that structural Fe(III) in clay minerals is reduced by aqueous Fe(II) and that electron transfer occurs when Fe(II) is sorbed to either basal planes and edge OH-groups of clay mineral. Findings from highly enriched isotope experiments suggest that up to 30 % of the Fe atoms in the structure of some clay minerals exhanges with aqueous Fe(II). First principles calculations usingmore » a small polaron hopping approach suggest surprisingly fast electron mobility at room temperature in a nontronite clay mineral and are consistent with temperature dependent Mössbauer data Fast electron mobility suggests that electrons may be able to conduct through the mineral fast enough to enable exchange of Fe between the aqueous phase and clay mineral structure. over the time periods we observed. Our findings suggest that Fe in clay minerals is not as stable as previously thought.« less

APPLE - An aeroelastic analysis system for turbomachines and propfans

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Bakhle, Milind A.; Srivastava, R.; Mehmed, Oral

1992-01-01

This paper reviews aeroelastic analysis methods for propulsion elements (advanced propellers, compressors and turbines) being developed and used at NASA Lewis Research Center. These aeroelastic models include both structural and aerodynamic components. The structural models include the typical section model, the beam model with and without disk flexibility, and the finite element blade model with plate bending elements. The aerodynamic models are based on the solution of equations ranging from the two-dimensional linear potential equation for a cascade to the three-dimensional Euler equations for multi-blade configurations. Typical results are presented for each aeroelastic model. Suggestions for further research are indicated. All the available aeroelastic models and analysis methods are being incorporated into a unified computer program named APPLE (Aeroelasticity Program for Propulsion at LEwis).

De novo protein structure prediction by dynamic fragment assembly and conformational space annealing.

PubMed

Lee, Juyong; Lee, Jinhyuk; Sasaki, Takeshi N; Sasai, Masaki; Seok, Chaok; Lee, Jooyoung

2011-08-01

Ab initio protein structure prediction is a challenging problem that requires both an accurate energetic representation of a protein structure and an efficient conformational sampling method for successful protein modeling. In this article, we present an ab initio structure prediction method which combines a recently suggested novel way of fragment assembly, dynamic fragment assembly (DFA) and conformational space annealing (CSA) algorithm. In DFA, model structures are scored by continuous functions constructed based on short- and long-range structural restraint information from a fragment library. Here, DFA is represented by the full-atom model by CHARMM with the addition of the empirical potential of DFIRE. The relative contributions between various energy terms are optimized using linear programming. The conformational sampling was carried out with CSA algorithm, which can find low energy conformations more efficiently than simulated annealing used in the existing DFA study. The newly introduced DFA energy function and CSA sampling algorithm are implemented into CHARMM. Test results on 30 small single-domain proteins and 13 template-free modeling targets of the 8th Critical Assessment of protein Structure Prediction show that the current method provides comparable and complementary prediction results to existing top methods. Copyright © 2011 Wiley-Liss, Inc.

A Review of Recent Aeroelastic Analysis Methods for Propulsion at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Bakhle, Milind A.; Srivastava, R.; Mehmed, Oral; Stefko, George L.

1993-01-01

This report reviews aeroelastic analyses for propulsion components (propfans, compressors and turbines) being developed and used at NASA LeRC. These aeroelastic analyses include both structural and aerodynamic models. The structural models include a typical section, a beam (with and without disk flexibility), and a finite-element blade model (with plate bending elements). The aerodynamic models are based on the solution of equations ranging from the two-dimensional linear potential equation to the three-dimensional Euler equations for multibladed configurations. Typical calculated results are presented for each aeroelastic model. Suggestions for further research are made. Many of the currently available aeroelastic models and analysis methods are being incorporated in a unified computer program, APPLE (Aeroelasticity Program for Propulsion at LEwis).

Active control of interior noise in model aircraft fuselages using piezoceramic actuators

NASA Technical Reports Server (NTRS)

Fuller, C. R.; Hansen, C. H.; Silcox, R. J.; Snyder, S. D.

1990-01-01

Active control of interior noise in model aircraft fuselages using piezoceramic actuators is experimentally studied. The actuators are bonded directly to the structure and error information is taken from up to two microphones located in the interior acoustic field. The results demonstrate that global attenuation of the order of 10 to 15 dB of interior noise can be achieved with piezoceramic actuators, irrespective of whether the shell system is vibrating at an acoustic or structural resonant frequency. The work also proves that active control using vibration (moment) inputs works well when a floor simulating that of an aircraft is installed in the model. This result suggests that the technique will be successful in controlling interior noise in realistic aircraft structures.

Automatic prediction of facial trait judgments: appearance vs. structural models.

PubMed

Rojas, Mario; Masip, David; Todorov, Alexander; Vitria, Jordi

2011-01-01

Evaluating other individuals with respect to personality characteristics plays a crucial role in human relations and it is the focus of attention for research in diverse fields such as psychology and interactive computer systems. In psychology, face perception has been recognized as a key component of this evaluation system. Multiple studies suggest that observers use face information to infer personality characteristics. Interactive computer systems are trying to take advantage of these findings and apply them to increase the natural aspect of interaction and to improve the performance of interactive computer systems. Here, we experimentally test whether the automatic prediction of facial trait judgments (e.g. dominance) can be made by using the full appearance information of the face and whether a reduced representation of its structure is sufficient. We evaluate two separate approaches: a holistic representation model using the facial appearance information and a structural model constructed from the relations among facial salient points. State of the art machine learning methods are applied to a) derive a facial trait judgment model from training data and b) predict a facial trait value for any face. Furthermore, we address the issue of whether there are specific structural relations among facial points that predict perception of facial traits. Experimental results over a set of labeled data (9 different trait evaluations) and classification rules (4 rules) suggest that a) prediction of perception of facial traits is learnable by both holistic and structural approaches; b) the most reliable prediction of facial trait judgments is obtained by certain type of holistic descriptions of the face appearance; and c) for some traits such as attractiveness and extroversion, there are relationships between specific structural features and social perceptions.

Quantitative structure-property relationship (QSPR) modeling of drug-loaded polymeric micelles via genetic function approximation.

PubMed

Wu, Wensheng; Zhang, Canyang; Lin, Wenjing; Chen, Quan; Guo, Xindong; Qian, Yu; Zhang, Lijuan

2015-01-01

Self-assembled nano-micelles of amphiphilic polymers represent a novel anticancer drug delivery system. However, their full clinical utilization remains challenging because the quantitative structure-property relationship (QSPR) between the polymer structure and the efficacy of micelles as a drug carrier is poorly understood. Here, we developed a series of QSPR models to account for the drug loading capacity of polymeric micelles using the genetic function approximation (GFA) algorithm. These models were further evaluated by internal and external validation and a Y-randomization test in terms of stability and generalization, yielding an optimization model that is applicable to an expanded materials regime. As confirmed by experimental data, the relationship between microstructure and drug loading capacity can be well-simulated, suggesting that our models are readily applicable to the quantitative evaluation of the drug-loading capacity of polymeric micelles. Our work may offer a pathway to the design of formulation experiments.

Entropy measure of credit risk in highly correlated markets

NASA Astrophysics Data System (ADS)

Gottschalk, Sylvia

2017-07-01

We compare the single and multi-factor structural models of corporate default by calculating the Jeffreys-Kullback-Leibler divergence between their predicted default probabilities when asset correlations are either high or low. Single-factor structural models assume that the stochastic process driving the value of a firm is independent of that of other companies. A multi-factor structural model, on the contrary, is built on the assumption that a single firm's value follows a stochastic process correlated with that of other companies. Our main results show that the divergence between the two models increases in highly correlated, volatile, and large markets, but that it is closer to zero in small markets, when asset correlations are low and firms are highly leveraged. These findings suggest that during periods of financial instability, when asset volatility and correlations increase, one of the models misreports actual default risk.

Quantitative Structure-Property Relationship (QSPR) Modeling of Drug-Loaded Polymeric Micelles via Genetic Function Approximation

PubMed Central

Lin, Wenjing; Chen, Quan; Guo, Xindong; Qian, Yu; Zhang, Lijuan

2015-01-01

Self-assembled nano-micelles of amphiphilic polymers represent a novel anticancer drug delivery system. However, their full clinical utilization remains challenging because the quantitative structure-property relationship (QSPR) between the polymer structure and the efficacy of micelles as a drug carrier is poorly understood. Here, we developed a series of QSPR models to account for the drug loading capacity of polymeric micelles using the genetic function approximation (GFA) algorithm. These models were further evaluated by internal and external validation and a Y-randomization test in terms of stability and generalization, yielding an optimization model that is applicable to an expanded materials regime. As confirmed by experimental data, the relationship between microstructure and drug loading capacity can be well-simulated, suggesting that our models are readily applicable to the quantitative evaluation of the drug-loading capacity of polymeric micelles. Our work may offer a pathway to the design of formulation experiments. PMID:25780923

Biologically Plausible, Human-Scale Knowledge Representation.

PubMed

Crawford, Eric; Gingerich, Matthew; Eliasmith, Chris

2016-05-01

Several approaches to implementing symbol-like representations in neurally plausible models have been proposed. These approaches include binding through synchrony (Shastri & Ajjanagadde, ), "mesh" binding (van der Velde & de Kamps, ), and conjunctive binding (Smolensky, ). Recent theoretical work has suggested that most of these methods will not scale well, that is, that they cannot encode structured representations using any of the tens of thousands of terms in the adult lexicon without making implausible resource assumptions. Here, we empirically demonstrate that the biologically plausible structured representations employed in the Semantic Pointer Architecture (SPA) approach to modeling cognition (Eliasmith, ) do scale appropriately. Specifically, we construct a spiking neural network of about 2.5 million neurons that employs semantic pointers to successfully encode and decode the main lexical relations in WordNet, which has over 100,000 terms. In addition, we show that the same representations can be employed to construct recursively structured sentences consisting of arbitrary WordNet concepts, while preserving the original lexical structure. We argue that these results suggest that semantic pointers are uniquely well-suited to providing a biologically plausible account of the structured representations that underwrite human cognition. Copyright © 2015 Cognitive Science Society, Inc.

Peptide aggregation and solvent electrostriction in a simple zwitterionic dipeptide via molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Bates, S. P.

2009-07-01

We investigate the structure of the glycyl-l-alanine dipeptide in aqueous solution at a 1:20 peptide:water concentration via classical, atomistic molecular dynamics simulations using the CHARMM22 force field, and compare to recent neutron diffraction data [S. E. McLain, A. K. Soper, and A. Watts, Eur. Biophys. J. 37, 647 (2008); S. E. McLain, A. K. Soper, I. Diadone, J. C. Smith, and A. Watts, Angew. Chem. Int. Ed. 47, 9059 (2008)]. Comparison between simulations and experiments is made using the static structure factor S (Q ) . The effect of water model (TIP3P, TIP4P, and SPC/E) upon the solution structure is investigated. Agreement between experiment and simulation is generally good across the entire Q range, although some model-dependent variation is observed, particularly in the predicted intensities of features in S (Q ) . Peptide aggregation is found to be driven by "hydrophilic" (often bifurcated) hydrogen bonds formed between carboxy and amine functional groups, although simulations suggest that the degree of aggregation is less than that observed experimentally. It is found that hydrophobic association is not significant, with hydrophobic hydration being preferred to association. Detailed examination of the solute structural motifs reveals the existence of bifurcated motifs that are suggested to be an artifact of the CHARMM force field, and may imply that classical force fields provide a flawed structural and dynamical description of such molecular fluids. Investigation of the water structure reveals the presence of an electrostrictive effect which manifests itself as an increase in the number of interstitial molecules in the water second coordination shell, in contradiction to suggestions that this phenomenon arises owing to hydrogen bond bending. Detailed analysis based upon two-dimensional distribution functions suggests an intimate link between the phenomenon of electrostriction and the behavior of water under high-pressure compression. We find the magnitude of the electrostrictive effect inferred from the neutron diffraction data to be greater than that found in the simulations. Investigation of the solvation structure suggests that the CHARMM force field overhydrates the terminal carboxy group, and that this overhydration is accompanied by the presence of bifurcated hydrogen bonds.

A Reaction-Diffusion Model for Synapse Growth and Long-Term Memory

NASA Astrophysics Data System (ADS)

Liu, Kang; Lisman, John; Hagan, Michael

Memory storage involves strengthening of synaptic transmission known as long-term potentiation (LTP). The late phase of LTP is associated with structural processes that enlarge the synapse. Yet, synapses must be stable, despite continual subunit turnover, over the lifetime of an encoded memory. These considerations suggest that synapses are variable-size stable structure (VSSS), meaning they can switch between multiple metastable structures with different sizes. The mechanisms underlying VSSS are poorly understood. While experiments and theory have suggested that the interplay between diffusion and receptor-scaffold interactions can lead to a preferred stable size for synaptic domains, such a mechanism cannot explain how synapses adopt widely different sizes. Here we develop a minimal reaction-diffusion model of VSSS for synapse growth, incorporating the recent observation from super-resolution microscopy that neural activity can build compositional heterogeneities within synaptic domains. We find that introducing such heterogeneities can change the stable domain size in a controlled manner. We discuss a potential connection between this model and experimental data on synapse sizes, and how it provides a possible mechanism to structurally encode graded long-term memory. We acknowledge the support from NSF INSPIRE Award number IOS-1526941 (KL, MFH, JL) and the Brandeis Center for Bioinspired Soft Materials, an NSF MRSEC, DMR- 1420382 (MFH).

Structural Validity of the Life Regard Index

ERIC Educational Resources Information Center

Steger, Michael F.

2007-01-01

Counselors and researchers interested in examining meaning in life often use the Life Regard Index (LRI; J. Battista & R. Almond, 1973). In this study, confirmatory factor analyses (CFAs) of several factor models based on J. Battista & R. Almond's work failed to support the structural validity of the LRI. CFA results suggested an influence of…

Family Structure States and Transitions: Associations with Children's Well-Being during Middle Childhood

ERIC Educational Resources Information Center

Magnuson, Katherine; Berger, Lawrence M.

2009-01-01

Using longitudinal data from the Maternal and Child Supplement of the National Longitudinal Survey of Youth (N = 3,862) and Hierarchical Linear Models, we estimated associations of family structure states and transitions with children's achievement and behavior trajectories during middle childhood. Results suggest that residing in a single-mother…

Extended Relation Metadata for SCORM-Based Learning Content Management Systems

ERIC Educational Resources Information Center

Lu, Eric Jui-Lin; Horng, Gwoboa; Yu, Chia-Ssu; Chou, Ling-Ying

2010-01-01

To increase the interoperability and reusability of learning objects, Advanced Distributed Learning Initiative developed a model called Content Aggregation Model (CAM) to describe learning objects and express relationships between learning objects. However, the suggested relations defined in the CAM can only describe structure-oriented…

Structural invariance of multiple intelligences, based on the level of execution.

PubMed

Almeida, Leandro S; Prieto, María Dolores; Ferreira, Arístides; Ferrando, Mercedes; Ferrandiz, Carmen; Bermejo, Rosario; Hernández, Daniel

2011-11-01

The independence of multiple intelligences (MI) of Gardner's theory has been debated since its conception. This article examines whether the one- factor structure of the MI theory tested in previous studies is invariant for low and high ability students. Two hundred ninety-four children (aged 5 to 7) participated in this study. A set of Gardner's Multiple Intelligence assessment tasks based on the Spectrum Project was used. To analyze the invariance of a general dimension of intelligence, the different models of behaviours were studied in samples of participants with different performance on the Spectrum Project tasks with Multi-Group Confirmatory Factor Analysis (MGCFA). Results suggest an absence of structural invariance in Gardner's tasks. Exploratory analyses suggest a three-factor structure for individuals with higher performance levels and a two-factor structure for individuals with lower performance levels.

Event Structure and Cognitive Control

PubMed Central

Reimer, Jason F.; Radvansky, Gabriel A.; Lorsbach, Thomas C.; Armendarez, Joseph J.

2017-01-01

Recently, a great deal of research has demonstrated that although everyday experience is continuous in nature, it is parsed into separate events. The aim of the present study was to examine whether event structure can influence the effectiveness of cognitive control. Across five experiments we varied the structure of events within the AX-CPT by shifting the spatial location of cues and probes on a computer screen. When location shifts were present, a pattern of AX-CPT performance consistent with enhanced cognitive control was found. To test whether the location shift effects were caused by the presence of event boundaries per se, other aspects of the AX-CPT were manipulated, such as the color of cues and probes and the inclusion of a distractor task during the cue-probe delay. Changes in cognitive control were not found under these conditions, suggesting that the location shift effects were specifically related to the formation of separate event models. Together, these results can be accounted for by the Event Horizon Model and a representation-based theory of cognitive control, and suggest that cognitive control can be influenced by the surrounding environmental structure. PMID:25603168

Using a Structural Equation Modelling Approach (SEM) to Examine Leadership of Heads of Subject Departments (HODs) as Perceived by Principals and Vice-Principals, Heads of Subject Departments and Teachers within "School Based Management" (SBM) Secondary Schools: Some Evidence from Hong Kong

ERIC Educational Resources Information Center

Au, Loretta; Wright, Nigel; Botton, Christopher

2003-01-01

This article reports the use of a Structural Equation Modelling (SEM) technique as a means of exploring our understanding of the leadership of Heads of Subject Departments within School Based Management (SBM) secondary schools in Hong Kong. Arguments made by Gronn (1999, 2000), Spillane et al. (2001) suggest that studies of leadership need to…

Crystal Structure Prediction via Deep Learning.

PubMed

Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

2018-06-06

We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

Igs expressed by chronic lymphocytic leukemia B cells show limited binding-site structure variability.

PubMed

Marcatili, Paolo; Ghiotto, Fabio; Tenca, Claudya; Chailyan, Anna; Mazzarello, Andrea N; Yan, Xiao-Jie; Colombo, Monica; Albesiano, Emilia; Bagnara, Davide; Cutrona, Giovanna; Morabito, Fortunato; Bruno, Silvia; Ferrarini, Manlio; Chiorazzi, Nicholas; Tramontano, Anna; Fais, Franco

2013-06-01

Ag selection has been suggested to play a role in chronic lymphocytic leukemia (CLL) pathogenesis, but no large-scale analysis has been performed so far on the structure of the Ag-binding sites (ABSs) of leukemic cell Igs. We sequenced both H and L chain V(D)J rearrangements from 366 CLL patients and modeled their three-dimensional structures. The resulting ABS structures were clustered into a small number of discrete sets, each containing ABSs with similar shapes and physicochemical properties. This structural classification correlates well with other known prognostic factors such as Ig mutation status and recurrent (stereotyped) receptors, but it shows a better prognostic value, at least in the case of one structural cluster for which clinical data were available. These findings suggest, for the first time, to our knowledge, on the basis of a structural analysis of the Ab-binding sites, that selection by a finite quota of antigenic structures operates on most CLL cases, whether mutated or unmutated.

Three-dimensional thermal structure and seismogenesis in the Tohoku and Hokkaido subduction system

NASA Astrophysics Data System (ADS)

van Keken, P. E.; Kita, S.; Nakajima, J.; Bengtson, A. K.; Hacker, B. R.; Abers, G. A.

2010-12-01

The Northern Japan arc is characterized by fast subduction of old oceanic lithosphere. The high density instrumentation and high seismicity make this an ideal natural laboratory to study the interplay between subduction zone dynamics, dehydration, migration of fluids, and seismogenesis. In this study we use high resolution finite element models to predict the thermal structure of the subduction slab below Tohoku (Northern Honshu) and Hokkaido. These models allow us to predict the pressure, temperature and mineralogy of the subducted crust and mantle. We use these models to predict the (p,T) conditions of earthquakes that are relocated with a precision of around 1 km by double difference techniques. Below Northern Hokkaido and Tohoku we find that the earthquake activity is strong in crust and the uppermost mantle for temperatures < 450 C. Above this temperature earthquakes occur more sporadically and have significantly reduced integrated seismic moment. The strongest 3D variations in this arc occur below southern Hokkaido. This 200 km wide region is characterized by a change in trench geometry, anomalously low heatflow and an anomalous velocity structure in the mantle wedge. Tomographic imaging suggest that continental crust is subducted to significant depth, thereby insulating the subducting slab from the hot mantle wedge at least at intermediate depths. The thermal insulation is also suggested by the deepening of the earthquakes in the slab (Kita et al., EPSL, 2010). This region may be characterized by active crustal erosion which would lead to a further blanketing of the crust by a sedimentary layer. Further modifications in thermal structure are possible due to the 3D wedge flow that is generated by the along-arc variations in trench geometry. We quantitatively verify the relative importance of these processes using 2D and 3D dynamical models. Without the seismically imaged crustal structure the earthquake temperatures are significantly elevated compared to the Tohoku and (northern) Hokkaido sections. If we take the modified crustal structure into account we find a (p,T) pattern that is quite similar to that in the other sections, suggesting that the processes that lead to earthquakes in crust and uppermost mantle of the downgoing slab are similar across the northern Japan arc.

Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway

PubMed Central

Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Pavlichin, Dmitri S.; Mabuchi, Hideo; Herschlag, Daniel

2016-01-01

The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations. PMID:27493222

Lagrange multiplier and Wess-Zumino variable as extra dimensions in the torus universe

NASA Astrophysics Data System (ADS)

Nejad, Salman Abarghouei; Dehghani, Mehdi; Monemzadeh, Majid

2018-01-01

We study the effect of the simplest geometry which is imposed via the topology of the universe by gauging non-relativistic particle model on torus and 3-torus with the help of symplectic formalism of constrained systems. Also, we obtain generators of gauge transformations for gauged models. Extracting corresponding Poisson structure of existed constraints, we show the effect of the shape of the universe on canonical structure of phase-spaces of models and suggest some phenomenology to prove the topology of the universe and probable non-commutative structure of the space. In addition, we show that the number of extra dimensions in the phase-spaces of gauged embedded models are exactly two. Moreover, in classical form, we talk over modification of Newton's second law in order to study the origin of the terms appeared in the gauged theory.

Structure and Function of the Intracellular Region of the Plexin-B1 Transmembrane Receptor*

PubMed Central

Tong, Yufeng; Hota, Prasanta K.; Penachioni, Junia Y.; Hamaneh, Mehdi B.; Kim, SoonJeung; Alviani, Rebecca S.; Shen, Limin; He, Hao; Tempel, Wolfram; Tamagnone, Luca; Park, Hee-Won; Buck, Matthias

2009-01-01

Members of the plexin family are unique transmembrane receptors in that they interact directly with Rho family small GTPases; moreover, they contain a GTPase-activating protein (GAP) domain for R-Ras, which is crucial for plexin-mediated regulation of cell motility. However, the functional role and structural basis of the interactions between the different intracellular domains of plexins remained unclear. Here we present the 2.4 Å crystal structure of the complete intracellular region of human plexin-B1. The structure is monomeric and reveals that the GAP domain is folded into one structure from two segments, separated by the Rho GTPase binding domain (RBD). The RBD is not dimerized, as observed previously. Instead, binding of a conserved loop region appears to compete with dimerization and anchors the RBD to the GAP domain. Cell-based assays on mutant proteins confirm the functional importance of this coupling loop. Molecular modeling based on structural homology to p120GAP·H-Ras suggests that Ras GTPases can bind to the plexin GAP region. Experimentally, we show that the monomeric intracellular plexin-B1 binds R-Ras but not H-Ras. These findings suggest that the monomeric form of the intracellular region is primed for GAP activity and extend a model for plexin activation. PMID:19843518

Semantic Elements in Deep Structures as Seen from a Modernist Definition of Clarity.

ERIC Educational Resources Information Center

Lemke, Alan

Typically, teachers approach ambiguity in student writing by suggesting that students focus on diction, syntax, and writing format; however, the works of modernists (including T.S. Eliot, Ludwig Wittgenstein, Karl Marx, and Pablo Picasso) suggest the importance of conceptions of semantic clarity. Transformational models for syntactic elements in…

Pseudomonas aeruginosa 4-Amino-4-Deoxychorismate Lyase: Spatial Conservation of an Active Site Tyrosine and Classification of Two Types of Enzyme

PubMed Central

O'Rourke, Patrick E. F.; Eadsforth, Thomas C.; Fyfe, Paul K.; Shepherd, Sharon M.; Hunter, William N.

2011-01-01

4-Amino-4-deoxychorismate lyase (PabC) catalyzes the formation of 4-aminobenzoate, and release of pyruvate, during folate biosynthesis. This is an essential activity for the growth of Gram-negative bacteria, including important pathogens such as Pseudomonas aeruginosa. A high-resolution (1.75 Å) crystal structure of PabC from P. aeruginosa has been determined, and sequence-structure comparisons with orthologous structures are reported. Residues around the pyridoxal 5′-phosphate cofactor are highly conserved adding support to aspects of a mechanism generic for enzymes carrying that cofactor. However, we suggest that PabC can be classified into two groups depending upon whether an active site and structurally conserved tyrosine is provided from the polypeptide that mainly forms an active site or from the partner subunit in the dimeric assembly. We considered that the conserved tyrosine might indicate a direct role in catalysis: that of providing a proton to reduce the olefin moiety of substrate as pyruvate is released. A threonine had previously been suggested to fulfill such a role prior to our observation of the structurally conserved tyrosine. We have been unable to elucidate an experimentally determined structure of PabC in complex with ligands to inform on mechanism and substrate specificity. Therefore we constructed a computational model of the catalytic intermediate docked into the enzyme active site. The model suggests that the conserved tyrosine helps to create a hydrophobic wall on one side of the active site that provides important interactions to bind the catalytic intermediate. However, this residue does not appear to participate in interactions with the C atom that undergoes an sp 2 to sp 3 conversion as pyruvate is produced. The model and our comparisons rather support the hypothesis that an active site threonine hydroxyl contributes a proton used in the reduction of the substrate methylene to pyruvate methyl in the final stage of the mechanism. PMID:21935381

Langevin Dynamics Simulations of Genome Packing in Bacteriophage

PubMed Central

Forrey, Christopher; Muthukumar, M.

2006-01-01

We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general. PMID:16617089

Langevin dynamics simulations of genome packing in bacteriophage.

PubMed

Forrey, Christopher; Muthukumar, M

2006-07-01

We use Langevin dynamics simulations to study the process by which a coarse-grained DNA chain is packaged within an icosahedral container. We focus our inquiry on three areas of interest in viral packing: the evolving structure of the packaged DNA condensate; the packing velocity; and the internal buildup of energy and resultant forces. Each of these areas has been studied experimentally, and we find that we can qualitatively reproduce experimental results. However, our findings also suggest that the phage genome packing process is fundamentally different than that suggested by the inverse spool model. We suggest that packing in general does not proceed in the deterministic fashion of the inverse-spool model, but rather is stochastic in character. As the chain configuration becomes compressed within the capsid, the structure, energy, and packing velocity all become dependent upon polymer dynamics. That many observed features of the packing process are rooted in condensed-phase polymer dynamics suggests that statistical mechanics, rather than mechanics, should serve as the proper theoretical basis for genome packing. Finally we suggest that, as a result of an internal protein unique to bacteriophage T7, the T7 genome may be significantly more ordered than is true for bacteriophage in general.

Highlighting the Structure-Function Relationship of the Brain with the Ising Model and Graph Theory

PubMed Central

Das, T. K.; Abeyasinghe, P. M.; Crone, J. S.; Sosnowski, A.; Laureys, S.; Owen, A. M.; Soddu, A.

2014-01-01

With the advent of neuroimaging techniques, it becomes feasible to explore the structure-function relationships in the brain. When the brain is not involved in any cognitive task or stimulated by any external output, it preserves important activities which follow well-defined spatial distribution patterns. Understanding the self-organization of the brain from its anatomical structure, it has been recently suggested to model the observed functional pattern from the structure of white matter fiber bundles. Different models which study synchronization (e.g., the Kuramoto model) or global dynamics (e.g., the Ising model) have shown success in capturing fundamental properties of the brain. In particular, these models can explain the competition between modularity and specialization and the need for integration in the brain. Graphing the functional and structural brain organization supports the model and can also highlight the strategy used to process and organize large amount of information traveling between the different modules. How the flow of information can be prevented or partially destroyed in pathological states, like in severe brain injured patients with disorders of consciousness or by pharmacological induction like in anaesthesia, will also help us to better understand how global or integrated behavior can emerge from local and modular interactions. PMID:25276772

A volumetric ablation model of EPDM considering complex physicochemical process in porous structure of char layer

NASA Astrophysics Data System (ADS)

Yang, Liu; Xiao-Jing, Yu; Jian-Ming, Ma; Yi-Wen, Guan; Jiang, Li; Qiang, Li; Sa, Yang

2017-06-01

A volumetric ablation model for EPDM (ethylene- propylene-diene monomer) is established in this paper. This model considers the complex physicochemical process in the porous structure of a char layer. An ablation physics model based on a porous structure of a char layer and another model of heterogeneous volumetric ablation char layer physics are then built. In the model, porosity is used to describe the porous structure of a char layer. Gas diffusion and chemical reactions are introduced to the entire porous structure. Through detailed formation analysis, the causes of the compact or loose structure in the char layer and chemical vapor deposition (CVD) reaction between pyrolysis gas and char layer skeleton are introduced. The Arrhenius formula is adopted to determine the methods for calculating carbon deposition rate C which is the consumption rate caused by thermochemical reactions in the char layer, and porosity evolution. The critical porosity value is used as a criterion for char layer porous structure failure under gas flow and particle erosion. This critical porosity value is obtained by fitting experimental parameters and surface porosity of the char layer. Linear ablation and mass ablation rates are confirmed with the critical porosity value. Results of linear ablation and mass ablation rate calculations generally coincide with experimental results, suggesting that the ablation analysis proposed in this paper can accurately reflect practical situations and that the physics and mathematics models built are accurate and reasonable.

Factor Structure, Reliability and Measurement Invariance of the Alberta Context Tool and the Conceptual Research Utilization Scale, for German Residential Long Term Care

PubMed Central

Hoben, Matthias; Estabrooks, Carole A.; Squires, Janet E.; Behrens, Johann

2016-01-01

We translated the Canadian residential long term care versions of the Alberta Context Tool (ACT) and the Conceptual Research Utilization (CRU) Scale into German, to study the association between organizational context factors and research utilization in German nursing homes. The rigorous translation process was based on best practice guidelines for tool translation, and we previously published methods and results of this process in two papers. Both instruments are self-report questionnaires used with care providers working in nursing homes. The aim of this study was to assess the factor structure, reliability, and measurement invariance (MI) between care provider groups responding to these instruments. In a stratified random sample of 38 nursing homes in one German region (Metropolregion Rhein-Neckar), we collected questionnaires from 273 care aides, 196 regulated nurses, 152 allied health providers, 6 quality improvement specialists, 129 clinical leaders, and 65 nursing students. The factor structure was assessed using confirmatory factor models. The first model included all 10 ACT concepts. We also decided a priori to run two separate models for the scale-based and the count-based ACT concepts as suggested by the instrument developers. The fourth model included the five CRU Scale items. Reliability scores were calculated based on the parameters of the best-fitting factor models. Multiple-group confirmatory factor models were used to assess MI between provider groups. Rather than the hypothesized ten-factor structure of the ACT, confirmatory factor models suggested 13 factors. The one-factor solution of the CRU Scale was confirmed. The reliability was acceptable (>0.7 in the entire sample and in all provider groups) for 10 of 13 ACT concepts, and high (0.90–0.96) for the CRU Scale. We could demonstrate partial strong MI for both ACT models and partial strict MI for the CRU Scale. Our results suggest that the scores of the German ACT and the CRU Scale for nursing homes are acceptably reliable and valid. However, as the ACT lacked strict MI, observed variables (or scale scores based on them) cannot be compared between provider groups. Rather, group comparisons should be based on latent variable models, which consider the different residual variances of each group. PMID:27656156

The influence of lateral Earth structure on glacial isostatic adjustment in Greenland

NASA Astrophysics Data System (ADS)

Milne, Glenn A.; Latychev, Konstantin; Schaeffer, Andrew; Crowley, John W.; Lecavalier, Benoit S.; Audette, Alexandre

2018-05-01

We present the first results that focus on the influence of lateral Earth structure on Greenland glacial isostatic adjustment (GIA) using a model that can explicitly incorporate 3-D Earth structure. In total, eight realisations of lateral viscosity structure were developed using four global seismic velocity models and two global lithosphere (elastic) thickness models. Our results show that lateral viscosity structure has a significant influence on model output of both deglacial relative sea level (RSL) changes and present-day rates of vertical land motion. For example, lateral structure changes the RSL predictions in the Holocene by several 10 s of metres in many locations relative to the 1-D case. Modelled rates of vertical land motion are also significantly affected, with differences from the 1-D case commonly at the mm/yr level and exceeding 2 mm/yr in some locations. The addition of lateral structure was unable to account for previously identified data-model RSL misfits in northern and southern Greenland, suggesting limitations in the adopted ice model (Lecavalier et al. 2014) and/or the existence of processes not included in our model. Our results show large data-model discrepancies in uplift rates when applying a 1-D viscosity model tuned to fit the RSL data; these discrepancies cannot be reconciled by adding the realisations of lateral structure considered here. In many locations, the spread in model output for the eight different 3-D Earth models is of similar amplitude or larger than the influence of lateral structure (as defined by the average of all eight model runs). This reflects the differences between the four seismic and two lithosphere models used and implies a large uncertainty in defining the GIA signal given that other aspects that contribute to this uncertainty (e.g. scaling from seismic velocity to viscosity) were not considered in this study. In order to reduce this large model uncertainty, an important next step is to develop more accurate constraints on Earth structure beneath Greenland based on regional geophysical data sets.

Differentiating Categories and Dimensions: Evaluating the Robustness of Taxometric Analyses

ERIC Educational Resources Information Center

Ruscio, John; Kaczetow, Walter

2009-01-01

Interest in modeling the structure of latent variables is gaining momentum, and many simulation studies suggest that taxometric analysis can validly assess the relative fit of categorical and dimensional models. The generation and parallel analysis of categorical and dimensional comparison data sets reduces the subjectivity required to interpret…

Structure and Etiology of Co-Occurring Internalizing and Externalizing Disorders in Adolescents

ERIC Educational Resources Information Center

Cosgrove, Victoria E.; Rhee, Soo H.; Gelhorn, Heather L.; Boeldt, Debra; Corley, Robin C.; Ehringer, Marissa A.; Young, Susan E.; Hewitt, John K.

2011-01-01

Several studies suggest that a two-factor model positing internalizing and externalizing factors explains the interrelationships among psychiatric disorders. However, it is unclear whether the covariation between internalizing and externalizing disorders is due to common genetic or environmental influences. We examined whether a model positing two…

Geophysical characteristics and crustal structure of greenstone terranes: Canadian Shield

NASA Technical Reports Server (NTRS)

Thomas, M. D.; Losier, L.; Thurston, P. C.; Gupta, V. K.; Gibb, R. A.; Grieve, R. A. F.

1986-01-01

Geophysical studies in the Canadian Shield have provided some insights into the tectonic setting of greenstone belts. Greenstone belts are not rooted in deep crustal structures. Geophysical techniques consistently indicate that greenstones are restricted to the uppermost 10 km or so of crust and are underlain by geophysically normal crust. Gravity models suggest that granitic elements are similarly restricted, although magnetic modelling suggests possible downward extension to the intermediate discontinuity around approx. 18 km. Seismic evidence demonstrates that steeply-dipping structure, which can be associated with the belts in the upper crust, is not present in the lower crust. Horizontal intermediate discontinuities mapped under adjacent greenstone and granitic components are not noticeably disrupted in the boundary zone. Geophysical evidence points to the presence of discontinuities between greenhouse-granite and adjacent metasedimentary erranes. Measured stratigraphic thicknesses of greenstone belts are often twice or more the vertical thicknesses determined from gravity modelling. Explantations advanced for the discrepancy include stratigraphy repeated by thrust faulting and/or listric normal faulting, mechanisms which are consistent with certain aspects of conceptual models of greenstone development. Where repetition is not a factor the gravity evidence points to removal of the root zones of greenstone belts. For one region, this has been attributed to magmatic stopping during resurgent caldera activity.

Temperature-Correlated Changes in Phytoplankton Community Structure Are Restricted to Polar Waters.

PubMed

Ward, Ben A

2015-01-01

Globally distributed observations of size-fractionated chlorophyll a and temperature were used to incorporate temperature dependence into an existing semi-empirical model of phytoplankton community size structure. The additional temperature-dependent term significantly increased the model's ability to both reproduce and predict observations of chlorophyll a size-fractionation at temperatures below 2°C. The most notable improvements were in the smallest (picoplankton) size-class, for which overall model fit was more than doubled, and predictive skill was increased by approximately 40%. The model was subsequently applied to generate global maps for three phytoplankton size classes, on the basis of satellite-derived estimates of surface chlorophyll a and sea surface temperature. Polar waters were associated with marked decline in the chlorophyll a biomass of the smallest cells, relative to lower latitude waters of equivalent total chlorophyll a. In the same regions a complementary increase was seen in the chlorophyll a biomass of larger size classes. These findings suggest that a warming and stratifying ocean will see a poleward expansion of the habitat range of the smallest phytoplankton, with the possible displacement of some larger groups that currently dominate. There was no evidence of a strong temperature dependence in tropical or sub-tropical regions, suggesting that future direct temperature effects on community structure at lower latitudes may be small.

Intraplate extensional tectonics of the eastern Basin-Range Inferencess on structural style from seismic reflection data, regional tectonics, and thermal-mechanical models of brittle-ductile deformation

NASA Technical Reports Server (NTRS)

Smith, R. B.; Bruhn, R. L.

1984-01-01

Using 1500 km of industry-released seismic reflection data, surface geology, velocity models from refraction data, and earthquake data, the large extensional structures in the crust of the eastern Basin-Range and its transition into the Middle Rocky Mountains and Colorado Plateau have been studied. It is suggested that the close spatial correlation between normal faults and thrust fault segmentation along the Wasatch Front reflects major east-trending structural and lithological boundaries inherited from tectonic processes associated with the evolution of the cordilleran miogeocline, which began in the Precambrian.

Atomistic materials modeling of complex systems: Carbynes, carbon nanotube devices and bulk metallic glasses

NASA Astrophysics Data System (ADS)

Luo, Weiqi

The key to understanding and predicting the behavior of materials is the knowledge of their structures. Many properties of materials samples are not solely determined by their average chemical compositions which one may easily control. Instead, they are profoundly influenced by structural features of different characteristic length scales. Starting in the last century, metallurgical engineering has mostly been microstructure engineering. With the further evolution of materials science, structural features of smaller length scales down to the atomic structure, have become of interest for the purpose of properties engineering and functionalizing materials and are, therefore, subjected to study. As computer modeling is becoming more powerful due to the dramatic increase of computational resources and software over the recent decades, there is an increasing demand for atomistic simulations with the goal of better understanding materials behavior on the atomic scale. Density functional theory (DFT) is a quantum mechanics based approach to calculate electron distribution, total energy and interatomic forces with high accuracy. From these, atomic structures and thermal effects can be predicted. However, DFT is mostly applied to relatively simple systems because it is computationally very demanding. In this thesis, the current limits of DFT applications are explored by studying relatively complex systems, namely, carbynes, carbon nanotube (CNT) devices and bulk metallic glasses (BMGs). Special care is taken to overcome the limitations set by small system sizes and time scales that often prohibit DFT from being applied to realistic systems under realistic external conditions. In the first study, we examine the possible existence of a third solid phase of carbon with linear bonding called carbyne, which has been suggested in the literature and whose formation has been suggested to be detrimental to high-temperature carbon materials. We have suggested potential structures for solid carbynes based on literature data and our calculations and have calculated their free energies by DFT as a function of temperature (0--4000 K) and pressure (0--180 kbar). We propose and verify a simplified approach to calculate the phonon density of states (DOS) to allow a fast calculation of free energies. We found that all carbyne structures have higher free energies than graphite in the whole temperature and pressure range of this investigation, making pure (carbon-only) carbynes at most meta-stable. The inclusion of impurities was studied as well and may be the key for a stable carbyne phase. For CNT devices which have been suggested to eventually replace current Si technology, there is currently no equivalent for the highly used Si process modeling methods ("Technology Computer Aided Design" (TCAD)). We suggest accelerated DFT molecular dynamics (MD) simulations as a method for process modeling and apply it to study the contact formation between CNTs and metal contacts consisting of Ti, Pd, Al, and Au. The temperature accelerated dynamics (TAD) technique was adopted to overcome the time limitations of MD simulations in general, which are especially severe for the computationally demanding DFT MD simulations. We found that CNTs undergo a structural transformation when brought into contact with certain metal electrodes (here, Ti and Al). This resulted in a dramatic decrease in electrical conductance of the device. We also show that the transformation depends on the size of CNTs due to the size-dependent elastic energy and on the electrode materials due to the electronegativity-dependent charge transfer. In the last study, DFT was used in conjunction with classical MD simulations to predict the electron density of a Cu46Zr54 BMG structure modeled by a 1000-atom cell. Whereas DFT is capable to calculate the electron distribution in the cell, it is too slow to simulate melting and structural relaxation, which we handle by classical MD within the Embedded Atom Method. We propose a new model to analyze the open volume distribution based on the electron density and compare it with the traditional hard sphere model. Results from both models agree well, while the former allows a significantly better physical insight into the open volume distribution. As an additional plus, its results can be connected to experimental results by techniques such as Positron Annihilation Spectroscopy (PAS).

Synchrotron Protein Footprinting Supports Substrate Translocation by ClpA via ATP-Induced Movements of the D2 Loop

PubMed Central

Bohon, Jen; Jennings, Laura D.; Phillips, Christine M.; Licht, Stuart; Chance, Mark R.

2010-01-01

SUMMARY Synchrotron x-ray protein footprinting is used to study structural changes upon formation of the ClpA hexamer. Comparative solvent accessibilities between ClpA monomer and ClpA hexamer samples are in agreement throughout most of the sequence with calculations based on two previously proposed hexameric models. The data differ substantially from the proposed models in two parts of the structure: the D1 sensor 1 domain and the D2 loop region. The results suggest that these two regions can access alternate conformations in which their solvent protection is greater than in the structural models based on crystallographic data. In combination with previously reported structural data, the footprinting data provide support for a revised model in which the D2 loop contacts the D1 sensor 1 domain in the ATP-bound form of the complex. These data provide the first direct experimental support for the nucleotide-dependent D2 loop conformational change previously proposed to mediate substrate translocation. PMID:18682217

THE VERTICAL X-SHAPED STRUCTURE IN THE MILKY WAY: EVIDENCE FROM A SIMPLE BOXY BULGE MODEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li Zhaoyu; Shen Juntai, E-mail: jshen@shao.ac.cn

2012-09-20

A vertical X-shaped structure in the Galactic bulge was recently reported. Here, we present evidence of a similar X-shaped structure in the Shen et al. 2010 bar/boxy bulge model that simultaneously matches the stellar kinematics successfully. The X-shaped structure is found in the central region of our bar/boxy bulge model and is qualitatively consistent with the observed one in many aspects. End-to-end separations of the X-shaped structure in the radial and vertical directions are roughly 3 kpc and 1.8 kpc, respectively. The X-shaped structure contains about 7% of light in the boxy bulge region, but it is significant enough tomore » be identified in observations. An X-shaped structure naturally arises in the formation of bar/boxy bulges and is mainly associated with orbits trapped around the vertically extended x{sub 1} family. Like the bar in our model, the X-shaped structure tilts away from the Sun-Galactic center line by 20 Degree-Sign . The X-shaped structure becomes increasingly symmetric about the disk plane, so the observed symmetry may indicate that it formed at least a few billion years ago. The existence of the vertical X-shaped structure suggests that the formation of the Milky Way bulge is shaped mainly by internal disk dynamical instabilities.« less

A nonlinear viscoelastic approach to durability predictions for polymer based composite structures

NASA Technical Reports Server (NTRS)

Brinson, Hal F.

1991-01-01

Current industry approaches for the durability assessment of metallic structures are briefly reviewed. For polymer based composite structures, it is suggested that new approaches must be adopted to include memory or viscoelastic effects which could lead to delayed failures that might not be predicted using current techniques. A durability or accelerated life assessment plan for fiber reinforced plastics (FRP) developed and documented over the last decade or so is reviewed and discussed. Limitations to the plan are outlined and suggestions to remove the limitations are given. These include the development of a finite element code to replace the previously used lamination theory code and the development of new specimen geometries to evaluate delamination failures. The new DCB model is reviewed and results are presented. Finally, it is pointed out that new procedures are needed to determine interfacial properties and current efforts underway to determine such properties are reviewed. Suggestions for additional efforts to develop a consistent and accurate durability predictive approach for FRP structures are outlined.

A nonlinear viscoelastic approach to durability predictions for polymer based composite structures

NASA Technical Reports Server (NTRS)

Brinson, Hal F.; Hiel, C. C.

1990-01-01

Current industry approaches for the durability assessment of metallic structures are briefly reviewed. For polymer based composite structures, it is suggested that new approaches must be adopted to include memory or viscoelastic effects which could lead to delayed failures that might not be predicted using current techniques. A durability or accelerated life assessment plan for fiber reinforced plastics (FRP) developed and documented over the last decade or so is reviewed and discussed. Limitations to the plan are outlined and suggestions to remove the limitations are given. These include the development of a finite element code to replace the previously used lamination theory code and the development of new specimen geometries to evaluate delamination failures. The new DCB model is reviewed and results are presented. Finally, it is pointed out that new procedures are needed to determine interfacial properties and current efforts underway to determine such properties are reviewed. Suggestions for additional efforts to develop a consistent and accurate durability predictive approach for FRP structures is outlined.

An anatomy of the projected North Atlantic warming hole in CMIP5 models

NASA Astrophysics Data System (ADS)

Menary, Matthew B.; Wood, Richard A.

2018-04-01

Global mean surface air temperature has increased over the past century and climate models project this trend to continue. However, the pattern of change is not homogeneous. Of particular interest is the subpolar North Atlantic, which has cooled in recent years and is projected to continue to warm less rapidly than the global mean. This is often termed the North Atlantic warming hole (WH). In climate model projections, the development of the WH is concomitant with a weakening of the Atlantic meridional overturning circulation (AMOC). Here, we further investigate the possible link between the AMOC and WH and the competing drivers of vertical mixing and surface heat fluxes. Across a large ensemble of 41 climate models we find that the spatial structure of the WH varies considerably from model to model but is generally upstream of the simulated deep water formation regions. A heat budget analysis suggests the formation of the WH is related to changes in ocean heat transport. Although the models display a plethora of AMOC mean states, they generally predict a weakening and shallowing of the AMOC also consistent with the evolving depth structure of the WH. A lagged regression analysis during the WH onset phase suggests that reductions in wintertime mixing lead a weakening of the AMOC by 5 years in turn leading initiation of the WH by 5 years. Inter-model differences in the evolution and structure of the WH are likely to lead to somewhat different projected climate impacts in nearby Europe and North America.

Final Report for Dynamic Models for Causal Analysis of Panel Data. Models for Change in Quantitative Variables, Part I Deterministic Models. Part II, Chapter 3.

ERIC Educational Resources Information Center

Hannan, Michael T.

This document is part of a series of chapters described in SO 011 759. Addressing the question of effective models to measure change and the change process, the author suggests that linear structural equation systems may be viewed as steady state outcomes of continuous-change models and have rich sociological grounding. Two interpretations of the…

Morphology suggests noseleaf and pinnae cooperate to enhance bat echolocation.

PubMed

Kuc, Roman

2010-11-01

A protruding noseleaf and concave pinna structures suggest that some bats may use these to enhance their echolocation capabilities. This paper considers two possible mechanisms that each exploit the combination of direct and delayed acoustic paths to achieve more complex emission or sensitivity echolocation patterns. The first is an emission mechanism, in which the protruding noseleaf vibrates to emit sound in both the forward and backward directions, and pinna structures reflect the backward emission to enhance the forward beam. The second is a reception mechanism, which has a direct echo path to the ear canal and a delayed path involving pinna structures reflecting onto the noseleaf and then into the ear canal. A model using Davis' Round-eared Bat illustrates that such direct and delayed acoustic paths provide target elevation cues. The model demonstrates the delayed pinna component can increase the on-axis emission strength, narrow the beam width, and sculpt frequency-dependent beam patterns useful for echolocation.

Structure of random discrete spacetime

NASA Technical Reports Server (NTRS)

Brightwell, Graham; Gregory, Ruth

1991-01-01

The usual picture of spacetime consists of a continuous manifold, together with a metric of Lorentzian signature which imposes a causal structure on the spacetime. A model, first suggested by Bombelli et al., is considered in which spacetime consists of a discrete set of points taken at random from a manifold, with only the causal structure on this set remaining. This structure constitutes a partially ordered set (or poset). Working from the poset alone, it is shown how to construct a metric on the space which closely approximates the metric on the original spacetime manifold, how to define the effective dimension of the spacetime, and how such quantities may depend on the scale of measurement. Possible desirable features of the model are discussed.

The structure of random discrete spacetime

NASA Technical Reports Server (NTRS)

Brightwell, Graham; Gregory, Ruth

1990-01-01

The usual picture of spacetime consists of a continuous manifold, together with a metric of Lorentzian signature which imposes a causal structure on the spacetime. A model, first suggested by Bombelli et al., is considered in which spacetime consists of a discrete set of points taken at random from a manifold, with only the causal structure on this set remaining. This structure constitutes a partially ordered set (or poset). Working from the poset alone, it is shown how to construct a metric on the space which closely approximates the metric on the original spacetime manifold, how to define the effective dimension of the spacetime, and how such quantities may depend on the scale of measurement. Possible desirable features of the model are discussed.

Testing the Mediating Role of Teachers' Self-Efficacy Beliefs in the Relationship between Sources of Efficacy Information and Students Achievement

ERIC Educational Resources Information Center

Mohamadi, Fatemeh Shaterian; Asadzadeh, Hassan

2012-01-01

The purpose of this study is to test the mediating role of teachers' self-efficacy beliefs in the relationship between sources of efficacy information and students achievement. For achieving this aim, this study suggests two alternative models, tested by Structural equation modeling (SEM) technique. In the first model, sources of efficacy…

Mediating Mental Models of Metals: Acknowledging the Priority of the Learner's Prior Learning

ERIC Educational Resources Information Center

Taber, Keith S.

2003-01-01

This paper describes the conceptualizations, or mental models, of the nature of the bonding and structure of metals of a group of U.K. college students. It is suggested that these mental models may be understood in terms of the students' prior learning about covalent and ionic bonding, and the prevalence of a common alternative conceptual…

Longitudinal Factor Structure of Posttraumatic Stress Symptoms Related to Intimate Partner Violence

ERIC Educational Resources Information Center

Krause, Elizabeth D.; Kaltman, Stacey; Goodman, Lisa A.; Dutton, Mary Ann

2007-01-01

Confirmatory factor analysis (CFA) studies have suggested that a model of posttraumatic stress disorder (PTSD) that is characterized by 4 factors is preferable to competing models. However, the composition of these 4 factors has varied across studies, with 1 model splitting avoidance and numbing symptoms (e.g., D. W. King, G. A. Leskin, L. A.…

Velocity-depth ambiguity and the seismic structure of large igneous provinces: a case study from the Ontong Java Plateau

NASA Astrophysics Data System (ADS)

Korenaga, Jun

2011-05-01

The seismic structure of large igneous provinces provides unique constraints on the nature of their parental mantle, allowing us to investigate past mantle dynamics from present crustal structure. To exploit this crust-mantle connection, however, it is prerequisite to quantify the uncertainty of a crustal velocity model, as it could suffer from considerable velocity-depth ambiguity. In this contribution, a practical strategy is suggested to estimate the model uncertainty by explicitly exploring the degree of velocity-depth ambiguity in the model space. In addition, wide-angle seismic data collected over the Ontong Java Plateau are revisited to provide a worked example of the new approach. My analysis indicates that the crustal structure of this gigantic plateau is difficult to reconcile with the melting of a pyrolitic mantle, pointing to the possibility of large-scale compositional heterogeneity in the convecting mantle.

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

Flutter of High-Speed Civil Transport Flexible Semispan Model: Time-Frequency Analysis

NASA Technical Reports Server (NTRS)

Chabalko, Christopher C.; Hajj, Muhammad R.; Silva, Walter A.

2006-01-01

Time/frequency analysis of fluctuations measured by pressure taps and strain gauges in the experimental studies of the flexible semispan model of a high-speed civil transport wing configuration is performed. The interest is in determining the coupling between the aerodynamic loads and structural motions that led to the hard flutter conditions and loss of the model. The results show that, away from the hard flutter point, the aerodynamic loads at all pressure taps near the wing tip and the structural motions contained the same frequency components. On the other hand, in the flow conditions leading to the hard flutter, the frequency content of the pressure fluctuations near the leading and trailing edges varied significantly. This led to contribution to the structural motions over two frequency ranges. The ratio of these ranges was near 2:1, which suggests the possibility of nonlinear structural coupling.

Landscape effects on diets of two canids in Northwestern Texas: A multinomial modeling approach

USGS Publications Warehouse

Lemons, P.R.; Sedinger, J.S.; Herzog, M.P.; Gipson, P.S.; Gilliland, R.L.

2010-01-01

Analyses of feces, stomach contents, and regurgitated pellets are common techniques for assessing diets of vertebrates and typically contain more than 1 food item per sampling unit. When analyzed, these individual food items have traditionally been treated as independent, which represents pseudoreplication. When food types are recorded as present or absent, these samples can be treated as multinomial vectors of food items, with each vector representing 1 realization of a possible diet. We suggest such data have a similar structure to capture histories for closed-capture, capturemarkrecapture data. To assess the effects of landscapes and presence of a potential competitor, we used closed-capture models implemented in program MARK into analyze diet data generated from feces of swift foxes (Vulpes velox) and coyotes (Canis latrans) in northwestern Texas. The best models of diet contained season and location for both swift foxes and coyotes, but year accounted for less variation, suggesting that landscape type is an important predictor of diets of both species. Models containing the effect of coyote reduction were not competitive (??QAICc 53.6685), consistent with the hypothesis that presence of coyotes did not influence diet of swift foxes. Our findings suggest that landscape type may have important influences on diets of both species. We believe that multinomial models represent an effective approach to assess hypotheses when diet studies have a data structure similar to ours. ?? 2010 American Society of Mammalogists.

Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove.

PubMed

Calderón, Luciano; Campagna, Leonardo; Wilke, Thomas; Lormee, Hervé; Eraud, Cyril; Dunn, Jenny C; Rocha, Gregorio; Zehtindjiev, Pavel; Bakaloudis, Dimitrios E; Metzger, Benjamin; Cecere, Jacopo G; Marx, Melanie; Quillfeldt, Petra

2016-11-07

Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove, Streptopelia turtur, is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations. Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size (Ne) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the Ne that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the Ne are coincident with recent changes in the availability of suitable habitat. We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.

Structural Analysis of 1995-2005 School Crime Supplement Datasets: Factors Influencing Students' Fear, Anxiety, and Avoidant Behaviors

ERIC Educational Resources Information Center

Mayer, Matthew J.

2010-01-01

The 1995-2005 School Crime Supplement datasets were analyzed using structural equation modeling. Converging evidence across multiple analyses suggests that secure school building policies may not be systematically linked to school disorder and may be more a reactive measure in response to other concerns. Most importantly, measures of incivility…

Evidence of Second-Order Factor Structure in a Diagnostic Problem Space: Implications for Medical Education.

ERIC Educational Resources Information Center

Papa, Frank J.; And Others

1997-01-01

Chest pain was identified as a specific medical problem space, and disease classes were modeled to define it. Results from a test taken by 628 medical residents indicate a second-order factor structure that suggests that chest pain is a multidimensional problem space. Implications for medical education are discussed. (SLD)

Exploratory Study of Factors Influencing Job-Related Stress in Japanese Psychiatric Nurses

PubMed Central

Yada, Hironori; Lu, Xi; Omori, Hisamitsu; Abe, Hiroshi; Matsuo, Hisae; Ishida, Yasushi; Katoh, Takahiko

2015-01-01

This study explored the factor structure of psychiatric nurses' job-related stress and examined the specificity of the related stressors using the job stressor scale of the Brief Job Stress Questionnaire (BJSQ). The stressor scale of the BJSQ was administered to 296 nurses and assistant nurses. Answers were examined statistically. Exploratory factor analysis was performed to identify factor structures; two factors (overload and job environment) were valid. Confirmatory factor analysis was conducted to examine the two-factor structure and found 11 items with factor loadings of >0.40 (model 1), 13 items with factor loadings from 0.30 to <0.40 (model 2), and 17 items with factor loadings from 0.20 to <0.30 (model 3) for one factor; model 1 demonstrated the highest goodness of fit. Then, we observed that the two-factor structure (model 1) showed a higher goodness of fit than the original six-factor structure. This differed from subscales based on general workers' job-related stressors, suggesting that the factor structure of psychiatric nurses' job-related stressors is specific. Further steps may be necessary to reduce job-related stress specifically related to overload including attention to many needs of patients and job environment including complex ethical dilemmas in psychiatric nursing. PMID:25922763

Exploratory study of factors influencing job-related stress in Japanese psychiatric nurses.

PubMed

Yada, Hironori; Lu, Xi; Omori, Hisamitsu; Abe, Hiroshi; Matsuo, Hisae; Ishida, Yasushi; Katoh, Takahiko

2015-01-01

This study explored the factor structure of psychiatric nurses' job-related stress and examined the specificity of the related stressors using the job stressor scale of the Brief Job Stress Questionnaire (BJSQ). The stressor scale of the BJSQ was administered to 296 nurses and assistant nurses. Answers were examined statistically. Exploratory factor analysis was performed to identify factor structures; two factors (overload and job environment) were valid. Confirmatory factor analysis was conducted to examine the two-factor structure and found 11 items with factor loadings of >0.40 (model 1), 13 items with factor loadings from 0.30 to <0.40 (model 2), and 17 items with factor loadings from 0.20 to <0.30 (model 3) for one factor; model 1 demonstrated the highest goodness of fit. Then, we observed that the two-factor structure (model 1) showed a higher goodness of fit than the original six-factor structure. This differed from subscales based on general workers' job-related stressors, suggesting that the factor structure of psychiatric nurses' job-related stressors is specific. Further steps may be necessary to reduce job-related stress specifically related to overload including attention to many needs of patients and job environment including complex ethical dilemmas in psychiatric nursing.

Structural Synaptic Plasticity Has High Memory Capacity and Can Explain Graded Amnesia, Catastrophic Forgetting, and the Spacing Effect

PubMed Central

Knoblauch, Andreas; Körner, Edgar; Körner, Ursula; Sommer, Friedrich T.

2014-01-01

Although already William James and, more explicitly, Donald Hebb's theory of cell assemblies have suggested that activity-dependent rewiring of neuronal networks is the substrate of learning and memory, over the last six decades most theoretical work on memory has focused on plasticity of existing synapses in prewired networks. Research in the last decade has emphasized that structural modification of synaptic connectivity is common in the adult brain and tightly correlated with learning and memory. Here we present a parsimonious computational model for learning by structural plasticity. The basic modeling units are “potential synapses” defined as locations in the network where synapses can potentially grow to connect two neurons. This model generalizes well-known previous models for associative learning based on weight plasticity. Therefore, existing theory can be applied to analyze how many memories and how much information structural plasticity can store in a synapse. Surprisingly, we find that structural plasticity largely outperforms weight plasticity and can achieve a much higher storage capacity per synapse. The effect of structural plasticity on the structure of sparsely connected networks is quite intuitive: Structural plasticity increases the “effectual network connectivity”, that is, the network wiring that specifically supports storage and recall of the memories. Further, this model of structural plasticity produces gradients of effectual connectivity in the course of learning, thereby explaining various cognitive phenomena including graded amnesia, catastrophic forgetting, and the spacing effect. PMID:24858841

Mathematics, thermodynamics, and modeling to address ten common misconceptions about protein structure, folding, and stability.

PubMed

Robic, Srebrenka

2010-01-01

To fully understand the roles proteins play in cellular processes, students need to grasp complex ideas about protein structure, folding, and stability. Our current understanding of these topics is based on mathematical models and experimental data. However, protein structure, folding, and stability are often introduced as descriptive, qualitative phenomena in undergraduate classes. In the process of learning about these topics, students often form incorrect ideas. For example, by learning about protein folding in the context of protein synthesis, students may come to an incorrect conclusion that once synthesized on the ribosome, a protein spends its entire cellular life time in its fully folded native confirmation. This is clearly not true; proteins are dynamic structures that undergo both local fluctuations and global unfolding events. To prevent and address such misconceptions, basic concepts of protein science can be introduced in the context of simple mathematical models and hands-on explorations of publicly available data sets. Ten common misconceptions about proteins are presented, along with suggestions for using equations, models, sequence, structure, and thermodynamic data to help students gain a deeper understanding of basic concepts relating to protein structure, folding, and stability.

A stochastic multiple imputation algorithm for missing covariate data in tree-structured survival analysis.

PubMed

Wallace, Meredith L; Anderson, Stewart J; Mazumdar, Sati

2010-12-20

Missing covariate data present a challenge to tree-structured methodology due to the fact that a single tree model, as opposed to an estimated parameter value, may be desired for use in a clinical setting. To address this problem, we suggest a multiple imputation algorithm that adds draws of stochastic error to a tree-based single imputation method presented by Conversano and Siciliano (Technical Report, University of Naples, 2003). Unlike previously proposed techniques for accommodating missing covariate data in tree-structured analyses, our methodology allows the modeling of complex and nonlinear covariate structures while still resulting in a single tree model. We perform a simulation study to evaluate our stochastic multiple imputation algorithm when covariate data are missing at random and compare it to other currently used methods. Our algorithm is advantageous for identifying the true underlying covariate structure when complex data and larger percentages of missing covariate observations are present. It is competitive with other current methods with respect to prediction accuracy. To illustrate our algorithm, we create a tree-structured survival model for predicting time to treatment response in older, depressed adults. Copyright © 2010 John Wiley & Sons, Ltd.

Structured Feedback Training for Time-Out: Efficacy and Efficiency in Comparison to a Didactic Method.

PubMed

Jensen, Scott A; Blumberg, Sean; Browning, Megan

2017-09-01

Although time-out has been demonstrated to be effective across multiple settings, little research exists on effective methods for training others to implement time-out. The present set of studies is an exploratory analysis of a structured feedback method for training time-out using repeated role-plays. The three studies examined (a) a between-subjects comparison to more a traditional didactic/video modeling method of time-out training, (b) a within-subjects comparison to traditional didactic/video modeling training for another skill, and (c) the impact of structured feedback training on in-home time-out implementation. Though findings are only preliminary and more research is needed, the structured feedback method appears across studies to be an efficient, effective method that demonstrates good maintenance of skill up to 3 months post training. Findings suggest, though do not confirm, a benefit of the structured feedback method over a more traditional didactic/video training model. Implications and further research on the method are discussed.

Quantitative theory of hydrophobic effect as a driving force of protein structure

PubMed Central

Perunov, Nikolay; England, Jeremy L

2014-01-01

Various studies suggest that the hydrophobic effect plays a major role in driving the folding of proteins. In the past, however, it has been challenging to translate this understanding into a predictive, quantitative theory of how the full pattern of sequence hydrophobicity in a protein shapes functionally important features of its tertiary structure. Here, we extend and apply such a phenomenological theory of the sequence-structure relationship in globular protein domains, which had previously been applied to the study of allosteric motion. In an effort to optimize parameters for the model, we first analyze the patterns of backbone burial found in single-domain crystal structures, and discover that classic hydrophobicity scales derived from bulk physicochemical properties of amino acids are already nearly optimal for prediction of burial using the model. Subsequently, we apply the model to studying structural fluctuations in proteins and establish a means of identifying ligand-binding and protein–protein interaction sites using this approach. PMID:24408023

Testing the simplex assumption underlying the Sport Motivation Scale: a structural equation modeling analysis.

PubMed

Li, F; Harmer, P

1996-12-01

Self-determination theory (Deci & Ryan, 1985) suggests that motivational orientation or regulatory styles with respect to various behaviors can be conceptualized along a continuum ranging from low (a motivation) to high (intrinsic motivation) levels of self-determination. This pattern is manifested in the rank order of correlations among these regulatory styles (i.e., adjacent correlations are expected to be higher than those more distant) and is known as a simplex structure. Using responses from the Sport Motivation Scale (Pelletier et al., 1995) obtained from a sample of 857 college students (442 men, 415 women), the present study tested the simplex structure underlying SMS subscales via structural equation modeling. Results confirmed the simplex model structure, indicating that the various motivational constructs are empirically organized from low to high self-determination. The simplex pattern was further found to be invariant across gender. Findings from this study support the construct validity of the SMS and have important implications for studies focusing on the influence of motivational orientation in sport.

A structural model for the flexural mechanics of nonwoven tissue engineering scaffolds.

PubMed

Engelmayr, George C; Sacks, Michael S

2006-08-01

The development of methods to predict the strength and stiffness of biomaterials used in tissue engineering is critical for load-bearing applications in which the essential functional requirements are primarily mechanical. We previously quantified changes in the effective stiffness (E) of needled nonwoven polyglycolic acid (PGA) and poly-L-lactic acid (PLLA) scaffolds due to tissue formation and scaffold degradation under three-point bending. Toward predicting these changes, we present a structural model for E of a needled nonwoven scaffold in flexure. The model accounted for the number and orientation of fibers within a representative volume element of the scaffold demarcated by the needling process. The spring-like effective stiffness of the curved fibers was calculated using the sinusoidal fiber shapes. Structural and mechanical properties of PGA and PLLA fibers and PGA, PLLA, and 50:50 PGA/PLLA scaffolds were measured and compared with model predictions. To verify the general predictive capability, the predicted dependence of E on fiber diameter was compared with experimental measurements. Needled nonwoven scaffolds were found to exhibit distinct preferred (PD) and cross-preferred (XD) fiber directions, with an E ratio (PD/XD) of approximately 3:1. The good agreement between the predicted and experimental dependence of E on fiber diameter (R2 = 0.987) suggests that the structural model can be used to design scaffolds with E values more similar to native soft tissues. A comparison with previous results for cell-seeded scaffolds (Engelmayr, G. C., Jr., et al., 2005, Biomaterials, 26(2), pp. 175-187) suggests, for the first time, that the primary mechanical effect of collagen deposition is an increase in the number of fiber-fiber bond points yielding effectively stiffer scaffold fibers. This finding indicated that the effects of tissue deposition on needled nonwoven scaffold mechanics do not follow a rule-of-mixtures behavior. These important results underscore the need for structural approaches in modeling the effects of engineered tissue formation on nonwoven scaffolds, and their potential utility in scaffold design.

Large-scale shell-model calculation with core excitations for neutron-rich nuclei beyond 132Sn

NASA Astrophysics Data System (ADS)

Jin, Hua; Hasegawa, Munetake; Tazaki, Shigeru; Kaneko, Kazunari; Sun, Yang

2011-10-01

The structure of neutron-rich nuclei with a few nucleons beyond 132Sn is investigated by means of large-scale shell-model calculations. For a considerably large model space, including neutron core excitations, a new effective interaction is determined by employing the extended pairing-plus-quadrupole model with monopole corrections. The model provides a systematical description for energy levels of A=133-135 nuclei up to high spins and reproduces available data of electromagnetic transitions. The structure of these nuclei is analyzed in detail, with emphasis of effects associated with core excitations. The results show evidence of hexadecupole correlation in addition to octupole correlation in this mass region. The suggested feature of magnetic rotation in 135Te occurs in the present shell-model calculation.

Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

PubMed Central

Chuang, Crystal K.; Rockel, Beate; Seyit, Gönül; Walian, Peter J.; Schönegge, Anne–Marie; Peters, Jürgen; Zwart, Petrus H.; Baumeister, Wolfgang; Jap, Bing K.

2010-01-01

Tripeptidyl peptidase II (TPP II) is the largest known eukaryotic protease (6MDa). It is believed to act downstream of the 26S proteasome cleaving tripeptides from the N– termini of longer peptides and it is implicated in numerous cellular processes. Here we report the structure of Drosophila TPP II determined by a hybrid approach: The structure of the dimer was solved by x–ray crystallography and docked into the three– dimensional map of the holocomplex obtained by single-particle cryo-electron microscopy. The resulting structure reveals the compartmentalization of the active sites inside a system of chambers and suggests the existence of a molecular ruler determining the size of the cleavage products. Furthermore, the structure suggests a model for activation of TPP II involving the relocation of a flexible loop and a repositioning of the active–site serine, coupling it to holocomplex assembly and active site sequestration. PMID:20676100

New perspectives on the geometry of the Albuquerque Basin, Rio Grande rift, New Mexico: Insights from geophysical models of rift-fill thickness

USGS Publications Warehouse

Grauch, V. J.; Connell, Sean D.

2013-01-01

Discrepancies among previous models of the geometry of the Albuquerque Basin motivated us to develop a new model using a comprehensive approach. Capitalizing on a natural separation between the densities of mainly Neogene basin fill (Santa Fe Group) and those of older rocks, we developed a three-dimensional (3D) geophysical model of syn-rift basin-fill thickness that incorporates well data, seismic-reflection data, geologic cross sections, and other geophysical data in a constrained gravity inversion. Although the resulting model does not show structures directly, it elucidates important aspects of basin geometry. The main features are three, 3–5-km-deep, interconnected structural depressions, which increase in size, complexity, and segmentation from north to south: the Santo Domingo, Calabacillas, and Belen subbasins. The increase in segmentation and complexity may reflect a transition of the Rio Grande rift from well-defined structural depressions in the north to multiple, segmented basins within a broader region of crustal extension to the south. The modeled geometry of the subbasins and their connections differs from a widely accepted structural model based primarily on seismic-reflection interpretations. Key elements of the previous model are an east-tilted half-graben block on the north separated from a west-tilted half-graben block on the south by a southwest-trending, scissor-like transfer zone. Instead, we find multiple subbasins with predominantly easterly tilts for much of the Albuquerque Basin, a restricted region of westward tilting in the southwestern part of the basin, and a northwesterly trending antiform dividing subbasins in the center of the basin instead of a major scissor-like transfer zone. The overall eastward tilt indicated by the 3D geophysical model generally conforms to stratal tilts observed for the syn-rift succession, implying a prolonged eastward tilting of the basin during Miocene time. An extensive north-south synform in the central part of the Belen subbasin suggests a possible path for the ancestral Rio Grande during late Miocene or early Pliocene time. Variations in rift-fill thickness correspond to pre-rift structures in several places, suggesting that a better understanding of pre-rift history may shed light on debates about structural inheritance within the rift.

Assembly and Channel Opening of Outer Membrane Protein in Tripartite Drug Efflux Pumps of Gram-negative Bacteria*

PubMed Central

Xu, Yongbin; Moeller, Arne; Jun, So-Young; Le, Minho; Yoon, Bo-Young; Kim, Jin-Sik; Lee, Kangseok; Ha, Nam-Chul

2012-01-01

Gram-negative bacteria are capable of expelling diverse xenobiotic substances from within the cell by use of three-component efflux pumps in which the energy-activated inner membrane transporter is connected to the outer membrane channel protein via the membrane fusion protein. In this work, we describe the crystal structure of the membrane fusion protein MexA from the Pseudomonas aeruginosa MexAB-OprM pump in the hexameric ring arrangement. Electron microscopy study on the chimeric complex of MexA and the outer membrane protein OprM reveals that MexA makes a tip-to-tip interaction with OprM, which suggests a docking model for MexA and OprM. This docking model agrees well with genetic results and depicts detailed interactions. Opening of the OprM channel is accompanied by the simultaneous exposure of a protein structure resembling a six-bladed cogwheel, which intermeshes with the complementary cogwheel structure in the MexA hexamer. Taken together, we suggest an assembly and channel opening model for the MexAB-OprM pump. This study provides a better understanding of multidrug resistance in Gram-negative bacteria. PMID:22308040

Correlation between surface reconstruction and polytypism in InAs nanowire selective area epitaxy

NASA Astrophysics Data System (ADS)

Liu, Ziyang; Merckling, Clement; Rooyackers, Rita; Richard, Olivier; Bender, Hugo; Mols, Yves; Vila, María; Rubio-Zuazo, Juan; Castro, Germán R.; Collaert, Nadine; Thean, Aaron; Vandervorst, Wilfried; Heyns, Marc

2017-12-01

The mechanism of widely observed intermixing of wurtzite and zinc-blende crystal structures in InAs nanowire (NW) grown by selective area epitaxy (SAE) is studied. We demonstrate that the crystal structure in InAs NW grown by SAE can be controlled using basic growth parameters, and wurtzitelike InAs NWs are achieved. We link the polytypic InAs NWs SAE to the reconstruction of the growth front (111)B surface. Surface reconstruction study of InAs (111) substrate and the following homoepitaxy experiment suggest that (111) planar defect nucleation is related to the (1 × 1) reconstruction of InAs (111)B surface. In order to reveal it more clearly, a model is presented to correlate growth temperature and arsenic partial pressure with InAs NW crystal structure. This model considers the transition between (1 × 1) and (2 × 2) surface reconstructions in the frame of adatom atoms adsorption/desorption, and the polytypism is thus linked to reconstruction quantitatively. The experimental data fit well with the model, which highly suggests that surface reconstruction plays an important role in the polytypism phenomenon in InAs NWs SAE.

Role of cerebellum in learning postural tasks.

PubMed

Ioffe, M E; Chernikova, L A; Ustinova, K I

2007-01-01

For a long time, the cerebellum has been known to be a structure related to posture and equilibrium control. According to the anatomic structure of inputs and internal structure of the cerebellum, its role in learning was theoretically reasoned and experimentally proved. The hypothesis of an inverse internal model based on feedback-error learning mechanism combines feedforward control by the cerebellum and feedback control by the cerebral motor cortex. The cerebellar cortex is suggested to acquire internal models of the body and objects in the external world. During learning of a new tool the motor cortex receives feedback from the realized movement while the cerebellum produces only feedforward command. To realize a desired movement without feedback of the realized movement, the cerebellum needs to form an inverse model of the hand/arm system. This suggestion was supported by FMRi data. The role of cerebellum in learning new postural tasks mainly concerns reorganization of natural synergies. A learned postural pattern in dogs has been shown to be disturbed after lesions of the cerebral motor cortex or cerebellar nuclei. In humans, learning voluntary control of center of pressure position is greatly disturbed after cerebellar lesions. However, motor cortex and basal ganglia are also involved in the feedback learning postural tasks.

Lateral Moho variations and the geometry of Main Himalayan Thrust beneath Nepal Himalayan orogen revealed by teleseismic receiver functions

NASA Astrophysics Data System (ADS)

He, Ping; Lei, Jianshe; Yuan, Xiaohui; Xu, Xiwei; Xu, Qiang; Liu, Zhikun; Mi, Qi; Zhou, Lianqing

2018-05-01

The lateral Moho variations and the geometry of the Main Himalayan Thrust under the Nepal Himalayan orogen are investigated to determine a new crustal model using a large number of high-quality receiver functions recorded by the HIMNT and HiCLIMB portable seismic networks. Our new model shows an evident and complicated lateral Moho depth variation of 8-16 km in the east-west direction, which is related to the surface tectonic features. These results suggest a non-uniformed crustal deformation, resulted from the splitting and/or tearing of the Indian plate during the northward subduction. Our migrated receiver function images illustrate a discernible ramp structure of the Main Himalayan Thrust with an abrupt downward bending close to the hypocenter of the 2015 Gorkha Mw 7.8 earthquake. The distribution of the aftershocks coincides with the present decollement structure. Integrating previous magnetotelluric soundings and tomographic results, our results suggest that the ramp-shaped structure within the Main Himalayan Thrust could enhance stress concentration leading to the nucleation of the large earthquake. Our new crustal model provides new clues to the formation of the Himalayan orogen.

PTSD's latent structure in Malaysian tsunami victims: assessing the newly proposed Dysphoric Arousal model.

PubMed

Armour, Cherie; Raudzah Ghazali, Siti; Elklit, Ask

2013-03-30

The underlying latent structure of Posttraumatic Stress Disorder (PTSD) is widely researched. However, despite a plethora of factor analytic studies, no single model has consistently been shown as superior to alternative models. The two most often supported models are the Emotional Numbing and the Dysphoria models. However, a recently proposed five-factor Dysphoric Arousal model has been gathering support over and above existing models. Data for the current study were gathered from Malaysian Tsunami survivors (N=250). Three competing models (Emotional Numbing/Dysphoria/Dysphoric Arousal) were specified and estimated using Confirmatory Factor Analysis (CFA). The Dysphoria model provided superior fit to the data compared to the Emotional Numbing model. However, using chi-square difference tests, the Dysphoric Arousal model showed a superior fit compared to both the Emotional Numbing and Dysphoria models. In conclusion, the current results suggest that the Dysphoric Arousal model better represents PTSD's latent structure and that items measuring sleeping difficulties, irritability/anger and concentration difficulties form a separate, unique PTSD factor. These results are discussed in relation to the role of Hyperarousal in PTSD's on-going symptom maintenance and in relation to the DSM-5. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Influence factors and forecast of carbon emission in China: structure adjustment for emission peak

NASA Astrophysics Data System (ADS)

Wang, B.; Cui, C. Q.; Li, Z. P.

2018-02-01

This paper introduced Principal Component Analysis and Multivariate Linear Regression Model to verify long-term balance relationships between Carbon Emissions and the impact factors. The integrated model of improved PCA and multivariate regression analysis model is attainable to figure out the pattern of carbon emission sources. Main empirical results indicate that among all selected variables, the role of energy consumption scale was largest. GDP and Population follow and also have significant impacts on carbon emission. Industrialization rate and fossil fuel proportion, which is the indicator of reflecting the economic structure and energy structure, have a higher importance than the factor of urbanization rate and the dweller consumption level of urban areas. In this way, some suggestions are put forward for government to achieve the peak of carbon emissions.

SL1 revisited: functional analysis of the structure and conformation of HIV-1 genome RNA.

PubMed

Sakuragi, Sayuri; Yokoyama, Masaru; Shioda, Tatsuo; Sato, Hironori; Sakuragi, Jun-Ichi

2016-11-11

The dimer initiation site/dimer linkage sequence (DIS/DLS) region of HIV is located on the 5' end of the viral genome and suggested to form complex secondary/tertiary structures. Within this structure, stem-loop 1 (SL1) is believed to be most important and an essential key to dimerization, since the sequence and predicted secondary structure of SL1 are highly stable and conserved among various virus subtypes. In particular, a six-base palindromic sequence is always present at the hairpin loop of SL1 and the formation of kissing-loop structure at this position between the two strands of genomic RNA is suggested to trigger dimerization. Although the higher-order structure model of SL1 is well accepted and perhaps even undoubted lately, there could be stillroom for consideration to depict the functional SL1 structure while in vivo (in virion or cell). In this study, we performed several analyses to identify the nucleotides and/or basepairing within SL1 which are necessary for HIV-1 genome dimerization, encapsidation, recombination and infectivity. We unexpectedly found that some nucleotides that are believed to contribute the formation of the stem do not impact dimerization or infectivity. On the other hand, we found that one G-C basepair involved in stem formation may serve as an alternative dimer interactive site. We also report on our further investigation of the roles of the palindromic sequences on viral replication. Collectively, we aim to assemble a more-comprehensive functional map of SL1 on the HIV-1 viral life cycle. We discovered several possibilities for a novel structure of SL1 in HIV-1 DLS. The newly proposed structure model suggested that the hairpin loop of SL1 appeared larger, and genome dimerization process might consist of more complicated mechanism than previously understood. Further investigations would be still required to fully understand the genome packaging and dimerization of HIV.

Homology modeling of a Class A GPCR in the inactive conformation: A quantitative analysis of the correlation between model/template sequence identity and model accuracy.

PubMed

Costanzi, Stefano; Skorski, Matthew; Deplano, Alessandro; Habermehl, Brett; Mendoza, Mary; Wang, Keyun; Biederman, Michelle; Dawson, Jessica; Gao, Jia

2016-11-01

With the present work we quantitatively studied the modellability of the inactive state of Class A G protein-coupled receptors (GPCRs). Specifically, we constructed models of one of the Class A GPCRs for which structures solved in the inactive state are available, namely the β 2 AR, using as templates each of the other class members for which structures solved in the inactive state are also available. Our results showed a detectable linear correlation between model accuracy and model/template sequence identity. This suggests that the likely accuracy of the homology models that can be built for a given receptor can be generally forecasted on the basis of the available templates. We also probed whether sequence alignments that allow for the presence of gaps within the transmembrane domains to account for structural irregularities afford better models than the classical alignment procedures that do not allow for the presence of gaps within such domains. As our results indicated, although the overall differences are very subtle, the inclusion of internal gaps within the transmembrane domains has a noticeable a beneficial effect on the local structural accuracy of the domain in question. Copyright © 2016 Elsevier Inc. All rights reserved.

Spontaneous parity violation and SUSY strong gauge theory

NASA Astrophysics Data System (ADS)

Haba, Naoyuki; Ohki, Hiroshi

2012-07-01

We suggest simple models of spontaneous parity violation in supersymmetric strong gauge theory. We focus on left-right symmetric model and investigate vacuum with spontaneous parity violation. Non-perturbative effects are calculable in supersymmetric gauge theory, and we suggest new models. Our models show confinement, so that we try to understand them by using a dual description of the theory. The left-right symmetry breaking and electroweak symmetry breaking are simultaneously occurred with the suitable energy scale hierarchy. This structure has several advantages compared to the MSSM. The scale of the Higgs mass (left-right breaking scale) and that of VEVs are different, so the SUSY little hierarchy problems are absent. The second model also induces spontaneous supersymmetry breaking [1].

Relationship between the Decomposition Process of Coarse Woody Debris and Fungal Community Structure as Detected by High-Throughput Sequencing in a Deciduous Broad-Leaved Forest in Japan

PubMed Central

Yamashita, Satoshi; Masuya, Hayato; Abe, Shin; Masaki, Takashi; Okabe, Kimiko

2015-01-01

We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of Fagus and Quercus in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of Fagus was greater than that of Quercus. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both Fagus and Quercus changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of Fagus was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of Quercus was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of Fagus coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process. PMID:26110605

Spatial structure increases the waiting time for cancer

PubMed Central

Martens, Erik A.; Kostadinov, Rumen; Maley, Carlo C.; Hallatschek, Oskar

2012-01-01

Cancer results from a sequence of genetic and epigenetic changes which lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells, and thus, to a selective advantage of pre-cancerous cells. The notion of cancer progression as an evolutionary process has been experiencing increasing interest in recent years. Many efforts have been made to better understand and predict the progression to cancer using mathematical models; these mostly consider the evolution of a well-mixed cell population, even though pre-cancerous cells often evolve in highly structured epithelial tissues. In this study, we propose a novel model of cancer progression that considers a spatially structured cell population where clones expand via adaptive waves. This model is used to assess two different paradigms of asexual evolution that have been suggested to delineate the process of cancer progression. The standard scenario of periodic selection assumes that driver mutations are accumulated strictly sequentially over time. However, when the mutation supply is sufficiently high, clones may arise simultaneously on distinct genetic backgrounds, and clonal adaptation waves interfere with each other. We find that in the presence of clonal interference, spatial structure increases the waiting time for cancer, leads to a patchwork structure of non-uniformly sized clones, decreases the survival probability of virtually neutral (passenger) mutations, and that genetic distance begins to increase over a characteristic length scale Lc. These characteristic features of clonal interference may help to predict the onset of cancers with pronounced spatial structure and to interpret spatially-sampled genetic data obtained from biopsies. Our estimates suggest that clonal interference likely occurs in the progression of colon cancer, and possibly other cancers where spatial structure matters. PMID:22707911

Spatial structure increases the waiting time for cancer

NASA Astrophysics Data System (ADS)

Martens, Erik A.; Kostadinov, Rumen; Maley, Carlo C.; Hallatschek, Oskar

2011-11-01

Cancer results from a sequence of genetic and epigenetic changes that lead to a variety of abnormal phenotypes including increased proliferation and survival of somatic cells and thus to a selective advantage of pre-cancerous cells. The notion of cancer progression as an evolutionary process has been attracting increasing interest in recent years. A great deal of effort has been made to better understand and predict the progression to cancer using mathematical models; these mostly consider the evolution of a well-mixed cell population, even though pre-cancerous cells often evolve in highly structured epithelial tissues. In this study, we propose a novel model of cancer progression that considers a spatially structured cell population where clones expand via adaptive waves. This model is used to assess two different paradigms of asexual evolution that have been suggested to delineate the process of cancer progression. The standard scenario of periodic selection assumes that driver mutations are accumulated strictly sequentially over time. However, when the mutation supply is sufficiently high, clones may arise simultaneously on distinct genetic backgrounds, and clonal adaptation waves interfere with each other. We find that in the presence of clonal interference, spatial structure increases the waiting time for cancer, leads to a patchwork structure of non-uniformly sized clones and decreases the survival probability of virtually neutral (passenger) mutations, and that genetic distance begins to increase over a characteristic length scale Lc. These characteristic features of clonal interference may help us to predict the onset of cancers with pronounced spatial structure and to interpret spatially sampled genetic data obtained from biopsies. Our estimates suggest that clonal interference likely occurs in the progression of colon cancer and possibly other cancers where spatial structure matters.

Modelling intelligent behavior

NASA Technical Reports Server (NTRS)

Green, H. S.; Triffet, T.

1993-01-01

An introductory discussion of the related concepts of intelligence and consciousness suggests criteria to be met in the modeling of intelligence and the development of intelligent materials. Methods for the modeling of actual structure and activity of the animal cortex have been found, based on present knowledge of the ionic and cellular constitution of the nervous system. These have led to the development of a realistic neural network model, which has been used to study the formation of memory and the process of learning. An account is given of experiments with simple materials which exhibit almost all properties of biological synapses and suggest the possibility of a new type of computer architecture to implement an advanced type of artificial intelligence.

Mass Spectrometry Based Identification of Geometric Isomers during Metabolic Stability Study of a New Cytotoxic Sulfonamide Derivatives Supported by Quantitative Structure-Retention Relationships

PubMed Central

Belka, Mariusz; Hewelt-Belka, Weronika; Sławiński, Jarosław; Bączek, Tomasz

2014-01-01

A set of 15 new sulphonamide derivatives, presenting antitumor activity have been subjected to a metabolic stability study. The results showed that besides products of biotransformation, some additional peaks occurred in chromatograms. Tandem mass spectrometry revealed the same mass and fragmentation pathway, suggesting that geometric isomerization occurred. Thus, to support this hypothesis, quantitative structure-retention relationships were applied. Human liver microsomes were used as an in vitro model of metabolism. The biotransformation reactions were tracked by liquid chromatography assay and additionally, fragmentation mass spectra were recorded. In silico molecular modeling at a semi-empirical level was conducted as a starting point for molecular descriptor calculations. A quantitative structure-retention relationship model was built applying multiple linear regression based on selected three-dimensional descriptors. The studied compounds revealed high metabolic stability, with a tendency to form hydroxylated biotransformation products. However, significant chemical instability in conditions simulating human body fluids was noticed. According to literature and MS data geometrical isomerization was suggested. The developed in sillico model was able to describe the relationship between the geometry of isomer pairs and their chromatographic retention properties, thus it supported the hypothesis that the observed pairs of peaks are most likely geometric isomers. However, extensive structural investigations are needed to fully identify isomers’ geometry. An effort to describe MS fragmentation pathways of novel chemical structures is often not enough to propose structures of potent metabolites and products of other chemical reactions that can be observed in compound solutions at early drug discovery studies. The results indicate that the relatively non-expensive and not time- and labor-consuming in sillico approach could be a good supportive tool assisting the identification of cis-trans isomers based on retention data. This methodology can be helpful during the structural identification of biotransformation and degradation products of new chemical entities - potential new drugs. PMID:24893169

Generic Features of Tertiary Chromatin Structure as Detected in Natural Chromosomes

PubMed Central

Müller, Waltraud G.; Rieder, Dietmar; Kreth, Gregor; Cremer, Christoph; Trajanoski, Zlatko; McNally, James G.

2004-01-01

Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different ∼400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or “beads”, referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters. PMID:15485905

Generalization Technique for 2D+SCALE Dhe Data Model

NASA Astrophysics Data System (ADS)

Karim, Hairi; Rahman, Alias Abdul; Boguslawski, Pawel

2016-10-01

Different users or applications need different scale model especially in computer application such as game visualization and GIS modelling. Some issues has been raised on fulfilling GIS requirement of retaining the details while minimizing the redundancy of the scale datasets. Previous researchers suggested and attempted to add another dimension such as scale or/and time into a 3D model, but the implementation of scale dimension faces some problems due to the limitations and availability of data structures and data models. Nowadays, various data structures and data models have been proposed to support variety of applications and dimensionality but lack research works has been conducted in terms of supporting scale dimension. Generally, the Dual Half Edge (DHE) data structure was designed to work with any perfect 3D spatial object such as buildings. In this paper, we attempt to expand the capability of the DHE data structure toward integration with scale dimension. The description of the concept and implementation of generating 3D-scale (2D spatial + scale dimension) for the DHE data structure forms the major discussion of this paper. We strongly believed some advantages such as local modification and topological element (navigation, query and semantic information) in scale dimension could be used for the future 3D-scale applications.

Narcissistic Personality Disorder and the Structure of Common Mental Disorders.

PubMed

Eaton, Nicholas R; Rodriguez-Seijas, Craig; Krueger, Robert F; Campbell, W Keith; Grant, Bridget F; Hasin, Deborah S

2017-08-01

Narcissistic personality disorder (NPD) shows high rates of comorbidity with mood, anxiety, substance use, and other personality disorders. Previous bivariate comorbidity investigations have left NPD multivariate comorbidity patterns poorly understood. Structural psychopathology research suggests that two transdiagnostic factors, internalizing (with distress and fear subfactors) and externalizing, account for comorbidity among common mental disorders. NPD has rarely been evaluated within this framework, with studies producing equivocal results. We investigated how NPD related to other mental disorders in the internalizing-externalizing model using diagnoses from a nationally representative sample (N = 34,653). NPD was best conceptualized as a distress disorder. NPD variance accounted for by transdiagnostic factors was modest, suggesting its variance is largely unique in the context of other common mental disorders. Results clarify NPD multivariate comorbidity, suggest avenues for classification and clinical endeavors, and highlight the need to understand vulnerable and grandiose narcissism subtypes' comorbidity patterns and structural relations.

Theoretical study of the ionospheric plasma cave in the equatorial ionization anomaly region

NASA Astrophysics Data System (ADS)

Chen, Yu-Tsung; Lin, C. H.; Chen, C. H.; Liu, J. Y.; Huba, J. D.; Chang, L. C.; Liu, H.-L.; Lin, J. T.; Rajesh, P. K.

2014-12-01

This paper investigates the physical mechanism of an unusual equatorial electron density structure, plasma cave, located underneath the equatorial ionization anomaly by using theoretical simulations. The simulation results provide important new understanding of the dynamics of the equatorial ionosphere. It has been suggested previously that unusual E>⇀×B>⇀ drifts might be responsible for the observed plasma cave structure, but model simulations in this paper suggest that the more likely cause is latitudinal meridional neutral wind variations. The neutral winds are featured by two divergent wind regions at off-equator latitudes and a convergent wind region around the magnetic equator, resulting in plasma divergences and convergence, respectively, to form the plasma caves structure. The tidal-decomposition analysis further suggests that the cave related meridional neutral winds and the intensity of plasma cave are highly associated with the migrating terdiurnal tidal component of the neutral winds.

Middle Childhood Antecedents to Progressions in Male Adolescent Substance Use: An Ecological Analysis of Risk and Protection.

ERIC Educational Resources Information Center

Dishion, Thomas J.; Capaldi, Deborah M.; Yoerger, Karen

1999-01-01

This study examined antecedents to early patterned alcohol and tobacco use and marijuana experimentation between ages 11 and 16 for an at-risk male sample. Findings suggested that family, peer, and child characteristics were inextricably connected within an ecology of development. A structural equation prediction model suggested a higher order…

Time domain simulation of novel photovoltaic materials

NASA Astrophysics Data System (ADS)

Chung, Haejun

Thin-film silicon-based solar cells have operated far from the Shockley- Queisser limit in all experiments to date. Novel light-trapping structures, however, may help address this limitation. Finite-difference time domain simulation methods offer the potential to accurately determine the light-trapping potential of arbitrary dielectric structures, but suffer from materials modeling problems. In this thesis, existing dispersion models for novel photovoltaic materials will be reviewed, and a novel dispersion model, known as the quadratic complex rational function (QCRF), will be proposed. It has the advantage of accurately fitting experimental semiconductor dielectric values over a wide bandwidth in a numerically stable fashion. Applying the proposed dispersion model, a statistically correlated surface texturing method will be suggested, and light absorption rates of it will be explained. In future work, these designs will be combined with other structures and optimized to help guide future experiments.

Discovering relevance knowledge in data: a growing cell structures approach.

PubMed

Azuaje, F; Dubitzky, W; Black, N; Adamson, K

2000-01-01

Both information retrieval and case-based reasoning systems rely on effective and efficient selection of relevant data. Typically, relevance in such systems is approximated by similarity or indexing models. However, the definition of what makes data items similar or how they should be indexed is often nontrivial and time-consuming. Based on growing cell structure artificial neural networks, this paper presents a method that automatically constructs a case retrieval model from existing data. Within the case-based reasoning (CBR) framework, the method is evaluated for two medical prognosis tasks, namely, colorectal cancer survival and coronary heart disease risk prognosis. The results of the experiments suggest that the proposed method is effective and robust. To gain a deeper insight and understanding of the underlying mechanisms of the proposed model, a detailed empirical analysis of the models structural and behavioral properties is also provided.

Structural Design Optimization of Doubly-Fed Induction Generators Using GeneratorSE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sethuraman, Latha; Fingersh, Lee J; Dykes, Katherine L

2017-11-13

A wind turbine with a larger rotor swept area can generate more electricity, however, this increases costs disproportionately for manufacturing, transportation, and installation. This poster presents analytical models for optimizing doubly-fed induction generators (DFIGs), with the objective of reducing the costs and mass of wind turbine drivetrains. The structural design for the induction machine includes models for the casing, stator, rotor, and high-speed shaft developed within the DFIG module in the National Renewable Energy Laboratory's wind turbine sizing tool, GeneratorSE. The mechanical integrity of the machine is verified by examining stresses, structural deflections, and modal properties. The optimization results aremore » then validated using finite element analysis (FEA). The results suggest that our analytical model correlates with the FEA in some areas, such as radial deflection, differing by less than 20 percent. But the analytical model requires further development for axial deflections, torsional deflections, and stress calculations.« less

Chemical structure-based predictive model for methanogenic anaerobic biodegradation potential.

PubMed

Meylan, William; Boethling, Robert; Aronson, Dallas; Howard, Philip; Tunkel, Jay

2007-09-01

Many screening-level models exist for predicting aerobic biodegradation potential from chemical structure, but anaerobic biodegradation generally has been ignored by modelers. We used a fragment contribution approach to develop a model for predicting biodegradation potential under methanogenic anaerobic conditions. The new model has 37 fragments (substructures) and classifies a substance as either fast or slow, relative to the potential to be biodegraded in the "serum bottle" anaerobic biodegradation screening test (Organization for Economic Cooperation and Development Guideline 311). The model correctly classified 90, 77, and 91% of the chemicals in the training set (n = 169) and two independent validation sets (n = 35 and 23), respectively. Accuracy of predictions of fast and slow degradation was equal for training-set chemicals, but fast-degradation predictions were less accurate than slow-degradation predictions for the validation sets. Analysis of the signs of the fragment coefficients for this and the other (aerobic) Biowin models suggests that in the context of simple group contribution models, the majority of positive and negative structural influences on ultimate degradation are the same for aerobic and methanogenic anaerobic biodegradation.

Economic evaluation in chronic pain: a systematic review and de novo flexible economic model.

PubMed

Sullivan, W; Hirst, M; Beard, S; Gladwell, D; Fagnani, F; López Bastida, J; Phillips, C; Dunlop, W C N

2016-07-01

There is unmet need in patients suffering from chronic pain, yet innovation may be impeded by the difficulty of justifying economic value in a field beset by data limitations and methodological variability. A systematic review was conducted to identify and summarise the key areas of variability and limitations in modelling approaches in the economic evaluation of treatments for chronic pain. The results of the literature review were then used to support the development of a fully flexible open-source economic model structure, designed to test structural and data assumptions and act as a reference for future modelling practice. The key model design themes identified from the systematic review included: time horizon; titration and stabilisation; number of treatment lines; choice/ordering of treatment; and the impact of parameter uncertainty (given reliance on expert opinion). Exploratory analyses using the model to compare a hypothetical novel therapy versus morphine as first-line treatments showed cost-effectiveness results to be sensitive to structural and data assumptions. Assumptions about the treatment pathway and choice of time horizon were key model drivers. Our results suggest structural model design and data assumptions may have driven previous cost-effectiveness results and ultimately decisions based on economic value. We therefore conclude that it is vital that future economic models in chronic pain are designed to be fully transparent and hope our open-source code is useful in order to aspire to a common approach to modelling pain that includes robust sensitivity analyses to test structural and parameter uncertainty.

Causal learning with local computations.

PubMed

Fernbach, Philip M; Sloman, Steven A

2009-05-01

The authors proposed and tested a psychological theory of causal structure learning based on local computations. Local computations simplify complex learning problems via cues available on individual trials to update a single causal structure hypothesis. Structural inferences from local computations make minimal demands on memory, require relatively small amounts of data, and need not respect normative prescriptions as inferences that are principled locally may violate those principles when combined. Over a series of 3 experiments, the authors found (a) systematic inferences from small amounts of data; (b) systematic inference of extraneous causal links; (c) influence of data presentation order on inferences; and (d) error reduction through pretraining. Without pretraining, a model based on local computations fitted data better than a Bayesian structural inference model. The data suggest that local computations serve as a heuristic for learning causal structure. Copyright 2009 APA, all rights reserved.

Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus

PubMed Central

Leyrat, Cedric; Renner, Max; Harlos, Karl; Grimes, Jonathan M.

2013-01-01

Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (Pced) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of Pced using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of Pced. Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (Pcore), that is surrounded by flexible regions with α-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales Pced structures suggests that Pced evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes. PMID:24224051

A viscoelastic fluid-structure interaction model for carotid arteries under pulsatile flow.

PubMed

Wang, Zhongjie; Wood, Nigel B; Xu, Xiao Yun

2015-05-01

In this study, a fluid-structure interaction model (FSI) incorporating viscoelastic wall behaviour is developed and applied to an idealized model of the carotid artery under pulsatile flow. The shear and bulk moduli of the arterial wall are described by Prony series, where the parameters can be derived from in vivo measurements. The aim is to develop a fully coupled FSI model that can be applied to realistic arterial geometries with normal or pathological viscoelastic wall behaviour. Comparisons between the numerical and analytical solutions for wall displacements demonstrate that the coupled model is capable of predicting the viscoelastic behaviour of carotid arteries. Comparisons are also made between the solid only and FSI viscoelastic models, and the results suggest that the difference in radial displacement between the two models is negligible. Copyright © 2015 John Wiley & Sons, Ltd.

Examining the Dynamic Structure of Daily Internalizing and Externalizing Behavior at Multiple Levels of Analysis

PubMed Central

Wright, Aidan G. C.; Beltz, Adriene M.; Gates, Kathleen M.; Molenaar, Peter C. M.; Simms, Leonard J.

2015-01-01

Psychiatric diagnostic covariation suggests that the underlying structure of psychopathology is not one of circumscribed disorders. Quantitative modeling of individual differences in diagnostic patterns has uncovered several broad domains of mental disorder liability, of which the Internalizing and Externalizing spectra have garnered the greatest support. These dimensions have generally been estimated from lifetime or past-year comorbidity patters, which are distal from the covariation of symptoms and maladaptive behavior that ebb and flow in daily life. In this study, structural models are applied to daily diary data (Median = 94 days) of maladaptive behaviors collected from a sample (N = 101) of individuals diagnosed with personality disorders (PDs). Using multilevel and unified structural equation modeling, between-person, within-person, and person-specific structures were estimated from 16 behaviors that are encompassed by the Internalizing and Externalizing spectra. At the between-person level (i.e., individual differences in average endorsement across days) we found support for a two-factor Internalizing–Externalizing model, which exhibits significant associations with corresponding diagnostic spectra. At the within-person level (i.e., dynamic covariation among daily behavior pooled across individuals) we found support for a more differentiated, four-factor, Negative Affect-Detachment-Hostility-Disinhibition structure. Finally, we demonstrate that the person-specific structures of associations between these four domains are highly idiosyncratic. PMID:26732546

OBSERVATIONS AND MAGNETIC FIELD MODELING OF A SOLAR POLAR CROWN PROMINENCE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Su Yingna; Van Ballegooijen, Adriaan, E-mail: ynsu@head.cfa.harvard.edu

2012-10-01

We present observations and magnetic field modeling of the large polar crown prominence that erupted on 2010 December 6. Combination of Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly (AIA) and STEREO{sub B}ehind/EUVI allows us to see the fine structures of this prominence both at the limb and on the disk. We focus on the structures and dynamics of this prominence before the eruption. This prominence contains two parts: an active region part containing mainly horizontal threads and a quiet-Sun part containing mainly vertical threads. On the northern side of the prominence channel, both AIA and EUVI observe bright features which appearmore » to be the lower legs of loops that go above then join in the filament. Filament materials are observed to frequently eject horizontally from the active region part to the quiet-Sun part. This ejection results in the formation of a dense-column structure (concentration of dark vertical threads) near the border between the active region and the quiet Sun. Using the flux rope insertion method, we create nonlinear force-free field models based on SDO/Helioseismic and Magnetic Imager line-of-sight magnetograms. A key feature of these models is that the flux rope has connections with the surroundings photosphere, so its axial flux varies along the filament path. The height and location of the dips of field lines in our models roughly replicate those of the observed prominence. Comparison between model and observations suggests that the bright features on the northern side of the channel are the lower legs of the field lines that turn into the flux rope. We suggest that plasma may be injected into the prominence along these field lines. Although the models fit the observations quiet well, there are also some interesting differences. For example, the models do not reproduce the observed vertical threads and cannot explain the formation of the dense-column structure.« less

Investigation of Secondary School, Undergraduate, and Graduate Learners' Mental Models of Ionic Bonding.

ERIC Educational Resources Information Center

Coll, Richard K.; Treagust, David F.

2003-01-01

Explores secondary school, undergraduate, and graduate level learners' mental models of bonding with ionic substances through an interview protocol involving the use of physical substances and a focus card containing depictions of ionic bonding and structure. Suggests that teachers and university faculty need to provide stronger links between the…

Compact Representations of Extended Causal Models

ERIC Educational Resources Information Center

Halpern, Joseph Y.; Hitchcock, Christopher

2013-01-01

Judea Pearl (2000) was the first to propose a definition of actual causation using causal models. A number of authors have suggested that an adequate account of actual causation must appeal not only to causal structure but also to considerations of "normality." In Halpern and Hitchcock (2011), we offer a definition of actual causation…

The Charlotte Action Research Project: A Model for Direct and Mutually Beneficial Community-University Engagement

ERIC Educational Resources Information Center

Morrell, Elizabeth; Sorensen, Janni; Howarth, Joe

2015-01-01

This article describes the evolution of the Charlotte Action Research Project (CHARP), a community-university partnership founded in 2008 at the University of North Carolina at Charlotte, and focuses particularly on the program's unique organizational structure. Research findings of a project evaluation suggest that the CHARP model's unique…

Contributions of Memory Circuits to Language: The Declarative/Procedural Model

ERIC Educational Resources Information Center

Ullman, Michael T.

2004-01-01

The structure of the brain and the nature of evolution suggest that, despite its uniqueness, language likely depends on brain systems that also subserve other functions. The declarative/procedural (DP) model claims that the mental lexicon of memorized word-specific knowledge depends on the largely temporal-lobe substrates of declarative memory,…

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bierlich, Christian; Gustafson, Gösta; Lönnblad, Leif

In models for hadron collisions based on string hadronization, the strings are usually treated as independent, allowing no interaction between the confined colour fields. In studies of nucleus collisions it has been suggested that strings close in space can fuse to form "colour ropes." Such ropes are expected to give more strange particles and baryons, which also has been suggested as a signal for plasma formation. Overlapping strings can also be expected in pp collisions, where usually no phase transition is expected. In particular at the high LHC energies the expected density of strings is quite high. To investigate possiblemore » effects of rope formation, we present a model in which strings are allowed to combine into higher multiplets, giving rise to increased production of baryons and strangeness, or recombine into singlet structures and vanish. Also a crude model for strings recombining into junction structures is considered, again giving rise to increased baryon production. The models are implemented in the DIPSY MC event generator, using PYTHIA8 for hadronization, and comparison to pp minimum bias data, reveals improvement in the description of identified particle spectra.« less

Effects of overlapping strings in pp collisions

DOE PAGES

Bierlich, Christian; Gustafson, Gösta; Lönnblad, Leif; ...

2015-03-26

In models for hadron collisions based on string hadronization, the strings are usually treated as independent, allowing no interaction between the confined colour fields. In studies of nucleus collisions it has been suggested that strings close in space can fuse to form "colour ropes." Such ropes are expected to give more strange particles and baryons, which also has been suggested as a signal for plasma formation. Overlapping strings can also be expected in pp collisions, where usually no phase transition is expected. In particular at the high LHC energies the expected density of strings is quite high. To investigate possiblemore » effects of rope formation, we present a model in which strings are allowed to combine into higher multiplets, giving rise to increased production of baryons and strangeness, or recombine into singlet structures and vanish. Also a crude model for strings recombining into junction structures is considered, again giving rise to increased baryon production. The models are implemented in the DIPSY MC event generator, using PYTHIA8 for hadronization, and comparison to pp minimum bias data, reveals improvement in the description of identified particle spectra.« less

Fluid Dynamics of Thrombosis in Transcatheter Aortic Valves

NASA Astrophysics Data System (ADS)

Seo, Jung Hee; Zhu, Chi; Dou, Zhongwang; Resar, Jon; Mittal, Rajat

2017-11-01

Transcatheter aortic valve replacement (TAVR) with bioprosthetic valves (BPV) has become highly prevalent in recent years. While one advantage of BPVs over mechanical ones is the lower incidence of valve thrombosis, recent clinical studies have suggested a higher than expected incidence of subclinical bioprosthetic valve thrombosis (BVT). Many factors that might affect the transvalvular hemodynamics including the valve position, orientation, stent, and interaction with the coronary flow, have been suggested, but the casual mechanisms of valve thrombosis are still unknown. In the present study, the hemodynamics associated with the formation of BVT is investigated using a novel, coupled flow-structure-biochemical computational modeling. A reduced degree of freedom, fluid-structure-interaction model is proposed for the efficient simulation of the hemodynamics and leaflet dynamics in the BPVs. Simple models to take into account the effects of the stent and coronary flows have also been developed. Simulations are performed for canonical models of BPVs in the aorta in various configurations and the results are examined to provide insights into the mechanisms for valve thrombosis. Supported by the NSF Grants IIS-1344772, CBET-1511200 and NSF XSEDE Grant TG-CTS100002.

Theoretical model for VITA-educed coherent structures in the wall region of a turbulent boundary layer

NASA Technical Reports Server (NTRS)

Landahl, Marten T.

1988-01-01

Experiments on wall-bounded shear flows (channel flows and boundary layers) have indicated that the turbulence in the region close to the wall exhibits a characteristic intermittently formed pattern of coherent structures. For a quantitative study of coherent structures it is necessary to make use of conditional sampling. One particularly successful sampling technique is the Variable Integration Time Averaging technique (VITA) first explored by Blackwelder and Kaplan (1976). In this, an event is assumed to occur when the short time variance exceeds a certain threshold multiple of the mean square signal. The analysis presented removes some assumptions in the earlier models in that the effects of pressure and viscosity are taken into account in an approximation based on the assumption that the near-wall structures are highly elongated in the streamwise direction. The appropriateness of this is suggested by the observations but is also self consistent with the results of the model which show that the streamwise dimension of the structure grows with time, so that the approximation should improve with the age of the structure.

Tubular growth and bead formation in the lyotropic lamellar phase of a lipid.

PubMed

Bhatia, Tripta; Hatwalne, Yashodhan; Madhusudana, N V

2015-07-28

We use fluorescence confocal polarised microscopy (FCPM) to study tubular growth upon hydration of dry DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) in water and water-glycerol mixtures. We have developed a model to relate the FCPM intensity profiles to the multilamellar structures of the tubules. Insertion of an additional patch inside a tubule produces a beaded structure, while a straight configuration is retained if the growth is on the outside. We use a simple model to suggest that reduction in overall curvature energy drives bead formation.

Weak low-frequency electromagnetic oscillations in water.

PubMed

Liboff, A R; Poggi, Claudio; Pratesi, Piero

2017-01-01

Recent observations of low-frequency electromagnetic oscillations in water suggest an inductive structural component. Accordingly, we assume a helical basis enabling us to model water as an LC tuned oscillator. A proposed tetrahedral structure consisting of three water molecules and one hydronium ion is incorporated into the Boerdijk-Coxeter tetrahelix to form long water chains that are shown to have resonance frequencies consistent with observation. This model also serves to explain separately reported claims of ion cyclotron resonance of hydronium ions, in that the tetrahelix provides a built-in path for helical proton-hopping.

A Descriptive Study of Nursing Peer-Review Programs in US Magnet® Hospitals.

PubMed

Roberts, Holli; Cronin, Sherill Nones

2017-04-01

The goal of this study was to assess the types of nursing peer review (NPR) programs in US Magnet® organizations. The 2 most predominant models of NPR programs in the literature are performance evaluation and clinical peer review. The literature on clinical peer review is primarily descriptive, outlining structures and anecdotal outcomes. Participants from hospitals holding Magnet recognition were selected using a stratified random-sampling method. A survey developed by the researchers assessed the presence of NPR. If clinical NPR was in place, program design, evaluation measurements, and barriers were explored. Findings suggest wide variability in NPR models. More than one-third of the respondents conduct peer evaluation as the only mechanism of NPR. Most hospitals with a clinical peer-review program reported a case review structure and process measurements not supported by data. The variations noted in this study suggest more research is needed to measure the effectiveness of NPR models and associated outcomes.

Cytoskeleton-mediated templating of complex cellulose-scaffolded extracellular structure and its association with oikosins in the urochordate Oikopleura.

PubMed

Sagane, Yoshimasa; Hosp, Julia; Zech, Karin; Thompson, Eric M

2011-05-01

Oriented cellulose deposition is critical to plant patterning and models suggest microtubules constrain cellulose synthase movements through the plasma membrane. Though widespread in plants, urochordates are the only animals that synthesize cellulose. We characterized the distinctive cellulose microfibril scaffold of the larvacean house and its interaction with house structural proteins (oikosins). Targeted disruption of cytoskeletal elements, secretory pathways, and plasma membrane organization, suggested a working model for templating extracellular cellulose microfibrils from animal cells that shows both convergence and differences to plant models. Specialized cortical F-actin arrays template microfibril orientation and glycosylphosphatidylinositol-anchored proteins in lipid rafts may act as scaffolding proteins in microfibril elongation. Microtubules deliver and maintain cellulose synthase complexes to specific cell membrane sites rather than orienting their movement through the membrane. Oikosins are incorporated into house compartments directly above their corresponding cellular field of expression and interact with the cellulose scaffold to a variable extent.

A model for the biological precipitation of Precambrian iron-formation

NASA Technical Reports Server (NTRS)

Laberge, G. L.

1986-01-01

A biological model for the precipitation of Precambrian iron formations is presented. Assuming an oxygen deficient atmosphere and water column to allow sufficient Fe solubility, it is proposed that local oxidizing environments, produced biologically, led to precipitation of iron formations. It is further suggested that spheroidal structures about 30 mm in diameter, which are widespread in low grade cherty rion formations, are relict forms of the organic walled microfossil Eosphaera tylerii. The presence of these structures suggests that the organism may have had a siliceous test, which allowed sufficient rigidity for accumulation and preservation. The model involves precipitation of ferric hydrates by oxidation of iron in the photic zone by a variety of photosynthetic organisms. Silica may have formed in the frustules of silica secreting organisms, including Eosphaera tylerii. Iron formates formed, therefore, by a sediment rain of biologically produced ferric hydrates and silica and other organic material. Siderite and hematite formed diagenetically on basin floors, and subsequent metamorphism produced magnetite and iron silicates.

Modelling the Evolution of Social Structure

PubMed Central

Sutcliffe, A. G.; Dunbar, R. I. M.; Wang, D.

2016-01-01

Although simple social structures are more common in animal societies, some taxa (mainly mammals) have complex, multi-level social systems, in which the levels reflect differential association. We develop a simulation model to explore the conditions under which multi-level social systems of this kind evolve. Our model focuses on the evolutionary trade-offs between foraging and social interaction, and explores the impact of alternative strategies for distributing social interaction, with fitness criteria for wellbeing, alliance formation, risk, stress and access to food resources that reward social strategies differentially. The results suggest that multi-level social structures characterised by a few strong relationships, more medium ties and large numbers of weak ties emerge only in a small part of the overall fitness landscape, namely where there are significant fitness benefits from wellbeing and alliance formation and there are high levels of social interaction. In contrast, ‘favour-the-few’ strategies are more competitive under a wide range of fitness conditions, including those producing homogeneous, single-level societies of the kind found in many birds and mammals. The simulations suggest that the development of complex, multi-level social structures of the kind found in many primates (including humans) depends on a capacity for high investment in social time, preferential social interaction strategies, high mortality risk and/or differential reproduction. These conditions are characteristic of only a few mammalian taxa. PMID:27427758

Crystal structure of LGR4-Rspo1 complex: insights into the divergent mechanisms of ligand recognition by leucine-rich repeat G-protein-coupled receptors (LGRs).

PubMed

Xu, Jin-Gen; Huang, Chunfeng; Yang, Zhengfeng; Jin, Mengmeng; Fu, Panhan; Zhang, Ni; Luo, Jian; Li, Dali; Liu, Mingyao; Zhou, Yan; Zhu, Yongqun

2015-01-23

Leucine-rich repeat G-protein-coupled receptors (LGRs) are a unique class of G-protein-coupled receptors characterized by a large extracellular domain to recognize ligands and regulate many important developmental processes. Among the three groups of LGRs, group B members (LGR4-6) recognize R-spondin family proteins (Rspo1-4) to stimulate Wnt signaling. In this study, we successfully utilized the "hybrid leucine-rich repeat technique," which fused LGR4 with the hagfish VLR protein, to obtain two recombinant human LGR4 proteins, LGR415 and LGR49. We determined the crystal structures of ligand-free LGR415 and the LGR49-Rspo1 complex. LGR4 exhibits a twisted horseshoe-like structure. Rspo1 adopts a flat and β-fold architecture and is bound in the concave surface of LGR4 in the complex through electrostatic and hydrophobic interactions. All the Rspo1-binding residues are conserved in LGR4-6, suggesting that LGR4-6 bind R-spondins through an identical surface. Structural analysis of our LGR4-Rspo1 complex with the previously determined LGR4 and LGR5 structures revealed that the concave surface of LGR4 is the sole binding site for R-spondins, suggesting a one-site binding model of LGR4-6 in ligand recognition. The molecular mechanism of LGR4-6 is distinct from the two-step mechanism of group A receptors LGR1-3 and the multiple-interface binding model of group C receptors LGR7-8, suggesting LGRs utilize the divergent mechanisms for ligand recognition. Our structures, together with previous reports, provide a comprehensive understanding of the ligand recognition by LGRs. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

A crustal seismic velocity model for the UK, Ireland and surrounding seas

USGS Publications Warehouse

Kelly, A.; England, R.W.; Maguire, Peter K.H.

2007-01-01

A regional model of the 3-D variation in seismic P-wave velocity structure in the crust of NW Europe has been compiled from wide-angle reflection/refraction profiles. Along each 2-D profile a velocity-depth function has been digitised at 5 km intervals. These 1-D velocity functions were mapped into three dimensions using ordinary kriging with weights determined to minimise the difference between digitised and interpolated values. An analysis of variograms of the digitised data suggested a radial isotropic weighting scheme was most appropriate. Horizontal dimensions of the model cells are optimised at 40 ?? 40 km and the vertical dimension at 1 km. The resulting model provides a higher resolution image of the 3-D variation in seismic velocity structure of the UK, Ireland and surrounding areas than existing models. The construction of the model through kriging allows the uncertainty in the velocity structure to be assessed. This uncertainty indicates the high density of data required to confidently interpolate the crustal velocity structure, and shows that for this region the velocity is poorly constrained for large areas away from the input data. ?? 2007 The Authors Journal compilation ?? 2007 RAS.

The topography of Ceres and implications for the formation of linear surface structures

NASA Astrophysics Data System (ADS)

Buczkowski, D.; Otto, K.; Ruesch, O.; Scully, J. E. C.; Williams, D. A.; Mest, S. C.; Schenk, P.; Jaumann, R.; Nathues, A.; Preusker, F.; Park, R. S.; Raymond, C. A.; Russell, C. T.

2015-12-01

NASA's Dawn spacecraft began orbiting the dwarf planet Ceres in April 2015. Framing Camera data from the Approach (1.3 km/px) and Survey (415 m/px) orbits include digital terrain models derived from processing stereo images. These models have supported various scientific studies of the surface. The eastern hemisphere of Ceres is topographically higher than the western hemisphere. Some of linear structures on Ceres (which include grooves, pit crater chains, fractures and troughs) appear to be radial to the large basins Urvara and Yalode, and most likely formed due to impact processes. However, set of regional linear structures (RLS) that do not have any obvious relationship to impact craters are found on the eastern hemisphere topographic high region. Many of the longer RLS are comprised of smaller structures that have linked together, suggestive of en echelon fractures. Polygonal craters, theorized to form when pervasive subsurface fracturing affects crater formation [1], are widespread on Ceres [2], and those proximal to the RLS have straight crater rims aligned with the grooves and troughs, suggesting that the RLS are fracture systems. A cross-section of one RLS is displayed in FC images of the Occator crater wall. Comparing these images to the digital terrain models show 1) that the structure dips ~60º and 2) there is downward motion on the hanging wall, implying normal faulting. The digital terrain models also reveal the presence of numerous positive relief features with sub-circular shapes. These dome-like features have been tentatively interpreted as volcanic/magmatic features [3]; other possibilities include salt domes. Analog models of domal uplift in areas of regional extension [4] predict patterns of linear structures similar to those observed in the RLS near Occator. Utilizing topography data provided by the Ceres digital terrain models, we assess the relationship between the RLS and nearby domes and topographic high regions to determine the mechanism by which the RLS may have formed. [1] Thomas, P.C. et al. (1999) Icarus, doi: 10.1006/icar.1999.6121 [2] Otto et al. (2015) EPSC2015-284 [3] Ruesch et al. [this meeting] [4] Sims et al. (2013) AAPG Bulletin, doi: 10.1306/02101209136

Normalized Shape and Location of Perturbed Craniofacial Structures in the Xenopus Tadpole Reveal an Innate Ability to Achieve Correct Morphology

PubMed Central

Vandenberg, Laura N.; Adams, Dany S.; Levin, Michael

2012-01-01

Background Embryonic development can often adjust its morphogenetic processes to counteract external perturbation. The existence of self-monitoring responses during pattern formation is of considerable importance to the biomedicine of birth defects, but has not been quantitatively addressed. To understand the computational capabilities of biological tissues in a molecularly-tractable model system, we induced craniofacial defects in Xenopus embryos, then tracked tadpoles with craniofacial deformities and used geometric morphometric techniques to characterize changes in the shape and position of the craniofacial structures. Results Canonical variate analysis revealed that the shapes and relative positions of perturbed jaws and branchial arches were corrected during the first few months of tadpole development. Analysis of the relative movements of the anterior-most structures indicates that misplaced structures move along the anterior-posterior and left-right axes in ways that are significantly different from their normal movements. Conclusions Our data suggest a model in which craniofacial structures utilize a measuring mechanism to assess and adjust their location relative to other local organs. Understanding the correction mechanisms at work in this system could lead to the better understanding of the adaptive decision-making capabilities of living tissues and suggest new approaches to correct birth defects in humans. PMID:22411736

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism

PubMed Central

Fernandes, Carlos A. H.; Pazin, Wallance M.; Dreyer, Thiago R.; Bicev, Renata N.; Cavalcante, Walter L. G.; Fortes-Dias, Consuelo L.; Ito, Amando S.; Oliveira, Cristiano L. P.; Fernandez, Roberto Morato; Fontes, Marcos R. M.

2017-01-01

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation. PMID:28256632

Biophysical studies suggest a new structural arrangement of crotoxin and provide insights into its toxic mechanism.

PubMed

Fernandes, Carlos A H; Pazin, Wallance M; Dreyer, Thiago R; Bicev, Renata N; Cavalcante, Walter L G; Fortes-Dias, Consuelo L; Ito, Amando S; Oliveira, Cristiano L P; Fernandez, Roberto Morato; Fontes, Marcos R M

2017-03-03

Crotoxin (CTX) is the main neurotoxin found in Crotalus durissus rattlesnake venoms being composed by a nontoxic and non-enzymatic component (CA) and a toxic phospholipase A 2 (CB). Previous crystallographic structures of CTX and CB provided relevant insights: (i) CTX structure showed a 1:1 molecular ratio between CA and CB, presenting three tryptophan residues in the CA/CB interface and one exposed to solvent; (ii) CB structure displayed a tetrameric conformation. This study aims to provide further information on the CTX mechanism of action by several biophysical methods. Our data show that isolated CB can in fact form tetramers in solution; however, these tetramers can be dissociated by CA titration. Furthermore, CTX exhibits a strong reduction in fluorescence intensity and lifetime compared with isolated CA and CB, suggesting that all tryptophan residues in CTX may be hidden by the CA/CB interface. By companying spectroscopy fluorescence and SAXS data, we obtained a new structural model for the CTX heterodimer in which all tryptophans are located in the interface, and the N-terminal region of CB is largely exposed to the solvent. Based on this model, we propose a toxic mechanism of action for CTX, involving the interaction of N-terminal region of CB with the target before CA dissociation.

Punishment can promote defection in group-structured populations.

PubMed

Powers, Simon T; Taylor, Daniel J; Bryson, Joanna J

2012-10-21

Pro-social punishment, whereby cooperators punish defectors, is often suggested as a mechanism that maintains cooperation in large human groups. Importantly, models that support this idea have to date only allowed defectors to be the target of punishment. However, recent empirical work has demonstrated the existence of anti-social punishment in public goods games. That is, individuals that defect have been found to also punish cooperators. Some recent theoretical studies have found that such anti-social punishment can prevent the evolution of pro-social punishment and cooperation. However, the evolution of anti-social punishment in group-structured populations has not been formally addressed. Previous work has informally argued that group-structure must favour pro-social punishment. Here we formally investigate how two demographic factors, group size and dispersal frequency, affect selection pressures on pro- and anti-social punishment. Contrary to the suggestions of previous work, we find that anti-social punishment can prevent the evolution of pro-social punishment and cooperation under a range of group structures. Given that anti-social punishment has now been found in all studied extant human cultures, the claims of previous models showing the co-evolution of pro-social punishment and cooperation in group-structured populations should be re-evaluated. Copyright © 2012 Elsevier Ltd. All rights reserved.

Off- and Along-Axis Slow Spreading Ridge Segment Characters: Insights From 3d Thermal Modeling

NASA Astrophysics Data System (ADS)

Gac, S.; Tisseau, C.; Dyment, J.

2001-12-01

Many observations along the Mid-Atlantic Ridge segments suggest a correlation between surface characters (length, axial morphology) and the thermal state of the segment. Thibaud et al. (1998) classify segments according to their thermal state: "colder" segments shorter than 30 km show a weak magmatic activity, and "hotter" segments as long as 90 km show a robust magmatic activity. The existence of such a correlation suggests that the thermal structure of a slow spreading ridge segment explains most of the surface observations. Here we test the physical coherence of such an integrated thermal model and evaluate it quantitatively. The different kinds of segment would constitute different phases in a segment evolution, the segment evolving progressively from a "colder" to a "hotter" so to a "colder" state. Here we test the consistency of such an evolution scheme. To test these hypotheses we have developed a 3D numerical model for the thermal structure and evolution of a slow spreading ridge segment. The thermal structure is controlled by the geometry and the dimensions of a permanently hot zone, imposed beneath the segment center, where is simulated the adiabatic ascent of magmatic material. To compare the model with the observations several geophysic quantities which depend on the thermal state are simulated: crustal thickness variations along axis, gravity anomalies (reflecting density variations) and earthquake maximum depth (corresponding to the 750° C isotherm depth). The thermal structure of a particular segment is constrained by comparing the simulated quantities to the real ones. Considering realistic magnetization parameters, the magnetic anomalies generated from the same thermal structure and evolution reproduce the observed magnetic anomaly amplitude variations along the segment. The thermal structures accounting for observations are determined for each kind of segment (from "colder" to "hotter"). The evolution of the thermal structure from the "colder" to the "hotter" segments gives credence to a temporal relationship between the different kinds of segment. The resulting thermal evolution model of slow spreading ridge segments may explain the rhomboedric shapes observed off-axis.

Inferring the relative resilience of alternative states

USGS Publications Warehouse

Angeler, David G.; Allen, Craig R.; Rojo, Carmen; Alvarez-Cobelas, Miguel; Rodrigo, Maria A.; Sanchez-Carrillo, Salvador

2013-01-01

Ecological systems may occur in alternative states that differ in ecological structures, functions and processes. Resilience is the measure of disturbance an ecological system can absorb before changing states. However, how the intrinsic structures and processes of systems that characterize their states affects their resilience remains unclear. We analyzed time series of phytoplankton communities at three sites in a floodplain in central Spain to assess the dominant frequencies or “temporal scales” in community dynamics and compared the patterns between a wet and a dry alternative state. The identified frequencies and cross-scale structures are expected to arise from positive feedbacks that are thought to reinforce processes in alternative states of ecological systems and regulate emergent phenomena such as resilience. Our analyses show a higher species richness and diversity but lower evenness in the dry state. Time series modeling revealed a decrease in the importance of short-term variability in the communities, suggesting that community dynamics slowed down in the dry relative to the wet state. The number of temporal scales at which community dynamics manifested, and the explanatory power of time series models, was lower in the dry state. The higher diversity, reduced number of temporal scales and the lower explanatory power of time series models suggest that species dynamics tended to be more stochastic in the dry state. From a resilience perspective our results highlight a paradox: increasing species richness may not necessarily enhance resilience. The loss of cross-scale structure (i.e. the lower number of temporal scales) in community dynamics across sites suggests that resilience erodes during drought. Phytoplankton communities in the dry state are therefore likely less resilient than in the wet state. Our case study demonstrates the potential of time series modeling to assess attributes that mediate resilience. The approach is useful for assessing resilience of alternative states across ecological and other complex systems.

Family Instability and Exposure to Violence in the Early Life Course.

PubMed

Cavanagh, Shannon E; Stritzel, Haley; Smith, Chelsea; Crosnoe, Robert

2017-10-11

Family instability has been linked with a host of outcomes across the early life course. This study extends this literature by connecting instability with violence in the community by examining the associations among family structure, family structure change, and secondary exposure to violence during adolescence across diverse segments of the population. Using longitudinal data from the Project on Human Development in Chicago Neighborhoods study, we found that living with a single parent and experiencing family structure changes were associated with secondary exposure to violence. Multiple group models suggest that partner change translated into more exposure for boys than girls. Findings also suggest that family instability may lead to more secondary exposure to violence for African American youth. © 2017 Society for Research on Adolescence.

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

PubMed

Kosinski, Jan; Gajda, Michal J; Cymerman, Iwona A; Kurowski, Michal A; Pawlowski, Marcin; Boniecki, Michal; Obarska, Agnieszka; Papaj, Grzegorz; Sroczynska-Obuchowicz, Paulina; Tkaczuk, Karolina L; Sniezynska, Paulina; Sasin, Joanna M; Augustyn, Anna; Bujnicki, Janusz M; Feder, Marcin

2005-01-01

In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts. 2005 Wiley-Liss, Inc.

The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition.

PubMed

Jauch, Ralf; Ng, Calista K L; Narasimhan, Kamesh; Kolatkar, Prasanna R

2012-04-01

It has recently been proposed that the sequence preferences of DNA-binding TFs (transcription factors) can be well described by models that include the positional interdependence of the nucleotides of the target sites. Such binding models allow for multiple motifs to be invoked, such as principal and secondary motifs differing at two or more nucleotide positions. However, the structural mechanisms underlying the accommodation of such variant motifs by TFs remain elusive. In the present study we examine the crystal structure of the HMG (high-mobility group) domain of Sox4 [Sry (sex-determining region on the Y chromosome)-related HMG box 4] bound to DNA. By comparing this structure with previously solved structures of Sox17 and Sox2, we observed subtle conformational differences at the DNA-binding interface. Furthermore, using quantitative electrophoretic mobility-shift assays we validated the positional interdependence of two nucleotides and the presence of a secondary Sox motif in the affinity landscape of Sox4. These results suggest that a concerted rearrangement of two interface amino acids enables Sox4 to accommodate primary and secondary motifs. The structural adaptations lead to altered dinucleotide preferences that mutually reinforce each other. These analyses underline the complexity of the DNA recognition by TFs and provide an experimental validation for the conceptual framework of positional interdependence and secondary binding motifs.

Subsurface Investigation of the Neogene Mygdonian Basin, Greece Using Magnetic Data

NASA Astrophysics Data System (ADS)

Ibraheem, Ismael M.; Gurk, Marcus; Tougiannidis, Nikolaos; Tezkan, Bülent

2018-02-01

A high-resolution ground and marine magnetic survey was executed to determine the structure of the subsurface and the thickness of the sedimentary cover in the Mygdonian Basin. A spacing of approximately 250 m or 500 m between measurement stations was selected to cover an area of 15 km × 22 km. Edge detectors such as total horizontal derivative (THDR), analytic signal (AS), tilt derivative (TDR), enhanced total horizontal gradient of tilt derivative (ETHDR) were applied to map the subsurface structure. Depth was estimated by power spectrum analysis, tilt derivative, source parameter imaging (SPI), and 2D-forward modeling techniques. Spectral analysis and SPI suggest a depth to the basement ranging from near surface to 600 m. For some selected locations, depth was also calculated using the TDR technique suggesting depths from 160 to 400 m. 2D forward magnetic modeling using existing boreholes as constraints was carried out along four selected profiles and confirmed the presence of alternative horsts and grabens formed by parallel normal faults. The dominant structural trends inferred from THDR, AS, TDR, and ETHDR are N-S, NW-SE, NE-SW and E-W. This corresponds with the known structural trends in the area. Finally, a detailed structural map showing the magnetic blocks and the structural architecture of the Mygdonian Basin was drawn up by collating all of the results.

A Framework for Modeling Competitive and Cooperative Computation in Retinal Processing

NASA Astrophysics Data System (ADS)

Moreno-Díaz, Roberto; de Blasio, Gabriel; Moreno-Díaz, Arminda

2008-07-01

The structure of the retina suggests that it should be treated (at least from the computational point of view), as a layered computer. Different retinal cells contribute to the coding of the signals down to ganglion cells. Also, because of the nature of the specialization of some ganglion cells, the structure suggests that all these specialization processes should take place at the inner plexiform layer and they should be of a local character, prior to a global integration and frequency-spike coding by the ganglion cells. The framework we propose consists of a layered computational structure, where outer layers provide essentially with band-pass space-time filtered signals which are progressively delayed, at least for their formal treatment. Specialization is supposed to take place at the inner plexiform layer by the action of spatio-temporal microkernels (acting very locally), and having a centerperiphery space-time structure. The resulting signals are then integrated by the ganglion cells through macrokernels structures. Practically all types of specialization found in different vertebrate retinas, as well as the quasilinear behavior in some higher vertebrates, can be modeled and simulated within this framework. Finally, possible feedback from central structures is considered. Though their relevance to retinal processing is not definitive, it is included here for the sake of completeness, since it is a formal requisite for recursiveness.

Integrating normal and abnormal personality structure: a proposal for DSM-V.

PubMed

Widiger, Thomas A

2011-06-01

The personality disorders section of the American Psychiatric Association's fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-V) is currently being developed. The purpose of the current paper is to encourage the authors of DSM-V to integrate normal and abnormal personality structure within a common, integrative model, and to suggest that the optimal choice for such an integration would be the five-factor model (FFM) of general personality structure. A proposal for the classification of personality disorder from the perspective of the FFM is provided. Discussed as well are implications and issues associated with an FFM of personality disorder, including validity, coverage, feasibility, clinical utility, and treatment implications.

Team assembly mechanisms determine collaboration network structure and team performance.

PubMed

Guimerà, Roger; Uzzi, Brian; Spiro, Jarrett; Amaral, Luís A Nunes

2005-04-29

Agents in creative enterprises are embedded in networks that inspire, support, and evaluate their work. Here, we investigate how the mechanisms by which creative teams self-assemble determine the structure of these collaboration networks. We propose a model for the self-assembly of creative teams that has its basis in three parameters: team size, the fraction of newcomers in new productions, and the tendency of incumbents to repeat previous collaborations. The model suggests that the emergence of a large connected community of practitioners can be described as a phase transition. We find that team assembly mechanisms determine both the structure of the collaboration network and team performance for teams derived from both artistic and scientific fields.

Event structure and cognitive control.

PubMed

Reimer, Jason F; Radvansky, Gabriel A; Lorsbach, Thomas C; Armendarez, Joseph J

2015-09-01

Recently, a great deal of research has demonstrated that although everyday experience is continuous in nature, it is parsed into separate events. The aim of the present study was to examine whether event structure can influence the effectiveness of cognitive control. Across 5 experiments we varied the structure of events within the AX-CPT by shifting the spatial location of cues and probes on a computer screen. When location shifts were present, a pattern of AX-CPT performance consistent with enhanced cognitive control was found. To test whether the location shift effects were caused by the presence of event boundaries per se, other aspects of the AX-CPT were manipulated, such as the color of cues and probes and the inclusion of a distractor task during the cue-probe delay. Changes in cognitive control were not found under these conditions, suggesting that the location shift effects were specifically related to the formation of separate event models. Together, these results can be accounted for by the Event Horizon Model and a representation-based theory of cognitive control, and suggest that cognitive control can be influenced by the surrounding environmental structure. (c) 2015 APA, all rights reserved).

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA

PubMed Central

2016-01-01

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results. PMID:27983843

Computational Assessment of Potassium and Magnesium Ion Binding to a Buried Pocket in GTPase-Associating Center RNA.

PubMed

Hayatshahi, Hamed S; Roe, Daniel R; Galindo-Murillo, Rodrigo; Hall, Kathleen B; Cheatham, Thomas E

2017-01-26

An experimentally well-studied model of RNA tertiary structures is a 58mer rRNA fragment, known as GTPase-associating center (GAC) RNA, in which a highly negative pocket walled by phosphate oxygen atoms is stabilized by a chelated cation. Although such deep pockets with more than one direct phosphate to ion chelation site normally include magnesium, as shown in one GAC crystal structure, another GAC crystal structure and solution experiments suggest potassium at this site. Both crystal structures also depict two magnesium ions directly bound to the phosphate groups comprising this controversial pocket. Here, we used classical molecular dynamics simulations as well as umbrella sampling to investigate the possibility of binding of potassium versus magnesium inside the pocket and to better characterize the chelation of one of the binding magnesium ions outside the pocket. The results support the preference of the pocket to accommodate potassium rather than magnesium and suggest that one of the closely binding magnesium ions can only bind at high magnesium concentrations, such as might be present during crystallization. This work illustrates the complementary utility of molecular modeling approaches with atomic-level detail in resolving discrepancies between conflicting experimental results.

Spatially localized structure-function relations in the elastic properties of sheared articular cartilage

NASA Astrophysics Data System (ADS)

Silverberg, Jesse; Bonassar, Lawrence; Cohen, Itai

2013-03-01

Contemporary developments in therapeutic tissue engineering have been enabled by basic research efforts in the field of biomechanics. Further integration of technology in medicine requires a deeper understanding of the mechanical properties of soft biological materials and the structural origins of their response under extreme stresses and strains. Drawing on the science generated by the ``Extreme Mechanics'' community, we present experimental results on the mechanical properties of articular cartilage, a hierarchically structured soft biomaterial found in the joints of mammalian long bones. Measurements of the spatially localized structure and mechanical properties will be compared with theoretical descriptions based on networks of deformed rods, poro-visco-elasticity, and standard continuum models. Discrepancies between experiment and theory will be highlighted, and suggestions for how models can be improved will be given.

Revealing the ISO/IEC 9126-1 Clique Tree for COTS Software Evaluation

NASA Technical Reports Server (NTRS)

Morris, A. Terry

2007-01-01

Previous research has shown that acyclic dependency models, if they exist, can be extracted from software quality standards and that these models can be used to assess software safety and product quality. In the case of commercial off-the-shelf (COTS) software, the extracted dependency model can be used in a probabilistic Bayesian network context for COTS software evaluation. Furthermore, while experts typically employ Bayesian networks to encode domain knowledge, secondary structures (clique trees) from Bayesian network graphs can be used to determine the probabilistic distribution of any software variable (attribute) using any clique that contains that variable. Secondary structures, therefore, provide insight into the fundamental nature of graphical networks. This paper will apply secondary structure calculations to reveal the clique tree of the acyclic dependency model extracted from the ISO/IEC 9126-1 software quality standard. Suggestions will be provided to describe how the clique tree may be exploited to aid efficient transformation of an evaluation model.

Algebra for Enterprise Ontology: towards analysis and synthesis of enterprise models

NASA Astrophysics Data System (ADS)

Suga, Tetsuya; Iijima, Junichi

2018-03-01

Enterprise modeling methodologies have made enterprises more likely to be the object of systems engineering rather than craftsmanship. However, the current state of research in enterprise modeling methodologies lacks investigations of the mathematical background embedded in these methodologies. Abstract algebra, a broad subfield of mathematics, and the study of algebraic structures may provide interesting implications in both theory and practice. Therefore, this research gives an empirical challenge to establish an algebraic structure for one aspect model proposed in Design & Engineering Methodology for Organizations (DEMO), which is a major enterprise modeling methodology in the spotlight as a modeling principle to capture the skeleton of enterprises for developing enterprise information systems. The results show that the aspect model behaves well in the sense of algebraic operations and indeed constructs a Boolean algebra. This article also discusses comparisons with other modeling languages and suggests future work.

Role of 0D peripheral vasculature model in fluid-structure interaction modeling of aneurysms

NASA Astrophysics Data System (ADS)

Torii, Ryo; Oshima, Marie; Kobayashi, Toshio; Takagi, Kiyoshi; Tezduyar, Tayfun E.

2010-06-01

Patient-specific simulations based on medical images such as CT and MRI offer information on the hemodynamic and wall tissue stress in patient-specific aneurysm configurations. These are considered important in predicting the rupture risk for individual aneurysms but are not possible to measure directly. In this paper, fluid-structure interaction (FSI) analyses of a cerebral aneurysm at the middle cerebral artery (MCA) bifurcation are presented. A 0D structural recursive tree model of the peripheral vasculature is incorporated and its impedance is coupled with the 3D FSI model to compute the outflow through the two branches accurately. The results are compared with FSI simulation with prescribed pressure variation at the outlets. The comparison shows that the pressure at the two outlets are nearly identical even with the peripheral vasculature model and the flow division to the two branches is nearly the same as what we see in the simulation without the peripheral vasculature model. This suggests that the role of the peripheral vasculature in FSI modeling of the MCA aneurysm is not significant.

From spatially variable streamflow to distributed hydrological models: Analysis of key modeling decisions

NASA Astrophysics Data System (ADS)

Fenicia, Fabrizio; Kavetski, Dmitri; Savenije, Hubert H. G.; Pfister, Laurent

2016-02-01

This paper explores the development and application of distributed hydrological models, focusing on the key decisions of how to discretize the landscape, which model structures to use in each landscape element, and how to link model parameters across multiple landscape elements. The case study considers the Attert catchment in Luxembourg—a 300 km2 mesoscale catchment with 10 nested subcatchments that exhibit clearly different streamflow dynamics. The research questions are investigated using conceptual models applied at hydrologic response unit (HRU) scales (1-4 HRUs) on 6 hourly time steps. Multiple model structures are hypothesized and implemented using the SUPERFLEX framework. Following calibration, space/time model transferability is tested using a split-sample approach, with evaluation criteria including streamflow prediction error metrics and hydrological signatures. Our results suggest that: (1) models using geology-based HRUs are more robust and capture the spatial variability of streamflow time series and signatures better than models using topography-based HRUs; this finding supports the hypothesis that, in the Attert, geology exerts a stronger control than topography on streamflow generation, (2) streamflow dynamics of different HRUs can be represented using distinct and remarkably simple model structures, which can be interpreted in terms of the perceived dominant hydrologic processes in each geology type, and (3) the same maximum root zone storage can be used across the three dominant geological units with no loss in model transferability; this finding suggests that the partitioning of water between streamflow and evaporation in the study area is largely independent of geology and can be used to improve model parsimony. The modeling methodology introduced in this study is general and can be used to advance our broader understanding and prediction of hydrological behavior, including the landscape characteristics that control hydrologic response, the dominant processes associated with different landscape types, and the spatial relations of catchment processes. This article was corrected on 14 MAR 2016. See the end of the full text for details.

The cross-national structure of mental disorders: results from the World Mental Health Surveys.

PubMed

de Jonge, Peter; Wardenaar, Klaas J; Lim, Carmen C W; Aguilar-Gaxiola, Sergio; Alonso, Jordi; Andrade, Laura Helena; Bunting, Brendan; Chatterji, Somnath; Ciutan, Marius; Gureje, Oye; Karam, Elie G; Lee, Sing; Medina-Mora, Maria Elena; Moskalewicz, Jacek; Navarro-Mateu, Fernando; Pennell, Beth-Ellen; Piazza, Marina; Posada-Villa, José; Torres, Yolanda; Kessler, Ronald C; Scott, Kate

2017-12-19

The patterns of comorbidity among mental disorders have led researchers to model the underlying structure of psychopathology. While studies have suggested a structure including internalizing and externalizing disorders, less is known with regard to the cross-national stability of this model. Moreover, little data are available on the placement of eating disorders, bipolar disorder and psychotic experiences (PEs) in this structure. We evaluated the structure of mental disorders with data from the World Health Organization Composite International Diagnostic Interview, including 15 lifetime mental disorders and six PEs. Respondents (n = 5478-15 499) were included from 10 high-, middle- and lower middle-income countries across the world aged 18 years or older. Confirmatory factor analyses (CFAs) were used to evaluate and compare the fit of different factor structures to the lifetime disorder data. Measurement invariance was evaluated with multigroup CFA (MG-CFA). A second-order model with internalizing and externalizing factors and fear and distress subfactors best described the structure of common mental disorders. MG-CFA showed that this model was stable across countries. Of the uncommon disorders, bipolar disorder and eating disorder were best grouped with the internalizing factor, and PEs with a separate factor. These results indicate that cross-national patterns of lifetime common mental-disorder comorbidity can be explained with a second-order underlying structure that is stable across countries and can be extended to also cover less common mental disorders.

Multi-region statistical shape model for cochlear implantation

NASA Astrophysics Data System (ADS)

Romera, Jordi; Kjer, H. Martin; Piella, Gemma; Ceresa, Mario; González Ballester, Miguel A.

2016-03-01

Statistical shape models are commonly used to analyze the variability between similar anatomical structures and their use is established as a tool for analysis and segmentation of medical images. However, using a global model to capture the variability of complex structures is not enough to achieve the best results. The complexity of a proper global model increases even more when the amount of data available is limited to a small number of datasets. Typically, the anatomical variability between structures is associated to the variability of their physiological regions. In this paper, a complete pipeline is proposed for building a multi-region statistical shape model to study the entire variability from locally identified physiological regions of the inner ear. The proposed model, which is based on an extension of the Point Distribution Model (PDM), is built for a training set of 17 high-resolution images (24.5 μm voxels) of the inner ear. The model is evaluated according to its generalization ability and specificity. The results are compared with the ones of a global model built directly using the standard PDM approach. The evaluation results suggest that better accuracy can be achieved using a regional modeling of the inner ear.

Weak data do not make a free lunch, only a cheap meal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Zhipu; Rajashankar, Kanagalaghatta; Dauter, Zbigniew, E-mail: dauter@anl.gov

2014-02-01

Refinement and analysis of four structures with various data resolution cutoffs suggests that at present there are no reliable criteria for judging the diffraction data resolution limit and the condition I/σ(I) = 2.0 is reasonable. However, extending the limit by about 0.2 Å beyond the resolution defined by this threshold does not deteriorate the quality of refined structures and in some cases may be beneficial. Four data sets were processed at resolutions significantly exceeding the criteria traditionally used for estimating the diffraction data resolution limit. The analysis of these data and the corresponding model-quality indicators suggests that the criteria ofmore » resolution limits widely adopted in the past may be somewhat conservative. Various parameters, such as R{sub merge} and I/σ(I), optical resolution and the correlation coefficients CC{sub 1/2} and CC*, can be used for judging the internal data quality, whereas the reliability factors R and R{sub free} as well as the maximum-likelihood target values and real-space map correlation coefficients can be used to estimate the agreement between the data and the refined model. However, none of these criteria provide a reliable estimate of the data resolution cutoff limit. The analysis suggests that extension of the maximum resolution by about 0.2 Å beyond the currently adopted limit where the I/σ(I) value drops to 2.0 does not degrade the quality of the refined structural models, but may sometimes be advantageous. Such an extension may be particularly beneficial for significantly anisotropic diffraction. Extension of the maximum resolution at the stage of data collection and structure refinement is cheap in terms of the required effort and is definitely more advisable than accepting a too conservative resolution cutoff, which is unfortunately quite frequent among the crystal structures deposited in the Protein Data Bank.« less

A structural model of teacher role stress, satisfaction, commitment, and intentions to leave: a comment on Conley and You (2009).

PubMed

Smith, Kenneth J

2010-04-01

Conley and You assessed the plausibility of three alternative model specifications of the relations between role stressors (i.e., role conflict, role ambiguity, and role overload) and organizational commitment, satisfaction, and turnover intentions among a sample of 178 teachers employed in four Southern California high schools. Using structural equations modeling procedures to evaluate their data, the authors reported the best fit for their "fully mediated effects" model wherein there was a "strong causal path from role ambiguity and role conflict --> satisfaction --> commitment --> intentions to leave" (p. 781). This note addresses methodological issues with the present study and provides suggestions for follow-up efforts designed to replicate and/or extend this line of research.

Evaluating model structure adequacy: The case of the Maggia Valley groundwater system, southern Switzerland

USGS Publications Warehouse

Hill, Mary C.; L. Foglia,; S. W. Mehl,; P. Burlando,

2013-01-01

Model adequacy is evaluated with alternative models rated using model selection criteria (AICc, BIC, and KIC) and three other statistics. Model selection criteria are tested with cross-validation experiments and insights for using alternative models to evaluate model structural adequacy are provided. The study is conducted using the computer codes UCODE_2005 and MMA (MultiModel Analysis). One recharge alternative is simulated using the TOPKAPI hydrological model. The predictions evaluated include eight heads and three flows located where ecological consequences and model precision are of concern. Cross-validation is used to obtain measures of prediction accuracy. Sixty-four models were designed deterministically and differ in representation of river, recharge, bedrock topography, and hydraulic conductivity. Results include: (1) What may seem like inconsequential choices in model construction may be important to predictions. Analysis of predictions from alternative models is advised. (2) None of the model selection criteria consistently identified models with more accurate predictions. This is a disturbing result that suggests to reconsider the utility of model selection criteria, and/or the cross-validation measures used in this work to measure model accuracy. (3) KIC displayed poor performance for the present regression problems; theoretical considerations suggest that difficulties are associated with wide variations in the sensitivity term of KIC resulting from the models being nonlinear and the problems being ill-posed due to parameter correlations and insensitivity. The other criteria performed somewhat better, and similarly to each other. (4) Quantities with high leverage are more difficult to predict. The results are expected to be generally applicable to models of environmental systems.

Structure of Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition Criteria for Obsessive–Compulsive Personality Disorder in Patients With Binge Eating Disorder

PubMed Central

Ansell, Emily B; Pinto, Anthony; Edelen, Maria Orlando; Grilo, Carlos M

2013-01-01

Objective To examine 1-, 2-, and 3-factor model structures through confirmatory analytic procedures for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) obsessive–compulsive personality disorder (OCPD) criteria in patients with binge eating disorder (BED). Method Participants were consecutive outpatients (n = 263) with binge eating disorder and were assessed with semi-structured interviews. The 8 OCPD criteria were submitted to confirmatory factor analyses in Mplus Version 4.2 (Los Angeles, CA) in which previously identified factor models of OCPD were compared for fit, theoretical relevance, and parsimony. Nested models were compared for significant improvements in model fit. Results Evaluation of indices of fit in combination with theoretical considerations suggest a multifactorial model is a significant improvement in fit over the current DSM-IV single-factor model of OCPD. Though the data support both 2- and 3-factor models, the 3-factor model is hindered by an underspecified third factor. Conclusion A multifactorial model of OCPD incorporating the factors perfectionism and rigidity represents the best compromise of fit and theory in modelling the structure of OCPD in patients with BED. A third factor representing miserliness may be relevant in BED populations but needs further development. The perfectionism and rigidity factors may represent distinct intrapersonal and interpersonal attempts at control and may have implications for the assessment of OCPD. PMID:19087485

Structure of diagnostic and statistical manual of mental disorders, fourth edition criteria for obsessive-compulsive personality disorder in patients with binge eating disorder.

PubMed

Ansell, Emily B; Pinto, Anthony; Edelen, Maria Orlando; Grilo, Carlos M

2008-12-01

To examine 1-, 2-, and 3-factor model structures through confirmatory analytic procedures for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) obsessive-compulsive personality disorder (OCPD) criteria in patients with binge eating disorder (BED). Participants were consecutive outpatients (n = 263) with binge eating disorder and were assessed with semi-structured interviews. The 8 OCPD criteria were submitted to confirmatory factor analyses in Mplus Version 4.2 (Los Angeles, CA) in which previously identified factor models of OCPD were compared for fit, theoretical relevance, and parsimony. Nested models were compared for significant improvements in model fit. Evaluation of indices of fit in combination with theoretical considerations suggest a multifactorial model is a significant improvement in fit over the current DSM-IV single- factor model of OCPD. Though the data support both 2- and 3-factor models, the 3-factor model is hindered by an underspecified third factor. A multifactorial model of OCPD incorporating the factors perfectionism and rigidity represents the best compromise of fit and theory in modelling the structure of OCPD in patients with BED. A third factor representing miserliness may be relevant in BED populations but needs further development. The perfectionism and rigidity factors may represent distinct intrapersonal and interpersonal attempts at control and may have implications for the assessment of OCPD.

Structural expression of a rolling hinge in the footwall of the Brenner Line normal fault, eastern Alps

NASA Astrophysics Data System (ADS)

Axen, Gary J.; Bartley, John M.; Selverstone, Jane

1995-12-01

The kinematic and temporal sequence of structures observed to overprint mylonites along the Brenner Line low-angle normal fault may record passage of the footwall through two rolling hinges, at the top and bottom of a ramp in the shear zone. The structures comprise west down brittle and brittle-ductile structures and east down brittle structures. PT conditions of formation (250° to >400°C and 2-23 km depth), obtained from analysis of oriented fluid inclusion planes, indicate that west down structures were formed at greater depths and temperatures, and therefore earlier, than the east down structures. These data suggest that the brittle structures formed under conditions that permit crystal-plastic deformation at long-term geologic strain rates and therefore probably reflect transient rapid strain rates and/or high fluid pressure. Structures inferred to have formed at a lower hinge are consistent with viscous flow models of rolling-hinge deformation and support the concept of a crustal asthenosphere. Such high temperatures at shallow crustal depth also suggest significant upward advection of heat by extensional unroofing of warm rocks, which may have reduced the flexural rigidity of the footwall and thus affected mechanical behavior at the upper rolling hinge. Exposed mylonitic foliation within a few hundred meters of the Brenner line and on top of the east-west trending anticlines in the footwall dips ˜15° west. Our data favor a ramp dip of ˜25° but permit a dip as great as 45°. Fluid inclusion data suggest that structures related to the hinge at the base of the ramp formed at depths of 12-25 km. If the average dip of the Brenner shear zone to those depths was 20°, intermediate between the favored ramp dip and the dip of exposed foliation, then the horizontal component of slip could be as high as 33-63 km. The two discrete sets of structures with opposite shear senses, formed in the temporal sequence indicated by PT data, are consistent with subvertical simple shear models of rolling-hinge strain. This kinematic pattern is not predicted by the flexural-failure model for rolling hinges. However, the predominance of normal slip at the upper hinge, which extends rather than shortens the mylonitic foliation, fails to match the subvertical simple shear model, which predicts shortening of the foliation there. One possible solution is that superposition of regional extension upon hinge-related stresses modified the rolling-hinge kinematics. Such a modified subvertical shear model can account for the observed small foliation-parallel extensional strains if the foliation was bent <5°-10° passing through the upper hinge. If more bending than that occurred, the data suggest rolling-hinge kinematics in which deformation is achieved by uniform-sense simple shear across the shear zone as in the subvertical simple shear model but in which material lines parallel to the shear-zone foliation and the detachment fault undergo very small length changes, presumably indicating that footwall rocks retained significant resistance to shear and underwent minimal permanent strain. The mechanics that would generate such a rolling hinge are uncertain but may incorporate aspects of both subvertical simple shear and flexural failure. An important kinematic consequence of such a rolling hinge is that all of the net slip across a normal fault, not only its horizontal component, is converted into horizontal extension. This implies a significantly larger magnitude of crustal extension across dipping normal faults whose footwalls passed through a rolling hinge than for those that did not develop along with a hinge.

Evaluating neighborhood structures for modeling intercity diffusion of large-scale dengue epidemics.

PubMed

Wen, Tzai-Hung; Hsu, Ching-Shun; Hu, Ming-Che

2018-05-03

Dengue fever is a vector-borne infectious disease that is transmitted by contact between vector mosquitoes and susceptible hosts. The literature has addressed the issue on quantifying the effect of individual mobility on dengue transmission. However, there are methodological concerns in the spatial regression model configuration for examining the effect of intercity-scale human mobility on dengue diffusion. The purposes of the study are to investigate the influence of neighborhood structures on intercity epidemic progression from pre-epidemic to epidemic periods and to compare definitions of different neighborhood structures for interpreting the spread of dengue epidemics. We proposed a framework for assessing the effect of model configurations on dengue incidence in 2014 and 2015, which were the most severe outbreaks in 70 years in Taiwan. Compared with the conventional model configuration in spatial regression analysis, our proposed model used a radiation model, which reflects population flow between townships, as a spatial weight to capture the structure of human mobility. The results of our model demonstrate better model fitting performance, indicating that the structure of human mobility has better explanatory power in dengue diffusion than the geometric structure of administration boundaries and geographic distance between centroids of cities. We also identified spatial-temporal hierarchy of dengue diffusion: dengue incidence would be influenced by its immediate neighboring townships during pre-epidemic and epidemic periods, and also with more distant neighbors (based on mobility) in pre-epidemic periods. Our findings suggest that the structure of population mobility could more reasonably capture urban-to-urban interactions, which implies that the hub cities could be a "bridge" for large-scale transmission and make townships that immediately connect to hub cities more vulnerable to dengue epidemics.

Hydrological model parameter dimensionality is a weak measure of prediction uncertainty

NASA Astrophysics Data System (ADS)

Pande, S.; Arkesteijn, L.; Savenije, H.; Bastidas, L. A.

2015-04-01

This paper shows that instability of hydrological system representation in response to different pieces of information and associated prediction uncertainty is a function of model complexity. After demonstrating the connection between unstable model representation and model complexity, complexity is analyzed in a step by step manner. This is done measuring differences between simulations of a model under different realizations of input forcings. Algorithms are then suggested to estimate model complexity. Model complexities of the two model structures, SAC-SMA (Sacramento Soil Moisture Accounting) and its simplified version SIXPAR (Six Parameter Model), are computed on resampled input data sets from basins that span across the continental US. The model complexities for SIXPAR are estimated for various parameter ranges. It is shown that complexity of SIXPAR increases with lower storage capacity and/or higher recession coefficients. Thus it is argued that a conceptually simple model structure, such as SIXPAR, can be more complex than an intuitively more complex model structure, such as SAC-SMA for certain parameter ranges. We therefore contend that magnitudes of feasible model parameters influence the complexity of the model selection problem just as parameter dimensionality (number of parameters) does and that parameter dimensionality is an incomplete indicator of stability of hydrological model selection and prediction problems.

Toward a blueprint for UDP-glucose pyrophosphorylase structure/function properties: homology-modeling analyses.

PubMed

Geisler, Matt; Wilczynska, Malgorzata; Karpinski, Stanislaw; Kleczkowski, Leszek A

2004-11-01

UDP-glucose pyrophosphorylase (UGPase) is an important enzyme of synthesis of sucrose, cellulose, and several other polysaccharides in all plants. The protein is evolutionarily conserved among eukaryotes, but has little relation, aside from its catalytic reaction, to UGPases of prokaryotic origin. Using protein homology modeling strategy, 3D structures for barley, poplar, and Arabidopsis UGPases have been derived, based on recently published crystal structure of human UDP-N-acetylglucosamine pyrophosphorylase. The derived 3D structures correspond to a bowl-shaped protein with the active site at a central groove, and a C-terminal domain that includes a loop (I-loop) possibly involved in dimerization. Data on a plethora of earlier described UGPase mutants from a variety of eukaryotic organisms have been revisited, and we have, in most cases, verified the role of each mutation in enzyme catalysis/regulation/structural integrity. We have also found that one of two alternatively spliced forms of poplar UGPase has a very short I-loop, suggesting differences in oligomerization ability of the two isozymes. The derivation of the structural model for plant UGPase should serve as a useful blueprint for further function/structure studies on this protein.

Family Structure and Adolescent Substance Use: An International Perspective.

PubMed

Hoffmann, John P

2017-11-10

Numerous studies indicate that family structure is a key correlate of adolescent substance use. Yet there are some important limitations to this research. Studies have been conducted mainly in the United States, with relatively few studies that have compared family structure and youth substance use across nations. There is also a lack of recognition of the complexity of family types prevalent in contemporary global society. Moreover, there remains a need to consider personal, interpersonal, and macro-level characteristics that may help account for the association between family structure and youth substance use. This study uses data from 37 countries to examine several models that purport to explain the association between family structure and substance use. The data are from the 2005-2006 WHO-sponsored Health Behaviour in School-Aged Children (HBSC) (n = 193,202). Multilevel models, including linear, probit, and structural equation models (SEMs), were used to test several hypotheses. The results suggest that time spent with friends largely accounted for the association between specific types of family structures and frequency of alcohol use and getting drunk, but that cannabis use was negatively associated with living with both biological parents irrespective of other factors.

Simulation of Canopy CO2/H2O Fluxes for a Rubber (Hevea Brasiliensis) Plantation in Central Cambodia: The Effect of the Regular Spacing of Planted Trees

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumagai, Tomo'omi; Mudd, Ryan; Miyazawa, Yoshiyuki

We developed a soil-vegetation-atmosphere transfer (SVAT) model applicable to simulating CO2 and H2O fluxes from the canopies of rubber plantations, which are characterized by distinct canopy clumping produced by regular spacing of plantation trees. Rubber (Hevea brasiliensis Müll. Arg.) plantations, which are rapidly expanding into both climatically optimal and sub-optimal environments throughout mainland Southeast Asia, potentially change the partitioning of water, energy, and carbon at multiple scales, compared with traditional land covers it is replacing. Describing the biosphere-atmosphere exchange in rubber plantations via SVAT modeling is therefore essential to understanding the impacts on environmental processes. The regular spacing of plantationmore » trees creates a peculiar canopy structure that is not well represented in most SVAT models, which generally assumes a non-uniform spacing of vegetation. Herein we develop a SVAT model applicable to rubber plantation and an evaluation method for its canopy structure, and examine how the peculiar canopy structure of rubber plantations affects canopy CO2 and H2O exchanges. Model results are compared with measurements collected at a field site in central Cambodia. Our findings suggest that it is crucial to account for intensive canopy clumping in order to reproduce observed rubber plantation fluxes. These results suggest a potentially optimal spacing of rubber trees to produce high productivity and water use efficiency.« less

A structural equation modelling approach examining the pathways between safety climate, behaviour performance and workplace slipping

PubMed Central

Swedler, David I; Verma, Santosh K; Huang, Yueng-Hsiang; Lombardi, David A; Chang, Wen-Ruey; Brennan, Melayne; Courtney, Theodore K

2015-01-01

Objective Safety climate has previously been associated with increasing safe workplace behaviours and decreasing occupational injuries. This study seeks to understand the structural relationship between employees’ perceptions of safety climate, performing a safety behaviour (ie, wearing slip-resistant shoes) and risk of slipping in the setting of limited-service restaurants. Methods At baseline, we surveyed 349 employees at 30 restaurants for their perceptions of their safety training and management commitment to safety as well as demographic data. Safety performance was identified as wearing slip-resistant shoes, as measured by direct observation by the study team. We then prospectively collected participants’ hours worked and number of slips weekly for the next 12 weeks. Using a confirmatory factor analysis, we modelled safety climate as a higher order factor composed of previously identified training and management commitment factors. Results The 349 study participants experienced 1075 slips during the 12-week follow-up. Confirmatory factor analysis supported modelling safety climate as a higher order factor composed of safety training and management commitment. In a structural equation model, safety climate indirectly affected prospective risk of slipping through safety performance, but no direct relationship between safety climate and slips was evident. Conclusions Results suggest that safety climate can reduce workplace slips through performance of a safety behaviour as well as suggesting a potential causal mechanism through which safety climate can reduce workplace injuries. Safety climate can be modelled as a higher order factor composed of safety training and management commitment. PMID:25710968

Dimensional Structure and Correlates of Posttraumatic Stress Symptoms Following Suspected Acute Coronary Syndrome

PubMed Central

Sumner, Jennifer A.; Kronish, Ian M.; Pietrzak, Robert H.; Shimbo, Daichi; Shaffer, Jonathan A.; Parsons, Faith E.; Edmondson, Donald

2015-01-01

Background Posttraumatic stress disorder (PTSD) is a heterogeneous construct, and some have suggested that PTSD triggered by acute coronary syndrome (ACS) may differ from PTSD due to prototypical traumas. Methods We conducted the first examination of the latent structure of PTSD symptoms after suspected ACS in 399 adults in the REactions to Acute Care and Hospitalization (REACH) study, an observational cohort study of patients recruited from the emergency department during evaluation for ACS. Using confirmatory factor analysis, we compared the 4-factor dysphoria, 4-factor numbing, and 5-factor dysphoric arousal models of PTSD. Results Although all models fit well, the dysphoria model was selected as the best-fitting model. Further, there was measurement invariance of the dysphoria model by sex. PTSD dimensions evidenced differential associations with indicators of threat perception during ACS evaluation and adherence to cardioprotective medication. Limitations One limitation of this investigation is the use of self-report measures. In addition, only one-third of the sample was diagnosed with ACS at discharge; the remaining participants received diagnoses such as chest pain without a cardiac diagnosis, another symptom/disease process (e.g., hypertensive chronic kidney disease), or another cardiac disease. Conclusions Findings suggest that suspected ACS-related PTSD symptoms are best-represented by a 4-factor structure distinguishing between specific (e.g., re-experiencing) and non-specific (dysphoria) symptoms of PTSD that has received support in the broader PTSD literature. PMID:26241667

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: from protein structure to nanodisk assemblies.

PubMed

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

2010-11-07

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

NASA Astrophysics Data System (ADS)

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.; Peterlik, Herwig; Jungbauer, Alois; Tscheliessnig, Rupert

2010-11-01

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on the basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.

Surface layer protein characterization by small angle x-ray scattering and a fractal mean force concept: From protein structure to nanodisk assemblies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Horejs, Christine; Pum, Dietmar; Sleytr, Uwe B.

2010-11-07

Surface layers (S-layers) are the most commonly observed cell surface structure of prokaryotic organisms. They are made up of proteins that spontaneously self-assemble into functional crystalline lattices in solution, on various solid surfaces, and interfaces. While classical experimental techniques failed to recover a complete structural model of an unmodified S-layer protein, small angle x-ray scattering (SAXS) provides an opportunity to study the structure of S-layer monomers in solution and of self-assembled two-dimensional sheets. For the protein under investigation we recently suggested an atomistic structural model by the use of molecular dynamics simulations. This structural model is now refined on themore » basis of SAXS data together with a fractal assembly approach. Here we show that a nondiluted critical system of proteins, which crystallize into monomolecular structures, might be analyzed by SAXS if protein-protein interactions are taken into account by relating a fractal local density distribution to a fractal local mean potential, which has to fulfill the Poisson equation. The present work demonstrates an important step into the elucidation of the structure of S-layers and offers a tool to analyze the structure of self-assembling systems in solution by means of SAXS and computer simulations.« less

Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1

PubMed Central

Ryu, Stephen I.; Shenoy, Krishna V.; Cunningham, John P.; Churchland, Mark M.

2016-01-01

Cortical firing rates frequently display elaborate and heterogeneous temporal structure. One often wishes to compute quantitative summaries of such structure—a basic example is the frequency spectrum—and compare with model-based predictions. The advent of large-scale population recordings affords the opportunity to do so in new ways, with the hope of distinguishing between potential explanations for why responses vary with time. We introduce a method that assesses a basic but previously unexplored form of population-level structure: when data contain responses across multiple neurons, conditions, and times, they are naturally expressed as a third-order tensor. We examined tensor structure for multiple datasets from primary visual cortex (V1) and primary motor cortex (M1). All V1 datasets were ‘simplest’ (there were relatively few degrees of freedom) along the neuron mode, while all M1 datasets were simplest along the condition mode. These differences could not be inferred from surface-level response features. Formal considerations suggest why tensor structure might differ across modes. For idealized linear models, structure is simplest across the neuron mode when responses reflect external variables, and simplest across the condition mode when responses reflect population dynamics. This same pattern was present for existing models that seek to explain motor cortex responses. Critically, only dynamical models displayed tensor structure that agreed with the empirical M1 data. These results illustrate that tensor structure is a basic feature of the data. For M1 the tensor structure was compatible with only a subset of existing models. PMID:27814353

A multiple-scales model of the shock-cell structure of imperfectly expanded supersonic jets

NASA Technical Reports Server (NTRS)

Tam, C. K. W.; Jackson, J. A.; Seiner, J. M.

1985-01-01

The present investigation is concerned with the development of an analytical model of the quasi-periodic shock-cell structure of an imperfectly expanded supersonic jet. The investigation represents a part of a program to develop a mathematical theory of broadband shock-associated noise of supersonic jets. Tam and Tanna (1982) have suggested that this type of noise is generated by the weak interaction between the quasi-periodic shock cells and the downstream-propagating large turbulence structures in the mixing layer of the jet. In the model developed in this paper, the effect of turbulence in the mixing layer of the jet is simulated by the addition of turbulent eddy-viscosity terms to the momentum equation. Attention is given to the mean-flow profile and the numerical solution, and a comparison of the numerical results with experimental data.

Structure and modeling of turbulence

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novikov, E.A.

The {open_quotes}vortex strings{close_quotes} scale l{sub s} {approximately} LRe{sup -3/10} (L-external scale, Re - Reynolds number) is suggested as a grid scale for the large-eddy simulation. Various aspects of the structure of turbulence and subgrid modeling are described in terms of conditional averaging, Markov processes with dependent increments and infinitely divisible distributions. The major request from the energy, naval, aerospace and environmental engineering communities to the theory of turbulence is to reduce the enormous number of degrees of freedom in turbulent flows to a level manageable by computer simulations. The vast majority of these degrees of freedom is in the small-scalemore » motion. The study of the structure of turbulence provides a basis for subgrid-scale (SGS) models, which are necessary for the large-eddy simulations (LES).« less

Assessing a dysphoric arousal model of acute stress disorder symptoms in a clinical sample of rape and bank robbery victims

PubMed Central

Hansen, Maj; Armour, Cherie; Elklit, Ask

2012-01-01

Background Since the introduction of Acute Stress Disorder (ASD) into the 4th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) research has focused on the ability of ASD to predict PTSD rather than focusing on addressing ASD's underlying latent structure. The few existing confirmatory factor analytic (CFA) studies of ASD have failed to reach a clear consensus regarding ASD's underlying dimensionality. Although, the discrepancy in the results may be due to varying ASD prevalence rates, it remains possible that the model capturing the latent structure of ASD has not yet been put forward. One such model may be a replication of a new five-factor model of PTSD, which separates the arousal symptom cluster into Dysphoric and Anxious Arousal. Given the pending DSM-5, uncovering ASD's latent structure is more pertinent than ever. Objective Using CFA, four different models of the latent structure of ASD were specified and tested: the proposed DSM-5 model, the DSM-IV model, a three factor model, and a five factor model separating the arousal symptom cluster. Method The analyses were based on a combined sample of rape and bank robbery victims, who all met the diagnostic criteria for ASD (N = 404) using the Acute Stress Disorder Scale. Results The results showed that the five factor model provided the best fit to the data. Conclusions The results of the present study suggest that the dimensionality of ASD may be best characterized as a five factor structure which separates dysphoric and anxious arousal items into two separate factors, akin to recent research on PTSD's latent structure. Thus, the current study adds to the debate about how ASD should be conceptualized in the pending DSM-5. PMID:22893845

Assessing a dysphoric arousal model of acute stress disorder symptoms in a clinical sample of rape and bank robbery victims.

PubMed

Hansen, Maj; Armour, Cherie; Elklit, Ask

2012-01-01

Since the introduction of Acute Stress Disorder (ASD) into the 4th edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV) research has focused on the ability of ASD to predict PTSD rather than focusing on addressing ASD's underlying latent structure. The few existing confirmatory factor analytic (CFA) studies of ASD have failed to reach a clear consensus regarding ASD's underlying dimensionality. Although, the discrepancy in the results may be due to varying ASD prevalence rates, it remains possible that the model capturing the latent structure of ASD has not yet been put forward. One such model may be a replication of a new five-factor model of PTSD, which separates the arousal symptom cluster into Dysphoric and Anxious Arousal. Given the pending DSM-5, uncovering ASD's latent structure is more pertinent than ever. USING CFA, FOUR DIFFERENT MODELS OF THE LATENT STRUCTURE OF ASD WERE SPECIFIED AND TESTED: the proposed DSM-5 model, the DSM-IV model, a three factor model, and a five factor model separating the arousal symptom cluster. The analyses were based on a combined sample of rape and bank robbery victims, who all met the diagnostic criteria for ASD (N = 404) using the Acute Stress Disorder Scale. The results showed that the five factor model provided the best fit to the data. The results of the present study suggest that the dimensionality of ASD may be best characterized as a five factor structure which separates dysphoric and anxious arousal items into two separate factors, akin to recent research on PTSD's latent structure. Thus, the current study adds to the debate about how ASD should be conceptualized in the pending DSM-5.

Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy

2014-08-19

The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup133 55–502) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one constructmore » of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332–1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes.« less

Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex*

PubMed Central

Kim, Seung Joong; Fernandez-Martinez, Javier; Sampathkumar, Parthasarathy; Martel, Anne; Matsui, Tsutomu; Tsuruta, Hiro; Weiss, Thomas M.; Shi, Yi; Markina-Inarrairaegui, Ane; Bonanno, Jeffery B.; Sauder, J. Michael; Burley, Stephen K.; Chait, Brian T.; Almo, Steven C.; Rout, Michael P.; Sali, Andrej

2014-01-01

The nuclear pore complex (NPC) is the sole passageway for the transport of macromolecules across the nuclear envelope. Nup133, a major component in the essential Y-shaped Nup84 complex, is a large scaffold protein of the NPC's outer ring structure. Here, we describe an integrative modeling approach that produces atomic models for multiple states of Saccharomyces cerevisiae (Sc) Nup133, based on the crystal structures of the sequence segments and their homologs, including the related Vanderwaltozyma polyspora (Vp) Nup133 residues 55 to 502 (VpNup13355–502) determined in this study, small angle X-ray scattering profiles for 18 constructs of ScNup133 and one construct of VpNup133, and 23 negative-stain electron microscopy class averages of ScNup1332–1157. Using our integrative approach, we then computed a multi-state structural model of the full-length ScNup133 and validated it with mutational studies and 45 chemical cross-links determined via mass spectrometry. Finally, the model of ScNup133 allowed us to annotate a potential ArfGAP1 lipid packing sensor (ALPS) motif in Sc and VpNup133 and discuss its potential significance in the context of the whole NPC; we suggest that ALPS motifs are scattered throughout the NPC's scaffold in all eukaryotes and play a major role in the assembly and membrane anchoring of the NPC in the nuclear envelope. Our results are consistent with a common evolutionary origin of Nup133 with membrane coating complexes (the protocoatomer hypothesis); the presence of the ALPS motifs in coatomer-like nucleoporins suggests an ancestral mechanism for membrane recognition present in early membrane coating complexes. PMID:25139911

Adolescent depressive symptoms in India, Australia and USA: Exploratory Structural Equation Modelling of cross-national invariance and predictions by gender and age.

PubMed

Lewis, Andrew J; Rowland, Bosco; Tran, Aiden; Solomon, Renatti F; Patton, George C; Catalano, Richard F; Toumbourou, John W

2017-04-01

The present study compares depressive symptoms in adolescents from three countries: Mumbai, India; Seattle, United States; and Melbourne, Australia measured using the Short Moods and Feelings Questionnaire (SMFQ). The study cross nationally compares SMFQ depressive symptom responses by age and gender. Data from a cross-nationally matched survey were used to compare factorial and measurement characteristics from samples of students from Grade 7 and 9 in Mumbai, India (n=3268) with the equivalent cohorts in the Washington State, USA (n=1907) and Victoria, Australia (n=1900). Exploratory Structural Equation Modelling (ESEM) was used to cross-nationally examine factor structure and measurement invariance. A number of reports suggesting that SMFQ is uni-dimensional were not supported in findings from any country. A model with two factors was a better fit and suggested a first factor clustering symptoms that were affective and physiologically based symptoms and a second factor of self-critical, cognitive symptoms. The two-factor model showed convincing cross national configural invariance and acceptable measurement invariance. The present findings revealed that adolescents in Mumbai, India, reported substantially higher depressive symptoms in both factors, but particularly for the self-critical dimension, as compared to their peers in Australia and the USA and that males in Mumbai report high levels of depressive symptoms than females in Mumbai. the cross sectional study collected data for adolescents in Melbourne and Seattle in 2002 and the data for adolescents in Mumbai was obtained in 2010-2011 CONCLUSIONS: These findings suggest that previous findings in developed nations of higher depressive symptoms amongst females compared to males may have an important cultural component and cannot be generalised as a universal feature of adolescent development. Copyright © 2017 Elsevier B.V. All rights reserved.

Electronic structures of Al-Si clusters and the magic number structure Al8Si4

NASA Astrophysics Data System (ADS)

Du, Ning; Su, Mingzhi; Chen, Hongshan

2018-02-01

The low-energy structures of Al8Sim (m = 1-6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al-Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al-Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si-Si, Si-Al and Al-Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

Insights into the structural basis of N2 and O6 substituted guanine derivatives as cyclin-dependent kinase 2 (CDK2) inhibitors: prediction of the binding modes and potency of the inhibitors by docking and ONIOM calculations.

PubMed

Alzate-Morales, Jans H; Caballero, Julio; Vergara Jague, Ariela; González Nilo, Fernando D

2009-04-01

N2 and O6 substituted guanine derivatives are well-known as potent and selective CDK2 inhibitors. The ability of molecular docking using the program AutoDock3 and the hybrid method ONIOM, to obtain some quantum chemical descriptors with the aim to successfully rank these inhibitors, was assessed. The quantum chemical descriptors were used to explain the affinity, of the series studied, by a model of the CDK2 binding site. The initial structures were obtained from docking studies and the ONIOM method was applied with only a single point energy calculation on the protein-ligand structure. We obtained a good correlation model between the ONIOM derived quantum chemical descriptor "H-bond interaction energy" and the experimental biological activity, with a correlation coefficient value of R = 0.80 for 75 compounds. To the best of our knowledge, this is the first time that both methodologies are used in conjunction in order to obtain a correlation model. The model suggests that electrostatic interactions are the principal driving force in this protein-ligand interaction. Overall, the approach was successful for the cases considered, and it suggests that could be useful for the design of inhibitors in the lead optimization phase of drug discovery.

Observing and modelling phytoplankton community structure in the North Sea

NASA Astrophysics Data System (ADS)

Ford, David A.; van der Molen, Johan; Hyder, Kieran; Bacon, John; Barciela, Rosa; Creach, Veronique; McEwan, Robert; Ruardij, Piet; Forster, Rodney

2017-03-01

Phytoplankton form the base of the marine food chain, and knowledge of phytoplankton community structure is fundamental when assessing marine biodiversity. Policy makers and other users require information on marine biodiversity and other aspects of the marine environment for the North Sea, a highly productive European shelf sea. This information must come from a combination of observations and models, but currently the coastal ocean is greatly under-sampled for phytoplankton data, and outputs of phytoplankton community structure from models are therefore not yet frequently validated. This study presents a novel set of in situ observations of phytoplankton community structure for the North Sea using accessory pigment analysis. The observations allow a good understanding of the patterns of surface phytoplankton biomass and community structure in the North Sea for the observed months of August 2010 and 2011. Two physical-biogeochemical ocean models, the biogeochemical components of which are different variants of the widely used European Regional Seas Ecosystem Model (ERSEM), were then validated against these and other observations. Both models were a good match for sea surface temperature observations, and a reasonable match for remotely sensed ocean colour observations. However, the two models displayed very different phytoplankton community structures, with one better matching the in situ observations than the other. Nonetheless, both models shared some similarities with the observations in terms of spatial features and inter-annual variability. An initial comparison of the formulations and parameterizations of the two models suggests that diversity between the parameter settings of model phytoplankton functional types, along with formulations which promote a greater sensitivity to changes in light and nutrients, is key to capturing the observed phytoplankton community structure. These findings will help inform future model development, which should be coupled with detailed validation studies, in order to help facilitate the wider application of marine biogeochemical modelling to user and policy needs.

The influence of vegetation height heterogeneity on forest and woodland bird species richness across the United States.

PubMed

Huang, Qiongyu; Swatantran, Anu; Dubayah, Ralph; Goetz, Scott J

2014-01-01

Avian diversity is under increasing pressures. It is thus critical to understand the ecological variables that contribute to large scale spatial distribution of avian species diversity. Traditionally, studies have relied primarily on two-dimensional habitat structure to model broad scale species richness. Vegetation vertical structure is increasingly used at local scales. However, the spatial arrangement of vegetation height has never been taken into consideration. Our goal was to examine the efficacies of three-dimensional forest structure, particularly the spatial heterogeneity of vegetation height in improving avian richness models across forested ecoregions in the U.S. We developed novel habitat metrics to characterize the spatial arrangement of vegetation height using the National Biomass and Carbon Dataset for the year 2000 (NBCD). The height-structured metrics were compared with other habitat metrics for statistical association with richness of three forest breeding bird guilds across Breeding Bird Survey (BBS) routes: a broadly grouped woodland guild, and two forest breeding guilds with preferences for forest edge and for interior forest. Parametric and non-parametric models were built to examine the improvement of predictability. Height-structured metrics had the strongest associations with species richness, yielding improved predictive ability for the woodland guild richness models (r(2) = ∼ 0.53 for the parametric models, 0.63 the non-parametric models) and the forest edge guild models (r(2) = ∼ 0.34 for the parametric models, 0.47 the non-parametric models). All but one of the linear models incorporating height-structured metrics showed significantly higher adjusted-r2 values than their counterparts without additional metrics. The interior forest guild richness showed a consistent low association with height-structured metrics. Our results suggest that height heterogeneity, beyond canopy height alone, supplements habitat characterization and richness models of forest bird species. The metrics and models derived in this study demonstrate practical examples of utilizing three-dimensional vegetation data for improved characterization of spatial patterns in species richness.

The Influence of Vegetation Height Heterogeneity on Forest and Woodland Bird Species Richness across the United States

PubMed Central

Huang, Qiongyu; Swatantran, Anu; Dubayah, Ralph; Goetz, Scott J.

2014-01-01

Avian diversity is under increasing pressures. It is thus critical to understand the ecological variables that contribute to large scale spatial distribution of avian species diversity. Traditionally, studies have relied primarily on two-dimensional habitat structure to model broad scale species richness. Vegetation vertical structure is increasingly used at local scales. However, the spatial arrangement of vegetation height has never been taken into consideration. Our goal was to examine the efficacies of three-dimensional forest structure, particularly the spatial heterogeneity of vegetation height in improving avian richness models across forested ecoregions in the U.S. We developed novel habitat metrics to characterize the spatial arrangement of vegetation height using the National Biomass and Carbon Dataset for the year 2000 (NBCD). The height-structured metrics were compared with other habitat metrics for statistical association with richness of three forest breeding bird guilds across Breeding Bird Survey (BBS) routes: a broadly grouped woodland guild, and two forest breeding guilds with preferences for forest edge and for interior forest. Parametric and non-parametric models were built to examine the improvement of predictability. Height-structured metrics had the strongest associations with species richness, yielding improved predictive ability for the woodland guild richness models (r2 = ∼0.53 for the parametric models, 0.63 the non-parametric models) and the forest edge guild models (r2 = ∼0.34 for the parametric models, 0.47 the non-parametric models). All but one of the linear models incorporating height-structured metrics showed significantly higher adjusted-r2 values than their counterparts without additional metrics. The interior forest guild richness showed a consistent low association with height-structured metrics. Our results suggest that height heterogeneity, beyond canopy height alone, supplements habitat characterization and richness models of forest bird species. The metrics and models derived in this study demonstrate practical examples of utilizing three-dimensional vegetation data for improved characterization of spatial patterns in species richness. PMID:25101782

Subduction zone guided waves in Northern Chile

NASA Astrophysics Data System (ADS)

Garth, Thomas; Rietbrock, Andreas

2016-04-01

Guided wave dispersion is observed in subduction zones as high frequency energy is retained and delayed by low velocity structure in the subducting slab, while lower frequency energy is able to travel at the faster velocities associated with the surrounding mantle material. As subduction zone guided waves spend longer interacting with the low velocity structure of the slab than any other seismic phase, they have a unique capability to resolve these low velocity structures. In Northern Chile, guided wave arrivals are clearly observed on two stations in the Chilean fore-arc on permanent stations of the IPOC network. High frequency (> 5 Hz) P-wave arrivals are delayed by approximately 2 seconds compared to the low frequency (< 2 Hz) P-wave arrivals. Full waveform finite difference modelling is used to test the low velocity slab structure that cause this P-wave dispersion. The synthetic waveforms produced by these models are compared to the recorded waveforms. Spectrograms are used to compare the relative arrival times of different frequencies, while the velocity spectra is used to constrain the relative amplitude of the arrivals. Constraining the waveform in these two ways means that the full waveform is also matched, and the low pass filtered observed and synthetic waveforms can be compared. A combined misfit between synthetic and observed waveforms is then calculated following Garth & Rietbrock (2014). Based on this misfit criterion we constrain the velocity model by using a grid search approach. Modelling the guided wave arrivals suggest that the observed dispersion cannot be solely accounted for by a single low velocity layer as suggested by previous guided wave studies. Including dipping low velocity normal fault structures in the synthetic model not only accounts for the observed strong P-wave coda, but also produces a clear first motion dispersion. We therefore propose that the lithospheric mantle of the subducting Nazca plate is highly hydrated at intermediate depths by dipping low velocity normal faults. Additionally, we show that the low velocity oceanic crust persists to depths of up to 200 km, well beyond the depth range where the eclogite transition is expected to have occurred. Our results suggest that young subducting lithosphere also has the potential to carry much larger amounts of water to the mantle than has previously been appreciated.

Penna model from the perspective of one geneticist

NASA Astrophysics Data System (ADS)

Cebrat, Stanis l̶aw

1998-09-01

Penna model of ageing predicts many phenomena in population dynamics. Since the model assumes that all genes in genomes are switched on chronologically and that there are no structural differences between male and female genomes, it cannot explain genetic death before birth and differences in mortality rates of men and women. I suggest adding the set of housekeeping genes, which are switched on during the embryo development, to the “death genes” of Penna model. Taking into account the large fraction of genes located on X chromosome whose deleterious mutations exert dominant effect on the male phenotype and recessive on the female phenotype would make it possible to avoid introducing somatic mutations as a cause of higher mortality of men. The modelling of linkage disequilibrium and its implications on eugenics have also been suggested.

Dynamical origins of the community structure of an online multi-layer society

NASA Astrophysics Data System (ADS)

Klimek, Peter; Diakonova, Marina; Eguíluz, Víctor M.; San Miguel, Maxi; Thurner, Stefan

2016-08-01

Social structures emerge as a result of individuals managing a variety of different social relationships. Societies can be represented as highly structured dynamic multiplex networks. Here we study the dynamical origins of the specific community structures of a large-scale social multiplex network of a human society that interacts in a virtual world of a massive multiplayer online game. There we find substantial differences in the community structures of different social actions, represented by the various layers in the multiplex network. Community sizes distributions are either fat-tailed or appear to be centered around a size of 50 individuals. To understand these observations we propose a voter model that is built around the principle of triadic closure. It explicitly models the co-evolution of node- and link-dynamics across different layers of the multiplex network. Depending on link and node fluctuation probabilities, the model exhibits an anomalous shattered fragmentation transition, where one layer fragments from one large component into many small components. The observed community size distributions are in good agreement with the predicted fragmentation in the model. This suggests that several detailed features of the fragmentation in societies can be traced back to the triadic closure processes.

Flutter Analysis for Turbomachinery Using Volterra Series

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing; Yao, Weigang

2014-01-01

The objective of this paper is to describe an accurate and efficient reduced order modeling method for aeroelastic (AE) analysis and for determining the flutter boundary. Without losing accuracy, we develop a reduced order model based on the Volterra series to achieve significant savings in computational cost. The aerodynamic force is provided by a high-fidelity solution from the Reynolds-averaged Navier-Stokes (RANS) equations; the structural mode shapes are determined from the finite element analysis. The fluid-structure coupling is then modeled by the state-space formulation with the structural displacement as input and the aerodynamic force as output, which in turn acts as an external force to the aeroelastic displacement equation for providing the structural deformation. NASA's rotor 67 blade is used to study its aeroelastic characteristics under the designated operating condition. First, the CFD results are validated against measured data available for the steady state condition. Then, the accuracy of the developed reduced order model is compared with the full-order solutions. Finally the aeroelastic solutions of the blade are computed and a flutter boundary is identified, suggesting that the rotor, with the material property chosen for the study, is structurally stable at the operating condition, free of encountering flutter.

The introspective may achieve more: Enhancing existing Geoscientific models with native-language emulated structural reflection

DOE PAGES

Ji, Xinye; Shen, Chaopeng

2017-09-28

Geoscientific models manage myriad and increasingly complex data structures as trans-disciplinary models are integrated. They often incur significant redundancy with cross-cutting tasks. Reflection, the ability of a program to inspect and modify its structure and behavior at runtime, is known as a powerful tool to improve code reusability, abstraction, and separation of concerns. Reflection is rarely adopted in high-performance Geoscientific models, especially with Fortran, where it was previously deemed implausible. Practical constraints of language and legacy often limit us to feather-weight, native-language solutions. We demonstrate the usefulness of a structural-reflection-emulating, dynamically-linked metaObjects, gd. We show real-world examples including data structuremore » self-assembly, effortless save/restart and upgrade to parallel I/O, recursive actions and batch operations. We share gd and a derived module that reproduces MATLAB-like structure in Fortran and C++. We suggest that both a gd representation and a Fortran-native representation are maintained to access the data, each for separate purposes. In conclusion, embracing emulated reflection allows generically-written codes that are highly re-usable across projects.« less

The introspective may achieve more: Enhancing existing Geoscientific models with native-language emulated structural reflection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Xinye; Shen, Chaopeng

Geoscientific models manage myriad and increasingly complex data structures as trans-disciplinary models are integrated. They often incur significant redundancy with cross-cutting tasks. Reflection, the ability of a program to inspect and modify its structure and behavior at runtime, is known as a powerful tool to improve code reusability, abstraction, and separation of concerns. Reflection is rarely adopted in high-performance Geoscientific models, especially with Fortran, where it was previously deemed implausible. Practical constraints of language and legacy often limit us to feather-weight, native-language solutions. We demonstrate the usefulness of a structural-reflection-emulating, dynamically-linked metaObjects, gd. We show real-world examples including data structuremore » self-assembly, effortless save/restart and upgrade to parallel I/O, recursive actions and batch operations. We share gd and a derived module that reproduces MATLAB-like structure in Fortran and C++. We suggest that both a gd representation and a Fortran-native representation are maintained to access the data, each for separate purposes. In conclusion, embracing emulated reflection allows generically-written codes that are highly re-usable across projects.« less

Meaningful questions: The acquisition of auxiliary inversion in a connectionist model of sentence production.

PubMed

Fitz, Hartmut; Chang, Franklin

2017-09-01

Nativist theories have argued that language involves syntactic principles which are unlearnable from the input children receive. A paradigm case of these innate principles is the structure dependence of auxiliary inversion in complex polar questions (Chomsky, 1968, 1975, 1980). Computational approaches have focused on the properties of the input in explaining how children acquire these questions. In contrast, we argue that messages are structured in a way that supports structure dependence in syntax. We demonstrate this approach within a connectionist model of sentence production (Chang, 2009) which learned to generate a range of complex polar questions from a structured message without positive exemplars in the input. The model also generated different types of error in development that were similar in magnitude to those in children (e.g., auxiliary doubling, Ambridge, Rowland, & Pine, 2008; Crain & Nakayama, 1987). Through model comparisons we trace how meaning constraints and linguistic experience interact during the acquisition of auxiliary inversion. Our results suggest that auxiliary inversion rules in English can be acquired without innate syntactic principles, as long as it is assumed that speakers who ask complex questions express messages that are structured into multiple propositions. Copyright © 2017 Elsevier B.V. All rights reserved.

Indicators of ecosystem function identify alternate states in the sagebrush steppe.

PubMed

Kachergis, Emily; Rocca, Monique E; Fernandez-Gimenez, Maria E

2011-10-01

Models of ecosystem change that incorporate nonlinear dynamics and thresholds, such as state-and-transition models (STMs), are increasingly popular tools for land management decision-making. However, few models are based on systematic collection and documentation of ecological data, and of these, most rely solely on structural indicators (species composition) to identify states and transitions. As STMs are adopted as an assessment framework throughout the United States, finding effective and efficient ways to create data-driven models that integrate ecosystem function and structure is vital. This study aims to (1) evaluate the utility of functional indicators (indicators of rangeland health, IRH) as proxies for more difficult ecosystem function measurements and (2) create a data-driven STM for the sagebrush steppe of Colorado, USA, that incorporates both ecosystem structure and function. We sampled soils, plant communities, and IRH at 41 plots with similar clayey soils but different site histories to identify potential states and infer the effects of management practices and disturbances on transitions. We found that many IRH were correlated with quantitative measures of functional indicators, suggesting that the IRH can be used to approximate ecosystem function. In addition to a reference state that functions as expected for this soil type, we identified four biotically and functionally distinct potential states, consistent with the theoretical concept of alternate states. Three potential states were related to management practices (chemical and mechanical shrub treatments and seeding history) while one was related only to ecosystem processes (erosion). IRH and potential states were also related to environmental variation (slope, soil texture), suggesting that there are environmental factors within areas with similar soils that affect ecosystem dynamics and should be noted within STMs. Our approach generated an objective, data-driven model of ecosystem dynamics for rangeland management. Our findings suggest that the IRH approximate ecosystem processes and can distinguish between alternate states and communities and identify transitions when building data-driven STMs. Functional indicators are a simple, efficient way to create data-driven models that are consistent with alternate state theory. Managers can use them to improve current model-building methods and thus apply state-and-transition models more broadly for land management decision-making.

Coupling of electromagnetic and structural dynamics for a wind turbine generator

NASA Astrophysics Data System (ADS)

Matzke, D.; Rick, S.; Hollas, S.; Schelenz, R.; Jacobs, G.; Hameyer, K.

2016-09-01

This contribution presents a model interface of a wind turbine generator to represent the reciprocal effects between the mechanical and the electromagnetic system. Therefore, a multi-body-simulation (MBS) model in Simpack is set up and coupled with a quasi-static electromagnetic (EM) model of the generator in Matlab/Simulink via co-simulation. Due to lack of data regarding the structural properties of the generator the modal properties of the MBS model are fitted with respect to results of an experimental modal analysis (EMA) on the reference generator. The used method and the results of this approach are presented in this paper. The MB S model and the interface are set up in such a way that the EM forces can be applied to the structure and the response of the structure can be fed back to the EM model. The results of this cosimulation clearly show an influence of the feedback of the mechanical response which is mainly damping in the torsional degree of freedom and effects due to eccentricity in radial direction. The accuracy of these results will be validated via test bench measurements and presented in future work. Furthermore it is suggested that the EM model should be adjusted in future works so that transient effects are represented.

NHF-McMaster Guideline on Care Models for Haemophilia Management.

PubMed

Pai, M; Key, N S; Skinner, M; Curtis, R; Feinstein, M; Kessler, C; Lane, S J; Makris, M; Riker, E; Santesso, N; Soucie, J M; Yeung, C H T; Iorio, A; Schünemann, H J

2016-07-01

This guideline was developed to identify evidence-based best practices in haemophilia care delivery, and discuss the range of care providers and services that are most important to optimize outcomes for persons with haemophilia (PWH) across the United States. The guideline was developed following specific methods described in detail in this supplement and based on the GRADE (Grading of Recommendations, Assessment, Development and Evaluation approach). Direct evidence from published literature and the haemophilia community, as well as indirect evidence from other chronic diseases, were reviewed, synthesized and applied to create evidence-based recommendations. The Guideline panel suggests that the integrated care model be used over non-integrated care models for PWH (conditional recommendation, moderate certainty in the evidence). For PWH with inhibitors and those at high risk for inhibitor development, the same recommendation was graded as strong, with moderate certainty in the evidence. The panel suggests that a haematologist, a specialized haemophilia nurse, a physical therapist, a social worker and round-the-clock access to a specialized coagulation laboratory be part of the integrated care team, over an integrated care team that does not include all of these components (conditional recommendation, very low certainty in the evidence). Based on available evidence, the integrated model of care in its current structure, is suggested for optimal care of PWH. There is a need for further appropriately designed studies that address unanswered questions about specific outcomes and the optimal structure of the integrated care delivery model in haemophilia. © 2016 John Wiley & Sons Ltd.

Lidar and Hyperspectral Remote Sensing for the Analysis of Coniferous Biomass Stocks and Fluxes

NASA Astrophysics Data System (ADS)

Halligan, K. Q.; Roberts, D. A.

2006-12-01

Airborne lidar and hyperspectral data can improve estimates of aboveground carbon stocks and fluxes through their complimentary responses to vegetation structure and biochemistry. While strong relationships have been demonstrated between lidar-estimated vegetation structural parameters and field data, research is needed to explore the portability of these methods across a range of topographic conditions, disturbance histories, vegetation type and climate. Additionally, research is needed to evaluate contributions of hyperspectral data in refining biomass estimates and determination of fluxes. To address these questions we are a conducting study of lidar and hyperspectral remote sensing data across sites including coniferous forests, broadleaf deciduous forests and a tropical rainforest. Here we focus on a single study site, Yellowstone National Park, where tree heights, stem locations, above ground biomass and basal area were mapped using first-return small-footprint lidar data. A new method using lidar intensity data was developed for separating the terrain and vegetation components in lidar data using a two-scale iterative local minima filter. Resulting Digital Terrain Models (DTM) and Digital Canopy Models (DCM) were then processed to retrieve a diversity of vertical and horizontal structure metrics. Univariate linear models were used to estimate individual tree heights while stepwise linear regression was used to estimate aboveground biomass and basal area. Three small-area field datasets were compared for their utility in model building and validation of vegetation structure parameters. All structural parameters were linearly correlated with lidar-derived metrics, with higher accuracies obtained where field and imagery data were precisely collocated . Initial analysis of hyperspectral data suggests that vegetation health metrics including measures of live and dead vegetation and stress indices may provide good indicators of carbon flux by mapping vegetation vigor or senescence. Additionally, the strength of hyperspectral data for vegetation classification suggests these data have additional utility for modeling carbon flux dynamics by allowing more accurate plant functional type mapping.

Charge structure in volcanic plumes: a comparison of plume properties predicted by an integral plume model to observations of volcanic lightning during the 2010 eruption of Eyjafjallajökull, Iceland.

PubMed

Woodhouse, Mark J; Behnke, Sonja A

Observations of volcanic lightning made using a lightning mapping array during the 2010 eruption of Eyjafjallajökull allow the trajectory and growth of the volcanic plume to be determined. The lightning observations are compared with predictions of an integral model of volcanic plumes that includes descriptions of the interaction with wind and the effects of moisture. We show that the trajectory predicted by the integral model closely matches the observational data and the model well describes the growth of the plume downwind of the vent. Analysis of the lightning signals reveals information on the dominant charge structure within the volcanic plume. During the Eyjafjallajökull eruption both monopole and dipole charge structures were observed in the plume. By using the integral plume model, we propose the varying charge structure is connected to the availability of condensed water and low temperatures at high altitudes in the plume, suggesting ice formation may have contributed to the generation of a dipole charge structure via thunderstorm-style ice-based charging mechanisms, though overall this charging mechanism is believed to have had only a weak influence on the production of lightning.

Hidden Markov model approach for identifying the modular framework of the protein backbone.

PubMed

Camproux, A C; Tuffery, P; Chevrolat, J P; Boisvieux, J F; Hazout, S

1999-12-01

The hidden Markov model (HMM) was used to identify recurrent short 3D structural building blocks (SBBs) describing protein backbones, independently of any a priori knowledge. Polypeptide chains are decomposed into a series of short segments defined by their inter-alpha-carbon distances. Basically, the model takes into account the sequentiality of the observed segments and assumes that each one corresponds to one of several possible SBBs. Fitting the model to a database of non-redundant proteins allowed us to decode proteins in terms of 12 distinct SBBs with different roles in protein structure. Some SBBs correspond to classical regular secondary structures. Others correspond to a significant subdivision of their bounding regions previously considered to be a single pattern. The major contribution of the HMM is that this model implicitly takes into account the sequential connections between SBBs and thus describes the most probable pathways by which the blocks are connected to form the framework of the protein structures. Validation of the SBBs code was performed by extracting SBB series repeated in recoding proteins and examining their structural similarities. Preliminary results on the sequence specificity of SBBs suggest promising perspectives for the prediction of SBBs or series of SBBs from the protein sequences.

The network organization of protein interactions in the spliceosome is reproduced by the simple rules of food-web models

PubMed Central

Pires, Mathias M.; Cantor, Maurício; Guimarães, Paulo R.; de Aguiar, Marcus A. M.; dos Reis, Sérgio F.; Coltri, Patricia P.

2015-01-01

The network structure of biological systems provides information on the underlying processes shaping their organization and dynamics. Here we examined the structure of the network depicting protein interactions within the spliceosome, the macromolecular complex responsible for splicing in eukaryotic cells. We show the interactions of less connected spliceosome proteins are nested subsets of the connections of the highly connected proteins. At the same time, the network has a modular structure with groups of proteins sharing similar interaction patterns. We then investigated the role of affinity and specificity in shaping the spliceosome network by adapting a probabilistic model originally designed to reproduce food webs. This food-web model was as successful in reproducing the structure of protein interactions as it is in reproducing interactions among species. The good performance of the model suggests affinity and specificity, partially determined by protein size and the timing of association to the complex, may be determining network structure. Moreover, because network models allow building ensembles of realistic networks while encompassing uncertainty they can be useful to examine the dynamics and vulnerability of intracelullar processes. Unraveling the mechanisms organizing the spliceosome interactions is important to characterize the role of individual proteins on splicing catalysis and regulation. PMID:26443080

[Quantitative relationship between gas chromatographic retention time and structural parameters of alkylphenols].

PubMed

Ruan, Xiaofang; Zhang, Ruisheng; Yao, Xiaojun; Liu, Mancang; Fan, Botao

2007-03-01

Alkylphenols are a group of permanent pollutants in the environment and could adversely disturb the human endocrine system. It is therefore important to effectively separate and measure the alkylphenols. To guide the chromatographic analysis of these compounds in practice, the development of quantitative relationship between the molecular structure and the retention time of alkylphenols becomes necessary. In this study, topological, constitutional, geometrical, electrostatic and quantum-chemical descriptors of 44 alkylphenols were calculated using a software, CODESSA, and these descriptors were pre-selected using the heuristic method. As a result, three-descriptor linear model (LM) was developed to describe the relationship between the molecular structure and the retention time of alkylphenols. Meanwhile, the non-linear regression model was also developed based on support vector machine (SVM) using the same three descriptors. The correlation coefficient (R(2)) for the LM and SVM was 0.98 and 0. 92, and the corresponding root-mean-square error was 0. 99 and 2. 77, respectively. By comparing the stability and prediction ability of the two models, it was found that the linear model was a better method for describing the quantitative relationship between the retention time of alkylphenols and the molecular structure. The results obtained suggested that the linear model could be applied for the chromatographic analysis of alkylphenols with known molecular structural parameters.

Structural Basis for the Inhibition of Gas Hydrates by α-Helical Antifreeze Proteins

PubMed Central

Sun, Tianjun; Davies, Peter L.; Walker, Virginia K.

2015-01-01

Kinetic hydrate inhibitors (KHIs) are used commercially to inhibit gas hydrate formation and growth in pipelines. However, improvement of these polymers has been constrained by the lack of verified molecular models. Since antifreeze proteins (AFPs) act as KHIs, we have used their solved x-ray crystallographic structures in molecular modeling to explore gas hydrate inhibition. The internal clathrate water network of the fish AFP Maxi, which extends to the protein’s outer surface, is remarkably similar to the {100} planes of structure type II (sII) gas hydrate. The crystal structure of this water web has facilitated the construction of in silico models for Maxi and type I AFP binding to sII hydrates. Here, we have substantiated our models with experimental evidence of Maxi binding to the tetrahydrofuran sII model hydrate. Both in silico and experimental evidence support the absorbance-inhibition mechanism proposed for KHI binding to gas hydrates. Based on the Maxi crystal structure we suggest that the inhibitor adsorbs to the gas hydrate lattice through the same anchored clathrate water mechanism used to bind ice. These results will facilitate the rational design of a next generation of effective green KHIs for the petroleum industry to ensure safe and efficient hydrocarbon flow. PMID:26488661

Combining shock barometry with numerical modeling: Insights into complex crater formation—The example of the Siljan impact structure (Sweden)

NASA Astrophysics Data System (ADS)

Holm-Alwmark, Sanna; Rae, Auriol S. P.; Ferrière, Ludovic; Alwmark, Carl; Collins, Gareth S.

2017-12-01

Siljan, central Sweden, is the largest known impact structure in Europe. It was formed at about 380 Ma, in the late Devonian period. The structure has been heavily eroded to a level originally located underneath the crater floor, and to date, important questions about the original size and morphology of Siljan remain unanswered. Here we present the results of a shock barometry study of quartz-bearing surface and drill core samples combined with numerical modeling using iSALE. The investigated 13 bedrock granitoid samples show that the recorded shock pressure decreases with increasing depth from 15 to 20 GPa near the (present) surface, to 10-15 GPa at 600 m depth. A best-fit model that is consistent with observational constraints relating to the present size of the structure, the location of the downfaulted sediments, and the observed surface and vertical shock barometry profiles is presented. The best-fit model results in a final crater (rim-to-rim) diameter of 65 km. According to our simulations, the original Siljan impact structure would have been a peak-ring crater. Siljan was formed in a mixed target of Paleozoic sedimentary rocks overlaying crystalline basement. Our modeling suggests that, at the time of impact, the sedimentary sequence was approximately 3 km thick. Since then, there has been around 4 km of erosion of the structure.

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network.

PubMed

Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

2014-04-07

Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird-plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought.

Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird–plant network

PubMed Central

Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

2014-01-01

Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird–plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

Fractal Interrelationships in Field and Seismic Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wilson, T.H.; Dominic, Jovita; Halverson, Joel

1997-10-01

Size scaling interrelationships are evaluated in this study using a fractal model. Fractal models of several geologic variables are examined and include fracture patterns, reflection travel times, structural relief, drainage, topographic relief and active fault patterns. The fractal properties of structural relief inferred from seismic data and structural cross sections provide a quantitative means to characterize and compare complex structural patterns. Studies were conducted using seismic data from the Granny Creek oil field in the Appalachian Plateau. Previous studies of the field reveal that subtle detached structures present on the limb of a larger structure are associated with enhanced productionmore » from the field. Vertical increases of fractal dimension across the zone of detachment provide a measure of the extent to which detachment has occurred. The increases of fractal dimension are greatest in the more productive areas of the field. A result with equally important ramifications is that fracture systems do not appear to be intrinsically fractal as is often suggested in the literature. While examples of nearly identical patterns can be found at different scales supporting the idea of self-similarity, these examples are often taken from different areas and from different lithologies. Examination of fracture systems at different scales in the Valley and Ridge Province suggest that their distribution become increasingly sparse with scale reduction, and therefore are dissimilar or non-fractal. Box counting data in all cases failed to yield a fractal regime. The results obtained from this analysis bring into question the general applicability of reservoir simulations employing fractal models of fracture distribution. The same conclusions were obtained from the analysis of 1D fracture patterns such as those that might appear in a horizontal well.« less

How Many Protein Sequences Fold to a Given Structure? A Coevolutionary Analysis.

PubMed

Tian, Pengfei; Best, Robert B

2017-10-17

Quantifying the relationship between protein sequence and structure is key to understanding the protein universe. A fundamental measure of this relationship is the total number of amino acid sequences that can fold to a target protein structure, known as the "sequence capacity," which has been suggested as a proxy for how designable a given protein fold is. Although sequence capacity has been extensively studied using lattice models and theory, numerical estimates for real protein structures are currently lacking. In this work, we have quantitatively estimated the sequence capacity of 10 proteins with a variety of different structures using a statistical model based on residue-residue co-evolution to capture the variation of sequences from the same protein family. Remarkably, we find that even for the smallest protein folds, such as the WW domain, the number of foldable sequences is extremely large, exceeding the Avogadro constant. In agreement with earlier theoretical work, the calculated sequence capacity is positively correlated with the size of the protein, or better, the density of contacts. This allows the absolute sequence capacity of a given protein to be approximately predicted from its structure. On the other hand, the relative sequence capacity, i.e., normalized by the total number of possible sequences, is an extremely tiny number and is strongly anti-correlated with the protein length. Thus, although there may be more foldable sequences for larger proteins, it will be much harder to find them. Lastly, we have correlated the evolutionary age of proteins in the CATH database with their sequence capacity as predicted by our model. The results suggest a trade-off between the opposing requirements of high designability and the likelihood of a novel fold emerging by chance. Published by Elsevier Inc.

The Radius and Entropy of a Magnetized, Rotating, Fully Convective Star: Analysis with Depth-dependent Mixing Length Theories

NASA Astrophysics Data System (ADS)

Ireland, Lewis G.; Browning, Matthew K.

2018-04-01

Some low-mass stars appear to have larger radii than predicted by standard 1D structure models; prior work has suggested that inefficient convective heat transport, due to rotation and/or magnetism, may ultimately be responsible. We examine this issue using 1D stellar models constructed using Modules for Experiments in Stellar Astrophysics (MESA). First, we consider standard models that do not explicitly include rotational/magnetic effects, with convective inhibition modeled by decreasing a depth-independent mixing length theory (MLT) parameter α MLT. We provide formulae linking changes in α MLT to changes in the interior specific entropy, and hence to the stellar radius. Next, we modify the MLT formulation in MESA to mimic explicitly the influence of rotation and magnetism, using formulations suggested by Stevenson and MacDonald & Mullan, respectively. We find rapid rotation in these models has a negligible impact on stellar structure, primarily because a star’s adiabat, and hence its radius, is predominantly affected by layers near the surface; convection is rapid and largely uninfluenced by rotation there. Magnetic fields, if they influenced convective transport in the manner described by MacDonald & Mullan, could lead to more noticeable radius inflation. Finally, we show that these non-standard effects on stellar structure can be fabricated using a depth-dependent α MLT: a non-magnetic, non-rotating model can be produced that is virtually indistinguishable from one that explicitly parameterizes rotation and/or magnetism using the two formulations above. We provide formulae linking the radially variable α MLT to these putative MLT reformulations.

Uncertainty analysis of terrestrial net primary productivity and net biome productivity in China during 1901-2005

NASA Astrophysics Data System (ADS)

Shao, Junjiong; Zhou, Xuhui; Luo, Yiqi; Zhang, Guodong; Yan, Wei; Li, Jiaxuan; Li, Bo; Dan, Li; Fisher, Joshua B.; Gao, Zhiqiang; He, Yong; Huntzinger, Deborah; Jain, Atul K.; Mao, Jiafu; Meng, Jihua; Michalak, Anna M.; Parazoo, Nicholas C.; Peng, Changhui; Poulter, Benjamin; Schwalm, Christopher R.; Shi, Xiaoying; Sun, Rui; Tao, Fulu; Tian, Hanqin; Wei, Yaxing; Zeng, Ning; Zhu, Qiuan; Zhu, Wenquan

2016-05-01

Despite the importance of net primary productivity (NPP) and net biome productivity (NBP), estimates of NPP and NBP for China are highly uncertain. To investigate the main sources of uncertainty, we synthesized model estimates of NPP and NBP for China from published literature and the Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP). The literature-based results showed that total NPP and NBP in China were 3.35 ± 1.25 and 0.14 ± 0.094 Pg C yr-1, respectively. Classification and regression tree analysis based on literature data showed that model type was the primary source of the uncertainty, explaining 36% and 64% of the variance in NPP and NBP, respectively. Spatiotemporal scales, land cover conditions, inclusion of the N cycle, and effects of N addition also contributed to the overall uncertainty. Results based on the MsTMIP data suggested that model structures were overwhelmingly important (>90%) for the overall uncertainty compared to simulations with different combinations of time-varying global change factors. The interannual pattern of NPP was similar among diverse studies and increased by 0.012 Pg C yr-1 during 1981-2000. In addition, high uncertainty in China's NPP occurred in areas with high productivity, whereas NBP showed the opposite pattern. Our results suggest that to significantly reduce uncertainty in estimated NPP and NBP, model structures should be substantially tested on the basis of empirical results. To this end, coordinated distributed experiments with multiple global change factors might be a practical approach that can validate specific structures of different models.

Comparison of the Motivational Climates Created during Multi-Activity Instruction and Sport Education

ERIC Educational Resources Information Center

Parker, Mitchum B.; Curtner-Smith, Matthew D.

2014-01-01

Previous research has suggested that sport education (SE) may be a superior curriculum model to multi-activity (MA) teaching because its pedagogies and structures create a task-involving motivational climate. The purpose of this study was to describe and compare the objective motivational climates teachers create within the MA and SE models.…

A Common Capacity Limitation for Response and Item Selection in Working Memory

ERIC Educational Resources Information Center

Janczyk, Markus

2017-01-01

Successful completion of any cognitive task requires selecting a particular action and the object the action is applied to. Oberauer (2009) suggested a working memory (WM) model comprising a declarative and a procedural part with analogous structures. One important assumption of this model is that both parts work independently of each other, and…

Thinking about Fashion Models' Looks: A Multidimensional Approach to the Structure of Perceived Physical Attractiveness.

ERIC Educational Resources Information Center

Ashmore, Richard D.; And Others

1996-01-01

Used a functional framework of the perception of female physical attractiveness in a sample of 96 college students viewing 96 photographs of female fashion models. Suggests perceivers should differentiate sexual (sexy), youthful, nonsexual (cute), and up-to-date clothed and groomed (trendy) dimensions. Indicates areas of both convergence and…

Impacts of the Deepwater Horizon oil spill evaluated using an end-to-end ecosystem model.

PubMed

Ainsworth, Cameron H; Paris, Claire B; Perlin, Natalie; Dornberger, Lindsey N; Patterson, William F; Chancellor, Emily; Murawski, Steve; Hollander, David; Daly, Kendra; Romero, Isabel C; Coleman, Felicia; Perryman, Holly

2018-01-01

We use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the oil spill with fisheries independent data. The model suggests that recruitment effects and fishery closures had little influence on biomass dynamics. However, at the assumed level of oil concentrations and toxicity, impacts on fish mortality and growth rates were large and commensurate with observations. Sensitivity analysis suggests the biomass of large reef fish decreased by 25% to 50% in areas most affected by the spill, and biomass of large demersal fish decreased even more, by 40% to 70%. Impacts on reef and demersal forage caused starvation mortality in predators and increased reliance on pelagic forage. Impacts on the food web translated effects of the spill far away from the oiled area. Effects on age structure suggest possible delayed impacts on fishery yields. Recovery of high-turnover populations generally is predicted to occur within 10 years, but some slower-growing populations may take 30+ years to fully recover.

Impacts of the Deepwater Horizon oil spill evaluated using an end-to-end ecosystem model

PubMed Central

Paris, Claire B.; Perlin, Natalie; Dornberger, Lindsey N.; Patterson, William F.; Chancellor, Emily; Murawski, Steve; Hollander, David; Daly, Kendra; Romero, Isabel C.; Coleman, Felicia; Perryman, Holly

2018-01-01

We use a spatially explicit biogeochemical end-to-end ecosystem model, Atlantis, to simulate impacts from the Deepwater Horizon oil spill and subsequent recovery of fish guilds. Dose-response relationships with expected oil concentrations were utilized to estimate the impact on fish growth and mortality rates. We also examine the effects of fisheries closures and impacts on recruitment. We validate predictions of the model by comparing population trends and age structure before and after the oil spill with fisheries independent data. The model suggests that recruitment effects and fishery closures had little influence on biomass dynamics. However, at the assumed level of oil concentrations and toxicity, impacts on fish mortality and growth rates were large and commensurate with observations. Sensitivity analysis suggests the biomass of large reef fish decreased by 25% to 50% in areas most affected by the spill, and biomass of large demersal fish decreased even more, by 40% to 70%. Impacts on reef and demersal forage caused starvation mortality in predators and increased reliance on pelagic forage. Impacts on the food web translated effects of the spill far away from the oiled area. Effects on age structure suggest possible delayed impacts on fishery yields. Recovery of high-turnover populations generally is predicted to occur within 10 years, but some slower-growing populations may take 30+ years to fully recover. PMID:29370187

Roles of glutamates and metal ions in a rationally designed nitric oxide reductase based on myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Y.W.; Robinson, H.; Yeung, N.

2010-05-11

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Roles of Glutamates and Metal ions in a Rationally Designed Nitric Oxide Reductase Based on Myoglobin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Y Lin; N Yeung; Y Gao

2011-12-31

A structural and functional model of bacterial nitric oxide reductase (NOR) has been designed by introducing two glutamates (Glu) and three histidines (His) in sperm whale myoglobin. X-ray structural data indicate that the three His and one Glu (V68E) residues bind iron, mimicking the putative FeB site in NOR, while the second Glu (I107E) interacts with a water molecule and forms a hydrogen bonding network in the designed protein. Unlike the first Glu (V68E), which lowered the heme reduction potential by {approx}110 mV, the second Glu has little effect on the heme potential, suggesting that the negatively charged Glu hasmore » a different role in redox tuning. More importantly, introducing the second Glu resulted in a {approx}100% increase in NOR activity, suggesting the importance of a hydrogen bonding network in facilitating proton delivery during NOR reactivity. In addition, EPR and X-ray structural studies indicate that the designed protein binds iron, copper, or zinc in the FeB site, each with different effects on the structures and NOR activities, suggesting that both redox activity and an intermediate five-coordinate heme-NO species are important for high NOR activity. The designed protein offers an excellent model for NOR and demonstrates the power of using designed proteins as a simpler and more well-defined system to address important chemical and biological issues.« less

Modulation of Endothelial Glycocalyx Structure under Inflammatory Conditions

PubMed Central

Kolářová, Hana; Ambrůzová, Barbora; Švihálková Šindlerová, Lenka; Klinke, Anna; Kubala, Lukáš

2014-01-01

The glycocalyx of the endothelium is an intravascular compartment that creates a barrier between circulating blood and the vessel wall. The glycocalyx is suggested to play an important role in numerous physiological processes including the regulation of vascular permeability, the prevention of the margination of blood cells to the vessel wall, and the transmission of shear stress. Various theoretical models and experimental approaches provide data about changes to the structure and functions of the glycocalyx under various types of inflammatory conditions. These alterations are suggested to promote inflammatory processes in vessels and contribute to the pathogenesis of number of diseases. In this review we summarize current knowledge about the modulation of the glycocalyx under inflammatory conditions and the consequences for the course of inflammation in vessels. The structure and functions of endothelial glycocalyx are briefly discussed in the context of methodological approaches regarding the determination of endothelial glycocalyx and the uncertainty and challenges involved in glycocalyx structure determination. In addition, the modulation of glycocalyx structure under inflammatory conditions and the possible consequences for pathogenesis of selected diseases and medical conditions (in particular, diabetes, atherosclerosis, ischemia/reperfusion, and sepsis) are summarized. Finally, therapeutic strategies to ameliorate glycocalyx dysfunction suggested by various authors are discussed. PMID:24803742

The Effects of Caregiving Resources on Perceived Health among Caregivers

PubMed Central

Hong, Michin; Harrington, Donna

2016-01-01

This study examined how various types of resources influence perceived health of caregivers. Guided by the conservation of resources theory, a caregiver health model was built and tested using structural equation modeling. The caregiver health model consisted of caregiving situations (functional limitations and cognitive impairments of older adults and caregiving time), resources (financial resources, mastery, social support, family harmony, and service utilization), caregiver burden, and perceived health of caregivers. The sample included 1,837 unpaid informal caregivers drawn from the 2004 National Long-Term Caregiver Survey. The model fit indices indicated that the first structural model did not fit well; however, the revised model yielded an excellent model fit. More stressful caregiving situations were associated with fewer resources and higher burden, whereas greater resources were associated with lower burden and better perceived health of caregivers. The results suggest explicit implications for social work research and practice on how to protect the health of caregivers. PMID:29206951

Fiber Diffraction Data Indicate a Hollow Core for the Alzheimer’s Aβ Three-fold Symmetric Fibril

PubMed Central

McDonald, Michele; Box, Hayden; Bian, Wen; Kendall, Amy; Tycko, Robert; Stubbs, Gerald

2012-01-01

Amyloid β protein (Aβ), the principal component of the extracellular plaques found in the brains of Alzheimer’s disease patients, forms fibrils well suited to structural study by X-ray fiber diffraction. Fiber diffraction patterns from the 40-residue form Aβ(1–40) confirm a number of features of a three-fold symmetric Aβ model from solid state NMR, but suggest that the fibrils have a hollow core, not present in the original ssNMR models. Diffraction patterns calculated from a revised hollow three-fold model with a more regular β-sheet structure are in much better agreement with the observed diffraction data than patterns calculated from the original ssNMR model. Refinement of a hollow-core model against ssNMR data led to a revised ssNMR model, similar to the fiber diffraction model. PMID:22903058

An Investigation of the Factor Structure and Convergent and Discriminant Validity of the Five-Factor Model Rating Form

ERIC Educational Resources Information Center

Samuel, Douglas B.; Mullins-Sweatt, Stephanie N.; Widiger, Thomas A.

2013-01-01

The Five-Factor Model Rating Form (FFMRF) is a one-page measure designed to provide an efficient assessment of the higher order domains of the Five Factor Model (FFM) as well as the more specific, lower order facets proposed by McCrae and Costa. Although previous research has suggested that the FFMRF's assessment of the lower order facets converge…

Modelling Wolbachia infection in a sex-structured mosquito population carrying West Nile virus.

PubMed

Farkas, József Z; Gourley, Stephen A; Liu, Rongsong; Yakubu, Abdul-Aziz

2017-09-01

Wolbachia is possibly the most studied reproductive parasite of arthropod species. It appears to be a promising candidate for biocontrol of some mosquito borne diseases. We begin by developing a sex-structured model for a Wolbachia infected mosquito population. Our model incorporates the key effects of Wolbachia infection including cytoplasmic incompatibility and male killing. We also allow the possibility of reduced reproductive output, incomplete maternal transmission, and different mortality rates for uninfected/infected male/female individuals. We study the existence and local stability of equilibria, including the biologically relevant and interesting boundary equilibria. For some biologically relevant parameter regimes there may be multiple coexistence steady states including, very importantly, a coexistence steady state in which Wolbachia infected individuals dominate. We also extend the model to incorporate West Nile virus (WNv) dynamics, using an SEI modelling approach. Recent evidence suggests that a particular strain of Wolbachia infection significantly reduces WNv replication in Aedes aegypti. We model this via increased time spent in the WNv-exposed compartment for Wolbachia infected female mosquitoes. A basic reproduction number [Formula: see text] is computed for the WNv infection. Our results suggest that, if the mosquito population consists mainly of Wolbachia infected individuals, WNv eradication is likely if WNv replication in Wolbachia infected individuals is sufficiently reduced.

Stress and Resilience in Functional Somatic Syndromes – A Structural Equation Modeling Approach

PubMed Central

Fischer, Susanne; Lemmer, Gunnar; Gollwitzer, Mario; Nater, Urs M.

2014-01-01

Background Stress has been suggested to play a role in the development and perpetuation of functional somatic syndromes. The mechanisms of how this might occur are not clear. Purpose We propose a multi-dimensional stress model which posits that childhood trauma increases adult stress reactivity (i.e., an individual's tendency to respond strongly to stressors) and reduces resilience (e.g., the belief in one's competence). This in turn facilitates the manifestation of functional somatic syndromes via chronic stress. We tested this model cross-sectionally and prospectively. Methods Young adults participated in a web survey at two time points. Structural equation modeling was used to test our model. The final sample consisted of 3′054 participants, and 429 of these participated in the follow-up survey. Results Our proposed model fit the data in the cross-sectional (χ2(21)  = 48.808, p<.001, CFI  = .995, TLI  = .992, RMSEA  = .021, 90% CI [.013.029]) and prospective analyses (χ2(21)  = 32.675, p<.05, CFI  = .982, TLI  = .969, RMSEA  = .036, 90% CI [.001.059]). Discussion Our findings have several clinical implications, suggesting a role for stress management training in the prevention and treatment of functional somatic syndromes. PMID:25396736

Principles of protein folding--a perspective from simple exact models.

PubMed Central

Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S.

1995-01-01

General principles of protein structure, stability, and folding kinetics have recently been explored in computer simulations of simple exact lattice models. These models represent protein chains at a rudimentary level, but they involve few parameters, approximations, or implicit biases, and they allow complete explorations of conformational and sequence spaces. Such simulations have resulted in testable predictions that are sometimes unanticipated: The folding code is mainly binary and delocalized throughout the amino acid sequence. The secondary and tertiary structures of a protein are specified mainly by the sequence of polar and nonpolar monomers. More specific interactions may refine the structure, rather than dominate the folding code. Simple exact models can account for the properties that characterize protein folding: two-state cooperativity, secondary and tertiary structures, and multistage folding kinetics--fast hydrophobic collapse followed by slower annealing. These studies suggest the possibility of creating "foldable" chain molecules other than proteins. The encoding of a unique compact chain conformation may not require amino acids; it may require only the ability to synthesize specific monomer sequences in which at least one monomer type is solvent-averse. PMID:7613459

Biophysical connectivity explains population genetic structure in a highly dispersive marine species

NASA Astrophysics Data System (ADS)

Truelove, Nathan K.; Kough, Andrew S.; Behringer, Donald C.; Paris, Claire B.; Box, Stephen J.; Preziosi, Richard F.; Butler, Mark J.

2017-03-01

Connectivity, the exchange of individuals among locations, is a fundamental ecological process that explains how otherwise disparate populations interact. For most marine organisms, dispersal occurs primarily during a pelagic larval phase that connects populations. We paired population structure from comprehensive genetic sampling and biophysical larval transport modeling to describe how spiny lobster ( Panulirus argus) population differentiation is related to biological oceanography. A total of 581 lobsters were genotyped with 11 microsatellites from ten locations around the greater Caribbean. The overall F ST of 0.0016 ( P = 0.005) suggested low yet significant levels of structuring among sites. An isolation by geographic distance model did not explain spatial patterns of genetic differentiation in P. argus ( P = 0.19; Mantel r = 0.18), whereas a biophysical connectivity model provided a significant explanation of population differentiation ( P = 0.04; Mantel r = 0.47). Thus, even for a widely dispersing species, dispersal occurs over a continuum where basin-wide larval retention creates genetic structure. Our study provides a framework for future explorations of wide-scale larval dispersal and marine connectivity by integrating empirical genetic research and probabilistic modeling.

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

PubMed Central

Huang, Ruili; Xia, Menghang; Sakamuru, Srilatha; Zhao, Jinghua; Shahane, Sampada A.; Attene-Ramos, Matias; Zhao, Tongan; Austin, Christopher P.; Simeonov, Anton

2016-01-01

Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure–activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing. PMID:26811972

Evaluating the Factor Validity of the Children's Organizational Skills Scale in Youth with ADHD.

PubMed

Molitor, Stephen J; Langberg, Joshua M; Evans, Steven W; Dvorsky, Melissa R; Bourchtein, Elizaveta; Eddy, Laura D; Smith, Zoe R; Oddo, Lauren E

2017-06-01

Children and adolescents with ADHD often have difficulties with organization, time management, and planning (OTMP) skills, and these skills are a common target of intervention. A limited array of tools for measuring these abilities in youth is available, and one of the most prominent measures is the Children's Organizational Skills Scale (COSS). Although the COSS fills an important need, a replication of the COSS factor structure outside of initial measure development has not been conducted in any population. Given that the COSS is frequently used in ADHD research, the current study evaluated the factor structure of the parent-rated COSS in a sample ( N = 619) of adolescents with ADHD. Results indicated that the original factor structure could be replicated, although the use of item parcels appeared to affect model fit statistics. An alternative bi-factor model was also tested that did not require the use of parcels, with results suggesting similar model fit in comparison to the original factor structure. Exploratory validity tests indicated that the domain-general factor of the bi-factor model appears related to broad executive functioning abilities.

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

PubMed

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

Three-dimensional structure of cofilin bound to monomeric actin derived by structural mass spectrometry data

PubMed Central

Kamal, J. K. Amisha; Benchaar, Sabrina A.; Takamoto, Keiji; Reisler, Emil; Chance, Mark R.

2007-01-01

The cytoskeletal protein, actin, has its structure and function regulated by cofilin. In the absence of an atomic resolution structure for the actin/cofilin complex, the mechanism of cofilin regulation is poorly understood. Theoretical studies based on the similarities of cofilin and gelsolin segment 1 proposed the cleft between subdomains 1 and 3 in actin as the cofilin binding site. We used radiolytic protein footprinting with mass spectrometry and molecular modeling to provide an atomic model of how cofilin binds to monomeric actin. Footprinting data suggest that cofilin binds to the cleft between subdomains 1 and 2 in actin and that cofilin induces further closure of the actin nucleotide cleft. Site-specific fluorescence data confirm these results. The model identifies key ionic and hydrophobic interactions at the binding interface, including hydrogen-bonding between His-87 of actin to Ser-89 of cofilin that may control the charge dependence of cofilin binding. This model and its implications fill an especially important niche in the actin field, owing to the fact that ongoing crystallization efforts of the actin/cofilin complex have so far failed. This 3D binary complex structure is derived from a combination of solution footprinting data and computational approaches and outlines a general method for determining the structure of such complexes. PMID:17470807

Modelling a 3D structure for EgDf1 from shape Echinococcus granulosus: putative epitopes, phosphorylation motifs and ligand

NASA Astrophysics Data System (ADS)

Paulino, M.; Esteves, A.; Vega, M.; Tabares, G.; Ehrlich, R.; Tapia, O.

1998-07-01

EgDf1 is a developmentally regulated protein from the parasite Echinococcus granulosus related to a family of hydrophobic ligand binding proteins. This protein could play a crucial role during the parasite life cycle development since this organism is unable to synthetize most of their own lipids de novo. Furthermore, it has been shown that two related protein from other parasitic platyhelminths (Fh15 from Fasciola hepatica and Sm14 from Schistosoma mansoni) are able to confer protective inmunity against experimental infection in animal models. A three-dimensional structure would help establishing structure/function relationships on a knowledge based manner. 3D structures for EgDf1 protein were modelled by using myelin P2 (mP2) and intestine fatty acid binding protein (I-FABP) as templates. Molecular dynamics techniques were used to validate the models. Template mP2 yielded the best 3D structure for EgDf1. Palmitic and oleic acids were docked inside EgDf1. The present theoretical results suggest definite location in the secondary structure of the epitopic regions, consensus phosphorylation motifs and oleic acid as a good ligand candidate to EgDf1. This protein might well be involved in the process of supplying hydrophobic metabolites for membrane biosynthesis and for signaling pathways.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leenheer, J.A.; Brown, G.K.; Cabaniss, S.E.

Fulvic acid, isolated from the Suwannee River, Georgia, was assessed for its ability to bind Ca{sup 2+}, Cd{sup 2+}, Cu{sup 2+}, Ni{sup 2+}, and Zn{sup 2+} ions at pH 6 before and after extensive fractionation that was designed to reveal the nature of metal binding functional groups. The binding constant for Ca{sup 2+} ion had the greatest increase of all the ions in a metal binding fraction that was selected for intensive characterization for the purpose of building quantitative average model structures. The metal binding fraction was characterized by quantitative {sup 13}C NMR, {sup 1}H NMR, and FT-IR spectrometry andmore » elemental, titrimetric, and molecular weight determinations. The characterization data revealed that carboxyl groups were clustered in short-chain aliphatic dibasic acid structures. The Ca{sup 2+} binding data suggested that ether-substituted oxysuccinic acid structures are good models for the metal binding sites at pH 6. Structural models were derived based upon oxidation and photolytic rearrangements of cutin, lignin, and tannin precursors. These structural models rich in substituted dibasic acid structures revealed polydentate binding sites with the potential for both inner-sphere and outer-sphere type binding. The majority of the fulvic acid molecule was involved with metal binding rather than a small substructural unit.« less

Improved Model for Predicting the Free Energy Contribution of Dinucleotide Bulges to RNA Duplex Stability.

PubMed

Tomcho, Jeremy C; Tillman, Magdalena R; Znosko, Brent M

2015-09-01

Predicting the secondary structure of RNA is an intermediate in predicting RNA three-dimensional structure. Commonly, determining RNA secondary structure from sequence uses free energy minimization and nearest neighbor parameters. Current algorithms utilize a sequence-independent model to predict free energy contributions of dinucleotide bulges. To determine if a sequence-dependent model would be more accurate, short RNA duplexes containing dinucleotide bulges with different sequences and nearest neighbor combinations were optically melted to derive thermodynamic parameters. These data suggested energy contributions of dinucleotide bulges were sequence-dependent, and a sequence-dependent model was derived. This model assigns free energy penalties based on the identity of nucleotides in the bulge (3.06 kcal/mol for two purines, 2.93 kcal/mol for two pyrimidines, 2.71 kcal/mol for 5'-purine-pyrimidine-3', and 2.41 kcal/mol for 5'-pyrimidine-purine-3'). The predictive model also includes a 0.45 kcal/mol penalty for an A-U pair adjacent to the bulge and a -0.28 kcal/mol bonus for a G-U pair adjacent to the bulge. The new sequence-dependent model results in predicted values within, on average, 0.17 kcal/mol of experimental values, a significant improvement over the sequence-independent model. This model and new experimental values can be incorporated into algorithms that predict RNA stability and secondary structure from sequence.

Structure of exotic light nuclei: Z = 2, 3, 4

NASA Astrophysics Data System (ADS)

Fortune, H. T.

2018-03-01

I examine the history and current state of knowledge of the structure of so-called "exotic" light nuclei with Z=2-4, from 7He to 16Be . I review the available experimental information and the models that have been applied to these nuclei. I pay particular attention to the interplay among energies, widths (or strengths), and microscopic structure. Throughout the presentation, I focus on a unified description of these nuclei. I point out contradictions within the data, and I suggest experiments that are still needed.

Impacts of model spatial resolution on the vertical structure of convection in the tropics

NASA Astrophysics Data System (ADS)

Bui, Hien Xuan; Yu, Jia-Yuh; Chou, Chia

2018-02-01

This study examined the impacts of model horizontal resolution on vertical structures of convection in the tropics by performing sensitivity experiments with the NCAR CESM1. It was found that contributions to the total precipitation between top-heavy and bottom-heavy convection are different among various resolutions. A coarser resolution tends to produce a greater contribution from top-heavy convection and, as a result, stronger precipitation in the western Pacific ITCZ; while there is less contribution from bottom-heavy convection and weaker precipitation in the eastern Pacific ITCZ. In the western Pacific ITCZ, where the convection is dominated by a top-heavy structure, the stronger precipitation in coarser resolution experiments is due to changes in temperature and moisture profiles associated with a warmer environment (i.e., thermodynamical effect). In the eastern Pacific ITCZ, where the convection is dictated by a bottom-heavy structure, the stronger precipitation in finer resolution experiments comes from changes in convection structure (i.e., dynamic effect) which favors a greater contribution of bottom-heavy convection as the model resolution goes higher. The moisture budget analysis further suggested that the very different behavior in precipitation tendencies in response to model resolution changes between the western and eastern Pacific ITCZs are determined mainly by changes in convective structure rather than changes in convective strength. This study pointed out the importance of model spatial resolution in reproducing a reasonable contribution to the total precipitation between top-heavy and bottom-heavy structure of convection in the tropical Pacific ITCZs.

Simulations of the flocculent spiral M33: what drives the spiral structure?

NASA Astrophysics Data System (ADS)

Dobbs, C. L.; Pettitt, A. R.; Corbelli, E.; Pringle, J. E.

2018-05-01

We perform simulations of isolated galaxies in order to investigate the likely origin of the spiral structure in M33. In our models, we find that gravitational instabilities in the stars and gas are able to reproduce the observed spiral pattern and velocity field of M33, as seen in HI, and no interaction is required. We also find that the optimum models have high levels of stellar feedback which create large holes similar to those observed in M33, whilst lower levels of feedback tend to produce a large amount of small scale structure, and undisturbed long filaments of high surface density gas, hardly detected in the M33 disc. The gas component appears to have a significant role in producing the structure, so if there is little feedback, both the gas and stars organise into clear spiral arms, likely due to a lower combined Q (using gas and stars), and the ready ability of cold gas to undergo spiral shocks. By contrast models with higher feedback have weaker spiral structure, especially in the stellar component, compared to grand design galaxies. We did not see a large difference in the behaviour of Qstars with most of these models, however, because Qstars stayed relatively constant unless the disc was more strongly unstable. Our models suggest that although the stars produce some underlying spiral structure, this is relatively weak, and the gas physics has a considerable role in producing the large scale structure of the ISM in flocculent spirals.

Structural hierarchy of autism spectrum disorder symptoms: an integrative framework.

PubMed

Kim, Hyunsik; Keifer, Cara M; Rodriguez-Seijas, Craig; Eaton, Nicholas R; Lerner, Matthew D; Gadow, Kenneth D

2018-01-01

In an attempt to resolve questions regarding the symptom classification of autism spectrum disorder (ASD), previous research generally aimed to demonstrate superiority of one model over another. Rather than adjudicating which model may be optimal, we propose an alternative approach that integrates competing models using Goldberg's bass-ackwards method, providing a comprehensive understanding of the underlying symptom structure of ASD. The study sample comprised 3,825 individuals, consecutive referrals to a university hospital developmental disabilities specialty clinic or a child psychiatry outpatient clinic. This study analyzed DSM-IV-referenced ASD symptom statements from parent and teacher versions of the Child and Adolescent Symptom Inventory-4R. A series of exploratory structural equation models was conducted in order to produce interpretable latent factors that account for multivariate covariance. Results indicated that ASD symptoms were structured into an interpretable hierarchy across multiple informants. This hierarchy includes five levels; key features of ASD bifurcate into different constructs with increasing specificity. This is the first study to examine an underlying structural hierarchy of ASD symptomatology using the bass-ackwards method. This hierarchy demonstrates how core features of ASD relate at differing levels of resolution, providing a model for conceptualizing ASD heterogeneity and a structure for integrating divergent theories of cognitive processes and behavioral features that define the disorder. These findings suggest that a more coherent and complete understanding of the structure of ASD symptoms may be reflected in a metastructure rather than at one level of resolution. © 2017 Association for Child and Adolescent Mental Health.

Atomic structures of fibrillar segments of hIAPP suggest tightly mated β-sheets are important for cytotoxicity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krotee, Pascal; Rodriguez, Jose A.; Sawaya, Michael R.

2017-01-03

hIAPP fibrils are associated with Type-II Diabetes, but the link of hIAPP structure to islet cell death remains elusive. Here we observe that hIAPP fibrils are cytotoxic to cultured pancreatic β-cells, leading us to determine the structure and cytotoxicity of protein segments composing the amyloid spine of hIAPP. Using the cryoEM method MicroED, we discover that one segment, 19–29 S20G, forms pairs of β-sheets mated by a dry interface that share structural features with and are similarly cytotoxic to full-length hIAPP fibrils. In contrast, a second segment, 15–25 WT, forms non-toxic labile β-sheets. These segments possess different structures and cytotoxicmore » effects, however, both can seed full-length hIAPP, and cause hIAPP to take on the cytotoxic and structural features of that segment. These results suggest that protein segment structures represent polymorphs of their parent protein and that segment 19–29 S20G may serve as a model for the toxic spine of hIAPP.« less

Exploratory structural equation modeling of personality data.

PubMed

Booth, Tom; Hughes, David J

2014-06-01

The current article compares the use of exploratory structural equation modeling (ESEM) as an alternative to confirmatory factor analytic (CFA) models in personality research. We compare model fit, factor distinctiveness, and criterion associations of factors derived from ESEM and CFA models. In Sample 1 (n = 336) participants completed the NEO-FFI, the Trait Emotional Intelligence Questionnaire-Short Form, and the Creative Domains Questionnaire. In Sample 2 (n = 425) participants completed the Big Five Inventory and the depression and anxiety scales of the General Health Questionnaire. ESEM models provided better fit than CFA models, but ESEM solutions did not uniformly meet cutoff criteria for model fit. Factor scores derived from ESEM and CFA models correlated highly (.91 to .99), suggesting the additional factor loadings within the ESEM model add little in defining latent factor content. Lastly, criterion associations of each personality factor in CFA and ESEM models were near identical in both inventories. We provide an example of how ESEM and CFA might be used together in improving personality assessment. © The Author(s) 2014.

Model structure identification for wastewater treatment simulation based on computational fluid dynamics.

PubMed

Alex, J; Kolisch, G; Krause, K

2002-01-01

The objective of this presented project is to use the results of an CFD simulation to automatically, systematically and reliably generate an appropriate model structure for simulation of the biological processes using CSTR activated sludge compartments. Models and dynamic simulation have become important tools for research but also increasingly for the design and optimisation of wastewater treatment plants. Besides the biological models several cases are reported about the application of computational fluid dynamics ICFD) to wastewater treatment plants. One aim of the presented method to derive model structures from CFD results is to exclude the influence of empirical structure selection to the result of dynamic simulations studies of WWTPs. The second application of the approach developed is the analysis of badly performing treatment plants where the suspicion arises that bad flow behaviour such as short cut flows is part of the problem. The method suggested requires as the first step the calculation of fluid dynamics of the biological treatment step at different loading situations by use of 3-dimensional CFD simulation. The result of this information is used to generate a suitable model structure for conventional dynamic simulation of the treatment plant by use of a number of CSTR modules with a pattern of exchange flows between the tanks automatically. The method is explained in detail and the application to the WWTP Wuppertal Buchenhofen is presented.

Maximum likelihood Bayesian model averaging and its predictive analysis for groundwater reactive transport models

USGS Publications Warehouse

Curtis, Gary P.; Lu, Dan; Ye, Ming

2015-01-01

While Bayesian model averaging (BMA) has been widely used in groundwater modeling, it is infrequently applied to groundwater reactive transport modeling because of multiple sources of uncertainty in the coupled hydrogeochemical processes and because of the long execution time of each model run. To resolve these problems, this study analyzed different levels of uncertainty in a hierarchical way, and used the maximum likelihood version of BMA, i.e., MLBMA, to improve the computational efficiency. This study demonstrates the applicability of MLBMA to groundwater reactive transport modeling in a synthetic case in which twenty-seven reactive transport models were designed to predict the reactive transport of hexavalent uranium (U(VI)) based on observations at a former uranium mill site near Naturita, CO. These reactive transport models contain three uncertain model components, i.e., parameterization of hydraulic conductivity, configuration of model boundary, and surface complexation reactions that simulate U(VI) adsorption. These uncertain model components were aggregated into the alternative models by integrating a hierarchical structure into MLBMA. The modeling results of the individual models and MLBMA were analyzed to investigate their predictive performance. The predictive logscore results show that MLBMA generally outperforms the best model, suggesting that using MLBMA is a sound strategy to achieve more robust model predictions relative to a single model. MLBMA works best when the alternative models are structurally distinct and have diverse model predictions. When correlation in model structure exists, two strategies were used to improve predictive performance by retaining structurally distinct models or assigning smaller prior model probabilities to correlated models. Since the synthetic models were designed using data from the Naturita site, the results of this study are expected to provide guidance for real-world modeling. Limitations of applying MLBMA to the synthetic study and future real-world modeling are discussed.

Factor Structure of the Wechsler Intelligence Scale for Children: Fourth Edition in Children with ADHD.

PubMed

Thaler, Nicholas S; Barchard, Kimberly A; Parke, Elyse; Jones, W Paul; Etcoff, Lewis M; Allen, Daniel N

2015-12-01

Recent evidence suggests that the factor structure of the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) is better explained by a five-factor model rather than the four-factor model in the standardization sample. The current study examined the WISC-IV's factor structure in a sample of children with ADHD. Participants included 314 children and adolescents who were diagnosed with ADHD. Confirmatory factor analysis was conducted on the 10 core subtests of the WISC-IV, and three models were examined including two based on Cattell-Horn-Carroll (CHC) theory. A five-factor model consisting of Gc, Gf, Gv, Gsm, and Gs factors provided the best fit for the data. The Perceptual Reasoning factor identified in the original four-factor model split into the two CHC factors, Gf and Gv, and cross-loaded the Symbol Search subtest onto the Gv factor. A five-factor model based on CHC theory provided superior fit for the WISC-IV in children with ADHD, as has been found with the standardization sample. © The Author(s) 2012.

Influence of the Institutional Structure of Surface Water Rights on Agricultural Production in the Central Valley

NASA Astrophysics Data System (ADS)

Nelson, K.; Burchfield, E. K.

2017-12-01

California's Central Valley region is one of the most productive agricultural systems on the planet. The high levels of agricultural production in this region require large amounts of fresh water for irrigation. However, the long-term availability of water required to sustain such levels of agricultural production has been questioned following the latest drought in California. In this study, we use Bayesian multilevel spatiotemporal modeling techniques to examine the influence of the institutional structure of surface water rights in the Central Valley on agricultural production during the recent drought. The R-INLA package is employed to account for spatial processes that have the potential to influence the effects of water right structures on crop productivity as well as on extent of cultivation. Model results suggest that seniority in surface water access significantly improves crop productivity on cultivated lands, but does not directly affect the ability to maintain cultivated extent. In addition, results suggest that areas with more junior surface water rights tend to reduce extent of cultivation, but maintain crop productivity, as cumulative drought stress increases.

A Model for the Ultrastructure of Bone Based on Electron Microscopy of Ion-Milled Sections

PubMed Central

McNally, Elizabeth A.; Schwarcz, Henry P.; Botton, Gianluigi A.; Arsenault, A. Larry

2012-01-01

The relationship between the mineral component of bone and associated collagen has been a matter of continued dispute. We use transmission electron microscopy (TEM) of cryogenically ion milled sections of fully-mineralized cortical bone to study the spatial and topological relationship between mineral and collagen. We observe that hydroxyapatite (HA) occurs largely as elongated plate-like structures which are external to and oriented parallel to the collagen fibrils. Dark field images suggest that the structures (“mineral structures”) are polycrystalline. They are approximately 5 nm thick, 70 nm wide and several hundred nm long. Using energy-dispersive X-ray analysis we show that approximately 70% of the HA occurs as mineral structures external to the fibrils. The remainder is found constrained to the gap zones. Comparative studies of other species suggest that this structural motif is ubiquitous in all vertebrates. PMID:22272230

MIS diode structure in As/+/ implanted CdS

NASA Technical Reports Server (NTRS)

Hutchby, J. A.

1977-01-01

Structure made by As implantation of carefully prepared high-conductivity CdS surfaces followed by Pt deposition and 450 C anneal display rectifying, although substantially different, I-V characteristics in the dark and during illumination with subband-gap light. Structures prepared in the same way on an unimplanted portion of the substrate have similar I-V characteristics, except that the forward turnover voltage for an illuminated unimplanted diode is much smaller than that for an implanted diode. It is suggested that the charge conduction in both structures is dominated by hole and/or electron tunneling through a metal-semiconductor potential barrier. The tunneling processes appear to be quite sensitive to subband-gap illumination, which causes the dramatic decreases of turnover voltages and apparent series resistances. The difference in turnover voltage appears to be caused by interface states between the Pt electrode and the implanted layer, which suggests a MIS model.

Subnetworks of percolation backbones to model karst systems around Tulum, Mexico

NASA Astrophysics Data System (ADS)

Hendrick, Martin; Renard, Philippe

2016-11-01

Karstic caves, which play a key role in groundwater transport, are often organized as complex connected networks resulting from the dissolution of carbonate rocks. In this work, we propose a new model to describe and study the structures of the two largest submersed karst networks in the world. Both of these networks are located in the area of Tulum (Quintana Roo, Mexico). In a previous work te{hendrick2016fractal} we showed that these networks behave as self-similar structures exhibiting well-defined scaling behaviours. In this paper, we suggest that these networks can be modeled using substructures of percolation clusters (θ-subnetworks) having similar structural behaviour (in terms of fractal dimension and conductivity exponent) to those observed in Tulum's karst networks. We show in addition that these θ-subnetworks correspond to structures that minimise a global function, where this global function includes energy dissipation by the viscous forces when water flows through the network, and the cost of network formation itself.

FTIR studies of gluten matrix dehydration after fibre polysaccharide addition.

PubMed

Nawrocka, Agnieszka; Krekora, Magdalena; Niewiadomski, Zbigniew; Miś, Antoni

2018-06-30

FTIR spectroscopy was used to determine changes in secondary structure, as well as water state, in gluten and model doughs supplemented by four fibre polysaccharides (microcrystalline cellulose, inulin, apple pectin and citrus pectin). The gluten and model doughs were obtained from commercially available wheat gluten and model flour, respectively. The polysaccharides were used in five concentrations: 3%, 6%, 9%, 12% and 18%. Analysis of the FTIR spectra indicated that polysaccharides could be divided into two groups: first - microcrystalline cellulose and inulin, second - apple and citrus pectins that induced opposite structural changes. Changes in secondary structure concern mainly β-sheets and β-turns that form aggregated β-structures, suggesting dehydration of the gluten matrix as a result of competition for water between gluten proteins and polysaccharides. Moreover, the positive band at ca. 1226 cm -1 in the spectra of pectin-modified samples indicates formation of 'ether' type hydrogen bonds between gluten proteins and pectins. Copyright © 2018 Elsevier Ltd. All rights reserved.

Structure refinement of membrane proteins via molecular dynamics simulations.

PubMed

Dutagaci, Bercem; Heo, Lim; Feig, Michael

2018-07-01

A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improvement of lipid-facing residues. Scoring with knowledge-based functions (DFIRE and RWplus) was found to be as good as scoring using implicit membrane-based scoring functions suggesting that differences in internal packing is more important than orientations relative to the membrane during the refinement of membrane protein homology models. © 2018 Wiley Periodicals, Inc.

A novel TctA citrate transporter from an activated sludge metagenome: structural and mechanistic predictions for the TTT family.

PubMed

Batista-García, Ramón Alberto; Sánchez-Reyes, Ayixon; Millán-Pacheco, César; González-Zuñiga, Víctor Manuel; Juárez, Soledad; Folch-Mallol, Jorge Luis; Pastor, Nina

2014-09-01

We isolated a putative citrate transporter of the tripartite tricarboxylate transporter (TTT) class from a metagenomic library of activated sludge from a sewage treatment plant. The transporter, dubbed TctA_ar, shares ∼50% sequence identity with TctA of Comamonas testosteroni (TctA_ct) and other β-Proteobacteria, and contains two 20-amino acid repeat signature sequences, considered a hallmark of this particular transporter class. The structures for both TctA_ar and TctA_ct were modeled with I-TASSER and two possible structures for this transporter family were proposed. Docking assays with citrate resulted in the corresponding sets of proposed critical residues for function. These models suggest functions for the 20-amino acid repeats in the context of the two different architectures. This constitutes the first attempt at structure modeling of the TTT family, to the best of our knowledge, and could aid functional understanding of this little-studied family. © 2014 Wiley Periodicals, Inc.

Insight into mitochondrial structure and function from electron tomography.

PubMed

Frey, T G; Renken, C W; Perkins, G A

2002-09-10

In recent years, electron tomography has provided detailed three-dimensional models of mitochondria that have redefined our concept of mitochondrial structure. The models reveal an inner membrane consisting of two components, the inner boundary membrane (IBM) closely apposed to the outer membrane and the cristae membrane that projects into the matrix compartment. These two components are connected by tubular structures of relatively uniform size called crista junctions. The distribution of crista junction sizes and shapes is predicted by a thermodynamic model based upon the energy of membrane bending, but proteins likely also play a role in determining the conformation of the inner membrane. Results of structural studies of mitochondria during apoptosis demonstrate that cytochrome c is released without detectable disruption of the outer membrane or extensive swelling of the mitochondrial matrix, suggesting the formation of an outer membrane pore large enough to allow passage of holo-cytochrome c. The possible compartmentation of inner membrane function between the IBM and the cristae membrane is also discussed.

X-ray absorption spectroscopy of LiBF 4 in propylene carbonate. A model lithium ion battery electrolyte

DOE PAGES

Smith, Jacob W.; Lam, Royce K.; Sheardy, Alex T.; ...

2014-08-20

Since their introduction into the commercial marketplace in 1991, lithium ion batteries have become increasingly ubiquitous in portable technology. Nevertheless, improvements to existing battery technology are necessary to expand their utility for larger-scale applications, such as electric vehicles. Advances may be realized from improvements to the liquid electrolyte; however, current understanding of the liquid structure and properties remains incomplete. X-ray absorption spectroscopy of solutions of LiBF 4 in propylene carbonate (PC), interpreted using first-principles electronic structure calculations within the eXcited electron and Core Hole (XCH) approximation, yields new insight into the solvation structure of the Li + ion in thismore » model electrolyte. By generating linear combinations of the computed spectra of Li +-associating and free PC molecules and comparing to the experimental spectrum, we find a Li +–solvent interaction number of 4.5. This result suggests that computational models of lithium ion battery electrolytes should move beyond tetrahedral coordination structures.« less

SELF-ORGANIZED BRAIDING AND THE STRUCTURE OF CORONAL LOOPS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berger, Mitchell A.; Asgari-Targhi, Mahboubeh, E-mail: m.berger@exeter.ac.u, E-mail: m.asgari@ucl.ac.u

2009-11-01

The Parker model for heating of the solar corona involves reconnection of braided magnetic flux elements. Much of this braiding is thought to occur at as yet unresolved scales, for example, braiding of threads within an extreme-ultraviolet or X-ray loop. However, some braiding may be still visible at scales accessible to TRACE or Hinode. We suggest that attempts to estimate the amount of braiding at these scales must take into account the degree of coherence of the braid structure. In this paper, we examine the effect of reconnection on the structure of a braided magnetic field. We demonstrate that simplemore » models of braided magnetic fields which balance the input of topological structure with reconnection evolve to a self-organized critical state. An initially random braid can become highly ordered, with coherence lengths obeying power-law distributions. The energy released during reconnection also obeys a power law. Our model gives more frequent (but smaller) energy releases nearer to the ends of a coronal loop.« less

Mobile Communication Via Satellite

NASA Technical Reports Server (NTRS)

Yan, Tsun-Yee; Naderi, Firouz M.

1988-01-01

System mixes real-time and delayed-transmission channels. Combination of L-band and SHF links connect fixed and mobile equipment on ground to satellite relay. Software and hardware architecture conforms structure of open-system-interconnection model suggested by International Standards Organization.

Crystal structure of the human astrovirus capsid spike.

PubMed

Dong, Jinhui; Dong, Liping; Méndez, Ernesto; Tao, Yizhi

2011-08-02

Astroviruses are single-stranded, plus-sense RNA viruses that infect both mammals and birds, causing gastroenteritis and other extraintestinal diseases. Clinical studies have established astroviruses as the second leading cause of viral diarrhea in young children. Here we report the crystal structure of the human astrovirus dimeric surface spike determined to 1.8-Å resolution. The overall structure of each spike/projection domain has a unique three-layered β-sandwiches fold, with a core, six-stranded β-barrel structure that is also found in the hepatitis E virus capsid protrusions, suggesting a closer phylogenetic relationship between these two viruses than previously acknowledged. Based on a hepatitis E virus capsid model, we performed homology modeling and produced a complete, T = 3 astrovirus capsid model with features remarkably similar to those observed in a cryoelectron microscopy reconstruction image of a human astrovirus. Mapping conserved residues onto the astrovirus projection domain revealed a putative receptor binding site with amino acid compositions characteristic for polysaccharide recognition. Our results will have an important impact on future characterization of astrovirus structure and function, and will likely have practical applications in the development of vaccines and antivirals.

Microphysical variability of Amazonian deep convective cores observed by CloudSat and simulated by a multi-scale modeling framework

NASA Astrophysics Data System (ADS)

Brant Dodson, J.; Taylor, Patrick C.; Branson, Mark

2018-05-01

Recently launched cloud observing satellites provide information about the vertical structure of deep convection and its microphysical characteristics. In this study, CloudSat reflectivity data is stratified by cloud type, and the contoured frequency by altitude diagrams reveal a double-arc structure in deep convective cores (DCCs) above 8 km. This suggests two distinct hydrometeor modes (snow versus hail/graupel) controlling variability in reflectivity profiles. The day-night contrast in the double arcs is about four times larger than the wet-dry season contrast. Using QuickBeam, the vertical reflectivity structure of DCCs is analyzed in two versions of the Superparameterized Community Atmospheric Model (SP-CAM) with single-moment (no graupel) and double-moment (with graupel) microphysics. Double-moment microphysics shows better agreement with observed reflectivity profiles; however, neither model variant captures the double-arc structure. Ultimately, the results show that simulating realistic DCC vertical structure and its variability requires accurate representation of ice microphysics, in particular the hail/graupel modes, though this alone is insufficient.

A unified genetic association test robust to latent population structure for a count phenotype.

PubMed

Song, Minsun

2018-06-04

Confounding caused by latent population structure in genome-wide association studies has been a big concern despite the success of genome-wide association studies at identifying genetic variants associated with complex diseases. In particular, because of the growing interest in association mapping using count phenotype data, it would be interesting to develop a testing framework for genetic associations that is immune to population structure when phenotype data consist of count measurements. Here, I propose a solution for testing associations between single nucleotide polymorphisms and a count phenotype in the presence of an arbitrary population structure. I consider a classical range of models for count phenotype data. Under these models, a unified test for genetic associations that protects against confounding was derived. An algorithm was developed to efficiently estimate the parameters that are required to fit the proposed model. I illustrate the proposed approach using simulation studies and an empirical study. Both simulated and real-data examples suggest that the proposed method successfully corrects population structure. Copyright © 2018 John Wiley & Sons, Ltd.

Applying the chronic care model to an employee benefits program: a qualitative inquiry.

PubMed

Schauer, Gillian L; Wilson, Mark; Barrett, Barbara; Honeycutt, Sally; Hermstad, April K; Kegler, Michelle C

2013-12-01

To assess how employee benefits programs may strengthen and/or complement elements of the chronic care model (CCM), a framework used by health systems to improve chronic illness care. A qualitative inquiry consisting of semi-structured interviews with employee benefit administrators and partners from a self-insured, self-administered employee health benefits program was conducted at a large family-owned business in southwest Georgia. Results indicate that the employer adapted and used many health system-related elements of the CCM in the design of their benefit program. Data also suggest that the employee benefits program contributed to self-management skills and to informing and activating patients to interact with the health system. Findings suggest that employee benefits programs can use aspects of the CCM in their own benefit design, and can structure their benefits to contribute to patient-related elements from the CCM.

Identification of novel Trypanosoma cruzi prolyl oligopeptidase inhibitors by structure-based virtual screening

NASA Astrophysics Data System (ADS)

de Almeida, Hugo; Leroux, Vincent; Motta, Flávia Nader; Grellier, Philippe; Maigret, Bernard; Santana, Jaime M.; Bastos, Izabela Marques Dourado

2016-12-01

We have previously demonstrated that the secreted prolyl oligopeptidase of Trypanosoma cruzi (POPTc80) is involved in the infection process by facilitating parasite migration through the extracellular matrix. We have built a 3D structural model where POPTc80 is formed by a catalytic α/β-hydrolase domain and a β-propeller domain, and in which the substrate docks at the inter-domain interface, suggesting a "jaw opening" gating access mechanism. This preliminary model was refined by molecular dynamics simulations and next used for a virtual screening campaign, whose predictions were tested by standard binding assays. This strategy was successful as all 13 tested molecules suggested from the in silico calculations were found out to be active POPTc80 inhibitors in the micromolar range (lowest K i at 667 nM). This work paves the way for future development of innovative drugs against Chagas disease.

Geophysical reassessment of the role of ancient crustal structures on the development of western Laurentia and Selwyn Basin, Yukon and Northwest Territories, Canada.

NASA Astrophysics Data System (ADS)

Hayward, N.

2017-12-01

The structure of the western margin of the North American craton (Laurentia) in the northern Canadian Cordillera and its role in the development of the Neoproterozoic-Early Paleozoic Selwyn Basin are reassessed through 3D inversion of a new compilation of aeromagnetic data and archival Bouguer gravity data. The region's tectonic history is obscured by partial burial beneath Selwyn Basin, and a tectonic overprint that includes terrane accretion, regional plutonism, and strike-slip faults with displacements of 100s and perhaps 1000s of kilometers. Despite the implied complexity, preliminary geological and geophysical based interpretations of the structure of the western margin of Laurentia, have been adopted with few refinements in over two decades. Regionally continuous, NE-trending, crustal lineaments, including the Fort Norman line and Leith Ridge fault, were interpreted as having had long-standing influence on the craton development, its western margin, and overlapping sedimentary basin. New results reveal limited evidence for the regional continuity of the NE-trending lineaments. Instead, models suggest that the structure of the Laurentian margin is characterised by segmentation on numerous shorter structures of varied strike. The western margin of the craton and its structures are bound by a NW-trending structure that connects with the Richardson Trough to the north and may have been active during rifting of the Misty Creek embayment. This boundary also marks the easternmost limit of both granitic intrusions in Selwyn Basin, which gravity models suggest are of greater extent than reflected on geological maps, and SEDEX occurrences. An ENE-trending structure beneath northern Selwyn Basin is interpreted as marking the southern edge of a previously unidentified cratonic promontory, akin to the Liard line that marks a transfer fault that bounds the promontory of the Macdonald Platform, south of Selwyn Basin. The ENE-trending structure is traced from the Tintina fault in the west to near to the Great Bear magmatic zone. The structure's regional continuity also limits the interpretation of a post-Cretaceous structure, inboard of the Tintina fault that could be responsible for 1000's km of dextral strike-slip ascribed to the Baja-BC terrane translation model.

Characterization of the recombinant copper chaperone (CCS) from the plant Glycine (G.) max.

PubMed

Sagasti, Sara; Yruela, Inmaculada; Bernal, Maria; Lujan, Maria A; Frago, Susana; Medina, Milagros; Picorel, Rafael

2011-02-01

The goal of the present work was to characterize the recombinant copper chaperone (CCS) from soybean. Very little is known about plant copper chaperones, which makes this study of current interest, and allows for a comparison with the better known homologues from yeast and humans. To obtain sizeable amounts of pure protein suitable for spectroscopic characterization, we cloned and overexpressed the G. max CCS chaperone in E. coli in the presence of 0.5 mM CuSO(4) and 0.5 mM ZnSO(4) in the broth. A pure protein preparation was obtained by using two IMAC steps and pH gradient chromatography. Most of the proteins were obtained as apo-form, devoid of copper atoms. The chaperone showed a high content (i.e., over 40%) of loops, turns and random coil as determined both by circular dichroism and homology modelling. The homology 3-D structural model suggests the protein might fold in three structural protein domains. The 3-D model along with the primary structure and spectroscopic data may suggest that copper atoms occupy the two metal binding sites, MKCEGC and CTC, within the N-terminal domain I and C-terminal domain III, respectively. But only one Zn-binding site was obtained spectroscopically.

Hydration of copper(II): new insights from density functional theory and the COSMO solvation model.

PubMed

Bryantsev, Vyacheslav S; Diallo, Mamadou S; van Duin, Adri C T; Goddard, William A

2008-09-25

The hydrated structure of the Cu(II) ion has been a subject of ongoing debate in the literature. In this article, we use density functional theory (B3LYP) and the COSMO continuum solvent model to characterize the structure and stability of [Cu(H2O)n](2+) clusters as a function of coordination number (4, 5, and 6) and cluster size (n = 4-18). We find that the most thermodynamically favored Cu(II) complexes in the gas phase have a very open four-coordinate structure. They are formed from a stable square-planar [Cu(H2O)8](2+) core stabilized by an unpaired electron in the Cu(II) ion d(x(2)-y(2)) orbital. This is consistent with cluster geometries suggested by recent mass-spectrometric experiments. In the aqueous phase, we find that the more compact five-coordinate square-pyramidal geometry is more stable than either the four-coordinate or six-coordinate clusters in agreement with recent combined EXAFS and XANES studies of aqueous solutions of Cu(II). However, a small energetic difference (approximately 1.4 kcal/mol) between the five- and six-coordinate models with two full hydration shells around the metal ion suggests that both forms may coexist in solution.

[Homeopathy and structure of water: a physical model].

PubMed

Kratky, K W

2004-02-01

Formerly, the author has suggested a relatively simple water model. There, the dynamical structure of a typical water cluster was investigated, being represented by the movement of a ball in an abstract energy landscape. Now the above-mentioned model is investigated in more detail to answer the following question: Are essential claims of homeopathy concerning potentiation (diluting and shaking) in agreement with science? Equations of motion are employed that represent vibrations of clusters. For the computer experiments, the formalism of Nosé-Hoover is used, the surrounding water being interpreted as a heat bath. Diluting corresponds to a shift of the energy landscape towards the pure solvent (water), shaking is accompanied by an increase of the contact to the heat bath. There is a tendency of the ball to be caught in local valleys of the energy landscape (metastable states) if the temperature is not too high and if the liquid is not shaken. Thus, even for a given landscape there are a variety of structures being durable for some time. The computer experiments suggest that the repeated process of potentiation eventually results in a specific metastable state of the pure solvent. The initial substance helps to obtain this goal, but is no longer necessary at last. Copyright 2004 S. Karger GmbH, Freiburg

An introductory review on gravitational-deformation induced structures, fabrics and modeling

NASA Astrophysics Data System (ADS)

Jaboyedoff, Michel; Penna, Ivanna; Pedrazzini, Andrea; Baroň, Ivo; Crosta, Giovanni B.

2013-10-01

Recent studies have pointed out a similarity between tectonics and slope tectonic-induced structures. Numerous studies have demonstrated that structures and fabrics previously interpreted as of purely geodynamical origin are instead the result of large slope deformation, and this led in the past to erroneous interpretations. Nevertheless, their limit seems not clearly defined, but it is somehow transitional. Some studies point out continuity between failures developing at surface with upper crust movements. In this contribution, the main studies which examine the link between rock structures and slope movements are reviewed. The aspects regarding model and scale of observation are discussed together with the role of pre-existing weaknesses in the rock mass. As slope failures can develop through progressive failure, structures and their changes in time and space can be recognized. Furthermore, recognition of the origin of these structures can help in avoiding misinterpretations of regional geology. This also suggests the importance of integrating different slope movement classifications based on distribution and pattern of deformation and the application of structural geology techniques. A structural geology approach in the landslide community is a tool that can greatly support the hazard quantification and related risks, because most of the physical parameters, which are used for landslide modeling, are derived from geotechnical tests or the emerging geophysical approaches.

Resistivity structure and geochemistry of the Jigokudani Valley hydrothermal system, Mt. Tateyama, Japan

NASA Astrophysics Data System (ADS)

Seki, Kaori; Kanda, Wataru; Tanbo, Toshiya; Ohba, Takeshi; Ogawa, Yasuo; Takakura, Shinichi; Nogami, Kenji; Ushioda, Masashi; Suzuki, Atsushi; Saito, Zenshiro; Matsunaga, Yasuo

2016-10-01

This study clarifies the hydrothermal system of Jigokudani Valley near Mt. Tateyama volcano in Japan by using a combination of audio-frequency magnetotelluric (AMT) survey and hot-spring water analysis in order to assess the potential of future phreatic eruptions in the area. Repeated phreatic eruptions in the area about 40,000 years ago produced the current valley morphology, which is now an active solfatara field dotted with hot springs and fumaroles indicative of a well-developed hydrothermal system. The three-dimensional (3D) resistivity structure of the hydrothermal system was modeled by using the results of an AMT survey conducted at 25 locations across the valley in 2013-2014. The model suggests the presence of a near-surface highly conductive layer of < 50 m in thickness across the entire valley, which is interpreted as a cap rock layer. Immediately below the cap rock is a relatively resistive body interpreted as a gas reservoir. Field measurements of temperature, pH, and electrical conductivity (EC) were taken at various hot springs across the valley, and 12 samples of hot-spring waters were analyzed for major ion chemistry and H2O isotopic ratios. All hot-spring waters had low pH and could be categorized into three types on the basis of the Cl-/SO 42 - concentration ratio, with all falling largely on a mixing line between magmatic fluids and local meteoric water (LMW). The geochemical analysis suggests that the hydrothermal system includes a two-phase zone of vapor-liquid. A comparison of the resistivity structure and the geochemically inferred structure suggests that a hydrothermal reservoir is present at a depth of approximately 500 m, from which hot-spring water differentiates into the three observed types. The two-phase zone appears to be located immediately beneath the cap rock structure. These findings suggest that the hydrothermal system of Jigokudani Valley exhibits a number of factors that could trigger a future phreatic eruption.

Molecular envelope and atomic model of an anti-terminated glyQS T-box regulator in complex with tRNAGly

PubMed Central

Chetnani, Bhaskar

2017-01-01

Abstract A T-box regulator or riboswitch actively monitors the levels of charged/uncharged tRNA and participates in amino acid homeostasis by regulating genes involved in their utilization or biosynthesis. It has an aptamer domain for cognate tRNA recognition and an expression platform to sense the charge state and modulate gene expression. These two conserved domains are connected by a variable linker that harbors additional secondary structural elements, such as Stem III. The structural basis for specific tRNA binding is known, but the structural basis for charge sensing and the role of other elements remains elusive. To gain new structural insights on the T-box mechanism, a molecular envelope was calculated from small angle X-ray scattering data for the Bacillus subtilis glyQS T-box riboswitch in complex with an uncharged tRNAGly. A structural model of an anti-terminated glyQS T-box in complex with its cognate tRNAGly was derived based on the molecular envelope. It shows the location and relative orientation of various secondary structural elements. The model was validated by comparing the envelopes of the wild-type complex and two variants. The structural model suggests that in addition to a possible regulatory role, Stem III could aid in preferential stabilization of the T-box anti-terminated state allowing read-through of regulated genes. PMID:28531275

Cognitive control over learning: Creating, clustering and generalizing task-set structure

PubMed Central

Collins, Anne G.E.; Frank, Michael J.

2013-01-01

Executive functions and learning share common neural substrates essential for their expression, notably in prefrontal cortex and basal ganglia. Understanding how they interact requires studying how cognitive control facilitates learning, but also how learning provides the (potentially hidden) structure, such as abstract rules or task-sets, needed for cognitive control. We investigate this question from three complementary angles. First, we develop a new computational “C-TS” (context-task-set) model inspired by non-parametric Bayesian methods, specifying how the learner might infer hidden structure and decide whether to re-use that structure in new situations, or to create new structure. Second, we develop a neurobiologically explicit model to assess potential mechanisms of such interactive structured learning in multiple circuits linking frontal cortex and basal ganglia. We systematically explore the link betweens these levels of modeling across multiple task demands. We find that the network provides an approximate implementation of high level C-TS computations, where manipulations of specific neural mechanisms are well captured by variations in distinct C-TS parameters. Third, this synergism across models yields strong predictions about the nature of human optimal and suboptimal choices and response times during learning. In particular, the models suggest that participants spontaneously build task-set structure into a learning problem when not cued to do so, which predicts positive and negative transfer in subsequent generalization tests. We provide evidence for these predictions in two experiments and show that the C-TS model provides a good quantitative fit to human sequences of choices in this task. These findings implicate a strong tendency to interactively engage cognitive control and learning, resulting in structured abstract representations that afford generalization opportunities, and thus potentially long-term rather than short-term optimality. PMID:23356780

Multi-model approach to assess the impact of climate change on runoff

NASA Astrophysics Data System (ADS)

Dams, J.; Nossent, J.; Senbeta, T. B.; Willems, P.; Batelaan, O.

2015-10-01

The assessment of climate change impacts on hydrology is subject to uncertainties related to the climate change scenarios, stochastic uncertainties of the hydrological model and structural uncertainties of the hydrological model. This paper focuses on the contribution of structural uncertainty of hydrological models to the overall uncertainty of the climate change impact assessment. To quantify the structural uncertainty of hydrological models, four physically based hydrological models (SWAT, PRMS and a semi- and fully distributed version of the WetSpa model) are set up for a catchment in Belgium. Each model is calibrated using four different objective functions. Three climate change scenarios with a high, mean and low hydrological impact are statistically perturbed from a large ensemble of climate change scenarios and are used to force the hydrological models. This methodology allows assessing and comparing the uncertainty introduced by the climate change scenarios with the uncertainty introduced by the hydrological model structure. Results show that the hydrological model structure introduces a large uncertainty on both the average monthly discharge and the extreme peak and low flow predictions under the climate change scenarios. For the low impact climate change scenario, the uncertainty range of the mean monthly runoff is comparable to the range of these runoff values in the reference period. However, for the mean and high impact scenarios, this range is significantly larger. The uncertainty introduced by the climate change scenarios is larger than the uncertainty due to the hydrological model structure for the low and mean hydrological impact scenarios, but the reverse is true for the high impact climate change scenario. The mean and high impact scenarios project increasing peak discharges, while the low impact scenario projects increasing peak discharges only for peak events with return periods larger than 1.6 years. All models suggest for all scenarios a decrease of the lowest flows, except for the SWAT model with the mean hydrological impact climate change scenario. The results of this study indicate that besides the uncertainty introduced by the climate change scenarios also the hydrological model structure uncertainty should be taken into account in the assessment of climate change impacts on hydrology. To make it more straightforward and transparent to include model structural uncertainty in hydrological impact studies, there is a need for hydrological modelling tools that allow flexible structures and methods to validate model structures in their ability to assess impacts under unobserved future climatic conditions.

Exploring psychometric properties of the interdisciplinary education perception scale in health graduate students.

PubMed

Leitch, Judith

2014-01-01

Designed as a measure of perceptions of collaboration, the original psychometric testing of the Interdisciplinary Education Perception Scale (IEPS) indicated a four-factor solution to this measure, although subsequent research has suggested a three-factor solution may have better fit indices. This study aimed to better understand psychometric properties of the IEPS in a new population, health graduate students in the United States, to determine which sub-scale structure may be a better fit. Additionally this research explores the IEPS through a targeted literature review and content analysis in combination with factor analysis to better understand what constructs are able to be assessed by this measure. Results showed that the three-factor model was the best fitting model for the IEPS, suggesting this structure should be used when looking at graduate-level health students. Results also suggested that the IEPS may be able to be as a measure of perceived professional prestige, for which there is currently no existing measure. The dimension of professional prestige should be explored in further research to create a more robust understanding of its role in collaboration between professions.

Homology Modeling of Class A G Protein-Coupled Receptors

PubMed Central

Costanzi, Stefano

2012-01-01

G protein-coupled receptors (GPCRs) are a large superfamily of membrane bound signaling proteins that hold great pharmaceutical interest. Since experimentally elucidated structures are available only for a very limited number of receptors, homology modeling has become a widespread technique for the construction of GPCR models intended to study the structure-function relationships of the receptors and aid the discovery and development of ligands capable of modulating their activity. Through this chapter, various aspects involved in the constructions of homology models of the serpentine domain of the largest class of GPCRs, known as class A or rhodopsin family, are illustrated. In particular, the chapter provides suggestions, guidelines and critical thoughts on some of the most crucial aspect of GPCR modeling, including: collection of candidate templates and a structure-based alignment of their sequences; identification and alignment of the transmembrane helices of the query receptor to the corresponding domains of the candidate templates; selection of one or more templates receptor; election of homology or de novo modeling for the construction of specific extracellular and intracellular domains; construction of the three-dimensional models, with special consideration to extracellular regions, disulfide bridges, and interhelical cavity; validation of the models through controlled virtual screening experiments. PMID:22323225

Corrosion Prediction with Parallel Finite Element Modeling for Coupled Hygro-Chemo Transport into Concrete under Chloride-Rich Environment

PubMed Central

Na, Okpin; Cai, Xiao-Chuan; Xi, Yunping

2017-01-01

The prediction of the chloride-induced corrosion is very important because of the durable life of concrete structure. To simulate more realistic durability performance of concrete structures, complex scientific methods and more accurate material models are needed. In order to predict the robust results of corrosion initiation time and to describe the thin layer from concrete surface to reinforcement, a large number of fine meshes are also used. The purpose of this study is to suggest more realistic physical model regarding coupled hygro-chemo transport and to implement the model with parallel finite element algorithm. Furthermore, microclimate model with environmental humidity and seasonal temperature is adopted. As a result, the prediction model of chloride diffusion under unsaturated condition was developed with parallel algorithms and was applied to the existing bridge to validate the model with multi-boundary condition. As the number of processors increased, the computational time decreased until the number of processors became optimized. Then, the computational time increased because the communication time between the processors increased. The framework of present model can be extended to simulate the multi-species de-icing salts ingress into non-saturated concrete structures in future work. PMID:28772714

Bidirectional Coupling between Astrocytes and Neurons Mediates Learning and Dynamic Coordination in the Brain: A Multiple Modeling Approach

PubMed Central

Wade, John J.; McDaid, Liam J.; Harkin, Jim; Crunelli, Vincenzo; Kelso, J. A. Scott

2011-01-01

In recent years research suggests that astrocyte networks, in addition to nutrient and waste processing functions, regulate both structural and synaptic plasticity. To understand the biological mechanisms that underpin such plasticity requires the development of cell level models that capture the mutual interaction between astrocytes and neurons. This paper presents a detailed model of bidirectional signaling between astrocytes and neurons (the astrocyte-neuron model or AN model) which yields new insights into the computational role of astrocyte-neuronal coupling. From a set of modeling studies we demonstrate two significant findings. Firstly, that spatial signaling via astrocytes can relay a “learning signal” to remote synaptic sites. Results show that slow inward currents cause synchronized postsynaptic activity in remote neurons and subsequently allow Spike-Timing-Dependent Plasticity based learning to occur at the associated synapses. Secondly, that bidirectional communication between neurons and astrocytes underpins dynamic coordination between neuron clusters. Although our composite AN model is presently applied to simplified neural structures and limited to coordination between localized neurons, the principle (which embodies structural, functional and dynamic complexity), and the modeling strategy may be extended to coordination among remote neuron clusters. PMID:22242121

[Critical phenomena, phase equilibria, and the temperature and structural optimum of homeostasis, as revealed by a model system water-biopolymer-electrolyte].

PubMed

Rozhkov, S P

2005-01-01

Equations of spinodal and two quasispinodals corresponding to critical and supercritical phase transitions leading to a rise of different dynamic structures of solution in the phase diagram of a model system water-biopolymer-electrolyte were obtained. The section of the phase diagram was considered where there exists the probability of quasi-equilibrium monomer-cluster and the principle of water-ion homeostasis is realized. Based on these results, a possible mechanism of origination of unspecific adaptation reactions of a biomolecular system at the stage of chemical evolution was suggested.

Transactional Process of African American Adolescents' Family Conflict and Violent Behavior.

PubMed

Choe, Daniel Ewon; Zimmerman, Marc A

2014-12-01

This is the first longitudinal study of urban African American adolescents that has examined bidirectional effects between their family conflict and violent behavior across all of high school. Structured interviews were administered to 681 students each year in high school at ages 15, 16 17, and 18 years. We used structural equation modeling to test a transactional model and found bidirectional effects between family conflict and violent behavior across the middle years of high school, while accounting for sex and socioeconomic status. Findings suggest a reciprocal process involving interpersonal conflict in African American families and adolescent engagement in youth violence.

Reply to Comment on Axial oxygen-centered lattice instabilities in YBa[sub 2]Cu[sub 3]O[sub 7]: An application of the analysis of extended x-ray-absorption fine structure in anharmonic systems' ''

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mustre de Leon, J.; Batistic, I.; Bishop, A.R.

1993-05-01

We assert that the one-site Cu(1)-O(4) model, suggested in the Comment by Thomsen and Cardona [Phys. Rev. B 47, 12 320 (1993)] is inconsistent with polarized x-ray-absorption fine-structure and diffraction results. We also show that the two-site Cu(1)-O(4) distribution is not inconsistent with optical measurements, although a rigid double-well modeling of this distribution is [Phys. Rev. Lett. 68, 3236 (1992)].

Behavior of road accidents: Structural time series approach

NASA Astrophysics Data System (ADS)

Junus, Noor Wahida Md; Ismail, Mohd Tahir; Arsad, Zainudin

2014-12-01

Road accidents become a major issue in contributing to the increasing number of deaths. Few researchers suggest that road accidents occur due to road structure and road condition. The road structure and condition may differ according to the area and volume of traffic of the location. Therefore, this paper attempts to look up the behavior of the road accidents in four main regions in Peninsular Malaysia by employing a structural time series (STS) approach. STS offers the possibility of modelling the unobserved component such as trends and seasonal component and it is allowed to vary over time. The results found that the number of road accidents is described by a different model. Perhaps, the results imply that the government, especially a policy maker should consider to implement a different approach in ways to overcome the increasing number of road accidents.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kufareva, Irina; Gustavsson, Martin; Zheng, Yi

Chemokines and their cell surface G protein–coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal the complicated and diverse structural foundations of small molecule antagonism and allostery, highlight the inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novelmore » epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.« less

Nonequilibrium phase transition in a self-activated biological network.

PubMed

Berry, Hugues

2003-03-01

We present a lattice model for a two-dimensional network of self-activated biological structures with a diffusive activating agent. The model retains basic and simple properties shared by biological systems at various observation scales, so that the structures can consist of individuals, tissues, cells, or enzymes. Upon activation, a structure emits a new mobile activator and remains in a transient refractory state before it can be activated again. Varying the activation probability, the system undergoes a nonequilibrium second-order phase transition from an active state, where activators are present, to an absorbing, activator-free state, where each structure remains in the deactivated state. We study the phase transition using Monte Carlo simulations and evaluate the critical exponents. As they do not seem to correspond to known values, the results suggest the possibility of a separate universality class.

Using Self-Organizing Neural Network Map Combined with Ward's Clustering Algorithm for Visualization of Students' Cognitive Structural Models about Aliveness Concept

PubMed Central

Ugulu, Ilker; Aydin, Halil

2016-01-01

We propose an approach to clustering and visualization of students' cognitive structural models. We use the self-organizing map (SOM) combined with Ward's clustering to conduct cluster analysis. In the study carried out on 100 subjects, a conceptual understanding test consisting of open-ended questions was used as a data collection tool. The results of analyses indicated that students constructed the aliveness concept by associating it predominantly with human. Motion appeared as the most frequently associated term with the aliveness concept. The results suggest that the aliveness concept has been constructed using anthropocentric and animistic cognitive structures. In the next step, we used the data obtained from the conceptual understanding test for training the SOM. Consequently, we propose a visualization method about cognitive structure of the aliveness concept. PMID:26819579

Polygamy and an absence of fine-scale structure in Dendroctonus ponderosae (Hopk.) (Coleoptera: Curcilionidae) confirmed using molecular markers

PubMed Central

Janes, J K; Roe, A D; Rice, A V; Gorrell, J C; Coltman, D W; Langor, D W; Sperling, F A H

2016-01-01

An understanding of mating systems and fine-scale spatial genetic structure is required to effectively manage forest pest species such as Dendroctonus ponderosae (mountain pine beetle). Here we used genome-wide single-nucleotide polymorphisms to assess the fine-scale genetic structure and mating system of D. ponderosae collected from a single stand in Alberta, Canada. Fine-scale spatial genetic structure was absent within the stand and the majority of genetic variation was best explained at the individual level. Relatedness estimates support previous reports of pre-emergence mating. Parentage assignment tests indicate that a polygamous mating system better explains the relationships among individuals within a gallery than the previously reported female monogamous/male polygynous system. Furthermore, there is some evidence to suggest that females may exploit the galleries of other females, at least under epidemic conditions. Our results suggest that current management models are likely to be effective across large geographic areas based on the absence of fine-scale genetic structure. PMID:26286666

Crystal structure of inhibitor of growth 4 (ING4) dimerization domain reveals functional organization of ING family of chromatin-binding proteins.

PubMed

Culurgioni, Simone; Muñoz, Inés G; Moreno, Alberto; Palacios, Alicia; Villate, Maider; Palmero, Ignacio; Montoya, Guillermo; Blanco, Francisco J

2012-03-30

The protein ING4 binds to histone H3 trimethylated at Lys-4 (H3K4me3) through its C-terminal plant homeodomain, thus recruiting the HBO1 histone acetyltransferase complex to target promoters. The structure of the plant homeodomain finger bound to an H3K4me3 peptide has been described, as well as the disorder and flexibility in the ING4 central region. We report the crystal structure of the ING4 N-terminal domain, which shows an antiparallel coiled-coil homodimer with each protomer folded into a helix-loop-helix structure. This arrangement suggests that ING4 can bind simultaneously two histone tails on the same or different nucleosomes. Dimerization has a direct impact on ING4 tumor suppressor activity because monomeric mutants lose the ability to induce apoptosis after genotoxic stress. Homology modeling based on the ING4 structure suggests that other ING dimers may also exist.

Crystallographic Studies of Prion Protein (PrP) Segments Suggest How Structural Changes Encoded by Polymorphism at Residue 129 Modulate Susceptibility to Human Prion Disease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Apostol, Marcin I.; Sawaya, Michael R.; Cascio, Duilio

2010-09-23

A single nucleotide polymorphism (SNP) in codon 129 of the human prion gene, leading to a change from methionine to valine at residue 129 of prion protein (PrP), has been shown to be a determinant in the susceptibility to prion disease. However, the molecular basis of this effect remains unexplained. In the current study, we determined crystal structures of prion segments having either Met or Val at residue 129. These 6-residue segments of PrP centered on residue 129 are 'steric zippers,' pairs of interacting {beta}-sheets. Both structures of these 'homozygous steric zippers' reveal direct intermolecular interactions between Met or Valmore » in one sheet and the identical residue in the mating sheet. These two structures, plus a structure-based model of the heterozygous Met-Val steric zipper, suggest an explanation for the previously observed effects of this locus on prion disease susceptibility and progression.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

A New Model for the Organizational Structure of Medical Record Departments in Hospitals in Iran

PubMed Central

Moghaddasi, Hamid; Hosseini, Azamossadat; Sheikhtaheri, Abbas

2006-01-01

The organizational structure of medical record departments in Iran is not appropriate for the efficient management of healthcare information. In addition, there is no strong information management division to provide comprehensive information management services in hospitals in Iran. Therefore, a suggested model was designed based on four main axes: 1) specifications of a Health Information Management Division, 2) specifications of a Healthcare Information Management Department, 3) the functions of the Healthcare Information Management Department, and 4) the units of the Healthcare Information Management Department. The validity of the model was determined through use of the Delphi technique. The results of the validation process show that the majority of experts agree with the model and consider it to be appropriate and applicable for hospitals in Iran. The model is therefore recommended for hospitals in Iran. PMID:18066362

Simple systems that exhibit self-directed replication

NASA Technical Reports Server (NTRS)

Reggia, James A.; Armentrout, Steven L.; Chou, Hui-Hsien; Peng, Yun

1993-01-01

Biological experience and intuition suggest that self-replication is an inherently complex phenomenon, and early cellular automata models support that conception. More recently, simpler computational models of self-directed replication called sheathed loops have been developed. It is shown here that 'unsheathing' these structures and altering certain assumptions about the symmetry of their components leads to a family of nontrivial self-replicating structures some substantially smaller and simpler than those previously reported. The dependence of replication time and transition function complexity on initial structure size, cell state symmetry, and neighborhood are examined. These results support the view that self-replication is not an inherently complex phenomenon but rather an emergent property arising from local interactions in systems that can be much simpler than is generally believed.

Structural properties of rutile TiO2 nanoparticles accumulated in a model of gastrointestinal epithelium elucidated by micro-beam x-ray absorption fine structure spectroscopy

NASA Astrophysics Data System (ADS)

Veronesi, G.; Brun, E.; Fayard, B.; Cotte, M.; Carrière, M.

2012-05-01

Micro-beam x-ray absorption fine structure spectroscopy was used to investigate rutile TiO2 nanoparticles internalized into gastrointestinal cells during their crossing of a gut model barrier. Nanoparticles diluted in culture medium tend to accumulate in cells after 48 h exposure; however, no spectral differences arise between particles in cellular and in acellular environments, as corroborated by quantitative analysis. This finding establishes that no modification of the lattice properties of the nanoparticles occurs upon interaction with the barrier. These measurements demonstrate the possibility of interrogating nanoparticles in situ within cells, suggesting a way to investigate their fate when incorporated in biological hosts.

Post-traumatic stress symptoms and structure among orphan and vulnerable children and adolescents in Zambia.

PubMed

Familiar, Itziar; Murray, Laura; Gross, Alden; Skavenski, Stephanie; Jere, Elizabeth; Bass, Judith

2014-11-01

Scant information exists on PTSD symptoms and structure in youth from developing countries. We describe the symptom profile and exposure to trauma experiences among 343 orphan and vulnerable children and adolescents from Zambia. We distinguished profiles of post-traumatic stress symptoms using latent class analysis. Average number of trauma-related symptoms (21.6; range 0-38) was similar across sex and age. Latent class model suggested 3 classes varying by level of severity: low (31% of the sample), medium (45% of the sample), and high (24% of the sample) symptomatology. Results suggest that PTSD is a continuously distributed latent trait.

Modeling of Glycerol-3-Phosphate Transporter Suggests a Potential ‘Tilt’ Mechanism involved in its Function

PubMed Central

Tsigelny, Igor F.; Greenberg, Jerry; Kouznetsova, Valentina; Nigam, Sanjay K.

2009-01-01

Many major facilitator superfamily (MFS) transporters have similar 12-transmembrane α-helical topologies with two six-helix halves connected by a long loop. In humans, these transporters participate in key physiological processes and are also, as in the case of members of the organic anion transporter (OAT) family, of pharmaceutical interest. Recently, crystal structures of two bacterial representatives of the MFS family — the glycerol-3-phosphate transporter (GlpT) and lac-permease (LacY) — have been solved and, because of assumptions regarding the high structural conservation of this family, there is hope that the results can be applied to mammalian transporters as well. Based on crystallography, it has been suggested that a major conformational “switching” mechanism accounts for ligand transport by MFS proteins. This conformational switch would then allow periodic changes in the overall transporter configuration, resulting in its cyclic opening to the periplasm or cytoplasm. Following this lead, we have modeled a possible “switch” mechanism in GlpT, using the concept of rotation of protein domains as in the DynDom program17 and membranephilic constraints predicted by the MAPAS program.23 We found that the minima of energies of intersubunit interactions support two alternate positions consistent with their transport properties. Thus, for GlpT, a “tilt” of 9°–10° rotation had the most favorable energetics of electrostatic interaction between the two halves of the transporter; moreover, this confirmation was sufficient to suggest transport of the ligand across the membrane. We conducted steered molecular dynamics simulations of the GlpT-ligand system to explore how glycerol-3-phosphate would be handled by the “tilted” structure, and obtained results generally consistent with experimental mutagenesis data. While biochemical data remain most consistent with a single-site alternating access model, our results raise the possibility that, while the “rocker switch” may apply to certain MFS transporters, intermediate “tilted” states may exist under certain circumstances or as transitional structures. While wet lab experimental confirmation is required, our results suggest that transport mechanisms in this transporter family should probably not be assumed to be conserved simply based on standard structural homology considerations. Furthermore, steered molecular dynamics elucidating energetic interactions of ligands with amino acid residues in an appropriately modeled transporter may have predictive value in understanding the impact of mutations and/or polymorphisms on transporter function. PMID:18942157

Investigation of Nonlinear Pressurization and Model Restart in MSC/NASTRAN for Modeling Thin Film Inflatable Structures

NASA Technical Reports Server (NTRS)

Smalley, Kurt B.; Tinker, Michael L.; Fischer, Richard T.

2001-01-01

This paper is written for the purpose of providing an introduction and set of guidelines for the use of a methodology for NASTRAN eigenvalue modeling of thin film inflatable structures. It is hoped that this paper will spare the reader from the problems and headaches the authors were confronted with during their investigation by presenting here not only an introduction and verification of the methodology, but also a discussion of the problems that this methodology can ensue. Our goal in this investigation was to verify the basic methodology through the creation and correlation of a simple model. An overview of thin film structures, their history, and their applications is given. Previous modeling work is then briefly discussed. An introduction is then given for the method of modeling. The specific mechanics of the method are then discussed in parallel with a basic discussion of NASTRAN s implementation of these mechanics. The problems encountered with the method are then given along with suggestions for their work-a-rounds. The methodology is verified through the correlation between an analytical model and modal test results of a thin film strut. Recommendations are given for the needed advancement of our understanding of this method and ability to accurately model thin film structures. Finally, conclusions are drawn regarding the usefulness of the methodology.

Structural analysis of β-prism lectin from Colocasia esculenta (L.) S chott.

PubMed

Vajravijayan, S; Pletnev, S; Pletnev, V Z; Nandhagopal, N; Gunasekaran, K

2016-10-01

The Mannose-binding β-Prism Colocasia esculenta lectin (β-PCL) was purified from tubers using ion exchange chromatography. The purified β-PCL appeared as a single band of ∼12kDa on SDS-PAGE. β-PCL crystallizes in trigonal space group P3121 and diffracted to a resolution of 2.1Å. The structure was solved using Molecular replacement using Crocus vernus lectin (PDB: 3MEZ) as a model. From the final refined model to an R-factor of 16.5% and an Rfree of 20.4%, it has been observed that the biological unit consists of two β-Prism domains augmented through C-terminals swap over to form one of faces for each domain. Cα superposition of individual domains of β-PCL with individual domains of other related structures and superposition of whole protein structures were carried out. The higher RMS deviation for the superposition of whole structures suggest that β-prism domains assume different orientation in each structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Resilience of branching and massive corals to wave loading under sea level rise--a coupled computational fluid dynamics-structural analysis.

PubMed

Baldock, Tom E; Karampour, Hassan; Sleep, Rachael; Vyltla, Anisha; Albermani, Faris; Golshani, Aliasghar; Callaghan, David P; Roff, George; Mumby, Peter J

2014-09-15

Measurements of coral structural strength are coupled with a fluid dynamics-structural analysis to investigate the resilience of coral to wave loading under sea level rise and a typical Great Barrier Reef lagoon wave climate. The measured structural properties were used to determine the wave conditions and flow velocities that lead to structural failure. Hydrodynamic modelling was subsequently used to investigate the type of the bathymetry where coral is most vulnerable to breakage under cyclonic wave conditions, and how sea level rise (SLR) changes this vulnerability. Massive corals are determined not to be vulnerable to wave induced structural damage, whereas branching corals are susceptible at wave induced orbital velocities exceeding 0.5m/s. Model results from a large suite of idealised bathymetry suggest that SLR of 1m or a loss of skeleton strength of order 25% significantly increases the area of reef flat where branching corals are exposed to damaging wave induced flows. Copyright © 2014 Elsevier Ltd. All rights reserved.

Three-dimensional structure of basal body triplet revealed by electron cryo-tomography

PubMed Central

Li, Sam; Fernandez, Jose-Jesus; Marshall, Wallace F; Agard, David A

2012-01-01

Basal bodies and centrioles play central roles in microtubule (MT)-organizing centres within many eukaryotes. They share a barrel-shaped cylindrical structure composed of nine MT triplet blades. Here, we report the structure of the basal body triplet at 33 Å resolution obtained by electron cryo-tomography and 3D subtomogram averaging. By fitting the atomic structure of tubulin into the EM density, we built a pseudo-atomic model of the tubulin protofilaments at the core of the triplet. The 3D density map reveals additional densities that represent non-tubulin proteins attached to the triplet, including a large inner circular structure in the basal body lumen, which functions as a scaffold to stabilize the entire basal body barrel. We found clear longitudinal structural variations along the basal body, suggesting a sequential and coordinated assembly mechanism. We propose a model in which δ-tubulin and other components participate in the assembly of the basal body. PMID:22157822

Structure and functions of internal working models of attachment and their role for emotion regulation.

PubMed

Zimmermann, P

1999-12-01

The concept of organization in the service of adaptation has been applied to attachment theory (Sroufe & Waters, 1977) as well as to a variety of life sciences (Ryan, Kuhi & Deci, 1997). Internal working models (IWMs) are postulated as providing organizing structure to the attachment behavior system controlling attachment behaviors toward caregivers and, with increasing age, autonomous individual adaptation. While many theoretical specifications have been suggested on that topic (e.g. Bretherton, 1987, 1990; Bretherton & Munholland, 1999; Main, Kaplan & Cassidy, 1985; Sroufe & Fleeson, 1986), empirical studies focusing directly on the structure or functions of internal working models are rare. Knowledge about the structure and functioning of IWMs could add to the understanding of the developmental influences of the attachment organization across the life-span. In this paper two topics will be addressed shortly and related to an empirical investigation concerning the relationship between attachment representations during late adolescence and emotion regulation patterns: (1) structure and functions of IWMs in terms of information-processing and emotion and behavior regulation; and (2) the transfer from IWMs of self-with-attachment figures to adaptive personality structures based on autonomous self-regulation.

A closer look at the lower-order structure of the Personality Inventory for DSM-5: comparison with the Five-Factor Model.

PubMed

Griffin, Sarah A; Samuel, Douglas B

2014-10-01

The Personality Inventory for DSM-5 (PID-5) was developed as a measure of the maladaptive personality trait model included within Section III of the DSM-5. Although preliminary findings have suggested the PID-5 has a five-factor structure that overlaps considerably with the Five-Factor Model (FFM) at the higher order level, there has been much less attention on the specific locations of the 25 lower-order traits. Joint exploratory factor analysis of the PID-5 traits and the 30 facets of the NEO-PI-R were used to determine the lower-order structure of the PID-5. Results indicated the PID-5's domain-level structure closely resembled the FFM. We also explored the placement of several lower-order facets that have not loaded consistently in previous studies. Overall, these results indicate that the PID-5 shares a common structure with the FFM and clarify the placement of some interstitial facets. More research investigating the lower-order facets is needed to determine how they fit into the hierarchical structure and explicate their relationships to existing measures of pathological traits. (PsycINFO Database Record (c) 2014 APA, all rights reserved).