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Sample records for all-atom structure validation

  1. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

    Science.gov (United States)

    Davis, Ian W; Leaver-Fay, Andrew; Chen, Vincent B; Block, Jeremy N; Kapral, Gary J; Wang, Xueyi; Murray, Laura W; Arendall, W Bryan; Snoeyink, Jack; Richardson, Jane S; Richardson, David C

    2007-07-01

    MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

  2. An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

    Science.gov (United States)

    Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

    2009-05-01

    Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

  3. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  4. The Dependence of All-Atom Statistical Potentials on Structural Training Database

    OpenAIRE

    Zhang, Chi; Liu, Song; Zhou, Hongyi; Zhou, Yaoqi

    2004-01-01

    An accurate statistical energy function that is suitable for the prediction of protein structures of all classes should be independent of the structural database used for energy extraction. Here, two high-resolution, low-sequence-identity structural databases of 333 α-proteins and 271 β-proteins were built for examining the database dependence of three all-atom statistical energy functions. They are RAPDF (residue-specific all-atom conditional probability discriminatory function), atomic KBP ...

  5. Protein structure prediction by all-atom free-energy refinement

    Directory of Open Access Journals (Sweden)

    Wenzel Wolfgang

    2007-03-01

    Full Text Available Abstract Background The reliable prediction of protein tertiary structure from the amino acid sequence remains challenging even for small proteins. We have developed an all-atom free-energy protein forcefield (PFF01 that we could use to fold several small proteins from completely extended conformations. Because the computational cost of de-novo folding studies rises steeply with system size, this approach is unsuitable for structure prediction purposes. We therefore investigate here a low-cost free-energy relaxation protocol for protein structure prediction that combines heuristic methods for model generation with all-atom free-energy relaxation in PFF01. Results We use PFF01 to rank and cluster the conformations for 32 proteins generated by ROSETTA. For 22/10 high-quality/low quality decoy sets we select near-native conformations with an average Cα root mean square deviation of 3.03 Å/6.04 Å. The protocol incorporates an inherent reliability indicator that succeeds for 78% of the decoy sets. In over 90% of these cases near-native conformations are selected from the decoy set. This success rate is rationalized by the quality of the decoys and the selectivity of the PFF01 forcefield, which ranks near-native conformations an average 3.06 standard deviations below that of the relaxed decoys (Z-score. Conclusion All-atom free-energy relaxation with PFF01 emerges as a powerful low-cost approach toward generic de-novo protein structure prediction. The approach can be applied to large all-atom decoy sets of any origin and requires no preexisting structural information to identify the native conformation. The study provides evidence that a large class of proteins may be foldable by PFF01.

  6. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations.

    Science.gov (United States)

    Raval, Alpan; Piana, Stefano; Eastwood, Michael P; Dror, Ron O; Shaw, David E

    2012-08-01

    Accurate computational prediction of protein structure represents a longstanding challenge in molecular biology and structure-based drug design. Although homology modeling techniques are widely used to produce low-resolution models, refining these models to high resolution has proven difficult. With long enough simulations and sufficiently accurate force fields, molecular dynamics (MD) simulations should in principle allow such refinement, but efforts to refine homology models using MD have for the most part yielded disappointing results. It has thus far been unclear whether MD-based refinement is limited primarily by accessible simulation timescales, force field accuracy, or both. Here, we examine MD as a technique for homology model refinement using all-atom simulations, each at least 100 μs long-more than 100 times longer than previous refinement simulations-and a physics-based force field that was recently shown to successfully fold a structurally diverse set of fast-folding proteins. In MD simulations of 24 proteins chosen from the refinement category of recent Critical Assessment of Structure Prediction (CASP) experiments, we find that in most cases, simulations initiated from homology models drift away from the native structure. Comparison with simulations initiated from the native structure suggests that force field accuracy is the primary factor limiting MD-based refinement. This problem can be mitigated to some extent by restricting sampling to the neighborhood of the initial model, leading to structural improvement that, while limited, is roughly comparable to the leading alternative methods.

  7. ALMOST: an all atom molecular simulation toolkit for protein structure determination.

    Science.gov (United States)

    Fu, Biao; Sahakyan, Aleksandr B; Camilloni, Carlo; Tartaglia, Gian Gaetano; Paci, Emanuele; Caflisch, Amedeo; Vendruscolo, Michele; Cavalli, Andrea

    2014-05-30

    Almost (all atom molecular simulation toolkit) is an open source computational package for structure determination and analysis of complex molecular systems including proteins, and nucleic acids. Almost has been designed with two primary goals: to provide tools for molecular structure determination using various types of experimental measurements as conformational restraints, and to provide methods for the analysis and assessment of structural and dynamical properties of complex molecular systems. The methods incorporated in Almost include the determination of structural and dynamical features of proteins using distance restraints derived from nuclear Overhauser effect measurements, orientational restraints obtained from residual dipolar couplings and the structural restraints from chemical shifts. Here, we present the first public release of Almost, highlight the key aspects of its computational design and discuss the main features currently implemented. Almost is available for the most common Unix-based operating systems, including Linux and Mac OS X. Almost is distributed free of charge under the GNU Public License, and is available both as a source code and as a binary executable from the project web site at http://www.open-almost.org. Interested users can follow and contribute to the further development of Almost on http://sourceforge.net/projects/almost.

  8. A real-time all-atom structural search engine for proteins.

    Directory of Open Access Journals (Sweden)

    Gabriel Gonzalez

    2014-07-01

    Full Text Available Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license, https://github.com/Gabriel439/suns-cmd (command line client, BSD license, and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license.

  9. A real-time all-atom structural search engine for proteins.

    Science.gov (United States)

    Gonzalez, Gabriel; Hannigan, Brett; DeGrado, William F

    2014-07-01

    Protein designers use a wide variety of software tools for de novo design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new "designability"-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).

  10. Simplified protein models can rival all atom simulations in predicting folding pathways and structure

    Science.gov (United States)

    Adhikari, Aashish N.; Freed, Karl F.; Sosnick, Tobin R.

    2014-01-01

    We demonstrate the ability of simultaneously determining a protein’s folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing native-like substructures or "foldons". Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R.O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that native-like propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the MD study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo. PMID:23889448

  11. All-atom Molecular Dynamics Simulationsand NMR Spectroscopy Study on Interactions and Structures in N-Glycylglycine Aqueous Solution

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Wen-juan Wu; Jing-man Huang; Xin Meng

    2011-01-01

    All-atom molecular dynamics (MD) simulation and the NMR spectra are used to investigate the interactions in N-glycylglycine aqueous solution.Different types of atoms exhibit different capability in forming hydrogen bonds by the radial distribution function analysis.Some typical dominant aggregates are found in different types of hydrogen bonds by the statistical hydrogen-bonding network.Moreover,temperature-dependent NMR are used to compare with the results of the MD simulations.The chemical shifts of the three hydrogen atoms all decrease with the temperature increasing which reveals that the hydrogen bonds are dominant in the glycylglycine aqueous solution.And the NMR results show agreement with the MD simulations.All-atom MD simulations and NMR spectra are successful in revealing the structures and interactions in the N-glycylglycine-water mixtures.

  12. Computational methods toward accurate RNA structure prediction using coarse-grained and all-atom models.

    Science.gov (United States)

    Krokhotin, Andrey; Dokholyan, Nikolay V

    2015-01-01

    Computational methods can provide significant insights into RNA structure and dynamics, bridging the gap in our understanding of the relationship between structure and biological function. Simulations enrich and enhance our understanding of data derived on the bench, as well as provide feasible alternatives to costly or technically challenging experiments. Coarse-grained computational models of RNA are especially important in this regard, as they allow analysis of events occurring in timescales relevant to RNA biological function, which are inaccessible through experimental methods alone. We have developed a three-bead coarse-grained model of RNA for discrete molecular dynamics simulations. This model is efficient in de novo prediction of short RNA tertiary structure, starting from RNA primary sequences of less than 50 nucleotides. To complement this model, we have incorporated additional base-pairing constraints and have developed a bias potential reliant on data obtained from hydroxyl probing experiments that guide RNA folding to its correct state. By introducing experimentally derived constraints to our computer simulations, we are able to make reliable predictions of RNA tertiary structures up to a few hundred nucleotides. Our refined model exemplifies a valuable benefit achieved through integration of computation and experimental methods.

  13. All-Atom Structural Models of the Transmembrane Domains of Insulin and Type 1 Insulin-Like Growth Factor Receptors.

    Science.gov (United States)

    Mohammadiarani, Hossein; Vashisth, Harish

    2016-01-01

    The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane-solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane-solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor.

  14. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

    Science.gov (United States)

    Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

    2014-10-16

    Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of

  15. Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

    Science.gov (United States)

    Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

    2012-12-07

    We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

  16. Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation.

    Science.gov (United States)

    Arnautova, Yelena A; Vorobjev, Yury N; Vila, Jorge A; Scheraga, Harold A

    2009-10-01

    Availability of energy functions which can discriminate native-like from non-native protein conformations is crucial for theoretical protein structure prediction and refinement of low-resolution protein models. This article reports the results of benchmark tests for scoring functions based on two all-atom ECEPP force fields, that is, ECEPP/3 and ECEPP05, and two implicit solvent models for a large set of protein decoys. The following three scoring functions are considered: (i) ECEPP05 plus a solvent-accessible surface area model with the parameters optimized with a set of protein decoys (ECEPP05/SA); (ii) ECEPP/3 plus the solvent-accessible surface area model of Ooi et al. (Proc Natl Acad Sci USA 1987;84:3086-3090) (ECEPP3/OONS); and (iii) ECEPP05 plus an implicit solvent model based on a solution of the Poisson equation with an optimized Fast Adaptive Multigrid Boundary Element (FAMBEpH) method (ECEPP05/FAMBEpH). Short Monte Carlo-with-Minimization (MCM) simulations, following local energy minimization, are used as a scoring method with ECEPP05/SA and ECEPP3/OONS potentials, whereas energy calculation is used with ECEPP05/FAMBEpH. The performance of each scoring function is evaluated by examining its ability to distinguish between native-like and non-native protein structures. The results of the tests show that the new ECEPP05/SA scoring function represents a significant improvement over the earlier ECEPP3/OONS version of the force field. Thus, it is able to rank native-like structures with C(alpha) root-mean-square-deviations below 3.5 A as lowest-energy conformations for 76% and within the top 10 for 87% of the proteins tested, compared with 69 and 80%, respectively, for ECEPP3/OONS. The use of the FAMBEpH solvation model, which provides a more accurate description of the protein-solvent interactions, improves the discriminative ability of the scoring function to 89%. All failed tests in which the native-like structures cannot be discriminated as those with low

  17. The Construction and Validation of All-Atom Bulk-Phase Models of Amorphous Polymers Using the TIGER2/TIGER3 Empirical Sampling Method.

    Science.gov (United States)

    Li, Xianfeng; Murthy, Sanjeeva; Latour, Robert A

    2011-07-12

    (butyl methacrylate), and DTB-succinate copolymer. Calculated glass transition temperature (T(g)) and structural parameter profile (S(q)) for each resulting polymer model were found to be in close agreement with experimental T(g) values and structural measurements obtained by x-ray diffraction, thus validating that the developed methods provide realistic models of amorphous polymer structure.

  18. All-atom structural models for complexes of insulin-like growth factors IGF1 and IGF2 with their cognate receptor.

    Science.gov (United States)

    Vashisth, Harish; Abrams, Cameron F

    2010-07-16

    Type 1 insulin-like growth factor receptor (IGF1R) is a membrane-spanning glycoprotein of the insulin receptor family that has been implicated in a variety of cancers. The key questions related to molecular mechanisms governing ligand recognition by IGF1R remain unanswered, partly due to the lack of testable structural models of apo or ligand-bound receptor complexes. Using a homology model of the IGF1R ectodomain IGF1RDeltabeta, we present the first experimentally consistent all-atom structural models of IGF1/IGF1RDeltabeta and IGF2/IGF1RDeltabeta complexes. Our explicit-solvent molecular dynamics (MD) simulation of apo-IGF1RDeltabeta shows that it displays asymmetric flexibility mechanisms that result in one of two binding pockets accessible to growth factors IGF1 and IGF2, as demonstrated via an MD-assisted Monte Carlo docking procedure. Our MD-generated ensemble of structures of apo and IGF1-bound IGF1RDeltabeta agrees reasonably well with published small-angle X-ray scattering data. We observe simultaneous contacts of each growth factor with sites 1 and 2 of IGF1R, suggesting cross-linking of receptor subunits. Our models provide direct evidence in favor of suggested electrostatic complementarity between the C-domain (IGF1) and the cysteine-rich domain (IGF1R). Our IGF1/IGF1RDeltabeta model provides structural bases for the observation that a single IGF1 molecule binds to IGF1RDeltabeta at low concentrations in small-angle X-ray scattering studies. We also suggest new possible structural bases for differences in the affinities of insulin, IGF1, and IGF2 for their noncognate receptors.

  19. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    Science.gov (United States)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  20. All-atom structural models of insulin binding to the insulin receptor in the presence of a tandem hormone-binding element.

    Science.gov (United States)

    Vashisth, Harish; Abrams, Cameron F

    2013-06-01

    Insulin regulates blood glucose levels in higher organisms by binding to and activating insulin receptor (IR), a constitutively homodimeric glycoprotein of the receptor tyrosine kinase (RTK) superfamily. Therapeutic efforts in treating diabetes have been significantly impeded by the absence of structural information on the activated form of the insulin/IR complex. Mutagenesis and photo-crosslinking experiments and structural information on insulin and apo-IR strongly suggest that the dual-chain insulin molecule, unlike the related single-chain insulin-like growth factors, binds to IR in a very different conformation than what is displayed in storage forms of the hormone. In particular, hydrophobic residues buried in the core of the folded insulin molecule engage the receptor. There is also the possibility of plasticity in the receptor structure based on these data, which may in part be due to rearrangement of the so-called CT-peptide, a tandem hormone-binding element of IR. These possibilities provide opportunity for large-scale molecular modeling to contribute to our understanding of this system. Using various atomistic simulation approaches, we have constructed all-atom structural models of hormone/receptor complexes in the presence of CT in its crystallographic position and a thermodynamically favorable displaced position. In the "displaced-CT" complex, many more insulin-receptor contacts suggested by experiments are satisfied, and our simulations also suggest that R-insulin potentially represents the receptor-bound form of hormone. The results presented in this work have further implications for the design of receptor-specific agonists/antagonists.

  1. Structural Interpretation of the Large Slowdown of Water Dynamics at Stacked Phospholipid Membranes for Decreasing Hydration Level: All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Carles Calero

    2016-04-01

    Full Text Available Hydration water determines the stability and function of phospholipid membranes as well as the interaction of membranes with other molecules. Experiments and simulations have shown that water dynamics slows down dramatically as the hydration decreases, suggesting that the interfacial water that dominates the average dynamics at low hydration is slower than water away from the membrane. Here, based on all-atom molecular dynamics simulations, we provide an interpretation of the slowdown of interfacial water in terms of the structure and dynamics of water–water and water–lipid hydrogen bonds (HBs. We calculate the rotational and translational slowdown of the dynamics of water confined in stacked phospholipid membranes at different levels of hydration, from completely hydrated to poorly hydrated membranes. For all hydrations, we analyze the distribution of HBs and find that water–lipids HBs last longer than water–water HBs and that at low hydration most of the water is in the interior of the membrane. We also show that water–water HBs become more persistent as the hydration is lowered. We attribute this effect (i to HBs between water molecules that form, in turn, persistent HBs with lipids; (ii to the hindering of the H-bonding switching between water molecules due to the lower water density at the interface; and (iii to the higher probability of water–lipid HBs as the hydration decreases. Our interpretation of the large dynamic slowdown in water under dehydration is potentially relevant in understanding membrane biophysics at different hydration levels.

  2. An Evolutionary Strategy for All-Atom Folding of the 60-Amino-Acid Bacterial Ribosomal Protein L20

    Science.gov (United States)

    Schug, A.; Wenzel, W.

    2006-01-01

    We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of “native content” in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence. PMID:16565067

  3. Structure validation in chemical crystallography.

    Science.gov (United States)

    Spek, Anthony L

    2009-02-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

  4. Structural system identification: Structural dynamics model validation

    Energy Technology Data Exchange (ETDEWEB)

    Red-Horse, J.R.

    1997-04-01

    Structural system identification is concerned with the development of systematic procedures and tools for developing predictive analytical models based on a physical structure`s dynamic response characteristics. It is a multidisciplinary process that involves the ability (1) to define high fidelity physics-based analysis models, (2) to acquire accurate test-derived information for physical specimens using diagnostic experiments, (3) to validate the numerical simulation model by reconciling differences that inevitably exist between the analysis model and the experimental data, and (4) to quantify uncertainties in the final system models and subsequent numerical simulations. The goal of this project was to develop structural system identification techniques and software suitable for both research and production applications in code and model validation.

  5. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    Science.gov (United States)

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  6. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  7. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  8. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    Science.gov (United States)

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  9. Beyond Modeling: All-Atom Olfactory Receptor Model Simulations

    Directory of Open Access Journals (Sweden)

    Peter C Lai

    2012-05-01

    Full Text Available Olfactory receptors (ORs are a type of GTP-binding protein-coupled receptor (GPCR. These receptors are responsible for mediating the sense of smell through their interaction with odor ligands. OR-odorant interactions marks the first step in the process that leads to olfaction. Computational studies on model OR structures can validate experimental functional studies as well as generate focused and novel hypotheses for further bench investigation by providing a view of these interactions at the molecular level. Here we have shown the specific advantages of simulating the dynamic environment that is associated with OR-odorant interactions. We present a rigorous methodology that ranges from the creation of a computationally-derived model of an olfactory receptor to simulating the interactions between an OR and an odorant molecule. Given the ubiquitous occurrence of GPCRs in the membranes of cells, we anticipate that our OR-developed methodology will serve as a model for the computational structural biology of all GPCRs.

  10. Intermolecular orientations in liquid acetonitrile: new insights based on diffraction measurements and all-atom simulations

    CERN Document Server

    Pothoczki, Szilvia

    2016-01-01

    Intermolecular correlations in liquid acetonitrile (CH3CN) have been revisited by calculating orientational correlation functions. In the present approach, hydrogen atoms are included, so that a concept applicable for molecules of (nearly) tetrahedral shape can be exploited. In this way molecular arrangements are elucidated not only for closest neighbours but also extending well beyond the first coordination sphere. Thus a complementary viewpoint is provided to the more popular dipole-dipole correlations. Our calculations are based on large structural models that were obtained by applying diffraction data and partial radial distribution functions from potential-based (all-atom) molecular dynamics simulation simultaneously, within the framework of the Reverse Monte Carlo method.

  11. Molecular dynamics simulation of protein adsorption at fluid interfaces: a comparison of all-atom and coarse-grained models.

    Science.gov (United States)

    Euston, Stephen R

    2010-10-11

    The adsorption of LTP at the decane-water interface was modeled using all-atom and coarse-grained (CG) molecular dynamics simulations. The CG model (300 ns simulation, 1200 ns scaled time) generates equilibrium adsorbed conformations in about 12 h, whereas the equivalent 1200 ns simulation would take about 300 days for the all-atom model. In both models the LTP molecule adsorbs with α-helical regions parallel to the interface with an average tilt angle normal to the interface of 73° for the all-atom model and 62° for the CG model. In the all-atom model, the secondary structure of the LTP is conserved upon adsorption. A considerable proportion of the N-terminal loop of LTP can be found in the decane phase for the all-atom model, whereas in the CG model the protein only penetrates as far as the mixed water-decane interfacial region. This difference may arise due to the different schemes used to parametrize force field parameters in the two models.

  12. Experimental validation of structural optimization methods

    Science.gov (United States)

    Adelman, Howard M.

    1992-01-01

    The topic of validating structural optimization methods by use of experimental results is addressed. The need for validating the methods as a way of effecting a greater and an accelerated acceptance of formal optimization methods by practicing engineering designers is described. The range of validation strategies is defined which includes comparison of optimization results with more traditional design approaches, establishing the accuracy of analyses used, and finally experimental validation of the optimization results. Examples of the use of experimental results to validate optimization techniques are described. The examples include experimental validation of the following: optimum design of a trussed beam; combined control-structure design of a cable-supported beam simulating an actively controlled space structure; minimum weight design of a beam with frequency constraints; minimization of the vibration response of helicopter rotor blade; minimum weight design of a turbine blade disk; aeroelastic optimization of an aircraft vertical fin; airfoil shape optimization for drag minimization; optimization of the shape of a hole in a plate for stress minimization; optimization to minimize beam dynamic response; and structural optimization of a low vibration helicopter rotor.

  13. Feature Extraction for Structural Dynamics Model Validation

    Energy Technology Data Exchange (ETDEWEB)

    Farrar, Charles [Los Alamos National Laboratory; Nishio, Mayuko [Yokohama University; Hemez, Francois [Los Alamos National Laboratory; Stull, Chris [Los Alamos National Laboratory; Park, Gyuhae [Chonnam Univesity; Cornwell, Phil [Rose-Hulman Institute of Technology; Figueiredo, Eloi [Universidade Lusófona; Luscher, D. J. [Los Alamos National Laboratory; Worden, Keith [University of Sheffield

    2016-01-13

    As structural dynamics becomes increasingly non-modal, stochastic and nonlinear, finite element model-updating technology must adopt the broader notions of model validation and uncertainty quantification. For example, particular re-sampling procedures must be implemented to propagate uncertainty through a forward calculation, and non-modal features must be defined to analyze nonlinear data sets. The latter topic is the focus of this report, but first, some more general comments regarding the concept of model validation will be discussed.

  14. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension

    DEFF Research Database (Denmark)

    Sonne, Jacob; Jensen, M.Ø.; Hansen, Flemming Yssing;

    2007-01-01

    represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting...... method. We tested the derived charges in molecular dynamics simulations of a fully hydrated DPPC bilayer. Only the simulation with the new restricted electrostatic potential charges shows significant improvements compared with simulations using the original CHARMM27 force field resulting in an area per...... fluid phase of DPPC bilayers can now be simulated in all-atom simulations in the NPT ensemble by employing our modified CHARMM27 force field....

  15. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

    Science.gov (United States)

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N

    2011-09-06

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  16. Multiscale approach for the construction of equilibrated all-atom models of a poly(ethylene glycol)-based hydrogel.

    Science.gov (United States)

    Li, Xianfeng; Murthy, N Sanjeeva; Becker, Matthew L; Latour, Robert A

    2016-06-24

    A multiscale modeling approach is presented for the efficient construction of an equilibrated all-atom model of a cross-linked poly(ethylene glycol) (PEG)-based hydrogel using the all-atom polymer consistent force field (PCFF). The final equilibrated all-atom model was built with a systematic simulation toolset consisting of three consecutive parts: (1) building a global cross-linked PEG-chain network at experimentally determined cross-link density using an on-lattice Monte Carlo method based on the bond fluctuation model, (2) recovering the local molecular structure of the network by transitioning from the lattice model to an off-lattice coarse-grained (CG) model parameterized from PCFF, followed by equilibration using high performance molecular dynamics methods, and (3) recovering the atomistic structure of the network by reverse mapping from the equilibrated CG structure, hydrating the structure with explicitly represented water, followed by final equilibration using PCFF parameterization. The developed three-stage modeling approach has application to a wide range of other complex macromolecular hydrogel systems, including the integration of peptide, protein, and/or drug molecules as side-chains within the hydrogel network for the incorporation of bioactivity for tissue engineering, regenerative medicine, and drug delivery applications.

  17. Feature extraction for structural dynamics model validation

    Energy Technology Data Exchange (ETDEWEB)

    Hemez, Francois [Los Alamos National Laboratory; Farrar, Charles [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory; Nishio, Mayuko [UNIV OF TOKYO; Worden, Keith [UNIV OF SHEFFIELD; Takeda, Nobuo [UNIV OF TOKYO

    2010-11-08

    This study focuses on defining and comparing response features that can be used for structural dynamics model validation studies. Features extracted from dynamic responses obtained analytically or experimentally, such as basic signal statistics, frequency spectra, and estimated time-series models, can be used to compare characteristics of structural system dynamics. By comparing those response features extracted from experimental data and numerical outputs, validation and uncertainty quantification of numerical model containing uncertain parameters can be realized. In this study, the applicability of some response features to model validation is first discussed using measured data from a simple test-bed structure and the associated numerical simulations of these experiments. issues that must be considered were sensitivity, dimensionality, type of response, and presence or absence of measurement noise in the response. Furthermore, we illustrate a comparison method of multivariate feature vectors for statistical model validation. Results show that the outlier detection technique using the Mahalanobis distance metric can be used as an effective and quantifiable technique for selecting appropriate model parameters. However, in this process, one must not only consider the sensitivity of the features being used, but also correlation of the parameters being compared.

  18. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    Directory of Open Access Journals (Sweden)

    Hyuntae Na

    2015-10-01

    Full Text Available Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  19. Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models.

    Science.gov (United States)

    Na, Hyuntae; Jernigan, Robert L; Song, Guang

    2015-10-01

    Dynamics can provide deep insights into the functional mechanisms of proteins and protein complexes. For large protein complexes such as GroEL/GroES with more than 8,000 residues, obtaining a fine-grained all-atom description of its normal mode motions can be computationally prohibitive and is often unnecessary. For this reason, coarse-grained models have been used successfully. However, most existing coarse-grained models use extremely simple potentials to represent the interactions within the coarse-grained structures and as a result, the dynamics obtained for the coarse-grained structures may not always be fully realistic. There is a gap between the quality of the dynamics of the coarse-grained structures given by all-atom models and that by coarse-grained models. In this work, we resolve an important question in protein dynamics computations--how can we efficiently construct coarse-grained models whose description of the dynamics of the coarse-grained structures remains as accurate as that given by all-atom models? Our method takes advantage of the sparseness of the Hessian matrix and achieves a high efficiency with a novel iterative matrix projection approach. The result is highly significant since it can provide descriptions of normal mode motions at an all-atom level of accuracy even for the largest biomolecular complexes. The application of our method to GroEL/GroES offers new insights into the mechanism of this biologically important chaperonin, such as that the conformational transitions of this protein complex in its functional cycle are even more strongly connected to the first few lowest frequency modes than with other coarse-grained models.

  20. Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models.

    Science.gov (United States)

    Liao, Chenyi; Zhao, Xiaochuan; Liu, Jiyuan; Schneebeli, Severin T; Shelley, John C; Li, Jianing

    2017-03-20

    The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.

  1. RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.

    Science.gov (United States)

    Wang, Xueyi; Kapral, Gary; Murray, Laura; Richardson, David; Richardson, Jane; Snoeyink, Jack

    2008-01-01

    Although accurate details in RNA structure are of great importance for understanding RNA function, the backbone conformation is difficult to determine, and most existing RNA structures show serious steric clashes (>or= 0.4 A overlap) when hydrogen atoms are taken into account. We have developed a program called RNABC (RNA Backbone Correction) that performs local perturbations to search for alternative conformations that avoid those steric clashes or other local geometry problems. Its input is an all-atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with problem areas specified. RNABC rebuilds a suite (the unit from sugar to sugar) by anchoring the phosphorus and base positions, which are clearest in crystallographic electron density, and reconstructing the other atoms using forward kinematics. Geometric parameters are constrained within user-specified tolerance of canonical or original values, and torsion angles are constrained to ranges defined through empirical database analyses. Several optimizations reduce the time required to search the many possible conformations. The output results are clustered and presented to the user, who can choose whether to accept one of the alternative conformations. Two test evaluations show the effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second on the worst problem suites (clusters of bad clashes, or serious sugar pucker outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems, and RNABC produced clash-free conformations with acceptable geometry for 71 of those (about 80%). For the 154 worst problem suites, RNABC proposed alternative conformations for 72. All but 8 of those were judged acceptable after examining electron density (where available) and local conformation. Thus, even for these worst cases, nearly half the time RNABC suggested corrections suitable to initiate further crystallographic refinement. The program is

  2. All-atom molecular dynamics studies of the full-length {beta}-amyloid peptides

    Energy Technology Data Exchange (ETDEWEB)

    Luttmann, Edgar [Department of Chemistry, Faculty of Science, University of Paderborn, Warburgerstr. 100, 33098 Paderborn (Germany); Fels, Gregor [Department of Chemistry, Faculty of Science, University of Paderborn, Warburgerstr. 100, 33098 Paderborn (Germany)], E-mail: fels@uni-paderborn.de

    2006-03-31

    {beta}-Amyloid peptides are believed to play an essential role in Alzheimer's disease (AD), due to their sedimentation in the form of {beta}-amyloid aggregates in the brain of AD-patients, and the in vitro neurotoxicity of oligomeric aggregates. The monomeric peptides come in different lengths of 39-43 residues, of which the 42 alloform seems to be most strongly associated with AD-symptoms. Structural information on these peptides to date comes from NMR studies in acidic solutions, organic solvents, or on shorter fragments of the peptide. In addition X-ray and solid-state NMR investigations of amyloid fibrils yield insight into the structure of the final aggregate and therefore define the endpoint of any conformational change of an A{beta}-monomer along the aggregation process. The conformational changes necessary to connect the experimentally known conformations are not yet understood and this process is an active field of research. In this paper, we report results from all-atom molecular dynamics simulations based on experimental data from four different peptides of 40 amino acids and two peptides consisting of 42 amino acids. The simulations allow for the analysis of intramolecular interactions and the role of structural features. In particular, they show the appearance of {beta}-turn in the region between amino acid 21 and 33, forming a hook-like shape as it is known to exist in the fibrillar A{beta}-structures. This folding does not depend on the formation of a salt bridge between Asp-23 and Lys-28 but requires the A{beta}(1-42) as such structure was not observed in the shorter system A{beta}(1-40)

  3. Molecular jamming—The cystine slipknot mechanical clamp in all-atom simulations

    Science.gov (United States)

    Pepłowski, Łukasz; Sikora, Mateusz; Nowak, Wiesław; Cieplak, Marek

    2011-02-01

    A recent survey of 17 134 proteins has identified a new class of proteins which are expected to yield stretching induced force peaks in the range of 1 nN. Such high force peaks should be due to forcing of a slip-loop through a cystine ring, i.e., by generating a cystine slipknot. The survey has been performed in a simple coarse grained model. Here, we perform all-atom steered molecular dynamics simulations on 15 cystine knot proteins and determine their resistance to stretching. In agreement with previous studies within a coarse grained structure based model, the level of resistance is found to be substantially higher than in proteins in which the mechanical clamp operates through shear. The large stretching forces arise through formation of the cystine slipknot mechanical clamp and the resulting steric jamming. We elucidate the workings of such a clamp in an atomic detail. We also study the behavior of five top strength proteins with the shear-based mechanostability in which no jamming is involved. We show that in the atomic model, the jamming state is relieved by moving one amino acid at a time and there is a choice in the selection of the amino acid that advances the first. In contrast, the coarse grained model also allows for a simultaneous passage of two amino acids.

  4. All-Atom Molecular Dynamics Simulation of Protein Translocation through an α-Hemolysin Nanopore

    KAUST Repository

    Di Marino, Daniele

    2015-08-06

    © 2015 American Chemical Society. Nanopore sensing is attracting the attention of a large and varied scientific community. One of the main issues in nanopore sensing is how to associate the measured current signals to specific features of the molecule under investigation. This is particularly relevant when the translocating molecule is a protein and the pore is sufficiently narrow to necessarily involve unfolding of the translocating protein. Recent experimental results characterized the cotranslocational unfolding of Thioredoxin (Trx) passing through an α-hemolisin pore, providing evidence for the existence of a multistep process. In this study we report the results of all-atom molecular dynamics simulations of the same system. Our data indicate that Trx translocation involves two main barriers. The first one is an unfolding barrier associated with a translocation intermediate where the N-terminal region of Trx is stuck at the pore entrance in a conformation that strongly resembles the native one. After the abrupt unfolding of the N-terminal region, the Trx enters the α-hemolisin vestibule. During this stage, the constriction is occupied not only by the translocating residue but also by a hairpin-like structure forming a tangle in the constriction. The second barrier is associated with the disentangling of this region.

  5. The psychiatric interview: validity, structure, and subjectivity.

    Science.gov (United States)

    Nordgaard, Julie; Sass, Louis A; Parnas, Josef

    2013-06-01

    There is a glaring gap in the psychiatric literature concerning the nature of psychiatric symptoms and signs, and a corresponding lack of epistemological discussion of psycho-diagnostic interviewing. Contemporary clinical neuroscience heavily relies on the use of fully structured interviews that are historically rooted in logical positivism and behaviorism. These theoretical approaches marked decisively the so-called "operational revolution in psychiatry" leading to the creation of DSM-III. This paper attempts to examine the theoretical assumptions that underlie the use of a fully structured psychiatric interview. We address the ontological status of pathological experience, the notions of symptom, sign, prototype and Gestalt, and the necessary second-person processes which are involved in converting the patient's experience (originally lived in the first-person perspective) into an "objective" (third person), actionable format, used for classification, treatment, and research. Our central thesis is that psychiatry targets the phenomena of consciousness, which, unlike somatic symptoms and signs, cannot be grasped on the analogy with material thing-like objects. We claim that in order to perform faithful distinctions in this particular domain, we need a more adequate approach, that is, an approach that is guided by phenomenologically informed considerations. Our theoretical discussion draws upon clinical examples derived from structured and semi-structured interviews. We conclude that fully structured interview is neither theoretically adequate nor practically valid in obtaining psycho-diagnostic information. Failure to address these basic issues may have contributed to the current state of malaise in the study of psychopathology.

  6. Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution.

    Science.gov (United States)

    McCullagh, Peter; Lake, Peter T; McCullagh, Martin

    2016-09-13

    An analytic method to assign optimal coarse-grained charges based on electrostatic potential matching is presented. This solution is the infinite size and density limit of grid-integration charge-fitting and is computationally more efficient by several orders of magnitude. The solution is also minimized with respect to coarse-grained positions which proves to be an extremely important step in reproducing the all-atom electrostatic potential. The joint optimal-charge optimal-position coarse-graining procedure is applied to a number of aggregating proteins using single-site per amino acid resolution. These models provide a good estimate of both the vacuum and Debye-Hückel screened all-atom electrostatic potentials in the vicinity and in the far-field of the protein. Additionally, these coarse-grained models are shown to approximate the all-atom dimerization electrostatic potential energy of 10 aggregating proteins with good accuracy.

  7. Accelerating all-atom MD simulations of lipids using a modified virtual-sites technique

    DEFF Research Database (Denmark)

    Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu

    2014-01-01

    We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation ...

  8. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Energy Technology Data Exchange (ETDEWEB)

    Markutsya, Sergiy [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Lamm, Monica H., E-mail: mhlamm@iastate.edu [Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States); Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011 (United States)

    2014-11-07

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  9. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

    Science.gov (United States)

    Markutsya, Sergiy; Lamm, Monica H.

    2014-11-01

    We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained from reference all-atom simulations. The agreement between the structural properties observed in the coarse-grained and all-atom simulations is also preserved. We discuss how this approach may be applied broadly to any existing coarse-graining method where the coarse-grained models are rigorously derived from all-atom reference systems.

  10. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  11. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals.

    Science.gov (United States)

    Kaushik, Ananth P; Clancy, Paulette

    2012-03-21

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), "capped" with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes.

  12. Explicit all-atom modeling of realistically sized ligand-capped nanocrystals

    KAUST Repository

    Kaushik, Ananth P.

    2012-01-01

    We present a study of an explicit all-atom representation of nanocrystals of experimentally relevant sizes (up to 6 nm), capped with alkyl chain ligands, in vacuum. We employ all-atom molecular dynamics simulation methods in concert with a well-tested intermolecular potential model, MM3 (molecular mechanics 3), for the studies presented here. These studies include determining the preferred conformation of an isolated single nanocrystal (NC), pairs of isolated NCs, and (presaging studies of superlattice arrays) unit cells of NC superlattices. We observe that very small NCs (3 nm) behave differently in a superlattice as compared to larger NCs (6 nm and above) due to the conformations adopted by the capping ligands on the NC surface. Short ligands adopt a uniform distribution of orientational preferences, including some that lie against the face of the nanocrystal. In contrast, longer ligands prefer to interdigitate. We also study the effect of changing ligand length and ligand coverage on the NCs on the preferred ligand configurations. Since explicit all-atom modeling constrains the maximum system size that can be studied, we discuss issues related to coarse-graining the representation of the ligands, including a comparison of two commonly used coarse-grained models. We find that care has to be exercised in the choice of coarse-grained model. The data provided by these realistically sized ligand-capped NCs, determined using explicit all-atom models, should serve as a reference standard for future models of coarse-graining ligands using united atom models, especially for self-assembly processes. © 2012 American Institute of Physics.

  13. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  14. All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Zai-you Tan; San-lai Luo

    2008-01-01

    N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

  15. An all-atom simulation study of the ordering of liquid squalane near a solid surface

    Science.gov (United States)

    Tsige, Mesfin; Patnaik, Soumya S.

    2008-05-01

    An all-atom molecular dynamics study using the OPLS force field has been carried out to obtain new insights in to the orientation and ordering of liquid squalane near a solid surface. As observed in previous experiments, the squalane molecules closest to a SiO 2 substrate are found to be tightly bound with their molecular axis preferentially parallel to the interface. Unlike linear alkanes, the squalane molecules are also found to lie preferentially parallel to the liquid/vapor interface. The simulation results predict that the molecular plane orientation of the squalane molecules changes from mainly parallel to perpendicular to the substrate in going further away from the substrate.

  16. Reproducible In-Silico Folding of a Four Helix 60 Amino Acid Protein in a Transferable All-Atom Forcefield

    Science.gov (United States)

    Schug, Alexander

    2005-03-01

    For predicting the protein tertiary structure one approach describes the native state of a protein as the global minimum of an appropiate free-energy forcefield. We have recently developed such a all-atom protein forcefield (PFF01). As major challenge remains the search for the global minimum for which we developed efficient methods. Using these we were able to predict the structure of helical proteins from different families ranging in size from 20 to 60 amino acids starting with random configurations. For the four helix 60 amino acid protein Bacterial Ribosomal Protein L20 (pdb code: 1GYZ) we used a simple client-master model for distributed computing. Starting from a set of random structures three phases of different folding simulations refined this set to a final one with 50 configurations. During this process the amount of native-like structures increased strongly. Six out of the ten structures best in energy approached the native structure within 5 åbackbone rmsd. The conformation with the lowest energy had a backbone rmsd value of 4.6 åtherefore correctly predicting the tertiary structure of 1GYZ.ReferencesA. Schug et al, Phys. Rev. Letters, 91:158102, 2003A. Schug et al, J. Am. Chem. Soc. (in press), 2004

  17. All-atom/coarse-grained hybrid predictions of distribution coefficients in SAMPL5

    Science.gov (United States)

    Genheden, Samuel; Essex, Jonathan W.

    2016-11-01

    We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based on a hybrid all-atom/coarse-grained model. The compounds were treated with the general Amber force field, whereas the solvent molecules were treated with the Elba coarse-grained model. Considering the simplicity of the solvent model and that we approximate the distribution coefficient with the partition coefficient of the neutral species, the predictions are of good accuracy. The correlation coefficient, R is 0.64, 82 % of the predictions have the correct sign and the mean absolute deviation is 1.8 log units. This is on a par with or better than the other simulation-based predictions in the challenge. We present an analysis of the deviations to experiments and compare the predictions to another submission that used all-atom solvent.

  18. Protein structure validation using a semi-empirical method

    OpenAIRE

    Lahiri, Tapobrata; Singh, Kalpana; Pal, Manoj Kumar; Verma, Gaurav

    2012-01-01

    Current practice of validating predicted protein structural model is knowledge-based where scoring parameters are derived from already known structures to obtain decision on validation out of this structure information. For example, the scoring parameter, Ramachandran Score gives percentage conformity with steric-property higher value of which implies higher acceptability. On the other hand, Force-Field Energy Score gives conformity with energy-wise stability higher value of which implies low...

  19. OPUS-PSP: an orientation-dependent statistical all-atom potential derived from side-chain packing.

    Science.gov (United States)

    Lu, Mingyang; Dousis, Athanasios D; Ma, Jianpeng

    2008-02-08

    Here we report an orientation-dependent statistical all-atom potential derived from side-chain packing, named OPUS-PSP. It features a basis set of 19 rigid-body blocks extracted from the chemical structures of all 20 amino acid residues. The potential is generated from the orientation-specific packing statistics of pairs of those blocks in a non-redundant structural database. The purpose of such an approach is to capture the essential elements of orientation dependence in molecular packing interactions. Tests of OPUS-PSP on commonly used decoy sets demonstrate that it significantly outperforms most of the existing knowledge-based potentials in terms of both its ability to recognize native structures and consistency in achieving high Z-scores across decoy sets. As OPUS-PSP excludes interactions among main-chain atoms, its success highlights the crucial importance of side-chain packing in forming native protein structures. Moreover, OPUS-PSP does not explicitly include solvation terms, and thus the potential should perform well when the solvation effect is difficult to determine, such as in membrane proteins. Overall, OPUS-PSP is a generally applicable potential for protein structure modeling, especially for handling side-chain conformations, one of the most difficult steps in high-accuracy protein structure prediction and refinement.

  20. In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field

    Science.gov (United States)

    Herges, T.; Wenzel, W.

    2005-01-01

    We report the reproducible first-principles folding of the 40 amino-acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy force field. Six of 20 simulations using an adapted basin-hopping method converged to better than 3Å backbone rms deviation to the experimental structure. Using over 60 000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

  1. In-silico folding of a three helix protein and characterization of its free-energy landscape in an all-atom forcefield

    CERN Document Server

    Herges, T

    2003-01-01

    We report the reproducible first-principles folding of the 40 amino acid, three-helix headpiece of the HIV accessory protein in a recently developed all-atom free-energy forcefield. Six of twenty simulations using an adapted basin-hopping method converged to better than 3 \\AA backbone RMS deviation to the experimental structure. Using over 60,000 low-energy conformations of this protein, we constructed a decoy tree that completely characterizes its folding funnel.

  2. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

    Science.gov (United States)

    Hoang Man, Viet; Van-Oanh, Nguyen-Thi; Derreumaux, Philippe; Li, Mai Suan; Roland, Christopher; Sagui, Celeste; Nguyen, Phuong H

    2016-04-28

    Since the discovery of the plant pathogen tobacco mosaic virus as the first viral entity in the late 1800s, viruses traditionally have been mainly thought of as pathogens for disease-resistances. However, viruses have recently been exploited as nanoplatforms with applications in biomedicine and materials science. To this aim, a large majority of current methods and tools have been developed to improve the physical stability of viral particles, which may be critical to the extreme physical or chemical conditions that viruses may encounter during purification, fabrication processes, storage and use. However, considerably fewer studies are devoted to developing efficient methods to degrade or recycle such enhanced stability biomaterials. With this in mind, we carry out all-atom nonequilibrium molecular dynamics simulation, inspired by the recently developed mid-infrared free-electron laser pulse technology, to dissociate viruses. Adopting the poliovirus as a representative example, we find that the primary step in the dissociation process is due to the strong resonance between the amide I vibrational modes of the virus and the tuned laser frequencies. This process is determined by a balance between the formation and dissociation of the protein shell, reflecting the highly plasticity of the virus. Furthermore, our method should provide a feasible approach to simulate viruses, which is otherwise too expensive for conventional equilibrium all-atom simulations of such very large systems. Our work shows a proof of concept which may open a new, efficient way to cleave or to recycle virus-based materials, provide an extremely valuable tool for elucidating mechanical aspects of viruses, and may well play an important role in future fighting against virus-related diseases.

  3. Structural Validity of the Multifactor Leadership Questionnaire.

    Science.gov (United States)

    Tepper, Bennett J.; Percy, Paul M.

    1994-01-01

    Two studies with 290 college students and 95 business managers investigated the latent structure of items from the Multifactor Leadership Questionnaire (MLQ). Results support models in which transformational and transactional leadership items load on separate factors and suggest that charismatic and inspirational leadership scales converge for…

  4. CING: an integrated residue-based structure validation program suite

    Energy Technology Data Exchange (ETDEWEB)

    Doreleijers, Jurgen F. [Radboud University Medical Centre, CMBI (Netherlands); Sousa da Silva, Alan W. [European Bioinformatics Institute, UniProt (United Kingdom); Krieger, Elmar [YASARA Biosciences GmbH (Austria); Nabuurs, Sander B. [Radboud University Medical Centre, CMBI (Netherlands); Spronk, Christian A. E. M. [Spronk NMR Consultancy UAB (Lithuania); Stevens, Tim J. [University of Cambridge, Department of Biochemistry (United Kingdom); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Vriend, Gert [Radboud University Medical Centre, CMBI (Netherlands); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry (United Kingdom)

    2012-11-15

    We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A red-orange-green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below {approx}20 % accompanied by red scores over {approx}50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.ukhttps://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis.

  5. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    Science.gov (United States)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Fujimoto, K.; Kojima, H.; Mizutani, K.; Nakagawa, A.; Nomoto, A.; Okazaki, S.

    2014-10-01

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  6. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution

    Energy Technology Data Exchange (ETDEWEB)

    Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)

    2014-10-28

    Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.

  7. High-throughput all-atom molecular dynamics simulations using distributed computing.

    Science.gov (United States)

    Buch, I; Harvey, M J; Giorgino, T; Anderson, D P; De Fabritiis, G

    2010-03-22

    Although molecular dynamics simulation methods are useful in the modeling of macromolecular systems, they remain computationally expensive, with production work requiring costly high-performance computing (HPC) resources. We review recent innovations in accelerating molecular dynamics on graphics processing units (GPUs), and we describe GPUGRID, a volunteer computing project that uses the GPU resources of nondedicated desktop and workstation computers. In particular, we demonstrate the capability of simulating thousands of all-atom molecular trajectories generated at an average of 20 ns/day each (for systems of approximately 30 000-80 000 atoms). In conjunction with a potential of mean force (PMF) protocol for computing binding free energies, we demonstrate the use of GPUGRID in the computation of accurate binding affinities of the Src SH2 domain/pYEEI ligand complex by reconstructing the PMF over 373 umbrella sampling windows of 55 ns each (20.5 mus of total data). We obtain a standard free energy of binding of -8.7 +/- 0.4 kcal/mol within 0.7 kcal/mol from experimental results. This infrastructure will provide the basis for a robust system for high-throughput accurate binding affinity prediction.

  8. All-atom models of the membrane-spanning domain of HIV-1 gp41 from metadynamics.

    Science.gov (United States)

    Gangupomu, Vamshi K; Abrams, Cameron F

    2010-11-17

    The 27-residue membrane-spanning domain (MSD) of the HIV-1 glycoprotein gp41 bears conserved sequence elements crucial to the biological function of the virus, in particular a conserved GXXXG motif and a midspan arginine. However, structure-based explanations for the roles of these and other MSD features remain unclear. Using molecular dynamics and metadynamics calculations of an all-atom, explicit solvent, and membrane-anchored model, we study the conformational variability of the HIV-1 gp41 MSD. We find that the MSD peptide assumes a stable tilted α-helical conformation in the membrane. However, when the side chain of the midspan Arg (694) "snorkels" to the outer leaflet of the viral membrane, the MSD assumes a metastable conformation where the highly-conserved N-terminal core (between Lys(681) and Arg(694) and containing the GXXXG motif) unfolds. In contrast, when the Arg(694) side chain snorkels to the inner leaflet, the MSD peptide assumes a metastable conformation consistent with experimental observations where the peptide kinks at Phe(697) to facilitate Arg(694) snorkeling. Both of these models suggest specific ways that gp41 may destabilize viral membrane, priming the virus for fusion with a target cell.

  9. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models

    Energy Technology Data Exchange (ETDEWEB)

    Kouza, Maksim, E-mail: mkouza@chem.uw.edu.pl; Kolinski, Andrzej [Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw (Poland); Co, Nguyen Truong [Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City (Viet Nam); Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City (Viet Nam); Nguyen, Phuong H. [Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris (France); Li, Mai Suan, E-mail: masli@ifpan.edu.pl [Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw (Poland)

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  10. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models.

    Science.gov (United States)

    Kouza, Maksim; Co, Nguyen Truong; Nguyen, Phuong H; Kolinski, Andrzej; Li, Mai Suan

    2015-04-14

    Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in

  11. Structural and Discriminant Validity of the Career Factors Inventory

    Science.gov (United States)

    Dickinson, Josephine; Tokar, David M.

    2004-01-01

    Using a sample of 350 college students, this study examined the structural and discriminant validity of the Career Factors Inventory (CFI; Chartrand, Robbins, Morrill, & Boggs, 1990), a multidimensional measure of career indecision intended to be scored for two informational indecision components (Need for Career Information and Need for…

  12. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  13. A validated approach for modeling collapse of steel structures

    Science.gov (United States)

    Saykin, Vitaliy Victorovich

    A civil engineering structure is faced with many hazardous conditions such as blasts, earthquakes, hurricanes, tornadoes, floods, and fires during its lifetime. Even though structures are designed for credible events that can happen during a lifetime of the structure, extreme events do happen and cause catastrophic failures. Understanding the causes and effects of structural collapse is now at the core of critical areas of national need. One factor that makes studying structural collapse difficult is the lack of full-scale structural collapse experimental test results against which researchers could validate their proposed collapse modeling approaches. The goal of this work is the creation of an element deletion strategy based on fracture models for use in validated prediction of collapse of steel structures. The current work reviews the state-of-the-art of finite element deletion strategies for use in collapse modeling of structures. It is shown that current approaches to element deletion in collapse modeling do not take into account stress triaxiality in vulnerable areas of the structure, which is important for proper fracture and element deletion modeling. The report then reviews triaxiality and its role in fracture prediction. It is shown that fracture in ductile materials is a function of triaxiality. It is also shown that, depending on the triaxiality range, different fracture mechanisms are active and should be accounted for. An approach using semi-empirical fracture models as a function of triaxiality are employed. The models to determine fracture initiation, softening and subsequent finite element deletion are outlined. This procedure allows for stress-displacement softening at an integration point of a finite element in order to subsequently remove the element. This approach avoids abrupt changes in the stress that would create dynamic instabilities, thus making the results more reliable and accurate. The calibration and validation of these models are

  14. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

    Science.gov (United States)

    Huang, Yandong; Chen, Wei; Wallace, Jason A; Shen, Jana

    2016-11-08

    Development of a pH stat to properly control solution pH in biomolecular simulations has been a long-standing goal in the community. Toward this goal recent years have witnessed the emergence of the so-called constant pH molecular dynamics methods. However, the accuracy and generality of these methods have been hampered by the use of implicit-solvent models or truncation-based electrostatic schemes. Here we report the implementation of the particle mesh Ewald (PME) scheme into the all-atom continuous constant pH molecular dynamics (CpHMD) method, enabling CpHMD to be performed with a standard MD engine at a fractional added computational cost. We demonstrate the performance using pH replica-exchange CpHMD simulations with titratable water for a stringent test set of proteins, HP36, BBL, HEWL, and SNase. With the sampling time of 10 ns per replica, most pKa's are converged, yielding the average absolute and root-mean-square deviations of 0.61 and 0.77, respectively, from experiment. Linear regression of the calculated vs experimental pKa shifts gives a correlation coefficient of 0.79, a slope of 1, and an intercept near 0. Analysis reveals inadequate sampling of structure relaxation accompanying a protonation-state switch as a major source of the remaining errors, which are reduced as simulation prolongs. These data suggest PME-based CpHMD can be used as a general tool for pH-controlled simulations of macromolecular systems in various environments, enabling atomic insights into pH-dependent phenomena involving not only soluble proteins but also transmembrane proteins, nucleic acids, surfactants, and polysaccharides.

  15. Protein structure validation and analysis with X-ray crystallography.

    Science.gov (United States)

    Papageorgiou, Anastassios C; Mattsson, Jesse

    2014-01-01

    X-ray crystallography is the main technique for the determination of protein structures. About 85 % of all protein structures known to date have been elucidated using X-ray crystallography. Knowledge of the three-dimensional structure of proteins can be used in various applications in biotechnology, biomedicine, drug design, and basic research and as a validation tool for protein modifications, ligand binding, and structural authenticity. Moreover, the requirement for pure, homogeneous, and stable protein solutions in crystallizations makes X-ray crystallography beneficial in other fields of protein research as well. Here, we describe the technique of X-ray protein crystallography and the steps involved for a successful three-dimensional crystal structure determination.

  16. Bayesian structural equation modeling method for hierarchical model validation

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Xiaomo [Department of Civil and Environmental Engineering, Vanderbilt University, Box 1831-B, Nashville, TN 37235 (United States)], E-mail: xiaomo.jiang@vanderbilt.edu; Mahadevan, Sankaran [Department of Civil and Environmental Engineering, Vanderbilt University, Box 1831-B, Nashville, TN 37235 (United States)], E-mail: sankaran.mahadevan@vanderbilt.edu

    2009-04-15

    A building block approach to model validation may proceed through various levels, such as material to component to subsystem to system, comparing model predictions with experimental observations at each level. Usually, experimental data becomes scarce as one proceeds from lower to higher levels. This paper presents a structural equation modeling approach to make use of the lower-level data for higher-level model validation under uncertainty, integrating several components: lower-level data, higher-level data, computational model, and latent variables. The method proposed in this paper uses latent variables to model two sets of relationships, namely, the computational model to system-level data, and lower-level data to system-level data. A Bayesian network with Markov chain Monte Carlo simulation is applied to represent the two relationships and to estimate the influencing factors between them. Bayesian hypothesis testing is employed to quantify the confidence in the predictive model at the system level, and the role of lower-level data in the model validation assessment at the system level. The proposed methodology is implemented for hierarchical assessment of three validation problems, using discrete observations and time-series data.

  17. Comparison and validation of community structures in complex networks

    Science.gov (United States)

    Gustafsson, Mika; Hörnquist, Michael; Lombardi, Anna

    2006-07-01

    The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the problem formulated this way is believed to be NP-hard, most effort has gone into the construction of search algorithms, and less to the question of other measures of community structures, similarities between various partitionings and the validation with respect to external information. Here we concentrate on a class of computer generated networks and on three well-studied real networks which constitute a bench-mark for network studies; the karate club, the US college football teams and a gene network of yeast. We utilize some standard ways of clustering data (originally not designed for finding community structures in networks) and show that these classical methods sometimes outperform the newer ones. We discuss various measures of the strength of the modular structure, and show by examples features and drawbacks. Further, we compare different partitions by applying some graph-theoretic concepts of distance, which indicate that one of the quality measures of the degree of modularity corresponds quite well with the distance from the true partition. Finally, we introduce a way to validate the partitionings with respect to external data when the nodes are classified but the network structure is unknown. This is here possible since we know everything of the computer generated networks, as well as the historical answer to how the karate club and the football teams are partitioned in reality. The partitioning of the gene network is validated by use of the Gene Ontology database, where we show that a community in general corresponds to a biological process.

  18. Local order parameters for use in driving homogeneous ice nucleation with all-atom models of water.

    Science.gov (United States)

    Reinhardt, Aleks; Doye, Jonathan P K; Noya, Eva G; Vega, Carlos

    2012-11-21

    We present a local order parameter based on the standard Steinhardt-Ten Wolde approach that is capable both of tracking and of driving homogeneous ice nucleation in simulations of all-atom models of water. We demonstrate that it is capable of forcing the growth of ice nuclei in supercooled liquid water simulated using the TIP4P/2005 model using over-biassed umbrella sampling Monte Carlo simulations. However, even with such an order parameter, the dynamics of ice growth in deeply supercooled liquid water in all-atom models of water are shown to be very slow, and so the computation of free energy landscapes and nucleation rates remains extremely challenging.

  19. Coulombic free energy and salt ion association per phosphate of all-atom models of DNA oligomer: dependence on oligomer size.

    Science.gov (United States)

    Shkel, Irina A; Record, M Thomas

    2012-08-23

    We investigate how the coulombic Gibbs free energy and salt ion association per phosphate charge of DNA oligomers vary with oligomer size (i.e. number of charged residues ∣ZD∣) at 0.15 M univalent salt by non-linear Poisson Boltzmann (NLPB) analysis of all-atom DNA models. Calculations of these quantities ([Formula: see text], [Formula: see text]) are performed for short and long double-stranded (ds) and single-stranded (ss) DNA oligomers, ranging from 4 to 118 phosphates (ds) and from 2 to 59 phosphates (ss). Behaviors of [Formula: see text] and [Formula: see text] as functions of ∣ZD∣ provide a measure of the range of the coulombic end effect and determine the size of an oligomer at which an interior region with the properties (per charge) of the infinite-length polyelectrolyte first appears. This size (10-11 phosphates at each end for ds DNA and 6-9 for ss DNA at 0.15 M salt) is in close agreement with values obtained previously by Monte Carlo and NLPB calculations for cylindrical models of polyions, and by analysis of binding of oligocations to DNA oligomers. Differences in [Formula: see text] and in [Formula: see text] between ss and ds DNA are used to predict effects of oligomeric size and salt concentration on duplex stability in the vicinity of 0.15 M salt. Results of all-atom calculations are compared with results of less structurally detailed models and with experimental data.

  20. Reparameterization of all-atom dipalmitoylphosphatidylcholine lipid parameters enables simulation of fluid bilayers at zero tension

    DEFF Research Database (Denmark)

    Sonne, Jacob; Jensen, M.Ø.; Hansen, Flemming Yssing;

    2007-01-01

    represented by the CHARMM energy function in this ensemble, we reparameterized the atomic partial charges in the lipid headgroup and upper parts of the acyl chains. The new charges were determined from the electron structure using both the Mulliken method and the restricted electrostatic potential fitting...

  1. All-atom molecular dynamics insights on preQ1 riboswitch aptamer

    Science.gov (United States)

    Gong, Zhou; Zhao, Yunjie; Chen, Changjun; Xiao, Yi

    2012-02-01

    Recently, a series of experiments have focused on two types of preQ1 riboswitch with known smallest aptamer. One of them is from Bacillus subtilis, which have been discussed before. The other one comes from T. tengcongensis, and Jenkins et al recently release its crystal structure in both ligand-bound and free state. These two types of riboswitch aptamer have similar structures but totally different functions. Consequently, contrast studies of these two preQ1 riboswitches will help us to understand the regulation function of riboswitch better. Here, we study the dynamical properties of two types of preQ1 riboswitches using molecular dynamics simulation. We find that the unfolding pathway of the two preQ1 aptamer domains in bound state are both hierarchical and have an intermediate state. We believe that such conformation would be a good candidate structure for ligand binding. On the other hand, in the absent of ligand, the preQ1 riboswitch from Bacillus subtilis can only form the stable state with P1-L3 triplex, while the preQ1 riboswitch from T. tengcongensis can form the conformation with pseudoknot shape. We suggest that such intermediate structures may perform regulation functions in the absent of ligand.

  2. Protein structure validation using a semi-empirical method

    Science.gov (United States)

    Lahiri, Tapobrata; Singh, Kalpana; Pal, Manoj Kumar; Verma, Gaurav

    2012-01-01

    Current practice of validating predicted protein structural model is knowledge-based where scoring parameters are derived from already known structures to obtain decision on validation out of this structure information. For example, the scoring parameter, Ramachandran Score gives percentage conformity with steric-property higher value of which implies higher acceptability. On the other hand, Force-Field Energy Score gives conformity with energy-wise stability higher value of which implies lower acceptability. Naturally, setting these two scoring parameters as target objectives sometimes yields a set of multiple models for the same protein for which acceptance based on a particular parameter, say, Ramachandran score, may not satisfy well with the acceptance of the same model based on other parameter, say, energy score. The confusion set of such models can further be resolved by introducing some parameters value of which are easily obtainable through experiment on the same protein. In this piece of work it was found that the confusion regarding final acceptance of a model out of multiple models of the same protein can be removed using a parameter Surface Rough Index which can be obtained through semi-empirical method from the ordinary microscopic image of heat denatured protein. PMID:23275692

  3. Hierarchical atom type definitions and extensible all-atom force fields.

    Science.gov (United States)

    Jin, Zhao; Yang, Chunwei; Cao, Fenglei; Li, Feng; Jing, Zhifeng; Chen, Long; Shen, Zhe; Xin, Liang; Tong, Sijia; Sun, Huai

    2016-03-15

    The extensibility of force field is a key to solve the missing parameter problem commonly found in force field applications. The extensibility of conventional force fields is traditionally managed in the parameterization procedure, which becomes impractical as the coverage of the force field increases above a threshold. A hierarchical atom-type definition (HAD) scheme is proposed to make extensible atom type definitions, which ensures that the force field developed based on the definitions are extensible. To demonstrate how HAD works and to prepare a foundation for future developments, two general force fields based on AMBER and DFF functional forms are parameterized for common organic molecules. The force field parameters are derived from the same set of quantum mechanical data and experimental liquid data using an automated parameterization tool, and validated by calculating molecular and liquid properties. The hydration free energies are calculated successfully by introducing a polarization scaling factor to the dispersion term between the solvent and solute molecules. © 2015 Wiley Periodicals, Inc.

  4. UCLA Loneliness Scale (Version 3): reliability, validity, and factor structure.

    Science.gov (United States)

    Russell, D W

    1996-02-01

    In this article I evaluated the psychometric properties of the UCLA Loneliness Scale (Version 3). Using data from prior studies of college students, nurses, teachers, and the elderly, analyses of the reliability, validity, and factor structure of this new version of the UCLA Loneliness Scale were conducted. Results indicated that the measure was highly reliable, both in terms of internal consistency (coefficient alpha ranging from .89 to .94) and test-retest reliability over a 1-year period (r = .73). Convergent validity for the scale was indicated by significant correlations with other measures of loneliness. Construct validity was supported by significant relations with measures of the adequacy of the individual's interpersonal relationships, and by correlations between loneliness and measures of health and well-being. Confirmatory factor analyses indicated that a model incorporating a global bipolar loneliness factor along with two method factor reflecting direction of item wording provided a very good fit to the data across samples. Implications of these results for future measurement research on loneliness are discussed.

  5. Predicting and validating protein interactions using network structure.

    Directory of Open Access Journals (Sweden)

    Pao-Yang Chen

    Full Text Available Protein interactions play a vital part in the function of a cell. As experimental techniques for detection and validation of protein interactions are time consuming, there is a need for computational methods for this task. Protein interactions appear to form a network with a relatively high degree of local clustering. In this paper we exploit this clustering by suggesting a score based on triplets of observed protein interactions. The score utilises both protein characteristics and network properties. Our score based on triplets is shown to complement existing techniques for predicting protein interactions, outperforming them on data sets which display a high degree of clustering. The predicted interactions score highly against test measures for accuracy. Compared to a similar score derived from pairwise interactions only, the triplet score displays higher sensitivity and specificity. By looking at specific examples, we show how an experimental set of interactions can be enriched and validated. As part of this work we also examine the effect of different prior databases upon the accuracy of prediction and find that the interactions from the same kingdom give better results than from across kingdoms, suggesting that there may be fundamental differences between the networks. These results all emphasize that network structure is important and helps in the accurate prediction of protein interactions. The protein interaction data set and the program used in our analysis, and a list of predictions and validations, are available at http://www.stats.ox.ac.uk/bioinfo/resources/PredictingInteractions.

  6. Feelings about culture scales: development, factor structure, reliability, and validity.

    Science.gov (United States)

    Maffini, Cara S; Wong, Y Joel

    2015-04-01

    Although measures of cultural identity, values, and behavior exist in the multicultural psychological literature, there is currently no measure that explicitly assesses ethnic minority individuals' positive and negative affect toward culture. Therefore, we developed 2 new measures called the Feelings About Culture Scale--Ethnic Culture and Feelings About Culture Scale--Mainstream American Culture and tested their psychometric properties. In 6 studies, we piloted the measures, conducted factor analyses to clarify their factor structure, and examined reliability and validity. The factor structure revealed 2 dimensions reflecting positive and negative affect for each measure. Results provided evidence for convergent, discriminant, criterion-related, and incremental validity as well as the reliability of the scales. The Feelings About Culture Scales are the first known measures to examine both positive and negative affect toward an individual's ethnic culture and mainstream American culture. The focus on affect captures dimensions of psychological experiences that differ from cognitive and behavioral constructs often used to measure cultural orientation. These measures can serve as a valuable contribution to both research and counseling by providing insight into the nuanced affective experiences ethnic minority individuals have toward culture.

  7. Nanosystem Self-Assembly Pathways Discovered via All-Atom Multiscale Analysis

    CERN Document Server

    Pankavich, Stephen

    2014-01-01

    We consider the self-assembly of composite structures from a group of nanocomponents, each consisting of particles within an $N$-atom system. Self-assembly pathways and rates for nanocomposites are derived via a multiscale analysis of the classical Liouville equation. From a reduced statistical framework, rigorous stochastic equations for population levels of beginning, intermediate, and final aggregates are also derived. It is shown that the definition of an assembly type is a self-consistency criterion that must strike a balance between precision and the need for population levels to be slowly varying relative to the time scale of atomic motion. The deductive multiscale approach is complemented by a qualitative notion of multicomponent association and the ensemble of exact atomic-level configurations consistent with them. In processes such as viral self-assembly from proteins and RNA or DNA, there are many possible intermediates, so that it is usually difficult to predict the most efficient assembly pathway...

  8. Structural validation as an input into seismic depth conversion to decrease assigned structural uncertainty

    Science.gov (United States)

    Totake, Yukitsugu; Butler, Robert W. H.; Bond, Clare E.

    2017-02-01

    While the interpretation of seismic reflection imagery is powerful and well established for evaluating subsurface structures it is never perfectly accurate. Structural validation techniques are widely used to geometrically test geological interpretations of seismic reflection data. Commonly these techniques are performed on depth sections converted from seismic time-based data using velocity models. Velocity model choices in seismic depth conversion have an impact on the final depth image and hence the structural geometry of interpretations. The impact of these choices in depth conversion on structural validation is rarely examined. Here we explore how multiple versions of a depth section, converted using different velocity models, influence the performance of structural validations for a fold-thrust structure from the deep water Niger Delta. The example illustrates that a range of kinematic models can validate the depth-converted profiles, regardless of the depth conversion choice and are thus poor diagnostic tools. Area-depth-strain (ADS) analysis can constrain the choice both of a kinematic model and the depth conversion, provided the seismic data allow the detachment level and excess areas to be recognised. Incorporation of ADS analysis within an interpretation-depth conversion workflow helps reduce assigned uncertainty in depth conversion, the seismic interpretation, and in the implicit geological model.

  9. Conformations of Carnosine in Aqueous Solutions by All-Atom Molecular Dynamics Simulations and 2D-NOSEY Spectrum

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Dan Wang; Wen-juan Wu

    2013-01-01

    All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution.Intramolecular distances,root-mean-square deviation,radius of gyration,and solvent-accessible surface are used to characterize the properties of the carnosine.Carnosine can shift between extended and folded states,but exists mostly in extended state in water.Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance (NMR) experiment.The NMR experimental results are consistent with the molecular dynamics simulations.

  10. Validating spatial structure in canopy water content using geostatistics

    Science.gov (United States)

    Sanderson, E. W.; Zhang, M. H.; Ustin, S. L.; Rejmankova, E.; Haxo, R. S.

    1995-01-01

    Heterogeneity in ecological phenomena are scale dependent and affect the hierarchical structure of image data. AVIRIS pixels average reflectance produced by complex absorption and scattering interactions between biogeochemical composition, canopy architecture, view and illumination angles, species distributions, and plant cover as well as other factors. These scales affect validation of pixel reflectance, typically performed by relating pixel spectra to ground measurements acquired at scales of 1m(exp 2) or less (e.g., field spectra, foilage and soil samples, etc.). As image analysis becomes more sophisticated, such as those for detection of canopy chemistry, better validation becomes a critical problem. This paper presents a methodology for bridging between point measurements and pixels using geostatistics. Geostatistics have been extensively used in geological or hydrogeolocial studies but have received little application in ecological studies. The key criteria for kriging estimation is that the phenomena varies in space and that an underlying controlling process produces spatial correlation between the measured data points. Ecological variation meets this requirement because communities vary along environmental gradients like soil moisture, nutrient availability, or topography.

  11. Using of Structural Equation Modeling Techniques in Cognitive Levels Validation

    Directory of Open Access Journals (Sweden)

    Natalija Curkovic

    2012-10-01

    Full Text Available When constructing knowledge tests, cognitive level is usually one of the dimensions comprising the test specifications with each item assigned to measure a particular level. Recently used taxonomies of the cognitive levels most often represent some modification of the original Bloom’s taxonomy. There are many concerns in current literature about existence of predefined cognitive levels. The aim of this article is to investigate can structural equation modeling techniques confirm existence of different cognitive levels. For the purpose of the research, a Croatian final high-school Mathematics exam was used (N = 9626. Confirmatory factor analysis and structural regression modeling were used to test three different models. Structural equation modeling techniques did not support existence of different cognitive levels in this case. There is more than one possible explanation for that finding. Some other techniques that take into account nonlinear behaviour of the items as well as qualitative techniques might be more useful for the purpose of the cognitive levels validation. Furthermore, it seems that cognitive levels were not efficient descriptors of the items and so improvements are needed in describing the cognitive skills measured by items.

  12. Comparison and validation of community structures in complex networks

    CERN Document Server

    Gustafsson, M; Lombardi, A; Gustafsson, Mika; Hornquist, Michael; Lombardi, Anna

    2006-01-01

    The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the problem formulated this way is NP-hard, most effort has gone into the construction of search algorithms, and less to the question of other measures of community structures, similarities between various partitionings and the validation with respect to external information. Here we concentrate on a class of computer generated networks and on three well-studied real networks which constitute a bench-mark for network studies; the karate club, the US college football teams and a gene network of yeast. We utilize some standard ways of clustering data (originally not designed for finding community structures in networks) and show that these classical methods sometimes outperform the newer ones. We discuss various measures of the strength of the modular structure, and show by examples f...

  13. All-atom simulation study of protein PTH(1-34) by using the Wang-Landau sampling method

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seung-Yeon [Korea National University of Transportation, Chungju (Korea, Republic of); Kwak, Woo-Seop [Chosun University, Gwangju (Korea, Republic of)

    2014-12-15

    We perform simulations of the N-terminal 34-residue protein fragment PTH(1-34), consisting of 581 atoms, of the 84-residue human parathyroid hormone by using the all-atom ECEPP/3 force field and the Wang-Landau sampling method. Through a massive high-performance computation, the density of states and the partition function Z(T), as a continuous function of T, are obtained for PTH(1-34). From the continuous partition function Z(T), the partition function zeros of PTH(1-34) are evaluated for the first time. From both the specific heat and the partition function zeros, two characteristic transition temperatures are obtained for the all-atom protein PTH(1-34). The higher transition temperature T{sub 1} and the lower transition temperature T{sub 2} of PTH(1-34) can be interpreted as the collapse temperature T{sub θ} and the folding temperature T{sub f} , respectively.

  14. Generation of Well-Relaxed All-Atom Models of Large Molecular Weight Polymer Melts: A Hybrid Particle-Continuum Approach Based on Particle-Field Molecular Dynamics Simulations.

    Science.gov (United States)

    De Nicola, Antonio; Kawakatsu, Toshihiro; Milano, Giuseppe

    2014-12-09

    A procedure based on Molecular Dynamics (MD) simulations employing soft potentials derived from self-consistent field (SCF) theory (named MD-SCF) able to generate well-relaxed all-atom structures of polymer melts is proposed. All-atom structures having structural correlations indistinguishable from ones obtained by long MD relaxations have been obtained for poly(methyl methacrylate) (PMMA) and poly(ethylene oxide) (PEO) melts. The proposed procedure leads to computational costs mainly related on system size rather than to the chain length. Several advantages of the proposed procedure over current coarse-graining/reverse mapping strategies are apparent. No parametrization is needed to generate relaxed structures of different polymers at different scales or resolutions. There is no need for special algorithms or back-mapping schemes to change the resolution of the models. This characteristic makes the procedure general and its extension to other polymer architectures straightforward. A similar procedure can be easily extended to the generation of all-atom structures of block copolymer melts and polymer nanocomposites.

  15. Density relaxation and particle motion characteristics in a non-ionic deep eutectic solvent (acetamide + urea): Time-resolved fluorescence measurements and all-atom molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Das, Anuradha; Das, Suman; Biswas, Ranjit, E-mail: ranjit@bose.res.in [Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata, West Bengal 700098 (India)

    2015-01-21

    Temperature dependent relaxation dynamics, particle motion characteristics, and heterogeneity aspects of deep eutectic solvents (DESs) made of acetamide (CH{sub 3}CONH{sub 2}) and urea (NH{sub 2}CONH{sub 2}) have been investigated by employing time-resolved fluorescence measurements and all-atom molecular dynamics simulations. Three different compositions (f) for the mixture [fCH{sub 3}CONH{sub 2} + (1 − f)NH{sub 2}CONH{sub 2}] have been studied in a temperature range of 328-353 K which is ∼120-145 K above the measured glass transition temperatures (∼207 K) of these DESs but much lower than the individual melting temperature of either of the constituents. Steady state fluorescence emission measurements using probe solutes with sharply different lifetimes do not indicate any dependence on excitation wavelength in these metastable molten systems. Time-resolved fluorescence anisotropy measurements reveal near-hydrodynamic coupling between medium viscosity and rotation of a dissolved dipolar solute. Stokes shift dynamics have been found to be too fast to be detected by the time-resolution (∼70 ps) employed, suggesting extremely rapid medium polarization relaxation. All-atom simulations reveal Gaussian distribution for particle displacements and van Hove correlations, and significant overlap between non-Gaussian (α{sub 2}) and new non-Gaussian (γ) heterogeneity parameters. In addition, no stretched exponential relaxations have been detected in the simulated wavenumber dependent acetamide dynamic structure factors. All these results are in sharp contrast to earlier observations for ionic deep eutectics with acetamide [Guchhait et al., J. Chem. Phys. 140, 104514 (2014)] and suggest a fundamental difference in interaction and dynamics between ionic and non-ionic deep eutectic solvent systems.

  16. Cholesterol Flip-Flop Dynamics in a Phospholipid Bilayer: A 10 Microsecond All-Atom Molecular Dynamics Simulation

    Science.gov (United States)

    Choubey, Amit; Nomura, Ken-Ichi; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya

    2012-02-01

    Cholesterol (CHOL) molecules play a key role in modulating the rigidity of cell membranes, and controlling intracellular transport and signal transduction. Using all-atom molecular dynamics and the parallel replica approach, we study the effect of CHOL molecules on mechanical stresses across a dipalmitoylphosphatidycholine (DPPC)-CHOL bilayer, and the mechanism by which CHOL molecules migrate from one bilayer leaflet to the other (flip-flop events). On average, we observe a CHOL flip-flop event in half-a-microsecond. Once a CHOL flip-flop event is triggered, the inter-leaflet migration occurs in about 62 nanoseconds. The energy barrier associated with flip-flop events is found to be 73 kJ/mol. Results for membrane rigidity as a function of CHOL concentration will also be presented.

  17. Analysis of Ligand-Receptor Association and Intermediate Transfer Rates in Multienzyme Nanostructures with All-Atom Brownian Dynamics Simulations.

    Science.gov (United States)

    Roberts, Christopher C; Chang, Chia-En A

    2016-08-25

    We present the second-generation GeomBD Brownian dynamics software for determining interenzyme intermediate transfer rates and substrate association rates in biomolecular complexes. Substrate and intermediate association rates for a series of enzymes or biomolecules can be compared between the freely diffusing disorganized configuration and various colocalized or complexed arrangements for kinetic investigation of enhanced intermediate transfer. In addition, enzyme engineering techniques, such as synthetic protein conjugation, can be computationally modeled and analyzed to better understand changes in substrate association relative to native enzymes. Tools are provided to determine nonspecific ligand-receptor association residence times, and to visualize common sites of nonspecific association of substrates on receptor surfaces. To demonstrate features of the software, interenzyme intermediate substrate transfer rate constants are calculated and compared for all-atom models of DNA origami scaffold-bound bienzyme systems of glucose oxidase and horseradish peroxidase. Also, a DNA conjugated horseradish peroxidase enzyme was analyzed for its propensity to increase substrate association rates and substrate local residence times relative to the unmodified enzyme. We also demonstrate the rapid determination and visualization of common sites of nonspecific ligand-receptor association by using HIV-1 protease and an inhibitor, XK263. GeomBD2 accelerates simulations by precomputing van der Waals potential energy grids and electrostatic potential grid maps, and has a flexible and extensible support for all-atom and coarse-grained force fields. Simulation software is written in C++ and utilizes modern parallelization techniques for potential grid preparation and Brownian dynamics simulation processes. Analysis scripts, written in the Python scripting language, are provided for quantitative simulation analysis. GeomBD2 is applicable to the fields of biophysics, bioengineering

  18. Estimation of Liposome Penetration Barriers of Drug Molecules with All-Atom and Coarse-Grained Models.

    Science.gov (United States)

    Genheden, Samuel; Eriksson, Leif A

    2016-09-13

    Liposomes are common carriers of drug molecules, providing enhanced delivery and accumulation of hydrophilic agents or larger biomolecules. Molecular simulations can be used to estimate key features of the drug molecules upon interaction with the liposomes, such as penetration barriers and localization. Herein, we investigate several aspects of the computational estimation of penetration barriers, viz. the potential of mean force (PMFs) along a vector spanning the membrane. First, we provide an evaluation of the all-atom (AA) and coarse-grained (CG) parametrization of 5-aminolevulinic acid (5-ALA) and two of its alkyl esters by computing n-octanol/water partition coefficients. We find that the CG parametrization of the esters performs significantly better than the CG model of 5-ALA, highlighting the difficulty to coarse-grain small, polar molecules. However, the expected trend in partition coefficients is reproduced also with the CG models. Second, we compare PMFs in a small membrane slab described with either the AA or CG models. Here, we are able to reproduce the all-atom PMF of 5-ALA with CG. However, for the alkyl esters it is unfortunately not possible to correctly reproduce both the depth and the penetration barrier of the PMF seen in the AA simulations with any of the tested CG models. We argue that it is more important to choose a CG parametrization that reproduces the depth of the PMF. Third, we compare, using the CG model, PMFs in the membrane slab with PMFs in a large, realistic liposome. We find similar depths but slightly different penetration barriers most likely due to differences in the lipid density along the membrane axis. Finally, we compute PMFs in liposomes with three different lipid compositions. Unfortunately, differences in the PMFs could not be quantified, and it remains to be investigated to what extent liposome simulations can fully reproduce experimental findings.

  19. Structure Modeling and Validation applied to Source Physics Experiments (SPEs)

    Science.gov (United States)

    Larmat, C. S.; Rowe, C. A.; Patton, H. J.

    2012-12-01

    The U. S. Department of Energy's Source Physics Experiments (SPEs) comprise a series of small chemical explosions used to develop a better understanding of seismic energy generation and wave propagation for low-yield explosions. In particular, we anticipate improved understanding of the processes through which shear waves are generated by the explosion source. Three tests, 100, 1000 and 1000 kg yields respectively, were detonated in the same emplacement hole and recorded on the same networks of ground motion sensors in the granites of Climax Stock at the Nevada National Security Site. We present results for the analysis and modeling of seismic waveforms recorded close-in on five linear geophone lines extending radially from ground zero, having offsets from 100 to 2000 m and station spacing of 100 m. These records exhibit azimuthal variations of P-wave arrival times, and phase velocity, spreading and attenuation properties of high-frequency Rg waves. We construct a 1D seismic body-wave model starting from a refraction analysis of P-waves and adjusting to address time-domain and frequency-domain dispersion measurements of Rg waves between 2 and 9 Hz. The shallowest part of the structure we address using the arrival times recorded by near-field accelerometers residing within 200 m of the shot hole. We additionally perform a 2D modeling study with the Spectral Element Method (SEM) to investigate which structural features are most responsible for the observed variations, in particular anomalously weak amplitude decay in some directions of this topographically complicated locality. We find that a near-surface, thin, weathered layer of varying thickness and low wave speeds plays a major role on the observed waveforms. We anticipate performing full 3D modeling of the seismic near-field through analysis and validation of waveforms on the 5 radial receiver arrays.

  20. Differential dynamics of the serotonin1A receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation.

    Science.gov (United States)

    Patra, Swarna M; Chakraborty, Sudip; Shahane, Ganesh; Prasanna, Xavier; Sengupta, Durba; Maiti, Prabal K; Chattopadhyay, Amitabha

    2015-01-01

    The serotonin1A receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin1A receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3 μs, to analyze the effect of cholesterol on the structure and dynamics of the serotonin1A receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin1A receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.

  1. Constructing a Validity Argument for the Objective Structured Assessment of Technical Skills (OSATS): A Systematic Review of Validity Evidence

    Science.gov (United States)

    Hatala, Rose; Cook, David A.; Brydges, Ryan; Hawkins, Richard

    2015-01-01

    In order to construct and evaluate the validity argument for the Objective Structured Assessment of Technical Skills (OSATS), based on Kane's framework, we conducted a systematic review. We searched MEDLINE, EMBASE, CINAHL, PsycINFO, ERIC, Web of Science, Scopus, and selected reference lists through February 2013. Working in duplicate, we selected…

  2. A Validation Study of the Dutch Childhood Trauma Questionnaire-Short Form: Factor Structure, Reliability, and Known-Groups Validity

    Science.gov (United States)

    Thombs, Brett D.; Bernstein, David P.; Lobbestael, Jill; Arntz, Arnoud

    2009-01-01

    Objective: The 28-item Childhood Trauma Questionnaire-Short Form (CTQ-SF) has been translated into at least 10 different languages. The validity of translated versions of the CTQ-SF, however, has generally not been examined. The objective of this study was to investigate the factor structure, internal consistency reliability, and known-groups…

  3. Development and Validation of a Coping with Discrimination Scale: Factor Structure, Reliability, and Validity

    Science.gov (United States)

    Wei, Meifen; Alvarez, Alvin N.; Ku, Tsun-Yao; Russell, Daniel W.; Bonett, Douglas G.

    2010-01-01

    Four studies were conducted to develop and validate the Coping With Discrimination Scale (CDS). In Study 1, an exploratory factor analysis (N = 328) identified 5 factors: Education/Advocacy, Internalization, Drug and Alcohol Use, Resistance, and Detachment, with internal consistency reliability estimates ranging from 0.72 to 0.90. In Study 2, a…

  4. Insights into the Tunnel Mechanism of Cholesteryl Ester Transfer Protein through All-atom Molecular Dynamics Simulations.

    Science.gov (United States)

    Lei, Dongsheng; Rames, Matthew; Zhang, Xing; Zhang, Lei; Zhang, Shengli; Ren, Gang

    2016-07-01

    Cholesteryl ester transfer protein (CETP) mediates cholesteryl ester (CE) transfer from the atheroprotective high density lipoprotein (HDL) cholesterol to the atherogenic low density lipoprotein cholesterol. In the past decade, this property has driven the development of CETP inhibitors, which have been evaluated in large scale clinical trials for treating cardiovascular diseases. Despite the pharmacological interest, little is known about the fundamental mechanism of CETP in CE transfer. Recent electron microscopy (EM) experiments have suggested a tunnel mechanism, and molecular dynamics simulations have shown that the flexible N-terminal distal end of CETP penetrates into the HDL surface and takes up a CE molecule through an open pore. However, it is not known whether a CE molecule can completely transfer through an entire CETP molecule. Here, we used all-atom molecular dynamics simulations to evaluate this possibility. The results showed that a hydrophobic tunnel inside CETP is sufficient to allow a CE molecule to completely transfer through the entire CETP within a predicted transfer time and at a rate comparable with those obtained through physiological measurements. Analyses of the detailed interactions revealed several residues that might be critical for CETP function, which may provide important clues for the effective development of CETP inhibitors and treatment of cardiovascular diseases.

  5. Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils.

    Science.gov (United States)

    Hoang Viet, Man; Derreumaux, Philippe; Nguyen, Phuong H

    2016-11-07

    The cavitation of gas bubbles in liquids has been applied to different disciplines in life and natural sciences, and in technologies. To obtain an appropriate theoretical description of effects induced by the bubble cavitation, we develop an all-atom nonequilibrium molecular-dynamics simulation method to simulate bubbles undergoing harmonic oscillation in size. This allows us to understand the mechanism of the bubble cavitation-induced liquid shear stress on surrounding objects. The method is then employed to simulate an Aβ fibril model in the presence of bubbles, and the results show that the bubble expansion and contraction exert water pressure on the fibril. This yields to the deceleration and acceleration of the fibril kinetic energy, facilitating the conformational transition between local free energy minima, and leading to the dissociation of the fibril. Our work, which is a proof-of-concept, may open a new, efficient way to dissociate amyloid fibrils using the bubble cavitation technique, and new venues to investigate the complex phenomena associated with amyloidogenesis.

  6. The Trait Emotional Intelligence Questionnaire: Internal Structure, Convergent, Criterion, and Incremental Validity in an Italian Sample

    Science.gov (United States)

    Andrei, Federica; Smith, Martin M.; Surcinelli, Paola; Baldaro, Bruno; Saklofske, Donald H.

    2016-01-01

    This study investigated the structure and validity of the Italian translation of the Trait Emotional Intelligence Questionnaire. Data were self-reported from 227 participants. Confirmatory factor analysis supported the four-factor structure of the scale. Hierarchical regressions also demonstrated its incremental validity beyond demographics, the…

  7. Uncovering the microscopic mechanism of strand exchange during RecA mediated homologous recombination using all-atom molecular dynamics simulations

    Science.gov (United States)

    Shankla, Manish; Yoo, Jejoong; Aksimentiev, Aleksei

    2012-02-01

    Homologous recombination (HR) is a key step during the repair process of double-stranded DNA (dsDNA) breakage. RecA is a protein that mediates HR in bacteria. RecA monomers polymerize on a single-stranded DNA (ssDNA) separated from the broken dsDNA to form a helical filament, thus allowing strand exchange to occur. Recent crystal structures depict each RecA monomer in contact with three contiguous nucleotides called DNA triplets. Surprisingly, the conformation of each triplet is similar to that of a triplet in B-form DNA. However, in the filament the neighboring triplets are separated by loops of the RecA proteins. Single molecule experiments demonstrated that strand exchange propagation occurs in 3 base-pair increments. However, the temporal resolution of the experiments was insufficient to determine the exact molecular mechanism of the triplet propagation. Using all-atom molecular dynamics simulations, we investigated the effect of both the RecA protein and the conformation of the bound ssDNA fragment on the stability of the duplex DNA intermediate formed during the strand-exchange process. Specifically, we report simulations of force-induced unzipping of duplex DNA in the presence and absence of the RecA filament that explored the effect of the triplet ladder conformation.

  8. All-atom molecular dynamics simulations reveal significant differences in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc1 complexes.

    Science.gov (United States)

    Kokhan, Oleksandr; Shinkarev, Vladimir P

    2011-02-02

    Antimycin A is the most frequently used specific and powerful inhibitor of the mitochondrial respiratory chain. We used all-atom molecular dynamics (MD) simulations to study the dynamic aspects of the interaction of antimycin A with the Q(i) site of the bacterial and bovine bc(1) complexes embedded in a membrane. The MD simulations revealed considerable conformational flexibility of antimycin and significant mobility of antimycin, as a whole, inside the Q(i) pocket. We conclude that many of the differences in antimycin binding observed in high-resolution x-ray structures may have a dynamic origin and result from fluctuations of protein and antimycin between multiple conformational states of similar energy separated by low activation barriers, as well as from the mobility of antimycin within the Q(i) pocket. The MD simulations also revealed a significant difference in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc(1) complexes. The strong hydrogen bond between antimycin and conserved Asp-228 (bovine numeration) was observed to be frequently broken in the bacterial bc(1) complex and only rarely in the bovine bc(1) complex. In addition, the distances between antimycin and conserved His-201 and Lys-227 were consistently larger in the bacterial bc(1) complex. The observed differences could be responsible for a weaker interaction of antimycin with the bacterial bc(1) complex.

  9. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  10. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations.

    Science.gov (United States)

    Ou, Shu-Ching; Cui, Di; Wezowicz, Matthew; Taufer, Michela; Patel, Sandeep

    2015-06-15

    In this study, we examine the temperature dependence of free energetics of nanotube association using graphical processing unit-enabled all-atom molecular dynamics simulations (FEN ZI) with two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution. Results suggest that the free energy, enthalpy and entropy changes for the association process are all reduced at the high temperature, in agreement with previous investigations using other hydrophobes. Via the decomposition of free energy into individual components, we found that solvent contribution (including water, anion, and cation contributions) is correlated with the spatial distribution of the corresponding species and is influenced distinctly by the temperature. We studied the spatial distribution and the structure of the solvent in different regions: intertube, intratube and the bulk solvent. By calculating the fluctuation of coarse-grained tube-solvent surfaces, we found that tube-water interfacial fluctuation exhibits the strongest temperature dependence. By taking ions to be a solvent-like medium in the absence of water, tube-anion interfacial fluctuation shows similar but weaker dependence on temperature, while tube-cation interfacial fluctuation shows no dependence in general. These characteristics are discussed via the malleability of their corresponding solvation shells relative to the nanotube surface. Hydrogen bonding profiles and tetrahedrality of water arrangement are also computed to compare the structure of solvent in the solvent bulk and intertube region. The hydrophobic confinement induces a relatively lower concentration environment in the intertube region, therefore causing different intertube solvent structures which depend on the tube separation. This study is relevant in the continuing discourse on hydrophobic interactions (as they impact generally a broad class of phenomena in biology, biochemistry, and materials science and soft condensed matter research), and

  11. Structured Programming Series. Volume 15. Validation and Verification Study

    Science.gov (United States)

    1975-05-22

    concept* b. Top down programming c . Structured programming In FORTRAN with a preprocessor d. Variation of HIPO* Including: *A1 though these are not...Structured programming technology components used In this project Include: a. Top down programming b. Structured programming c . Program design

  12. Experimentally validated finite element model of electrocaloric multilayer ceramic structures

    Energy Technology Data Exchange (ETDEWEB)

    Smith, N. A. S., E-mail: nadia.smith@npl.co.uk, E-mail: maciej.rokosz@npl.co.uk, E-mail: tatiana.correia@npl.co.uk; Correia, T. M., E-mail: nadia.smith@npl.co.uk, E-mail: maciej.rokosz@npl.co.uk, E-mail: tatiana.correia@npl.co.uk [National Physical Laboratory, Hampton Road, TW11 0LW Middlesex (United Kingdom); Rokosz, M. K., E-mail: nadia.smith@npl.co.uk, E-mail: maciej.rokosz@npl.co.uk, E-mail: tatiana.correia@npl.co.uk [National Physical Laboratory, Hampton Road, TW11 0LW Middlesex (United Kingdom); Department of Materials, Imperial College London, London SW7 2AZ (United Kingdom)

    2014-07-28

    A novel finite element model to simulate the electrocaloric response of a multilayer ceramic capacitor (MLCC) under real environment and operational conditions has been developed. The two-dimensional transient conductive heat transfer model presented includes the electrocaloric effect as a source term, as well as accounting for radiative and convective effects. The model has been validated with experimental data obtained from the direct imaging of MLCC transient temperature variation under application of an electric field. The good agreement between simulated and experimental data, suggests that the novel experimental direct measurement methodology and the finite element model could be used to support the design of optimised electrocaloric units and operating conditions.

  13. Theoretical temperature model with experimental validation for CLIC Accelerating Structures

    CERN Document Server

    Aasly, Sara Hegdahl; Vamvakas, Alex; Alme, Johan; Haustveit, Svein

    Micron level stability of the Compact Linear Collider (CLIC) components is one of the main requirements to meet the luminosity goal for the future $48 \\,km$ long underground linear accelerator. The radio frequency (RF) power used for beam acceleration causes heat generation within the aligned structures, resulting in mechanical movements and structural deformations. A dedicated control of the air- and water- cooling system in the tunnel is therefore crucial to improve alignment accuracy. This thesis investigates the thermo-mechanical behavior of the CLIC Accelerating Structure (AS). In CLIC, the AS must be aligned to a precision of $10\\,\\mu m$. The thesis shows that a relatively simple theoretical model can be used within reasonable accuracy to predict the temperature response of an AS as a function of the applied RF power. During failure scenarios or maintenance interventions, the RF power is turned off resulting in no heat dissipation and decrease in the overall temperature of the components. The theoretica...

  14. Validation methods for low-resolution fitting of atomic structures to electron microscopy data

    OpenAIRE

    Xu, Xiao-Ping; Volkmann, Niels

    2015-01-01

    Fitting of atomic-resolution structures into reconstructions from electron cryo-microscopy is routinely used to understand the structure and function of macromolecular machines. Despite the fact that a plethora of fitting methods has been developed over recent years, standard protocols for quality assessment and validation of these fits have not been established. Here, we present the general concepts underlying current validation ideas as they relate to fitting of atomic-resolution models int...

  15. Experimental validation of the interaction between combustion and structural vibration

    NARCIS (Netherlands)

    Huls, Rob; Boer, de André; Kok, Jim; Hoogt, van der Peter

    2005-01-01

    To decrease NOx emissions from combustion systems, lean premixed combustion is used. A disadvantage is the increase in sound pressure levels in the combustor, resulting in an increased excitation of the surrounding structure: the liner. This causes fatigue, which limits the life time of the combusto

  16. A Novel Validity Index for Evaluating the Item Ordering Structure Based on Q-matrix Theory

    Directory of Open Access Journals (Sweden)

    Hsiang-Chuan Liu

    2013-06-01

    Full Text Available Before then, no validity index can be used for evaluating the item ordering structure for cognition diagnosis. In this study, based on the Q-matrix theory, an ideal item ordering structure without slip and guess for an efficient test is proposed by using the set containing relation operation. It can be viewed as a criterion of the item ordering structure for a given test. Furthermore, a novel criterion-related validity index for evaluating the item ordering structure of any item ordering algorithm is proposed, it is more useful for cognition diagnosis.

  17. Validation of Superelement Modelling of Complex Offshore Support Structures

    DEFF Research Database (Denmark)

    Wang, Shaofeng; Larsen, Torben J.; Hansen, Anders Melchior

    2016-01-01

    Modern large MW wind turbines today are installed at larger water depth than applicable for traditional monopile substructure. It appears that foundation types such as jacket and tripod are gaining more popularity for these locations. For certification purposes, a full set of design load calculat......Modern large MW wind turbines today are installed at larger water depth than applicable for traditional monopile substructure. It appears that foundation types such as jacket and tripod are gaining more popularity for these locations. For certification purposes, a full set of design load...... calculations consisting of up to thousands design load cases needs to be evaluated. However, even the simplest aero-elastic model of such structures has many more DOFs than monopile, resulting in excessive computation burden. In order to deal with this problem, the superelement method has been introduced...... for modelling such structures. One superelement method has been proven very promising in the previous project of Wave Loads [1] and a fundamental question in such DOFs reduction methods is which modes that are essential and which modes can be neglected. For the jacket structure, the introduction of a gravity...

  18. Structural Health Monitoring 2007: Quantification, Validation, and Implementation

    Science.gov (United States)

    2007-11-30

    Fritzen, C.-P., Klinkov, M., University of Siegen 15:05 ~ 15:25 Online Wind Load Estimation for Offshore Wind Energy Plants p. 1905 Raimund Rolfes...Stephan Zerbst, Gerrit Haake, Johannes Reetz, , Jerome P. LynchUniversity of Hannover 15:25 ~ 15:45 Integral SHM-System for Offshore Wind Energy Turbines...15:40 Concept for Structural Damage Identification of Offshore Wind Energy Plants p. 1881 Zhan-Sheng GUO, Shanghai University 12:00 ~ 13:00 14

  19. Latent structure and construct validity of the reinforcement sensitivity questionnaire

    Directory of Open Access Journals (Sweden)

    Mitrović Dušanka

    2008-01-01

    Full Text Available The Revised reinforcement sensitivity theory contains three basic systems: Behavioral inhibition system (BAS, Behavioral activation system (BIS and the Fight/ Flight/ Freeze (FFF system. In this model, BIS is a system for detection of potential conflict or threat, and FFFS differs three basic patterns of reaction to actual or perceived danger. In Study 1, which was aimed at the examination of the latent structure of the RSQ, was conducted on a sample of 472 participants of both genders. The best - fitting model suggests that, at the top level of hierarchy, three dimensions exist, which are analogous to the BIS, BAS and FFF. The last dimension contains three subordinate dimensions, which represent the subsystems of the FFF. Study 2, in which 203 subjects participated, was aimed at examination of the relations between the dimensions of the Revised reinforcement sensitivity theory and dimensions of the PEN model. Confirmatory factor analyses of the RSQ and EPQ-R dimensions revealed that the best-fitting model comprised three latent dimensions, the first one being analogous to the BIS - Neuroticism, the second one to the BAS - Extraversion, and the third to the Aggressiveness- Psychoticism. The structure of the latent dimensions is in accordance with the expectations. The results state that fear and anxiety (which neurophysiological distinction is emphasized by Gray, are substantively similar on the behavioral level. Also, the results suggest that the Freeze dimension is probably closer to the BIS system than to the FFF.

  20. A model of the lung structure and its validation.

    Science.gov (United States)

    Fung, Y C

    1988-05-01

    As a framework to describe the structure of the lung, a theory is presented under the assumptions that all alveoli are initially equal and space filling, are ventilated as uniformly as possible, and obey the laws of elasticity. A combination of the tetrakaidecahedron (14-hedron) and the order-2 14-hedron formed by 14 14-hedra surrounding a central one that is perforated for ventilation meets the requirements. Alveolar ductal tree is formed by these order-2 polyhedra. Equilibrium and elasticity require the alveolar mouths to be curved and convex toward the alveolar wall. Perforation of additional walls causes a variety of alveolar shapes. The predicted shapes of the alveoli, the shapes of alveolar mouths, the lengths of sacs and ducts, the statistics of the dihedral angles, stars, corners, lines, dots, and vertices compare well with available morphometric data. The vascular and bronchial trees are joined at the alveolar level: each arteriole supplies 0.75 and each venule drains 0.72 order-2 polyhedra.

  1. Factorial Structure of the Career Decision Scale: Incremental Validity of the Five-Factor Domains

    Science.gov (United States)

    Feldt, Ronald C.; Ferry, Ashley; Bullock, Melinda; Camarotti-Carvalho, Ana; Collingwood, Melinda; Eilers, Scott; Meyer, Luke; Nurre, Emily; Woelfel, Cheryl

    2010-01-01

    For comparison of one-, three-, and four-factor structures of the Indecision scale of the Career Decision Scale, results of confirmatory factor analysis (N = 686) indicated the best fit for the three-factor structure. Multiple regression analysis results indicated incremental validity of the five-factor model for predicting dimensions of career…

  2. The Dynamic Similitude Design Method of Thin Walled Structures and Experimental Validation

    Directory of Open Access Journals (Sweden)

    Zhong Luo

    2016-01-01

    Full Text Available For the applicability of dynamic similitude models of thin walled structures, such as engine blades, turbine discs, and cylindrical shells, the dynamic similitude design of typical thin walled structures is investigated. The governing equation of typical thin walled structures is firstly unified, which guides to establishing dynamic scaling laws of typical thin walled structures. Based on the governing equation, geometrically complete scaling law of the typical thin walled structure is derived. In order to determine accurate distorted scaling laws of typical thin walled structures, three principles are proposed and theoretically proved by combining the sensitivity analysis and governing equation. Taking the thin walled annular plate as an example, geometrically complete and distorted scaling laws can be obtained based on the principles of determining dynamic scaling laws. Furthermore, the previous five orders’ accurate distorted scaling laws of thin walled annular plates are presented and numerically validated. Finally, the effectiveness of the similitude design method is validated by experimental annular plates.

  3. Validity and Reliability of pre-internship Objective Structured Clinical Examination in Shiraz Medical School

    Directory of Open Access Journals (Sweden)

    NARGES VASEGHI

    2013-07-01

    Full Text Available Introduction: Objective Structured Clinical Examination (OSCE is one of the most appropriate methods for assessment of clinical skills.Validity and reliability assurance is a mandatory factor for any assessment tool. In Shiraz University of Medical Sciences, medical students’ clinical competences are evaluated by a pre-internship OSCE. This study is designed to examine the validity and reliability of this exam. Validity is the extent to which the test measures what it intends to measure. Reliability refers to the accuracy of measurement and the consistency of test results. Methods: Content validity was evaluated by expert opinion about blueprinting and station checklists. To determine the construct validity, station scores correlation with the total OSCE score and inter station correlations were calculated. The inter examiner reliability was assessed by coefficient of correlation. Results: Content validity was established by alignment between the curriculum and the blueprint using expert opinion. Correlation of the station scores with the total OSCE score were positive and statistically significant in all stations except the 16th station (suturing. Inter examiner reliability coefficients of correlations ranged 0.33 – 0.99, with an average of 0.83. Conclusions: Our findings support the assumption that the pre-internship OSCE is valid, reliable and suitable to assess students’ clinical competence. Validity and reliability studies should be performed for all new assessment tools, particularly in high-stakes assessments.

  4. Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database.

    Science.gov (United States)

    Hawkins, Paul C D; Skillman, A Geoffrey; Warren, Gregory L; Ellingson, Benjamin A; Stahl, Matthew T

    2010-04-26

    Here, we present the algorithm and validation for OMEGA, a systematic, knowledge-based conformer generator. The algorithm consists of three phases: assembly of an initial 3D structure from a library of fragments; exhaustive enumeration of all rotatable torsions using values drawn from a knowledge-based list of angles, thereby generating a large set of conformations; and sampling of this set by geometric and energy criteria. Validation of conformer generators like OMEGA has often been undertaken by comparing computed conformer sets to experimental molecular conformations from crystallography, usually from the Protein Databank (PDB). Such an approach is fraught with difficulty due to the systematic problems with small molecule structures in the PDB. Methods are presented to identify a diverse set of small molecule structures from cocomplexes in the PDB that has maximal reliability. A challenging set of 197 high quality, carefully selected ligand structures from well-solved models was obtained using these methods. This set will provide a sound basis for comparison and validation of conformer generators in the future. Validation results from this set are compared to the results using structures of a set of druglike molecules extracted from the Cambridge Structural Database (CSD). OMEGA is found to perform very well in reproducing the crystallographic conformations from both these data sets using two complementary metrics of success.

  5. All-atom Molecular-level Computational Simulations of Planar Longitudinal Shockwave Interactions with Polyurea, Soda-lime Glass and Polyurea/Glass Interfaces

    Science.gov (United States)

    2014-01-01

    All-atom molecular-level computational simulations of planar longitudinal shockwave interactions with polyurea, soda- lime glass and polyurea/glass...of this paper is to study the mechanical response of polyurea, soda- lime glass (glass, for short), polyurea/glass/polyurea and glass/polyurea/glass...methods, the interaction of shockwaves with material boundaries. Keywords Polyurea, Material interface, Shockwaves, Soda- lime glass Paper type Research

  6. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations

    Indian Academy of Sciences (India)

    Surjit B Dixit; Mihaly Mezei; David L Beveridge

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute–solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interactmore strongly with watermolecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning’s counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 Å from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general

  7. The Obsessive Compulsive Cocaine Scale: assessment of factor structure, reliability, and validity.

    Science.gov (United States)

    Jardin, Bianca F; Larowe, Steven D; Hall, Brian J; Malcolm, Robert J

    2011-12-01

    The present study assessed the factor structure, reliability, test retest, convergent validity, and predictive validity of the Obsessive Compulsive Cocaine Scale (OCCS), a newly developed questionnaire adapted from the Obsessive Compulsive Drinking Scale (OCDS). The questionnaire was administered to 189 cocaine-dependent individuals participating in two medication treatment trials for cocaine dependence. Confirmatory factor analysis of this measure revealed that it primarily assesses two factors, obsessions and compulsions. In addition, the data provided strong support for the internal consistency, test-retest reliability, predictive validity, and convergent validity of this two-factor measure. Overall, the data provide support for the psychometric strength of a modified version of the OCDS specifically designed to assess obsessive and compulsive cocaine use among those with cocaine dependence.

  8. Factorial Structure and Validity of the Quantified Behavior Test Plus (Qb+©).

    Science.gov (United States)

    Hirsch, Oliver; Christiansen, Hanna

    2016-03-14

    This study investigates the factorial structure and validity of the Quantified Behavior Test Plus (Qb+©), a computerized test to objectively evaluate the three attention deficit/hyperactivity disorder core symptoms, hyperactivity, inattention, and impulsivity, independently. Confirmatory and exploratory factor analyses were conducted with an outpatient sample of 773 subjects ≥12 years old. In a second sample of 297 patients ≥16 years, a multitrait-multimethod analysis was performed to examine concurrent and discriminant validity. The discriminative power of the Qb+ was investigated using a general linear model and logistic regression analysis. The three factorial structure (Hyperactivity, Inattention, Impulsivity) was verified in the confirmatory factor analysis. Fit indices demonstrated a good model fit and factor loadings were almost all moderate to high. In the multitrait-multimethod analysis, the criterion for convergent validity was fulfilled. The discriminant validity of the Qb+ was partially supported. Significant but small gender and age effects were found. In the logistic regression analysis, omission errors and reaction time variability, belonging to the Inattention factor, were able to discriminate between subjects with and without attention deficit/hyperactivity disorder. The internal structure of the Qb+ was verified. Its validity was partially supported. Results regarding discriminative power were mixed.

  9. Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

    Science.gov (United States)

    van de Streek, Jacco; Neumann, Marcus A

    2010-10-01

    This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

  10. Assessing the diagnostic validity of a structured psychiatric interview in a first-admission hospital sample

    DEFF Research Database (Denmark)

    Frederiksen, Julie Elisabeth Nordgaard; Revsbech, Rasmus; Sæbye, Ditte

    2012-01-01

    The use of structured psychiatric interviews performed by non-clinicians is frequent for research purposes and is becoming increasingly common in clini-cal practice. The validity of such interviews has rarely been evaluated empirically. In this study of a sample of 100 diagnostically heterogeneous...

  11. The Reliability, Validity, and Usefulness of the Objective Structured Clinical Examination (OSCE) in Dental Education

    Science.gov (United States)

    Graham, Roseanna

    2010-01-01

    This study evaluated the reliability, validity, and educational usefulness of a comprehensive, multidisciplinary Objective Structured Clinical Examination (OSCE) in dental education. The OSCE was administered to dental students at the Columbia University College of Dental Medicine (CDM) before they entered clinical training. Participants in this…

  12. The Reliability, Validity, and Evaluation of the Objective Structured Clinical Examination in Podiatry (Chiropody).

    Science.gov (United States)

    Woodburn, Jim; Sutcliffe, Nick

    1996-01-01

    The Objective Structured Clinical Examination (OSCE), initially developed for undergraduate medical education, has been adapted for assessment of clinical skills in podiatry students. A 12-month pilot study found the test had relatively low levels of reliability, high construct and criterion validity, and good stability of performance over time.…

  13. Testing the structural and cross-cultural validity of the KIDSCREEN-27 quality of life questionnaire

    NARCIS (Netherlands)

    Robitail, S.; Ravens-Sieberer, U.; Simeoni, M.-C.; Rajmil, L.; Bruil, J.; Power, M.; Duer, W.; Cloetta, B.; Czemy, L.; Mazur, J.; Czimbalmos, A.; Tountas, Y.; Hagquist, C.; Kilroe, J.; Auquier, P.; Fuerth, K.; Czerny, L.; Erhart, M.; Nickel, J.; Kurth, B.-M.; Gosch, A.; Von Rüden, U.; Dimitrakakis, C.; Aszman, A.; Flannery, E.; Detmar, S.; Veripps, E.; Mierzejeswka, E.; Berra, S.; Tebé, C.; Herdman, M.; Alonso, J.; Abel, T.; Bisegger, C.; Farley, C.; Atherton, C.; Phillips, K.

    2007-01-01

    Objectives: The aim of this study is to assess the structural and cross-cultural validity of the KIDSCREEN-27 questionnaire. Methods: The 27-item version of the KIDSCREEN instrument was derived from a longer 52-item version and was administered to young people aged 8-18 years in 13 European countrie

  14. Implicit structural inversion of gravity data using linear programming, a validation study

    NARCIS (Netherlands)

    Zon, A.T. van; Roy Chowdhury, K.

    2010-01-01

    In this study, a regional scale gravity data set has been inverted to infer the structure (topography) of the top of the basement underlying sub-horizontal strata. We apply our method to this real data set for further proof of concept, validation and benchmarking against results from an earlier forw

  15. Validation of the Transient Structural Response of a Threaded Assembly: Phase I

    Energy Technology Data Exchange (ETDEWEB)

    Doebling, Scott W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hemez, Francois M. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Robertson, Amy N. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Maupin, Ryan D. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Schultze, John F. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cundy, Amanda L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Hylok, Jeff E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2004-04-01

    This report explores the application of model validation techniques in structural dynamics. The problem of interest is the propagation of an explosive-driven mechanical shock through a complex threaded joint. The study serves the purpose of assessing whether validating a large-size computational model is feasible, which unit experiments are required, and where the main sources of uncertainty reside. The results documented here are preliminary, and the analyses are exploratory in nature. The results obtained to date reveal several deficiencies of the analysis, to be rectified in future work.

  16. Development and Ground-Test Validation of Fiber Optic Sensor Attachment Techniques for Hot Structures Applications

    Science.gov (United States)

    Piazza, Anthony; Hudson, Larry D.; Richards, W. Lance

    2005-01-01

    Fiber Optic Strain Measurements: a) Successfully attached silica fiber optic sensors to both metallics and composites; b) Accomplished valid EFPI strain measurements to 1850 F; c) Successfully attached EFPI sensors to large scale hot-structures; and d) Attached and thermally validated FBG bond and epsilon(sub app). Future Development a) Improve characterization of sensors on C-C and C-SiC substrates; b) Apply application to other composites such as SiC-SiC; c) Assist development of interferometer based Sapphire sensor currently being conducted under a Phase II SBIR; and d) Complete combined thermal/mechanical testing of FBG on composite substrates in controlled laboratory environment.

  17. Contribution to the validation of thermal ratchetting prevision methods in metallic structures; Contribution a la validation des methodes de prevision du rochet thermique dans les structures metalliques

    Energy Technology Data Exchange (ETDEWEB)

    Rakotovelo, A.M

    1998-03-01

    This work concerns the steady state assessment in the metallic structures subjected to thermomechanical cyclic loadings in biaxial stress state. The effect of the short time mechanical overloads is also investigated. The first chapter is devoted to a bibliographic research concerning the behaviour of the materials and the structures in the cyclic plasticity. Some works relate to the experimental aspect as well as the numerical one for the steady state assessment of such structures are presented. The experimental part of the study is presented in the second chapter. The experimental device was carried out in order to prescribe tension and torsion forces combined with cyclic thermal loading. Some tests was then carried out, among these tests certain include some overloads in tension or torsion. The last chapter describes the numerical calculations using different models (linear isotropic hardening, linear kinematic hardening and elasto-viscoplastic Chaboche's model) and the application of some simplified methods for the ratchetting assessment in the structures. We have considered two categories of methods. The first one is based on an elastic analysis (Bree's diagram, 3 Sm rule, efficiency rule) and the second one combines elastic analysis and elastoplastic analysis of the first cycle (Gatt's and Taleb's methods). The results of this study have enabled: to validate in the biaxial stress state an expression which takes into account the effect of mechanical short time overloads; to test the performances of considered models to describe the evolution of the structure during the first cycle and to take into account the effect of short time overloads. Among the considered models, the elastoplastic Chaboche's model seems to be the most accurate to describe the structure's behaviour during the first cycles; to validate some simplified methods. Certain methods based only on elastic analysis (Bee's diagram and efficiency rule) seem not

  18. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

    Science.gov (United States)

    Wallace, Jason A; Shen, Jana K

    2012-11-14

    Recent development of constant pH molecular dynamics (CpHMD) methods has offered promise for adding pH-stat in molecular dynamics simulations. However, until now the working pH molecular dynamics (pHMD) implementations are dependent in part or whole on implicit-solvent models. Here we show that proper treatment of long-range electrostatics and maintaining charge neutrality of the system are critical for extending the continuous pHMD framework to the all-atom representation. The former is achieved here by adding forces to titration coordinates due to long-range electrostatics based on the generalized reaction field method, while the latter is made possible by a charge-leveling technique that couples proton titration with simultaneous ionization or neutralization of a co-ion in solution. We test the new method using the pH-replica-exchange CpHMD simulations of a series of aliphatic dicarboxylic acids with varying carbon chain length. The average absolute deviation from the experimental pK(a) values is merely 0.18 units. The results show that accounting for the forces due to extended electrostatics removes the large random noise in propagating titration coordinates, while maintaining charge neutrality of the system improves the accuracy in the calculated electrostatic interaction between ionizable sites. Thus, we believe that the way is paved for realizing pH-controlled all-atom molecular dynamics in the near future.

  19. ProTSAV: A protein tertiary structure analysis and validation server.

    Science.gov (United States)

    Singh, Ankita; Kaushik, Rahul; Mishra, Avinash; Shanker, Asheesh; Jayaram, B

    2016-01-01

    Quality assessment of predicted model structures of proteins is as important as the protein tertiary structure prediction. A highly efficient quality assessment of predicted model structures directs further research on function. Here we present a new server ProTSAV, capable of evaluating predicted model structures based on some popular online servers and standalone tools. ProTSAV furnishes the user with a single quality score in case of individual protein structure along with a graphical representation and ranking in case of multiple protein structure assessment. The server is validated on ~64,446 protein structures including experimental structures from RCSB and predicted model structures for CASP targets and from public decoy sets. ProTSAV succeeds in predicting quality of protein structures with a specificity of 100% and a sensitivity of 98% on experimentally solved structures and achieves a specificity of 88%and a sensitivity of 91% on predicted protein structures of CASP11 targets under 2Å.The server overcomes the limitations of any single server/method and is seen to be robust in helping in quality assessment. ProTSAV is freely available at http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp.

  20. Construct validity of the reporter-interpreter-manager-educator structure for assessing students' patient encounter skills

    DEFF Research Database (Denmark)

    Tolsgaard, Martin G.; Arendrup, Henrick; Lindhardt, Bjarne O.

    2012-01-01

    PURPOSE: The aim of this study, done in Denmark, was to explore the construct validity of a Reporter-Interpreter-Manager-Educator (RIME)-structured scoring format for assessing patient encounter skills. METHOD: The authors developed a RIME-structured scoring form and explored its construct validity...... (carried out during 2009-2010) was an observational study of patient encounter skills where clinician examiners used the scoring form in end-of-clerkship oral examinations of three consecutive cohorts of a total of 547 fourth-year medical students. RESULTS: In the experimental study, RIME scores showed...... in managing patient encounters when assessed according to an advanced criterion. However, clinician examiners may tacitly score the elements according to what can be expected at a certain level of student experience....

  1. SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

    Directory of Open Access Journals (Sweden)

    Parida Swarup K

    2012-08-01

    Full Text Available Abstract Background Single nucleotide polymorphism (SNP validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. Results Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%. Of these 325 (84.6% showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. Conclusions SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.

  2. Validation of a unique concept for a low-cost, lightweight space-deployable antenna structure

    Science.gov (United States)

    Freeland, R. E.; Bilyeu, G. D.; Veal, G. R.

    1993-01-01

    An experiment conducted in the framework of a NASA In-Space Technology Experiments Program based on a concept of inflatable deployable structures is described. The concept utilizes very low inflation pressure to maintain the required geometry on orbit and gravity-induced deflection of the structure precludes any meaningful ground-based demonstrations of functions performance. The experiment is aimed at validating and characterizing the mechanical functional performance of a 14-m-diameter inflatable deployable reflector antenna structure in the orbital operational environment. Results of the experiment are expected to significantly reduce the user risk associated with using large space-deployable antennas by demonstrating the functional performance of a concept that meets the criteria for low-cost, lightweight, and highly reliable space-deployable structures.

  3. Full-Scale Structural and NDI Validation Tests of Bonded Composite Doublers for Commercial Aircraft Applications

    Energy Technology Data Exchange (ETDEWEB)

    Roach, D.; Walkington, P.

    1999-02-01

    Composite doublers, or repair patches, provide an innovative repair technique which can enhance the way aircraft are maintained. Instead of riveting multiple steel or aluminum plates to facilitate an aircraft repair, it is possible to bond a single Boron-Epoxy composite doubler to the damaged structure. Most of the concerns surrounding composite doubler technology pertain to long-term survivability, especially in the presence of non-optimum installations, and the validation of appropriate inspection procedures. This report focuses on a series of full-scale structural and nondestructive inspection (NDI) tests that were conducted to investigate the performance of Boron-Epoxy composite doublers. Full-scale tests were conducted on fuselage panels cut from retired aircraft. These full-scale tests studied stress reductions, crack mitigation, and load transfer capabilities of composite doublers using simulated flight conditions of cabin pressure and axial stress. Also, structures which modeled key aspects of aircraft structure repairs were subjected to extreme tension, shear and bending loads to examine the composite laminate's resistance to disbond and delamination flaws. Several of the structures were loaded to failure in order to determine doubler design margins. Nondestructive inspections were conducted throughout the test series in order to validate appropriate techniques on actual aircraft structure. The test results showed that a properly designed and installed composite doubler is able to enhance fatigue life, transfer load away from damaged structure, and avoid the introduction of new stress risers (i.e. eliminate global reduction in the fatigue life of the structure). Comparisons with test data obtained prior to the doubler installation revealed that stresses in the parent material can be reduced 30%--60% through the use of the composite doubler. Tests to failure demonstrated that the bondline is able to transfer plastic strains into the doubler and that

  4. Valuing structured professional judgment: predictive validity, decision-making, and the clinical-actuarial conflict.

    Science.gov (United States)

    Falzer, Paul R

    2013-01-01

    Structured professional judgment (SPJ) has received considerable attention as an alternative to unstructured clinical judgment and actuarial assessment, and as a means of resolving their ongoing conflict. However, predictive validity studies have typically relied on receiver operating characteristic (ROC) analysis, the same technique commonly used to validate actuarial assessment tools. This paper presents SPJ as distinct from both unstructured clinical judgment and actuarial assessment. A key distinguishing feature of SPJ is the contribution of modifiable factors, either dynamic or protective, to summary risk ratings. With modifiable factors, the summary rating scheme serves as a prognostic model rather than a classification procedure. However, prognostic models require more extensive and thorough predictive validity testing than can be provided by ROC analysis. It is proposed that validation should include calibration and reclassification techniques, as well as additional measures of discrimination. Several techniques and measures are described and illustrated. The paper concludes by tracing the limitations of ROC analysis to its philosophical foundation and its origin as a statistical theory of decision-making. This foundation inhibits the performance of crucial tasks, such as determining the sufficiency of a risk assessment and examining the evidentiary value of statistical findings. The paper closes by noting a current effort to establish a viable and complementary relationship between SPJ and decision-making theory.

  5. Protein structure validation by generalized linear model root-mean-square deviation prediction.

    Science.gov (United States)

    Bagaria, Anurag; Jaravine, Victor; Huang, Yuanpeng J; Montelione, Gaetano T; Güntert, Peter

    2012-02-01

    Large-scale initiatives for obtaining spatial protein structures by experimental or computational means have accentuated the need for the critical assessment of protein structure determination and prediction methods. These include blind test projects such as the critical assessment of protein structure prediction (CASP) and the critical assessment of protein structure determination by nuclear magnetic resonance (CASD-NMR). An important aim is to establish structure validation criteria that can reliably assess the accuracy of a new protein structure. Various quality measures derived from the coordinates have been proposed. A universal structural quality assessment method should combine multiple individual scores in a meaningful way, which is challenging because of their different measurement units. Here, we present a method based on a generalized linear model (GLM) that combines diverse protein structure quality scores into a single quantity with intuitive meaning, namely the predicted coordinate root-mean-square deviation (RMSD) value between the present structure and the (unavailable) "true" structure (GLM-RMSD). For two sets of structural models from the CASD-NMR and CASP projects, this GLM-RMSD value was compared with the actual accuracy given by the RMSD value to the corresponding, experimentally determined reference structure from the Protein Data Bank (PDB). The correlation coefficients between actual (model vs. reference from PDB) and predicted (model vs. "true") heavy-atom RMSDs were 0.69 and 0.76, for the two datasets from CASD-NMR and CASP, respectively, which is considerably higher than those for the individual scores (-0.24 to 0.68). The GLM-RMSD can thus predict the accuracy of protein structures more reliably than individual coordinate-based quality scores.

  6. Solute and solvent dynamics in confined equal-sized aqueous environments of charged and neutral reverse micelles: a combined dynamic fluorescence and all-atom molecular dynamics simulation study.

    Science.gov (United States)

    Guchhait, Biswajit; Biswas, Ranjit; Ghorai, Pradip K

    2013-03-28

    Here a combined dynamic fluorescence and all-atom molecular dynamics simulation study of aqueous pool-size dependent solvation energy and rotational relaxations of a neutral dipolar solute, C153, trapped in AOT (charged) and IGPAL (neutral) reverse micelles (RMs) at 298 K, is described. RMs in simulations have been represented by a reduced model where SPC/E water molecules interact with a trapped C153 that possesses realistic charge distributions for both ground and excited states. In large aqueous pools, measured average solvation and rotation rates are smaller for the neutral RMs than those in charged ones. Interestingly, while the measured average solvation and rotation rates increase with pool size for the charged RMs, the average rotation rates for the neutral RMs exhibit a reverse dependence. Simulations have qualitatively reproduced this experimental trend and suggested interfacial location for the solute for all cases. The origin for the subnanosecond Stokes shift dynamics has been investigated and solute-interface interaction contribution quantified. Simulated layer-wise translational and rotational diffusions of water molecules re-examine the validity of the core-shell model and provide a resolution to a debate regarding the origin of the subnanosecond solvation component in dynamic Stokes shift measurements with aqueous RMs but not detected in ultrafast IR measurements.

  7. Development, Administration, and Structural Validity of a Brief, Computerized Neurocognitive Battery.

    Science.gov (United States)

    Moore, Tyler M; Gur, Ruben C; Thomas, Michael L; Brown, Gregory G; Nock, Matthew K; Savitt, Adam P; Keilp, John G; Heeringa, Steven; Ursano, Robert J; Stein, Murray B

    2017-01-01

    The Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS) is a research project aimed at identifying risk and protective factors for suicide and related mental health outcomes among Army Soldiers. The New Soldier Study component of Army STARRS included the assessment of a range of cognitive- and emotion-processing domains linked to brain systems related to suicidal behavior including posttraumatic stress disorder, mood disorders, substance use disorders, and impulsivity. We describe the design and application of the Army STARRS neurocognitive test battery to a sample of 56,824 soldiers. We investigate its structural and concurrent validity through factor analysis and correlation of scores with demographics. We conclude that, in addition to being composed of previously well-validated measures, the Army STARRS neurocognitive battery as a whole demonstrates good psychometric properties. Correlations of scores with age and sex differences mostly replicate previously published findings, highlighting moderate to large effect sizes even within this restricted age range. Factor structures of scores conform to theoretical expectations. This neurocognitive battery provides a brief, valid measurement of neurocognition that may be helpful in predicting mental health and military performance. These measures can be integrated with neuroimaging to offer a powerful tool for assessing neurocognition in Servicemembers.

  8. Construct Validity of the Social Provisions Scale: A Bifactor Exploratory Structural Equation Modeling Approach.

    Science.gov (United States)

    Perera, Harsha N

    2016-12-01

    Extant theory posits well-differentiated dimensions of perceived social support as measured using the Social Provisions Scale (SPS). However, evidence is inconsistent with this multidimensionality perspective, with SPS factor correlations near unity and higher between-factor than within-factor item correlations. This article reports on research investigating the internal structure, gender invariance, and predictive validity of SPS scores. The analyses are conducted in a novel bifactor exploratory structural equation modeling (ESEM) framework, which is designed to account for presumed psychometric multidimensionality in SPS items due to (a) their fallibility as pure indicators of the constructs they are purported to measure and (b) the coexistence of general and specific factors. Based on 376 item responses, evidence was obtained for a bifactor-ESEM representation of the SPS data. In addition, support was found for the invariance of item thresholds and the latent mean invariance of six of the seven SPS factors in the retained solution. Only mean levels of Social Integration were found to differ by gender, with men scoring higher than women. Finally, evidence was obtained for the predictive validity of SPS scores with respect to loneliness and psychological well-being. Quite apart from yielding evidence validating the SPS, this research demonstrates the utility of bifactor ESEM for psychological assessment.

  9. Validation and Factor Structure of the French-Language Version of the Emotional Appetite Questionnaire (EMAQ)

    Science.gov (United States)

    Bourdier, Léna; Lalanne, Christophe; Morvan, Yannick; Kern, Laurence; Romo, Lucia; Berthoz, Sylvie

    2017-01-01

    The concept of Emotional Eating (EE) is increasingly considered to be implicated in overeating and obesity, and in different subtypes of eating disorders. Among the self-report questionnaires assessing EE, the Emotional Appetite Questionnaire (EMAQ) includes recent advances in this area: it evaluates a broad range of emotions and situations both positive and negative, and the way they modulate food intake (decrease, stability, or increase). The main objective of our study was to further investigate the psychometric properties of the French version of the EMAQ in a large sample of students. Participants completed the EMAQ (n = 679), the DEBQ (Dutch Eating Behavior Questionnaire) (n = 75) and the CIDI-eating disorders screening (Composite International Diagnostic Interview) (n = 604). Factorial structure, reliability, and validity of the EMAQ were tested. Factorial analyses supported a two-factor (Positive and Negative) structure. The internal consistency indices were satisfactory and results suggest good test–retest reliability for the scale. Convergent and discriminant validity were confirmed from the significant correlations observed between the EMAQ scores and the DEBQ-EE subscale scores. Regarding associations with weight, whereas EMAQ negative scores were positively correlated with BMI, EMAQ positive scores were negatively correlated with BMI. Finally, EMAQ scores differed significantly depending on gender and risk for bulimia nervosa. This study supports the validity and the reliability of the EMAQ, which appears to be a promising instrument to better understand individual differences that could modulate food intake. PMID:28386243

  10. The Structure of Preschoolers' Emotion Knowledge: Model Equivalence and Validity Using a Structural Equation Modeling Approach

    Science.gov (United States)

    Bassett, Hideko Hamada; Denham, Susanne; Mincic, Melissa; Graling, Kelly

    2012-01-01

    Research Findings: A theory-based 2-factor structure of preschoolers' emotion knowledge (i.e., recognition of emotional expression and understanding of emotion-eliciting situations) was tested using confirmatory factor analysis. Compared to 1- and 3-factor models, the 2-factor model showed a better fit to the data. The model was found to be…

  11. The Revised Identity Style Inventory: Factor Structure and Validity in Italian Speaking Students

    Science.gov (United States)

    Monacis, Lucia; de Palo, Valeria; Sinatra, Maria; Berzonsky, Michael D.

    2016-01-01

    The purpose of this study was to evaluate the factor structure and convergent and discriminant validity of scores on an Italian translation of the Revised Identity Style Inventory (ISI-5) with samples of 237 adolescents (50 males, Mage = 18.04, SD = .86) and 268 university students (42 males, Mage = 22.71, SD = 3.70). Confirmatory Factor Analysis indicated that a three-factor solution provided a good fit, which was invariant across age and sex groups. The theoretically relationships between scores on the ISI and scores on measures of reasoning and identity processes, identity commitment, and social desirability were partially consistent, thus further studies are needed to give more evidence to the convergent and discriminant validity. PMID:27378980

  12. Ab initio prediction of the polymorphic structures of pyrazinamide: A validation study

    Directory of Open Access Journals (Sweden)

    David Stephen Arputhara

    2016-01-01

    Full Text Available A validation study to predict the possible stable polymorphs of Pyrazinamide within a low energy conformational region of the flexible torsion angle was made through a potential energy surface (PES scan by gas phase optimisation using the MP2/6-31G(d,p method. Hypothetical crystal structures with favourable packing density for each of the stable conformers generated from the PES scan were generated using a global search with a repulsion only potential field. The densest crystal structures with stable energy were analyzed with more accurate lattice energy minimisation via distributed multipole analysis using a repulsion-dispersion potential. The stability of the predicted crystal structures with similar close packing to the known experimental polymorphs of Pyrazinamide molecule was analyzed by inspecting their intermolecular short contacts. Studies to analyze the second derivative mechanical properties from the hessian matrix were carried out to emphasise the thermodynamic stability of predicted polymorphs of Pyrazinamide.

  13. Validation of the magnetic energy vs. helicity scaling in solar magnetic structures

    CERN Document Server

    Tziotziou, K; Georgoulis, M K; Archontis, V

    2014-01-01

    We assess the validity of the free magnetic energy - relative magnetic helicity diagram for solar magnetic structures. We used two different methods of calculating the free magnetic energy and the relative magnetic helicity budgets: a classical, volume-calculation nonlinear force-free (NLFF) method applied to finite coronal magnetic structures and a surface-calculation NLFF derivation that relies on a single photospheric or chromospheric vector magnetogram. Both methods were applied to two different data sets, namely synthetic active-region cases obtained by three-dimensional magneto-hydrodynamic (MHD) simulations and observed active-region cases, which include both eruptive and noneruptive magnetic structures. The derived energy--helicity diagram shows a consistent monotonic scaling between relative helicity and free energy with a scaling index 0.84$\\pm$0.05 for both data sets and calculation methods. It also confirms the segregation between noneruptive and eruptive active regions and the existence of thresh...

  14. Development and Validation of a Novel Bird Strike Resistant Composite Leading Edge Structure

    Science.gov (United States)

    Kermanidis, Th.; Labeas, G.; Sunaric, M.; Ubels, L.

    2005-11-01

    A novel design of a fibre-reinforced composite Leading Edge (LE) of a Horizontal Tail Plain (HTP) is proposed. The development and validation approach of the innovative composite LE structure are described. The main design goal is the satisfactory impact resistance of the novel composite LE in the case of bird strike. The design concept is based on the absorption of the major portion of the bird kinetic energy by the composite skins, in order to protect the ribs and the inner LE structure from damaging, thus preserving the tail plane functionality for safe landing. To this purpose, the LE skin is fabricated from specially designed composite panels, so called ‘tensor skin’ panels, comprising folded layers, which unfold under the impact load and increase the energy absorption capability of the LE. A numerical model simulating the bird strike process is developed and bird strike experimental testing is performed, in order to validate the proposed layout and prove the capability of the structure to successfully withstand the impact loading. The numerical modelling issues and the critical parameters of the simulation are discussed. The present work is part of the European Aeronautics Research Project, ‘Crashworthiness of aircraft for high velocity impact CRAHVI’ [1].

  15. Impact of Cross-Axis Structural Dynamics on Validation of Linear Models for Space Launch System

    Science.gov (United States)

    Pei, Jing; Derry, Stephen D.; Zhou Zhiqiang; Newsom, Jerry R.

    2014-01-01

    A feasibility study was performed to examine the advisability of incorporating a set of Programmed Test Inputs (PTIs) during the Space Launch System (SLS) vehicle flight. The intent of these inputs is to provide validation to the preflight models for control system stability margins, aerodynamics, and structural dynamics. During October 2009, Ares I-X program was successful in carrying out a series of PTI maneuvers which provided a significant amount of valuable data for post-flight analysis. The resulting data comparisons showed excellent agreement with the preflight linear models across the frequency spectrum of interest. However unlike Ares I-X, the structural dynamics associated with the SLS boost phase configuration are far more complex and highly coupled in all three axes. This presents a challenge when implementing this similar system identification technique to SLS. Preliminary simulation results show noticeable mismatches between PTI validation and analytical linear models in the frequency range of the structural dynamics. An alternate approach was examined which demonstrates the potential for better overall characterization of the system frequency response as well as robustness of the control design.

  16. Prediction of vibration characteristics in beam structure using sub-scale modeling with experimental validation

    Science.gov (United States)

    Zai, Behzad Ahmed; Sami, Saad; Khan, M. Amir; Ahmad, Furqan; Park, Myung Kyun

    2015-09-01

    Geometric or sub-scale modeling techniques are used for the evaluation of large and complex dynamic structures to ensure accurate reproduction of load path and thus leading to true dynamic characteristics of such structures. The sub-scale modeling technique is very effective in the prediction of vibration characteristics of original large structure when the experimental testing is not feasible due to the absence of a large testing facility. Previous researches were more focused on free and harmonic vibration case with little or no consideration for readily encountered random vibration. A sub-scale modeling technique is proposed for estimating the vibration characteristics of any large scale structure such as Launch vehicles, Mega structures, etc., under various vibration load cases by utilizing precise scaled-down model of that dynamic structure. In order to establish an analytical correlation between the original structure and its scaled models, different scale models of isotropic cantilever beam are selected and analyzed under various vibration conditions( i.e. free, harmonic and random) using finite element package ANSYS. The developed correlations are also validated through experimental testing. The prediction made from the vibratory response of the scaled-down beam through the established sets of correlation are found similar to the response measured from the testing of original beam structure. The established correlations are equally applicable in the prediction of dynamic characteristics of any complex structure through its scaled-down models. This paper presents modified sub-scale modeling technique that enables accurate prediction of vibration characteristics of large and complex structure under not only sinusoidal but also for random vibrations.

  17. Synthesis, crystal structure and charge-distribution validation of β-Na4Cu(MoO43 adopting the alluadite structure-type

    Directory of Open Access Journals (Sweden)

    Wassim Dridi

    2016-08-01

    Full Text Available Single crystals of a new variety of tetrasodium copper(II tris[molybdate(VI], Na4Cu(MoO43, have been synthesized by solid-state reactions and characterized by single-crystal X-ray diffraction. This alluaudite structure-type is characterized by the presence of infinite layers of composition (Cu/Na2Mo3O14 parallel to the (100 plane, which are linked by MoO4 tetrahedra, forming a three-dimensional framework containing two types of hexagonal channels in which Na+ cations reside. The Cu2+ and Na2+ cations are located at the same general site with occupancies of 0.5. All atoms are on general positions except for one Mo, two Na (site symmetry 2 and another Na (site symmetry -1 atom. One O atom is split into two separate positions with occupancies of 0.5. The title compound is isotypic with Na5Sc(MoO44 and Na3In2As3O12. The structure model is supported by bond-valence-sum (BVS and charge-distribution CHARDI methods. β-Na4Cu(MoO43 is compared and discussed with the K4Cu(MoO43 and α-Na4Cu(MoO43 structures.

  18. Assessing the diagnostic validity of a structured psychiatric interview in a first-admission hospital sample

    DEFF Research Database (Denmark)

    Frederiksen, Julie Elisabeth Nordgaard; Revsbech, Rasmus; Sæbye, Ditte

    2012-01-01

    , first-admitted inpatients, the results of an assessment with the Structured Clinical Interview for DSM-IV (SCID), yielding a DSM-IV diagnosis and performed by a trained non-clinician, were compared with a consensus lifetime best diagnostic estimate (DSM-IV) by two experienced research clinicians, based...... performed by non-clinicians are not recommendable for clinical work and should only be used in research with certain precautions. It is suggested that a revival of systematic theoretical and practical training in psychopathology is an obvious way forward in order to improve the validity and therapeutic...

  19. The reliability, validity, and usefulness of the Objective Structured Clinical Examination (OSCE) in dental education

    Science.gov (United States)

    Graham, Roseanna

    This study evaluated the reliability, validity, and educational usefulness of a comprehensive, multidisciplinary Objective Structured Clinical Examination (OSCE) in dental education. The OSCE was administered to dental students at the Columbia University College of Dental Medicine (CDM) before they entered clinical training. Participants in this study included CDM's class of 2010 which consisted of 78 students. The overall reliability of the examination was measured via calculation of Cronbach's alpha. Content validity was examined through evaluation of the OSCE by three experienced clinical faculty members. Predictive validity was evaluated by correlating student grades on the OSCE to future clinical performance as measured by number of clinical points achieved during the third year of training. Student perceptions regarding the educational usefulness of the examination were evaluated through a 12-question Liken-type survey and focus group interviews analyzed using a phenomenological approach. Findings of the study indicated the OSCE was a highly reliable examination (alpha=0.86) with high content validity and a moderately high correlation to future clinical performance (r=.614, p<.0001). Overall, student perceptions of the educational usefulness of the OSCE were positive as based on their responses to a 5-point Likert scale (1=strongly disagree and 5=strongly agree). They reported that the exam required the ability to think critically and problem-solve (4.0 +/- 0.85), assessed clinically relevant skills (4.59 +/- 0.69), helped identify clinical weaknesses (4.16 +/- 0.90), and was a learning experience (4.58 +/- 0.84). Findings from the qualitative portion of the study identified four main themes including the student perception that the OSCE is a unique assessment experience that required integration and application of knowledge. Recommendations for the use of the OSCE to improve clinical teaching and the implications of this study relating to the expanded use of

  20. Validity boundary of orbital-free molecular dynamics method corresponding to thermal ionization of shell structure

    Science.gov (United States)

    Gao, Chang; Zhang, Shen; Kang, Wei; Wang, Cong; Zhang, Ping; He, X. T.

    2016-11-01

    With 6LiD as an example, we show that the applicable region of the orbital-free molecular dynamics (OFMD) method in a large temperature range is determined by the thermal ionization process of bound electrons in shell structures. The validity boundary of the OFMD method is defined roughly by the balance point of the average thermal energy of an electron and the ionization energy of the lowest localized electronic state. This theoretical proposition is based on the observation that the deviation of the OFMD method originates from its less accurate description to the charge density in partially ionized shells, as compared with the results of the extended first-principles molecular dynamics method, which well reproduces the charge density of shell structures.

  1. The Skin Picking Impact Scale: Factor structure, validity and development of a short version.

    Science.gov (United States)

    Snorrason, Ivar; Olafsson, Ragnar P; Flessner, Christopher A; Keuthen, Nancy J; Franklin, Martin E; Woods, Douglas W

    2013-08-01

    In the present study, we examined the psychometric properties of the Skin Picking Impact Scale (SPIS; Keuthen, Deckersbach, Wilhelm et al., 2001), a 10 item self-report questionnaire designed to assess the psychosocial impact of skin picking disorder (SPD). Participants were 650 individuals who met criteria for SPD in an online survey. Exploratory and confirmatory factor analyses demonstrated a unitary factor structure with high internal consistency (α = 0.94). Consequently, we constructed an abbreviated 4-item version that retained good internal consistency (α = 0.87) and a robust factor structure. Both the short and the full versions demonstrated discriminant and convergent/concurrent validity. In conclusion, the findings indicate that both versions are psychometrically sound measures of SPD related psychosocial impact; however, some potential limitations of the full scale are discussed.

  2. Out-of-sample validation for structured expert judgment of Asian carp establishment in Lake Erie.

    Science.gov (United States)

    Cooke, Roger M; Wittmann, Marion E; Lodge, David M; Rothlisberger, John D; Rutherford, Edward S; Zhang, Hongyan; Mason, Doran M

    2014-10-01

    Structured expert judgment (SEJ) is used to quantify the uncertainty of nonindigenous fish (bighead carp [Hypophthalmichthys nobilis] and silver carp [H. molitrix]) establishment in Lake Erie. The classical model for structured expert judgment model is applied. Forming a weighted combination (called a decision maker) of experts' distributions, with weights derived from performance on a set of calibration variables from the experts' field, exhibits greater statistical accuracy and greater informativeness than simple averaging with equal weights. New methods of cross validation are applied and suggest that performance characteristics relative to equal weighting could be predicted with a small number (1-2) of calibration variables. The performance-based decision maker is somewhat degraded on out-of-sample prediction, but remained superior to the equal weight decision maker in terms of statistical accuracy and informativeness.

  3. Validation of an immersed thick boundary method for simulating fluid-structure interactions of deformable membranes

    Science.gov (United States)

    Sigüenza, J.; Mendez, S.; Ambard, D.; Dubois, F.; Jourdan, F.; Mozul, R.; Nicoud, F.

    2016-10-01

    This paper constitutes an extension of the work of Mendez et al. (2014) [36], for three-dimensional simulations of deformable membranes under flow. An immersed thick boundary method is used, combining the immersed boundary method with a three-dimensional modeling of the structural part. The immersed boundary method is adapted to unstructured grids for the fluid resolution, using the reproducing kernel particle method. An unstructured finite-volume flow solver for the incompressible Navier-Stokes equations is coupled with a finite-element solver for the structure. The validation process relying on a number of test cases proves the efficiency of the method, and its robustness is illustrated when computing the dynamics of a tri-leaflet aortic valve. The proposed immersed thick boundary method is able to tackle applications involving both thin and thick membranes/closed and open membranes, in significantly high Reynolds number flows and highly complex geometries.

  4. Creating a Test Validated Structural Dynamic Finite Element Model of the X-56A Aircraft

    Science.gov (United States)

    Pak, Chan-Gi; Truong, Samson

    2014-01-01

    Small modeling errors in the finite element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of the Multi Utility Technology Test-bed, X-56A aircraft, is the flight demonstration of active flutter suppression, and therefore in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of the X-56A aircraft. The ground vibration test-validated structural dynamic finite element model of the X-56A aircraft is created in this study. The structural dynamic finite element model of the X-56A aircraft is improved using a model tuning tool. In this study, two different weight configurations of the X-56A aircraft have been improved in a single optimization run. Frequency and the cross-orthogonality (mode shape) matrix were the primary focus for improvement, while other properties such as center of gravity location, total weight, and offdiagonal terms of the mass orthogonality matrix were used as constraints. The end result was a more improved and desirable structural dynamic finite element model configuration for the X-56A aircraft. Improved frequencies and mode shapes in this study increased average flutter speeds of the X-56A aircraft by 7.6% compared to the baseline model.

  5. Creating a Test-Validated Finite-Element Model of the X-56A Aircraft Structure

    Science.gov (United States)

    Pak, Chan-Gi; Truong, Samson

    2014-01-01

    Small modeling errors in a finite-element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of the X-56A Multi-Utility Technology Testbed aircraft is the flight demonstration of active flutter suppression and, therefore, in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of the X-56A aircraft. The ground-vibration test-validated structural dynamic finite-element model of the X-56A aircraft is created in this study. The structural dynamic finite-element model of the X-56A aircraft is improved using a model-tuning tool. In this study, two different weight configurations of the X-56A aircraft have been improved in a single optimization run. Frequency and the cross-orthogonality (mode shape) matrix were the primary focus for improvement, whereas other properties such as c.g. location, total weight, and off-diagonal terms of the mass orthogonality matrix were used as constraints. The end result was an improved structural dynamic finite-element model configuration for the X-56A aircraft. Improved frequencies and mode shapes in this study increased average flutter speeds of the X-56A aircraft by 7.6% compared to the baseline model.

  6. Validation of a three-dimensional facial scanning system based on structured light techniques.

    Science.gov (United States)

    Ma, Lili; Xu, Tianmin; Lin, Jiuxiang

    2009-06-01

    The aim of this study was to validate a newly developed three-dimensional (3D) structured light scanning system in recording the facial morphology. The validation was performed in three aspects including accuracy, precision and reliability. The accuracy and precision were investigated using a plaster model with 19 marked landmarks. The accuracy was determined by comparing the coordinates from the 3D images and from the coordinates measure machine (CMM). The precision was quantified through the repeated landmarks location on 3D images. The reliability was investigated in 10 adult volunteers. Each was scanned five times in 3 weeks. The 3D images acquired at different times were compared with each other to measure the reliability. We found that the accuracy was 0.93 mm, the precision was 0.79 mm, the reliability was 0.2mm. These findings suggested that the structured light scanning system was accurate, precise and reliable to record the facial morphology for both clinic and research purposes.

  7. The tilt-dependent potential of mean force of a pair of DNA oligomers from all-atom molecular dynamics simulations

    Science.gov (United States)

    Cortini, Ruggero; Cheng, Xiaolin; Smith, Jeremy C.

    2017-03-01

    Electrostatic interactions between DNA molecules have been extensively studied experimentally and theoretically, but several aspects (e.g. its role in determining the pitch of the cholesteric DNA phase) still remain unclear. Here, we performed large-scale all-atom molecular dynamics simulations in explicit water and 150 mM sodium chloride, to reconstruct the potential of mean force (PMF) of two DNA oligomers 24 base pairs long as a function of their interaxial angle and intermolecular distance. We find that the potential of mean force is dominated by total DNA charge, and not by the helical geometry of its charged groups. The theory of homogeneously charged cylinders fits well all our simulation data, and the fit yields the optimal value of the total compensated charge on DNA to  ≈65% of its total fixed charge (arising from the phosphorous atoms), close to the value expected from Manning’s theory of ion condensation. The PMF calculated from our simulations does not show a significant dependence on the handedness of the angle between the two DNA molecules, or its size is on the order of 1{{k}\\text{B}}T . Thermal noise for molecules of the studied length seems to mask the effect of detailed helical charge patterns of DNA. The fact that in monovalent salt the effective interaction between two DNA molecules is independent on the handedness of the tilt may suggest that alternative mechanisms are required to understand the cholesteric phase of DNA.

  8. $C_6$ coefficients and dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table

    CERN Document Server

    Gould, Tim

    2016-01-01

    Using time-dependent density functional theory (tdDFT) with exchange kernels we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ns in rows 1-6 of the periodic table. These are then integrated over frequency to produce $C_6$ coefficients. Results are presented under different models: straight tdDFT calculations using two different kernels, "benchmark" tdDFT calculations corrected by more accurate quantum chemical and experimental data, and "benchmark" tdDFT with frozen orbital anions. Parametrisations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, $C_{6,XY}\\propto [\\alpha_X(0)\\alpha_Y(0)]^{0.73}$ is found between $C_6$ coefficients and static polarizabilities $\\alpha(0)$. The relationship $C_{6,XY}=2C_{6,X}C_{6,Y}/[\\alpha_X/\\alpha_YC_{6,Y}+\\alpha_Y/\\alpha_XC_{6,X}]$ is tested and found to work well ($30$\\% errors) in a small fraction of cases.

  9. Effects of water models on binding affinity: evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase.

    Science.gov (United States)

    Nguyen, Trang Truc; Viet, Man Hoang; Li, Mai Suan

    2014-01-01

    The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding pocket in CHARMM. However, for three remaining force fields ΔG(bind) decays with increase of water density. SPC/E provides the lowest binding free energy for any force field, while the water effect is the most pronounced in CHARMM. In agreement with the popular GROMACS recommendation, the binding score obtained by combinations of AMBER-TIP3P, OPLS-TIP4P, and GROMOS-SPC is the most relevant to the experiments. For wild-type neuraminidase we have found that SPC is more suitable for CHARMM than TIP3P recommended by GROMACS for studying ligand binding. However, our study for three of its mutants reveals that TIP3P is presumably the best choice for CHARMM.

  10. C6 Coefficients and Dipole Polarizabilities for All Atoms and Many Ions in Rows 1-6 of the Periodic Table.

    Science.gov (United States)

    Gould, Tim; Bučko, Tomáš

    2016-08-09

    Using time-dependent density functional theory (TDDFT) with exchange kernels, we calculate and test imaginary frequency-dependent dipole polarizabilities for all atoms and many ions in rows 1-6 of the periodic table. These are then integrated over frequency to produce C6 coefficients. Results are presented under different models: straight TDDFT calculations using two different kernels; "benchmark" TDDFT calculations corrected by more accurate quantum chemical and experimental data; and "benchmark" TDDFT with frozen orbital anions. Parametrizations are presented for 411+ atoms and ions, allowing results to be easily used by other researchers. A curious relationship, C6,XY ∝ [αX(0)αY(0)](0.73), is found between C6 coefficients and static polarizabilities α(0). The relationship C6,XY = 2C6,XC6,Y/[(αX/αY)C6,Y + (αY/αX)C6,X] is tested and found to work well (30% errors) in a small fraction of cases.

  11. Development and preliminary validation of the spondyloarthritis research consortium of Canada magnetic resonance imaging sacroiliac joint structural score

    DEFF Research Database (Denmark)

    Maksymowych, Walter P; Wichuk, Stephanie; Chiowchanwisawakit, Praveena

    2015-01-01

    OBJECTIVE: There is an unmet need for reliable assessment of structural progression in the sacroiliac joints (SIJ) of patients with spondyloarthritis (SpA), but radiography is unreliable and lacks responsiveness. We aimed to develop and validate a new scoring method for structural lesions based...... on magnetic resonance imaging (MRI), the Spondyloarthritis Research Consortium of Canada (SPARCC) SIJ Structural Score (SSS). METHODS: The SSS method for assessment of structural lesions is based on T1-weighted spin echo MRI, validated lesion definitions, slice selection according to well-defined anatomical...

  12. Application of stereology for two-phase flow structure validation in fluidized bed reactors

    Directory of Open Access Journals (Sweden)

    Anweiler Stanisław

    2016-01-01

    Full Text Available Paper describes a novel method for two-phase gas-solid flow structure validation in fluidized bed reactors. Investigation is based on application of stereology techniques. This is an innovative approach in the field of fluidization phenomena research. Study is focused on the analysis of flow structure images, obtained with high-speed visualization of the fluidization process. Fluidization is conducted in transparent narrow channel, where plastic balls are fluidized by air. Applied stereological analysis is grounded on the linear method and on the method of random and directed secants. This enables 2-dimensional image measurement and 3-dimensional stereological extrapolation. The major result is that for each two-phase gas-solid flow structure a set of stereological parameters exists. This enables quantification of the process. It has been found that the observation of inter-relation of all stereological parameters, during the changing of the flow structure, can be used for system control. The basic conclusion is that knowledge about the character of the changes may be used for constant process adjustment for various two phase systems such as gas-solid or gas-liquid.

  13. Objective Structured Clinical Examinations Provide Valid Clinical Skills Assessment in Emergency Medicine Education

    Directory of Open Access Journals (Sweden)

    Wallenstein, Joshua

    2014-12-01

    Full Text Available Introduction: Evaluation of emergency medicine (EM learners based on observed performance in the emergency department (ED is limited by factors such as reproducibility and patient safety. EM educators depend on standardized and reproducible assessments such as the objective structured clinical examination (OSCE. The validity of the OSCE as an evaluation tool in EM education has not been previously studied. The objective was to assess the validity of a novel management-focused OSCE as an evaluation instrument in EM education through demonstration of performance correlation with established assessment methods and case item analysis. Methods: We conducted a prospective cohort study of fourth-year medical students enrolled in a required EM clerkship. Students enrolled in the clerkship completed a five-station EM OSCE. We used Pearson’s coefficient to correlate OSCE performance with performance in the ED based on completed faculty evaluations. Indices of difficulty and discrimination were computed for each scoring item. Results: We found a moderate and statistically-significant correlation between OSCE score and ED performance score [r(239 =0.40, p<0.001]. Of the 34 OSCE testing items the mean index of difficulty was 63.0 (SD =23.0 and the mean index of discrimination was 0.52 (SD =0.21. Conclusion: Student performance on the OSCE correlated with their observed performance in the ED, and indices of difficulty and differentiation demonstrated alignment with published best-practice testing standards. This evidence, along with other attributes of the OSCE, attest to its validity. Our OSCE can be further improved by modifying testing items that performed poorly and by examining and maximizing the inter-rater reliability of our evaluation instrument. [West J Emerg Med. 2015;16(1:121–126.

  14. Psychometrics and life history strategy: the structure and validity of the High K Strategy Scale.

    Science.gov (United States)

    Copping, Lee T; Campbell, Anne; Muncer, Steven

    2014-03-22

    In this paper, we critically review the conceptualization and implementation of psychological measures of life history strategy associated with Differential K theory. The High K Strategy Scale (HKSS: Giosan, 2006) was distributed to a large British sample (n = 809) with the aim of assessing its factor structure and construct validity in relation to theoretically relevant life history variables: age of puberty, age of first sexual encounter, and number of sexual partners. Exploratory and confirmatory factor analyses indicated that the HKSS in its current form did not show an adequate statistical fit to the data. Modifications to improve fit indicated four correlated factors (personal capital, environmental stability, environmental security, and social capital). Later puberty in women was positively associated with measures of the environment and personal capital. Among men, contrary to Differential K predictions but in line with female mate preferences, earlier sexual debut and more sexual partners were positively associated with more favorable environments and higher personal and social capital. We raise concerns about the use of psychometric indicators of lifestyle and personality as proxies for life history strategy when they have not been validated against objective measures derived from contemporary life history theory and when their status as causes, mediators, or correlates has not been investigated.

  15. Structure and Validity of Affect Knowledge Test (AKT) in a Sample of Italian Preschoolers.

    Science.gov (United States)

    Sette, Stefania; Bassett, Hideko H; Baumgartner, Emma; Denham, Susanne A

    2015-01-01

    The authors' main goals were to examine whether the Affect Knowledge Test's (AKT) factor structure would be represented by a two-factor model (i.e., emotion recognition and situation knowledge) or by a one-factor model in Italian preschoolers (N = 164; M = 4.24 years, SD = 1.09 years). The concurrent validity of the AKT was further examined using measures of social competence. The findings replicated a model of emotion knowledge, with emotion recognition and situation knowledge as distinct but interrelated factors. Gender and age differences showed that older children and girls displayed higher scores in situation knowledge than younger children and boys. Additionally, our validity model of the AKT demonstrated that emotion recognition preceded situation knowledge, which in turn was positively related to children's sensitive or cooperative behaviors and negatively associated with anxious or withdrawn behaviors. Our results suggest that the use of the AKT may help the teachers to evaluate children's level on emotional knowledge that in turn might impact on children's positive social relationships within classroom in Italy.

  16. Validation of Flight Control Law Based on LFT and Structured Singular Value

    Institute of Scientific and Technical Information of China (English)

    ZHOU Xi; LIU Lin; CHEN Zong-ji; DUAN Hai-bin

    2007-01-01

    The main goal of flight clearance is to use the structured singular value (μ) analysis of the flight control system when some parameters in the system vary in a certain range. As theμ-analysis can only be done on a linear fractional transformation (LFT) model, the first step of flight clearance is to generate the LFT model of the flight control system. In this paper, based on the introduction of basic theory of LFT and μ-analysis, an X-fighter is chosen as an example to utilize the proposed methods. In order to realize the flight clearance process automatically, a novel software package based on MATLAB programming language is developed. The results of simulation experiments validate the feasibility and effectiveness of the novel methods proposed in this paper.

  17. The structure and validity of directional measures of appearance social comparison among emerging adults in China.

    Science.gov (United States)

    Liao, Jun; Jackson, Todd; Chen, Hong

    2014-09-01

    We evaluated the structure and validity of the Upward Appearance Comparison Scale (UPACS) and Downward Appearance Comparison Scale (DACS) (O'Brien et al., 2009) in Chinese samples. In Study 1, principal component analysis on an initial sample (427 women, 123 men) and confirmatory factor analysis on another sample (447 women, 121 men) found that a 15-item, two component model had the best overall fit. Derived components had moderate correlations with most conceptually related measures and low correlations with less conceptually related indices. Study 2 participants (310 women, 201 men) completed the UPACS and DACS as well as measures of disordered eating, fatness concern, and negative affect; they were re-assessed one year later. Baseline UPACS scores predicted changes in disordered eating for women and fatness concerns for men, independent of initial disturbances, but DACS responses were not related to outcomes. Findings highlighted the potential utility of derived UPACS and DACS within a Chinese context.

  18. Validation of a computer based objective structured clinical examination in the assessment of undergraduate dermatology courses

    Directory of Open Access Journals (Sweden)

    Feroze Kaliyadan

    2014-01-01

    Full Text Available Many teaching centers have now adopted objective structured clinical examination (OSCE as an assessment method for undergraduate dermatology courses. A modification of the standard OSCE in dermatology is computer based or electronic OSCE (eOSCE. We attempted to validate the use of a computer-based OSCE in dermatology in a group of fifth year medical students. The scores of the students in the computer-based OSCE showed a strong positive correlation with the scores on the clinical presentation (Pearson′s co-efficient - 0.923, P value <0.000, significant at the 0.01 level and a good correlation with overall scores of the student (Pearson′s co-efficient - 0.728, P value <0.000, significant at the 0.01 level, indicating that this is a reliable method for assessment in dermatology. Generally, the students′ feedback regarding the methods was positive.

  19. Structural validity of the Pittsburgh Sleep Quality Index in Chinese undergraduate students: A confirmatory factor analysis

    Directory of Open Access Journals (Sweden)

    Suran Guo

    2016-08-01

    Full Text Available The purpose of this study was to examine the structural validity of the Pittsburgh Sleep Quality Index (PSQI in Chinese undergraduate students. A cross-sectional questionnaire survey with 631 Chinese undergraduate students was conducted, and the questionnaire package included a measure of demographic characteristics, Pittsburgh Sleep Quality Index (PSQI, Chinese editions of Center for Epidemiologic Studies-Depression, State- Trait Anxiety Inventory, Rumination Response Scale, and Perceived Social Support Scale. Results showed that the item use of sleep medicine was not suitable for use with this population, that a two-factor model provided the best fit to the data as assessed through confirmatory factor analysis, and that other indices were consistently correlated with the sleep quality but not the sleep efficiency factor.

  20. [Voice-related quality of life: structure, validity and factors of the German questionnaire].

    Science.gov (United States)

    Schwanfelder, Carla; Eysholdt, Ulrich; Rosanowski, Frank; Graessel, Elmar

    2008-01-01

    In this study, structure and validity of the German version of the Voice-Related Quality of Life (V-RQOL) questionnaire and its correlation to age, gender, and type of dysphonia (organic vs. functional) were assessed. Correlations of the V-RQOL result on the one hand and emotional and physical complaints on the other hand were investigated. Data were collected in 62 adult patients with dysphonia of benign origin and the following results were found: the German version of the V-RQOL questionnaire describes voice-related quality of life in one single value. Age, gender and type of dysphonia do not influence its result. Dysphonic patients present with an increased number of emotional and physical complaints when compared with normative values derived from the literature. However, not all of these complaints correlate with voice-related quality of life at a significant level.

  1. Investigating the validity of a structured interview protocol for assessing the preferences of children with autism spectrum disorders

    NARCIS (Netherlands)

    Verschuur, R.; Didden, H.C.M.; Meer, L. van der; Achmadi, D.; Kagohara, D.; Green, V.A.; Lang, R.; Lancioni, G.E.

    2011-01-01

    PURPOSE: To investigate the congruent validity of a structured interview protocol for assessing the preferences of seven children with autism spectrum disorder (ASD). METHOD: Using the structured interview protocol described by Green et al., parents were asked to provide a rank ordering of their chi

  2. The Structural Validity of the Perceived Traits of the "Ideal Student" Multi-Faceted Theory among Education Students

    Science.gov (United States)

    Maslovaty, Nava; Cohen, Arie; Furman, Sari

    2008-01-01

    The article presents a multi-faceted theory of "ideal high school student" traits. The trait system, as defined by several theories, is a translation of the teachers' belief system into educational objectives. The study focused on Bloom's taxonomies and the structural validity of its principles, using Similarity Structure Analysis. Aware of the…

  3. Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

    Science.gov (United States)

    Orellana, Laura; Yoluk, Ozge; Carrillo, Oliver; Orozco, Modesto; Lindahl, Erik

    2016-08-01

    Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.

  4. Hydrologic validation of a structure-from-motion DEM derived from low-altitude UAV imagery

    Science.gov (United States)

    Steiner, Florian; Marzolff, Irene; d'Oleire-Oltmanns, Sebastian

    2015-04-01

    The increasing ease of use of current Unmanned Aerial Vehicles (UAVs) and 3D image processing software has spurred the number of applications relying on high-resolution topographic datasets. Of particular significance in this field is "structure from motion" (SfM), a photogrammetric technique used to generate low-cost digital elevation models (DEMs) for erosion budgeting, measuring of glaciers/lava-flows, archaeological applications and others. It was originally designed to generate 3D-models of buildings, based on unordered collections of images and has become increasingly common in geoscience applications during the last few years. Several studies on the accuracy of this technique already exist, in which the SfM data is mostly compared with Lidar-generated terrain data. The results are mainly positive, indicating that the technique is suitable for such applications. This work aims at validating very high resolution SfM DEMs with a different approach: Not the original elevation data is validated, but data on terrain-related hydrological and geomorphometric parameters derived from the DEM. The study site chosen for this analysis is an abandoned agricultural field near the city of Taroudant, in the semi-arid southern part of Morocco. The site is characterized by aggressive rill and gully erosion and is - apart from sparsely scattered shrub cover - mainly featureless. An area of 5.7 ha, equipped with 30 high-precision ground control points (GCPs), was covered with an unmanned aerial vehicle (UAV) in two different heights (85 and 170 m). A selection of 160 images was used to generate several high-resolution DEMs (2 and 5 cm resolution) of the area using the fully automated SfM software AGISOFT Photoscan. For comparison purposes, a conventional photogrammetry-based workflow using the Leica Photogrammetry Suite was used to generate a DEM with a resolution of 5 cm (LPS DEM). The evaluation is done by comparison of the SfM DEM with the derived orthoimages and the LPS DEM

  5. [Factor structure validity of the social capital scale used at baseline in the ELSA-Brasil study].

    Science.gov (United States)

    Souto, Ester Paiva; Vasconcelos, Ana Glória Godoi; Chor, Dora; Reichenheim, Michael E; Griep, Rosane Härter

    2016-07-21

    This study aims to analyze the factor structure of the Brazilian version of the Resource Generator (RG) scale, using baseline data from the Brazilian Longitudinal Health Study in Adults (ELSA-Brasil). Cross-validation was performed in three random subsamples. Exploratory factor analysis using exploratory structural equation models was conducted in the first two subsamples to diagnose the factor structure, and confirmatory factor analysis was used in the third to corroborate the model defined by the exploratory analyses. Based on the 31 initial items, the model with the best fit included 25 items distributed across three dimensions. They all presented satisfactory convergent validity (values greater than 0.50 for the extracted variance) and precision (values greater than 0.70 for compound reliability). All factor correlations were below 0.85, indicating full discriminative factor validity. The RG scale presents acceptable psychometric properties and can be used in populations with similar characteristics.

  6. Validated linear dynamic model of electrically-shunted magnetostrictive transducers with application to structural vibration control

    Science.gov (United States)

    Scheidler, Justin J.; Asnani, Vivake M.

    2017-03-01

    This paper presents a linear model of the fully-coupled electromechanical behavior of a generally-shunted magnetostrictive transducer. The impedance and admittance representations of the model are reported. The model is used to derive the effect of the shunt’s electrical impedance on the storage modulus and loss factor of the transducer without neglecting the inherent resistance of the transducer’s coil. The expressions are normalized and then shown to also represent generally-shunted piezoelectric materials that have a finite leakage resistance. The generalized expressions are simplified for three shunts: resistive, series resistive-capacitive, and inductive, which are considered for shunt damping, resonant shunt damping, and stiffness tuning, respectively. For each shunt, the storage modulus and loss factor are plotted for a wide range of the normalized parameters. Then, important trends and their impact on different applications are discussed. An experimental validation of the transducer model is presented for the case of resistive and resonant shunts. The model closely predicts the measured response for a variety of operating conditions. This paper also introduces a model for the dynamic compliance of a vibrating structure that is coupled to a magnetostrictive transducer for shunt damping and resonant shunt damping applications. This compliance is normalized and then shown to be analogous to that of a structure that is coupled to a piezoelectric material. The derived analogies allow for the observations and equations in the existing literature on structural vibration control using shunted piezoelectric materials to be directly applied to the case of shunted magnetostrictive transducers.

  7. Reliability and Validity of Objective Structured Clinical Examination for Residents of Obstetrics and Gynecology at Kermanshah University of Medical Sciences

    Directory of Open Access Journals (Sweden)

    Nasrin Jalilian

    2012-11-01

    Full Text Available Introduction: Objective structured clinical examination (OSCE is used for the evaluation of the clinical competence in medicine for which it is essential to measure validity and reliability. This study aimed to investigate the validity and reliability of OSCE for residents of obstetrics and gynecology at Kermanshah University of Medical Sciences in 2011.Methods: A descriptive-correlation study was designed and the data of OSCE for obstetrics and gynecology were collected via learning behavior checklists in method stations and multiple choice questions in question stations. The data were analyzed through Pearson correlation coefficient and Cronbach's alpha, using SPSS software (version 16. To determine the criterion validity, correlation of OSCE scores with scores of resident promotion test, direct observation of procedural skills, and theoretical knowledge was determined; for reliability, however, Cronbach's alpha was used. Total sample consisted of 25 participants taking part in 14 stations. P value of less than 0.05 was considered as significant.Results: The mean OSCE scores was 22.66 (±6.85. Criterion validity of the stations with resident promotion theoretical test, first theoretical knowledge test, second theoretical knowledge, and direct observation of procedural skills (DOPS was 0.97, 0.74, 0.49, and 0.79, respectively. In question stations, criterion validity was 0.15, and total validity of OSCE was 0.77.Conclusion: Findings of the present study indicated acceptable validity and reliability of OSCE for residents of obstetrics and gynecology.

  8. Structural damage localization by outlier analysis of signal-processed mode shapes - Analytical and experimental validation

    Science.gov (United States)

    Ulriksen, M. D.; Damkilde, L.

    2016-02-01

    Contrary to global modal parameters such as eigenfrequencies, mode shapes inherently provide structural information on a local level. Therefore, this particular modal parameter and its derivatives are utilized extensively for damage identification. Typically, more or less advanced mathematical methods are employed to identify damage-induced discontinuities in the spatial mode shape signals, hereby, potentially, facilitating damage detection and/or localization. However, by being based on distinguishing damage-induced discontinuities from other signal irregularities, an intrinsic deficiency in these methods is the high sensitivity towards measurement noise. In the present paper, a damage localization method which, compared to the conventional mode shape-based methods, has greatly enhanced robustness towards measurement noise is proposed. The method is based on signal processing of a spatial mode shape by means of continuous wavelet transformation (CWT) and subsequent application of a generalized discrete Teager-Kaiser energy operator (GDTKEO) to identify damage-induced mode shape discontinuities. In order to evaluate whether the identified discontinuities are in fact damage-induced, outlier analysis is conducted by applying the Mahalanobis metric to major principal scores of the sensor-located bands of the signal-processed mode shape. The method is tested analytically and benchmarked with other mode shape-based damage localization approaches on the basis of a free-vibrating beam and validated experimentally in the context of a residential-sized wind turbine blade subjected to an impulse load.

  9. Validating estimates of the growth rate of structure with modified gravity simulations

    CERN Document Server

    Barreira, Alexandre; Schmidt, Fabian

    2016-01-01

    We perform a consistent end-to-end validation of estimates of the growth rate of structure, described by the parameter combination $f\\sigma_8$, in modified gravity cosmologies. We consider an analysis pipeline based on the redshift-space distortion modelling of the clustering wedges statistic of the galaxy correlation function and apply it to mock catalogues of $\\Lambda{\\rm CDM}$ and the normal branch of DGP cosmologies. We employ a halo occupation distribution approach to construct our mocks, which we ensure resemble the CMASS sample from BOSS in terms of the total galaxy number density and large scale amplitude of the power spectrum monopole. We show that the clustering wedges model successfully recovers the true growth rate difference between DGP and $\\Lambda{\\rm CDM}$, even for cases with over 40% enhancement in $f\\sigma_8$ compared to $\\Lambda{\\rm CDM}$. The unbiased performance of the clustering wedges model allows us to use the growth rate values estimated from the BOSS LOWZ and CMASS samples to constr...

  10. Calibration and validation of FLFArs -- a new flood loss function for Australian residential structures

    Science.gov (United States)

    Hasanzadeh Nafari, R.; Ngo, T.; Lehman, W.

    2016-01-01

    Rapid urbanisation, climate change and unsustainable developments are increasing the risk of floods. Flood is a frequent natural hazard that has significant financial consequences for Australia. The emergency response system in Australia is very successful and has saved many lives over the years. However, the preparedness for natural disaster impacts in terms of loss reduction and damage mitigation has been less successful. In this paper, a newly derived flood loss function for Australian residential structures (FLFArs) has been presented and calibrated by using historic data collected from an extreme event in Queensland, Australia, that occurred in 2013. Afterwards, the performance of the method developed in this work (contrasted to one Australian model and one model from USA) has been compared with the observed damage data collected from a 2012 flood event in Maranoa, Queensland. Based on this analysis, validation of the selected methodologies has been performed in terms of Australian geographical conditions. Results obtained from the new empirically based function (FLFArs) and the other models indicate that it is apparent that the precision of flood damage models is strongly dependent on selected stage damage curves, and flood damage estimation without model calibration might result in inaccurate predictions of losses. Therefore, it is very important to be aware of the associated uncertainties in flood risk assessment, especially if models have not been calibrated with real damage data.

  11. Structural and construct validity of the Whiplash Disability Questionnaire in adults with acute whiplash-associated disorders

    DEFF Research Database (Denmark)

    Stupar, Maja; Côté, Pierre; Beaton, Dorcas E

    2015-01-01

    included insurance claimants who were aged 18 years or older and diagnosed with acute WAD Grades I to III. All participants completed the WDQ, a 13-item questionnaire scored from 0 (no disability) to 130 (complete disability). We assessed the factor structure of the WDQ and tested its construct validity...... that the WDQ includes two factors: daily activities and emotional status. This factor structure remained stable in sensitivity analyses (eg, zeros imputed for missing values, and the item with the most missing values or resulting in complex loading excluded). Strong correlations were found between the total......: The WDQ includes two factors and has strong construct validity in individuals with acute WAD. Our results demonstrate that the WDQ is valid for use as an overall summative scale or as the daily activities and emotional subscales in clinical and research settings to determine disability status....

  12. Structural validity of the Dutch-language version of the WAIS-III in a psychiatric sample

    NARCIS (Netherlands)

    Heijden, P. van der; Bos, P. van den; Mol, B.; Kessels, R.P.C.

    2013-01-01

    The Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV; Wechsler, 2008 ) no longer provides the "traditional" Verbal IQ and Performance IQ deviation scores. In the current study, we investigated the structural validity of these scores in the scale's predecessor, the WAIS-Third Edition (WAIS-I

  13. Structural Validity of the Dutch-Language Version of the WAIS-III in a Psychiatric Sample

    NARCIS (Netherlands)

    Heijden, P.T. van der; Bos, P. van den; Mol, B.A.W.; Kessels, R.P.C.

    2013-01-01

    The Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV; Wechsler, 2008) no longer provides the traditional Verbal IQ and Performance IQ deviation scores. In the current study, we investigated the structural validity of these scores in the scale's predecessor, the WAIS-Third Edition (WAIS-III;

  14. Construct Validity of an Objective Structured Clinical Examination (OSCE) in Psychiatry: Associations with the Clinical Skills Examination and Other Indicators

    Science.gov (United States)

    Park, Robin S.; Chibnall, John T.; Blaskiewicz, Robert J.; Furman, Gail E.; Powell, Jill K.; Mohr, Clinton J.

    2004-01-01

    Objective: The construct validity of checklist and global process scores for an objective structured clinical examination (OSCE) in psychiatry was assessed. Multiple regression analysis was used to predict psychiatry OSCE scores from the clinical skills examination, an obstetrics/gynecology (OB/GYN) OSCE, and the National Board of Medical…

  15. [New biological active derivatives of indomethacin and acetylsalicylic acid. Synthesis, physico-chemical characterisation and structure validation].

    Science.gov (United States)

    Stan, Catalina; Stefanache, Alina; Dumitrache, M

    2006-01-01

    It is well known that niflumic acid glycinamide has a good antiinflammatory action useful in gum inflammatory diseases. The objective of this study was to obtain new glycinamides of acetylsalicylic acid and indomethacin, which could have a better antiinflammatory action than niflumic acid glycinamide. The study presents the synthesis, physico-chemical characterisation and structure validation of these glycinamides.

  16. Cross-Validation of the Factor Structure of the Aberrant Behavior Checklist for Persons with Mental Retardation.

    Science.gov (United States)

    Bihm, Elson M.; Poindexter, Ann R.

    1991-01-01

    The original factor structure of the Aberrant Behavior Checklist was cross-validated with a U.S. sample of 470 persons with moderate to profound mental retardation (27 percent nonambulatory). Results replicated previous findings, suggesting that the original five factors (irritability, lethargy, stereotypic behavior, hyperactivity, and…

  17. Convergence among Data Sources, Response Bias, and Reliability and Validity of a Structured Job Analysis Questionnaire.

    Science.gov (United States)

    Smith, Jack E.; Hakel, Milton D.

    1979-01-01

    Examined are questions pertinent to the use of the Position Analysis Questionnaire: Who can use the PAQ reliably and validly? Must one rely on trained job analysts? Can people having no direct contact with the job use the PAQ reliably and validly? Do response biases influence PAQ responses? (Author/KC)

  18. Adaptation of the Body Image after Breast Cancer Questionnaire in the Polish context: factorial structure and validity of the scale

    Directory of Open Access Journals (Sweden)

    Romuald Derbis

    2016-01-01

    Full Text Available Background Valid assessment of body image is salient in therapy and rehabilitation of women suffering from breast cancer. Adequate instruments are still lacking in this domain. To overcome this limitation two aims were formulated in the study. First, we tested the factorial structure of the Body Image after Breast Cancer Questionnaire (BIBCQ developed by Baxter (1998 in Canada, in the Polish context. Then, we tested the construct validity of the scale. The scale is based on a multidimensional concept of the body image of chronically ill individuals proposed by Vamos (1993. Participants and procedure A group of 270 women at the mean age of 55 (range of 23-81 with breast cancer who underwent conservation, mastectomy, or lumpectomy surgery was sampled in the Amazonki community. Results Confirmatory factor analysis was used to test the factorial structure of the instrument. To test the convergent validity, scales assessing body self, body image, self-esteem, and depression were used. Divergent validity was analyzed in the context of the social desirability construct. Discriminant validity was based on comparisons between women who had undergone lumpectomy or mastectomy surgery. The results showed that within two out of six subscales proposed by Baxter, two additional subscales had to be distinguished. However, some differences in comparisons with previous validation studies were also found. Conclusions The BIBCQ scale was found to be a valid multidimensional tool of body image assessment in the Polish context. The results are discussed in terms of cross-cultural differences in body image perception in breast cancer patients and guidelines for the scale’s implementation in the Polish context.

  19. AOCS Performance and Stability Validation for a 160-m Solar Sail with Control-Structure Interactions

    Science.gov (United States)

    Wie, Bong; Murphy, David

    2005-01-01

    Future solar sail missions, such as NASA's Solar Polar Imager Vision, will require sails with dimensions on the order of 50-500 m. We are examining a square sail design with moving mass (trim control mass, TCM) and quadrant rotation primary actuators plus pulsed plasma thrusters (PPTs) at the mast tips for backup attitude control. Quadrant rotation is achieved via roll stabilizer bars (RSB) at the mast tips. At these sizes, given the gossamer nature of the sail supporting structures, flexible modes may be low enough to interact with the control system, especially as these actuators are located on the flexible structure itself and not on the rigid core. This paper develops a practical analysis of the flexible interactions using state-space systems and modal data from finite element models of the system. Torsion and bending of the masts during maneuvers could significantly affect the function of the actuators while activation of the membrane modes could adversely affect the thrust vector direction and magnitude. Analysis of the RSB and TCM dynamics for developing high-fidelity simulations is included. For control analysis of the flexible system, standard finite-element models of the flexible sail body are loaded and the modal data is used to create a modal coordinate state-space system. Key parameters include which modes to include, which nodes are of interest for force inputs and displacement outputs, connecting nodes through which external forces and torques are applied from the flex body to the core, any nominal momentum in the system, and any steady rates. The system is linearized about the nominal attitude and rate. The state-space plant can then be analyzed with a state-space controller, and Bode, Nyquist, step and impulse responses generated. The approach is general for any rigid core with a flexible appendage. This paper develops a compensator for a simple two-mass flex system and extrapolates the results to the solar sail. A finite element model of the 20 m

  20. Validation of HFCS-I on Calculation of High-Frequency Parameters of Helical Slow-Wave Structures

    Science.gov (United States)

    Zhu, Xiaofang; Yang, Zhonghai; Li, Bin; Li, Jianqing; Xu, Li

    2010-02-01

    To validate HFCS-I, a newly developed design tool for high frequency circuits of microwave tubes, the high-frequency parameters (including dispersion, interaction impedance and attenuation constant) of a typical helical slow-wave structure (SWS) for millimetre wave travelling-wave tube are calculated by HFCS-I and MAFIA. Both the direct calculation method and the Non-Resonant Perturbation (NRP) technique are adopted to get the interaction impedance. The obtained high-frequency parameters from HFCS-I and MAFIA are compared in detail and the consistency has proved the reliability and validity of HFCS-I.

  1. On-orbit validation system for space structure composite actuators Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This SBIR project delivers an On-orbit Validation System (OVS) that provides performance and durability data for Macro Fiber Composite (MFC) active piezocomposite...

  2. Reliability and Validity of the Objective Structured Clinical Examination in the Evaluation of Clinical Skills of Midwifery Students (Kashan, 2014

    Directory of Open Access Journals (Sweden)

    Saeideh Nasiri

    2015-09-01

    Full Text Available This study was conducted to determine the validity and reliability of OSCE in evaluating the clinical skills of midwifery students at Kashan University of Medical Sciences in 2014. This descriptive-correlational study was carried out on 23 senior midwifery students. The OSCE scores were calculated according to the structured objective checklists. Content and criterion validity and reliability were also assessed. The obtained data were analyzed by SPSS-16 using ANOVA and Spearman correlation coefficients. There was a significant relationship between the clinical scores and the OSCE score (P=0.03. The reliability results of the evaluation of stations by two observers showed that the lowest and highest correlation coefficients between observers were 0.58 and 1.00, respectively. Owing to good reliability and validity of this test in the first period of its implementation in Kashan, it can be recommended for subsequent periods as part of the final exam for midwifery students.

  3. Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

    Science.gov (United States)

    Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

    2003-12-01

    Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

  4. Structural and incremental validity of the Wechsler Adult Intelligence Scale-Fourth Edition with a clinical sample.

    Science.gov (United States)

    Nelson, Jason M; Canivez, Gary L; Watkins, Marley W

    2013-06-01

    Structural and incremental validity of the Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV; Wechsler, 2008a) was examined with a sample of 300 individuals referred for evaluation at a university-based clinic. Confirmatory factor analysis indicated that the WAIS-IV structure was best represented by 4 first-order factors as well as a general intelligence factor in a direct hierarchical model. The general intelligence factor accounted for the most common and total variance among the subtests. Incremental validity analyses indicated that the Full Scale IQ (FSIQ) generally accounted for medium to large portions of academic achievement variance. For all measures of academic achievement, the first-order factors combined accounted for significant achievement variance beyond that accounted for by the FSIQ, but individual factor index scores contributed trivial amounts of achievement variance. Implications for interpreting WAIS-IV results are discussed.

  5. The factor structure, metrical properties, and convergent validity of the third edition (1999 of the locus of control inventory

    Directory of Open Access Journals (Sweden)

    Johann M Schepers

    2006-02-01

    Full Text Available The principal objective of the study was to examine the factor structure and metrical properties of the third edition (1999 of the Locus of Control Inventory (LCI. A corollary of the study was to examine the convergent validity of the instrument. After a thorough revision and extension of the scale to 88 items it was applied to a sample of 2091 first-year university students. Particular attention was paid to the shortcomings revealed in a study by de Bruin (2004. An iterative principal factor analysis of the scale was done. The three-factor-structure previously found was substantiated by the analysis. The obtained factors were interpreted as Autonomy, External Control and Internal Control. Highly acceptable reliabilities were obtained. As far as validity is concerned it was found that Internal Control and Autonomy are strongly related to Psychological Wellness and External Control negatively to Stress Management. The implications of the findings are discussed.

  6. All-Atom Molecular-Level Computational Analyses of Polyurea/Fused-Silica Interfacial Decohesion Caused by Impinging Tensile Stress-Waves

    Science.gov (United States)

    2014-01-01

    Interfacial decohesion, Reactive forcefields Paper type Research paper International Journal of Structural Integrity Vol. 5 No. 4, 2014 pp. 339-367 © Emerald ...interaction was conducted to provide additional insight into the outcome of the stress-wave/interface interactions. 4. Results and discussion The main emphasis

  7. The DUNDRUM-1 structured professional judgment for triage to appropriate levels of therapeutic security: retrospective-cohort validation study.

    LENUS (Irish Health Repository)

    Flynn, Grainne

    2011-01-01

    The assessment of those presenting to prison in-reach and court diversion services and those referred for admission to mental health services is a triage decision, allocating the patient to the appropriate level of therapeutic security. This is a critical clinical decision. We set out to improve on unstructured clinical judgement. We collated qualitative information and devised an 11 item structured professional judgment instrument for this purpose then tested for validity.

  8. A Multiscale Finite Element Model Validation Method of Composite Cable-Stayed Bridge Based on Structural Health Monitoring System

    Directory of Open Access Journals (Sweden)

    Rumian Zhong

    2015-01-01

    Full Text Available A two-step response surface method for multiscale finite element model (FEM updating and validation is presented with respect to Guanhe Bridge, a composite cable-stayed bridge in the National Highway number G15, in China. Firstly, the state equations of both multiscale and single-scale FEM are established based on the basic equation in structural dynamic mechanics to update the multiscale coupling parameters and structural parameters. Secondly, based on the measured data from the structural health monitoring (SHM system, a Monte Carlo simulation is employed to analyze the uncertainty quantification and transmission, where the uncertainties of the multiscale FEM and measured data were considered. The results indicate that the relative errors between the calculated and measured frequencies are less than 2%, and the overlap ratio indexes of each modal frequency are larger than 80% without the average absolute value of relative errors. These demonstrate that the proposed method can be applied to validate the multiscale FEM, and the validated FEM can reflect the current conditions of the real bridge; thus it can be used as the basis for bridge health monitoring, damage prognosis (DP, and safety prognosis (SP.

  9. Toward validation of a structural approach to conceptualizing psychopathology: A special section of the Journal of Abnormal Psychology.

    Science.gov (United States)

    Krueger, Robert F; Tackett, Jennifer L; MacDonald, Angus

    2016-11-01

    Traditionally, psychopathology has been conceptualized in terms of polythetic categories derived from committee deliberations and enshrined in authoritative psychiatric nosologies-most notably the Diagnostic and Statistical Manual of Mental Disorders (DSM; American Psychiatric Association [APA], 2013). As the limitations of this form of classification have become evident, empirical data have been increasingly relied upon to investigate the structure of psychopathology. These efforts have borne fruit in terms of an increasingly consistent set of psychopathological constructs closely connected with similar personality constructs. However, the work of validating these constructs using convergent sources of data is an ongoing enterprise. This special section collects several new efforts to use structural approaches to study the validity of this empirically based organizational scheme for psychopathology. Inasmuch as a structural approach reflects the natural organization of psychopathology, it has great potential to facilitate comprehensive organization of information on the correlates of psychopathology, providing evidence for the convergent and discriminant validity of an empirical approach to classification. Here, we highlight several themes that emerge from this burgeoning literature. (PsycINFO Database Record

  10. Common Structural Design Features of Rubrics May Represent a Threat to Validity

    Science.gov (United States)

    Humphry, Stephen Mark; Heldsinger, Sandra Allison

    2014-01-01

    Rubrics for assessing student performance are often seen as providing rich information about complex skills. Despite their widespread usage, however, little empirical research has focused on whether it is possible for rubrics to validly meet their intended purposes. The authors examine a rubric used to assess students' writing in a large-scale…

  11. Age Differences in Personality Structure Revisited: Studies in Validity, Stability, and Change

    Science.gov (United States)

    Costa, Paul T., Jr.; McCrae, Robert R.

    1978-01-01

    Construct validity and longitudinal stability evidence for three cluster dimensions of personality identified as Anxiety, Extraversion, and Openness is examined in a sample of adult males. Correlations with Allport-Vernon-Lindsay Value scales, Cornell Medical Index scores, Eysenck E and N scales, and factors from the SVIB are presented. (Author)

  12. Creating a Test Validated Structural Dynamic Finite Element Model of the Multi-Utility Technology Test Bed Aircraft

    Science.gov (United States)

    Pak, Chan-Gi; Truong, Samson S.

    2014-01-01

    Small modeling errors in the finite element model will eventually induce errors in the structural flexibility and mass, thus propagating into unpredictable errors in the unsteady aerodynamics and the control law design. One of the primary objectives of Multi Utility Technology Test Bed, X-56A, aircraft is the flight demonstration of active flutter suppression, and therefore in this study, the identification of the primary and secondary modes for the structural model tuning based on the flutter analysis of X-56A. The ground vibration test validated structural dynamic finite element model of the X-56A is created in this study. The structural dynamic finite element model of the X-56A is improved using a model tuning tool. In this study, two different weight configurations of the X-56A have been improved in a single optimization run.

  13. Crack Detection in Fibre Reinforced Plastic Structures Using Embedded Fibre Bragg Grating Sensors: Theory, Model Development and Experimental Validation.

    Directory of Open Access Journals (Sweden)

    G F Pereira

    Full Text Available In a fibre-reinforced polymer (FRP structure designed using the emerging damage tolerance and structural health monitoring philosophy, sensors and models that describe crack propagation will enable a structure to operate despite the presence of damage by fully exploiting the material's mechanical properties. When applying this concept to different structures, sensor systems and damage types, a combination of damage mechanics, monitoring technology, and modelling is required. The primary objective of this article is to demonstrate such a combination. This article is divided in three main topics: the damage mechanism (delamination of FRP, the structural health monitoring technology (fibre Bragg gratings to detect delamination, and the finite element method model of the structure that incorporates these concepts into a final and integrated damage-monitoring concept. A novel method for assessing a crack growth/damage event in fibre-reinforced polymer or structural adhesive-bonded structures using embedded fibre Bragg grating (FBG sensors is presented by combining conventional measured parameters, such as wavelength shift, with parameters associated with measurement errors, typically ignored by the end-user. Conjointly, a novel model for sensor output prediction (virtual sensor was developed using this FBG sensor crack monitoring concept and implemented in a finite element method code. The monitoring method was demonstrated and validated using glass fibre double cantilever beam specimens instrumented with an array of FBG sensors embedded in the material and tested using an experimental fracture procedure. The digital image correlation technique was used to validate the model prediction by correlating the specific sensor response caused by the crack with the developed model.

  14. Crack Detection in Fibre Reinforced Plastic Structures Using Embedded Fibre Bragg Grating Sensors: Theory, Model Development and Experimental Validation.

    Science.gov (United States)

    Pereira, G F; Mikkelsen, L P; McGugan, M

    2015-01-01

    In a fibre-reinforced polymer (FRP) structure designed using the emerging damage tolerance and structural health monitoring philosophy, sensors and models that describe crack propagation will enable a structure to operate despite the presence of damage by fully exploiting the material's mechanical properties. When applying this concept to different structures, sensor systems and damage types, a combination of damage mechanics, monitoring technology, and modelling is required. The primary objective of this article is to demonstrate such a combination. This article is divided in three main topics: the damage mechanism (delamination of FRP), the structural health monitoring technology (fibre Bragg gratings to detect delamination), and the finite element method model of the structure that incorporates these concepts into a final and integrated damage-monitoring concept. A novel method for assessing a crack growth/damage event in fibre-reinforced polymer or structural adhesive-bonded structures using embedded fibre Bragg grating (FBG) sensors is presented by combining conventional measured parameters, such as wavelength shift, with parameters associated with measurement errors, typically ignored by the end-user. Conjointly, a novel model for sensor output prediction (virtual sensor) was developed using this FBG sensor crack monitoring concept and implemented in a finite element method code. The monitoring method was demonstrated and validated using glass fibre double cantilever beam specimens instrumented with an array of FBG sensors embedded in the material and tested using an experimental fracture procedure. The digital image correlation technique was used to validate the model prediction by correlating the specific sensor response caused by the crack with the developed model.

  15. Structural Design of the DTU-ESA MM-Wave Validation Standard Antenna

    DEFF Research Database (Denmark)

    Branner, Kim; Berring, Peter; Markussen, Christen Malte;

    2015-01-01

    A new specially designed antenna to be used for inter-comparisons and validation of antenna test facilities is under development in cooperation between DTU and TICRA under a contract from the European Space Agency. The antenna is designed to be extremely thermally and mechanically stable in the r...... to verify that they can be met. The paper also discusses the challenges of integrating an aluminum feed cluster with high thermal expansion coefficient in a CFRP support frame with very low thermal expansion coefficient.......A new specially designed antenna to be used for inter-comparisons and validation of antenna test facilities is under development in cooperation between DTU and TICRA under a contract from the European Space Agency. The antenna is designed to be extremely thermally and mechanically stable...

  16. VALIDATING QUALITY PROCESS MANAGEMENT INSTRUMENT FOR HIGHER EDUCATION USING STRUCTURAL EQUATION MODELLING

    Directory of Open Access Journals (Sweden)

    David Jimoh Kayode

    2016-06-01

    Full Text Available This study attempts to validate process management scale using rigorous validation procedures. An adapted questionnaire comprising 77 items was administered to faculty members in two public universities in Nigeria. The data gathered were analyzed using exploratory factor analysis and confirmatory factor analysis with SPSS 20.0 and SmartPLS 3.1.2 respectively. The findings of this study shows that process management is a third order reflective model with multidimensional constructs. The two dimension of process management administrative process and academic process has four and five dimensions respectively. The process management scale will therefore facilitate the identifications of elements that influence the effectiveness of higher education. The practical implications and methodological limitations are discussed.

  17. A Study of Factor Structur, Validity and Reliabileaty of Pro-social Tendencies

    Directory of Open Access Journals (Sweden)

    Mohammdbagher Kajbaf

    2010-07-01

    Full Text Available AbstractThe purpose of this study is to examine the validity and reliability of pro-social tendencies scale amongstudents at the university of Isfahan. The population in this study compised whole undergraduate students ofthe university of Isfahan in the educational year 1387-88. By using a simple randomized samplingcommensurate with Cohen & others (2000 formula, some 300 subjects were selected. Scales usedconcurrently were: Carlo et al's pro-social tendencies (with 25 items, Rushton et al's global pro-socialbehavior (with 20 items, Davis' empathic concern (with 7 items, Nickell et al's altruistic Values (with 4items and Steele et al's Social responsibility motivation (with 4 items. All of the above scales wereadministered concurrently for studying the validity and reliability of pro-social tendencies. Data wasanalyzed and studied using coronbach's Alpha, Spearman-Brown and Guttman's coefficients, factor analysis(with principal component and varimax rotation and concurrent validity (the correlation between scales.Results showed that the coronbach's Alpha for pro-social tendencies, global pro-social behavior, empathicconcern, altruistic values and social responsibility motivation were 0.861, 0.845, 0.600, 0.500 and 0.782respectively. The result of factor analysis showed five factors for pro-social tendencies: anonymouse, publicaltruistic,emotional, dire and compliant pro-social behaviors.

  18. Modal test and analysis: Multiple tests concept for improved validation of large space structure mathematical models

    Science.gov (United States)

    Wada, B. K.; Kuo, C-P.; Glaser, R. J.

    1986-01-01

    For the structural dynamic analysis of large space structures, the technology in structural synthesis and the development of structural analysis software have increased the capability to predict the dynamic characteristics of the structural system. The various subsystems which comprise the system are represented by various displacement functions; the displacement functions are then combined to represent the total structure. Experience has indicated that even when subsystem mathematical models are verified by test, the mathematical representations of the total system are often in error because the mathematical model of the structural elements which are significant when loads are applied at the interconnection points are not adequately verified by test. A multiple test concept, based upon the Multiple Boundary Condition Test (MBCT), is presented which will increase the accuracy of the system mathematical model by improving the subsystem test and test/analysis correlation procedure.

  19. Damage Theory Validation

    DEFF Research Database (Denmark)

    Simonsen, Bo Cerup

    1998-01-01

    This report contains a series of validation examples for the theoretical model implemented in the computer program DAMAGE. note that the validation examples are for assembled structures.......This report contains a series of validation examples for the theoretical model implemented in the computer program DAMAGE. note that the validation examples are for assembled structures....

  20. Using the De Jong Gierveld Loneliness Scale With Early Adolescents: Factor Structure, Reliability, Stability, and External Validity.

    Science.gov (United States)

    Grygiel, Paweł; Humenny, Grzegorz; Rębisz, Sławomir

    2016-12-08

    The present investigation is the first examination of the factor structures, reliability, external validity, longitudinal invariance, and stability of the De Jong Gierveld Loneliness Scale (DJGLS), as used with early adolescents. It is based on a two-wave, large, representative sample of Polish primary school pupils. The results demonstrate that the model most reflective of the factor structure of the DJGLS is the bifactor model, which assumes the occurrence of one, highly reliable, general factor (overall sense of loneliness) and two, relatively irrelevant, subfactors. Essential unidimensionality (the general factor accounting for three fourth of the common variance) suggest that the interpretation of the subfactors over and above the general factor is inappropriate. The longitudinal confirmatory factor analysis indicated that the bifactor structure of the DJGLS is invariant over time. Correlations with self-rated loneliness, sociometric acceptance/rejection, social self-efficacy, identification with class group, family structure, and gender provide support for the validity of the DJGLS. This implies that it could be used as a measure of loneliness in adolescence, which does not involve references to the school context, making it possible to conduct studies that go beyond school period and compare the intensity of the feeling of loneliness in that group with other age groups.

  1. Assessment of family functioning in Caucasian and Hispanic Americans: reliability, validity, and factor structure of the Family Assessment Device.

    Science.gov (United States)

    Aarons, Gregory A; McDonald, Elizabeth J; Connelly, Cynthia D; Newton, Rae R

    2007-12-01

    The purpose of this study was to examine the factor structure, reliability, and validity of the Family Assessment Device (FAD) among a national sample of Caucasian and Hispanic American families receiving public sector mental health services. A confirmatory factor analysis conducted to test model fit yielded equivocal findings. With few exceptions, indices of model fit, reliability, and validity were poorer for Hispanic Americans compared with Caucasian Americans. Contrary to our expectation, an exploratory factor analysis did not result in a better fitting model of family functioning. Without stronger evidence supporting a reformulation of the FAD, we recommend against such a course of action. Findings highlight the need for additional research on the role of culture in measurement of family functioning.

  2. Structure and Profiles of Basic Motor Competencies in the Third Grade-Validation of the Test Instrument MOBAK-3.

    Science.gov (United States)

    Herrmann, Christian; Seelig, Harald

    2016-11-21

    Basic motor competencies are defined as motor performance dispositions that evolve from specific requirements in sports and exercise. After validating the MOBAK-1 instrument for first graders, we developed the MOBAK-3 for the assessment of basic motor competencies in third graders. We investigated the factorial and diagnostic validity of this instrument in a sample of 323 children (age: M = 9.2 years, SD = .39; sex: boys, n = 158, girls, n = 165). A confirmatory factor analysis verified the theoretical structure with the two factors Locomotion and Object Control. By means of latent class analysis, we identified five latent classes that were connected with external criteria. We concluded that the MOBAK-3 effectively evaluates the basic motor competencies of 8- to 10-year-old students.

  3. Validation of a numerical 3-D fluid-structure interaction model for a prosthetic valve based on experimental PIV measurements.

    Science.gov (United States)

    Guivier-Curien, Carine; Deplano, Valérie; Bertrand, Eric

    2009-10-01

    A numerical 3-D fluid-structure interaction (FSI) model of a prosthetic aortic valve was developed, based on a commercial computational fluid dynamics (CFD) software program using an Arbitrary Eulerian Lagrangian (ALE) formulation. To make sure of the validity of this numerical model, an equivalent experimental model accounting for both the geometrical features and the hydrodynamic conditions was also developed. The leaflet and the flow behaviours around the bileaflet valve were investigated numerically and experimentally by performing particle image velocimetry (PIV) measurements. Through quantitative and qualitative comparisons, it was shown that the leaflet behaviour and the velocity fields were similar in both models. The present study allows the validation of a fully coupled 3-D FSI numerical model. The promising numerical tool could be therefore used to investigate clinical issues involving the aortic valve.

  4. Psychometric Properties and Structural Validity of the Short Version of the Personality Beliefs Questionnaire (PBQ-SF

    Directory of Open Access Journals (Sweden)

    Rubén Darío Manrique Hernández

    2016-06-01

    Full Text Available The Personality Belief Questionnaire- Short Form (PBQ-SF is an assessment instrument of personality beliefs based on the cognitive theory that states that these are characterized by a specific pattern of dysfunctional thoughts. The objective of this study was to establish the psychometric properties and structural validity of the PBQ-SF questionnaire in Colombian adults from 18 to 35 years old. To carry out the above and with permission of the author the validation process was initiated following a thorough and rigorous process that led to a final version of the PBQ-SF applied to 1423 persons born in Colombia and living in nine Colombian cities. Analysis of internal consistency among the items (Cronbach´s alpha, confirmatory factor analysis and calculus of goodness of fit estimators were performed. It was found that the Internal consistency of the domains varied from 0,65 for avoidant disorder up to 0,83 for paranoid disorder.

  5. Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    In this thesis, my work involving dierent aspects of protein structure determination by computer modeling is presented. Determination of several protein's native fold were carried out with Markov chain Monte Carlo simulations in the PHAISTOS protein structure simulation framework, utilizing...... to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...

  6. Structure simulation in unidirectionally solidified turbine blade by dendrite envelope tracking model (Ⅱ): model validation and defects prediction

    Institute of Scientific and Technical Information of China (English)

    WANG Tong-min; SU Yan-qing; GUO Jing-jie; I. OHNAKA; H. YASUDA

    2006-01-01

    The developed model was validated by the checking of grain preferential growth orientation and the solidification experiment with low melting point alloy of Sn-21%Bi(mole fraction). It was also applied to predict the structure defects (e.g. stray grain) of unidirectionally solidified turbine blade. The results show that the developed model is reliable and has the following abilities: 1) reduce the misorientation caused by the orthogonal mesh used in simulation; 2) well reproduce the growth competition among the different-preferential-direction grains with less than 10% relative error; 3) predict the structure defect of stray grain with the accuracy over 80%; 4) optimize the grain selector to better obtain a single crystal avoiding the multigrain defect; 5) simulate the structure evolution (nucleation and growth) of the directional and single crystal turbine blade.

  7. Out-of-sample validation for structured expert judgment of Asian carp establishment in Lake Erie

    NARCIS (Netherlands)

    Cooke, R.M.; Wittmann, M.E.; Lodge, D.M.; Rothlisberger, J.D.; Rutherford, E.S.; Zhang, H.; Mason, D.M.

    2014-01-01

    Structured expert judgment (SEJ) is used to quantify the uncertainty of nonindigenous fish (bighead carp [Hypophthalmichthys nobilis] and silver carp [H. molitrix]) establishment in Lake Erie. The classical model for structured expert judgment model is applied. Forming a weighted combination (called

  8. Verification and Validation of Numerical Models for Air/Water Flow on Coastal and Navigation Fluid-Structure Interaction Applications

    Science.gov (United States)

    Kees, C. E.; Farthing, M.; Dimakopoulos, A.; DeLataillade, T.

    2015-12-01

    Performance analysis and optimization of coastal and navigation structures is becoming feasible due to recent improvements in numerical methods for multiphase flows and the steady increase in capacity and availability of high performance computing resources. Now that the concept of fully three-dimensional air/water flow modelling for real world engineering analysis is achieving acceptance by the wider engineering community, it is critical to expand careful comparative studies on verification,validation, benchmarking, and uncertainty quantification for the variety of competing numerical methods that are continuing to evolve. Furthermore, uncertainty still remains about the relevance of secondary processes such as surface tension, air compressibility, air entrainment, and solid phase (structure) modelling so that questions about continuum mechanical theory and mathematical analysis of multiphase flow are still required. Two of the most popular and practical numerical approaches for large-scale engineering analysis are the Volume-Of-Fluid (VOF) and Level Set (LS) approaches. In this work we will present a publically available verification and validation test set for air-water-structure interaction problems as well as computational and physical model results including a hybrid VOF-LS method, traditional VOF methods, and Smoothed Particle Hydrodynamics (SPH) results. The test set repository and test problem formats will also be presented in order to facilitate future comparative studies and reproduction of scientific results.

  9. Structural validity and reliability of the Positive and Negative Affect Schedule (PANAS: Evidence from a large Brazilian community sample

    Directory of Open Access Journals (Sweden)

    Hudson W. de Carvalho

    2013-06-01

    Full Text Available Objective: Positive and negative affect are the two psychobiological-dispositional dimensions reflecting proneness to positive and negative activation that influence the extent to which individuals experience life events as joyful or as distressful. The Positive and Negative Affect Schedule (PANAS is a structured questionnaire that provides independent indexes of positive and negative affect. This study aimed to validate a Brazilian interview-version of the PANAS by means of factor and internal consistency analysis. Methods: A representative community sample of 3,728 individuals residing in the cities of São Paulo and Rio de Janeiro, Brazil, voluntarily completed the PANAS. Exploratory structural equation model analysis was based on maximum likelihood estimation and reliability was calculated via Cronbach's alpha coefficient. Results: Our results provide support for the hypothesis that the PANAS reliably measures two distinct dimensions of positive and negative affect. Conclusion: The structure and reliability of the Brazilian version of the PANAS are consistent with those of its original version. Taken together, these results attest the validity of the Brazilian adaptation of the instrument.

  10. [Validation of the structure and resources of nosocomial infection control team in hospitals ascribed to VINCat program in Catalonia, Spain].

    Science.gov (United States)

    Limón, Enrique; Pujol, Miquel; Gudiol, Francesc

    2014-07-01

    The main objective of this study was to validate the structure of the infection control team (ICT) in the hospitals adhered to VINCat program and secondary objective was to establish the consistency of resources of each center with the requirements established by the program. Qualitative research consisting of an ethnographic study using participant observation during the years 2008-2010. The centers were stratified in three groups by complexity and beds. The instrument was a semistructured interview to members of the ICT. The transcription of the interview was sent to informants for validation. In November 2010 a questionnaire regarding human resources and number hours dedicated to the ICT was sent. During 2008-2010, 65 centers had been adhered to VINCat program. In 2010, the ICT of Group I hospitals had a mean of two physician, one in full-time and one nurse for every 230 beds. In Group II, one physician part-time and one nurse per 180 beds and in Group III a physician and a nurse for every 98 beds, both part-time. In 2010, all hospitals had a structured ICT, an operative infection committee, and a hospital member representing the center at the program as well as enough electronic resources. The hospitals participating in the program have now VINCat an adequate surveillance structure and meet the minimum technical and human resources required to provide high-quality data. However human resources are not guaranteed.

  11. Validity evidence based on internal structure of scores on the Spanish version of the Self-Description Questionnaire-II.

    Science.gov (United States)

    Ingles, Cándido J; Torregrosa, María S; Hidalgo, María D; Nuñez, Jose C; Castejón, Juan L; García-Fernández, Jose M; Valles, Antonio

    2012-03-01

    The aim of this study was to analyze the reliability and validity evidence of scores on the Spanish version of Self-Description Questionnaire II (SDQ-II). The instrument was administered in a sample of 2022 Spanish students (51.1% boys) from grades 7 to 10. Confirmatory factor analysis (CFA) was used to examine validity evidence based on internal structure drawn from the scores on the SDQ-II. CFA replicated the correlated II first-order factor structure. Furthermore, hierarchical confirmatory factor analysis (HCFA) was used to examine the hierarchical ordering of self-concept, as measured by scores on the Spanish version of the SDQ-II. Although a series of HCFA models were tested to assess academic and non-academic components organization, support for those hierarchical models was weaker than for the correlated 11 first-order factor structure. Results also indicated that scores on the Spanish version of the SDQ-II had internal consistency and test-retest reliability estimates within an acceptable range.

  12. Extending modal testing technology for model validation of engineering structures with sparse nonlinearities: A first case study

    Science.gov (United States)

    delli Carri, Arnaldo; Weekes, B.; Di Maio, Dario; Ewins, D. J.

    2017-02-01

    Modal testing is widely used today as a means of validating theoretical (Finite Element) models for the dynamic analysis of engineering structures, prior to these models being used for optimisation of product design. Current model validation methodology is confined to linear models and is primarily concerned with (i) correcting inaccurate model parameters and (ii) ensuring that sufficient elements are included for these cases, using measured data. Basic experience is that this works quite well, largely because the weaknesses in the models are relatively sparse and, as a result, are usually identifiable and correctable. The current state-of-the-art in linear model validation has contributed to an awareness that residual errors in FE models are increasingly the consequence of some unrepresented nonlinearity in the structure. In these cases, additional, higher order parameters are required to improve the model so that it can represent the nonlinear behaviour. This is opposed to the current practice of simply refining the mesh. Again, these nonlinear features are generally localised, and are often associated with joints. We seek to provide a procedure for extending existing modal testing to enable these nonlinear elements to be addressed using current nonlinear identification methods directed at detection, characterisation, location and then quantification - in order to enhance the elements in an FE model as necessary to describe nonlinear dynamic behaviour. Emphasis is placed on the outcome of these extended methods to relate specifically to the physical behaviour of the relevant components of the structure, rather than to the nonlinear response characteristics that are the result of their presence.

  13. Design and validation of wireless acceleration sensor network for structural health monitoring

    Institute of Scientific and Technical Information of China (English)

    Yu Yan; Ou Jinping

    2006-01-01

    A wireless sensor network is proposed to monitor the acceleration of structures for the purpose of structural health monitoring of civil engineering structures. Using commercially available parts, several modules are constructed and integrated into complete wireless sensors and base stations. The communication protocol is designed and the fusion arithmetic of the temperature and acceleration is embedded in the wireless sensor node so that the measured acceleration values are more accurate. Measures are adopted to finish energy optimization, which is an important issue for a wireless sensor network. The test is performed on an offshore platform model, and the experimental results are given to show the feasibility of the designed wireless sensor network.

  14. Assessing the Reliability, Factor Structure, and Validity of the African Self-Consciousness Scale in a General Population of African Americans.

    Science.gov (United States)

    Stokes, Julie E.; And Others

    1994-01-01

    This paper investigates the psychometric properties of the African Self-Consciousness (ASC) Scale in a noncollege heterogeneous population of 147 African Americans to determine the reliability and validity of the ASC Scale. Based on analysis of the scale's reliability, factor structure, and construct validity, the study shows the ASC Scale to be a…

  15. Assessing Social Validity of School-Wide Positive Behavior Support Plans: Evidence for the Reliability and Structure of the Primary Intervention Rating Scale

    Science.gov (United States)

    Lane, Kathleen Lynne; Kalberg, Jemma Robertson; Bruhn, Allison Leigh; Driscoll, Steven A.; Wehby, Joseph H.; Elliott, Stephen N.

    2009-01-01

    This study provides initial evidence for the reliability and structural validity of scores from the Primary Intervention Rating Scale (Lane, Robertson, & Wehby, 2002), an adapted version of the Intervention Rating Profile-15 (Witt & Elliott, 1985) designed to assess faculty's perceptions of social validity of primary prevention plans prior…

  16. Structural validity of the tonic immobility scale in a population exposed to trauma: evidence from two large Brazilian samples.

    Directory of Open Access Journals (Sweden)

    Michael Reichenheim

    Full Text Available BACKGROUND: Tonic Immobility is a temporary state of motor inhibition in situations involving extreme fear. The first scale developed for its assessment was the 10-item Tonic Immobility Scale (TIS. However, there are still few studies on its structural (dimensional validity. The objective of this study was to reassess the factor structure of the TIS applied to representative samples exposed to general trauma of two Brazilian mega-cities. METHODS: The sample comprised 3,223 participants reporting at least one traumatic experience. In São Paulo (n = 2,148, a Confirmatory Factor Analysis (CFA first tested the originally proposed two-dimensional structure. This was followed by sequential Exploratory Structural Equation Models to identify the best fitting model, and subsequently tested in Rio de Janeiro (n = 1,075 via CFA. Alternative reduced versions were further explored using the aggregate sample. Model-based Item Response Theory (IRT location parameters were also investigated. RESULTS: An absence of factor-based convergent and discriminant validity rejected the original proposition. However, the one-dimensional structure still held several residual correlations. Further exploration indicated the sustainability of reduced versions with seven (alternative A and six (alternative B items. Both presented excellent fit and no relevant residual item correlation. According to the IRT location parameters, items in alternative B covered a wider range of the latent trait. The Loevinger's H scalability coefficients underscored this pattern. CONCLUSIONS: The original model did not hold. A one-factor solution was the most tenable in both large samples, but with significant item residual correlations, indicating that content redundancies persisted. Further reduced and simplified versions of the TIS proved promising. Although studies are yet to be carried out in other settings, it is the authors' impression that the restricted versions of the TIS are

  17. A Quantitative Structure Activity Relationship for acute oral toxicity of pesticides on rats: Validation, domain of application and prediction.

    Science.gov (United States)

    Hamadache, Mabrouk; Benkortbi, Othmane; Hanini, Salah; Amrane, Abdeltif; Khaouane, Latifa; Si Moussa, Cherif

    2016-02-13

    Quantitative Structure Activity Relationship (QSAR) models are expected to play an important role in the risk assessment of chemicals on humans and the environment. In this study, we developed a validated QSAR model to predict acute oral toxicity of 329 pesticides to rats because a few QSAR models have been devoted to predict the Lethal Dose 50 (LD50) of pesticides on rats. This QSAR model is based on 17 molecular descriptors, and is robust, externally predictive and characterized by a good applicability domain. The best results were obtained with a 17/9/1 Artificial Neural Network model trained with the Quasi Newton back propagation (BFGS) algorithm. The prediction accuracy for the external validation set was estimated by the Q(2)ext and the root mean square error (RMS) which are equal to 0.948 and 0.201, respectively. 98.6% of external validation set is correctly predicted and the present model proved to be superior to models previously published. Accordingly, the model developed in this study provides excellent predictions and can be used to predict the acute oral toxicity of pesticides, particularly for those that have not been tested as well as new pesticides.

  18. Validity and reliability of the Structured Clinical Interview for the Trauma and Loss Spectrum (SCI-TALS

    Directory of Open Access Journals (Sweden)

    Conversano Ciro

    2008-01-01

    Full Text Available Abstract Background DSM-IV identifies three stress response disorders (acute stress Disorder (ASD, post-traumatic stress Disorder (PTSD and adjustment disorders (AD that derive from specific life events. An additional condition of complicated grief (CG, well described in the literature, is triggered by bereavement. This paper reports on the reliability and validity of the Structured Clinical Interview for Trauma and Loss Spectrum (SCI-TALS developed to assess the spectrum of stress response. The instrument is based on a spectrum model that emphasizes soft signs, low-grade symptoms, subthreshold syndromes, as well as temperamental and personality traits comprising clinical and subsyndromal manifestations. Methods Study participants, enrolled at 6 Italian Departments of Psychiatry located at six sites, included consecutive patients with PTSD, 44 with CG and a comparative group of 48 unselected controls. Results We showed good reliability and validity of the SCI-TALS. Domain scores were significantly higher in participants with PTSD or CG compared to controls. There were high correlations between specific SCI-TALS domains and corresponding scores on established measures of similar constructs. Participants endorsing grief and loss events reported similar scores on all instruments, except those with CG who scored significantly higher on the domain of grief reactions. Conclusion These findings provide strong support for the internal consistency, the discriminant validity and the reliability of the SCI-TALS. These results also support the existence of a specific grief-related condition and the proposal that different forms of stress response have similar manifestations.

  19. Exploring RNA structure by integrative molecular modelling

    DEFF Research Database (Denmark)

    Masquida, Benoît; Beckert, Bertrand; Jossinet, Fabrice

    2010-01-01

    RNA molecular modelling is adequate to rapidly tackle the structure of RNA molecules. With new structured RNAs constituting a central class of cellular regulators discovered every year, the need for swift and reliable modelling methods is more crucial than ever. The pragmatic method based...... on interactive all-atom molecular modelling relies on the observation that specific structural motifs are recurrently found in RNA sequences. Once identified by a combination of comparative sequence analysis and biochemical data, the motifs composing the secondary structure of a given RNA can be extruded...... in three dimensions (3D) and used as building blocks assembled manually during a bioinformatic interactive process. Comparing the models to the corresponding crystal structures has validated the method as being powerful to predict the RNA topology and architecture while being less accurate regarding...

  20. Stress and structural damage sensing piezospectroscopic coatings validated with digital image correlation

    Directory of Open Access Journals (Sweden)

    Gregory Freihofer

    2015-03-01

    Full Text Available The piezospectroscopic effect, relating a material’s stress state and spectral signature, has recently demonstrated tailorable sensitivity when the photo-luminescent alpha alumina is distributed in nanoparticulate form within a matrix. Here, the stress-sensing behavior of an alumina-epoxy nanoparticle coating, applied to a composite substrate in an open hole tension configuration, is validated with the biaxial strain field concurrently determined through digital image correlation. The coating achieved early detection of composite failure initiation at 77% failure load, and subsequently tracked stress distribution in the immediate vicinity of the crack as it progressed, demonstrating non-invasive stress and damage detection with multi-scale spatial resolution.

  1. Is structured observation a valid technique to measure handwashing behavior? Use of acceleration sensors embedded in soap to assess reactivity to structured observation.

    Science.gov (United States)

    Ram, Pavani K; Halder, Amal K; Granger, Stewart P; Jones, Therese; Hall, Peter; Hitchcock, David; Wright, Richard; Nygren, Benjamin; Islam, M Sirajul; Molyneaux, John W; Luby, Stephen P

    2010-11-01

    Structured observation is often used to evaluate handwashing behavior. We assessed reactivity to structured observation in rural Bangladesh by distributing soap containing acceleration sensors and performing structured observation 4 days later. Sensors recorded the number of times soap was moved. In 45 participating households, the median number of sensor soap movements during the 5-hour time block on pre-observation days was 3.7 (range 0.3-10.6). During the structured observation, the median number of sensor soap movements was 5.0 (range 0-18.0), a 35% increase, P = 0.0004. Compared with the same 5-hour time block on pre-observation days, the number of sensor soap movements increased during structured observation by ≥ 20% in 62% of households, and by ≥ 100% in 22% of households. The increase in sensor soap movements during structured observation, compared with pre-observation days, indicates substantial reactivity to the presence of the observer. These findings call into question the validity of structured observation for measurement of handwashing behavior.

  2. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    CERN Document Server

    Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...

  3. Validation of in utero tractography of human fetal commissural and internal capsule fibers with histological structure tensor analysis

    Directory of Open Access Journals (Sweden)

    Christian eMitter

    2015-12-01

    Full Text Available Diffusion tensor imaging (DTI and tractography offer the unique possibility to visualize the developing white matter macroanatomy of the human fetal brain in vivo and in utero and are currently under investigation for their potential use in the diagnosis of developmental pathologies of the human central nervous system. However, in order to establish in utero DTI as a clinical imaging tool, an independent comparison between macroscopic imaging and microscopic histology data in the same subject is needed. The present study aimed to cross-validate normal as well as abnormal in utero tractography results of commissural and internal capsule fibers in human fetal brains using postmortem histological structure tensor (ST analysis. In utero tractography findings from two structurally unremarkable and five abnormal fetal brains were compared to the results of postmortem ST analysis applied to digitalized whole hemisphere sections of the same subjects. An approach to perform ST-based deterministic tractography in histological sections was implemented to overcome limitations in correlating in utero tractography to postmortem histology data. ST analysis and histology-based tractography of fetal brain sections enabled the direct assessment of the anisotropic organization and main fiber orientation of fetal telencephalic layers on a micro- and macroscopic scale, and validated in utero tractography results of corpus callosum and internal capsule fiber tracts. Cross-validation of abnormal in utero tractography results could be achieved in four subjects with agenesis of the corpus callosum and in two cases with malformations of internal capsule fibers. In addition, potential limitations of current DTI-based in utero tractography could be demonstrated in several brain regions. Combining the three-dimensional nature of DTI-based in utero tractography with the microscopic resolution provided by histological ST analysis may ultimately facilitate a more complete

  4. Discriminant and concurrent validity of a simplified DSM-based structured diagnostic instrument for the assessment of autism spectrum disorders in youth and young adults

    Directory of Open Access Journals (Sweden)

    Joshi Gagan

    2011-12-01

    Full Text Available Abstract Background To evaluate the concurrent and discriminant validity of a brief DSM-based structured diagnostic interview for referred individuals with autism spectrum disorders (ASDs. Methods To test concurrent validity, we assessed the structured interview's agreement in 123 youth with the expert clinician assessment and the Social Responsiveness Scale (SRS. Discriminant validity was examined using 1563 clinic-referred youth. Results The structured diagnostic interview and SRS were highly sensitive indicators of the expert clinician assessment. Equally strong was the agreement between the structured interview and SRS. We found evidence for high specificity for the structured interview. Conclusions A simplified DSM-based ASD structured diagnostic interview could serve as a useful diagnostic aid in the assessment of subjects with ASDs in clinical and research settings.

  5. Assessment of the structural validity of the domestic violence healthcare providers’ survey questionnaire using a Nigerian sample

    Science.gov (United States)

    John, Ime A; Lawoko, Stephen

    2010-01-01

    Abstract: Background: There has been increased advocacy to involve healthcare providers in the prevention of intimate partner violence (IPV) through screening for it in healthcare. Yet, only one in ten providers screen for IPV, suggesting barriers. Understanding the readiness of healthcare providers to screen for IPV is therefore paramount. The Domestic Violence Healthcare Provider Survey Scales (DVHPSS) is a previously validated, comprehensive scale to study readiness of healthcare providers to screen for IPV. However, an understanding of its usefulness in the Sub-Saharan African context remains elusive. The current study undertook to examine the structural validity of the DVHPSS in Nigeria. Methods: Exploratory factor analysis and Cronbach's Alpha were run to reveal the factorial structure and reliability of the instrument/subscales respectively. Established thresholds were used to determine significant factor loadings and alphas coefficient. Results: A six factor model emerged, with 2 factors similar to the original scale, another two differing slightly and a further two factors resulting from a splitting up of the original combination of victim/provider safety to having distinct victim and provider safety subscales. Conclusions: With slight modifications, the DVHPSS can be use to study IPV screening among Nigerian healthcare professionals. Introducing screening protocols could promote better understanding of crucial questions that were lost in the analysis. PMID:21483202

  6. Assessment of the structural validity of the domestic violence healthcare providers’ survey questionnaire using a Nigerian sample

    Directory of Open Access Journals (Sweden)

    Stephen Lawoko

    2010-07-01

    Full Text Available BACKGROUND: There has been increased advocacy to involve healthcare providers in the prevention of intimate partner violence (IPV through screening for it in healthcare. Yet, only one in ten providers screen for IPV, suggesting barriers. Understanding the readiness of healthcare providers to screen for IPV is therefore paramount. The Domestic Violence Healthcare Provider Survey Scales (DVHPSS is a previously validated, comprehensive scale to study readiness of healthcare providers to screen for IPV. However, an understanding of its usefulness in the Sub-Saharan African context remains elusive. The current study undertook to examine the structural validity of the DVHPSS in Nigeria. METHODS: Exploratory factor analysis and Cronbach's Alpha were run to reveal the factorial structure and reliability of the instrument/subscales respectively. Established thresholds were used to determine significant factor loadings and alphas coefficient. RESULTS: A six factor model emerged, with 2 factors similar to the original scale, another two differing slightly and a further two factors resulting from a splitting up of the original combination of victim/provider safety to having distinct victim and provider safety subscales. CONCLUSIONS: With slight modifications, the DVHPSS can be use to study IPV screening among Nigerian healthcare professionals. Introducing screening protocols could promote better understanding of crucial questions that were lost in the analysis.

  7. Structural relations between coping strategies and Burnout syndrome on health workers: A study of external and construct validity

    Directory of Open Access Journals (Sweden)

    Fernando Austria Corrales

    2012-03-01

    Full Text Available The aim of this study was to validate hypothesized structural and functional relationships between coping strategies and factors associated with burnout syndrome in independent samples of health workers from different hospitals and hospital care settings. We applied the Maslach Burnout Inventory and the scale of Coping with Extreme Risks adapted to the Mexican population, we analyzed the responses of 354 health workers in a tertiary hospital and 300 from a reference hospital. The samples were intentional, non-probability, quota. The group was formed by nurses, paramedics, diagnostics services, physicians and resident physicians. Results confirmed the factor structure of the instruments in the twosamples and showed that the use of active coping strategies (control, information seeking, social support, among others has protective effects on the factors associated withthe syndrome (emotional exhaustion, depersonalization and personal fulfillment at work, regardless of the sample, context and type of hospital care. We discuss the results andtheir implications in relation to external validity and findings in other related research.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott (Michigan); (Kansas); (HWMRI)

    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) 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.

  9. DNDC Model Calibration, Validation and Quantification of Structural Uncertainty to Support Rice Methane Offset Protocols

    Science.gov (United States)

    Salas, W.; Ducey, M. J.; Li, C.

    2014-12-01

    Agriculture represents an important near-term option for GHG offsets. Currently, the most widely accepted low-cost approaches to quantify N2O and CH4 emissions are based on emission factors. Given that N2O and CH4 emissions from agricultural practices exhibit high spatial and temporal variability, emission factors are not very sensitive to estimate this variability in emissions at the farm level, even when the emission factors are regional. It is clear that if agricultural offset projects are going to include N2O and CH4 reductions, then process-based biogeochemical models are potentially important tools to quantify emission reductions within offset protocols. The question remains how good a model's performance is with respect to emission reductions. As PBM, are integrated into protocols for agricultural GHG offsets, comprehensive and systematic validation is needed to statistically quantify uncertainties in model-based estimates of GHG emission reductions that are obtained by standardized approach to parameterization and calibration that can be applied across a whole region. The DNDC model was validated against 88 datasets of rice methane emissions. Data were collected at sites in California and MidSouth. In addition to examining the magnitude of the measured versus modeled emissions, we analyzed model performance for estimating the changes in emissions associated with a change in management practices (e.g. dry versus wet seeded rice, different fertilizer rates, etc.). We analyzed 100 pairs of modeled and measured emission reductions. DNDC model performance and uncertainty was quantified using a suite of statistical measures. First, we examined how well the modeled emissions differences match the field-measured differences on a case-by-case basis and also on average, using a combination of Monte Carlo approaches and equivalence testing. Although modeled emissions for individual fields show a slight bias, emissions reductions for baseline:treatment pairs fall close

  10. The Student Perception of University Support and Structure Scale: Development and Validation

    Science.gov (United States)

    Wintre, Maxine G.; Gates, Shawn K. E.; Pancer, W. Mark; Pratt, Michael S.; Polivy, Janet; Birnie-Lefcovitch, S.; Adams, Gerald

    2009-01-01

    A new scale, the Student Perception of University Support and Structure Scale (SPUSS), was developed for research on the transition to university. The scale was based on concepts derived from Baumrind's (1971) theory of parenting styles. Data were obtained from two separate cohorts of freshmen (n=759 and 397) attending six Canadian universities of…

  11. The PANAS Structure Revisited: On the Validity of a Bifactor Model in Community and Forensic Samples

    Science.gov (United States)

    Leue, Anja; Beauducel, Andre

    2011-01-01

    The Positive and Negative Affect Schedule (PANAS) is a widely used inventory for the assessment of affect in psychology and other applied sciences. Despite its popularity, the structure of the PANAS is still under debate. On the one hand, there is evidence of the traditional 2-factor model with Positive Affect (PA) and Negative Affect (NA) as…

  12. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  13. Factor Structure and Validation of the Dimensional Assessment of Personality Questionnaire (DAPQ

    Directory of Open Access Journals (Sweden)

    Dino Krupić

    2015-12-01

    Full Text Available The last decade was extremely dynamic in the field of personality disorder. The extensive research has resulted with significant changes in conceptualization and assessment of personality psychopathology. DSM 5 has introduced a hybrid diagnostic model of personality disorders, which leads toward implementing dimensional instead of categorical approach to personality disorders. There are many questionnaires aimed to measure dimensions of personality psychopathology. However, they contain a large number of items, which may present a methodological problem in conducting research on large samples. Hence, the aim of this study is to present development of a short questionnaire aimed to measure main dimensions of personality psychopathology. The questionnaire, named Dimensional Assessment of Personality Traits Questionnaire (DAPTQ, contains 62 items distributed into 5 main scales; Negative Emotionality, Detachment, Compulsivity, Psychoticism and Antagonism, and two additional scales Grandiosity and Attention Seeking. Study was conducted on the sample of 456 high school students from Osijek and Koprivnica. The DAPTQ, YPI, LEXI - 70 and Ryff Scales of Psychological Well-Being were administered. Results indicate good psychometric properties, namely content, construct and convergent validity and reliability, of all scales of the DAPTQ. This paper discusses some measurement issues concerning personality psychopathology in adolescents' population and the ways in which they could be overcome.

  14. Lidar Altimeter Measurements of Canopy Structure: Methods and Validation for Closed Canopy, Broadleaf Forests

    Science.gov (United States)

    Harding, D. J.; Lefsky, M. A.; Parker, G. G.; Blair, J. B.

    1999-01-01

    Lidar altimeter observations of vegetated landscapes provide a time-resolved measure of laser pulse backscatter energy from canopy surfaces and the underlying ground. Airborne lidar altimeter data was acquired using the Scanning Lidar Imager of Canopies by Echo Recovery (SLICER) for a successional sequence of four, closed-canopy, deciduous forest stands in eastern Maryland. The four stands were selected so as to include a range of canopy structures of importance to forest ecosystem function, including variation in the height and roughness of the outer-most canopy surface and the vertical organization of canopy stories and gaps. The character of the SLICER backscatter signal is described and a method is developed that accounts for occlusion of the laser energy by canopy surfaces, transforming the backscatter signal to a canopy height profile (CHP) that quantitatively represents the relative vertical distribution of canopy surface area. The transformation applies an increased weighting to the backscatter amplitude as a function of closure through the canopy and assumes a horizontally random distribution of the canopy components. SLICER CHPs, averaged over areas of overlap where lidar ground tracks intersect, are shown to be highly reproducible. CHP transects across the four stands reveal spatial variations in vegetation, at the scale of the individual 10 m diameter laser footprints, within and between stands. Averaged SLICER CHPs are compared to analogous height profile results derived from ground-based sightings to plant intercepts measured on plots within the four stands. Tbe plots were located on the segments of the lidar ground tracks from which averaged SLICER CHPs were derived, and the ground observations were acquired within two weeks of the SLICER data acquisition to minimize temporal change. The differences in canopy structure between the four stands is similarly described by the SLICER and ground-based CHP results, however a Chi-square test of similarity

  15. [Structural validity of miokinetic psychodiagnosis-revised and digitalyzed (MKP-RD) lineograms].

    Science.gov (United States)

    Tous, Josep M; Viadé, Albert; Muiños, Rubén

    2007-05-01

    In this study, we have applied a principal components analysis to the data obtained from a graphical record of motor behaviour performed without vision. The data was obtained from two samples, one made up of men and the other one made up of women. Hand dominance was controlled in both samples. Five independent factors were obtained: Factor I (Tendency to increase or decrease the length), Factor II (Tendency to deviate in a sagittal direction), Factor V (Tendency to deviate in a frontal direction); two factors (III and IV) were found in a transversal direction. This factor structure did not depend on sex, because the same structure was found in both sexes, nor it could be explained by learning, because the same factors appeared for each hand, except for Factors III and IV which were different for each hand. This study supports different motor dispositions as foundations of behaviour tendencies.

  16. Structural damage identification in wind turbine blades using piezoelectric active sensing with ultrasonic validation

    Energy Technology Data Exchange (ETDEWEB)

    Claytor, Thomas N [Los Alamos National Laboratory; Ammerman, Curtt N [Los Alamos National Laboratory; Park, Gyu Hae [Los Alamos National Laboratory; Farinholt, Kevin M [Los Alamos National Laboratory; Farrar, Charles R [Los Alamos National Laboratory; Atterbury, Marie K [Los Alamos National Laboratory

    2010-01-01

    This paper gives a brief overview of a new project at LANL in structural damage identification for wind turbines. This project makes use of modeling capabilities and sensing technology to understand realistic blade loading on large turbine blades, with the goal of developing the technology needed to automatically detect early damage. Several structural health monitoring (SHM) techniques using piezoelectric active materials are being investigated for the development of wireless, low power sensors that interrogate sections of the wind turbine blade using Lamb wave propagation data, frequency response functions (FRFs), and time-series analysis methods. The modeling and sensor research will be compared with extensive experimental testing, including wind tunnel experiments, load and fatigue tests, and ultrasonic scans - on small- to mid-scale turbine blades. Furthermore, this study will investigate the effect of local damage on the global response of the blade by monitoring low-frequency response changes.

  17. Experiments to Populate and Validate a Processing Model for Polyurethane Foam: Additional Data for Structural Foams.

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Rekha R.; Celina, Mathias C.; Giron, Nicholas Henry; Long, Kevin Nicholas; Russick, Edward M.

    2015-01-01

    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-18 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 o 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.

  18. Experiments to Populate and Validate a Processing Model for Polyurethane Foam: Additional Data for Structural Foams

    Energy Technology Data Exchange (ETDEWEB)

    Rao, Rekha R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Celina, Mathias C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Giron, Nicholas Henry [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Long, Kevin Nicholas [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russick, Edward M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-01-01

    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-18 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.

  19. Simple structures test for elastic-plastic strain acceptance criterion validation

    Energy Technology Data Exchange (ETDEWEB)

    Trimble, T.F. [Electric Boat Corp., Groton, CT (United States); Krech, G.R. [Wyle Labs., Inc., Huntsville, AL (United States)

    1997-11-01

    A Simple Structures Test Program was performed where several cantilevered beam and fixed-end beam test specimens (fabricated from HY-80 steel) were subjected to a series of analytically predetermined rapidly applied transient dynamic input loads. The primary objective of the test program was to obtain dynamic nonlinear response for simple structures subjected to these load inputs. Data derived from these tests was subsequently used to correlate to analysis predictions to assess the capability to analytically predict elastic-plastic nonlinear material behavior in structures using typical time-dependent (transient) design methods and the ABAQUS finite element analysis code. The installation of a significant amount of instrumentation on these specimens and post-test measurements enabled the monitoring and recording of strain levels, displacements, accelerations, and permanent set. An assessment of modeling parameters such as the element type and mesh refinement was made using these test results. In addition, currently available material models and the incremental time step procedure used in the transient analyses were evaluated. Comparison of test data to analysis results shows that displacements, accelerations, and peak strain can be predicted with a reasonable level of accuracy using detailed solid models of the tested specimens. Permanent set is overpredicted by a factor of approximately two. However, the accuracy of the prediction of permanent set is being enhanced by updating material modeling in the ABAQUS code to account for effects of strain reversal in oscillatory behavior of dynamically loaded specimens.

  20. Fuzzy structure theory modeling of sound-insulation layers in complex vibroacoustic uncertain systems: theory and experimental validation.

    Science.gov (United States)

    Fernandez, Charles; Soize, Christian; Gagliardini, Laurent

    2009-01-01

    The fuzzy structure theory was introduced 20 years ago in order to model the effects of complex subsystems imprecisely known on a master structure. This theory was only aimed at structural dynamics. In this paper, an extension of that theory is proposed in developing an elastoacoustic element useful to model sound-insulation layers for computational vibroacoustics of complex systems. The simplified model constructed enhances computation time and memory allocation because the number of physical and generalized degrees of freedom in the computational vibroacoustic model is not increased. However, these simplifications introduce model uncertainties. In order to take into account these uncertainties, the nonparametric probabilistic approach recently introduced is used. A robust simplified model for sound-insulation layers is then obtained. This model is controlled by a small number of physical and dispersion parameters. First, the extension of the fuzzy structure theory to elastoacoustic element is presented. Second, the computational vibroacoustic model including such an elastoacoustic element to model sound-insulation layer is given. Then, a design methodology to identify the model parameters with experiments is proposed and is experimentally validated. Finally, the theory is applied to an uncertain vibroacoustic system.

  1. Traffic weigh-in-motion (WIM measurements and validation of the Texas perpetual pavement structural design concept

    Directory of Open Access Journals (Sweden)

    Lubinda F. Walubita

    2011-01-01

    Full Text Available Over the past few years, the State of Texas has used perpetual pavement (PP structures on its heavily trafficked highways, where the expected 20-year truck-traffic estimate of 80 kN ESALs (equivalent single axle loads is in excess of 30 million. As a means to validate the Texas PP structural design concept and to make optimal future truck-traffic design recommendations, traffic Weigh In-Motion (WIM measurements were conducted and analyzed for two PP projects. The findings indicated that the initial 80 kN ESAL traffic design estimates for PP were comparable to the projections based on the actual measured WIM traffic data. However, underestimation of the hot mix asphalt layer dynamic moduli resulted in conservative designs for the PP structures. In addition, based on the successful use of the automated WIM data stations for traffic data collection, the paper highlights possible applications and advantages (as compared to conventional manual collection of traffic data of using detailed WIM traffic data information for future analyses of both highway operation and pavement structural design.

  2. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

  3. Optimization and Validation of Rotating Current Excitation with GMR Array Sensors for Riveted Structures Inspection

    Directory of Open Access Journals (Sweden)

    Chaofeng Ye

    2016-09-01

    Full Text Available In eddy current non-destructive testing of a multi-layered riveted structure, rotating current excitation, generated by orthogonal coils, is advantageous in providing sensitivity to defects of all orientations. However, when used with linear array sensors, the exciting magnetic flux density ( B x of the orthogonal coils is not uniform over the sensor region, resulting in an output signal magnitude that depends on the relative location of the defect to the sensor array. In this paper, the rotating excitation coil is optimized to achieve a uniform B x field in the sensor array area and minimize the probe size. The current density distribution of the coil is optimized using the polynomial approximation method. A non-uniform coil design is derived from the optimized current density distribution. Simulation results, using both an optimized coil and a conventional coil, are generated using the finite element method (FEM model. The signal magnitude for an optimized coil is seen to be more robust with respect to offset of defects from the coil center. A novel multilayer coil structure, fabricated on a multi-layer printed circuit board, is used to build the optimized coil. A prototype probe with the optimized coil and 32 giant magnetoresistive (GMR sensors is built and tested on a two-layer riveted aluminum sample. Experimental results show that the optimized probe has better defect detection capability compared with a conventional non-optimized coil.

  4. Analysis of foot structural damage in rheumatoid arthritis: clinical evaluation by validated measures and serological correlations

    Directory of Open Access Journals (Sweden)

    E. Bartoloni Bocci

    2011-06-01

    Full Text Available Objective: To examine foot involvement in rheumatoid arthritis (RA and to characterize structural alterations in patients with anti-cyclic citrullinated peptide (CCP antibody-positive and -negative disease. Methods: Seventy-eight patients with RA with foot pain were consecutively enrolled. The Manchester Hallux Valgus (MHV rating scale was used to evaluate the hallux valgus deformity degree. The Foot Posture Index (FPI6, a novel, foot-specific outcome measure, was adopted in order to quantify variation in the position of the foot. The findings were correlated with disease duration and presence or absence of anti-CCP antibodies. Results: About 84.6% patients had different degrees of hallux valgus and 65.4% subjects had a pronated foot. These two foot alterations were prevalently found in patients with long-standing disease and circulating anti-CCP antibodies. On the contrary, RA patients without anti-CCP and early disease essentially displayed a supinated foot without relevant hallux valgus deformity. Conclusion: Our findings allowed to identify different anatomic foot alterations in RA patients according to disease duration and negative prognostic factors such as anti-CCP antibodies. Our findings support the role of an accurate analysis of foot structural damage and may suggest the usefulness of a correct plantar orthosis prescription also in early phases of the disease.

  5. Validity of quadratic two-source spherical wave structure functions in analysis of beam propagation through generalized atmospheric turbulence

    Science.gov (United States)

    Chen, Chunyi; Yang, Huamin; Kavehrad, Mohsen; Tong, Shoufeng; Li, Yanfang

    2014-12-01

    Two distinct methods based on which two different quadratic-form expressions for the two-source spherical wave structure function (WSF) can be derived are reviewed. The validity of closed-form expressions for the beam-wave cross-spectral density function (CSDF) due to generalized atmospheric turbulence featuring an arbitrary spectral index ranging from 3 to 4, developed based on the quadratic two-source spherical WSFs, is examined in detail. New formulations for the conditions under which the said closed-form expressions for the beam-wave CSDF are strictly valid are developed and several novel interesting findings are elucidated. In particular, the closed-form beam-wave CSDF derived based on the small-separation asymptotic two-source spherical WSF can be considered a rigorous asymptotic solution under the strong-turbulence condition only when the separation distance between the two observation points is much smaller than the inner scale of turbulence; moreover it is also a rigorous asymptotic solution when a certain relation among the initial beam radius, initial transverse coherence width and inner scale holds, regardless of the turbulence strength and spectral index. On the other hand, the accuracy of the closed-form beam-wave CSDF derived based on the large-separation-approximation two-source spherical WSF depends on the spectral index, and a spectral index closer to 4 results in better accuracy.

  6. Original article Reliability, factor structure, and construct validity of the Polish version of the sport imagery ability measure

    Directory of Open Access Journals (Sweden)

    Dagmara Budnik-Przybylska

    2014-12-01

    Full Text Available Background An important component of mental training in sport is the utilization of positive imagery. The “human brain cannot distinguish between an imagined experience and a real experience. The same areas of the brain light up in an imagined experience or imagined performance as in a real experience or performance. For that reason, positive performance imagery has enormous potential” (Orlick, 2008, p. 101. Imagery “has been described as a centre pillar of applied sport psychology” research (Morris, Spittle, & Perry, 2004, p. 344. The aim of the present study was to examine reliability and validity characteristics of the Polish language version of the Sport Imagery Ability Measure (SIAM. Participants and procedure Polish athletes (N = 316 from a range of sports and competitive levels completed the 48 item SIAM. The participants (163 male, 153 female were aged between 12 and 57 years (M = 22.15, SD = 8.25. Results Results indicated that the SIAM had sound internal consistency and maintained good stability over a 3-week period. Confirmatory factor analysis demonstrated that the a priori 3-factor structure of the SIAM resulted in a set of acceptable and poor fit indices (CFI = .91, NFI = .90, RMSEA = .12. Finally, differences in athletes’ imagery abilities were examined in relation to competitive level, gender, and age. Conclusions Overall, results generally supported the reliability and construct validity of the Polish version of the SIAM.

  7. Validity of young children's self-reports of their emotion in response to structured laboratory tasks.

    Science.gov (United States)

    Durbin, C Emily

    2010-08-01

    Can young children report coherently on their emotions, and how do their reports contribute to our understanding of emotional development? Two-hundred six children ages 3 to 6 years participated in structured laboratory tasks designed to elicit a range of positive and negative emotions and indicated their emotional state following each task. Children's reports of their emotions meaningfully varied along with the nature of the different tasks during which they were collected (i.e., reports of negative and positive emotions differed across tasks designed to elicit those states). There were no sex differences on reports of any emotion and only small age differences. Multilevel modeling analyses demonstrated that children's self-reports of each emotion converged significantly with objective coding of expressions of those emotions across laboratory tasks; higher convergence for some emotions was associated with older age, higher verbal intelligence, and greater emotion-recognition abilities.

  8. Constitutive Theories for Woven Composite Structures Subjected to Shock Loading; Experimental Validation Using a Conical Shock Tube

    Directory of Open Access Journals (Sweden)

    David R. Hufner

    2012-01-01

    Full Text Available Woven polymer-based composites are currently used in a wide range of marine applications. These materials often exhibit highly nonlinear, rate dependent, anisotropic behavior under shock loadings. Correlation to transient response data, beyond an initial peak, is often difficult. The state of damage evolves throughout the time history and the unloading response varies based on the amount, and nature of, the accumulated damage. Constitutive theories that address the loading and unloading responses have been developed and integrated with each other. A complete theory, applicable to transient dynamic analysis, is presented. The model is implemented within the commercial finite element code, Abaqus, in the form of a user material subroutine. In this study, the conical shock tube is used to experimentally reproduce the high strain rates and fluid structure interactions typical of underwater shock loadings. The conical shock tube data is used to validate analytical model predictions. Simulation results are in good agreement with test data.

  9. Extending the Newns-Anderson model to molecules with floppy degrees of freedom. Validation by electronic structure calculations

    CERN Document Server

    Baldea, Ioan

    2012-01-01

    In cases where reorganization is important, present theoretical studies of molecular transport have inherently to resort to models. The Newns-Anderson model is ubiquitous for this purpose but, to author's knowledge, attempts to validate/challenge this model by microscopic calculations are missing in the literature. In this work, results of electronic structure calculations are presented, which demonstrate that the conventional Newns-Anderson model fails to describe redox-active tunneling junctions of recent experimental interest. For the case considered, the ($4, 4^\\prime$)-bipyridine molecule, the failure traces back to the floppy degree of freedom represented by the relative rotation of the two pyridine rings. Expressions that generalize the Newns-Anderson model are deduced, which include significant anharmonicities. These expressions can be straightforwardly utilized as input information in calculations of the partially coherent transport.

  10. The Feeding Practices and Structure Questionnaire (FPSQ-28): A parsimonious version validated for longitudinal use from 2 to 5 years.

    Science.gov (United States)

    Jansen, Elena; Williams, Kate E; Mallan, Kimberley M; Nicholson, Jan M; Daniels, Lynne A

    2016-05-01

    Prospective studies and intervention evaluations that examine change over time assume that measurement tools measure the same construct at each occasion. In the area of parent-child feeding practices, longitudinal measurement properties of the questionnaires used are rarely verified. To ascertain that measured change in feeding practices reflects true change rather than change in the assessment, structure, or conceptualisation of the constructs over time, this study examined longitudinal measurement invariance of the Feeding Practices and Structure Questionnaire (FPSQ) subscales (9 constructs; 40 items) across 3 time points. Mothers participating in the NOURISH trial reported their feeding practices when children were aged 2, 3.7, and 5 years (N = 404). Confirmatory Factor Analysis (CFA) within a structural equation modelling framework was used. Comparisons of initial cross-sectional models followed by longitudinal modelling of subscales, resulted in the removal of 12 items, including two redundant or poorly performing subscales. The resulting 28-item FPSQ-28 comprised 7 multi-item subscales: Reward for Behaviour, Reward for Eating, Persuasive Feeding, Overt Restriction, Covert Restriction, Structured Meal Setting and Structured Meal Timing. All subscales showed good fit over 3 time points and each displayed at least partial scalar (thresholds equal) longitudinal measurement invariance. We recommend the use of a separate single item indicator to assess the family meal setting. This is the first study to examine longitudinal measurement invariance in a feeding practices questionnaire. Invariance was established, indicating that the subscales of the shortened FPSQ-28 can be used with mothers to validly assess change in 7 feeding constructs in samples of children aged 2-5 years of age.

  11. Validating two-dimensional leadership models on three-dimensionally structured fish schools

    Science.gov (United States)

    Nagy, Máté; Holbrook, Robert I.; Biro, Dora; Burt de Perera, Theresa

    2017-01-01

    Identifying leader–follower interactions is crucial for understanding how a group decides where or when to move, and how this information is transferred between members. Although many animal groups have a three-dimensional structure, previous studies investigating leader–follower interactions have often ignored vertical information. This raises the question of whether commonly used two-dimensional leader–follower analyses can be used justifiably on groups that interact in three dimensions. To address this, we quantified the individual movements of banded tetra fish (Astyanax mexicanus) within shoals by computing the three-dimensional trajectories of all individuals using a stereo-camera technique. We used these data firstly to identify and compare leader–follower interactions in two and three dimensions, and secondly to analyse leadership with respect to an individual's spatial position in three dimensions. We show that for 95% of all pairwise interactions leadership identified through two-dimensional analysis matches that identified through three-dimensional analysis, and we reveal that fish attend to the same shoalmates for vertical information as they do for horizontal information. Our results therefore highlight that three-dimensional analyses are not always required to identify leader–follower relationships in species that move freely in three dimensions. We discuss our results in terms of the importance of taking species' sensory capacities into account when studying interaction networks within groups.

  12. Genetic and structural validation of Aspergillus fumigatus UDP-N-acetylglucosamine pyrophosphorylase as an antifungal target.

    Science.gov (United States)

    Fang, Wenxia; Du, Ting; Raimi, Olawale G; Hurtado-Guerrero, Ramon; Urbaniak, Michael D; Ibrahim, Adel F M; Ferguson, Michael A J; Jin, Cheng; van Aalten, Daan M F

    2013-08-01

    The sugar nucleotide UDP-N-acetylglucosamine (UDP-GlcNAc) is an essential metabolite in both prokaryotes and eukaryotes. In fungi, it is the precursor for the synthesis of chitin, an essential component of the fungal cell wall. UDP-N-acetylglucosamine pyrophosphorylase (UAP) is the final enzyme in eukaryotic UDP-GlcNAc biosynthesis, converting UTP and N-acetylglucosamine-1-phosphate (GlcNAc-1P) to UDP-GlcNAc. As such, this enzyme may provide an attractive target against pathogenic fungi. Here, we demonstrate that the fungal pathogen Aspergillus fumigatus possesses an active UAP (AfUAP1) that shows selectivity for GlcNAc-1P as the phosphosugar substrate. A conditional mutant, constructed by replacing the native promoter of the A. fumigatus uap1 gene with the Aspergillus nidulans alcA promoter, revealed that uap1 is essential for cell survival and important for cell wall synthesis and morphogenesis. The crystal structure of AfUAP1 was determined and revealed exploitable differences in the active site compared with the human enzyme. Thus AfUAP1 could represent a novel antifungal target and this work will assist the future discovery of small molecule inhibitors against this enzyme.

  13. Validity of semi-quantitative scale for brain MRI in unilateral cerebral palsy due to periventricular white matter lesions: Relationship with hand sensorimotor function and structural connectivity

    Directory of Open Access Journals (Sweden)

    Simona Fiori

    2015-01-01

    Conclusion: The sqMRI scale demonstrates first evidence of construct validity against impaired motor and sensory function measures and brain structural connectivity in a cohort of children with UCP due to PWM lesions. More severe lesions correlated with poorer paretic hand sensorimotor function and impaired structural connectivity in the hemisphere contralateral to the clinical side of hemiplegia. The quantitative structural MRI scoring may be a useful clinical tool for studying brain structure–function relationships but requires further validation in other populations of CP.

  14. An Examination of the Structural, Discriminant, Nomological, and Incremental Predictive Validity of the MSCEIT[copyright sign] V2.0

    Science.gov (United States)

    Rode, Joseph C.; Mooney, Christine H.; Arthaud-Day, Marne L.; Near, Janet P.; Rubin, Robert S.; Baldwin, Timothy T.; Bommer, William H.

    2008-01-01

    We examined the structural, discriminant, nomological, and incremental predictive validity of a behavioral measure of emotional intelligence, using data from two undergraduate student samples. Covariance structure modeling indicated that the eight subscales of the MSCEIT(C) V2.0 were best modeled with a solution consisting of three first-order…

  15. Simulation of planar soft tissues using a structural constitutive model: Finite element implementation and validation.

    Science.gov (United States)

    Fan, Rong; Sacks, Michael S

    2014-06-27

    Computational implementation of physical and physiologically realistic constitutive models is critical for numerical simulation of soft biological tissues in a variety of biomedical applications. It is well established that the highly nonlinear and anisotropic mechanical behaviors of soft tissues are an emergent behavior of the underlying tissue microstructure. In the present study, we have implemented a structural constitutive model into a finite element framework specialized for membrane tissues. We noted that starting with a single element subjected to uniaxial tension, the non-fibrous tissue matrix must be present to prevent unrealistic tissue deformations. Flexural simulations were used to set the non-fibrous matrix modulus because fibers have little effects on tissue deformation under three-point bending. Multiple deformation modes were simulated, including strip biaxial, planar biaxial with two attachment methods, and membrane inflation. Detailed comparisons with experimental data were undertaken to insure faithful simulations of both the macro-level stress-strain insights into adaptations of the fiber architecture under stress, such as fiber reorientation and fiber recruitment. Results indicated a high degree of fidelity and demonstrated interesting microstructural adaptions to stress and the important role of the underlying tissue matrix. Moreover, we apparently resolve a discrepancy in our 1997 study (Billiar and Sacks, 1997. J. Biomech. 30 (7), 753-756) where we observed that under strip biaxial stretch the simulated fiber splay responses were not in good agreement with the experimental results, suggesting non-affine deformations may have occurred. However, by correctly accounting for the isotropic phase of the measured fiber splay, good agreement was obtained. While not the final word, these simulations suggest that affine fiber kinematics for planar collagenous tissues is a reasonable assumption at the macro level. Simulation tools such as these are

  16. Development and experimental validation of a numerical tool for structural health and usage monitoring systems based on chirped grating sensors.

    Science.gov (United States)

    Bettini, Paolo; Guerreschi, Erika; Sala, Giuseppe

    2015-01-01

    The interest of the aerospace industries in structural health and usage monitoring systems is continuously increasing. Among the techniques available in literature those based on Fibre Bragg Grating sensors are much promising thanks to their peculiarities. Different Chirped Bragg Grating sensor configurations have been investigated in this paper. Starting from a numerical model capable of simulating the spectral response of a grating subjected to a generic strain profile (direct problem), a new code has been developed, allowing strain reconstruction from the experimental validation of the program, carried out through different loading cases applied on a chirped grating. The wavelength of the reflection spectrum for a chirped FBG has a one-to-one correspondence to the position along the gauge section, thus allowing strain reconstruction over the entire sensor length. Tests conducted on chirped FBGs also evidenced their potential for SHM applications, if coupled with appropriate numerical strain reconstructions tools. Finally, a new class of sensors-Draw Tower Grating arrays-has been studied. These sensors are applicable to distributed sensing and load reconstruction over large structures, thanks to their greater length. Three configurations have been evaluated, having different spatial and spectral characteristics, in order to explore possible applications of such sensors to SHM systems.

  17. Validation and Benchmarking of a Practical Free Magnetic Energy and Relative Magnetic Helicity Budget Calculation in Solar Magnetic Structures

    CERN Document Server

    Moraitis, K; Georgoulis, M K; Archontis, V

    2014-01-01

    In earlier works we introduced and tested a nonlinear force-free (NLFF) method designed to self-consistently calculate the free magnetic energy and the relative magnetic helicity budgets of the corona of observed solar magnetic structures. The method requires, in principle, only a single, photospheric or low-chromospheric, vector magnetogram of a quiet-Sun patch or an active region and performs calculations in the absence of three-dimensional magnetic and velocity-field information. In this work we strictly validate this method using three-dimensional coronal magnetic fields. Benchmarking employs both synthetic, three-dimensional magnetohydrodynamic simulations and nonlinear force-free field extrapolations of the active-region solar corona. We find that our time-efficient NLFF method provides budgets that differ from those of more demanding semi-analytical methods by a factor of ~3, at most. This difference is expected from the physical concept and the construction of the method. Temporal correlations show mo...

  18. Structural validity of the Dutch-language version of the WAIS-III in a psychiatric sample.

    Science.gov (United States)

    van der Heijden, Paul; van den Bos, Pancras; Mol, Bart; Kessels, Roy P C

    2013-01-01

    The Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV; Wechsler, 2008 ) no longer provides the "traditional" Verbal IQ and Performance IQ deviation scores. In the current study, we investigated the structural validity of these scores in the scale's predecessor, the WAIS-Third Edition (WAIS-III; Wechsler, 1997c ), which is still widely used in clinical practice, especially outside the United States. Confirmative (CFA) and exploratory factor analyses (EFA) were performed on WAIS-III data from a Dutch sample of 247 psychiatric patients. Four competing models were tested in the CFA on 11 subtests. The model that fit the data best was a model in which subtests loaded on the four factor indexes (i.e., 3 Verbal Comprehension subtests, 3 Perceptual Organization subtests, 3 Working Memory subtests, and 2 Processing Speed subtests) as proposed by the manual (Wechsler, 1997b ). In the EFA on 13 subtests with four factors extracted, all subtests were found to load on the factors in accordance with the WAIS-III test manual. However, Picture Arrangement, Arithmetic, and Picture Completion showed only moderate loadings on the proposed factors. Implications for clinical practice are discussed.

  19. Weight pressures in sport: examining the factor structure and incremental validity of the weight pressures in sport - females.

    Science.gov (United States)

    Reel, Justine J; Petrie, Trent A; SooHoo, Sonya; Anderson, Carlin M

    2013-04-01

    Due to pressures within the sport environment, such as from coaches, teammates, uniforms and judges, female athletes may develop unhealthy eating practices to lose weight or change their body size/shape to become more competitive and meet societal and sport-related physique ideals. However, up until the development of the Weight Pressures in Sport for Females (WPS-F; Reel, SooHoo, Petrie, Greenleaf, & Carter, 2010) there was no way to quantify sport-specific weight pressures with female athletes. In this study, the psychometric properties of the scale were further examined using a sample of 414 female collegiate athletes. Sample 1 [n=207; M=19.27 years; SD=1.16] and Sample 2 [n=207; M=19.19 years; SD=1.66] participants were of a similar age and were used for exploratory and confirmatory analyses respectively. A two factor structure was confirmed and it was established that the scale was unique from general sociocultural pressures that all women experience, predicting female athletes' internalization, body dissatisfaction, dietary intent, and bulimic symptomatology. Specifically, the following factors, Coach and Sport Pressures about Weight (Factor 1) and Pressures Regarding Appearance and Performance (Factor 2), were found to have strong internal consistency and the emerging reliable and valid WPS-F has practical implications for screening and identifying weight-related sport pressures within female athletes. WPS-F can also serve to educate sport professionals about environmental pressures so that disordered eating and body image disturbances can be prevented.

  20. Validation of the Penn Inventory of Scrupulosity (PIOS) in scrupulous and nonscrupulous patients: Revision of factor structure and psychometrics.

    Science.gov (United States)

    Huppert, Jonathan D; Fradkin, Isaac

    2016-06-01

    Scrupulosity, or obsessive-compulsive symptoms related to religiosity or religion, is a common presentation of obsessive compulsive disorder (OCD), and it is important to elucidate its phenomenology and measurement. Today, the most widespread questionnaire for the assessment of scrupulosity is the Penn Inventory of Scrupulosity (PIOS). The current study examines the psychometric properties of the PIOS in outpatient, treatment-seeking patients. Results of a confirmatory factor analysis suggested an unsatisfactory fit for previously suggested factor structures. A follow-up exploratory factor analysis suggested that a bifactor model was the most suitable solution. In addition, the scores of the PIOS and its revised subscales were found to have moderate-good concurrent validity; however, its scores discriminated poorly between patients with scrupulous obsessions and patients with OCD and other repugnant obsessions. Group differences and receiver operating characteristics (ROC) analyses both indicated that the PIOS is more suitable in discriminating scrupulous obsessions in Christian patients but not in other religious groups (i.e., Jews, nonreligious patients). Additional analyses revealed that the co-occurrence of scrupulous and other repugnant obsessions is also moderated by religious affiliation. These results raise questions in terms of grouping scrupulosity with other repugnant obsessions and suggest for the need of culturally sensitive instruments of scrupulosity. (PsycINFO Database Record

  1. The Structured Clinical Interview for DSM-5 Internet Gaming Disorder: Development and Validation for Diagnosing IGD in Adolescents

    Science.gov (United States)

    Koo, Hoon Jung; Han, Doug Hyun; Park, Sung-Yong

    2017-01-01

    Objective This study aimed to develop and validate a Structured Clinical Interview for Internet Gaming Disorder (SCI-IGD) in adolescents. Methods First, we generated preliminary items of the SCI-IGD based on the information from the DSM-5 literature reviews and expert consultations. Next, a total of 236 adolescents, from both community and clinical settings, were recruited to evaluate the psychometric properties of the SCI-IGD. Results First, the SCI-IGD was found to be consistent over the time period of about one month. Second, diagnostic concordances between the SCI-IGD and clinician's diagnostic impression were good to excellent. The Likelihood Ratio Positive and the Likelihood Ratio Negative estimates for the diagnosis of SCI-IGD were 10.93 and 0.35, respectively, indicating that SCI-IGD was ‘very useful test’ for identifying the presence of IGD and ‘useful test’ for identifying the absence of IGD. Third, SCI-IGD could identify disordered gamers from non-disordered gamers. Conclusion The implications and limitations of the study are also discussed. PMID:28096871

  2. Construct Validity of the Braden Scale for Pressure Ulcer Assessment in Acute Care: A Structural Equation Modeling Approach.

    Science.gov (United States)

    Chen, Hong-Lin; Cao, Ying-Juan; Shen, Wang-Qin; Zhu, Bin

    2017-02-01

    The Braden Scale is the most widely used pressure ulcer risk assessment system in the world. To investigate its construct validity using structural equation modeling (SEM), a secondary analysis of retrospective data of patients admitted to an acute care facility was conducted using the records of 2588 patients who were at risk for pressure ulcers and admitted between January 2013 and December 2013. Data were extracted to an Excel sheet and analyzed, including demographic characteristics (ie, patients age, gender, weight, and disease spectrum), as well as total Braden scores and subscale scores. The SEM was set according to modification indices suggestion. The original Braden Scale model was supported by χ2(9) = 22.854, CFI = 0.902, GFI = 0.974, root mean square error of approximation (RMSEA) = 0.092, indicating inadequate model fit. After modification according to software indices, χ2(2) = 2.052, CFI = 0.999, GFI = 0.999, RMSEA = 0.020 indicated an acceptable fit of the model (final model). The factor loadings of 6 subscales were all significant (P <.001), with .147 for nutrition, .137 for activity, .167 for friction and shear, .825 for sensory perception, .626 for mobility, and .556 for moisture subscale. The nutrition, activity, and friction and shear subscales were corrected to examine their relationships with other Braden Scale subscales (nutrition with activity [φ -0.063], activity with friction/shear [φ 0.136], and nutrition (φ friction/shear [0.159]). The factor loadings ranged from -0.067 to 0.159. These findings suggest the original Braden Scale has inadequate construct validity for acute care patients and that new risk-predicting scales should be designed based on data mining. Second, according to the factor loadings in the SEM, the most important risk factor in the Braden Scale for this patient population is sensory perception, followed by mobility and moisture. This suggests practitioners should pay particular attention to pressure ulcer prevention

  3. Optical techniques as validation tools for finite element modeling of biomechanical structures, demonstrated in bird ear research

    Science.gov (United States)

    Muyshondt, Pieter; De Greef, Daniël; Soons, Joris; Dirckx, Joris J. J.

    2014-05-01

    In this paper we demonstrate the potential of stroboscopic digital holography and laser vibrometry as tools to gather vibration data and validate modelling results in complex biomechanical systems, in this case the avian middle ear. Whereas the middle ear of all mammal species contains three ossicles, birds only feature one ossicle, the columella. Despite this far simpler design, the hearing range of most birds is comparable to mammals, and is adapted to operate under very diverse atmospheric circumstances. This makes the investigation of the avian middle ear potentially very meaningful, since it could provide knowledge that can improve the design of prosthetic ossicle replacements in humans such as a TORP (Total Ossicle Replacement Prosthesis). In order to better understand the mechanics of the bird's hearing, we developed a finite element model that simulates the transmission of an incident acoustic wave on the eardrum via the middle ear structures to the fluid of the inner ear. The model is based on geometry extracted from stained μCT data and is validated using results from stroboscopic digital holography measurements on the eardrum and LDV measurements on the columella footplate. This technique uses very short high-power laser pulses that are synchronized to the membrane's vibration phase to measure the dynamic response of the bird's eardrum to an incident acoustic stimulus. Vibration magnitude as well as phase relative to the sound wave can be deduced from the results, the latter being of great importance in the elastic characterization of the tympanic membrane. In this work, the setup and results from the optical measurements, as well as the properties and optimization of the finite element model are presented. Observed phase variations across the eardrum's surface on the holography results strongly suggest the presence of internal energy losses in the membrane due to damping. Therefore, a viscoelastic characterisation of the model based on a complex

  4. Modeling validation to structural flaws in the foundations of oil tanks; Validacao de modelagem para estudo de alteracoes estruturais em fundacoes de tanques de petroleo

    Energy Technology Data Exchange (ETDEWEB)

    Couto, Larissa Goncalves; Leite, Sandro Passos, E-mail: leite_sp@ig.com.br [Fundacao Tecnico-Educacional Souza Marques, Rio de Janeiro, RJ (Brazil). Faculdade de Engenharia; Pereira, Walsan Wagner [Instituto de Radioprotecao e Dosimetria, (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

    2014-07-01

    This paper presents the modeling of an experiment used to study the application of backscattered neutrons in the identification of structural flaws in the foundations of oil tanks. This modeling was a preliminary validation procedure of the method of calculation, performed with the radiation transport code MCNP, to study the application of backscattered neutrons as inspection tool. (author)

  5. A Validational Study of the Structured Interview of Symptoms Associated with Sexual Abuse (SASA) Using Three Samples of Sexually Abused, Allegedly Abused, and Nonabused Boys.

    Science.gov (United States)

    Wells, Robert; McCann, John; Adams, Joyce; Voris, Joan; Dahl, Barbara

    1997-01-01

    A study validated the use of a structured parent interview regarding emotional, behavioral, and physical symptoms by comparing results among 22 sexually abused boys whose perpetrator confessed, 47 boys evaluated in a sexual abuse clinic but without a history of perpetrator confession, and 52 nonabused boys (ages 3-15). (Author/CR)

  6. The Inventory of Teacher-Student Relationships: Factor Structure, Reliability, and Validity among African American Youth in Low-Income Urban Schools

    Science.gov (United States)

    Murray, Christopher; Zvoch, Keith

    2011-01-01

    This study investigates the factor structure, reliability, and validity of the Inventory of Teacher-Student Relationships (IT-SR), a measure that was developed by adapting the widely used Inventory of Parent and Peer Attachments (Armsden & Greenberg, 1987) for use in the context of teacher-student relationships. The instrument was field tested…

  7. The Theory of Planned Behavior (TPB) and Pre-Service Teachers' Technology Acceptance: A Validation Study Using Structural Equation Modeling

    Science.gov (United States)

    Teo, Timothy; Tan, Lynde

    2012-01-01

    This study applies the theory of planned behavior (TPB), a theory that is commonly used in commercial settings, to the educational context to explain pre-service teachers' technology acceptance. It is also interested in examining its validity when used for this purpose. It has found evidence that the TPB is a valid model to explain pre-service…

  8. Reliability and validity assessment of an apathy scale for home-care patients with Parkinson's disease: a structural equation modeling analysis.

    Science.gov (United States)

    Morita, Hiroaki; Kannari, Kazuya

    2016-06-01

    [Purpose] Based on the Starkstein Apathy Scale, an apathy scale was developed for home-care patients with Parkinson's disease using structural equation modeling (SEM), with which the data compatibility of extraction factors can be verified. [Subjects and Methods] The participants were 122 home-care patients with Parkinson's disease (mean age: 70.9 ± 7.8 years) who were member of the Aomori branch or Tohoku/Hokkaido block of the Japan Parkinson's Disease Association. A questionnaire survey (anonymous, self-administered) was carried out by distributing and collecting questionnaires by mail or a collective survey at a workshop. Construct validity was evaluated by confirmatory factor analysis using SEM. Internal consistency was investigated using Cronbach's alpha coefficient. Criterion-related validity was assessed by correlation analysis with the total score of the Beck Depression Inventory. [Results] Concerning construct validity, 11 of the 14 question items of the original scale were extracted. Cronbach's α of this scale was 0.939. For criterion-related validity, Spearman's rank correlation coefficient was 0.831. [Conclusion] The construct validity, internal consistency, and criterion-related validity of the 11-item apathy scale were confirmed. The 11-item apathy scale can serve as a useful tool for the efficient and effective assessment of rehabilitation, establishment of rehabilitation goals and programs for patients with Parkinson's disease.

  9. Development and validation of a bedside risk score for MRSA among patients hospitalized with complicated skin and skin structure infections

    Directory of Open Access Journals (Sweden)

    Zilberberg Marya D

    2012-07-01

    Full Text Available Abstract Background Methicillin-resistant Staphylococcus aureus (MRSA is a frequent cause of complicated skin and skin structure infections (cSSSI. Patients with MRSA require different empiric treatment than those with non-MRSA infections, yet no accurate tools exist to aid in stratifying the risk for a MRSA cSSSI. We sought to develop a simple bedside decision rule to tailor empiric coverage more accurately. Methods We conducted a large multicenter (N=62 hospitals retrospective cohort study in a US-based database between April 2005 and March 2009. All adult initial admissions with ICD-9-CM codes specific to cSSSI were included. Patients admitted with MRSA vs. non-MRSA were compared with regard to baseline demographic, clinical and hospital characteristics. We developed and validated a model to predict the risk of MRSA, and compared its performance via sensitivity, specificity and other classification statistics to the healthcare-associated (HCA infection risk factors. Results Of the 7,183 patients with cSSSI, 2,387 (33.2% had MRSA. Factors discriminating MRSA from non-MRSA were age, African-American race, no evidence of diabetes mellitus, cancer or renal dysfunction, and prior history of cardiac dysrhythmia. The score ranging from 0 to 8 points exhibited a consistent dose–response relationship. A MRSA score of 5 or higher was superior to the HCA classification in all characteristics, while that of 4 or higher was superior on all metrics except specificity. Conclusions MRSA is present in 1/3 of all hospitalized cSSSI. A simple bedside risk score can help discriminate the risk for MRSA vs. other pathogens with improved accuracy compared to the HCA definition.

  10. Extended criteria and predictors in college admission: Exploring the structure of study success and investigating the validity of domain knowledge

    Directory of Open Access Journals (Sweden)

    OLGA KUNINA

    2007-06-01

    Full Text Available The utility of aptitude tests and intelligence measures in the prediction of the success in college is one of the empirically best supported results in ability research. However, the structure of the criterion “study success” has not been appropriately investigated so far. Moreover, it remains unclear which aspect of intelligence – fluid intelligence or crystallized intelligence – has the major impact on the prediction. In three studies we have investigated the dimensionality of the criterion achievements as well as the relative contributions of competing ability predictors. In the first study, the dimensionality of college grades was explored in a sample of 629 alumni. A measurement model with two correlated latent factors distinguishing undergraduate college grades on the one hand from graduate college grades on the other hand had the best fit to the data. In the second study, a group of 179 graduate students completed a Psychology knowledge test and provided available college grades in undergraduate studies. A model separating a general latent factor for Psychology knowledge from a nested method factor for college grades, and a second nested factor for “experimental orientation” had the best fit to the data. In the third study the predictive power of domain specific knowledge tests in Mathematics, English, and Biology was investigated. A sample of 387 undergraduate students in this prospective study additionally completed a compilation of fluid intelligence tests. The results of this study indicate as expected that: a ability measures are incrementally predictive over school grades in predicting exam grades; and b that knowledge tests from relevant domains were incrementally predictive over fluid intelligence. The results of these studies suggest that criteria for college admission tests deserve and warrant more attention, and that domain specific ability indicators can contribute to the predictive validity of established

  11. Cross-validation of the structure of a transiently formed and low populated FF domain folding intermediate determined by relaxation dispersion NMR and CS-Rosetta.

    Science.gov (United States)

    Barette, Julia; Velyvis, Algirdas; Religa, Tomasz L; Korzhnev, Dmitry M; Kay, Lewis E

    2012-06-14

    We have recently reported the atomic resolution structure of a low populated and transiently formed on-pathway folding intermediate of the FF domain from human HYPA/FBP11 [Korzhnev, D. M.; Religa, T. L.; Banachewicz, W.; Fersht, A. R.; Kay, L.E. Science 2011, 329, 1312-1316]. The structure was determined on the basis of backbone chemical shift and bond vector orientation restraints of the invisible intermediate state measured using relaxation dispersion nuclear magnetic resonance (NMR) spectroscopy that were subsequently input into the database structure determination program, CS-Rosetta. As a cross-validation of the structure so produced, we present here the solution structure of a mimic of the folding intermediate that is highly populated in solution, obtained from the wild-type domain by mutagenesis that destabilizes the native state. The relaxation dispersion/CS-Rosetta structures of the intermediate are within 2 Å of those of the mimic, with the nonnative interactions in the intermediate also observed in the mimic. This strongly confirms the structure of the FF domain folding intermediate, in particular, and validates the use of relaxation dispersion derived restraints in structural studies of invisible excited states, in general.

  12. Reliability and validity of a semi-structured DSM-based diagnostic interview module for the assessment of Attention Deficit Hyperactivity Disorder in adult psychiatric outpatients.

    Science.gov (United States)

    Gorlin, Eugenia I; Dalrymple, Kristy; Chelminski, Iwona; Zimmerman, Mark

    2016-08-30

    Despite growing recognition that the symptoms and functional impairments of Attention Deficit/Hyperactivity Disorder (ADHD) persist into adulthood, only a few psychometrically sound diagnostic measures have been developed for the assessment of ADHD in adults, and none have been validated for use in a broad treatment-seeking psychiatric sample. The current study presents the reliability and validity of a semi-structured DSM-based diagnostic interview module for ADHD, which was administered to 1194 adults presenting to an outpatient psychiatric practice. The module showed excellent internal consistency and interrater reliability, good convergent and discriminant validity (as indexed by relatively high correlations with self-report measures of ADHD and ADHD-related constructs and little or no correlation with other, non-ADHD symptom domains), and good construct validity (as indexed by significantly higher rates of psychosocial impairment and self-reported family history of ADHD in individuals who meet criteria for an ADHD diagnosis). This instrument is thus a reliable and valid diagnostic tool for the detection of ADHD in adults presenting for psychiatric evaluation and treatment.

  13. Field Evaluations Test Plan for Validation of Alternative Low-Emission Surface Preparation/Depainting Technologies for Structural Steel

    Science.gov (United States)

    Lewis, Pattie

    2005-01-01

    Headquarters National Aeronautics and Space Administration (NASA) chartered the Acquisition Pollution Prevention (AP2) Office to coordinate agency activities affecting pollution prevention issues identified during system and component acquisition and sustainment processes. The primary objectives of the AP2 Office are to: (1) Reduce or eliminate the use of hazardous materials (HazMats) or hazardous processes at manufacturing, remanufacturing, and sustainment locations. (2) Avoid duplication of effort in actions required to reduce or eliminate HazMats through joint center cooperation and technology sharing. To achieve a substrate condition suitable for the application of a coating system, both new and old (in-situ) substrates must undergo some type of surface preparation and/or depainting operation to ensure adhesion of the new coating system. The level of cleanliness or anchor profile desired is typically a function of the type of coating to be applied and the specification being adhered to. In high performance environments, cleanliness and surface profile requirements for carbon steel (the dominant substrate for facilities, structures and equipment) dictates the use of abrasive media. Many of the abrasive media currently used across NASA and Air Force Space Command (AFSPC) installations generate large quantities of fugitive particulate emissions and waste. The high quantities of airborne dust and waste generated from these operations pose significant environmental concern. Efforts to contain emissions and the reduce quantity of waste generated have significant implications on project cost; this is often a deterrent to engaging in maintenance activities. In response to recent technological developments and NASA's and AFSPC's need to undertake environmentally conscious corrosion prevention projects, a review of the industry needs to be undertaken to evaluate surface preparation technologies (materials and processes) for embrace. This project will identify, evaluate

  14. The DUNDRUM-1 structured professional judgment for triage to appropriate levels of therapeutic security: retrospective-cohort validation study

    Directory of Open Access Journals (Sweden)

    O'Neill Conor

    2011-03-01

    Full Text Available Abstract Background The assessment of those presenting to prison in-reach and court diversion services and those referred for admission to mental health services is a triage decision, allocating the patient to the appropriate level of therapeutic security. This is a critical clinical decision. We set out to improve on unstructured clinical judgement. We collated qualitative information and devised an 11 item structured professional judgment instrument for this purpose then tested for validity. Methods All those assessed following screening over a three month period at a busy remand committals prison (n = 246 were rated in a retrospective cohort design blind to outcome. Similarly, all those admitted to a mental health service from the same prison in-reach service over an overlapping two year period were rated blind to outcome (n = 100. Results The 11 item scale had good internal consistency (Cronbach's alpha = 0.95 and inter-rater reliability. The scale score did not correlate with the HCR-20 'historical' score. For the three month sample, the receiver operating characteristic area under the curve (AUC for those admitted to hospital was 0.893 (95% confidence interval 0.843 to 0.943. For the two year sample, AUC distinguished at each level between those admitted to open wards, low secure units or a medium/high secure service. Open wards v low secure units AUC = 0.805 (95% CI 0.680 to 0.930; low secure v medium/high secure AUC = 0.866, (95% CI 0.784 to 0.949. Item to outcome correlations were significant for all 11 items. Conclusions The DUNDRUM-1 triage security scale and its items performed to criterion levels when tested against the real world outcome. This instrument can be used to ensure consistency in decision making when deciding who to admit to secure forensic hospitals. It can also be used to benchmark admission thresholds between services and jurisdictions. In this study we found some divergence between assessed need and actual placement

  15. Validating the German version of the Quality of Relationship Inventory: confirming the three-factor structure and report of psychometric properties.

    Directory of Open Access Journals (Sweden)

    Iris Reiner

    Full Text Available Research on psychosocial influences such as relationship characteristics has received increased attention in the clinical as well as social-psychological field. Several studies demonstrated that the quality of relationships, in particular with respect to the perceived support within intimate relationships, profoundly affects individuals' mental and physical health. There is, however, a limited choice of valid and internationally known assessments of relationship quality in Germany. We report the validation of the German version of the Quality of Relationships Inventory (QRI. First, we evaluated its factor structure in a representative German sample of 1.494 participants by means of confirmatory factor analysis. Our findings support the previously proposed three-factor structure. Second, importance and satisfaction with different relationship domains (family/children and relationship/sexuality were linked with the QRI scales, demonstrating high construct validity. Finally, we report sex and age differences regarding the perceived relationship support, conflict and depth in our German sample. In conclusion, the QRI is a reliable and valid measurement to assess social support in romantic relationships in the German population.

  16. STRUCTURE AND VALIDATION OF A CONTEXTUAL QUALITY OF LIFE SCALE FOR PEOPLE WITH INTELLECTUAL DISABILITIES IN SOCIAL SERVICES: AN ORGANIZATION-ORIENTED MEASURE FROM AN EXTERNAL PERSPECTIVE

    Directory of Open Access Journals (Sweden)

    Carolina Moliner

    2013-09-01

    Full Text Available The aim of this study is to develop and validate a scale on the Quality of Life (QoL of people with intellectual disabilities as assessed by family members (external perspective. The instrument measures improvement in QoL due to actions by organizations delivering services to individuals with intellectual disabilities (organization-oriented measure. In order to design the items for the scale, focus groups were set up with professionals dedicated to attending to individuals with intellectual disabilities. An initial scale of 20 items was constructed by consensus. A total of 1195 family members answered the questionnaire. In order to assess the structure of the scale, EFA recommended deleting 3 overlapping items. The final scale consisted of 17 items (α=95 and was composed of four main dimensions: self-determination (SD, social inclusion (SI, rights (RI and overall improvement (OI, which explained 74.83% of the variance. Finally, the consistency and validity were assessed. Convergent validity and discriminant validity were satisfactory. Moreover, CFA confirmed the structure of the scale. Main conclusions, limitations and practical implications are discussed.

  17. Magnetic Decoupling Design and Experimental Validation of a Radial-Radial Flux Compound-Structure Permanent-Magnet Synchronous Machine for HEVs

    Directory of Open Access Journals (Sweden)

    Zhiyi Song

    2012-10-01

    Full Text Available The radial-radial flux compound-structure permanent-magnet synchronous machine (CS-PMSM, integrated by two concentrically arranged permanent-magnet electric machines, is an electromagnetic power-splitting device for hybrid electric vehicles (HEVs. As the two electric machines share a rotor as structural and magnetic common part, their magnetic paths are coupled, leading to possible mutual magnetic-field interference and complex control. In this paper, a design method to ensure magnetic decoupling with minimum yoke thickness of the common rotor is investigated. A prototype machine is designed based on the proposed method, and the feasibility of magnetic decoupling and independent control is validated by experimental tests of mutual influence. The CS-PMSM is tested by a designed driving cycle, and functions to act as starter motor, generator and to help the internal combustion engine (ICE operate at optimum efficiency are validated.

  18. Assessing adult attachment across different contexts: validation of the Portuguese version of the experiences in Close Relationships-Relationship Structures questionnaire.

    Science.gov (United States)

    Moreira, Helena; Martins, Teresa; Gouveia, Maria João; Canavarro, Maria Cristina

    2015-01-01

    The Experiences in Close Relationships-Relationship Structures questionnaire (ECR-RS) is one of the most recent measures of adult attachment. This instrument provides a contextual assessment of attachment-related anxiety and avoidance by measuring these dimensions in various close relationships (mother, father, partner, friend). To further explore its psychometric properties and cross-cultural adequacy, this study presents the validation of the ECR-RS in a sample of Portuguese community individuals (N = 236). The Portuguese version showed adequate reliability and construct validity. The original 2-factor structure was confirmed through confirmatory factor analysis. The ECR-RS is a psychometrically robust measure of attachment, representing an important advance in the measurement of adult attachment.

  19. Organizational Leadership Assessment in Servant Organizations: Adaptation for Turkish Culture, Language Validity and Examination of Factor Structure

    Directory of Open Access Journals (Sweden)

    Hakkı KAHVECİ

    2012-06-01

    Full Text Available The purpose of this study is to adapt Laub’s (1999 Organizational Leadership Assessment in Servant Organizations to Turkish literaturate on servant leadership. Validity and reliability analyzes were conducted. The original instrument included 60 questions and six dimensions. Data was collected from primaryschool teachers in Eskişehir and Balıkesir. Descriptive statistics and exploratory factor analyis were used to analyze the data. Resulst indicated that, a valid and relaible instrument included 54 questions with two dimensions.

  20. The Impact of Structural Break(s on the Validity of Purchasing Power Parity in Turkey: Evidence from Zivot-Andrews and Lagrange Multiplier Unit Root Tests

    Directory of Open Access Journals (Sweden)

    Hakan Kum

    2012-01-01

    Full Text Available This study examines the validity of the purchasing power parity (PPP in Turkey for annual data from 1953 to 2009. While results from both the ADF unit root and the DF-GLS unit root test indicate mixed results, PPP holds for Turkey with the presence of structural breaks which are obtained by Zivot and Andrews and Lagrange Multiplier unit root tests.

  1. Structures' validation profiles in Transmission of Imaging and Data (TRIAD) for automated National Clinical Trials Network (NCTN) clinical trial digital data quality assurance.

    Science.gov (United States)

    Giaddui, Tawfik; Yu, Jialu; Manfredi, Denise; Linnemann, Nancy; Hunter, Joanne; O'Meara, Elizabeth; Galvin, James; Bialecki, Brian; Xiao, Ying

    2016-01-01

    Transmission of Imaging and Data (TRIAD) is a standard-based system built by the American College of Radiology to provide the seamless exchange of images and data for accreditation of clinical trials and registries. Scripts of structures' names validation profiles created in TRIAD are used in the automated submission process. It is essential for users to understand the logistics of these scripts for successful submission of radiation therapy cases with less iteration.

  2. Using Structural Equation Modeling to Validate the Theory of Planned Behavior as a Model for Predicting Student Cheating

    Science.gov (United States)

    Mayhew, Matthew J.; Hubbard, Steven M.; Finelli, Cynthia J.; Harding, Trevor S.; Carpenter, Donald D.

    2009-01-01

    The purpose of this paper is to validate the use of a modified Theory of Planned Behavior (TPB) for predicting undergraduate student cheating. Specifically, we administered a survey assessing how the TPB relates to cheating along with a measure of moral reasoning (DIT- 2) to 527 undergraduate students across three institutions; and analyzed the…

  3. Factor Structure of the Schalock and Keith Quality of Life Questionnaire (QOL-Q): Validation on Mexican and Spanish Samples

    Science.gov (United States)

    Caballo, C.; Crespo, M.; Jenaro, C.; Verdugo, M. A.; Martinez, J. L.

    2005-01-01

    Background: The Quality of Life Questionnaire (QOL-Q) is used widely to evaluate the quality of life of persons with intellectual disability (ID). Its validity for use with Spanish-speaking cultures has been demonstrated for individuals with visual disabilities, but not for those with physical or intellectual disabilities. Such was the purpose of…

  4. Structural Validity of the MACI Psychopathy and Narcissism Scales: Evidence of Multidimensionality and Implications for Use in Research and Screening

    Science.gov (United States)

    Penney, Stephanie R.; Moretti, Marlene M.; Da Silva, Kimberley S.

    2008-01-01

    This study investigated the psychometric properties and predictive validity of three self-report scales (the Psychopathy Content Scale, the Psychopathy-16 scale, and the Egotistic scale) derived from the Millon Adolescent Clinical Inventory (MACI) to screen for the presence of psychopathic and narcissistic personality characteristics. Exploratory…

  5. Construct validity evidence for the Male Role Norms Inventory-Short Form: A structural equation modeling approach using the bifactor model.

    Science.gov (United States)

    Levant, Ronald F; Hall, Rosalie J; Weigold, Ingrid K; McCurdy, Eric R

    2016-10-01

    The construct validity of the Male Role Norms Inventory-Short Form (MRNI-SF) was assessed using a latent variable approach implemented with structural equation modeling (SEM). The MRNI-SF was specified as having a bifactor structure, and validation scales were also specified as latent variables. The latent variable approach had the advantages of separating effects of general and specific factors and controlling for some sources of measurement error. Data (N = 484) were from a diverse sample (38.8% men of color, 22.3% men of diverse sexualities) of community-dwelling and college men who responded to an online survey. The construct validity of the MRNI-SF General Traditional Masculinity Ideology factor was supported for all 4 of the proposed latent correlations with: (a) Male Role Attitudes Scale; (b) general factor of Conformity to Masculine Norms Inventory-46; (c) higher-order factor of Gender Role Conflict Scale; and (d) Personal Attributes Questionnaire-Masculinity Scale. Significant correlations with relevant other latent factors provided concurrent validity evidence for the MRNI-SF specific factors of Negativity toward Sexual Minorities, Importance of Sex, Restrictive Emotionality, and Toughness, with all 8 of the hypothesized relationships supported. However, 3 relationships concerning Dominance were not supported. (The construct validity of the remaining 2 MRNI-SF specific factors-Avoidance of Femininity and Self-Reliance through Mechanical Skills was not assessed.) Comparisons were made, and meaningful differences noted, between the latent correlations emphasized in this study and their raw variable counterparts. Results are discussed in terms of the advantages of an SEM approach and the unique characteristics of the bifactor model. (PsycINFO Database Record

  6. Direct-contact condensers for open-cycle OTEC applications: Model validation with fresh water experiments for structured packings

    Energy Technology Data Exchange (ETDEWEB)

    Bharathan, D.; Parsons, B.K.; Althof, J.A.

    1988-10-01

    The objective of the reported work was to develop analytical methods for evaluating the design and performance of advanced high-performance heat exchangers for use in open-cycle thermal energy conversion (OC-OTEC) systems. This report describes the progress made on validating a one-dimensional, steady-state analytical computer of fresh water experiments. The condenser model represents the state of the art in direct-contact heat exchange for condensation for OC-OTEC applications. This is expected to provide a basis for optimizing OC-OTEC plant configurations. Using the model, we examined two condenser geometries, a cocurrent and a countercurrent configuration. This report provides detailed validation results for important condenser parameters for cocurrent and countercurrent flows. Based on the comparisons and uncertainty overlap between the experimental data and predictions, the model is shown to predict critical condenser performance parameters with an uncertainty acceptable for general engineering design and performance evaluations. 33 refs., 69 figs., 38 tabs.

  7. Direct-contact condensers for open-cycle OTEC applications: Model validation with fresh water experiments for structured packings

    Science.gov (United States)

    Bharathan, D.; Parsons, B. K.; Althof, J. A.

    1988-10-01

    The objective of the reported work was to develop analytical methods for evaluating the design and performance of advanced high-performance heat exchangers for use in open-cycle thermal energy conversion (OC-OTEC) systems. This report describes the progress made on validating a one-dimensional, steady-state analytical computer of fresh water experiments. The condenser model represents the state of the art in direct-contact heat exchange for condensation for OC-OTEC applications. This is expected to provide a basis for optimizing OC-OTEC plant configurations. Using the model, we examined two condenser geometries, a cocurrent and a countercurrent configuration. This report provides detailed validation results for important condenser parameters for cocurrent and countercurrent flows. Based on the comparisons and uncertainty overlap between the experimental data and predictions, the model is shown to predict critical condenser performance parameters with an uncertainty acceptable for general engineering design and performance evaluations.

  8. Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

    Science.gov (United States)

    van de Streek, Jacco; Neumann, Marcus A

    2014-12-01

    In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

  9. Assessment of the structural validity of the domestic violence healthcare providers’ survey questionnaire using a Nigerian sample

    OpenAIRE

    Stephen Lawoko; Ime Akpan John

    2010-01-01

    Abstract: Background: There has been increased advocacy to involve healthcare providers in the prevention of intimate partner violence (IPV) through screening for it in healthcare. Yet, only one in ten providers screen for IPV, suggesting barriers. Understanding the readiness of healthcare providers to screen for IPV is therefore paramount. The Domestic Violence Healthcare Provider Survey Scales (DVHPSS) is a previously validated, comprehensive scale to study readiness of healthcare providers...

  10. A coarse-grained protein force field for folding and structure prediction.

    Science.gov (United States)

    Maupetit, Julien; Tuffery, P; Derreumaux, Philippe

    2007-11-01

    We have revisited the protein coarse-grained optimized potential for efficient structure prediction (OPEP). The training and validation sets consist of 13 and 16 protein targets. Because optimization depends on details of how the ensemble of decoys is sampled, trial conformations are generated by molecular dynamics, threading, greedy, and Monte Carlo simulations, or taken from publicly available databases. The OPEP parameters are varied by a genetic algorithm using a scoring function which requires that the native structure has the lowest energy, and the native-like structures have energy higher than the native structure but lower than the remote conformations. Overall, we find that OPEP correctly identifies 24 native or native-like states for 29 targets and has very similar capability to the all-atom discrete optimized protein energy model (DOPE), found recently to outperform five currently used energy models.

  11. Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

    DEFF Research Database (Denmark)

    van de Streek, Jacco; Neumann, Marcus A

    2014-01-01

    is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.......In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published...... minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom...

  12. The Psychometric Properties of the Center for Epidemiologic Studies Depression Scale in Chinese Primary Care Patients: Factor Structure, Construct Validity, Reliability, Sensitivity and Responsiveness.

    Directory of Open Access Journals (Sweden)

    Weng Yee Chin

    Full Text Available The Center for Epidemiologic Studies Depression Scale (CES-D is a commonly used instrument to measure depressive symptomatology. Despite this, the evidence for its psychometric properties remains poorly established in Chinese populations. The aim of this study was to validate the use of the CES-D in Chinese primary care patients by examining factor structure, construct validity, reliability, sensitivity and responsiveness.The psychometric properties were assessed amongst a sample of 3686 Chinese adult primary care patients in Hong Kong. Three competing factor structure models were examined using confirmatory factor analysis. The original CES-D four-structure model had adequate fit, however the data was better fit into a bi-factor model. For the internal construct validity, corrected item-total correlations were 0.4 for most items. The convergent validity was assessed by examining the correlations between the CES-D, the Patient Health Questionnaire 9 (PHQ-9 and the Short Form-12 Health Survey (version 2 Mental Component Summary (SF-12 v2 MCS. The CES-D had a strong correlation with the PHQ-9 (coefficient: 0.78 and SF-12 v2 MCS (coefficient: -0.75. Internal consistency was assessed by McDonald's omega hierarchical (ωH. The ωH value for the general depression factor was 0.855. The ωH values for "somatic", "depressed affect", "positive affect" and "interpersonal problems" were 0.434, 0.038, 0.738 and 0.730, respectively. For the two-week test-retest reliability, the intraclass correlation coefficient was 0.91. The CES-D was sensitive in detecting differences between known groups, with the AUC >0.7. Internal responsiveness of the CES-D to detect positive and negative changes was satisfactory (with p value 0.2. The CES-D was externally responsive, with the AUC>0.7.The CES-D appears to be a valid, reliable, sensitive and responsive instrument for screening and monitoring depressive symptoms in adult Chinese primary care patients. In its original

  13. Crack Detection in Fibre Reinforced Plastic Structures Using Embedded Fibre Bragg Grating Sensors: Theory, Model Development and Experimental Validation

    DEFF Research Database (Denmark)

    Pereira, Gilmar Ferreira; Mikkelsen, Lars Pilgaard; McGugan, Malcolm

    2015-01-01

    properties. When applying this concept to different structures, sensor systems and damage types, a combination of damage mechanics, monitoring technology, and modelling is required. The primary objective of this article is to demonstrate such a combination. This article is divided in three main topics......In a fibre-reinforced polymer (FRP) structure designed using the emerging damage tolerance and structural health monitoring philosophy, sensors and models that describe crack propagation will enable a structure to operate despite the presence of damage by fully exploiting the material’s mechanical...... a crack growth/damage event in fibre-reinforced polymer or structural adhesive-bonded structures using embedded fibre Bragg grating (FBG) sensors is presented by combining conventional measured parameters, such as wavelength shift, with parameters associated with measurement errors, typically ignored...

  14. Validity and reliability of a structured interview for early detection and risk assessment of parenting and developmental problems in young children: a cross-sectional study

    Directory of Open Access Journals (Sweden)

    van Stel Henk F

    2012-06-01

    Full Text Available Abstract Background Preventive child health care is well suited for the early detection of parenting and developmental problems. However, as far as the younger age group is concerned, there are no validated early detection instruments which cover both the child and its environment. Therefore, we have developed a broad-scope structured interview which assesses parents’ concerns and their need for support, using both the parental perspective and the experience of the child health care nurse: the Structured Problem Analysis of Raising Kids (SPARK. This study reports the psychometric characteristics of the SPARK. Method A cross-sectional study of 2012 18-month-old children, living in Zeeland, a province of the Netherlands. Inter-rater reliability was assessed in 67 children. Convergent validity was assessed by comparing SPARK-domains with domains in self-report questionnaires on child development and parenting stress. Discriminative validity was assessed by comparing different outcomes of the SPARK between groups with different levels of socio-economic status and by performing an extreme-groups comparison. The user experience of both parents and nurses was assessed with the aid of an online survey. Results The response rate was 92.1% for the SPARK. Self-report questionnaires were returned in the case of 66.9% of the remaining 1721 children. There was selective non-reporting: 33.1% of the questionnaires were not returned, covering 65.2% of the children with a high-risk label according to the SPARK (p  Conclusion The SPARK discriminates between children with a high, increased and low risk of parenting and developmental problems. It does so in a reliable way, but more research is needed on aspects of validity and in other populations.

  15. Factor Structure and Construct Validity of the Eating Disorder Examination-Questionnaire in College Students: Further Support for a Modified Brief Version

    Science.gov (United States)

    Grilo, Carlos M.; Reas, Deborah L.; Hopwood, Christopher J.; Crosby, Ross D.

    2014-01-01

    Objective The Eating Disorder Examination-Questionnaire (EDE-Q) is widely used in research studies across clinical and non-clinical groups. Relatively little is known about psychometric properties of this measure and the available literature has not supported the proposed scale structure. The current study evaluated the factor structure and construct validity of the EDE-Q in a non-clinical study group of young adults. Method Participants were 801 young adults (573 females, 228 males) enrolled at a large public university in the Midwestern United States who completed the EDE-Q and a battery of behavioral and psychological measures. Results Confirmatory factor analysis (CFA) revealed an inadequate fit for the original EDE-Q structure but revealed a good fit for an alternative structure suggested by recent research with predominately overweight/obese samples. CFA supported a modified 7-item, 3-factor structure; the three factors were interpreted as dietary restraint, shape/weight overvaluation, and body dissatisfaction. Factor loadings and item intercepts were invariant across sex and overweight status. The three factors had less redundancy than the original EDE-Q scales and demonstrated improved convergent and discriminant validity in relation to relevant other measures. Discussion These factor-analytic findings, which replicate findings from studies with diverse predominately overweight/obese samples, supported a modified 7-item, 3-factor structure for the EDE-Q with improved psychometric characteristics. The findings provide further empirical support for the distinction between body dissatisfaction and overvaluation and have implications for assessment and research. These findings need to be replicated in samples of persons with eating-disorder psychopathology including those with anorexia nervosa, bulimia nervosa, and allied states. PMID:25346071

  16. Structure prediction of GPCRs using piecewise homologs and application to the human CCR5 chemokine receptor: validation through agonist and antagonist docking.

    Science.gov (United States)

    Arumugam, Karthik; Crouzy, Serge; Chevigne, Andy; Seguin-Devaux, Carole; Schmit, Jean-Claude

    2014-01-01

    This article describes the construction and validation of a three-dimensional model of the human CC chemokine receptor 5 (CCR5) receptor using multiple homology modeling. A new methodology is presented where we built each secondary structural model of the protein separately from distantly related homologs of known structure. The reliability of our approach for G-protein coupled receptors was assessed through the building of the human C-X-C chemokine receptor type 4 (CXCR4) receptor of known crystal structure. The models are refined using molecular dynamics simulations and energy minimizations using CHARMM, a classical force field for proteins. Finally, docking models of both the natural agonists and the antagonists of the receptors CCR5 and CXCR4 are proposed. This study explores the possible binding process of ligands to the receptor cavity of chemokine receptors at molecular and atomic levels. We proposed few crucial residues in receptors binding to agonist/antagonist for further validation through experimental analysis. In particular, our study provides better understanding of the blockage mechanism of the chemokine receptors CCR5 and CXCR4, and may help the identification of new lead compounds for drug development in HIV infection, inflammatory diseases, and cancer metastasis.

  17. A validation of the Experiences in Close Relationships-Relationship Structures scale (ECR-RS) in adolescents

    DEFF Research Database (Denmark)

    Donbaek, Dagmar Feddern; Elklit, Ask

    2014-01-01

    Emerging evidence points toward a two-dimensional attachment construct: avoidance and anxiety. The Experiences in Close Relationships-Relationship Structures scale (ECR-RS; Fraley, Heffernan, Vicary, & Brumbaugh, 2011) is a questionnaire assessing two-dimensional relationship-specific attachment...... structures in adults and, hence, moves beyond the traditional focus on romantic relationships. The present article explored the psychometric abilities of the ECR-RS across parental and best friend domains in a sample of 15 to 18-year-olds (n = 1999). Two oblique factors were revealed across domains...... attachment structures....

  18. Three dimensional stereolithography models of cancellous bone structures from muCT data: testing and validation of finite element results.

    Science.gov (United States)

    Dobson, C A; Sisias, G; Phillips, R; Fagan, M J; Langton, C M

    2006-04-01

    Stereolithography (STL) models of complex cancellous bone structures have been produced from three-dimensional micro-computed tomography data sets of human cancellous bone histological samples from four skeletal sites. The STL models have been mechanically tested and the derived stiffness compared with that predicted by finite element analysis. The results show a strong correlation (R2 = 0.941) between the predicted and calculated stiffnesses of the structures and show promise for the use of STL as an additional technique to complement the use of finite element models, for the assessment of the mechanical properties of complex cancellous bone structures.

  19. Reliability, factor structure, and validity of the German version of the Trauma Symptom Checklist for Children in a sample of adolescents

    Directory of Open Access Journals (Sweden)

    Simone Matulis

    2015-10-01

    Full Text Available Background: The Trauma Symptom Checklist for Children (TSC-C is the most widely used self-report scale to assess trauma-related symptoms in children and adolescents on six clinical scales. The purpose of the present study was to develop a German version of the TSC-C and to investigate its psychometric properties, such as factor structure, reliability, and validity, in a sample of German adolescents. Method: A normative sample of N=583 and a clinical sample of N=41 adolescents with a history of physical or sexual abuse aged between 13 and 21 years participated in the study. Results: The Confirmatory Factor Analysis on the six-factor model (anger, anxiety, depression, dissociation, posttraumatic stress, and sexual concerns with the subdimensions preoccupation and distress revealed acceptable to good fit statistics in the normative sample. One item had to be excluded from the German version of the TSC-C because the factor loading was too low. All clinical scales presented acceptable to good reliability, with Cronbach's α's ranging from .80 to .86 in the normative sample and from .72 to .87 in the clinical sample. Concurrent validity was also demonstrated by the high correlations between the TSC-C scales and instruments measuring similar psychopathology. TSC-C scores reliably differentiated between adolescents with trauma history and those without trauma history, indicating discriminative validity. Conclusions: In conclusion, the German version of the TSC-C is a reliable and valid instrument for assessing trauma-related symptoms on six different scales in adolescents aged between 13 and 21 years.

  20. The Eating Disorder Assessment for DSM-5 (EDA-5): Development and Validation of a Structured Interview for Feeding and Eating Disorders

    Science.gov (United States)

    Sysko, Robyn; Glasofer, Deborah R.; Hildebrandt, Tom; Klimek, Patrycja; Mitchell, James E.; Berg, Kelly C.; Peterson, Carol B.; Wonderlich, Stephen A.; Walsh, B. Timothy

    2016-01-01

    Objective Existing measures for DSM-IV eating disorder diagnoses have notable limitations, and there are important differences between DSM-IV and DSM-5 feeding and eating disorders. This study developed and validated a new semi-structured interview, the Eating Disorders Assessment for DSM-5 (EDA-5). Method Two studies evaluated the utility of the EDA-5. Study 1 compared the diagnostic validity of the EDA-5 to the Eating Disorder Examination (EDE) and evaluated the test-retest reliability of the new measure. Study 2 compared the diagnostic validity of an EDA-5 electronic application (“app”) to clinician interview and self-report assessments. Results In Study 1, the kappa for EDE and EDA-5 eating disorder diagnoses was 0.74 across all diagnoses (n= 64), with a range of κ=0.65 for Other Specified Feeding or Eating Disorder (OSFED)/Unspecified Feeding or Eating Disorder (USFED) to κ=0.90 for Binge Eating Disorder (BED). The EDA-5 test-retest kappa coefficient was 0.87 across diagnoses. For Study 2, clinical interview versus “app” conditions revealed a kappa of 0.83 for all eating disorder diagnoses (n=71). Across individual diagnostic categories, kappas ranged from 0.56 for OSFED/USFED to 0.94 for BN. Discussion High rates of agreement were found between diagnoses by EDA-5 and the EDE, and EDA-5 and clinical interviews. As this study supports the validity of the EDA-5 to generate DSM-5 eating disorders and the reliability of these diagnoses, the EDA-5 may be an option for the assessment of Anorexia Nervosa, Bulimia Nervosa, and BED. Additional research is needed to evaluate the utility of the EDA-5 in assessing DSM-5 feeding disorders. PMID:25639562

  1. Validation of Methods for Computational Catalyst Design: Geometries, Structures, and Energies of Neutral and Charged Silver Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Duanmu, Kaining; Truhlar, Donald G.

    2015-04-30

    We report a systematic study of small silver clusters, Agn, Agn+, and Agn–, n = 1–7. We studied all possible isomers of clusters with n = 5–7. We tested 42 exchange–correlation functionals, and we assess these functionals for their accuracy in three respects: geometries (quantitative prediction of internuclear distances), structures (the nature of the lowest-energy structure, for example, whether it is planar or nonplanar), and energies. We find that the ingredients of exchange–correlation functionals are indicators of their success in predicting geometries and structures: local exchange–correlation functionals are generally better than hybrid functionals for geometries; functionals depending on kinetic energy density are the best for predicting the lowest-energy isomer correctly, especially for predicting two-dimensional to three-dimenstional transitions correctly. The accuracy for energies is less sensitive to the ingredient list. Our findings could be useful for guiding the selection of methods for computational catalyst design.

  2. Testing of the OMERACT 8 draft validation criteria for a soluble biomarker reflecting structural damage in rheumatoid arthritis: a systematic literature search on 5 candidate biomarkers

    DEFF Research Database (Denmark)

    Syversen, Silje W; Landewe, Robert; van der Heijde, Désirée;

    2009-01-01

    OBJECTIVE: To test the OMERACT 8 draft validation criteria for soluble biomarkers by assessing the strength of literature evidence in support of 5 candidate biomarkers. METHODS: A systematic literature search was conducted on the 5 soluble biomarkers RANKL, osteoprotegerin (OPG), matrix...... metalloprotease (MMP-3), urine C-telopeptide of types I and II collagen (U-CTX-I and U CTX-II), focusing on the 14 OMERACT 8 criteria. Two electronic voting exercises were conducted to address: (1) strength of evidence for each biomarker as reflecting structural damage according to each individual criterion...... and the importance of each individual criterion; (2) overall strength of evidence in support of each of the 5 candidate biomarkers as reflecting structural damage endpoints in rheumatoid arthritis (RA) and identification of omissions to the criteria set. RESULTS: The search identified 111 articles. The strength...

  3. Assessment of Dysfunctional Cognitions in Binge-Eating Disorder: Factor Structure and Validity of the Mizes Anorectic Cognitions Questionnaire-Revised (MAC-R)

    Science.gov (United States)

    Carrard, Isabelle; Rothen, Stephane; Kruseman, Maaike; Khazaal, Yasser

    2017-01-01

    Background: Dysfunctional cognitions regarding weight and shape and their implications for self-esteem are considered core features of anorexia nervosa and bulimia nervosa. However, they have also been associated with the severity of binge eating disorder (BED). Therefore, they should be screened with appropriate instruments to tailor treatment to individual patient needs. The Mizes Anorectic Cognitions-Revised (MAC-R) is a self-report questionnaire that lists dysfunctional cognitions related to three hypothesized core beliefs typical of the psychopathology of eating disorders: weight and eating as the basis of approval from others; the belief that rigid self-control is fundamental to self-worth; and the rigidity of weight- and eating-regulation efforts. Objectives: The goal of the study was to confirm the factor structure and to assess the validity of the MAC-R among a sample that met full-threshold and subthreshold criteria for BED. Methods: We used data of women meeting full-threshold (n = 94) and subthreshold (n = 22) criteria for BED to conduct confirmatory factor analyses and to compute Spearman's correlations, in order to assess factorial, convergent, and discriminant validity. Results: Two models having a structure of three factors with or without a total score proved to be acceptable. The MAC-R total score was correlated with questionnaires assessing dimensions related to eating disorder psychopathology, adding to the validity of the questionnaire. Conclusion: These results were similar to those found in studies on the psychometric properties of the MAC among samples with anorexia nervosa or bulimia nervosa, encouraging the use of the MAC-R as a research or clinical tool in order to further document the core beliefs underlying BED. PMID:28261139

  4. Detection of Q-Matrix Misspecification Using Two Criteria for Validation of Cognitive Structures under the Least Squares Distance Model

    Science.gov (United States)

    Romero, Sonia J.; Ordoñez, Xavier G.; Ponsoda, Vincente; Revuelta, Javier

    2014-01-01

    Cognitive Diagnostic Models (CDMs) aim to provide information about the degree to which individuals have mastered specific attributes that underlie the success of these individuals on test items. The Q-matrix is a key element in the application of CDMs, because contains links item-attributes representing the cognitive structure proposed for solve…

  5. In silico identification and crystal structure validation of caspase-3 inhibitors without a P1 aspartic acid moiety

    Science.gov (United States)

    Ganesan, Rajkumar; Jelakovic, Stjepan; Mittl, Peer R. E.; Caflisch, Amedeo; Grütter, Markus G.

    2011-01-01

    Using a fragment-based docking procedure, several small-molecule inhibitors of caspase-3 were identified and tested and the crystal structures of three inhibitor complexes were determined. The crystal structures revealed that one inhibitor (NSC 18508) occupies only the S1 subsite, while two other inhibitors (NSC 89167 and NSC 251810) bind only to the prime part of the substrate-binding site. One of the major conformational changes observed in all three caspase-3–inhibitor complexes is a rotation of the Tyr204 side chain, which blocks the S2 subsite. In addition, the structural variability of the residues shaping the S1–S4 as well as the S1′ subsites supports an induced-fit mechanism for the binding of the inhibitors in the active site. The high-resolution crystal structures reported here provide novel insights into the architecture of the substrate-binding site, which might be useful for the design of more potent caspase inhibitors. PMID:21821879

  6. The Construct Validity of Scores on the Ways of Coping Questionnaire: Confirmatory Analysis of Alternative Factor Structures.

    Science.gov (United States)

    Edwards, Jeffrey R.; O'Neill, Regina M.

    1998-01-01

    Confirmatory factor analysis was used to evaluate alternative factor structures, based on previous exploratory factor analyses and coping dimensions derived from the theory of R. Lazarus, for the Ways of Coping Questionnaire (S. Folkman and R. Lazarus, 1988). Results from responses of 654 college graduates provide little support for the factor…

  7. The Disruptive Behavior Rating Scale--Parent Version (DBRS-PV): Factor Analytic Structure and Validity among Young Preschool Children

    Science.gov (United States)

    Friedman-Weieneth, Julie L.; Doctoroff, Greta L.; Harvey, Elizabeth A.; Goldstein, Lauren H.

    2009-01-01

    Objective: Despite recognition that disruptive behavior disorders often begin early in development, existing assessment tools are largely based on research with school-aged children. Further empirical work is needed to evaluate the utility of these tools in younger children. Methods: The present study investigated the factor structure, internal…

  8. Proton affinities of maingroup-element hydrides and noble gases: trends across the periodic table, structural effects, and DFT validation.

    Science.gov (United States)

    Swart, Marcel; Rösler, Ernst; Bickelhaupt, F Matthias

    2006-10-01

    We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15-17 and the noble gases, that is, group 18, and periods 1-6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases.

  9. Proton Affinities of Anionic Bases:  Trends Across the Periodic Table, Structural Effects, and DFT Validation.

    Science.gov (United States)

    Swart, Marcel; Bickelhaupt, F Matthias

    2006-03-01

    We have carried out an extensive exploration of the gas-phase basicity of archetypal anionic bases across the periodic system using the generalized gradient approximation of density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities:  BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 1.6 kcal/mol for the proton affinity at 0 K with respect to high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the anionic conjugate bases of all main-group-element hydrides of groups 14-17 and periods 2-6. We have also studied the effect of stepwise methylation of the protophilic center of the second- and third-period bases.

  10. A general psychopathology factor (P factor) in children: Structural model analysis and external validation through familial risk and child global executive function.

    Science.gov (United States)

    Martel, Michelle M; Pan, Pedro M; Hoffmann, Maurício S; Gadelha, Ary; do Rosário, Maria C; Mari, Jair J; Manfro, Gisele G; Miguel, Eurípedes C; Paus, Tomás; Bressan, Rodrigo A; Rohde, Luis A; Salum, Giovanni A

    2017-01-01

    High rates of comorbidities and poor validity of disorder diagnostic criteria for mental disorders hamper advances in mental health research. Recent work has suggested the utility of continuous cross-cutting dimensions, including general psychopathology and specific factors of externalizing and internalizing (e.g., distress and fear) syndromes. The current study evaluated the reliability of competing structural models of psychopathology and examined external validity of the best fitting model on the basis of family risk and child global executive function (EF). A community sample of 8,012 families from Brazil with children ages 6-12 years completed structured interviews about the child and parental psychiatric syndromes, and a subsample of 2,395 children completed tasks assessing EF (i.e., working memory, inhibitory control, and time processing). Confirmatory factor analyses tested a series of structural models of psychopathology in both parents and children. The model with a general psychopathology factor ("P factor") with 3 specific factors (fear, distress, and externalizing) exhibited the best fit. The general P factor accounted for most of the variance in all models, with little residual variance explained by each of the 3 specific factors. In addition, associations between child and parental factors were mainly significant for the P factors and nonsignificant for the specific factors from the respective models. Likewise, the child P factor-but not the specific factors-was significantly associated with global child EF. Overall, our results provide support for a latent overarching P factor characterizing child psychopathology, supported by familial associations and child EF. (PsycINFO Database Record

  11. A non-linear wave decomposition model for efficient wave–structure interaction. Part A: Formulation, validations and analysis

    DEFF Research Database (Denmark)

    Ducrozet, Guillaume; Engsig-Karup, Allan Peter; Bingham, Harry B.;

    2014-01-01

    This paper deals with the development of an enhanced model for solving wave–wave and wave–structure interaction problems. We describe the application of a non-linear splitting method originally suggested by Di Mascio et al. [1], to the high-order finite difference model developed by Bingham et al....... [2] and extended by Engsig-Karup et al. [3] and [4]. The enhanced strategy is based on splitting all solution variables into incident and scattered fields, where the incident field is assumed to be known and only the scattered field needs to be computed by the numerical model. Although this splitting...

  12. Factor Structure and Validity of the Body Parts Satisfaction Scale: Results from the 1972 Psychology Today Survey

    Directory of Open Access Journals (Sweden)

    David Frederick

    2014-07-01

    Full Text Available In 1972, the first major national study on body image was conducted under the auspices of Psychology Today. Body image was assessed with the Body Parts Satisfaction Scale, which examined the dissatisfaction people experienced with 24 aspects of their bodies. Despite the continued reliance on this scale and reference to the study, data on the factor structure of this measure in a sample of adults have never been published, and citations of the original scale have relied on an unpublished manuscript (Bohrnstedt, 1977. An exploratory factor analysis conducted on 2,013 adults revealed factors for men (Face, Sex Organ, Height, Lower Body, Mid Torso, Upper Torso, Height and women (Face, Sex Organ, Height, Lower Torso, Mid Torso, Extremities, Breast. The factors were weakly to moderately intercorrelated, suggesting the scale can be analyzed by items, by subscales, or by total score. People who reported more dissatisfaction with their body also tended to report lower self-esteem and less comfort interacting with members of the other sex. The analyses provide a useful comparison point for researchers looking to examine gender differences in dissatisfaction with specific aspects of the body, as well as the factor structures linking these items.

  13. Validity of a self-reported diagnosis of depression among participants in a cohort study using the Structured Clinical Interview for DSM-IV (SCID-I

    Directory of Open Access Journals (Sweden)

    Pla Jorge

    2008-06-01

    Full Text Available Abstract Background Depression assessment in population studies is usually based on depressive symptoms scales. However, the use of scales could lead to the choice of an arbitrary cut-off point depending on the sample characteristics and on the patient diagnosis. Thus, the use of a medical diagnosis of depression could be a more appropriate approach. Objective To validate a self-reported physician diagnosis of depression using the Structured Clinical Interview for DSM-IV (SCID-I as Gold Standard and to assess the factors associated to a valid self-reported diagnosis. Methods The SUN Project is a cohort study based on university graduates followed-up through postal questionnaires. The response to the question included in the questionnaire: Have you ever been diagnosed of depression by a physician? was compared to that obtained through the SCID-I applied by a psychiatrist or a clinical psychologist. The percentages of confirmed depression and non-depression were assessed for the overall sample and according to several characteristics. Logistic regression models were fitted to ascertain the association between different factors and a correct classification regarding depression status. Results The percentage of confirmed depression was 74.2%; 95% confidence interval (95% CI = 63.3–85.1. Out of 42 participants who did not report a depression diagnosis in the questionnaire, 34 were free of the disease (%confirmed non-depression = 81.1%; 95% CI = 69.1–92.9. The probability of being a true positive was higher among ex-smokers and non-smokers and among those overweight or obese but the differences were not statistically significant. Conclusion The validity of a self-reported diagnosis of depression in the SUN cohort is adequate. Thus, this question about depression diagnosis could be used in further investigations regarding this disease in this graduate cohort study.

  14. Measuring trauma and stressful events in childhood and adolescence among patients with first-episode psychosis: initial factor structure, reliability, and validity of the Trauma Experiences Checklist.

    Science.gov (United States)

    Cristofaro, Sarah L; Cleary, Sean D; Ramsay Wan, Claire; Broussard, Beth; Chapman, Colby; Haggard, Patrick J; Jananeh, Sara; Myers, Neely L; Compton, Michael T

    2013-12-15

    Past trauma and stressful events, especially in childhood and adolescence, are common among individuals with serious mental illnesses like schizophrenia. Traumatic experiences are thought to be a socio-environmental risk factor not only for poorer outcomes, but also potentially for the onset of these disorders. Because improved measurement tools are needed, we developed and studied, among 205 first-episode psychosis patients, the factor structure, internal consistency reliability, and initial validity of the Trauma Experiences Checklist (TEC), our measure of trauma and stressful events during childhood/adolescence. We assessed validity of subscales using correlations with Childhood Trauma Questionnaire-Short Form, Parental Harsh Discipline, Violence Exposure, and TEC-Informant Version scores. Exploratory factor analysis resulted in two internally consistent subscales (Cronbach's α=0.79 and 0.80, respectively), interpersonal abuse and family stress, and violence, death, and legal involvement. Scores from the former subscale were substantially associated with CTQ-SF physical, emotional, and sexual abuse (r=0.42-0.57, all p<0.001) and Violence Exposure (r=0.49, p<0.001). On the other hand, violence, death, and legal involvement scores were most highly correlated with Violence Exposure (r=0.49, p<0.001), and not with most CTQ-SF subscales. The TEC is a potentially useful tool in assessing diverse traumatic life events across various social contexts during childhood and adolescence.

  15. The French Version of the Screen for Child Anxiety Related Emotional Disorders-Revised (Scared-R: Factor Structure, Convergent and Divergent Validity in a Sample of Teenagers

    Directory of Open Access Journals (Sweden)

    Martine Bouvard

    2013-06-01

    Full Text Available The principal objective of this study is to provide data on the French version of the SCARED-R. This article investigates the factor structure of the French version of the Screen for Child Anxiety Related Emotional Disorders-Revised (SCARED-R and its convergent and divergent validity. 704 normal adolescents aged 10 to 19 years completed the questionnaires in their classrooms. A sub-sample of 595 adolescents also completed an anxiety questionnaire (the French version of the Fear Survey Schedule for Children-Revised, FSSC-R and a depression questionnaire (the French version of the Center for Epidemiological Studies Depression Scale, CES-D. Confirmatory factor analysis of the SCARED-R suggested reasonable fit for the 9-factor model. The comparison of the convergent and divergent validity revealed that the SCARED-R total score and five SCARED-R subscales (SAD, Social Phobia and the three Specific Phobias correlated more strongly with anxiety than depression. The other SCARED-R subscales (GAD, Panic Disorder, OCD and PTSD are positively related to levels of anxiety and depression. Altogether, the French version of the SCARED-R showed reasonable psychometric properties.

  16. Numerical modeling and experimental validation of the acoustic transmission of aircraft's double-wall structures including sound package

    Science.gov (United States)

    Rhazi, Dilal

    In the field of aeronautics, reducing the harmful effects of acoustics constitutes a major concern at the international level and justifies the call for further research, particularly in Canada where aeronautics is a key economic sector, which operates in a context of global competition. Aircraft sidewall structure is usually of a double wall construction with a curved ribbed metallic skin and a lightweight composite or sandwich trim separated by a cavity filled with a noise control treatment. The latter is of a great importance in the transport industry, and continues to be of interest in many engineering applications. However, the insertion loss noise control treatment depends on the excitation of the supporting structure. In particular, Turbulent Boundary Layer is of interest to several industries. This excitation is difficult to simulate in laboratory conditions, given the prohibiting costs and difficulties associated with wind tunnel and in-flight tests. Numerical simulation is the only practical way to predict the response to such excitations and to analyze effects of design changes to the response to such excitation. Another kinds of excitations encountered in industrial are monopole, rain on the Roof and diffuse acoustic field. Deterministic methods can calculate in each point the spectral response of the system. Most known are numerical methods such as finite elements and boundary elements methods. These methods generally apply to the low frequency where modal behavior of the structure dominates. However, the high limit of calculation in frequency of these methods cannot be defined in a strict way because it is related to the capacity of data processing and to the nature of the studied mechanical system. With these challenges in mind, and with limitations of the main numerical codes on the market, the manufacturers have expressed the need for simple models immediately available as early as the stage of preliminary drafts. This thesis represents an attempt

  17. Complementary numerical–experimental benchmarking for shape optimization and validation of structures subjected to wave and current forces

    DEFF Research Database (Denmark)

    Markus, D.; Ferri, Francesco; Wüchner, R.

    2015-01-01

    that focuses on differences in load curves resulting from 2D and 3D flows. It is shown that the major trends predicted by the numerical simulations are also captured in the experiment, highlighting the potential of CFD as a powerful tool for shape optimization studies. The overall aim of the paper...... variations of the structure on the resulting horizontal forces. Steady current conditions, dynamic loading due to waves, and combined wave–current scenarios are considered. A clear focus is put on simplicity and reproducibility, allowing for efficient testing of related methods and codes. This is achieved...... by defining a simple test geometry, altered in one design variable only, and by designing the test case such that a two dimensional analysis of the flow fields is possible. The force sensitivities to changes in the geometry are determined both numerically and experimentally for a great bandwidth of different...

  18. Population genetic structure of Tomicus piniperda L. (Curculionidae: Scolytinae) on different pine species and validation of T. destruens (Woll.).

    Science.gov (United States)

    Kerdelhué, Carole; Roux-Morabito, Géraldine; Forichon, Julien; Chambon, Jean-Michel; Robert, Annelaure; Lieutier, François

    2002-03-01

    Genetic diversity and population structure of Tomicus piniperda was assessed using mitochondrial sequences on 16 populations sampled on 6 pine species in France. Amplifications of Internal transcribed space 1 (ITS1) were also performed. Our goals were to determine the taxonomic status of the Mediterranean ecotype T. piniperda destruens, and to test for host plant or geographical isolation effect on population genetic structure. We showed that T. piniperda clusters in two mtDNA haplotypic groups. Clade A corresponds to insects sampled in continental France on Pinus sylvestris, P. pinaster and P. uncinata, whereas clade B gathers the individuals sampled in Corsica on P. pinaster and P. radiata and in continental France on P. pinea and P. halepensis. Insects belonging to clade A and clade B also consistently differ in the length of ITS1. Individuals belonging to both clades were found once in sympatry on P. pinaster. Genetic distances between clades are similar to those measured between distinct species of Tomicus. We concluded that clade B actually corresponds to the destruens ecotype and forms a good species, T. destruens. Analyses of molecular variance ( amova ) were conducted separately on T. destruens and T. piniperda to test for an effect of either geographical isolation or host species. Interestingly, the effect of host plant was significant for T. piniperda only, while the effect of geographical isolation was not. Pine species therefore seems to act as a significant barrier to gene flow, even if host race formation is not observed. These results still need to be confirmed by nuclear markers.

  19. Control of Flexible Joint Manipulator via Variable Structure Rule-Based Fuzzy Control and Chaos Anti-Control with Experimental Validation

    Directory of Open Access Journals (Sweden)

    Mojtaba Rostami Kandroodi

    2014-03-01

    Full Text Available This paper presents a variable structure rule-based fuzzy control for trajectory tracking and vibration control of a flexible joint manipulator by using chaotic anti-control. Based on Lyapunov stability theory for variable structure control and fuzzy rules, the nonlinear controller and some generic sufficient conditions for global asymptotic control are attained. The fuzzy rules are directly constructed subject to a Lyapunov function obtained from variable structure surfaces such that the error dynamics of control problem satisfy stability in the Lyapunov sense. Also in this study, the anti-control is applied to reduce the deflection angle of flexible joint system. To achieve this goal, the chaos dynamic must be created in the flexible joint system. So, the flexible joint system has been synchronized to chaotic gyroscope system. In this study, control and anti-control concepts are applied to achieve the high quality performance of flexible joint system. It is tried to design a controller which is capable to satisfy the control and anti- control aims. The performances of the proposed control are examined in terms of input tracking capability, level of vibration reduction and time response specifications. Finally, the efficacy of the proposed method is validated through experimentation on QUANSER’s flexible-joint manipulator.

  20. The joint WAIS-III and WMS-III factor structure: development and cross-validation of a six-factor model of cognitive functioning.

    Science.gov (United States)

    Tulsky, David S; Price, Larry R

    2003-06-01

    During the standardization of the Wechsler Adult Intelligence Scale (3rd ed.; WAIS-III) and the Wechsler Memory Scale (3rd ed.; WMS-III) the participants in the normative study completed both scales. This "co-norming" methodology set the stage for full integration of the 2 tests and the development of an expanded structure of cognitive functioning. Until now, however, the WAIS-III and WMS-III had not been examined together in a factor analytic study. This article presents a series of confirmatory factor analyses to determine the joint WAIS-III and WMS-III factor structure. Using a structural equation modeling approach, a 6-factor model that included verbal, perceptual, processing speed, working memory, auditory memory, and visual memory constructs provided the best model fit to the data. Allowing select subtests to load simultaneously on 2 factors improved model fit and indicated that some subtests are multifaceted. The results were then replicated in a large cross-validation sample (N = 858).

  1. Potential Alternatives Report for Validation of Alternative Low-Emission Surface PreparationlDepainting Technologies for Structural Steel

    Science.gov (United States)

    Lewis, Pattie

    2006-01-01

    For this project, particulates and solvents used during the depainting process of steel structures were the identified hazardous material (HazMat) targeted for elimination or reduction. This Potential Alternatives Report (PAR) provides technical analyses of identified alternatives to the current coating removal processes, criteria used to select alternatives for further analysis, and a list of those alternatives recommended for testing. The initial coating removal alternatives list was compiled using literature searches and center participant recommendations. The involved project participants initially considered fifteen (15) alternatives. In late 2004, stakeholders down-selected the list and identified specific processes as potential alternatives to the current depainting methods. The selected alternatives were: 1. Plastic Blast Media 2. Hard Abrasive Media 3. Sponge Blast Media 4. Mechanical Removal with Vacuum Attachment 5. Liquid Nitrogen 6. Laser Coating Removal Available information about these processes was used to analyze the technical merits and the potential environmental, safety, and occupational health (ESOH) impacts of these methods. A preliminary cost benefit analysis will be performed to determine if implementation of alternative technologies is economically justified. NASA AP2

  2. Acoustic guided waves in cylindrical solid-fluid structures: Modeling with a sweeping frequency finite element method and experimental validation

    Science.gov (United States)

    Liu, Yang; D'Angelo, Ralph M.; Sinha, Bikash K.; Zeroug, Smaine

    2017-02-01

    Modeling and understanding the complex elastic-wave physics prevalent in solid-fluid cylindrically-layered structures is of importance in many NDE fields, and most pertinently in the domain of well integrity evaluation of cased holes in the oil and gas industry. Current sonic measurements provide viable techniques for well integrity evaluation yet their practical effectiveness is hampered by the current lack of knowledge of acoustic wave fields particularly in complicated cased-hole geometry where for instance two or more nested steel strings are present in the borehole. In this article, we propose and implement a Sweeping Frequency Finite Element Method (SFFEM) for acoustic guided waves simulation in complex geometries that include double steel strings cemented to each other and to the formation and where the strings may be non-concentric. Transient dynamic finite element models are constructed with sweeping frequency signals being applied as the excitation sources. The sources and receivers disposition simulate current sonic measurement tools deployed in the oilfield. Synthetic wavetrains are recorded and processed with modified matrix pencil method to isolate both the dispersive and non-dispersive propagating guided wave modes. Scaled experiments of fluid-filled double strings with dimensions mimicking the real ones encountered in the field have also been carried out to generate reference data. A comparison of the experimental and numerical results indicates that the SFFEM is capable of accurately reproducing the rich and intricate higher-order multiple wave fields observed experimentally in the fluid-filled double string geometries.

  3. The Herdecke questionnaire on quality of life (HLQ: Validation of factorial structure and development of a short form within a naturopathy treated in-patient collective

    Directory of Open Access Journals (Sweden)

    Beer Andre-Michael

    2005-07-01

    Full Text Available Abstract Background Quality of life (QoL of patients has become a central evaluation parameter that also acts as an aid for decisions related to treatment strategies particularly for patients with chronic illnesses. In Germany, one of the newer instruments attempting to measure distinct QoL aspects is the "Herdecke Questionnaire for Quality of Life" (HLQ. In this study, we aimed to validate the HLQ with respect to its factorial structure, and to develop a short form. The validation has been carried out in relation to other questionnaires including the SF-36 Health Survey, the Mood-Scale Bf-S, the Giessen Physical Complaints Questionnaire GBB-24 and McGill's Pain Perception Scale SES. Methods Data for this study derived from a model project on the treatment of patients using naturopathy methods in Blankenstein Hospital, Hattingen. In total, 2,461 patients between the ages of 16 and 92 years (mean age: 58.0 ± 13.4 years were included in this study. Most of the patients (62% suffered from rheumatic diseases. Factorial validation of the HLQ, it's reliability and external consistency analysis and the development of a short form were carried out using the SPSS software. Results Structural analysis of the HLQ-items pointed to a 6-factor model. The internal consistency of both the long and the short version is excellent (Cronbach's α is 0.935 for the HLQ-L and 0.862 for the HLQ-S. The highest reliability in the HLQ-L was obtained for the "Initiative Power and Interest" scale, the lowest for the 2-item scales "Digestive Well-Being" and the "Physical Complaints". However, the scales found by factor analysis herein were only in part congruent with the original 5-scale model which was approved a multitrait analysis approach. The new instrument shows good correlations with several scales of other relevant QoL instruments. The scales "Initiative Power and Interest", "Social Interaction", "Mental Balance", "Motility", "Physical Complaints", "Digestive Well

  4. Creating space for citizenship: The impact of group structure on validating the voices of people with dementia.

    Science.gov (United States)

    Wiersma, Elaine C; O'Connor, Deborah L; Loiselle, Lisa; Hickman, Kathy; Heibein, Bill; Hounam, Brenda; Mann, Jim

    2016-05-01

    Recently, there has been increasing attention given to finding ways to help people diagnosed with dementia 'live well' with their condition. Frequently however, the attention has been placed on the family care partner as the foundation for creating a context that supports the person with dementia to live well. A recent participatory action research (PAR) study highlighted the importance of beginning to challenge some of the assumptions around how best to include family, especially within a context of supporting citizenship. Three advisory groups consisting of 20 people with dementia, 13 care partners, and three service providers, were set up in three locations across Canada to help develop a self-management program for people with dementia. The hubs met monthly for up to two years. One of the topics that emerged as extremely important to consider in the structuring of the program revolved around whether or not these groups should be segregated to include only people with dementia. A thematic analysis of these ongoing discussions coalesced around four inter-related themes: creating safe spaces; maintaining voice and being heard; managing the balancing act; and the importance of solidarity Underpinning these discussions was the fifth theme, recognition that 'one size doesn't fit all'. Overall an important finding was that the presence of family care-partners could have unintended consequences in relation to creating the space for active citizenship to occur in small groups of people with dementia although it could also offer some opportunities. The involvement of care partners in groups with people with dementia is clearly one that is complex without an obvious answer and dependent on a variety of factors to inform a solution, which can and should be questioned and revisited.

  5. Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.

    Science.gov (United States)

    Maltsev, Alexander S; Grishaev, Alexander; Roche, Julien; Zasloff, Michael; Bax, Ad

    2014-03-12

    The antibiotic squalamine forms a lyotropic liquid crystal at very low concentrations in water (0.3-3.5% w/v), which remains stable over a wide range of temperature (1-40 °C) and pH (4-8). Squalamine is positively charged, and comparison of the alignment of ubiquitin relative to 36 previously reported alignment conditions shows that it differs substantially from most of these, but is closest to liquid crystalline cetyl pyridinium bromide. High precision residual dipolar couplings (RDCs) measured for the backbone (1)H-(15)N, (15)N-(13)C', (1)H(α)-(13)C(α), and (13)C'-(13)C(α) one-bond interactions in the squalamine medium fit well to the static structural model previously derived from NMR data. Inclusion into the structure refinement procedure of these RDCs, together with (1)H-(15)N and (1)H(α)-(13)C(α) RDCs newly measured in Pf1, results in improved agreement between alignment-induced changes in (13)C' chemical shift, (3)JHNHα values, and (13)C(α)-(13)C(β) RDCs and corresponding values predicted by the structure, thereby validating the high quality of the single-conformer structural model. This result indicates that fitting of a single model to experimental data provides a better description of the average conformation than does averaging over previously reported NMR-derived ensemble representations. The latter can capture dynamic aspects of a protein, thus making the two representations valuable complements to one another.

  6. Structural insight into tetrameric hTRPV1 from homology modeling, molecular docking, molecular dynamics simulation, virtual screening, and bioassay validations.

    Science.gov (United States)

    Feng, Zhiwei; Pearce, Larry V; Xu, Xiaomeng; Yang, Xiaole; Yang, Peng; Blumberg, Peter M; Xie, Xiang-Qun

    2015-03-23

    The transient receptor potential vanilloid type 1 (TRPV1) is a heat-activated cation channel protein, which contributes to inflammation, acute and persistent pain. Antagonists of human TRPV1 (hTRPV1) represent a novel therapeutic approach for the treatment of pain. Developing various antagonists of hTRPV1, however, has been hindered by the unavailability of a 3D structure of hTRPV1. Recently, the 3D structures of rat TRPV1 (rTRPV1) in the presence and absence of ligand have been reported as determined by cryo-EM. rTRPV1 shares 85.7% sequence identity with hTRPV1. In the present work, we constructed and reported the 3D homology tetramer model of hTRPV1 based on the cryo-EM structures of rTRPV1. Molecular dynamics (MD) simulations, energy minimizations, and prescreen were applied to select and validate the best model of hTRPV1. The predicted binding pocket of hTRPV1 consists of two adjacent monomers subunits, which were congruent with the experimental rTRPV1 data and the cyro-EM structures of rTRPV1. The detailed interactions between hTRPV1 and its antagonists or agonists were characterized by molecular docking, which helped us to identify the important residues. Conformational changes of hTRPV1 upon antagonist/agonist binding were also explored by MD simulation. The different movements of compounds led to the different conformational changes of monomers in hTRPV1, indicating that TRPV1 works in a concerted way, resembling some other channel proteins such as aquaporins. We observed that the selective filter was open when hTRPV1 bound with an agonist during MD simulation. For the lower gate of hTRPV1, we observed large similarities between hTRPV1 bound with antagonist and with agonist. A five-point pharmacophore model based on several antagonists was established, and the structural model was used to screen in silico for new antagonists for hTRPV1. By using the 3D TRPV1 structural model above, the pilot in silico screening has begun to yield promising hits with

  7. Direct atomic structure determination by the inspection of structural phase.

    Science.gov (United States)

    Nakashima, Philip N H; Moodie, Alexander F; Etheridge, Joanne

    2013-08-27

    A century has passed since Bragg solved the first atomic structure using diffraction. As with this first structure, all atomic structures to date have been deduced from the measurement of many diffracted intensities using iterative and statistical methods. We show that centrosymmetric atomic structures can be determined without the need to measure or even record a diffracted intensity. Instead, atomic structures can be determined directly and quickly from the observation of crystallographic phases in electron diffraction patterns. Furthermore, only a few phases are required to achieve high resolution. This represents a paradigm shift in structure determination methods, which we demonstrate with the moderately complex α-Al2O3. We show that the observation of just nine phases enables the location of all atoms with a resolution of better than 0.1 Å. This level of certainty previously required the measurement of thousands of diffracted intensities.

  8. Alignment validation

    Energy Technology Data Exchange (ETDEWEB)

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias

    2008-09-06

    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  9. SANSMIC Validation.

    Energy Technology Data Exchange (ETDEWEB)

    Weber, Paula D.; Rudeen, David Keith; Lord, David L.

    2014-08-01

    SANSMIC is solution mining software that was developed and utilized by SNL in its role as geotechnical advisor to the US DOE SPR for planning purposes. Three SANSMIC leach modes - withdrawal, direct, and reverse leach - have been revalidated with multiple test cases for each mode. The withdrawal mode was validated using high quality data from recent leach activity while the direct and reverse modes utilized data from historical cavern completion reports. Withdrawal results compared very well with observed data, including the location and size of shelves due to string breaks with relative leached volume differences ranging from 6 - 10% and relative radius differences from 1.5 - 3%. Profile comparisons for the direct mode were very good with relative leached volume differences ranging from 6 - 12% and relative radius differences from 5 - 7%. First, second, and third reverse configurations were simulated in order to validate SANSMIC over a range of relative hanging string and OBI locations. The first-reverse was simulated reasonably well with relative leached volume differences ranging from 1 - 9% and relative radius differences from 5 - 12%. The second-reverse mode showed the largest discrepancies in leach profile. Leached volume differences ranged from 8 - 12% and relative radius differences from 1 - 10%. In the third-reverse, relative leached volume differences ranged from 10 - 13% and relative radius differences were %7E4 %. Comparisons to historical reports were quite good, indicating that SANSMIC is essentially the same as documented and validated in the early 1980's.

  10. The DUNDRUM Quartet: validation of structured professional judgement instruments DUNDRUM-3 assessment of programme completion and DUNDRUM-4 assessment of recovery in forensic mental health services

    Directory of Open Access Journals (Sweden)

    McDonnell Kim

    2011-07-01

    Full Text Available Abstract Background Moving a forensic mental health patient from one level of therapeutic security to a lower level or to the community is influenced by more than risk assessment and risk management. We set out to construct and validate structured professional judgement instruments for consistency and transparency in decision making Methods Two instruments were developed, the seven-item DUNDRUM-3 programme completion instrument and the six item DUNDRUM-4 recovery instrument. These were assessed for all 95 forensic patients at Ireland's only forensic mental health hospital. Results The two instruments had good internal consistency (Cronbach's alpha 0.911 and 0.887. Scores distinguished those allowed no leave or accompanied leave from those with unaccompanied leave (ANOVA F = 38.1 and 50.3 respectively, p Conclusions The DUNDRUM-3 programme completion items distinguished significantly between levels of therapeutic security while the DUNDRUM-4 recovery items consistently distinguished those given unaccompanied leave outside the hospital and those in the lowest levels of therapeutic security. This data forms the basis for a prospective study of outcomes now underway.

  11. Identification of gefitinib off-targets using a structure-based systems biology approach; their validation with reverse docking and retrospective data mining

    Science.gov (United States)

    Verma, Nidhi; Rai, Amit Kumar; Kaushik, Vibha; Brünnert, Daniela; Chahar, Kirti Raj; Pandey, Janmejay; Goyal, Pankaj

    2016-01-01

    Gefitinib, an EGFR tyrosine kinase inhibitor, is used as FDA approved drug in breast cancer and non-small cell lung cancer treatment. However, this drug has certain side effects and complications for which the underlying molecular mechanisms are not well understood. By systems biology based in silico analysis, we identified off-targets of gefitinib that might explain side effects of this drugs. The crystal structure of EGFR-gefitinib complex was used for binding pocket similarity searches on a druggable proteome database (Sc-PDB) by using IsoMIF Finder. The top 128 hits of putative off-targets were validated by reverse docking approach. The results showed that identified off-targets have efficient binding with gefitinib. The identified human specific off-targets were confirmed and further analyzed for their links with biological process and clinical disease pathways using retrospective studies and literature mining, respectively. Noticeably, many of the identified off-targets in this study were reported in previous high-throughput screenings. Interestingly, the present study reveals that gefitinib may have positive effects in reducing brain and bone metastasis, and may be useful in defining novel gefitinib based treatment regime. We propose that a system wide approach could be useful during new drug development and to minimize side effect of the prospective drug. PMID:27653775

  12. Identification of gefitinib off-targets using a structure-based systems biology approach; their validation with reverse docking and retrospective data mining.

    Science.gov (United States)

    Verma, Nidhi; Rai, Amit Kumar; Kaushik, Vibha; Brünnert, Daniela; Chahar, Kirti Raj; Pandey, Janmejay; Goyal, Pankaj

    2016-09-22

    Gefitinib, an EGFR tyrosine kinase inhibitor, is used as FDA approved drug in breast cancer and non-small cell lung cancer treatment. However, this drug has certain side effects and complications for which the underlying molecular mechanisms are not well understood. By systems biology based in silico analysis, we identified off-targets of gefitinib that might explain side effects of this drugs. The crystal structure of EGFR-gefitinib complex was used for binding pocket similarity searches on a druggable proteome database (Sc-PDB) by using IsoMIF Finder. The top 128 hits of putative off-targets were validated by reverse docking approach. The results showed that identified off-targets have efficient binding with gefitinib. The identified human specific off-targets were confirmed and further analyzed for their links with biological process and clinical disease pathways using retrospective studies and literature mining, respectively. Noticeably, many of the identified off-targets in this study were reported in previous high-throughput screenings. Interestingly, the present study reveals that gefitinib may have positive effects in reducing brain and bone metastasis, and may be useful in defining novel gefitinib based treatment regime. We propose that a system wide approach could be useful during new drug development and to minimize side effect of the prospective drug.

  13. The DUNDRUM Quartet: validation of structured professional judgement instruments DUNDRUM-3 assessment of programme completion and DUNDRUM-4 assessment of recovery in forensic mental health services.

    LENUS (Irish Health Repository)

    O'Dwyer, Sarah

    2011-07-03

    Abstract Background Moving a forensic mental health patient from one level of therapeutic security to a lower level or to the community is influenced by more than risk assessment and risk management. We set out to construct and validate structured professional judgement instruments for consistency and transparency in decision making Methods Two instruments were developed, the seven-item DUNDRUM-3 programme completion instrument and the six item DUNDRUM-4 recovery instrument. These were assessed for all 95 forensic patients at Ireland\\'s only forensic mental health hospital. Results The two instruments had good internal consistency (Cronbach\\'s alpha 0.911 and 0.887). Scores distinguished those allowed no leave or accompanied leave from those with unaccompanied leave (ANOVA F = 38.1 and 50.3 respectively, p < 0.001). Scores also distinguished those in acute\\/high security units from those in medium or in low secure\\/pre-discharge units. Each individual item distinguished these levels of need significantly. The DUNDRUM-3 and DUNDRUM-4 correlated moderately with measures of dynamic risk and with the CANFOR staff rated unmet need (Spearman r = 0.5, p < 0.001). Conclusions The DUNDRUM-3 programme completion items distinguished significantly between levels of therapeutic security while the DUNDRUM-4 recovery items consistently distinguished those given unaccompanied leave outside the hospital and those in the lowest levels of therapeutic security. This data forms the basis for a prospective study of outcomes now underway.

  14. A scoring framework for predicting protein structures

    Science.gov (United States)

    Zou, Xiaoqin

    2013-03-01

    We have developed a statistical mechanics-based iterative method to extract statistical atomic interaction potentials from known, non-redundant protein structures. Our method circumvents the long-standing reference state problem in deriving traditional knowledge-based scoring functions, by using rapid iterations through a physical, global convergence function. The rapid convergence of this physics-based method, unlike other parameter optimization methods, warrants the feasibility of deriving distance-dependent, all-atom statistical potentials to keep the scoring accuracy. The derived potentials, referred to as ITScore/Pro, have been validated using three diverse benchmarks: the high-resolution decoy set, the AMBER benchmark decoy set, and the CASP8 decoy set. Significant improvement in performance has been achieved. Finally, comparisons between the potentials of our model and potentials of a knowledge-based scoring function with a randomized reference state have revealed the reason for the better performance of our scoring function, which could provide useful insight into the development of other physical scoring functions. The potentials developed in the present study are generally applicable for structural selection in protein structure prediction.

  15. Testing of the preliminary OMERACT validation criteria for a biomarker to be regarded as reflecting structural damage endpoints in rheumatoid arthritis clinical trials: the example of C-reactive protein

    DEFF Research Database (Denmark)

    Keeling, Stephanie O; Landewe, Robert; van der Heijde, Desiree;

    2007-01-01

    OBJECTIVE: A list of 14 criteria for guiding the validation of a soluble biomarker as reflecting structural damage endpoints in rheumatoid arthritis (RA) clinical trials was drafted by an international working group after a Delphi consensus exercise. C-reactive protein (CRP), a soluble biomarker...

  16. Predictive validity of measurements of clinical competence using the team objective structured bedside assessment (TOSBA): assessing the clinical competence of final year medical students.

    LENUS (Irish Health Repository)

    Meagher, Frances M

    2009-11-01

    The importance of valid and reliable assessment of student competence and performance is gaining increased recognition. Provision of valid patient-based formative assessment is an increasing challenge for clinical teachers in a busy hospital setting. A formative assessment tool that reliably predicts performance in the summative setting would be of value to both students and teachers.

  17. Validation through Understanding Test-Taking Strategies: An Illustration With the CELPIP-General Reading Pilot Test Using Structural Equation Modeling

    Science.gov (United States)

    Wu, Amery D.; Stone, Jake E.

    2016-01-01

    This article explores an approach for test score validation that examines test takers' strategies for taking a reading comprehension test. The authors formulated three working hypotheses about score validity pertaining to three types of test-taking strategy (comprehending meaning, test management, and test-wiseness). These hypotheses were…

  18. Developing and validating predictive decision tree models from mining chemical structural fingerprints and high–throughput screening data in PubChem

    Directory of Open Access Journals (Sweden)

    Bryant Stephen H

    2008-09-01

    Full Text Available Abstract Background Recent advances in high-throughput screening (HTS techniques and readily available compound libraries generated using combinatorial chemistry or derived from natural products enable the testing of millions of compounds in a matter of days. Due to the amount of information produced by HTS assays, it is a very challenging task to mine the HTS data for potential interest in drug development research. Computational approaches for the analysis of HTS results face great challenges due to the large quantity of information and significant amounts of erroneous data produced. Results In this study, Decision Trees (DT based models were developed to discriminate compound bioactivities by using their chemical structure fingerprints provided in the PubChem system http://pubchem.ncbi.nlm.nih.gov. The DT models were examined for filtering biological activity data contained in four assays deposited in the PubChem Bioassay Database including assays tested for 5HT1a agonists, antagonists, and HIV-1 RT-RNase H inhibitors. The 10-fold Cross Validation (CV sensitivity, specificity and Matthews Correlation Coefficient (MCC for the models are 57.2~80.5%, 97.3~99.0%, 0.4~0.5 respectively. A further evaluation was also performed for DT models built for two independent bioassays, where inhibitors for the same HIV RNase target were screened using different compound libraries, this experiment yields enrichment factor of 4.4 and 9.7. Conclusion Our results suggest that the designed DT models can be used as a virtual screening technique as well as a complement to traditional approaches for hits selection.

  19. The effect of validating and invalidating communication on satisfaction, pain and affect in nurses suffering from low back pain during a semi-structured interview.

    Science.gov (United States)

    Vangronsveld, K L; Linton, S J

    2012-02-01

    When physicians interview patients with ambiguous or nonspecific symptoms, they often try to reassure them with the purpose of explaining that no dangerous illness or disease is causing the symptoms. Unfortunately the evidence suggests that patients with benign (back) pain instead feel misunderstood, frustrated and unsatisfied with the consultation. Validation is a communication method that focuses on understanding and empathy as a platform for problem solving and it may be applicable for interviews in medical settings. The aim of this study was to examine the effects of validation on patient satisfaction, pain and affect. To this end 28 nurses with (re)current back pain were recruited and randomly assigned to be interviewed in a validating or invalidating condition. Patient satisfaction, affect, pain, disability, pain catastrophizing, and fear of movement were assessed immediately after the interview. The results show that the participants in the validated group were more satisfied with the interview than participants in the invalidating condition. Moreover, they showed a significant decrease on all measures of negative affect as well as for pain. For example, there was a significant between group difference in frustration where frustration decreased in the validation group, while it increased in the invalidation condition. A validating communication style seems to be beneficial for enhancing patient satisfaction, as well as diminishing negative affect and pain intensity ratings. Our results suggest that validation might be a viable technique to use in clinical examinations of patients suffering pain.

  20. A Stability-Indicating HPLC-DAD Method for Determination of Stiripentol: Development, Validation, Kinetics, Structure Elucidation and Application to Commercial Dosage Form

    OpenAIRE

    Hany W. Darwish; Abdelhameed, Ali S; Mohamed I. Attia; Bakheit, Ahmed H.; Khalil, Nasr Y; Al-Majed, Abdulrahman A.

    2014-01-01

    A rapid, simple, sensitive, and accurate isocratic reversed-phase stability-indicating high performance liquid chromatography method has been developed and validated for the determination of stiripentol and its degradation product in its bulk form and pharmaceutical dosage form. Chromatographic separation was achieved on a Symmetry C18 column and quantification was achieved using photodiode array detector (DAD). The method was validated in accordance with the ICH requirements showing specific...

  1. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

    Science.gov (United States)

    Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; Kathuria, Sagar V.; Bilsel, Osman; Matthews, C. Robert; Lane, T. J.; Pande, Vijay S.

    2017-01-01

    The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. Here, we report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. This prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. Using these results, we then predict incisive single molecule FRET experiments as a means of model validation. This study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments. PMID:28272524

  2. Clinical Validation of Atlas-Based Auto-Segmentation of Multiple Target Volumes and Normal Tissue (Swallowing/Mastication) Structures in the Head and Neck

    Energy Technology Data Exchange (ETDEWEB)

    Teguh, David N. [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands); Levendag, Peter C., E-mail: p.levendag@erasmusmc.nl [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands); Voet, Peter W.J.; Al-Mamgani, Abrahim [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands); Han Xiao; Wolf, Theresa K.; Hibbard, Lyndon S. [Elekta-CMS Software, Maryland Heights, MO 63043 (United States); Nowak, Peter; Akhiat, Hafid; Dirkx, Maarten L.P.; Heijmen, Ben J.M.; Hoogeman, Mischa S. [Department of Radiation Oncology, Erasmus Medical Center-Daniel den Hoed Cancer Center, Rotterdam (Netherlands)

    2011-11-15

    Purpose: To validate and clinically evaluate autocontouring using atlas-based autosegmentation (ABAS) of computed tomography images. Methods and Materials: The data from 10 head-and-neck patients were selected as input for ABAS, and neck levels I-V and 20 organs at risk were manually contoured according to published guidelines. The total contouring times were recorded. Two different ABAS strategies, multiple and single subject, were evaluated, and the similarity of the autocontours with the atlas contours was assessed using Dice coefficients and the mean distances, using the leave-one-out method. For 12 clinically treated patients, 5 experienced observers edited the autosegmented contours. The editing times were recorded. The Dice coefficients and mean distances were calculated among the clinically used contours, autocontours, and edited autocontours. Finally, an expert panel scored all autocontours and the edited autocontours regarding their adequacy relative to the published atlas. Results: The time to autosegment all the structures using ABAS was 7 min/patient. No significant differences were observed in the autosegmentation accuracy for stage N0 and N+ patients. The multisubject atlas performed best, with a Dice coefficient and mean distance of 0.74 and 2 mm, 0.67 and 3 mm, 0.71 and 2 mm, 0.50 and 2 mm, and 0.78 and 2 mm for the salivary glands, neck levels, chewing muscles, swallowing muscles, and spinal cord-brainstem, respectively. The mean Dice coefficient and mean distance of the autocontours vs. the clinical contours was 0.8 and 2.4 mm for the neck levels and salivary glands, respectively. For the autocontours vs. the edited autocontours, the mean Dice coefficient and mean distance was 0.9 and 1.6 mm, respectively. The expert panel scored 100% of the autocontours as a 'minor deviation, editable' or better. The expert panel scored 88% of the edited contours as good compared with 83% of the clinical contours. The total editing time was 66 min

  3. Reappraisal of OMERACT 8 draft validation criteria for a soluble biomarker reflecting structural damage endpoints in rheumatoid arthritis, psoriatic arthritis, and spondyloarthritis

    DEFF Research Database (Denmark)

    Maksymowych, Walter P; Landewé, Robert; Tak, Paul-Peter

    2009-01-01

    and the principle objectives of the validation process were clarified at a meeting of the working group in London, December 2007. A new framework was proposed after the following steps were conducted: (A) A systematic review of the literature focusing on the draft criteria and a preselected group of biomarkers (MMP...

  4. The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.

    Science.gov (United States)

    Snyder, David A; Grullon, Jennifer; Huang, Yuanpeng J; Tejero, Roberto; Montelione, Gaetano T

    2014-02-01

    Maximizing the scientific impact of NMR-based structure determination requires robust and statistically sound methods for assessing the precision of NMR-derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR-derived structures as targets in the CASP competition. FindCore (Snyder and Montelione, Proteins 2005;59:673-686) is a superimposition independent method for identifying a core atom set and partitioning that set into domains. However, as FindCore optimizes superimposition by sensitively excluding not-well-defined atoms, the FindCore core may not comprise all atoms suitable for use in certain applications of NMR structures, including the CASP assessment process. Adapting the FindCore approach to assess predicted models against experimental NMR structures in CASP10 required modification of the FindCore method. This paper describes conventions and a standard protocol to calculate an "Expanded FindCore" atom set suitable for validation and application in biological and biophysical contexts. A key application of the Expanded FindCore method is to identify a core set of atoms in the experimental NMR structure for which it makes sense to validate predicted protein structure models. We demonstrate the application of this Expanded FindCore method in characterizing well-defined regions of 18 NMR-derived CASP10 target structures. The Expanded FindCore protocol defines "expanded core atom sets" that match an expert's intuition of which parts of the structure are sufficiently well defined to use in assessing CASP model predictions. We also illustrate the impact of this analysis on the CASP GDT assessment scores.

  5. Validation of community robustness

    CERN Document Server

    Carissimo, Annamaria; Defeis, Italia

    2016-01-01

    The large amount of work on community detection and its applications leaves unaddressed one important question: the statistical validation of the results. In this paper we present a methodology able to clearly detect if the community structure found by some algorithms is statistically significant or is a result of chance, merely due to edge positions in the network. Given a community detection method and a network of interest, our proposal examines the stability of the partition recovered against random perturbations of the original graph structure. To address this issue, we specify a perturbation strategy and a null model to build a set of procedures based on a special measure of clustering distance, namely Variation of Information, using tools set up for functional data analysis. The procedures determine whether the obtained clustering departs significantly from the null model. This strongly supports the robustness against perturbation of the algorithm used to identify the community structure. We show the r...

  6. Steklite, KAl(SO4)2: A finding at the Tolbachik Volcano, Kamchatka, Russia, validating its status as a mineral species and crystal structure

    Science.gov (United States)

    Murashko, M. N.; Pekov, I. V.; Krivovichev, S. V.; Chernyatyeva, A. P.; Yapaskurt, V. O.; Zadov, A. E.; Zelensky, M. E.

    2013-12-01

    Steklite KAl(SO4)2 has been found in sublimates of the Yadovitaya (Poisonous) fumarole at the second cinder cone of the northern breach of the Great Fissure Tolbachik Eruption, Tolbachik volcano, Kamchatka Peninsula, Russia. Steklite was approved as a valid mineral species by the Commission on New Minerals, Nomenclature, and Mineral Classification of the International Mineralogical Association on June 2, 2011 (IMA no. 2011-041). The name steklite is left for this mineral, as it was named by Chesnokov et al. (1995) for its technogenic analog from a burnt dump of coal mine no. 47 at Kopeisk, the Southern Urals, Russia. It is named after the Russian word steklo, meaning glass, in allusion to the visual similarity of its lamellae to thin glass platelets. At Tolbachik, steklite is associated with alumoklyuchevskite, langbeinite, euchlorine, fedotovite, chalcocyanite, hematite, and lyonsite. It occurs as hexagonal or irregular-shaped lamellar crystals with the major form {001} reaching 30 μm in thickness and 0.2 mm (occasionally up to 1 mm) in width. The crystals are frequently split. They are combined into openwork aggregates or thin crusts up to 1.5 × 2.5 cm in area. Steklite is transparent and colorless, with vitreous luster. The cleavage is perfect, parallel to (001). The mineral is brittle. The Mohs' hardness is 2.5. D calc is 2.797 g/cm3. Steklite is optically uniaxial, (-), ω = 1.546(2), ɛ = 1.533(3). The chemical composition (wt %, electron-microprobe data) is as follows: 0.09 Na2O, 18.12 K2O, 0.08 CaO, 0.03 MnO, 2.02 Fe2O3, 18.18 Al2O3, 61.80 SO3. The total is 100.37. The empirical formula calculated on the basis of eight O atoms is: (K0.997Na0.008Ca0.004)Σ1.009(Al0.925Fe{0.066/3+}Mg0.003Mn0.001)Σ0.995S2.01O8. Steklite is trigonal, space group P321, a = 4.7281(3), c = 7.9936(5) Å, V = 154.76(17)Å3, Z =1. The strongest reflections in the X-ray powder diffraction pattern ( d, Å- I[ hkl]) are: 8.02-34[001], 4.085-11[100], 3.649-100[011, 101], 2

  7. Validated dynamic flow model

    DEFF Research Database (Denmark)

    Knudsen, Torben

    2011-01-01

    The purpose with this deliverable 2.5 is to use fresh experimental data for validation and selection of a flow model to be used for control design in WP3-4. Initially the idea was to investigate the models developed in WP2. However, in the project it was agreed to include and focus on a additive...... model turns out not to be useful for prediction of the flow. Moreover, standard Box Jenkins model structures and multiple output auto regressive models proves to be superior as they can give useful predictions of the flow....

  8. Validated spectrophotometric method for the determination, spectroscopic characterization and thermal structural analysis of duloxetine with 1,2-naphthoquinone-4-sulphonate

    Science.gov (United States)

    Ulu, Sevgi Tatar; Elmali, Fikriye Tuncel

    2012-03-01

    A novel, selective, sensitive and simple spectrophotometric method was developed and validated for the determination of the antidepressant duloxetine hydrochloride in pharmaceutical preparation. The method was based on the reaction of duloxetine hydrochloride with 1,2-naphthoquinone-4-sulphonate (NQS) in alkaline media to yield orange colored product. The formation of this complex was also confirmed by UV-visible, FTIR, 1H NMR, Mass spectra techniques and thermal analysis. This method was validated for various parameters according to ICH guidelines. Beer's law is obeyed in a range of 5.0-60 μg/mL at the maximum absorption wavelength of 480 nm. The detection limit is 0.99 μg/mL and the recovery rate is in a range of 98.10-99.57%. The proposed methods was validated and applied to the determination of duloxetine hydrochloride in pharmaceutical preparation. The results were statistically analyzed and compared to those of a reference UV spectrophotometric method.

  9. A Stability-Indicating HPLC-DAD Method for Determination of Stiripentol: Development, Validation, Kinetics, Structure Elucidation and Application to Commercial Dosage Form

    Directory of Open Access Journals (Sweden)

    Hany W. Darwish

    2014-01-01

    Full Text Available A rapid, simple, sensitive, and accurate isocratic reversed-phase stability-indicating high performance liquid chromatography method has been developed and validated for the determination of stiripentol and its degradation product in its bulk form and pharmaceutical dosage form. Chromatographic separation was achieved on a Symmetry C18 column and quantification was achieved using photodiode array detector (DAD. The method was validated in accordance with the ICH requirements showing specificity, linearity (r2=0.9996, range of 1–25 μg/mL, precision (relative standard deviation lower than 2%, accuracy (mean recovery 100.08±1.73, limits of detection and quantitation (LOD = 0.024 and LOQ = 0.081 μg/mL, and robustness. Stiripentol was subjected to various stress conditions and it has shown marked stability under alkaline hydrolytic stress conditions, thermal, oxidative, and photolytic conditions. Stiripentol degraded only under acidic conditions, forming a single degradation product which was well resolved from the pure drug with significantly different retention time values. This degradation product was characterized by 1H-NMR and 13C-NMR spectroscopy as well as ion trap mass spectrometry. The results demonstrated that the method would have a great value when applied in quality control and stability studies for stiripentol.

  10. The General Assessment of Personality Disorder (GAPD): factor structure, incremental validity of self-pathology, and relations to DSM-IV personality disorders.

    Science.gov (United States)

    Hentschel, Annett G; Livesley, W John

    2013-01-01

    Recent developments in the classification of personality disorder, especially moves toward more dimensional systems, create the need to assess general personality disorder apart from individual differences in personality pathology. The General Assessment of Personality Disorder (GAPD) is a self-report questionnaire designed to evaluate general personality disorder. The measure evaluates 2 major components of disordered personality: self or identity problems and interpersonal dysfunction. This study explores whether there is a single factor reflecting general personality pathology as proposed by the Diagnostic and Statistical Manual of Mental Disorders (5th ed.), whether self-pathology has incremental validity over interpersonal pathology as measured by GAPD, and whether GAPD scales relate significantly to Diagnostic and Statistical Manual of Mental Disorders (4th ed. [DSM-IV]) personality disorders. Based on responses from a German psychiatric sample of 149 participants, parallel analysis yielded a 1-factor model. Self Pathology scales of the GAPD increased the predictive validity of the Interpersonal Pathology scales of the GAPD. The GAPD scales showed a moderate to high correlation for 9 of 12 DSM-IV personality disorders.

  11. A Stability-Indicating HPLC-DAD Method for Determination of Stiripentol: Development, Validation, Kinetics, Structure Elucidation and Application to Commercial Dosage Form.

    Science.gov (United States)

    Darwish, Hany W; Abdelhameed, Ali S; Attia, Mohamed I; Bakheit, Ahmed H; Khalil, Nasr Y; Al-Majed, Abdulrahman A

    2014-01-01

    A rapid, simple, sensitive, and accurate isocratic reversed-phase stability-indicating high performance liquid chromatography method has been developed and validated for the determination of stiripentol and its degradation product in its bulk form and pharmaceutical dosage form. Chromatographic separation was achieved on a Symmetry C18 column and quantification was achieved using photodiode array detector (DAD). The method was validated in accordance with the ICH requirements showing specificity, linearity (r (2) = 0.9996, range of 1-25 μg/mL), precision (relative standard deviation lower than 2%), accuracy (mean recovery 100.08 ± 1.73), limits of detection and quantitation (LOD = 0.024 and LOQ = 0.081 μg/mL), and robustness. Stiripentol was subjected to various stress conditions and it has shown marked stability under alkaline hydrolytic stress conditions, thermal, oxidative, and photolytic conditions. Stiripentol degraded only under acidic conditions, forming a single degradation product which was well resolved from the pure drug with significantly different retention time values. This degradation product was characterized by (1)H-NMR and (13)C-NMR spectroscopy as well as ion trap mass spectrometry. The results demonstrated that the method would have a great value when applied in quality control and stability studies for stiripentol.

  12. An attempt to validate the ultra-accelerated microbar and the concrete performance test with the degree of AAR-induced damage observed in concrete structures

    Energy Technology Data Exchange (ETDEWEB)

    Leemann, Andreas, E-mail: andreas.leemann@empa.ch [Empa, Dübendorf (Switzerland); Merz, Christine [Holcim (Schweiz) AG, Würenlingen (Switzerland)

    2013-07-15

    There is little knowledge about the relation between AAR-induced damage observed in structures and the expansion potential obtained with accelerated tests. In this study, aggregates used in structures damaged by AAR were tested with the microbar test (MBT/AFNOR XP 18-594) and the concrete performance test (CPT/AFNOR P18-454). After the tests, the samples were examined using optical and scanning electron microscopy. Based on the results, the significance of the microbar test has to be examined very critically. The agreement of measured expansion, reacted rock types and the composition of the reaction products between the on-site concrete and the reproduced concrete subjected to the CPT clearly indicates that the reaction mechanisms in the structure and in the concrete performance test are comparable. As such, the concrete performance test seems to be an appropriate tool to test the potential reactivity of specific concrete mixtures.

  13. Brief report: The Identity Style Inventory (ISI-3) and the Utrecht-Management of Identity Commitments Scale (U-MICS): factor structure, reliability, and convergent validity in French-speaking university students.

    Science.gov (United States)

    Zimmermann, Grégoire; Mahaim, Elodie Biermann; Mantzouranis, Gregory; Genoud, Philippe A; Crocetti, Elisabetta

    2012-04-01

    The purpose of this study was to evaluate the factor structure and the reliability of the French versions of the Identity Style Inventory (ISI-3) and the Utrecht-Management of Identity Commitments Scale (U-MICS) in a sample of college students (N = 457, 18-25 years old). Confirmatory factor analyses confirmed the hypothesized three-factor solution of the ISI-3 identity styles (i.e. informational, normative, and diffuse-avoidant styles), the one-factor solution of the ISI-3 identity commitment, and the three-factor structure of the U-MICS (i.e. commitment, in-depth exploration, and reconsideration of commitment). Additionally, theoretically consistent and meaningful associations among the ISI-3, U-MICS, and Ego Identity Process Questionnaire (EIPQ) confirmed convergent validity. Overall, the results of the present study indicate that the French versions of the ISI-3 and UMICS are useful instruments for assessing identity styles and processes, and provide additional support to the cross-cultural validity of these tools.

  14. Analysis and experimental validation of the middle-frequency vibro-acoustic coupling property for aircraft structural model based on the wave coupling hybrid FE-SEA method

    Science.gov (United States)

    Yan, Yunju; Li, Pengbo; Lin, Huagang

    2016-06-01

    The finite element (FE) method is suitable for low frequency analysis and the statistical energy analysis (SEA) for high frequency analysis, but the vibro-acoustic coupling analysis at middle frequency, especially with a certain range of uncertainty system, requires some new methods. A hybrid FE-SEA method is proposed in this study and the Monte Carlo method is used to check the hybrid FE-SEA method through the energy response analysis of a beam-plate built-up structure with some uncertainty, and the results show that two kinds of calculation results match well consistently. Taking the advantage of the hybrid FE-SEA method, the structural vibration and the cabin noise field responses under the vibro-acoustic coupling for an aircraft model are numerically analyzed, and, also, the corresponding experiment is carried out to verify the simulated results. Results show that the structural vibration responses at low frequency accord well with the experiment, but the error at high frequency is greater. The error of sound pressure response level in cabin throughout the spectrum is less than 3 dB. The research proves the reliability of the method proposed in this paper. This indicates that the proposed method can overcome the strict limitations of the traditional method for a large complex structure with uncertainty factors, and it can also avoid the disadvantages of solving complex vibro-acoustic system using the finite element method or statistical energy analysis in the middle frequency.

  15. WAIS-IV and WISC-IV Structural Validity: Alternate Methods, Alternate Results. Commentary on Weiss et al. (2013a) and Weiss et al. (2013b)

    Science.gov (United States)

    Canivez, Gary L.; Kush, Joseph C.

    2013-01-01

    Weiss, Keith, Zhu, and Chen (2013a) and Weiss, Keith, Zhu, and Chen (2013b), this issue, report examinations of the factor structure of the Wechsler Adult Intelligence Scale-Fourth Edition (WAIS-IV) and Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV), respectively; comparing Wechsler Hierarchical Model (W-HM) and…

  16. The Anxiety Sensitivity Index--Revised: Confirmatory Factor Analyses, Structural Invariance in Caucasian and African American Samples, and Score Reliability and Validity

    Science.gov (United States)

    Arnau, Randolph C.; Broman-Fulks, Joshua J.; Green, Bradley A.; Berman, Mitchell E.

    2009-01-01

    The most commonly used measure of anxiety sensitivity is the 36-item Anxiety Sensitivity Index--Revised (ASI-R). Exploratory factor analyses have produced several different factors structures for the ASI-R, but an acceptable fit using confirmatory factor analytic approaches has only been found for a 21-item version of the instrument. We evaluated…

  17. The Structure of Self-Serving Cognitive Distortions: A Validation of the "How I Think" Questionnaire in a Sample of Italian Adolescents

    Science.gov (United States)

    Bacchini, Dario; De Angelis, Grazia; Affuso, Gaetana; Brugman, Daniel

    2016-01-01

    This study aims to investigate the structure of self-serving cognitive distortions (CD), evaluating the psychometric properties of the How I Think Questionnaire in a sample of Italian adolescents. A confirmatory factor analysis supported the distinction between four categories of CD and the use of a single second-order dimension of CD. Reliability…

  18. Validating the student-teacher relationship scale: testing factor structure and measurement invariance across child gender and age in a Dutch sample

    NARCIS (Netherlands)

    Koomen, H.M.Y.; Verschueren, K.; van Schooten, E.; Jak, S.; Pianta, R.C.

    2012-01-01

    The Student-Teacher Relationship Scale (STRS) is widely used to examine teachers' relationships with young students in terms of closeness, conflict, and dependency. This study aimed to verify the dimensional structure of the STRS with confirmatory factor analysis, test its measurement invariance acr

  19. Validating an Objective Structured Clinical Examination (OSCE) as a Method for Selecting Foreign Medical Graduates for a Pre-Internship Program.

    Science.gov (United States)

    Cohen, Robert; And Others

    1991-01-01

    A study supported use of the objective structured clinical examination for screening foreign medical graduates (n=67) wishing to enter a preinternship program in at the University of Toronto. However, it also showed that appropriate training for the candidates was the internship, not preinternship, program. (MSE)

  20. Extending Structural Analyses of the Rosenberg Self-Esteem Scale to Consider Criterion-Related Validity: Can Composite Self-Esteem Scores Be Good Enough?

    Science.gov (United States)

    Donnellan, M Brent; Ackerman, Robert A; Brecheen, Courtney

    2016-01-01

    Although the Rosenberg Self-Esteem Scale (RSES) is the most widely used measure of global self-esteem in the literature, there are ongoing disagreements about its factor structure. This methodological debate informs how the measure should be used in substantive research. Using a sample of 1,127 college students, we test the overall fit of previously specified models for the RSES, including a newly proposed bifactor solution (McKay, Boduszek, & Harvey, 2014 ). We extend previous work by evaluating how various latent factors from these structural models are related to a set of criterion variables frequently studied in the self-esteem literature. A strict unidimensional model poorly fit the data, whereas models that accounted for correlations between negatively and positively keyed items tended to fit better. However, global factors from viable structural models had similar levels of association with criterion variables and with the pattern of results obtained with a composite global self-esteem variable calculated from observed scores. Thus, we did not find compelling evidence that different structural models had substantive implications, thereby reducing (but not eliminating) concerns about the integrity of the self-esteem literature based on overall composite scores for the RSES.

  1. Multi-institutional Quantitative Evaluation and Clinical Validation of Smart Probabilistic Image Contouring Engine (SPICE) Autosegmentation of Target Structures and Normal Tissues on Computer Tomography Images in the Head and Neck, Thorax, Liver, and Male Pelvis Areas

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Mingyao [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri (United States); Bzdusek, Karl [Philips Healthcare, Fitchburg, Wisconsin (United States); Brink, Carsten [Institute of Clinical Research, University of Southern Denmark, Odense (Denmark); Laboratory of Radiation Physics, Odense University Hospital, Odense (Denmark); Eriksen, Jesper Grau [Department of Oncology, Odense University Hospital, Odense (Denmark); Hansen, Olfred [Institute of Clinical Research, University of Southern Denmark, Odense (Denmark); Department of Oncology, Odense University Hospital, Odense (Denmark); Jensen, Helle Anita [Department of Oncology, Odense University Hospital, Odense (Denmark); Gay, Hiram A.; Thorstad, Wade [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri (United States); Widder, Joachim; Brouwer, Charlotte L.; Steenbakkers, Roel J.H.M.; Vanhauten, Hubertus A.M. [Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen (Netherlands); Cao, Jeffrey Q.; McBrayne, Gail [London Regional Cancer Centre, Ontario (Canada); Patel, Salil H. [Department of Radiation Oncology, Rhode Island Hospital, Providence, Rhode Island (United States); Cannon, Donald M. [Department of Human Oncology, University of Wisconsin—Madison (United States); Hardcastle, Nicholas [Department of Physical Science, Peter MacCallum Cancer Centre, Melbourne (Australia); Tomé, Wolfgang A. [Montefiore Medical Center and Institute of Onco-Physics, Albert Einstein College of Medicine, Bronx, New York (United States); Guckenberg, Matthias [University of Würzburg, Department of Radiation Oncology, Würzburg (Germany); Parikh, Parag J., E-mail: pparikh@radonc.wustl.edu [Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri (United States)

    2013-11-15

    Purpose: Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE). Methods and Materials: CT images of 125 treated patients (32 head and neck [HN], 40 thorax, 23 liver, and 30 prostate) in 7 independent institutions were autosegmented using SPICE and computational times were recorded. The number of structures autocontoured were 25 for the HN, 7 for the thorax, 3 for the liver, and 6 for the male pelvis regions. Using the clinical contours as reference, autocontours of 22 selected structures were quantitatively evaluated using Dice Similarity Coefficient (DSC) and Mean Slice-wise Hausdorff Distance (MSHD). All 40 autocontours were evaluated by a radiation oncologist from the institution that treated the patients. Results: The mean computational times to autosegment all the structures using SPICE were 3.1 to 11.1 minutes per patient. For the HN region, the mean DSC was >0.70 for all evaluated structures, and the MSHD ranged from 3.2 to 10.0 mm. For the thorax region, the mean DSC was 0.95 for the lungs and 0.90 for the heart, and the MSHD ranged from 2.8 to 12.8 mm. For the liver region, the mean DSC was >0.92 for all structures, and the MSHD ranged from 5.2 to 15.9 mm. For the male pelvis region, the mean DSC was >0.76 for all structures, and the MSHD ranged from 4.8 to 10.5 mm. Out of the 40 autocontoured structures reviews by experts, 25 were scored useful as autocontoured or with minor edits for at least 90% of the patients and 33 were scored useful autocontoured or with minor edits for at least 80% of the patients. Conclusions: Compared with manual contouring, autosegmentation using SPICE for the HN, thorax, liver, and male pelvis regions is efficient and shows significant promise for clinical utility.

  2. Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

    OpenAIRE

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-01-01

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic sta...

  3. Structural basis for species specific inhibition of 17β-hydroxysteroid dehydrogenase type 1 (17β-HSD1: computational study and biological validation.

    Directory of Open Access Journals (Sweden)

    Tobias Klein

    Full Text Available 17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1 catalyzes the reduction of estrone to estradiol, which is the most potent estrogen in humans. Inhibition of 17β-HSD1 and thereby reducing the intracellular estradiol concentration is thus a promising approach for the treatment of estrogen dependent diseases. In the past, several steroidal and non-steroidal inhibitors of 17β-HSD1 have been described but so far there is no cocrystal structure of the latter in complex with 17β-HSD1. However, a distinct knowledge of active site topologies and protein-ligand interactions is a prerequisite for structure-based drug design and optimization. An elegant strategy to enhance this knowledge is to compare inhibition values obtained for one compound toward ortholog proteins from various species, which are highly conserved in sequence and differ only in few residues. In this study the inhibitory potencies of selected members of different non-steroidal inhibitor classes toward marmoset 17β-HSD1 were determined and the data were compared with the values obtained for the human enzyme. A species specific inhibition profile was observed in the class of the (hydroxyphenylnaphthols. Using a combination of computational methods, including homology modelling, molecular docking, MD simulation, and binding energy calculation, a reasonable model of the three-dimensional structure of marmoset 17β-HSD1 was developed and inhibition data were rationalized on the structural basis. In marmoset 17β-HSD1, residues 190 to 196 form a small α-helix, which induces conformational changes compared to the human enzyme. The docking poses suggest these conformational changes as determinants for species specificity and energy decomposition analysis highlighted the outstanding role of Asn152 as interaction partner for inhibitor binding. In summary, this strategy of comparing the biological activities of inhibitors toward highly conserved ortholog proteins might be an alternative to

  4. Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides.

    Science.gov (United States)

    Chin, Stacy L; Lu, Qing; Dane, Eric L; Dominguez, Laura; McKnight, Christopher J; Straub, John E; Grinstaff, Mark W

    2016-05-25

    Poly-amido-saccharides (PAS) are carbohydrate-based, enantiopure synthetic polymers in which sugar repeat units are joined by amide linkages. This unique and relatively rigid pyranose backbone contributes to their defined helical secondary structure and remarkable chemical properties. Glucose- (glc-) and galactose- (gal-) PAS 10-mer structures are synthesized and investigated with molecular dynamics (MD) simulations and experimental measurements. Quantum mechanical DFT energy minimization calculations, as well as experimental observables including circular dichroism, (1)H,(13)C-HSQC, and (1)H,(1)H-NOESY 2D-NMR studies, validated the all-atom simulation models produced using a modified CHARMM force field. Water radial distribution functions show distinct differences in the glc- and gal-PAS systems that correlate well with observed differences in solubility between gal-PASs and glc-PASs. The computational analysis and MD simulations are in good agreement with experimental results, validating the proposed models as reliable representations of novel glc- and gal-PASs.

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

    Science.gov (United States)

    Fabris, Daniele; Yu, Eizadora T.

    2010-01-01

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

  6. Validation of the k-filtering technique for a signal composed of random-phase plane waves and non-random coherent structures

    Directory of Open Access Journals (Sweden)

    O. W. Roberts

    2014-12-01

    Full Text Available Recent observations of astrophysical magnetic fields have shown the presence of fluctuations being wave-like (propagating in the plasma frame and those described as being structure-like (advected by the plasma bulk velocity. Typically with single-spacecraft missions it is impossible to differentiate between these two fluctuations, due to the inherent spatio-temporal ambiguity associated with a single point measurement. However missions such as Cluster which contain multiple spacecraft have allowed for temporal and spatial changes to be resolved, using techniques such as k filtering. While this technique does not assume Taylor's hypothesis it requires both weak stationarity of the time series and that the fluctuations can be described by a superposition of plane waves with random phases. In this paper we test whether the method can cope with a synthetic signal which is composed of a combination of non-random-phase coherent structures with a mean radius d and a mean separation λ, as well as plane waves with random phase.

  7. Validation of the k-filtering technique for a signal composed of random phase plane waves and non-random coherent structures

    Directory of Open Access Journals (Sweden)

    O. W. Roberts

    2014-08-01

    Full Text Available Recent observations of astrophysical magnetic fields have shown the presence of fluctuations being wave-like (propagating in the plasma frame and those described as being structure-like (advected by the plasma bulk velocity. Typically with single spacecraft missions it is impossible to differentiate between these two fluctuations, due to the inherent spatio-temporal ambiguity associated with a single point measurement. However missions such as Cluster which contain multiple spacecraft have allowed temporal and spatial changes to be resolved, with techniques such as the k-filtering technique. While this technique does not assume Taylor's hypothesis as is necessary with single spacecraft missions, it does require weak stationarity of the time series, and that the fluctuations can be described by a superposition of plane waves with random phase. In this paper we test whether the method can cope with a synthetic signal which is composed of a combination of non-random phase coherent structures with a mean radius d and a mean separation λ, as well as plane waves with random phase.

  8. Psychological Test Validity

    Directory of Open Access Journals (Sweden)

    Gessmann H.-W.

    2015-02-01

    Full Text Available This paper presents a theoretical overview of current aspects about the validity problems of psychological tests. The article demonstrates the importance of the development of psychological tests and the scientific studies of their validity, describes the different types of validity and the possible ways of measurement and determination of the validity coefficients. The paper is recommended for researchers, whose work is dedicated to the development, modification or adaptation of the psychological test.

  9. Principles of Proper Validation

    DEFF Research Database (Denmark)

    Esbensen, Kim; Geladi, Paul

    2010-01-01

    Validation in chemometrics is presented using the exemplar context of multivariate calibration/prediction. A phenomenological analysis of common validation practices in data analysis and chemometrics leads to formulation of a set of generic Principles of Proper Validation (PPV), which is based...

  10. Validating the Student-Teacher Relationship Scale: testing factor structure and measurement invariance across child gender and age in a Dutch sample.

    Science.gov (United States)

    Koomen, Helma M Y; Verschueren, Karine; van Schooten, Erik; Jak, Suzanne; Pianta, Robert C

    2012-04-01

    The Student-Teacher Relationship Scale (STRS) is widely used to examine teachers' relationships with young students in terms of closeness, conflict, and dependency. This study aimed to verify the dimensional structure of the STRS with confirmatory factor analysis, test its measurement invariance across child gender and age, improve its measurement of the dependency construct, and extend its age range. Teachers completed a slightly adapted STRS for a Dutch sample of 2335 children aged 3 to 12. Overall, the 3-factor model showed an acceptable fit. Results indicated metric invariance across gender and age up to 8years. Scalar invariance generally did not hold. Lack of metric invariance at ages 8 to 12 primarily involved Conflict items, whereas scale differences across gender and age primarily involved Closeness items. The adapted Dependency scale showed strong invariance and higher internal consistencies than the original scale for this Dutch sample. Importantly, the revealed non-invariance for gender and age did not influence mean group comparisons.

  11. Validation and structural characterization of the LEDGF/p75-MLL interface as a new target for the treatment of MLL-dependent leukemia.

    Science.gov (United States)

    Cermáková, Kateřina; Tesina, Petr; Demeulemeester, Jonas; El Ashkar, Sara; Méreau, Hélène; Schwaller, Juerg; Rezáčová, Pavlína; Veverka, Vaclav; De Rijck, Jan

    2014-09-15

    Mixed lineage leukemia (MLL) fusion-driven acute leukemias represent a genetically distinct subset of leukemias with poor prognosis. MLL forms a ternary complex with the lens epithelium-derived growth factor (LEDGF/p75) and MENIN. LEDGF/p75, a chromatin reader recognizing H3K36me3 marks, contributes to the association of the MLL multiprotein complex to chromatin. Formation of this complex is critical for the development of MLL leukemia. Available X-ray data represent only a partial structure of the LEDGF/p75-MLL-MENIN complex. Using nuclear magnetic resonance spectroscopy, we identified an additional LEDGF/p75-MLL interface, which overlaps with the binding site of known LEDGF/p75 interactors-HIV-1 integrase, PogZ, and JPO2. Binding of these proteins or MLL to LEDGF/p75 is mutually exclusive. The resolved structure, as well as mutational analysis, shows that the interaction is primarily sustained via two aromatic residues of MLL (F148 and F151). Colony-forming assays in MLL-AF9(+) leukemic cells expressing MLL interaction-defective LEDGF/p75 mutants revealed that this interaction is essential for transformation. Finally, we show that the clonogenic growth of primary murine MLL-AF9-expressing leukemic blasts is selectively impaired upon overexpression of a LEDGF/p75-binding cyclic peptide CP65, originally developed to inhibit the LEDGF/p75-HIV-1 integrase interaction. The newly defined protein-protein interface therefore represents a new target for the development of therapeutics against LEDGF/p75-dependent MLL fusion-driven leukemic disorders. Cancer Res; 74(18); 5139-51. ©2014 AACR.

  12. Statistical mechanics-based method to extract atomic distance-dependent potentials from protein structures.

    Science.gov (United States)

    Huang, Sheng-You; Zou, Xiaoqin

    2011-09-01

    In this study, we have developed a statistical mechanics-based iterative method to extract statistical atomic interaction potentials from known, nonredundant protein structures. Our method circumvents the long-standing reference state problem in deriving traditional knowledge-based scoring functions, by using rapid iterations through a physical, global convergence function. The rapid convergence of this physics-based method, unlike other parameter optimization methods, warrants the feasibility of deriving distance-dependent, all-atom statistical potentials to keep the scoring accuracy. The derived potentials, referred to as ITScore/Pro, have been validated using three diverse benchmarks: the high-resolution decoy set, the AMBER benchmark decoy set, and the CASP8 decoy set. Significant improvement in performance has been achieved. Finally, comparisons between the potentials of our model and potentials of a knowledge-based scoring function with a randomized reference state have revealed the reason for the better performance of our scoring function, which could provide useful insight into the development of other physical scoring functions. The potentials developed in this study are generally applicable for structural selection in protein structure prediction.

  13. Toward the discovery of novel anti-HIV drugs. Second-generation inhibitors of the cellular ATPase DDX3 with improved anti-HIV activity: synthesis, structure-activity relationship analysis, cytotoxicity studies, and target validation.

    Science.gov (United States)

    Maga, Giovanni; Falchi, Federico; Radi, Marco; Botta, Lorenzo; Casaluce, Gianni; Bernardini, Martina; Irannejad, Hamid; Manetti, Fabrizio; Garbelli, Anna; Samuele, Alberta; Zanoli, Samantha; Esté, José A; Gonzalez, Emmanuel; Zucca, Elisa; Paolucci, Stefania; Baldanti, Fausto; De Rijck, Jan; Debyser, Zeger; Botta, Maurizio

    2011-08-01

    A hit optimization protocol applied to the first nonnucleoside inhibitor of the ATPase activity of human DEAD-box RNA helicase DDX3 led to the design and synthesis of second-generation rhodanine derivatives with better inhibitory activity toward cellular DDX3 and HIV-1 replication. Additional DDX3 inhibitors were identified among triazine compounds. Biological data were rationalized in terms of structure-activity relationships and docking simulations. Antiviral activity and cytotoxicity of selected DDX3 inhibitors are reported and discussed. A thorough analysis confirmed human DDX3 as a valid anti-HIV target. The compounds described herein represent a significant advance in the pursuit of novel drugs that target HIV-1 host cofactors.

  14. Testing of the preliminary OMERACT validation criteria for a biomarker to be regarded as reflecting structural damage endpoints in rheumatoid arthritis clinical trials: the example of C-reactive protein

    DEFF Research Database (Denmark)

    Keeling, Stephanie O; Landewe, Robert; van der Heijde, Desiree;

    2007-01-01

    OBJECTIVE: A list of 14 criteria for guiding the validation of a soluble biomarker as reflecting structural damage endpoints in rheumatoid arthritis (RA) clinical trials was drafted by an international working group after a Delphi consensus exercise. C-reactive protein (CRP), a soluble biomarker...... of individual criteria in the draft set. METHODS: A systematic literature review was conducted to elicit evidence in support of each specific criterion composing the 14-criteria draft set. A summary of the key literature findings per criterion was presented to both the working group and to participants......-based survey. RESULTS: Minimal data were extracted from the literature pertaining to those criteria listed under the category of truth. Ratings for strength of evidence were moderate to low (

  15. Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.

    Directory of Open Access Journals (Sweden)

    Alessandro Marchiori

    Full Text Available Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs. The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC and propylthiouracil (PROP. We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.

  16. Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding.

    Science.gov (United States)

    Marchiori, Alessandro; Capece, Luciana; Giorgetti, Alejandro; Gasparini, Paolo; Behrens, Maik; Carloni, Paolo; Meyerhof, Wolfgang

    2013-01-01

    Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs). The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC) and propylthiouracil (PROP). We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG) method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.

  17. How much do incentives affect car purchase? Agent-based microsimulation of consumer choice of new cars. Part 1. Model structure, simulation of bounded rationality, and model validation

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Michel G.; Haan, Peter de [ETH Zurich, Institute for Environmental Decisions, Natural and Social Science Interface, Universitaetstr. 22, CHN J 73.2, 8092 Zurich (Switzerland)

    2009-03-15

    This article presents an agent-based microsimulation capable of forecasting the effects of policy levers that influence individual choices of new passenger cars. The fundamental decision-making units are households distinguished by sociodemographic characteristics and car ownership. A two-stage model of individual decision processes is employed. In the first stage, individual choice sets are constructed using simple, non-compensatory rules that are based on previously owned cars. Second, decision makers evaluate alternatives in their individual choice set using a multi-attributive weighting rule. The attribute weights are based on a multinomial logit model for cross-country policy analysis in European countries. Additionally, prospect theory and the notion of mental accounting are used to model the perception of monetary values. The microsimulation forecasts actual market observations with high accuracy, both on the level of aggregate market characteristics as well as on a highly resolved level of distributions of market shares. The presented approach is useful for the assessment of policies that influence individual purchase decisions of new passenger cars; it allows accounting for a highly resolved car fleet and differentiated consumer segments. As a result, the complexity of incentive schemes can be represented and detailed structural changes can be investigated. (author)

  18. Validación de un cuestionario de contexto para evaluar sistemas educativos con Modelos de Ecuaciones Estructurales. [Validation of a context questionnaire for the evaluation of educational systems with Structural Equations Modeling].

    Directory of Open Access Journals (Sweden)

    González-Montesinos, Manuel-Jorge

    2010-12-01

    Full Text Available This work shows the use of Structural Equations Modeling (SEM methodology to validate the conceptual structure of context questionnaires employed in national and international studies that evaluate the educational achievement of students. Unfortunately, evaluation agencies do not assign the same amount of technical resources to context questionnaires as those allotted to achievement tests, consequently the former are rarely subject to validity studies. In order to show the use of SEM methodology, a questionnaire was selected, which was employed by the National Institute for the Evaluation of Education to investigate the background factors associated with educational achievement of elementary school students in the third grade. It was administered to a national representative sample of 55,312 students. This questionnaire is analyzed according to SEM procedures of confirmatory factor analysis (CFA. The obtained results provide evidence for the constructive validity of this tool. Este trabajo tiene el propósito de mostrar el uso de la metodología de Modelos de Ecuaciones Estructurales (SEM para validar la estructura conceptual de cuestionarios de contexto que se utilizan en los estudios nacionales e internacionales para evaluar el logro educativo de los escolares. Desgraciadamente, los organismos evaluadores no destinan los mismos recursos técnicos a los cuestionarios de contexto que a las pruebas de aprendizaje, por lo que rara vez los primeros son sujetos a estudios de validez. Para mostrar el uso de la metodología SEM, se seleccionó el cuestionario dirigido a alumnos que utilizó el Instituto Nacional para la Evaluación de la Educación (INEE para conocer los factores de contexto asociados el logro educativo de los estudiantes de tercero de primaria, el que se aplicó a una muestra representativa nacional de 55, 312 alumnos. A dicho instrumento se le aplican los supuestos y procedimientos del análisis factorial confirmatorio (AFC y se

  19. Death Anxiety, Reliability, Validity, and Factorial Structure of the Farsi Form of the Arabic Scale of Death Anxiety in Iranian Old-Aged Persons

    Directory of Open Access Journals (Sweden)

    Mahboubeh Dadfar

    2016-01-01

    Full Text Available The present study is aimed at examining the level of death anxiety and the sex-related differences among old-aged Iranian individuals sample to compare the old-aged persons with young college students and to explore the psychometric properties of the Arabic Scale of Death Anxiety (ASDA factors in old-aged sample. A sample of 146 volunteer Iranian individuals took part in the study. The mean ages were 68.58 (SD = 7.10, men 68.81 (SD = 7.44 and women 68.28 (SD = 6.76, respectively. The mean score of the ASDA was 51.09 (SD = 20.19. Cronbach’s alpha of the ASDA was found to be high (0.94; and Spearman-Brown coefficient was 0.92. Women had a significantly higher mean total score on the ASDA. Old-aged individuals had a significantly higher mean ASDA total score than younger college students (M age = 25.77. The factor analysis of the ASDA items yielded three factors accounting for 67.88% of the total variance labeled (F1 fear of dead people and tombs; (F2 fear of lethal disease and postmortem events; and (F3 death fear. These factors were highly replicable with previous factors extracted from a middle-aged Kuwaiti sample. On the basis of the present results, there are the following three general conclusions: death anxiety is not significantly correlated with age; the sex-related differences on death anxiety are striking in the Iranian samples; and the ASDA has a highly replicable factor structure among two Iranian and Arab countries.

  20. Multi-institutional Quantitative Evaluation and Clinical Validation of Smart Probabilistic Image Contouring Engine (SPICE) Autosegmentation of Target Structures and Normal Tissues on Computer Tomography Images in the Head and Neck, Thorax, Liver, and Male Pelvis Areas

    DEFF Research Database (Denmark)

    Zhu, Mingyao; Bzdusek, Karl; Brink, Carsten

    2013-01-01

    Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE).......Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE)....

  1. Computational modeling and validation studies of 3-D structure of neuraminidase protein of H1N1 influenza A virus and subsequent in silico elucidation of piceid analogues as its potent inhibitors.

    Science.gov (United States)

    Gupta, Chhedi Lal; Akhtar, Salman; Bajpaib, Preeti; Kandpal, K N; Desai, G S; Tiwari, Ashok K

    2013-01-01

    Emergence of the drug resistant variants of the Influenza A virus in the recent years has aroused a great need for the development of novel neuraminidase inhibitors for controlling the pandemic. The neuraminidase (NA) protein of the influenza virus has been the most potential target for the anti-influenza. However, in the absence of any experimental structure of the drug targeting NA protein of H1N1 influenza A virus as zanamivir and oseltamivir, the comprehensive study of the interaction of the drug molecules with the target protein has been missing. Hence in this study a computational 3-D structure of neuraminidase of H1N1 influenza A virus has been developed using homology modeling technique, and the same was validated for its reliability by ProSA web server in term of energy profile & Z scores and PROCHECK program followed by Ramachandran plot. Further, the developed 3-D model had been employed for docking studies with the class of compounds as Piceid and its analogs. In this context, two novel compounds (ChemBank ID 2110359 and 3075417) were found to be more potent inhibitors of neuraminidase than control drugs as zanamivir and oseltamivir in terms of their robust binding energies, strong inhibition constant (Ki) and better hydrogen bond interactions between the protein-ligand complex. The interaction of these compounds with NA protein has been significantly studied at the molecular level.

  2. Validation Measures in CMMI

    OpenAIRE

    Khraiwesh, Mahmoud

    2011-01-01

    Validation is one of the software engineering disciplines that help build quality into software. The major objective of software validation process is to determine that the software performs its intended functions correctly and provide information about its quality and reliability. This paper identifies general measures for the specific goals and its specific practices of Validation Process Area (PA) in Capability Maturity Model Integration (CMMI). CMMI is developed by Software Engineering In...

  3. Validation of simulation models

    DEFF Research Database (Denmark)

    Rehman, Muniza; Pedersen, Stig Andur

    2012-01-01

    of models with regards to their purpose, character, field of application and time dimension inherently calls for a similar diversity in validation approaches. A classification of models in terms of the mentioned elements is presented and used to shed light on possible types of validation leading...... of models has been somewhat narrow-minded reducing the notion of validation to establishment of truth. This article puts forward the diversity in applications of simulation models that demands a corresponding diversity in the notion of validation....

  4. An SAT® Validity Primer

    Science.gov (United States)

    Shaw, Emily J.

    2015-01-01

    This primer should provide the reader with a deeper understanding of the concept of test validity and will present the recent available validity evidence on the relationship between SAT® scores and important college outcomes. In addition, the content examined on the SAT will be discussed as well as the fundamental attention paid to the fairness of…

  5. An Estimation Method of a Constitutive-law for the Rod Model of DNA using Discrete-Structure Simulations

    CERN Document Server

    Hinkle, Adam R; Palanthandalam-Madapusi, Harish J

    2009-01-01

    The continuum-rod model has emerged as an efficient tool to describe the long-length-scale structural-deformations of DNA which are critical to understanding the nature of many biological processes such as gene expression. However, a significant challenge in continuum-mechanics-based modeling of DNA is to estimate its constitutive law, which follows from its interatomic bond-stiffness. Experiments and all-atom molecular dynamics (MD) simulations have suggested that the constitutive law is nonlinear and non-homogeneous (sequence-dependent) along the length of DNA. In this paper, we present an estimation method and a validation study using discrete-structure simulations. We consider a simple cantilever-rod with an artificially constructed, discrete lattice-structure which gives rise to a constitutive law. Large deformations are then simulated. An effective constitutive-law is estimated from these deformations using inverse methods. Finally, we test the estimated law by employing it in the continuum rod-model an...

  6. Construct validity and factor structure of the pittsburgh sleep quality index and epworth sleepiness scale in a multi-national study of African, South East Asian and South American college students.

    Directory of Open Access Journals (Sweden)

    Bizu Gelaye

    Full Text Available The Pittsburgh Sleep Quality Index (PSQI and the Epworth Sleepiness Scale (ESS are questionnaires used to assess sleep quality and excessive daytime sleepiness in clinical and population-based studies. The present study aimed to evaluate the construct validity and factor structure of the PSQI and ESS questionnaires among young adults in four countries (Chile, Ethiopia, Peru and Thailand.A cross-sectional study was conducted among 8,481 undergraduate students. Students were invited to complete a self-administered questionnaire that collected information about lifestyle, demographic, and sleep characteristics. In each country, the construct validity and factorial structures of PSQI and ESS questionnaires were tested through exploratory and confirmatory factor analyses (EFA and CFA.The largest component-total correlation coefficient for sleep quality as assessed using PSQI was noted in Chile (r = 0.71 while the smallest component-total correlation coefficient was noted for sleep medication use in Peru (r = 0.28. The largest component-total correlation coefficient for excessive daytime sleepiness as assessed using ESS was found for item 1 (sitting/reading in Chile (r = 0.65 while the lowest item-total correlation was observed for item 6 (sitting and talking to someone in Thailand (r = 0.35. Using both EFA and CFA a two-factor model was found for PSQI questionnaire in Chile, Ethiopia and Thailand while a three-factor model was found for Peru. For the ESS questionnaire, we noted two factors for all four countries.Overall, we documented cross-cultural comparability of sleep quality and excessive daytime sleepiness measures using the PSQI and ESS questionnaires among Asian, South American and African young adults. Although both the PSQI and ESS were originally developed as single-factor questionnaires, the results of our EFA and CFA revealed the multi- dimensionality of the scales suggesting limited usefulness of the global PSQI and ESS

  7. Checklists for external validity

    DEFF Research Database (Denmark)

    Dyrvig, Anne-Kirstine; Kidholm, Kristian; Gerke, Oke;

    2014-01-01

    RATIONALE, AIMS AND OBJECTIVES: The quality of the current literature on external validity varies considerably. An improved checklist with validated items on external validity would aid decision-makers in judging similarities among circumstances when transferring evidence from a study setting...... to an implementation setting. In this paper, currently available checklists on external validity are identified, assessed and used as a basis for proposing a new improved instrument. METHOD: A systematic literature review was carried out in Pubmed, Embase and Cinahl on English-language papers without time restrictions....... The retrieved checklist items were assessed for (i) the methodology used in primary literature, justifying inclusion of each item; and (ii) the number of times each item appeared in checklists. RESULTS: Fifteen papers were identified, presenting a total of 21 checklists for external validity, yielding a total...

  8. Bibliometrics for Social Validation.

    Science.gov (United States)

    Hicks, Daniel J

    2016-01-01

    This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community; it is formally independent of the technical validation of methods, and is frequently studied in history, philosophy, and social studies of science using qualitative methods. The quantitative methods introduced here find that high-throughput toxicology methods are spread throughout a large and well-connected research community, which suggests high social validation. Further assessment of social validation involving mixed qualitative and quantitative methods are discussed in the conclusion.

  9. Bibliometrics for Social Validation

    Science.gov (United States)

    2016-01-01

    This paper introduces a bibliometric, citation network-based method for assessing the social validation of novel research, and applies this method to the development of high-throughput toxicology research at the US Environmental Protection Agency. Social validation refers to the acceptance of novel research methods by a relevant scientific community; it is formally independent of the technical validation of methods, and is frequently studied in history, philosophy, and social studies of science using qualitative methods. The quantitative methods introduced here find that high-throughput toxicology methods are spread throughout a large and well-connected research community, which suggests high social validation. Further assessment of social validation involving mixed qualitative and quantitative methods are discussed in the conclusion. PMID:28005974

  10. Validación estructural del Wong-Law Emotional Intelligence Scale (WLEIS: estudio preliminar en adultos / Structural validation of the Wong-Law Emotional Intelligence Scale (WLEIS: preliminary study in adults

    Directory of Open Access Journals (Sweden)

    César Merino Soto

    2016-06-01

    structure validity of the WLEIS in Peruvian adults. There were 120 participants (72 women between 17 and 59 years old who responded to the questionnaire mediated by the internet. The internal structure was analyzed using structural equations methodology. A satisfactory structure of 4 factors and high factorial loads of items was found. The inter-factorial correlations were high or moderately high – and the internal consistency was good. It is concluded that the first results are acceptable – to assume that the Wong-Law model is also apparently generalizable.

  11. On validation of multibody musculoskeletal models

    DEFF Research Database (Denmark)

    Lund, Morten Enemark; de Zee, Mark; Andersen, Michael Skipper;

    2012-01-01

    This paper reviews the opportunities to validate multibody musculoskeletal models in view of the current transition of musculoskeletal modelling from a research topic to a practical simulation tool in product design, healthcare and other important applications. This transition creates a new need...... for improvement of the validation of multibody musculoskeletal models are pointed out and directions for future research in the field are proposed. It is our hope that a more structured approach to model validation can help to improve the credibility of musculoskeletal models....

  12. Model Validation Status Review

    Energy Technology Data Exchange (ETDEWEB)

    E.L. Hardin

    2001-11-28

    The primary objective for the Model Validation Status Review was to perform a one-time evaluation of model validation associated with the analysis/model reports (AMRs) containing model input to total-system performance assessment (TSPA) for the Yucca Mountain site recommendation (SR). This review was performed in response to Corrective Action Request BSC-01-C-01 (Clark 2001, Krisha 2001) pursuant to Quality Assurance review findings of an adverse trend in model validation deficiency. The review findings in this report provide the following information which defines the extent of model validation deficiency and the corrective action needed: (1) AMRs that contain or support models are identified, and conversely, for each model the supporting documentation is identified. (2) The use for each model is determined based on whether the output is used directly for TSPA-SR, or for screening (exclusion) of features, events, and processes (FEPs), and the nature of the model output. (3) Two approaches are used to evaluate the extent to which the validation for each model is compliant with AP-3.10Q (Analyses and Models). The approaches differ in regard to whether model validation is achieved within individual AMRs as originally intended, or whether model validation could be readily achieved by incorporating information from other sources. (4) Recommendations are presented for changes to the AMRs, and additional model development activities or data collection, that will remedy model validation review findings, in support of licensing activities. The Model Validation Status Review emphasized those AMRs that support TSPA-SR (CRWMS M&O 2000bl and 2000bm). A series of workshops and teleconferences was held to discuss and integrate the review findings. The review encompassed 125 AMRs (Table 1) plus certain other supporting documents and data needed to assess model validity. The AMRs were grouped in 21 model areas representing the modeling of processes affecting the natural and

  13. Validity in Qualitative Evaluation

    Directory of Open Access Journals (Sweden)

    Vasco Lub

    2015-12-01

    Full Text Available This article provides a discussion on the question of validity in qualitative evaluation. Although validity in qualitative inquiry has been widely reflected upon in the methodological literature (and is still often subject of debate, the link with evaluation research is underexplored. Elaborating on epistemological and theoretical conceptualizations by Guba and Lincoln and Creswell and Miller, the article explores aspects of validity of qualitative research with the explicit objective of connecting them with aspects of evaluation in social policy. It argues that different purposes of qualitative evaluations can be linked with different scientific paradigms and perspectives, thus transcending unproductive paradigmatic divisions as well as providing a flexible yet rigorous validity framework for researchers and reviewers of qualitative evaluations.

  14. Validation Measures in CMMI

    CERN Document Server

    Khraiwesh, Mahmoud

    2011-01-01

    Validation is one of the software engineering disciplines that help build quality into software. The major objective of software validation process is to determine that the software performs its intended functions correctly and provide information about its quality and reliability. This paper identifies general measures for the specific goals and its specific practices of Validation Process Area (PA) in Capability Maturity Model Integration (CMMI). CMMI is developed by Software Engineering Institute (SEI). CMMI is a framework for improvement and assessment of a software development process. CMMI needs a measurement program that is practical. The method we used to define the measures is to apply the Goal Question Metrics (GQM) paradigm to the specific goals and its specific practices of Validation Process Area in CMMI.

  15. On Validating Boolean Optimizers

    CERN Document Server

    Morgado, Antonio

    2011-01-01

    Boolean optimization finds a wide range of application domains, that motivated a number of different organizations of Boolean optimizers since the mid 90s. Some of the most successful approaches are based on iterative calls to an NP oracle, using either linear search, binary search or the identification of unsatisfiable sub-formulas. The increasing use of Boolean optimizers in practical settings raises the question of confidence in computed results. For example, the issue of confidence is paramount in safety critical settings. One way of increasing the confidence of the results computed by Boolean optimizers is to develop techniques for validating the results. Recent work studied the validation of Boolean optimizers based on branch-and-bound search. This paper complements existing work, and develops methods for validating Boolean optimizers that are based on iterative calls to an NP oracle. This entails implementing solutions for validating both satisfiable and unsatisfiable answers from the NP oracle. The wo...

  16. Structure of Adverse Events Risk Perception Scale and its reliability and validity among clinical nurses%临床护士不良事件风险感知量表的构建及信效度检验

    Institute of Scientific and Technical Information of China (English)

    毛秋云; 赵伯莲; 刘春玲; 张伟

    2016-01-01

    目的:构建临床护士不良事件风险感知量表,并进行信效度检验。方法:通过半结构访谈与开放问卷调查形成量表初稿,然后经专家咨询及预调查进行修改。抽取917名泰安市二、三级医院临床护士进行信效度检验,对量表进行修改并形成终稿。结果:总量表全部条目内容效度指数(CVI)为0.91,各条目CVI为0.71~1.00;利用项目分析和探索性因子分析最终确定20个条目、3个维度,分别为患者照护风险、系统流程风险和护士操作风险,累积方差贡献率为60.374%;验证性因子分析拟合总体较理想(χ2/df=2.427、GFI=0.936、AGFI=0.917、RMSEA=0.049、NFI=0.915、CFI=0.948、IFI=0.948);量表总体Cronbach’s α系数为0.939,各维度Cronbach’s α系数均大于0.70;各条目与量表总分的相关系数为0.46~0.77(P<0.01)。结论:临床护士不良事件风险感知量表体现出护理服务自身的特点,量表具有良好的信度和效度,可作为临床护士不良事件风险感知的测评工具。%Objective: To explore the structure of Adverse Events Risk Perception Scale and to test its reliability and validity among clinical nurses. Methods: The draft questionnaire was designed by semi-structure interview and open questionnaire survey, and then revised through Delphi Method and a preliminary test. The reliability and validity of the scale were tested among 917 nurses in Taian city. Data were analyzed by SPSS 19.0 software and AMOS 17.0 software. Results: A scale with three factors and 20 items was identiifed by using item analysis and exploratory factor analysis. These three factors could explain 60.374% of the variance. The overall content Validity Index (CVI) was 0.91, while the CVI for each item was ranged from 0.71 to 1.00. The conifrmatory factor analysis revealed a good ift of the model to the data based on various ift indices (χ2/df=2.427, GFI=0.936, AGFI=0.917, RMSEA=0

  17. Verification and validation benchmarks.

    Energy Technology Data Exchange (ETDEWEB)

    Oberkampf, William Louis; Trucano, Timothy Guy

    2007-02-01

    Verification and validation (V&V) are the primary means to assess the accuracy and reliability of computational simulations. V&V methods and procedures have fundamentally improved the credibility of simulations in several high-consequence fields, such as nuclear reactor safety, underground nuclear waste storage, and nuclear weapon safety. Although the terminology is not uniform across engineering disciplines, code verification deals with assessing the reliability of the software coding, and solution verification deals with assessing the numerical accuracy of the solution to a computational model. Validation addresses the physics modeling accuracy of a computational simulation by comparing the computational results with experimental data. Code verification benchmarks and validation benchmarks have been constructed for a number of years in every field of computational simulation. However, no comprehensive guidelines have been proposed for the construction and use of V&V benchmarks. For example, the field of nuclear reactor safety has not focused on code verification benchmarks, but it has placed great emphasis on developing validation benchmarks. Many of these validation benchmarks are closely related to the operations of actual reactors at near-safety-critical conditions, as opposed to being more fundamental-physics benchmarks. This paper presents recommendations for the effective design and use of code verification benchmarks based on manufactured solutions, classical analytical solutions, and highly accurate numerical solutions. In addition, this paper presents recommendations for the design and use of validation benchmarks, highlighting the careful design of building-block experiments, the estimation of experimental measurement uncertainty for both inputs and outputs to the code, validation metrics, and the role of model calibration in validation. It is argued that the understanding of predictive capability of a computational model is built on the level of

  18. Introduction to Validity

    Institute of Scientific and Technical Information of China (English)

    张楠

    2015-01-01

    The designing of a test paper strictly follows the specification of the relevant Testing Syllabus, which covers various skills and abilities needed for real communicative situation. A test with high content validity is likely to have a positive impact upon the teaching. Therefore, a test with a high content validity will undoubtedly promote the college English education and it will certainly facilitate the implementation of the Syllabus.

  19. Structure of the antimicrobial beta-hairpin peptide protegrin-1 in a DLPC lipid bilayer investigated by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2007-01-01

    All atom molecular dynamics simulations of the 18-residue beta-hairpin antimicrobial peptide protegrin-1 (PG-1, RGGRLCYCRRRFCVCVGR-NH(2)) in a fully hydrated dilauroylphosphatidylcholine (DLPC) lipid bilayer have been implemented. The goal of the reported work is to investigate the structure of t...

  20. Selective refinement and selection of near-native models in protein structure prediction.

    Science.gov (United States)

    Zhang, Jiong; Barz, Bogdan; Zhang, Jingfen; Xu, Dong; Kosztin, Ioan

    2015-10-01

    In recent years in silico protein structure prediction reached a level where fully automated servers can generate large pools of near-native structures. However, the identification and further refinement of the best structures from the pool of models remain problematic. To address these issues, we have developed (i) a target-specific selective refinement (SR) protocol; and (ii) molecular dynamics (MD) simulation based ranking (SMDR) method. In SR the all-atom refinement of structures is accomplished via the Rosetta Relax protocol, subject to specific constraints determined by the size and complexity of the target. The best-refined models are selected with SMDR by testing their relative stability against gradual heating through all-atom MD simulations. Through extensive testing we have found that Mufold-MD, our fully automated protein structure prediction server updated with the SR and SMDR modules consistently outperformed its previous versions.

  1. Novel computational methodologies for structural modeling of spacious ligand binding sites of G-protein-coupled receptors: development and application to human leukotriene B4 receptor.

    Science.gov (United States)

    Ishino, Yoko; Harada, Takanori

    2012-01-01

    This paper describes a novel method to predict the activated structures of G-protein-coupled receptors (GPCRs) with high accuracy, while aiming for the use of the predicted 3D structures in in silico virtual screening in the future. We propose a new method for modeling GPCR thermal fluctuations, where conformation changes of the proteins are modeled by combining fluctuations on multiple time scales. The core idea of the method is that a molecular dynamics simulation is used to calculate average 3D coordinates of all atoms of a GPCR protein against heat fluctuation on the picosecond or nanosecond time scale, and then evolutionary computation including receptor-ligand docking simulations functions to determine the rotation angle of each helix of a GPCR protein as a movement on a longer time scale. The method was validated using human leukotriene B4 receptor BLT1 as a sample GPCR. Our study demonstrated that the proposed method was able to derive the appropriate 3D structure of the active-state GPCR which docks with its agonists.

  2. Validation of analytical methods

    Directory of Open Access Journals (Sweden)

    Xavier Rius, F.

    2002-03-01

    Full Text Available In this paper we shall discuss the concept of method validation, describe the various elements and explain its close relationship with fitness for purpose. Method validation is based on the assumption that a series of requirements are fulfilled and we shall explain how these requirements are selected, the way in which evidence is supplied and what work has to be carried out in the laboratory. The basic principles of method validation and the different ways to validate a methodology, by inter-laboratory comparison or performing an in-house validation, are also described.En este artículo se discute el concepto de validación del método, se describen los elementos que la componen y se explica la fuerte relación entre la validación y las características de ajuste. El método de validación se basa en el cumplimiento de una serie de requerimientos, se explica como seleccionar esos requerimientos, la forma en que se suministran evidencias, y que trabajo se debe llevar a cabo en el laboratorio. También se describen, los principios básicos del método de validación y los diferentes caminos para validar una metodología, tanto en la comparación entre laboratorios o como cuando se lleva a cabo una validación dentro del laboratorio.

  3. Validation of Serious Games

    Directory of Open Access Journals (Sweden)

    Katinka van der Kooij

    2015-09-01

    Full Text Available The application of games for behavioral change has seen a surge in popularity but evidence on the efficacy of these games is contradictory. Anecdotal findings seem to confirm their motivational value whereas most quantitative findings from randomized controlled trials (RCT are negative or difficult to interpret. One cause for the contradictory evidence could be that the standard RCT validation methods are not sensitive to serious games’ effects. To be able to adapt validation methods to the properties of serious games we need a framework that can connect properties of serious game design to the factors that influence the quality of quantitative research outcomes. The Persuasive Game Design model [1] is particularly suitable for this aim as it encompasses the full circle from game design to behavioral change effects on the user. We therefore use this model to connect game design features, such as the gamification method and the intended transfer effect, to factors that determine the conclusion validity of an RCT. In this paper we will apply this model to develop guidelines for setting up validation methods for serious games. This way, we offer game designers and researchers handles on how to develop tailor-made validation methods.

  4. Rapid Robot Design Validation Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Energid Technologies will create a comprehensive software infrastructure for rapid validation of robot designs. The software will support push-button validation...

  5. Rapid Robot Design Validation Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Energid Technologies will create a comprehensive software infrastructure for rapid validation of robotic designs. The software will support push-button validation...

  6. Shift Verification and Validation

    Energy Technology Data Exchange (ETDEWEB)

    Pandya, Tara M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Evans, Thomas M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Davidson, Gregory G [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Johnson, Seth R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Godfrey, Andrew T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-09-07

    This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over a burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.

  7. Validation and Variability

    DEFF Research Database (Denmark)

    Carusi, Annamaria

    2014-01-01

    as inter-subject variability. This need is simultaneously social and epistemic: social as systems biologists attempt to engage with the interests and concerns of clinicians and others in applied medical research; epistemic as they attempt to develop new strategies to cope with variability in the validation...... and experimentally inclined modellers on one hand, and attempts to forge new collaborations with medical scientists on the other. Apart from the scientific interest of the population of models approach for tackling variability, the trial also offers a good illustration of the epistemology of experiment......-facing modelling. I claim that it shows the extent to which experiment-facing modelling and validation require the establishment of criteria for comparing models and experiments that enable them to be linked together. These 'grounds of comparability' are the broad framework in which validation experiments...

  8. Shift Verification and Validation

    Energy Technology Data Exchange (ETDEWEB)

    Pandya, Tara M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Evans, Thomas M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Davidson, Gregory G [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Johnson, Seth R. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Godfrey, Andrew T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-09-07

    This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of LightWater Reactors (CASL). Fivemain types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over a burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.

  9. Space Shuttle navigation validation

    Science.gov (United States)

    Ragsdale, A.

    The validation of the guidance, navigation, and control system of the Space Shuttle is explained. The functions of the ascent, on-board, and entry mission phases software of the navigation system are described. The common facility testing, which evaluates the simulations to be used in the navigation validation, is examined. The standard preflight analysis of the operational modes of the navigation software and the post-flight navigation analysis are explained. The conversion of the data into a useful reference frame and the use of orbit parameters in the analysis of the data are discussed. Upon entry the data received are converted to flags, ratios, and residuals in order to evaluate performance and detect errors. Various programs developed to support navigation validation are explained. A number of events that occurred with the Space Shuttle's navigation system are described.

  10. The validation of metaphors

    OpenAIRE

    Verhulst, F.

    2001-01-01

    In this paper we introduce models as metaphors for the description of reality We consider a number of case studies of contemporary research pollution of the NorthSea the ow eld of theWadden Sea drillstring dynamics the use of metaphors in psychoanalysis In all these cases validation of the results takes a very dierent form Also this validation is certainly not in agreement with the picture of scienti c research projected by textbook examples In the discussion we draw some conclusions on the u...

  11. Validating Animal Models

    Directory of Open Access Journals (Sweden)

    Nina Atanasova

    2015-06-01

    Full Text Available In this paper, I respond to the challenge raised against contemporary experimental neurobiology according to which the field is in a state of crisis because of the multiple experimental protocols employed in different laboratories and strengthening their reliability that presumably preclude the validity of neurobiological knowledge. I provide an alternative account of experimentation in neurobiology which makes sense of its experimental practices. I argue that maintaining a multiplicity of experimental protocols and strengthening their reliability are well justified and they foster rather than preclude the validity of neurobiological knowledge. Thus, their presence indicates thriving rather than crisis of experimental neurobiology.

  12. The dialogic validation

    DEFF Research Database (Denmark)

    Musaeus, Peter

    2005-01-01

    This paper is inspired by dialogism and the title is a paraphrase on Bakhtin's (1981) "The Dialogic Imagination". The paper investigates how dialogism can inform the process of validating inquiry-based qualitative research. The paper stems from a case study on the role of recognition in apprentic......This paper is inspired by dialogism and the title is a paraphrase on Bakhtin's (1981) "The Dialogic Imagination". The paper investigates how dialogism can inform the process of validating inquiry-based qualitative research. The paper stems from a case study on the role of recognition...

  13. Neurofilament ELISA validation.

    NARCIS (Netherlands)

    Petzold, A.; Altintas, A.; Andreoni, L.; Bartos, A.; Berthele, A.; Blankenstein, M.A.; Buee, L.; Castellazzi, M.; Cepok, S.; Comabella, M.; Constantinescu, C.S.; Deisenhammer, F.; Deniz, G.; Erten, G.; Espino, M.; Fainardi, E.; Franciotta, D.; Freedman, M.S.; Giedraitis, V.; Gilhus, N.E.; Giovannoni, G.; Glabinski, A.; Grieb, P.; Hartung, H.P.; Hemmer, B.; Herukka, S.K.; Hintzen, R.; Ingelsson, M.; Jackson, S.; Jacobsen, S.; Jafari, N.; Jalosinski, M.; Jarius, S.; Kapaki, E.; Kieseier, B.C.; Koel-Simmelink, M.J.; Kornhuber, J.; Kuhle, J.; Kurzepa, J.; Lalive, P.H.; Lannfelt, L.; Lehmensiek, V.; Lewczuk, P.; Livrea, P.; Marnetto, F.; Martino, D.; Menge, T.; Norgren, N.; Papuc, E.; Paraskevas, G.P.; Pirttila, T.; Rajda, C.; Rejdak, K.; Ricny, J.; Ripova, D.; Rosengren, L.; Ruggieri, M.; Schraen, S.; Shaw, G.; Sindic, C.; Siva, A.; Stigbrand, T.; Stonebridge, I.; Topcular, B.; Trojano, M.; Tumani, H.; Twaalfhoven, H.A.; Vecsei, L.; Pesch, V. Van; Stichele, H. van der; Vedeler, C.; Verbeek, M.M.; Villar, L.M.; Weissert, R.; Wildemann, B.; Yang, C.; Yao, K.; Teunissen, C.E.

    2010-01-01

    BACKGROUND: Neurofilament proteins (Nf) are highly specific biomarkers for neuronal death and axonal degeneration. As these markers become more widely used, an inter-laboratory validation study is required to identify assay criteria for high quality performance. METHODS: The UmanDiagnostics NF-light

  14. A valid licence

    NARCIS (Netherlands)

    Spoolder, H.A.M.; Ingenbleek, P.T.M.

    2010-01-01

    A valid licence Tuesday, April 20, 2010 Dr Hans Spoolder and Dr Paul Ingenbleek, of Wageningen University and Research Centres, share their thoughts on improving farm animal welfare in Europe At the presentation of the European Strategy 2020 on 3rd March, President Barroso emphasised the need for Eu

  15. The validation of metaphors

    NARCIS (Netherlands)

    Verhulst, F.

    2001-01-01

    In this paper we introduce models as metaphors for the description of reality We consider a number of case studies of contemporary research pollution of the NorthSea the ow eld of theWadden Sea drillstring dynamics the use of metaphors in psychoanalysis In all these cases validation of the resu

  16. Validation and test report

    DEFF Research Database (Denmark)

    Pedersen, Jens Meldgaard; Andersen, T. Bull

    2012-01-01

    . As a consequence of extensive movement artefacts seen during dynamic contractions, the following validation and test report consists of a report that investigates the physiological responses to a static contraction in a standing and a supine position. Eight subjects performed static contractions of the ankle...

  17. Statistical Analysis and validation

    NARCIS (Netherlands)

    Hoefsloot, H.C.J.; Horvatovich, P.; Bischoff, R.

    2013-01-01

    In this chapter guidelines are given for the selection of a few biomarker candidates from a large number of compounds with a relative low number of samples. The main concepts concerning the statistical validation of the search for biomarkers are discussed. These complicated methods and concepts are

  18. Validation of the Drinking Motives Questionnaire

    DEFF Research Database (Denmark)

    Fernandes-Jesus, Maria; Beccaria, Franca; Demant, Jakob Johan;

    2016-01-01

    • This paper assesses the validity of the DMQ-R (Cooper, 1994) among university students in six different European countries. • Results provide support for similar DMQ-R factor structures across countries. • Drinking motives have similar meanings among European university students....

  19. Validation of the organizational culture assessment instrument.

    Science.gov (United States)

    Heritage, Brody; Pollock, Clare; Roberts, Lynne

    2014-01-01

    Organizational culture is a commonly studied area in industrial/organizational psychology due to its important role in workplace behaviour, cognitions, and outcomes. Jung et al.'s [1] review of the psychometric properties of organizational culture measurement instruments noted many instruments have limited validation data despite frequent use in both theoretical and applied situations. The Organizational Culture Assessment Instrument (OCAI) has had conflicting data regarding its psychometric properties, particularly regarding its factor structure. Our study examined the factor structure and criterion validity of the OCAI using robust analysis methods on data gathered from 328 (females = 226, males = 102) Australian employees. Confirmatory factor analysis supported a four factor structure of the OCAI for both ideal and current organizational culture perspectives. Current organizational culture data demonstrated expected reciprocally-opposed relationships between three of the four OCAI factors and the outcome variable of job satisfaction but ideal culture data did not, thus indicating possible weak criterion validity when the OCAI is used to assess ideal culture. Based on the mixed evidence regarding the measure's properties, further examination of the factor structure and broad validity of the measure is encouraged.

  20. Validation of the organizational culture assessment instrument.

    Directory of Open Access Journals (Sweden)

    Brody Heritage

    Full Text Available Organizational culture is a commonly studied area in industrial/organizational psychology due to its important role in workplace behaviour, cognitions, and outcomes. Jung et al.'s [1] review of the psychometric properties of organizational culture measurement instruments noted many instruments have limited validation data despite frequent use in both theoretical and applied situations. The Organizational Culture Assessment Instrument (OCAI has had conflicting data regarding its psychometric properties, particularly regarding its factor structure. Our study examined the factor structure and criterion validity of the OCAI using robust analysis methods on data gathered from 328 (females = 226, males = 102 Australian employees. Confirmatory factor analysis supported a four factor structure of the OCAI for both ideal and current organizational culture perspectives. Current organizational culture data demonstrated expected reciprocally-opposed relationships between three of the four OCAI factors and the outcome variable of job satisfaction but ideal culture data did not, thus indicating possible weak criterion validity when the OCAI is used to assess ideal culture. Based on the mixed evidence regarding the measure's properties, further examination of the factor structure and broad validity of the measure is encouraged.

  1. Validity of the Decisional Process Inventory.

    Science.gov (United States)

    Marco, Cynthia D.; Hartung, Paul J.; Newman, Isadore; Parr, Patricia

    2003-01-01

    The Gestalt-based Decisional Process Inventory and measures of career indecision and vocational identity were completed by 201 subjects. Results supported the inventory's ability to differentiate by career choice states. Concurrent validity was supported, but confirmatory factor analysis did not support the factor structure regarding measurement…

  2. A logic generator and validator

    Energy Technology Data Exchange (ETDEWEB)

    Szabo, J.; Cain, D.G.; Okrent, D.

    1985-05-01

    The on-line monitoring of a power plant (or any process plant) has three primary functions: data acquisition, data analysis, and data presentation. Relative to the second of these functions, advanced methods for generating reliable data analysis computer codes are presented. The results are illustrated for a safety parameter display system that provides operators with a computer-graphic summary of a nuclear power plant's safety status. In the conventional method of analysis code production, the systems analyst or designer generates rules by which the plant status is being evaluated, while the transcription of those rules to a computer code is done separately by a programmer. Subsequently, the analysis code produced by the programmer must be validated against the specifications prepared by the systems analyst. A logic generator and logic validator are presented to streamline these processes. The logic generator acquires the relevant specifications through a systematic dialogue with the designer and then translates them automatically into an efficient computer logic code, thus solvin the problem of a designer who is not a programmer interfacing with a programmer who is not a designer. The logic generator enhances code reliability in two ways. First, it encourages the systems analyst to produce more reliable and relevant specifications because of the logical structured order in which the interactive session is being conducted. Second, because of the mass production mode b which the logic codes are being generated, proving once the correctness of the code production process ensures the accuracy of all codes to be generated in the future. In the postproduction stage, a logic validator enhances code reliability by displaying a structura overview of the data analysis code, allowing the user an additional opportunity for code evaluation.

  3. CIPS Validation Data Plan

    Energy Technology Data Exchange (ETDEWEB)

    Nam Dinh

    2012-03-01

    This report documents analysis, findings and recommendations resulted from a task 'CIPS Validation Data Plan (VDP)' formulated as an POR4 activity in the CASL VUQ Focus Area (FA), to develop a Validation Data Plan (VDP) for Crud-Induced Power Shift (CIPS) challenge problem, and provide guidance for the CIPS VDP implementation. The main reason and motivation for this task to be carried at this time in the VUQ FA is to bring together (i) knowledge of modern view and capability in VUQ, (ii) knowledge of physical processes that govern the CIPS, and (iii) knowledge of codes, models, and data available, used, potentially accessible, and/or being developed in CASL for CIPS prediction, to devise a practical VDP that effectively supports the CASL's mission in CIPS applications.

  4. UTSim2 validation

    Science.gov (United States)

    Grandin, Robert; Gray, Tim

    2017-02-01

    The Center for NDE (CNDE) at Iowa State University has a long history of developing physics models for NDE and packaging these models into simulation tools which make the modeling capabilities accessible to CNDEs industrial sponsors. Recent work at CNDE has led to the development of a new ultrasonic simulation package, UTSim2, which aims to continue this tradition of supporting industrial application of CNDE models. In order to meet this goal, UTSim2 has been designed as an extensible software package which can support previously-developed physics models as well as future models yet to be developed. Initial work has focused on the implementation of a Gauss-Hermite beam model, a paraxial approximation, which is implemented as part of the Thompson-Gray measurement model. This paper will present recent validation results and include comparisons against both previously-validated model output and newly-performed experiments.

  5. Self-Validating Thermocouple

    Science.gov (United States)

    Perotti, Jose M. (Inventor); Mata, Carlos T. (Inventor); Santiago, Josephine B. (Inventor); Vokrot, Peter (Inventor); Zavala, Carlos E. (Inventor); Burns, Bradley M. (Inventor)

    2010-01-01

    Self-Validating Thermocouple (SVT) Systems capable of detecting sensor probe open circuits, short circuits, and unnoticeable faults such as a probe debonding and probe degradation are useful in the measurement of temperatures. SVT Systems provide such capabilities by incorporating a heating or excitation element into the measuring junction of the thermocouple. By heating the measuring junction and observing the decay time for the detected DC voltage signal, it is possible to indicate whether the thermocouple is bonded or debonded. A change in the thermal transfer function of the thermocouple system causes a change in the rise and decay times of the thermocouple output. Incorporation of the excitation element does not interfere with normal thermocouple operation, thus further allowing traditional validation procedures as well.

  6. Validating MEDIQUAL Constructs

    Science.gov (United States)

    Lee, Sang-Gun; Min, Jae H.

    In this paper, we validate MEDIQUAL constructs through the different media users in help desk service. In previous research, only two end-users' constructs were used: assurance and responsiveness. In this paper, we extend MEDIQUAL constructs to include reliability, empathy, assurance, tangibles, and responsiveness, which are based on the SERVQUAL theory. The results suggest that: 1) five MEDIQUAL constructs are validated through the factor analysis. That is, importance of the constructs have relatively high correlations between measures of the same construct using different methods and low correlations between measures of the constructs that are expected to differ; and 2) five MEDIQUAL constructs are statistically significant on media users' satisfaction in help desk service by regression analysis.

  7. Indian Ocean Validation,

    Science.gov (United States)

    1987-09-01

    block number) 20. DISTRIBUTION/ AVAILABILTY OF ABSTRACT 21. ABSTRACT SECURITY CLASSIFICATION UNCLASSIFIEDIJNLIMITE0 (-1 SAME AS RPT. E3 DTIC USERS \\ .1...characteristics as received. A priori guidance on usage is a major reason for undertaking validation in general and developing coverage guidance in...particular method for predicting estimated SNRs is reasonably accurate. Actual signal usage was highly supportive of the theoretical model. One would also

  8. Seismic Data Gathering and Validation

    Energy Technology Data Exchange (ETDEWEB)

    Coleman, Justin [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-02-01

    Three recent earthquakes in the last seven years have exceeded their design basis earthquake values (so it is implied that damage to SSC’s should have occurred). These seismic events were recorded at North Anna (August 2011, detailed information provided in [Virginia Electric and Power Company Memo]), Fukushima Daichii and Daini (March 2011 [TEPCO 1]), and Kaswazaki-Kariwa (2007, [TEPCO 2]). However, seismic walk downs at some of these plants indicate that very little damage occurred to safety class systems and components due to the seismic motion. This report presents seismic data gathered for two of the three events mentioned above and recommends a path for using that data for two purposes. One purpose is to determine what margins exist in current industry standard seismic soil-structure interaction (SSI) tools. The second purpose is the use the data to validated seismic site response tools and SSI tools. The gathered data represents free field soil and in-structure acceleration time histories data. Gathered data also includes elastic and dynamic soil properties and structural drawings. Gathering data and comparing with existing models has potential to identify areas of uncertainty that should be removed from current seismic analysis and SPRA approaches. Removing uncertainty (to the extent possible) from SPRA’s will allow NPP owners to make decisions on where to reduce risk. Once a realistic understanding of seismic response is established for a nuclear power plant (NPP) then decisions on needed protective measures, such as SI, can be made.

  9. Adapforms: A framework for creating and validating adaptive forms

    DEFF Research Database (Denmark)

    Bohøj, Morten; Bouvin, Niels Olof; Gammelmark, Henrik

    2011-01-01

    AdapForms is a framework for adaptive forms, consisting of a form de nition language designating structure and constraints upon acceptable input, and a software architecture that continuously validates and adapts the form presented to the user. The validation is performed server-side, which enabl...... the use of complex business logic without duplicate code. Thus, the state of the form is kept persistently at the server, and the system ensures that all submitted forms are valid and type safe...

  10. Protein structure prediction: assembly of secondary structure elements by basin-hopping.

    Science.gov (United States)

    Hoffmann, Falk; Vancea, Ioan; Kamat, Sanjay G; Strodel, Birgit

    2014-10-20

    The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.

  11. Excavator Design Validation

    Science.gov (United States)

    Pholsiri, Chalongrath; English, James; Seberino, Charles; Lim, Yi-Je

    2010-01-01

    The Excavator Design Validation tool verifies excavator designs by automatically generating control systems and modeling their performance in an accurate simulation of their expected environment. Part of this software design includes interfacing with human operations that can be included in simulation-based studies and validation. This is essential for assessing productivity, versatility, and reliability. This software combines automatic control system generation from CAD (computer-aided design) models, rapid validation of complex mechanism designs, and detailed models of the environment including soil, dust, temperature, remote supervision, and communication latency to create a system of high value. Unique algorithms have been created for controlling and simulating complex robotic mechanisms automatically from just a CAD description. These algorithms are implemented as a commercial cross-platform C++ software toolkit that is configurable using the Extensible Markup Language (XML). The algorithms work with virtually any mobile robotic mechanisms using module descriptions that adhere to the XML standard. In addition, high-fidelity, real-time physics-based simulation algorithms have also been developed that include models of internal forces and the forces produced when a mechanism interacts with the outside world. This capability is combined with an innovative organization for simulation algorithms, new regolith simulation methods, and a unique control and study architecture to make powerful tools with the potential to transform the way NASA verifies and compares excavator designs. Energid's Actin software has been leveraged for this design validation. The architecture includes parametric and Monte Carlo studies tailored for validation of excavator designs and their control by remote human operators. It also includes the ability to interface with third-party software and human-input devices. Two types of simulation models have been adapted: high-fidelity discrete

  12. Development and validation of the Alcohol Myopia Scale.

    Science.gov (United States)

    Lac, Andrew; Berger, Dale E

    2013-09-01

    Alcohol myopia theory conceptualizes the ability of alcohol to narrow attention and how this demand on mental resources produces the impairments of self-inflation, relief, and excess. The current research was designed to develop and validate a scale based on this framework. People who were alcohol users rated items representing myopic experiences arising from drinking episodes in the past month. In Study 1 (N = 260), the preliminary 3-factor structure was supported by exploratory factor analysis. In Study 2 (N = 289), the 3-factor structure was substantiated with confirmatory factor analysis, and it was superior in fit to an empirically indefensible 1-factor structure. The final 14-item scale was evaluated with internal consistency reliability, discriminant validity, convergent validity, criterion validity, and incremental validity. The alcohol myopia scale (AMS) illuminates conceptual underpinnings of this theory and yields insights for understanding the tunnel vision that arises from intoxication.

  13. The Fundamental Framework of Remote Sensing Validation System

    Science.gov (United States)

    Jiang, X.-G.; Xi, X.-H.; Wu, M.-J.; Li, Z.-L.

    2009-04-01

    Remote sensing is a very complicated course. It is influenced by many factors, such as speciality of remote sensing sensor, radiant transmission characteristic of atmosphere, work environment of remote sensing platform, data transmission, data reception, data processing, and property of observed object etc. Whether the received data is consistent with the design specifications? Can the data meet the demands of remote sensing applications? How about the accuracy of the data products, retrieval products and application products of remote sensing? It is essential to carry out the validation to assess the data quality and application potential. Validation is effective approach to valuate remote sensing products. It is the significant link between remote sensing data and information. Research on remote sensing validation is very important for sensor development, data quality analysis and control. This paper focuses on the study of remote sensing validation and validation system. Different from the previous work done by other researchers, we study the validation from the viewpoint of systematic engineering considering that validation is involved with many aspects as talked about. Validation is not just a single and simple course. It is complicated system. Validation system is the important part of whole earth observation system. First of all, in this paper the category of remote sensing validation is defined. Remote sensing validation includes not only the data products validation, but also the retrieval products validation and application products validation. Second, the new concept, remote sensing validation system, is proposed. Then, the general framework, software structure and functions of validation system are studied and put forward. The validation system is composed of validation field module, data acquirement module, data processing module, data storage and management module, data scaling module, and remote sensing products validation module. And finally the

  14. Multi-institutional Quantitative Evaluation and Clinical Validation of Smart Probabilistic Image Contouring Engine (SPICE) Autosegmentation of Target Structures and Normal Tissues on Computer Tomography Images in the Head and Neck, Thorax, Liver, and Male Pelvis Areas

    NARCIS (Netherlands)

    Zhu, Mingyao; Bzdusek, Karl; Brink, Carsten; Eriksen, Jesper Grau; Hansen, Olfred; Jensen, Helle Anita; Gay, Hiram A.; Thorstad, Wade; Widder, Joachim; Brouwer, Charlotte L.; Steenbakkers, Roel J. H. M.; Vanhauten, Hubertus A. M.; Cao, Jeffrey Q.; McBrayne, Gail; Patel, Salil H.; Cannon, Donald M.; Hardcastle, Nicholas; Tome, Wolfgang A.; Guckenberg, Matthias; Parikh, Parag J.

    2013-01-01

    Purpose: Clinical validation and quantitative evaluation of computed tomography (CT) image autosegmentation using Smart Probabilistic Image Contouring Engine (SPICE). Methods and Materials: CT images of 125 treated patients (32 head and neck [HN], 40 thorax, 23 liver, and 30 prostate) in 7 independe

  15. Unconstrained Structure Formation in Coarse-Grained Protein Simulations

    Science.gov (United States)

    Bereau, Tristan

    The ability of proteins to fold into well-defined structures forms the basis of a wide variety of biochemical functions in and out of the cell membrane. Many of these processes, however, operate at time- and length-scales that are currently unattainable by all-atom computer simulations. To cope with this difficulty, increasingly more accurate and sophisticated coarse-grained models are currently being developed. In the present thesis, we introduce a solvent-free coarse-grained model for proteins. Proteins are modeled by four beads per amino acid, providing enough backbone resolution to allow for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. By studying both helical and extended conformations we make sure the force field is not biased towards any particular secondary structure. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed. The model is subsequently applied to various biophysical problems: (i) kinetics of folding of two model peptides, (ii) large-scale amyloid-beta oligomerization, and (iii) protein folding cooperativity. The last topic---defined by the nature of the finite-size thermodynamic transition exhibited upon folding---was investigated from a microcanonical perspective: the accurate evaluation of the density of states can unambiguously characterize the nature of the transition, unlike its corresponding canonical analysis. Extending the results of lattice simulations and theoretical models, we find that it is the interplay between secondary structure and the loss of non-native tertiary contacts which determines the nature of the transition. Finally, we combine the peptide model with a high-resolution, solvent-free, lipid

  16. Measuring Long-Distance Romantic Relationships: A Validity Study

    Science.gov (United States)

    Pistole, M. Carole; Roberts, Amber

    2011-01-01

    This study investigated aspects of construct validity for the scores of a new long-distance romantic relationship measure. A single-factor structure of the long-distance romantic relationship index emerged, with convergent and discriminant evidence of external validity, high internal consistency reliability, and applied utility of the scores.…

  17. Test Validation and the MKT Measures: Generalizations and Conclusions

    Science.gov (United States)

    Schilling, Stephen G.; Blunk, Merrie; Hill, Heather C.

    2007-01-01

    In this paper, the authors complete the summative stage of the validity argument approach, then use their experiences to reflect on the validity argument as a method. They begin by evaluating the inferences and assumptions of the interpretive argument for the MKT measures. Then they examine both the form and the structure of the interpretive…

  18. Validation of the Chinese Expanded Euthanasia Attitude Scale

    Science.gov (United States)

    Chong, Alice Ming-Lin; Fok, Shiu-Yeu

    2013-01-01

    This article reports the validation of the Chinese version of an expanded 31-item Euthanasia Attitude Scale. A 4-stage validation process included a pilot survey of 119 college students and a randomized household survey with 618 adults in Hong Kong. Confirmatory factor analysis confirmed a 4-factor structure of the scale, which can therefore be…

  19. Validity and reliability of the Structured Clinical Interview for Mood Spectrum: Brazilian version (SCIMOODS-VB Validade e confiabilidade da versão brasileira da Entrevista Clínica Estruturada para o Espectro do Humor (SCIMOODS-VB

    Directory of Open Access Journals (Sweden)

    Roberto Ratzke

    2011-03-01

    Full Text Available OBJECTIVE: The aim of this study was to translate the Structured Clinical Interview for Mood Spectrum into Brazilian Portuguese, measuring its reliability, validity, and defining scores for bipolar disorders. METHOD: Questionnaire was translated (into Brazilian Portuguese and back-translated into English. Sample consisted of 47 subjects with bipolar disorder, 47 with major depressive disorder, 18 with schizophrenia and 22 controls. Inter-rater reliability was tested in 20 subjects with bipolar disorder and MDD. Internal consistency was measured using the Kuder Richardson formula. Forward stepwise discriminant analysis was performed. Scores were compared between groups; manic (M, depressive (D and total (T threshold scores were calculated through receiver operating characteristic (ROC curves. RESULTS: Kuder Richardson coefficients were between 0.86 and 0.94. Intraclass correlation coefficient was 0.96 (CI 95 % 0.93-0.97. Subjects with bipolar disorder had higher M and T, and similar D scores, when compared to major depressive disorder (ANOVA, p OBJETIVO: Traduzir e validar para o português a Entrevista Clínica Estruturada para Distúrbios do Humor, mensurando sua validade, confiabilidade, bem como definindo os escores para transtornos bipolares. MÉTODO: A entrevista foi traduzida (para o português e novamente traduzida para o inglês. A amostra incluiu 47 indivíduos com transtornos bipolares, 47 com transtorno depressivo maior, 18 com esquizofrenia e 22 controles. A confiabilidade entre avaliadores foi testada em 20 indivíduos com transtornos bipolares e transtorno depressivo maior. A consistência interna foi mensurada por meio da fórmula de Kuder Richardson. Análise discriminante foi realizada. Escores dos diversos grupos foram comparados; limiares para mania (M, depressão (D e valores totais foram calculados usando curvas de "receiver operating characteristic" (ROC. RESULTADOS: Coeficientes de Kuder Richardson ficaram entre 0,86 e 0

  20. Reliability and validity in research.

    Science.gov (United States)

    Roberts, Paula; Priest, Helena

    This article examines reliability and validity as ways to demonstrate the rigour and trustworthiness of quantitative and qualitative research. The authors discuss the basic principles of reliability and validity for readers who are new to research.

  1. Validation of the Social Appearance Anxiety Scale: factor, convergent, and divergent validity.

    Science.gov (United States)

    Levinson, Cheri A; Rodebaugh, Thomas L

    2011-09-01

    The Social Appearance Anxiety Scale (SAAS) was created to assess fear of overall appearance evaluation. Initial psychometric work indicated that the measure had a single-factor structure and exhibited excellent internal consistency, test-retest reliability, and convergent validity. In the current study, the authors further examined the factor, convergent, and divergent validity of the SAAS in two samples of undergraduates. In Study 1 (N = 323), the authors tested the factor structure, convergent, and divergent validity of the SAAS with measures of the Big Five personality traits, negative affect, fear of negative evaluation, and social interaction anxiety. In Study 2 (N = 118), participants completed a body evaluation that included measurements of height, weight, and body fat content. The SAAS exhibited excellent convergent and divergent validity with self-report measures (i.e., self-esteem, trait anxiety, ethnic identity, and sympathy), predicted state anxiety experienced during the body evaluation, and predicted body fat content. In both studies, results confirmed a single-factor structure as the best fit to the data. These results lend additional support for the use of the SAAS as a valid measure of social appearance anxiety.

  2. Software Validation using Power Profiles

    OpenAIRE

    Lencevicius, Raimondas; Metz, Edu; Ran, Alexander

    2002-01-01

    The validation of modern software systems incorporates both functional and quality requirements. This paper proposes a validation approach for software quality requirement - its power consumption. This approach validates whether the software produces the desired results with a minimum expenditure of energy. We present energy requirements and an approach for their validation using a power consumption model, test-case specification, software traces, and power measurements. Three different appro...

  3. Measuring avoidance of pain : validation of the Acceptance and Action Questionnaire II-pain version

    NARCIS (Netherlands)

    Reneman, Michiel F.; Kleen, Marco; Trompetter, Hester R.; Schiphorst Preuper, Henrica R.; Koeke, Albere; van Baalen, Bianca; Schreurs, Karlein M. G.

    2014-01-01

    Psychometric research on widely used questionnaires aimed at measuring experiential avoidance of chronic pain has led to inconclusive results. To test the structural validity, internal consistency, and construct validity of a recently developed short questionnaire: the Acceptance and Action Question

  4. Criterion-related validity of screening for exposure to torture

    DEFF Research Database (Denmark)

    Montgomery, Edith; Foldspang, Anders

    1994-01-01

    %, respectively, without significant differences concerning the refugee's gender. It is concluded that refugees' own testimonies of torture appear fairly valid. This enables anamnestic torture prevalence estimation in refugee groups, based on pre-structured interview techniques. Rehabilitation and Research Centre...

  5. Determining Validity in Qualitative Inquiry.

    Science.gov (United States)

    Creswell, John W.; Miller, Dana L.

    2000-01-01

    Suggests that the choice of validity procedures in qualitative inquiry is governed by two perspectives: the lens researchers choose to validate their studies and the researchers' paradigm assumptions. The article advances a two-dimensional framework to help researchers identify appropriate validity procedures for their studies. Nine validity…

  6. Sensitivity validation technique for sequential kriging metamodel

    Energy Technology Data Exchange (ETDEWEB)

    Huh, Seung Kyun; Lee, Jin Min; Lee, Tae Hee [Hanyang Univ., Seoul (Korea, Republic of)

    2012-08-15

    Metamodels have been developed with a variety of design optimization techniques in the field of structural engineering over the last decade because they are efficient, show excellent prediction performance, and provide easy interconnections into design frameworks. To construct a metamodel, a sequential procedure involving steps such as the design of experiments, metamodeling techniques, and validation techniques is performed. Because validation techniques can measure the accuracy of the metamodel, the number of presampled points for an accurate kriging metamodel is decided by the validation technique in the sequential kriging metamodel. Because the interpolation model such as the kriging metamodel based on computer experiments passes through responses at presampled points, additional analyses or reconstructions of the meta models are required to measure the accuracy of the meta model if existing validation techniques are applied. In this study, we suggest a sensitivity validation that does not require additional analyses or reconstructions of the meta models. Fourteen two dimensional mathematical problems and an engineering problem are illustrated to show the feasibility of the suggested method.

  7. Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration

    DEFF Research Database (Denmark)

    Maciejewski, A.; Pasenkiewicz-Gierula, M.; Cramariuc, O.

    2014-01-01

    . In the present study, we determined the parameters for torsion angles in the phosphatidylcholine and glycerol moieties and in the acyl chains, as well the partial atomic charges. In these calculations, we used three methods: (1) Hartree-Fock (HF), (2) second order Moller-Plesset perturbation theory (MP2), and (3...... one was found to be able to satisfactorily reproduce experimental data for the lipid bilayer. The successful DPPC model was obtained from MP2 calculations in an implicit polar environment (PCM)....

  8. Model Validation in Ontology Based Transformations

    Directory of Open Access Journals (Sweden)

    Jesús M. Almendros-Jiménez

    2012-10-01

    Full Text Available Model Driven Engineering (MDE is an emerging approach of software engineering. MDE emphasizes the construction of models from which the implementation should be derived by applying model transformations. The Ontology Definition Meta-model (ODM has been proposed as a profile for UML models of the Web Ontology Language (OWL. In this context, transformations of UML models can be mapped into ODM/OWL transformations. On the other hand, model validation is a crucial task in model transformation. Meta-modeling permits to give a syntactic structure to source and target models. However, semantic requirements have to be imposed on source and target models. A given transformation will be sound when source and target models fulfill the syntactic and semantic requirements. In this paper, we present an approach for model validation in ODM based transformations. Adopting a logic programming based transformational approach we will show how it is possible to transform and validate models. Properties to be validated range from structural and semantic requirements of models (pre and post conditions to properties of the transformation (invariants. The approach has been applied to a well-known example of model transformation: the Entity-Relationship (ER to Relational Model (RM transformation.

  9. Convergent Validity of the PUTS

    Directory of Open Access Journals (Sweden)

    Valerie Cathérine Brandt

    2016-04-01

    Full Text Available Premonitory urges are a cardinal feature in Gilles de la Tourette syndrome. Severity of premonitory urges can be assessed with the Premonitory Urge for Tic Disorders Scale (PUTS. However, convergent validity of the measure has been difficult to assess due to the lack of other urge measures.We investigated the relationship between average real-time urge intensity assessed by an in-house developed real-time urge monitor, measuring urge intensity continuously for 5mins on a visual analogue scale, and general urge intensity assessed by the PUTS in 22 adult Tourette patients (mean age 29.8+/- 10.3; 19 male. Additionally, underlying factors of premonitory urges assessed by the PUTS were investigated in the adult sample using factor analysis and were replicated in 40 children and adolescents diagnosed with Tourette syndrome (mean age 12.05 +/- 2.83 SD, 31 male.Cronbach’s alpha for the PUTS10 was acceptable (α = .79 in the adult sample. Convergent validity between average real-time urge intensity scores (as assessed with the real-time urge monitor and the 10-item version of the PUTS (r = .64 and the 9-item version of the PUTS (r = .66 was good. A factor analysis including the 10 items of the PUTS and average real-time urge intensity scores revealed three factors. One factor included the average real-time urge intensity score and appeared to measure urge intensity, while the other two factors can be assumed to reflect the (sensory quality of urges and subjective control, respectively. The factor structure of the 10 PUTS items alone was replicated in a sample of children and adolescents.The results indicate that convergent validity between the PUTS and the real-time urge assessment monitor is good. Furthermore, the results suggest that the PUTS might assess more than one dimension of urges and it may be worthwhile developing different sub-scales of the PUTS assessing premonitory urges in terms of intensity and quality, as well as subjectively

  10. Efficient sampling in fragment-based protein structure prediction using an estimation of distribution algorithm.

    Directory of Open Access Journals (Sweden)

    David Simoncini

    Full Text Available Fragment assembly is a powerful method of protein structure prediction that builds protein models from a pool of candidate fragments taken from known structures. Stochastic sampling is subsequently used to refine the models. The structures are first represented as coarse-grained models and then as all-atom models for computational efficiency. Many models have to be generated independently due to the stochastic nature of the sampling methods used to search for the global minimum in a complex energy landscape. In this paper we present EdaFold(AA, a fragment-based approach which shares information between the generated models and steers the search towards native-like regions. A distribution over fragments is estimated from a pool of low energy all-atom models. This iteratively-refined distribution is used to guide the selection of fragments during the building of models for subsequent rounds of structure prediction. The use of an estimation of distribution algorithm enabled EdaFold(AA to reach lower energy levels and to generate a higher percentage of near-native models. [Formula: see text] uses an all-atom energy function and produces models with atomic resolution. We observed an improvement in energy-driven blind selection of models on a benchmark of EdaFold(AA in comparison with the [Formula: see text] AbInitioRelax protocol.

  11. Validation of the holyoake codependency index.

    Science.gov (United States)

    Dear, Greg E; Roberts, Clare M

    2005-07-01

    Some clinicians working with families with alcohol or other drug problems continue to use the codependency model to guide their practice despite the limited empirical support for this approach. Research into codependency has been hampered by the lack of psychometrically sound instruments. The Holyoake Codependency Index (HCI; G. E. Dear & C. M. Roberts, 2000) is a 13-item self-report measure of codependent traits that has previously shown adequate to high reliability, initial evidence of construct validity, and an internal structure that is consistent across samples. In the 4 studies reported here, the internal structure of the HCI was confirmed using confirmatory factor analysis, and further evidence of construct validity was found in that the HCI subscales showed meaningful associations with other psychological and demographic variables.

  12. Validation of Rheological Models of Typical Structures : an Attempt to Work Out an Insurance-Quality Procedure Validation des modèles rhéologiques sur ouvrages types : une tentative de démarche d'assurance-qualité

    Directory of Open Access Journals (Sweden)

    Meimon Y.

    2006-11-01

    Full Text Available For four years now, a validation of models for typical structuresgroup has been constituted inside the GRECO group on Rheology of Geomaterialssponsored by CNRS (French National Research Council. It has been working on the development of a methodology for validating rheological models of geomaterials. The aim was to reduce the gap between the theory and the practice of geomechanical computing. In a first step, the group work has been applied to shallow fondations. A complete validation process, which can be understood as an insurance-quality procedure, has been worked out, ranging from validation on the basis of homogeneous laboratory tests to validation based on boundary problems. Partial computerization of validation has been achieved with the help of a suitable software environment. A databank of laboratory and centrifuge tests has been created. An attempt has been made to define qualification criteria for models. Numerous rheological models have been applied, including some relatively sophisticated ones. This work has reached the point where the generalization of the procedure can been foreseen within the wider setting of the validation of geomechanical programs. Les travaux de validation Durant quatre ans (1986-1989, le groupe Validation des Modèles sur Ouvrages Typesdu GRECO CNRS Rhéologie des Géomatériaux , s'est efforcé de développer une méthodologie de validation des modèles rhéologiques de géomatériaux dans le but de réduire le décalage entre théorie et pratique des calculs en géomécanique, en appuyant son travail sur l'ouvrage type fondation superficielleet sur une collaboration étroite entre des équipes universitaires et des centres techniques et industriels. Les principaux travaux du groupe, constitué, d'une part de laboratoires universitaires français ou européen (École Centrale de Lyon (ECL, École Centrale de Paris (ECP, École Nationale des Travaux Publics de l'État (ENTPE, Institut de Mécanique de

  13. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

    Science.gov (United States)

    Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

    2016-08-25

    The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

  14. Design and analysis tool validation

    Energy Technology Data Exchange (ETDEWEB)

    Judkoff, R.

    1981-07-01

    The Solar Energy Research Institute (SERI) is developing a procedure for the validation of Building Energy Analysis Simulation Codes (BEAS). These codes are being used increasingly in the building design process, both directly and as the basis for simplified design tools and guidelines. The importance of the validity of the BEAS in predicting building energy performance is obvious when one considers the money and energy that could be wasted by energy-inefficient designs. However, to date, little or no systematic effort has been made to ensure the validity of the various BEAS. The validation work at SERI consists of three distinct parts: Comparative Study, Analytical Verification, and Empirical Validation. The procedures have been developed for the first two parts and have been implemented on a sampling of the major BEAS; results have shown major problems in one of the BEAS tested. Furthermore, when one building design was run using several of the BEAS, large differences were found in the predicted annual cooling and heating loads. The empirical validation procedure has been developed, and five two-zone test cells have been constructed for validation; a summer validation run will take place as soon as the data acquisition system is completed. Additionally, a test validation exercise is now in progress using the low-cal house to fine-tune the empirical validation procedure and better define monitoring data requirements.

  15. Developing and validating an Academic Listening Questionnaire

    Directory of Open Access Journals (Sweden)

    Vahid Aryadoust

    2012-09-01

    Full Text Available This article reports on the development and administration of the Academic Listening Self-rating Questionnaire (ALSA. The ALSA was developed on the basis of a proposed model of academic listening comprising six related components. The researchers operationalized the model, subjected items to iterative rounds of content analysis, and administered the finalized questionnaire to international ESL (English as a second language students in Malaysian and Australian universities. Structural equation modeling and rating scale modeling of data provided content-related, substantive, and structural validity evidence for the instrument. The researchers explain the utility of the questionnaire for educational and assessment purposes.

  16. Verification, Validation and Accreditation

    Science.gov (United States)

    2011-05-03

    bilinear- elastoplastic model linear-elastic model primary structural material linear-elastic model component occurrence [1.2] [1.1] length 2 + Product...139 Libraries & Databases Classification Codes, Materials, Personnel, Procedures, … b0. Federated Descriptive Models Damaged Stability FEA Abaqus

  17. Validation of Sexological Worldview

    Directory of Open Access Journals (Sweden)

    Justin A. Sitron

    2012-01-01

    Full Text Available The authors originally posited that a new construct must be developed to measure the success of affective training for sexologists, particularly the Sexuality Attitudes Reassessment (SAR modality. Couching their critique in studies that have been conducted to measure the SAR’s effectiveness as a method used to evoke perspective transformation and more sensitive and humanistic service provision, the authors argued that the development of a professional’s sexological worldview would be a more accurate construct than attitude change to measure when considering the outcomes of SAR training. This study in the United States used a two-phase qualitative approach to validate the proposed sexological worldview construct. In the first phase, they surveyed a panel of 16 sexologists regarding their original proposed definition of sexological worldview and refined it. In the second phase, they completed 30 one-on-one interviews with a convenience sample of sexologists and sexology students. Using an inductive content analysis of the interview transcripts, seven themes emerged in support of the proposed definition of sexological worldview, including its components and its developmental characteristics. The article concludes with a discussion of the implications for the use of the construct for the training of sexologists.

  18. Simulation Validation for Societal Systems

    Science.gov (United States)

    2006-09-01

    06806-01, the DHS EMW-2004-GR-0816 with ODU, and the ONR under the Biodefense project N00014-06-1-0252. Additional support was provided by CASOS at...data o DARPA SDI hospital and clinics visit data for five cities o DARPA ADS hospital and clinics visit data for five cities o DARPA PDTS hospital...and clinics visit data for five cities 6.5 Validation Scenarios I examine two validation scenarios. Validation Scenario I examines the

  19. Developing a validation for environmental sustainability

    Science.gov (United States)

    Adewale, Bamgbade Jibril; Mohammed, Kamaruddeen Ahmed; Nawi, Mohd Nasrun Mohd; Aziz, Zulkifli

    2016-08-01

    One of the agendas for addressing environmental protection in construction is to reduce impacts and make the construction activities more sustainable. This important consideration has generated several research interests within the construction industry, especially considering the construction damaging effects on the ecosystem, such as various forms of environmental pollution, resource depletion and biodiversity loss on a global scale. Using Partial Least Squares-Structural Equation Modeling technique, this study validates environmental sustainability (ES) construct in the context of large construction firms in Malaysia. A cross-sectional survey was carried out where data was collected from Malaysian large construction firms using a structured questionnaire. Results of this study revealed that business innovativeness and new technology are important in determining environmental sustainability (ES) of the Malaysian construction firms. It also established an adequate level of internal consistency reliability, convergent validity and discriminant validity for each of this study's constructs. And based on this result, it could be suggested that the indicators for organisational innovativeness dimensions (business innovativeness and new technology) are useful to measure these constructs in order to study construction firms' tendency to adopt environmental sustainability (ES) in their project execution.

  20. Diversity Management: Seeking Validation

    Directory of Open Access Journals (Sweden)

    M. Tony Bledsoe

    2011-01-01

    Full Text Available Diversity management is widely valued in higher education today, but closer examination often reveals a lack of action to support the level of diversity that institutions claim to embrace in many of their strategic documents. This paper includes an assessment of diversity management within South Carolina’s technical colleges and an examination of survey results.  It is a companion study to a prior study of diversity in North Carolina Independent Colleges and Universities (NCICU.  The purpose of that research was to review campus-wide documents and structure of schools in the NCICU to determine diversity transparency (Bledsoe/Oatsvall.

  1. Model validation, science and application

    NARCIS (Netherlands)

    Builtjes, P.J.H.; Flossmann, A.

    1998-01-01

    Over the last years there is a growing interest to try to establish a proper validation of atmospheric chemistry-transport (ATC) models. Model validation deals with the comparison of model results with experimental data, and in this way adresses both model uncertainty and uncertainty in, and adequac

  2. Cleaning Validation of Fermentation Tanks

    DEFF Research Database (Denmark)

    Salo, Satu; Friis, Alan; Wirtanen, Gun

    2008-01-01

    Reliable test methods for checking cleanliness are needed to evaluate and validate the cleaning process of fermentation tanks. Pilot scale tanks were used to test the applicability of various methods for this purpose. The methods found to be suitable for validation of the clenlinees were visula o...

  3. Compiler validates units and dimensions

    Science.gov (United States)

    Levine, F. E.

    1980-01-01

    Software added to compiler for automated test system for Space Shuttle decreases computer run errors by providing offline validation of engineering units used system command programs. Validation procedures are general, though originally written for GOAL, a free-form language that accepts "English-like" statements, and may be adapted to other programming languages.

  4. Concurrent Validity and Holland's Theory

    Science.gov (United States)

    Gaffey, Robert L.; Walsh, W. Bruce

    1974-01-01

    This study was designed to explore two areas: (1) the concurrent validity of Holland's theory for employed men using four different operational definitions of vocational orientation, and (2) the relationships among all possible combinations of same named scales across the four inventories. Findings tend to support the concurrent validity of…

  5. Cultural Validation of the Maslach Burnout Inventory for Korean Students

    Science.gov (United States)

    Shin, Hyojung; Puig, Ana; Lee, Jayoung; Lee, Ji Hee; Lee, Sang Min

    2011-01-01

    The purpose of this study was to examine the factorial validity of the MBI-SS in Korean students. Specifically, we investigated whether the original three-factor structure of the MBI-SS was appropriate for use with Korean students. In addition, by running multi-group structural equation model analyses with factorial invariance tests simultaneously…

  6. Construct validity of the Moral Development Scale for Professionals (MDSP).

    Science.gov (United States)

    Söderhamn, Olle; Bjørnestad, John Olav; Skisland, Anne; Cliffordson, Christina

    2011-01-01

    The aim of this study was to investigate the construct validity of the Moral Development Scale for Professionals (MDSP) using structural equation modeling. The instrument is a 12-item self-report instrument, developed in the Scandinavian cultural context and based on Kohlberg's theory. A hypothesized simplex structure model underlying the MDSP was tested through structural equation modeling. Validity was also tested as the proportion of respondents older than 20 years that reached the highest moral level, which according to the theory should be small. A convenience sample of 339 nursing students with a mean age of 25.3 years participated. Results confirmed the simplex model structure, indicating that MDSP reflects a moral construct empirically organized from low to high. A minority of respondents >20 years of age (13.5%) scored more than 80% on the highest moral level. The findings support the construct validity of the MDSP and the stages and levels in Kohlberg's theory.

  7. Distributed Trust Management for Validating SLA Choreographies

    Science.gov (United States)

    Haq, Irfan Ul; Alnemr, Rehab; Paschke, Adrian; Schikuta, Erich; Boley, Harold; Meinel, Christoph

    For business workflow automation in a service-enriched environment such as a grid or a cloud, services scattered across heterogeneous Virtual Organizations (VOs) can be aggregated in a producer-consumer manner, building hierarchical structures of added value. In order to preserve the supply chain, the Service Level Agreements (SLAs) corresponding to the underlying choreography of services should also be incrementally aggregated. This cross-VO hierarchical SLA aggregation requires validation, for which a distributed trust system becomes a prerequisite. Elaborating our previous work on rule-based SLA validation, we propose a hybrid distributed trust model. This new model is based on Public Key Infrastructure (PKI) and reputation-based trust systems. It helps preventing SLA violations by identifying violation-prone services at service selection stage and actively contributes in breach management at the time of penalty enforcement.

  8. Beliefs about language development: construct validity evidence.

    Science.gov (United States)

    Donahue, Mavis L; Fu, Qiong; Smith, Everett V

    2012-01-01

    Understanding language development is incomplete without recognizing children's sociocultural environments, including adult beliefs about language development. Yet there is a need for data supporting valid inferences to assess these beliefs. The current study investigated the psychometric properties of data from a survey (MODeL) designed to explore beliefs in the popular culture, and their alignment with more formal theories. Support for the content, substantive, structural, generalizability, and external aspects of construct validity of the data were investigated. Subscales representing Behaviorist, Cognitive, Nativist, and Sociolinguistic models were identified as dimensions of beliefs. More than half of the items showed a high degree of consensus, suggesting culturally-transmitted beliefs. Behaviorist ideas were most popular. Bilingualism and ethnicity were related to Cognitive and Sociolinguistic beliefs. Identifying these beliefs may clarify the nature of child-directed speech, and enable the design of language intervention programs that are congruent with family and cultural expectations.

  9. Development and validation of the Cancer Exercise Stereotypes Scale.

    Science.gov (United States)

    Falzon, Charlène; Sabiston, Catherine; Bergamaschi, Alessandro; Corrion, Karine; Chalabaev, Aïna; D'Arripe-Longueville, Fabienne

    2014-01-01

    The objective of this study was to develop and validate a French-language questionnaire measuring stereotypes related to exercise in cancer patients: The Cancer Exercise Stereotypes Scale (CESS). Four successive steps were carried out with 806 participants. First, a preliminary version was developed on the basis of the relevant literature and qualitative interviews. A test of clarity then led to the reformulation of six of the 30 items. Second, based on the modification indices of the first confirmatory factorial analysis, 11 of the 30 initial items were deleted. A new factorial structure analysis showed a good fit and validated a 19-item instrument with five subscales. Third, the stability of the instrument was tested over time. Last, tests of construct validity were conducted to examine convergent validity and discriminant validity. The French-language CESS appears to have good psychometric qualities and can be used to test theoretical tenets and inform intervention strategies on ways to foster exercise in cancer patients.

  10. Reducing Validity in Epistemic ATL to Validity in Epistemic CTL

    Directory of Open Access Journals (Sweden)

    Dimitar P. Guelev

    2013-03-01

    Full Text Available We propose a validity preserving translation from a subset of epistemic Alternating-time Temporal Logic (ATL to epistemic Computation Tree Logic (CTL. The considered subset of epistemic ATL is known to have the finite model property and decidable model-checking. This entails the decidability of validity but the implied algorithm is unfeasible. Reducing the validity problem to that in a corresponding system of CTL makes the techniques for automated deduction for that logic available for the handling of the apparently more complex system of ATL.

  11. Brief Report: The Identity Style Inventory (ISI-3) and the Utrecht-Management of Identity Commitments Scale (U-MICS)--Factor Structure, Reliability, and Convergent Validity in French-Speaking University Students

    Science.gov (United States)

    Zimmermann, Gregoire; Mahaim, Elodie Biermann; Mantzouranis, Gregory; Genoud, Philippe A.; Crocetti, Elisabetta

    2012-01-01

    The purpose of this study was to evaluate the factor structure and the reliability of the French versions of the Identity Style Inventory (ISI-3) and the Utrecht-Management of Identity Commitments Scale (U-MICS) in a sample of college students (N = 457, 18-25 years old). Confirmatory factor analyses confirmed the hypothesized three-factor solution…

  12. In situ structure and dynamics of DNA origami determined through molecular dynamics simulations.

    Science.gov (United States)

    Yoo, Jejoong; Aksimentiev, Aleksei

    2013-12-10

    The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-atom molecular dynamics simulations that characterized the structural and mechanical properties of DNA origami objects in unprecedented microscopic detail. When simulated in an aqueous environment, the structures of DNA origami objects depart from their idealized targets as a result of steric, electrostatic, and solvent-mediated forces. Whereas the global structural features of such relaxed conformations conform to the target designs, local deformations are abundant and vary in magnitude along the structures. In contrast to their free-solution conformation, the Holliday junctions in the DNA origami structures adopt a left-handed antiparallel conformation. We find the DNA origami structures undergo considerable temporal fluctuations on both local and global scales. Analysis of such structural fluctuations reveals the local mechanical properties of the DNA origami objects. The lattice type of the structures considerably affects global mechanical properties such as bending rigidity. Our study demonstrates the potential of all-atom molecular dynamics simulations to play a considerable role in future development of the DNA origami field by providing accurate, quantitative assessment of local and global structural and mechanical properties of DNA origami objects.

  13. The Particle Cleanliness Validation System

    Energy Technology Data Exchange (ETDEWEB)

    Stowers, I.F.; Ravizza, D.L.

    2001-12-21

    The Particle Cleanliness Validation System (PCVS) is a combination of a surface particle collection tool and a microscope based data, reduction system for determining the particle cleanliness of mechanical and optical surfaces at LLNL. Livermore is currently constructing the National Ignition Facility (NIF), a large 192 beam laser system for studying fusion physics. The laser is entirely enclosed. in aluminum and stainless steel vessels containing several environments; air, argon, and vacuum. It contains uncoated optics as well as hard dielectric coated and softer solgel coated optics which are, to varying degrees, sensitive to opaque particles, translucent particles, and molecular contamination. To quantify the particulate matter on structural surfaces during vendor cleaning and installation, a novel instrument has been developed to-both collect surface particles and to quantify the number and size distribution of these particles. The particles are collected on membrane filter paper which is ''swiped'' on a test surface for a proscribed distance to collect sufficient particles to significantly exceed the cleanliness of the filter paper. The swipe paper is then placed into a cassette for protection from further. contamination and transported to a microscope with x-y motorized stage and image analysis software, The surface of the swipe paper is scanned to determine both the background particle level of the paper, the cassette cover, and the portion of the paper which made contact with the test surface. The cumulative size distribution of the collected particles are displayed in size bins from 5 to 200 {micro}m. The quantity of particles exceeding 5 {micro}m is used to compute the IEST-STD-1246D cleanliness Level. Eight image analysis microscopes have been constructed for use with several dozen particle collection tools. About 30,000 cleanliness measurements have been taken to assure the clean construction and operation of the NIF laser system.

  14. [Authentic leadership. Concept and validation of the ALQ in Spain].

    Science.gov (United States)

    Moriano, Juan A; Molero, Fernando; Lévy Mangin, Jean-Pierre

    2011-04-01

    This study presents the validation of the Authentic Leadership Questionnaire (ALQ) in a sample of more than 600 Spanish employees. This questionnaire measures four distinct but related substantive components of authentic leadership. These components are: self-awareness, relational transparency, balanced processing, and internalized moral perspective. Structural equation modeling confirmed that the Spanish version of ALQ has high reliability and predictive validity for important leadership outputs such as perceived effectiveness of leadership, followers' extra effort and satisfaction with the leader.

  15. Emotional intelligence: new ability or renowned traits? An investigation of the convergent, discriminant and incremental validity

    OpenAIRE

    Wan Husin, Wan Nurul Izza

    2017-01-01

    Despite the recent popularity of the concept of emotional intelligence, several researchers question current emotional intelligence tests on several grounds including their lack of construct validity and unstable factor structure. This thesis aims to investigate the construct validity of emotional intelligence. In particular, the present study seeks to (1) confirm the factorial validity of emotional intelligence, (2) examine the convergent validity between a performance-based test and self-re...

  16. The development and validation of the Workplace Ostracism Scale.

    Science.gov (United States)

    Ferris, D Lance; Brown, Douglas J; Berry, Joseph W; Lian, Huiwen

    2008-11-01

    This article outlines the development of a 10-item measure of workplace ostracism. Using 6 samples (including multisource and multiwave data), the authors developed a reliable scale with a unidimensional factor structure that replicated across 4 separate samples. The scale possessed both convergent and discriminant validity, and criterion-related validity was demonstrated through the scale's relation with basic needs, well-being, job attitudes, job performance, and withdrawal. Overall, the present study suggests that the Workplace Ostracism Scale is a reliable and valid measure and that the workplace ostracism construct has important implications for both individuals and organizations.

  17. Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

    Science.gov (United States)

    Sterpone, Fabio; Nguyen, Phuong H; Kalimeri, Maria; Derreumaux, Philippe

    2013-10-08

    We have derived new effective interactions that improve the description of ion-pairs in the OPEP coarse-grained force field without introducing explicit electrostatic terms. The iterative Boltzmann inversion method was used to extract these potentials from all atom simulations by targeting the radial distribution function of the distance between the center of mass of the side-chains. The new potentials have been tested on several systems that differ in structural properties, thermodynamic stabilities and number of ion-pairs. Our modeling, by refining the packing of the charged amino-acids, impacts the stability of secondary structure motifs and the population of intermediate states during temperature folding/unfolding; it also improves the aggregation propensity of peptides. The new version of the OPEP force field has the potentiality to describe more realistically a large spectrum of situations where salt-bridges are key interactions.

  18. Validation of computationally predicted substrates for laccase

    Directory of Open Access Journals (Sweden)

    Reena

    2014-10-01

    Full Text Available Present study reports the validation (oxidation of computationally predicted oxidation of xenobiotic contaminants by commercially available pure laccase from Trametes versicolor. Selected contaminants were predicted as potential targets for laccase oxidation by using in-silico docking tool. The oxidation by laccase was measured by change in absorbance at specific λ max of each compound. Sinapic acid and tyrosine were taken as positive and negative controls, respectively. Oxidation was observed in m-chlorophenol, 2,4 di-chlorophenol, 2,4,6 tri-chlorophenol, captan, atrazine and thiodicarb, except malathion, which showed no activity. It could be speculated that the predicted substrates showing oxidation shared homology at structural and chemical level with positive control compounds. In case of malathion, structural non-homology with sinapic acid could be attributed to its inactivity towards laccase that required further structural analysis. Thus, a remediation tool proposing an advanced remediation approach combining the application of theoretical in-silico method and subsequent experimental validation using pure laccase could be proposed. As number and type of xenobiotics increase, the unfeasibility to screen them experimentally for bioremediation also rise. This approach would be useful to reduce the time and cost required in other screening methods.

  19. White Bear Suppression Inventory: Structure, Reliability and Validity of the Chinese Version%思维压抑量表:中文版的结构、信度及效度

    Institute of Scientific and Technical Information of China (English)

    Marcus A.Rodriguez; 贾珂; 钱铭怡

    2012-01-01

    Objective: To test the reliability and validity of the Chinese version of White Bear Suppression Inventory (WBSI) among a Chinese student sample. Methods: A convenience sample of 125 college students completed the WBSI and Beck Depression Inventory; a randomly selected subsample of 33 students participated in the retest in 4 weeks. A second sample of 383 college students completed the WBSI, Penn State Worry Questionnaire, Impact of Event Scale-Revised, and Thought-Action Fusion Scale. A third sample of 334 college students completed the WBSI, State-Trait Anxiety Inventory, Padua Inventory, and a measure of Chinese superstition. Results: EFA results revealed 3 factors (intrusive thoughts, thought suppression and self-distraction), which accounted for 52.4% of the total variance. CFA results provided support for a 3-factor model (x2/d?3.45, CFI=0.91, TU=0.89, RMSEA=0.07, SRMR=0.06). Internal consistency and test-retest coefficients for the WBSI梩otal were 0.87 and 0.59 respectively. WBSI-total scores were significantly higher for female participants. Criterion-related validity results revealed positive significant correlations between WBSI and depression (r=0.29), trait-anxiety (r=0.42), PTSD symptomology (r=0.42), OCD (0.30), and GAD (r=0.44). SEM results also provided support for a model wherein thought suppression mediates the relationship between superstition and obsessive-compulsive symptoms. Conclusion: The Chinese version of the WBSI is found to have good reliability and validity.%目的:在大学生群体中对思维压抑量表(White Bear Suppression Inventory,WBSI)进行修订并考察其信效度.方法:采用方便取样方法,对样本一的125名大学生施测WBSI及贝克抑郁问卷,以检验该量表的效度,并随机选取其中33名学生,在初测4周后进行了重测;对样本二的383名大学生施测WBSI、宾州忧虑问卷、事件影响量表-修订版及想法行为混淆量表.对样本三的334名大学生施测WBSI、帕多瓦量

  20. QDB: Validated Plasma Chemistries Database

    Science.gov (United States)

    Rahimi, Sara; Hamilton, James; Hill, Christian; Tennyson, Jonathan; UCL Team

    2016-09-01

    One of most challenging recurring problems when modelling plasmas is the lack of data. This lack of complete and validated datasets hinders research on plasma processes and curbs development of industrial Applications. We will describe the QDB project which aims to fill this missing link by provide a platform for exchange and validation of chemistry datasets. The database will collate published data on both electron scattering and heavy particle reactions and also facilitates and encourages peer-to-peer data sharing by its users. This data platform is rigorously supported by the validation methodical validation of the datasetsan automated chemistry generator employed; this methodology identifies missing reactions in chemistries which although important are currently unreported in the literature and employs mathematical methods to analyze the importance of these chemistries. Gaps in the datasets are filled using in house theoretical methods.