Empirical evaluation of neutral interactions in host-parasite networks.

PubMed

Canard, E F; Mouquet, N; Mouillot, D; Stanko, M; Miklisova, D; Gravel, D

2014-04-01

While niche-based processes have been invoked extensively to explain the structure of interaction networks, recent studies propose that neutrality could also be of great importance. Under the neutral hypothesis, network structure would simply emerge from random encounters between individuals and thus would be directly linked to species abundance. We investigated the impact of species abundance distributions on qualitative and quantitative metrics of 113 host-parasite networks. We analyzed the concordance between neutral expectations and empirical observations at interaction, species, and network levels. We found that species abundance accurately predicts network metrics at all levels. Despite host-parasite systems being constrained by physiology and immunology, our results suggest that neutrality could also explain, at least partially, their structure. We hypothesize that trait matching would determine potential interactions between species, while abundance would determine their realization.

A knowledge-based potential with an accurate description of local interactions improves discrimination between native and near-native protein conformations.

PubMed

Ferrada, Evandro; Vergara, Ismael A; Melo, Francisco

2007-01-01

The correct discrimination between native and near-native protein conformations is essential for achieving accurate computer-based protein structure prediction. However, this has proven to be a difficult task, since currently available physical energy functions, empirical potentials and statistical scoring functions are still limited in achieving this goal consistently. In this work, we assess and compare the ability of different full atom knowledge-based potentials to discriminate between native protein structures and near-native protein conformations generated by comparative modeling. Using a benchmark of 152 near-native protein models and their corresponding native structures that encompass several different folds, we demonstrate that the incorporation of close non-bonded pairwise atom terms improves the discriminating power of the empirical potentials. Since the direct and unbiased derivation of close non-bonded terms from current experimental data is not possible, we obtained and used those terms from the corresponding pseudo-energy functions of a non-local knowledge-based potential. It is shown that this methodology significantly improves the discrimination between native and near-native protein conformations, suggesting that a proper description of close non-bonded terms is important to achieve a more complete and accurate description of native protein conformations. Some external knowledge-based energy functions that are widely used in model assessment performed poorly, indicating that the benchmark of models and the specific discrimination task tested in this work constitutes a difficult challenge.

PSPP: A Protein Structure Prediction Pipeline for Computing Clusters

DTIC Science & Technology

2009-07-01

Evanseck JD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. Journal of Physical Chemistry B 102...dimensional (3-D) protein structures are critical for the understanding of molecular mechanisms of living systems. Traditionally, X-ray crystallography...disordered proteins are often responsible for molecular recognition, molecular assembly, protein modifica- tion, and entropic chain activities in organisms [26

Unraveling the disease consequences and mechanisms of modular structure in animal social networks

PubMed Central

Leu, Stephan T.; Cross, Paul C.; Hudson, Peter J.; Bansal, Shweta

2017-01-01

Disease risk is a potential cost of group living. Although modular organization is thought to reduce this cost in animal societies, empirical evidence toward this hypothesis has been conflicting. We analyzed empirical social networks from 43 animal species to motivate our study of the epidemiological consequences of modular structure in animal societies. From these empirical studies, we identified the features of interaction patterns associated with network modularity and developed a theoretical network model to investigate when and how subdivisions in social networks influence disease dynamics. Contrary to prior work, we found that disease risk is largely unaffected by modular structure, although social networks beyond a modular threshold experience smaller disease burden and longer disease duration. Our results illustrate that the lowering of disease burden in highly modular social networks is driven by two mechanisms of modular organization: network fragmentation and subgroup cohesion. Highly fragmented social networks with cohesive subgroups are able to structurally trap infections within a few subgroups and also cause a structural delay to the spread of disease outbreaks. Finally, we show that network models incorporating modular structure are necessary only when prior knowledge suggests that interactions within the population are highly subdivided. Otherwise, null networks based on basic knowledge about group size and local contact heterogeneity may be sufficient when data-limited estimates of epidemic consequences are necessary. Overall, our work does not support the hypothesis that modular structure universally mitigates the disease impact of group living. PMID:28373567

Unraveling the disease consequences and mechanisms of modular structure in animal social networks

USGS Publications Warehouse

Sah, Pratha; Leu, Stephan T.; Cross, Paul C.; Hudson, Peter J.; Bansal, Shweta

2017-01-01

Disease risk is a potential cost of group living. Although modular organization is thought to reduce this cost in animal societies, empirical evidence toward this hypothesis has been conflicting. We analyzed empirical social networks from 43 animal species to motivate our study of the epidemiological consequences of modular structure in animal societies. From these empirical studies, we identified the features of interaction patterns associated with network modularity and developed a theoretical network model to investigate when and how subdivisions in social networks influence disease dynamics. Contrary to prior work, we found that disease risk is largely unaffected by modular structure, although social networks beyond a modular threshold experience smaller disease burden and longer disease duration. Our results illustrate that the lowering of disease burden in highly modular social networks is driven by two mechanisms of modular organization: network fragmentation and subgroup cohesion. Highly fragmented social networks with cohesive subgroups are able to structurally trap infections within a few subgroups and also cause a structural delay to the spread of disease outbreaks. Finally, we show that network models incorporating modular structure are necessary only when prior knowledge suggests that interactions within the population are highly subdivided. Otherwise, null networks based on basic knowledge about group size and local contact heterogeneity may be sufficient when data-limited estimates of epidemic consequences are necessary. Overall, our work does not support the hypothesis that modular structure universally mitigates the disease impact of group living.

Unraveling the disease consequences and mechanisms of modular structure in animal social networks.

PubMed

Sah, Pratha; Leu, Stephan T; Cross, Paul C; Hudson, Peter J; Bansal, Shweta

2017-04-18

Disease risk is a potential cost of group living. Although modular organization is thought to reduce this cost in animal societies, empirical evidence toward this hypothesis has been conflicting. We analyzed empirical social networks from 43 animal species to motivate our study of the epidemiological consequences of modular structure in animal societies. From these empirical studies, we identified the features of interaction patterns associated with network modularity and developed a theoretical network model to investigate when and how subdivisions in social networks influence disease dynamics. Contrary to prior work, we found that disease risk is largely unaffected by modular structure, although social networks beyond a modular threshold experience smaller disease burden and longer disease duration. Our results illustrate that the lowering of disease burden in highly modular social networks is driven by two mechanisms of modular organization: network fragmentation and subgroup cohesion. Highly fragmented social networks with cohesive subgroups are able to structurally trap infections within a few subgroups and also cause a structural delay to the spread of disease outbreaks. Finally, we show that network models incorporating modular structure are necessary only when prior knowledge suggests that interactions within the population are highly subdivided. Otherwise, null networks based on basic knowledge about group size and local contact heterogeneity may be sufficient when data-limited estimates of epidemic consequences are necessary. Overall, our work does not support the hypothesis that modular structure universally mitigates the disease impact of group living.

Modelling and simulation of complex sociotechnical systems: envisioning and analysing work environments

PubMed Central

Hettinger, Lawrence J.; Kirlik, Alex; Goh, Yang Miang; Buckle, Peter

2015-01-01

Accurate comprehension and analysis of complex sociotechnical systems is a daunting task. Empirically examining, or simply envisioning the structure and behaviour of such systems challenges traditional analytic and experimental approaches as well as our everyday cognitive capabilities. Computer-based models and simulations afford potentially useful means of accomplishing sociotechnical system design and analysis objectives. From a design perspective, they can provide a basis for a common mental model among stakeholders, thereby facilitating accurate comprehension of factors impacting system performance and potential effects of system modifications. From a research perspective, models and simulations afford the means to study aspects of sociotechnical system design and operation, including the potential impact of modifications to structural and dynamic system properties, in ways not feasible with traditional experimental approaches. This paper describes issues involved in the design and use of such models and simulations and describes a proposed path forward to their development and implementation. Practitioner Summary: The size and complexity of real-world sociotechnical systems can present significant barriers to their design, comprehension and empirical analysis. This article describes the potential advantages of computer-based models and simulations for understanding factors that impact sociotechnical system design and operation, particularly with respect to process and occupational safety. PMID:25761227

Investigation on the structure of liquid N-methylformamide-dimethylsulfoxide mixtures

NASA Astrophysics Data System (ADS)

Cordeiro, João M. M.; Soper, Alan K.

2011-03-01

The structures of liquid mixtures of N-methylformamide (NMF) and dimethyl sulfoxide (DMSO) at two concentrations (80% and 50% NMF) are investigated using a combination of neutron diffraction augmented with isotopic substitution and empirical potential structure refinement simulations. The results indicate that the NMF and DMSO molecules are hydrogen-bonded to one another with a preference for NMF-DMSO hydrogen bonding, compared to the NMF-NMF ones. The liquid is orientationally structured as a consequence of these hydrogen bonds between molecules. NMF-DMSO dimers are very stable species in the bulk of the mixture. The structure of the dimers is such that the angle between the molecular dipole moments is around 60°. The NMF molecules are well solvated in DMSO with potential implications for peptides solvation in this solvent.

A Simplified Model of Local Structure in Aqueous Proline Amino Acid Revealed by First-Principles Molecular Dynamics Simulations

PubMed Central

Troitzsch, Raphael Z.; Tulip, Paul R.; Crain, Jason; Martyna, Glenn J.

2008-01-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data. PMID:18790850

Molecular modeling and dynamics simulations of PNP from Streptococcus agalactiae.

PubMed

Caceres, Rafael Andrade; Saraiva Timmers, Luis Fernando; Dias, Raquel; Basso, Luiz Augusto; Santos, Diogenes Santiago; de Azevedo, Walter Filgueira

2008-05-01

This work describes for the first time a structural model of purine nucleoside phosphorylase from Streptococcus agalactiae (SaPNP). PNP catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is a potential target for the development of antibacterial drugs. We modeled the complexes of SaPNP with 15 different ligands in order to determine the structural basis for the specificity of these ligands against SaPNP. The application of a novel empirical scoring function to estimate the affinity of a ligand for a protein was able to identify the ligands with high affinity for PNPs. The analysis of molecular dynamics trajectory for SaPNP indicates that the functionally important motifs have a very stable structure. This new structural model together with a novel empirical scoring function opens the possibility to explorer larger library of compounds in order to identify the new inhibitors for PNPs in virtual screening projects.

A simplified model of local structure in aqueous proline amino acid revealed by first-principles molecular dynamics simulations.

PubMed

Troitzsch, Raphael Z; Tulip, Paul R; Crain, Jason; Martyna, Glenn J

2008-12-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data.

Carl gustav jung, quantum physics and the spiritual mind: a mystical vision of the twenty-first century.

PubMed

Valadas Ponte, Diogo; Schäfer, Lothar

2013-12-01

We describe similarities in the ontology of quantum physics and of Carl Gustav Jung's psychology. In spite of the fact that physics and psychology are usually considered as unrelated, in the last century, both of these disciplines have led at the same time to revolutionary changes in the Western understanding of the cosmic order, discovering a non-empirical realm of the universe that doesn't consist of material things but of forms. These forms are real, even though they are invisible, because they have the potential to appear in the empirical world and act in it. We present arguments that force us to believe, that the empirical world is an emanation out of a cosmic realm of potentiality, whose forms can appear as physical structures in the external world and as archetypal concepts in our mind. Accordingly, the evolution of life now appears no longer as a process of the adaptation of species to their environment, but as the adaptation of minds to increasingly complex forms that exist in the cosmic potentiality. The cosmic connection means that the human mind is a mystical mind.

Carl Gustav Jung, Quantum Physics and the Spiritual Mind: A Mystical Vision of the Twenty-First Century

PubMed Central

Valadas Ponte, Diogo; Schäfer, Lothar

2013-01-01

We describe similarities in the ontology of quantum physics and of Carl Gustav Jung’s psychology. In spite of the fact that physics and psychology are usually considered as unrelated, in the last century, both of these disciplines have led at the same time to revolutionary changes in the Western understanding of the cosmic order, discovering a non-empirical realm of the universe that doesn’t consist of material things but of forms. These forms are real, even though they are invisible, because they have the potential to appear in the empirical world and act in it. We present arguments that force us to believe, that the empirical world is an emanation out of a cosmic realm of potentiality, whose forms can appear as physical structures in the external world and as archetypal concepts in our mind. Accordingly, the evolution of life now appears no longer as a process of the adaptation of species to their environment, but as the adaptation of minds to increasingly complex forms that exist in the cosmic potentiality. The cosmic connection means that the human mind is a mystical mind. PMID:25379259

A general intermolecular force field based on tight-binding quantum chemical calculations

NASA Astrophysics Data System (ADS)

Grimme, Stefan; Bannwarth, Christoph; Caldeweyher, Eike; Pisarek, Jana; Hansen, Andreas

2017-10-01

A black-box type procedure is presented for the generation of a molecule-specific, intermolecular potential energy function. The method uses quantum chemical (QC) information from our recently published extended tight-binding semi-empirical scheme (GFN-xTB) and can treat non-covalently bound complexes and aggregates with almost arbitrary chemical structure. The necessary QC information consists of the equilibrium structure, Mulliken atomic charges, charge centers of localized molecular orbitals, and also of frontier orbitals and orbital energies. The molecular pair potential includes model density dependent Pauli repulsion, penetration, as well as point charge electrostatics, the newly developed D4 dispersion energy model, Drude oscillators for polarization, and a charge-transfer term. Only one element-specific and about 20 global empirical parameters are needed to cover systems with nuclear charges up to radon (Z = 86). The method is tested for standard small molecule interaction energy benchmark sets where it provides accurate intermolecular energies and equilibrium distances. Examples for structures with a few hundred atoms including charged systems demonstrate the versatility of the approach. The method is implemented in a stand-alone computer code which enables rigid-body, global minimum energy searches for molecular aggregation or alignment.

Critical Factors in Cultural Immersion: A Synthesis of Relevant Literature

ERIC Educational Resources Information Center

Barden, Sejal M.; Cashwell, Craig S.

2013-01-01

This synthesis of the literature on cross-cultural immersion experiences gives emphasis to the need for effective pedagogy for enhancing multicultural counseling competency, with cultural immersion being a potentially valuable training tool. The authors examine the empirical literature towards identifying both helpful and hindering structural and…

Caring potentials in the shadows of power, correction, and discipline—Forensic psychiatric care in the light of the work of Michel Foucault

PubMed Central

Hörberg, Ulrica; Dahlberg, Karin

2015-01-01

The aim of this article is to shed light on contemporary forensic psychiatric care through a philosophical examination of the empirical results from two lifeworld phenomenological studies from the perspective of patients and carers, by using the French philosopher Michel Foucault's historical–philosophical work. Both empirical studies were conducted in a forensic psychiatric setting. The essential results of the two empirical studies were reexamined in a phenomenological meaning analysis to form a new general structure in accordance with the methodological principles of Reflective Lifeworld Research. This general structure shows how the caring on the forensic psychiatric wards appears to be contradictory, in that it is characterized by an unreflective (non-)caring attitude and contributes to an inconsistent and insecure existence. The caring appears to have a corrective approach and thus lacks a clear caring structure, a basic caring approach that patients in forensic psychiatric services have a great need of. To gain a greater understanding of forensic psychiatric caring, the new empirical results were further examined in the light of Foucault's historical–philosophical work. The philosophical examination is presented in terms of the three meaning constituents: Caring as correction and discipline, The existence of power, and Structures and culture in care. The philosophical examination illustrates new meaning nuances of the corrective and disciplinary nature of forensic psychiatric care, its power, and how this is materialized in caring, and what this does to the patients. The examination reveals embedded difficulties in forensic psychiatric care and highlights a need to revisit the aim of such care. PMID:26319100

Caring potentials in the shadows of power, correction, and discipline - Forensic psychiatric care in the light of the work of Michel Foucault.

PubMed

Hörberg, Ulrica; Dahlberg, Karin

2015-01-01

The aim of this article is to shed light on contemporary forensic psychiatric care through a philosophical examination of the empirical results from two lifeworld phenomenological studies from the perspective of patients and carers, by using the French philosopher Michel Foucault's historical-philosophical work. Both empirical studies were conducted in a forensic psychiatric setting. The essential results of the two empirical studies were reexamined in a phenomenological meaning analysis to form a new general structure in accordance with the methodological principles of Reflective Lifeworld Research. This general structure shows how the caring on the forensic psychiatric wards appears to be contradictory, in that it is characterized by an unreflective (non-)caring attitude and contributes to an inconsistent and insecure existence. The caring appears to have a corrective approach and thus lacks a clear caring structure, a basic caring approach that patients in forensic psychiatric services have a great need of. To gain a greater understanding of forensic psychiatric caring, the new empirical results were further examined in the light of Foucault's historical-philosophical work. The philosophical examination is presented in terms of the three meaning constituents: Caring as correction and discipline, The existence of power, and Structures and culture in care. The philosophical examination illustrates new meaning nuances of the corrective and disciplinary nature of forensic psychiatric care, its power, and how this is materialized in caring, and what this does to the patients. The examination reveals embedded difficulties in forensic psychiatric care and highlights a need to revisit the aim of such care.

Bond-orientational order in liquid Si

NASA Technical Reports Server (NTRS)

Wang, Z. Q.; Stroud, D.

1991-01-01

Bond-orientational order in liquid Si via Monte Carlo simulation in conjuncation with empirical two- and three-body potentials of the form proposed by Stillinger and Weber are studied. Bond-orientational order (BOO) is described in terms of combinations of spherical harmonic functions. Liquid Si is found to have pronounced short-range BOO corresponding to l = 3, as expected for a structure with local tetrahedral order. No long-range BOO is found either in the equilibrium or the supercooled liquid. When the three-body potential is artificially removed, the tetrahedral bond-orientation order disappears and the liquid assumes a close-packed structure.

Assessing the accuracy of improved force-matched water models derived from Ab initio molecular dynamics simulations.

PubMed

Köster, Andreas; Spura, Thomas; Rutkai, Gábor; Kessler, Jan; Wiebeler, Hendrik; Vrabec, Jadran; Kühne, Thomas D

2016-07-15

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force-matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force-matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Methane hydrate formation and decomposition: structural studies via neutron diffraction and empirical potential structure refinement.

PubMed

Thompson, Helen; Soper, Alan K; Buchanan, Piers; Aldiwan, Nawaf; Creek, Jefferson L; Koh, Carolyn A

2006-04-28

Neutron diffraction studies with hydrogen/deuterium isotope substitution measurements are performed to investigate the water structure at the early, medium, and late periods of methane clathrate hydrate formation and decomposition. These measurements are coupled with simultaneous gas consumption measurements to track the formation of methane hydrate from a gas/water mixture, and then the complete decomposition of hydrate. Empirical potential structure refinement computer simulations are used to analyze the neutron diffraction data and extract from the data the water structure in the bulk methane hydrate solution. The results highlight the significant changes in the water structure of the remaining liquid at various stages of hydrate formation and decomposition, and give further insight into the way in which hydrates form. The results also have important implications on the memory effect, suggesting that the water structure in the presence of hydrate crystallites is significantly different at equivalent stages of forming compared to decomposing. These results are in sharp contrast to the previously reported cases when all remaining hydrate crystallites are absent from the solution. For these systems there is no detectable change in the water structure or the methane hydration shell before hydrate formation and after decomposition. Based on the new results presented in this paper, it is clear that the local water structure is affected by the presence of hydrate crystallites, which may in turn be responsible for the "history" or "memory" effect where the production of hydrate from a solution of formed and then subsequently melted hydrate is reportedly much quicker than producing hydrate from a fresh water/gas mixture.

Heuristic lipophilicity potential for computer-aided rational drug design.

PubMed

Du, Q; Arteca, G A; Mezey, P G

1997-09-01

In this contribution we suggest a heuristic molecular lipophilicity potential (HMLP), which is a structure-based technique requiring no empirical indices of atomic lipophilicity. The input data used in this approach are molecular geometries and molecular surfaces. The HMLP is a modified electrostatic potential, combined with the averaged influences from the molecular environment. Quantum mechanics is used to calculate the electron density function rho(r) and the electrostatic potential V(r), and from this information a lipophilicity potential L(r) is generated. The HMLP is a unified lipophilicity and hydrophilicity potential. The interactions of dipole and multipole moments, hydrogen bonds, and charged atoms in a molecule are included in the hydrophilic interactions in this model. The HMLP is used to study hydrogen bonds and water-octanol partition coefficients in several examples. The calculated results show that the HMLP gives qualitatively and quantitatively correct, as well as chemically reasonable, results in cases where comparisons are available. These comparisons indicate that the HMLP has advantages over the empirical lipophilicity potential in many aspects. The HMLP is a three-dimensional and easily visualizable representation of molecular lipophilicity, suggested as a potential tool in computer-aided three-dimensional drug design.

Structures of 38-atom gold-platinum nanoalloy clusters

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

Ong, Yee Pin; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

Bimetallic nanoclusters, such as gold-platinum nanoclusters, are nanomaterials promising wide range of applications. We perform a numerical study of 38-atom gold-platinum nanoalloy clusters, Au{sub n}Pt{sub 38−n} (0 ≤ n ≤ 38), to elucidate the geometrical structures of these clusters. The lowest-energy structures of these bimetallic nanoclusters at the semi-empirical level are obtained via a global-minimum search algorithm known as parallel tempering multi-canonical basin hopping plus genetic algorithm (PTMBHGA), in which empirical Gupta many-body potential is used to describe the inter-atomic interactions among the constituent atoms. The structures of gold-platinum nanoalloy clusters are predicted to be core-shell segregated nanoclusters. Gold atomsmore » are observed to preferentially occupy the surface of the clusters, while platinum atoms tend to occupy the core due to the slightly smaller atomic radius of platinum as compared to gold’s. The evolution of the geometrical structure of 38-atom Au-Pt clusters displays striking similarity with that of 38-atom Au-Cu nanoalloy clusters as reported in the literature.« less

Exchange repulsive potential adaptable for electronic structure changes during chemical reactions

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

Yokogawa, D., E-mail: d.yokogawa@chem.nagoya-u.ac.jp

2015-04-28

Hybrid methods combining quantum mechanical (QM) and classical calculations are becoming important tools in chemistry. The popular approach to calculate the interaction between QM and classical calculations employs interatomic potentials. In most cases, the interatomic potential is constructed of an electrostatic (ES) potential and a non-ES potential. Because QM treatment is employed in the calculation of the ES potential, the electronic change can be considered in this ES potential. However, QM treatment of the non-ES potential is difficult because of high computational cost. To overcome this difficulty of evaluating the non-ES potential, we proposed an exchange repulsive potential as themore » main part of the non-ES potential on the basis of a QM approach. This potential is independent of empirical parameters and adaptable for electronic structure. We combined this potential with the reference interaction site model self-consistent field explicitly including spatial electron density distribution and successfully applied it to the chemical reactions in aqueous phase.« less

Empirical relations between large wood transport and catchment characteristics

NASA Astrophysics Data System (ADS)

Steeb, Nicolas; Rickenmann, Dieter; Rickli, Christian; Badoux, Alexandre

2017-04-01

The transport of vast amounts of large wood (LW) in water courses can considerably aggravate hazardous situations during flood events, and often strongly affects resulting flood damage. Large wood recruitment and transport are controlled by various factors which are difficult to assess and the prediction of transported LW volumes is difficult. Such information are, however, important for engineers and river managers to adequately dimension retention structures or to identify critical stream cross-sections. In this context, empirical formulas have been developed to estimate the volume of transported LW during a flood event (Rickenmann, 1997; Steeb et al., 2017). The data base of existing empirical wood load equations is, however, limited. The objective of the present study is to test and refine existing empirical equations, and to derive new relationships to reveal trends in wood loading. Data have been collected for flood events with LW occurrence in Swiss catchments of various sizes. This extended data set allows us to derive statistically more significant results. LW volumes were found to be related to catchment and transport characteristics, such as catchment size, forested area, forested stream length, water discharge, sediment load, or Melton ratio. Both the potential wood load and the fraction that is effectively mobilized during a flood event (effective wood load) are estimated. The difference of potential and effective wood load allows us to derive typical reduction coefficients that can be used to refine spatially explicit GIS models for potential LW recruitment.

Retrieving hydrological connectivity from empirical causality in karst systems

NASA Astrophysics Data System (ADS)

Delforge, Damien; Vanclooster, Marnik; Van Camp, Michel; Poulain, Amaël; Watlet, Arnaud; Hallet, Vincent; Kaufmann, Olivier; Francis, Olivier

2017-04-01

Because of their complexity, karst systems exhibit nonlinear dynamics. Moreover, if one attempts to model a karst, the hidden behavior complicates the choice of the most suitable model. Therefore, both intense investigation methods and nonlinear data analysis are needed to reveal the underlying hydrological connectivity as a prior for a consistent physically based modelling approach. Convergent Cross Mapping (CCM), a recent method, promises to identify causal relationships between time series belonging to the same dynamical systems. The method is based on phase space reconstruction and is suitable for nonlinear dynamics. As an empirical causation detection method, it could be used to highlight the hidden complexity of a karst system by revealing its inner hydrological and dynamical connectivity. Hence, if one can link causal relationships to physical processes, the method should show great potential to support physically based model structure selection. We present the results of numerical experiments using karst model blocks combined in different structures to generate time series from actual rainfall series. CCM is applied between the time series to investigate if the empirical causation detection is consistent with the hydrological connectivity suggested by the karst model.

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

PubMed

Eyrich, V A; Standley, D M; Friesner, R A

1999-05-14

We report the tertiary structure predictions for 95 proteins ranging in size from 17 to 160 residues starting from known secondary structure. Predictions are obtained from global minimization of an empirical potential function followed by the application of a refined atomic overlap potential. The minimization strategy employed represents a variant of the Monte Carlo plus minimization scheme of Li and Scheraga applied to a reduced model of the protein chain. For all of the cases except beta-proteins larger than 75 residues, a native-like structure, usually 4-6 A root-mean-square deviation from the native, is located. For beta-proteins larger than 75 residues, the energy gap between native-like structures and the lowest energy structures produced in the simulation is large, so that low RMSD structures are not generated starting from an unfolded state. This is attributed to the lack of an explicit hydrogen bond term in the potential function, which we hypothesize is necessary to stabilize large assemblies of beta-strands. Copyright 1999 Academic Press.

Participative Decision Making in Schools: A Mediating-Moderating Analytical Framework for Understanding School and Teacher Outcomes

ERIC Educational Resources Information Center

Somech, Anit

2010-01-01

The increasing emergence of participation in decision making (PDM) in schools reflects the widely shared belief that flatter management and decentralized authority structures carry the potential for promoting school effectiveness. However, the literature indicates a discrepancy between the intuitive appeal of PDM and empirical evidence in respect…

An Empirical Study of Earth Covered Schools in Oklahoma. Final Report.

ERIC Educational Resources Information Center

Zaccor, James V.

A study of earth-covered schools in Oklahoma was conducted for the Federal Emergency Management Agency (FEMA) to assess the viability of these structures as learning and teaching environments, as cost beneficial investments, and as potential shelters from natural and man-made disasters. The study was aimed at identifying what information is…

Music on the Move: Methodological Applications of Bernstein's Concepts in a Secondary School Music Context

ERIC Educational Resources Information Center

McPhail, Graham J.

2016-01-01

In 2002 Parlo Singh outlined Bernstein's theory of the pedagogic device, elaborating the potential in Bernstein's complex theoretical framework for empirical research. In particular, Singh suggests that Bernstein's concepts provide the means of making explicit the macro and micro structuring of knowledge into pedagogic communication. More…

Family Migration and Labor Force Outcomes: Sex Differences in Occupational Context

ERIC Educational Resources Information Center

Shauman, Kimberlee A.; Noonan, Mary C.

2007-01-01

Empirical analyses of sex differences in the career consequences of family migration have focused on adjudicating between the human capital and the gender-role explanations but have ignored the potential influence of gender inequality in the structure of the labor market. In this paper we estimate conditional difference-in-difference models with…

Molecular dynamic simulations reveal the structural determinants of fatty acid binding to oxy-myoglobin

USDA-ARS?s Scientific Manuscript database

The mechanism(s) by which fatty acids are sequestered and transported in muscle have not been fully elucidated. A potential key player in this process is the protein myoglobin (Mb). Indeed, there is a catalogue of empirical evidence supporting direct interaction of globins with fatty acid metabolite...

A semi-empirical model for the estimation of maximum horizontal displacement due to liquefaction-induced lateral spreading

USGS Publications Warehouse

Faris, Allison T.; Seed, Raymond B.; Kayen, Robert E.; Wu, Jiaer

2006-01-01

During the 1906 San Francisco Earthquake, liquefaction-induced lateral spreading and resultant ground displacements damaged bridges, buried utilities, and lifelines, conventional structures, and other developed works. This paper presents an improved engineering tool for the prediction of maximum displacement due to liquefaction-induced lateral spreading. A semi-empirical approach is employed, combining mechanistic understanding and data from laboratory testing with data and lessons from full-scale earthquake field case histories. The principle of strain potential index, based primary on correlation of cyclic simple shear laboratory testing results with in-situ Standard Penetration Test (SPT) results, is used as an index to characterized the deformation potential of soils after they liquefy. A Bayesian probabilistic approach is adopted for development of the final predictive model, in order to take fullest advantage of the data available and to deal with the inherent uncertainties intrinstiic to the back-analyses of field case histories. A case history from the 1906 San Francisco Earthquake is utilized to demonstrate the ability of the resultant semi-empirical model to estimate maximum horizontal displacement due to liquefaction-induced lateral spreading.

Development of interatomic potentials appropriate for simulation of devitrification of Al 90Sm 10 alloy

DOE PAGES

Mendelev, M. I.; Zhang, F.; Ye, Z.; ...

2015-04-23

In this study, a semi-empirical potential for the Al 90Sm 10 alloy is presented. The potential provides satisfactory reproduction of pure Al properties, the formation energies of a set of Al–Sm crystal phases with Sm content about 10%, and the structure of the liquid Al 90Sm 10 alloy. During molecular dynamics simulation in which the liquid alloy is cooled at a rate of 10 10 K/s, the developed potential produces a glass structure with lower ab initio energy than that produced by ab initio molecular dynamics (AIMD) itself using a typical AIMD cooling rate of 8 ∙10 13 K/s. Basedmore » on these facts the developed potential should be suitable for simulations of phase transformations in the Al 90Sm 10 alloy.« less

Potential utility of three-dimensional temperature and salinity fields estimated from satellite altimetry and Argo data for improving mesoscale reproducibility in regional ocean modeling

NASA Astrophysics Data System (ADS)

Kanki, R.; Uchiyama, Y.; Miyazaki, D.; Takano, A.; Miyazawa, Y.; Yamazaki, H.

2014-12-01

Mesoscale oceanic structure and variability are required to be reproduced as accurately as possible in realistic regional ocean modeling. Uchiyama et al. (2012) demonstrated with a submesoscale eddy-resolving JCOPE2-ROMS downscaling oceanic modeling system that the mesoscale reproducibility of the Kuroshio meandering along Japan is significantly improved by introducing a simple restoration to data which we call "TS nudging" (a.k.a. robust diagnosis) where the prognostic temperature and salinity fields are weakly nudged four-dimensionally towards the assimilative JCOPE2 reanalysis (Miyazawa et al., 2009). However, there is not always a reliable reanalysis for oceanic downscaling in an arbitrary region and at an arbitrary time, and therefore alternative dataset should be prepared. Takano et al. (2009) proposed an empirical method to estimate mesoscale 3-D thermal structure from the near real-time AVISO altimetry data along with the ARGO float data based on the two-layer model of Goni et al. (1996). In the present study, we consider the TS data derived from this method as a candidate. We thus conduct a synoptic forward modeling of the Kuroshio using the JCOPE2-ROMS downscaling system to explore potential utility of this empirical TS dataset (hereinafter TUM-TS) by carrying out two runs with the T-S nudging towards 1) the JCOPE2-TS and 2) TUM-TS fields.　An example of the comparison between the two ROMS test runs is shown in the attached figure showing the annually averaged surface EKE. Both of TUM-TS and JCOPE2-TS are found to help reproducing the mesoscale variance of the Koroshio and its extension as well as its mean paths, surface KE and EKE reasonably well. Therefore, the AVISO-ARGO derived empirical 3-D TS estimation is potentially exploitable for the dataset to conduct the T-S nudging to reproduce mesoscale oceanic structure.

A review of failure models for unidirectional ceramic matrix composites under monotonic loads

NASA Technical Reports Server (NTRS)

Tripp, David E.; Hemann, John H.; Gyekenyesi, John P.

1989-01-01

Ceramic matrix composites offer significant potential for improving the performance of turbine engines. In order to achieve their potential, however, improvements in design methodology are needed. In the past most components using structural ceramic matrix composites were designed by trial and error since the emphasis of feasibility demonstration minimized the development of mathematical models. To understand the key parameters controlling response and the mechanics of failure, the development of structural failure models is required. A review of short term failure models with potential for ceramic matrix composite laminates under monotonic loads is presented. Phenomenological, semi-empirical, shear-lag, fracture mechanics, damage mechanics, and statistical models for the fast fracture analysis of continuous fiber unidirectional ceramic matrix composites under monotonic loads are surveyed.

Empirical analysis of knowledge bases to support structured output in the Arden syntax.

PubMed

Jenders, Robert A

2013-01-01

Structured output has been suggested for the Arden Syntax to facilitate interoperability. Tabulate the components of WRITE statements in a corpus of medical logic modules (MLMs)in order to validate requiring structured output. WRITE statements were tabulated in 258 MLMs from 2 organizations. In a total of 351 WRITE statements, email destinations (226) predominated, and 39 orders and 40 coded output elements also were tabulated. Free-text strings predominated as the message data. Arden WRITE statements contain considerable potentially structured data now included as free text. A future, normative structured WRITE statement must address a variety of data types and destinations.

Overview of data and conceptual approaches for derivation of quantitative structure-activity relationships for ecotoxicological effects of organic chemicals.

PubMed

Bradbury, Steven P; Russom, Christine L; Ankley, Gerald T; Schultz, T Wayne; Walker, John D

2003-08-01

The use of quantitative structure-activity relationships (QSARs) in assessing potential toxic effects of organic chemicals on aquatic organisms continues to evolve as computational efficiency and toxicological understanding advance. With the ever-increasing production of new chemicals, and the need to optimize resources to assess thousands of existing chemicals in commerce, regulatory agencies have turned to QSARs as essential tools to help prioritize tiered risk assessments when empirical data are not available to evaluate toxicological effects. Progress in designing scientifically credible QSARs is intimately associated with the development of empirically derived databases of well-defined and quantified toxicity endpoints, which are based on a strategic evaluation of diverse sets of chemical structures, modes of toxic action, and species. This review provides a brief overview of four databases created for the purpose of developing QSARs for estimating toxicity of chemicals to aquatic organisms. The evolution of QSARs based initially on general chemical classification schemes, to models founded on modes of toxic action that range from nonspecific partitioning into hydrophobic cellular membranes to receptor-mediated mechanisms is summarized. Finally, an overview of expert systems that integrate chemical-specific mode of action classification and associated QSAR selection for estimating potential toxicological effects of organic chemicals is presented.

Semi-empirical model for prediction of unsteady forces on an airfoil with application to flutter

NASA Technical Reports Server (NTRS)

Mahajan, Aparajit J.; Kaza, Krishna Rao V.

1992-01-01

A semi-empirical model is described for predicting unsteady aerodynamic forces on arbitrary airfoils under mildly stalled and unstalled conditions. Aerodynamic forces are modeled using second order ordinary differential equations for lift and moment with airfoil motion as the input. This model is simultaneously integrated with structural dynamics equations to determine flutter characteristics for a two degrees-of-freedom system. Results for a number of cases are presented to demonstrate the suitability of this model to predict flutter. Comparison is made to the flutter characteristics determined by a Navier-Stokes solver and also the classical incompressible potential flow theory.

Semi-empirical model for prediction of unsteady forces on an airfoil with application to flutter

NASA Technical Reports Server (NTRS)

Mahajan, A. J.; Kaza, K. R. V.; Dowell, E. H.

1993-01-01

A semi-empirical model is described for predicting unsteady aerodynamic forces on arbitrary airfoils under mildly stalled and unstalled conditions. Aerodynamic forces are modeled using second order ordinary differential equations for lift and moment with airfoil motion as the input. This model is simultaneously integrated with structural dynamics equations to determine flutter characteristics for a two degrees-of-freedom system. Results for a number of cases are presented to demonstrate the suitability of this model to predict flutter. Comparison is made to the flutter characteristics determined by a Navier-Stokes solver and also the classical incompressible potential flow theory.

'A civilizing mission'? Austrian medicine and the reform of medical structures in the Ottoman Empire, 1838-1850.

PubMed

Chahrour, Marcel

2007-12-01

During the 1840s, physicians from the Habsburg Empire played a decisive role in the reform of medical structures in the Ottoman Empire. This paper discusses different aspects of this scientific and cultural encounter. It emphasizes the importance of Austrian health care structures as a model for the work of these physicians in the Ottoman Empire and studies the role of the medical school ran by the Austrians as a means of representing, on the one hand, the reformatory efforts of the Ottoman Empire and, on the other hand, the motivations of the Habsburg monarchy for an involvement in Ottoman health care affairs, strongly bound up with its own quarantine politics towards the Ottoman Empire.

Impact of Online Instructional Game Features on College Students' Perceived Motivational Support and Cognitive Investment: A Structural Equation Modeling Study

ERIC Educational Resources Information Center

Huang, Wenhao David; Johnson, Tristan E.; Han, Seung-Hyun Caleb

2013-01-01

Colleges and universities have begun to understand the instructional potential of digital game-based learning (DGBL) due to digital games' immersive features. These features, however, might overload learners as excessive motivational and cognitive stimuli thus impeding intended learning. Current research, however, lacks empirical evidences to…

Influence of Additive and Multiplicative Structure and Direction of Comparison on the Reversal Error

ERIC Educational Resources Information Center

González-Calero, José Antonio; Arnau, David; Laserna-Belenguer, Belén

2015-01-01

An empirical study has been carried out to evaluate the potential of word order matching and static comparison as explanatory models of reversal error. Data was collected from 214 undergraduate students who translated a set of additive and multiplicative comparisons expressed in Spanish into algebraic language. In these multiplicative comparisons…

A fitting empirical potential for NiTi alloy and its application

NASA Astrophysics Data System (ADS)

Ren, Guowu; Tang, Tiegang; Sehitoglu, Huseyin

Due to its superelastic behavior, NiTi shape memory alloy receives considerable attentions over a wide range of industrial and commercial applications. Limited to its complex structural transformation and multiple variants, semiempirical potentials for performing large-scale molecular dynamics simulations to investigate the atomistic mechanical process, are very few. In this work, we construct a new interatomic potential for the NiTi alloy by fitting to experimental or ab initio data. The fitting potential correctly predicts the lattice parameter, structural stability, equation of state for cubic B2(austenite) and monoclinic B19'(martensite) phases. In particular the elastic properties(three elastic constants for B2 and thirteen ones for B19') are in satisfactory agreement with the experiments or ab initio calculations. Furthermore, we apply this potential to conduct the molecular dynamics simulations of the mechanical behavior for NiTi alloy and the results capture its reversible transformation.

Evidence for structural plasticity in humans: comment on Thomas and Baker (2012).

PubMed

Erickson, Kirk I

2013-06-01

Thomas and Baker (2012) have provided a balanced and critical review of the scientific evidence claiming that training interventions have the capacity to alter the structural morphology of the brain. Here I provide some additional considerations when reading and interpreting both the review and the original empirical articles. Research proposing to examine the capacity for structural brain plasticity needs to contemplate methodological issues and factors that could moderate or mask potentially interesting effects. Overall, although this area of research is in need of circumspection, it also could have transformative implications if structural brain plasticity in humans is possible. Copyright © 2012 Elsevier Inc. All rights reserved.

Does appropriate empiric antibiotic therapy modify intensive care unit-acquired Enterobacteriaceae bacteraemia mortality and discharge?

PubMed

Pouwels, K B; Van Kleef, E; Vansteelandt, S; Batra, R; Edgeworth, J D; Smieszek, T; Robotham, J V

2017-05-01

Conflicting results have been found regarding outcomes of intensive care unit (ICU)-acquired Enterobacteriaceae bacteraemia and the potentially modifying effect of appropriate empiric antibiotic therapy. To evaluate these associations while adjusting for potential time-varying confounding using methods from the causal inference literature. Patients who stayed more than two days in two general ICUs in England between 2002 and 2006 were included in this cohort study. Marginal structural models with inverse probability weighting were used to estimate the mortality and discharge associated with Enterobacteriaceae bacteraemia and the impact of appropriate empiric antibiotic therapy on these outcomes. Among 3411 ICU admissions, 195 (5.7%) ICU-acquired Enterobacteriaceae bacteraemia cases occurred. Enterobacteriaceae bacteraemia was associated with an increased daily risk of ICU death [cause-specific hazard ratio (HR): 1.48; 95% confidence interval (CI): 1.10-1.99] and a reduced daily risk of ICU discharge (HR: 0.66; 95% CI: 0.54-0.80). Appropriate empiric antibiotic therapy did not significantly modify ICU mortality (HR: 1.08; 95% CI: 0.59-1.97) or discharge (HR: 0.91; 95% CI: 0.63-1.32). ICU-acquired Enterobacteriaceae bacteraemia was associated with an increased daily risk of ICU mortality. Furthermore, the daily discharge rate was also lower after acquiring infection, even when adjusting for time-varying confounding using appropriate methodology. No evidence was found for a beneficial modifying effect of appropriate empiric antibiotic therapy on ICU mortality and discharge. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

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

PubMed

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.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

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

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) 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 Cα 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 Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since 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. PMID:18837035

Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.

PubMed

Bellucci, Michael A; Coker, David F

2011-07-28

We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent. © 2011 American Institute of Physics

Experiential knowledge of expert coaches can help identify informational constraints on performance of dynamic interceptive actions.

PubMed

Greenwood, Daniel; Davids, Keith; Renshaw, Ian

2014-01-01

Coordination of dynamic interceptive movements is predicated on cyclical relations between an individual's actions and information sources from the performance environment. To identify dynamic informational constraints, which are interwoven with individual and task constraints, coaches' experiential knowledge provides a complementary source to support empirical understanding of performance in sport. In this study, 15 expert coaches from 3 sports (track and field, gymnastics and cricket) participated in a semi-structured interview process to identify potential informational constraints which they perceived to regulate action during run-up performance. Expert coaches' experiential knowledge revealed multiple information sources which may constrain performance adaptations in such locomotor pointing tasks. In addition to the locomotor pointing target, coaches' knowledge highlighted two other key informational constraints: vertical reference points located near the locomotor pointing target and a check mark located prior to the locomotor pointing target. This study highlights opportunities for broadening the understanding of perception and action coupling processes, and the identified information sources warrant further empirical investigation as potential constraints on athletic performance. Integration of experiential knowledge of expert coaches with theoretically driven empirical knowledge represents a promising avenue to drive future applied science research and pedagogical practice.

Siting of prison complex above abandoned underground coal mine

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

Marino, G.G.

1998-10-01

This paper discusses in detail the process undertaken to mitigate the effects of any future mine subsidence on prison structures proposed above old abandoned underground workings. The site for a proposed prison complex purchased by the state of Indiana was located in west-central Indiana and was undermined by an old abandoned room and pillar mine. Based on a study of the mine map and subsurface verification of the extent of mining it was determined that all prison buildings and important structures could be placed above solid coal to the north. However, one masonry building was located within the potential drawmore » zone of mine works that still contained significant mine voids. Based on empirical data the subsidence potential was estimated and the building was designed accordingly to be mine subsidence resistant. It was decided that a phase 2 prison complex should be constructed adjacent to and just south of the phase 1 complex. This complex would be directly above the underground workings. Subsequently, an extensive subsurface investigation program was undertaken to (1) ascertain whether or not mine areas where buildings would be located were already collapsed and thus only nominal, if any, subsidence could occur in the future and (2) verify the presence of solid coal areas within the mine as indicated on the mine map. Based on all the site information gathered subsidence profiles were developed from an empirical database of subsidence events in the Illinois coal basin. As a result of this work many structures on the site required no or nominal subsidence considerations. However, for others that could be affected potentially by future subsidence movement preliminary subsidence resistant designs were completed using the expected level of potential subsidence movement.« less

Aiming at a Moving Target: Theoretical and Methodological Considerations in the Study of Intraindividual Goal Conflict between Personal Goals

PubMed Central

Gorges, Julia; Grund, Axel

2017-01-01

Multiple-goal pursuit and conflict between personal life-defining goals can be considered part of everyday business in most individuals' lives. Given the potentially detrimental effects of goal conflict—for example, impaired well-being or poor performance—the literature on goal conflict is surprisingly scattered due to heterogeneous methodological approaches and technical terms. Little empirical research has addressed the conceptualization of goal conflict against the background of differing understandings from a structure-like and a process-like perspective. In the present article, we outline theoretical foundations of goal conflict from two perspectives: a structure- and a process-like perspective. Based on a comparative analysis and integration of these two perspectives, we systematically review empirical studies on goal conflict over 30 years of research. In doing so, we identify and discuss important conceptual dimensions of goal conflict, namely, goal conflict as a cognitive construct and an experiential instance, a focus on goal interrelations or on specific goal properties, and resource vs. inherent conflict, and the potential of these distinctions to further research on goal conflict. Finally, we present major challenges and pose questions that need to be addressed by future research. PMID:29201013

Aiming at a Moving Target: Theoretical and Methodological Considerations in the Study of Intraindividual Goal Conflict between Personal Goals.

PubMed

Gorges, Julia; Grund, Axel

2017-01-01

Multiple-goal pursuit and conflict between personal life-defining goals can be considered part of everyday business in most individuals' lives. Given the potentially detrimental effects of goal conflict-for example, impaired well-being or poor performance-the literature on goal conflict is surprisingly scattered due to heterogeneous methodological approaches and technical terms. Little empirical research has addressed the conceptualization of goal conflict against the background of differing understandings from a structure-like and a process-like perspective. In the present article, we outline theoretical foundations of goal conflict from two perspectives: a structure- and a process-like perspective. Based on a comparative analysis and integration of these two perspectives, we systematically review empirical studies on goal conflict over 30 years of research. In doing so, we identify and discuss important conceptual dimensions of goal conflict, namely, goal conflict as a cognitive construct and an experiential instance, a focus on goal interrelations or on specific goal properties, and resource vs. inherent conflict, and the potential of these distinctions to further research on goal conflict. Finally, we present major challenges and pose questions that need to be addressed by future research.

Host specificity in vascular epiphytes: a review of methodology, empirical evidence and potential mechanisms

PubMed Central

Wagner, Katrin; Mendieta-Leiva, Glenda; Zotz, Gerhard

2015-01-01

Information on the degree of host specificity is fundamental for an understanding of the ecology of structurally dependent plants such as vascular epiphytes. Starting with the seminal paper of A.F.W. Schimper on epiphyte ecology in the late 19th century over 200 publications have dealt with the issue of host specificity in vascular epiphytes. We review and critically discuss this extensive literature. The available evidence indicates that host ranges of vascular epiphytes are largely unrestricted while a certain host bias is ubiquitous. However, tree size and age and spatial autocorrelation of tree and epiphyte species have not been adequately considered in most statistical analyses. More refined null expectations and adequate replication are needed to allow more rigorous conclusions. Host specificity could be caused by a large number of tree traits (e.g. bark characteristics and architectural traits), which influence epiphyte performance. After reviewing the empirical evidence for their relevance, we conclude that future research should use a more comprehensive approach by determining the relative importance of various potential mechanisms acting locally and by testing several proposed hypotheses regarding the relative strength of host specificity in different habitats and among different groups of structurally dependent flora. PMID:25564514

Semi-empirical quantum evaluation of peptide - MHC class II binding

NASA Astrophysics Data System (ADS)

González, Ronald; Suárez, Carlos F.; Bohórquez, Hugo J.; Patarroyo, Manuel A.; Patarroyo, Manuel E.

2017-01-01

Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing the costs of investigation into vaccine development. This study involved using two semi-empirical quantum chemistry methods (PM7 and FMO-DFTB) for computing the binding energies of peptides bonded to HLA-DR1 and HLA-DR2. We found that key stabilising water molecules involved in the peptide binding mechanism were required for finding high correlation with IC50 experimental values. Our proposal is computationally non-intensive, and is a reliable alternative for studying pMHC binding interactions.

Delineating the Structure of Normal and Abnormal Personality: An Integrative Hierarchical Approach

PubMed Central

Markon, Kristian E.; Krueger, Robert F.; Watson, David

2008-01-01

Increasing evidence indicates that normal and abnormal personality can be treated within a single structural framework. However, identification of a single integrated structure of normal and abnormal personality has remained elusive. Here, a constructive replication approach was used to delineate an integrative hierarchical account of the structure of normal and abnormal personality. This hierarchical structure, which integrates many Big Trait models proposed in the literature, replicated across a meta-analysis as well as an empirical study, and across samples of participants as well as measures. The proposed structure resembles previously suggested accounts of personality hierarchy and provides insight into the nature of personality hierarchy more generally. Potential directions for future research on personality and psychopathology are discussed. PMID:15631580

Delineating the structure of normal and abnormal personality: an integrative hierarchical approach.

PubMed

Markon, Kristian E; Krueger, Robert F; Watson, David

2005-01-01

Increasing evidence indicates that normal and abnormal personality can be treated within a single structural framework. However, identification of a single integrated structure of normal and abnormal personality has remained elusive. Here, a constructive replication approach was used to delineate an integrative hierarchical account of the structure of normal and abnormal personality. This hierarchical structure, which integrates many Big Trait models proposed in the literature, replicated across a meta-analysis as well as an empirical study, and across samples of participants as well as measures. The proposed structure resembles previously suggested accounts of personality hierarchy and provides insight into the nature of personality hierarchy more generally. Potential directions for future research on personality and psychopathology are discussed.

Structural Patterns in Empirical Research Articles: A Cross-Disciplinary Study

ERIC Educational Resources Information Center

Lin, Ling; Evans, Stephen

2012-01-01

This paper presents an analysis of the major generic structures of empirical research articles (RAs), with a particular focus on disciplinary variation and the relationship between the adjacent sections in the introductory and concluding parts. The findings were derived from a close "manual" analysis of 433 recent empirical RAs from high-impact…

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

PubMed

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

2015-03-01

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

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Entrapment and near Miss: A Comparative Analysis of Psycho-Structural Elements in Gambling Games and Massively Multiplayer Online Role-Playing Games

ERIC Educational Resources Information Center

Karlsen, Faltin

2011-01-01

While massively multiplayer online role-playing games like World of Warcraft are often accused of leading to excessive and harmful playing, the only gaming activity that is internationally recognized as a pathological disorder is excessive gambling. The present article seeks to establish empirical data on potential harmful online gaming through a…

Quantitative evaluation of simulated functional brain networks in graph theoretical analysis.

PubMed

Lee, Won Hee; Bullmore, Ed; Frangou, Sophia

2017-02-01

There is increasing interest in the potential of whole-brain computational models to provide mechanistic insights into resting-state brain networks. It is therefore important to determine the degree to which computational models reproduce the topological features of empirical functional brain networks. We used empirical connectivity data derived from diffusion spectrum and resting-state functional magnetic resonance imaging data from healthy individuals. Empirical and simulated functional networks, constrained by structural connectivity, were defined based on 66 brain anatomical regions (nodes). Simulated functional data were generated using the Kuramoto model in which each anatomical region acts as a phase oscillator. Network topology was studied using graph theory in the empirical and simulated data. The difference (relative error) between graph theory measures derived from empirical and simulated data was then estimated. We found that simulated data can be used with confidence to model graph measures of global network organization at different dynamic states and highlight the sensitive dependence of the solutions obtained in simulated data on the specified connection densities. This study provides a method for the quantitative evaluation and external validation of graph theory metrics derived from simulated data that can be used to inform future study designs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

An EQT-cDFT approach to determine thermodynamic properties of confined fluids.

PubMed

Mashayak, S Y; Motevaselian, M H; Aluru, N R

2015-06-28

We present a continuum-based approach to predict the structure and thermodynamic properties of confined fluids at multiple length-scales, ranging from a few angstroms to macro-meters. The continuum approach is based on the empirical potential-based quasi-continuum theory (EQT) and classical density functional theory (cDFT). EQT is a simple and fast approach to predict inhomogeneous density and potential profiles of confined fluids. We use EQT potentials to construct a grand potential functional for cDFT. The EQT-cDFT-based grand potential can be used to predict various thermodynamic properties of confined fluids. In this work, we demonstrate the EQT-cDFT approach by simulating Lennard-Jones fluids, namely, methane and argon, confined inside slit-like channels of graphene. We show that the EQT-cDFT can accurately predict the structure and thermodynamic properties, such as density profiles, adsorption, local pressure tensor, surface tension, and solvation force, of confined fluids as compared to the molecular dynamics simulation results.

Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates.

PubMed

Martos-Villa, Ruben; Francisco-Márquez, Misaela; Mata, M Pilar; Sainz-Díaz, C Ignacio

2013-07-01

Methane hydrates are highly present in sea-floors and in other planets and their moons. Hence, these compounds are of great interest for environment, global climate change, energy resources, and Cosmochemistry. The knowledge of stability and physical-chemical properties of methane hydrate crystal structure is important for evaluating some new green becoming technologies such as, strategies to produce natural gas from marine methane hydrates and simultaneously store CO2 as hydrates. However, some aspects related with their stability, spectroscopic and other chemical-physical properties of both hydrates are not well understood yet. The structure and stability of crystal structure of methane and CO2 hydrates have been investigated by means of calculations with empirical interatomic potentials and quantum-mechanical methods based on Hartree-Fock and Density Functional Theory (DFT) approximations. Molecular Dynamic simulations have been also performed exploring different configurations reproducing the experimental crystallographic properties. Spectroscopic properties have also been studied. Frequency shifts of the main vibration modes were observed upon the formation of these hydrates, confirming that vibration stretching peaks of C-H at 2915cm(-1) and 2905cm(-1) are due to methane in small and large cages, respectively. Similar effect is observed in the CO2 clathrates. The guest-host binding energy in these clathrates calculated with different methods are compared and discussed in terms of adequacy of empirical potentials and DFT methods for describing the interactions between gas guest and the host water cage, proving an exothermic nature of methane and CO2 hydrates formation process. Copyright © 2013 Elsevier Inc. All rights reserved.

Modeling relations in nature and eco-informatics: a practical application of rosennean complexity.

PubMed

Kineman, John J

2007-10-01

The purpose of eco-informatics is to communicate critical information about organisms and ecosystems. To accomplish this, it must reflect the complexity of natural systems. Present information systems are designed around mechanistic concepts that do not capture complexity. Robert Rosen's relational theory offers a way of representing complexity in terms of information entailments that are part of an ontologically implicit 'modeling relation'. This relation has corresponding epistemological components that can be captured empirically, the components being structure (associated with model encoding) and function (associated with model decoding). Relational complexity, thus, provides a long-awaited theoretical underpinning for these concepts that ecology has found indispensable. Structural information pertains to the material organization of a system, which can be represented by data. Functional information specifies potential change, which can be inferred from experiment and represented as models or descriptions of state transformations. Contextual dependency (of structure or function) implies meaning. Biological functions imply internalized or system-dependent laws. Complexity can be represented epistemologically by relating structure and function in two different ways. One expresses the phenomenal relation that exists in any present or past instance, and the other draws the ontology of a system into the empirical world in terms of multiple potentials subject to natural forms of selection and optimality. These act as system attractors. Implementing these components and their theoretical relations in an informatics system will provide more-complete ecological informatics than is possible from a strictly mechanistic point of view. This approach will enable many new possibilities for supporting science and decision making.

Inferring multi-scale neural mechanisms with brain network modelling

PubMed Central

Schirner, Michael; McIntosh, Anthony Randal; Jirsa, Viktor; Deco, Gustavo

2018-01-01

The neurophysiological processes underlying non-invasive brain activity measurements are incompletely understood. Here, we developed a connectome-based brain network model that integrates individual structural and functional data with neural population dynamics to support multi-scale neurophysiological inference. Simulated populations were linked by structural connectivity and, as a novelty, driven by electroencephalography (EEG) source activity. Simulations not only predicted subjects' individual resting-state functional magnetic resonance imaging (fMRI) time series and spatial network topologies over 20 minutes of activity, but more importantly, they also revealed precise neurophysiological mechanisms that underlie and link six empirical observations from different scales and modalities: (1) resting-state fMRI oscillations, (2) functional connectivity networks, (3) excitation-inhibition balance, (4, 5) inverse relationships between α-rhythms, spike-firing and fMRI on short and long time scales, and (6) fMRI power-law scaling. These findings underscore the potential of this new modelling framework for general inference and integration of neurophysiological knowledge to complement empirical studies. PMID:29308767

A discrete structure of the brain waves.

NASA Astrophysics Data System (ADS)

Dabaghian, Yuri; Perotti, Luca; oscillons in biological rhythms Collaboration; physics of biological rhythms Team

A physiological interpretation of the biological rhythms, e.g., of the local field potentials (LFP) depends on the mathematical approaches used for the analysis. Most existing mathematical methods are based on decomposing the signal into a set of ``primitives,'' e.g., sinusoidal harmonics, and correlating them with different cognitive and behavioral phenomena. A common feature of all these methods is that the decomposition semantics is presumed from the onset, and the goal of the subsequent analysis reduces merely to identifying the combination that best reproduces the original signal. We propose a fundamentally new method in which the decomposition components are discovered empirically, and demonstrate that it is more flexible and more sensitive to the signal's structure than the standard Fourier method. Applying this method to the rodent LFP signals reveals a fundamentally new structure of these ``brain waves.'' In particular, our results suggest that the LFP oscillations consist of a superposition of a small, discrete set of frequency modulated oscillatory processes, which we call ``oscillons''. Since these structures are discovered empirically, we hypothesize that they may capture the signal's actual physical structure, i.e., the pattern of synchronous activity in neuronal ensembles. Proving this hypothesis will help to advance our principal understanding of the neuronal synchronization mechanisms and reveal new structure within the LFPs and other biological oscillations. NSF 1422438 Grant, Houston Bioinformatics Endowment Fund.

Structure and Dynamics of the Thermohaline Staircases in the Beaufort Gyre

DTIC Science & Technology

2007-09-01

diffusive layering created by heating a salt gradient from below, after Figure 6 (Kelley 2003) A is the first quasi - stationary interface. B is the...sources Crapper (1975), Turner (1965), and Newell (1984) from Kelley (1990). The solid line is the empirical fit....12 Figure 11. Schematic of Ice...Salinity, Potential Temperature and Density plots show thermohaline xi step characteristics. b) Sound velocity profiles showing the step data

Mass density fluctuations in quantum and classical descriptions of liquid water

NASA Astrophysics Data System (ADS)

Galib, Mirza; Duignan, Timothy T.; Misteli, Yannick; Baer, Marcel D.; Schenter, Gregory K.; Hutter, Jürg; Mundy, Christopher J.

2017-06-01

First principles molecular dynamics simulation protocol is established using revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with Grimme's third generation of dispersion (D3) correction to describe the properties of water at ambient conditions. This study also demonstrates the consistency of the structure of water across both isobaric (NpT) and isothermal (NVT) ensembles. Going beyond the standard structural benchmarks for liquid water, we compute properties that are connected to both local structure and mass density fluctuations that are related to concepts of solvation and hydrophobicity. We directly compare our revPBE results to the Becke-Lee-Yang-Parr (BLYP) plus Grimme dispersion corrections (D2) and both the empirical fixed charged model (SPC/E) and many body interaction potential model (MB-pol) to further our understanding of how the computed properties herein depend on the form of the interaction potential.

Mass density fluctuations in quantum and classical descriptions of liquid water

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

Galib, Mirza; Duignan, Timothy T.; Misteli, Yannick

First principles molecular dynamics simulation protocol is established using revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with Grimme's third generation of dispersion (D3) correction to describe properties of water at ambient conditions. This study also demonstrates the consistency of the structure of water across both isobaric (NpT) and isothermal (NVT) ensembles. Going beyond the standard structural benchmarks for liquid water, we compute properties that are connected to both local structure and mass density fluctuations that are related to concepts of solvation and hydrophobicity. We directly compare our revPBE results to the Becke-Lee-Yang-Parr (BLYP) plus Grimme dispersion corrections (D2) and bothmore » the empirical fixed charged model (SPC/E) and many body interaction potential model (MB-pol) to further our understanding of how the computed properties herein depend on the form of the interaction potential.« less

Theoretical and Empirical Analysis of a Spatial EA Parallel Boosting Algorithm.

PubMed

Kamath, Uday; Domeniconi, Carlotta; De Jong, Kenneth

2018-01-01

Many real-world problems involve massive amounts of data. Under these circumstances learning algorithms often become prohibitively expensive, making scalability a pressing issue to be addressed. A common approach is to perform sampling to reduce the size of the dataset and enable efficient learning. Alternatively, one customizes learning algorithms to achieve scalability. In either case, the key challenge is to obtain algorithmic efficiency without compromising the quality of the results. In this article we discuss a meta-learning algorithm (PSBML) that combines concepts from spatially structured evolutionary algorithms (SSEAs) with concepts from ensemble and boosting methodologies to achieve the desired scalability property. We present both theoretical and empirical analyses which show that PSBML preserves a critical property of boosting, specifically, convergence to a distribution centered around the margin. We then present additional empirical analyses showing that this meta-level algorithm provides a general and effective framework that can be used in combination with a variety of learning classifiers. We perform extensive experiments to investigate the trade-off achieved between scalability and accuracy, and robustness to noise, on both synthetic and real-world data. These empirical results corroborate our theoretical analysis, and demonstrate the potential of PSBML in achieving scalability without sacrificing accuracy.

Disordered Atom Molecular Potential for Water Parameterized against Neutron Diffraction Data. Application to the Structure of Ice Ih.

PubMed

Soper, Alan K

2015-07-23

A disordered atom molecular potential (DAMP) for water is described that accurately accounts for the observed neutron interference differential scattering cross sections for light water, heavy water, and two different mixtures of these liquids (x = 0.5 and x = 0.64, where x is the mole fraction of light water in the mixtures) at T = 283 K. This potential, when used in a NVT Monte Carlo computer simulation, produces an intermolecular pressure of ∼0 kbar and a configurational energy of approximately -50 kJ/mol, close to the values found in the ambient liquid at this temperature. The same potential is used as the reference potential in an empirical potential structure refinement of ice diffraction data at T = 258 K measured at the same time as the water data and under the same conditions. Particularly intriguing is the finding that the O···O-H angle in ice, which would be 0° for a linear hydrogen bond, is actually more disordered in ice than in the liquid. A rationalization of these findings is presented. It remains to be seen whether this potential has any value other than simply as a description of the ambient liquid structure.

The Problem of Empirical Redundancy of Constructs in Organizational Research: An Empirical Investigation

ERIC Educational Resources Information Center

Le, Huy; Schmidt, Frank L.; Harter, James K.; Lauver, Kristy J.

2010-01-01

Construct empirical redundancy may be a major problem in organizational research today. In this paper, we explain and empirically illustrate a method for investigating this potential problem. We applied the method to examine the empirical redundancy of job satisfaction (JS) and organizational commitment (OC), two well-established organizational…

Structural Priming: A Critical Review

PubMed Central

Pickering, Martin J.; Ferreira, Victor S.

2009-01-01

Repetition is a central phenomenon of behavior, and researchers make extensive use of it to illuminate psychological functioning. In the language sciences, a ubiquitous form of such repetition is structural priming, a tendency to repeat or better process a current sentence because of its structural similarity to a previously experienced (“prime”) sentence (Bock, 1986). The recent explosion of research in structural priming has made it the dominant means of investigating the processes involved in the production (and increasingly, comprehension) of complex expressions such as sentences. This review considers its implications for the representation of syntax and the mechanisms of production, comprehension, and their relationship. It then addresses the potential functions of structural priming, before turning to its implications for first language acquisition, bilingualism, and aphasia We close with theoretical and empirical recommendations for future investigations. PMID:18444704

Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.

PubMed

Blazquez-Navarro, Arturo; Schachtner, Thomas; Stervbo, Ulrik; Sefrin, Anett; Stein, Maik; Westhoff, Timm H; Reinke, Petra; Klipp, Edda; Babel, Nina; Neumann, Avidan U; Or-Guil, Michal

2018-05-01

BK virus (BKV) associated nephropathy affects 1-10% of kidney transplant recipients, leading to graft failure in about 50% of cases. Immune responses against different BKV antigens have been shown to have a prognostic value for disease development. Data currently suggest that the structural antigens and regulatory antigens of BKV might each trigger a different mode of action of the immune response. To study the influence of different modes of action of the cellular immune response on BKV clearance dynamics, we have analysed the kinetics of BKV plasma load and anti-BKV T cell response (Elispot) in six patients with BKV associated nephropathy using ODE modelling. The results show that only a small number of hypotheses on the mode of action are compatible with the empirical data. The hypothesis with the highest empirical support is that structural antigens trigger blocking of virus production from infected cells, whereas regulatory antigens trigger an acceleration of death of infected cells. These differential modes of action could be important for our understanding of BKV resolution, as according to the hypothesis, only regulatory antigens would trigger a fast and continuous clearance of the viral load. Other hypotheses showed a lower degree of empirical support, but could potentially explain the clearing mechanisms of individual patients. Our results highlight the heterogeneity of the dynamics, including the delay between immune response against structural versus regulatory antigens, and its relevance for BKV clearance. Our modelling approach is the first that studies the process of BKV clearance by bringing together viral and immune kinetics and can provide a framework for personalised hypotheses generation on the interrelations between cellular immunity and viral dynamics.

Photoacoustic imaging optimization with raw signal deconvolution and empirical mode decomposition

NASA Astrophysics Data System (ADS)

Guo, Chengwen; Wang, Jing; Qin, Yu; Zhan, Hongchen; Yuan, Jie; Cheng, Qian; Wang, Xueding

2018-02-01

Photoacoustic (PA) signal of an ideal optical absorb particle is a single N-shape wave. PA signals of a complicated biological tissue can be considered as the combination of individual N-shape waves. However, the N-shape wave basis not only complicates the subsequent work, but also results in aliasing between adjacent micro-structures, which deteriorates the quality of the final PA images. In this paper, we propose a method to improve PA image quality through signal processing method directly working on raw signals, which including deconvolution and empirical mode decomposition (EMD). During the deconvolution procedure, the raw PA signals are de-convolved with a system dependent point spread function (PSF) which is measured in advance. Then, EMD is adopted to adaptively re-shape the PA signals with two constraints, positive polarity and spectrum consistence. With our proposed method, the built PA images can yield more detail structural information. Micro-structures are clearly separated and revealed. To validate the effectiveness of this method, we present numerical simulations and phantom studies consist of a densely distributed point sources model and a blood vessel model. In the future, our study might hold the potential for clinical PA imaging as it can help to distinguish micro-structures from the optimized images and even measure the size of objects from deconvolved signals.

RNA design rules from a massive open laboratory

PubMed Central

Lee, Jeehyung; Kladwang, Wipapat; Lee, Minjae; Cantu, Daniel; Azizyan, Martin; Kim, Hanjoo; Limpaecher, Alex; Gaikwad, Snehal; Yoon, Sungroh; Treuille, Adrien; Das, Rhiju

2014-01-01

Self-assembling RNA molecules present compelling substrates for the rational interrogation and control of living systems. However, imperfect in silico models—even at the secondary structure level—hinder the design of new RNAs that function properly when synthesized. Here, we present a unique and potentially general approach to such empirical problems: the Massive Open Laboratory. The EteRNA project connects 37,000 enthusiasts to RNA design puzzles through an online interface. Uniquely, EteRNA participants not only manipulate simulated molecules but also control a remote experimental pipeline for high-throughput RNA synthesis and structure mapping. We show herein that the EteRNA community leveraged dozens of cycles of continuous wet laboratory feedback to learn strategies for solving in vitro RNA design problems on which automated methods fail. The top strategies—including several previously unrecognized negative design rules—were distilled by machine learning into an algorithm, EteRNABot. Over a rigorous 1-y testing phase, both the EteRNA community and EteRNABot significantly outperformed prior algorithms in a dozen RNA secondary structure design tests, including the creation of dendrimer-like structures and scaffolds for small molecule sensors. These results show that an online community can carry out large-scale experiments, hypothesis generation, and algorithm design to create practical advances in empirical science. PMID:24469816

Empirical temperature-dependent intermolecular potentials determined by data mining from crystal data

NASA Astrophysics Data System (ADS)

Hofmann, D. W. M.; Kuleshova, L. N.

2018-05-01

Modern force fields are accurate enough to describe thermal effects in molecular crystals. Here, we have extended our earlier approach to discrete force fields for various temperatures to a force field with a continuous function. For the parametrisation of the force field, we used data mining on experimental structures with the temperature as an additional descriptor. The obtained force field can be used to minimise energy at a finite temperature and for molecular dynamics with zero-K potentials. The applicability of the method has been demonstrated for the prediction of crystal density, temperature density gradients and transition temperature.

Irregularity, volatility, risk, and financial market time series

PubMed Central

Pincus, Steve; Kalman, Rudolf E.

2004-01-01

The need to assess subtle, potentially exploitable changes in serial structure is paramount in the analysis of financial data. Herein, we demonstrate the utility of approximate entropy (ApEn), a model-independent measure of sequential irregularity, toward this goal, by several distinct applications. We consider both empirical data and models, including composite indices (Standard and Poor's 500 and Hang Seng), individual stock prices, the random-walk hypothesis, and the Black–Scholes and fractional Brownian motion models. Notably, ApEn appears to be a potentially useful marker of system stability, with rapid increases possibly foreshadowing significant changes in a financial variable. PMID:15358860

An evolutionary algorithm that constructs recurrent neural networks.

PubMed

Angeline, P J; Saunders, G M; Pollack, J B

1994-01-01

Standard methods for simultaneously inducing the structure and weights of recurrent neural networks limit every task to an assumed class of architectures. Such a simplification is necessary since the interactions between network structure and function are not well understood. Evolutionary computations, which include genetic algorithms and evolutionary programming, are population-based search methods that have shown promise in many similarly complex tasks. This paper argues that genetic algorithms are inappropriate for network acquisition and describes an evolutionary program, called GNARL, that simultaneously acquires both the structure and weights for recurrent networks. GNARL's empirical acquisition method allows for the emergence of complex behaviors and topologies that are potentially excluded by the artificial architectural constraints imposed in standard network induction methods.

The siting of a prison complex above an abandoned underground coal mine

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

Marino, G.G.

1997-12-31

This paper discusses in detail the process undertaken to mitigate the effects of any future mine subsidence on prison structures proposed above old abandoned underground workings. The site for a proposed prison complex purchased by the State of Indiana was located in west-central Indiana and was undermined by an old abandoned room and pillar mine. The original plan for construction consisted of one phase. Based on a study of the mine map and subsurface verification of the extent of mining it was determined that all prison buildings and important structures could be placed above solid coal to the north. Onemore » masonry building, however, was located within the potential draw zone of mine works which still contained significant mine voids. Based on empirical data the subsidence potential was estimated and the building was accordingly designed to be mine subsidence resistant. It was decided that a phase two prison complex should be constructed adjacent to and just south of the Phase I complex. This complex would be directly above the underground workings. The first stage of design was to minimize subsidence potential by positioning the exposure of significant structures to the subjacent mining assuming the mine map was sufficiently accurate. Subsequently, an extensive subsurface investigation program was then undertaken to: (1) ascertain whether or not mine areas where buildings would be located were already collapsed and thus only nominal, if any, subsidence could occur in the future; and (2) verify the presence of solid coal areas within the mine as indicated on the mine map. Based on all the site information gathered subsidence profiles were developed from an empirical data base of subsidence events in the Illinois Coal Basin. As a result of this work many structures on the site required no or nominal subsidence considerations.« less

New interatomic potential for Mg–Al–Zn alloys with specific application to dilute Mg-based alloys

NASA Astrophysics Data System (ADS)

Dickel, Doyl E.; Baskes, Michael I.; Aslam, Imran; Barrett, Christopher D.

2018-06-01

Because of its very large c/a ratio, zinc has proven to be a difficult element to model using semi-empirical classical potentials. It has been shown, in particular, that for the modified embedded atom method (MEAM), a potential cannot simultaneously have an hcp ground state and c/a ratio greater than ideal. As an alloying element, however, useful zinc potentials can be generated by relaxing the condition that hcp be the lowest energy structure. In this paper, we present a MEAM zinc potential, which gives accurate material properties for the pure state, as well as a MEAM ternary potential for the Mg–Al–Zn system which will allow the atomistic modeling of a wide class of alloys containing zinc. The effects of zinc in simple Mg–Zn for this potential is demonstrated and these results verify the accuracy for the new potential in these systems.

An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data.

PubMed

Wang, Yejun; MacKenzie, Keith D; White, Aaron P

2015-05-07

As sequencing costs are being lowered continuously, RNA-seq has gradually been adopted as the first choice for comparative transcriptome studies with bacteria. Unlike microarrays, RNA-seq can directly detect cDNA derived from mRNA transcripts at a single nucleotide resolution. Not only does this allow researchers to determine the absolute expression level of genes, but it also conveys information about transcript structure. Few automatic software tools have yet been established to investigate large-scale RNA-seq data for bacterial transcript structure analysis. In this study, 54 directional RNA-seq libraries from Salmonella serovar Typhimurium (S. Typhimurium) 14028s were examined for potential relationships between read mapping patterns and transcript structure. We developed an empirical method, combined with statistical tests, to automatically detect key transcript features, including transcriptional start sites (TSSs), transcriptional termination sites (TTSs) and operon organization. Using our method, we obtained 2,764 TSSs and 1,467 TTSs for 1331 and 844 different genes, respectively. Identification of TSSs facilitated further discrimination of 215 putative sigma 38 regulons and 863 potential sigma 70 regulons. Combining the TSSs and TTSs with intergenic distance and co-expression information, we comprehensively annotated the operon organization in S. Typhimurium 14028s. Our results show that directional RNA-seq can be used to detect transcriptional borders at an acceptable resolution of ±10-20 nucleotides. Technical limitations of the RNA-seq procedure may prevent single nucleotide resolution. The automatic transcript border detection methods, statistical models and operon organization pipeline that we have described could be widely applied to RNA-seq studies in other bacteria. Furthermore, the TSSs, TTSs, operons, promoters and unstranslated regions that we have defined for S. Typhimurium 14028s may constitute valuable resources that can be used for comparative analyses with other Salmonella serotypes.

Physical–chemical determinants of coil conformations in globular proteins

PubMed Central

Perskie, Lauren L; Rose, George D

2010-01-01

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α-helices and/or β-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue. PMID:20512968

Peierls potential of screw dislocations in bcc transition metals: Predictions from density functional theory

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

Weinberger, Christopher R.; Tucker, Garritt J.; Foiles, Stephen M.

2013-02-01

It is well known that screw dislocation motion dominates the plastic deformation in body-centered-cubic metals at low temperatures. The nature of the nonplanar structure of screw dislocations gives rise to high lattice friction, which results in strong temperature and strain rate dependence of plastic flow. Thus the nature of the Peierls potential, which is responsible for the high lattice resistance, is an important physical property of the material. However, current empirical potentials give a complicated picture of the Peierls potential. Here, we investigate the nature of the Peierls potential using density functional theory in the bcc transition metals. The resultsmore » show that the shape of the Peierls potential is sinusoidal for every material investigated. Furthermore, we show that the magnitude of the potential scales strongly with the energy per unit length of the screw dislocation in the material.« less

A charge optimized many-body potential for titanium nitride (TiN).

PubMed

Cheng, Y-T; Liang, T; Martinez, J A; Phillpot, S R; Sinnott, S B

2014-07-02

This work presents a new empirical, variable charge potential for TiN systems in the charge-optimized many-body potential framework. The potential parameters were determined by fitting them to experimental data for the enthalpy of formation, lattice parameters, and elastic constants of rocksalt structured TiN. The potential does a good job of describing the fundamental physical properties (defect formation and surface energies) of TiN relative to the predictions of first-principles calculations. This potential is used in classical molecular dynamics simulations to examine the interface of fcc-Ti(0 0 1)/TiN(0 0 1) and to characterize the adsorption of oxygen atoms and molecules on the TiN(0 0 1) surface. The results indicate that the potential is well suited to model TiN thin films and to explore the chemistry associated with their oxidation.

Investigating the potential of e-Learning in healthcare postgraduate curricula: a structural equation model.

PubMed

Katharaki, Maria; Daskalakis, Stelios; Mantas, John

2010-01-01

The objective of this paper is to assess the future adaptability of e-Learning platforms within postgraduate modules. An ongoing empirical assessment was conducted amongst postgraduate students, based on the Technology Acceptance Model (TAM). The current paper presents the outcomes from the second phase of a survey, involving fifty six participants. Data analysis was performed using a structural equation model, based on partial least squares. Results highlighted the very strong effect of perceived usefulness and perceived ease of use to attitude towards using e-Learning platforms. Consequently, attitude towards use proved to be a very strong predictor of behavioral intention. Perceived usefulness, on the contrary, did not prove to have an effect to behavioral intention. Implications on the potential of using e-Learning platforms are discussed along with limitations and future directions of the study.

Transition mixing study empirical model report

NASA Technical Reports Server (NTRS)

Srinivasan, R.; White, C.

1988-01-01

The empirical model developed in the NASA Dilution Jet Mixing Program has been extended to include the curvature effects of transition liners. This extension is based on the results of a 3-D numerical model generated under this contract. The empirical model results agree well with the numerical model results for all tests cases evaluated. The empirical model shows faster mixing rates compared to the numerical model. Both models show drift of jets toward the inner wall of a turning duct. The structure of the jets from the inner wall does not exhibit the familiar kidney-shaped structures observed for the outer wall jets or for jets injected in rectangular ducts.

Assessment of current atomic scale modelling methods for the investigation of nuclear fuels under irradiation: Example of uranium dioxide

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

Bertolus, Marjorie; Krack, Matthias; Freyss, Michel

Multiscale approaches are developed to build more physically based kinetic and mechanical mesoscale models to enhance the predictive capability of fuel performance codes and increase the efficiency of the development of the safer and more innovative nuclear materials needed in the future. Atomic scale methods, and in particular electronic structure and empirical potential methods, form the basis of this multiscale approach. It is therefore essential to know the accuracy of the results computed at this scale if we want to feed them into higher scale models. We focus here on the assessment of the description of interatomic interactions in uraniummore » dioxide using on the one hand electronic structure methods, in particular in the density functional theory (DFT) framework and on the other hand empirical potential methods. These two types of methods are complementary, the former enabling to get results from a minimal amount of input data and further insight into the electronic and magnetic properties, while the latter are irreplaceable for studies where a large number of atoms needs to be considered. We consider basic properties as well as specific ones, which are important for the description of nuclear fuel under irradiation. These are especially energies, which are the main data passed to higher scale models. We limit ourselves to uranium dioxide.« less

Foundations of quantum gravity: The role of principles grounded in empirical reality

NASA Astrophysics Data System (ADS)

Holman, Marc

2014-05-01

When attempting to assess the strengths and weaknesses of various principles in their potential role of guiding the formulation of a theory of quantum gravity, it is crucial to distinguish between principles which are strongly supported by empirical data - either directly or indirectly - and principles which instead (merely) rely heavily on theoretical arguments for their justification. Principles in the latter category are not necessarily invalid, but their a priori foundational significance should be regarded with due caution. These remarks are illustrated in terms of the current standard models of cosmology and particle physics, as well as their respective underlying theories, i.e., essentially general relativity and quantum (field) theory. For instance, it is clear that both standard models are severely constrained by symmetry principles: an effective homogeneity and isotropy of the known universe on the largest scales in the case of cosmology and an underlying exact gauge symmetry of nuclear and electromagnetic interactions in the case of particle physics. However, in sharp contrast to the cosmological situation, where the relevant symmetry structure is more or less established directly on observational grounds, all known, nontrivial arguments for the "gauge principle" are purely theoretical (and far less conclusive than usually advocated). Similar remarks apply to the larger theoretical structures represented by general relativity and quantum (field) theory, where - actual or potential - empirical principles, such as the (Einstein) equivalence principle or EPR-type nonlocality, should be clearly differentiated from theoretical ones, such as general covariance or renormalizability. It is argued that if history is to be of any guidance, the best chance to obtain the key structural features of a putative quantum gravity theory is by deducing them, in some form, from the appropriate empirical principles (analogous to the manner in which, say, the idea that gravitation is a curved spacetime phenomenon is arguably implied by the equivalence principle). Theoretical principles may still be useful however in formulating a concrete theory (analogous to the manner in which, say, a suitable form of general covariance can still act as a sieve for separating theories of gravity from one another). It is subsequently argued that the appropriate empirical principles for deducing the key structural features of quantum gravity should at least include (i) quantum nonlocality, (ii) irreducible indeterminacy (or, essentially equivalently, given (i), relativistic causality), (iii) the thermodynamic arrow of time, (iv) homogeneity and isotropy of the observable universe on the largest scales. In each case, it is explained - when appropriate - how the principle in question could be implemented mathematically in a theory of quantum gravity, why it is considered to be of fundamental significance and also why contemporary accounts of it are insufficient. For instance, the high degree of uniformity observed in the Cosmic Microwave Background is usually regarded as theoretically problematic because of the existence of particle horizons, whereas the currently popular attempts to resolve this situation in terms of inflationary models are, for a number of reasons, less than satisfactory. However, rather than trying to account for the required empirical features dynamically, an arguably much more fruitful approach consists in attempting to account for these features directly, in the form of a lawlike initial condition within a theory of quantum gravity.

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

Zhang, Y.; Ashcraft, R.; Mendelev, M. I.

The state-of-the-art experimental and atomistic simulation techniques were utilized to study the structure of the liquid and amorphous Ni62Nb38 alloy. First, the ab initio molecular dynamics (AIMD) simulation was performed at rather high temperature where the time limitations of the AIMD do not prevent to reach the equilibrium liquid structure. A semi-empirical potential of the Finnis-Sinclair (FS) type was developed to almost exactly reproduce the AIMD partial pair correlation functions (PPCFs) in a classical molecular dynamics simulation. This simulation also showed that the FS potential well reproduces the bond angle distributions. The FS potential was then employed to elongate themore » AIMD PPCFs and determine the total structure factor (TSF) which was found to be in excellent agreement with X-ray TSF obtained within the present study demonstrating the reliability of the AIMD for the simulation of the structure of the liquid Ni–Nb alloys as well as the reliability of the developed FS potential. The glass structure obtained with the developed potential was also found to be in excellent agreement with the X-ray data. The analysis of the structure revealed that a network of the icosahedra clusters centered on Ni atoms is forming during cooling the liquid alloy down to T g and the Nb Z14, Z15, and Z16 clusters are attached to this network. This network is the main feature of the Ni 62Nb 38 alloy and further investigations of the properties of this alloy should be based on study of the behavior of this network.« less

Characterization of material properties for mechanistic-empirical pavement design in Wyoming : final report.

DOT National Transportation Integrated Search

2016-12-01

The Wyoming Department of Transportation (WYDOT) recently transitioned from the empirical AASHTO Design for Design of Pavement Structures to the Mechanistic Empirical Pavement Design Guide (MEPDG) as their standard pavement design procedure. A compre...

Fine structure of spectral properties for random correlation matrices: An application to financial markets

NASA Astrophysics Data System (ADS)

Livan, Giacomo; Alfarano, Simone; Scalas, Enrico

2011-07-01

We study some properties of eigenvalue spectra of financial correlation matrices. In particular, we investigate the nature of the large eigenvalue bulks which are observed empirically, and which have often been regarded as a consequence of the supposedly large amount of noise contained in financial data. We challenge this common knowledge by acting on the empirical correlation matrices of two data sets with a filtering procedure which highlights some of the cluster structure they contain, and we analyze the consequences of such filtering on eigenvalue spectra. We show that empirically observed eigenvalue bulks emerge as superpositions of smaller structures, which in turn emerge as a consequence of cross correlations between stocks. We interpret and corroborate these findings in terms of factor models, and we compare empirical spectra to those predicted by random matrix theory for such models.

Statistical Mechanical Model for Adsorption Coupled with SAFT-VR Mie Equation of State.

PubMed

Franco, Luís F M; Economou, Ioannis G; Castier, Marcelo

2017-10-24

We extend the SAFT-VR Mie equation of state to calculate adsorption isotherms by considering explicitly the residual energy due to the confinement effect. Assuming a square-well potential for the fluid-solid interactions, the structure imposed by the fluid-solid interface is calculated using two different approaches: an empirical expression proposed by Travalloni et al. ( Chem. Eng. Sci. 65 , 3088 - 3099 , 2010 ), and a new theoretical expression derived by applying the mean value theorem. Adopting the SAFT-VR Mie ( Lafitte et al. J. Chem. Phys. , 139 , 154504 , 2013 ) equation of state to describe the fluid-fluid interactions, and solving the phase equilibrium criteria, we calculate adsorption isotherms for light hydrocarbons adsorbed in a carbon molecular sieve and for carbon dioxide, nitrogen, and water adsorbed in a zeolite. Good results are obtained from the model using either approach. Nonetheless, the theoretical expression seems to correlate better the experimental data than the empirical one, possibly implying that a more reliable way to describe the structure ensures a better description of the thermodynamic behavior.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores.

PubMed

Law, Y K; Hassanali, A A

2018-03-14

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores

NASA Astrophysics Data System (ADS)

Law, Y. K.; Hassanali, A. A.

2018-03-01

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

Empirical Bayes method for reducing false discovery rates of correlation matrices with block diagonal structure.

PubMed

Pacini, Clare; Ajioka, James W; Micklem, Gos

2017-04-12

Correlation matrices are important in inferring relationships and networks between regulatory or signalling elements in biological systems. With currently available technology sample sizes for experiments are typically small, meaning that these correlations can be difficult to estimate. At a genome-wide scale estimation of correlation matrices can also be computationally demanding. We develop an empirical Bayes approach to improve covariance estimates for gene expression, where we assume the covariance matrix takes a block diagonal form. Our method shows lower false discovery rates than existing methods on simulated data. Applied to a real data set from Bacillus subtilis we demonstrate it's ability to detecting known regulatory units and interactions between them. We demonstrate that, compared to existing methods, our method is able to find significant covariances and also to control false discovery rates, even when the sample size is small (n=10). The method can be used to find potential regulatory networks, and it may also be used as a pre-processing step for methods that calculate, for example, partial correlations, so enabling the inference of the causal and hierarchical structure of the networks.

A Novel Approach for Blast-Induced Flyrock Prediction Based on Imperialist Competitive Algorithm and Artificial Neural Network

PubMed Central

Marto, Aminaton; Jahed Armaghani, Danial; Tonnizam Mohamad, Edy; Makhtar, Ahmad Mahir

2014-01-01

Flyrock is one of the major disturbances induced by blasting which may cause severe damage to nearby structures. This phenomenon has to be precisely predicted and subsequently controlled through the changing in the blast design to minimize potential risk of blasting. The scope of this study is to predict flyrock induced by blasting through a novel approach based on the combination of imperialist competitive algorithm (ICA) and artificial neural network (ANN). For this purpose, the parameters of 113 blasting operations were accurately recorded and flyrock distances were measured for each operation. By applying the sensitivity analysis, maximum charge per delay and powder factor were determined as the most influential parameters on flyrock. In the light of this analysis, two new empirical predictors were developed to predict flyrock distance. For a comparison purpose, a predeveloped backpropagation (BP) ANN was developed and the results were compared with those of the proposed ICA-ANN model and empirical predictors. The results clearly showed the superiority of the proposed ICA-ANN model in comparison with the proposed BP-ANN model and empirical approaches. PMID:25147856

Semi-empirical studies of atomic structure. Progress report, 1 July 1982-1 February 1983

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

Curtis, L.J.

1983-01-01

A program of studies of the properties of the heavy and highly ionized atomic systems which often occur as contaminants in controlled fusion devices is continuing. The project combines experimental measurements by fast-ion-beam excitation with semi-empirical data parametrizations to identify and exploit regularities in the properties of these very heavy and very highly ionized systems. The increasing use of spectroscopic line intensities as diagnostics for determining thermonuclear plasma temperatures and densities requires laboratory observation and analysis of such spectra, often to accuracies that exceed the capabilities of ab initio theoretical methods for these highly relativistic many electron systems. Through themore » acquisition and systematization of empirical data, remarkably precise methods for predicting excitation energies, transition wavelengths, transition probabilities, level lifetimes, ionization potentials, core polarizabilities, and core penetrabilities are being developed and applied. Although the data base for heavy, highly ionized atoms is still sparse, parametrized extrapolations and interpolations along isoelectronic, homologous, and Rydberg sequences are providing predictions for large classes of quantities, with a precision that is sharpened by subsequent measurements.« less

A novel approach for blast-induced flyrock prediction based on imperialist competitive algorithm and artificial neural network.

PubMed

Marto, Aminaton; Hajihassani, Mohsen; Armaghani, Danial Jahed; Mohamad, Edy Tonnizam; Makhtar, Ahmad Mahir

2014-01-01

Flyrock is one of the major disturbances induced by blasting which may cause severe damage to nearby structures. This phenomenon has to be precisely predicted and subsequently controlled through the changing in the blast design to minimize potential risk of blasting. The scope of this study is to predict flyrock induced by blasting through a novel approach based on the combination of imperialist competitive algorithm (ICA) and artificial neural network (ANN). For this purpose, the parameters of 113 blasting operations were accurately recorded and flyrock distances were measured for each operation. By applying the sensitivity analysis, maximum charge per delay and powder factor were determined as the most influential parameters on flyrock. In the light of this analysis, two new empirical predictors were developed to predict flyrock distance. For a comparison purpose, a predeveloped backpropagation (BP) ANN was developed and the results were compared with those of the proposed ICA-ANN model and empirical predictors. The results clearly showed the superiority of the proposed ICA-ANN model in comparison with the proposed BP-ANN model and empirical approaches.

Building blocks for correlated superconductors and magnets

DOE PAGES

Sarrao, J. L.; Ronning, F.; Bauer, E. D.; ...

2015-04-01

Recent efforts at Los Alamos to discover strongly correlated superconductors and hard ferromagnets are reviewed. While serendipity remains a principal engine of materials discovery, design principles and structural building blocks are beginning to emerge that hold potential for predictive discovery. In addition, successes over the last decade with the so-called “115” strongly correlated superconductors are summarized, and more recent efforts to translate these insights and principles to novel hard magnets are discussed. While true “materials by design” remains a distant aspiration, progress is being made in coupling empirical design principles to electronic structure simulation to accelerate and guide materials designmore » and synthesis.« less

High Performance Graphene Nano-ribbon Thermoelectric Devices by Incorporation and Dimensional Tuning of Nanopores

PubMed Central

Sharafat Hossain, Md; Al-Dirini, Feras; Hossain, Faruque M.; Skafidas, Efstratios

2015-01-01

Thermoelectric properties of Graphene nano-ribbons (GNRs) with nanopores (NPs) are explored for a range of pore dimensions in order to achieve a high performance two-dimensional nano-scale thermoelectric device. We reduce thermal conductivity of GNRs by introducing pores in them in order to enhance their thermoelectric performance. The electrical properties (Seebeck coefficient and conductivity) of the device usually degrade with pore inclusion; however, we tune the pore to its optimal dimension in order to minimize this degradation, enhancing the overall thermoelectric performance (high ZT value) of our device. We observe that the side channel width plays an important role to achieve optimal performance while the effect of pore length is less pronounced. This result is consistent with the fact that electronic conduction in GNRs is dominated along its edges. Ballistic transport regime is assumed and a semi-empirical method using Huckel basis set is used to obtain the electrical properties, while the phononic system is characterized by Tersoff empirical potential model. The proposed device structure has potential applications as a nanoscale local cooler and as a thermoelectric power generator. PMID:26083450

High Performance Graphene Nano-ribbon Thermoelectric Devices by Incorporation and Dimensional Tuning of Nanopores.

PubMed

Hossain, Md Sharafat; Al-Dirini, Feras; Hossain, Faruque M; Skafidas, Efstratios

2015-06-17

Thermoelectric properties of Graphene nano-ribbons (GNRs) with nanopores (NPs) are explored for a range of pore dimensions in order to achieve a high performance two-dimensional nano-scale thermoelectric device. We reduce thermal conductivity of GNRs by introducing pores in them in order to enhance their thermoelectric performance. The electrical properties (Seebeck coefficient and conductivity) of the device usually degrade with pore inclusion; however, we tune the pore to its optimal dimension in order to minimize this degradation, enhancing the overall thermoelectric performance (high ZT value) of our device. We observe that the side channel width plays an important role to achieve optimal performance while the effect of pore length is less pronounced. This result is consistent with the fact that electronic conduction in GNRs is dominated along its edges. Ballistic transport regime is assumed and a semi-empirical method using Huckel basis set is used to obtain the electrical properties, while the phononic system is characterized by Tersoff empirical potential model. The proposed device structure has potential applications as a nanoscale local cooler and as a thermoelectric power generator.

Structural analysis of graphene and h-BN: A molecular dynamics approach

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

Thomas, Siby; Ajith, K. M., E-mail: ajith@nitk.ac.in; Valsakumar, M. C.

2016-05-06

Classical molecular dynamics simulation is employed to analyze pair correlations in graphene and h-BN at various temperatures to explore the integrity of their respective structures. As the temperature increases, the height fluctuations in the out-of-plane direction of both graphene and h-BN are found to increase. The positional spread of atoms also increases with temperature. Thus the amplitude of the peak positions in the radial distribution function (RDF) decreases with temperature. It is found that FWHM of peaks in the RDF of h-BN is smaller as compared to those of graphene which implies that the structure of h-BN is more robustmore » as compared to that of graphene with respect to their respective empirical potential.« less

Empirical evaluation of decision support systems: Needs, definitions, potential methods, and an example pertaining to waterfowl management

USGS Publications Warehouse

Sojda, R.S.

2007-01-01

Decision support systems are often not empirically evaluated, especially the underlying modelling components. This can be attributed to such systems necessarily being designed to handle complex and poorly structured problems and decision making. Nonetheless, evaluation is critical and should be focused on empirical testing whenever possible. Verification and validation, in combination, comprise such evaluation. Verification is ensuring that the system is internally complete, coherent, and logical from a modelling and programming perspective. Validation is examining whether the system is realistic and useful to the user or decision maker, and should answer the question: “Was the system successful at addressing its intended purpose?” A rich literature exists on verification and validation of expert systems and other artificial intelligence methods; however, no single evaluation methodology has emerged as preeminent. At least five approaches to validation are feasible. First, under some conditions, decision support system performance can be tested against a preselected gold standard. Second, real-time and historic data sets can be used for comparison with simulated output. Third, panels of experts can be judiciously used, but often are not an option in some ecological domains. Fourth, sensitivity analysis of system outputs in relation to inputs can be informative. Fifth, when validation of a complete system is impossible, examining major components can be substituted, recognizing the potential pitfalls. I provide an example of evaluation of a decision support system for trumpeter swan (Cygnus buccinator) management that I developed using interacting intelligent agents, expert systems, and a queuing system. Predicted swan distributions over a 13-year period were assessed against observed numbers. Population survey numbers and banding (ringing) studies may provide long term data useful in empirical evaluation of decision support.

Evaluating the efficiency of nuclear energy policies: an empirical examination for 26 countries.

PubMed

Gozgor, Giray; Demir, Ender

2017-08-01

The decarbonization of the global economy is an urgent concern. As a potential solution, it can be important to understand the efficiency of nuclear energy policies. For this purpose, the paper analyzes whether there is a unit root in nuclear energy consumption in 26 countries and it uses the unit root tests with two endogenous (unknown) structural breaks. The paper finds that nuclear energy consumption is stationary around a level and the time trend in 25 of 26 countries and nuclear energy consumption contains a unit root only in France. The paper also discusses the potential implications of the findings.

Time-varying volatility in Malaysian stock exchange: An empirical study using multiple-volatility-shift fractionally integrated model

NASA Astrophysics Data System (ADS)

Cheong, Chin Wen

2008-02-01

This article investigated the influences of structural breaks on the fractionally integrated time-varying volatility model in the Malaysian stock markets which included the Kuala Lumpur composite index and four major sectoral indices. A fractionally integrated time-varying volatility model combined with sudden changes is developed to study the possibility of structural change in the empirical data sets. Our empirical results showed substantial reduction in fractional differencing parameters after the inclusion of structural change during the Asian financial and currency crises. Moreover, the fractionally integrated model with sudden change in volatility performed better in the estimation and specification evaluations.

Development of Alabama traffic factors for use in mechanistic-empirical pavement design.

DOT National Transportation Integrated Search

2015-02-01

The pavement engineering community is moving toward design practices that use mechanistic-empirical (M-E) approaches to the design and analysis of pavement structures. This effort is : embodied in the Mechanistic-Empirical Pavement Design Guide (MEPD...

Empirical Mining of Large Data Sets Already Helps to Solve Practical Ecological Problems; A Panoply of Working Examples (Invited)

NASA Astrophysics Data System (ADS)

Hargrove, W. W.; Hoffman, F. M.; Kumar, J.; Spruce, J.; Norman, S. P.

2013-12-01

Here we present diverse examples where empirical mining and statistical analysis of large data sets have already been shown to be useful for a wide variety of practical decision-making problems within the realm of large-scale ecology. Because a full understanding and appreciation of particular ecological phenomena are possible only after hypothesis-directed research regarding the existence and nature of that process, some ecologists may feel that purely empirical data harvesting may represent a less-than-satisfactory approach. Restricting ourselves exclusively to process-driven approaches, however, may actually slow progress, particularly for more complex or subtle ecological processes. We may not be able to afford the delays caused by such directed approaches. Rather than attempting to formulate and ask every relevant question correctly, empirical methods allow trends, relationships and associations to emerge freely from the data themselves, unencumbered by a priori theories, ideas and prejudices that have been imposed upon them. Although they cannot directly demonstrate causality, empirical methods can be extremely efficient at uncovering strong correlations with intermediate "linking" variables. In practice, these correlative structures and linking variables, once identified, may provide sufficient predictive power to be useful themselves. Such correlation "shadows" of causation can be harnessed by, e.g., Bayesian Belief Nets, which bias ecological management decisions, made with incomplete information, toward favorable outcomes. Empirical data-harvesting also generates a myriad of testable hypotheses regarding processes, some of which may even be correct. Quantitative statistical regionalizations based on quantitative multivariate similarity have lended insights into carbon eddy-flux direction and magnitude, wildfire biophysical conditions, phenological ecoregions useful for vegetation type mapping and monitoring, forest disease risk maps (e.g., sudden oak death), global aquatic ecoregion risk maps for aquatic invasives, and forest vertical structure ecoregions (e.g., using extensive LiDAR data sets). Multivariate Spatio-Temporal Clustering, which quantitatively places alternative future conditions on a common footing with present conditions, allows prediction of present and future shifts in tree species ranges, given alternative climatic change forecasts. ForWarn, a forest disturbance detection and monitoring system mining 12 years of national 8-day MODIS phenology data, has been operating since 2010, producing national maps every 8 days showing many kinds of potential forest disturbances. Forest resource managers can view disturbance maps via a web-based viewer, and alerts are issued when particular forest disturbances are seen. Regression-based decadal trend analysis showing long-term forest thrive and decline areas, and individual-based, brute-force supercomputing to map potential movement corridors and migration routes across landscapes will also be discussed. As significant ecological changes occur with increasing rapidity, such empirical data-mining approaches may be the most efficient means to help land managers find the best, most-actionable policies and decision strategies.

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model

PubMed Central

Gordon, J.A.; Freedman, B.R.; Zuskov, A.; Iozzo, R.V.; Birk, D.E.; Soslowsky, L.J.

2015-01-01

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn−/−) and biglycan-null (Bgn−/−) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. PMID:25888014

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model.

PubMed

Gordon, J A; Freedman, B R; Zuskov, A; Iozzo, R V; Birk, D E; Soslowsky, L J

2015-07-16

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn(-/-)) and biglycan-null (Bgn(-/-)) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Increasing Chemical Space Coverage by Combining Empirical and Computational Fragment Screens

PubMed Central

2015-01-01

Most libraries for fragment-based drug discovery are restricted to 1,000–10,000 compounds, but over 500,000 fragments are commercially available and potentially accessible by virtual screening. Whether this larger set would increase chemotype coverage, and whether a computational screen can pragmatically prioritize them, is debated. To investigate this question, a 1281-fragment library was screened by nuclear magnetic resonance (NMR) against AmpC β-lactamase, and hits were confirmed by surface plasmon resonance (SPR). Nine hits with novel chemotypes were confirmed biochemically with KI values from 0.2 to low mM. We also computationally docked 290,000 purchasable fragments with chemotypes unrepresented in the empirical library, finding 10 that had KI values from 0.03 to low mM. Though less novel than those discovered by NMR, the docking-derived fragments filled chemotype holes from the empirical library. Crystal structures of nine of the fragments in complex with AmpC β-lactamase revealed new binding sites and explained the relatively high affinity of the docking-derived fragments. The existence of chemotype holes is likely a general feature of fragment libraries, as calculation suggests that to represent the fragment substructures of even known biogenic molecules would demand a library of minimally over 32,000 fragments. Combining computational and empirical fragment screens enables the discovery of unexpected chemotypes, here by the NMR screen, while capturing chemotypes missing from the empirical library and tailored to the target, with little extra cost in resources. PMID:24807704

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Structural and functional hyperconnectivity within the sensorimotor system in xenomelia.

PubMed

Hänggi, Jürgen; Vitacco, Deborah A; Hilti, Leonie M; Luechinger, Roger; Kraemer, Bernd; Brugger, Peter

2017-03-01

Xenomelia is a rare condition characterized by the persistent and compulsive desire for the amputation of one or more physically healthy limbs. We highlight the neurological underpinnings of xenomelia by assessing structural and functional connectivity by means of whole-brain connectome and network analyses of regions previously implicated in empirical research in this condition. We compared structural and functional connectivity between 13 xenomelic men with matched controls using diffusion tensor imaging combined with fiber tractography and resting state functional magnetic resonance imaging. Altered connectivity in xenomelia within the sensorimotor system has been predicted. We found subnetworks showing structural and functional hyperconnectivity in xenomelia compared with controls. These subnetworks were lateralized to the right hemisphere and mainly comprised by nodes belonging to the sensorimotor system. In the connectome analyses, the paracentral lobule, supplementary motor area, postcentral gyrus, basal ganglia, and the cerebellum were hyperconnected to each other, whereas in the xenomelia-specific network analyses, hyperconnected nodes have been found in the superior parietal lobule, primary and secondary somatosensory cortex, premotor cortex, basal ganglia, thalamus, and insula. Our study provides empirical evidence of structural and functional hyperconnectivity within the sensorimotor system including those regions that are core for the reconstruction of a coherent body image. Aberrant connectivity is a common response to focal neurological damage. As exemplified here, it may affect different brain regions differentially. Due to the small sample size, our findings must be interpreted cautiously and future studies are needed to elucidate potential associations between hyperconnectivity and limb disownership reported in xenomelia.

Empirical molecular-dynamics study of diffusion in liquid semiconductors

NASA Astrophysics Data System (ADS)

Yu, W.; Wang, Z. Q.; Stroud, D.

1996-11-01

We report the results of an extensive molecular-dynamics study of diffusion in liquid Si and Ge (l-Si and l-Ge) and of impurities in l-Ge, using empirical Stillinger-Weber (SW) potentials with several choices of parameters. We use a numerical algorithm in which the three-body part of the SW potential is decomposed into products of two-body potentials, thereby permitting the study of large systems. One choice of SW parameters agrees very well with the observed l-Ge structure factors. The diffusion coefficients D(T) at melting are found to be approximately 6.4×10-5 cm2/s for l-Si, in good agreement with previous calculations, and about 4.2×10-5 and 4.6×10-5 cm2/s for two models of l-Ge. In all cases, D(T) can be fitted to an activated temperature dependence, with activation energies Ed of about 0.42 eV for l-Si, and 0.32 or 0.26 eV for two models of l-Ge, as calculated from either the Einstein relation or from a Green-Kubo-type integration of the velocity autocorrelation function. D(T) for Si impurities in l-Ge is found to be very similar to the self-diffusion coefficient of l-Ge. We briefly discuss possible reasons why the SW potentials give D(T)'s substantially lower than ab initio predictions.

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

NASA Astrophysics Data System (ADS)

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.; Jin, Wencan; Dadap, Jerry I.; Hybertsen, Mark S.; Osgood, Richard M.

2018-04-01

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n =1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energy and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. This opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.

Structural determinants for the inhibitory ligands of orotidine-5′-monophosphate decarboxylase

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

Meza-Avina, Maria Elena; Wei, Lianhu; Liu, Yan

2010-06-14

In recent years, orotidine-5{prime}-monophosphate decarboxylase (ODCase) has gained renewed attention as a drug target. As a part of continuing efforts to design novel inhibitors of ODCase, we undertook a comprehensive study of potent, structurally diverse ligands of ODCase and analyzed their structural interactions in the active site of ODCase. These ligands comprise of pyrazole or pyrimidine nucleotides including the mononucleotide derivatives of pyrazofurin, barbiturate ribonucleoside, and 5-cyanouridine, as well as, in a computational approach, 1,4-dihydropyridine-based non-nucleoside inhibitors such as nifedipine and nimodipine. All these ligands bind in the active site of ODCase exhibiting distinct interactions paving the way to designmore » novel inhibitors against this interesting enzyme. We propose an empirical model for the ligand structure for rational modifications in new drug design and potentially new lead structures.« less

Development and Validation of the Agency for Healthcare Research and Quality Measures of Potentially Preventable Emergency Department (ED) Visits: The ED Prevention Quality Indicators for General Health Conditions.

PubMed

Davies, Sheryl; Schultz, Ellen; Raven, Maria; Wang, Nancy Ewen; Stocks, Carol L; Delgado, Mucio Kit; McDonald, Kathryn M

2017-10-01

To develop and validate rates of potentially preventable emergency department (ED) visits as indicators of community health. Agency for Healthcare Research and Quality, Healthcare Cost and Utilization Project 2008-2010 State Inpatient Databases and State Emergency Department Databases. Empirical analyses and structured panel reviews. Panels of 14-17 clinicians and end users evaluated a set of ED Prevention Quality Indicators (PQIs) using a Modified Delphi process. Empirical analyses included assessing variation in ED PQI rates across counties and sensitivity of those rates to county-level poverty, uninsurance, and density of primary care physicians (PCPs). ED PQI rates varied widely across U.S. communities. Indicator rates were significantly associated with county-level poverty, median income, Medicaid insurance, and levels of uninsurance. A few indicators were significantly associated with PCP density, with higher rates in areas with greater density. A clinical and an end-user panel separately rated the indicators as having strong face validity for most uses evaluated. The ED PQIs have undergone initial validation as indicators of community health with potential for use in public reporting, population health improvement, and research. © Health Research and Educational Trust.

Using neutrons, X-rays and nuclear magnetism to determine the role of transition metal oxide inclusions on both glass structure and stability in automotive glass enamels.

PubMed

Bowron, Daniel T; Booth, Jonathan; Barrow, Nathan S; Sutton, Patricia; Johnson, Simon R

2018-05-23

Low levels of transition metal oxides in alkali borosilicate glass systems can drastically influence crystallisation and phase separation properties. We investigated the non-monotonic effect of manganese doping on suppressing crystallisation, and the influence on optical properties by iron oxide doping, in terms of local atomic structure. Structural models based on empirical potential structure refinement were generated from neutron and X-ray scattering data, and compared against multinuclear solid-state NMR. This revealed that a 2.5% manganese doping had a disruptive effect on the entire glass network, supressing crystallisation of an undesired bismuth silicate phase, and that iron species preferentially locate near borate tetrahedra. Preventing phase separation and controlling crystallisation behaviour of glass are critical to the ultimate properties of automotive glass enamels.

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

PubMed

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

Raman structural studies of the nickel electrode

NASA Technical Reports Server (NTRS)

Cornilsen, B. C.

1985-01-01

Raman spectroscopy is sensitive to empirically controlled nickel electrode structural variations, and has unique potential for structural characterization of these materials. How the structure relates to electrochemical properties is examined so that the latter can be more completely understood, controlled, and optimized. Electrodes were impregnated and cycled, and cyclic voltammetry is being used for electrochemical characterization. Structural variation was observed which has escaped detection using other methods. Structural changes are induced by: (1) cobalt doping, (2) the state of change or discharge, (3) the preparation conditions and type of buffer used, and (4) the formation process. Charged active mass has an NiOOH-type structure, agreeing with X-ray diffraction results. Discharged active mass, however, is not isostructural with beta-Ni(OH)2. Chemically prepared alpha phases are not isostructural either. A disordered structural model, containing point defects, is proposed for the cycled materials. This model explains K(+) incorporation. Band assignments were made and spectra interpreted for beta-Ni(OH)2, electrochemical NiOOH and chemically precipitated NiOOH.

On the structure of an aqueous propylene glycol solution.

PubMed

Rhys, Natasha H; Gillams, Richard J; Collins, Louise E; Callear, Samantha K; Lawrence, M Jayne; McLain, Sylvia E

2016-12-14

Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.

On the structure of an aqueous propylene glycol solution

NASA Astrophysics Data System (ADS)

Rhys, Natasha H.; Gillams, Richard J.; Collins, Louise E.; Callear, Samantha K.; Lawrence, M. Jayne; McLain, Sylvia E.

2016-12-01

Using a combination of neutron diffraction and empirical potential structure refinement computational modelling, the interactions in a 30 mol. % aqueous solution of propylene glycol (PG), which govern both the hydration and association of this molecule in solution, have been assessed. From this work it appears that PG is readily hydrated, where the most prevalent hydration interactions were found to be through both the PG hydroxyl groups but also alkyl groups typically considered hydrophobic. Hydration interactions of PG dominate the solution over PG self-self interactions and there is no evidence of more extensive association. This hydration behavior for PG in solutions suggests that the preference of PG to be hydrated rather than to be self-associated may translate into a preference for PG to bind to lipids rather than itself, providing a potential explanation for how PG is able to enhance the apparent solubility of drug molecules in vivo.

Implicit and Explicit Preference Structures in Models of Labor Supply.

ERIC Educational Resources Information Center

Dickinson, Jonathan

The study of labor supply is directed to a theoretical methodology under which the choice of the general functional form of the income-leisure preference structure may be regarded as an empirical question. The author has reviewed the common functional forms employed in empirical labor supply models and has characterized the inherent preference…

Effect of annealing on structural changes and oxygen diffusion in amorphous HfO2 using classical molecular dynamics

NASA Astrophysics Data System (ADS)

Shen, Wenqing; Kumari, Niru; Gibson, Gary; Jeon, Yoocharn; Henze, Dick; Silverthorn, Sarah; Bash, Cullen; Kumar, Satish

2018-02-01

Non-volatile memory is a promising alternative to present memory technologies. Oxygen vacancy diffusion has been widely accepted as one of the reasons for the resistive switching mechanism of transition-metal-oxide based resistive random access memory. In this study, molecular dynamics simulation is applied to investigate the diffusion coefficient and activation energy of oxygen in amorphous hafnia. Two sets of empirical potential, Charge-Optimized Many-Body (COMB) and Morse-BKS (MBKS), were considered to investigate the structural and diffusion properties at different temperatures. COMB predicts the activation energy of 0.53 eV for the temperature range of 1000-2000 K, while MBKS predicts 2.2 eV at high temperature (1600-2000 K) and 0.36 eV at low temperature (1000-1600 K). Structural changes and appearance of nano-crystalline phases with increasing temperature might affect the activation energy of oxygen diffusion predicted by MBKS, which is evident from the change in coordination number distribution and radial distribution function. None of the potentials make predictions that are fully consistent with density functional theory simulations of both the structure and diffusion properties of HfO2. This suggests the necessity of developing a better multi-body potential that considers charge exchange.

Minimum stiffness criteria for ring frame stiffeners of space launch vehicles

NASA Astrophysics Data System (ADS)

Friedrich, Linus; Schröder, Kai-Uwe

2016-12-01

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

Structure of S-shaped growth in innovation diffusion

NASA Astrophysics Data System (ADS)

Shimogawa, Shinsuke; Shinno, Miyuki; Saito, Hiroshi

2012-05-01

A basic question on innovation diffusion is why the growth curve of the adopter population in a large society is often S shaped. From macroscopic, microscopic, and mesoscopic viewpoints, the growth of the adopter population is observed as the growth curve, individual adoptions, and differences among individual adoptions, respectively. The S shape can be explained if an empirical model of the growth curve can be deduced from models of microscopic and mesoscopic structures. However, even the structure of growth curve has not been revealed yet because long-term extrapolations by proposed models of S-shaped curves are unstable and it has been very difficult to predict the long-term growth and final adopter population. This paper studies the S-shaped growth from the viewpoint of social regularities. Simple methods to analyze power laws enable us to extract the structure of the growth curve directly from the growth data of recent basic telecommunication services. This empirical model of growth curve is singular at the inflection point and a logarithmic function of time after this point, which explains the unstable extrapolations obtained using previously proposed models and the difficulty in predicting the final adopter population. Because the empirical S curve can be expressed in terms of two power laws of the regularity found in social performances of individuals, we propose the hypothesis that the S shape represents the heterogeneity of the adopter population, and the heterogeneity parameter is distributed under the regularity in social performances of individuals. This hypothesis is so powerful as to yield models of microscopic and mesoscopic structures. In the microscopic model, each potential adopter adopts the innovation when the information accumulated by the learning about the innovation exceeds a threshold. The accumulation rate of information is heterogeneous among the adopter population, whereas the threshold is a constant, which is the opposite of previously proposed models. In the mesoscopic model, flows of innovation information incoming to individuals are organized as dimorphic and partially clustered. These microscopic and mesoscopic models yield the empirical model of the S curve and explain the S shape as representing the regularities of information flows generated through a social self-organization. To demonstrate the validity and importance of the hypothesis, the models of three level structures are applied to reveal the mechanism determining and differentiating diffusion speeds. The empirical model of S curves implies that the coefficient of variation of the flow rates determines the diffusion speed for later adopters. Based on this property, a model describing the inside of information flow clusters can be given, which provides a formula interconnecting the diffusion speed, cluster populations, and a network topological parameter of the flow clusters. For two recent basic telecommunication services in Japan, the formula represents the variety of speeds in different areas and enables us to explain speed gaps between urban and rural areas and between the two services. Furthermore, the formula provides a method to estimate the final adopter population.

Theoretical Study of Diamond-Like Carbons and Nucleation of Diamond

NASA Astrophysics Data System (ADS)

Lee, Choon-Heung

Different forms of amorphous carbon and hydrocarbons with varying elastic and optical properties, hardness, density and hydrogen content exist depending on the preparation technique. The structure can vary from graphitic to diamond -like, i.e., from mainly threefold coordinated to mainly four-fold coordinated. In order to study the properties of such materials, microscopic models must be developed. These studies include the modelling of crosslinked defective graphite, diamond nucleation along the graphite edges, and diamond-like carbons. Tamor's proposed structure for diamondlike carbon consists of crosslinked graphitic regions. We studied a concrete realization of this model in which the cross -links are produced by shortening the interplanar bond lengths. The model study was accomplished with a pure rhombohedral graphite cell. For this study we used a semi-empirical potential based on Tersoff's environment-dependent potential which contains angular terms. It is enhanced by a long-range potential which describes the interplanar interactions. We found a configuration corresponding to a local minimum. More general features such as the randomness of the distribution of cross-links are needed for a realistic model. A model study of diamond/graphite interfaces was motivated by recent observations by Li and Angus. They observed a significant enhancement of diamond nucleation on the graphite edge planes with the preferential orientation relationship: {0001} _{g} | {111 }_{d}, < 1120 >_{g} | < 101>_{d}. Two possible interface structures were studied using the Tersoff potential. We found that the models have comparable low interface energies even if they contain some dangling bonds. Moreover, lower interface energies were found when the dangling bonds of the non-bonded diamond layer were satisfied with hydrogen. We have proposed a growth mechanism based on this study. Finally, we constructed realistic models of dense amorphous carbon. The WWW (introduced earlier for a-Si by Wooten, Winer and Weaire) model was the starting structure. The effects of clustering of the threefold coordinated atoms in pairs, chains, or graphitic (planar hexagonal clusters) were studied. The resulting models were relaxed using the Tersoff potential. Their electronic structures were studied using an empirical tight-binding scheme with parameters adjusted to reproduce the diamond and graphite band-structures. The models were found to have densities of ~ 3 g/cm^3 and bulk moduli of ~3.1 Mbar. Localized dangling bonds and pi - pi^* states were found within the wide gap of the WWW model consistent with optical gaps of the order of 0.5-2 eV. Hydrogen atoms were introduced to remove some of the dangling bonds. The models were found to account for the essential features of ion-beam deposited amorphous carbon and hydrogenated amorphous carbon.

Emergent Hydrological Regimes in Amazonia Determine Vegetation Productivity and Structure.

NASA Astrophysics Data System (ADS)

Ahlström, A.; Canadell, J.; Schurgers, G.; Berry, J. A.; Guan, K.; Jackson, R. B.

2016-12-01

The Amazon rain forest has a disproportionate significance for global CO2 storage and biodiversity. Earth system models (ESMs) that estimate future climate and vegetation show little agreement in simulations in Amazonia. Here we show that evapotranspiration (ET), gross primary productivity (GPP) and above ground biomass in both models and empirical data align on an emergent hydrologically determined relationship that describes a functional relationship with annual precipitation (P). The physical relationship describes the potential for plant productivity and has a breakpoint at 2000 mm annual precipitation, where the system transitions between water and radiation limitation of annual ET. While ESM GPP is generally underestimated due to a low-bias in their internally generated P, their response to annual precipitation generally matches empirical data. It is different for biomass: ESMs show some ability in capturing biomass levels in the energy-limited wet hydrological regime above 2000 mm annual precipitation but they do not fully capture the biomass structure tipping point found in empirical data at the hydrological regime breakpoint that coincide with the forest-savanna transition. This discrepancy is likely due to the relatively simple representation of disturbances, primarily fires, and vegetation dynamics found in ESMs, and implies that ESMs likely overestimate the resilience to a potential future drying of the Amazon. Future elevated CO2 may increase plant water use efficiency and shift GPP upwards, but it will not affect the breakpoint between the regimes or the susceptibility of the forest which are both determined by precipitation and its role in determining the hydrological regime. This analysis reconciles and explains the findings of many studies on the Amazon. Our results suggests that future Amazonian biomass is governed by changes in precipitation, vegetation dynamics and disturbances, none of which are well predicted and represented by ESMs. Improvements of these processes are the most pressing challenges for more accurate future predictions on the fate of the Amazon and the global tropics.

An EQT-based cDFT approach for thermodynamic properties of confined fluid mixtures

NASA Astrophysics Data System (ADS)

Motevaselian, M. H.; Aluru, N. R.

2017-04-01

We present an empirical potential-based quasi-continuum theory (EQT) to predict the structure and thermodynamic properties of confined fluid mixtures. The central idea in the EQT is to construct potential energies that integrate important atomistic details into a continuum-based model such as the Nernst-Planck equation. The EQT potentials can be also used to construct the excess free energy functional, which is required for the grand potential in the classical density functional theory (cDFT). In this work, we use the EQT-based grand potential to predict various thermodynamic properties of a confined binary mixture of hydrogen and methane molecules inside graphene slit channels of different widths. We show that the EQT-cDFT predictions for the structure, surface tension, solvation force, and local pressure tensor profiles are in good agreement with the molecular dynamics simulations. Moreover, we study the effect of different bulk compositions and channel widths on the thermodynamic properties. Our results reveal that the composition of methane in the mixture can significantly affect the ordering of molecules and thermodynamic properties under confinement. In addition, we find that graphene is selective to methane molecules.

Learning to Read Empirical Articles in General Psychology

ERIC Educational Resources Information Center

Sego, Sandra A.; Stuart, Anne E.

2016-01-01

Many students, particularly underprepared students, struggle to identify the essential information in empirical articles. We describe a set of assignments for instructing general psychology students to dissect the structure of such articles. Students in General Psychology I read empirical articles and answered a set of general, factual questions…

Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization.

PubMed Central

Henriques, D. A.; Ladbury, J. E.; Jackson, R. M.

2000-01-01

The prediction of binding energies from the three-dimensional (3D) structure of a protein-ligand complex is an important goal of biophysics and structural biology. Here, we critically assess the use of empirical, solvent-accessible surface area-based calculations for the prediction of the binding of Src-SH2 domain with a series of tyrosyl phosphopeptides based on the high-affinity ligand from the hamster middle T antigen (hmT), where the residue in the pY+ 3 position has been changed. Two other peptides based on the C-terminal regulatory site of the Src protein and the platelet-derived growth factor receptor (PDGFR) are also investigated. Here, we take into account the effects of proton linkage on binding, and test five different surface area-based models that include different treatments for the contributions to conformational change and protein solvation. These differences relate to the treatment of conformational flexibility in the peptide ligand and the inclusion of proximal ordered solvent molecules in the surface area calculations. This allowed the calculation of a range of thermodynamic state functions (deltaCp, deltaS, deltaH, and deltaG) directly from structure. Comparison with the experimentally derived data shows little agreement for the interaction of SrcSH2 domain and the range of tyrosyl phosphopeptides. Furthermore, the adoption of the different models to treat conformational change and solvation has a dramatic effect on the calculated thermodynamic functions, making the predicted binding energies highly model dependent. While empirical, solvent-accessible surface area based calculations are becoming widely adopted to interpret thermodynamic data, this study highlights potential problems with application and interpretation of this type of approach. There is undoubtedly some agreement between predicted and experimentally determined thermodynamic parameters: however, the tolerance of this approach is not sufficient to make it ubiquitously applicable. PMID:11106171

Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

PubMed

Shim, Jihyun; Mackerell, Alexander D

2011-05-01

A significant number of drug discovery efforts are based on natural products or high throughput screens from which compounds showing potential therapeutic effects are identified without knowledge of the target molecule or its 3D structure. In such cases computational ligand-based drug design (LBDD) can accelerate the drug discovery processes. LBDD is a general approach to elucidate the relationship of a compound's structure and physicochemical attributes to its biological activity. The resulting structure-activity relationship (SAR) may then act as the basis for the prediction of compounds with improved biological attributes. LBDD methods range from pharmacophore models identifying essential features of ligands responsible for their activity, quantitative structure-activity relationships (QSAR) yielding quantitative estimates of activities based on physiochemical properties, and to similarity searching, which explores compounds with similar properties as well as various combinations of the above. A number of recent LBDD approaches involve the use of multiple conformations of the ligands being studied. One of the basic components to generate multiple conformations in LBDD is molecular mechanics (MM), which apply an empirical energy function to relate conformation to energies and forces. The collection of conformations for ligands is then combined with functional data using methods ranging from regression analysis to neural networks, from which the SAR is determined. Accordingly, for effective application of LBDD for SAR determinations it is important that the compounds be accurately modelled such that the appropriate range of conformations accessible to the ligands is identified. Such accurate modelling is largely based on use of the appropriate empirical force field for the molecules being investigated and the approaches used to generate the conformations. The present chapter includes a brief overview of currently used SAR methods in LBDD followed by a more detailed presentation of issues and limitations associated with empirical energy functions and conformational sampling methods.

Transforming graphene nanoribbons into nanotubes by use of point defects.

PubMed

Sgouros, A; Sigalas, M M; Papagelis, K; Kalosakas, G

2014-03-26

Using molecular dynamics simulations with semi-empirical potentials, we demonstrate a method to fabricate carbon nanotubes (CNTs) from graphene nanoribbons (GNRs), by periodically inserting appropriate structural defects into the GNR crystal structure. We have found that various defect types initiate the bending of GNRs and eventually lead to the formation of CNTs. All kinds of carbon nanotubes (armchair, zigzag, chiral) can be produced with this method. The structural characteristics of the resulting CNTs, and the dependence on the different type and distribution of the defects, were examined. The smallest (largest) CNT obtained had a diameter of ∼ 5 Å (∼ 39 Å). Proper manipulation of ribbon edges controls the chirality of the CNTs formed. Finally, the effect of randomly distributed defects on the ability of GNRs to transform into CNTs is considered.

A universal preconditioner for simulating condensed phase materials.

PubMed

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

A universal preconditioner for simulating condensed phase materials

NASA Astrophysics Data System (ADS)

Packwood, David; Kermode, James; Mones, Letif; Bernstein, Noam; Woolley, John; Gould, Nicholas; Ortner, Christoph; Csányi, Gábor

2016-04-01

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor of two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.

Chimera states in brain networks: Empirical neural vs. modular fractal connectivity

NASA Astrophysics Data System (ADS)

Chouzouris, Teresa; Omelchenko, Iryna; Zakharova, Anna; Hlinka, Jaroslav; Jiruska, Premysl; Schöll, Eckehard

2018-04-01

Complex spatiotemporal patterns, called chimera states, consist of coexisting coherent and incoherent domains and can be observed in networks of coupled oscillators. The interplay of synchrony and asynchrony in complex brain networks is an important aspect in studies of both the brain function and disease. We analyse the collective dynamics of FitzHugh-Nagumo neurons in complex networks motivated by its potential application to epileptology and epilepsy surgery. We compare two topologies: an empirical structural neural connectivity derived from diffusion-weighted magnetic resonance imaging and a mathematically constructed network with modular fractal connectivity. We analyse the properties of chimeras and partially synchronized states and obtain regions of their stability in the parameter planes. Furthermore, we qualitatively simulate the dynamics of epileptic seizures and study the influence of the removal of nodes on the network synchronizability, which can be useful for applications to epileptic surgery.

The ACTIVE conceptual framework as a structural equation model.

PubMed

Gross, Alden L; Payne, Brennan R; Casanova, Ramon; Davoudzadeh, Pega; Dzierzewski, Joseph M; Farias, Sarah; Giovannetti, Tania; Ip, Edward H; Marsiske, Michael; Rebok, George W; Schaie, K Warner; Thomas, Kelsey; Willis, Sherry; Jones, Richard N

2018-01-01

Background/Study Context: Conceptual frameworks are analytic models at a high level of abstraction. Their operationalization can inform randomized trial design and sample size considerations. The Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) conceptual framework was empirically tested using structural equation modeling (N=2,802). ACTIVE was guided by a conceptual framework for cognitive training in which proximal cognitive abilities (memory, inductive reasoning, speed of processing) mediate treatment-related improvement in primary outcomes (everyday problem-solving, difficulty with activities of daily living, everyday speed, driving difficulty), which in turn lead to improved secondary outcomes (health-related quality of life, health service utilization, mobility). Measurement models for each proximal, primary, and secondary outcome were developed and tested using baseline data. Each construct was then combined in one model to evaluate fit (RMSEA, CFI, normalized residuals of each indicator). To expand the conceptual model and potentially inform future trials, evidence of modification of structural model parameters was evaluated by age, years of education, sex, race, and self-rated health status. Preconceived measurement models for memory, reasoning, speed of processing, everyday problem-solving, instrumental activities of daily living (IADL) difficulty, everyday speed, driving difficulty, and health-related quality of life each fit well to the data (all RMSEA < .05; all CFI > .95). Fit of the full model was excellent (RMSEA = .038; CFI = .924). In contrast with previous findings from ACTIVE regarding who benefits from training, interaction testing revealed associations between proximal abilities and primary outcomes are stronger on average by nonwhite race, worse health, older age, and less education (p < .005). Empirical data confirm the hypothesized ACTIVE conceptual model. Findings suggest that the types of people who show intervention effects on cognitive performance potentially may be different from those with the greatest chance of transfer to real-world activities.

Simulations of water nano-confined between corrugated planes

NASA Astrophysics Data System (ADS)

Zubeltzu, Jon; Artacho, Emilio

2017-11-01

Water confined to nanoscale widths in two dimensions between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water to the imposition of a periodicity in the confinement by means of computer simulations, both using empirical potentials and from first-principles. For that we propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude of the oscillation. We do it for a triangular lattice, with several values of the lattice parameter: one which is ideal for commensuration with layers of Ih ice and other values that would correspond to more realistic substrates. For the former, the phase diagram shows an overall rise of the melting temperature. The liquid maintains a bi-layer triangular structure, however, despite the fact that it is not favoured by the external periodicity. The first-principles liquid is significantly affected by the modulation in its layering and stacking even at relatively small amplitudes of the confinement modulation. Beyond some critical modulation amplitude, the hexatic phase present in flat confinement is replaced by a trilayer crystalline phase unlike any of the phases encountered for flat confinement. For more realistic lattice parameters, the liquid does not display higher tendency to freeze, but it clearly shows inhomogeneous behaviour as the strength of the rugosity increases. In spite of this expected inhomogeneity, the structural and dynamical response of the liquid is surprisingly insensitive to the external modulation. Although the first-principles calculations give a more triangular liquid than the one observed with empirical potentials (TIP4P/2005), both agree remarkably well for the main conclusions of the study.

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

Motevaselian, M. H.; Mashayak, S. Y.; Aluru, N. R., E-mail: aluru@illinois.edu

Empirical potential-based quasi-continuum theory (EQT) provides a route to incorporate atomistic detail into continuum framework such as the Nernst-Planck equation. EQT can also be used to construct a grand potential functional for classical density functional theory (cDFT). The combination of EQT and cDFT provides a simple and fast approach to predict the inhomogeneous density, potential profiles, and thermodynamic properties of confined fluids. We extend the EQT-cDFT approach to confined fluid mixtures and demonstrate it by simulating a mixture of methane and hydrogen inside slit-like channels of graphene. We show that the EQT-cDFT predictions for the structure of the confined fluidmore » mixture compare well with the molecular dynamics simulation results. In addition, our results show that graphene slit nanopores exhibit a selective adsorption of methane over hydrogen.« less

Predicting protein complex geometries with a neural network.

PubMed

Chae, Myong-Ho; Krull, Florian; Lorenzen, Stephan; Knapp, Ernst-Walter

2010-03-01

A major challenge of the protein docking problem is to define scoring functions that can distinguish near-native protein complex geometries from a large number of non-native geometries (decoys) generated with noncomplexed protein structures (unbound docking). In this study, we have constructed a neural network that employs the information from atom-pair distance distributions of a large number of decoys to predict protein complex geometries. We found that docking prediction can be significantly improved using two different types of polar hydrogen atoms. To train the neural network, 2000 near-native decoys of even distance distribution were used for each of the 185 considered protein complexes. The neural network normalizes the information from different protein complexes using an additional protein complex identity input neuron for each complex. The parameters of the neural network were determined such that they mimic a scoring funnel in the neighborhood of the native complex structure. The neural network approach avoids the reference state problem, which occurs in deriving knowledge-based energy functions for scoring. We show that a distance-dependent atom pair potential performs much better than a simple atom-pair contact potential. We have compared the performance of our scoring function with other empirical and knowledge-based scoring functions such as ZDOCK 3.0, ZRANK, ITScore-PP, EMPIRE, and RosettaDock. In spite of the simplicity of the method and its functional form, our neural network-based scoring function achieves a reasonable performance in rigid-body unbound docking of proteins. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

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

McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.

2015-09-01

In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expandmore » the number of potential types of graphene electronic devices.« less

Effects of Experimental Learning--Outcomes of an Empirical Study in the Vocational Field of Structural Engineering

ERIC Educational Resources Information Center

Bünning, Frank

2013-01-01

Pedagogic approaches to TVET offer a limited range of teaching strategies which make use of experimental learning. Thus experiments were developed for teachers of structural engineering and timber processing technologies and were subject to empirical evaluation by a researcher at the Otto-von-Guericke-University Magdeburg and Kassel University.…

Role of local network oscillations in resting-state functional connectivity.

PubMed

Cabral, Joana; Hugues, Etienne; Sporns, Olaf; Deco, Gustavo

2011-07-01

Spatio-temporally organized low-frequency fluctuations (<0.1 Hz), observed in BOLD fMRI signal during rest, suggest the existence of underlying network dynamics that emerge spontaneously from intrinsic brain processes. Furthermore, significant correlations between distinct anatomical regions-or functional connectivity (FC)-have led to the identification of several widely distributed resting-state networks (RSNs). This slow dynamics seems to be highly structured by anatomical connectivity but the mechanism behind it and its relationship with neural activity, particularly in the gamma frequency range, remains largely unknown. Indeed, direct measurements of neuronal activity have revealed similar large-scale correlations, particularly in slow power fluctuations of local field potential gamma frequency range oscillations. To address these questions, we investigated neural dynamics in a large-scale model of the human brain's neural activity. A key ingredient of the model was a structural brain network defined by empirically derived long-range brain connectivity together with the corresponding conduction delays. A neural population, assumed to spontaneously oscillate in the gamma frequency range, was placed at each network node. When these oscillatory units are integrated in the network, they behave as weakly coupled oscillators. The time-delayed interaction between nodes is described by the Kuramoto model of phase oscillators, a biologically-based model of coupled oscillatory systems. For a realistic setting of axonal conduction speed, we show that time-delayed network interaction leads to the emergence of slow neural activity fluctuations, whose patterns correlate significantly with the empirically measured FC. The best agreement of the simulated FC with the empirically measured FC is found for a set of parameters where subsets of nodes tend to synchronize although the network is not globally synchronized. Inside such clusters, the simulated BOLD signal between nodes is found to be correlated, instantiating the empirically observed RSNs. Between clusters, patterns of positive and negative correlations are observed, as described in experimental studies. These results are found to be robust with respect to a biologically plausible range of model parameters. In conclusion, our model suggests how resting-state neural activity can originate from the interplay between the local neural dynamics and the large-scale structure of the brain. Copyright © 2011 Elsevier Inc. All rights reserved.

A Simulation Study of Threats to Validity in Quasi-Experimental Designs: Interrelationship between Design, Measurement, and Analysis.

PubMed

Holgado-Tello, Fco P; Chacón-Moscoso, Salvador; Sanduvete-Chaves, Susana; Pérez-Gil, José A

2016-01-01

The Campbellian tradition provides a conceptual framework to assess threats to validity. On the other hand, different models of causal analysis have been developed to control estimation biases in different research designs. However, the link between design features, measurement issues, and concrete impact estimation analyses is weak. In order to provide an empirical solution to this problem, we use Structural Equation Modeling (SEM) as a first approximation to operationalize the analytical implications of threats to validity in quasi-experimental designs. Based on the analogies established between the Classical Test Theory (CTT) and causal analysis, we describe an empirical study based on SEM in which range restriction and statistical power have been simulated in two different models: (1) A multistate model in the control condition (pre-test); and (2) A single-trait-multistate model in the control condition (post-test), adding a new mediator latent exogenous (independent) variable that represents a threat to validity. Results show, empirically, how the differences between both the models could be partially or totally attributed to these threats. Therefore, SEM provides a useful tool to analyze the influence of potential threats to validity.

A Simulation Study of Threats to Validity in Quasi-Experimental Designs: Interrelationship between Design, Measurement, and Analysis

PubMed Central

Holgado-Tello, Fco. P.; Chacón-Moscoso, Salvador; Sanduvete-Chaves, Susana; Pérez-Gil, José A.

2016-01-01

The Campbellian tradition provides a conceptual framework to assess threats to validity. On the other hand, different models of causal analysis have been developed to control estimation biases in different research designs. However, the link between design features, measurement issues, and concrete impact estimation analyses is weak. In order to provide an empirical solution to this problem, we use Structural Equation Modeling (SEM) as a first approximation to operationalize the analytical implications of threats to validity in quasi-experimental designs. Based on the analogies established between the Classical Test Theory (CTT) and causal analysis, we describe an empirical study based on SEM in which range restriction and statistical power have been simulated in two different models: (1) A multistate model in the control condition (pre-test); and (2) A single-trait-multistate model in the control condition (post-test), adding a new mediator latent exogenous (independent) variable that represents a threat to validity. Results show, empirically, how the differences between both the models could be partially or totally attributed to these threats. Therefore, SEM provides a useful tool to analyze the influence of potential threats to validity. PMID:27378991

Practice management: observations, issues, and empirical evidence.

PubMed

Wong, H M; Braithwaite, J

2001-02-01

The primary objective of this study is to provide objective, empirical, evidence-based practice management information. This is a hitherto under-researched area of considerable interest for both the practitioner and educator. A questionnaire eliciting a mix of structured and free text responses was administered to a random sample of 480 practitioners who are members of the American Academy of Periodontology. Potential respondents not in private practice were excluded and the next listed person substituted. The results provide demographic and descriptive information about some of the main issues and problems facing practice managers, central to which are information technology (IT), financial, people management, and marketing. Human resource and marketing management appear to represent the biggest challenges. Periodontists running practices would prefer more information, development, and support in dealing with IT, finance, marketing, and people management. The empirical evidence reported here suggests that although tailored educational programs on key management issues at both undergraduate and postgraduate levels have become ubiquitous, nevertheless some respondents seek further training opportunities. Evidence-based practice management information will be invaluable to the clinician considering strategic and marketing planning, and also for those responsible for the design and conduct of predoctoral and postdoctoral programs.

Application of Tight-Binding Method in Atomistic Simulation of Covalent Materials

NASA Astrophysics Data System (ADS)

Isik, Ahmet

1994-05-01

The primary goal of this thesis is to develop and apply molecular dynamics simulation methods to elemental and binary covalent materials (Si, C, SiC) based on the tight-binding (TB) model of atomic cohesion in studies of bulk and deformation properties far from equilibrium. A second purpose is to compare results with those obtained using empirical interatomic potential functions in order to elucidate the applicability of models of interatomic interactions which do not take into account explicitly electronic structure effects. We have calculated the former by using a basis set consisting of four atomic orbitals, one for the s state and three for the p states, constructing a TB Hamiltonian in the usual Slater-Koster parametrization, and diagonalizing the Hamiltonian matrix at the origin of the Brillouin zone. For the repulsive part of the energy we employ a function in the form of inverse power law with screening which is then fitted to the bulk modulus and lattice parameter of several stable polytypes, results calculated by ab initio methods in the literature. Three types of applications have been investigated to demonstrate the utility of the present TB models and their advantages relative to empirical potentials. In the case of Si we show the calculated cohesive energy agrees to within a few percent with the ab initio local-density approximation (LDA) results. In addition, for clusters up to 10 atoms we find most of the energies and equilibrium structures to be in good agreement with LDA results (the failure of the empirical potential of Stillinger and Weber (SW) is well known). In the case of C clusters our TB model gives ring and chain structures which have been found both experimentally and by LDA calculations. In the second application we have applied our TB model of Si to investigate the core structure and energetics of partial dislocations on the glide plane and reconstruction antiphase defect (APD). For the 90^circ partial we show that the TB description gives the correct asymetric reconstruction previously found by LDA. For the 30^circ partial, TB gives better bond angles in the dislocation core. For the APD we have obtained a binding energy and activation for migration which are somewhat larger than the SW values, but the conclusion remains that APD is a low-energy defect which should be quite mobile. In the third application we formulate a simple TB model for SiC where the coefficients of the two-center integrals in Si-C interactions are taken to be simple averages of Si-Si and C-C integrals. Fitting is done on two polytypes, zincblende and rocksalt structures, and a simulated annealing procedure is used. The TB results are found in good agreement with LDA and experimental results in the cohesive energy, acoustic phonon modes, and elastic constants. (Abstract shortened by UMI.).

Modelling nutritional mutualisms: challenges and opportunities for data integration.

PubMed

Clark, Teresa J; Friel, Colleen A; Grman, Emily; Shachar-Hill, Yair; Friesen, Maren L

2017-09-01

Nutritional mutualisms are ancient, widespread, and profoundly influential in biological communities and ecosystems. Although much is known about these interactions, comprehensive answers to fundamental questions, such as how resource availability and structured interactions influence mutualism persistence, are still lacking. Mathematical modelling of nutritional mutualisms has great potential to facilitate the search for comprehensive answers to these and other fundamental questions by connecting the physiological and genomic underpinnings of mutualisms with ecological and evolutionary processes. In particular, when integrated with empirical data, models enable understanding of underlying mechanisms and generalisation of principles beyond the particulars of a given system. Here, we demonstrate how mathematical models can be integrated with data to address questions of mutualism persistence at four biological scales: cell, individual, population, and community. We highlight select studies where data has been or could be integrated with models to either inform model structure or test model predictions. We also point out opportunities to increase model rigour through tighter integration with data, and describe areas in which data is urgently needed. We focus on plant-microbe systems, for which a wealth of empirical data is available, but the principles and approaches can be generally applied to any nutritional mutualism. © 2017 John Wiley & Sons Ltd/CNRS.

Characterizing the Response of Composite Panels to a Pyroshock Induced Environment Using Design of Experiments Methodology

NASA Technical Reports Server (NTRS)

Parsons, David S.; Ordway, David; Johnson, Kenneth

2013-01-01

This experimental study seeks to quantify the impact various composite parameters have on the structural response of a composite structure in a pyroshock environment. The prediction of an aerospace structure's response to pyroshock induced loading is largely dependent on empirical databases created from collections of development and flight test data. While there is significant structural response data due to pyroshock induced loading for metallic structures, there is much less data available for composite structures. One challenge of developing a composite pyroshock response database as well as empirical prediction methods for composite structures is the large number of parameters associated with composite materials. This experimental study uses data from a test series planned using design of experiments (DOE) methods. Statistical analysis methods are then used to identify which composite material parameters most greatly influence a flat composite panel's structural response to pyroshock induced loading. The parameters considered are panel thickness, type of ply, ply orientation, and pyroshock level induced into the panel. The results of this test will aid in future large scale testing by eliminating insignificant parameters as well as aid in the development of empirical scaling methods for composite structures' response to pyroshock induced loading.

Characterizing the Response of Composite Panels to a Pyroshock Induced Environment using Design of Experiments Methodology

NASA Technical Reports Server (NTRS)

Parsons, David S.; Ordway, David O.; Johnson, Kenneth L.

2013-01-01

This experimental study seeks to quantify the impact various composite parameters have on the structural response of a composite structure in a pyroshock environment. The prediction of an aerospace structure's response to pyroshock induced loading is largely dependent on empirical databases created from collections of development and flight test data. While there is significant structural response data due to pyroshock induced loading for metallic structures, there is much less data available for composite structures. One challenge of developing a composite pyroshock response database as well as empirical prediction methods for composite structures is the large number of parameters associated with composite materials. This experimental study uses data from a test series planned using design of experiments (DOE) methods. Statistical analysis methods are then used to identify which composite material parameters most greatly influence a flat composite panel's structural response to pyroshock induced loading. The parameters considered are panel thickness, type of ply, ply orientation, and pyroshock level induced into the panel. The results of this test will aid in future large scale testing by eliminating insignificant parameters as well as aid in the development of empirical scaling methods for composite structures' response to pyroshock induced loading.

Softly-confined water cluster between freestanding graphene sheets

NASA Astrophysics Data System (ADS)

Agustian, Rifan; Akaishi, Akira; Nakamura, Jun

2018-01-01

Confined water could adopt new forms not seen in the open air, such as a two-dimensional (2D) square ice trapped between two graphene sheets [Algara-Siller et al., Nature 519, 443-445 (2015)]. In this study, in order to investigate how the flexibility of graphene affects the confined structure of water molecules, we employed classical molecular dynamics simulations with Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential to produce a soft-confining property of graphene. We discovered various solid-like structures of water molecules ranging from two-dimensional to three-dimensional structure encapsulated between two freestanding graphene sheets even at room temperature (300K). A small amount of water encapsulation leads to a layered two-dimensional form with triangular structure. On the other hand, large amounts of water molecules take a three-dimensional flying-saucer-like form with the square ice intra-layer structure. There is also a metastable state where both two-dimensional and three-dimensional structures coexist.

Vibration assessment and structural monitoring of the Basilica of Maxentius in Rome

NASA Astrophysics Data System (ADS)

Pau, Annamaria; Vestroni, Fabrizio

2013-12-01

The present paper addresses the analysis of the ambient vibrations of the Basilica of Maxentius in Rome. This monument, in the city centre and close to busy roads, was the largest vaulted structure in the Roman Empire. Today, only one aisle of the structure remains, suffering from a complex crack scenario. The ambient vibration response is used to investigate traffic induced vibration and compare this to values that could be a potential cause of structural damage according to international standards. Using output-only methods, natural frequencies and mode shapes are obtained from the response, allowing comparison with predictions made with a finite element model. Notwithstanding simplifications regarding material behavior and crack pattern in the finite element model, an agreement between numerical and experimental results is reached once selected mechanical parameters are adjusted. A knowledge of modal characteristics and the availability of an updated model may be a first step of a structural monitoring program that could reveal any decay over time in the structural integrity of the monument.

Structure Shapes Dynamics and Directionality in Diverse Brain Networks: Mathematical Principles and Empirical Confirmation in Three Species

NASA Astrophysics Data System (ADS)

Moon, Joon-Young; Kim, Junhyeok; Ko, Tae-Wook; Kim, Minkyung; Iturria-Medina, Yasser; Choi, Jee-Hyun; Lee, Joseph; Mashour, George A.; Lee, Uncheol

2017-04-01

Identifying how spatially distributed information becomes integrated in the brain is essential to understanding higher cognitive functions. Previous computational and empirical studies suggest a significant influence of brain network structure on brain network function. However, there have been few analytical approaches to explain the role of network structure in shaping regional activities and directionality patterns. In this study, analytical methods are applied to a coupled oscillator model implemented in inhomogeneous networks. We first derive a mathematical principle that explains the emergence of directionality from the underlying brain network structure. We then apply the analytical methods to the anatomical brain networks of human, macaque, and mouse, successfully predicting simulation and empirical electroencephalographic data. The results demonstrate that the global directionality patterns in resting state brain networks can be predicted solely by their unique network structures. This study forms a foundation for a more comprehensive understanding of how neural information is directed and integrated in complex brain networks.

Autonomous Vehicles Require Socio-Political Acceptance—An Empirical and Philosophical Perspective on the Problem of Moral Decision Making

PubMed Central

Bergmann, Lasse T.; Schlicht, Larissa; Meixner, Carmen; König, Peter; Pipa, Gordon; Boshammer, Susanne; Stephan, Achim

2018-01-01

Autonomous vehicles, though having enormous potential, face a number of challenges. As a computer system interacting with society on a large scale and human beings in particular, they will encounter situations, which require moral assessment. What will count as right behavior in such situations depends on which factors are considered to be both morally justified and socially acceptable. In an empirical study we investigated what factors people recognize as relevant in driving situations. The study put subjects in several “dilemma” situations, which were designed to isolate different and potentially relevant factors. Subjects showed a surprisingly high willingness to sacrifice themselves to save others, took the age of potential victims in a crash into consideration and were willing to swerve onto a sidewalk if this saved more lives. The empirical insights are intended to provide a starting point for a discussion, ultimately yielding societal agreement whereby the empirical insights should be balanced with philosophical considerations. PMID:29541023

Autonomous Vehicles Require Socio-Political Acceptance-An Empirical and Philosophical Perspective on the Problem of Moral Decision Making.

PubMed

Bergmann, Lasse T; Schlicht, Larissa; Meixner, Carmen; König, Peter; Pipa, Gordon; Boshammer, Susanne; Stephan, Achim

2018-01-01

Autonomous vehicles, though having enormous potential, face a number of challenges. As a computer system interacting with society on a large scale and human beings in particular, they will encounter situations, which require moral assessment. What will count as right behavior in such situations depends on which factors are considered to be both morally justified and socially acceptable. In an empirical study we investigated what factors people recognize as relevant in driving situations. The study put subjects in several "dilemma" situations, which were designed to isolate different and potentially relevant factors. Subjects showed a surprisingly high willingness to sacrifice themselves to save others, took the age of potential victims in a crash into consideration and were willing to swerve onto a sidewalk if this saved more lives. The empirical insights are intended to provide a starting point for a discussion, ultimately yielding societal agreement whereby the empirical insights should be balanced with philosophical considerations.

Transcranial magnetic stimulation: Improved coil design for deep brain investigation

NASA Astrophysics Data System (ADS)

Crowther, L. J.; Marketos, P.; Williams, P. I.; Melikhov, Y.; Jiles, D. C.; Starzewski, J. H.

2011-04-01

This paper reports on a design for a coil for transcranial magnetic stimulation. The design shows potential for improving the penetration depth of the magnetic field, allowing stimulation of subcortical structures within the brain. The magnetic and induced electric fields in the human head have been calculated with finite element electromagnetic modeling software and compared with empirical measurements. Results show that the coil design used gives improved penetration depth, but also indicates the likelihood of stimulation of additional tissue resulting from the spatial distribution of the magnetic field.

Systemic risk measures

NASA Astrophysics Data System (ADS)

Guerra, Solange Maria; Silva, Thiago Christiano; Tabak, Benjamin Miranda; de Souza Penaloza, Rodrigo Andrés; de Castro Miranda, Rodrigo César

2016-01-01

In this paper we present systemic risk measures based on contingent claims approach and banking sector multivariate density. We also apply network measures to analyze bank common risk exposure. The proposed measures aim to capture credit risk stress and its potential to become systemic. These indicators capture not only individual bank vulnerability, but also the stress dependency structure between them. Furthermore, these measures can be quite useful for identifying systemically important banks. The empirical results show that these indicators capture with considerable fidelity the moments of increasing systemic risk in the Brazilian banking sector in recent years.

A comparison of choline:urea and choline:oxalic acid deep eutectic solvents at 338 K

NASA Astrophysics Data System (ADS)

Gilmore, Mark; Moura, Leila M.; Turner, Adam H.; Swadźba-Kwaśny, Małgorzata; Callear, Samantha K.; McCune, Jade A.; Scherman, Oren A.; Holbrey, John D.

2018-05-01

1:2 choline chloride:urea and 1:1 choline chloride:oxalic acid deep eutectic solvents are compared at 338 K using liquid-phase neutron diffraction with H/D isotopic substitution to obtain differential neutron scattering cross sections and fitting of models to the experimental data using Empirical Potential Structure Refinement. In comparison to the previously reported study of choline chloride:urea at 303 K, we observed significant weakening and lengthening of choline-OH⋯Cl- and choline-OH⋯hydrogen-bond acceptor correlations.

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

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

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n = 1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energymore » and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. Finally, this opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.« less

Excitation and characterization of image potential state electrons on quasi-free-standing graphene

DOE PAGES

Lin, Yi; Li, Yunzhe; Sadowski, Jerzy T.; ...

2018-04-09

We investigate the band structure of image potential states in quasi-free-standing graphene (QFG) monolayer islands using angle-resolved two-photon-photoemission spectroscopy. Direct probing by low-energy electron diffraction shows that QFG is formed following oxygen intercalation into the graphene-Ir(111) interface. Despite the apparent decoupling of the monolayer graphene from the Ir substrate, we find that the binding energy of the n = 1 image potential state on these QFG islands increases by 0.17 eV, as compared to the original Gr/Ir(111) interface. We use calculations based on density-functional theory to construct an empirical, one-dimensional potential that quantitatively reproduces the image potential state binding energymore » and links the changes in the interface structure to the shift in energy. Specifically, two factors contribute comparably to this energy shift: a deeper potential well arising from the presence of intercalated oxygen adatoms and a wider potential well associated with the increase in the graphene-Ir distance. While image potential states have not been observed previously on QFG by photoemission, our paper now demonstrates that they may be strongly excited in a well-defined QFG system produced by oxygen intercalation. Finally, this opens an opportunity for studying the surface electron dynamics in QFG systems, beyond those found in typical nonintercalated graphene-on-substrate systems.« less

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

Shirkov, Leonid; Makarewicz, Jan, E-mail: jama@amu.edu.pl

An ab initio intermolecular potential energy surface (PES) has been constructed for the benzene-krypton (BKr) van der Waals (vdW) complex. The interaction energy has been calculated at the coupled cluster level of theory with single, double, and perturbatively included triple excitations using different basis sets. As a result, a few analytical PESs of the complex have been determined. They allowed a prediction of the complex structure and its vibrational vdW states. The vibrational energy level pattern exhibits a distinct polyad structure. Comparison of the equilibrium structure, the dipole moment, and vibrational levels of BKr with their experimental counterparts has allowedmore » us to design an optimal basis set composed of a small Dunning’s basis set for the benzene monomer, a larger effective core potential adapted basis set for Kr and additional midbond functions. Such a basis set yields vibrational energy levels that agree very well with the experimental ones as well as with those calculated from the available empirical PES derived from the microwave spectra of the BKr complex. The basis proposed can be applied to larger complexes including Kr because of a reasonable computational cost and accurate results.« less

Structural study of Na2O-B2O3-SiO2 glasses from molecular simulations using a polarizable force field.

PubMed

Pacaud, Fabien; Delaye, Jean-Marc; Charpentier, Thibault; Cormier, Laurent; Salanne, Mathieu

2017-10-28

Sodium borosilicate glasses Na 2 O-B 2 O 3 -SiO 2 (NBS) are complex systems from a structural point of view. Three main building units are present: tetrahedral SiO 4 and BO 4 (B IV ) and triangular BO 3 (B III ). One of the salient features of these compounds is the change of the B III /B IV ratio with the alkali concentration, which is very difficult to capture in force fields-based molecular dynamics simulations. In this work, we develop a polarizable force field that is able to reproduce the boron coordination and more generally the structure of several NBS systems in the glass and in the melt. The parameters of the potential are fitted from density functional theory calculations only, in contrast with the existing empirical potentials for NBS systems. This ensures a strong improvement on the transferability of the parameters from one composition to another. Using this new force field, the structure of NBS systems is validated against neutron diffraction and nuclear magnetic resonance experiments. A special focus is given to the distribution of B III /B IV with respect to the composition and the temperature.

Investigation of empirical damping laws for the space shuttle

NASA Technical Reports Server (NTRS)

Bernstein, E. L.

1973-01-01

An analysis of dynamic test data from vibration testing of a number of aerospace vehicles was made to develop an empirical structural damping law. A systematic attempt was made to fit dissipated energy/cycle to combinations of all dynamic variables. The best-fit laws for bending, torsion, and longitudinal motion are given, with error bounds. A discussion and estimate are made of error sources. Programs are developed for predicting equivalent linear structural damping coefficients and finding the response of nonlinearly damped structures.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

PubMed

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift.

Influence of strain on dislocation core in silicon

NASA Astrophysics Data System (ADS)

Pizzagalli, L.; Godet, J.; Brochard, S.

2018-05-01

First principles, density functional-based tight binding and semi-empirical interatomic potentials calculations are performed to analyse the influence of large strains on the structure and stability of a 60? dislocation in silicon. Such strains typically arise during the mechanical testing of nanostructures like nanopillars or nanoparticles. We focus on bi-axial strains in the plane normal to the dislocation line. Our calculations surprisingly reveal that the dislocation core structure largely depends on the applied strain, for strain levels of about 5%. In the particular case of bi-axial compression, the transformation of the dislocation to a locally disordered configuration occurs for similar strain magnitudes. The formation of an opening, however, requires larger strains, of about 7.5%. Furthermore, our results suggest that electronic structure methods should be favoured to model dislocation cores in case of large strains whenever possible.

A universal preconditioner for simulating condensed phase materials

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

Packwood, David; Ortner, Christoph, E-mail: c.ortner@warwick.ac.uk; Kermode, James, E-mail: j.r.kermode@warwick.ac.uk

2016-04-28

We introduce a universal sparse preconditioner that accelerates geometry optimisation and saddle point search tasks that are common in the atomic scale simulation of materials. Our preconditioner is based on the neighbourhood structure and we demonstrate the gain in computational efficiency in a wide range of materials that include metals, insulators, and molecular solids. The simple structure of the preconditioner means that the gains can be realised in practice not only when using expensive electronic structure models but also for fast empirical potentials. Even for relatively small systems of a few hundred atoms, we observe speedups of a factor ofmore » two or more, and the gain grows with system size. An open source Python implementation within the Atomic Simulation Environment is available, offering interfaces to a wide range of atomistic codes.« less

Structure determination in 55-atom Li-Na and Na-K nanoalloys.

PubMed

Aguado, Andrés; López, José M

2010-09-07

The structure of 55-atom Li-Na and Na-K nanoalloys is determined through combined empirical potential (EP) and density functional theory (DFT) calculations. The potential energy surface generated by the EP model is extensively sampled by using the basin hopping technique, and a wide diversity of structural motifs is reoptimized at the DFT level. A composition comparison technique is applied at the DFT level in order to make a final refinement of the global minimum structures. For dilute concentrations of one of the alkali atoms, the structure of the pure metal cluster, namely, a perfect Mackay icosahedron, remains stable, with the minority component atoms entering the host cluster as substitutional impurities. At intermediate concentrations, the nanoalloys adopt instead a core-shell polyicosahedral (p-Ih) packing, where the element with smaller atomic size and larger cohesive energy segregates to the cluster core. The p-Ih structures show a marked prolate deformation, in agreement with the predictions of jelliumlike models. The electronic preference for a prolate cluster shape, which is frustrated in the 55-atom pure clusters due to the icosahedral geometrical shell closing, is therefore realized only in the 55-atom nanoalloys. An analysis of the electronic densities of states suggests that photoelectron spectroscopy would be a sufficiently sensitive technique to assess the structures of nanoalloys with fixed size and varying compositions.

Hydration of Caffeine at High Temperature by Neutron Scattering and Simulation Studies.

PubMed

Tavagnacco, L; Brady, J W; Bruni, F; Callear, S; Ricci, M A; Saboungi, M L; Cesàro, A

2015-10-22

The solvation of caffeine in water is examined with neutron diffraction experiments at 353 K. The experimental data, obtained by taking advantage of isotopic H/D substitution in water, were analyzed by empirical potential structure refinement (EPSR) in order to extract partial structure factors and site-site radial distribution functions. In parallel, molecular dynamics (MD) simulations were carried out to interpret the data and gain insight into the intermolecular interactions in the solutions and the solvation process. The results obtained with the two approaches evidence differences in the individual radial distribution functions, although both confirm the presence of caffeine stacks at this temperature. The two approaches point to different accessibility of water to the caffeine sites due to different stacking configurations.

Structure and electrochemical behaviour of 4,7-diazaheptyl-trimethoxy-silane and vinyl-trialkoxy-silane adsorbed at silver surface

NASA Astrophysics Data System (ADS)

Łuczak, Teresa; Pankiewicz, Radosław; Łęska, Bogusława; Schroeder, Grzegorz; Bełtowska-Brzezinska, Maria; Brzezinski, Bogumil

2006-12-01

Novel self-assembled monolayers were obtained on silver using 4,7-diazaheptyl-trimethoxy-silane (SiN) and vinyl-trialkoxy-silane (SiVA, where the alkyl group is 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60-eicozaoxa- hexaheptaconan). It was shown that thus modified metal surface was protected against electrooxidation. A densely packed monolayer remained stable and did not desorb from the Ag electrode on the potential cycling. The structure of SiN and SiVA as well as their complexes with Li + cations were calculated and visualised by the AM1d and PM5 semi-empirical methods.

Empirical correspondence between trophic transfer efficiency in freshwater food webs and the slope of their size spectra.

PubMed

Mehner, Thomas; Lischke, Betty; Scharnweber, Kristin; Attermeyer, Katrin; Brothers, Soren; Gaedke, Ursula; Hilt, Sabine; Brucet, Sandra

2018-06-01

The density of organisms declines with size, because larger organisms need more energy than smaller ones and energetic losses occur when larger organisms feed on smaller ones. A potential expression of density-size distributions are Normalized Biomass Size Spectra (NBSS), which plot the logarithm of biomass independent of taxonomy within bins of logarithmic organismal size, divided by the bin width. Theoretically, the NBSS slope of multi-trophic communities is exactly -1.0 if the trophic transfer efficiency (TTE, ratio of production rates between adjacent trophic levels) is 10% and the predator-prey mass ratio (PPMR) is fixed at 10 4 . Here we provide evidence from four multi-trophic lake food webs that empirically estimated TTEs correspond to empirically estimated slopes of the respective community NBSS. Each of the NBSS considered pelagic and benthic organisms spanning size ranges from bacteria to fish, all sampled over three seasons in 1 yr. The four NBSS slopes were significantly steeper than -1.0 (range -1.14 to -1.19, with 95% CIs excluding -1). The corresponding average TTEs were substantially lower than 10% in each of the four food webs (range 1.0% to 3.6%, mean 1.85%). The overall slope merging all biomass-size data pairs from the four systems (-1.17) was almost identical to the slope predicted from the arithmetic mean TTE of the four food webs (-1.18) assuming a constant PPMR of 10 4 . Accordingly, our empirical data confirm the theoretically predicted quantitative relationship between TTE and the slope of the biomass-size distribution. Furthermore, we show that benthic and pelagic organisms can be merged into a community NBSS, but future studies have yet to explore potential differences in habitat-specific TTEs and PPMRs. We suggest that community NBSS may provide valuable information on the structure of food webs and their energetic pathways, and can result in improved accuracy of TTE-estimates. © 2018 by the Ecological Society of America.

Defining Characteristics and Potential Consequences of Caretaking Burden Among Children Living in Urban Poverty

PubMed Central

McMahon, Thomas J.; Luthar, Suniya S.

2012-01-01

Parentification of children has not been the focus of much empirical research. Consequently, this study was designed to explore the defining characteristics and potential consequences of caretaking burden in a sample of 356 children living in urban poverty. In a series of multivariate analyses, characteristics of the children, vocational-educational status of their mothers, and family structure correlated with caretaking burden more consistently than psychiatric, substance use, or personality problems in the mothers. Moreover, responsibility to care for mother, more so than responsibility for household chores or the care of siblings, consistently correlated with the psychosocial adjustment of the children. However, even the highest levels of caretaking burden were not consistently associated with clinically significant compromise of psychosocial adjustment. PMID:17535125

A Density Functional Approach to Polarizable Models: A Kim-Gordon-Response Density Interaction Potential for Molecular Simulations

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

Tabacchi, G; Hutter, J; Mundy, C

2005-04-07

A combined linear response--frozen electron density model has been implemented in a molecular dynamics scheme derived from an extended Lagrangian formalism. This approach is based on a partition of the electronic charge distribution into a frozen region described by Kim-Gordon theory, and a response contribution determined by the instaneous ionic configuration of the system. The method is free from empirical pair-potentials and the parameterization protocol involves only calculations on properly chosen subsystems. They apply this method to a series of alkali halides in different physical phases and are able to reproduce experimental structural and thermodynamic properties with an accuracy comparablemore » to Kohn-Sham density functional calculations.« less

Family Structure and Long-Term Care Insurance Purchase

PubMed Central

Van Houtven, Courtney Harold; Coe, Norma B.; Konetzka, R. Tamara

2015-01-01

While it has long been assumed that family structure and potential sources of informal care play a large role in the purchase decisions for long-term care insurance (LTCI), current empirical evidence is inconclusive. Our study examines the relationship between family structure and LTCI purchase and addresses several major limitations of the prior literature by using a long panel of data and considering modern family relationships, such as presence of stepchildren. We find that family structure characteristics from one’s own generation, particularly about one’s spouse, are associated with purchase, but that few family structure attributes from the younger generation have an influence. Family factors that may indicate future caregiver supply are negatively associated with purchase: having a coresidential child, signaling close proximity, and having a currently working spouse, signaling a healthy and able spouse, that LTC planning has not occurred yet, or that there is less need for asset protection afforded by LTCI. Dynamic factors, such as increasing wealth or turning 65, are associated with higher likelihood of LTCI purchase. PMID:25760583

Underground structures increasing the intrinsic vulnerability of urban groundwater: Sensitivity analysis and development of an empirical law based on a groundwater age modelling approach

NASA Astrophysics Data System (ADS)

Attard, Guillaume; Rossier, Yvan; Eisenlohr, Laurent

2017-09-01

In a previous paper published in Journal of Hydrology, it was shown that underground structures are responsible for a mixing process between shallow and deep groundwater that can favour the spreading of urban contamination. In this paper, the impact of underground structures on the intrinsic vulnerability of urban aquifers was investigated. A sensitivity analysis was performed using a 2D deterministic modelling approach based on the reservoir theory generalized to hydrodispersive systems to better understand this mixing phenomenon and the mixing affected zone (MAZ) caused by underground structures. It was shown that the maximal extent of the MAZ caused by an underground structure is reached approximately 20 years after construction. Consequently, underground structures represent a long-term threat for deep aquifer reservoirs. Regarding the construction process, draining operations have a major impact and favour large-scale mixing between shallow and deep groundwater. Consequently, dewatering should be reduced and enclosed as much as possible. The role played by underground structures' dimensions was assessed. The obstruction of the first aquifer layer caused by construction has the greatest influence on the MAZ. The cumulative impact of several underground structures was assessed. It was shown that the total MAZ area increases linearly with underground structures' density. The role played by materials' properties and hydraulic gradient were assessed. Hydraulic conductivity, anisotropy and porosity have the strongest influence on the development of MAZ. Finally, an empirical law was derived to estimate the MAZ caused by an underground structure in a bi-layered aquifer under unconfined conditions. This empirical law, based on the results of the sensitivity analysis developed in this paper, allows for the estimation of MAZ dimensions under known material properties and underground structure dimensions. This empirical law can help urban planners assess the area of influence of underground structures and protect urban strategic reservoirs.

Molecular dynamics simulations for mechanical properties of borophene: parameterization of valence force field model and Stillinger-Weber potential

PubMed Central

Zhou, Yu-Ping; Jiang, Jin-Wu

2017-01-01

While most existing theoretical studies on the borophene are based on first-principles calculations, the present work presents molecular dynamics simulations for the lattice dynamical and mechanical properties in borophene. The obtained mechanical quantities are in good agreement with previous first-principles calculations. The key ingredients for these molecular dynamics simulations are the two efficient empirical potentials developed in the present work for the interaction of borophene with low-energy triangular structure. The first one is the valence force field model, which is developed with the assistance of the phonon dispersion of borophene. The valence force field model is a linear potential, so it is rather efficient for the calculation of linear quantities in borophene. The second one is the Stillinger-Weber potential, whose parameters are derived based on the valence force field model. The Stillinger-Weber potential is applicable in molecular dynamics simulations of nonlinear physical or mechanical quantities in borophene. PMID:28349983

Stability and thermal behavior of molybdenum disulfide nanotubes: Nonequilibrium molecular dynamics simulation using REBO potential

NASA Astrophysics Data System (ADS)

Ahadi, Zohreh; Shadman Lakmehsari, Muhammad; Kumar Singh, Sandeep; Davoodi, Jamal

2017-12-01

This study is an attempt to perform equilibrium molecular dynamics and non-equilibrium molecular dynamics (NEMD) to evaluate the stability and thermal behavior of molybdenum disulfide nanotubes (MoS2NTs) by reactive empirical bond order potential. The stability of nanotubes, cohesive energy, isobaric heat capacity, and enthalpies of fusion in armchair and zigzag structures with different radii were calculated. The observed results illustrate that SWMoS2NTs, which have larger diameters, are more stable with more negative energy than the smaller ones. Moreover, it was found that the melting point is increased with an increase in the nanotube's radius. During the melting process, the structural transformation of nanotubes was investigated using a mean-square displacement and radial distribution function diagrams. Afterwards, using a NEMD simulation, the thermal conductivity of nanotubes with various diameters was calculated at a constant nanotube length. The obtained results show that the thermal conductivity coefficient increases with increasing nanotube diameters when the nanotube length is constant.

Development of the talent development environment questionnaire for sport.

PubMed

Martindale, Russell J J; Collins, Dave; Wang, John C K; McNeill, Michael; Lee, Kok Sonk; Sproule, John; Westbury, Tony

2010-09-01

As sporting challenge at the elite level becomes ever harder, maximizing effectiveness of the talent development pathway is crucial. Reflecting this need, this paper describes the development of the Talent Development Environment Questionnaire, which has been designed to facilitate the development of sporting potential to world-class standard. The questionnaire measures the experiences of developing athletes in relation to empirically identified "key features" of effective talent development environments. The first phase involved the generation of questionnaire items with clear content and face validity. The second phase explored the factor structure and reliability. This was carried out with 590 developing athletes through application of exploratory factor analysis with oblique rotation, principal axis factoring extraction and cronbach alpha tests. This yielded a 59-item, seven-factor structure with good internal consistency (0.616-0.978). The Talent Development Environment Questionnaire appears to be a promising psychometric instrument that can potentially be useful for education and formative review in applied settings, and as a measurement tool in talent development research.

Implementation and local calibration of the MEPDG transfer functions in Wyoming.

DOT National Transportation Integrated Search

2015-11-01

The Wyoming Department of Transportation (WYDOT) currently uses the empirical AASHTO Design for Design of : Pavement Structures as their standard pavement design procedure. WYDOT plans to transition to the Mechanistic : Empirical Pavement Design Guid...

Prediction of the Dynamic Yield Strength of Metals Using Two Structural-Temporal Parameters

NASA Astrophysics Data System (ADS)

Selyutina, N. S.; Petrov, Yu. V.

2018-02-01

The behavior of the yield strength of steel and a number of aluminum alloys is investigated in a wide range of strain rates, based on the incubation time criterion of yield and the empirical models of Johnson-Cook and Cowper-Symonds. In this paper, expressions for the parameters of the empirical models are derived through the characteristics of the incubation time criterion; a satisfactory agreement of these data and experimental results is obtained. The parameters of the empirical models can depend on some strain rate. The independence of the characteristics of the incubation time criterion of yield from the loading history and their connection with the structural and temporal features of the plastic deformation process give advantage of the approach based on the concept of incubation time with respect to empirical models and an effective and convenient equation for determining the yield strength in a wider range of strain rates.

Stochastic Formalism for Thermally Driven Distribution Frontier: A Nonempirical Approach to the Potential Escape Problem

NASA Astrophysics Data System (ADS)

Akashi, Ryosuke; Nagornov, Yuri S.

2018-06-01

We develop a non-empirical scheme to search for the minimum-energy escape paths from the minima of the potential surface to unknown saddle points nearby. A stochastic algorithm is constructed to move the walkers up the surface through the potential valleys. This method employs only the local gradient and diagonal part of the Hessian matrix of the potential. An application to a two-dimensional model potential is presented to demonstrate the successful finding of the paths to the saddle points. The present scheme could serve as a starting point toward first-principles simulation of rare events across the potential basins free from empirical collective variables.

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

PubMed

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

2018-01-01

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

Development of 7TM receptor-ligand complex models using ligand-biased, semi-empirical helix-bundle repacking in torsion space: application to the agonist interaction of the human dopamine D2 receptor.

PubMed

Malo, Marcus; Persson, Ronnie; Svensson, Peder; Luthman, Kristina; Brive, Lars

2013-03-01

Prediction of 3D structures of membrane proteins, and of G-protein coupled receptors (GPCRs) in particular, is motivated by their importance in biological systems and the difficulties associated with experimental structure determination. In the present study, a novel method for the prediction of 3D structures of the membrane-embedded region of helical membrane proteins is presented. A large pool of candidate models are produced by repacking of the helices of a homology model using Monte Carlo sampling in torsion space, followed by ranking based on their geometric and ligand-binding properties. The trajectory is directed by weak initial restraints to orient helices towards the original model to improve computation efficiency, and by a ligand to guide the receptor towards a chosen conformational state. The method was validated by construction of the β1 adrenergic receptor model in complex with (S)-cyanopindolol using bovine rhodopsin as template. In addition, models of the dopamine D2 receptor were produced with the selective and rigid agonist (R)-N-propylapomorphine ((R)-NPA) present. A second quality assessment was implemented by evaluating the results from docking of a library of 29 ligands with known activity, which further discriminated between receptor models. Agonist binding and recognition by the dopamine D2 receptor is interpreted using the 3D structure model resulting from the approach. This method has a potential for modeling of all types of helical transmembrane proteins for which a structural template with sequence homology sufficient for homology modeling is not available or is in an incorrect conformational state, but for which sufficient empirical information is accessible.

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow.

PubMed

Whittaker, Kerry A; Rynearson, Tatiana A

2017-03-07

The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations ( F ST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a , a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time.

Multiple ligand-binding modes in bacterial R67 dihydrofolate reductase

NASA Astrophysics Data System (ADS)

Alonso, Hernán; Gillies, Malcolm B.; Cummins, Peter L.; Bliznyuk, Andrey A.; Gready, Jill E.

2005-03-01

R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor structural homology with the chromosomal DHFR. It presents a highly symmetrical toroidal structure, where four identical monomers contribute to the unique central active-site pore. Two reactants (dihydrofolate, DHF), two cofactors (NADPH) or one of each (R67•DHF•NADPH) can be found simultaneously within the active site, the last one being the reactive ternary complex. As the positioning of the ligands has proven elusive to empirical determination, we addressed the problem from a theoretical perspective. Several potential structures of the ternary complex were generated using the docking programs AutoDock and FlexX. The variability among the final poses, many of which conformed to experimental data, prompted us to perform a comparative scoring analysis and molecular dynamics simulations to assess the stability of the complexes. Analysis of ligand-ligand and ligand-protein interactions along the 4 ns trajectories of eight different structures allowed us to identify important inter-ligand contacts and key protein residues. Our results, combined with published empirical data, clearly suggest that multipe binding modes of the ligands are possible within R67 DHFR. While the pterin ring of DHF and the nicotinamide ring of NADPH assume a stacked endo-conformation at the centre of the pore, probably assisted by V66, Q67 and I68, the tails of the molecules extend towards opposite ends of the cavity, adopting multiple configurations in a solvent rich-environment where hydrogen-bond interactions with K32 and Y69 may play important roles.

[The leadership style as a mitigator of the insurgence of mobbing risk. Results from an empirical research on Italian nurses].

PubMed

Caporale, Loretta; Palese, Alvisa; Bortoluzzi, Guido

2012-01-01

The influence of the organizational factors in mobbing onset, is supported by several studies. The leadership style is considered as one of its main antecedents. To investigate the relation between the leadership style adopted by the Nurse Coordinator and the diffusion of "negative actions", main indicator and antecedent of mobbing onset. Empirical study that involved 175 nurses and obstetricians of a Public Hospital Corporation in North Italy. Data has been collected via a semi-structured and anonymous questionnaire. The results confirm the hypothesis that the adoption of a non-collaborative leadership style goes with a greater diffusion of "negative actions" among the nurses. To intervene on organizational variables, such as the leadership style, allows to reduce the working unease and, therefore, the factors which are linked to it and which bear on the provided relief quality. The results of this study underline the Nurse Coordinator role in preventing and thwarting the onset of "negative actions", which are a potential source for mobbing onset.

The moral sense of humanitarian actors: an empirical exploration.

PubMed

Rességuier, Anaïs

2018-01-01

This paper examines humanitarianism's moral positioning above private and political interests to save lives and alleviate suffering. It does not aim to assess the legitimacy of this stance, but rather to probe the way in which humanitarian actors relate to this moral dimension in their everyday work. It investigates empirically humanitarian ethics from the perspective of humanitarian actors, drawing on interviews conducted in Beirut, Lebanon, in 2014. As it is exploratory, three key conceptual innovations were required. The first of these is the introduction of the tools developed to consider a neglected reality: humanitarian actors' 'moral sense' vis-à-vis the humanitarian sector's 'moral culture'. Second, the study shows how the sector's moral culture is structured around the notion of 'concern for persons in need'. Third, it analyses the way in which the sector and its actors handle the asymmetrical relationships encountered daily. Ultimately this paper seeks to valorise humanitarian actors' creativity in their common practices and explore potential challenges to it. © 2018 The Author(s). Disasters © Overseas Development Institute, 2018.

Development of hypersonic engine seals: Flow effects of preload and engine pressures

NASA Technical Reports Server (NTRS)

Cai, Zhong; Mutharasan, Rajakkannu; Ko, Frank K.; Steinetz, Bruce M.

1993-01-01

A new type of engine seal is being developed to meet the needs of advanced hypersonic engines. A seal braided of emerging high temperature ceramic fibers comprised of a sheath-core construction was selected for study based on its low leakage rates. Flexible, low-leakage, high temperature seals are required to seal the movable engine panels of advanced ramjet-scramjet engines either preventing potentially dangerous leakage into backside engine cavities or limiting the purge coolant flow rates through the seals. To predict the leakage through these flexible, porous seal structures as a function of preload and engine pressures, new analytical flow models are required. An empirical leakage resistance/preload model is proposed to characterize the observed decrease in leakage with increasing preload. Empirically determined compression modulus and preload factor are used to correlate experimental leakage data for a wide range of seal architectures. Good agreement between measured and predicted values are observed over a range of engine pressures and seal preloads.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04344e Click here for additional data file.

PubMed Central

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1–0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural change may be due to force field deficiencies. The overall accuracy of the empirical methods are slightly improved by annealing the CHARMM structure with ProCS15, which may suggest that the minor structural changes introduced by ProCS15-based annealing improves the accuracy of the protein structures. Having established that QM-based chemical shift prediction can deliver the same accuracy as empirical shift predictors we hope this can help increase the accuracy of related approaches such as QM/MM or linear scaling approaches or interpreting protein structural dynamics from QM-derived chemical shift. PMID:28451325

Base course resilient modulus for the mechanistic-empirical pavement design guide.

DOT National Transportation Integrated Search

2011-11-01

The Mechanistic-Empirical Pavement Design Guidelines (MEPDG) recommend use of modulus in lieu of structural number for base layer thickness design. Modulus is nonlinear with respect to effective confinement stress, loading strain, and moisture. For d...

Calibration of the MEPDG transfer functions in Georgia : task order 2 report.

DOT National Transportation Integrated Search

2015-03-28

The Georgia Department of Transportation (GDOT) currently uses the empirical 1972 AASHTO Interim Guide for : Design of Pavement Structures as their standard pavement design procedure. However, GDOT plans to transition to the : Mechanistic Empirical P...

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters

NASA Astrophysics Data System (ADS)

Hey, John C.; Doyle, Emily J.; Chen, Yuting; Johnston, Roy L.

2018-03-01

We present putative global minima for the micro-hydrated sulfite SO32-(H2O)N and chlorate ClO32(H2O)N systems in the range 3≤N≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤N≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems. This article is part of the theme issue `Modern theoretical chemistry'.

Isomers and energy landscapes of micro-hydrated sulfite and chlorate clusters.

PubMed

Hey, John C; Doyle, Emily J; Chen, Yuting; Johnston, Roy L

2018-03-13

We present putative global minima for the micro-hydrated sulfite SO 3 2- (H 2 O) N and chlorate ClO 3 - (H 2 O) N systems in the range 3≤ N ≤15 found using basin-hopping global structure optimization with an empirical potential. We present a structural analysis of the hydration of a large number of minimized structures for hydrated sulfite and chlorate clusters in the range 3≤ N ≤50. We show that sulfite is a significantly stronger net acceptor of hydrogen bonding within water clusters than chlorate, completely suppressing the appearance of hydroxyl groups pointing out from the cluster surface (dangling OH bonds), in low-energy clusters. We also present a qualitative analysis of a highly explored energy landscape in the region of the global minimum of the eight water hydrated sulfite and chlorate systems.This article is part of the theme issue 'Modern theoretical chemistry'. © 2018 The Authors.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals.

PubMed

Wilson, S R; Mendelev, M I

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

NASA Astrophysics Data System (ADS)

Wilson, S. R.; Mendelev, M. I.

2016-04-01

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, we found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).

The atomic scale structure of CXV carbon: wide-angle x-ray scattering and modeling studies.

PubMed

Hawelek, L; Brodka, A; Dore, J C; Honkimaki, V; Burian, A

2013-11-13

The disordered structure of commercially available CXV activated carbon produced from finely powdered wood-based carbon has been studied using the wide-angle x-ray scattering technique, molecular dynamics and density functional theory simulations. The x-ray scattering data has been converted to the real space representation in the form of the pair correlation function via the Fourier transform. Geometry optimizations using classical molecular dynamics based on the reactive empirical bond order potential and density functional theory at the B3LYP/6-31g* level have been performed to generate nanoscale models of CXV carbon consistent with the experimental data. The final model of the structure comprises four chain-like and buckled graphitic layers containing a small percentage of four-fold coordinated atoms (sp(3) defects) in each layer. The presence of non-hexagonal rings in the atomic arrangement has been also considered.

Faces of integration.

PubMed

Williams, Paul; Sullivan, Helen

2009-12-22

Two central themes permeate this paper-the interplay between structure and agency in integration processes and the extent to which this is mediated through sensemaking by individual actors. The empirical base for the paper is provided by case study research from Wales which draws on examples of different types of integration in health and social care. The individual case studies highlight different interpretations of integration set against a background of the resources involved, processes employed and outcomes achieved. A wide ranging discussion exposes the complex interplay and dynamics between structural factors and the manner in which they enable or constrain integration, and individual actors realising their potential agency through leadership, professionalism and boundary spanning to influence outcomes. The importance of structure and agency complementing each other to determine effective integration is emphasised, together with the scope that is available for interpretation and meaning by individual actors within the contested discourse of integration.

Faces of integration

PubMed Central

Williams, Paul; Sullivan, Helen

2009-01-01

Theme Two central themes permeate this paper—the interplay between structure and agency in integration processes and the extent to which this is mediated through sensemaking by individual actors. Case study The empirical base for the paper is provided by case study research from Wales which draws on examples of different types of integration in health and social care. The individual case studies highlight different interpretations of integration set against a background of the resources involved, processes employed and outcomes achieved. Discussion A wide ranging discussion exposes the complex interplay and dynamics between structural factors and the manner in which they enable or constrain integration, and individual actors realising their potential agency through leadership, professionalism and boundary spanning to influence outcomes. The importance of structure and agency complementing each other to determine effective integration is emphasised, together with the scope that is available for interpretation and meaning by individual actors within the contested discourse of integration. PMID:20087420

Clinical and pharmacokinetic drug evaluation of delafloxacin for the treatment of acute bacterial skin and skin structure infections.

PubMed

Bassetti, Matteo; Pecori, Davide; Cojutti, Piergiorgio; Righi, Elda; Pea, Federico

2017-11-01

In the era of multi-drug resistant pathogens, the adequate treatment of skin and skin structure infections remains a challenge for clinicians. Delafloxacin, with its broad spectrum against Gram-positive, Gram-negative and anaerobic organisms, represents a new therapeutic option in this setting, especially when coverage of methicillin-resistant Staphylococcus aureus is required in the empirical or targeted approach. Areas covered: In this drug evaluation, the Authors have reviewed the pharmacokinetic and pharmacodynamic characteristics of delafloxacin. In addition, recent data on clinical efficacy and safety from clinical trials have been included. Expert opinion: Delafloxacin represents an attractive therapeutic option due to a broad antimicrobial and favorable pharmacokinetic and pharmacodynamic profile. Several in vitro studies have demonstrated the low potential for resistance selection if used in empirical regimens. Delafloxacin is a promising candidate for the treatment of Gram-positive infections, especially if co-infection with other pathogens is suspected. This is because of the very low MIC of the agent for Gram-positive (including MRSA) and anaerobic bacteria and because of the wide spectrum of activity against Gram-negative organisms. For these interesting microbiological and PK/PD characteristics we expect future uses of this drug in other indications such as diabetic foot infection, osteomyelitis, prosthetic joint infections, abdominal infections and central nervous system infections.

Measuring 3D point configurations in pictorial space

PubMed Central

Wagemans, Johan; van Doorn, Andrea J; Koenderink, Jan J

2011-01-01

We propose a novel method to probe the depth structure of the pictorial space evoked by paintings. The method involves an exocentric pointing paradigm that allows one to find the slope of the geodesic connection between any pair of points in pictorial space. Since the locations of the points in the picture plane are known, this immediately yields the depth difference between the points. A set of depth differences between all pairs of points from an N-point (N > 2) configuration then yields the configuration in depth up to an arbitrary depth offset. Since an N-point configuration implies N(N−1) (ordered) pairs, the number of observations typically far exceeds the number of inferred depths. This yields a powerful check on the geometrical consistency of the results. We report that the remaining inconsistencies are fully accounted for by the spread encountered in repeated observations. This implies that the concept of ‘pictorial space’ indeed has an empirical significance. The method is analyzed and empirically verified in considerable detail. We report large quantitative interobserver differences, though the results of all observers agree modulo a certain affine transformation that describes the basic cue ambiguities. This is expected on the basis of a formal analysis of monocular optical structure. The method will prove useful in a variety of potential applications. PMID:23145227

Network structure and concentration fluctuations in a series of elemental, binary, and tertiary liquids and glasses.

PubMed

Soper, Alan K

2010-10-13

Liquids and glasses continue to produce a lively debate about the nature of the disordered structure in these materials, and whether it is driven by longer range concentration or density fluctuations. One factor often lacking in these studies is an overview of a wide range of structures from which common features of and differences between materials can be identified. Here I examine the structure of a wide range of chain and network, elemental, binary and tertiary liquids and glasses, using available x-ray and neutron diffraction data and combining them with empirical potential structure refinement. Calculation of the Bhatia-Thornton number-number and concentration-concentration structure factors and distribution functions highlights common structural motifs that run through many of the series. It is found that the greatest structural overlap occurs where the nearest-neighbour and second-neighbour coordination numbers are similar for different materials. As these coordination numbers increase, so the structures undergo a sequence of characteristic changes involving increasingly bent bond angle distributions and increased packing fractions. In these regards liquid and amorphous phosphorus appear to be in a structural class of their own, combining both chain-like and network-like characteristics.

Perceived sexual harassment at work: meta-analysis and structural model of antecedents and consequences.

PubMed

Topa Cantisano, Gabriela; Morales Domínguez, J F; Depolo, Marco

2008-05-01

Although sexual harassment has been extensively studied, empirical research has not led to firm conclusions about its antecedents and consequences, both at the personal and organizational level. An extensive literature search yielded 42 empirical studies with 60 samples. The matrix correlation obtained through meta-analytic techniques was used to test a structural equation model. Results supported the hypotheses regarding organizational environmental factors as main predictors of harassment.

Assessing musical skills in autistic children who are not savants.

PubMed

Heaton, Pamela

2009-05-27

Descriptions of autistic musical savants suggest that they possess extraordinary skills within the domain. However, until recently little was known about the musical skills and potential of individuals with autism who are not savants. The results from these more recent studies investigating music perception, cognition and learning in musically untrained children with autism have revealed a pattern of abilities that are either enhanced or spared. For example, increased sensitivity to musical pitch and timbre is frequently observed, and studies investigating perception of musical structure and emotions have consistently failed to reveal deficits in autism. While the phenomenon of the savant syndrome is of considerable theoretical interest, it may have led to an under-consideration of the potential talents and skills of that vast majority of autistic individuals, who do not meet savant criteria. Data from empirical studies show that many autistic children possess musical potential that can and should be developed.

Assessing musical skills in autistic children who are not savants

PubMed Central

Heaton, Pamela

2009-01-01

Descriptions of autistic musical savants suggest that they possess extraordinary skills within the domain. However, until recently little was known about the musical skills and potential of individuals with autism who are not savants. The results from these more recent studies investigating music perception, cognition and learning in musically untrained children with autism have revealed a pattern of abilities that are either enhanced or spared. For example, increased sensitivity to musical pitch and timbre is frequently observed, and studies investigating perception of musical structure and emotions have consistently failed to reveal deficits in autism. While the phenomenon of the savant syndrome is of considerable theoretical interest, it may have led to an under-consideration of the potential talents and skills of that vast majority of autistic individuals, who do not meet savant criteria. Data from empirical studies show that many autistic children possess musical potential that can and should be developed. PMID:19528029

Melt-growth dynamics in CdTe crystals

DOE PAGES

Zhou, X. W.; Ward, D. K.; Wong, B. M.; ...

2012-06-01

We use a new, quantum-mechanics-based bond-order potential (BOP) to reveal melt growth dynamics and fine scale defect formation mechanisms in CdTe crystals. Previous molecular dynamics simulations of semiconductors have shown qualitatively incorrect behavior due to the lack of an interatomic potential capable of predicting both crystalline growth and property trends of many transitional structures encountered during the melt → crystal transformation. Here, we demonstrate successful molecular dynamics simulations of melt growth in CdTe using a BOP that significantly improves over other potentials on property trends of different phases. Our simulations result in a detailed understanding of defect formation during themore » melt growth process. Equally important, we show that the new BOP enables defect formation mechanisms to be studied at a scale level comparable to empirical molecular dynamics simulation methods with a fidelity level approaching quantum-mechanical methods.« less

Violent Crime in Post-Civil War Guatemala: Causes and Policy Implications

DTIC Science & Technology

2015-03-01

on field research and case studies in Honduras, Bolivia, and Argentina. Bailey’s Security Trap theory is comprehensive in nature and derived from... research question. The second phase uses empirical data and comparative case studies to validate or challenge selected arguments that potentially...Contextual relevancy, historical inference, Tools: Empirics and case conclusions empirical data studies Figme2. Sample Research Methodology E

Physician practice management organizations: their prospects and performance.

PubMed

Conrad, D A; Koos, S; Harney, A; Haase, M

1999-09-01

As physician organizations adapt their incentives, processes, and structures to accommodate the demands of an increasingly competitive and performance-sensitive external environment, the development of more effective administrative and managerial mechanisms becomes critical to success. The emergence of physician practice management companies (PPMCs) represents a potentially positive step for physician practices seeking increased economies of scale through consolidation, as well as enhanced access to financial capital. However, economic and finance theory, coupled with some empirical "arithmetic" regarding the financial and operational performance of leading publicly traded PPMCs, suggest caution in one's forecasts of the future prospects for these evolving corporate forms.

Evidence-Based Best Practices for Outpatient Management of Warfarin.

PubMed

Rose, Adam J; Vaiana, Mary

2018-06-01

Many best practices have been described for organizing a clinic to manage warfarin. Although these practices may have face validity, they may not be based on empirical analysis. Here, we describe our decade-long effort to apply the Structure-Process-Outcome model of quality measurement as a basis for measuring and improving outpatient warfarin management in the Veterans Health Administration. The purpose of the article is to raise awareness of this body of work with pharmacists who could potentially incorporate the findings of this work into their own practice settings. We conclude with concrete suggestions for immediate implementation in clinical settings.

Development of traffic data input resources for the mechanistic empirical pavement design process.

DOT National Transportation Integrated Search

2011-12-12

The Mechanistic-Empirical Pavement Design Guide (MEPDG) for New and Rehabilitated Pavement Structures uses : nationally based data traffic inputs and recommends that state DOTs develop their own site-specific and regional : values. To support the MEP...

Development of local calibration factors and design criteria values for mechanistic-empirical pavement design.

DOT National Transportation Integrated Search

2015-08-01

A mechanistic-empirical (ME) pavement design procedure allows for analyzing and selecting pavement structures based : on predicted distress progression resulting from stresses and strains within the pavement over its design life. The Virginia : Depar...

Local structure of molten AuGa 2 under pressure: Evidence for coordination change and planetary implications

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

Kalkan, Bora; Godwal, Budhiram; Raju, Selva Vennila

In situ x-ray diffraction measurements and inverse Monte Carlo simulations of pair distribution functions were used to characterize the local structure of molten AuGa 2 up to 16 GPa and 940 K. Our results document systematic changes in liquid structure due to a combination of bond compression and coordination increase. Empirical potential structure refinement shows the first-neighbor coordination of Ga around Au and of Au around Ga to increase from about 8 to 10 and 4 to 5, respectively between 0 and 16 GPa, and the inferred changes in liquid structure can explain the observed melting-point depression of AuGa2 upmore » to 5 GPa. As intermetallic AuGa 2 is an analogue for metallic SiO 2 at much higher pressures, our results imply that structural changes documented for non-metallic silicate melts below 100 GPa are followed by additional coordination changes in the metallic state at pressures in the 0.2–1 TPa range achieved inside large planets.« less

Local structure of molten AuGa 2 under pressure: Evidence for coordination change and planetary implications

DOE PAGES

Kalkan, Bora; Godwal, Budhiram; Raju, Selva Vennila; ...

2018-05-01

In situ x-ray diffraction measurements and inverse Monte Carlo simulations of pair distribution functions were used to characterize the local structure of molten AuGa 2 up to 16 GPa and 940 K. Our results document systematic changes in liquid structure due to a combination of bond compression and coordination increase. Empirical potential structure refinement shows the first-neighbor coordination of Ga around Au and of Au around Ga to increase from about 8 to 10 and 4 to 5, respectively between 0 and 16 GPa, and the inferred changes in liquid structure can explain the observed melting-point depression of AuGa2 upmore » to 5 GPa. As intermetallic AuGa 2 is an analogue for metallic SiO 2 at much higher pressures, our results imply that structural changes documented for non-metallic silicate melts below 100 GPa are followed by additional coordination changes in the metallic state at pressures in the 0.2–1 TPa range achieved inside large planets.« less

Relaxation of structural parameters and potential coefficients of nonrigid molecules. General symmetry properties and application to ab initio study of 1,2-difluoroethane

NASA Astrophysics Data System (ADS)

Ha, T.-K.; Günthard, H. H.

1989-07-01

Structural parameters like bond length, bond angles, etc. and harmonic and anharmonic potential coefficients of molecules with internal rotation, inversion or puckering modes are generally assumed to vary with the large amplitude internal coordinates in a concerted manner (relaxation). Taking the coordinate vectors of the nuclear configuration of semirigid molecules with relaxation (SRMRs) as functions of relaxing structural parameters and finite amplitude internal coordinate, the isometric group of SRMRs is discussed and the irreducible representations of the latter are shown to classify into engendered and nonengendered ones. On this basis a concept of equivalent sets of nuclei SRMRs is introduced and an analytical expression is derived which defines the most general functional form of relaxation increments of all common types of structural parameters compatible with isometric symmetry. This formula is shown to be a close analog of an analytical expression defining the transformations induced by the isometric group of infinitesimal internal coordinates associated with typical structural parameters. Furthermore analogous formulae are given for the most general form of the relaxation of harmonic potential coefficients as a function of finite internal coordinates. The general relations are illustrated by ab initio calculations for 1,2-difluoroethane at the MP4/DZP//HF/4-31G* level for twelve values of the dihedral angle including complete structure optimization. The potential to internal rotation is found to be in essential agreement with experimentally derived data. For a complete set of ab initio structural parameters the associated relaxation increments are represented as Fourier series, which are shown to confirm the form predicted by the general formula and the isometric group of 1,2-difluoroethane. Depending on type of the structural parameters (bond length, bond angles, etc.), the associated relaxation increments appear to follow some simple rules. Similarly a complete set of harmonic potential coefficients derived from the ab initio calculations will be analyzed in terms of Fourier series and shown to conform to the symmetry requirements of the symmetry group. Relaxation of potential coefficients is found to amount to up to ≈5% for some types of diagonal and nondiagonal terms and to reflect certain "topological" rules similar to regularities of harmonic potential constants of quasi-rigid molecules found in empirical determinations of valence force fields.

Flood loss modelling with FLF-IT: a new flood loss function for Italian residential structures

NASA Astrophysics Data System (ADS)

Hasanzadeh Nafari, Roozbeh; Amadio, Mattia; Ngo, Tuan; Mysiak, Jaroslav

2017-07-01

The damage triggered by different flood events costs the Italian economy millions of euros each year. This cost is likely to increase in the future due to climate variability and economic development. In order to avoid or reduce such significant financial losses, risk management requires tools which can provide a reliable estimate of potential flood impacts across the country. Flood loss functions are an internationally accepted method for estimating physical flood damage in urban areas. In this study, we derived a new flood loss function for Italian residential structures (FLF-IT), on the basis of empirical damage data collected from a recent flood event in the region of Emilia-Romagna. The function was developed based on a new Australian approach (FLFA), which represents the confidence limits that exist around the parameterized functional depth-damage relationship. After model calibration, the performance of the model was validated for the prediction of loss ratios and absolute damage values. It was also contrasted with an uncalibrated relative model with frequent usage in Europe. In this regard, a three-fold cross-validation procedure was carried out over the empirical sample to measure the range of uncertainty from the actual damage data. The predictive capability has also been studied for some sub-classes of water depth. The validation procedure shows that the newly derived function performs well (no bias and only 10 % mean absolute error), especially when the water depth is high. Results of these validation tests illustrate the importance of model calibration. The advantages of the FLF-IT model over other Italian models include calibration with empirical data, consideration of the epistemic uncertainty of data, and the ability to change parameters based on building practices across Italy.

A main sequence for quasars

NASA Astrophysics Data System (ADS)

Marziani, Paola; Dultzin, Deborah; Sulentic, Jack W.; Del Olmo, Ascensión; Negrete, C. A.; Martínez-Aldama, Mary L.; D'Onofrio, Mauro; Bon, Edi; Bon, Natasa; Stirpe, Giovanna M.

2018-03-01

The last 25 years saw a major step forward in the analysis of optical and UV spectroscopic data of large quasar samples. Multivariate statistical approaches have led to the definition of systematic trends in observational properties that are the basis of physical and dynamical modeling of quasar structure. We discuss the empirical correlates of the so-called “main sequence” associated with the quasar Eigenvector 1, its governing physical parameters and several implications on our view of the quasar structure, as well as some luminosity effects associated with the virialized component of the line emitting regions. We also briefly discuss quasars in a segment of the main sequence that includes the strongest FeII emitters. These sources show a small dispersion around a well-defined Eddington ratio value, a property which makes them potential Eddington standard candles.

Ab initio and empirical energy landscapes of (MgF2)n clusters (n = 3, 4).

PubMed

Neelamraju, S; Schön, J C; Doll, K; Jansen, M

2012-01-21

We explore the energy landscape of (MgF(2))(3) on both the empirical and ab initio level using the threshold algorithm. In order to determine the energy landscape and the dynamics of the trimer we investigate not only the stable isomers but also the barriers separating these isomers. Furthermore, we study the probability flows in order to estimate the stability of all the isomers found. We find that there is reasonable qualitative agreement between the ab initio and empirical potential, and important features such as sub-basins and energetic barriers follow similar trends. However, we observe that the energies are systematically different for the less compact clusters, when comparing empirical and ab initio energies. Since the underlying motivation of this work is to identify the possible clusters present in the gas phase during a low-temperature atom beam deposition synthesis of MgF(2), we employ the same procedure to additionally investigate the energy landscape of the tetramer. For this case, however, we use only the empirical potential.

State of the art for ab initio vs empirical potentials for HeH+ (2e-), BeH+ (4e-), BeH (5e-), Li2 (6e-) and BH (6e-)

NASA Astrophysics Data System (ADS)

Dattani, Nike

For large internuclear distances, the potential energy between two atoms is known analytically, based on constants that are calculated from atomic ab initio rather than molecular ab initio. This analytic form can be built into models for molecular potentials that are fitted to spectroscopic data. Such empirical potentials constitute the most accurate molecular potentials known. For HeH+, and BeH+, the long-range form of the potential is based only on the polarizabilities for He and H respectively, for which we have included up to 4th order QED corrections. For BeH, the best ab initio potential matches all but one observed vibrational spacing to < 1 cm- accuracy, and for Li2 the discrepancy in the spacings is < 0.08 cm-1 for all vibrational levels. But experimental methods such as photoassociation require the absolute energies, not spacings, and these are still several in several cm-1 disagreement. So empirical potentials are still the only reliable way to predict energies for few-electron systems. We also give predictions for various unobserved ''halo nucleonic molecules'' containing the ''halo'' isotopes: 6,8He, 11Li, 11,14Be and 8 , 17 , 19B.

Structural qualia: a solution to the hard problem of consciousness.

PubMed

Loorits, Kristjan

2014-01-01

The hard problem of consciousness has been often claimed to be unsolvable by the methods of traditional empirical sciences. It has been argued that all the objects of empirical sciences can be fully analyzed in structural terms but that consciousness is (or has) something over and above its structure. However, modern neuroscience has introduced a theoretical framework in which also the apparently non-structural aspects of consciousness, namely the so called qualia or qualitative properties, can be analyzed in structural terms. That framework allows us to see qualia as something compositional with internal structures that fully determine their qualitative nature. Moreover, those internal structures can be identified which certain neural patterns. Thus consciousness as a whole can be seen as a complex neural pattern that misperceives some of its own highly complex structural properties as monadic and qualitative. Such neural pattern is analyzable in fully structural terms and thereby the hard problem is solved.

Structural qualia: a solution to the hard problem of consciousness

PubMed Central

Loorits, Kristjan

2014-01-01

The hard problem of consciousness has been often claimed to be unsolvable by the methods of traditional empirical sciences. It has been argued that all the objects of empirical sciences can be fully analyzed in structural terms but that consciousness is (or has) something over and above its structure. However, modern neuroscience has introduced a theoretical framework in which also the apparently non-structural aspects of consciousness, namely the so called qualia or qualitative properties, can be analyzed in structural terms. That framework allows us to see qualia as something compositional with internal structures that fully determine their qualitative nature. Moreover, those internal structures can be identified which certain neural patterns. Thus consciousness as a whole can be seen as a complex neural pattern that misperceives some of its own highly complex structural properties as monadic and qualitative. Such neural pattern is analyzable in fully structural terms and thereby the hard problem is solved. PMID:24672510

Gender differences in the factor structure of posttraumatic stress disorder symptoms in war-exposed adolescents.

PubMed

Armour, Cherie; Elhai, Jon D; Layne, Christopher M; Shevlin, Mark; Duraković-Belko, Elvira; Djapo, Nermin; Pynoos, Robert S

2011-05-01

DSM-IV's three-factor model of posttraumatic stress disorder (PTSD) is rarely empirically supported, whereas other four-factor models (King et al., 1998; Simms, Watson, & Doebbeling, 2002) have proven to be better representations of PTSD's latent structure. To date, a clear consensus as to which model provides the best representation of PTSD's underlying dimensions has yet to be reached. The current study investigated whether gender is associated with factor structure differences using the King et al. (1998) model of reexperiencing, avoidance, numbing, and hyperarousal PTSD symptoms. Participants were war-exposed Bosnian secondary/high school boys and girls (N=1572) assessed nearly two years after the 1992-1995 Bosnian conflict. Confirmatory factor analytic tests of measurement invariance across PTSD model parameters revealed many significant sex-linked differences. Implications regarding the potential role of gender as a moderator of the King et al. (1998) model's factor structure are discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations.

PubMed

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-14

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiC x O 6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young's modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young's modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations

NASA Astrophysics Data System (ADS)

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-01

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Health lifestyle theory and the convergence of agency and structure.

PubMed

Cockerham, William C

2005-03-01

This article utilizes the agency-structure debate as a framework for constructing a health lifestyle theory. No such theory currently exists, yet the need for one is underscored by the fact that many daily lifestyle practices involve considerations of health outcomes. An individualist paradigm has influenced concepts of health lifestyles in several disciplines, but this approach neglects the structural dimensions of such lifestyles and has limited applicability to the empirical world. The direction of this article is to present a theory of health lifestyles that includes considerations of both agency and structure, with an emphasis upon restoring structure to its appropriate position. The article begins by defining agency and structure, followed by presentation of a health lifestyle model and the theoretical and empirical studies that support it.

The Osmotic Potential of Polyethylene Glycol 6000 1

PubMed Central

Michel, Burlyn E.; Kaufmann, Merrill R.

1973-01-01

Osmotic potential (ψs) of aqueous solutions of polyethylene glycol 6000 (PEG-6000) was curvilinearly related to concentration. At given concentrations, ψs increased linearly with temperature. The effects of concentration and temperature on ψs of PEG-6000 solutions differ from those for most salts and sugars and apparently are related to structural changes in the PEG polymer. Measurements of ψs with thermocouple psychrometers are more negative than those with a vapor pressure osmometer, with the psychrometer probably giving the more nearly correct ψs for bulk solutions. An empirical equation permits calculation of ψs from known concentrations of PEG-6000 over a temperature range of 15 to 35 C. Viscometery and gravimetric analysis are convenient methods by which the concentrations of PEG-6000 solutions may be measured. PMID:16658439

The osmotic potential of polyethylene glycol 6000.

PubMed

Michel, B E; Kaufmann, M R

1973-05-01

Osmotic potential (psi(s)) of aqueous solutions of polyethylene glycol 6000 (PEG-6000) was curvilinearly related to concentration. At given concentrations, psi(s) increased linearly with temperature. The effects of concentration and temperature on psi(s) of PEG-6000 solutions differ from those for most salts and sugars and apparently are related to structural changes in the PEG polymer. Measurements of psi(s) with thermocouple psychrometers are more negative than those with a vapor pressure osmometer, with the psychrometer probably giving the more nearly correct psi(s) for bulk solutions. An empirical equation permits calculation of psi(s) from known concentrations of PEG-6000 over a temperature range of 15 to 35 C. Viscometery and gravimetric analysis are convenient methods by which the concentrations of PEG-6000 solutions may be measured.

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen.

PubMed

Andersen, J; Voute, A; Mihrin, D; Heimdal, J; Berg, R W; Torsson, M; Wugt Larsen, R

2017-06-28

The true global potential energy minimum configuration of the formaldehyde dimer (CH 2 O) 2 , including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of C s and C 2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar C s configuration of (CH 2 O) 2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol -1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol -1 for the dissociation energy D 0 of this global potential energy minimum.

Solid-liquid interface free energies of pure bcc metals and B2 phases

DOE PAGES

Wilson, S. R.; Gunawardana, K. G. S. H.; Mendelev, M. I.

2015-04-07

The solid-liquid interface (SLI) free energy was determined from molecular dynamics (MD) simulation for several body centered cubic (bcc) metals and B2 metallic compounds (space group: Pm3¯m ; prototype: CsCl). In order to include a bcc metal with a low melting temperature in our study, a semi-empirical potential was developed for Na. Two additional synthetic “Na” potentials were also developed to explore the effect of liquid structure and latent heat on the SLI free energy. The obtained MD data were compared with the empirical Turnbull, Laird, and Ewing relations. All three relations are found to predict the general trend observedmore » in the MD data for bcc metals obtained within the present study. However, only the Laird and Ewing relations are able to predict the trend obtained within the sequence of “Na” potentials. The Laird relation provides the best prediction for our MD data and other MD data for bcc metals taken from the literature. Overall, the Laird relation also agrees well with our B2 data but requires a proportionality constant that is substantially different from the bcc case. It also fails to explain a considerable difference between the SLI free energies of some B2 phases which have nearly the same melting temperature. In contrast, this difference is satisfactorily described by the Ewing relation. Thus, the Ewing relation obtained from the bcc dataset also provides a reasonable description of the B2 data.« less

Probing the global potential energy minimum of (CH2O)2: THz absorption spectrum of (CH2O)2 in solid neon and para-hydrogen

NASA Astrophysics Data System (ADS)

Andersen, J.; Voute, A.; Mihrin, D.; Heimdal, J.; Berg, R. W.; Torsson, M.; Wugt Larsen, R.

2017-06-01

The true global potential energy minimum configuration of the formaldehyde dimer (CH2O)2, including the presence of a single or a double weak intermolecular CH⋯O hydrogen bond motif, has been a long-standing subject among both experimentalists and theoreticians as two different energy minima conformations of Cs and C2h symmetry have almost identical energies. The present work demonstrates how the class of large-amplitude hydrogen bond vibrational motion probed in the THz region provides excellent direct spectroscopic observables for these weak intermolecular CH⋯O hydrogen bond motifs. The combination of concentration dependency measurements, observed isotopic spectral shifts associated with H/D substitutions and dedicated annealing procedures, enables the unambiguous assignment of three large-amplitude infrared active hydrogen bond vibrational modes for the non-planar Cs configuration of (CH2O)2 embedded in cryogenic neon and enriched para-hydrogen matrices. A (semi)-empirical value for the change of vibrational zero-point energy of 5.5 ± 0.3 kJ mol-1 is proposed for the dimerization process. These THz spectroscopic observations are complemented by CCSD(T)-F12/aug-cc-pV5Z (electronic energies) and MP2/aug-cc-pVQZ (force fields) electronic structure calculations yielding a (semi)-empirical value of 13.7 ± 0.3 kJ mol-1 for the dissociation energy D0 of this global potential energy minimum.

Solid-liquid interface free energies of pure bcc metals and B2 phases

NASA Astrophysics Data System (ADS)

Wilson, S. R.; Gunawardana, K. G. S. H.; Mendelev, M. I.

2015-04-01

The solid-liquid interface (SLI) free energy was determined from molecular dynamics (MD) simulation for several body centered cubic (bcc) metals and B2 metallic compounds (space group: P m 3 ¯ m ; prototype: CsCl). In order to include a bcc metal with a low melting temperature in our study, a semi-empirical potential was developed for Na. Two additional synthetic "Na" potentials were also developed to explore the effect of liquid structure and latent heat on the SLI free energy. The obtained MD data were compared with the empirical Turnbull, Laird, and Ewing relations. All three relations are found to predict the general trend observed in the MD data for bcc metals obtained within the present study. However, only the Laird and Ewing relations are able to predict the trend obtained within the sequence of "Na" potentials. The Laird relation provides the best prediction for our MD data and other MD data for bcc metals taken from the literature. Overall, the Laird relation also agrees well with our B2 data but requires a proportionality constant that is substantially different from the bcc case. It also fails to explain a considerable difference between the SLI free energies of some B2 phases which have nearly the same melting temperature. In contrast, this difference is satisfactorily described by the Ewing relation. Moreover, the Ewing relation obtained from the bcc dataset also provides a reasonable description of the B2 data.

Solid-liquid interface free energies of pure bcc metals and B2 phases.

PubMed

Wilson, S R; Gunawardana, K G S H; Mendelev, M I

2015-04-07

The solid-liquid interface (SLI) free energy was determined from molecular dynamics (MD) simulation for several body centered cubic (bcc) metals and B2 metallic compounds (space group: Pm3̄m; prototype: CsCl). In order to include a bcc metal with a low melting temperature in our study, a semi-empirical potential was developed for Na. Two additional synthetic "Na" potentials were also developed to explore the effect of liquid structure and latent heat on the SLI free energy. The obtained MD data were compared with the empirical Turnbull, Laird, and Ewing relations. All three relations are found to predict the general trend observed in the MD data for bcc metals obtained within the present study. However, only the Laird and Ewing relations are able to predict the trend obtained within the sequence of "Na" potentials. The Laird relation provides the best prediction for our MD data and other MD data for bcc metals taken from the literature. Overall, the Laird relation also agrees well with our B2 data but requires a proportionality constant that is substantially different from the bcc case. It also fails to explain a considerable difference between the SLI free energies of some B2 phases which have nearly the same melting temperature. In contrast, this difference is satisfactorily described by the Ewing relation. Moreover, the Ewing relation obtained from the bcc dataset also provides a reasonable description of the B2 data.

Default contagion risks in Russian interbank market

NASA Astrophysics Data System (ADS)

Leonidov, A. V.; Rumyantsev, E. L.

2016-06-01

Systemic risks of default contagion in the Russian interbank market are investigated. The analysis is based on considering the bow-tie structure of the weighted oriented graph describing the structure of the interbank loans. A probabilistic model of interbank contagion explicitly taking into account the empirical bow-tie structure reflecting functionality of the corresponding nodes (borrowers, lenders, borrowers and lenders simultaneously), degree distributions and disassortativity of the interbank network under consideration based on empirical data is developed. The characteristics of contagion-related systemic risk calculated with this model are shown to be in agreement with those of explicit stress tests.

An optimum organizational structure for a large earth-orbiting multidisciplinary space base. Ph.D. Thesis - Fla. State Univ., 1973

NASA Technical Reports Server (NTRS)

Ragusa, J. M.

1975-01-01

An optimum hypothetical organizational structure was studied for a large earth-orbiting, multidisciplinary research and applications space base manned by a crew of technologists. Because such a facility does not presently exist, in situ empirical testing was not possible. Study activity was, therefore, concerned with the identification of a desired organizational structural model rather than with the empirical testing of the model. The essential finding of this research was that a four-level project type total matrix model will optimize the efficiency and effectiveness of space base technologists.

An optimum organizational structure for a large earth-orbiting multidisciplinary Space Base

NASA Technical Reports Server (NTRS)

Ragusa, J. M.

1973-01-01

The purpose of this exploratory study was to identify an optimum hypothetical organizational structure for a large earth-orbiting multidisciplinary research and applications (R&A) Space Base manned by a mixed crew of technologists. Since such a facility does not presently exist, in situ empirical testing was not possible. Study activity was, therefore, concerned with the identification of a desired organizational structural model rather than the empirical testing of it. The essential finding of this research was that a four-level project type 'total matrix' model will optimize the efficiency and effectiveness of Space Base technologists.

The ACTIVE conceptual framework as a structural equation model

PubMed Central

Gross, Alden L.; Payne, Brennan R.; Casanova, Ramon; Davoudzadeh, Pega; Dzierzewski, Joseph M.; Farias, Sarah; Giovannetti, Tania; Ip, Edward H.; Marsiske, Michael; Rebok, George W.; Schaie, K. Warner; Thomas, Kelsey; Willis, Sherry; Jones, Richard N.

2018-01-01

Background/Study Context Conceptual frameworks are analytic models at a high level of abstraction. Their operationalization can inform randomized trial design and sample size considerations. Methods The Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) conceptual framework was empirically tested using structural equation modeling (N=2,802). ACTIVE was guided by a conceptual framework for cognitive training in which proximal cognitive abilities (memory, inductive reasoning, speed of processing) mediate treatment-related improvement in primary outcomes (everyday problem-solving, difficulty with activities of daily living, everyday speed, driving difficulty), which in turn lead to improved secondary outcomes (health-related quality of life, health service utilization, mobility). Measurement models for each proximal, primary, and secondary outcome were developed and tested using baseline data. Each construct was then combined in one model to evaluate fit (RMSEA, CFI, normalized residuals of each indicator). To expand the conceptual model and potentially inform future trials, evidence of modification of structural model parameters was evaluated by age, years of education, sex, race, and self-rated health status. Results Preconceived measurement models for memory, reasoning, speed of processing, everyday problem-solving, instrumental activities of daily living (IADL) difficulty, everyday speed, driving difficulty, and health-related quality of life each fit well to the data (all RMSEA < .05; all CFI > .95). Fit of the full model was excellent (RMSEA = .038; CFI = .924). In contrast with previous findings from ACTIVE regarding who benefits from training, interaction testing revealed associations between proximal abilities and primary outcomes are stronger on average by nonwhite race, worse health, older age, and less education (p < .005). Conclusions Empirical data confirm the hypothesized ACTIVE conceptual model. Findings suggest that the types of people who show intervention effects on cognitive performance potentially may be different from those with the greatest chance of transfer to real-world activities. PMID:29303475

wACSF—Weighted atom-centered symmetry functions as descriptors in machine learning potentials

NASA Astrophysics Data System (ADS)

Gastegger, M.; Schwiedrzik, L.; Bittermann, M.; Berzsenyi, F.; Marquetand, P.

2018-06-01

We introduce weighted atom-centered symmetry functions (wACSFs) as descriptors of a chemical system's geometry for use in the prediction of chemical properties such as enthalpies or potential energies via machine learning. The wACSFs are based on conventional atom-centered symmetry functions (ACSFs) but overcome the undesirable scaling of the latter with an increasing number of different elements in a chemical system. The performance of these two descriptors is compared using them as inputs in high-dimensional neural network potentials (HDNNPs), employing the molecular structures and associated enthalpies of the 133 855 molecules containing up to five different elements reported in the QM9 database as reference data. A substantially smaller number of wACSFs than ACSFs is needed to obtain a comparable spatial resolution of the molecular structures. At the same time, this smaller set of wACSFs leads to a significantly better generalization performance in the machine learning potential than the large set of conventional ACSFs. Furthermore, we show that the intrinsic parameters of the descriptors can in principle be optimized with a genetic algorithm in a highly automated manner. For the wACSFs employed here, we find however that using a simple empirical parametrization scheme is sufficient in order to obtain HDNNPs with high accuracy.

Development of flexible pavement database for local calibration of MEPDG : volume 1.

DOT National Transportation Integrated Search

2011-06-01

The new mechanistic-empirical pavement design guide (MEPDG), based on the National Cooperative Highway : Research Program (NCHRP) study 1-37A, replaces the widely used but more empirical 1993 AASHTO Guide : for Design of Pavement Structures. The MEPD...

Improved characterization of truck traffic volumes and axle loads for mechanistic-empirical pavement design.

DOT National Transportation Integrated Search

2012-12-01

The recently developed mechanistic-empirical pavement design guide (MEPDG) requires a multitude of traffic : inputs to be defined for the design of pavement structures, including the initial two-way annual average daily truck : traffic (AADTT), direc...

Inter-atomic potentials for radiation damage studies in CePO4 monazite

NASA Astrophysics Data System (ADS)

Jolley, Kenny; Asuvathraman, Rajaram; Smith, Roger

2017-02-01

An original empirical potential used for modelling phosphate glasses is adapted to be suitable for use with monazite (CePO4) so as to have a consistent formulation for radiation damage studies of phosphates. This is done by adding a parameterisation for the Ce-O interaction to the existing potential set. The thermal and structural properties of the resulting computer model are compared to experimental results. The parameter set gives a stable monazite structure where the volume of the unit cell is almost identical to that measured experimentally, but with some shrinkage in the a and b lengths and a small expansion in the c direction compared to experiment. The thermal expansion, specific heat capacity and estimates of the melting point are also determined. The estimate of the melting temperature of 2500 K is comparable to the experimental value of 2318 ± 20 K, but the simulated thermal expansion of 49 ×10-6 K-1 is larger than the usually reported value. The simulated specific heat capacity at constant pressure was found to be approximately constant at 657 J kg-1 K-1 in the range 300-1000 K, however, this is not observed experimentally or in more detailed ab initio calculations.

A modified Embedded-Atom Method interatomic potential for uranium-silicide

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

Beeler, Benjamin; Baskes, Michael; Andersson, David

Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel bene ts from higher thermal conductivity and higher ssile density compared to uranium dioxide (UO 2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling e orts are underway to address this gap in knowledge. In this study, a semi-empirical modi ed Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is ttedmore » to the formation energy, defect energies and structural properties of U 3Si 2. The primary phase of interest (U 3Si 2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.« less

A modified Embedded-Atom Method interatomic potential for uranium-silicide

DOE PAGES

Beeler, Benjamin; Baskes, Michael; Andersson, David; ...

2017-08-18

Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel bene ts from higher thermal conductivity and higher ssile density compared to uranium dioxide (UO 2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling e orts are underway to address this gap in knowledge. In this study, a semi-empirical modi ed Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is ttedmore » to the formation energy, defect energies and structural properties of U 3Si 2. The primary phase of interest (U 3Si 2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.« less

A modified Embedded-Atom Method interatomic potential for uranium-silicide

NASA Astrophysics Data System (ADS)

Beeler, Benjamin; Baskes, Michael; Andersson, David; Cooper, Michael W. D.; Zhang, Yongfeng

2017-11-01

Uranium-silicide (U-Si) fuels are being pursued as a possible accident tolerant fuel (ATF). This uranium alloy fuel benefits from higher thermal conductivity and higher fissile density compared to uranium dioxide (UO2). In order to perform engineering scale nuclear fuel performance simulations, the material properties of the fuel must be known. Currently, the experimental data available for U-Si fuels is rather limited. Thus, multiscale modeling efforts are underway to address this gap in knowledge. In this study, a semi-empirical modified Embedded-Atom Method (MEAM) potential is presented for the description of the U-Si system. The potential is fitted to the formation energy, defect energies and structural properties of U3Si2. The primary phase of interest (U3Si2) is accurately described over a wide temperature range and displays good behavior under irradiation and with free surfaces. The potential can also describe a variety of U-Si phases across the composition spectrum.

Leaf Extraction and Analysis Framework Graphical User Interface: Segmenting and Analyzing the Structure of Leaf Veins and Areoles1[W][OA

PubMed Central

Price, Charles A.; Symonova, Olga; Mileyko, Yuriy; Hilley, Troy; Weitz, Joshua S.

2011-01-01

Interest in the structure and function of physical biological networks has spurred the development of a number of theoretical models that predict optimal network structures across a broad array of taxonomic groups, from mammals to plants. In many cases, direct tests of predicted network structure are impossible given the lack of suitable empirical methods to quantify physical network geometry with sufficient scope and resolution. There is a long history of empirical methods to quantify the network structure of plants, from roots, to xylem networks in shoots and within leaves. However, with few exceptions, current methods emphasize the analysis of portions of, rather than entire networks. Here, we introduce the Leaf Extraction and Analysis Framework Graphical User Interface (LEAF GUI), a user-assisted software tool that facilitates improved empirical understanding of leaf network structure. LEAF GUI takes images of leaves where veins have been enhanced relative to the background, and following a series of interactive thresholding and cleaning steps, returns a suite of statistics and information on the structure of leaf venation networks and areoles. Metrics include the dimensions, position, and connectivity of all network veins, and the dimensions, shape, and position of the areoles they surround. Available for free download, the LEAF GUI software promises to facilitate improved understanding of the adaptive and ecological significance of leaf vein network structure. PMID:21057114

Leaf extraction and analysis framework graphical user interface: segmenting and analyzing the structure of leaf veins and areoles.

PubMed

Price, Charles A; Symonova, Olga; Mileyko, Yuriy; Hilley, Troy; Weitz, Joshua S

2011-01-01

Interest in the structure and function of physical biological networks has spurred the development of a number of theoretical models that predict optimal network structures across a broad array of taxonomic groups, from mammals to plants. In many cases, direct tests of predicted network structure are impossible given the lack of suitable empirical methods to quantify physical network geometry with sufficient scope and resolution. There is a long history of empirical methods to quantify the network structure of plants, from roots, to xylem networks in shoots and within leaves. However, with few exceptions, current methods emphasize the analysis of portions of, rather than entire networks. Here, we introduce the Leaf Extraction and Analysis Framework Graphical User Interface (LEAF GUI), a user-assisted software tool that facilitates improved empirical understanding of leaf network structure. LEAF GUI takes images of leaves where veins have been enhanced relative to the background, and following a series of interactive thresholding and cleaning steps, returns a suite of statistics and information on the structure of leaf venation networks and areoles. Metrics include the dimensions, position, and connectivity of all network veins, and the dimensions, shape, and position of the areoles they surround. Available for free download, the LEAF GUI software promises to facilitate improved understanding of the adaptive and ecological significance of leaf vein network structure.

How closely do many-body potentials describe the structure and dynamics of Cu-Zr glass-forming alloy?

NASA Astrophysics Data System (ADS)

Lad, K. N.; Jakse, N.; Pasturel, A.

2017-03-01

Molecular dynamics investigations of the structure and dynamics of Cu64.5Zr35.5 metallic glass-forming alloy have been carried out using five different semi-empirical, many-body interaction potentials based on the Finnis-Sinclair model [M. I. Mendelev et al., J. Appl. Phys. 102, 043501 (2007) (MSK); M. I. Mendelev et al., Philos. Mag. 89, 967 (2009) (MKOSYP); L. Ward et al., e-print arXiv:1209.0619 (2012) (WAFW)] and the embedded-atom model [Y. Q. Cheng et al., Phys. Rev. Lett. 102, 245501 (2009) (CMS) and N. Jakse et al., Phys. Rev. B 85, 174201 (2012) (JNP)]. Although the total static structure factor of the alloy for all the five interaction potentials is, in general, found to be in good agreement with the experimental results, the investigation of a local structure in terms of icosahedral short-range order reveals that the effect of the interaction potential (especially the cohesive part) on the structure of the alloy is not as trivial as it seems. For MSK and JNP potentials, the self-intermediate scattering function Fs(q, t), q-dependence of the structural relaxation time τα in the low-q region, and the self-diffusion coefficient, Ds, for Cu-atoms in the alloy are in excellent agreement with the experimental results. The results for MKOSYP, CMS, and WAFW potentials deviate significantly from the experiment and suggest the dynamics of the alloy to be faster. The difference in the description of the dynamics of the alloy by different potentials is found to be due to the difference in the relevant energy scales corresponding to the temperature scales. τα and Ds exhibit Arrhenius temperature dependence in the high temperature regime above the melting temperature. We also suggest that the attractive forces influence the dynamics of the liquid alloy significantly, which is against the mere perturbative role assigned to the attractive forces in the van der Waals picture of liquids that has been challenged in the recent years. As the five interaction potentials are frequently employed to study thermodynamic, mechanical, and transport properties of Cu-Zr alloys, our study also provides a suitability check for these potentials.

Causal diagrams for empirical legal research: a methodology for identifying causation, avoiding bias and interpreting results

PubMed Central

VanderWeele, Tyler J.; Staudt, Nancy

2014-01-01

In this paper we introduce methodology—causal directed acyclic graphs—that empirical researchers can use to identify causation, avoid bias, and interpret empirical results. This methodology has become popular in a number of disciplines, including statistics, biostatistics, epidemiology and computer science, but has yet to appear in the empirical legal literature. Accordingly we outline the rules and principles underlying this new methodology and then show how it can assist empirical researchers through both hypothetical and real-world examples found in the extant literature. While causal directed acyclic graphs are certainly not a panacea for all empirical problems, we show they have potential to make the most basic and fundamental tasks, such as selecting covariate controls, relatively easy and straightforward. PMID:25685055

A Modified Empirical Wavelet Transform for Acoustic Emission Signal Decomposition in Structural Health Monitoring.

PubMed

Dong, Shaopeng; Yuan, Mei; Wang, Qiusheng; Liang, Zhiling

2018-05-21

The acoustic emission (AE) method is useful for structural health monitoring (SHM) of composite structures due to its high sensitivity and real-time capability. The main challenge, however, is how to classify the AE data into different failure mechanisms because the detected signals are affected by various factors. Empirical wavelet transform (EWT) is a solution for analyzing the multi-component signals and has been used to process the AE data. In order to solve the spectrum separation problem of the AE signals, this paper proposes a novel modified separation method based on local window maxima (LWM) algorithm. It searches the local maxima of the Fourier spectrum in a proper window, and automatically determines the boundaries of spectrum segmentations, which helps to eliminate the impact of noise interference or frequency dispersion in the detected signal and obtain the meaningful empirical modes that are more related to the damage characteristics. Additionally, both simulation signal and AE signal from the composite structures are used to verify the effectiveness of the proposed method. Finally, the experimental results indicate that the proposed method performs better than the original EWT method in identifying different damage mechanisms of composite structures.

A Modified Empirical Wavelet Transform for Acoustic Emission Signal Decomposition in Structural Health Monitoring

PubMed Central

Dong, Shaopeng; Yuan, Mei; Wang, Qiusheng; Liang, Zhiling

2018-01-01

The acoustic emission (AE) method is useful for structural health monitoring (SHM) of composite structures due to its high sensitivity and real-time capability. The main challenge, however, is how to classify the AE data into different failure mechanisms because the detected signals are affected by various factors. Empirical wavelet transform (EWT) is a solution for analyzing the multi-component signals and has been used to process the AE data. In order to solve the spectrum separation problem of the AE signals, this paper proposes a novel modified separation method based on local window maxima (LWM) algorithm. It searches the local maxima of the Fourier spectrum in a proper window, and automatically determines the boundaries of spectrum segmentations, which helps to eliminate the impact of noise interference or frequency dispersion in the detected signal and obtain the meaningful empirical modes that are more related to the damage characteristics. Additionally, both simulation signal and AE signal from the composite structures are used to verify the effectiveness of the proposed method. Finally, the experimental results indicate that the proposed method performs better than the original EWT method in identifying different damage mechanisms of composite structures. PMID:29883411

[Crop geometry identification based on inversion of semiempirical BRDF models].

PubMed

Huang, Wen-jiang; Wang, Jin-di; Mu, Xi-han; Wang, Ji-hua; Liu, Liang-yun; Liu, Qiang; Niu, Zheng

2007-10-01

Investigations have been made on identification of erective and horizontal varieties by bidirectional canopy reflected spectrum and semi-empirical bidirectional reflectance distribution function (BRDF) models. The qualitative effect of leaf area index (LAI) and average leaf angle (ALA) on crop canopy reflected spectrum was studied. The structure parameter sensitive index (SPEI) based on the weight for the volumetric kernel (fvol), the weight for the geometric kernel (fgeo), and the weight for constant corresponding to isotropic reflectance (fiso), was defined in the present study for crop geometry identification. However, the weights associated with the kernels of semi-empirical BRDF model do not have a direct relationship with measurable biophysical parameters. Therefore, efforts have focused on trying to find the relation between these semi-empirical BRDF kernel weights and various vegetation structures. SPEI was proved to be more sensitive to identify crop geometry structures than structural scattering index (SSI) and normalized difference f-index (NDFI), SPEI could be used to distinguish erective and horizontal geometry varieties. So, it is feasible to identify horizontal and erective varieties of wheat by bidirectional canopy reflected spectrum.

Analysis of Virginia-specific traffic data inputs for use with the mechanistic-empirical pavement design guide.

DOT National Transportation Integrated Search

2010-02-01

This study developed traffic inputs for use with the Guide for the Mechanistic-Empirical Design of New & Rehabilitated Pavement Structures (MEPDG) in Virginia and sought to determine if the predicted distresses showed differences between site-specifi...

Empirical potential influence and effect of temperature on the mechanical properties of pristine and defective hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Thomas, Siby; Ajith, K. M.; Valsakumar, M. C.

2017-06-01

The major objective of this work is to present results of a classical molecular dynamics study to investigate the effect of changing the cut-off distance in the empirical potential on the stress-strain relation and also the temperature dependent Young’s modulus of pristine and defective hexagonal boron nitride. As the temperature increases, the computed Young’s modulus shows a significant decrease along both the armchair and zigzag directions. The computed Young’s modulus shows a trend in keeping with the structural anisotropy of h-BN. The variation of Young’s modulus with system size is elucidated. The observed mechanical strength of h-BN is significantly affected by the vacancy and Stone-Wales type defects. The computed room temperature Young’s modulus of pristine h-BN is 755 GPa and 769 GPa respectively along the armchair and zigzag directions. The decrease of Young’s modulus with increase in temperature has been analyzed and the results show that the system with zigzag edge shows a higher value of Young’s modulus in comparison to that with armchair edge. As the temperature increases, the computed stiffness decreases and the system with zigzag edge possesses a higher value of stiffness as compared to the armchair counterpart and this behaviour is consistent with the variation of Young’s modulus. The defect analysis shows that presence of vacancy type defects leads to a higher Young’s modulus, in the studied range with different percentage of defect concentration, in comparison with Stone-Wales defect. The variations in the peak position of the computed radial distribution function reveals the changes in the structural features of systems with zigzag and armchair edges in the presence of applied stress.

Influence of highly distinctive structural properties on the excitability of pyramidal neurons in monkey visual and prefrontal cortices

PubMed Central

Amatrudo, Joseph M.; Weaver, Christina M.; Crimins, Johanna L.; Hof, Patrick R.; Rosene, Douglas L.; Luebke, Jennifer I.

2012-01-01

Whole-cell patch-clamp recordings and high-resolution 3D morphometric analyses of layer 3 pyramidal neurons in in vitro slices of monkey primary visual cortex (V1) and dorsolateral granular prefrontal cortex (dlPFC) revealed that neurons in these two brain areas possess highly distinctive structural and functional properties. Area V1 pyramidal neurons are much smaller than dlPFC neurons, with significantly less extensive dendritic arbors and far fewer dendritic spines. Relative to dlPFC neurons, V1 neurons have a significantly higher input resistance, depolarized resting membrane potential and higher action potential (AP) firing rates. Most V1 neurons exhibit both phasic and regular-spiking tonic AP firing patterns, while dlPFC neurons exhibit only tonic firing. Spontaneous postsynaptic currents are lower in amplitude and have faster kinetics in V1 than in dlPFC neurons, but are no different in frequency. Three-dimensional reconstructions of V1 and dlPFC neurons were incorporated into computational models containing Hodgkin-Huxley and AMPA- and GABAA-receptor gated channels. Morphology alone largely accounted for observed passive physiological properties, but led to AP firing rates that differed more than observed empirically, and to synaptic responses that opposed empirical results. Accordingly, modeling predicts that active channel conductances differ between V1 and dlPFC neurons. The unique features of V1 and dlPFC neurons are likely fundamental determinants of area-specific network behavior. The compact electrotonic arbor and increased excitability of V1 neurons support the rapid signal integration required for early processing of visual information. The greater connectivity and dendritic complexity of dlPFC neurons likely support higher level cognitive functions including working memory and planning. PMID:23035077

Torsion-wagging tunneling and vibrational states in hydrazine determined from its ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Łodyga, Wiesław; Makarewicz, Jan

2012-05-01

Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Møller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state rav structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm-1 and 3454 cm-1, respectively, are in reasonable agreement with the empirical estimates of 2072 cm-1 and 3312 cm-1, respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997), 10.1006/jmsp.1997.7271]. However, the empirical torsion barrier of 934 cm-1 appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm-1 and 2706 cm-1, respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.

Confirmatory factor analysis of the Child Oral Health Impact Profile (Korean version).

PubMed

Cho, Young Il; Lee, Soonmook; Patton, Lauren L; Kim, Hae-Young

2016-04-01

Empirical support for the factor structure of the Child Oral Health Impact Profile (COHIP) has not been fully established. The purposes of this study were to evaluate the factor structure of the Korean version of the COHIP (COHIP-K) empirically using confirmatory factor analysis (CFA) based on the theoretical framework and then to assess whether any of the factors in the structure could be grouped into a simpler single second-order factor. Data were collected through self-reported COHIP-K responses from a representative community sample of 2,236 Korean children, 8-15 yr of age. Because a large inter-factor correlation of 0.92 was estimated in the original five-factor structure, the two strongly correlated factors were combined into one factor, resulting in a four-factor structure. The revised four-factor model showed a reasonable fit with appropriate inter-factor correlations. Additionally, the second-order model with four sub-factors was reasonable with sufficient fit and showed equal fit to the revised four-factor model. A cross-validation procedure confirmed the appropriateness of the findings. Our analysis empirically supported a four-factor structure of COHIP-K, a summarized second-order model, and the use of an integrated summary COHIP score. © 2016 Eur J Oral Sci.

Scaling of strength and lifetime probability distributions of quasibrittle structures based on atomistic fracture mechanics

PubMed Central

Bažant, Zdeněk P.; Le, Jia-Liang; Bazant, Martin Z.

2009-01-01

The failure probability of engineering structures such as aircraft, bridges, dams, nuclear structures, and ships, as well as microelectronic components and medical implants, must be kept extremely low, typically <10−6. The safety factors needed to ensure it have so far been assessed empirically. For perfectly ductile and perfectly brittle structures, the empirical approach is sufficient because the cumulative distribution function (cdf) of random material strength is known and fixed. However, such an approach is insufficient for structures consisting of quasibrittle materials, which are brittle materials with inhomogeneities that are not negligible compared with the structure size. The reason is that the strength cdf of quasibrittle structure varies from Gaussian to Weibullian as the structure size increases. In this article, a recently proposed theory for the strength cdf of quasibrittle structure is refined by deriving it from fracture mechanics of nanocracks propagating by small, activation-energy-controlled, random jumps through the atomic lattice. This refinement also provides a plausible physical justification of the power law for subcritical creep crack growth, hitherto considered empirical. The theory is further extended to predict the cdf of structural lifetime at constant load, which is shown to be size- and geometry-dependent. The size effects on structure strength and lifetime are shown to be related and the latter to be much stronger. The theory fits previously unexplained deviations of experimental strength and lifetime histograms from the Weibull distribution. Finally, a boundary layer method for numerical calculation of the cdf of structural strength and lifetime is outlined. PMID:19561294

Detection of internal structure by scattered light intensity: Application to kidney cell sorting

NASA Technical Reports Server (NTRS)

Goolsby, C. L.; Kunze, M. E.

1985-01-01

Scattered light measurements in flow cytometry were sucessfully used to distinguish cells on the basis of differing morphology and internal structure. Differences in scattered light patterns due to changes in internal structure would be expected to occur at large scattering angles. Practically, the results of these calculations suggest that in experimental situations an array of detectors would be useful. Although in general the detection of the scattered light intensity at several intervals within the 10 to 60 region would be sufficient, there are many examples where increased sensitivity could be acheived at other angles. The ability to measure at many different angular intervals would allow the experimenter to empirically select the optimum intervals for the varying conditions of cell size, N/C ratio, granule size and internal structure from sample to sample. The feasibility of making scattered light measurements at many different intervals in flow cytometry was demonstrated. The implementation of simplified versions of these techniques in conjunction with independant measurements of cell size could potentially improve the usefulness of flow cytometry in the study of the internal structure of cells.

Search for memory effects in methane hydrate: structure of water before hydrate formation and after hydrate decomposition.

PubMed

Buchanan, Piers; Soper, Alan K; Thompson, Helen; Westacott, Robin E; Creek, Jefferson L; Hobson, Greg; Koh, Carolyn A

2005-10-22

Neutron diffraction with HD isotope substitution has been used to study the formation and decomposition of the methane clathrate hydrate. Using this atomistic technique coupled with simultaneous gas consumption measurements, we have successfully tracked the formation of the sI methane hydrate from a water/gas mixture and then the subsequent decomposition of the hydrate from initiation to completion. These studies demonstrate that the application of neutron diffraction with simultaneous gas consumption measurements provides a powerful method for studying the clathrate hydrate crystal growth and decomposition. We have also used neutron diffraction to examine the water structure before the hydrate growth and after the hydrate decomposition. From the neutron-scattering curves and the empirical potential structure refinement analysis of the data, we find that there is no significant difference between the structure of water before the hydrate formation and the structure of water after the hydrate decomposition. Nor is there any significant change to the methane hydration shell. These results are discussed in the context of widely held views on the existence of memory effects after the hydrate decomposition.

Power in health care organizations: contemplations from the first-line management perspective.

PubMed

Isosaari, Ulla

2011-01-01

The aim of this paper is to examine health care organizations' power structures from the first-line management perspective. What liable power structures derive from the theoretical bases of bureaucratic, professional and result based organizations, and what power type do health care organizations represent, according to the empirical data? The paper seeks to perform an analysis using Mintzberg's power configurations of instrument, closed system, meritocracy and political arena. The empirical study was executed at the end of 2005 through a survey in ten Finnish hospital districts in both specialized and primary care. Respondents were all first-line managers in the area and a sample of staff members from internal disease, surgical and psychiatric units, as well as out-patient and primary care units. The number of respondents was 1,197 and the response percentage was 38. The data were analyzed statistically. As a result, it can be seen that a certain kind of organization structure supports the generation of a certain power type. A bureaucratic organization generates an instrument or closed system organization, a professional organization generates meritocracy and also political arena, and a result-based organization has a connection to political arena and meritocracy. First line managers regarded health care organizations as instruments when staff regarded them mainly as meritocracies having features of political arena. Managers felt their position to be limited by rules, whereas staff members regarded their position as having lots of space and influence potential. If the organizations seek innovative and active managers at the unit level, they should change the organizational structure and redistribute the work so that there could be more space for meaningful management. This research adds to the literature and gives helpful suggestions that will be of interest to those in the position of first-line management in health care.

An Investigation of Document Partitions.

ERIC Educational Resources Information Center

Shaw, W. M., Jr.

1986-01-01

Empirical significance of document partitions is investigated as a function of index term-weight and similarity thresholds. Results show the same empirically preferred partitions can be detected by two independent strategies: an analysis of cluster-based retrieval analysis and an analysis of regularities in the underlying structure of the document…

Supervision for School Psychologists in Training: Developing a Framework from Empirical Findings

ERIC Educational Resources Information Center

Gibbs, Simon; Atkinson, Cathy; Woods, Kevin; Bond, Caroline; Hill, Vivian; Howe, Julia; Morris, Sue

2016-01-01

Similar to other professional disciplines, the importance of supervision within school psychology has attracted considerable attention within recent years. Despite this, systematic review of current literature reveals a dearth of empirical literature proposing underlying theoretical structures. This study extends recent qualitative research by…

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

PubMed

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

2011-08-01

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

Determinants of environmental audit frequency: the role of firm organizational structure.

PubMed

Earnhart, Dietrich; Leonard, J Mark

2013-10-15

This study empirically examines the extent of environmental management practiced by US chemical manufacturing facilities, as reflected in the number of environmental internal audits conducted annually. As its focus, this study analyzes the effects of firm-level organizational structure on facility-level environmental management practices. For this empirical analysis, the study exploits unique data from a survey distributed to all U.S. chemical manufacturing permitted to discharge wastewater in 2001; the data reflect internal audits conducted during the years 1999-2001. Empirical results reveal differences in auditing behavior based on whether facilities are owned by publicly held or non-publicly held firms, owned by U.S.-based or non-U.S.-based firms, and owned by larger or smaller firms. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Appearance of psychopathic tendencies among children and adolescents].

PubMed

Pataky, Nóra; Körmendi, Attila

2010-01-01

There has been a growing body of researches about psychopathic tendencies appearing among children and adolescents. First generation studies differentiated psychopathic constellation from conduct problems in childhood and pointed out that the presence of these traits predict unpleasant therapeutic prognosis and is partly independent from quality of parenting. The factor structure of constellation is similar to the factor structure of adult psychopaths. Surveying the structure became clear that C/U traits are the core of the child and adolescent psychopathic constellation. This paper summarize results of empirical studies connected to C/U traits among children and adolescents. We introduce debatable questions about child and adolescent psychopathic traits and connected empirical studies.

The Small World of Psychopathology

PubMed Central

Borsboom, Denny; Cramer, Angélique O. J.; Schmittmann, Verena D.; Epskamp, Sacha; Waldorp, Lourens J.

2011-01-01

Background Mental disorders are highly comorbid: people having one disorder are likely to have another as well. We explain empirical comorbidity patterns based on a network model of psychiatric symptoms, derived from an analysis of symptom overlap in the Diagnostic and Statistical Manual of Mental Disorders-IV (DSM-IV). Principal Findings We show that a) half of the symptoms in the DSM-IV network are connected, b) the architecture of these connections conforms to a small world structure, featuring a high degree of clustering but a short average path length, and c) distances between disorders in this structure predict empirical comorbidity rates. Network simulations of Major Depressive Episode and Generalized Anxiety Disorder show that the model faithfully reproduces empirical population statistics for these disorders. Conclusions In the network model, mental disorders are inherently complex. This explains the limited successes of genetic, neuroscientific, and etiological approaches to unravel their causes. We outline a psychosystems approach to investigate the structure and dynamics of mental disorders. PMID:22114671

Empirical Bayes estimation of proportions with application to cowbird parasitism rates

USGS Publications Warehouse

Link, W.A.; Hahn, D.C.

1996-01-01

Bayesian models provide a structure for studying collections of parameters such as are considered in the investigation of communities, ecosystems, and landscapes. This structure allows for improved estimation of individual parameters, by considering them in the context of a group of related parameters. Individual estimates are differentially adjusted toward an overall mean, with the magnitude of their adjustment based on their precision. Consequently, Bayesian estimation allows for a more credible identification of extreme values in a collection of estimates. Bayesian models regard individual parameters as values sampled from a specified probability distribution, called a prior. The requirement that the prior be known is often regarded as an unattractive feature of Bayesian analysis and may be the reason why Bayesian analyses are not frequently applied in ecological studies. Empirical Bayes methods provide an alternative approach that incorporates the structural advantages of Bayesian models while requiring a less stringent specification of prior knowledge. Rather than requiring that the prior distribution be known, empirical Bayes methods require only that it be in a certain family of distributions, indexed by hyperparameters that can be estimated from the available data. This structure is of interest per se, in addition to its value in allowing for improved estimation of individual parameters; for example, hypotheses regarding the existence of distinct subgroups in a collection of parameters can be considered under the empirical Bayes framework by allowing the hyperparameters to vary among subgroups. Though empirical Bayes methods have been applied in a variety of contexts, they have received little attention in the ecological literature. We describe the empirical Bayes approach in application to estimation of proportions, using data obtained in a community-wide study of cowbird parasitism rates for illustration. Since observed proportions based on small sample sizes are heavily adjusted toward the mean, extreme values among empirical Bayes estimates identify those species for which there is the greatest evidence of extreme parasitism rates. Applying a subgroup analysis to our data on cowbird parasitism rates, we conclude that parasitism rates for Neotropical Migrants as a group are no greater than those of Resident/Short-distance Migrant species in this forest community. Our data and analyses demonstrate that the parasitism rates for certain Neotropical Migrant species are remarkably low (Wood Thrush and Rose-breasted Grosbeak) while those for others are remarkably high (Ovenbird and Red-eyed Vireo).

Development of glue type potentials for the Al-Pb system: computer simulation of Pb/Al interfaces and phase diagram calculation

NASA Astrophysics Data System (ADS)

Landa, Alex; Wynblatt, Paul; Siegel, Donald; Adams, Jim; Johnson, Erik; Dahmen, Uli

2000-03-01

Empirical many-body potentials have been constructed for the Al-Pb system using the ``force matching" method. The potentials have been fitted to a set of the ground state physical quantities calculated within ab initio approach and a massive quantum mechanical forces database for samples of bulk Al-Pb liquid alloys generated using ab initio molecular dynamics program VASP. Monte Carlo simulations using these potentials have been employed to compute an Al-Pb phase diagram, which is in fair agreement with experimental data, and to model the structure of (111) and (100) Pb/Al interfaces. The calculated free energy ratios for the Pb/Al 100 and 111 interfaces are in good agreement with recent high-resolution transmission electron microscopy measurements. The constructed glue potentials correctly reflects the large change in anisotropy which is observed experimentally between isolated Pb crystals and Pb crystals embedded in Al. Support by the DOE under grants DE-FG02-99ER45773 and DE-AC03-76SF00098, the NSF under grant DMR9619353 and the Danish Natural Sciences Research Council.

Using Empirical Data to Estimate Potential Functions in Commodity Markets: Some Initial Results

NASA Astrophysics Data System (ADS)

Shen, C.; Haven, E.

2017-12-01

This paper focuses on estimating real and quantum potentials from financial commodities. The log returns of six common commodities are considered. We find that some phenomena, such as the vertical potential walls and the time scale issue of the variation on returns, also exists in commodity markets. By comparing the quantum and classical potentials, we attempt to demonstrate that the information within these two types of potentials is different. We believe this empirical result is consistent with the theoretical assumption that quantum potentials (when embedded into social science contexts) may contain some social cognitive or market psychological information, while classical potentials mainly reflect `hard' market conditions. We also compare the two potential forces and explore their relationship by simply estimating the Pearson correlation between them. The Medium or weak interaction effect may indicate that the cognitive system among traders may be affected by those `hard' market conditions.

Branch-point energies and the band-structure lineup at Schottky contacts and heterostrucures

NASA Astrophysics Data System (ADS)

Mönch, Winfried

2011-06-01

Empirical branch-point energies of Si, the group-III nitrides AlN, GaN, and InN, and the group-II and group-III oxides MgO, ZnO, Al2O3 and In2O3 are determined from experimental valance-band offsets of their heterostructures. For Si, GaN, and MgO, these values agree with the branch-point energies obtained from the barrier heights of their Schottky contacts. The empirical branch-point energies of Si and the group-III nitrides are in very good agreement with results of previously published calculations using quite different approaches such as the empirical tight-binding approximation and modern electronic-structure theory. In contrast, the empirical branch-point energies of the group-II and group-III oxides do not confirm the respective theoretical results. As at Schottky contacts, the band-structure lineup at heterostructures is also made up of a zero-charge-transfer term and an intrinsic electric-dipole contribution. Hence, valence-band offsets are not equal to the difference of the branch-point energies of the two semiconductors forming the heterostructure. The electric-dipole term may be described by the electronegativity difference of the two solids in contact. A detailed analysis of experimental Si Schottky barrier heights and heterostructure valence-band offsets explains and proves these conclusions.

When can efforts to control nuisance and invasive species backfire?

USGS Publications Warehouse

Zipkin, E.F.; Kraft, C.E.; Cooch, E.G.; Sullivan, P.J.

2009-01-01

Population control through harvest has the potential to reduce the abundance of nuisance and invasive species. However, demographic structure and density-dependent processes can confound removal efforts and lead to undesirable consequences, such as overcompensation (an increase in abundance in response to harvest) and instability (population cycling or chaos). Recent empirical studies have demonstrated the potential for increased mortality (such as that caused by harvest) to lead to overcompensation and instability in plant, insect, and fish populations. We developed a general population model with juvenile and adult stages to help determine the conditions under which control harvest efforts can produce unintended outcomes. Analytical and simulation analyses of the model demonstrated that the potential for overcompensation as a result of harvest was significant for species with high fecundity, even when annual stage-specific survivorship values were fairly low. Population instability as a result of harvest occurred less frequently and was only possible with harvest strategies that targeted adults when both fecundity and adult survivorship were high. We considered these results in conjunction with current literature on nuisance and invasive species to propose general guidelines for assessing the risks associated with control harvest based on life history characteristics of target populations. Our results suggest that species with high per capita fecundity (over discrete breeding periods), short juvenile stages, and fairly constant survivorship rates are most likely to respond undesirably to harvest. It is difficult to determine the extent to which overcompensation and instability could occur during real-world removal efforts, and more empirical removal studies should be undertaken to evaluate population-level responses to control harvests. Nevertheless, our results identify key issues that have been seldom acknowledged and are potentially generic across taxa. ?? 2009 by the Ecological Society ot America.

When can efforts to control nuisance and invasive species backfire?

PubMed

Zipkin, Elise F; Kraft, Clifford E; Cooch, Evan G; Sullivan, Patrick J

2009-09-01

Population control through harvest has the potential to reduce the abundance of nuisance and invasive species. However, demographic structure and density-dependent processes can confound removal efforts and lead to undesirable consequences, such as overcompensation (an increase in abundance in response to harvest) and instability (population cycling or chaos). Recent empirical studies have demonstrated the potential for increased mortality (such as that caused by harvest) to lead to overcompensation and instability in plant, insect, and fish populations. We developed a general population model with juvenile and adult stages to help determine the conditions under which control harvest efforts can produce unintended outcomes. Analytical and simulation analyses of the model demonstrated that the potential for overcompensation as a result of harvest was significant for species with high fecundity, even when annual stage-specific survivorship values were fairly low. Population instability as a result of harvest occurred less frequently and was only possible with harvest strategies that targeted adults when both fecundity and adult survivorship were high. We considered these results in conjunction with current literature on nuisance and invasive species to propose general guidelines for assessing the risks associated with control harvest based on life history characteristics of target populations. Our results suggest that species with high per capita fecundity (over discrete breeding periods), short juvenile stages, and fairly constant survivorship rates are most likely to respond undesirably to harvest. It is difficult to determine the extent to which overcompensation and instability could occur during real-world removal efforts, and more empirical removal studies should be undertaken to evaluate population-level responses to control harvests. Nevertheless, our results identify key issues that have been seldom acknowledged and are potentially generic across taxa.

Retrieval Interference in Syntactic Processing: The Case of Reflexive Binding in English.

PubMed

Patil, Umesh; Vasishth, Shravan; Lewis, Richard L

2016-01-01

It has been proposed that in online sentence comprehension the dependency between a reflexive pronoun such as himself/herself and its antecedent is resolved using exclusively syntactic constraints. Under this strictly syntactic search account, Principle A of the binding theory-which requires that the antecedent c-command the reflexive within the same clause that the reflexive occurs in-constrains the parser's search for an antecedent. The parser thus ignores candidate antecedents that might match agreement features of the reflexive (e.g., gender) but are ineligible as potential antecedents because they are in structurally illicit positions. An alternative possibility accords no special status to structural constraints: in addition to using Principle A, the parser also uses non-structural cues such as gender to access the antecedent. According to cue-based retrieval theories of memory (e.g., Lewis and Vasishth, 2005), the use of non-structural cues should result in increased retrieval times and occasional errors when candidates partially match the cues, even if the candidates are in structurally illicit positions. In this paper, we first show how the retrieval processes that underlie the reflexive binding are naturally realized in the Lewis and Vasishth (2005) model. We present the predictions of the model under the assumption that both structural and non-structural cues are used during retrieval, and provide a critical analysis of previous empirical studies that failed to find evidence for the use of non-structural cues, suggesting that these failures may be Type II errors. We use this analysis and the results of further modeling to motivate a new empirical design that we use in an eye tracking study. The results of this study confirm the key predictions of the model concerning the use of non-structural cues, and are inconsistent with the strictly syntactic search account. These results present a challenge for theories advocating the infallibility of the human parser in the case of reflexive resolution, and provide support for the inclusion of agreement features such as gender in the set of retrieval cues.

Retrieval Interference in Syntactic Processing: The Case of Reflexive Binding in English

PubMed Central

Patil, Umesh; Vasishth, Shravan; Lewis, Richard L.

2016-01-01

It has been proposed that in online sentence comprehension the dependency between a reflexive pronoun such as himself/herself and its antecedent is resolved using exclusively syntactic constraints. Under this strictly syntactic search account, Principle A of the binding theory—which requires that the antecedent c-command the reflexive within the same clause that the reflexive occurs in—constrains the parser's search for an antecedent. The parser thus ignores candidate antecedents that might match agreement features of the reflexive (e.g., gender) but are ineligible as potential antecedents because they are in structurally illicit positions. An alternative possibility accords no special status to structural constraints: in addition to using Principle A, the parser also uses non-structural cues such as gender to access the antecedent. According to cue-based retrieval theories of memory (e.g., Lewis and Vasishth, 2005), the use of non-structural cues should result in increased retrieval times and occasional errors when candidates partially match the cues, even if the candidates are in structurally illicit positions. In this paper, we first show how the retrieval processes that underlie the reflexive binding are naturally realized in the Lewis and Vasishth (2005) model. We present the predictions of the model under the assumption that both structural and non-structural cues are used during retrieval, and provide a critical analysis of previous empirical studies that failed to find evidence for the use of non-structural cues, suggesting that these failures may be Type II errors. We use this analysis and the results of further modeling to motivate a new empirical design that we use in an eye tracking study. The results of this study confirm the key predictions of the model concerning the use of non-structural cues, and are inconsistent with the strictly syntactic search account. These results present a challenge for theories advocating the infallibility of the human parser in the case of reflexive resolution, and provide support for the inclusion of agreement features such as gender in the set of retrieval cues. PMID:27303315

From Decent Work to Decent Lives: Positive Self and Relational Management (PS&RM) in the Twenty-First Century

PubMed Central

Di Fabio, Annamaria; Kenny, Maureen E.

2016-01-01

The aim of the present study is to empirically test the theoretical model, Positive Self and Relational Management (PS&RM), for a sample of 184 Italian university students. The PS&RM model specifies the development of individuals' strengths, potentials, and talents across the lifespan and with regard to the dialect of self in relationship. PS&RM is defined theoretically by three constructs: Positive Lifelong Life Management, Positive Lifelong Self-Management, Positive Lifelong Relational Management. The three constructs are operationalized as follows: Positive Lifelong Life Management is measured by the Positive and Negative Affect Schedule (PANAS), the Satisfaction With Life Scale (SWLS), the Meaningful Life Measure (MLM), and the Authenticity Scale (AS); Positive Lifelong Self-Management is measured by the Intrapreneurial Self-Capital Scale (ISC), the Career Adapt-Abilities Scale (CAAS), and the Life Project Reflexivity Scale (LPRS); and Positive Lifelong Relational Management is measured by the Trait Emotional Intelligence Questionnaire (TEIQue), the Multidimensional Scale for Perceived Social Support (MSPSS), and the Positive Relational Management Scale (PRMS). Confirmatory factor analysis of the PS&RM model was completed using structural equation modeling. The theoretical PS&RM model was empirically tested as defined by the three hypothesized constructs. Empirical support for this model offers a framework for further research and the design of preventive interventions to promote decent work and decent lives in the twenty-first century. PMID:27047406

Estimating the effects of 17α-ethinylestradiol on stochastic population growth rate of fathead minnows: a population synthesis of empirically derived vital rates.

PubMed

Schwindt, Adam R; Winkelman, Dana L

2016-09-01

Urban freshwater streams in arid climates are wastewater effluent dominated ecosystems particularly impacted by bioactive chemicals including steroid estrogens that disrupt vertebrate reproduction. However, more understanding of the population and ecological consequences of exposure to wastewater effluent is needed. We used empirically derived vital rate estimates from a mesocosm study to develop a stochastic stage-structured population model and evaluated the effect of 17α-ethinylestradiol (EE2), the estrogen in human contraceptive pills, on fathead minnow Pimephales promelas stochastic population growth rate. Tested EE2 concentrations ranged from 3.2 to 10.9 ng L(-1) and produced stochastic population growth rates (λ S ) below 1 at the lowest concentration, indicating potential for population decline. Declines in λ S compared to controls were evident in treatments that were lethal to adult males despite statistically insignificant effects on egg production and juvenile recruitment. In fact, results indicated that λ S was most sensitive to the survival of juveniles and female egg production. More broadly, our results document that population model results may differ even when empirically derived estimates of vital rates are similar among experimental treatments, and demonstrate how population models integrate and project the effects of stressors throughout the life cycle. Thus, stochastic population models can more effectively evaluate the ecological consequences of experimentally derived vital rates.

Evaluation of current Louisiana flexible pavement structures using PMS data and new mechanistic-empirical pavement design guide.

DOT National Transportation Integrated Search

2012-04-01

The new Mechanistic-Empirical Pavement Design Guide (MEPDG) developed under the National Cooperative Highway Research Program (NCHRP) Project 1-37A represents a major change as compared to the 1993 AASHTO Pavement Design Guide. The MEPDG provides a r...

Evaluation of current Louisiana flexible pavement structures using PMS data and new mechanistic-empirical pavement design guide : tech summary.

DOT National Transportation Integrated Search

2012-04-01

The new Mechanistic-Empirical Pavement Design Guide (MEPDG) developed under the National Cooperative Highway : Research Program (NCHRP) Project 1-37A represents a major change as compared to the 1993 AASHTO Pavement : Design Guide. MEPDG provides a r...

Content-Related Knowledge of Biology Teachers from Secondary Schools: Structure and learning opportunities

NASA Astrophysics Data System (ADS)

Großschedl, Jörg; Mahler, Daniela; Kleickmann, Thilo; Harms, Ute

2014-09-01

Teachers' content-related knowledge is a key factor influencing the learning progress of students. Different models of content-related knowledge have been proposed by educational researchers; most of them take into account three categories: content knowledge, pedagogical content knowledge, and curricular knowledge. As there is no consensus about the empirical separability (i.e. empirical structure) of content-related knowledge yet, a total of 134 biology teachers from secondary schools completed three tests which were to capture each of the three categories of content-related knowledge. The empirical structure of content-related knowledge was analyzed by Rasch analysis, which suggests content-related knowledge to be composed of (1) content knowledge, (2) pedagogical content knowledge, and (3) curricular knowledge. Pedagogical content knowledge and curricular knowledge are highly related (rlatent = .70). The latent correlations between content knowledge and pedagogical content knowledge (rlatent = .48)-and curricular knowledge, respectively (rlatent = .35)-are moderate to low (all ps < .001). Beyond the empirical structure of content-related knowledge, different learning opportunities for teachers were investigated with regard to their relationship to content knowledge, pedagogical content knowledge, and curricular knowledge acquisition. Our results show that an in-depth training in teacher education, professional development, and teacher self-study are positively related to particular categories of content-related knowledge. Furthermore, our results indicate that teaching experience is negatively related to curricular knowledge, compared to no significant relationship with content knowledge and pedagogical content knowledge.

The many roles of "explanation" in science education: a case study

NASA Astrophysics Data System (ADS)

Rocksén, Miranda

2016-12-01

In this paper the role of explanations is discussed in relation to possible consequences originating in the polysemy of the word explanation. The present study is a response to conceptual confusions that have arisen in the intersection between theory and practice, and between science education literature and communication in authentic science classroom settings. Science classroom communication is examined in terms of one teacher's word use during eleven lessons about evolution. The study contributes empirical examples of how disciplinary norms of valid explanations are manifested in science classroom communication. A dialogical analysis shows how the teacher provides three conversational structures: asking for acts of explanation, providing opportunities to talk about what explanations are in this context and providing opportunities to talk about explanations constructed by students. These three structures facilitate the process of learning how to evaluate and justify explanations. Three potential meanings of the word "explanation" are pointed to: an everyday meaning, a pedagogical-professional meaning and a scientific meaning of the word. It is suggested that the co-existence of these three potential meanings has communicative consequences in science education.

Implications of the Hierarchical Structure of Psychopathology for Psychiatric Neuroimaging.

PubMed

Zald, David H; Lahey, Benjamin B

2017-05-01

Research into the neurobiological substrates of psychopathology has been impeded by heterogeneity within diagnostic categories, comorbidity among mental disorders, and the presence of symptoms that transcend diagnostic categories. Solutions to these issues increasingly focus neurobiological research on isolated or narrow groupings of symptoms or functional constructs rather than categorical diagnoses. Here we argue for a more integrative approach that also incorporates the broad hierarchical structure of psychopathological symptoms and their etiological mechanisms. This approach places clinical neuroscience research in the context of a hierarchy of empirically defined factors of symptoms such as internalizing disorders, externalizing disorders, and the general factor of psychopathology. Application of this hierarchical approach has the potential to reveal neural substrates that nonspecifically contribute to multiple forms of psychopathology and their comorbidity, and in doing so, facilitate the study of mechanisms that are specific to single dimensions and subsets of symptoms. Neurobiological research on the hierarchy of dimensions of psychopathology is only just beginning to emerge, but has the potential to radically alter our understanding of the neurobiology of abnormal behavior.

In- and Ga-based inorganic double perovskites with direct bandgaps for photovoltaic applications.

PubMed

Dai, Jun; Ma, Liang; Ju, Minggang; Huang, Jinsong; Zeng, Xiao Cheng

2017-08-16

Double perovskites in the form of A 2 B'B''X 6 (A = Cs, B' = Ag, B'' = Bi) have been reported as potential alternatives to lead-containing organometal trihalide perovskites. However, all double perovskites synthesized to date exhibit indirect bandgaps >1.95 eV, which are undesirable for photovoltaic and optoelectronic applications. Herein, we report a comprehensive computer-aided screening of In- and Ga-based double perovskites for potential photovoltaic applications. To this end, several preconditions are implemented for the screening of optimal candidates, which include structural stability, electronic bandgaps, and optical absorption. Importantly, four In- and Ga-based double perovskites are identified to possess direct bandgaps within the desirable range of 0.9-1.6 eV for photovoltaic applications. Dominant optical absorption of the four double perovskites is found to be in the UV range. The structural and thermal stability of the four double perovskites are examined using both the empirical Goldschmidt ratio and convex-hull calculations. Only Cs 2 AgInBr 6 is predicted to be thermodynamically stable.

Implications of the Hierarchical Structure of Psychopathology for Psychiatric Neuroimaging

PubMed Central

Zald, David H.; Lahey, Benjamin B.

2017-01-01

Research into the neurobiological substrates of psychopathology has been impeded by heterogeneity within diagnostic categories, comorbidity among mental disorders, and the presence of symptoms that transcend diagnostic categories. Solutions to these issues increasingly focus neurobiological research on isolated or narrow groupings of symptoms or functional constructs rather than categorical diagnoses. Here we argue for a more integrative approach that also incorporates the broad hierarchical structure of psychopathological symptoms and their etiological mechanisms. This approach places clinical neuroscience research in the context of a hierarchy of empirically defined factors of symptoms such as internalizing disorders, externalizing disorders, and the general factor of psychopathology. Application of this hierarchical approach has the potential to reveal neural substrates that nonspecifically contribute to multiple forms of psychopathology and their comorbidity, and in doing so, facilitate the study of mechanisms that are specific to single dimensions and subsets of symptoms. Neurobiological research on the hierarchy of dimensions of psychopathology is only just beginning to emerge, but has the potential to radically alter our understanding of the neurobiology of abnormal behavior. PMID:28713866

An Empirical Model for Estimating the Probability of Electrical Short Circuits from Tin Whiskers. Part 2

NASA Technical Reports Server (NTRS)

Courey, Karim; Wright, Clara; Asfour, Shihab; Onar, Arzu; Bayliss, Jon; Ludwig, Larry

2009-01-01

In this experiment, an empirical model to quantify the probability of occurrence of an electrical short circuit from tin whiskers as a function of voltage was developed. This empirical model can be used to improve existing risk simulation models. FIB and TEM images of a tin whisker confirm the rare polycrystalline structure on one of the three whiskers studied. FIB cross-section of the card guides verified that the tin finish was bright tin.

Symposium Introduction: Papers on 'Modeling National Health Expenditures'.

PubMed

Getzen, Thomas E; Okunade, Albert A

2017-07-01

Significant contributions have been made since the World Health Organization published Brian Abel-Smith's pioneering comparative study of national health expenditures more than 50 years ago. There have been major advances in theories, model specifications, methodological approaches, and data structures. This introductory essay provides a historical context for this line of work, highlights four newly published studies that move health economics research forward, and indicates several important areas of challenging but potentially fruitful research to strengthen future contributions to the literature and make empirical findings more useful for evaluating health policy decisions. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Delusions and the Right Hemisphere: A Review of the Case for the Right Hemisphere as a Mediator of Reality-Based Belief.

PubMed

Gurin, Lindsey; Blum, Sonja

2017-01-01

Delusions are beliefs that remain fixed despite evidence that they are incorrect. Although the precise neural mechanism of delusional belief remains to be elucidated, there is a predominance of right-hemisphere lesions among patients with delusional syndromes accompanied by structural pathology, suggesting that right-hemisphere lesions, or networks with key nodes in the right hemisphere, may be playing a role. The authors discuss the potential theoretical basis and empiric support for a specific right-hemisphere role in delusion production, drawing on its roles in pragmatic communication; perceptual integration; attentional surveillance and anomaly/novelty detection; and belief updating.

Does export product quality matter for CO2 emissions? Evidence from China.

PubMed

Gozgor, Giray; Can, Muhlis

2017-01-01

This paper re-estimates the environmental Kuznets curve (EKC) in China. To this end, it uses the unit root tests with structural breaks and the autoregressive-distributed lag (ARDL) estimations over the period 1971-2010. The special role is given to the impact of export product quality on CO 2 emissions in the empirical models. The paper finds that the EKC hypothesis is applicable in China. It also observes the positive effect from energy consumption to CO 2 emissions. In addition, it finds that the export product quality is negatively associated with CO 2 emissions. The paper also argues potential implications.

[Management of dog bite trauma of the external genital organs].

PubMed

Dubosq, Francis; Traxer, Olivier; Boublil, Véronique; Gattegno, Bernard; Thibault, Philippe

2004-04-01

Animal bites to the scrotum are rare, but potentially serious. In the light of a personal case, the authors discuss the management of these lesions. An animal bite comprises a triple infectious risk: bacterial, tetanus and rabies. Surgical exploration is indicated for assessment of the structures involved and debridement. The morbidity is related to the severity of the bite and the waiting time before consultation, and complications are rare. Orchidectomy is sometimes necessary, as in the case reported here, and the patient must be warned about this possibility. Antibiotic therapy is empirical: tetracycline and anti-anaerobe antibiotic. Rabies and tetanus prophylaxis must be performed according to vaccine guidelines.

Thermodynamic properties of semiconductor compounds studied based on Debye-Waller factors

NASA Astrophysics Data System (ADS)

Van Hung, Nguyen; Toan, Nguyen Cong; Ba Duc, Nguyen; Vuong, Dinh Quoc

2015-08-01

Thermodynamic properties of semiconductor compounds have been studied based on Debye-Waller factors (DWFs) described by the mean square displacement (MSD) which has close relation with the mean square relative displacement (MSRD). Their analytical expressions have been derived based on the statistical moment method (SMM) and the empirical many-body Stillinger-Weber potentials. Numerical results for the MSDs of GaAs, GaP, InP, InSb, which have zinc-blende structure, are found to be in reasonable agreement with experiment and other theories. This paper shows that an elements value for MSD is dependent on the binary semiconductor compound within which it resides.

Multivariate Qst–Fst Comparisons: A Neutrality Test for the Evolution of the G Matrix in Structured Populations

PubMed Central

Martin, Guillaume; Chapuis, Elodie; Goudet, Jérôme

2008-01-01

Neutrality tests in quantitative genetics provide a statistical framework for the detection of selection on polygenic traits in wild populations. However, the existing method based on comparisons of divergence at neutral markers and quantitative traits (Qst–Fst) suffers from several limitations that hinder a clear interpretation of the results with typical empirical designs. In this article, we propose a multivariate extension of this neutrality test based on empirical estimates of the among-populations (D) and within-populations (G) covariance matrices by MANOVA. A simple pattern is expected under neutrality: D = 2Fst/(1 − Fst)G, so that neutrality implies both proportionality of the two matrices and a specific value of the proportionality coefficient. This pattern is tested using Flury's framework for matrix comparison [common principal-component (CPC) analysis], a well-known tool in G matrix evolution studies. We show the importance of using a Bartlett adjustment of the test for the small sample sizes typically found in empirical studies. We propose a dual test: (i) that the proportionality coefficient is not different from its neutral expectation [2Fst/(1 − Fst)] and (ii) that the MANOVA estimates of mean square matrices between and among populations are proportional. These two tests combined provide a more stringent test for neutrality than the classic Qst–Fst comparison and avoid several statistical problems. Extensive simulations of realistic empirical designs suggest that these tests correctly detect the expected pattern under neutrality and have enough power to efficiently detect mild to strong selection (homogeneous, heterogeneous, or mixed) when it is occurring on a set of traits. This method also provides a rigorous and quantitative framework for disentangling the effects of different selection regimes and of drift on the evolution of the G matrix. We discuss practical requirements for the proper application of our test in empirical studies and potential extensions. PMID:18245845

Detonation Product EOS Studies: Using ISLS to Refine Cheetah

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

Zaug, J M; Howard, W M; Fried, L E

2001-08-08

Knowledge of an effective interatomic potential function underlies any effort to predict or rationalize the properties of solids and liquids. The experiments we undertake are directed towards determination of equilibrium and dynamic properties of simple fluids at densities sufficiently high that traditional computational methods and semi-empirical forms successful at ambient conditions may require reconsideration. In this paper we present high-pressure and temperature experimental sound speed data on a simple fluid, methanol. Impulsive Stimulated Light Scattering (ISLS) conducted on diamond-anvil cell (DAC) encapsulated samples offers an experimental approach to determine cross-pair potential interactions through equation of state determinations. In addition themore » kinetics of structural relaxation in fluids can be studied. We compare our experimental results with our thermochemical computational model Cheetah. Computational models are systematically improved with each addition of experimental data.« less

Sampling the energy landscape of Pt13 with metadynamics

NASA Astrophysics Data System (ADS)

Pavan, Luca; Di Paola, Cono; Baletto, Francesca

2013-02-01

The potential energy surface of a metallic nanoparticle formed by 13 atoms of platinum is efficiently explored using metadynamics in combination with empirical potential molecular dynamics. The scenario obtained is wider and more complex of what was previously reported: more than thirty independent energy basins are found, corresponding to different local minima of Pt. It is demonstrated that in almost all the cases these motifs are local minima even at ab-initio level, hence proving the effectiveness of the method to sample the energy landscape. A classification of the minima in structural families is proposed, and a discussion regarding the shape and the connections between energy basins is reported. ISSPIC 16 - 16th International Symposium on Small Particles and Inorganic Clusters, edited by Kristiaan Temst, Margriet J. Van Bael, Ewald Janssens, H.-G. Boyen and Françoise Remacle.

Integration of the radiation belt environment model into the space weather modeling framework

NASA Astrophysics Data System (ADS)

Glocer, A.; Toth, G.; Fok, M.; Gombosi, T.; Liemohn, M.

2009-11-01

We have integrated the Fok radiation belt environment (RBE) model into the space weather modeling framework (SWMF). RBE is coupled to the global magnetohydrodynamics component (represented by the Block-Adaptive-Tree Solar-wind Roe-type Upwind Scheme, BATS-R-US, code) and the Ionosphere Electrodynamics component of the SWMF, following initial results using the Weimer empirical model for the ionospheric potential. The radiation belt (RB) model solves the convection-diffusion equation of the plasma in the energy range of 10 keV to a few MeV. In stand-alone mode RBE uses Tsyganenko's empirical models for the magnetic field, and Weimer's empirical model for the ionospheric potential. In the SWMF the BATS-R-US model provides the time dependent magnetic field by efficiently tracing the closed magnetic field-lines and passing the geometrical and field strength information to RBE at a regular cadence. The ionosphere electrodynamics component uses a two-dimensional vertical potential solver to provide new potential maps to the RBE model at regular intervals. We discuss the coupling algorithm and show some preliminary results with the coupled code. We run our newly coupled model for periods of steady solar wind conditions and compare our results to the RB model using an empirical magnetic field and potential model. We also simulate the RB for an active time period and find that there are substantial differences in the RB model results when changing either the magnetic field or the electric field, including the creation of an outer belt enhancement via rapid inward transport on the time scale of tens of minutes.

Protection of large predators in a marine reserve alters size-dependent prey mortality

PubMed Central

Gaines, Steven D.; Hamilton, Scott L.; Warner, Robert R.

2017-01-01

Where predator–prey interactions are size-dependent, reductions in predator size owing to fishing has the potential to disrupt the ecological role of top predators in marine ecosystems. In southern California kelp forests, we investigated the size-dependence of the interaction between herbivorous sea urchins and one of their predators, California sheephead (Semicossyphus pulcher). Empirical tests examined how differences in predator size structure between reserve and fished areas affected size-specific urchin mortality. Sites inside marine reserves had greater sheephead size and biomass, while empirical feeding trials indicated that larger sheephead were required to successfully consume urchins of increasing test diameter. Evaluations of the selectivity of sheephead for two urchin species indicated that shorter-spined purple urchins were attacked more frequently and successfully than longer-spined red urchins of the same size class, particularly at the largest test diameters. As a result of these size-specific interactions and the higher biomass of large sheephead inside reserves, urchin mortality rates were three times higher inside the reserve for both species. In addition, urchin mortality rates decreased with urchin size, and very few large urchins were successfully consumed in fished areas. The truncation of sheephead size structure that commonly occurs owing to fishing will probably result in reductions in urchin mortality, which may reduce the resilience of kelp beds to urchin barren formation. By contrast, the recovery of predator size structure in marine reserves may restore this resilience, but may be delayed until fish grow to sizes capable of consuming larger urchins. PMID:28123086

Influence of magnetic field strength and image registration strategy on voxel-based morphometry in a study of Alzheimer's disease.

PubMed

Marchewka, Artur; Kherif, Ferath; Krueger, Gunnar; Grabowska, Anna; Frackowiak, Richard; Draganski, Bogdan

2014-05-01

Multi-centre data repositories like the Alzheimer's Disease Neuroimaging Initiative (ADNI) offer a unique research platform, but pose questions concerning comparability of results when using a range of imaging protocols and data processing algorithms. The variability is mainly due to the non-quantitative character of the widely used structural T1-weighted magnetic resonance (MR) images. Although the stability of the main effect of Alzheimer's disease (AD) on brain structure across platforms and field strength has been addressed in previous studies using multi-site MR images, there are only sparse empirically-based recommendations for processing and analysis of pooled multi-centre structural MR data acquired at different magnetic field strengths (MFS). Aiming to minimise potential systematic bias when using ADNI data we investigate the specific contributions of spatial registration strategies and the impact of MFS on voxel-based morphometry in AD. We perform a whole-brain analysis within the framework of Statistical Parametric Mapping, testing for main effects of various diffeomorphic spatial registration strategies, of MFS and their interaction with disease status. Beyond the confirmation of medial temporal lobe volume loss in AD, we detect a significant impact of spatial registration strategy on estimation of AD related atrophy. Additionally, we report a significant effect of MFS on the assessment of brain anatomy (i) in the cerebellum, (ii) the precentral gyrus and (iii) the thalamus bilaterally, showing no interaction with the disease status. We provide empirical evidence in support of pooling data in multi-centre VBM studies irrespective of disease status or MFS. Copyright © 2013 Wiley Periodicals, Inc.

Multidimensional Knowledge Structures.

ERIC Educational Resources Information Center

Schuh, Kathy L.

Multidimensional knowledge structures, described from a constructivist perspective and aligned with the "Mind as Rhizome" metaphor, provide support for constructivist learning strategies. This qualitative study was conducted to seek empirical support for a description of multidimensional knowledge structures, focusing on the…

Empirical potential for molecular simulation of graphene nanoplatelets

NASA Astrophysics Data System (ADS)

Bourque, Alexander J.; Rutledge, Gregory C.

2018-04-01

A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ˜15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets.

PHEPS: web-based pH-dependent Protein Electrostatics Server

PubMed Central

Kantardjiev, Alexander A.; Atanasov, Boris P.

2006-01-01

PHEPS (pH-dependent Protein Electrostatics Server) is a web service for fast prediction and experiment planning support, as well as for correlation and analysis of experimentally obtained results, reflecting charge-dependent phenomena in globular proteins. Its implementation is based on long-term experience (PHEI package) and the need to explain measured physicochemical characteristics at the level of protein atomic structure. The approach is semi-empirical and based on a mean field scheme for description and evaluation of global and local pH-dependent electrostatic properties: protein proton binding; ionic sites proton population; free energy electrostatic term; ionic groups proton affinities (pKa,i) and their Coulomb interaction with whole charge multipole; electrostatic potential of whole molecule at fixed pH and pH-dependent local electrostatic potentials at user-defined set of points. The speed of calculation is based on fast determination of distance-dependent pair charge-charge interactions as empirical three exponential function that covers charge–charge, charge–dipole and dipole–dipole contributions. After atomic coordinates input, all standard parameters are used as defaults to facilitate non-experienced users. Special attention was given to interactive addition of non-polypeptide charges, extra ionizable groups with intrinsic pKas or fixed ions. The output information is given as plain-text, readable by ‘RasMol’, ‘Origin’ and the like. The PHEPS server is accessible at . PMID:16845042

A technology selection framework for supporting delivery of patient-oriented health interventions in developing countries

PubMed Central

Chan, Connie V.; Kaufman, David R.

2009-01-01

Health information technologies (HIT) have great potential to advance health care globally. In particular, HIT can provide innovative approaches and methodologies to overcome the range of access and resource barriers specific to developing countries. However, there is a paucity of models and empirical evidence informing the technology selection process in these settings. We propose a framework for selecting patient-oriented technologies in developing countries. The selection guidance process is structured by a set of filters that impose particular constraints and serve to narrow the space of possible decisions. The framework consists of three levels of factors: 1) situational factors, 2) the technology and its relationship with health interventions and with target patients, and 3) empirical evidence. We demonstrate the utility of the framework in the context of mobile phones for behavioral health interventions to reduce risk factors for cardiovascular disease. This framework can be applied to health interventions across health domains to explore how and whether available technologies can support delivery of the associated types of interventions and with the target populations. PMID:19796709

Source Characteristics of the Northern Longitudinal Valley, Taiwan Derived from Broadband Strong-Motion Simulation

NASA Astrophysics Data System (ADS)

Wen, Yi-Ying

2018-02-01

The 2014 M L 5.9 Fanglin earthquake occurred at the northern end of the aftershock distribution of the 2013 M L 6.4 Ruisui event and caused strong ground shaking and some damage in the northern part of the Longitudinal Valley. We carried out the strong-motion simulation of the 2014 Fanglin event in the broadband frequency range (0.4-10 Hz) using the empirical Green's function method and then integrated the source models to investigate the source characteristics of the 2013 Ruisui and 2014 Fanglin events. The results show that the dimension of strong motion generation area of the 2013 Ruisui event is smaller, whereas that of the 2014 Fanglin event is comparable with the empirical estimation of inland crustal earthquakes, which indicates the different faulting behaviors. Furthermore, the localized high PGV patch might be caused by the radiation energy amplified by the local low-velocity structure in the northern Longitudinal Valley. Additional study issues are required for building up the knowledge of the potential seismic hazard related to moderate-large events for various seismogenic areas in Taiwan.

Measurement, methods, and divergent patterns: Reassessing the effects of same-sex parents.

PubMed

Cheng, Simon; Powell, Brian

2015-07-01

Scholars have noted that survey analysis of small subsamples-for example, same-sex parent families-is sensitive to researchers' analytical decisions, and even small differences in coding can profoundly shape empirical patterns. As an illustration, we reassess the findings of a recent article by Regnerus regarding the implications of being raised by gay and lesbian parents. Taking a close look at the New Family Structures Study (NFSS), we demonstrate the potential for misclassifying a non-negligible number of respondents as having been raised by parents who had a same-sex romantic relationship. We assess the implications of these possible misclassifications, along with other methodological considerations, by reanalyzing the NFSS in seven steps. The reanalysis offers evidence that the empirical patterns showcased in the original Regnerus article are fragile-so fragile that they appear largely a function of these possible misclassifications and other methodological choices. Our replication and reanalysis of Regnerus's study offer a cautionary illustration of the importance of double checking and critically assessing the implications of measurement and other methodological decisions in our and others' research. Copyright © 2015 Elsevier Inc. All rights reserved.

Health policy--why research it and how: health political science.

PubMed

de Leeuw, Evelyne; Clavier, Carole; Breton, Eric

2014-09-23

The establishment of policy is key to the implementation of actions for health. We review the nature of policy and the definition and directions of health policy. In doing so, we explicitly cast a health political science gaze on setting parameters for researching policy change for health. A brief overview of core theories of the policy process for health promotion is presented, and illustrated with empirical evidence. The key arguments are that (a) policy is not an intervention, but drives intervention development and implementation; (b) understanding policy processes and their pertinent theories is pivotal for the potential to influence policy change; (c) those theories and associated empirical work need to recognise the wicked, multi-level, and incremental nature of elements in the process; and, therefore, (d) the public health, health promotion, and education research toolbox should more explicitly embrace health political science insights. The rigorous application of insights from and theories of the policy process will enhance our understanding of not just how, but also why health policy is structured and implemented the way it is.

Physical-chemical processes of diamond grinding

NASA Astrophysics Data System (ADS)

Lobanov, D. V.; Arhipov, P. V.; Yanyushkin, A. S.; Skeeba, V. Yu

2017-10-01

The article focuses on the relevance of the research into the problem of diamond abrasive metal-bonded tool performance loss with a view to enhancing the effectiveness of high-strength materials finishing processing. The article presents the results of theoretical and empirical studies of loading layer formation on the surface of diamond wheels during processing high-strength materials. The theoretical part deals with the physical and chemical processes at the contact area of the diamond wheel and work surface with the viewpoint of the electrochemical potentials equilibrium state. We defined dependencies for calculating the loading layer dimensions. The practical part of work centers on various electron-microscopic, spectral and X-ray diffraction studies of the metal-bonded wheel samples during diamond grinding. The analysis of the research results revealed the composition and structure of the loading layer. The validity of the theoretical data is confirmed by sufficient convergence of the calculated values with the results of empirical research. In order to reduce the intensity of loading and improve the cutting properties of metal-bonded diamond abrasive tools, it is recommended to use combined methods for more efficient processing of high-strength materials.

Suicide Risk Assessment Training for Psychology Doctoral Programs: Core Competencies and a Framework for Training

PubMed Central

Cramer, Robert J.; Johnson, Shara M.; McLaughlin, Jennifer; Rausch, Emilie M.; Conroy, Mary Alice

2014-01-01

Clinical and counseling psychology programs currently lack adequate evidence-based competency goals and training in suicide risk assessment. To begin to address this problem, this article proposes core competencies and an integrated training framework that can form the basis for training and research in this area. First, we evaluate the extent to which current training is effective in preparing trainees for suicide risk assessment. Within this discussion, sample and methodological issues are reviewed. Second, as an extension of these methodological training issues, we integrate empirically- and expert-derived suicide risk assessment competencies from several sources with the goal of streamlining core competencies for training purposes. Finally, a framework for suicide risk assessment training is outlined. The approach employs Objective Structured Clinical Examination (OSCE) methodology, an approach commonly utilized in medical competency training. The training modality also proposes the Suicide Competency Assessment Form (SCAF), a training tool evaluating self- and observer-ratings of trainee core competencies. The training framework and SCAF are ripe for empirical evaluation and potential training implementation. PMID:24672588

Suicide Risk Assessment Training for Psychology Doctoral Programs: Core Competencies and a Framework for Training.

PubMed

Cramer, Robert J; Johnson, Shara M; McLaughlin, Jennifer; Rausch, Emilie M; Conroy, Mary Alice

2013-02-01

Clinical and counseling psychology programs currently lack adequate evidence-based competency goals and training in suicide risk assessment. To begin to address this problem, this article proposes core competencies and an integrated training framework that can form the basis for training and research in this area. First, we evaluate the extent to which current training is effective in preparing trainees for suicide risk assessment. Within this discussion, sample and methodological issues are reviewed. Second, as an extension of these methodological training issues, we integrate empirically- and expert-derived suicide risk assessment competencies from several sources with the goal of streamlining core competencies for training purposes. Finally, a framework for suicide risk assessment training is outlined. The approach employs Objective Structured Clinical Examination (OSCE) methodology, an approach commonly utilized in medical competency training. The training modality also proposes the Suicide Competency Assessment Form (SCAF), a training tool evaluating self- and observer-ratings of trainee core competencies. The training framework and SCAF are ripe for empirical evaluation and potential training implementation.

Near transferable phenomenological n-body potentials for noble metals

NASA Astrophysics Data System (ADS)

Pontikis, Vassilis; Baldinozzi, Gianguido; Luneville, Laurence; Simeone, David

2017-09-01

We present a semi-empirical model of cohesion in noble metals with suitable parameters reproducing a selected set of experimental properties of perfect and defective lattices in noble metals. It consists of two short-range, n-body terms accounting respectively for attractive and repulsive interactions, the former deriving from the second moment approximation of the tight-binding scheme and the latter from the gas approximation of the kinetic energy of electrons. The stability of the face centred cubic versus the hexagonal compact stacking is obtained via a long-range, pairwise function of customary use with ionic pseudo-potentials. Lattice dynamics, molecular statics, molecular dynamics and nudged elastic band calculations show that, unlike previous potentials, this cohesion model reproduces and predicts quite accurately thermodynamic properties in noble metals. In particular, computed surface energies, largely underestimated by existing empirical cohesion models, compare favourably with measured values, whereas predicted unstable stacking-fault energy profiles fit almost perfectly ab initio evaluations from the literature. All together the results suggest that this semi-empirical model is nearly transferable.

Near transferable phenomenological n-body potentials for noble metals.

PubMed

Pontikis, Vassilis; Baldinozzi, Gianguido; Luneville, Laurence; Simeone, David

2017-09-06

We present a semi-empirical model of cohesion in noble metals with suitable parameters reproducing a selected set of experimental properties of perfect and defective lattices in noble metals. It consists of two short-range, n-body terms accounting respectively for attractive and repulsive interactions, the former deriving from the second moment approximation of the tight-binding scheme and the latter from the gas approximation of the kinetic energy of electrons. The stability of the face centred cubic versus the hexagonal compact stacking is obtained via a long-range, pairwise function of customary use with ionic pseudo-potentials. Lattice dynamics, molecular statics, molecular dynamics and nudged elastic band calculations show that, unlike previous potentials, this cohesion model reproduces and predicts quite accurately thermodynamic properties in noble metals. In particular, computed surface energies, largely underestimated by existing empirical cohesion models, compare favourably with measured values, whereas predicted unstable stacking-fault energy profiles fit almost perfectly ab initio evaluations from the literature. All together the results suggest that this semi-empirical model is nearly transferable.

The Conceptualisation and Measurement of DSM-5 Internet Gaming Disorder: The Development of the IGD-20 Test

PubMed Central

Pontes, Halley M.; Király, Orsolya; Demetrovics, Zsolt; Griffiths, Mark D.

2014-01-01

Background Over the last decade, there has been growing concern about ‘gaming addiction’ and its widely documented detrimental impacts on a minority of individuals that play excessively. The latest (fifth) edition of the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders (DSM-5) included nine criteria for the potential diagnosis of Internet Gaming Disorder (IGD) and noted that it was a condition that warranted further empirical study. Aim: The main aim of this study was to develop a valid and reliable standardised psychometrically robust tool in addition to providing empirically supported cut-off points. Methods A sample of 1003 gamers (85.2% males; mean age 26 years) from 57 different countries were recruited via online gaming forums. Validity was assessed by confirmatory factor analysis (CFA), criterion-related validity, and concurrent validity. Latent profile analysis was also carried to distinguish disordered gamers from non-disordered gamers. Sensitivity and specificity analyses were performed to determine an empirical cut-off for the test. Results The CFA confirmed the viability of IGD-20 Test with a six-factor structure (salience, mood modification, tolerance, withdrawal, conflict and relapse) for the assessment of IGD according to the nine criteria from DSM-5. The IGD-20 Test proved to be valid and reliable. According to the latent profile analysis, 5.3% of the total participants were classed as disordered gamers. Additionally, an optimal empirical cut-off of 71 points (out of 100) seemed to be adequate according to the sensitivity and specificity analyses carried. Conclusions The present findings support the viability of the IGD-20 Test as an adequate standardised psychometrically robust tool for assessing internet gaming disorder. Consequently, the new instrument represents the first step towards unification and consensus in the field of gaming studies. PMID:25313515

A Time-dependent Heliospheric Model Driven by Empirical Boundary Conditions

NASA Astrophysics Data System (ADS)

Kim, T. K.; Arge, C. N.; Pogorelov, N. V.

2017-12-01

Consisting of charged particles originating from the Sun, the solar wind carries the Sun's energy and magnetic field outward through interplanetary space. The solar wind is the predominant source of space weather events, and modeling the solar wind propagation to Earth is a critical component of space weather research. Solar wind models are typically separated into coronal and heliospheric parts to account for the different physical processes and scales characterizing each region. Coronal models are often coupled with heliospheric models to propagate the solar wind out to Earth's orbit and beyond. The Wang-Sheeley-Arge (WSA) model is a semi-empirical coronal model consisting of a potential field source surface model and a current sheet model that takes synoptic magnetograms as input to estimate the magnetic field and solar wind speed at any distance above the coronal region. The current version of the WSA model takes the Air Force Data Assimilative Photospheric Flux Transport (ADAPT) model as input to provide improved time-varying solutions for the ambient solar wind structure. When heliospheric MHD models are coupled with the WSA model, density and temperature at the inner boundary are treated as free parameters that are tuned to optimal values. For example, the WSA-ENLIL model prescribes density and temperature assuming momentum flux and thermal pressure balance across the inner boundary of the ENLIL heliospheric MHD model. We consider an alternative approach of prescribing density and temperature using empirical correlations derived from Ulysses and OMNI data. We use our own modeling software (Multi-scale Fluid-kinetic Simulation Suite) to drive a heliospheric MHD model with ADAPT-WSA input. The modeling results using the two different approaches of density and temperature prescription suggest that the use of empirical correlations may be a more straightforward, consistent method.

Dissociative identity disorder: An empirical overview.

PubMed

Dorahy, Martin J; Brand, Bethany L; Sar, Vedat; Krüger, Christa; Stavropoulos, Pam; Martínez-Taboas, Alfonso; Lewis-Fernández, Roberto; Middleton, Warwick

2014-05-01

Despite its long and auspicious place in the history of psychiatry, dissociative identity disorder (DID) has been associated with controversy. This paper aims to examine the empirical data related to DID and outline the contextual challenges to its scientific investigation. The overview is limited to DID-specific research in which one or more of the following conditions are met: (i) a sample of participants with DID was systematically investigated, (ii) psychometrically-sound measures were utilised, (iii) comparisons were made with other samples, (iv) DID was differentiated from other disorders, including other dissociative disorders, (v) extraneous variables were controlled or (vi) DID diagnosis was confirmed. Following an examination of challenges to research, data are organised around the validity and phenomenology of DID, its aetiology and epidemiology, the neurobiological and cognitive correlates of the disorder, and finally its treatment. DID was found to be a complex yet valid disorder across a range of markers. It can be accurately discriminated from other disorders, especially when structured diagnostic interviews assess identity alterations and amnesia. DID is aetiologically associated with a complex combination of developmental and cultural factors, including severe childhood relational trauma. The prevalence of DID appears highest in emergency psychiatric settings and affects approximately 1% of the general population. Psychobiological studies are beginning to identify clear correlates of DID associated with diverse brain areas and cognitive functions. They are also providing an understanding of the potential metacognitive origins of amnesia. Phase-oriented empirically-guided treatments are emerging for DID. The empirical literature on DID is accumulating, although some areas remain under-investigated. Existing data show DID as a complex, valid and not uncommon disorder, associated with developmental and cultural variables, that is amenable to psychotherapeutic intervention.

An upper bound on the electrical conductivity of hydrated oceanic mantle at the onset of dehydration melting

NASA Astrophysics Data System (ADS)

Naif, Samer

2018-01-01

Electrical conductivity soundings provide important constraints on the thermal and hydration state of the mantle. Recent seafloor magnetotelluric surveys have imaged the electrical conductivity structure of the oceanic upper mantle over a variety of plate ages. All regions show high conductivity (0.02 to 0.2 S/m) at 50 to 150 km depths that cannot be explained with a sub-solidus dry mantle regime without unrealistic temperature gradients. Instead, the conductivity observations require either a small amount of water stored in nominally anhydrous minerals or the presence of interconnected partial melts. This ambiguity leads to dramatically different interpretations on the origin of the asthenosphere. Here, I apply the damp peridotite solidus together with plate cooling models to determine the amount of H2O needed to induce dehydration melting as a function of depth and plate age. Then, I use the temperature and water content estimates to calculate the electrical conductivity of the oceanic mantle with a two-phase mixture of olivine and pyroxene from several competing empirical conductivity models. This represents the maximum potential conductivity of sub-solidus oceanic mantle at the limit of hydration. The results show that partial melt is required to explain the subset of the high conductivity observations beneath young seafloor, irrespective of which empirical model is applied. In contrast, the end-member empirical models predict either nearly dry (<20 wt ppm H2O) or slightly damp (<200 wt ppm H2O) asthenosphere for observations of mature seafloor. Since the former estimate is too dry compared with geochemical constraints from mid-ocean ridge basalts, this suggests the effect of water on mantle conductivity is less pronounced than currently predicted by the conductive end-member empirical model.

The conceptualisation and measurement of DSM-5 Internet Gaming Disorder: the development of the IGD-20 Test.

PubMed

Pontes, Halley M; Király, Orsolya; Demetrovics, Zsolt; Griffiths, Mark D

2014-01-01

Over the last decade, there has been growing concern about 'gaming addiction' and its widely documented detrimental impacts on a minority of individuals that play excessively. The latest (fifth) edition of the American Psychiatric Association's Diagnostic and Statistical Manual of Mental Disorders (DSM-5) included nine criteria for the potential diagnosis of Internet Gaming Disorder (IGD) and noted that it was a condition that warranted further empirical study. The main aim of this study was to develop a valid and reliable standardised psychometrically robust tool in addition to providing empirically supported cut-off points. A sample of 1003 gamers (85.2% males; mean age 26 years) from 57 different countries were recruited via online gaming forums. Validity was assessed by confirmatory factor analysis (CFA), criterion-related validity, and concurrent validity. Latent profile analysis was also carried to distinguish disordered gamers from non-disordered gamers. Sensitivity and specificity analyses were performed to determine an empirical cut-off for the test. The CFA confirmed the viability of IGD-20 Test with a six-factor structure (salience, mood modification, tolerance, withdrawal, conflict and relapse) for the assessment of IGD according to the nine criteria from DSM-5. The IGD-20 Test proved to be valid and reliable. According to the latent profile analysis, 5.3% of the total participants were classed as disordered gamers. Additionally, an optimal empirical cut-off of 71 points (out of 100) seemed to be adequate according to the sensitivity and specificity analyses carried. The present findings support the viability of the IGD-20 Test as an adequate standardised psychometrically robust tool for assessing internet gaming disorder. Consequently, the new instrument represents the first step towards unification and consensus in the field of gaming studies.

Developmant of a Reparametrized Semi-Empirical Force Field to Compute the Rovibrational Structure of Large PAHs

NASA Astrophysics Data System (ADS)

Fortenberry, Ryan

The Spitzer Space Telescope observation of spectra most likely attributable to diverse and abundant populations of polycyclic aromatic hydrocarbons (PAHs) in space has led to tremendous interest in these molecules as tracers of the physical conditions in different astrophysical regions. A major challenge in using PAHs as molecular tracers is the complexity of the spectral features in the 3-20 μm region. The large number and vibrational similarity of the putative PAHs responsible for these spectra necessitate determination for the most accurate basis spectra possible for comparison. It is essential that these spectra be established in order for the regions explored with the newest generation of observatories such as SOFIA and JWST to be understood. Current strategies to develop these spectra for individual PAHs involve either matrixisolation IR measurements or quantum chemical calculations of harmonic vibrational frequencies. These strategies have been employed to develop the successful PAH IR spectral database as a repository of basis functions used to fit astronomically observed spectra, but they are limited in important ways. Both techniques provide an adequate description of the molecules in their electronic, vibrational, and rotational ground state, but these conditions do not represent energetically hot regions for PAHs near strong radiation fields of stars and are not direct representations of the gas phase. Some non-negligible matrix effects are known in condensed-phase studies, and the inclusion of anharmonicity in quantum chemical calculations is essential to generate physically-relevant results especially for hot bands. While scaling factors in either case can be useful, they are agnostic to the system studied and are not robustly predictive. One strategy that has emerged to calculate the molecular vibrational structure uses vibrational perturbation theory along with a quartic force field (QFF) to account for higher-order derivatives of the potential energy surface. QFFs can regularly predict the fundamental vibrational frequencies to within 5 cm-1 of experimentally measured values. This level of accuracy represents a reduction in discrepancies by an order of magnitude compared with harmonic frequencies calculated with density functional theory (DFT). The major limitation of the QFF strategy is that the level of electronic-structure theory required to develop a predictive force field is prohibitively time consuming for molecular systems larger than 5 atoms. Recent advances in QFF techniques utilizing informed DFT approaches have pushed the size of the systems studied up to 24 heavy atoms, but relevant PAHs can have up to hundreds of atoms. We have developed alternative electronic-structure methods that maintain the accuracy of the coupled-cluster calculations extrapolated to the complete basis set limit with relativistic and core correlation corrections applied: the CcCR QFF. These alternative methods are based on simplifications of Hartree—Fock theory in which the computationally intensive two-electron integrals are approximated using empirical parameters. These methods reduce computational time to orders of magnitude less than the CcCR calculations. We have derived a set of optimized empirical parameters to minimize the difference molecular ions of astrochemical significance. We have shown that it is possible to derive a set of empirical parameters that will produce RMS energy differences of less than 2 cm- 1 for our test systems. We are proposing to adopt this reparameterization strategy and some of the lessons learned from the informed DFT studies to create a semi-empirical method whose tremendous speed will allow us to study the rovibrational structure of large PAHs with up to 100s of carbon atoms.

High frequency flow-structural interaction in dense subsonic fluids

NASA Technical Reports Server (NTRS)

Liu, Baw-Lin; Ofarrell, J. M.

1995-01-01

Prediction of the detailed dynamic behavior in rocket propellant feed systems and engines and other such high-energy fluid systems requires precise analysis to assure structural performance. Designs sometimes require placement of bluff bodies in a flow passage. Additionally, there are flexibilities in ducts, liners, and piping systems. A design handbook and interactive data base have been developed for assessing flow/structural interactions to be used as a tool in design and development, to evaluate applicable geometries before problems develop, or to eliminate or minimize problems with existing hardware. This is a compilation of analytical/empirical data and techniques to evaluate detailed dynamic characteristics of both the fluid and structures. These techniques have direct applicability to rocket engine internal flow passages, hot gas drive systems, and vehicle propellant feed systems. Organization of the handbook is by basic geometries for estimating Strouhal numbers, added mass effects, mode shapes for various end constraints, critical onset flow conditions, and possible structural response amplitudes. Emphasis is on dense fluids and high structural loading potential for fatigue at low subsonic flow speeds where high-frequency excitations are possible. Avoidance and corrective measure illustrations are presented together with analytical curve fits for predictions compiled from a comprehensive data base.

The validation and preference among different EAM potentials to describe the solid-liquid transition of aluminum

NASA Astrophysics Data System (ADS)

Jiang, Yewei; Luo, Jie; Wu, Yongquan

2017-06-01

Empirical potential is vital to the classic atomic simulation, especially for the study of phase transitions, as well as the solid-interface. In this paper, we attempt to set up a uniform procedure for the validation among different potentials before the formal simulation study of phase transitions of metals. Two main steps are involved: (1) the prediction of the structures of both solid and liquid phases and their mutual transitions, i.e. melting and crystallization; (2) the prediction of vital thermodynamic (the equilibrium melting point at ambient pressure) and dynamic properties (the degrees of superheating and undercooling). We applied this procedure to the testing of seven published embedded-atom potentials (MKBA (Mendelev et al 2008 Philos. Mag. 88 1723), MFMP (Mishin et al 1999 Phys. Rev. B 59 3393), MDSL (Sturgeon and Laird 2000 Phys. Rev. B 62 14720), ZM (Zope and Mishin 2003 Phys. Rev. B 68 024102), LEA (Liu et al 2004 Model. Simul. Mater. Sci. Eng. 12 665), WKG (Winey et al 2009 Model. Simul. Mater. Sci. Eng. 17 055004) and ZJW (Zhou et al 2004 Phys. Rev. B 69 144113)) for the description of the solid-liquid transition of Al. All the predictions of structure, melting point and superheating/undercooling degrees were compared with the experiments or theoretical calculations. Then, two of them, MKBA and MDSL, were proven suitable for the study of the solid-liquid transition of Al while the residuals were unqualified. However, potential MKBA is more accurate to predict the structures of solid and liquid, while MDSL works a little better in the thermodynamic and dynamic predictions of solid-liquid transitions.

Protein comparability assessments and potential applicability of high throughput biophysical methods and data visualization tools to compare physical stability profiles

PubMed Central

Alsenaidy, Mohammad A.; Jain, Nishant K.; Kim, Jae H.; Middaugh, C. Russell; Volkin, David B.

2014-01-01

In this review, some of the challenges and opportunities encountered during protein comparability assessments are summarized with an emphasis on developing new analytical approaches to better monitor higher-order protein structures. Several case studies are presented using high throughput biophysical methods to collect protein physical stability data as function of temperature, agitation, ionic strength and/or solution pH. These large data sets were then used to construct empirical phase diagrams (EPDs), radar charts, and comparative signature diagrams (CSDs) for data visualization and structural comparisons between the different proteins. Protein samples with different sizes, post-translational modifications, and inherent stability are presented: acidic fibroblast growth factor (FGF-1) mutants, different glycoforms of an IgG1 mAb prepared by deglycosylation, as well as comparisons of different formulations of an IgG1 mAb and granulocyte colony stimulating factor (GCSF). Using this approach, differences in structural integrity and conformational stability profiles were detected under stress conditions that could not be resolved by using the same techniques under ambient conditions (i.e., no stress). Thus, an evaluation of conformational stability differences may serve as an effective surrogate to monitor differences in higher-order structure between protein samples. These case studies are discussed in the context of potential utility in protein comparability studies. PMID:24659968

Protein comparability assessments and potential applicability of high throughput biophysical methods and data visualization tools to compare physical stability profiles.

PubMed

Alsenaidy, Mohammad A; Jain, Nishant K; Kim, Jae H; Middaugh, C Russell; Volkin, David B

2014-01-01

In this review, some of the challenges and opportunities encountered during protein comparability assessments are summarized with an emphasis on developing new analytical approaches to better monitor higher-order protein structures. Several case studies are presented using high throughput biophysical methods to collect protein physical stability data as function of temperature, agitation, ionic strength and/or solution pH. These large data sets were then used to construct empirical phase diagrams (EPDs), radar charts, and comparative signature diagrams (CSDs) for data visualization and structural comparisons between the different proteins. Protein samples with different sizes, post-translational modifications, and inherent stability are presented: acidic fibroblast growth factor (FGF-1) mutants, different glycoforms of an IgG1 mAb prepared by deglycosylation, as well as comparisons of different formulations of an IgG1 mAb and granulocyte colony stimulating factor (GCSF). Using this approach, differences in structural integrity and conformational stability profiles were detected under stress conditions that could not be resolved by using the same techniques under ambient conditions (i.e., no stress). Thus, an evaluation of conformational stability differences may serve as an effective surrogate to monitor differences in higher-order structure between protein samples. These case studies are discussed in the context of potential utility in protein comparability studies.

Structure and stability of small Li2 +(X2Σ+ g )-Xen (n = 1-6) clusters

NASA Astrophysics Data System (ADS)

Saidi, Sameh; Ghanmi, Chedli; Berriche, Hamid

2014-04-01

We have studied the structure and stability of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters for special symmetry groups. The potential energy surfaces of these clusters, are described using an accurate ab initio approach based on non-empirical pseudopotential, parameterized l-dependent polarization potential and analytic potential forms for the Li+Xe and Xe-Xe interactions. The pseudopotential technique has reduced the number of active electrons of Li2 +(X2Σ+ g )-Xe n ( n = 1-6) clusters to only one electron, the Li valence electron. The core-core interactions for Li+Xe are included using accurate CCSD(T) potential fitted using the analytical form of Tang and Toennies. For the Xe-Xe potential interactions we have used the analytical form of Lennard Jones (LJ6 - 12). The potential energy surfaces of the Li2 +(X2Σ+ g )Xe n ( n = 1-6) clusters are performed for a fixed distance of the Li2 +(X2Σ+ g ) alkali dimer, its equilibrium distance. They are used to extract information on the stability of the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters. For each n, the stability of the different isomers is examined by comparing their potential energy surfaces. Moreover, we have determined the quantum energies ( D 0), the zero-point-energies (ZPE) and the ZPE%. To our best knowledge, there are neither experimental nor theoretical works realized for the Li2 +(X2Σ+ g Xe n ( n = 1-6) clusters, our results are presented for the first time.

Next generation interatomic potentials for condensed systems

NASA Astrophysics Data System (ADS)

Handley, Christopher Michael; Behler, Jörg

2014-07-01

The computer simulation of condensed systems is a challenging task. While electronic structure methods like density-functional theory (DFT) usually provide a good compromise between accuracy and efficiency, they are computationally very demanding and thus applicable only to systems containing up to a few hundred atoms. Unfortunately, many interesting problems require simulations to be performed on much larger systems involving thousands of atoms or more. Consequently, more efficient methods are urgently needed, and a lot of effort has been spent on the development of a large variety of potentials enabling simulations with significantly extended time and length scales. Most commonly, these potentials are based on physically motivated functional forms and thus perform very well for the applications they have been designed for. On the other hand, they are often highly system-specific and thus cannot easily be transferred from one system to another. Moreover, their numerical accuracy is restricted by the intrinsic limitations of the imposed functional forms. In recent years, several novel types of potentials have emerged, which are not based on physical considerations. Instead, they aim to reproduce a set of reference electronic structure data as accurately as possible by using very general and flexible functional forms. In this review we will survey a number of these methods. While they differ in the choice of the employed mathematical functions, they all have in common that they provide high-quality potential-energy surfaces, while the efficiency is comparable to conventional empirical potentials. It has been demonstrated that in many cases these potentials now offer a very interesting new approach to study complex systems with hitherto unreached accuracy.

Signs of universality in the structure of culture

NASA Astrophysics Data System (ADS)

Băbeanu, Alexandru-Ionuţ; Talman, Leandros; Garlaschelli, Diego

2017-11-01

Understanding the dynamics of opinions, preferences and of culture as whole requires more use of empirical data than has been done so far. It is clear that an important role in driving this dynamics is played by social influence, which is the essential ingredient of many quantitative models. Such models require that all traits are fixed when specifying the "initial cultural state". Typically, this initial state is randomly generated, from a uniform distribution over the set of possible combinations of traits. However, recent work has shown that the outcome of social influence dynamics strongly depends on the nature of the initial state. If the latter is sampled from empirical data instead of being generated in a uniformly random way, a higher level of cultural diversity is found after long-term dynamics, for the same level of propensity towards collective behavior in the short-term. Moreover, if the initial state is randomized by shuffling the empirical traits among people, the level of long-term cultural diversity is in-between those obtained for the empirical and uniformly random counterparts. The current study repeats the analysis for multiple empirical data sets, showing that the results are remarkably similar, although the matrix of correlations between cultural variables clearly differs across data sets. This points towards robust structural properties inherent in empirical cultural states, possibly due to universal laws governing the dynamics of culture in the real world. The results also suggest that this dynamics might be characterized by criticality and involve mechanisms beyond social influence.

Solute–solute correlations responsible for the prepeak in structure factors of undercooled Al-rich liquids: A molecular dynamics study

DOE PAGES

Zhang, Feng; Sun, Yang; Ye, Zhuo; ...

2015-05-06

In this study, we have performed molecular dynamics simulations on a typical Al-based alloy Al 90Sm 10. The short-range and medium-range correlations of the system are reliably produced by ab initio calculations, whereas the long-range correlations are obtained with the assistance of a semi-empirical potential well-fitted to ab initio data. Our calculations show that a prepeak in the structure factor of this system emerges well above the melting temperature, and the intensity of the prepeak increases with increasing undercooling of the liquid. These results are in agreement with x-ray diffraction experiments. The interplay between the short-range order of the systemmore » originating from the large affinity between Al and Sm atoms, and the intrinsic repulsion between Sm atoms gives rise to a stronger correlation in the second peak than the first peak in the Sm–Sm partial pair correlation function (PPCF), which in turn produces the prepeak in the structure factor.« less

Competition between conceptual relations affects compound recognition: the role of entropy.

PubMed

Schmidtke, Daniel; Kuperman, Victor; Gagné, Christina L; Spalding, Thomas L

2016-04-01

Previous research has suggested that the conceptual representation of a compound is based on a relational structure linking the compound's constituents. Existing accounts of the visual recognition of modifier-head or noun-noun compounds posit that the process involves the selection of a relational structure out of a set of competing relational structures associated with the same compound. In this article, we employ the information-theoretic metric of entropy to gauge relational competition and investigate its effect on the visual identification of established English compounds. The data from two lexical decision megastudies indicates that greater entropy (i.e., increased competition) in a set of conceptual relations associated with a compound is associated with longer lexical decision latencies. This finding indicates that there exists competition between potential meanings associated with the same complex word form. We provide empirical support for conceptual composition during compound word processing in a model that incorporates the effect of the integration of co-activated and competing relational information.

The application of quantum mechanics in structure-based drug design.

PubMed

Mucs, Daniel; Bryce, Richard A

2013-03-01

Computational chemistry has become an established and valuable component in structure-based drug design. However the chemical complexity of many ligands and active sites challenges the accuracy of the empirical potentials commonly used to describe these systems. Consequently, there is a growing interest in utilizing electronic structure methods for addressing problems in protein-ligand recognition. In this review, the authors discuss recent progress in the development and application of quantum chemical approaches to modeling protein-ligand interactions. The authors specifically consider the development of quantum mechanics (QM) approaches for studying large molecular systems pertinent to biology, focusing on protein-ligand docking, protein-ligand binding affinities and ligand strain on binding. Although computation of binding energies remains a challenging and evolving area, current QM methods can underpin improved docking approaches and offer detailed insights into ligand strain and into the nature and relative strengths of complex active site interactions. The authors envisage that QM will become an increasingly routine and valued tool of the computational medicinal chemist.

A novel structure-aware sparse learning algorithm for brain imaging genetics.

PubMed

Du, Lei; Jingwen, Yan; Kim, Sungeun; Risacher, Shannon L; Huang, Heng; Inlow, Mark; Moore, Jason H; Saykin, Andrew J; Shen, Li

2014-01-01

Brain imaging genetics is an emergent research field where the association between genetic variations such as single nucleotide polymorphisms (SNPs) and neuroimaging quantitative traits (QTs) is evaluated. Sparse canonical correlation analysis (SCCA) is a bi-multivariate analysis method that has the potential to reveal complex multi-SNP-multi-QT associations. Most existing SCCA algorithms are designed using the soft threshold strategy, which assumes that the features in the data are independent from each other. This independence assumption usually does not hold in imaging genetic data, and thus inevitably limits the capability of yielding optimal solutions. We propose a novel structure-aware SCCA (denoted as S2CCA) algorithm to not only eliminate the independence assumption for the input data, but also incorporate group-like structure in the model. Empirical comparison with a widely used SCCA implementation, on both simulated and real imaging genetic data, demonstrated that S2CCA could yield improved prediction performance and biologically meaningful findings.

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

Callear, Samantha K.; Imberti, Silvia; Johnston, Andrew

The aqueous solution of dopamine hydrochloride has been investigated using neutron and X-ray total scattering data together with Monte-Carlo based modelling using Empirical Potential Structure Refinement. The conformation of the protonated dopamine molecule is presented and the results compared to the conformations found in crystal structures, dopamine-complexed protein crystal structures and predicted from theoretical calculations and pharmacophoric models. It is found that protonated dopamine adopts a range of conformations in solution, highlighting the low rotational energy barrier between different conformations, with the preferred conformation being trans-perpendicular. The interactions between each of the species present (protonated dopamine molecules, water molecules, andmore » chloride anions) have been determined and are discussed with reference to interactions observed in similar systems both in the liquid and crystalline state, and predicted from theoretical calculations. The expected strong hydrogen bonds between the strong hydrogen bond donors and acceptors are observed, together with evidence of weaker CH hydrogen bonds and π interactions also playing a significant role in determining the arrangement of adjacent molecules.« less

From bismuth oxide/hydroxide precursor clusters towards stable oxides: Proton transfer reactions and structural reorganization govern the stability of [Bi18O13(OH)10]-nitrate clusters

NASA Astrophysics Data System (ADS)

Walther, M.; Zahn, D.

2018-01-01

Structural relaxation and stability of a Bi18-cluster as obtained from association of [Bi6O4(OH)4](NO3)6 precursor clusters in DMSO solution is investigated from a combination of quantum chemical calculations and μs-scale molecular dynamics simulations using empirical interaction potentials. The Bi18-cluster undergoes a OH⋯OH proton transfer reaction, followed by considerable structural relaxation. While the aggregation of the Bi18-cluster is induced by the dissociation of a single nitrate ion leading to [Bi6O4(OH)4](NO3)5+ as an activated precursor species that can bind two more Bi6-clusters, we find the [Bi18O13(OH)10](NO3)18-x+x species (explored for x = 1-6) rather inert against either nitrate dissociation, collision with Bi6-precursors or combinations thereof.

Modeling of time dependent localized flow shear stress and its impact on cellular growth within additive manufactured titanium implants

PubMed Central

Zhang, Ziyu; Yuan, Lang; Lee, Peter D; Jones, Eric; Jones, Julian R

2014-01-01

Bone augmentation implants are porous to allow cellular growth, bone formation and fixation. However, the design of the pores is currently based on simple empirical rules, such as minimum pore and interconnects sizes. We present a three-dimensional (3D) transient model of cellular growth based on the Navier–Stokes equations that simulates the body fluid flow and stimulation of bone precursor cellular growth, attachment, and proliferation as a function of local flow shear stress. The model's effectiveness is demonstrated for two additive manufactured (AM) titanium scaffold architectures. The results demonstrate that there is a complex interaction of flow rate and strut architecture, resulting in partially randomized structures having a preferential impact on stimulating cell migration in 3D porous structures for higher flow rates. This novel result demonstrates the potential new insights that can be gained via the modeling tool developed, and how the model can be used to perform what-if simulations to design AM structures to specific functional requirements. PMID:24664988

On the solvation of the phosphocholine headgroup in an aqueous propylene glycol solution

NASA Astrophysics Data System (ADS)

Rhys, Natasha H.; Al-Badri, Mohamed Ali; Ziolek, Robert M.; Gillams, Richard J.; Collins, Louise E.; Lawrence, M. Jayne; Lorenz, Christian D.; McLain, Sylvia E.

2018-04-01

The atomic-scale structure of the phosphocholine (PC) headgroup in 30 mol. % propylene glycol (PG) in an aqueous solution has been investigated using a combination of neutron diffraction with isotopic substitution experiments and computer simulation techniques—molecular dynamics and empirical potential structure refinement. Here, the hydration of the PC headgroup remains largely intact compared with the hydration of this group in a bilayer and in a bulk water solution, with the PG molecules showing limited interactions with the headgroup. When direct PG interactions with PC do occur, they are most likely to coordinate to the 3+N (CH 3 ) motifs. Further, PG does not affect the bulk water structure and the addition of PC does not perturb the PG-solvent interactions. This suggests that the reason why PG is able to penetrate into membranes easily is that it does not form strong-hydrogen bonding or electrostatic interactions with the headgroup allowing it to easily move across the membrane barrier.

A unified relation for the solid-liquid interface free energy of pure FCC, BCC, and HCP metals

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

Wilson, S. R.; Mendelev, M. I., E-mail: mendelev@ameslab.gov

2016-04-14

We study correlations between the solid-liquid interface (SLI) free energy and bulk material properties (melting temperature, latent heat, and liquid structure) through the determination of SLI free energies for bcc and hcp metals from molecular dynamics (MD) simulation. Values obtained for the bcc metals in this study were compared to values predicted by the Turnbull, Laird, and Ewing relations on the basis of previously published MD simulation data. We found that of these three empirical relations, the Ewing relation better describes the MD simulation data. Moreover, whereas the original Ewing relation contains two constants for a particular crystal structure, wemore » found that the first coefficient in the Ewing relation does not depend on crystal structure, taking a common value for all three phases, at least for the class of the systems described by embedded-atom method potentials (which are considered to provide a reasonable approximation for metals).« less

N-Loop Learning: Part II--An Empirical Investigation

ERIC Educational Resources Information Center

Simonin, Bernard L.

2017-01-01

Purpose: Through a survey of firm's experiences with strategic alliances and a structural equation modeling approach, the aim of this study is to stimulate further interest in modeling and empirical research in the area of N-loop learning. Although the concepts of single-loop and double-loop learning, in particular, are well established in the…

Empirical Studies of Interactions of Semantic Roles: The Agent and Patient in Mandarin Chinese

ERIC Educational Resources Information Center

Yue, Kun

2010-01-01

This dissertation investigates the interaction between form and function in Mandarin Chinese by empirically examining the interactions of core semantic roles (Agent and Patient) and the syntactic representation of those interactions in semantically transitive events. First, I demonstrate that syntactic structures and functions are intertwined with…

Understanding Transactional Distance in Web-Based Learning Environments: An Empirical Study

ERIC Educational Resources Information Center

Huang, Xiaoxia; Chandra, Aruna; DePaolo, Concetta A.; Simmons, Lakisha L.

2016-01-01

Transactional distance is an important pedagogical theory in distance education that calls for more empirical support. The purpose of this study was to verify the theory by operationalizing and examining the relationship of (1) dialogue, structure and learner autonomy to transactional distance, and (2) environmental factors and learner demographic…

Modeling Lolium perenne L. roots in the presence of empirical black holes

USDA-ARS?s Scientific Manuscript database

Plant root models are designed for understanding structural or functional aspects of root systems. When a process is not thoroughly understood, a black box object is used. However, when a process exists but empirical data do not indicate its existence, you have a black hole. The object of this re...

Empirical modeling of dynamic behaviors of pneumatic artificial muscle actuators.

PubMed

Wickramatunge, Kanchana Crishan; Leephakpreeda, Thananchai

2013-11-01

Pneumatic Artificial Muscle (PAM) actuators yield muscle-like mechanical actuation with high force to weight ratio, soft and flexible structure, and adaptable compliance for rehabilitation and prosthetic appliances to the disabled as well as humanoid robots or machines. The present study is to develop empirical models of the PAM actuators, that is, a PAM coupled with pneumatic control valves, in order to describe their dynamic behaviors for practical control design and usage. Empirical modeling is an efficient approach to computer-based modeling with observations of real behaviors. Different characteristics of dynamic behaviors of each PAM actuator are due not only to the structures of the PAM actuators themselves, but also to the variations of their material properties in manufacturing processes. To overcome the difficulties, the proposed empirical models are experimentally derived from real physical behaviors of the PAM actuators, which are being implemented. In case studies, the simulated results with good agreement to experimental results, show that the proposed methodology can be applied to describe the dynamic behaviors of the real PAM actuators. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Stellar atmospheric structural patterns

NASA Technical Reports Server (NTRS)

Thomas, R. N.

1983-01-01

The thermodynamics of stellar atmospheres is discussed. Particular attention is given to the relation between theoretical modeling and empirical evidence. The characteristics of distinctive atmospheric regions and their radical structures are discussed.

Attachment-Based Family Therapy: A Review of the Empirical Support.

PubMed

Diamond, Guy; Russon, Jody; Levy, Suzanne

2016-09-01

Attachment-based family therapy (ABFT) is an empirically supported treatment designed to capitalize on the innate, biological desire for meaningful and secure relationships. The therapy is grounded in attachment theory and provides an interpersonal, process-oriented, trauma-focused approach to treating adolescent depression, suicidality, and trauma. Although a process-oriented therapy, ABFT offers a clear structure and road map to help therapists quickly address attachment ruptures that lie at the core of family conflict. Several clinical trials and process studies have demonstrated empirical support for the model and its proposed mechanism of change. This article provides an overview of the clinical model and the existing empirical support for ABFT. © 2016 Family Process Institute.

Differentiating between appraisal process and product in cognitive theories of posttraumatic stress

PubMed Central

Nanney, John T.; Constans, Joseph I.; Kimbrell, Timothy A.; Kramer, Teresa L.; Pyne, Jeffrey M.

2014-01-01

Biased appraisal is central to cognitive theories of posttraumatic stress, but little research has examined the potentially distinct meanings of the term. The on-going process of appraising social information and the beliefs that emerge as products of that process can be distinguished conceptually. The present study sought to examine if these two meanings are empirically distinct as well, and if so, to begin exploring potential relations between these appraisal constructs and posttraumatic stress symptoms. Soldiers (N = 424) preparing for deployment to Iraq or Afghanistan were administered measures of each construct. Results of confirmatory factor analysis suggest that the appraisal process and the products of that process (i.e., beliefs) are indeed distinct. Structural equation models are consistent with cognitive bias and social information processing literatures which posit that a biased appraisal process may contribute to the development of dysfunctional beliefs and posttraumatic stress symptoms following trauma. The potential utility of distinctly conceptualizing and measuring the appraisal process in both clinical and research settings is discussed. PMID:26147520

Differentiating between appraisal process and product in cognitive theories of posttraumatic stress.

PubMed

Nanney, John T; Constans, Joseph I; Kimbrell, Timothy A; Kramer, Teresa L; Pyne, Jeffrey M

2015-07-01

Biased appraisal is central to cognitive theories of posttraumatic stress, but little research has examined the potentially distinct meanings of the term. The ongoing process of appraising social information and the beliefs that emerge as products of that process can be distinguished conceptually. This study sought to examine whether these 2 meanings are empirically distinct as well, and if so, to begin exploring potential relations between these appraisal constructs and posttraumatic stress symptoms. Soldiers (N = 424) preparing for deployment to Iraq or Afghanistan were administered measures of each construct. Results of confirmatory factor analysis suggest that the appraisal process and the products of that process (i.e., beliefs) are indeed distinct. Structural equation models are consistent with cognitive bias and social information processing literatures, which posit that a biased appraisal process may contribute to the development of dysfunctional beliefs and posttraumatic stress symptoms following trauma. The potential utility of distinctly conceptualizing and measuring the appraisal process in both clinical and research settings is discussed. (c) 2015 APA, all rights reserved).

Critical assessment of Pt surface energy - An atomistic study

NASA Astrophysics Data System (ADS)

Kim, Jin-Soo; Seol, Donghyuk; Lee, Byeong-Joo

2018-04-01

Despite the fact that surface energy is a fundamental quantity in understanding surface structure of nanoparticle, the results of experimental measurements and theoretical calculations for the surface energy of pure Pt show a wide range of scattering. It is necessary to further ensure the surface energy of Pt to find the equilibrium shape and atomic configuration in Pt bimetallic nanoparticles accurately. In this article, we critically assess and optimize the Pt surface energy using a semi-empirical atomistic approach based on the second nearest-neighbor modified embedded-atom method interatomic potential. That is, the interatomic potential of pure Pt was adjusted in a way that the surface segregation tendency in a wide range of Pt binary alloys is reproduced in accordance with experimental information. The final optimized Pt surface energy (mJ/m2) is 2036 for (100) surface, 2106 for (110) surface, and 1502 for (111) surface. The potential can be utilized to find the equilibrium shape and atomic configuration of Pt bimetallic nanoparticles more accurately.

Mapping Topographic Structure in White Matter Pathways with Level Set Trees

PubMed Central

Kent, Brian P.; Rinaldo, Alessandro; Yeh, Fang-Cheng; Verstynen, Timothy

2014-01-01

Fiber tractography on diffusion imaging data offers rich potential for describing white matter pathways in the human brain, but characterizing the spatial organization in these large and complex data sets remains a challenge. We show that level set trees–which provide a concise representation of the hierarchical mode structure of probability density functions–offer a statistically-principled framework for visualizing and analyzing topography in fiber streamlines. Using diffusion spectrum imaging data collected on neurologically healthy controls (N = 30), we mapped white matter pathways from the cortex into the striatum using a deterministic tractography algorithm that estimates fiber bundles as dimensionless streamlines. Level set trees were used for interactive exploration of patterns in the endpoint distributions of the mapped fiber pathways and an efficient segmentation of the pathways that had empirical accuracy comparable to standard nonparametric clustering techniques. We show that level set trees can also be generalized to model pseudo-density functions in order to analyze a broader array of data types, including entire fiber streamlines. Finally, resampling methods show the reliability of the level set tree as a descriptive measure of topographic structure, illustrating its potential as a statistical descriptor in brain imaging analysis. These results highlight the broad applicability of level set trees for visualizing and analyzing high-dimensional data like fiber tractography output. PMID:24714673

Ferroelectricity in corundum derivatives

NASA Astrophysics Data System (ADS)

Ye, Meng; Vanderbilt, David

The search for new ferroelectric (FE) materials holds promise for broadening our understanding of FE mechanisms and extending the range of application of FE materials. The known FE materials LiNbO3 can be regarded as derived from the A2O3 corundum structure with cation ordering. Here we consider more general binary (AB O3) and ternary (A2 BB' O6) corundum derivatives as an extended class of potential FE materials, motivated by the fact that some members of this class have recently been synthesized. There are four structure types for these corundum derivatives, and the number of cation combinations is enormous, but in many cases the energy barriers for polarization reversal may be too large to allow FE behavior. Here we present a first-principles study of the polar structure, coherent FE barrier, and domain-wall switching barrier for a representative set of polar corundum derivatives, allowing us to identify several potentially new FE materials. We also discuss the conditions under which ferroelectricity is compatible with magnetic ordering. Finally, we identify several empirical measures that can provide a rule of thumb for estimating the barrier energies. Our results should assist in the experimental search for new FE materials in the corundum derivative family. This work is supported by ONR Grant No. N-00014-12-1-1035.

The phase diagram of water at negative pressures: virtual ices.

PubMed

Conde, M M; Vega, C; Tribello, G A; Slater, B

2009-07-21

The phase diagram of water at negative pressures as obtained from computer simulations for two models of water, TIP4P/2005 and TIP5P is presented. Several solid structures with lower densities than ice Ih, so-called virtual ices, were considered as possible candidates to occupy the negative pressure region of the phase diagram of water. In particular the empty hydrate structures sI, sII, and sH and another, recently proposed, low-density ice structure. The relative stabilities of these structures at 0 K was determined using empirical water potentials and density functional theory calculations. By performing free energy calculations and Gibbs-Duhem integration the phase diagram of TIP4P/2005 was determined at negative pressures. The empty hydrates sII and sH appear to be the stable solid phases of water at negative pressures. The phase boundary between ice Ih and sII clathrate occurs at moderate negative pressures, while at large negative pressures sH becomes the most stable phase. This behavior is in reasonable agreement with what is observed in density functional theory calculations.

Characterization and optimization of spiral eddy current coils for in-situ crack detection

NASA Astrophysics Data System (ADS)

Mandache, Catalin

2018-03-01

In-situ condition-based maintenance is making strides in the aerospace industry and it is seen as an alternative to scheduled, time-based maintenance. With fatigue cracks originating from fastener holes as the main reason for structural failures, embedded eddy current coils are a viable non-invasive solution for their timely detection. The development and potential broad use of these coils are motivated by a few consistent arguments: (i) inspection of structures of complicated geometries and hard to access areas, that often require disassembly, (ii) alternative to regular inspection actions that could introduce inadvertent damage, (iii) for structures that have short inspection intervals, and (iv) for repaired structures where fastener holes contain bushings and prevent further bolt-hole inspections. Since the spiral coils are aiming at detecting radial cracks emanating from the fastener holes, their design parameters should allow for high inductance, low ohmic losses and power requirements, as well as optimal size and high sensitivity to discontinuities. In this study, flexible, surface conformable, spiral eddy current coils are empirically investigated on mock-up specimens, while numerical analysis is performed for their optimization and design improvement.

A review of covariate selection for non-experimental comparative effectiveness research.

PubMed

Sauer, Brian C; Brookhart, M Alan; Roy, Jason; VanderWeele, Tyler

2013-11-01

This paper addresses strategies for selecting variables for adjustment in non-experimental comparative effectiveness research and uses causal graphs to illustrate the causal network that relates treatment to outcome. Variables in the causal network take on multiple structural forms. Adjustment for a common cause pathway between treatment and outcome can remove confounding, whereas adjustment for other structural types may increase bias. For this reason, variable selection would ideally be based on an understanding of the causal network; however, the true causal network is rarely known. Therefore, we describe more practical variable selection approaches based on background knowledge when the causal structure is only partially known. These approaches include adjustment for all observed pretreatment variables thought to have some connection to the outcome, all known risk factors for the outcome, and all direct causes of the treatment or the outcome. Empirical approaches, such as forward and backward selection and automatic high-dimensional proxy adjustment, are also discussed. As there is a continuum between knowing and not knowing the causal, structural relations of variables, we recommend addressing variable selection in a practical way that involves a combination of background knowledge and empirical selection and that uses high-dimensional approaches. This empirical approach can be used to select from a set of a priori variables based on the researcher's knowledge to be included in the final analysis or to identify additional variables for consideration. This more limited use of empirically derived variables may reduce confounding while simultaneously reducing the risk of including variables that may increase bias. Copyright © 2013 John Wiley & Sons, Ltd.

A Review of Covariate Selection for Nonexperimental Comparative Effectiveness Research

PubMed Central

Sauer, Brian C.; Brookhart, Alan; Roy, Jason; Vanderweele, Tyler

2014-01-01

This paper addresses strategies for selecting variables for adjustment in non-experimental comparative effectiveness research (CER), and uses causal graphs to illustrate the causal network that relates treatment to outcome. Variables in the causal network take on multiple structural forms. Adjustment for on a common cause pathway between treatment and outcome can remove confounding, while adjustment for other structural types may increase bias. For this reason variable selection would ideally be based on an understanding of the causal network; however, the true causal network is rarely know. Therefore, we describe more practical variable selection approaches based on background knowledge when the causal structure is only partially known. These approaches include adjustment for all observed pretreatment variables thought to have some connection to the outcome, all known risk factors for the outcome, and all direct causes of the treatment or the outcome. Empirical approaches, such as forward and backward selection and automatic high-dimensional proxy adjustment, are also discussed. As there is a continuum between knowing and not knowing the causal, structural relations of variables, we recommend addressing variable selection in a practical way that involves a combination of background knowledge and empirical selection and that uses the high-dimensional approaches. This empirical approach can be used to select from a set of a priori variables based on the researcher’s knowledge to be included in the final analysis or to identify additional variables for consideration. This more limited use of empirically-derived variables may reduce confounding while simultaneously reducing the risk of including variables that may increase bias. PMID:24006330

Analysis of the local structure around Cr3+ centers in perovskite KMgF3 using both ab initio (DFT) and semi-empirical (SPM) calculations

NASA Astrophysics Data System (ADS)

Emül, Y.; Erbahar, D.; Açıkgöz, M.

2014-11-01

The local structure around Cr3+ centers in perovskite KMgF3 crystal have been investigated through the applications of both an ab-initio, density functional theory (DFT), and a semi empirical, superposition model (SPM), analyses. A supercell approach is used for DFT calculations. All the tetragonal (Cr3+-VMg and Cr3+-Li+), trigonal (Cr3+-VK), and CrF5O cluster centers have been considered with various structural models based on the previously suggested experimental inferences. The significant structural changes around the Cr3+ centers induced by Mg2+ or K+ vacancies and the Li substitution at those vacancy sites have been determined and discussed by means of charge distribution. This study provides insight on both the roles of Mg2+ and K+ vacancies and Li+ ion in the local structural properties around Cr3+ centers in KMgF3.

A genetic-algorithm approach for assessing the liquefaction potential of sandy soils

NASA Astrophysics Data System (ADS)

Sen, G.; Akyol, E.

2010-04-01

The determination of liquefaction potential is required to take into account a large number of parameters, which creates a complex nonlinear structure of the liquefaction phenomenon. The conventional methods rely on simple statistical and empirical relations or charts. However, they cannot characterise these complexities. Genetic algorithms are suited to solve these types of problems. A genetic algorithm-based model has been developed to determine the liquefaction potential by confirming Cone Penetration Test datasets derived from case studies of sandy soils. Software has been developed that uses genetic algorithms for the parameter selection and assessment of liquefaction potential. Then several estimation functions for the assessment of a Liquefaction Index have been generated from the dataset. The generated Liquefaction Index estimation functions were evaluated by assessing the training and test data. The suggested formulation estimates the liquefaction occurrence with significant accuracy. Besides, the parametric study on the liquefaction index curves shows a good relation with the physical behaviour. The total number of misestimated cases was only 7.8% for the proposed method, which is quite low when compared to another commonly used method.

Higher Education Structure and Education Outcomes: Evidence from the USA

ERIC Educational Resources Information Center

Koedel, Cory

2014-01-01

This paper documents substantial differences across states in their higher education (HE) structures and highlights several empirical relationships between these structures and individuals' HE outcomes. Not surprisingly, individuals who are exposed to more-fractionalized HE structures are more likely to attend small public universities and…

Empirical estimates to reduce modeling uncertainties of soil organic carbon in permafrost regions: a review of recent progress and remaining challenges

USGS Publications Warehouse

Mishra, U.; Jastrow, J.D.; Matamala, R.; Hugelius, G.; Koven, C.D.; Harden, Jennifer W.; Ping, S.L.; Michaelson, G.J.; Fan, Z.; Miller, R.M.; McGuire, A.D.; Tarnocai, C.; Kuhry, P.; Riley, W.J.; Schaefer, K.; Schuur, E.A.G.; Jorgenson, M.T.; Hinzman, L.D.

2013-01-01

The vast amount of organic carbon (OC) stored in soils of the northern circumpolar permafrost region is a potentially vulnerable component of the global carbon cycle. However, estimates of the quantity, decomposability, and combustibility of OC contained in permafrost-region soils remain highly uncertain, thereby limiting our ability to predict the release of greenhouse gases due to permafrost thawing. Substantial differences exist between empirical and modeling estimates of the quantity and distribution of permafrost-region soil OC, which contribute to large uncertainties in predictions of carbon–climate feedbacks under future warming. Here, we identify research challenges that constrain current assessments of the distribution and potential decomposability of soil OC stocks in the northern permafrost region and suggest priorities for future empirical and modeling studies to address these challenges.

The Civic Effects of Schools: Theory and Empirics

ERIC Educational Resources Information Center

Bischoff, Kendra

2016-01-01

In concert with policy trends, theory and research on the ways in which school context affects student outcomes have focused almost exclusively on academic achievement in recent years. Given the fundamental role that schools should play in civic education, and the potential for schools to affect civic equality, more empirical and theoretical…

Gathering Empirical Evidence Concerning Links between Computer Aided Design (CAD) and Creativity

ERIC Educational Resources Information Center

Musta'amal, Aede Hatib; Norman, Eddie; Hodgson, Tony

2009-01-01

Discussion is often reported concerning potential links between computer-aided designing and creativity, but there is a lack of systematic enquiry to gather empirical evidence concerning such links. This paper reports an indication of findings from other research studies carried out in contexts beyond general education that have sought evidence…

A Glimpse of Challenges and Benefits Associated with Collaborative Postgraduate Programmes in Sub-Saharan African Universities

ERIC Educational Resources Information Center

Mundia, Lisho C.

2017-01-01

The paper presents empirical findings on the potential benefits and challenges associated with collaborative postgraduate programs between African universities. It reflects the empirical benefits and challenges towards a collaborative master in the fields of Earth Observation, Geographical Information Science (GIS) and Remote Sensing. The research…

Why Do People Need Self-Esteem? A Theoretical and Empirical Review

ERIC Educational Resources Information Center

Pyszczynsi, Tom; Greenberg, Jeff; Solomon, Sheldon; Arndt, Jamie; Schimel, Jeff

2004-01-01

Terror management theory (TMT; J. Greenberg, T. Pyszczynski, & S. Solomon, 1986) posits that people are motivated to pursue positive self-evaluations because self-esteem provides a buffer against the omnipresent potential for anxiety engendered by the uniquely human awareness of mortality. Empirical evidence relevant to the theory is reviewed…

An Empirical Assessment of an Activity to Teach Sensory Change in Aging

ERIC Educational Resources Information Center

Dickinson, Paige E.; Schwarzmueller, April; Martin, Bret

2014-01-01

This study empirically tested the effectiveness of a brief, inexpensive aging simulation activity to educate traditional-aged students about sensory declines and their potential causes in older adulthood development. Students in a life-span development course wore specific props (e.g., thick gloves, earplugs, and obscured glasses) to simulate…

A Poststructuralist View on Student's Project Groups: Possibilities and Limitations

ERIC Educational Resources Information Center

Christensen, Gerd

2016-01-01

The aim of this paper is to demonstrate how poststructuralism and social constructionism can contribute to the empirical research on groups in problem-based learning (PBL). The paper outlines the analytical complexity and shows, through empirical examples, the potentials and limitations of this perspective as an alternative to traditional group…

Plant water potential improves prediction of empirical stomatal models.

PubMed

Anderegg, William R L; Wolf, Adam; Arango-Velez, Adriana; Choat, Brendan; Chmura, Daniel J; Jansen, Steven; Kolb, Thomas; Li, Shan; Meinzer, Frederick; Pita, Pilar; Resco de Dios, Víctor; Sperry, John S; Wolfe, Brett T; Pacala, Stephen

2017-01-01

Climate change is expected to lead to increases in drought frequency and severity, with deleterious effects on many ecosystems. Stomatal responses to changing environmental conditions form the backbone of all ecosystem models, but are based on empirical relationships and are not well-tested during drought conditions. Here, we use a dataset of 34 woody plant species spanning global forest biomes to examine the effect of leaf water potential on stomatal conductance and test the predictive accuracy of three major stomatal models and a recently proposed model. We find that current leaf-level empirical models have consistent biases of over-prediction of stomatal conductance during dry conditions, particularly at low soil water potentials. Furthermore, the recently proposed stomatal conductance model yields increases in predictive capability compared to current models, and with particular improvement during drought conditions. Our results reveal that including stomatal sensitivity to declining water potential and consequent impairment of plant water transport will improve predictions during drought conditions and show that many biomes contain a diversity of plant stomatal strategies that range from risky to conservative stomatal regulation during water stress. Such improvements in stomatal simulation are greatly needed to help unravel and predict the response of ecosystems to future climate extremes.

Biomedical Research Ethics Committees in sub-Saharan Africa: a collective review of their structure, functioning, and outcomes.

PubMed

Silaigwana, Blessing; Wassenaar, Douglas

2015-04-01

Research Ethics Committees (RECs) are mandated to protect human participants by conducting ethical reviews of biomedical research. To date, there is a dearth of information on the structure, functioning, and outcomes of RECs in Africa. This article reviews empirical studies investigating African RECs, with the aim of providing an overview of what is known and identifying gaps in our knowledge. We conducted a literature search of the EBSCO, PubMed, and Google Scholar electronic databases. Twenty-three empirical studies reporting on the structure, functions, and outcomes of African RECs were included in our analysis. The review yielded limited systematic data on RECs in Africa. Available empirical evidence suggests that challenges hampering the effective functioning of RECs included lack of membership diversity, scarcity of resources, insufficient training of members, inadequate capacity to review and monitor studies, and lack of national ethics guidelines and accreditation. Relatively little data on the review outcomes of African RECs were described. There is an ongoing need for concerted efforts from various stakeholders to support capacity development and enhancement of African RECs. © The Author(s) 2015.

Skeletonization of Gridded Potential-Field Images

NASA Astrophysics Data System (ADS)

Gao, L.; Morozov, I. B.

2012-12-01

A new approach to skeletonization was developed for gridded potential-field data. Generally, skeletonization is a pattern-recognition technique allowing automatic recognition of near-linear features in the images, measurement of their parameters, and analyzing them for similarities. Our approach decomposes the images into arbitrarily-oriented "wavelets" characterized by positive or negative amplitudes, orientation angles, spatial dimensions, polarities, and other attributes. Orientations of the wavelets are obtained by scanning the azimuths to detect the strike direction of each anomaly. The wavelets are connected according to the similarities of these attributes, which leads to a "skeleton" map of the potential-field data. In addition, 2-D filtering is conducted concurrently with the wavelet-identification process, which allows extracting parameters of background trends and reduces the adverse effects of low-frequency background (which is often strong in potential-field maps) on skeletonization.. By correlating the neighboring wavelets, linear anomalies are identified and characterized. The advantages of this algorithm are the generality and isotropy of feature detection, as well as being specifically designed for gridded data. With several options for background-trend extraction, the stability for identification of lineaments is improved and optimized. The algorithm is also integrated in a powerful processing system which allows combining it with numerous other tools, such as filtering, computation of analytical signal, empirical mode decomposition, and various types of plotting. The method is applied to potential-field data for the Western Canada Sedimentary Basin, in a study area which extends from southern Saskatchewan into southwestern Manitoba. The target is the structure of crystalline basement beneath Phanerozoic sediments. The examples illustrate that skeletonization aid in the interpretation of complex structures at different scale lengths. The results indicate that this method is useful for identifying structures in complex geophysical images and for automatic extraction of their attributes as well as for quantitative characterization and analysis of potential-field images. Skeletonized potential-field images should also be useful for inversion.

Traditional healing practices among American Muslims: perceptions of community leaders in southeast Michigan.

PubMed

Alrawi, Sara; Fetters, Michael D; Killawi, Amal; Hammad, Adnan; Padela, Aasim

2012-06-01

Despite growing numbers of American Muslims, little empirical work exists on their use of traditional healing practices. We explored the types of traditional healing practices used by American Muslims in southeast Michigan. Twelve semi-structured interviews with American Muslim community leaders identified through a community-academic steering committee were conducted. Using a framework coding structure, a multidisciplinary investigative team identified themes describing traditional healing practices. Traditional healing practices can be categorized into three domains: Islamic religious text based practices, Islamic worship practices, and folk healing practices. Each domain may further contain therapies such as spiritual healing, medicinal herbs, mind body therapy, and dietary prescriptions. Traditional healing practices are utilized in three capacities of care: primary, secondary, and integrative. Our findings demonstrate that American Muslims actively utilize traditional healing practices. Healthcare practitioners caring for this population should be aware of the potential influence of these practices on health behaviors.

Structural equation modeling in pediatric psychology: overview and review of applications.

PubMed

Nelson, Timothy D; Aylward, Brandon S; Steele, Ric G

2008-08-01

To describe the use of structural equation modeling (SEM) in the Journal of Pediatric Psychology (JPP) and to discuss the usefulness of SEM applications in pediatric psychology research. The use of SEM in JPP between 1997 and 2006 was examined and compared to leading journals in clinical psychology, clinical child psychology, and child development. SEM techniques were used in <4% of the empirical articles appearing in JPP between 1997 and 2006. SEM was used less frequently in JPP than in other clinically relevant journals over the past 10 years. However, results indicated a recent increase in JPP studies employing SEM techniques. SEM is an under-utilized class of techniques within pediatric psychology research, although investigations employing these methods are becoming more prevalent. Despite its infrequent use to date, SEM is a potentially useful tool for advancing pediatric psychology research with a number of advantages over traditional statistical methods.

Solvatochromism and prototropic reactions of 2-quinoxalinone

NASA Astrophysics Data System (ADS)

Santra, Swadeshmukul; Dogra, Sneh K.

1996-06-01

Spectral characteristics of 2-quinoxalinone (QNH) in twelve different solvents and those of N-methyl-2-quinoxalinone (QNM) and 2-methoxyquinoxaline (QOM) in five solvents have been studied. Spectral data, along with prototropic reactions have confirmed that QNH possesses a cyclic amide structure. Charge density and electrostatic potential energy mapping calculations carried out using semi-empirical quantum mechanical methods predict that the monocations of QNH and QNM are formed by protonating carbonyl O-11, whereas that of QOM, by protonating, N-1. Dications of all the molecules are formed by protonating N-4. Deprotonation of QNH takes place after QNH reorganizing to enol form, whereas CNDO/S-CI calculations predict that monoanion formed by deprotonation has a structure where charge density is delocalized over C-2, N-1 and O-11. p Ka and pK a∗ values for the various prototropic reactions have been measured and discussed.

Elementary Students as Active Agents in Their Learning: An Empirical Study of the Connections between Assessment Practices and Student Metacognition

ERIC Educational Resources Information Center

Braund, Heather; DeLuca, Christopher

2018-01-01

This study explored how elementary teachers leveraged and structured student-involved formative assessment to promote metacognition and self-regulation. Research has suggested a connection between formative assessment practices (e.g., self-assessment and peer-assessment) and metacognition. However, this connection has limited empirical support,…

Development of a simplified flexible pavement design protocol for New York State Department of Transportation based on the AASHTO mechanistic-empirical pavement design guide : final report.

DOT National Transportation Integrated Search

2017-01-01

The New York State Department of Transportation (NYSDOT) has used the AASHTO 1993 Design Guide for the design of new flexible pavement structures for more than two decades. The AASHTO 1993 Guide is based on the empirical design equations developed fr...

Empirical Modeling of Information Communication Technology Usage Behaviour among Business Education Teachers in Tertiary Colleges of a Developing Country

ERIC Educational Resources Information Center

Isiyaku, Dauda Dansarki; Ayub, Ahmad Fauzi Mohd; Abdulkadir, Suhaida

2015-01-01

This study has empirically tested the fitness of a structural model in explaining the influence of two exogenous variables (perceived enjoyment and attitude towards ICTs) on two endogenous variables (behavioural intention and teachers' Information Communication Technology (ICT) usage behavior), based on the proposition of Technology Acceptance…

"Next Time, Just Remember the Story": Unlearning Empire in Silko's "Ceremony"

ERIC Educational Resources Information Center

Akins, Adrienne

2012-01-01

In this article, the author discusses the unlearning empire in Leslie Marmon Silko's novel titled "Ceremony." "Ceremony' has received a wealth of critical attention. A number of scholars have identified the novel's treatment of education as a colonizing force used by the white American power structure to coerce assimilation of American Indians.…

Preparation of the implementation plan of AASHTO Mechanistic-Empirical Pavement Design Guide (M-EPDG) in Connecticut : Phase II : expanded sensitivity analysis and validation with pavement management data.

DOT National Transportation Integrated Search

2017-02-08

The study re-evaluates distress prediction models using the Mechanistic-Empirical Pavement Design Guide (MEPDG) and expands the sensitivity analysis to a wide range of pavement structures and soils. In addition, an extensive validation analysis of th...

Methodological support for the further abstraction of and philosophical examination of empirical findings in the context of caring science.

PubMed

Lindberg, Elisabeth; Österberg, Sofia A; Hörberg, Ulrica

2016-01-01

Phenomena in caring science are often complex and laden with meanings. Empirical research with the aim of capturing lived experiences is one way of revealing the complexity. Sometimes, however, results from empirical research need to be further discussed. One way is to further abstract the result and/or philosophically examine it. This has previously been performed and presented in scientific journals and doctoral theses, contributing to a greater understanding of phenomena in caring science. Although the intentions in many of these publications are laudable, the lack of methodological descriptions as well as a theoretical and systematic foundation can contribute to an ambiguity concerning how the results have emerged during the analysis. The aim of this paper is to describe the methodological support for the further abstraction of and/or philosophical examination of empirical findings. When trying to systematize the support procedures, we have used a reflective lifeworld research (RLR) approach. Based on the assumptions in RLR, this article will present methodological support for a theoretical examination that can include two stages. In the first stage, data from several (two or more) empirical results on an essential level are synthesized into a general structure. Sometimes the analysis ends with the general structure, but sometimes there is a need to proceed further. The second stage can then be a philosophical examination, in which the general structure is discussed in relation to a philosophical text, theory, or concept. It is important that the theories are brought in as the final stage after the completion of the analysis. Core dimensions of the described methodological support are, in accordance with RLR, openness, bridling, and reflection. The methodological support cannot be understood as fixed stages, but rather as a guiding light in the search for further meanings.

A cost-effectiveness analysis of "test" versus "treat" patients hospitalized with suspected influenza in Hong Kong.

PubMed

You, Joyce H S; Chan, Eva S K; Leung, Maggie Y K; Ip, Margaret; Lee, Nelson L S

2012-01-01

Seasonal and 2009 H1N1 influenza viruses may cause severe diseases and result in excess hospitalization and mortality in the older and younger adults, respectively. Early antiviral treatment may improve clinical outcomes. We examined potential outcomes and costs of test-guided versus empirical treatment in patients hospitalized for suspected influenza in Hong Kong. We designed a decision tree to simulate potential outcomes of four management strategies in adults hospitalized for severe respiratory infection suspected of influenza: "immunofluorescence-assay" (IFA) or "polymerase-chain-reaction" (PCR)-guided oseltamivir treatment, "empirical treatment plus PCR" and "empirical treatment alone". Model inputs were derived from literature. The average prevalence (11%) of influenza in 2010-2011 (58% being 2009 H1N1) among cases of respiratory infections was used in the base-case analysis. Primary outcome simulated was cost per quality-adjusted life-year (QALY) expected (ICER) from the Hong Kong healthcare providers' perspective. In base-case analysis, "empirical treatment alone" was shown to be the most cost-effective strategy and dominated the other three options. Sensitivity analyses showed that "PCR-guided treatment" would dominate "empirical treatment alone" when the daily cost of oseltamivir exceeded USD18, or when influenza prevalence was <2.5% and the predominant circulating viruses were not 2009 H1N1. Using USD50,000 as the threshold of willingness-to-pay, "empirical treatment alone" and "PCR-guided treatment" were cost-effective 97% and 3% of time, respectively, in 10,000 Monte-Carlo simulations. During influenza epidemics, empirical antiviral treatment appears to be a cost-effective strategy in managing patients hospitalized with severe respiratory infection suspected of influenza, from the perspective of healthcare providers in Hong Kong.

DEVELOPMENT OF STRUCTURE ACTIVITY RELATIONSHIPS FOR ASSESSING ECOLOGICAL RISKS

EPA Science Inventory

In the field of environmental toxicology, structure activity relationships (SARs) have developed as scientifically-credible tools for predicting the effects of chemicals when little or no empirical data are available.

CONSIDERATION OF REACTION INTERMEDIATES IN STRUCTURE-ACTIVITY RELATIONSHIPS: A KEY TO UNDERSTANDING AND PREDICTION

EPA Science Inventory

Consideration of Reaction Intermediates in Structure- Activity Relationships: A Key to Understanding and Prediction

A structure-activity relationship (SAR) represents an empirical means for generalizing chemical information relative to biological activity, and is frequent...

The Potential of Digital Technologies to Support Literacy Instruction Relevant to the Common Core State Standards

ERIC Educational Resources Information Center

Hutchison, Amy C.; Colwell, Jamie

2014-01-01

Digital tools have the potential to transform instruction and promote literacies outlined in the Common Core State Standards. Empirical research is examined to illustrate this potential in grades 6-12 instruction.

Application of the Semi-Empirical Force-Limiting Approach for the CoNNeCT SCAN Testbed

NASA Technical Reports Server (NTRS)

Staab, Lucas D.; McNelis, Mark E.; Akers, James C.; Suarez, Vicente J.; Jones, Trevor M.

2012-01-01

The semi-empirical force-limiting vibration method was developed and implemented for payload testing to limit the structural impedance mismatch (high force) that occurs during shaker vibration testing. The method has since been extended for use in analytical models. The Space Communications and Navigation Testbed (SCAN Testbed), known at NASA as, the Communications, Navigation, and Networking re-Configurable Testbed (CoNNeCT), project utilized force-limiting testing and analysis following the semi-empirical approach. This paper presents the steps in performing a force-limiting analysis and then compares the results to test data recovered during the CoNNeCT force-limiting random vibration qualification test that took place at NASA Glenn Research Center (GRC) in the Structural Dynamics Laboratory (SDL) December 19, 2010 to January 7, 2011. A compilation of lessons learned and considerations for future force-limiting tests is also included.

Probabilistic empirical prediction of seasonal climate: evaluation and potential applications

NASA Astrophysics Data System (ADS)

Dieppois, B.; Eden, J.; van Oldenborgh, G. J.

2017-12-01

Preparing for episodes with risks of anomalous weather a month to a year ahead is an important challenge for governments, non-governmental organisations, and private companies and is dependent on the availability of reliable forecasts. The majority of operational seasonal forecasts are made using process-based dynamical models, which are complex, computationally challenging and prone to biases. Empirical forecast approaches built on statistical models to represent physical processes offer an alternative to dynamical systems and can provide either a benchmark for comparison or independent supplementary forecasts. Here, we present a new evaluation of an established empirical system used to predict seasonal climate across the globe. Forecasts for surface air temperature, precipitation and sea level pressure are produced by the KNMI Probabilistic Empirical Prediction (K-PREP) system every month and disseminated via the KNMI Climate Explorer (climexp.knmi.nl). K-PREP is based on multiple linear regression and built on physical principles to the fullest extent with predictive information taken from the global CO2-equivalent concentration, large-scale modes of variability in the climate system and regional-scale information. K-PREP seasonal forecasts for the period 1981-2016 will be compared with corresponding dynamically generated forecasts produced by operational forecast systems. While there are many regions of the world where empirical forecast skill is extremely limited, several areas are identified where K-PREP offers comparable skill to dynamical systems. We discuss two key points in the future development and application of the K-PREP system: (a) the potential for K-PREP to provide a more useful basis for reference forecasts than those based on persistence or climatology, and (b) the added value of including K-PREP forecast information in multi-model forecast products, at least for known regions of good skill. We also discuss the potential development of stakeholder-driven applications of the K-PREP system, including empirical forecasts for circumboreal fire activity.

Detonation product EOS studies: Using ISLS to refine CHEETAH

NASA Astrophysics Data System (ADS)

Zaug, Joseph; Fried, Larry; Hansen, Donald

2001-06-01

Knowledge of an effective interatomic potential function underlies any effort to predict or rationalize the properties of solids and liquids. The experiments we undertake are directed towards determination of equilibrium and dynamic properties of simple fluids at densities sufficiently high that traditional computational methods and semi-empirical forms successful at ambient conditions may require reconsideration. In this paper we present high-pressure and temperature experimental sound speed data on a suite of non-ideal simple fluids and fluid mixtures. Impulsive Stimulated Light Scattering conducted in the diamond-anvil cell offers an experimental approach to determine cross-pair potential interactions through equation of state determinations. In addition the kinetics of structural relaxation in fluids can be studied. We compare our experimental results with our thermochemical computational model CHEETAH. Computational models are systematically improved with each addition of experimental data. Experimentally grounded computational models provide a good basis to confidently understand the chemical nature of reactions at extreme conditions.

Detonation Product EOS Studies: Using ISLS to Refine Cheetah

NASA Astrophysics Data System (ADS)

Zaug, J. M.; Howard, W. M.; Fried, L. E.; Hansen, D. W.

2002-07-01

Knowledge of an effective interatomic potential function underlies any effort to predict or rationalize the properties of solids and liquids. The experiments we undertake are directed towards determination of equilibrium and dynamic properties of simple fluids at densities sufficiently high that traditional computational methods and semi-empirical forms successful at ambient conditions may require reconsideration. In this paper we present high-pressure and temperature experimental sound speed data on a simple fluid, methanol. Impulsive Stimulated Light Scattering (ISLS) conducted on diamond-anvil cell (DAC) encapsulated samples offers an experimental approach to determine cross-pair potential interactions through equation of state determinations. In addition the kinetics of structural relaxation in fluids can be studied. We compare our experimental results with our thermochemical computational model Cheetah. Experimentally grounded computational models provide a good basis to confidently understand the chemical nature of reactions at extreme conditions.

On Estimation of Contamination from Hydrogen Cyanide in Carbon Monoxide Line-intensity Mapping

NASA Astrophysics Data System (ADS)

Chung, Dongwoo T.; Li, Tony Y.; Viero, Marco P.; Church, Sarah E.; Wechsler, Risa H.

2017-09-01

Line-intensity mapping surveys probe large-scale structure through spatial variations in molecular line emission from a population of unresolved cosmological sources. Future such surveys of carbon monoxide line emission, specifically the CO(1-0) line, face potential contamination from a disjointed population of sources emitting in a hydrogen cyanide emission line, HCN(1-0). This paper explores the potential range of the strength of HCN emission and its effect on the CO auto power spectrum, using simulations with an empirical model of the CO/HCN-halo connection. We find that effects on the observed CO power spectrum depend on modeling assumptions but are very small for our fiducial model, which is based on current understanding of the galaxy-halo connection. Given the fiducial model, we expect the bias in overall CO detection significance due to HCN to be less than 1%.

Research on response spectrum of dam based on scenario earthquake

NASA Astrophysics Data System (ADS)

Zhang, Xiaoliang; Zhang, Yushan

2017-10-01

Taking a large hydropower station as an example, the response spectrum based on scenario earthquake is determined. Firstly, the potential source of greatest contribution to the site is determined on the basis of the results of probabilistic seismic hazard analysis (PSHA). Secondly, the magnitude and epicentral distance of the scenario earthquake are calculated according to the main faults and historical earthquake of the potential seismic source zone. Finally, the response spectrum of scenario earthquake is calculated using the Next Generation Attenuation (NGA) relations. The response spectrum based on scenario earthquake method is less than the probability-consistent response spectrum obtained by PSHA method. The empirical analysis shows that the response spectrum of scenario earthquake considers the probability level and the structural factors, and combines the advantages of the deterministic and probabilistic seismic hazard analysis methods. It is easy for people to accept and provide basis for seismic engineering of hydraulic engineering.

On Estimation of Contamination from Hydrogen Cyanide in Carbon Monoxide Line-intensity Mapping

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

Chung, Dongwoo T.; Li, Tony Y.; Viero, Marco P.

Line-intensity mapping surveys probe large-scale structure through spatial variations in molecular line emission from a population of unresolved cosmological sources. Future such surveys of carbon monoxide line emission, specifically the CO(1-0) line, face potential contamination from a disjointed population of sources emitting in a hydrogen cyanide emission line, HCN(1-0). This paper explores the potential range of the strength of HCN emission and its effect on the CO auto power spectrum, using simulations with an empirical model of the CO/HCN–halo connection. We find that effects on the observed CO power spectrum depend on modeling assumptions but are very small for ourmore » fiducial model, which is based on current understanding of the galaxy–halo connection. Given the fiducial model, we expect the bias in overall CO detection significance due to HCN to be less than 1%.« less

On Estimation of Contamination from Hydrogen Cyanide in Carbon Monoxide Line-intensity Mapping

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

Chung, Dongwoo T.; Li, Tony Y.; Viero, Marco P.

Here, line-intensity mapping surveys probe large-scale structure through spatial variations in molecular line emission from a population of unresolved cosmological sources. Future such surveys of carbon monoxide line emission, specifically the CO(1-0) line, face potential contamination from a disjointed population of sources emitting in a hydrogen cyanide emission line, HCN(1-0). This paper explores the potential range of the strength of HCN emission and its effect on the CO auto power spectrum, using simulations with an empirical model of the CO/HCN–halo connection. We find that effects on the observed CO power spectrum depend on modeling assumptions but are very small formore » our fiducial model, which is based on current understanding of the galaxy–halo connection. Given the fiducial model, we expect the bias in overall CO detection significance due to HCN to be less than 1%.« less

The spatial scaling of species interaction networks.

PubMed

Galiana, Nuria; Lurgi, Miguel; Claramunt-López, Bernat; Fortin, Marie-Josée; Leroux, Shawn; Cazelles, Kevin; Gravel, Dominique; Montoya, José M

2018-05-01

Species-area relationships (SARs) are pivotal to understand the distribution of biodiversity across spatial scales. We know little, however, about how the network of biotic interactions in which biodiversity is embedded changes with spatial extent. Here we develop a new theoretical framework that enables us to explore how different assembly mechanisms and theoretical models affect multiple properties of ecological networks across space. We present a number of testable predictions on network-area relationships (NARs) for multi-trophic communities. Network structure changes as area increases because of the existence of different SARs across trophic levels, the preferential selection of generalist species at small spatial extents and the effect of dispersal limitation promoting beta-diversity. Developing an understanding of NARs will complement the growing body of knowledge on SARs with potential applications in conservation ecology. Specifically, combined with further empirical evidence, NARs can generate predictions of potential effects on ecological communities of habitat loss and fragmentation in a changing world.

On Estimation of Contamination from Hydrogen Cyanide in Carbon Monoxide Line-intensity Mapping

DOE PAGES

Chung, Dongwoo T.; Li, Tony Y.; Viero, Marco P.; ...

2017-08-31

Here, line-intensity mapping surveys probe large-scale structure through spatial variations in molecular line emission from a population of unresolved cosmological sources. Future such surveys of carbon monoxide line emission, specifically the CO(1-0) line, face potential contamination from a disjointed population of sources emitting in a hydrogen cyanide emission line, HCN(1-0). This paper explores the potential range of the strength of HCN emission and its effect on the CO auto power spectrum, using simulations with an empirical model of the CO/HCN–halo connection. We find that effects on the observed CO power spectrum depend on modeling assumptions but are very small formore » our fiducial model, which is based on current understanding of the galaxy–halo connection. Given the fiducial model, we expect the bias in overall CO detection significance due to HCN to be less than 1%.« less

Oceanography and life history predict contrasting genetic population structure in two Antarctic fish species.

PubMed

Young, Emma F; Belchier, Mark; Hauser, Lorenz; Horsburgh, Gavin J; Meredith, Michael P; Murphy, Eugene J; Pascoal, Sonia; Rock, Jennifer; Tysklind, Niklas; Carvalho, Gary R

2015-06-01

Understanding the key drivers of population connectivity in the marine environment is essential for the effective management of natural resources. Although several different approaches to evaluating connectivity have been used, they are rarely integrated quantitatively. Here, we use a 'seascape genetics' approach, by combining oceanographic modelling and microsatellite analyses, to understand the dominant influences on the population genetic structure of two Antarctic fishes with contrasting life histories, Champsocephalus gunnari and Notothenia rossii. The close accord between the model projections and empirical genetic structure demonstrated that passive dispersal during the planktonic early life stages is the dominant influence on patterns and extent of genetic structuring in both species. The shorter planktonic phase of C. gunnari restricts direct transport of larvae between distant populations, leading to stronger regional differentiation. By contrast, geographic distance did not affect differentiation in N. rossii, whose longer larval period promotes long-distance dispersal. Interannual variability in oceanographic flows strongly influenced the projected genetic structure, suggesting that shifts in circulation patterns due to climate change are likely to impact future genetic connectivity and opportunities for local adaptation, resilience and recovery from perturbations. Further development of realistic climate models is required to fully assess such potential impacts.

Electronic and magnetic properties of small rhodium clusters

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

Soon, Yee Yeen; Yoon, Tiem Leong; Lim, Thong Leng

2015-04-24

We report a theoretical study of the electronic and magnetic properties of rhodium-atomic clusters. The lowest energy structures at the semi-empirical level of rhodium clusters are first obtained from a novel global-minimum search algorithm, known as PTMBHGA, where Gupta potential is used to describe the atomic interaction among the rhodium atoms. The structures are then re-optimized at the density functional theory (DFT) level with exchange-correlation energy approximated by Perdew-Burke-Ernzerhof generalized gradient approximation. For the purpose of calculating the magnetic moment of a given cluster, we calculate the optimized structure as a function of the spin multiplicity within the DFT framework.more » The resultant magnetic moments with the lowest energies so obtained allow us to work out the magnetic moment as a function of cluster size. Rhodium atomic clusters are found to display a unique variation in the magnetic moment as the cluster size varies. However, Rh{sub 4} and Rh{sub 6} are found to be nonmagnetic. Electronic structures of the magnetic ground-state structures are also investigated within the DFT framework. The results are compared against those based on different theoretical approaches available in the literature.« less

Structure of Aqueous Trehalose Solution by Neutron Diffraction and Structural Modeling.

PubMed

Olsson, Christoffer; Jansson, Helén; Youngs, Tristan; Swenson, Jan

2016-12-15

The molecular structure of an aqueous solution of the disaccharide trehalose (C 12 H 22 O 11 ) has been studied by neutron diffraction and empirical potential structure refinement modeling. Six different isotope compositions with 33 wt % trehalose (corresponding to 38 water molecules per trehalose molecule) were measured to ensure that water-water, trehalose-water, and trehalose-trehalose correlations were accurately determined. In fact, this is the first neutron diffraction study of an aqueous trehalose solution in which also the nonexchangeable hydrogen atoms in trehalose are deuterated. With this approach, it was possible to determine that (1) there is a substantial hydrogen bonding between trehalose and water (∼11 hydrogen bonds per trehalose molecule), which is in contrast to previous neutron diffraction studies, and (2) there is no tendency of clustering of trehalose, in contrast to what is generally observed by molecular dynamics simulations and experimentally found for other disaccharides. Thus, the results give the structural picture that trehalose prefers to interact with water and participate in a hydrogen-bonded network. This strong network character of the solution might be one of the key reasons for its extraordinary stabilization effect on biological materials.

On the role of general system theory for functional neuroimaging.

PubMed

Stephan, Klaas Enno

2004-12-01

One of the most important goals of neuroscience is to establish precise structure-function relationships in the brain. Since the 19th century, a major scientific endeavour has been to associate structurally distinct cortical regions with specific cognitive functions. This was traditionally accomplished by correlating microstructurally defined areas with lesion sites found in patients with specific neuropsychological symptoms. Modern neuroimaging techniques with high spatial resolution have promised an alternative approach, enabling non-invasive measurements of regionally specific changes of brain activity that are correlated with certain components of a cognitive process. Reviewing classic approaches towards brain structure-function relationships that are based on correlational approaches, this article argues that these approaches are not sufficient to provide an understanding of the operational principles of a dynamic system such as the brain but must be complemented by models based on general system theory. These models reflect the connectional structure of the system under investigation and emphasize context-dependent couplings between the system elements in terms of effective connectivity. The usefulness of system models whose parameters are fitted to measured functional imaging data for testing hypotheses about structure-function relationships in the brain and their potential for clinical applications is demonstrated by several empirical examples.

Trends and structural shifts in health tourism: evidence from seasonal time-series data on health-related travel spending by Canada during 1970-2010.

PubMed

Loh, Chung-Ping A

2015-05-01

There has been a growing interest in better understanding the trends and determinants of health tourism activities. While much of the expanding literature on health tourism offers theoretical or qualitative discussion, empirical evidences has been lacking. This study employs Canada's outbound health tourism activities as an example to examine the trends in health tourism and its association with changing domestic health care market characteristics. A time-series model that accounts for potential structural changes in the trend is employed to analyze the quarterly health-related travel spending series reported in the Balance of Payments Statistics (BOPS) during 1970-2010 (n = 156). We identified a structural shift point which marks the start of an accelerated growth of health tourism and a flattened seasonality in such activities. We found that the health tourism activities of Canadian consumers increase when the private investment in medical facilities declines or when the private MPI increases during the years following the structural-change. We discussed the possible linkage of the structural shift to the General Agreement on Trade in Services (GATS), which went into effect in January, 1995. Copyright © 2015 Elsevier Ltd. All rights reserved.

FROM FINANCE TO COSMOLOGY: THE COPULA OF LARGE-SCALE STRUCTURE

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

Scherrer, Robert J.; Berlind, Andreas A.; Mao, Qingqing

2010-01-01

Any multivariate distribution can be uniquely decomposed into marginal (one-point) distributions, and a function called the copula, which contains all of the information on correlations between the distributions. The copula provides an important new methodology for analyzing the density field in large-scale structure. We derive the empirical two-point copula for the evolved dark matter density field. We find that this empirical copula is well approximated by a Gaussian copula. We consider the possibility that the full n-point copula is also Gaussian and describe some of the consequences of this hypothesis. Future directions for investigation are discussed.

A classification of ecological boundaries

USGS Publications Warehouse

Strayer, D.L.; Power, M.E.; Fagan, W.F.; Pickett, S.T.A.; Belnap, J.

2003-01-01

Ecologists use the term boundary to refer to a wide range of real and conceptual structures. Because imprecise terminology may impede the search for general patterns and theories about ecological boundaries, we present a classification of the attributes of ecological boundaries to aid in communication and theory development. Ecological boundaries may differ in their origin and maintenance, their spatial structure, their function, and their temporal dynamics. A classification system based on these attributes should help ecologists determine whether boundaries are truly comparable. This system can be applied when comparing empirical studies, comparing theories, and testing theoretical predictions against empirical results.

Structural diversity effect on hashtag adoption in Twitter

NASA Astrophysics Data System (ADS)

Zhang, Aihua; Zheng, Mingxing; Pang, Bowen

2018-03-01

With online social network developing rapidly these years, user' behavior in online social network has attracted a lot of attentions to it. In this paper, we study Twitter user's behavior of hashtag adoption from the perspective of social contagion and focus on "structure diversity" effect on individual's behavior in Twitter. We achieve data through Twitter's API by crawling and build a users' network to carry on empirical research. The Girvan-Newman (G-N) algorithm is used to analyze the structural diversity of user's ego network, and Logistic regression model is adopted to examine the hypothesis. The findings of our empirical study indicate that user' behavior in online social network is indeed influenced by his friends and his decision is significantly affected by the number of groups that these friends belong to, which we call structural diversity.

Empirical Correction to the Likelihood Ratio Statistic for Structural Equation Modeling with Many Variables.

PubMed

Yuan, Ke-Hai; Tian, Yubin; Yanagihara, Hirokazu

2015-06-01

Survey data typically contain many variables. Structural equation modeling (SEM) is commonly used in analyzing such data. The most widely used statistic for evaluating the adequacy of a SEM model is T ML, a slight modification to the likelihood ratio statistic. Under normality assumption, T ML approximately follows a chi-square distribution when the number of observations (N) is large and the number of items or variables (p) is small. However, in practice, p can be rather large while N is always limited due to not having enough participants. Even with a relatively large N, empirical results show that T ML rejects the correct model too often when p is not too small. Various corrections to T ML have been proposed, but they are mostly heuristic. Following the principle of the Bartlett correction, this paper proposes an empirical approach to correct T ML so that the mean of the resulting statistic approximately equals the degrees of freedom of the nominal chi-square distribution. Results show that empirically corrected statistics follow the nominal chi-square distribution much more closely than previously proposed corrections to T ML, and they control type I errors reasonably well whenever N ≥ max(50,2p). The formulations of the empirically corrected statistics are further used to predict type I errors of T ML as reported in the literature, and they perform well.

Waiting time distribution in public health care: empirics and theory.

PubMed

Dimakou, Sofia; Dimakou, Ourania; Basso, Henrique S

2015-12-01

Excessive waiting times for elective surgery have been a long-standing concern in many national healthcare systems in the OECD. How do the hospital admission patterns that generate waiting lists affect different patients? What are the hospitals characteristics that determine waiting times? By developing a model of healthcare provision and analysing empirically the entire waiting time distribution we attempt to shed some light on those issues. We first build a theoretical model that describes the optimal waiting time distribution for capacity constraint hospitals. Secondly, employing duration analysis, we obtain empirical representations of that distribution across hospitals in the UK from 1997-2005. We observe important differences on the 'scale' and on the 'shape' of admission rates. Scale refers to how quickly patients are treated and shape represents trade-offs across duration-treatment profiles. By fitting the theoretical to the empirical distributions we estimate the main structural parameters of the model and are able to closely identify the main drivers of these empirical differences. We find that the level of resources allocated to elective surgery (budget and physical capacity), which determines how constrained the hospital is, explains differences in scale. Changes in benefits and costs structures of healthcare provision, which relate, respectively, to the desire to prioritise patients by duration and the reduction in costs due to delayed treatment, determine the shape, affecting short and long duration patients differently. JEL Classification I11; I18; H51.

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

Estimating the effects of 17α-ethinylestradiol on stochastic population growth rate of fathead minnows: a population synthesis of empirically derived vital rates

USGS Publications Warehouse

Schwindt, Adam R.; Winkelman, Dana L.

2016-01-01

Urban freshwater streams in arid climates are wastewater effluent dominated ecosystems particularly impacted by bioactive chemicals including steroid estrogens that disrupt vertebrate reproduction. However, more understanding of the population and ecological consequences of exposure to wastewater effluent is needed. We used empirically derived vital rate estimates from a mesocosm study to develop a stochastic stage-structured population model and evaluated the effect of 17α-ethinylestradiol (EE2), the estrogen in human contraceptive pills, on fathead minnow Pimephales promelas stochastic population growth rate. Tested EE2 concentrations ranged from 3.2 to 10.9 ng L−1 and produced stochastic population growth rates (λ S ) below 1 at the lowest concentration, indicating potential for population decline. Declines in λ S compared to controls were evident in treatments that were lethal to adult males despite statistically insignificant effects on egg production and juvenile recruitment. In fact, results indicated that λ S was most sensitive to the survival of juveniles and female egg production. More broadly, our results document that population model results may differ even when empirically derived estimates of vital rates are similar among experimental treatments, and demonstrate how population models integrate and project the effects of stressors throughout the life cycle. Thus, stochastic population models can more effectively evaluate the ecological consequences of experimentally derived vital rates.

Invasive Infection with Fusarium chlamydosporum in a Patient with Aplastic Anemia

PubMed Central

Segal, Brahm H.; Walsh, Thomas J.; Liu, Johnson M.; Wilson, Jon D.; Kwon-Chung, Kyung J.

1998-01-01

We report the first case of invasive disease caused by Fusarium chlamydosporum. The patient had aplastic anemia with prolonged neutropenia and was treated with immunosuppressive therapy. While she was receiving empirical amphotericin B, a dark crusted lesion developed on her nasal turbinate. Histologic analysis revealed invasive hyaline hyphae and some darkly pigmented structures that resembled conidia of dematiaceous molds. Only after the mold was grown in culture were characteristic colonial morphology, phialides, conidia, and chlamydospores evident, thus permitting the identification of F. chlamydosporum. This case illustrates the ever-increasing spectrum of pathogenic Fusarium spp. in immunocompromised patients and emphasizes the potential pitfalls in histologic diagnosis, which may have important treatment implications. PMID:9620419

Neurocognitive mechanisms of mathematical giftedness: A literature review.

PubMed

Zhang, Li; Gan, John Q; Wang, Haixian

2017-01-01

Mathematically gifted children/adolescents have demonstrated exceptional abilities and traits in logical reasoning, mental imagery, and creative thinking. In the field of cognitive neuroscience, the past studies on mathematically gifted brains have concentrated on investigating event-related brain activation regions, cerebral laterality of cognitive functions, functional specialization that is uniquely dedicated for specific cognitive purposes, and functional interactions among discrete brain regions. From structural and functional perspectives, these studies have witnessed both "general" and "unique" neural characteristics of mathematically gifted brains. In this article, the theoretical background, empirical studies, and neurocognitive mechanisms of mathematically gifted children/adolescents are reviewed. Based on the integration of the findings, some potential directions for the future research are identified and discussed.

A genetic atlas of human admixture history.

PubMed

Hellenthal, Garrett; Busby, George B J; Band, Gavin; Wilson, James F; Capelli, Cristian; Falush, Daniel; Myers, Simon

2014-02-14

Modern genetic data combined with appropriate statistical methods have the potential to contribute substantially to our understanding of human history. We have developed an approach that exploits the genomic structure of admixed populations to date and characterize historical mixture events at fine scales. We used this to produce an atlas of worldwide human admixture history, constructed by using genetic data alone and encompassing over 100 events occurring over the past 4000 years. We identified events whose dates and participants suggest they describe genetic impacts of the Mongol empire, Arab slave trade, Bantu expansion, first millennium CE migrations in Eastern Europe, and European colonialism, as well as unrecorded events, revealing admixture to be an almost universal force shaping human populations.

Semiempirical studies of atomic structure. Progress report, 1 July 1984-1 January 1985

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

Curtis, L.J.

1985-01-01

Through the acquisition and systematization of empirical data, remarkably precise methods for predicting excitation energies, transition wavelengths, transition probabilities, level lifetimes, ionization potentials, core polarizabilities, and core penetrabilities have been and are being developed and applied. Although the data base for heavy, highly ionized atoms is still sparse, much new information has become available since this program was begun in 1980. The purpose of the project is to perform needed measurements and to utilize the available data through parametrized extrapolations and interpolations along isoelectronic, homologous, and Rydberg sequences to provide predictions for large classes of quantities with a precision thatmore » is sharpened by subsequent measurements.« less

The Pathways from a Behavior Change Communication Intervention to Infant and Young Child Feeding in Bangladesh Are Mediated and Potentiated by Maternal Self-Efficacy.

PubMed

Zongrone, Amanda A; Menon, Purnima; Pelto, Gretel H; Habicht, Jean-Pierre; Rasmussen, Kathleen M; Constas, Mark A; Vermeylen, Francoise; Khaled, Adiba; Saha, Kuntal K; Stoltzfus, Rebecca J

2018-02-01

Although self-efficacy is a potential determinant of feeding and care behaviors, there is limited empirical analysis of the role of maternal self-efficacy in low- and middle-income countries. In the context of behavior change interventions (BCIs) addressing complementary feeding (CF), it is possible that maternal self-efficacy can mediate or enhance intervention impacts. In the context of a BCI in Bangladesh, we studied the role of maternal self-efficacy for CF (MSE-CF) for 2 CF behaviors with the use of a theoretically grounded empirical model of determinants to illustrate the potential roles of MSE-CF. We developed and tested a locally relevant scale for MSE-CF and included it in a survey (n = 457 mothers of children aged 6-24 mo) conducted as part of a cluster-randomized evaluation. Qualitative research was used to inform the selection of 2 intervention-targeted behaviors: feeding green leafy vegetables in the last 24 h (GLV) and on-time introduction of egg (EGG) between 6 and 8 mo of age. We then examined direct, mediated, and potentiated paths of MSE-CF in relation to the impacts of the BCI on these behaviors with the use of regression and structural equation modeling. GLV and EGG were higher in the intensive group than in the nonintensive control group (16.0 percentage points for GLV; P < 0.001; 11.2 percentage points for EGG; P = 0.037). For GLV, MSE-CF mediated (β = 0.345, P = 0.010) and potentiated (β = 0.390, P = 0.038) the effect of the intensive group. In contrast, MSE-CF did not mediate or potentiate the effect of the intervention on EGG. MSE-CF was a significant mediator and potentiator for GLV but not for EGG. The divergent findings highlight the complex determinants of individual specific infant and young child feeding behaviors. The study shows the value of measuring behavioral determinants, such as MSE-CF, that affect a caregiver's capability to adopt intervention-targeted behaviors.

Simulating sunflower canopy temperatures to infer root-zone soil water potential

NASA Technical Reports Server (NTRS)

Choudhury, B. J.; Idso, S. B.

1983-01-01

A soil-plant-atmosphere model for sunflower (Helianthus annuus L.), together with clear sky weather data for several days, is used to study the relationship between canopy temperature and root-zone soil water potential. Considering the empirical dependence of stomatal resistance on insolation, air temperature and leaf water potential, a continuity equation for water flux in the soil-plant-atmosphere system is solved for the leaf water potential. The transpirational flux is calculated using Monteith's combination equation, while the canopy temperature is calculated from the energy balance equation. The simulation shows that, at high soil water potentials, canopy temperature is determined primarily by air and dew point temperatures. These results agree with an empirically derived linear regression equation relating canopy-air temperature differential to air vapor pressure deficit. The model predictions of leaf water potential are also in agreement with observations, indicating that measurements of canopy temperature together with a knowledge of air and dew point temperatures can provide a reliable estimate of the root-zone soil water potential.

The Effect of Classroom Structure on Verbal and Physical Aggression among Peers: A Short-Term Longitudinal Study

ERIC Educational Resources Information Center

Bergsmann, Evelyn M.; Van De Schoot, Rens; Schober, Barbara; Finsterwald, Monika; Spiel, Christiane

2013-01-01

Teachers promote student learning and well-being in school by establishing a supportive classroom structure. The term "classroom structure" refers to how teachers design tasks, maintain authority, and evaluate student achievement. Although empirical studies have shown the relation of classroom structure to student motivation, achievement, and…

Cognitive neuroenhancement: false assumptions in the ethical debate.

PubMed

Heinz, Andreas; Kipke, Roland; Heimann, Hannah; Wiesing, Urban

2012-06-01

The present work critically examines two assumptions frequently stated by supporters of cognitive neuroenhancement. The first, explicitly methodological, assumption is the supposition of effective and side effect-free neuroenhancers. However, there is an evidence-based concern that the most promising drugs currently used for cognitive enhancement can be addictive. Furthermore, this work describes why the neuronal correlates of key cognitive concepts, such as learning and memory, are so deeply connected with mechanisms implicated in the development and maintenance of addictive behaviour so that modification of these systems may inevitably run the risk of addiction to the enhancing drugs. Such a potential risk of addiction could only be falsified by in-depth empirical research. The second, implicit, assumption is that research on neuroenhancement does not pose a serious moral problem. However, the potential for addiction, along with arguments related to research ethics and the potential social impact of neuroenhancement, could invalidate this assumption. It is suggested that ethical evaluation needs to consider the empirical data as well as the question of whether and how such empirical knowledge can be obtained.

A Proposed Integration Environment for Enhanced User Interaction and Value-Adding of Electronic Documents: An Empirical Evaluation.

ERIC Educational Resources Information Center

Liew, Chern Li; Chennupati, K. R.; Foo, Schubert

2001-01-01

Explores the potential and impact of an innovative information environment in enhancing user activities in using electronic documents for various tasks, and to support the value-adding of these e-documents. Discusses the conceptual design and prototyping of a proposed environment, PROPIE. Presents an empirical and formative evaluation of the…

Learning Analytics and Educational Data Mining in Practice: A Systematic Literature Review of Empirical Evidence

ERIC Educational Resources Information Center

Papamitsiou, Zacharoula; Economides, Anastasios A.

2014-01-01

This paper aims to provide the reader with a comprehensive background for understanding current knowledge on Learning Analytics (LA) and Educational Data Mining (EDM) and its impact on adaptive learning. It constitutes an overview of empirical evidence behind key objectives of the potential adoption of LA/EDM in generic educational strategic…

A Systematic Literature Review of Empirical Evidence on Computer Games and Serious Games

ERIC Educational Resources Information Center

Connolly, Thomas M.; Boyle, Elizabeth A.; MacArthur, Ewan; Hainey, Thomas; Boyle, James M.

2012-01-01

This paper examines the literature on computer games and serious games in regard to the potential positive impacts of gaming on users aged 14 years or above, especially with respect to learning, skill enhancement and engagement. Search terms identified 129 papers reporting empirical evidence about the impacts and outcomes of computer games and…

Trends of Empirical Research in South Korean Mental Health Social Work

ERIC Educational Resources Information Center

Song, In Han; Lee, Eun Jung

2017-01-01

Since the introduction of evidence-based practice in South Korea, it has gained significant attention for its potential to promote the efficacy of social work services and to integrate knowledge and practice in mental health social work. In order to see how empirical research in South Korean mental health social work has changed, we examined…

A Taxonomy of Care for Youth: Results of an Empirical Development Procedure

ERIC Educational Resources Information Center

Evenboer, K. Els; Huyghen, Anne-Marie N.; Tuinstra, Jolanda; Knorth, Erik J.; Reijneveld, Sijmen A.

2012-01-01

Purpose: Statements about potentially effective components of interventions in child and youth care are hard to make because of a lack of a standardized instruments for classifying the most salient care characteristics. The aim of this study is to present an empirically developed taxonomy of care for youth (Tocfy) which is feasible for use in…

Analytic Empirical Potential and its Comparison to State of the Art ab initio Calculations for the 6e^- Excited b(1^3Π_u)-STATE of Li_2.

NASA Astrophysics Data System (ADS)

Dattani, Nikesh S.; Le Roy, Robert J.

2015-06-01

Despite only having 6e^-, the most sophisticated Li_2(b,1^3Π_u) calculation has an r_e that disagrees with the empirical value by over 1500% of the latter's uncertainty, and energy spacings that disagree with those of the empirical potential by up to over 1.5cm-1. The discrepancy here is far more than for the ground state of the 5e^- system BeH, for which the best ab initio calculation gives an r_e which disagrees with the empirical value by less than 200% of the latter's uncertainty. In addition to this discrepancy, other reasons motivating the construction of an analytic empirical potential for Li_2(b,1^3Π_u) include (1) the fact that it is the most deeply bound Li_2 state, (2) it is the only Li_2 state out of the lowest five, for which no analytic empirical potential has yet been built, (3) the state it mixes with, the A(1^1σ_u)-state, is one of the most thoroughly characterized molecular states, but has a small gap of missing data in part of the region where it mixes with the b-state, and (4) it is one of the states accessible by new ultra-high precision techniques based on photoassociation. Finally (5) there is currently a discrepancy between the most sophisticated 3e- ab initio calculation, and the most current empirical value, for the first Li(^2S)-Li(^2P) interaction term (C_3), despite the latter being the most precise experimentally determined oscillator strength for any system, by an order of magnitude^e. The b-state is one of the states that has this exact C_3 interaction term. Musial & Kucharski (2014) J. Chem. Theor. Comp. 10, 1200. Dattani N. S. (2015) J. Mol. Spec. http://dx.doi.org/10.1016/j.jms.2014.09.005. Semczuk M., Li X., Gunton W., Haw M., Dattani N. S., Witz J., Mills A., Jones D. J., Madison K. W. (2013) Phys. Rev. A 87, 052505 Gunton W., Semczuk M., Dattani N. S., Madison K. W. (2013) Phys. Rev. A 88, 062510 Tang L.-Y., Yan Z.-C., Shi T.-Y., Mitroy J (2011) Phys. Rev. A 84, 052502. Le Roy R. J., Dattani N. S., Coxon J. A., Ross A. J., Crozet P., Linton C. (2009) J. Chem Phys. 131, 204309

The relevance of time series in molecular ecology and conservation biology.

PubMed

Habel, Jan C; Husemann, Martin; Finger, Aline; Danley, Patrick D; Zachos, Frank E

2014-05-01

The genetic structure of a species is shaped by the interaction of contemporary and historical factors. Analyses of individuals from the same population sampled at different points in time can help to disentangle the effects of current and historical forces and facilitate the understanding of the forces driving the differentiation of populations. The use of such time series allows for the exploration of changes at the population and intraspecific levels over time. Material from museum collections plays a key role in understanding and evaluating observed population structures, especially if large numbers of individuals have been sampled from the same locations at multiple time points. In these cases, changes in population structure can be assessed empirically. The development of new molecular markers relying on short DNA fragments (such as microsatellites or single nucleotide polymorphisms) allows for the analysis of long-preserved and partially degraded samples. Recently developed techniques to construct genome libraries with a reduced complexity and next generation sequencing and their associated analysis pipelines have the potential to facilitate marker development and genotyping in non-model species. In this review, we discuss the problems with sampling and available marker systems for historical specimens and demonstrate that temporal comparative studies are crucial for the estimation of important population genetic parameters and to measure empirically the effects of recent habitat alteration. While many of these analyses can be performed with samples taken at a single point in time, the measurements are more robust if multiple points in time are studied. Furthermore, examining the effects of habitat alteration, population declines, and population bottlenecks is only possible if samples before and after the respective events are included. © 2013 The Authors. Biological Reviews © 2013 Cambridge Philosophical Society.

Consumptive and nonconsumptive effects of cannibalism in fluctuating age-structured populations.

PubMed

Wissinger, Scott A; Whiteman, Howard H; Denoël, Mathieu; Mumford, Miranda L; Aubee, Catherine B

2010-02-01

Theory and empirical studies suggest that cannibalism in age-structured populations can regulate recruitment depending on the intensity of intraspecific competition between cannibals and victims and the nature of the cannibalism window, i.e., which size classes interact as cannibals and victims. Here we report on a series of experiments that quantify that window for age-structured populations of salamander larvae and paedomorphic adults. We determined body size limits on cannibalism in microcosms and then the consumptive and nonconsumptive (injuries, foraging and activity, diet, growth) effects on victims in mesocosms with seminatural levels of habitat complexity and alternative prey. We found that cannibalism by the largest size classes (paedomorphs and > or = age 3+ yr larvae) occurs mainly on young-of-the-year (YOY) victims. Surviving YOY and other small larvae had increased injuries, reduced activity levels, and reduced growth rates in the presence of cannibals. Data on YOY survival in an experiment in which we manipulated the density of paedomorphs combined with historical data on the number of cannibals in natural populations indicate that dominant cohorts of paedomorphs can cause observed recruitment failures. Dietary data indicate that ontogenetic shifts in diet should preclude strong intraspecific competition between YOY and cannibals in this species. Thus our results are consistent with previous empirical and theoretical work that suggests that recruitment regulation by cannibalism is most likely when YOY are vulnerable to cannibalism but have low dietary overlap with cannibals. Understanding the role of cannibalism in regulating recruitment in salamander populations is timely, given the widespread occurrences of amphibian decline. Previous studies have focused on extrinsic (including anthropogenic) factors that affect amphibian population dynamics, whereas the data presented here combined with long-term field observations suggest the potential for intrinsically driven population cycles.

Structure-based design of ligands for protein basic domains: Application to the HIV-1 Tat protein

NASA Astrophysics Data System (ADS)

Filikov, Anton V.; James, Thomas L.

1998-05-01

A methodology has been developed for designing ligands to bind a flexible basic protein domain where the structure of the domain is essentially known. It is based on an empirical binding free energy function developed for highly charged complexes and on Monte Carlo simulations in internal coordinates with both the ligand and the receptor being flexible. HIV-1 encodes a transactivating regulatory protein called Tat. Binding of the basic domain of Tat to TAR RNA is required for efficient transcription of the viral genome. The structure of a biologically active peptide containing the Tat basic RNA-binding domain is available from NMR studies. The goal of the current project is to design a ligand which will bind to that basic domain and potentially inhibit the TAR-Tat interaction. The basic domain contains six arginine and two lysine residues. Our strategy was to design a ligand for arginine first and then a superligand for the basic domain by joining arginine ligands with a linker. Several possible arginine ligands were obtained by searching the Available Chemicals Directory with DOCK 3.5 software. Phytic acid, which can potentially bind multiple arginines, was chosen as a building block for the superligand. Calorimetric binding studies of several compounds to methylguanidine and Arg-/Lys-containing peptides were performed. The data were used to develop an empirical binding free energy function for prediction of affinity of the ligands for the Tat basic domain. Modeling of the conformations of the complexes with both the superligand and the basic domain being flexible has been carried out via Biased Probability Monte Carlo (BPMC) simulations in internal coordinates (ICM 2.6 suite of programs). The simulations used parameters to ensure correct folding, i.e., consistent with the experimental NMR structure of a 25-residue Tat peptide, from a random starting conformation. Superligands for the basic domain were designed by joining together two molecules of phytic acid with peptidic and peptidomimetic linkers. The linkers were refined by varying the length and side chains of the linking residues, carrying out BPMC simulations, and evaluation of the binding free energy for the best energy conformation. The dissociation constant of the best ligand designed is estimated to be in the low- to mid-nanomolar range.

Influence of Using Challenging Tasks in Biology Classrooms on Students' Cognitive Knowledge Structure: An Empirical Video Study

ERIC Educational Resources Information Center

Nawani, Jigna; Rixius, Julia; Neuhaus, Birgit J.

2016-01-01

Empirical analysis of secondary biology classrooms revealed that, on average, 68% of teaching time in Germany revolved around processing tasks. Quality of instruction can thus be assessed by analyzing the quality of tasks used in classroom discourse. This quasi-experimental study analyzed how teachers used tasks in 38 videotaped biology lessons…

How to measure the impacts of antibiotic resistance and antibiotic development on empiric therapy: new composite indices.

PubMed

Hughes, Josie S; Hurford, Amy; Finley, Rita L; Patrick, David M; Wu, Jianhong; Morris, Andrew M

2016-12-16

We aimed to construct widely useable summary measures of the net impact of antibiotic resistance on empiric therapy. Summary measures are needed to communicate the importance of resistance, plan and evaluate interventions, and direct policy and investment. As an example, we retrospectively summarised the 2011 cumulative antibiogram from a Toronto academic intensive care unit. We developed two complementary indices to summarise the clinical impact of antibiotic resistance and drug availability on empiric therapy. The Empiric Coverage Index (ECI) measures susceptibility of common bacterial infections to available empiric antibiotics as a percentage. The Empiric Options Index (EOI) varies from 0 to 'the number of treatment options available', and measures the empiric value of the current stock of antibiotics as a depletable resource. The indices account for drug availability and the relative clinical importance of pathogens. We demonstrate meaning and use by examining the potential impact of new drugs and threatening bacterial strains. In our intensive care unit coverage of device-associated infections measured by the ECI remains high (98%), but 37-44% of treatment potential measured by the EOI has been lost. Without reserved drugs, the ECI is 86-88%. New cephalosporin/β-lactamase inhibitor combinations could increase the EOI, but no single drug can compensate for losses. Increasing methicillin-resistant Staphylococcus aureus (MRSA) prevalence would have little overall impact (ECI=98%, EOI=4.8-5.2) because many Gram-positives are already resistant to β-lactams. Aminoglycoside resistance, however, could have substantial clinical impact because they are among the few drugs that provide coverage of Gram-negative infections (ECI=97%, EOI=3.8-4.5). Our proposed indices summarise the local impact of antibiotic resistance on empiric coverage (ECI) and available empiric treatment options (EOI) using readily available data. Policymakers and drug developers can use the indices to help evaluate and prioritise initiatives in the effort against antimicrobial resistance. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Error estimates for (semi-)empirical dispersion terms and large biomacromolecules.

PubMed

Korth, Martin

2013-10-14

The first-principles modeling of biomaterials has made tremendous advances over the last few years with the ongoing growth of computing power and impressive developments in the application of density functional theory (DFT) codes to large systems. One important step forward was the development of dispersion corrections for DFT methods, which account for the otherwise neglected dispersive van der Waals (vdW) interactions. Approaches at different levels of theory exist, with the most often used (semi-)empirical ones based on pair-wise interatomic C6R(-6) terms. Similar terms are now also used in connection with semiempirical QM (SQM) methods and density functional tight binding methods (SCC-DFTB). Their basic structure equals the attractive term in Lennard-Jones potentials, common to most force field approaches, but they usually use some type of cutoff function to make the mixing of the (long-range) dispersion term with the already existing (short-range) dispersion and exchange-repulsion effects from the electronic structure theory methods possible. All these dispersion approximations were found to perform accurately for smaller systems, but error estimates for larger systems are very rare and completely missing for really large biomolecules. We derive such estimates for the dispersion terms of DFT, SQM and MM methods using error statistics for smaller systems and dispersion contribution estimates for the PDBbind database of protein-ligand interactions. We find that dispersion terms will usually not be a limiting factor for reaching chemical accuracy, though some force fields and large ligand sizes are problematic.

Climate change alters stability and species potential interactions in a large marine ecosystem.

PubMed

Griffith, Gary P; Strutton, Peter G; Semmens, Jayson M

2018-01-01

We have little empirical evidence of how large-scale overlaps between large numbers of marine species may have altered in response to human impacts. Here, we synthesized all available distribution data (>1 million records) since 1992 for 61 species of the East Australian marine ecosystem, a global hot spot of ocean warming and continuing fisheries exploitation. Using a novel approach, we constructed networks of the annual changes in geographical overlaps between species. Using indices of changes in species overlap, we quantified changes in the ecosystem stability, species robustness, species sensitivity and structural keystone species. We then compared the species overlap indices with environmental and fisheries data to identify potential factors leading to the changes in distributional overlaps between species. We found that the structure of the ecosystem has changed with a decrease in asymmetrical geographical overlaps between species. This suggests that the ecosystem has become less stable and potentially more susceptible to environmental perturbations. Most species have shown a decrease in overlaps with other species. The greatest decrease in species overlap robustness and sensitivity to the loss of other species has occurred in the pelagic community. Some demersal species have become more robust and less sensitive. Pelagic structural keystone species, predominately the tunas and billfish, have been replaced by demersal fish species. The changes in species overlap were strongly correlated with regional oceanographic changes, in particular increasing ocean warming and the southward transport of warmer and saltier water with the East Australian Current, but less correlated with fisheries catch. Our study illustrates how large-scale multispecies distribution changes can help identify structural changes in marine ecosystems associated with climate change. © 2017 John Wiley & Sons Ltd.

Understanding Complex Natural Systems by Articulating Structure-Behavior-Function Models

ERIC Educational Resources Information Center

Vattam, Swaroop S.; Goel, Ashok K.; Rugaber, Spencer; Hmelo-Silver, Cindy E.; Jordan, Rebecca; Gray, Steven; Sinha, Suparna

2011-01-01

Artificial intelligence research on creative design has led to Structure-Behavior-Function (SBF) models that emphasize functions as abstractions for organizing understanding of physical systems. Empirical studies on understanding complex systems suggest that novice understanding is shallow, typically focusing on their visible structures and…

The Structural Algebra Option: A Discussion Paper.

ERIC Educational Resources Information Center

Kirshner, David

The goal of this paper is to renew interest in the structural option to algebra instruction. Concern for the usual secondary school algebra curriculum related to simplifying expressions, solving equations, and rationalizing numerators and denominators is viewed from three pedagogical approaches: (1) structural approach, (2) empirical approach, and…

The potential of the inventory of learning styles to study students' learning patterns in three types of medical curricula.

PubMed

Van der Veken, J; Valcke, M; Muijtjens, A; De Maeseneer, J; Derese, A

2008-01-01

Introducing innovative curricular designs can be evaluating by scrutinizing the learning patterns students use. Studying the potential of Vermunt's Inventory of Learning Styles (ILS) in detecting differences in student learning patterns in different medical curricula. Cross-sectional between-subjects comparison of ILS-scores in third-year medical students in a conventional, an integrated contextual and a PBL-curriculum using one-way post hoc ANOVA. Response rate was 85%: 197 conventional, 130 integrated contextual and 301 PBL students. The results show a differential impact from the three curricula. In relation to processing strategies, the students in the problem-based curriculum showed less rote learning and rehearsing, greater variety in sources of knowledge used and less ability to express study content in a personal manner than did the students in the conventional curriculum. The students of the integrated contextual curriculum showed more structuring of subject matter by integrating different aspects into a whole. In relation to regulation strategies, the students in the problem-based curriculum showed significantly more self-regulation of learning content and the students in the integrated contextual curriculum showed lower levels of regulation. As to learning orientations, the students in the problem-based curriculum showed less ambivalence and the students of the conventional curriculum were less vocationally oriented. The study provides empirical support for expected effects of traditional and innovative curricula which thus far were not well supported by empirical studies.

Predicting Reduction Rates of Energetic Nitroaromatic Compounds Using Calculated One-Electron Reduction Potentials

DOE PAGES

Salter-Blanc, Alexandra; Bylaska, Eric J.; Johnston, Hayley; ...

2015-02-11

The evaluation of new energetic nitroaromatic compounds (NACs) for use in green munitions formulations requires models that can predict their environmental fate. The susceptibility of energetic NACs to nitro reduction might be predicted from correlations between rate constants (k) for this reaction and one-electron reduction potentials (E1NAC) / 0.059 V, but the mechanistic implications of such correlations are inconsistent with evidence from other methods. To address this inconsistency, we have reevaluated existing kinetic data using a (non-linear) free-energy relationship (FER) based on the Marcus theory of outer-sphere electron transfer. For most reductants, the results are inconsistent with rate limitation bymore » an initial, outer-sphere electron transfer, suggesting that the strong correlation between k and E1NAC is justified only as an empirical model. This empirical correlation was used to calibrate a new quantitative structure-activity relationship (QSAR) using previously reported values of k for non-energetic NAC reduction by Fe(II) porphyrin and newly reported values of E1NAC determined using density functional theory at the B3LYP/6-311++G(2d,2p) level with the COSMO solvation model. The QSAR was then validated for energetic NACs using newly measured kinetic data for 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), and 2,4-dinitroanisole (DNAN). The data show close agreement with the QSAR, supporting its applicability to energetic NACs.« less

Efficacy beliefs predict collaborative practice among intensive care unit nurses.

PubMed

Le Blanc, Pascale M; Schaufeli, Wilmar B; Salanova, Marisa; Llorens, Susana; Nap, Raoul E

2010-03-01

This paper is a report of an investigation of whether intensive care nurses' efficacy beliefs predict future collaborative practice, and to test the potential mediating role of team commitment in this relationship. Recent empirical studies in the field of work and organizational psychology have demonstrated that (professional) efficacy beliefs are reciprocally related to workers' resources and well-being over time, resulting in a positive gain spiral. Moreover, there is ample evidence that workers' affective commitment to their organization or work-team is related to desirable work behaviours such as citizenship behaviour. A longitudinal design was applied to questionnaire data from the EURICUS-project. Structural Equation Modelling was used to analyse the data. The sample consisted of 372 nurses working in 29 different European intensive care units. Data were collected in 1997 and 1998. However, our research model deals with fundamental psychosocial processes that are not time-dependent. Moreover, recent empirical literature shows that there is still room for improvement in ICU collaborative practice. The hypotheses that (i) the relationship between efficacy beliefs and collaborative practice is mediated by team commitment and (ii) efficacy beliefs, team commitment and collaborative practice are reciprocally related were supported, suggesting a potential positive gain spiral of efficacy beliefs. Healthcare organizations should create working environments that provide intensive care unit nurses with sufficient resources to perform their job well. Further research is needed to design and evaluate interventions for the enhancement of collaborative practice in intensive care units.

A theoretical method for the analysis and design of axisymmetric bodies. [flow distribution and incompressible fluids

NASA Technical Reports Server (NTRS)

Beatty, T. D.

1975-01-01

A theoretical method is presented for the computation of the flow field about an axisymmetric body operating in a viscous, incompressible fluid. A potential flow method was used to determine the inviscid flow field and to yield the boundary conditions for the boundary layer solutions. Boundary layer effects in the forces of displacement thickness and empirically modeled separation streamlines are accounted for in subsequent potential flow solutions. This procedure is repeated until the solutions converge. An empirical method was used to determine base drag allowing configuration drag to be computed.

Development of vulnerability curves to typhoon hazards based on insurance policy and claim dataset

NASA Astrophysics Data System (ADS)

Mo, Wanmei; Fang, Weihua; li, Xinze; Wu, Peng; Tong, Xingwei

2016-04-01

Vulnerability refers to the characteristics and circumstances of an exposure that make it vulnerable to the effects of some certain hazards. It can be divided into physical vulnerability, social vulnerability, economic vulnerabilities and environmental vulnerability. Physical vulnerability indicates the potential physical damage of exposure caused by natural hazards. Vulnerability curves, quantifying the loss ratio against hazard intensity with a horizontal axis for the intensity and a vertical axis for the Mean Damage Ratio (MDR), is essential to the vulnerability assessment and quantitative evaluation of disasters. Fragility refers to the probability of diverse damage states under different hazard intensity, revealing a kind of characteristic of the exposure. Fragility curves are often used to quantify the probability of a given set of exposure at or exceeding a certain damage state. The development of quantitative fragility and vulnerability curves is the basis of catastrophe modeling. Generally, methods for quantitative fragility and vulnerability assessment can be categorized into empirical, analytical and expert opinion or judgment-based ones. Empirical method is one of the most popular methods and it relies heavily on the availability and quality of historical hazard and loss dataset, which has always been a great challenge. Analytical method is usually based on the engineering experiments and it is time-consuming and lacks built-in validation, so its credibility is also sometimes criticized widely. Expert opinion or judgment-based method is quite effective in the absence of data but the results could be too subjective so that the uncertainty is likely to be underestimated. In this study, we will present the fragility and vulnerability curves developed with empirical method based on simulated historical typhoon wind, rainfall and induced flood, and insurance policy and claim datasets of more than 100 historical typhoon events. Firstly, an insurance exposure classification system is built according to structure type, occupation type and insurance coverage. Then MDR estimation method based on considering insurance policy structure and claim information is proposed and validated. Following that, fragility and vulnerability curves of the major exposure types for construction, homeowner insurance and enterprise property insurance are fitted with empirical function based on the historical dataset. The results of this study can not only help understand catastrophe risk and mange insured disaster risks, but can also be applied in other disaster risk reduction efforts.

Style Matching or Ability Building? An Empirical Study on FD Learners' Learning in Well-Structured and Ill-Structured Asynchronous Online Learning Environments

ERIC Educational Resources Information Center

Zheng, Robert Z.; Flygare, Jill A.; Dahl, Laura B.

2009-01-01

The present study investigated (1) the impact of cognitive styles on learner performance in well-structured and ill-structured learning, and (2) scaffolding as a cognitive tool to improve learners' cognitive abilities, especially field dependent (FD) learners' ability to thrive in an ill-structured learning environment. Two experiments were…

Varieties of Organizational Conflict

ERIC Educational Resources Information Center

Pondy, Louis R.

1969-01-01

The viewpoints and findings of the seven empirical studies of organizational conflict contained in this issue are compared and contrasted. A distinction is made between conflict within a stable organization structure and conflict aimed at changing the organization structure. (Author)

The Molecular Structure of Penicillin

ERIC Educational Resources Information Center

Bentley, Ronald

2004-01-01

Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

Structural pierce into molecular mechanism underlying Clostridium perfringens Epsilon toxin function.

PubMed

Khalili, Saeed; Jahangiri, Abolfazl; Hashemi, Zahra Sadat; Khalesi, Bahman; Mard-Soltani, Maysam; Amani, Jafar

2017-03-01

Epsilon toxin of the Clostridium perfringens garnered a lot of attention due to its potential for toxicity in humans, extreme potency for cytotoxicity in mice and lack of any approved therapeutics prescribed for human. However, the intricacies of the Epsilon toxin action mechanism are yet to be understood. In this regard, various in silico tools have been exploited to model and refine the 3D structure of the toxin and its two receptors. The receptor proteins were embedded into designed lipid membranes within an aqueous and ionized environment. Thereafter, the modeled structures subjected to series of consecutive molecular dynamics runs to achieve the most natural like coordination for each model. Ultimately, protein-protein interaction analyses were performed to understand the probable action mechanism. The obtained results successfully confirmed the accuracy of employed methods to achieve high quality models for the toxin and its receptors within their lipid bilayers. Molecular dynamics analyses lead the structures to a more native like coordination. Moreover, the results of previous empirical studies were confirmed, while new insights for action mechanisms including the detailed roles of Hepatitis A virus cellular receptor 1 (HAVCR1) and Myelin and lymphocyte protein (MAL) proteins were achieved. In light of previous and our observations, we suggested novel models which elucidated the existing interplay between potential players of Epsilon toxin action mechanism with detailed structural evidences. These models would pave the way to have more robust understanding of the Epsilon toxin biology, more precise vaccine construction and more successful drug (inhibitor) design. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dependency structure and scaling properties of financial time series are related

PubMed Central

Morales, Raffaello; Di Matteo, T.; Aste, Tomaso

2014-01-01

We report evidence of a deep interplay between cross-correlations hierarchical properties and multifractality of New York Stock Exchange daily stock returns. The degree of multifractality displayed by different stocks is found to be positively correlated to their depth in the hierarchy of cross-correlations. We propose a dynamical model that reproduces this observation along with an array of other empirical properties. The structure of this model is such that the hierarchical structure of heterogeneous risks plays a crucial role in the time evolution of the correlation matrix, providing an interpretation to the mechanism behind the interplay between cross-correlation and multifractality in financial markets, where the degree of multifractality of stocks is associated to their hierarchical positioning in the cross-correlation structure. Empirical observations reported in this paper present a new perspective towards the merging of univariate multi scaling and multivariate cross-correlation properties of financial time series. PMID:24699417

Dependency structure and scaling properties of financial time series are related

NASA Astrophysics Data System (ADS)

Morales, Raffaello; Di Matteo, T.; Aste, Tomaso

2014-04-01

We report evidence of a deep interplay between cross-correlations hierarchical properties and multifractality of New York Stock Exchange daily stock returns. The degree of multifractality displayed by different stocks is found to be positively correlated to their depth in the hierarchy of cross-correlations. We propose a dynamical model that reproduces this observation along with an array of other empirical properties. The structure of this model is such that the hierarchical structure of heterogeneous risks plays a crucial role in the time evolution of the correlation matrix, providing an interpretation to the mechanism behind the interplay between cross-correlation and multifractality in financial markets, where the degree of multifractality of stocks is associated to their hierarchical positioning in the cross-correlation structure. Empirical observations reported in this paper present a new perspective towards the merging of univariate multi scaling and multivariate cross-correlation properties of financial time series.

Water in a Soft Confinement: Structure of Water in Amorphous Sorbitol.

PubMed

Shalaev, Evgenyi; Soper, Alan K

2016-07-28

The structure of water in 70 wt % sorbitol-30 wt % water mixture is investigated by wide-angle neutron scattering (WANS) as a function of temperature. WANS data are analyzed using empirical potential structure refinement to obtain the site-site radial distribution functions (RDFs). Orientational structure of water is represented using OW-OW-OW triangles distributions and a tetrahedrality parameter, q, while water-water correlation function is used to estimate size of water clusters. Water structure in the sorbitol matrix is compared with that of water confined in nanopores of MCM41. The results indicate the existence of voids in the sorbitol matrix with the length scale of approximately 5 Å, which are filled by water. At 298 K, positional water structure in these voids is similar to that of water in MCM41, whereas there is a difference in the tetrahedral (orientational) arrangement. Cooling to 213 K strengthens tetrahedrality, with the orientational order of water in sorbitol becoming similar to that of confined water in MCM41 at 210 K, whereas further cooling to 100 K does not introduce any additional changes in the tetrahedrality. The results obtained allow us to propose, for the first time, that such confinement of water in a sorbitol matrix is the main reason for the lack of ice formation in this system.

An empirical examination of the factor structure of compassion.

PubMed

Gu, Jenny; Cavanagh, Kate; Baer, Ruth; Strauss, Clara

2017-01-01

Compassion has long been regarded as a core part of our humanity by contemplative traditions, and in recent years, it has received growing research interest. Following a recent review of existing conceptualisations, compassion has been defined as consisting of the following five elements: 1) recognising suffering, 2) understanding the universality of suffering in human experience, 3) feeling moved by the person suffering and emotionally connecting with their distress, 4) tolerating uncomfortable feelings aroused (e.g., fear, distress) so that we remain open to and accepting of the person suffering, and 5) acting or being motivated to act to alleviate suffering. As a prerequisite to developing a high quality compassion measure and furthering research in this field, the current study empirically investigated the factor structure of the five-element definition using a combination of existing and newly generated self-report items. This study consisted of three stages: a systematic consultation with experts to review items from existing self-report measures of compassion and generate additional items (Stage 1), exploratory factor analysis of items gathered from Stage 1 to identify the underlying structure of compassion (Stage 2), and confirmatory factor analysis to validate the identified factor structure (Stage 3). Findings showed preliminary empirical support for a five-factor structure of compassion consistent with the five-element definition. However, findings indicated that the 'tolerating' factor may be problematic and not a core aspect of compassion. This possibility requires further empirical testing. Limitations with items from included measures lead us to recommend against using these items collectively to assess compassion. Instead, we call for the development of a new self-report measure of compassion, using the five-element definition to guide item generation. We recommend including newly generated 'tolerating' items in the initial item pool, to determine whether or not factor-level issues are resolved once item-level issues are addressed.

Assessing Knowledge Structures.

ERIC Educational Resources Information Center

Yacci, Michael

This paper presents two general approaches to the assessment of knowledge structures, the first of which entails the building of empirical evidence to support cognitive theory. This type of assessment is concerned with attempting to prove the existence of various knowledge structures; that is, evidence that leads to the construct validity of these…

The Acceptance of Universalism: The Importance of Selected Aspects of School Structure.

ERIC Educational Resources Information Center

Martin, Robert A.

This report describes a study that investigated empirically the relationships between selected aspects of the organizational structure of elementary schools and the extent to which students endorsed the norm of universalism. Four aspects of structure were studied: degree of departmentalization, school enrollment, student-teacher ratio, and extent…

Exploratory and Confirmatory Factor Analyses of the Structured Interview for Disorders of Extreme Stress

ERIC Educational Resources Information Center

Scoboria, Alan; Ford, Julian; Lin, Hsiu-ju; Frisman, Linda

2008-01-01

Two studies were conducted to provide the first empirical examination of the factor structure of a revised version of the clinically derived Structured Interview for Disorders of Extreme Stress, a structured interview designed to assess associated features of posttraumatic stress disorder (PTSD) thought to be related to early onset, interpersonal,…

Empirical Analysis of Farm Credit Risk under the Structure Model

ERIC Educational Resources Information Center

Yan, Yan

2009-01-01

The study measures farm credit risk by using farm records collected by Farm Business Farm Management (FBFM) during the period 1995-2004. The study addresses the following questions: (1) whether farm's financial position is fully described by the structure model, (2) what are the determinants of farm capital structure under the structure model, (3)…

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

Morris, J.R.; Lu, Z.Y.; Xiang, J.B.

We have examined a variety of structures for the (510) symmetric tilt boundary in Si, using first-principles calculations. These calculations show that the observed structure in Si is the lowest energy structure. This structure is more complicated than what is necessary to preserve four-fold coordination. We compare the results to classical and tight-binding models, in order to test these empirical problems.

Analytic Empirical Potentials for all Stable Isotopologues of the Ground X(^1Σ^+) State of ZnO from Purely Rotational Measurements

NASA Astrophysics Data System (ADS)

Dattani, Nikesh S.; Zack, Lindsay; Sun, Ming; Johnson, Erin R.; Le Roy, Robert; Ziurys, Lucy

2014-06-01

We report eight new ultra-high precision (±5 kHz) measurements of purely rotational N(1←0) transitions in several vibrational states of all stable isotopologues of the ground X(11Σ+) -state of ZnO. Combined with previous high-resolution (±50 kHz) measurements of purely rotational transitions between higher rotational states for the same system, we are able to build analytic potentials for 64Zn16O, 66Zn16O, 67Zn16O, 68Zn16O, and 70Zn16O, that are in full agreement with all known spectroscopic measurements of the system. Despite there being absolutely no vibrational information, our empirical potentials are able to determine the size of the vibrational spacings and the bond lengths, each with a precision of more than two orders of magnitude greater than the most precise empirical values previously known. We then use the XDM method to calculate values for the C6, C8, and C10 long-range constants for this molecule, and use these to accurately anchor the long-range regions of the potentials, where no measurements have yet been performed. In the region lying between the short-range measurements and the long-range theory on which our potentials are based, our final analytic global potentials are in very good agreement with state of the art ab initio potentials. L. N. Zack, R. L. Pulliam, L. M. Ziurys, J. Mol. Spec., 256, 186-191 (2009).

Parents' Involvement in Inclusive Education: An Empirical Test for the Psycho-Educational Development of Learners with Special Education Needs (SENs)

ERIC Educational Resources Information Center

Afolabi, Olusegun Emmanuel

2014-01-01

There is mounting evidence that involvement paradigm is a major strategy that supports positive learning outcomes and is critically vital for educating learners with special educational needs (SENs). To illuminate the parental involvement concept and potential in a concrete context, this paper explains 1) the empirical literature that explains the…

Empirical population and public health ethics: A review and critical analysis to advance robust empirical-normative inquiry.

PubMed

Knight, Rod

2016-05-01

The field of population and public health ethics (PPHE) has yet to fully embrace the generation of evidence as an important project. This article reviews the philosophical debates related to the 'empirical turn' in clinical bioethics, and critically analyses how PPHE has and can engage with the philosophical implications of generating empirical data within the task of normative inquiry. A set of five conceptual and theoretical issues pertaining to population health that are unresolved and could potentially benefit from empirical PPHE approaches to normative inquiry are discussed. Each issue differs from traditional empirical bioethical approaches, in that they emphasize (1) concerns related to the population, (2) 'upstream' policy-relevant health interventions - within and outside of the health care system and (3) the prevention of illness and disease. Within each theoretical issue, a conceptual example from population and public health approaches to HIV prevention and health promotion is interrogated. Based on the review and critical analysis, this article concludes that empirical-normative approaches to population and public health ethics would be most usefully pursued as an iterative project (rather than as a linear project), in which the normative informs the empirical questions to be asked and new empirical evidence constantly directs conceptualizations of what constitutes morally robust public health practices. Finally, a conceptualization of an empirical population and public health ethics is advanced in order to open up new interdisciplinary 'spaces', in which empirical and normative approaches to ethical inquiry are transparently (and ethically) integrated. © The Author(s) 2015.

Identifying Early Childhood Personality Dimensions Using the California Child Q-Set and Prospective Associations With Behavioral and Psychosocial Development.

PubMed

Wilson, Sylia; Schalet, Benjamin D; Hicks, Brian M; Zucker, Robert A

2013-08-01

The present study used an empirical, "bottom-up" approach to delineate the structure of the California Child Q-Set (CCQ), a comprehensive set of personality descriptors, in a sample of 373 preschool-aged children. This approach yielded two broad trait dimensions, Adaptive Socialization (emotional stability, compliance, intelligence) and Anxious Inhibition (emotional/behavioral introversion). Results demonstrate the value of using empirical derivation to investigate the structure of personality in young children, speak to the importance of early-evident personality traits for adaptive development, and are consistent with a growing body of evidence indicating that personality structure in young children is similar, but not identical to, that in adults, suggesting a model of broad personality dimensions in childhood that evolve into narrower traits in adulthood.

Temporal structure of neuronal population oscillations with empirical model decomposition

NASA Astrophysics Data System (ADS)

Li, Xiaoli

2006-08-01

Frequency analysis of neuronal oscillation is very important for understanding the neural information processing and mechanism of disorder in the brain. This Letter addresses a new method to analyze the neuronal population oscillations with empirical mode decomposition (EMD). Following EMD of neuronal oscillation, a series of intrinsic mode functions (IMFs) are obtained, then Hilbert transform of IMFs can be used to extract the instantaneous time frequency structure of neuronal oscillation. The method is applied to analyze the neuronal oscillation in the hippocampus of epileptic rats in vivo, the results show the neuronal oscillations have different descriptions during the pre-ictal, seizure onset and ictal periods of the epileptic EEG at the different frequency band. This new method is very helpful to provide a view for the temporal structure of neural oscillation.

Around the macrolide - Impact of 3D structure of macrocycles on lipophilicity and cellular accumulation.

PubMed

Koštrun, Sanja; Munic Kos, Vesna; Matanović Škugor, Maja; Palej Jakopović, Ivana; Malnar, Ivica; Dragojević, Snježana; Ralić, Jovica; Alihodžić, Sulejman

2017-06-16

The aim of this study was to investigate lipophilicity and cellular accumulation of rationally designed azithromycin and clarithromycin derivatives at the molecular level. The effect of substitution site and substituent properties on a global physico-chemical profile and cellular accumulation of investigated compounds was studied using calculated structural parameters as well as experimentally determined lipophilicity. In silico models based on the 3D structure of molecules were generated to investigate conformational effect on studied properties and to enable prediction of lipophilicity and cellular accumulation for this class of molecules based on non-empirical parameters. The applicability of developed models was explored on a validation and test sets and compared with previously developed empirical models. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Undermining and Strengthening Social Networks through Network Modification

PubMed Central

Mellon, Jonathan; Yoder, Jordan; Evans, Daniel

2016-01-01

Social networks have well documented effects at the individual and aggregate level. Consequently it is often useful to understand how an attempt to influence a network will change its structure and consequently achieve other goals. We develop a framework for network modification that allows for arbitrary objective functions, types of modification (e.g. edge weight addition, edge weight removal, node removal, and covariate value change), and recovery mechanisms (i.e. how a network responds to interventions). The framework outlined in this paper helps both to situate the existing work on network interventions but also opens up many new possibilities for intervening in networks. In particular use two case studies to highlight the potential impact of empirically calibrating the objective function and network recovery mechanisms as well as showing how interventions beyond node removal can be optimised. First, we simulate an optimal removal of nodes from the Noordin terrorist network in order to reduce the expected number of attacks (based on empirically predicting the terrorist collaboration network from multiple types of network ties). Second, we simulate optimally strengthening ties within entrepreneurial ecosystems in six developing countries. In both cases we estimate ERGM models to simulate how a network will endogenously evolve after intervention. PMID:27703198

Undermining and Strengthening Social Networks through Network Modification.

PubMed

Mellon, Jonathan; Yoder, Jordan; Evans, Daniel

2016-10-05

Social networks have well documented effects at the individual and aggregate level. Consequently it is often useful to understand how an attempt to influence a network will change its structure and consequently achieve other goals. We develop a framework for network modification that allows for arbitrary objective functions, types of modification (e.g. edge weight addition, edge weight removal, node removal, and covariate value change), and recovery mechanisms (i.e. how a network responds to interventions). The framework outlined in this paper helps both to situate the existing work on network interventions but also opens up many new possibilities for intervening in networks. In particular use two case studies to highlight the potential impact of empirically calibrating the objective function and network recovery mechanisms as well as showing how interventions beyond node removal can be optimised. First, we simulate an optimal removal of nodes from the Noordin terrorist network in order to reduce the expected number of attacks (based on empirically predicting the terrorist collaboration network from multiple types of network ties). Second, we simulate optimally strengthening ties within entrepreneurial ecosystems in six developing countries. In both cases we estimate ERGM models to simulate how a network will endogenously evolve after intervention.

Undermining and Strengthening Social Networks through Network Modification

NASA Astrophysics Data System (ADS)

Mellon, Jonathan; Yoder, Jordan; Evans, Daniel

2016-10-01

Social networks have well documented effects at the individual and aggregate level. Consequently it is often useful to understand how an attempt to influence a network will change its structure and consequently achieve other goals. We develop a framework for network modification that allows for arbitrary objective functions, types of modification (e.g. edge weight addition, edge weight removal, node removal, and covariate value change), and recovery mechanisms (i.e. how a network responds to interventions). The framework outlined in this paper helps both to situate the existing work on network interventions but also opens up many new possibilities for intervening in networks. In particular use two case studies to highlight the potential impact of empirically calibrating the objective function and network recovery mechanisms as well as showing how interventions beyond node removal can be optimised. First, we simulate an optimal removal of nodes from the Noordin terrorist network in order to reduce the expected number of attacks (based on empirically predicting the terrorist collaboration network from multiple types of network ties). Second, we simulate optimally strengthening ties within entrepreneurial ecosystems in six developing countries. In both cases we estimate ERGM models to simulate how a network will endogenously evolve after intervention.

Transcranial direct current stimulation in obsessive-compulsive disorder: emerging clinical evidence and considerations for optimal montage of electrodes.

PubMed

Senço, Natasha M; Huang, Yu; D'Urso, Giordano; Parra, Lucas C; Bikson, Marom; Mantovani, Antonio; Shavitt, Roseli G; Hoexter, Marcelo Q; Miguel, Eurípedes C; Brunoni, André R

2015-07-01

Neuromodulation techniques for obsessive-compulsive disorder (OCD) treatment have expanded with greater understanding of the brain circuits involved. Transcranial direct current stimulation (tDCS) might be a potential new treatment for OCD, although the optimal montage is unclear. To perform a systematic review on meta-analyses of repetitive transcranianal magnetic stimulation (rTMS) and deep brain stimulation (DBS) trials for OCD, aiming to identify brain stimulation targets for future tDCS trials and to support the empirical evidence with computer head modeling analysis. Systematic reviews of rTMS and DBS trials on OCD in Pubmed/MEDLINE were searched. For the tDCS computational analysis, we employed head models with the goal of optimally targeting current delivery to structures of interest. Only three references matched our eligibility criteria. We simulated four different electrodes montages and analyzed current direction and intensity. Although DBS, rTMS and tDCS are not directly comparable and our theoretical model, based on DBS and rTMS targets, needs empirical validation, we found that the tDCS montage with the cathode over the pre-supplementary motor area and extra-cephalic anode seems to activate most of the areas related to OCD.

How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

PubMed Central

Jørgensen, J. S.; Sidky, E. Y.

2015-01-01

We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization. PMID:25939620

How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography.

PubMed

Jørgensen, J S; Sidky, E Y

2015-06-13

We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization.

[Everyday life and solidarity in north-east German rural communities - first qualitative results of the Rural Health Study].

PubMed

Nebelung, C; Forkel, J A; Elkeles, T

2010-03-01

There have been increasing discussions in the health sciences in recent years about socio-spatial influences on health activities. The starting point has been the growing territorial inequality in spatial development resources, which has an effect on the participatory chances of people in structurally weak regions. The concept of "peripherisation" is used to describe this change. Empirical investigations of socio-spatial resources at the local level are rare, because the theoretical preconditions have not been elaborated sufficiently for the theoretical modelling to be recognised for hypothesis-based empirical investigations. At the centre of this theorisation are analyses of the "social capital" of every-day actions. As part of the Rural Health Study 2008 at the University of Applied Science Neubrandenburg (involving a longitudinal analysis with quantitative surveys in 14 rural communities in north-eastern Germany 1973, 1994, 2008), a qualitative approach was also adopted with case and community studies. The first results are compared with the state of the literature. Case studies are presented showing strategies for adaptation and improvement of the individual's situation, and also the daily solidarity of people in villages. Development potentials are outlined. Georg Thieme Verlag KG Stuttgart. New York.

[Empirical therapeutic approach to infection by resistant gram positive (acute bacterial skin and skin structure infections and health care pneumonia). Value of risk factors].

PubMed

González-DelCastillo, J; Núñez-Orantos, M J; Candel, F J; Martín-Sánchez, F J

2016-09-01

Antibiotic treatment inadequacy is common in these sites of infection and may have implications for the patient's prognosis. In acute bacterial skin and skin structure infections, the document states that for the establishment of an adequate treatment it must be assessed the severity, the patient comorbidity and the risk factors for multidrug-resistant microorganism. The concept of health care-associated pneumonia is discussed and leads to errors in the etiologic diagnosis and therefore in the selection of antibiotic treatment. This paper discusses how to perform this approach to the possible etiology to guide empirical treatment.

[Contribution to the history of pharmacology (the early Roman empire)].

PubMed

Tesařová, Drahomíra

2014-01-01

This article is a contribution to the history of pharmacology in the early Roman empire. It contains texts mainly written in Latin: the works of Aulus Cornelius Celsus, Scribonius Largus and Plinius Maior (Pliny the Elder). It describes their structure and contributions to the history of medicine and gives examples of some prescriptions and drugs in the original language and in Czech.

Implications of alternative field-sampling designs on Landsat-based mapping of stand age and carbon stocks in Oregon forests

Treesearch

Maureen V. Duane; Warren B. Cohen; John L. Campbell; Tara Hudiburg; David P. Turner; Dale Weyermann

2010-01-01

Empirical models relating forest attributes to remotely sensed metrics are widespread in the literature and underpin many of our efforts to map forest structure across complex landscapes. In this study we compared empirical models relating Landsat reflectance to forest age across Oregon using two alternate sets of ground data: one from a large (n ~ 1500) systematic...

Estimating and Identifying Unspecified Correlation Structure for Longitudinal Data

PubMed Central

Hu, Jianhua; Wang, Peng; Qu, Annie

2014-01-01

Identifying correlation structure is important to achieving estimation efficiency in analyzing longitudinal data, and is also crucial for drawing valid statistical inference for large size clustered data. In this paper, we propose a nonparametric method to estimate the correlation structure, which is applicable for discrete longitudinal data. We utilize eigenvector-based basis matrices to approximate the inverse of the empirical correlation matrix and determine the number of basis matrices via model selection. A penalized objective function based on the difference between the empirical and model approximation of the correlation matrices is adopted to select an informative structure for the correlation matrix. The eigenvector representation of the correlation estimation is capable of reducing the risk of model misspecification, and also provides useful information on the specific within-cluster correlation pattern of the data. We show that the proposed method possesses the oracle property and selects the true correlation structure consistently. The proposed method is illustrated through simulations and two data examples on air pollution and sonar signal studies. PMID:26361433

Synthesis of novel Schiff's bases of highly potential biological activities and their structure investigation.

PubMed

Zayed, Ehab M; Zayed, M A

2015-05-15

Novel bisaldehyde-hydrazide Schiff's bases AS1 (2,2'-(ethane-1,2-diylbis(oxy))dibenzaldehyde terephthalohydrazide) and AS2 (N',N'″-(((ethane-1,2-diylbis(oxy))bis(2,1-phenylene))bis(methanylylidene))di(benzohydrazide)) were prepared as new macrocyclic compounds via condensation reactions. AS1 had been prepared by condensation between (2,2'-(ethane-1,2-diylbis(oxy))dibenzaldehyde) bisaldehyde and terephthalohydrazide in a ratio1:1. AS2 had been obtained by condensation between (2,2'-(ethane-1,2-diylbis(oxy))dibenzaldehyde) bisaldehyde and benzohydrazide in ratio 1:2. The structures of AS1 and AS2 were characterized by elemental analysis (EA), mass (MS), FT-IR and (1)H-NMR spectra, and thermal analyses (TG, DTG). The activation thermodynamic parameters such as ΔE(∗), ΔH(∗), ΔS(∗) and ΔG(∗) were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bonds responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities had been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillus subtilis and Staphylococcus aurous bacteria in order to assess their anti-microbial potential. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthesis of novel Schiff's bases of highly potential biological activities and their structure investigation

NASA Astrophysics Data System (ADS)

Zayed, Ehab M.; Zayed, M. A.

2015-05-01

Novel bisaldehyde-hydrazide Schiff's bases AS1 (2,2‧-(ethane-1,2-diylbis(oxy))dibenzaldehyde terephthalohydrazide) and AS2 (N‧,N‧″-(((ethane-1,2-diylbis(oxy))bis(2,1-phenylene))bis(methanylylidene))di(benzohydrazide)) were prepared as new macrocyclic compounds via condensation reactions. AS1 had been prepared by condensation between (2,2‧-(ethane-1,2-diylbis(oxy))dibenzaldehyde) bisaldehyde and terephthalohydrazide in a ratio1:1. AS2 had been obtained by condensation between (2,2‧-(ethane-1,2-diylbis(oxy))dibenzaldehyde) bisaldehyde and benzohydrazide in ratio 1:2. The structures of AS1 and AS2 were characterized by elemental analysis (EA), mass (MS), FT-IR and 1H-NMR spectra, and thermal analyses (TG, DTG). The activation thermodynamic parameters such as ΔE∗, ΔH∗, ΔS∗ and ΔG∗ were calculated from the TG curves using Coats-Redfern method. It is important to investigate their molecular structures to know the active groups and weak bonds responsible for their biological activities. Consequently in the present work, the obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculations (MOCS) using PM3 procedure. Their biological activities had been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillus subtilis and Staphylococcus aurous bacteria in order to assess their anti-microbial potential.

Selected approaches for rational drug design and high throughput screening to identify anti-cancer molecules.

PubMed

Hedvat, Michael; Emdad, Luni; Das, Swadesh K; Kim, Keetae; Dasgupta, Santanu; Thomas, Shibu; Hu, Bin; Zhu, Shan; Dash, Rupesh; Quinn, Bridget A; Oyesanya, Regina A; Kegelman, Timothy P; Sokhi, Upneet K; Sarkar, Siddik; Erdogan, Eda; Menezes, Mitchell E; Bhoopathi, Praveen; Wang, Xiang-Yang; Pomper, Martin G; Wei, Jun; Wu, Bainan; Stebbins, John L; Diaz, Paul W; Reed, John C; Pellecchia, Maurizio; Sarkar, Devanand; Fisher, Paul B

2012-11-01

Structure-based modeling combined with rational drug design, and high throughput screening approaches offer significant potential for identifying and developing lead compounds with therapeutic potential. The present review focuses on these two approaches using explicit examples based on specific derivatives of Gossypol generated through rational design and applications of a cancer-specificpromoter derived from Progression Elevated Gene-3. The Gossypol derivative Sabutoclax (BI-97C1) displays potent anti-tumor activity against a diverse spectrum of human tumors. The model of the docked structure of Gossypol bound to Bcl-XL provided a virtual structure-activity-relationship where appropriate modifications were predicted on a rational basis. These structure-based studies led to the isolation of Sabutoclax, an optically pure isomer of Apogossypol displaying superior efficacy and reduced toxicity. These studies illustrate the power of combining structure-based modeling with rational design to predict appropriate derivatives of lead compounds to be empirically tested and evaluated for bioactivity. Another approach to cancer drug discovery utilizes a cancer-specific promoter as readouts of the transformed state. The promoter region of Progression Elevated Gene-3 is such a promoter with cancer-specific activity. The specificity of this promoter has been exploited as a means of constructing cancer terminator viruses that selectively kill cancer cells and as a systemic imaging modality that specifically visualizes in vivo cancer growth with no background from normal tissues. Screening of small molecule inhibitors that suppress the Progression Elevated Gene-3-promoter may provide relevant lead compounds for cancer therapy that can be combined with further structure-based approaches leading to the development of novel compounds for cancer therapy.

The First Empirical Determination of the Fe10+ and Fe13+ Freeze-in Distances in the Solar Corona

NASA Astrophysics Data System (ADS)

Boe, Benjamin; Habbal, Shadia; Druckmüller, Miloslav; Landi, Enrico; Kourkchi, Ehsan; Ding, Adalbert; Starha, Pavel; Hutton, Joseph

2018-06-01

Heavy ions are markers of the physical processes responsible for the density and temperature distribution throughout the fine-scale magnetic structures that define the shape of the solar corona. One of their properties, whose empirical determination has remained elusive, is the “freeze-in” distance (R f ) where they reach fixed ionization states that are adhered to during their expansion with the solar wind. We present the first empirical inference of R f for {Fe}}{10+} and {Fe}}{13+} derived from multi-wavelength imaging observations of the corresponding Fe XI ({Fe}}{10+}) 789.2 nm and Fe XIV ({Fe}}{13+}) 530.3 nm emission acquired during the 2015 March 20 total solar eclipse. We find that the two ions freeze-in at different heliocentric distances. In polar coronal holes (CHs) R f is around 1.45 R ⊙ for {Fe}}{10+} and below 1.25 R ⊙ for {Fe}}{13+}. Along open field lines in streamer regions, R f ranges from 1.4 to 2 R ⊙ for {Fe}}{10+} and from 1.5 to 2.2 R ⊙ for {Fe}}{13+}. These first empirical R f values: (1) reflect the differing plasma parameters between CHs and streamers and structures within them, including prominences and coronal mass ejections; (2) are well below the currently quoted values derived from empirical model studies; and (3) place doubt on the reliability of plasma diagnostics based on the assumption of ionization equilibrium beyond 1.2 R ⊙.

Multi-scale predictive modeling of nano-material and realistic electron devices

NASA Astrophysics Data System (ADS)

Palaria, Amritanshu

Among the challenges faced in further miniaturization of electronic devices, heavy influence of the detailed atomic configuration of the material(s) involved, which often differs significantly from that of the bulk material(s), is prominent. Device design has therefore become highly interrelated with material engineering at the atomic level. This thesis aims at outlining, with examples, a multi-scale simulation procedure that allows one to integrate material and device aspects of nano-electronic design to predict behavior of novel devices with novel material. This is followed in four parts: (1) An approach that combines a higher time scale reactive force field analysis with density functional theory to predict structure of new material is demonstrated for the first time for nanowires. Novel stable structures for very small diameter silicon nanowires are predicted. (2) Density functional theory is used to show that the new nanowire structures derived in 1 above have properties different from diamond core wires even though the surface bonds in some may be similar to the surface of bulk silicon. (3) Electronic structure of relatively large-scale germanium sections of realistically strained Si/strained Ge/ strained Si nanowire heterostructures is computed using empirical tight binding and it is shown that the average non-homogeneous strain in these structures drives their interesting non-conventional electronic characteristics such as hole effective masses which decrease as the wire cross-section is reduced. (4) It is shown that tight binding, though empirical in nature, is not necessarily limited to the material and atomic structure for which the parameters have been empirically derived, but that simple changes may adapt the derived parameters to new bond environments. Si (100) surface electronic structure is obtained from bulk Si parameters.

Investigating the potential for ethnic group harm in collaborative genomics research in Africa: Is ethnic stigmatisation likely?

PubMed Central

de Vries, Jantina; Jallow, Muminatou; Williams, Thomas N.; Kwiatkowski, Dominic; Parker, Michael; Fitzpatrick, Raymond

2013-01-01

A common assumption in genomics research is that the use of ethnic categories has the potential to lead to ethnic stigmatisation – particularly when the research is done on minority populations. Yet few empirical studies have sought to investigate the relation between genomics and stigma, and fewer still with a focus on Africa. In this paper, we investigate the potential for genomics research to lead to harms to ethnic groups. We carried out 49 semi-structured, open-ended interviews with stakeholders in a current medical genomics research project in Africa, MalariaGEN. Interviews were conducted with MalariaGEN researchers, fieldworkers, members of three ethics committees who reviewed MalariaGEN project proposals, and with members of the two funding bodies providing support to the MalariaGEN project. Interviews were conducted in Kenya, The Gambia and the UK between June 2008 and October 2009. They covered a range of aspects relating to the use of ethnicity in the genomics project, including views on adverse effects of the inclusion of ethnicity in such research. Drawing on the empirical data, we argue that the risk of harm to ethnic groups is likely to be more acute in specific types of genomics research. We develop a typology of research questions and projects that carry a greater risk of harm to the populations included in genomics research. We conclude that the potential of generating harm to ethnic groups in genomics research is present if research includes populations that are already stigmatised or discriminated against, or where the research investigates questions with particular normative implications. We identify a clear need for genomics researchers to take account of the social context of the work they are proposing to do, including understanding the local realities and relations between ethnic groups, and whether diseases are already stigmatised. PMID:22749442

Computational modeling of high-entropy alloys: Structures, thermodynamics and elasticity

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

Gao, Michael C.; Gao, Pan; Hawk, Jeffrey A.

This study provides a short review on computational modeling on the formation, thermodynamics, and elasticity of single-phase high-entropy alloys (HEAs). Hundreds of predicted single-phase HEAs were re-examined using various empirical thermo-physical parameters. Potential BCC HEAs (CrMoNbTaTiVW, CrMoNbReTaTiVW, and CrFeMoNbReRuTaVW) were suggested based on CALPHAD modeling. The calculated vibrational entropies of mixing are positive for FCC CoCrFeNi, negative for BCC MoNbTaW, and near-zero for HCP CoOsReRu. The total entropies of mixing were observed to trend in descending order: CoCrFeNi > CoOsReRu > MoNbTaW. Calculated lattice parameters agree extremely well with averaged values estimated from the rule of mixtures (ROM) if themore » same crystal structure is used for the elements and the alloy. The deviation in the calculated elastic properties from ROM for select alloys is small but is susceptible to the choice used for the structures of pure components.« less

Computational modeling of high-entropy alloys: Structures, thermodynamics and elasticity

DOE PAGES

Gao, Michael C.; Gao, Pan; Hawk, Jeffrey A.; ...

2017-10-12

This study provides a short review on computational modeling on the formation, thermodynamics, and elasticity of single-phase high-entropy alloys (HEAs). Hundreds of predicted single-phase HEAs were re-examined using various empirical thermo-physical parameters. Potential BCC HEAs (CrMoNbTaTiVW, CrMoNbReTaTiVW, and CrFeMoNbReRuTaVW) were suggested based on CALPHAD modeling. The calculated vibrational entropies of mixing are positive for FCC CoCrFeNi, negative for BCC MoNbTaW, and near-zero for HCP CoOsReRu. The total entropies of mixing were observed to trend in descending order: CoCrFeNi > CoOsReRu > MoNbTaW. Calculated lattice parameters agree extremely well with averaged values estimated from the rule of mixtures (ROM) if themore » same crystal structure is used for the elements and the alloy. The deviation in the calculated elastic properties from ROM for select alloys is small but is susceptible to the choice used for the structures of pure components.« less

Simulating Spatial Growth Patterns in Developing Countries: A Case of Shama in the Western Region of Ghana.

NASA Astrophysics Data System (ADS)

Inkoom, J. N.; Nyarko, B. K.

2014-12-01

The integration of geographic information systems (GIS) and agent-based modelling (ABM) can be an efficient tool to improve spatial planning practices. This paper utilizes GIS and ABM approaches to simulate spatial growth patterns of settlement structures in Shama. A preliminary household survey on residential location decision-making choice served as the behavioural rule for household agents in the model. Physical environment properties of the model were extracted from a 2005 image implemented in NetLogo. The resulting growth pattern model was compared with empirical growth patterns to ascertain the model's accuracy. The paper establishes that the development of unplanned structures and its evolving structural pattern are a function of land price, proximity to economic centres, household economic status and location decision-making patterns. The application of the proposed model underlines its potential for integration into urban planning policies and practices, and for understanding residential decision-making processes in emerging cities in developing countries. Key Words: GIS; Agent-based modelling; Growth patterns; NetLogo; Location decision making; Computational Intelligence.

Metabolomic approaches for orange origin discrimination by ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry.

PubMed

Díaz, Ramon; Pozo, Oscar J; Sancho, Juan V; Hernández, Félix

2014-08-15

In this work, hybrid quadrupole time-of-flight mass spectrometer (QTOF MS) coupled to ultra high performance liquid chromatography (UHPLC) has been used for biomarkers identification for correct authentication of Valencia (Spain) oranges. Differentiation from foreign Argentinean, Brazilian and South African oranges has been carried out using XCMS application and multivariate analysis to UHPLC-(Q)TOF MS data acquired in both, positive and negative ionisation modes. Several markers have been found and corroborated by analysing two seasons samples. A seasonal independent marker was found and its structure elucidated using accurate mass data and MS(E) fragmentation spectrum information. Empirical formula was searched in Reaxys database applying sub-structure filtering from the fragments obtained. Three possible structures were found and citrusin D, a compound present in sweet oranges, has been identified as the most plausible as it fits better with the product ion scan performed for this compound. As a result of data obtained in this work, citrusin D is suggested as a potential marker to distinguish the geographic origin of oranges. Copyright © 2014 Elsevier Ltd. All rights reserved.

Modeling of time dependent localized flow shear stress and its impact on cellular growth within additive manufactured titanium implants.

PubMed

Zhang, Ziyu; Yuan, Lang; Lee, Peter D; Jones, Eric; Jones, Julian R

2014-11-01

Bone augmentation implants are porous to allow cellular growth, bone formation and fixation. However, the design of the pores is currently based on simple empirical rules, such as minimum pore and interconnects sizes. We present a three-dimensional (3D) transient model of cellular growth based on the Navier-Stokes equations that simulates the body fluid flow and stimulation of bone precursor cellular growth, attachment, and proliferation as a function of local flow shear stress. The model's effectiveness is demonstrated for two additive manufactured (AM) titanium scaffold architectures. The results demonstrate that there is a complex interaction of flow rate and strut architecture, resulting in partially randomized structures having a preferential impact on stimulating cell migration in 3D porous structures for higher flow rates. This novel result demonstrates the potential new insights that can be gained via the modeling tool developed, and how the model can be used to perform what-if simulations to design AM structures to specific functional requirements. © 2014 Wiley Periodicals, Inc.

Structural and configurational properties of nanoconfined monolayer ice from first principles

PubMed Central

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations. PMID:26728125

Structural and configurational properties of nanoconfined monolayer ice from first principles

NASA Astrophysics Data System (ADS)

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations.

Living in the branches: population dynamics and ecological processes in dendritic networks

USGS Publications Warehouse

Grant, E.H.C.; Lowe, W.H.; Fagan, W.F.

2007-01-01

Spatial structure regulates and modifies processes at several levels of ecological organization (e.g. individual/genetic, population and community) and is thus a key component of complex systems, where knowledge at a small scale can be insufficient for understanding system behaviour at a larger scale. Recent syntheses outline potential applications of network theory to ecological systems, but do not address the implications of physical structure for network dynamics. There is a specific need to examine how dendritic habitat structure, such as that found in stream, hedgerow and cave networks, influences ecological processes. Although dendritic networks are one type of ecological network, they are distinguished by two fundamental characteristics: (1) both the branches and the nodes serve as habitat, and (2) the specific spatial arrangement and hierarchical organization of these elements interacts with a species' movement behaviour to alter patterns of population distribution and abundance, and community interactions. Here, we summarize existing theory relating to ecological dynamics in dendritic networks, review empirical studies examining the population- and community-level consequences of these networks, and suggest future research integrating spatial pattern and processes in dendritic systems.

Effect of the cation model on the equilibrium structure of poly-L-glutamate in aqueous sodium chloride solution

NASA Astrophysics Data System (ADS)

Marchand, Gabriel; Soetens, Jean-Christophe; Jacquemin, Denis; Bopp, Philippe A.

2015-12-01

We demonstrate that different sets of Lennard-Jones parameters proposed for the Na+ ion, in conjunction with the empirical combining rules routinely used in simulation packages, can lead to essentially different equilibrium structures for a deprotonated poly-L-glutamic acid molecule (poly-L-glutamate) dissolved in a 0.3M aqueous NaCl solution. It is, however, difficult to discriminate a priori between these model potentials; when investigating the structure of the Na+-solvation shell in bulk NaCl solution, all parameter sets lead to radial distribution functions and solvation numbers in broad agreement with the available experimental data. We do not find any such dependency of the equilibrium structure on the parameters associated with the Cl- ion. This work does not aim at recommending a particular set of parameters for any particular purpose. Instead, it stresses the model dependence of simulation results for complex systems such as biomolecules in solution and thus the difficulties if simulations are to be used for unbiased predictions, or to discriminate between contradictory experiments. However, this opens the possibility of validating a model specifically in view of analyzing experimental data believed to be reliable.

Computational prediction of atomic structures of helical membrane proteins aided by EM maps.

PubMed

Kovacs, Julio A; Yeager, Mark; Abagyan, Ruben

2007-09-15

Integral membrane proteins pose a major challenge for protein-structure prediction because only approximately 100 high-resolution structures are available currently, thereby impeding the development of rules or empirical potentials to predict the packing of transmembrane alpha-helices. However, when an intermediate-resolution electron microscopy (EM) map is available, it can be used to provide restraints which, in combination with a suitable computational protocol, make structure prediction feasible. In this work we present such a protocol, which proceeds in three stages: 1), generation of an ensemble of alpha-helices by flexible fitting into each of the density rods in the low-resolution EM map, spanning a range of rotational angles around the main helical axes and translational shifts along the density rods; 2), fast optimization of side chains and scoring of the resulting conformations; and 3), refinement of the lowest-scoring conformations with internal coordinate mechanics, by optimizing the van der Waals, electrostatics, hydrogen bonding, torsional, and solvation energy contributions. In addition, our method implements a penalty term through a so-called tethering map, derived from the EM map, which restrains the positions of the alpha-helices. The protocol was validated on three test cases: GpA, KcsA, and MscL.

Some properties of solid helium and helium nanoclusters using the effective HFD-like interaction potential: Adsorption and desorption inside carbon nanotube

NASA Astrophysics Data System (ADS)

Abbaspour, M.; Akbarzadeh, H.; Banihashemi, S. Z.; Sotoudeh, A.

2018-02-01

We have calculated the zero equation of state of solid helium using a two-body Hartree-Fock dispersion (HFD)-like potential from molecular dynamics (MD) simulation. To take many-body forces into account, our simple and accurate empirical expression is used with the HFD-like potential without requiring an expensive three-body calculation. This potential model also includes the quantum effects for helium at low temperatures. The results indicate that our effective HFD-like potential improves the prediction of the classical two-body results to get better agreement with experiment than many other two-body and three-body potentials of helium reported in the literature. We have also simulated the adsorption and desorption processes of the (He)55, (He)147, (He)309, (He)561, and (He)923 icosahedral nanoclusters confined into the different armchair and zigzag CNTs from 0 to 50 K using our effective model. We have observed an interesting phenomenon at 0 K for helium. The nanoclusters adsorb to the inner CNT wall as a melting process. But, the heavier noble gas clusters (such as Ne and Xe) show the different behavior than the He clusters. They form a multilayered solid structure into the CNT at zero temperature and adsorb into the inner wall of the CNT at higher temperatures. Our results for He clusters show that the absolute value of the adsorption energy increases as the size of the nanocluster increases. The desorption process begins at a certain temperature and represents itself by a jump in the configurational energy values. We have also investigated the structural and dynamical properties of the confined helium nanoclusters during the adsorption and desorption processes at different temperatures.

Empirical approaches to metacommunities: a review and comparison with theory.

PubMed

Logue, Jürg B; Mouquet, Nicolas; Peter, Hannes; Hillebrand, Helmut

2011-09-01

Metacommunity theory has advanced understanding of how spatial dynamics and local interactions shape community structure and biodiversity. Here, we review empirical approaches to metacommunities, both observational and experimental, pertaining to how well they relate to and test theoretical metacommunity paradigms and how well they capture the realities of natural ecosystems. First, we show that the species-sorting and mass-effects paradigms are the most commonly tested and supported paradigms. Second, the dynamics observed can often be ascribed to two or more of the four non-exclusive paradigms. Third, empirical approaches relate only weakly to the concise assumptions and predictions made by the paradigms. Consequently, we suggest major avenues of improvement for empirical metacommunity approaches, including the integration across theoretical approaches and the incorporation of evolutionary and meta-ecosystem dynamics. We hope for metacommunity ecology to thereby bridge existing gaps between empirical and theoretical work, thus becoming a more powerful framework to understand dynamics across ecosystems. Copyright © 2011 Elsevier Ltd. All rights reserved.

Empirical fitness landscapes and the predictability of evolution.

PubMed

de Visser, J Arjan G M; Krug, Joachim

2014-07-01

The genotype-fitness map (that is, the fitness landscape) is a key determinant of evolution, yet it has mostly been used as a superficial metaphor because we know little about its structure. This is now changing, as real fitness landscapes are being analysed by constructing genotypes with all possible combinations of small sets of mutations observed in phylogenies or in evolution experiments. In turn, these first glimpses of empirical fitness landscapes inspire theoretical analyses of the predictability of evolution. Here, we review these recent empirical and theoretical developments, identify methodological issues and organizing principles, and discuss possibilities to develop more realistic fitness landscape models.

Predictive vs. Empiric Assessment of Schistosomiasis: Implications for Treatment Projections in Ghana

PubMed Central

Kabore, Achille; Biritwum, Nana-Kwadwo; Downs, Philip W.; Soares Magalhaes, Ricardo J.; Zhang, Yaobi; Ottesen, Eric A.

2013-01-01

Background Mapping the distribution of schistosomiasis is essential to determine where control programs should operate, but because it is impractical to assess infection prevalence in every potentially endemic community, model-based geostatistics (MBG) is increasingly being used to predict prevalence and determine intervention strategies. Methodology/Principal Findings To assess the accuracy of MBG predictions for Schistosoma haematobium infection in Ghana, school surveys were evaluated at 79 sites to yield empiric prevalence values that could be compared with values derived from recently published MBG predictions. Based on these findings schools were categorized according to WHO guidelines so that practical implications of any differences could be determined. Using the mean predicted values alone, 21 of the 25 empirically determined ‘high-risk’ schools requiring yearly praziquantel would have been undertreated and almost 20% of the remaining schools would have been treated despite empirically-determined absence of infection – translating into 28% of the children in the 79 schools being undertreated and 12% receiving treatment in the absence of any demonstrated need. Conclusions/Significance Using the current predictive map for Ghana as a spatial decision support tool by aggregating prevalence estimates to the district level was clearly not adequate for guiding the national program, but the alternative of assessing each school in potentially endemic areas of Ghana or elsewhere is not at all feasible; modelling must be a tool complementary to empiric assessments. Thus for practical usefulness, predictive risk mapping should not be thought of as a one-time exercise but must, as in the current study, be an iterative process that incorporates empiric testing and model refining to create updated versions that meet the needs of disease control operational managers. PMID:23505584

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster.

PubMed

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S

2017-05-28

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au 147 ), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au 147 , and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au 147 is performed, and it is concluded that Au 147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Experimental Validation of a Forward Looking Interferometer for Detection of Clear Air Turbulence due to Mountain Waves

NASA Technical Reports Server (NTRS)

Schaffner, Philip R.; Daniels, Taumi S.; West, Leanne L.; Gimmestad, Gary G.; Lane, Sarah E.; Burdette, Edward M.; Smith, William L.; Kireev, Stanislav; Cornman, Larry; Sharman, Robert D.

2012-01-01

The Forward-Looking Interferometer (FLI) is an airborne sensor concept for detection and estimation of potential atmospheric hazards to aircraft. The FLI concept is based on high-resolution Infrared Fourier Transform Spectrometry technologies that have been developed for satellite remote sensing. The FLI is being evaluated for its potential to address multiple hazards, during all phases of flight, including clear air turbulence, volcanic ash, wake vortices, low slant range visibility, dry wind shear, and icing. In addition, the FLI is being evaluated for its potential to detect hazardous runway conditions during landing, such as wet or icy asphalt or concrete. The validation of model-based instrument and hazard simulation results is accomplished by comparing predicted performance against empirical data. In the mountain lee wave data collected in the previous FLI project, the data showed a damped, periodic mountain wave structure. The wave data itself will be of use in forecast and nowcast turbulence products such as the Graphical Turbulence Guidance and Graphical Turbulence Guidance Nowcast products. Determining how turbulence hazard estimates can be derived from FLI measurements will require further investigation.

Spherical harmonics based descriptor for neural network potentials: Structure and dynamics of Au147 nanocluster

NASA Astrophysics Data System (ADS)

Jindal, Shweta; Chiriki, Siva; Bulusu, Satya S.

2017-05-01

We propose a highly efficient method for fitting the potential energy surface of a nanocluster using a spherical harmonics based descriptor integrated with an artificial neural network. Our method achieves the accuracy of quantum mechanics and speed of empirical potentials. For large sized gold clusters (Au147), the computational time for accurate calculation of energy and forces is about 1.7 s, which is faster by several orders of magnitude compared to density functional theory (DFT). This method is used to perform the global minimum optimizations and molecular dynamics simulations for Au147, and it is found that its global minimum is not an icosahedron. The isomer that can be regarded as the global minimum is found to be 4 eV lower in energy than the icosahedron and is confirmed from DFT. The geometry of the obtained global minimum contains 105 atoms on the surface and 42 atoms in the core. A brief study on the fluxionality in Au147 is performed, and it is concluded that Au147 has a dynamic surface, thus opening a new window for studying its reaction dynamics.

Is Structural Subtyping Useful? An Empirical Study

DTIC Science & Technology

2009-12-01

Mellon University Pittsburgh, PA 15213 Abstract Structural subtyping is popular in research languages , but all mainstream object-oriented languages use...nominal subtyping. Since languages with structural subtyping are not in widespread use, the empiri- cal questions of whether and how structural...will provide guidance for language designers who are considering use of this subtyping discipline. Report Documentation Page Form ApprovedOMB No

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

Morris, J.R.; Lu, Z.Y.; Ring, D.M.

The authors have examined a variety of structures for the {l_brace}510{r_brace} symmetric tilt boundary in Si, using first-principles calculations. These calculations show that the observed structure in Si is the lowest energy structure. This structure is more complicated than what is necessary to preserve four-fold coordination. They compare the results to classical and tight-binding models, in order to test these empirical approaches.

Organizational Structure, Collegial Trust, and College Faculty Teaching Efficacy: A Case Study

ERIC Educational Resources Information Center

Okpogba, Desmond

2011-01-01

The purpose of this mixed-method study was to explore the relationship between faculty self-efficacy, organizational structure, and collegial trust. The concepts of teacher self-efficacy, organizational structure, and collegial trust were used to investigate any possible empirical relationships existing between these variables in a private,…

The Role of Structural Characteristics in Problematic Video Game Play: An Empirical Study

ERIC Educational Resources Information Center

King, Daniel L.; Delfabbro, Paul H.; Griffiths, Mark D.

2011-01-01

The research literature suggests that the structural characteristics of video games may play a considerable role in the initiation, development and maintenance of problematic video game playing. The present study investigated the role of structural characteristics in video game playing behaviour within a sample of 421 video game players aged…

Age-Related Progressions in Story Structure in Young Children's Narratives

ERIC Educational Resources Information Center

Khan, Kiren S.; Gugiu, Mihaiela R.; Justice, Laura M.; Bowles, Ryan P.; Skibbe, Lori E.; Piasta, Shayne B.

2016-01-01

Purpose: Prior theoretical and empirical work has referenced several broad stages of narrative development, particularly in terms of young children's understanding of story structure. However, there is considerable variation in how story structure has been defined and assessed across these studies. The aims of the present study were threefold: (a)…

The Effect of Knowledge Linking Levels in Biology Lessons upon Students' Knowledge Structure

ERIC Educational Resources Information Center

Wadouh, Julia; Liu, Ning; Sandmann, Angela; Neuhaus, Birgit J.

2014-01-01

Knowledge structure is an important aspect for defining students' competency in biology learning, but how knowledge structure is influenced by the teaching process in naturalistic biology classroom settings has scarcely been empirically investigated. In this study, 49 biology lessons in the teaching unit "blood and circulatory system" in…

Research notes : measuring the strain of the road.

DOT National Transportation Integrated Search

2005-09-01

This study will monitor the pavement structure to investigate if the assumptions used in a mechanistic-empirical design analysis are valid, or if adjustments are needed. The study will be assessing the reaction of the pavement structure to traffic lo...

Assessing the bioaccumulation potential of ionizable organic compounds: Current knowledge and research priorities

EPA Science Inventory

The objective of the present study is to review current knowledge regarding the bioaccumulation potential of IOCs, with a focus on the availability of empirical data for fish. Aspects of the bioaccumulation potential of IOCs in fish that can be characterized relatively well inclu...

A new empirical potential energy function for Ar2

NASA Astrophysics Data System (ADS)

Myatt, Philip T.; Dham, Ashok K.; Chandrasekhar, Pragna; McCourt, Frederick R. W.; Le Roy, Robert J.

2018-06-01

A critical re-analysis of all available spectroscopic and virial coefficient data for Ar2 has been used to determine an improved empirical analytic potential energy function that has been 'tuned' to optimise its agreement with viscosity, diffusion and thermal diffusion data, and whose short-range behaviour is in reasonably good agreement with the most recent ab initio calculations for this system. The recommended Morse/long-range potential function is smooth and differentiable at all distances, and incorporates both the correct theoretically predicted long-range behaviour and the correct limiting short-range functional behaviour. The resulting value of the well depth is ? cm-1 and the associated equilibrium distance is re = 3.766 (±0.002) Å, while the 40Ar s-wave scattering length is -714 Å.

Optimizing empiric therapy for Gram-negative bloodstream infections in children.

PubMed

Chao, Y; Reuter, C; Kociolek, L K; Patel, R; Zheng, X; Patel, S J

2018-06-01

Antimicrobial stewardship can be challenging in children with bloodstream infections (BSIs) caused by Gram-negative bacilli (GNB). This retrospective cohort study explored how data elements in the electronic health record could potentially optimize empiric antibiotic therapy for BSIs caused by GNB, via the construction of customized antibiograms for categorical GNB infections and identification of opportunities to minimize organism-drug mismatch and decrease time to effective therapy. Our results suggest potential strategies that could be implemented at key decision points in prescribing at initiation, modification, and targeting of therapy. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.