Domain size sensitivities of landfalling eastern Pacific atmospheric rivers

NASA Astrophysics Data System (ADS)

McClenny, E. E.; Ullrich, P. A.; Grotjahn, R.; Guan, B.; Waliser, D. E.

2017-12-01

Atmospheric rivers (ARs) concentrate a majority of mid-latitude latent heat transport into narrow bands. ARs making landfall along the North American coast typically originate in the waters surrounding Hawaii. We explore here the effects of explicitly simulating this "genesis region" on AR characteristics. We do this using two models and three domains centered on the North American coast. The Weather Research and Forecast (WRF) model, forced by National Center for Environmental Prediction Final Reanalysis data, provides a representative regional model. The simulation domains include: 1. Just off the coastline (100-130W), 2. The coastline to the Pacific just east of Hawaii (100-155W), and 3. The coastline to the Pacific west of Hawaii (100-180W). The Variable Resolution Community Earth System Model simulates ARs while preserving global interactions. In this global model, "domain" refers to the mesh refinement region, each of which corresponds to one of the three previously described WRF domains. We compare ARs from the wet season (October-April) for water years 2009-2017 in the test models against those found in the Modern Era Retrospective Reanalysis 2 (MERRA2). We objectively detect events with the global AR detection algorithm introduced in Guan and Waliser (2015). Comparisons between all model configurations and the reference MERRA2 data will be assessed by characteristics including landfall location (meridional distributions, including quartile ranges and standard deviations of landfalls across the coast), as well as vapor flux and precipitation (in terms of both the contribution of ARs to the larger regional climatology and any differences in the intensity of individual AR events across runs).

Applied Routh approximation

NASA Technical Reports Server (NTRS)

Merrill, W. C.

1978-01-01

The Routh approximation technique for reducing the complexity of system models was applied in the frequency domain to a 16th order, state variable model of the F100 engine and to a 43d order, transfer function model of a launch vehicle boost pump pressure regulator. The results motivate extending the frequency domain formulation of the Routh method to the time domain in order to handle the state variable formulation directly. The time domain formulation was derived and a characterization that specifies all possible Routh similarity transformations was given. The characterization was computed by solving two eigenvalue-eigenvector problems. The application of the time domain Routh technique to the state variable engine model is described, and some results are given. Additional computational problems are discussed, including an optimization procedure that can improve the approximation accuracy by taking advantage of the transformation characterization.

Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis

PubMed Central

Parks, Joseph W.; Kappel, Kalli; Das, Rhiju; Stone, Michael D.

2017-01-01

Maintenance of telomeres by telomerase permits continuous proliferation of rapidly dividing cells, including the majority of human cancers. Despite its direct biomedical significance, the architecture of the human telomerase complex remains unknown. Generating homogeneous telomerase samples has presented a significant barrier to developing improved structural models. Here we pair single-molecule Förster resonance energy transfer (smFRET) measurements with Rosetta modeling to map the conformations of the essential telomerase RNA core domain within the active ribonucleoprotein. FRET-guided modeling places the essential pseudoknot fold distal to the active site on a protein surface comprising the C-terminal element, a domain that shares structural homology with canonical polymerase thumb domains. An independently solved medium-resolution structure of Tetrahymena telomerase provides a blind test of our modeling methodology and sheds light on the structural homology of this domain across diverse organisms. Our smFRET-Rosetta models reveal nanometer-scale rearrangements within the RNA core domain during catalysis. Taken together, our FRET data and pseudoatomic molecular models permit us to propose a possible mechanism for how RNA core domain rearrangement is coupled to template hybrid elongation. PMID:28096444

Evapotranspiration Within the Groundwater Model Domain of the Tuba City, Arizona, Disposal Site Interim Report

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

None, None

The revised groundwater model includes estimates of evapotranspiration (ET). The types of vegetation and the influences of ET on groundwater hydrology vary within the model domain. Some plant species within the model domain, classified as phreatophytes, survive by extracting groundwater. ET within these plant communities can result in a net discharge of groundwater if ET exceeds precipitation. Other upland desert plants within the model domain survive on meteoric water, potentially limiting groundwater recharge if ET is equivalent to precipitation. For all plant communities within the model domain, excessive livestock grazing or other disturbances can tip the balance to a netmore » groundwater recharge. This task characterized and mapped vegetation within the groundwater model domain at the Tuba City, Arizona, Site, and then applied a remote sensing algorithm to estimate ET for each vegetation type. The task was designed to address five objectives: 1. Characterize and delineate different vegetation or ET zones within the groundwater model domain, focusing on the separation of plant communities with phreatophytes that survive by tapping groundwater and upland plant communities that are dependent on precipitation. 2. Refine a remote sensing method, developed to estimate ET at the Monument Valley site, for application at the Tuba City site. 3. Estimate recent seasonal and annual ET for all vegetation zones, separating phreatophytic and upland plant communities within the Tuba City groundwater model domain. 4. For selected vegetation zones, estimate ET that might be achieved given a scenario of limited livestock grazing. 5. Analyze uncertainty of ET estimates for each vegetation zone and for the entire groundwater model domain.« less

A High-Resolution Model of the Beaufort Sea Circulation

NASA Astrophysics Data System (ADS)

Hedstrom, K.; Danielson, S. L.; Curchitser, E. N.; Lemieux, J. F.; Kasper, J.

2016-02-01

Configuration of and results from a coupled sea-ice ocean model of the Beaufort Sea shelf at 900 m resolution will be shown. Challenging features of the domain include large fresh water flux from the MacKenzie River, seasonal land-fast ice, and ice-covered open boundary conditions. A pan-Arctic domain provides boundary fields for both the ocean and sea-ice models (Regional Ocean Modeling System - myroms.org). Both models are forced with river inputs from the ARDAT climatology (Whitefield et al., 2015), which includes heat content as well as flow rate. Coastal discharges are prescribed as lateral inflows distributed over the depth of the ocean-land interface. New in the Beaufort domain is the use of a landfast ice parameterization (Lemieux, 2015), which adds a large bottom stress to the ice when the estimated keel depth approaches that of the ocean.

Vibration sensing in flexible structures using a distributed-effect modal domain optical fiber sensor

NASA Technical Reports Server (NTRS)

Reichard, Karl M.; Lindner, Douglas K.; Claus, Richard O.

1991-01-01

Modal domain optical fiber sensors have recently been employed in the implementation of system identification algorithms and the closed-loop control of vibrations in flexible structures. The mathematical model of the modal domain optical fiber sensor used in these applications, however, only accounted for the effects of strain in the direction of the fiber's longitudinal axis. In this paper, we extend this model to include the effects of arbitrary stress. Using this sensor model, we characterize the sensor's sensitivity and dynamic range.

Structural insights into SAM domain-mediated tankyrase oligomerization.

PubMed

DaRosa, Paul A; Ovchinnikov, Sergey; Xu, Wenqing; Klevit, Rachel E

2016-09-01

Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP-ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain-mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head-to-tail polymer that facilitates TNKS self-association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM-TNKS2 SAM) hetero-oligomeric structures mediated by their SAM domains. Though wild-type tankyrase proteins have very low solubility, model-based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP-ribosyl)ation (PARylation) and PARylation-dependent ubiquitylation. © 2016 The Protein Society.

Pathogen blocks host death receptor signalling by arginine GlcNAcylation of death domains.

PubMed

Li, Shan; Zhang, Li; Yao, Qing; Li, Lin; Dong, Na; Rong, Jie; Gao, Wenqing; Ding, Xiaojun; Sun, Liming; Chen, Xing; Chen, She; Shao, Feng

2013-09-12

The tumour necrosis factor (TNF) family is crucial for immune homeostasis, cell death and inflammation. These cytokines are recognized by members of the TNF receptor (TNFR) family of death receptors, including TNFR1 and TNFR2, and FAS and TNF-related apoptosis-inducing ligand (TRAIL) receptors. Death receptor signalling requires death-domain-mediated homotypic/heterotypic interactions between the receptor and its downstream adaptors, including TNFR1-associated death domain protein (TRADD) and FAS-associated death domain protein (FADD). Here we discover that death domains in several proteins, including TRADD, FADD, RIPK1 and TNFR1, were directly inactivated by NleB, an enteropathogenic Escherichia coli (EPEC) type III secretion system effector known to inhibit host nuclear factor-κB (NF-κB) signalling. NleB contained an unprecedented N-acetylglucosamine (GlcNAc) transferase activity that specifically modified a conserved arginine in these death domains (Arg 235 in the TRADD death domain). NleB GlcNAcylation (the addition of GlcNAc onto a protein side chain) of death domains blocked homotypic/heterotypic death domain interactions and assembly of the oligomeric TNFR1 complex, thereby disrupting TNF signalling in EPEC-infected cells, including NF-κB signalling, apoptosis and necroptosis. Type-III-delivered NleB also blocked FAS ligand and TRAIL-induced cell death by preventing formation of a FADD-mediated death-inducing signalling complex (DISC). The arginine GlcNAc transferase activity of NleB was required for bacterial colonization in the mouse model of EPEC infection. The mechanism of action of NleB represents a new model by which bacteria counteract host defences, and also a previously unappreciated post-translational modification.

Evidence in Support of the Independent Channel Model Describing the Sensorimotor Control of Human Stance Using a Humanoid Robot

PubMed Central

Pasma, Jantsje H.; Assländer, Lorenz; van Kordelaar, Joost; de Kam, Digna; Mergner, Thomas; Schouten, Alfred C.

2018-01-01

The Independent Channel (IC) model is a commonly used linear balance control model in the frequency domain to analyze human balance control using system identification and parameter estimation. The IC model is a rudimentary and noise-free description of balance behavior in the frequency domain, where a stable model representation is not guaranteed. In this study, we conducted firstly time-domain simulations with added noise, and secondly robot experiments by implementing the IC model in a real-world robot (PostuRob II) to test the validity and stability of the model in the time domain and for real world situations. Balance behavior of seven healthy participants was measured during upright stance by applying pseudorandom continuous support surface rotations. System identification and parameter estimation were used to describe the balance behavior with the IC model in the frequency domain. The IC model with the estimated parameters from human experiments was implemented in Simulink for computer simulations including noise in the time domain and robot experiments using the humanoid robot PostuRob II. Again, system identification and parameter estimation were used to describe the simulated balance behavior. Time series, Frequency Response Functions, and estimated parameters from human experiments, computer simulations, and robot experiments were compared with each other. The computer simulations showed similar balance behavior and estimated control parameters compared to the human experiments, in the time and frequency domain. Also, the IC model was able to control the humanoid robot by keeping it upright, but showed small differences compared to the human experiments in the time and frequency domain, especially at high frequencies. We conclude that the IC model, a descriptive model in the frequency domain, can imitate human balance behavior also in the time domain, both in computer simulations with added noise and real world situations with a humanoid robot. This provides further evidence that the IC model is a valid description of human balance control. PMID:29615886

Evidence in Support of the Independent Channel Model Describing the Sensorimotor Control of Human Stance Using a Humanoid Robot.

PubMed

Pasma, Jantsje H; Assländer, Lorenz; van Kordelaar, Joost; de Kam, Digna; Mergner, Thomas; Schouten, Alfred C

2018-01-01

The Independent Channel (IC) model is a commonly used linear balance control model in the frequency domain to analyze human balance control using system identification and parameter estimation. The IC model is a rudimentary and noise-free description of balance behavior in the frequency domain, where a stable model representation is not guaranteed. In this study, we conducted firstly time-domain simulations with added noise, and secondly robot experiments by implementing the IC model in a real-world robot (PostuRob II) to test the validity and stability of the model in the time domain and for real world situations. Balance behavior of seven healthy participants was measured during upright stance by applying pseudorandom continuous support surface rotations. System identification and parameter estimation were used to describe the balance behavior with the IC model in the frequency domain. The IC model with the estimated parameters from human experiments was implemented in Simulink for computer simulations including noise in the time domain and robot experiments using the humanoid robot PostuRob II. Again, system identification and parameter estimation were used to describe the simulated balance behavior. Time series, Frequency Response Functions, and estimated parameters from human experiments, computer simulations, and robot experiments were compared with each other. The computer simulations showed similar balance behavior and estimated control parameters compared to the human experiments, in the time and frequency domain. Also, the IC model was able to control the humanoid robot by keeping it upright, but showed small differences compared to the human experiments in the time and frequency domain, especially at high frequencies. We conclude that the IC model, a descriptive model in the frequency domain, can imitate human balance behavior also in the time domain, both in computer simulations with added noise and real world situations with a humanoid robot. This provides further evidence that the IC model is a valid description of human balance control.

Domain modeling and grid generation for multi-block structured grids with application to aerodynamic and hydrodynamic configurations

NASA Technical Reports Server (NTRS)

Spekreijse, S. P.; Boerstoel, J. W.; Vitagliano, P. L.; Kuyvenhoven, J. L.

1992-01-01

About five years ago, a joint development was started of a flow simulation system for engine-airframe integration studies on propeller as well as jet aircraft. The initial system was based on the Euler equations and made operational for industrial aerodynamic design work. The system consists of three major components: a domain modeller, for the graphical interactive subdivision of flow domains into an unstructured collection of blocks; a grid generator, for the graphical interactive computation of structured grids in blocks; and a flow solver, for the computation of flows on multi-block grids. The industrial partners of the collaboration and NLR have demonstrated that the domain modeller, grid generator and flow solver can be applied to simulate Euler flows around complete aircraft, including propulsion system simulation. Extension to Navier-Stokes flows is in progress. Delft Hydraulics has shown that both the domain modeller and grid generator can also be applied successfully for hydrodynamic configurations. An overview is given about the main aspects of both domain modelling and grid generation.

From scenarios to domain models: processes and representations

NASA Astrophysics Data System (ADS)

Haddock, Gail; Harbison, Karan

1994-03-01

The domain specific software architectures (DSSA) community has defined a philosophy for the development of complex systems. This philosophy improves productivity and efficiency by increasing the user's role in the definition of requirements, increasing the systems engineer's role in the reuse of components, and decreasing the software engineer's role to the development of new components and component modifications only. The scenario-based engineering process (SEP), the first instantiation of the DSSA philosophy, has been adopted by the next generation controller project. It is also the chosen methodology of the trauma care information management system project, and the surrogate semi-autonomous vehicle project. SEP uses scenarios from the user to create domain models and define the system's requirements. Domain knowledge is obtained from a variety of sources including experts, documents, and videos. This knowledge is analyzed using three techniques: scenario analysis, task analysis, and object-oriented analysis. Scenario analysis results in formal representations of selected scenarios. Task analysis of the scenario representations results in descriptions of tasks necessary for object-oriented analysis and also subtasks necessary for functional system analysis. Object-oriented analysis of task descriptions produces domain models and system requirements. This paper examines the representations that support the DSSA philosophy, including reference requirements, reference architectures, and domain models. The processes used to create and use the representations are explained through use of the scenario-based engineering process. Selected examples are taken from the next generation controller project.

Techniques for determining physical zones of influence

DOEpatents

Hamann, Hendrik F; Lopez-Marrero, Vanessa

2013-11-26

Techniques for analyzing flow of a quantity in a given domain are provided. In one aspect, a method for modeling regions in a domain affected by a flow of a quantity is provided which includes the following steps. A physical representation of the domain is provided. A grid that contains a plurality of grid-points in the domain is created. Sources are identified in the domain. Given a vector field that defines a direction of flow of the quantity within the domain, a boundary value problem is defined for each of one or more of the sources identified in the domain. Each of the boundary value problems is solved numerically to obtain a solution for the boundary value problems at each of the grid-points. The boundary problem solutions are post-processed to model the regions affected by the flow of the quantity on the physical representation of the domain.

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation.

PubMed

Mourad, Raphaël; Cuvier, Olivier

2016-05-01

Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1.

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

PubMed Central

Mourad, Raphaël; Cuvier, Olivier

2016-01-01

Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression. A current challenge is to identify the key molecular drivers of this 3D structure. Several genomic features, such as architectural proteins and functional elements, were shown to be enriched at topological domain borders using classical enrichment tests. Here we propose multiple logistic regression to identify those genomic features that positively or negatively influence domain border establishment or maintenance. The model is flexible, and can account for statistical interactions among multiple genomic features. Using both simulated and real data, we show that our model outperforms enrichment test and non-parametric models, such as random forests, for the identification of genomic features that influence domain borders. Using Drosophila Hi-C data at a very high resolution of 1 kb, our model suggests that, among architectural proteins, BEAF-32 and CP190 are the main positive drivers of 3D domain borders. In humans, our model identifies well-known architectural proteins CTCF and cohesin, as well as ZNF143 and Polycomb group proteins as positive drivers of domain borders. The model also reveals the existence of several negative drivers that counteract the presence of domain borders including P300, RXRA, BCL11A and ELK1. PMID:27203237

Scattering from phase-separated vesicles. I. An analytical form factor for multiple static domains

DOE PAGES

Heberle, Frederick A.; Anghel, Vinicius N. P.; Katsaras, John

2015-08-18

This is the first in a series of studies considering elastic scattering from laterally heterogeneous lipid vesicles containing multiple domains. Unique among biophysical tools, small-angle neutron scattering can in principle give detailed information about the size, shape and spatial arrangement of domains. A general theory for scattering from laterally heterogeneous vesicles is presented, and the analytical form factor for static domains with arbitrary spatial configuration is derived, including a simplification for uniformly sized round domains. The validity of the model, including series truncation effects, is assessed by comparison with simulated data obtained from a Monte Carlo method. Several aspects ofmore » the analytical solution for scattering intensity are discussed in the context of small-angle neutron scattering data, including the effect of varying domain size and number, as well as solvent contrast. Finally, the analysis indicates that effects of domain formation are most pronounced when the vesicle's average scattering length density matches that of the surrounding solvent.« less

Modeling software systems by domains

NASA Technical Reports Server (NTRS)

Dippolito, Richard; Lee, Kenneth

1992-01-01

The Software Architectures Engineering (SAE) Project at the Software Engineering Institute (SEI) has developed engineering modeling techniques that both reduce the complexity of software for domain-specific computer systems and result in systems that are easier to build and maintain. These techniques allow maximum freedom for system developers to apply their domain expertise to software. We have applied these techniques to several types of applications, including training simulators operating in real time, engineering simulators operating in non-real time, and real-time embedded computer systems. Our modeling techniques result in software that mirrors both the complexity of the application and the domain knowledge requirements. We submit that the proper measure of software complexity reflects neither the number of software component units nor the code count, but the locus of and amount of domain knowledge. As a result of using these techniques, domain knowledge is isolated by fields of engineering expertise and removed from the concern of the software engineer. In this paper, we will describe kinds of domain expertise, describe engineering by domains, and provide relevant examples of software developed for simulator applications using the techniques.

On domain modelling of the service system with its application to enterprise information systems

NASA Astrophysics Data System (ADS)

Wang, J. W.; Wang, H. F.; Ding, J. L.; Furuta, K.; Kanno, T.; Ip, W. H.; Zhang, W. J.

2016-01-01

Information systems are a kind of service systems and they are throughout every element of a modern industrial and business system, much like blood in our body. Types of information systems are heterogeneous because of extreme uncertainty in changes in modern industrial and business systems. To effectively manage information systems, modelling of the work domain (or domain) of information systems is necessary. In this paper, a domain modelling framework for the service system is proposed and its application to the enterprise information system is outlined. The framework is defined based on application of a general domain modelling tool called function-context-behaviour-principle-state-structure (FCBPSS). The FCBPSS is based on a set of core concepts, namely: function, context, behaviour, principle, state and structure and system decomposition. Different from many other applications of FCBPSS in systems engineering, the FCBPSS is applied to both infrastructure and substance systems, which is novel and effective to modelling of service systems including enterprise information systems. It is to be noted that domain modelling of systems (e.g. enterprise information systems) is a key to integration of heterogeneous systems and to coping with unanticipated situations facing to systems.

Challenges in Requirements Engineering: A Research Agenda for Conceptual Modeling

NASA Astrophysics Data System (ADS)

March, Salvatore T.; Allen, Gove N.

Domains for which information systems are developed deal primarily with social constructions—conceptual objects and attributes created by human intentions and for human purposes. Information systems play an active role in these domains. They document the creation of new conceptual objects, record and ascribe values to their attributes, initiate actions within the domain, track activities performed, and infer conclusions based on the application of rules that govern how the domain is affected when socially-defined and identified causal events occur. Emerging applications of information technologies evaluate such business rules, learn from experience, and adapt to changes in the domain. Conceptual modeling grammars aimed at representing their system requirements must include conceptual objects, socially-defined events, and the rules pertaining to them. We identify challenges to conceptual modeling research and pose an ontology of the artificial as a step toward meeting them.

Individual negative symptoms and domains - Relevance for assessment, pathomechanisms and treatment.

PubMed

Kaiser, Stefan; Lyne, John; Agartz, Ingrid; Clarke, Mary; Mørch-Johnsen, Lynn; Faerden, Ann

2017-08-01

The negative symptoms of schizophrenia can be divided into two domains. Avolition/apathy includes the individual symptoms of avolition, asociality and anhedonia. Diminished expression includes blunted affect and alogia. Until now, causes and treatment of negative symptoms have remained a major challenge, which is partially related to the focus on negative symptoms as a broad entity. Here, we propose that negative symptoms may become more tractable when the different domains and individual symptoms are taken into account. There is now increasing evidence that the relationship with clinical variables - in particular outcome - differs between the domains of avolition/apathy and diminished expression. Regarding models of negative symptom formation, those relevant to avolition/apathy are now converging on processes underlying goal-directed behavior and dysfunctions of the reward system. In contrast, models of the diminished expression domains are only beginning to emerge. The aim of this article is to review the specific clinical, behavioral and neural correlates of individual symptoms and domains as a better understanding of these areas may facilitate specific treatment approaches. Copyright © 2016 Elsevier B.V. All rights reserved.

A cognitive-behavioral model of Internet gaming disorder: theoretical underpinnings and clinical implications.

PubMed

Dong, Guangheng; Potenza, Marc N

2014-11-01

Cognitive contributions to the behaviors observed in substance and non-substance addictions have been investigated and characterized. Based on models of drug addictions and the extant literature on Internet gaming disorder (IGD), we propose a cognitive-behavioral model for conceptualizing IGD. The model focuses on three domains and their roles in addictive behaviors. The three domains include motivational drives related to reward-seeking and stress-reduction, behavioral control relating to executive inhibition, and decision-making that involves weighing the pros and cons of engaging in motivated behaviors. Based on this model, we propose how behavioral therapies might target these domains in the treatment of IGD. Copyright © 2014 Elsevier Ltd. All rights reserved.

Reference Architecture Model Enabling Standards Interoperability.

PubMed

Blobel, Bernd

2017-01-01

Advanced health and social services paradigms are supported by a comprehensive set of domains managed by different scientific disciplines. Interoperability has to evolve beyond information and communication technology (ICT) concerns, including the real world business domains and their processes, but also the individual context of all actors involved. So, the system must properly reflect the environment in front and around the computer as essential and even defining part of the health system. This paper introduces an ICT-independent system-theoretical, ontology-driven reference architecture model allowing the representation and harmonization of all domains involved including the transformation into an appropriate ICT design and implementation. The entire process is completely formalized and can therefore be fully automated.

Structural bioinformatics of the human spliceosomal proteome

PubMed Central

Korneta, Iga; Magnus, Marcin; Bujnicki, Janusz M.

2012-01-01

In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258–338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540–683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome. PMID:22573172

Forecasting space weather: Can new econometric methods improve accuracy?

NASA Astrophysics Data System (ADS)

Reikard, Gordon

2011-06-01

Space weather forecasts are currently used in areas ranging from navigation and communication to electric power system operations. The relevant forecast horizons can range from as little as 24 h to several days. This paper analyzes the predictability of two major space weather measures using new time series methods, many of them derived from econometrics. The data sets are the A p geomagnetic index and the solar radio flux at 10.7 cm. The methods tested include nonlinear regressions, neural networks, frequency domain algorithms, GARCH models (which utilize the residual variance), state transition models, and models that combine elements of several techniques. While combined models are complex, they can be programmed using modern statistical software. The data frequency is daily, and forecasting experiments are run over horizons ranging from 1 to 7 days. Two major conclusions stand out. First, the frequency domain method forecasts the A p index more accurately than any time domain model, including both regressions and neural networks. This finding is very robust, and holds for all forecast horizons. Combining the frequency domain method with other techniques yields a further small improvement in accuracy. Second, the neural network forecasts the solar flux more accurately than any other method, although at short horizons (2 days or less) the regression and net yield similar results. The neural net does best when it includes measures of the long-term component in the data.

The use of typed lambda calculus for comprehension and construction of simulation models in the domain of ecology

NASA Technical Reports Server (NTRS)

Uschold, Michael

1992-01-01

We are concerned with two important issues in simulation modelling: model comprehension and model construction. Model comprehension is limited because many important choices taken during the modelling process are not documented. This makes it difficult for models to be modified or used by others. A key factor hindering model construction is the vast modelling search space which must be navigated. This is exacerbated by the fact that many modellers are unfamiliar with the terms and concepts catered to by current tools. The root of both problems is the lack of facilities for representing or reasoning about domain concepts in current simulation technology. The basis for our achievements in both of these areas is the development of a language with two distinct levels; one for representing domain information, and the other for representing the simulation model. Of equal importance, is the fact that we make formal connections between these two levels. The domain we are concerned with is ecological modelling. This language, called Elklogic, is based on the typed lambda calculus. Important features include a rich type structure, the use of various higher order functions, and semantics. This enables complex expressions to be constructed from relatively few primitives. The meaning of each expression can be determined in terms of the domain, the simulation model, or the relationship between the two. We describe a novel representation for sets and substructure, and a variety of other general concepts that are especially useful in the ecological domain. We use the type structure in a novel way: for controlling the modelling search space, rather than a proof search space. We facilitate model comprehension by representing modelling decisions that are embodied in the simulation model. We represent the simulation model separately from, but in terms of a domain mode. The explicit links between the two models constitute the modelling decisions. The semantics of Elklogic enables English text to be generated to explain the simulation model in domain terms.

INITIAL VALIDATION OF THE ASSESSMENT OF PARENTING TOOL: A TASK- AND DOMAIN-LEVEL MEASURE OF PARENTING SELF-EFFICACY FOR PARENTS OF INFANTS FROM BIRTH TO 24 MONTHS OF AGE.

PubMed

Moran, Tracy E; Polanin, Joshua R; Evenson, Amber L; Troutman, Beth R; Franklin, Christina L

2016-05-01

Parenting self-efficacy (PSE) includes parents' self-perceptions regarding their capabilities in performing the numerous and changing tasks associated with parenting a specific child (i.e., domain-specific PSE) as well as their self-perceptions in the parenting role overall (i.e., domain-general PSE). Prior literature has demonstrated PSE's relations with numerous constructs significant to mental health and the parent-infant relationship. Prior measures of PSE have been limited by focusing on only domain-specific or domain-general PSE, ignoring the importance of infant development to PSE, and other psychometric limitations. This article presents sound psychometric data for a new measure of PSE, the Assessment of Parenting Tool (APT). The APT includes task-level items on the Domain-Specific subscale (APT-DS) for each age-referenced version of the measure as well as a domain-general subscale that taps overall PSE within the first 24 months' postpartum. Initial construct validity of the measure is established, particularly for parents of infants aged 3 months and older. A stable, three-factor structure for the domain-general subscale includes "coping with being a parent," "attuned parenting," and "self-perceived model parenting." Future directions for the APT, including a revised checklist format for the domain-specific subscale, are included. © 2016 Michigan Association for Infant Mental Health.

The Women's Health Care Empowerment Model as a Catalyst for Change in Developing Countries.

PubMed

Mitroi, Lavinia R; Sahak, Medina; Sherzai, Ayesha Z; Sherzai, Dean

2016-01-01

Women's empowerment has been attempted through a number of different fields including the realms of politics, finance, and education, yet none of these domains are as promising as health care. Here we review preliminary work in this domain and introduce a model for women's empowerment through involvement in health care, titled the "women's health care empowerment model." Principles upon which our model is built include: acknowledging the appropriate definition of empowerment within the cultural context, creating a women's network for communication, integrating local culture and tradition into training women, and increasing the capability of women to care for their children and other women.

Threading structural model of the manganese-stabilizing protein PsbO reveals presence of two possible beta-sandwich domains.

PubMed

Pazos, F; Heredia, P; Valencia, A; de las Rivas, J

2001-12-01

The manganese-stabilizing protein (PsbO) is an essential component of photosystem II (PSII) and is present in all oxyphotosynthetic organisms. PsbO allows correct water splitting and oxygen evolution by stabilizing the reactions driven by the manganese cluster. Despite its important role, its structure and detailed functional mechanism are still unknown. In this article we propose a structural model based on fold recognition and molecular modeling. This model has additional support from a study of the distribution of characteristics of the PsbO sequence family, such as the distribution of conserved, apolar, tree-determinants, and correlated positions. Our threading results consistently showed PsbO as an all-beta (beta) protein, with two homologous beta domains of approximately 120 amino acids linked by a flexible Proline-Glycine-Glycine (PGG) motif. These features are compatible with a general elongated and flexible architecture, in which the two domains form a sandwich-type structure with Greek key topology. The first domain is predicted to include 8 to 9 beta-strands, the second domain 6 to 7 beta-strands. An Ig-like beta-sandwich structure was selected as a template to build the 3-D model. The second domain has, between the strands, long-loops rich in Pro and Gly that are difficult to model. One of these long loops includes a highly conserved region (between P148 and P174) and a short alpha-helix (between E181 and N188)). These regions are characteristic parts of PsbO and show that the second domain is not so similar to the template. Overall, the model was able to account for much of the experimental data reported by several authors, and it would allow the detection of key residues and regions that are proposed in this article as essential for the structure and function of PsbO. Copyright 2001 Wiley-Liss, Inc.

The Arctic Marine Pulses Model: Linking Contiguous Domains in the Pacific Arctic Region

NASA Astrophysics Data System (ADS)

Moore, S. E.; Stabeno, P. J.

2016-02-01

The Pacific Arctic marine ecosystem extends from the northern Bering Sea, across the Chukchi and into the East Siberian and Beaufort seas. Food webs in this domain are short, a simplicity that belies the biophysical complexity underlying trophic linkages from primary production to humans. Existing biophysical models, such as pelagic-benthic coupling and advective processes, provide frameworks for connecting certain aspects of the marine food web, but do not offer a full accounting of events that occur seasonally across the Pacific Arctic. In the course of the Synthesis of Arctic Research (SOAR) project, a holistic Arctic Marine Pulses (AMP) model was developed that depicts seasonal biophysical `pulses' across a latitudinal gradient, and linking four previously-described contiguous domains, including the: (i) Pacific-Arctic domain = the focal region; (ii) seasonal ice zone domain; (iii) Pacific marginal domain; and (iv) riverine coastal domain. The AMP model provides a spatial-temporal framework to guide research on dynamic ecosystem processes during this period of rapid biophysical changes in the Pacific Arctic. Some of the processes included in the model, such as pelagic-benthic coupling in the Northern Bering and Chukchi seas, and advection and upwelling along the Beaufort shelf, are already the focus of sampling via the Distributed Biological Observatory (DBO) and other research programs. Other aspects such as biological processes associated with the seasonal ice zone and trophic responses to riverine outflow have received less attention. The AMP model could be enhanced by the application of visualization tools to provide a means to watch a season unfold in space and time. The capability to track sea ice dynamics and water masses and to move nutrients, prey and upper-trophic predators in space and time would provide a strong foundation for the development of predictive human-inclusive ecosystem models for the Pacific Arctic.

A Multi-Domain Model of Risk Factors for ODD Symptoms in a Community Sample of 4-Year-Olds

ERIC Educational Resources Information Center

Lavigne, John V.; Gouze, Karen R.; Hopkins, Joyce; Bryant, Fred B.; LeBailly, Susan A.

2012-01-01

Few studies have been designed to assess the pathways by which risk factors are associated with symptoms of psychopathology across multiple domains, including contextual factors, parental depression, parenting, and child characteristics. The present study examines a cross-sectional model of risk factors for symptoms of Oppositional Defiant…

Parallel distributed, reciprocal Monte Carlo radiation in coupled, large eddy combustion simulations

NASA Astrophysics Data System (ADS)

Hunsaker, Isaac L.

Radiation is the dominant mode of heat transfer in high temperature combustion environments. Radiative heat transfer affects the gas and particle phases, including all the associated combustion chemistry. The radiative properties are in turn affected by the turbulent flow field. This bi-directional coupling of radiation turbulence interactions poses a major challenge in creating parallel-capable, high-fidelity combustion simulations. In this work, a new model was developed in which reciprocal monte carlo radiation was coupled with a turbulent, large-eddy simulation combustion model. A technique wherein domain patches are stitched together was implemented to allow for scalable parallelism. The combustion model runs in parallel on a decomposed domain. The radiation model runs in parallel on a recomposed domain. The recomposed domain is stored on each processor after information sharing of the decomposed domain is handled via the message passing interface. Verification and validation testing of the new radiation model were favorable. Strong scaling analyses were performed on the Ember cluster and the Titan cluster for the CPU-radiation model and GPU-radiation model, respectively. The model demonstrated strong scaling to over 1,700 and 16,000 processing cores on Ember and Titan, respectively.

Theoretical Methods of Domain Structures in Ultrathin Ferroelectric Films: A Review

PubMed Central

Liu, Jianyi; Chen, Weijin; Wang, Biao; Zheng, Yue

2014-01-01

This review covers methods and recent developments of the theoretical study of domain structures in ultrathin ferroelectric films. The review begins with an introduction to some basic concepts and theories (e.g., polarization and its modern theory, ferroelectric phase transition, domain formation, and finite size effects, etc.) that are relevant to the study of domain structures in ultrathin ferroelectric films. Basic techniques and recent progress of a variety of important approaches for domain structure simulation, including first-principles calculation, molecular dynamics, Monte Carlo simulation, effective Hamiltonian approach and phase field modeling, as well as multiscale simulation are then elaborated. For each approach, its important features and relative merits over other approaches for modeling domain structures in ultrathin ferroelectric films are discussed. Finally, we review recent theoretical studies on some important issues of domain structures in ultrathin ferroelectric films, with an emphasis on the effects of interfacial electrostatics, boundary conditions and external loads. PMID:28788198

A multi-domain trust management model for supporting RFID applications of IoT

PubMed Central

Li, Feng

2017-01-01

The use of RFID technology in complex and distributed environments often leads to a multi-domain RFID system, in which trust establishment among entities from heterogeneous domains without past interaction or prior agreed policy, is a challenge. The current trust management mechanisms in the literature do not meet the specific requirements in multi-domain RFID systems. Therefore, this paper analyzes the special challenges on trust management in multi-domain RFID systems, and identifies the implications and the requirements of the challenges on the solutions to the trust management of multi-domain RFID systems. A multi-domain trust management model is proposed, which provides a hierarchical trust management framework include a diversity of trust evaluation and establishment approaches. The simulation results and analysis show that the proposed method has excellent ability to deal with the trust relationships, better security, and higher accuracy rate. PMID:28708855

A multi-domain trust management model for supporting RFID applications of IoT.

PubMed

Wu, Xu; Li, Feng

2017-01-01

The use of RFID technology in complex and distributed environments often leads to a multi-domain RFID system, in which trust establishment among entities from heterogeneous domains without past interaction or prior agreed policy, is a challenge. The current trust management mechanisms in the literature do not meet the specific requirements in multi-domain RFID systems. Therefore, this paper analyzes the special challenges on trust management in multi-domain RFID systems, and identifies the implications and the requirements of the challenges on the solutions to the trust management of multi-domain RFID systems. A multi-domain trust management model is proposed, which provides a hierarchical trust management framework include a diversity of trust evaluation and establishment approaches. The simulation results and analysis show that the proposed method has excellent ability to deal with the trust relationships, better security, and higher accuracy rate.

Factor analytical study of the short version of the World Health Organization Quality of Life Instrument.

PubMed

Ohaeri, Jude U; Olusina, Adewunmi K; Al-Abassi, Abdul-Hamid M

2004-01-01

The domains of the 26-item World Health Organization Quality of Life Instrument (WHOQOL-Bref) contain heterogeneous items and do not encompass the logical constructs of subjective quality of life (QOL). We compared the WHO 4-domain and 6-domain models of the WHOQOL-Bref with the 8-domain model that we obtained from factor analysis (FA). Data from 118 recently recovered Nigerian psychotic patients were used in confirmatory factor analysis (CFA) to assess goodness of fit and clarity of concept. Our FA model had superior goodness of fit for CFA and provided clarity of concept. Analysis of the WHOQOL-Bref should consider the domains from FA and include 'overall QOL' as an item and dependent variable. Subjective QOL is an aggregate of the following constructs: satisfaction with life circumstances; fulfillment of needs, and opportunity for experience in the milieu.

Reuse: A knowledge-based approach

NASA Technical Reports Server (NTRS)

Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui

1992-01-01

This paper describes our research in automating the reuse process through the use of application domain models. Application domain models are explicit formal representations of the application knowledge necessary to understand, specify, and generate application programs. Furthermore, they provide a unified repository for the operational structure, rules, policies, and constraints of a specific application area. In our approach, domain models are expressed in terms of a transaction-based meta-modeling language. This paper has described in detail the creation and maintenance of hierarchical structures. These structures are created through a process that includes reverse engineering of data models with supplementary enhancement from application experts. Source code is also reverse engineered but is not a major source of domain model instantiation at this time. In the second phase of the software synthesis process, program specifications are interactively synthesized from an instantiated domain model. These specifications are currently integrated into a manual programming process but will eventually be used to derive executable code with mechanically assisted transformations. This research is performed within the context of programming-in-the-large types of systems. Although our goals are ambitious, we are implementing the synthesis system in an incremental manner through which we can realize tangible results. The client/server architecture is capable of supporting 16 simultaneous X/Motif users and tens of thousands of attributes and classes. Domain models have been partially synthesized from five different application areas. As additional domain models are synthesized and additional knowledge is gathered, we will inevitably add to and modify our representation. However, our current experience indicates that it will scale and expand to meet our modeling needs.

Time-domain simulation of constitutive relations for nonlinear acoustics including relaxation for frequency power law attenuation media modeling

NASA Astrophysics Data System (ADS)

Jiménez, Noé; Camarena, Francisco; Redondo, Javier; Sánchez-Morcillo, Víctor; Konofagou, Elisa E.

2015-10-01

We report a numerical method for solving the constitutive relations of nonlinear acoustics, where multiple relaxation processes are included in a generalized formulation that allows the time-domain numerical solution by an explicit finite differences scheme. Thus, the proposed physical model overcomes the limitations of the one-way Khokhlov-Zabolotskaya-Kuznetsov (KZK) type models and, due to the Lagrangian density is implicitly included in the calculation, the proposed method also overcomes the limitations of Westervelt equation in complex configurations for medical ultrasound. In order to model frequency power law attenuation and dispersion, such as observed in biological media, the relaxation parameters are fitted to both exact frequency power law attenuation/dispersion media and also empirically measured attenuation of a variety of tissues that does not fit an exact power law. Finally, a computational technique based on artificial relaxation is included to correct the non-negligible numerical dispersion of the finite difference scheme, and, on the other hand, improve stability trough artificial attenuation when shock waves are present. This technique avoids the use of high-order finite-differences schemes leading to fast calculations. The present algorithm is especially suited for practical configuration where spatial discontinuities are present in the domain (e.g. axisymmetric domains or zero normal velocity boundary conditions in general). The accuracy of the method is discussed by comparing the proposed simulation solutions to one dimensional analytical and k-space numerical solutions.

Translating hydrologically-relevant variables from the ice sheet model SICOPOLIS to the Greenland Analog Project hydrologic modeling domain

NASA Astrophysics Data System (ADS)

Vallot, Dorothée; Applegate, Patrick; Pettersson, Rickard

2013-04-01

Projecting future climate and ice sheet development requires sophisticated models and extensive field observations. Given the present state of our knowledge, it is very difficult to say what will happen with certainty. Despite the ongoing increase in atmospheric greenhouse gas concentrations, the possibility that a new ice sheet might form over Scandinavia in the far distant future cannot be excluded. The growth of a new Scandinavian Ice Sheet would have important consequences for buried nuclear waste repositories. The Greenland Analogue Project, initiated by the Swedish Nuclear Fuel and Waste Management Company (SKB), is working to assess the effects of a possible future ice sheet on groundwater flow by studying a constrained domain in Western Greenland by field measurements (including deep bedrock drilling in front of the ice sheet) combined with numerical modeling. To address the needs of the GAP project, we interpolated results from an ensemble of ice sheet model runs to the smaller and more finely resolved modeling domain used in the GAP project's hydrologic modeling. Three runs have been chosen with three fairly different positive degree-day factors among those that reproduced the modern ice margin at the borehole position. The interpolated results describe changes in hydrologically-relevant variables over two time periods, 115 ka to 80 ka, and 20 ka to 1 ka. In the first of these time periods, the ice margin advances over the model domain; in the second time period, the ice margin retreats over the model domain. The spatially-and temporally dependent variables that we treated include the ice thickness, basal melting rate, surface mass balance, basal temperature, basal thermal regime (frozen or thawed), surface temperature, and basal water pressure. The melt flux is also calculated.

NED-IIS: An Intelligent Information System for Forest Ecosystem Management

Treesearch

W.D. Potter; S. Somasekar; R. Kommineni; H.M. Rauscher

1999-01-01

We view Intelligent Information System (IIS) as composed of a unified knowledge base, database, and model base. The model base includes decision support models, forecasting models, and cvsualization models for example. In addition, we feel that the model base should include domain specific porblems solving modules as well as decision support models. This, then,...

PEST domain mutations in Notch receptors comprise an oncogenic driver segment in triple-negative breast cancer sensitive to a γ-secretase inhibitor.

PubMed

Wang, Kai; Zhang, Qin; Li, Danan; Ching, Keith; Zhang, Cathy; Zheng, Xianxian; Ozeck, Mark; Shi, Stephanie; Li, Xiaorong; Wang, Hui; Rejto, Paul; Christensen, James; Olson, Peter

2015-03-15

To identify and characterize novel, activating mutations in Notch receptors in breast cancer and to determine response to the gamma secretase inhibitor (GSI) PF-03084014. We used several computational approaches, including novel algorithms, to analyze next-generation sequencing data and related omic datasets from The Cancer Genome Atlas (TCGA) breast cancer cohort. Patient-derived xenograft (PDX) models were sequenced, and Notch-mutant models were treated with PF-03084014. Gene-expression and functional analyses were performed to study the mechanism of activation through mutation and inhibition by PF-03084014. We identified mutations within and upstream of the PEST domains of NOTCH1, NOTCH2, and NOTCH3 in the TCGA dataset. Mutations occurred via several genetic mechanisms and compromised the function of the PEST domain, a negative regulatory domain commonly mutated in other cancers. Focal amplifications of NOTCH2 and NOTCH3 were also observed, as were heterodimerization or extracellular domain mutations at lower incidence. Mutations and amplifications often activated the Notch pathway as evidenced by increased expression of canonical Notch target genes, and functional mutations were significantly enriched in the triple-negative breast cancer subtype (TNBC). PDX models were also identified that harbored PEST domain mutations, and these models were highly sensitive to PF-03084014. This work suggests that Notch-altered breast cancer constitutes a bona fide oncogenic driver segment with the most common alteration being PEST domain mutations present in multiple Notch receptors. Importantly, functional studies suggest that this newly identified class can be targeted with Notch inhibitors, including GSIs. ©2015 American Association for Cancer Research.

Nonequilibrium ferroelectric-ferroelastic 10 nm nanodomains: wrinkles, period-doubling, and power-law relaxation

NASA Astrophysics Data System (ADS)

Scott, James F.; Evans, Donald M.; Katiyar, Ram S.; McQuaid, Raymond G. P.; Gregg, J. Marty

2017-08-01

Since the 1935 work of Landau-Lifshitz and of Kittel in 1946 all ferromagnetic, ferroelectric, and ferroelastic domains have been thought to be straight-sided with domain widths proportional to the square root of the sample thickness. We show in the present work that this is not true. We also discover period doubling domains predicted by Metaxas et al (2008 Phys. Rev. Lett. 99 217208) and modeled by Wang and Zhao (2015 Sci. Rep. 5 8887). We examine non-equilibrium ferroic domain structures in perovskite oxides with respect to folding, wrinkling, and relaxation and suggest that structures are kinetically limited and in the viscous flow regime predicted by Metaxas et al in 2008 but never observed experimentally. Comparisons are made with liquid crystals and hydrodynamic instabilities, including chevrons, and fractional power-law relaxation. As Shin et al (2016 Soft Matter 12 3502) recently emphasized: ‘An understanding of how these folds initiate, propagate, and interact with each other is still lacking’. Inside each ferroelastic domain are ferroelectric 90° nano-domains with 10 nm widths and periodicity in agreement with the 10 nm theoretical minima predicted by Feigl et al (2014 Nat. Commun. 5 4677). Evidence is presented for domain-width period doubling, which is common in polymer films but unknown in ferroic domains. A discussion of the folding-to-period doubling phase transition model of Wang and Zhao is included.

Shared acoustic codes underlie emotional communication in music and speech—Evidence from deep transfer learning

PubMed Central

Schuller, Björn

2017-01-01

Music and speech exhibit striking similarities in the communication of emotions in the acoustic domain, in such a way that the communication of specific emotions is achieved, at least to a certain extent, by means of shared acoustic patterns. From an Affective Sciences points of view, determining the degree of overlap between both domains is fundamental to understand the shared mechanisms underlying such phenomenon. From a Machine learning perspective, the overlap between acoustic codes for emotional expression in music and speech opens new possibilities to enlarge the amount of data available to develop music and speech emotion recognition systems. In this article, we investigate time-continuous predictions of emotion (Arousal and Valence) in music and speech, and the Transfer Learning between these domains. We establish a comparative framework including intra- (i.e., models trained and tested on the same modality, either music or speech) and cross-domain experiments (i.e., models trained in one modality and tested on the other). In the cross-domain context, we evaluated two strategies—the direct transfer between domains, and the contribution of Transfer Learning techniques (feature-representation-transfer based on Denoising Auto Encoders) for reducing the gap in the feature space distributions. Our results demonstrate an excellent cross-domain generalisation performance with and without feature representation transfer in both directions. In the case of music, cross-domain approaches outperformed intra-domain models for Valence estimation, whereas for Speech intra-domain models achieve the best performance. This is the first demonstration of shared acoustic codes for emotional expression in music and speech in the time-continuous domain. PMID:28658285

Shared acoustic codes underlie emotional communication in music and speech-Evidence from deep transfer learning.

PubMed

Coutinho, Eduardo; Schuller, Björn

2017-01-01

Music and speech exhibit striking similarities in the communication of emotions in the acoustic domain, in such a way that the communication of specific emotions is achieved, at least to a certain extent, by means of shared acoustic patterns. From an Affective Sciences points of view, determining the degree of overlap between both domains is fundamental to understand the shared mechanisms underlying such phenomenon. From a Machine learning perspective, the overlap between acoustic codes for emotional expression in music and speech opens new possibilities to enlarge the amount of data available to develop music and speech emotion recognition systems. In this article, we investigate time-continuous predictions of emotion (Arousal and Valence) in music and speech, and the Transfer Learning between these domains. We establish a comparative framework including intra- (i.e., models trained and tested on the same modality, either music or speech) and cross-domain experiments (i.e., models trained in one modality and tested on the other). In the cross-domain context, we evaluated two strategies-the direct transfer between domains, and the contribution of Transfer Learning techniques (feature-representation-transfer based on Denoising Auto Encoders) for reducing the gap in the feature space distributions. Our results demonstrate an excellent cross-domain generalisation performance with and without feature representation transfer in both directions. In the case of music, cross-domain approaches outperformed intra-domain models for Valence estimation, whereas for Speech intra-domain models achieve the best performance. This is the first demonstration of shared acoustic codes for emotional expression in music and speech in the time-continuous domain.

A Joint Method of Envelope Inversion Combined with Hybrid-domain Full Waveform Inversion

NASA Astrophysics Data System (ADS)

CUI, C.; Hou, W.

2017-12-01

Full waveform inversion (FWI) aims to construct high-precision subsurface models by fully using the information in seismic records, including amplitude, travel time, phase and so on. However, high non-linearity and the absence of low frequency information in seismic data lead to the well-known cycle skipping problem and make inversion easily fall into local minima. In addition, those 3D inversion methods that are based on acoustic approximation ignore the elastic effects in real seismic field, and make inversion harder. As a result, the accuracy of final inversion results highly relies on the quality of initial model. In order to improve stability and quality of inversion results, multi-scale inversion that reconstructs subsurface model from low to high frequency are applied. But, the absence of very low frequencies (< 3Hz) in field data is still bottleneck in the FWI. By extracting ultra low-frequency data from field data, envelope inversion is able to recover low wavenumber model with a demodulation operator (envelope operator), though the low frequency data does not really exist in field data. To improve the efficiency and viability of the inversion, in this study, we proposed a joint method of envelope inversion combined with hybrid-domain FWI. First, we developed 3D elastic envelope inversion, and the misfit function and the corresponding gradient operator were derived. Then we performed hybrid-domain FWI with envelope inversion result as initial model which provides low wavenumber component of model. Here, forward modeling is implemented in the time domain and inversion in the frequency domain. To accelerate the inversion, we adopt CPU/GPU heterogeneous computing techniques. There were two levels of parallelism. In the first level, the inversion tasks are decomposed and assigned to each computation node by shot number. In the second level, GPU multithreaded programming is used for the computation tasks in each node, including forward modeling, envelope extraction, DFT (discrete Fourier transform) calculation and gradients calculation. Numerical tests demonstrated that the combined envelope inversion + hybrid-domain FWI could obtain much faithful and accurate result than conventional hybrid-domain FWI. The CPU/GPU heterogeneous parallel computation could improve the performance speed.

SUPERFAMILY 1.75 including a domain-centric gene ontology method.

PubMed

de Lima Morais, David A; Fang, Hai; Rackham, Owen J L; Wilson, Derek; Pethica, Ralph; Chothia, Cyrus; Gough, Julian

2011-01-01

The SUPERFAMILY resource provides protein domain assignments at the structural classification of protein (SCOP) superfamily level for over 1400 completely sequenced genomes, over 120 metagenomes and other gene collections such as UniProt. All models and assignments are available to browse and download at http://supfam.org. A new hidden Markov model library based on SCOP 1.75 has been created and a previously ignored class of SCOP, coiled coils, is now included. Our scoring component now uses HMMER3, which is in orders of magnitude faster and produces superior results. A cloud-based pipeline was implemented and is publicly available at Amazon web services elastic computer cloud. The SUPERFAMILY reference tree of life has been improved allowing the user to highlight a chosen superfamily, family or domain architecture on the tree of life. The most significant advance in SUPERFAMILY is that now it contains a domain-based gene ontology (GO) at the superfamily and family levels. A new methodology was developed to ensure a high quality GO annotation. The new methodology is general purpose and has been used to produce domain-based phenotypic ontologies in addition to GO.

The International River Interface Cooperative: Public Domain Software for River Flow and Morphodynamics (Invited)

NASA Astrophysics Data System (ADS)

Nelson, J. M.; Shimizu, Y.; McDonald, R.; Takebayashi, H.

2009-12-01

The International River Interface Cooperative is an informal organization made up of academic faculty and government scientists with the goal of developing, distributing and providing education for a public-domain software interface for modeling river flow and morphodynamics. Formed in late 2007, the group released the first version of this interface (iRIC) in late 2009. iRIC includes models for two and three-dimensional flow, sediment transport, bed evolution, groundwater-surface water interaction, topographic data processing, and habitat assessment, as well as comprehensive data and model output visualization, mapping, and editing tools. All the tools in iRIC are specifically designed for use in river reaches and utilize common river data sets. The models are couched within a single graphical user interface so that a broad spectrum of models are available to users without learning new pre- and post-processing tools. The first version of iRIC was developed by combining the USGS public-domain Multi-Dimensional Surface Water Modeling System (MD_SWMS), developed at the USGS Geomorphology and Sediment Transport Laboratory in Golden, Colorado, with the public-domain river modeling code NAYS developed by the Universities of Hokkaido and Kyoto, Mizuho Corporation, and the Foundation of the River Disaster Prevention Research Institute in Sapporo, Japan. Since this initial effort, other Universities and Agencies have joined the group, and the interface has been expanded to allow users to integrate their own modeling code using Executable Markup Language (XML), which provides easy access and expandability to the iRIC software interface. In this presentation, the current components of iRIC are described and results from several practical modeling applications are presented to illustrate the capabilities and flexibility of the software. In addition, some future extensions to iRIC are demonstrated, including software for Lagrangian particle tracking and the prediction of bedform development and response to time-varying flows. Education and supporting documentation for iRIC, including detailed tutorials, are available at www.i-ric.org. The iRIC model codes, interface, and all supporting documentation are in the public domain.

Cognitive ability, academic achievement and academic self-concept: extending the internal/external frame of reference model.

PubMed

Chen, Ssu-Kuang; Hwang, Fang-Ming; Yeh, Yu-Chen; Lin, Sunny S J

2012-06-01

Marsh's internal/external (I/E) frame of reference model depicts the relationship between achievement and self-concept in specific academic domains. Few efforts have been made to examine concurrent relationships among cognitive ability, achievement, and academic self-concept (ASC) within an I/E model framework. To simultaneously examine the influences of domain-specific cognitive ability and grades on domain self-concept in an extended I/E model, including the indirect effect of domain-specific cognitive ability on domain self-concept via grades. Tenth grade respondents (628 male, 452 female) to a national adolescent survey conducted in Taiwan. Respondents completed surveys designed to measure maths and verbal aptitudes. Data on Maths and Chinese class grades and self-concepts were also collected. Statistically significant and positive path coefficients were found between cognitive ability and self-concept in the same domain (direct effect) and between these two constructs via grades (indirect effect). The cross-domain effects of either ability or grades on ASC were negatively significant. Taiwanese 10th graders tend to evaluate their ASCs based on a mix of ability and achievement, with achievement as a mediator exceeding ability as a predictor. In addition, the cross-domain effects suggest that Taiwanese students are likely to view Maths and verbal abilities and achievements as distinctly different. ©2011 The British Psychological Society.

A Steric-inhibition model for regulation of nucleotide exchange via the Dock180 family of GEFs.

PubMed

Lu, Mingjian; Kinchen, Jason M; Rossman, Kent L; Grimsley, Cynthia; Hall, Matthew; Sondek, John; Hengartner, Michael O; Yajnik, Vijay; Ravichandran, Kodi S

2005-02-22

CDM (CED-5, Dock180, Myoblast city) family members have been recently identified as novel, evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases . They regulate multiple processes, including embryonic development, cell migration, apoptotic-cell engulfment, tumor invasion, and HIV-1 infection, in diverse model systems . However, the mechanism(s) of regulation of CDM proteins has not been well understood. Here, our studies on the prototype member Dock180 reveal a steric-inhibition model for regulating the Dock180 family of GEFs. At basal state, the N-terminal SH3 domain of Dock180 binds to the distant catalytic Docker domain and negatively regulates the function of Dock180. Further studies revealed that the SH3:Docker interaction sterically blocks Rac access to the Docker domain. Interestingly, ELMO binding to the SH3 domain of Dock180 disrupted the SH3:Docker interaction, facilitated Rac access to the Docker domain, and contributed to the GEF activity of the Dock180/ELMO complex. Additional genetic rescue studies in C. elegans suggested that the regulation of the Docker-domain-mediated GEF activity by the SH3 domain and its adjoining region is evolutionarily conserved. This steric-inhibition model may be a general mechanism for regulating multiple SH3-domain-containing Dock180 family members and may have implications for a variety of biological processes.

Sub-cellular force microscopy in single normal and cancer cells

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

Babahosseini, H.; Carmichael, B.; Strobl, J.S.

2015-08-07

This work investigates the biomechanical properties of sub-cellular structures of breast cells using atomic force microscopy (AFM). The cells are modeled as a triple-layered structure where the Generalized Maxwell model is applied to experimental data from AFM stress-relaxation tests to extract the elastic modulus, the apparent viscosity, and the relaxation time of sub-cellular structures. The triple-layered modeling results allow for determination and comparison of the biomechanical properties of the three major sub-cellular structures between normal and cancerous cells: the up plasma membrane/actin cortex, the mid cytoplasm/nucleus, and the low nuclear/integrin sub-domains. The results reveal that the sub-domains become stiffer andmore » significantly more viscous with depth, regardless of cell type. In addition, there is a decreasing trend in the average elastic modulus and apparent viscosity of the all corresponding sub-cellular structures from normal to cancerous cells, which becomes most remarkable in the deeper sub-domain. The presented modeling in this work constitutes a unique AFM-based experimental framework to study the biomechanics of sub-cellular structures. - Highlights: • The cells are modeled as a triple-layered structure using Generalized Maxwell model. • The sub-domains include membrane/cortex, cytoplasm/nucleus, and nuclear/integrin. • Biomechanics of corresponding sub-domains are compared among normal and cancer cells. • Viscoelasticity of sub-domains show a decreasing trend from normal to cancer cells. • The decreasing trend becomes most significant in the deeper sub-domain.« less

On the maximum-entropy/autoregressive modeling of time series

NASA Technical Reports Server (NTRS)

Chao, B. F.

1984-01-01

The autoregressive (AR) model of a random process is interpreted in the light of the Prony's relation which relates a complex conjugate pair of poles of the AR process in the z-plane (or the z domain) on the one hand, to the complex frequency of one complex harmonic function in the time domain on the other. Thus the AR model of a time series is one that models the time series as a linear combination of complex harmonic functions, which include pure sinusoids and real exponentials as special cases. An AR model is completely determined by its z-domain pole configuration. The maximum-entropy/autogressive (ME/AR) spectrum, defined on the unit circle of the z-plane (or the frequency domain), is nothing but a convenient, but ambiguous visual representation. It is asserted that the position and shape of a spectral peak is determined by the corresponding complex frequency, and the height of the spectral peak contains little information about the complex amplitude of the complex harmonic functions.

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

PubMed Central

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

2009-01-01

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

Protein sorting by lipid phase-like domains supports emergent signaling function in B lymphocyte plasma membranes.

PubMed

Stone, Matthew B; Shelby, Sarah A; Núñez, Marcos F; Wisser, Kathleen; Veatch, Sarah L

2017-02-01

Diverse cellular signaling events, including B cell receptor (BCR) activation, are hypothesized to be facilitated by domains enriched in specific plasma membrane lipids and proteins that resemble liquid-ordered phase-separated domains in model membranes. This concept remains controversial and lacks direct experimental support in intact cells. Here, we visualize ordered and disordered domains in mouse B lymphoma cell membranes using super-resolution fluorescence localization microscopy, demonstrate that clustered BCR resides within ordered phase-like domains capable of sorting key regulators of BCR activation, and present a minimal, predictive model where clustering receptors leads to their collective activation by stabilizing an extended ordered domain. These results provide evidence for the role of membrane domains in BCR signaling and a plausible mechanism of BCR activation via receptor clustering that could be generalized to other signaling pathways. Overall, these studies demonstrate that lipid mediated forces can bias biochemical networks in ways that broadly impact signal transduction.

Tyrosine Phosphorylation of the Lyn Src Homology 2 (SH2) Domain Modulates Its Binding Affinity and Specificity*

PubMed Central

Jin, Lily L.; Wybenga-Groot, Leanne E.; Tong, Jiefei; Taylor, Paul; Minden, Mark D.; Trudel, Suzanne; McGlade, C. Jane; Moran, Michael F.

2015-01-01

Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y194 impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y194 on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases. PMID:25587033

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates

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

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The 'cell interaction domain' is proposed to regulatemore » dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The 'matrix interaction domain' may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging.« less

Frequency Domain Modeling of SAW Devices

NASA Technical Reports Server (NTRS)

Wilson, W. C.; Atkinson, G. M.

2007-01-01

New SAW sensors for integrated vehicle health monitoring of aerospace vehicles are being investigated. SAW technology is low cost, rugged, lightweight, and extremely low power. However, the lack of design tools for MEMS devices in general, and for Surface Acoustic Wave (SAW) devices specifically, has led to the development of tools that will enable integrated design, modeling, simulation, analysis and automatic layout generation of SAW devices. A frequency domain model has been created. The model is mainly first order, but it includes second order effects from triple transit echoes. This paper presents the model and results from the model for a SAW delay line device.

The PYRIN domain: A member of the death domain-fold superfamily

PubMed Central

Fairbrother, Wayne J.; Gordon, Nathaniel C.; Humke, Eric W.; O'Rourke, Karen M.; Starovasnik, Melissa A.; Yin, Jian-Ping; Dixit, Vishva M.

2001-01-01

PYRIN domains were identified recently as putative protein–protein interaction domains at the N-termini of several proteins thought to function in apoptotic and inflammatory signaling pathways. The ∼95 residue PYRIN domains have no statistically significant sequence homology to proteins with known three-dimensional structure. Using secondary structure prediction and potential-based fold recognition methods, however, the PYRIN domain is predicted to be a member of the six-helix bundle death domain-fold superfamily that includes death domains (DDs), death effector domains (DEDs), and caspase recruitment domains (CARDs). Members of the death domain-fold superfamily are well established mediators of protein–protein interactions found in many proteins involved in apoptosis and inflammation, indicating further that the PYRIN domains serve a similar function. An homology model of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1, a member of the Apaf-1/Ced-4 family of proteins, was constructed using the three-dimensional structures of the FADD and p75 neurotrophin receptor DDs, and of the Apaf-1 and caspase-9 CARDs, as templates. Validation of the model using a variety of computational techniques indicates that the fold prediction is consistent with the sequence. Comparison of a circular dichroism spectrum of the PYRIN domain of CARD7/DEFCAP/NAC/NALP1 with spectra of several proteins known to adopt the death domain-fold provides experimental support for the structure prediction. PMID:11514682

Aeroelastic Modeling of X-56A Stiff-Wing Configuration Flight Test Data

NASA Technical Reports Server (NTRS)

Grauer, Jared A.; Boucher, Matthew J.

2017-01-01

Aeroelastic stability and control derivatives for the X-56A Multi-Utility Technology Testbed (MUTT), in the stiff-wing configuration, were estimated from flight test data using the output-error method. Practical aspects of the analysis are discussed. The orthogonal phase-optimized multisine inputs provided excellent data information for aeroelastic modeling. Consistent parameter estimates were determined using output error in both the frequency and time domains. The frequency domain analysis converged faster and was less sensitive to starting values for the model parameters, which was useful for determining the aeroelastic model structure and obtaining starting values for the time domain analysis. Including a modal description of the structure from a finite element model reduced the complexity of the estimation problem and improved the modeling results. Effects of reducing the model order on the short period stability and control derivatives were investigated.

Mechanisms for integration of information models across related domains

NASA Astrophysics Data System (ADS)

Atkinson, Rob

2010-05-01

It is well recognised that there are opportunities and challenges in cross-disciplinary data integration. A significant barrier, however, is creating a conceptual model of the combined domains and the area of integration. For example, a groundwater domain application may require information from several related domains: geology, hydrology, water policy, etc. Each domain may have its own data holdings and conceptual models, but these will share various common concepts (eg. The concept of an aquifer). These areas of semantic overlap present significant challenges, firstly to choose a single representation (model) of a concept that appears in multiple disparate models,, then to harmonise these other models with the single representation. In addition, models may exist at different levels of abstraction depending on how closely aligned they are with a particular implementation. This makes it hard for modellers in one domain to introduce elements from another domain without either introducing a specific style of implementation, or conversely dealing with a set of abstract patterns that are hard to integrate with existing implementations. Models are easier to integrate if they are broken down into small units, with common concepts implemented using common models from well-known, and predictably managed shared libraries. This vision however requires development of a set of mechanisms (tools and procedures) for implementing and exploiting libraries of model components. These mechanisms need to handle publication, discovery, subscription, versioning and implementation of models in different forms. In this presentation a coherent suite of such mechanisms is proposed, using a scenario based on re-use of geosciences models. This approach forms the basis of a comprehensive strategy to empower domain modellers to create more interoperable systems. The strategy address a range of concerns and practice, and includes methodologies, an accessible toolkit, improvements to available modelling software, a community of practice and design of model registries. These mechanisms have been used to decouple the generation of simplified data products from a data and metadata maintenance environment, where the simplified products conform to implementation styles, and the data maintenance environment is a modular, extensible implementation of a more complete set of related domain models. Another case study is the provisioning of authoritative place names (a gazetteer) from more complex multi-lingual and historical archives of related place name usage.

Three-dimensional time domain model of lightning including corona effects

NASA Technical Reports Server (NTRS)

Podgorski, Andrew S.

1991-01-01

A new 3-D lightning model that incorporates the effect of corona is described for the first time. The new model is based on a Thin Wire Time Domain Lightning (TWTDL) Code developed previously. The TWTDL Code was verified during the 1985 and 1986 lightning seasons by the measurements conducted at the 553 m CN Tower in Toronto, Ontario. The inclusion of corona in the TWTDL code allowed study of the corona effects on the lightning current parameters and the associated electric field parameters.

Synthetic Modifications In the Frequency Domain for Finite Element Model Update and Damage Detection

DTIC Science & Technology

2017-09-01

Sensitivity-based finite element model updating and structural damage detection has been limited by the number of modes available in a vibration test and...increase the number of modes and corresponding sensitivity data by artificially constraining the structure under test, producing a large number of... structural modifications to the measured data, including both springs-to-ground and mass modifications. This is accomplished with frequency domain

Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain.

PubMed

Narayanan, Sunilkumar Puthenpurackal; Nair, Divya Gopalakrishnan; Schaal, Daniel; Barbosa de Aguiar, Marisa; Wenzel, Sabine; Kremer, Werner; Schwarzinger, Stephan; Kalbitzer, Hans Robert

2016-06-24

Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23-230) as detected by [(1)H, (15)N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn(2+)-binding to the octarepeat motif.

Structural transitions in full-length human prion protein detected by xenon as probe and spin labeling of the N-terminal domain

PubMed Central

Narayanan, Sunilkumar Puthenpurackal; Nair, Divya Gopalakrishnan; Schaal, Daniel; Barbosa de Aguiar, Marisa; Wenzel, Sabine; Kremer, Werner; Schwarzinger, Stephan; Kalbitzer, Hans Robert

2016-01-01

Fatal neurodegenerative disorders termed transmissible spongiform encephalopathies (TSEs) are associated with the accumulation of fibrils of misfolded prion protein PrP. The noble gas xenon accommodates into four transiently enlarged hydrophobic cavities located in the well-folded core of human PrP(23–230) as detected by [1H, 15N]-HSQC spectroscopy. In thermal equilibrium a fifth xenon binding site is formed transiently by amino acids A120 to L125 of the presumably disordered N-terminal domain and by amino acids K185 to T193 of the well-folded domain. Xenon bound PrP was modelled by restraint molecular dynamics. The individual microscopic and macroscopic dissociation constants could be derived by fitting the data to a model including a dynamic opening and closing of the cavities. As observed earlier by high pressure NMR spectroscopy xenon binding influences also other amino acids all over the N-terminal domain including residues of the AGAAAAGA motif indicating a structural coupling between the N-terminal domain and the core domain. This is in agreement with spin labelling experiments at positions 93 or 107 that show a transient interaction between the N-terminus and the start of helix 2 and the end of helix 3 of the core domain similar to that observed earlier by Zn2+-binding to the octarepeat motif. PMID:27341298

Development of a Finite-Difference Time Domain (FDTD) Model for Propagation of Transient Sounds in Very Shallow Water.

PubMed

Sprague, Mark W; Luczkovich, Joseph J

2016-01-01

This finite-difference time domain (FDTD) model for sound propagation in very shallow water uses pressure and velocity grids with both 3-dimensional Cartesian and 2-dimensional cylindrical implementations. Parameters, including water and sediment properties, can vary in each dimension. Steady-state and transient signals from discrete and distributed sources, such as the surface of a vibrating pile, can be used. The cylindrical implementation uses less computation but requires axial symmetry. The Cartesian implementation allows asymmetry. FDTD calculations compare well with those of a split-step parabolic equation. Applications include modeling the propagation of individual fish sounds, fish aggregation sounds, and distributed sources.

Beliefs about cervical cancer and Pap test: a new Chilean questionnaire.

PubMed

Urrutia, Maria-Teresa; Hall, Rosemary

2013-06-01

The purpose of this study was to develop and validate a questionnaire to examine women's beliefs about cervical cancer and the Pap test in Chilean women. The questionnaire, developed following the guidelines by Robert de Vellis, is based on the Health Belief Model. The content validity index was 0.93 upon review by 10 Chilean experts. A cross-sectional design was implemented to validate the questionnaire. The sample included 333 women recruited from a women's healthcare center in Santiago, Chile. Exploratory factor analysis was used to evaluate validity and coefficient α to evaluate reliability. After six models were computed, the questionnaire was reduced from 53 to 28 items. The new questionnaire, CPC-28 (in Spanish, Creencias, Papanicolaou, Cancer -28), includes six domains: the barriers domain to take a Pap test, the cues to action domain, the severity domain, the need to have a Pap test domain, the susceptibility to cervical cancer domain, and the benefit domain. The unexpected salient factor "need to have a Pap test" was found as part of the susceptibility domain proposed in the initial questionnaire. This finding is an important topic for future research. The CPC-28 questionnaire explained 49% of the total variance, and the reliability was .735. It was concluded that the CPC-28 questionnaire will have important implications on research, education, and administration across disciplines. Nursing curricula and healthcare providers must stress the importance and reinforce the importance of prevention of cervical cancer and regular Pap test screenings. © 2013 Sigma Theta Tau International.

An EarthCube Roadmap for Cross-Domain Interoperability in the Geosciences: Governance Aspects

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Couch, A.; Richard, S. M.; Valentine, D. W.; Stocks, K.; Murphy, P.; Lehnert, K. A.

2012-12-01

The goal of cross-domain interoperability is to enable reuse of data and models outside the original context in which these data and models are collected and used and to facilitate analysis and modeling of physical processes that are not confined to disciplinary or jurisdictional boundaries. A new research initiative of the U.S. National Science Foundation, called EarthCube, is developing a roadmap to address challenges of interoperability in the earth sciences and create a blueprint for community-guided cyberinfrastructure accessible to a broad range of geoscience researchers and students. Infrastructure readiness for cross-domain interoperability encompasses the capabilities that need to be in place for such secondary or derivative-use of information to be both scientifically sound and technically feasible. In this initial assessment we consider the following four basic infrastructure components that need to be present to enable cross-domain interoperability in the geosciences: metadata catalogs (at the appropriate community defined granularity) that provide standard discovery services over datasets, data access services, models and other resources of the domain; vocabularies that support unambiguous interpretation of domain resources and metadata; services used to access data repositories and other resources including models, visualizations and workflows; and formal information models that define structure and semantics of the information returned on service requests. General standards for these components have been proposed; they form the backbone of large scale integration activities in the geosciences. By utilizing these standards, EarthCube research designs can take advantage of data discovery across disciplines using the commonality in key data characteristics related to shared models of spatial features, time measurements, and observations. Data can be discovered via federated catalogs and linked nomenclatures from neighboring domains, while standard data services can be used to transparently compile composite data products. Key questions addressed in this presentation are: (1) How to define and assess readiness of existing domain information systems for cross-domain re-use? (2) How to determine EarthCube development priorities given a multitude of use cases that involve cross-domain data flows? and (3) How to involve a wider community of geoscientists in the development and curation of cross-domain resources and incorporate community feedback in the CI design? Answering them involves consideration of governance mechanisms for cross-domain interoperability: while domain information systems and projects developed governance mechanisms, managing cross-domain CI resources and supporting cross-domain information re-use hasn't been the development focus at the scale of the geosciences. We present a cross-domain readiness model as enabling effective communication among scientists, governance bodies, and information providers. We also present an initial readiness assessment and a cross-domain connectivity map for the geosciences, and outline processes for eliciting user requirements, setting priorities, and obtaining community consensus.

Fitting the Jigsaw of Citation: Information Visualization in Domain Analysis.

ERIC Educational Resources Information Center

Chen, Chaomei; Paul, Ray J.; O'Keefe, Bob

2001-01-01

Discusses the role of information visualization in modeling and representing intellectual structures associated with scientific disciplines and visualizes the domain of computer graphics based on bibliographic data from author cocitation patterns. Highlights include author cocitation maps, citation time lines, animation of a high-dimensional…

Three-dimensional electrical resistivity model of a nuclear waste disposal site

NASA Astrophysics Data System (ADS)

Rucker, Dale F.; Levitt, Marc T.; Greenwood, William J.

2009-12-01

A three-dimensional (3D) modeling study was completed on a very large electrical resistivity survey conducted at a nuclear waste site in eastern Washington. The acquisition included 47 pole-pole two-dimensional (2D) resistivity profiles collected along parallel and orthogonal lines over an area of 850 m × 570 m. The data were geo-referenced and inverted using EarthImager3D (EI3D). EI3D runs on a Microsoft 32-bit operating system (e.g. WIN-2K, XP) with a maximum usable memory of 2 GB. The memory limits the size of the domain for the inversion model to 200 m × 200 m, based on the survey electrode density. Therefore, a series of increasing overlapping models were run to evaluate the effectiveness of dividing the survey area into smaller subdomains. The results of the smaller subdomains were compared to the inversion results of a single domain over a larger area using an upgraded form of EI3D that incorporates multi-processing capabilities and 32 GB of RAM memory. The contours from the smaller subdomains showed discontinuity at the boundaries between the adjacent models, which do not match the hydrogeologic expectations given the nature of disposal at the site. At several boundaries, the contours of the low resistivity areas close, leaving the appearance of disconnected plumes or open contours at boundaries are not met with a continuance of the low resistivity plume into the adjacent subdomain. The model results of the single large domain show a continuous monolithic plume within the central and western portion of the site, directly beneath the elongated trenches. It is recommended that where possible, the domain not be subdivided, but instead include as much of the domain as possible given the memory of available computing resources.

A Logic for Inclusion of Administrative Domains and Administrators in Multi-domain Authorization

NASA Astrophysics Data System (ADS)

Iranmanesh, Zeinab; Amini, Morteza; Jalili, Rasool

Authorization policies for an administrative domain or a composition of multiple domains in multi-domain environments are determined by either one administrator or multiple administrators' cooperation. Several logic-based models for multi-domain environments' authorization have been proposed; however, they have not considered administrators and administrative domains in policies' representation. In this paper, we propose the syntax, proof theory, and semantics of a logic for multi-domain authorization policies including administrators and administrative domains. Considering administrators in policies provides the possibility of presenting composite administration having applicability in many collaborative applications. Indeed, administrators and administrative domains stated in policies can be used in authorization. The presented logic is based on modal logic and utilizes two calculi named the calculus of administrative domains and the calculus of administrators. It is also proved that the logic is sound. A case study is presented signifying the logic application in practical projects.

Design of Xen Hybrid Multiple Police Model

NASA Astrophysics Data System (ADS)

Sun, Lei; Lin, Renhao; Zhu, Xianwei

2017-10-01

Virtualization Technology has attracted more and more attention. As a popular open-source virtualization tools, XEN is used more and more frequently. Xsm, XEN security model, has also been widespread concern. The safety status classification has not been established in the XSM, and it uses the virtual machine as a managed object to make Dom0 a unique administrative domain that does not meet the minimum privilege. According to these questions, we design a Hybrid multiple police model named SV_HMPMD that organically integrates multiple single security policy models include DTE,RBAC,BLP. It can fullfill the requirement of confidentiality and integrity for security model and use different particle size to different domain. In order to improve BLP’s practicability, the model introduce multi-level security labels. In order to divide the privilege in detail, we combine DTE with RBAC. In order to oversize privilege, we limit the privilege of domain0.

An Empirical Human Controller Model for Preview Tracking Tasks.

PubMed

van der El, Kasper; Pool, Daan M; Damveld, Herman J; van Paassen, Marinus Rene M; Mulder, Max

2016-11-01

Real-life tracking tasks often show preview information to the human controller about the future track to follow. The effect of preview on manual control behavior is still relatively unknown. This paper proposes a generic operator model for preview tracking, empirically derived from experimental measurements. Conditions included pursuit tracking, i.e., without preview information, and tracking with 1 s of preview. Controlled element dynamics varied between gain, single integrator, and double integrator. The model is derived in the frequency domain, after application of a black-box system identification method based on Fourier coefficients. Parameter estimates are obtained to assess the validity of the model in both the time domain and frequency domain. Measured behavior in all evaluated conditions can be captured with the commonly used quasi-linear operator model for compensatory tracking, extended with two viewpoints of the previewed target. The derived model provides new insights into how human operators use preview information in tracking tasks.

Efficient Power Network Analysis with Modeling of Inductive Effects

NASA Astrophysics Data System (ADS)

Zeng, Shan; Yu, Wenjian; Hong, Xianlong; Cheng, Chung-Kuan

In this paper, an efficient method is proposed to accurately analyze large-scale power/ground (P/G) networks, where inductive parasitics are modeled with the partial reluctance. The method is based on frequency-domain circuit analysis and the technique of vector fitting [14], and obtains the time-domain voltage response at given P/G nodes. The frequency-domain circuit equation including partial reluctances is derived, and then solved with the GMRES algorithm with rescaling, preconditioning and recycling techniques. With the merit of sparsified reluctance matrix and iterative solving techniques for the frequency-domain circuit equations, the proposed method is able to handle large-scale P/G networks with complete inductive modeling. Numerical results show that the proposed method is orders of magnitude faster than HSPICE, several times faster than INDUCTWISE [4], and capable of handling the inductive P/G structures with more than 100, 000 wire segments.

Structure of Serum Amyloid A Suggests a Mechanism for Selective Lipoprotein Binding and Functions: SAA as a Hub in Macromolecular Interaction Networks

PubMed Central

Frame, Nicholas M.; Gursky, Olga

2016-01-01

Serum amyloid A is a major acute-phase plasma protein that modulates innate immunity and cholesterol homeostasis. We combine sequence analysis with x-ray crystal structures to postulate that SAA acts as an intrinsically disordered hub mediating interactions among proteins, lipids and proteoglycans. A structural model of lipoprotein-bound SAA monomer is proposed wherein two α-helices from the N-domain form a concave hydrophobic surface that binds lipoproteins. A C-domain, connected to the N-domain via a flexible linker, binds polar/charged ligands including cell receptors, bridging them with lipoproteins and re-routing cholesterol transport. Our model is supported by the SAA cleavage in the inter-domain linker to generate the 1–76 fragment deposited in reactive amyloidosis. This model sheds new light on functions of this enigmatic protein. PMID:26918388

A Functional Approach to Hyperspectral Image Analysis in the Cloud

NASA Astrophysics Data System (ADS)

Wilson, A.; Lindholm, D. M.; Coddington, O.; Pilewskie, P.

2017-12-01

Hyperspectral image volumes are very large. A hyperspectral image analysis (HIA) may use 100TB of data, a huge barrier to their use. Hylatis is a new NASA project to create a toolset for HIA. Through web notebook and cloud technology, Hylatis will provide a more interactive experience for HIA by defining and implementing concepts and operations for HIA, identified and vetted by subject matter experts, and callable within a general purpose language, particularly Python. Hylatis leverages LaTiS, a data access framework developed at LASP. With an OPeNDAP compliant interface plus additional server side capabilities, the LaTiS API provides a uniform interface to virtually any data source, and has been applied to various storage systems, including: file systems, databases, remote servers, and in various domains including: space science, systems administration and stock quotes. In the LaTiS architecture, data `adapters' read data into a data model, where server-side computations occur. Data `writers' write data from the data model into the desired format. The Hylatis difference is the data model. In LaTiS, data are represented as mathematical functions of independent and dependent variables. Domain semantics are not present at this level, but are instead present in higher software layers. The benefit of a domain agnostic, mathematical representation is having the power of math, particularly functional algebra, unconstrained by domain semantics. This agnosticism supports reusable server side functionality applicable in any domain, such as statistical, filtering, or projection operations. Algorithms to aggregate or fuse data can be simpler because domain semantics are separated from the math. Hylatis will map the functional model onto the Spark relational interface, thereby adding a functional interface to that big data engine.This presentation will discuss Hylatis goals, strategies, and current state.

3D transient electromagnetic simulation using a modified correspondence principle for wave and diffusion fields

NASA Astrophysics Data System (ADS)

Hu, Y.; Ji, Y.; Egbert, G. D.

2015-12-01

The fictitious time domain method (FTD), based on the correspondence principle for wave and diffusion fields, has been developed and used over the past few years primarily for marine electromagnetic (EM) modeling. Here we present results of our efforts to apply the FTD approach to land and airborne TEM problems which can reduce the computer time several orders of magnitude and preserve high accuracy. In contrast to the marine case, where sources are in the conductive sea water, we must model the EM fields in the air; to allow for topography air layers must be explicitly included in the computational domain. Furthermore, because sources for most TEM applications generally must be modeled as finite loops, it is useful to solve directly for the impulse response appropriate to the problem geometry, instead of the point-source Green functions typically used for marine problems. Our approach can be summarized as follows: (1) The EM diffusion equation is transformed to a fictitious wave equation. (2) The FTD wave equation is solved with an explicit finite difference time-stepping scheme, with CPML (Convolutional PML) boundary conditions for the whole computational domain including the air and earth , with FTD domain source corresponding to the actual transmitter geometry. Resistivity of the air layers is kept as low as possible, to compromise between efficiency (longer fictitious time step) and accuracy. We have generally found a host/air resistivity contrast of 10-3 is sufficient. (3)A "Modified" Fourier Transform (MFT) allow us recover system's impulse response from the fictitious time domain to the diffusion (frequency) domain. (4) The result is multiplied by the Fourier transformation （FT） of the real source current avoiding time consuming convolutions in the time domain. (5) The inverse FT is employed to get the final full waveform and full time response of the system in the time domain. In general, this method can be used to efficiently solve most time-domain EM simulation problems for non-point sources.

Generating Dynamic Persistence in the Time Domain

NASA Astrophysics Data System (ADS)

Guerrero, A.; Smith, L. A.; Smith, L. A.; Kaplan, D. T.

2001-12-01

Many dynamical systems present long-range correlations. Physically, these systems vary from biological to economical, including geological or urban systems. Important geophysical candidates for this type of behaviour include weather (or climate) and earthquake sequences. Persistence is characterised by slowly decaying correlation function; that, in theory, never dies out. The Persistence exponent reflects the degree of memory in the system and much effort has been expended creating and analysing methods that successfully estimate this parameter and model data that exhibits persistence. The most widely used methods for generating long correlated time series are not dynamical systems in the time domain, but instead are derived from a given spectral density. Little attention has been drawn to modelling persistence in the time domain. The time domain approach has the advantage that an observation at certain time can be calculated using previous observations which is particularly suitable when investigating the predictability of a long memory process. We will describe two of these methods in the time domain. One is a traditional approach using fractional ARIMA (autoregressive and moving average) models; the second uses a novel approach to extending a given series using random Fourier basis functions. The statistical quality of the two methods is compared, and they are contrasted with weather data which shows, reportedly, persistence. The suitability of this approach both for estimating predictability and for making predictions is discussed.

A probabilistic model for detecting rigid domains in protein structures.

PubMed

Nguyen, Thach; Habeck, Michael

2016-09-01

Large-scale conformational changes in proteins are implicated in many important biological functions. These structural transitions can often be rationalized in terms of relative movements of rigid domains. There is a need for objective and automated methods that identify rigid domains in sets of protein structures showing alternative conformational states. We present a probabilistic model for detecting rigid-body movements in protein structures. Our model aims to approximate alternative conformational states by a few structural parts that are rigidly transformed under the action of a rotation and a translation. By using Bayesian inference and Markov chain Monte Carlo sampling, we estimate all parameters of the model, including a segmentation of the protein into rigid domains, the structures of the domains themselves, and the rigid transformations that generate the observed structures. We find that our Gibbs sampling algorithm can also estimate the optimal number of rigid domains with high efficiency and accuracy. We assess the power of our method on several thousand entries of the DynDom database and discuss applications to various complex biomolecular systems. The Python source code for protein ensemble analysis is available at: https://github.com/thachnguyen/motion_detection : mhabeck@gwdg.de. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Reports on block rotations, fault domains and crustal deformation

NASA Technical Reports Server (NTRS)

Nur, Amos

1990-01-01

Studies of block rotations, fault domains and crustal deformation in the western United States, Israel, and China are discussed. Topics include a three-dimensional model of crustal fracture by distributed fault sets, distributed deformation and block rotation in 3D, stress field rotation, and multiple strike slip fault sets.

Skyrmions from Instantons inside Domain Walls

NASA Astrophysics Data System (ADS)

Eto, Minoru; Nitta, Muneto; Ohashi, Keisuke; Tong, David

2005-12-01

Some years ago, Atiyah and Manton described a method to construct approximate Skyrmion solutions from Yang-Mills instantons. Here we present a dynamical realization of this construction using domain walls in a five-dimensional gauge theory. The non-Abelian gauge symmetry is broken in each vacuum but restored in the core of the domain wall, allowing instantons to nestle inside the wall. We show that the world volume dynamics of the wall is given by the Skyrme model, including the four-derivative term, and the instantons appear as domain wall Skyrmions.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1993-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a testbed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

Construction of an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Friedland, Peter; Keller, Richard M.; Mckay, Christopher P.; Sims, Michael H.; Thompson, David E.

1992-01-01

Scientific model-building can be a time intensive and painstaking process, often involving the development of large complex computer programs. Despite the effort involved, scientific models cannot be distributed easily and shared with other scientists. In general, implemented scientific models are complicated, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing, using and sharing models. The proposed tool will include an interactive intelligent graphical interface and a high-level domain-specific modeling language. As a test bed for this research, we propose to develop a software prototype in the domain of planetary atmospheric modeling.

Tyrosine phosphorylation of the Lyn Src homology 2 (SH2) domain modulates its binding affinity and specificity.

PubMed

Jin, Lily L; Wybenga-Groot, Leanne E; Tong, Jiefei; Taylor, Paul; Minden, Mark D; Trudel, Suzanne; McGlade, C Jane; Moran, Michael F

2015-03-01

Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y(194) impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y(194) on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

The role of internal duplication in the evolution of multi-domain proteins.

PubMed

Nacher, J C; Hayashida, M; Akutsu, T

2010-08-01

Many proteins consist of several structural domains. These multi-domain proteins have likely been generated by selective genome growth dynamics during evolution to perform new functions as well as to create structures that fold on a biologically feasible time scale. Domain units frequently evolved through a variety of genetic shuffling mechanisms. Here we examine the protein domain statistics of more than 1000 organisms including eukaryotic, archaeal and bacterial species. The analysis extends earlier findings on asymmetric statistical laws for proteome to a wider variety of species. While proteins are composed of a wide range of domains, displaying a power-law decay, the computation of domain families for each protein reveals an exponential distribution, characterizing a protein universe composed of a thin number of unique families. Structural studies in proteomics have shown that domain repeats, or internal duplicated domains, represent a small but significant fraction of genome. In spite of its importance, this observation has been largely overlooked until recently. We model the evolutionary dynamics of proteome and demonstrate that these distinct distributions are in fact rooted in an internal duplication mechanism. This process generates the contemporary protein structural domain universe, determines its reduced thickness, and tames its growth. These findings have important implications, ranging from protein interaction network modeling to evolutionary studies based on fundamental mechanisms governing genome expansion.

Empowerment variables for rehabilitation clients on perceived beliefs concerning work quality of life domains.

PubMed

Tschopp, Molly K; Frain, Michael P; Bishop, Malachy

2009-01-01

This article describes and presents an initial analysis of variables generally associated with empowerment towards perceived beliefs concerning quality of life work domains for individuals with disabilities. The model examines the domains of importance, satisfaction, control and degree of interference of disability that an individual feels towards work. The internet based study used results from 70 individuals with disabilities in varying aspects of work. The variables composing empowerment that correlated strongly with the work domains include: self-advocacy, self-efficacy, perceived stigma, and family resiliency as measured through coping. Quality of Life concerning work was measured through the DSC-C a domain specific QOL instrument.

Life sciences domain analysis model

PubMed Central

Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H

2012-01-01

Objective Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. Materials and methods The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. Results The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. Discussion The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. Conclusions The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science. PMID:22744959

Optimal vibration control of a rotating plate with self-sensing active constrained layer damping

NASA Astrophysics Data System (ADS)

Xie, Zhengchao; Wong, Pak Kin; Lo, Kin Heng

2012-04-01

This paper proposes a finite element model for optimally controlled constrained layer damped (CLD) rotating plate with self-sensing technique and frequency-dependent material property in both the time and frequency domain. Constrained layer damping with viscoelastic material can effectively reduce the vibration in rotating structures. However, most existing research models use complex modulus approach to model viscoelastic material, and an additional iterative approach which is only available in frequency domain has to be used to include the material's frequency dependency. It is meaningful to model the viscoelastic damping layer in rotating part by using the anelastic displacement fields (ADF) in order to include the frequency dependency in both the time and frequency domain. Also, unlike previous ones, this finite element model treats all three layers as having the both shear and extension strains, so all types of damping are taken into account. Thus, in this work, a single layer finite element is adopted to model a three-layer active constrained layer damped rotating plate in which the constraining layer is made of piezoelectric material to work as both the self-sensing sensor and actuator under an linear quadratic regulation (LQR) controller. After being compared with verified data, this newly proposed finite element model is validated and could be used for future research.

Structure of a two-CAP-domain protein from the human hookworm parasite Necator americanus

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

Asojo, Oluwatoyin A., E-mail: oasojo@unmc.edu

2011-05-01

The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite N. americanus refined to a resolution limit of 2.2 Å is presented. Major proteins secreted by the infective larval stage hookworms upon host entry include Ancylostoma secreted proteins (ASPs), which are characterized by one or two CAP (cysteine-rich secretory protein/antigen 5/pathogenesis related-1) domains. The CAP domain has been reported in diverse phylogenetically unrelated proteins, but has no confirmed function. The first structure of a two-CAP-domain protein, Na-ASP-1, from the major human hookworm parasite Necator americanus was refined to a resolution limit of 2.2 Å. The structuremore » was solved by molecular replacement (MR) using Na-ASP-2, a one-CAP-domain ASP, as the search model. The correct MR solution could only be obtained by truncating the polyalanine model of Na-ASP-2 and removing several loops. The structure reveals two CAP domains linked by an extended loop. Overall, the carboxyl-terminal CAP domain is more similar to Na-ASP-2 than to the amino-terminal CAP domain. A large central cavity extends from the amino-terminal CAP domain to the carboxyl-terminal CAP domain, encompassing the putative CAP-binding cavity. The putative CAP-binding cavity is a characteristic cavity in the carboxyl-terminal CAP domain that contains a His and Glu pair. These residues are conserved in all single-CAP-domain proteins, but are absent in the amino-terminal CAP domain. The conserved His residues are oriented such that they appear to be capable of directly coordinating a zinc ion as observed for CAP proteins from reptile venoms. This first structure of a two-CAP-domain ASP can serve as a template for homology modeling of other two-CAP-domain proteins.« less

The critical domain size of stochastic population models.

PubMed

Reimer, Jody R; Bonsall, Michael B; Maini, Philip K

2017-02-01

Identifying the critical domain size necessary for a population to persist is an important question in ecology. Both demographic and environmental stochasticity impact a population's ability to persist. Here we explore ways of including this variability. We study populations with distinct dispersal and sedentary stages, which have traditionally been modelled using a deterministic integrodifference equation (IDE) framework. Individual-based models (IBMs) are the most intuitive stochastic analogues to IDEs but yield few analytic insights. We explore two alternate approaches; one is a scaling up to the population level using the Central Limit Theorem, and the other a variation on both Galton-Watson branching processes and branching processes in random environments. These branching process models closely approximate the IBM and yield insight into the factors determining the critical domain size for a given population subject to stochasticity.

Quantum model of a hysteresis in a single-domain magnetically soft ferromagnetic

NASA Astrophysics Data System (ADS)

Ignatiev, V. K.; Lebedev, N. G.; Orlov, A. A.

2018-01-01

A quantum model of a single-domain magnetically soft ferromagnetic is proposed. The α-Fe crystal in a state of the saturation magnetization and a variable magnetic field is considered as a sample. The method of an effective Hamiltonian, including the operators of the Zeeman energy, the spin-orbit interaction and the interaction with the crystal field, is used in the model. An expansion of trial single-electron wave function in a series in small parameter of the spin-orbit interaction is suggested to account for the magnetic anisotropy. Within the framework of the Heisenberg representation, the nonlinear equations of motion for the magnetization and the orbital moment of single domain are obtained. Parameters of the modelling Hamiltonian are found from a comparison with experimental data on the magnetic anisotropy of iron. A phenomenological term of the magnetic friction is introduced into equation of the magnetization motion. Nonlinear equations are solved numerically by the Runge-Kutta method. A dependence of the single domain magnetization on magnetic field intensity has a characteristic form of a hysteresis loop which parameters are quantitatively coordinated with experimental data of researches of magnetic properties of nanoparticles of iron and iron oxide. The method is extended for modelling the magnetization dynamics of multi-domain ferromagnetic in the approximation of a strong crystal field.

A Knowledge Navigation Method for the Domain of Customers' Services of Mobile Communication Corporations in China

NASA Astrophysics Data System (ADS)

Wu, Jiangning; Wang, Xiaohuan

Rapidly increasing amount of mobile phone users and types of services leads to a great accumulation of complaining information. How to use this information to enhance the quality of customers' services is a big issue at present. To handle this kind of problem, the paper presents an approach to construct a domain knowledge map for navigating the explicit and tacit knowledge in two ways: building the Topic Map-based explicit knowledge navigation model, which includes domain TM construction, a semantic topic expansion algorithm and VSM-based similarity calculation; building Social Network Analysis-based tacit knowledge navigation model, which includes a multi-relational expert navigation algorithm and the criterions to evaluate the performance of expert networks. In doing so, both the customer managers and operators in call centers can find the appropriate knowledge and experts quickly and exactly. The experimental results show that the above method is very powerful for knowledge navigation.

qFeature

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

2015-09-14

This package contains statistical routines for extracting features from multivariate time-series data which can then be used for subsequent multivariate statistical analysis to identify patterns and anomalous behavior. It calculates local linear or quadratic regression model fits to moving windows for each series and then summarizes the model coefficients across user-defined time intervals for each series. These methods are domain agnostic-but they have been successfully applied to a variety of domains, including commercial aviation and electric power grid data.

Analysis instruments for the performance of Advanced Practice Nursing.

PubMed

Sevilla-Guerra, Sonia; Zabalegui, Adelaida

2017-11-29

Advanced Practice Nursing has been a reality in the international context for several decades and recently new nursing profiles have been developed in Spain as well that follow this model. The consolidation of these advanced practice roles has also led to of the creation of tools that attempt to define and evaluate their functions. This study aims to identify and explore the existing instruments that enable the domains of Advanced Practice Nursing to be defined. A review of existing international questionnaires and instruments was undertaken, including an analysis of the design process, the domains/dimensions defined, the main results and an exploration of clinimetric properties. Seven studies were analysed but not all proved to be valid, stable or reliable tools. One included tool was able to differentiate between the functions of the general nurse and the advanced practice nurse by the level of activities undertaken within the five domains described. These tools are necessary to evaluate the scope of advanced practice in new nursing roles that correspond to other international models of competencies and practice domains. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

A 2-D Interface Element for Coupled Analysis of Independently Modeled 3-D Finite Element Subdomains

NASA Technical Reports Server (NTRS)

Kandil, Osama A.

1998-01-01

Over the past few years, the development of the interface technology has provided an analysis framework for embedding detailed finite element models within finite element models which are less refined. This development has enabled the use of cascading substructure domains without the constraint of coincident nodes along substructure boundaries. The approach used for the interface element is based on an alternate variational principle often used in deriving hybrid finite elements. The resulting system of equations exhibits a high degree of sparsity but gives rise to a non-positive definite system which causes difficulties with many of the equation solvers in general-purpose finite element codes. Hence the global system of equations is generally solved using, a decomposition procedure with pivoting. The research reported to-date for the interface element includes the one-dimensional line interface element and two-dimensional surface interface element. Several large-scale simulations, including geometrically nonlinear problems, have been reported using the one-dimensional interface element technology; however, only limited applications are available for the surface interface element. In the applications reported to-date, the geometry of the interfaced domains exactly match each other even though the spatial discretization within each domain may be different. As such, the spatial modeling of each domain, the interface elements and the assembled system is still laborious. The present research is focused on developing a rapid modeling procedure based on a parametric interface representation of independently defined subdomains which are also independently discretized.

Application of Boosting Regression Trees to Preliminary Cost Estimation in Building Construction Projects

PubMed Central

2015-01-01

Among the recent data mining techniques available, the boosting approach has attracted a great deal of attention because of its effective learning algorithm and strong boundaries in terms of its generalization performance. However, the boosting approach has yet to be used in regression problems within the construction domain, including cost estimations, but has been actively utilized in other domains. Therefore, a boosting regression tree (BRT) is applied to cost estimations at the early stage of a construction project to examine the applicability of the boosting approach to a regression problem within the construction domain. To evaluate the performance of the BRT model, its performance was compared with that of a neural network (NN) model, which has been proven to have a high performance in cost estimation domains. The BRT model has shown results similar to those of NN model using 234 actual cost datasets of a building construction project. In addition, the BRT model can provide additional information such as the importance plot and structure model, which can support estimators in comprehending the decision making process. Consequently, the boosting approach has potential applicability in preliminary cost estimations in a building construction project. PMID:26339227

Application of Boosting Regression Trees to Preliminary Cost Estimation in Building Construction Projects.

PubMed

Shin, Yoonseok

2015-01-01

Among the recent data mining techniques available, the boosting approach has attracted a great deal of attention because of its effective learning algorithm and strong boundaries in terms of its generalization performance. However, the boosting approach has yet to be used in regression problems within the construction domain, including cost estimations, but has been actively utilized in other domains. Therefore, a boosting regression tree (BRT) is applied to cost estimations at the early stage of a construction project to examine the applicability of the boosting approach to a regression problem within the construction domain. To evaluate the performance of the BRT model, its performance was compared with that of a neural network (NN) model, which has been proven to have a high performance in cost estimation domains. The BRT model has shown results similar to those of NN model using 234 actual cost datasets of a building construction project. In addition, the BRT model can provide additional information such as the importance plot and structure model, which can support estimators in comprehending the decision making process. Consequently, the boosting approach has potential applicability in preliminary cost estimations in a building construction project.

Forecasting volcanic air pollution in Hawaii: Tests of time series models

NASA Astrophysics Data System (ADS)

Reikard, Gordon

2012-12-01

Volcanic air pollution, known as vog (volcanic smog) has recently become a major issue in the Hawaiian islands. Vog is caused when volcanic gases react with oxygen and water vapor. It consists of a mixture of gases and aerosols, which include sulfur dioxide and other sulfates. The source of the volcanic gases is the continuing eruption of Mount Kilauea. This paper studies predicting vog using statistical methods. The data sets include time series for SO2 and SO4, over locations spanning the west, south and southeast coasts of Hawaii, and the city of Hilo. The forecasting models include regressions and neural networks, and a frequency domain algorithm. The most typical pattern for the SO2 data is for the frequency domain method to yield the most accurate forecasts over the first few hours, and at the 24 h horizon. The neural net places second. For the SO4 data, the results are less consistent. At two sites, the neural net generally yields the most accurate forecasts, except at the 1 and 24 h horizons, where the frequency domain technique wins narrowly. At one site, the neural net and the frequency domain algorithm yield comparable errors over the first 5 h, after which the neural net dominates. At the remaining site, the frequency domain method is more accurate over the first 4 h, after which the neural net achieves smaller errors. For all the series, the average errors are well within one standard deviation of the actual data at all the horizons. However, the errors also show irregular outliers. In essence, the models capture the central tendency of the data, but are less effective in predicting the extreme events.

Wave Propagation, Scattering and Imaging Using Dual-domain One-way and One-return Propagators

NASA Astrophysics Data System (ADS)

Wu, R.-S.

- Dual-domain one-way propagators implement wave propagation in heterogeneous media in mixed domains (space-wavenumber domains). One-way propagators neglect wave reverberations between heterogeneities but correctly handle the forward multiple-scattering including focusing/defocusing, diffraction, refraction and interference of waves. The algorithm shuttles between space-domain and wavenumber-domain using FFT, and the operations in the two domains are self-adaptive to the complexity of the media. The method makes the best use of the operations in each domain, resulting in efficient and accurate propagators. Due to recent progress, new versions of dual-domain methods overcame some limitations of the classical dual-domain methods (phase-screen or split-step Fourier methods) and can propagate large-angle waves quite accurately in media with strong velocity contrasts. These methods can deliver superior image quality (high resolution/high fidelity) for complex subsurface structures. One-way and one-return (De Wolf approximation) propagators can be also applied to wave-field modeling and simulations for some geophysical problems. In the article, a historical review and theoretical analysis of the Born, Rytov, and De Wolf approximations are given. A review on classical phase-screen or split-step Fourier methods is also given, followed by a summary and analysis of the new dual-domain propagators. The applications of the new propagators to seismic imaging and modeling are reviewed with several examples. For seismic imaging, the advantages and limitations of the traditional Kirchhoff migration and time-space domain finite-difference migration, when applied to 3-D complicated structures, are first analyzed. Then the special features, and applications of the new dual-domain methods are presented. Three versions of GSP (generalized screen propagators), the hybrid pseudo-screen, the wide-angle Padé-screen, and the higher-order generalized screen propagators are discussed. Recent progress also makes it possible to use the dual-domain propagators for modeling elastic reflections for complex structures and long-range propagations of crustal guided waves. Examples of 2-D and 3-D imaging and modeling using GSP methods are given.

Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

PubMed

Subbotina, Julia; Yarov-Yarovoy, Vladimir; Lees-Miller, James; Durdagi, Serdar; Guo, Jiqing; Duff, Henry J; Noskov, Sergei Yu

2010-11-01

The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed. © 2010 Wiley-Liss, Inc.

Guideline appraisal with AGREE II: Systematic review of the current evidence on how users handle the 2 overall assessments.

PubMed

Hoffmann-Eßer, Wiebke; Siering, Ulrich; Neugebauer, Edmund A M; Brockhaus, Anne Catharina; Lampert, Ulrike; Eikermann, Michaela

2017-01-01

The Appraisal of Guidelines for Research & Evaluation (AGREE) II instrument is the most commonly used guideline appraisal tool. It includes 23 appraisal criteria (items) organized within 6 domains and 2 overall assessments (1. overall guideline quality; 2. recommendation for use). The aim of this systematic review was twofold. Firstly, to investigate how often AGREE II users conduct the 2 overall assessments. Secondly, to investigate the influence of the 6 domain scores on each of the 2 overall assessments. A systematic bibliographic search was conducted for publications reporting guideline appraisals with AGREE II. The impact of the 6 domain scores on the overall assessment of guideline quality was examined using a multiple linear regression model. Their impact on the recommendation for use (possible answers: "yes", "yes, with modifications", "no") was examined using a multinomial regression model. 118 relevant publications including 1453 guidelines were identified. 77.1% of the publications reported results for at least one overall assessment, but only 32.2% reported results for both overall assessments. The results of the regression analyses showed a statistically significant influence of all domains on overall guideline quality, with Domain 3 (rigour of development) having the strongest influence. For the recommendation for use, the results showed a significant influence of Domains 3 to 5 ("yes" vs. "no") and Domains 3 and 5 ("yes, with modifications" vs. "no"). The 2 overall assessments of AGREE II are underreported by guideline assessors. Domains 3 and 5 have the strongest influence on the results of the 2 overall assessments, while the other domains have a varying influence. Within a normative approach, our findings could be used as guidance for weighting individual domains in AGREE II to make the overall assessments more objective. Alternatively, a stronger content analysis of the individual domains could clarify their importance in terms of guideline quality. Moreover, AGREE II should require users to transparently present how they conducted the assessments.

Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

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

Wei, Guowei; Baker, Nathan A.

2016-11-11

This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In thesemore » approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.« less

Toward mechanistic models of action-oriented and detached cognition.

PubMed

Pezzulo, Giovanni

2016-01-01

To be successful, the research agenda for a novel control view of cognition should foresee more detailed, computationally specified process models of cognitive operations including higher cognition. These models should cover all domains of cognition, including those cognitive abilities that can be characterized as online interactive loops and detached forms of cognition that depend on internally generated neuronal processing.

Domain and Specification Models for Software Engineering

NASA Technical Reports Server (NTRS)

Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui

1992-01-01

This paper discusses our approach to representing application domain knowledge for specific software engineering tasks. Application domain knowledge is embodied in a domain model. Domain models are used to assist in the creation of specification models. Although many different specification models can be created from any particular domain model, each specification model is consistent and correct with respect to the domain model. One aspect of the system-hierarchical organization is described in detail.

Anti-staphylococcal activities of lysostaphin and LytM catalytic domain

PubMed Central

2012-01-01

Background Lysostaphin and the catalytic domain of LytM cleave pentaglycine crossbridges of Staphylococcus aureus peptidoglycan. The bacteriocin lysostaphin is secreted by Staphylococcus simulans biovar staphylolyticus and directed against the cell walls of competing S. aureus. LytM is produced by S. aureus as a latent autolysin and can be activated in vitro by the removal of an N-terminal domain and occluding region. Results We compared the efficacies of the lysostaphin and LytM catalytic domains using a newly developed model of chronic S. aureus infected eczema. Lysostaphin was effective, like in other models. In contrast, LytM was not significantly better than control. The different treatment outcomes could be correlated with in vitro properties of the proteins, including proteolytic stability, affinity to cell wall components other than peptidoglycan, and sensitivity to the ionic milieu. Conclusions Although lysostaphin and LytM cleave the same peptide bond in the peptidoglycan, the two enzymes have very different environmental requirements what is reflected in their contrasting performance in mouse eczema model. PMID:22672475

A Nodal Domain Integration Model of Two-Dimensional Heat and Soil-Water Flow Coupled by Soil-Water Phase Change.

DTIC Science & Technology

1987-06-01

WORK UNIT ELEMENT NO. NO NO ACCESSION NO I I ICWIS 31711 11 TITLE (Include Security Classification) A Nodal Domain Integration Model of Two...t.5% Unclassified."- .-,,. PREFACE This report was prepared by Ted Hromadka, Director of Water Re- sources, Williamson and Schmid. The work was...performed for CRREL under Contract 84-M-1691 and was funded by the Directorate of Civil Works , Office of the Chief of Engineers, under Civil Works Order No

A Simple and Efficient Computational Approach to Chafed Cable Time-Domain Reflectometry Signature Prediction

NASA Technical Reports Server (NTRS)

Kowalski, Marc Edward

2009-01-01

A method for the prediction of time-domain signatures of chafed coaxial cables is presented. The method is quasi-static in nature, and is thus efficient enough to be included in inference and inversion routines. Unlike previous models proposed, no restriction on the geometry or size of the chafe is required in the present approach. The model is validated and its speed is illustrated via comparison to simulations from a commercial, three-dimensional electromagnetic simulator.

System modeling with the DISC framework: evidence from safety-critical domains.

PubMed

Reiman, Teemu; Pietikäinen, Elina; Oedewald, Pia; Gotcheva, Nadezhda

2012-01-01

The objective of this paper is to illustrate the development and application of the Design for Integrated Safety Culture (DISC) framework for system modeling by evaluating organizational potential for safety in nuclear and healthcare domains. The DISC framework includes criteria for good safety culture and a description of functions that the organization needs to implement in order to orient the organization toward the criteria. Three case studies will be used to illustrate the utilization of the DISC framework in practice.

A Common Mechanism Underlying Food Choice and Social Decisions.

PubMed

Krajbich, Ian; Hare, Todd; Bartling, Björn; Morishima, Yosuke; Fehr, Ernst

2015-10-01

People make numerous decisions every day including perceptual decisions such as walking through a crowd, decisions over primary rewards such as what to eat, and social decisions that require balancing own and others' benefits. The unifying principles behind choices in various domains are, however, still not well understood. Mathematical models that describe choice behavior in specific contexts have provided important insights into the computations that may underlie decision making in the brain. However, a critical and largely unanswered question is whether these models generalize from one choice context to another. Here we show that a model adapted from the perceptual decision-making domain and estimated on choices over food rewards accurately predicts choices and reaction times in four independent sets of subjects making social decisions. The robustness of the model across domains provides behavioral evidence for a common decision-making process in perceptual, primary reward, and social decision making.

A Common Mechanism Underlying Food Choice and Social Decisions

PubMed Central

Krajbich, Ian; Hare, Todd; Bartling, Björn; Morishima, Yosuke; Fehr, Ernst

2015-01-01

People make numerous decisions every day including perceptual decisions such as walking through a crowd, decisions over primary rewards such as what to eat, and social decisions that require balancing own and others’ benefits. The unifying principles behind choices in various domains are, however, still not well understood. Mathematical models that describe choice behavior in specific contexts have provided important insights into the computations that may underlie decision making in the brain. However, a critical and largely unanswered question is whether these models generalize from one choice context to another. Here we show that a model adapted from the perceptual decision-making domain and estimated on choices over food rewards accurately predicts choices and reaction times in four independent sets of subjects making social decisions. The robustness of the model across domains provides behavioral evidence for a common decision-making process in perceptual, primary reward, and social decision making. PMID:26460812

Numerical Model Sensitivity to Heterogeneous Satellite Derived Vegetation Roughness

NASA Technical Reports Server (NTRS)

Jasinski, Michael; Eastman, Joseph; Borak, Jordan

2011-01-01

The sensitivity of a mesoscale weather prediction model to a 1 km satellite-based vegetation roughness initialization is investigated for a domain within the south central United States. Three different roughness databases are employed: i) a control or standard lookup table roughness that is a function only of land cover type, ii) a spatially heterogeneous roughness database, specific to the domain, that was previously derived using a physically based procedure and Moderate Resolution Imaging Spectroradiometer (MODIS) imagery, and iii) a MODIS climatologic roughness database that like (i) is a function only of land cover type, but possesses domain specific mean values from (ii). The model used is the Weather Research and Forecast Model (WRF) coupled to the Community Land Model within the Land Information System (LIS). For each simulation, a statistical comparison is made between modeled results and ground observations within a domain including Oklahoma, Eastern Arkansas, and Northwest Louisiana during a 4-day period within IHOP 2002. Sensitivity analysis compares the impact the three roughness initializations on time-series temperature, precipitation probability of detection (POD), average wind speed, boundary layer height, and turbulent kinetic energy (TKE). Overall, the results indicate that, for the current investigation, replacement of the standard look-up table values with the satellite-derived values statistically improves model performance for most observed variables. Such natural roughness heterogeneity enhances the surface wind speed, PBL height and TKE production up to 10 percent, with a lesser effect over grassland, and greater effect over mixed land cover domains.

Exact model reduction of combinatorial reaction networks

PubMed Central

Conzelmann, Holger; Fey, Dirk; Gilles, Ernst D

2008-01-01

Background Receptors and scaffold proteins usually possess a high number of distinct binding domains inducing the formation of large multiprotein signaling complexes. Due to combinatorial reasons the number of distinguishable species grows exponentially with the number of binding domains and can easily reach several millions. Even by including only a limited number of components and binding domains the resulting models are very large and hardly manageable. A novel model reduction technique allows the significant reduction and modularization of these models. Results We introduce methods that extend and complete the already introduced approach. For instance, we provide techniques to handle the formation of multi-scaffold complexes as well as receptor dimerization. Furthermore, we discuss a new modeling approach that allows the direct generation of exactly reduced model structures. The developed methods are used to reduce a model of EGF and insulin receptor crosstalk comprising 5,182 ordinary differential equations (ODEs) to a model with 87 ODEs. Conclusion The methods, presented in this contribution, significantly enhance the available methods to exactly reduce models of combinatorial reaction networks. PMID:18755034

Preparing Addiction Specialists to Include Case Management and Vocational Rehabilitation Services in the Treatment Model for Problem Gamblers

ERIC Educational Resources Information Center

Glenn, Margaret K.; Diaz, Sebastian R.; Hawley, Carolyn

2009-01-01

Professionals in the field of addictions view problems associated with recovery management across multiple domains. This exploratory study utilized concept mapping and pattern matching methodology to conceptualize the resulting 7 domains of concern for treatment and aftercare of problem and pathological gamblers. The information can be used by…

VENI, video, VICI: The merging of computer and video technologies

NASA Technical Reports Server (NTRS)

Horowitz, Jay G.

1993-01-01

The topics covered include the following: High Definition Television (HDTV) milestones; visual information bandwidth; television frequency allocation and bandwidth; horizontal scanning; workstation RGB color domain; NTSC color domain; American HDTV time-table; HDTV image size; digital HDTV hierarchy; task force on digital image architecture; open architecture model; future displays; and the ULTIMATE imaging system.

Birth and death of protein domains: A simple model of evolution explains power law behavior

PubMed Central

Karev, Georgy P; Wolf, Yuri I; Rzhetsky, Andrey Y; Berezovskaya, Faina S; Koonin, Eugene V

2002-01-01

Background Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution. Results A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i) domain birth (duplication with divergence), ii) death (inactivation and/or deletion), and iii) innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer). This formalism can be described as a birth, death and innovation model (BDIM). The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational models, are considered in details and the distributions of the equilibrium frequencies of domain families of different size are determined for each case. We apply the BDIM formalism to the analysis of the domain family size distributions in prokaryotic and eukaryotic proteomes and show an excellent fit between these empirical data and a particular form of the model, the second-order balanced linear BDIM. Calculation of the parameters of these models suggests surprisingly high innovation rates, comparable to the total domain birth (duplication) and elimination rates, particularly for prokaryotic genomes. Conclusions We show that a straightforward model of genome evolution, which does not explicitly include selection, is sufficient to explain the observed distributions of domain family sizes, in which power laws appear as asymptotic. However, for the model to be compatible with the data, there has to be a precise balance between domain birth, death and innovation rates, and this is likely to be maintained by selection. The developed approach is oriented at a mathematical description of evolution of domain composition of proteomes, but a simple reformulation could be applied to models of other evolving networks with preferential attachment. PMID:12379152

Birth and death of protein domains: a simple model of evolution explains power law behavior.

PubMed

Karev, Georgy P; Wolf, Yuri I; Rzhetsky, Andrey Y; Berezovskaya, Faina S; Koonin, Eugene V

2002-10-14

Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution. A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i) domain birth (duplication with divergence), ii) death (inactivation and/or deletion), and iii) innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer). This formalism can be described as a birth, death and innovation model (BDIM). The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational models, are considered in details and the distributions of the equilibrium frequencies of domain families of different size are determined for each case. We apply the BDIM formalism to the analysis of the domain family size distributions in prokaryotic and eukaryotic proteomes and show an excellent fit between these empirical data and a particular form of the model, the second-order balanced linear BDIM. Calculation of the parameters of these models suggests surprisingly high innovation rates, comparable to the total domain birth (duplication) and elimination rates, particularly for prokaryotic genomes. We show that a straightforward model of genome evolution, which does not explicitly include selection, is sufficient to explain the observed distributions of domain family sizes, in which power laws appear as asymptotic. However, for the model to be compatible with the data, there has to be a precise balance between domain birth, death and innovation rates, and this is likely to be maintained by selection. The developed approach is oriented at a mathematical description of evolution of domain composition of proteomes, but a simple reformulation could be applied to models of other evolving networks with preferential attachment.

Assessment of Energy Removal Impacts on Physical Systems: Hydrodynamic Model Domain Expansion and Refinement, and Online Dissemination of Model Results

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

Yang, Zhaoqing; Khangaonkar, Tarang; Wang, Taiping

In this report we describe the 1) the expansion of the PNNL hydrodynamic model domain to include the continental shelf along the coasts of Washington, Oregon, and Vancouver Island; and 2) the approach and progress in developing the online/Internet disseminations of model results and outreach efforts in support of the Puget Sound Operational Forecast System (PS-OPF). Submittal of this report completes the work on Task 2.1.2, Effects of Physical Systems, Subtask 2.1.2.1, Hydrodynamics, for fiscal year 2010 of the Environmental Effects of Marine and Hydrokinetic Energy project.

A numerical study of thermal stratification due to transient natural convection in densified liquid propellant tanks

NASA Astrophysics Data System (ADS)

Manalo, Lawrence B.

A comprehensive, non-equilibrium, two-domain (liquid and vapor), physics based, mathematical model is developed to investigate the onset and growth of the natural circulation and thermal stratification inside cryogenic propellant storage tanks due to heat transfer from the surroundings. A two-dimensional (planar) model is incorporated for the liquid domain while a lumped, thermodynamic model is utilized for the vapor domain. The mathematical model in the liquid domain consists of the conservation of mass, momentum, and energy equations and incorporates the Boussinesq approximation (constant fluid density except in the buoyancy term of the momentum equation). In addition, the vapor is assumed to behave like an ideal gas with uniform thermodynamic properties. Furthermore, the time-dependent nature of the heat leaks from the surroundings to the propellant (due to imperfect tank insulation) is considered. Also, heterogeneous nucleation, although not significant in the temperature range of study, has been included. The transport of mass and energy between the liquid and vapor domains leads to transient ullage vapor temperatures and pressures. (The latter of which affects the saturation temperature of the liquid at the liquid-vapor interface.) This coupling between the two domains is accomplished through an energy balance (based on a micro-layer concept) at the interface. The resulting governing, non-linear, partial differential equations (which include a Poisson's equation for determining the pressure distribution) in the liquid domain are solved by an implicit, finite-differencing technique utilizing a non-uniform (stretched) mesh (in both directions) for predicting the velocity and temperature fields. (The accuracy of the numerical scheme is validated by comparing the model's results to a benchmark numerical case as well as to available experimental data.) The mass, temperature, and pressure of the vapor is determined by using a simple explicit finite-differencing technique. With the model at hand, the effects of variable fluid transport/thermo-physical properties, levels of initial sub-cooling, operating pressure, and initial liquid aspect ratio on the natural circulation patterns and thermal stratification are numerically investigated. Liquid oxygen (LOx) is the primary working fluid in the study. However, a simulation with liquid nitrogen (LN2) as the propellant is also carried out for comparison purposes.

Bridging Multidimensional Models of Ethnic-Racial and Gender Identity Among Ethnically Diverse Emerging Adults.

PubMed

Wilson, Antoinette R; Leaper, Campbell

2016-08-01

The purpose of this study was to integrate and validate a multidimensional model of ethnic-racial identity and gender identity borrowing constructs and measures based on social identity and gender identity theories. Participants included 662 emerging adults (M age  = 19.86 years; 75 % female) who self-identified either as Asian American, Latino/a, or White European American. We assessed the following facets separately for ethnic-racial identity and gender identity: centrality, in-group affect, in-group ties, self-perceived typicality, and felt conformity pressure. Within each identity domain (gender or ethnicity/race), the five dimensions generally indicated small-to-moderate correlations with one another. Also, correlations between domains for each dimension (e.g., gender typicality and ethnic-racial typicality) were mostly moderate in magnitude. We also noted some group variations based on participants' ethnicity/race and gender in how strongly particular dimensions were associated with self-esteem. Finally, participants who scored positively on identity dimensions for both gender and ethnic-racial domains indicated higher self-esteem than those who scored high in only one domain or low in both domains. We recommend the application of multidimensional models to study social identities in multiple domains as they may relate to various outcomes during development.

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

PubMed Central

Jost, Daniel; Carrivain, Pascal; Cavalli, Giacomo; Vaillant, Cédric

2014-01-01

Genomes of eukaryotes are partitioned into domains of functionally distinct chromatin states. These domains are stably inherited across many cell generations and can be remodeled in response to developmental and external cues, hence contributing to the robustness and plasticity of expression patterns and cell phenotypes. Remarkably, recent studies indicate that these 1D epigenomic domains tend to fold into 3D topologically associated domains forming specialized nuclear chromatin compartments. However, the general mechanisms behind such compartmentalization including the contribution of epigenetic regulation remain unclear. Here, we address the question of the coupling between chromatin folding and epigenome. Using polymer physics, we analyze the properties of a block copolymer model that accounts for local epigenomic information. Considering copolymers build from the epigenomic landscape of Drosophila, we observe a very good agreement with the folding patterns observed in chromosome conformation capture experiments. Moreover, this model provides a physical basis for the existence of multistability in epigenome folding at sub-chromosomal scale. We show how experiments are fully consistent with multistable conformations where topologically associated domains of the same epigenomic state interact dynamically with each other. Our approach provides a general framework to improve our understanding of chromatin folding during cell cycle and differentiation and its relation to epigenetics. PMID:25092923

Proposal for constructing an advanced software tool for planetary atmospheric modeling

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Sims, Michael H.; Podolak, Esther; Mckay, Christopher P.; Thompson, David E.

1990-01-01

Scientific model building can be a time intensive and painstaking process, often involving the development of large and complex computer programs. Despite the effort involved, scientific models cannot easily be distributed and shared with other scientists. In general, implemented scientific models are complex, idiosyncratic, and difficult for anyone but the original scientist/programmer to understand. We believe that advanced software techniques can facilitate both the model building and model sharing process. We propose to construct a scientific modeling software tool that serves as an aid to the scientist in developing and using models. The proposed tool will include an interactive intelligent graphical interface and a high level, domain specific, modeling language. As a testbed for this research, we propose development of a software prototype in the domain of planetary atmospheric modeling.

Protein domains of unknown function are essential in bacteria.

PubMed

Goodacre, Norman F; Gerloff, Dietlind L; Uetz, Peter

2013-12-31

More than 20% of all protein domains are currently annotated as "domains of unknown function" (DUFs). About 2,700 DUFs are found in bacteria compared with just over 1,500 in eukaryotes. Over 800 DUFs are shared between bacteria and eukaryotes, and about 300 of these are also present in archaea. A total of 2,786 bacterial Pfam domains even occur in animals, including 320 DUFs. Evolutionary conservation suggests that many of these DUFs are important. Here we show that 355 essential proteins in 16 model bacterial species contain 238 DUFs, most of which represent single-domain proteins, clearly establishing the biological essentiality of DUFs. We suggest that experimental research should focus on conserved and essential DUFs (eDUFs) for functional analysis given their important function and wide taxonomic distribution, including bacterial pathogens. The functional units of proteins are domains. Typically, each domain has a distinct structure and function. Genomes encode thousands of domains, and many of the domains have no known function (domains of unknown function [DUFs]). They are often ignored as of little relevance, given that many of them are found in only a few genomes. Here we show that many DUFs are essential DUFs (eDUFs) based on their presence in essential proteins. We also show that eDUFs are often essential even if they are found in relatively few genomes. However, in general, more common DUFs are more often essential than rare DUFs.

Extracting Low-Frequency Information from Time Attenuation in Elastic Waveform Inversion

NASA Astrophysics Data System (ADS)

Guo, Xuebao; Liu, Hong; Shi, Ying; Wang, Weihong

2017-03-01

Low-frequency information is crucial for recovering background velocity, but the lack of low-frequency information in field data makes inversion impractical without accurate initial models. Laplace-Fourier domain waveform inversion can recover a smooth model from real data without low-frequency information, which can be used for subsequent inversion as an ideal starting model. In general, it also starts with low frequencies and includes higher frequencies at later inversion stages, while the difference is that its ultralow frequency information comes from the Laplace-Fourier domain. Meanwhile, a direct implementation of the Laplace-transformed wavefield using frequency domain inversion is also very convenient. However, because broad frequency bands are often used in the pure time domain waveform inversion, it is difficult to extract the wavefields dominated by low frequencies in this case. In this paper, low-frequency components are constructed by introducing time attenuation into the recorded residuals, and the rest of the method is identical to the traditional time domain inversion. Time windowing and frequency filtering are also applied to mitigate the ambiguity of the inverse problem. Therefore, we can start at low frequencies and to move to higher frequencies. The experiment shows that the proposed method can achieve a good inversion result in the presence of a linear initial model and records without low-frequency information.

Determination of the extra buffering distance in the one-way nesting procedure for the regional ocean

NASA Astrophysics Data System (ADS)

Hwang, Jin Hwan; Pham, Van Sy

2017-04-01

The Big-Brother Experiment (BBE) evaluates the effect of domain size on the ocean regional circulation model (ORCMs) in the downscaling and nesting from the ocean global circulation (OGCMs). The BBE first establishes a mimic ocean global circulation models (M-OGCMs) data and employs a ORCM to simulate for a highly resolved large domain. This M-OGCM's results were then filtered to remove short scales then used for boundary and initial conditions of the nested ORCMs, which have the same resolution to the M-OGCMs. The various sizes of domain were embedded in the M-OGCMs and the cases were simulated to see the effect of domain size with the extra buffering distance to the results of the ORCMs. The diagnostic variables including temperature, salinity and vorticity of the nested domain are then compared with those of the M-OGCMs before filtering. Differences between them can address the errors associating with the sizes of the domain, which are not attributed unambiguously to models errors or observational errors. The results showed that domain size significantly impacts on the results of ORCMs. As the domain size of the ORCM becomes lager, the distance of the extra space between the area of interest and the updated LBCs increases. So, the results of ORCMs perform more highly correlated with the M-OGCM. But, there are a certain optimal sizes of the OGCMs, which could be larger than nested ORCMs' domain size from 2 to 10 times, depending on the computational costs. Key words: domain size, error, ocean regional circulation model, Big-Brother Experiment. Acknowledgement: This research was supported by grants from the Korean Ministry of Oceans and Fisheries entitled "Development of integrated estuarine management system" and a National Research Foundation of Korea (NRF) Grant (No. 2015R1A5A 7037372) funded by MSIP of Korea. The authors thank the Integrated Research Institute of Construction and Environmental Engineering of Seoul National University for administrative support.

Alterations in comprehensive geriatric assessment decrease survival of elderly patients with cancer.

PubMed

Frasca, M; Soubeyran, P; Bellera, C; Rainfray, M; Leffondre, K; Mathoulin-Pélissier, S

2018-02-01

A comprehensive geriatric assessment (CGA) evaluating several domains of health is recommended for elderly patients with cancer. Effects of altered domains on the risk of death in this population need to be clarified. The aim of this study was to estimate the independent association of each CGA domain to overall survival (OS). Patients included in the ONCODAGE cohort completed a CGA at baseline. Cox models (one per domain) estimated the hazard ratio (HR) of death for each CGA domain. Directed Acyclic Graphs (DAGs) selected specific sets of adjustment factors for each model. The analysis included 1264 patients (mean age: 78 years, women: 70%). Median follow-up was 5.2 years, and 446 patients died. Each altered domain had a detrimental effect on survival, sometimes dependent on gender, age, education or time from inclusion. Nutritional status had a time-varying effect, with higher mortality rates if altered only within the first 3 years of follow-up. In case of altered mobility, the risk of death was higher only for the youngest patients and, in case of altered autonomy, only for the youngest women. An altered neurological state led to higher mortality rates; this effect increased with the level of education. Patients with altered psychological status or more than four comorbidities at baseline had also higher mortality rates. Patients with an altered CGA domain have a higher risk of death than those without any alteration. The effect of some alterations is different in some subgroups or at a given time of the treatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

MOCASSIN-prot: a multi-objective clustering approach for protein similarity networks.

PubMed

Keel, Brittney N; Deng, Bo; Moriyama, Etsuko N

2018-04-15

Proteins often include multiple conserved domains. Various evolutionary events including duplication and loss of domains, domain shuffling, as well as sequence divergence contribute to generating complexities in protein structures, and consequently, in their functions. The evolutionary history of proteins is hence best modeled through networks that incorporate information both from the sequence divergence and the domain content. Here, a game-theoretic approach proposed for protein network construction is adapted into the framework of multi-objective optimization, and extended to incorporate clustering refinement procedure. The new method, MOCASSIN-prot, was applied to cluster multi-domain proteins from ten genomes. The performance of MOCASSIN-prot was compared against two protein clustering methods, Markov clustering (TRIBE-MCL) and spectral clustering (SCPS). We showed that compared to these two methods, MOCASSIN-prot, which uses both domain composition and quantitative sequence similarity information, generates fewer false positives. It achieves more functionally coherent protein clusters and better differentiates protein families. MOCASSIN-prot, implemented in Perl and Matlab, is freely available at http://bioinfolab.unl.edu/emlab/MOCASSINprot. emoriyama2@unl.edu. Supplementary data are available at Bioinformatics online.

Rasch analysis of the UK Functional Assessment Measure in patients with complex disability after stroke.

PubMed

Medvedev, Oleg N; Turner-Stokes, Lynne; Ashford, Stephen; Siegert, Richard J

2018-02-28

To determine whether the UK Functional Assessment Measure (UK FIM+FAM) fits the Rasch model in stroke patients with complex disability and, if so, to derive a conversion table of Rasch-transformed interval level scores. The sample included a UK multicentre cohort of 1,318 patients admitted for specialist rehabilitation following a stroke. Rasch analysis was conducted for the 30-item scale including 3 domains of items measuring physical, communication and psychosocial functions. The fit of items to the Rasch model was examined using 3 different analytical approaches referred to as "pathways". The best fit was achieved in the pathway where responses from motor, communication and psychosocial domains were summarized into 3 super-items and where some items were split because of differential item functioning (DIF) relative to left and right hemisphere location (χ2 (10) = 14.48, p = 0.15). Re-scoring of items showing disordered thresholds did not significantly improve the overall model fit. The UK FIM+FAM with domain super-items satisfies expectations of the unidimensional Rasch model without the need for re-scoring. A conversion table was produced to convert the total scale scores into interval-level data based on person estimates of the Rasch model. The clinical benefits of interval-transformed scores require further evaluation.

The basic tilted helix bundle domain of the prolyl isomerase FKBP25 is a novel double-stranded RNA binding module

PubMed Central

Dilworth, David; Bonnafous, Pierre; Edoo, Amiirah Bibi; Bourbigot, Sarah; Pesek-Jardim, Francy; Gudavicius, Geoff; Serpa, Jason J.; Petrotchenko, Evgeniy V.; Borchers, Christoph H.

2017-01-01

Abstract Prolyl isomerases are defined by a catalytic domain that facilitates the cis–trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors. An independent mobility of the BTHB and FKBP catalytic domains supports a model by which the N-terminus of FKBP25 is anchored to regions of dsRNA, whereas the FKBP domain is free to interact with neighboring proteins. Apart from the identification of the BTHB as a new dsRNA-binding module, this domain adds to the growing list of auxiliary functions used by prolyl isomerases to define their primary cellular targets. PMID:29036638

Recombinant Domain V of Human Perlecan Is a Bioactive Vascular Proteoglycan.

PubMed

Rnjak-Kovacina, Jelena; Tang, Fengying; Lin, Xiaoting; Whitelock, John M; Lord, Megan S

2017-12-01

The C-terminal domain V of the extracellular matrix proteoglycan perlecan plays unique and often divergent roles in a number of biological processes, including angiogenesis, vascular cell interactions, wound healing, and autophagy. Recombinant forms of domain V have been proposed as therapeutic agents for the treatment of cancer, stroke, and the development of cardiovascular devices and bioartificial tissues. However, the effect of domain V appears to be related to the differences in domain V structure and function observed in different expression systems and environments and exactly how this occurs is not well understood. In this study, the sequence from amino acid 3626 to 4391 of the perlecan protein core, which includes domain V, is expressed in HEK-293 cells and purified as a secreted product from conditioned media. This recombinant domain V (rDV) is expressed as a proteoglycan decorated with heparan sulfate and chondroitin sulfate chains and supports endothelial cell interactions to the same extent as full-length perlecan. This expression system serves as an important model of recombinant proteoglycan expression, as well as a source of biologically active rDV for therapeutic applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Learning and serial effects on verbal memory in mild cognitive impairment.

PubMed

Campos-Magdaleno, María; Díaz-Bóveda, Rosalía; Juncos-Rabadán, Onésimo; Facal, David; Pereiro, Arturo X

2016-01-01

The objective of this study was to examine different patterns of learning and episodic memory in 3 mild cognitive impairment (MCI) groups and a control group by administering the California Verbal Learning Test (CVLT) and using serial position effect as a principal variable. The study sample included 3 groups of patients with MCI (n = 90) divided into single-domain amnestic, multiple-domain amnestic, and multiple-domain nonamnestic MCI and a group of healthy controls (n = 60). We compared the performance of each group on several CVLT measures used in previous research, and we included a new measure that provides specific information about the serial effect. Data showed a similar pattern of learning and memory impairment in both amnestic MCI groups (i.e., no differences between the multiple-domain and single-domain subtypes); the recency effect was significantly higher in both amnestic MCI groups than in all other groups, and the primacy effect was only lower in the multiple-domain amnestic MCI subtype. Verbal learning and memory profiles of patients with amnestic MCI were very similar, independent of the presence of deficits in cognitive domains other than episodic memory. Results are discussed in light of the unitary-store model of memory.

Along-strike complex geometry of subduction zones - an experimental approach

NASA Astrophysics Data System (ADS)

Midtkandal, I.; Gabrielsen, R. H.; Brun, J.-P.; Huismans, R.

2012-04-01

Recent knowledge of the great geometric and dynamic complexity insubduction zones, combined with new capacity for analogue mechanical and numerical modeling has sparked a number of studies on subduction processes. Not unexpectedly, such models reveal a complex relation between physical conditions during subduction initiation, strength profile of the subducting plate, the thermo-dynamic conditions and the subduction zones geometries. One rare geometrical complexity of subduction that remains particularly controversial, is the potential for polarity shift in subduction systems. The present experiments were therefore performed to explore the influence of the architecture, strength and strain velocity on complexities in subduction zones, focusing on along-strike variation of the collision zone. Of particular concern were the consequences for the geometry and kinematics of the transition zones between segments of contrasting subduction direction. Although the model design to some extent was inspired by the configuration along the Iberian - Eurasian suture zone, the results are also of significance for other orogens with complex along-strike geometries. The experiments were set up to explore the initial state of subduction only, and were accordingly terminated before slab subduction occurred. The model wasbuilt from layers of silicone putty and sand, tailored to simulate the assumed lithospheric geometries and strength-viscosity profiles along the plate boundary zone prior to contraction, and comprises two 'continental' plates separated by a thinner 'oceanic' plate that represents the narrow seaway. The experiment floats on a substrate of sodiumpolytungstate, representing mantle. 24 experimental runs were performed, varying the thickness (and thus strength) of the upper mantle lithosphere, as well as the strain rate. Keeping all other parameters identical for each experiment, the models were shortened by a computer-controlled jackscrew while time-lapse images were recorded. After completion, the models were saturated with water and frozen, allowing for sectioning and profile inspection. The experiments were invariably characterized by different along-strike patterns of deformation, so that three distinct structural domains could be distinguished in all cases. Model descriptions are subdivided accordingly, including domain CC, simulating a continent-continent collision, domain OC, characterized by continent-ocean-continent collision and domain T, representing the transition zone between domain CC and domain OC. The latter zone varied in width and complexity depending on the contrast in structural style developed in the two other domains; in cases where domain OC developed very differently from domain CC, the transition zone was generally wider and more complex. A typical experiment displayed the following features and strain history: In domain CC two principal thrust sheets are displayed, which obviously developed in an in-sequence foreland-directed fashion. The lowermost detachment nucleated at the base of the High Strength Lithospheric Mantle analogue, whereas the uppermost thrust was anchored within the "lower crust". The two thrusts operated in concert, the surface trace of the deepest dominating in the west, and the shallowest in the east. The kinematic development of domain CC could be subdivided into four stages, including initiation of a symmetrical anticline with a minute amplitude and situated directly above the velocity discontinuity defined by the plate contact (stage 1), contemporaneous development of the two thrusts (stage 2) and an associated asymmetrical anticline (stage 3) with a central collapse graben in the latest phase (stage 4). It is noted that the segment CC as seen in a clear majority of the experiments followed this pattern of development. In contrast, the configuration of domain OC displayed greater variation, and included north and south-directed subduction, folding, growth of pop-up-structures and triangle zones. In the "ocean crust" domain, stage 1 was characterized by the growth of a fault-propagation anticline with an E-W-oriented fold axis, ending with the surfacing of a north-vergent thrust. In stage 2, the contraction was concentrated to the south in the oceanic domain, again ending with the surfacing of a thrust, here with top-south transport. By continued movement (stage 3), the thrust fault propagated towards the east, crossing into the "continental" domain and linking with the fault systems of the segment CC. The structure of domain T is dominated by the interference of faults propagating westwards from the domain CC and eastwards from the domain OC, respectively. The zone of overlap in the experiment was significant, and its central part had the geometry of a double "crocodile structure" (sensuMeissner 1989), separating the two areas of northerly and southerly subduction. Hence, its development is less easily subdivided into stages. Reference: Meissner,R., 1989: Rupture, creep lamellae and crocodiles: happenings in the continental crust. Terra Nova, 1, 17-28.

Effects of clinically relevant MPL mutations in the transmembrane domain revealed at the atomic level through computational modeling.

PubMed

Lee, Tai-Sung; Kantarjian, Hagop; Ma, Wanlong; Yeh, Chen-Hsiung; Giles, Francis; Albitar, Maher

2011-01-01

Mutations in the thrombopoietin receptor (MPL) may activate relevant pathways and lead to chronic myeloproliferative neoplasms (MPNs). The mechanisms of MPL activation remain elusive because of a lack of experimental structures. Modern computational biology techniques were utilized to explore the mechanisms of MPL protein activation due to various mutations. Transmembrane (TM) domain predictions, homology modeling, ab initio protein structure prediction, and molecular dynamics (MD) simulations were used to build structural dynamic models of wild-type and four clinically observed mutants of MPL. The simulation results suggest that S505 and W515 are important in keeping the TM domain in its correct position within the membrane. Mutations at either of these two positions cause movement of the TM domain, altering the conformation of the nearby intracellular domain in unexpected ways, and may cause the unwanted constitutive activation of MPL's kinase partner, JAK2. Our findings represent the first full-scale molecular dynamics simulations of the wild-type and clinically observed mutants of the MPL protein, a critical element of the MPL-JAK2-STAT signaling pathway. In contrast to usual explanations for the activation mechanism that are based on the relative translational movement between rigid domains of MPL, our results suggest that mutations within the TM region could result in conformational changes including tilt and rotation (azimuthal) angles along the membrane axis. Such changes may significantly alter the conformation of the adjacent and intrinsically flexible intracellular domain. Hence, caution should be exercised when interpreting experimental evidence based on rigid models of cytokine receptors or similar systems.

The Regional Climate Model Evaluation System: A Systematic Evaluation Of CORDEX Simulations Using Obs4MIPs

NASA Astrophysics Data System (ADS)

Goodman, A.; Lee, H.; Waliser, D. E.; Guttowski, W.

2017-12-01

Observation-based evaluations of global climate models (GCMs) have been a key element for identifying systematic model biases that can be targeted for model improvements and for establishing uncertainty associated with projections of global climate change. However, GCMs are limited in their ability to represent physical phenomena which occur on smaller, regional scales, including many types of extreme weather events. In order to help facilitate projections in changes of such phenomena, simulations from regional climate models (RCMs) for 14 different domains around the world are being provided by the Coordinated Regional Climate Downscaling Experiment (CORDEX; www.cordex.org). However, although CORDEX specifies standard simulation and archiving protocols, these simulations are conducted independently by individual research and modeling groups representing each of these domains often with different output requirements and data archiving and exchange capabilities. Thus, with respect to similar efforts using GCMs (e.g., the Coupled Model Intercomparison Project, CMIP), it is more difficult to achieve a standardized, systematic evaluation of the RCMs for each domain and across all the CORDEX domains. Using the Regional Climate Model Evaluation System (RCMES; rcmes.jpl.nasa.gov) developed at JPL, we are developing easy to use templates for performing systematic evaluations of CORDEX simulations. Results from the application of a number of evaluation metrics (e.g., biases, centered RMS, and pattern correlations) will be shown for a variety of physical quantities and CORDEX domains. These evaluations are performed using products from obs4MIPs, an activity initiated by DOE and NASA, and now shepherded by the World Climate Research Program's Data Advisory Council.

The use of ZFP lossy floating point data compression in tornado-resolving thunderstorm simulations

NASA Astrophysics Data System (ADS)

Orf, L.

2017-12-01

In the field of atmospheric science, numerical models are used to produce forecasts of weather and climate and serve as virtual laboratories for scientists studying atmospheric phenomena. In both operational and research arenas, atmospheric simulations exploiting modern supercomputing hardware can produce a tremendous amount of data. During model execution, the transfer of floating point data from memory to the file system is often a significant bottleneck where I/O can dominate wallclock time. One way to reduce the I/O footprint is to compress the floating point data, which reduces amount of data saved to the file system. In this presentation we introduce LOFS, a file system developed specifically for use in three-dimensional numerical weather models that are run on massively parallel supercomputers. LOFS utilizes the core (in-memory buffered) HDF5 driver and includes compression options including ZFP, a lossy floating point data compression algorithm. ZFP offers several mechanisms for specifying the amount of lossy compression to be applied to floating point data, including the ability to specify the maximum absolute error allowed in each compressed 3D array. We explore different maximum error tolerances in a tornado-resolving supercell thunderstorm simulation for model variables including cloud and precipitation, temperature, wind velocity and vorticity magnitude. We find that average compression ratios exceeding 20:1 in scientifically interesting regions of the simulation domain produce visually identical results to uncompressed data in visualizations and plots. Since LOFS splits the model domain across many files, compression ratios for a given error tolerance can be compared across different locations within the model domain. We find that regions of high spatial variability (which tend to be where scientifically interesting things are occurring) show the lowest compression ratios, whereas regions of the domain with little spatial variability compress extremely well. We observe that the overhead for compressing data with ZFP is low, and that compressing data in memory reduces the amount of memory overhead needed to store the virtual files before they are flushed to disk.

Ribosomal small subunit domains radiate from a central core

NASA Astrophysics Data System (ADS)

Gulen, Burak; Petrov, Anton S.; Okafor, C. Denise; Vander Wood, Drew; O'Neill, Eric B.; Hud, Nicholas V.; Williams, Loren Dean

2016-02-01

The domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2‧OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.

Modeling NDT piezoelectric ultrasonic transmitters.

PubMed

San Emeterio, J L; Ramos, A; Sanz, P T; Ruíz, A; Azbaid, A

2004-04-01

Ultrasonic NDT applications are frequently based on the spike excitation of piezoelectric transducers by means of efficient pulsers which usually include a power switching device (e.g. SCR or MOS-FET) and some rectifier components. In this paper we present an approximate frequency domain electro-acoustic model for pulsed piezoelectric ultrasonic transmitters which, by integrating partial models of the different stages (driving electronics, tuning/matching networks and broadband piezoelectric transducer), allows the computation of the emission transfer function and output force temporal waveform. An approximate frequency domain model is used for the evaluation of the electrical driving pulse from the spike generator. Tuning circuits, interconnecting cable and mechanical impedance matching layers are modeled by means of transmission lines and the classical quadripole approach. The KLM model is used for the piezoelectric transducer. In addition, a PSPICE scheme is used for an alternative simulation of the broadband driving spike, including the accurate evaluation of non-linear driving effects. Several examples illustrate the capabilities of the specifically developed software.

Model of a ternary complex between activated factor VII, tissue factor and factor IX.

PubMed

Chen, Shu-wen W; Pellequer, Jean-Luc; Schved, Jean-François; Giansily-Blaizot, Muriel

2002-07-01

Upon binding to tissue factor, FVIIa triggers coagulation by activating vitamin K-dependent zymogens, factor IX (FIX) and factor X (FX). To understand recognition mechanisms in the initiation step of the coagulation cascade, we present a three-dimensional model of the ternary complex between FVIIa:TF:FIX. This model was built using a full-space search algorithm in combination with computational graphics. With the known crystallographic complex FVIIa:TF kept fixed, the FIX docking was performed first with FIX Gla-EGF1 domains, followed by the FIX protease/EGF2 domains. Because the FIXa crystal structure lacks electron density for the Gla domain, we constructed a chimeric FIX molecule that contains the Gla-EGF1 domains of FVIIa and the EGF2-protease domains of FIXa. The FVIIa:TF:FIX complex has been extensively challenged against experimental data including site-directed mutagenesis, inhibitory peptide data, haemophilia B database mutations, inhibitor antibodies and a novel exosite binding inhibitor peptide. This FVIIa:TF:FIX complex provides a powerful tool to study the regulation of FVIIa production and presents new avenues for developing therapeutic inhibitory compounds of FVIIa:TF:substrate complex.

A phenological mid-domain effect in flowering diversity.

PubMed

Morales, Manuel A; Dodge, Gary J; Inouye, David W

2005-01-01

In this paper, we test the mid-domain hypothesis as an explanation for observed patterns of flowering diversity in two sub-alpine communities of insect-pollinated plants. Observed species richness patterns showed an early-season increase in richness, a mid-season peak, and a late-season decrease. We show that a "mid-domain" null model can qualitatively match this pattern of flowering species richness, with R(2) values typically greater than 60%. We find significant or marginally significant departures from expected patterns of diversity for only 3 out of 12 year-site combinations. On the other hand, we do find a consistent pattern of departure when comparing observed versus null-model predicted flowering diversity averaged across years. Our results therefore support the hypothesis that ecological factors shape patterns of flowering phenology, but that the strength or nature of these environmental forcings may differ between years or the two habitats we studied, or may depend on species-specific characteristics of these plant communities. We conclude that mid-domain null models provide an important baseline from which to test departure of expected patterns of flowering diversity across temporal domains. Geometric constraints should be included first in the list of factors that drive seasonal patterns of flowering diversity.

Roles and responsibilities of the nursing scholar.

PubMed

Conard, Patricia L; Pape, Tess Theresa

2014-01-01

Scholarship is an important facet of the nursing profession. There are many components, virtues, and roles and responsibilities of a nursing scholar practicing in today's ever-changing health care environment. Scholarship was redefined by Boyer to include scholarly activities in addition to research. Boyer's Model of Scholarship includes four interrelated and overlapping domains of discovery, integration, application, and teaching. Each domain is explained with examples for the pediatric nurse scholar, which includes roles in academia as well as in the practice setting. Pediatric nurses are key to scholarship in nursing because they work to improve the care of children.

Challenges associated with the prediction of tropical storms in the Bay of Bengal when using the WRF model

NASA Astrophysics Data System (ADS)

Machineni, N.; Veldore, V.; Mesquita, M. D. S.

2016-12-01

Accuracy in predicting tropical cyclones over low lying coastal regions is pivotal for understanding storm tracks and their subsequent impacts. The present study highlights the challenges in predicting the Bay of Bengal (BOB) cyclone "AILA" (during 23rd to 25th May 2009) using the Weather Research and Forecast model, Advanced research core module (WRF-ARW). The model configuration uses a two-way interactive nested domain with 10 km resolution over BOB. Its initial and boundary conditions are driven from the NCEP FNL operational global analysis data at every 6 hours. A total of 74 sensitivity experiments were conducted to test the following factors and levels: a) parametrization schemes: two microphysics and two cumulus physics schemes used to select appropriate combination over study region, b) model domain:including/excluding Himalayas, c) vertical resolution: eight various increasing/decreasing vertical levels have been carried out to evaluate the storm track dependencies on these factors, d) domain size: and increasing (decreasing) the grid points of model domain in east-west direction shows that approximately 50-100 km track difference for every two points. Our results show that, the experiments including the Himalayas provide a better representation of cyclone track and speed. In order to reduce the computational time required to do such tremendous amount of experiment, we hypothesize to use statistical tools of experimental design which can involve all the factors that determine the cyclone tracks. A proper experimental design might provide unbiased results and also we might need less number of experiments.

Challenges associated with the prediction of tropical storms in the Bay of Bengal when using the WRF model

NASA Astrophysics Data System (ADS)

Machineni, Nehru; Veldore, Vidyunmala; Mesquita, Michel d. S.

2017-04-01

Accuracy in predicting tropical cyclones over low lying coastal regions is pivotal for understanding storm tracks and their subsequent impacts. The present study highlights the challenges in predicting the Bay of Bengal (BOB) cyclone "AILA" (during 23rd to 25th May 2009) using the Weather Research and Forecast model, Advanced research core module (WRF-ARW). The model configuration uses a two-way interactive nested domain with 10 km resolution over BOB. Its initial and boundary conditions are driven from the NCEP FNL operational global analysis data at every 6 hours. A total of 74 sensitivity experiments were conducted to test the following factors and levels: a) parametrization schemes: two microphysics and two cumulus physics schemes used to select appropriate combination over study region, b) model domain:including/excluding Himalayas, c) vertical resolution: eight various increasing/decreasing vertical levels have been carried out to evaluate the storm track dependencies on these factors, d) domain size: and increasing (decreasing) the grid points of model domain in east-west direction shows that approximately 50-100 km track difference for every two points. Our results show that, the experiments including the Himalayas provide a better representation of cyclone track and speed. In order to reduce the computational time required to do such tremendous amount of experiment, we hypothesize to use statistical tools of experimental design which can involve all the factors that determine the cyclone tracks. A proper experimental design might provide unbiased results and also we might need less number of experiments.

Evaluation of different time domain peak models using extreme learning machine-based peak detection for EEG signal.

PubMed

Adam, Asrul; Ibrahim, Zuwairie; Mokhtar, Norrima; Shapiai, Mohd Ibrahim; Cumming, Paul; Mubin, Marizan

2016-01-01

Various peak models have been introduced to detect and analyze peaks in the time domain analysis of electroencephalogram (EEG) signals. In general, peak model in the time domain analysis consists of a set of signal parameters, such as amplitude, width, and slope. Models including those proposed by Dumpala, Acir, Liu, and Dingle are routinely used to detect peaks in EEG signals acquired in clinical studies of epilepsy or eye blink. The optimal peak model is the most reliable peak detection performance in a particular application. A fair measure of performance of different models requires a common and unbiased platform. In this study, we evaluate the performance of the four different peak models using the extreme learning machine (ELM)-based peak detection algorithm. We found that the Dingle model gave the best performance, with 72 % accuracy in the analysis of real EEG data. Statistical analysis conferred that the Dingle model afforded significantly better mean testing accuracy than did the Acir and Liu models, which were in the range 37-52 %. Meanwhile, the Dingle model has no significant difference compared to Dumpala model.

Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

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

Yang, Xiaojing; Kuk, Jane; Moffat, Keith

2008-11-12

Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 {angstrom} resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an 'arm' structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common andmore » may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity.« less

Deep Correlated Holistic Metric Learning for Sketch-Based 3D Shape Retrieval.

PubMed

Dai, Guoxian; Xie, Jin; Fang, Yi

2018-07-01

How to effectively retrieve desired 3D models with simple queries is a long-standing problem in computer vision community. The model-based approach is quite straightforward but nontrivial, since people could not always have the desired 3D query model available by side. Recently, large amounts of wide-screen electronic devices are prevail in our daily lives, which makes the sketch-based 3D shape retrieval a promising candidate due to its simpleness and efficiency. The main challenge of sketch-based approach is the huge modality gap between sketch and 3D shape. In this paper, we proposed a novel deep correlated holistic metric learning (DCHML) method to mitigate the discrepancy between sketch and 3D shape domains. The proposed DCHML trains two distinct deep neural networks (one for each domain) jointly, which learns two deep nonlinear transformations to map features from both domains into a new feature space. The proposed loss, including discriminative loss and correlation loss, aims to increase the discrimination of features within each domain as well as the correlation between different domains. In the new feature space, the discriminative loss minimizes the intra-class distance of the deep transformed features and maximizes the inter-class distance of the deep transformed features to a large margin within each domain, while the correlation loss focused on mitigating the distribution discrepancy across different domains. Different from existing deep metric learning methods only with loss at the output layer, our proposed DCHML is trained with loss at both hidden layer and output layer to further improve the performance by encouraging features in the hidden layer also with desired properties. Our proposed method is evaluated on three benchmarks, including 3D Shape Retrieval Contest 2013, 2014, and 2016 benchmarks, and the experimental results demonstrate the superiority of our proposed method over the state-of-the-art methods.

Large scale healthcare data integration and analysis using the semantic web.

PubMed

Timm, John; Renly, Sondra; Farkash, Ariel

2011-01-01

Healthcare data interoperability can only be achieved when the semantics of the content is well defined and consistently implemented across heterogeneous data sources. Achieving these objectives of interoperability requires the collaboration of experts from several domains. This paper describes tooling that integrates Semantic Web technologies with common tools to facilitate cross-domain collaborative development for the purposes of data interoperability. Our approach is divided into stages of data harmonization and representation, model transformation, and instance generation. We applied our approach on Hypergenes, an EU funded project, where we use our method to the Essential Hypertension disease model using a CDA template. Our domain expert partners include clinical providers, clinical domain researchers, healthcare information technology experts, and a variety of clinical data consumers. We show that bringing Semantic Web technologies into the healthcare interoperability toolkit increases opportunities for beneficial collaboration thus improving patient care and clinical research outcomes.

Hindcasting of Storm Surges, Currents, and Waves at Lower Delaware Bay during Hurricane Isabel

NASA Astrophysics Data System (ADS)

Salehi, M.

2017-12-01

Hurricanes are a major threat to coastal communities and infrastructures including nuclear power plants located in low-lying coastal zones. In response, their sensitive elements should be protected by smart design to withstand against drastic impact of such natural phenomena. Accurate and reliable estimate of hurricane attributes is the first step to that effort. Numerical models have extensively grown over the past few years and are effective tools in modeling large scale natural events such as hurricane. The impact of low probability hurricanes on the lower Delaware Bay is investigated using dynamically coupled meteorological, hydrodynamic, and wave components of Delft3D software. Efforts are made to significantly reduce the computational overburden of performing such analysis for the industry, yet keeping the same level of accuracy at the area of study (AOS). The model is comprised of overall and nested domains. The overall model domain includes portion of Atlantic Ocean, Delaware, and Chesapeake bays. The nested model domain includes Delaware Bay, its floodplain, and portion of the continental shelf. This study is portion of a larger modeling effort to study the impact of low probability hurricanes on sensitive infrastructures located at the coastal zones prone to hurricane activity. The AOS is located on the east bank of Delaware Bay almost 16 miles upstream of its mouth. Model generated wind speed, significant wave height, water surface elevation, and current are calibrated for hurricane Isabel (2003). The model calibration results agreed reasonably well with field observations. Furthermore, sensitivity of surge and wave responses to various hurricane parameters was tested. In line with findings from other researchers, accuracy of wind field played a major role in hindcasting the hurricane attributes.

Advantages and limitations of the Five Domains model for assessing welfare impacts associated with vertebrate pest control.

PubMed

Beausoleil, N J; Mellor, D J

2015-01-01

Many pest control activities have the potential to impact negatively on the welfare of animals, and animal welfare is an important consideration in the development, implementation and evaluation of ethically defensible vertebrate pest control. Thus, reliable and accurate methods for assessing welfare impacts are required. The Five Domains model provides a systematic method for identifying potential or actual welfare impacts associated with an event or situation in four physical or functional domains (nutrition, environment, health or functional status, behaviour) and one mental domain (overall mental or affective state). Here we evaluate the advantages and limitations of the Five Domains model for this purpose and illustrate them using specific examples from a recent assessment of the welfare impacts of poisons used to lethally control possums in New Zealand. The model has a number of advantages which include the following: the systematic identification of a wide range of impacts associated with a variety of control tools; the production of relative rankings of tools in terms of their welfare impacts; the easy incorporation of new information into assessments; and the highlighting of additional information needed. For example, a recent analysis of sodium fluoroacetate (1080) poisoning in possums revealed the need for more information on the period from the onset of clinical signs to the point at which consciousness is lost, as well as on the level of consciousness during or after the occurrence of muscle spasms and seizures. The model is also valuable because it clearly separates physical or functional and affective impacts, encourages more comprehensive consideration of negative affective experiences than has occurred in the past, and allows development and evaluation of targeted mitigation strategies. Caution must be used in interpreting and applying the outputs of the model, most importantly because relative rankings or grades are fundamentally qualitative in nature. Certain domains are more useful for evaluating impacts associated with slower/longer-acting tools than for faster-acting methods, and it may be easier to identify impacts in some domains than others. Overall, we conclude that the Five Domains model advances evaluation of the animal welfare impacts of vertebrate pest control methods, provided users are cognisant of its limitations.

Accelerating advances in continental domain hydrologic modeling

USGS Publications Warehouse

Archfield, Stacey A.; Clark, Martyn; Arheimer, Berit; Hay, Lauren E.; McMillan, Hilary; Kiang, Julie E.; Seibert, Jan; Hakala, Kirsti; Bock, Andrew R.; Wagener, Thorsten; Farmer, William H.; Andreassian, Vazken; Attinger, Sabine; Viglione, Alberto; Knight, Rodney; Markstrom, Steven; Over, Thomas M.

2015-01-01

In the past, hydrologic modeling of surface water resources has mainly focused on simulating the hydrologic cycle at local to regional catchment modeling domains. There now exists a level of maturity among the catchment, global water security, and land surface modeling communities such that these communities are converging toward continental domain hydrologic models. This commentary, written from a catchment hydrology community perspective, provides a review of progress in each community toward this achievement, identifies common challenges the communities face, and details immediate and specific areas in which these communities can mutually benefit one another from the convergence of their research perspectives. Those include: (1) creating new incentives and infrastructure to report and share model inputs, outputs, and parameters in data services and open access, machine-independent formats for model replication or reanalysis; (2) ensuring that hydrologic models have: sufficient complexity to represent the dominant physical processes and adequate representation of anthropogenic impacts on the terrestrial water cycle, a process-based approach to model parameter estimation, and appropriate parameterizations to represent large-scale fluxes and scaling behavior; (3) maintaining a balance between model complexity and data availability as well as uncertainties; and (4) quantifying and communicating significant advancements toward these modeling goals.

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

PubMed Central

Mohammadiarani, Hossein; Vashisth, Harish

2016-01-01

The receptor tyrosine kinase superfamily comprises many cell-surface receptors including the insulin receptor (IR) and type 1 insulin-like growth factor receptor (IGF1R) that are constitutively homodimeric transmembrane glycoproteins. Therefore, these receptors require ligand-triggered domain rearrangements rather than receptor dimerization for activation. Specifically, binding of peptide ligands to receptor ectodomains transduces signals across the transmembrane domains for trans-autophosphorylation in cytoplasmic kinase domains. The molecular details of these processes are poorly understood in part due to the absence of structures of full-length receptors. Using MD simulations and enhanced conformational sampling algorithms, we present all-atom structural models of peptides containing 51 residues from the transmembrane and juxtamembrane regions of IR and IGF1R. In our models, the transmembrane regions of both receptors adopt helical conformations with kinks at Pro961 (IR) and Pro941 (IGF1R), but the C-terminal residues corresponding to the juxtamembrane region of each receptor adopt unfolded and flexible conformations in IR as opposed to a helix in IGF1R. We also observe that the N-terminal residues in IR form a kinked-helix sitting at the membrane–solvent interface, while homologous residues in IGF1R are unfolded and flexible. These conformational differences result in a larger tilt-angle of the membrane-embedded helix in IGF1R in comparison to IR to compensate for interactions with water molecules at the membrane–solvent interfaces. Our metastable/stable states for the transmembrane domain of IR, observed in a lipid bilayer, are consistent with a known NMR structure of this domain determined in detergent micelles, and similar states in IGF1R are consistent with a previously reported model of the dimerized transmembrane domains of IGF1R. Our all-atom structural models suggest potentially unique structural organization of kinase domains in each receptor. PMID:27379020

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates*S⃞

PubMed Central

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej; McAuliffe, Jon D.; Turner, Kevin R.; Di Lullo, Gloria A.; Chen, Steven; Antipova, Olga; Perumal, Shiamalee; Ala-Kokko, Leena; Forlino, Antonella; Cabral, Wayne A.; Barnes, Aileen M.; Marini, Joan C.; Antonio, James D. San

2008-01-01

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The “cell interaction domain” is proposed to regulate dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The “matrix interaction domain” may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging. PMID:18487200

Psychotic experiences and disability: Findings from the Collaborative Psychiatric Epidemiology Surveys.

PubMed

Oh, Hans; Koyanagi, Ai; Kelleher, Ian; DeVylder, Jordan

2018-03-01

Psychotic experiences are associated with a number of poor clinical outcomes, including multimorbid psychopathology, suicidal behavior, and poor treatment response. We wished to investigate the relationship between psychotic experiences and disability, including the following domains: cognition, mobility, self-care, social interaction, role functioning, and days out of role. We used three nationally representative and racially/ethnically diverse samples of the general US adult population: the National Comorbidity Survey Replication (NCS-R), the National Latino and Asian American Survey (NLAAS), and the National Survey of American Life (NSAL). Multi-variable logistic regression analyses were used to assess the associations between lifetime psychotic experiences (visual and auditory hallucinatory experiences and delusional ideation; WHO Composite International Diagnostic Interview psychosis screen) and 30-day impairments in functioning across disability domains (using the WHO Disability Assessment Schedule II). In all three samples, models were adjusted for socio-demographics and co-occurring psychiatric disorders. In the NCS-R, models were also adjusted for chronic health conditions. Across all three studies, our adjusted models showed that people with disability had anywhere from about 1.5 to over 3 times the odds of reporting lifetime psychotic experiences, depending on the domain. This was true for each disability domain, except self-care in the NLAAS and in the NSAL. Psychotic experiences are markers of risk for disability across a wide range of domains. This may explain the elevated rates of service utilization among individuals who report psychotic experiences and supports the need to assess for and respond to psychotic experiences even in the absence of psychotic disorder. Copyright © 2017 Elsevier B.V. All rights reserved.

A Multidisciplinary Model for Development of Intelligent Computer-Assisted Instruction.

ERIC Educational Resources Information Center

Park, Ok-choon; Seidel, Robert J.

1989-01-01

Proposes a schematic multidisciplinary model to help developers of intelligent computer-assisted instruction (ICAI) identify the types of required expertise and integrate them into a system. Highlights include domain types and expertise; knowledge acquisition; task analysis; knowledge representation; student modeling; diagnosis of learning needs;…

Assessment of existing Sierra/Fuego capabilities related to grid-to-rod-fretting (GTRF).

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

Turner, Daniel Zack; Rodriguez, Salvador B.

2011-06-01

The following report presents an assessment of existing capabilities in Sierra/Fuego applied to modeling several aspects of grid-to-rod-fretting (GTRF) including: fluid dynamics, heat transfer, and fluid-structure interaction. We compare the results of a number of Fuego simulations with relevant sources in the literature to evaluate the accuracy, efficiency, and robustness of using Fuego to model the aforementioned aspects. Comparisons between flow domains that include the full fuel rod length vs. a subsection of the domain near the spacer show that tremendous efficiency gains can be obtained by truncating the domain without loss of accuracy. Thermal analysis reveals the extent tomore » which heat transfer from the fuel rods to the coolant is improved by the swirling flow created by the mixing vanes. Lastly, coupled fluid-structure interaction analysis shows that the vibrational modes of the fuel rods filter out high frequency turbulent pressure fluctuations. In general, these results allude to interesting phenomena for which further investigation could be quite fruitful.« less

Simultaneous prediction of binding free energy and specificity for PDZ domain-peptide interactions

NASA Astrophysics Data System (ADS)

Crivelli, Joseph J.; Lemmon, Gordon; Kaufmann, Kristian W.; Meiler, Jens

2013-12-01

Interactions between protein domains and linear peptides underlie many biological processes. Among these interactions, the recognition of C-terminal peptides by PDZ domains is one of the most ubiquitous. In this work, we present a mathematical model for PDZ domain-peptide interactions capable of predicting both affinity and specificity of binding based on X-ray crystal structures and comparative modeling with R osetta. We developed our mathematical model using a large phage display dataset describing binding specificity for a wild type PDZ domain and 91 single mutants, as well as binding affinity data for a wild type PDZ domain binding to 28 different peptides. Structural refinement was carried out through several R osetta protocols, the most accurate of which included flexible peptide docking and several iterations of side chain repacking and backbone minimization. Our findings emphasize the importance of backbone flexibility and the energetic contributions of side chain-side chain hydrogen bonds in accurately predicting interactions. We also determined that predicting PDZ domain-peptide interactions became increasingly challenging as the length of the peptide increased in the N-terminal direction. In the training dataset, predicted binding energies correlated with those derived through calorimetry and specificity switches introduced through single mutations at interface positions were recapitulated. In independent tests, our best performing protocol was capable of predicting dissociation constants well within one order of magnitude of the experimental values and specificity profiles at the level of accuracy of previous studies. To our knowledge, this approach represents the first integrated protocol for predicting both affinity and specificity for PDZ domain-peptide interactions.

The Swiss Transplant Cohort Study's framework for assessing lifelong psychosocial factors in solid-organ transplants.

PubMed

De Geest, Sabina; Burkhalter, Hanna; Berben, Lut; Bogert, Laura Jane; Denhaerynck, Kris; Glass, Tracy R; Goetzmann, Lutz; Kirsch, Monika; Kiss, Alexander; Koller, Michael T; Piot-Ziegler, Chantal; Schmidt-Trucksäss, Arno

2013-09-01

Understanding outcomes after transplant requires a biopsychosocial model that includes biomedical and psychosocial factors. The latter, to date, are assessed only in a limited way as part of transplant registries or cohort studies. The Swiss Transplant Cohort Study (STCS) is a nationwide open cohort study (starting May 2008) to systematically and prospectively assess psychosocial factors. This article describes the framework underpinning STCS's psychosocial assessment. The STCS framework was adapted from the multidimensional conceptual perspective of Dew et al to describe transplant psychosocial domains and specific outcomes by adding a time perspective, a system perspective, and interaction among domains. We propose a multidimensional, multilevel biopsychosocial framework representing mutually influencing domains from before to after transplant, and exemplify each domain by factors included in STCS and their measurement. The transplant patient, centrally positioned, is described by clinical and sociodemographic characteristics (eg, socioeconomic status, educational, professional, and relationship status). The following psychosocial domains further describe the patient: (1) physical/functional (eg, perceived health status, sleep quality, daytime sleepiness), (2) psychological (eg, depression, stress), (3) behavioral (eg, medication adherence, smoking, drug use, physical activity, sun protection), (4) social (eg, work capacity/return to work), and (5) global quality of life. Factors associated with health care system level (eg, trust in transplant team) are also included in the model. The STCS's psychosocial framework provides a basis for studying the interplay of biomedical, sociodemographic, psychosocial, behavioral, and health care system factors in view of transplant outcomes and therefore has the potential to guide biopsychosocial transplant research.

A rational fraction polynomials model to study vertical dynamic wheel-rail interaction

NASA Astrophysics Data System (ADS)

Correa, N.; Vadillo, E. G.; Santamaria, J.; Gómez, J.

2012-04-01

This paper presents a model designed to study vertical interactions between wheel and rail when the wheel moves over a rail welding. The model focuses on the spatial domain, and is drawn up in a simple fashion from track receptances. The paper obtains the receptances from a full track model in the frequency domain already developed by the authors, which includes deformation of the rail section and propagation of bending, elongation and torsional waves along an infinite track. Transformation between domains was secured by applying a modified rational fraction polynomials method. This obtains a track model with very few degrees of freedom, and thus with minimum time consumption for integration, with a good match to the original model over a sufficiently broad range of frequencies. Wheel-rail interaction is modelled on a non-linear Hertzian spring, and consideration is given to parametric excitation caused by the wheel moving over a sleeper, since this is a moving wheel model and not a moving irregularity model. The model is used to study the dynamic loads and displacements emerging at the wheel-rail contact passing over a welding defect at different speeds.

Crystal structure of tandem type III fibronectin domains from Drosophila neuroglian at 2.0 A.

PubMed

Huber, A H; Wang, Y M; Bieber, A J; Bjorkman, P J

1994-04-01

We report the crystal structure of two adjacent fibronectin type III repeats from the Drosophila neural cell adhesion molecule neuroglian. Each domain consists of two antiparallel beta sheets and is folded topologically identically to single fibronectin type III domains from the extracellular matrix proteins tenascin and fibronectin. beta bulges and left-handed polyproline II helices disrupt the regular beta sheet structure of both neuroglian domains. The hydrophobic interdomain interface includes a metal-binding site, presumably involved in stabilizing the relative orientation between domains and predicted by sequence comparision to be present in the vertebrate homolog molecule L1. The neuroglian domains are related by a near perfect 2-fold screw axis along the longest molecular dimension. Using this relationship, a model for arrays of tandem fibronectin type III repeats in neuroglian and other molecules is proposed.

New optical and radio frequency angular tropospheric refraction models for deep space applications

NASA Technical Reports Server (NTRS)

Berman, A. L.; Rockwell, S. T.

1976-01-01

The development of angular tropospheric refraction models for optical and radio frequency usage is presented. The models are compact analytic functions, finite over the entire domain of elevation angle, and accurate over large ranges of pressure, temperature, and relative humidity. Additionally, FORTRAN subroutines for each of the models are included.

Evaluation properties of the French version of the OUT-PATSAT35 satisfaction with care questionnaire according to classical and item response theory analyses.

PubMed

Panouillères, M; Anota, A; Nguyen, T V; Brédart, A; Bosset, J F; Monnier, A; Mercier, M; Hardouin, J B

2014-09-01

The present study investigates the properties of the French version of the OUT-PATSAT35 questionnaire, which evaluates the outpatients' satisfaction with care in oncology using classical analysis (CTT) and item response theory (IRT). This cross-sectional multicenter study includes 692 patients who completed the questionnaire at the end of their ambulatory treatment. CTT analyses tested the main psychometric properties (convergent and divergent validity, and internal consistency). IRT analyses were conducted separately for each OUT-PATSAT35 domain (the doctors, the nurses or the radiation therapists and the services/organization) by models from the Rasch family. We examined the fit of the data to the model expectations and tested whether the model assumptions of unidimensionality, monotonicity and local independence were respected. A total of 605 (87.4%) respondents were analyzed with a mean age of 64 years (range 29-88). Internal consistency for all scales separately and for the three main domains was good (Cronbach's α 0.74-0.98). IRT analyses were performed with the partial credit model. No disordered thresholds of polytomous items were found. Each domain showed high reliability but fitted poorly to the Rasch models. Three items in particular, the item about "promptness" in the doctors' domain and the items about "accessibility" and "environment" in the services/organization domain, presented the highest default of fit. A correct fit of the Rasch model can be obtained by dropping these items. Most of the local dependence concerned items about "information provided" in each domain. A major deviation of unidimensionality was found in the nurses' domain. CTT showed good psychometric properties of the OUT-PATSAT35. However, the Rasch analysis revealed some misfitting and redundant items. Taking the above problems into consideration, it could be interesting to refine the questionnaire in a future study.

The sensitivity of precipitation simulations to the soot aerosol presence

NASA Astrophysics Data System (ADS)

Palamarchuk, Iuliia; Ivanov, Sergiy; Mahura, Alexander; Ruban, Igor

2016-04-01

The role of aerosols in nonlinear feedbacks on atmospheric processes is in a focus of many researches. Particularly, the importance of black carbon particles for evolution of physical weather including precipitation formation and release is investigated by numerical modelling as well as observation networks. However, certain discrepancies between results obtained by different methods are remained. The increasing of complexity in numerical weather modelling systems leads to enlarging a volume of output data and promises to reveal new aspects in complexity of interactions and feedbacks. The Harmonie-38h1.2 model with the AROME physical package is used to study changes in precipitation life-cycle under black carbon polluted conditions. A model configuration includes a radar data assimilation procedure on a high resolution domain covering the Scandinavia region. Model results show that precipitation rate and distribution as well as other variables of atmospheric dynamics and physics over the domain are sensitive to aerosol concentrations. The attention should also be paid to numerical aspects, such as a list of observation types involved in assimilation. The use of high resolution radar information allows to include mesoscale features in initial conditions and to decrease the growth rate of a model error with the lead time.

Real-Time Dynamic Modeling - Data Information Requirements and Flight Test Results

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.; Smith, Mark S.

2008-01-01

Practical aspects of identifying dynamic models for aircraft in real time were studied. Topics include formulation of an equation-error method in the frequency domain to estimate non-dimensional stability and control derivatives in real time, data information content for accurate modeling results, and data information management techniques such as data forgetting, incorporating prior information, and optimized excitation. Real-time dynamic modeling was applied to simulation data and flight test data from a modified F-15B fighter aircraft, and to operational flight data from a subscale jet transport aircraft. Estimated parameter standard errors and comparisons with results from a batch output-error method in the time domain were used to demonstrate the accuracy of the identified real-time models.

Real-Time Dynamic Modeling - Data Information Requirements and Flight Test Results

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.; Smith, Mark S.

2010-01-01

Practical aspects of identifying dynamic models for aircraft in real time were studied. Topics include formulation of an equation-error method in the frequency domain to estimate non-dimensional stability and control derivatives in real time, data information content for accurate modeling results, and data information management techniques such as data forgetting, incorporating prior information, and optimized excitation. Real-time dynamic modeling was applied to simulation data and flight test data from a modified F-15B fighter aircraft, and to operational flight data from a subscale jet transport aircraft. Estimated parameter standard errors, prediction cases, and comparisons with results from a batch output-error method in the time domain were used to demonstrate the accuracy of the identified real-time models.

Computational Modeling and Numerical Methods for Spatiotemporal Calcium Cycling in Ventricular Myocytes

PubMed Central

Nivala, Michael; de Lange, Enno; Rovetti, Robert; Qu, Zhilin

2012-01-01

Intracellular calcium (Ca) cycling dynamics in cardiac myocytes is regulated by a complex network of spatially distributed organelles, such as sarcoplasmic reticulum (SR), mitochondria, and myofibrils. In this study, we present a mathematical model of intracellular Ca cycling and numerical and computational methods for computer simulations. The model consists of a coupled Ca release unit (CRU) network, which includes a SR domain and a myoplasm domain. Each CRU contains 10 L-type Ca channels and 100 ryanodine receptor channels, with individual channels simulated stochastically using a variant of Gillespie’s method, modified here to handle time-dependent transition rates. Both the SR domain and the myoplasm domain in each CRU are modeled by 5 × 5 × 5 voxels to maintain proper Ca diffusion. Advanced numerical algorithms implemented on graphical processing units were used for fast computational simulations. For a myocyte containing 100 × 20 × 10 CRUs, a 1-s heart time simulation takes about 10 min of machine time on a single NVIDIA Tesla C2050. Examples of simulated Ca cycling dynamics, such as Ca sparks, Ca waves, and Ca alternans, are shown. PMID:22586402

Alpha1 LASSO data bundles Lamont, OK

DOE Data Explorer

Gustafson, William Jr; Vogelmann, Andrew; Endo, Satoshi; Toto, Tami; Xiao, Heng; Li, Zhijin; Cheng, Xiaoping; Krishna, Bhargavi (ORCID:000000018828528X)

2016-08-03

A data bundle is a unified package consisting of LASSO LES input and output, observations, evaluation diagnostics, and model skill scores. LES input includes model configuration information and forcing data. LES output includes profile statistics and full domain fields of cloud and environmental variables. Model evaluation data consists of LES output and ARM observations co-registered on the same grid and sampling frequency. Model performance is quantified by skill scores and diagnostics in terms of cloud and environmental variables.

Extend MANPADS M&S Capabilities to Include Energetic Materials, Fragmentation Effects, and Wing Flutter Response

DTIC Science & Technology

2005-12-31

MANPADS missile is modeled using LSDYNA . It has 187600 nodes, 52802 shell elements with 13 shell materials, 112200 solid elements with 1804 solid...model capability that includes impact, detonation, penetration, and wing flutter response. This work extends an existing body on body missile model...the missile as well as the expansion of the surrounding fluids was modeled in the Eulerian domain. The Jones-Wilkins-Lee (JWL) equation of state was

A Framework for Understanding Physics Students' Computational Modeling Practices

ERIC Educational Resources Information Center

Lunk, Brandon Robert

2012-01-01

With the growing push to include computational modeling in the physics classroom, we are faced with the need to better understand students' computational modeling practices. While existing research on programming comprehension explores how novices and experts generate programming algorithms, little of this discusses how domain content…

The Meta-Ontology Model of the Fishdisease Diagnostic Knowledge Based on Owl

NASA Astrophysics Data System (ADS)

Shi, Yongchang; Gao, Wen; Hu, Liang; Fu, Zetian

For improving available and reusable of knowledge in fish disease diagnosis (FDD) domain and facilitating knowledge acquisition, an ontology model of FDD knowledge was developed based on owl according to FDD knowledge model. It includes terminology of terms in FDD knowledge and hierarchies of their class.

Contributions of physical and cognitive impairments to self-reported driving difficulty in chronic whiplash-associated disorders.

PubMed

Takasaki, Hiroshi; Treleaven, Julia; Johnston, Venerina; Jull, Gwendolen

2013-08-15

Cross-sectional. To conduct a preliminary analysis of the physical, cognitive, and psychological domains contributing to self-reported driving difficulty after adjusting for neck pain, dizziness, and relevant demographics in chronic whiplash-associated disorders (WAD) using hierarchical regression modeling. Pain is a risk factor for car crashes, and dizziness may affect fitness to drive. Both symptoms are common in chronic WAD and difficulty driving is a common complaint in this group. Chronic WAD is often accompanied by physical, cognitive, and psychological impairments. These impairments may contribute to self-reported driving difficulty beyond neck pain, dizziness, and relevant demographics. Forty individuals with chronic WAD participated. Dependent variables were the magnitude of self-reported driving difficulty assessed in the strategic, tactical, and operational levels of the Neck Pain Driving Index. Three models were developed to assess the contributions of independent variables (physical, cognitive, and psychological domains) to each of the 3 dependent variables after adjusting for neck pain intensity, dizziness, and driving demographics. The measures included were: physical domain-range and maximum speed of head rotation, performances during gaze stability, eye-head coordination, and visual dependency tests; cognitive domain-self-reported cognitive symptoms including fatigue and the trail making tests; and psychological domain-general stress, traumatic stress, depression, and fear of neck movements and driving. Symptom duration was relevant to driving difficulty in the strategic and tactical levels. The cognitive domain increased statistical power to estimate the strategic and operational levels (P < 0.1) beyond other contributors. The physical domain increased statistical power to estimate the tactical level (P < 0.1) beyond other contributors. Physical and cognitive impairments independently contributed to self-reported driving difficulty in chronic WAD beyond neck pain, dizziness, and symptom duration. 3.

Effect of the centrifugal force on domain chaos in Rayleigh-Bénard convection.

PubMed

Becker, Nathan; Scheel, J D; Cross, M C; Ahlers, Guenter

2006-06-01

Experiments and simulations from a variety of sample sizes indicated that the centrifugal force significantly affects the domain-chaos state observed in rotating Rayleigh-Bénard convection-patterns. In a large-aspect-ratio sample, we observed a hybrid state consisting of domain chaos close to the sample center, surrounded by an annulus of nearly stationary nearly radial rolls populated by occasional defects reminiscent of undulation chaos. Although the Coriolis force is responsible for domain chaos, by comparing experiment and simulation we show that the centrifugal force is responsible for the radial rolls. Furthermore, simulations of the Boussinesq equations for smaller aspect ratios neglecting the centrifugal force yielded a domain precession-frequency f approximately epsilon(mu) with mu approximately equal to 1 as predicted by the amplitude-equation model for domain chaos, but contradicted by previous experiment. Additionally the simulations gave a domain size that was larger than in the experiment. When the centrifugal force was included in the simulation, mu and the domain size were consistent with experiment.

Dependence of the ferroelectric domain shape on the electric field of the microscope tip

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

Starkov, Alexander S.; Starkov, Ivan A., E-mail: starkov@feec.vutbr.cz

2015-08-21

A theory of an equilibrium shape of the domain formed in an electric field of a scanning force microscope (SFM) tip is proposed. We do not assume a priori that the domain has a fixed form. The shape of the domain is defined by the minimum of the free energy of the ferroelectric. This energy includes the energy of the depolarization field, the energy of the domain wall, and the energy of the interaction between the domain and the electric field of the SFM tip. The contributions of the apex and conical part of the tip are examined. Moreover, inmore » the proposed approach, any narrow tip can be considered. The surface energy is determined on the basis of the Ginzburg-Landau-Devonshire theory and takes into account the curvature of the domain wall. The variation of the free energy with respect to the domain shape leads to an integro-differential equation, which must be solved numerically. Model results are illustrated for lithium tantalate ceramics.« less

Study of human phonation in a full-body domain

NASA Astrophysics Data System (ADS)

Saurabh, Shakti; Bodony, Daniel

2015-11-01

The generation and propagation of the human voice is studied in two-dimensions using a full-body domain, using direct numerical simulation. The fluid/air in the vocal tract is modeled as a compressible and viscous fluid interacting with the non-linear, viscoelastic vocal folds (VF). The VF tissue material properties are multi-layered, with varying stiffness, and a finite-strain model is utilized and implemented in a quadratic finite element code. The fluid-solid domains are coupled through a boundary-fitted interface and utilize a Poisson equation-based mesh deformation method. The full-body domain includes the near VF region, the vocal tract, a simplified model of the soft palate and mouth, and extends out into the acoustic far-field. A new kind of inflow boundary condition based upon a quasi-one-dimensional formulation with constant sub-glottal volume velocity, which is linked to the VF movement, has been adopted. The sound pressure levels (SPL) measured are realistic and we analyze their connection to the VF dynamics and glottal and vocal tract geometries. Supported by the National Science Foundation (CAREER award number 1150439).

Description of waves in inhomogeneous domains using Heun's equation

NASA Astrophysics Data System (ADS)

Bednarik, M.; Cervenka, M.

2018-04-01

There are a number of model equations describing electromagnetic, acoustic or quantum waves in inhomogeneous domains and some of them are of the same type from the mathematical point of view. This isomorphism enables us to use a unified approach to solving the corresponding equations. In this paper, the inhomogeneity is represented by a trigonometric spatial distribution of a parameter determining the properties of an inhomogeneous domain. From the point of view of modeling, this trigonometric parameter function can be smoothly connected to neighboring constant-parameter regions. For this type of distribution, exact local solutions of the model equations are represented by the local Heun functions. As the interval for which the solution is sought includes two regular singular points. For this reason, a method is proposed which resolves this problem only based on the local Heun functions. Further, the transfer matrix for the considered inhomogeneous domain is determined by means of the proposed method. As an example of the applicability of the presented solutions the transmission coefficient is calculated for the locally periodic structure which is given by an array of asymmetric barriers.

Predicting Health Care Utilization in Marginalized Populations: Black, Female, Street-based Sex Workers

PubMed Central

Varga, Leah M.; Surratt, Hilary L.

2014-01-01

Background Patterns of social and structural factors experienced by vulnerable populations may negatively affect willingness and ability to seek out health care services, and ultimately, their health. Methods The outcome variable was utilization of health care services in the previous 12 months. Using Andersen’s Behavioral Model for Vulnerable Populations, we examined self-reported data on utilization of health care services among a sample of 546 Black, street-based female sex workers in Miami, Florida. To evaluate the impact of each domain of the model on predicting health care utilization, domains were included in the logistic regression analysis by blocks using the traditional variables first and then adding the vulnerable domain variables. Findings The most consistent variables predicting health care utilization were having a regular source of care and self-rated health. The model that included only enabling variables was the most efficient model in predicting health care utilization. Conclusions Any type of resource, link, or connection to or with an institution, or any consistent point of care contributes significantly to health care utilization behaviors. A consistent and reliable source for health care may increase health care utilization and subsequently decrease health disparities among vulnerable and marginalized populations, as well as contribute to public health efforts that encourage preventive health. PMID:24657047

Ontology-Driven Business Modelling: Improving the Conceptual Representation of the REA Ontology

NASA Astrophysics Data System (ADS)

Gailly, Frederik; Poels, Geert

Business modelling research is increasingly interested in exploring how domain ontologies can be used as reference models for business models. The Resource Event Agent (REA) ontology is a primary candidate for ontology-driven modelling of business processes because the REA point of view on business reality is close to the conceptual modelling perspective on business models. In this paper Ontology Engineering principles are employed to reengineer REA in order to make it more suitable for ontology-driven business modelling. The new conceptual representation of REA that we propose uses a single representation formalism, includes a more complete domain axiomatizat-ion (containing definitions of concepts, concept relations and ontological axioms), and is proposed as a generic model that can be instantiated to create valid business models. The effects of these proposed improvements on REA-driven business modelling are demonstrated using a business modelling example.

Models of the Joint Structure of Domain-Related and Global Distress: Implications for the Reconciliation of Quality of Life and Mental Health Perspectives

ERIC Educational Resources Information Center

Magee, William; St-Arnaud, Sebastien

2012-01-01

Research on subjective wellbeing includes studies of both domain-related and global distress. The mental health literature, though, focuses almost exclusively on global distress. This seems to be partly due to a common belief that psychological distress, and the moods that comprise distress, necessarily lack referential content. However, if that…

Modeling Urban Air Quality in the Berlin-Brandenburg Region: Evaluation of a WRF-Chem Setup

NASA Astrophysics Data System (ADS)

Kuik, F.; Churkina, G.; Butler, T. M.; Lauer, A.; Mar, K. A.

2015-12-01

Air pollution is the number one environmental cause of premature deaths in Europe. Despite extensive regulations, air pollution remains a challenging issue, especially in urban areas. For studying air quality in the Berlin-Brandenburg region of Germany the Weather Research and Forecasting Model with Chemistry (WRF-Chem) is set up and evaluated against meteorological and air quality observations from monitoring stations as well as from a field campaign conducted in 2014 (incl. black carbon, VOCs as well as mobile measurements of particle size distribution and particle mass). The model setup includes 3 nested domains with horizontal resolutions of 15km, 3km, and 1km, online biogenic emissions using MEGAN 2.0, and anthropogenic emissions from the TNO-MACC-II inventory. This work serves as a basis for future studies on different aspects of air pollution in the Berlin-Brandenburg region, including how heat waves affect emissions of biogenic volatile organic compounds (BVOC) from urban vegetation (summer 2006) and the impact of selected traffic measures on air quality in the Berlin-Brandenburg area (summer 2014). The model represents the meteorology as observed in the region well for both periods. An exception is the heat wave period in 2006, where the temperature simulated with 3km and 1km resolutions is biased low by around 2°C for urban built-up stations. First results of simulations with chemistry show that, on average, WRF-Chem simulates concentrations of O3 well. However, the 8 hr maxima are underestimated, and the minima are overestimated. While NOx daily means are modeled reasonably well for urban stations, they are overestimated for suburban stations. PM10 concentrations are underestimated by the model. The biases and correlation coefficients of simulated O3, NOx, and PM10 in comparison to surface observations do not show improvements for the 1km domain in comparison to the 3km domain. To improve the model performance of the 1km domain we will include an updated emission inventory (TNO-MACC-III) as well as the interpolation of the emission data from 7km to a 1km resolution.

Generating target system specifications from a domain model using CLIPS

NASA Technical Reports Server (NTRS)

Sugumaran, Vijayan; Gomaa, Hassan; Kerschberg, Larry

1991-01-01

The quest for reuse in software engineering is still being pursued and researchers are actively investigating the domain modeling approach to software construction. There are several domain modeling efforts reported in the literature and they all agree that the components that are generated from domain modeling are more conducive to reuse. Once a domain model is created, several target systems can be generated by tailoring the domain model or by evolving the domain model and then tailoring it according to the specified requirements. This paper presents the Evolutionary Domain Life Cycle (EDLC) paradigm in which a domain model is created using multiple views, namely, aggregation hierarchy, generalization/specialization hierarchies, object communication diagrams and state transition diagrams. The architecture of the Knowledge Based Requirements Elicitation Tool (KBRET) which is used to generate target system specifications is also presented. The preliminary version of KBRET is implemented in the C Language Integrated Production System (CLIPS).

An evaluation of evaluative personality terms: a comparison of the big seven and five-factor model in predicting psychopathology.

PubMed

Durrett, Christine; Trull, Timothy J

2005-09-01

Two personality models are compared regarding their relationship with personality disorder (PD) symptom counts and with lifetime Axis I diagnoses. These models share 5 similar domains, and the Big 7 model also includes 2 domains assessing self-evaluation: positive and negative valence. The Big 7 model accounted for more variance in PDs than the 5-factor model, primarily because of the association of negative valence with most PDs. Although low-positive valence was associated with most Axis I diagnoses, the 5-factor model generally accounted for more variance in Axis I diagnoses than the Big 7 model. Some predicted associations between self-evaluation and psychopathology were not found, and unanticipated associations emerged. These findings are discussed regarding the utility of evaluative terms in clinical assessment.

Time-domain full-waveform inversion of Rayleigh and Love waves in presence of free-surface topography

NASA Astrophysics Data System (ADS)

Pan, Yudi; Gao, Lingli; Bohlen, Thomas

2018-05-01

Correct estimation of near-surface seismic-wave velocity when encountering lateral heterogeneity and free surface topography is one of the challenges to current shallow seismic. We propose to use time-domain full-waveform inversion (FWI) of surface waves, including both Rayleigh and Love waves, to solve this problem. We adopt a 2D time-domain finite-difference method with an improved vacuum formulation (IVF) to simulate shallow-seismic Rayleigh wave in presence of free-surface topography. We modify the IVF for SH-wave equation for the simulation of Love wave in presence of topographic free surface and prove its accuracy by benchmark tests. Checkboard model tests are performed in both cases when free-surface topography is included or neglected in FWI. Synthetic model containing a dipping planar free surface and lateral heterogeneity was then tested, in both cases of considering and neglecting free-surface topography. Both checkerboard and synthetic models show that Rayleigh- and Love-wave FWI have similar ability of reconstructing near-surface structures when free-surface topography is considered, while Love-wave FWI could reconstruct near-surface structures better than Rayleigh-wave when free-surface topography is neglected.

The international river interface cooperative: Public domain flow and morphodynamics software for education and applications

NASA Astrophysics Data System (ADS)

Nelson, Jonathan M.; Shimizu, Yasuyuki; Abe, Takaaki; Asahi, Kazutake; Gamou, Mineyuki; Inoue, Takuya; Iwasaki, Toshiki; Kakinuma, Takaharu; Kawamura, Satomi; Kimura, Ichiro; Kyuka, Tomoko; McDonald, Richard R.; Nabi, Mohamed; Nakatsugawa, Makoto; Simões, Francisco R.; Takebayashi, Hiroshi; Watanabe, Yasunori

2016-07-01

This paper describes a new, public-domain interface for modeling flow, sediment transport and morphodynamics in rivers and other geophysical flows. The interface is named after the International River Interface Cooperative (iRIC), the group that constructed the interface and many of the current solvers included in iRIC. The interface is entirely free to any user and currently houses thirteen models ranging from simple one-dimensional models through three-dimensional large-eddy simulation models. Solvers are only loosely coupled to the interface so it is straightforward to modify existing solvers or to introduce other solvers into the system. Six of the most widely-used solvers are described in detail including example calculations to serve as an aid for users choosing what approach might be most appropriate for their own applications. The example calculations range from practical computations of bed evolution in natural rivers to highly detailed predictions of the development of small-scale bedforms on an initially flat bed. The remaining solvers are also briefly described. Although the focus of most solvers is coupled flow and morphodynamics, several of the solvers are also specifically aimed at providing flood inundation predictions over large spatial domains. Potential users can download the application, solvers, manuals, and educational materials including detailed tutorials at www.-i-ric.org. The iRIC development group encourages scientists and engineers to use the tool and to consider adding their own methods to the iRIC suite of tools.

The international river interface cooperative: Public domain flow and morphodynamics software for education and applications

USGS Publications Warehouse

Nelson, Jonathan M.; Shimizu, Yasuyuki; Abe, Takaaki; Asahi, Kazutake; Gamou, Mineyuki; Inoue, Takuya; Iwasaki, Toshiki; Kakinuma, Takaharu; Kawamura, Satomi; Kimura, Ichiro; Kyuka, Tomoko; McDonald, Richard R.; Nabi, Mohamed; Nakatsugawa, Makoto; Simoes, Francisco J.; Takebayashi, Hiroshi; Watanabe, Yasunori

2016-01-01

This paper describes a new, public-domain interface for modeling flow, sediment transport and morphodynamics in rivers and other geophysical flows. The interface is named after the International River Interface Cooperative (iRIC), the group that constructed the interface and many of the current solvers included in iRIC. The interface is entirely free to any user and currently houses thirteen models ranging from simple one-dimensional models through three-dimensional large-eddy simulation models. Solvers are only loosely coupled to the interface so it is straightforward to modify existing solvers or to introduce other solvers into the system. Six of the most widely-used solvers are described in detail including example calculations to serve as an aid for users choosing what approach might be most appropriate for their own applications. The example calculations range from practical computations of bed evolution in natural rivers to highly detailed predictions of the development of small-scale bedforms on an initially flat bed. The remaining solvers are also briefly described. Although the focus of most solvers is coupled flow and morphodynamics, several of the solvers are also specifically aimed at providing flood inundation predictions over large spatial domains. Potential users can download the application, solvers, manuals, and educational materials including detailed tutorials at www.-i-ric.org. The iRIC development group encourages scientists and engineers to use the tool and to consider adding their own methods to the iRIC suite of tools.

Care episode retrieval: distributional semantic models for information retrieval in the clinical domain.

PubMed

Moen, Hans; Ginter, Filip; Marsi, Erwin; Peltonen, Laura-Maria; Salakoski, Tapio; Salanterä, Sanna

2015-01-01

Patients' health related information is stored in electronic health records (EHRs) by health service providers. These records include sequential documentation of care episodes in the form of clinical notes. EHRs are used throughout the health care sector by professionals, administrators and patients, primarily for clinical purposes, but also for secondary purposes such as decision support and research. The vast amounts of information in EHR systems complicate information management and increase the risk of information overload. Therefore, clinicians and researchers need new tools to manage the information stored in the EHRs. A common use case is, given a--possibly unfinished--care episode, to retrieve the most similar care episodes among the records. This paper presents several methods for information retrieval, focusing on care episode retrieval, based on textual similarity, where similarity is measured through domain-specific modelling of the distributional semantics of words. Models include variants of random indexing and the semantic neural network model word2vec. Two novel methods are introduced that utilize the ICD-10 codes attached to care episodes to better induce domain-specificity in the semantic model. We report on experimental evaluation of care episode retrieval that circumvents the lack of human judgements regarding episode relevance. Results suggest that several of the methods proposed outperform a state-of-the art search engine (Lucene) on the retrieval task.

Care episode retrieval: distributional semantic models for information retrieval in the clinical domain

PubMed Central

2015-01-01

Patients' health related information is stored in electronic health records (EHRs) by health service providers. These records include sequential documentation of care episodes in the form of clinical notes. EHRs are used throughout the health care sector by professionals, administrators and patients, primarily for clinical purposes, but also for secondary purposes such as decision support and research. The vast amounts of information in EHR systems complicate information management and increase the risk of information overload. Therefore, clinicians and researchers need new tools to manage the information stored in the EHRs. A common use case is, given a - possibly unfinished - care episode, to retrieve the most similar care episodes among the records. This paper presents several methods for information retrieval, focusing on care episode retrieval, based on textual similarity, where similarity is measured through domain-specific modelling of the distributional semantics of words. Models include variants of random indexing and the semantic neural network model word2vec. Two novel methods are introduced that utilize the ICD-10 codes attached to care episodes to better induce domain-specificity in the semantic model. We report on experimental evaluation of care episode retrieval that circumvents the lack of human judgements regarding episode relevance. Results suggest that several of the methods proposed outperform a state-of-the art search engine (Lucene) on the retrieval task. PMID:26099735

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

Homology Modeling of Class A G Protein-Coupled Receptors

PubMed Central

Costanzi, Stefano

2012-01-01

G protein-coupled receptors (GPCRs) are a large superfamily of membrane bound signaling proteins that hold great pharmaceutical interest. Since experimentally elucidated structures are available only for a very limited number of receptors, homology modeling has become a widespread technique for the construction of GPCR models intended to study the structure-function relationships of the receptors and aid the discovery and development of ligands capable of modulating their activity. Through this chapter, various aspects involved in the constructions of homology models of the serpentine domain of the largest class of GPCRs, known as class A or rhodopsin family, are illustrated. In particular, the chapter provides suggestions, guidelines and critical thoughts on some of the most crucial aspect of GPCR modeling, including: collection of candidate templates and a structure-based alignment of their sequences; identification and alignment of the transmembrane helices of the query receptor to the corresponding domains of the candidate templates; selection of one or more templates receptor; election of homology or de novo modeling for the construction of specific extracellular and intracellular domains; construction of the three-dimensional models, with special consideration to extracellular regions, disulfide bridges, and interhelical cavity; validation of the models through controlled virtual screening experiments. PMID:22323225

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

Refinement of a Conceptual Model for Adolescent Readiness to Engage in End-of-Life Discussions.

PubMed

Bell, Cynthia J; Zimet, Gregory D; Hinds, Pamela S; Broome, Marion E; McDaniel, Anna M; Mays, Rose M; Champion, Victoria L

Adolescents living with incurable cancer require ongoing support to process grief, emotions, and information as disease progresses including treatment options (phase 1 clinical trials and/or hospice/palliative care). Little is known about how adolescents become ready for such discussions. The purpose of this study was to explore the process of adolescent readiness for end-of-life preparedness discussions, generating a theoretical understanding for guiding clinical conversations when curative options are limited. We explored 2 in-depth cases across time using case-study methodology. An à priori conceptual model based on current end-of-life research guided data collection and analysis. Multiple sources including in-depth adolescent interviews generated data collection on model constructs. Analysis followed a logical sequence establishing a chain of evidence linking raw data to study conclusions. Synthesis and data triangulation across cases and time led to theoretical generalizations. Initially, we proposed a linear process of readiness with 3 domains: a cognitive domain (awareness), an emotional domain (acceptance), and a behavioral domain (willingness), which preceded preparedness. Findings led to conceptual model refinement showing readiness is a dynamic internal process that interacts with preparedness. Current awareness context facilitates the type of preparedness discussions (cognitive or emotional). Furthermore, social constraint inhibits discussions. Data support theoretical understanding of the dynamism of readiness. Future research that validates adolescent conceptualization will ensure age-appropriate readiness representation. Understanding the dynamic process of readiness for engaging in end-of-life preparedness provides clinician insight for guiding discussions that facilitate shared decision making and promote quality of life for adolescents and their families.

On the likelihood of single-peaked preferences.

PubMed

Lackner, Marie-Louise; Lackner, Martin

2017-01-01

This paper contains an extensive combinatorial analysis of the single-peaked domain restriction and investigates the likelihood that an election is single-peaked. We provide a very general upper bound result for domain restrictions that can be defined by certain forbidden configurations. This upper bound implies that many domain restrictions (including the single-peaked restriction) are very unlikely to appear in a random election chosen according to the Impartial Culture assumption. For single-peaked elections, this upper bound can be refined and complemented by a lower bound that is asymptotically tight. In addition, we provide exact results for elections with few voters or candidates. Moreover, we consider the Pólya urn model and the Mallows model and obtain lower bounds showing that single-peakedness is considerably more likely to appear for certain parameterizations.

The Coherence Formation Model of Illustrated Text Comprehension: A Path Model of Attention to Multimedia Text

ERIC Educational Resources Information Center

Fitzhugh, Shannon Leigh

2012-01-01

The study reported here tests a model that includes several factors thought to contribute to the comprehension of static multimedia learning materials (i.e. background knowledge, working memory, attention to components as measured with eye movement measures). The model examines the effects of working memory capacity, domain specific (biology) and…

Functional and topological characteristics of mammalian regulatory domains

PubMed Central

Symmons, Orsolya; Uslu, Veli Vural; Tsujimura, Taro; Ruf, Sandra; Nassari, Sonya; Schwarzer, Wibke; Ettwiller, Laurence; Spitz, François

2014-01-01

Long-range regulatory interactions play an important role in shaping gene-expression programs. However, the genomic features that organize these activities are still poorly characterized. We conducted a large operational analysis to chart the distribution of gene regulatory activities along the mouse genome, using hundreds of insertions of a regulatory sensor. We found that enhancers distribute their activities along broad regions and not in a gene-centric manner, defining large regulatory domains. Remarkably, these domains correlate strongly with the recently described TADs, which partition the genome into distinct self-interacting blocks. Different features, including specific repeats and CTCF-binding sites, correlate with the transition zones separating regulatory domains, and may help to further organize promiscuously distributed regulatory influences within large domains. These findings support a model of genomic organization where TADs confine regulatory activities to specific but large regulatory domains, contributing to the establishment of specific gene expression profiles. PMID:24398455

A role for chromatin topology in imprinted domain regulation.

PubMed

MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

2016-02-01

Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

Running SW4 On New Commodity Technology Systems (CTS-1) Platform

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

Rodgers, Arthur J.; Petersson, N. Anders; Pitarka, Arben

We have recently been running earthquake ground motion simulations with SW4 on the new capacity computing systems, called the Commodity Technology Systems - 1 (CTS-1) at Lawrence Livermore National Laboratory (LLNL). SW4 is a fourth order time domain finite difference code developed by LLNL and distributed by the Computational Infrastructure for Geodynamics (CIG). SW4 simulates seismic wave propagation in complex three-dimensional Earth models including anelasticity and surface topography. We are modeling near-fault earthquake strong ground motions for the purposes of evaluating the response of engineered structures, such as nuclear power plants and other critical infrastructure. Engineering analysis of structures requiresmore » the inclusion of high frequencies which can cause damage, but are often difficult to include in simulations because of the need for large memory to model fine grid spacing on large domains.« less

The development of efficient numerical time-domain modeling methods for geophysical wave propagation

NASA Astrophysics Data System (ADS)

Zhu, Lieyuan

This Ph.D. dissertation focuses on the numerical simulation of geophysical wave propagation in the time domain including elastic waves in solid media, the acoustic waves in fluid media, and the electromagnetic waves in dielectric media. This thesis shows that a linear system model can describe accurately the physical processes of those geophysical waves' propagation and can be used as a sound basis for modeling geophysical wave propagation phenomena. The generalized stability condition for numerical modeling of wave propagation is therefore discussed in the context of linear system theory. The efficiency of a series of different numerical algorithms in the time-domain for modeling geophysical wave propagation are discussed and compared. These algorithms include the finite-difference time-domain method, pseudospectral time domain method, alternating directional implicit (ADI) finite-difference time domain method. The advantages and disadvantages of these numerical methods are discussed and the specific stability condition for each modeling scheme is carefully derived in the context of the linear system theory. Based on the review and discussion of these existing approaches, the split step, ADI pseudospectral time domain (SS-ADI-PSTD) method is developed and tested for several cases. Moreover, the state-of-the-art stretched-coordinate perfect matched layer (SCPML) has also been implemented in SS-ADI-PSTD algorithm as the absorbing boundary condition for truncating the computational domain and absorbing the artificial reflection from the domain boundaries. After algorithmic development, a few case studies serve as the real-world examples to verify the capacities of the numerical algorithms and understand the capabilities and limitations of geophysical methods for detection of subsurface contamination. The first case is a study using ground penetrating radar (GPR) amplitude variation with offset (AVO) for subsurface non-aqueous-liquid (NAPL) contamination. The numerical AVO study reveals that the normalized residual polarization (NRP) variation with offset does not respond to subsurface NAPL existence when the offset is close to or larger than its critical value (which corresponds to critical incident angle) because the air and head waves dominate the recorded wave field and severely interfere with reflected waves in the TEz wave field. Thus it can be concluded that the NRP AVO/GPR method is invalid when source-receiver angle offset is close to or greater than its critical value due to incomplete and severely distorted reflection information. In other words, AVO is not a promising technique for detection of the subsurface NAPL, as claimed by some researchers. In addition, the robustness of the newly developed numerical algorithms is also verified by the AVO study for randomly-arranged layered media. Meanwhile, this case study also demonstrates again that the full-wave numerical modeling algorithms are superior to ray tracing method. The second case study focuses on the effect of the existence of a near-surface fault on the vertically incident P- and S- plane waves. The modeling results show that both P-wave vertical incidence and S-wave vertical incidence cases are qualified fault indicators. For the plane S-wave vertical incidence case, the horizontal location of the upper tip of the fault (the footwall side) can be identified without much effort, because all the recorded parameters on the surface including the maximum velocities and the maximum accelerations, and even their ratios H/V, have shown dramatic changes when crossing the upper tip of the fault. The centers of the transition zone of the all the curves of parameters are almost directly above the fault tip (roughly the horizontal center of the model). Compared with the case of the vertically incident P-wave source, it has been found that the S-wave vertical source is a better indicator for fault location, because the horizontal location of the tip of that fault cannot be clearly identified with the ratio of the horizontal to vertical velocity for the P-wave incident case.

Exploring and modelling impacts of third molar experience on quality of life: a real-time qualitative study using Twitter.

PubMed

Hanna, Kamal; Sambrook, Paul; Armfield, Jason M; Brennan, David S

2017-10-01

This study had two objectives: (i) to explore and model domains describing the real-time impact of third molars (TMs) on quality of life (QoL); and (ii) to assess the percentage coverage, in some generic health-related quality of life (HRQoL) and oral health-related quality of life (OHRQoL) instruments, of the TM QoL domains identified in this study. A global cross-sectional sample of tweets containing 'wisdom tooth' over a 1-week period retrieved 3,537 tweets. After random quota sampling, classification and filtering, only 843 tweets were included in the thematic analysis. A TM QoL model was constructed based on the associations of the identified domains. Domains for the selected generic HRQoL and OHRQoL instruments were plotted against the domains identified in the study to calculate the percentage coverage for each. The QoL domains identified were pain (n = 348, 41%), mood (n = 173, 20%), anxiety and fear (n = 54, 7%), enjoying food (n = 41, 4%), coping (n = 37, 4%), daily activities (n = 34, 4%), sleep (n = 24, 2%), social life (n = 19, 2%), physical health (n = 17, 2%), ability to think (n = 9, 1%), self-care (n = 8, 1%) and sporting & recreation (n = 2, <1%). The Assessment Quality of Life instrument (AQoL-8D) covers 87% of the TM QoL domains, while the rest of the HRQoL and OHRQoL instruments cover 33-60%. This study shows how Twitter can be used to obtain real-time QoL data, which might be used to model how TMs impact on QoL. The TM QoL domains identified in the study were generally under-represented among the generic OHRQoL instruments assessed while, the HRQoL AQoL-8D covered most of the TM QoL domains. The QoL domains identified in the study might be used to develop a new OHRQoL measure for TMs. © 2017 FDI World Dental Federation.

Clinical modeling--a critical analysis.

PubMed

Blobel, Bernd; Goossen, William; Brochhausen, Mathias

2014-01-01

Modeling clinical processes (and their informational representation) is a prerequisite for optimally enabling and supporting high quality and safe care through information and communication technology and meaningful use of gathered information. The paper investigates existing approaches to clinical modeling, thereby systematically analyzing the underlying principles, the consistency with and the integration opportunity to other existing or emerging projects, as well as the correctness of representing the reality of health and health services. The analysis is performed using an architectural framework for modeling real-world systems. In addition, fundamental work on the representation of facts, relations, and processes in the clinical domain by ontologies is applied, thereby including the integration of advanced methodologies such as translational and system medicine. The paper demonstrates fundamental weaknesses and different maturity as well as evolutionary potential in the approaches considered. It offers a development process starting with the business domain and its ontologies, continuing with the Reference Model-Open Distributed Processing (RM-ODP) related conceptual models in the ICT ontology space, the information and the computational view, and concluding with the implementation details represented as engineering and technology view, respectively. The existing approaches reflect at different levels the clinical domain, put the main focus on different phases of the development process instead of first establishing the real business process representation and therefore enable quite differently and partially limitedly the domain experts' involvement. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Multidisciplinary model-based-engineering for laser weapon systems: recent progress

NASA Astrophysics Data System (ADS)

Coy, Steve; Panthaki, Malcolm

2013-09-01

We are working to develop a comprehensive, integrated software framework and toolset to support model-based engineering (MBE) of laser weapons systems. MBE has been identified by the Office of the Director, Defense Science and Engineering as one of four potentially "game-changing" technologies that could bring about revolutionary advances across the entire DoD research and development and procurement cycle. To be effective, however, MBE requires robust underlying modeling and simulation technologies capable of modeling all the pertinent systems, subsystems, components, effects, and interactions at any level of fidelity that may be required in order to support crucial design decisions at any point in the system development lifecycle. Very often the greatest technical challenges are posed by systems involving interactions that cut across two or more distinct scientific or engineering domains; even in cases where there are excellent tools available for modeling each individual domain, generally none of these domain-specific tools can be used to model the cross-domain interactions. In the case of laser weapons systems R&D these tools need to be able to support modeling of systems involving combined interactions among structures, thermal, and optical effects, including both ray optics and wave optics, controls, atmospheric effects, target interaction, computational fluid dynamics, and spatiotemporal interactions between lasing light and the laser gain medium. To address this problem we are working to extend Comet™, to add the addition modeling and simulation capabilities required for this particular application area. In this paper we will describe our progress to date.

Growth- and Stress-Induced PASTA Kinase Phosphorylation in Enterococcus faecalis.

PubMed

Labbe, Benjamin D; Kristich, Christopher J

2017-11-01

Transmembrane Ser/Thr kinases containing extracellular PASTA domains are ubiquitous among Actinobacteria and Firmicutes Such PASTA kinases regulate critical processes, including antibiotic resistance, cell division, toxin production, and virulence, and are essential for viability in certain organisms. Based on in vitro studies with purified extracellular and intracellular fragments of PASTA kinases, a model for signaling has been proposed, in which the extracellular PASTA domains bind currently undefined ligands (typically thought to be peptidoglycan, or fragments thereof) to drive kinase dimerization, which leads to enhanced kinase autophosphorylation and enhanced phosphorylation of substrates. However, this model has not been rigorously tested in vivo Enterococcus faecalis is a Gram-positive intestinal commensal and major antibiotic-resistant opportunistic pathogen. In E. faecalis , the PASTA kinase IreK drives intrinsic resistance to cell wall-active antimicrobials, suggesting that such antimicrobials may trigger IreK signaling. Here we show that IreK responds to cell wall stress in vivo by enhancing its phosphorylation and that of a downstream substrate. This response requires both the extracellular PASTA domains and specific phosphorylatable residues in the kinase domain. Thus, our results provide in vivo evidence, with an intact full-length PASTA kinase in its native physiological environment, that supports the prevailing model of PASTA kinase signaling. In addition, we show that IreK responds to a signal associated with growth and/or cell division, in the absence of cell wall-active antimicrobials. Surprisingly, the ability of IreK to respond to growth and/or division does not require the extracellular PASTA domains, suggesting that IreK monitors multiple parameters for sensory input in vivo IMPORTANCE Transmembrane Ser/Thr kinases containing extracellular PASTA domains are ubiquitous among Actinobacteria and Firmicutes and regulate critical processes. The prevailing model for signaling by PASTA kinases proposes that the extracellular PASTA domains bind ligands to drive kinase dimerization, enhanced autophosphorylation, and enhanced phosphorylation of substrates. However, this model has not been rigorously tested in vivo We show that the PASTA kinase IreK of Enterococcus faecalis responds to cell wall stress in vivo by enhancing its phosphorylation and that of a downstream substrate. This response requires the PASTA domains and phosphorylatable residues in the kinase domain. Thus, our results provide in vivo evidence, with an intact full-length PASTA kinase in its native physiological environment, that supports the prevailing model of PASTA kinase signaling. Copyright © 2017 American Society for Microbiology.

Growth- and Stress-Induced PASTA Kinase Phosphorylation in Enterococcus faecalis

PubMed Central

Labbe, Benjamin D.

2017-01-01

ABSTRACT Transmembrane Ser/Thr kinases containing extracellular PASTA domains are ubiquitous among Actinobacteria and Firmicutes. Such PASTA kinases regulate critical processes, including antibiotic resistance, cell division, toxin production, and virulence, and are essential for viability in certain organisms. Based on in vitro studies with purified extracellular and intracellular fragments of PASTA kinases, a model for signaling has been proposed, in which the extracellular PASTA domains bind currently undefined ligands (typically thought to be peptidoglycan, or fragments thereof) to drive kinase dimerization, which leads to enhanced kinase autophosphorylation and enhanced phosphorylation of substrates. However, this model has not been rigorously tested in vivo. Enterococcus faecalis is a Gram-positive intestinal commensal and major antibiotic-resistant opportunistic pathogen. In E. faecalis, the PASTA kinase IreK drives intrinsic resistance to cell wall-active antimicrobials, suggesting that such antimicrobials may trigger IreK signaling. Here we show that IreK responds to cell wall stress in vivo by enhancing its phosphorylation and that of a downstream substrate. This response requires both the extracellular PASTA domains and specific phosphorylatable residues in the kinase domain. Thus, our results provide in vivo evidence, with an intact full-length PASTA kinase in its native physiological environment, that supports the prevailing model of PASTA kinase signaling. In addition, we show that IreK responds to a signal associated with growth and/or cell division, in the absence of cell wall-active antimicrobials. Surprisingly, the ability of IreK to respond to growth and/or division does not require the extracellular PASTA domains, suggesting that IreK monitors multiple parameters for sensory input in vivo. IMPORTANCE Transmembrane Ser/Thr kinases containing extracellular PASTA domains are ubiquitous among Actinobacteria and Firmicutes and regulate critical processes. The prevailing model for signaling by PASTA kinases proposes that the extracellular PASTA domains bind ligands to drive kinase dimerization, enhanced autophosphorylation, and enhanced phosphorylation of substrates. However, this model has not been rigorously tested in vivo. We show that the PASTA kinase IreK of Enterococcus faecalis responds to cell wall stress in vivo by enhancing its phosphorylation and that of a downstream substrate. This response requires the PASTA domains and phosphorylatable residues in the kinase domain. Thus, our results provide in vivo evidence, with an intact full-length PASTA kinase in its native physiological environment, that supports the prevailing model of PASTA kinase signaling. PMID:28808126

Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain.

PubMed

Raghav, Pawan Kumar; Verma, Yogesh Kumar; Gangenahalli, Gurudutta U

2012-05-01

B-cell lymphoma (Bcl-2) protein is an anti-apoptotic member of the Bcl-2 family. It is functionally demarcated into four Bcl-2 homology (BH) domains: BH1, BH2, BH3, BH4, one flexible loop domain (FLD), a transmembrane domain (TM), and an X domain. Bcl-2's BH domains have clearly been elucidated from a structural perspective, whereas the conformation of FLD has not yet been predicted, despite its important role in regulating apoptosis through its interactions with JNK-1, PKC, PP2A phosphatase, caspase 3, MAP kinase, ubiquitin, PS1, and FKBP38. Many important residues that regulate Bcl-2 anti-apoptotic activity are present in this domain, for example Asp34, Thr56, Thr69, Ser70, Thr74, and Ser87. The structural elucidation of the FLD would likely help in attempts to accurately predict the effect of mutating these residues on the overall structure of the protein and the interactions of other proteins in this domain. Therefore, we have generated an increased quality model of the Bcl-2 protein including the FLD through modeling. Further, molecular dynamics (MD) simulations were used for FLD optimization, to predict the flexibility, and to determine the stability of the folded FLD. In addition, essential dynamics (ED) was used to predict the collective motions and the essential subspace relevant to Bcl-2 protein function. The predicted average structure and ensemble of MD-simulated structures were submitted to the Protein Model Database (PMDB), and the Bcl-2 structures obtained exhibited enhanced quality. This study should help to elucidate the structural basis for Bcl-2 anti-apoptotic activity regulation through its binding to other proteins via the FLD.

Blunt Snout Bream (Megalobrama amblycephala) MyD88 and TRAF6: Characterisation, Comparative Homology Modelling and Expression

PubMed Central

Tran, Ngoc Tuan; Liu, Han; Jakovlić, Ivan; Wang, Wei-Min

2015-01-01

MyD88 and TRAF6 play an essential role in the innate immune response in most animals. This study reports the full-length MaMyD88 and MaTRAF6 genes identified from the blunt snout bream (Megalobrama amblycephala) transcriptome profile. MaMyD88 is 2501 base pairs (bp) long, encoding a putative protein of 284 amino acids (aa), including the N-terminal DEATH domain of 78 aa and the C-terminal TIR domain of 138 aa. MaTRAF6 is 2252 bp long, encoding a putative protein of 542 aa, including the N-terminal low-complexity region, RING domain (40 aa), a coiled-coil region (64 aa) and C-terminal MATH domain (147 aa). Coding regions of MaMyD88 and MaTRAF6 genomic sequences consisted of five and six exons, respectively. Physicochemical and functional characteristics of the proteins were analysed. Alpha helices were dominant in the secondary structure of the proteins. Homology models of the MaMyD88 and MaTRAF6 domains were constructed applying the comparative modelling method. RT-qPCR was used to analyse the expression of MaMyD88 and MaTRAF6 mRNA transcripts in response to Aeromonas hydrophila challenge. Both genes were highly upregulated in the liver, spleen and kidney during the first 24 h after the challenge. While MyD88 and TRAF6 have been reported in various aquatic species, this is the first report and characterisation of these genes in blunt snout bream. This research also provides evidence of the important roles of these two genes in the blunt snout bream innate immune system. PMID:25830478

A new percolation model for composite solid electrolytes and dispersed ionic conductors

NASA Astrophysics Data System (ADS)

Risyad Hasyim, Muhammad; Lanagan, Michael T.

2018-02-01

Composite solid electrolytes (CSEs) including conductor/insulator composites known as dispersed ionic conductors (DICs) have motivated the development of novel percolation models that describe their conductivity. Despite the long history, existing models lack in one or more key areas: (1) rigorous foundation for their physical theory, (2) explanation for non-universal conductor-insulator transition, (3) classification of DICs, and (4) extension to frequency-domain. This work describes a frequency-domain effective medium approximation (EMA) of a bond percolation model for CSEs. The EMA is derived entirely from Maxwell’s equations and contains basic microstructure parameters. The model was applied successfully to several composite systems from literature. Simulations and fitting of literature data address these key areas and illustrate the interplay between space charge layer properties and bulk microstructure.

Including Magnetostriction in Micromagnetic Models

NASA Astrophysics Data System (ADS)

Conbhuí, Pádraig Ó.; Williams, Wyn; Fabian, Karl; Nagy, Lesleis

2016-04-01

The magnetic anomalies that identify crustal spreading are predominantly recorded by basalts formed at the mid-ocean ridges, whose magnetic signals are dominated by iron-titanium-oxides (Fe3-xTixO4), so called "titanomagnetites", of which the Fe2.4Ti0.6O4 (TM60) phase is the most common. With sufficient quantities of titanium present, these minerals exhibit strong magnetostriction. To date, models of these grains in the pseudo-single domain (PSD) range have failed to accurately account for this effect. In particular, a popular analytic treatment provided by Kittel (1949) for describing the magnetostrictive energy as an effective increase of the anisotropy constant can produce unphysical strains for non-uniform magnetizations. I will present a rigorous approach based on work by Brown (1966) and by Kroner (1958) for including magnetostriction in micromagnetic codes which is suitable for modelling hysteresis loops and finding remanent states in the PSD regime. Preliminary results suggest the more rigorously defined micromagnetic models exhibit higher coercivities and extended single domain ranges when compared to more simplistic approaches.

Recent developments in learning control and system identification for robots and structures

NASA Technical Reports Server (NTRS)

Phan, M.; Juang, J.-N.; Longman, R. W.

1990-01-01

This paper reviews recent results in learning control and learning system identification, with particular emphasis on discrete-time formulation, and their relation to adaptive theory. Related continuous-time results are also discussed. Among the topics presented are proportional, derivative, and integral learning controllers, time-domain formulation of discrete learning algorithms. Newly developed techniques are described including the concept of the repetition domain, and the repetition domain formulation of learning control by linear feedback, model reference learning control, indirect learning control with parameter estimation, as well as related basic concepts, recursive and non-recursive methods for learning identification.

Performing Verification and Validation in Reuse-Based Software Engineering

NASA Technical Reports Server (NTRS)

Addy, Edward A.

1999-01-01

The implementation of reuse-based software engineering not only introduces new activities to the software development process, such as domain analysis and domain modeling, it also impacts other aspects of software engineering. Other areas of software engineering that are affected include Configuration Management, Testing, Quality Control, and Verification and Validation (V&V). Activities in each of these areas must be adapted to address the entire domain or product line rather than a specific application system. This paper discusses changes and enhancements to the V&V process, in order to adapt V&V to reuse-based software engineering.

Control systems using modal domain optical fiber sensors for smart structure applications

NASA Technical Reports Server (NTRS)

Lindner, Douglas K.; Reichard, Karl M.

1991-01-01

Recently, a new class of sensors has emerged for structural control which respond to environmental changes over a significant gauge length; these sensors are called distributed-effect sensors. These sensors can be fabricated with spatially varying sensitivity to the distributed measurand, and can be configured to measure a variety of structural parameters which can not be measured directly using point sensors. Examples of distributed-effect sensors include piezoelectric film, holographic sensors, and modal domain optical fiber sensors. Optical fiber sensors are particularly attractive for smart structure applications because they are flexible, have low mass, and can easily be embedded directly into materials. In this paper we describe the implementation of weighted modal domain optical fiber sensors. The mathematical model of the modal domain optical fiber sensor model is described and used to derive an expression for the sensor sensitivity. The effects of parameter variations on the sensor sensitivity are demonstrated to illustrate methods of spatially varying the sensor sensitivity.

Coupled Data Assimilation for Integrated Earth System Analysis and Prediction: Goals, Challenges, and Recommendations

NASA Technical Reports Server (NTRS)

Penny, Stephen G.; Akella, Santha; Buehner, Mark; Chevallier, Matthieu; Counillon, Francois; Draper, Clara; Frolov, Sergey; Fujii, Yosuke; Karspeck, Alicia; Kumar, Arun

2017-01-01

The purpose of this report is to identify fundamental issues for coupled data assimilation (CDA), such as gaps in science and limitations in forecasting systems, in order to provide guidance to the World Meteorological Organization (WMO) on how to facilitate more rapid progress internationally. Coupled Earth system modeling provides the opportunity to extend skillful atmospheric forecasts beyond the traditional two-week barrier by extracting skill from low-frequency state components such as the land, ocean, and sea ice. More generally, coupled models are needed to support seamless prediction systems that span timescales from weather, subseasonal to seasonal (S2S), multiyear, and decadal. Therefore, initialization methods are needed for coupled Earth system models, either applied to each individual component (called Weakly Coupled Data Assimilation - WCDA) or applied the coupled Earth system model as a whole (called Strongly Coupled Data Assimilation - SCDA). Using CDA, in which model forecasts and potentially the state estimation are performed jointly, each model domain benefits from observations in other domains either directly using error covariance information known at the time of the analysis (SCDA), or indirectly through flux interactions at the model boundaries (WCDA). Because the non-atmospheric domains are generally under-observed compared to the atmosphere, CDA provides a significant advantage over single-domain analyses. Next, we provide a synopsis of goals, challenges, and recommendations to advance CDA: Goals: (a) Extend predictive skill beyond the current capability of NWP (e.g. as demonstrated by improving forecast skill scores), (b) produce physically consistent initial conditions for coupled numerical prediction systems and reanalyses (including consistent fluxes at the domain interfaces), (c) make best use of existing observations by allowing observations from each domain to influence and improve the full earth system analysis, (d) develop a robust observation-based identification and understanding of mechanisms that determine the variability of weather and climate, (e) identify critical weaknesses in coupled models and the earth observing system, (f) generate full-field estimates of unobserved or sparsely observed variables, (g) improve the estimation of the external forcings causing changes to climate, (h) transition successes from idealized CDA experiments to real-world applications. Challenges: (a) Modeling at the interfaces between interacting components of coupled Earth system models may be inadequate for estimating uncertainty or error covariances between domains, (b) current data assimilation methods may be insufficient to simultaneously analyze domains containing multiple spatiotemporal scales of interest, (c) there is no standardization of observation data or their delivery systems across domains, (d) the size and complexity of many large-scale coupled Earth system models makes it is difficult to accurately represent uncertainty due to model parameters and coupling parameters, (e) model errors lead to local biases that can transfer between the different Earth system components and lead to coupled model biases and long-term model drift, (e) information propagation across model components with different spatiotemporal scales is extremely complicated, and must be improved in current coupled modeling frameworks, (h) there is insufficient knowledge on how to represent evolving errors in non-atmospheric model components (e.g. as sea ice, land and ocean) on the timescales of NWP.

A core observational data model for enhancing the interoperability of ontologically annotated environmental data

NASA Astrophysics Data System (ADS)

Schildhauer, M.; Bermudez, L. E.; Bowers, S.; Dibner, P. C.; Gries, C.; Jones, M. B.; McGuinness, D. L.; Cao, H.; Cox, S. J.; Kelling, S.; Lagoze, C.; Lapp, H.; Madin, J.

2010-12-01

Research in the environmental sciences often requires accessing diverse data, collected by numerous data providers over varying spatiotemporal scales, incorporating specialized measurements from a range of instruments. These measurements are typically documented using idiosyncratic, disciplinary specific terms, and stored in management systems ranging from desktop spreadsheets to the Cloud, where the information is often further decomposed or stylized in unpredictable ways. This situation creates major informatics challenges for broadly discovering, interpreting, and merging the data necessary for integrative earth science research. A number of scientific disciplines have recognized these issues, and been developing semantically enhanced data storage frameworks, typically based on ontologies, to enable communities to better circumscribe and clarify the content of data objects within their domain of practice. There is concern, however, that cross-domain compatibility of these semantic solutions could become problematic. We describe here our efforts to address this issue by developing a core, unified Observational Data Model, that should greatly facilitate interoperability among the semantic solutions growing organically within diverse scientific domains. Observational Data Models have emerged independently from several distinct scientific communities, including the biodiversity sciences, ecology, evolution, geospatial sciences, and hydrology, to name a few. Informatics projects striving for data integration within each of these domains had converged on identifying "observations" and "measurements" as fundamental abstractions that provide useful "templates" through which scientific data can be linked— at the structural, composited, or even cell value levels— to domain terms stored in ontologies or other forms of controlled vocabularies. The Scientific Observations Network, SONet (http://sonet.ecoinformatics.org) brings together a number of these observational data efforts, and is harmonizing their models. The specific observational data models currently under consideration include the OGC's Observations and Measurements Encoding Standard, O&M; the ecological community's Extensible Observation Ontology, OBOE'; the evolutionary community's Entity-Quality model, EQ; and the VSTO core classes, intended for describing atmospheric and solar-terrestrial phenomena, VSTO.OWL. These models all share high structural similarities, expressed in different languages (e.g. UML or OWL), and are intended for use with very different forms of data. The main focus of this talk will be describing these Observational Data Models, and more importantly, how harmonizing these will catalyze semantically enhanced access to large additional data resources across the earth and life sciences.

Verification and validation of a Work Domain Analysis with turing machine task analysis.

PubMed

Rechard, J; Bignon, A; Berruet, P; Morineau, T

2015-03-01

While the use of Work Domain Analysis as a methodological framework in cognitive engineering is increasing rapidly, verification and validation of work domain models produced by this method are becoming a significant issue. In this article, we propose the use of a method based on Turing machine formalism named "Turing Machine Task Analysis" to verify and validate work domain models. The application of this method on two work domain analyses, one of car driving which is an "intentional" domain, and the other of a ship water system which is a "causal domain" showed the possibility of highlighting improvements needed by these models. More precisely, the step by step analysis of a degraded task scenario in each work domain model pointed out unsatisfactory aspects in the first modelling, like overspecification, underspecification, omission of work domain affordances, or unsuitable inclusion of objects in the work domain model. Copyright © 2014 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

PubMed

Liu, Bernard A

2017-01-01

Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.

Ground Operations Autonomous Control and Integrated Health Management

NASA Technical Reports Server (NTRS)

Daniels, James

2014-01-01

The Ground Operations Autonomous Control and Integrated Health Management plays a key role for future ground operations at NASA. The software that is integrated into this system is called G2 2011 Gensym. The purpose of this report is to describe the Ground Operations Autonomous Control and Integrated Health Management with the use of the G2 Gensym software and the G2 NASA toolkit for Integrated System Health Management (ISHM) which is a Computer Software Configuration Item (CSCI). The decision rationale for the use of the G2 platform is to develop a modular capability for ISHM and AC. Toolkit modules include knowledge bases that are generic and can be applied in any application domain module. That way, there's a maximization of reusability, maintainability, and systematic evolution, portability, and scalability. Engine modules are generic, while application modules represent the domain model of a specific application. Furthermore, the NASA toolkit, developed since 2006 (a set of modules), makes it possible to create application domain models quickly, using pre-defined objects that include sensors and components libraries for typical fluid, electrical, and mechanical systems.

A Critique of Selected References on Educational Cost Effectiveness with a Resource - Utility Model To Improve Resource Allocation.

ERIC Educational Resources Information Center

Cleckner, John

The author reviews five cost-effectiveness basic models including log-log correlational, general utility theory, simultaneous equations, nonlinear theoretical, and feedback. Several suggestions are made to improve the models and increase the domain of problems that can be considered by the models. In the second part of the paper, the author…

A hybrid-domain approach for modeling climate data time series

NASA Astrophysics Data System (ADS)

Wen, Qiuzi H.; Wang, Xiaolan L.; Wong, Augustine

2011-09-01

In order to model climate data time series that often contain periodic variations, trends, and sudden changes in mean (mean shifts, mostly artificial), this study proposes a hybrid-domain (HD) algorithm, which incorporates a time domain test and a newly developed frequency domain test through an iterative procedure that is analogue to the well known backfitting algorithm. A two-phase competition procedure is developed to address the confounding issue between modeling periodic variations and mean shifts. A variety of distinctive features of climate data time series, including trends, periodic variations, mean shifts, and a dependent noise structure, can be modeled in tandem using the HD algorithm. This is particularly important for homogenization of climate data from a low density observing network in which reference series are not available to help preserve climatic trends and long-term periodic variations, preventing them from being mistaken as artificial shifts. The HD algorithm is also powerful in estimating trend and periodicity in a homogeneous data time series (i.e., in the absence of any mean shift). The performance of the HD algorithm (in terms of false alarm rate and hit rate in detecting shifts/cycles, and estimation accuracy) is assessed via a simulation study. Its power is further illustrated through its application to a few climate data time series.

Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods

PubMed Central

Chasin, Rachel; Rumshisky, Anna; Uzuner, Ozlem; Szolovits, Peter

2014-01-01

Objective To evaluate state-of-the-art unsupervised methods on the word sense disambiguation (WSD) task in the clinical domain. In particular, to compare graph-based approaches relying on a clinical knowledge base with bottom-up topic-modeling-based approaches. We investigate several enhancements to the topic-modeling techniques that use domain-specific knowledge sources. Materials and methods The graph-based methods use variations of PageRank and distance-based similarity metrics, operating over the Unified Medical Language System (UMLS). Topic-modeling methods use unlabeled data from the Multiparameter Intelligent Monitoring in Intensive Care (MIMIC II) database to derive models for each ambiguous word. We investigate the impact of using different linguistic features for topic models, including UMLS-based and syntactic features. We use a sense-tagged clinical dataset from the Mayo Clinic for evaluation. Results The topic-modeling methods achieve 66.9% accuracy on a subset of the Mayo Clinic's data, while the graph-based methods only reach the 40–50% range, with a most-frequent-sense baseline of 56.5%. Features derived from the UMLS semantic type and concept hierarchies do not produce a gain over bag-of-words features in the topic models, but identifying phrases from UMLS and using syntax does help. Discussion Although topic models outperform graph-based methods, semantic features derived from the UMLS prove too noisy to improve performance beyond bag-of-words. Conclusions Topic modeling for WSD provides superior results in the clinical domain; however, integration of knowledge remains to be effectively exploited. PMID:24441986

A Constructive Neural-Network Approach to Modeling Psychological Development

ERIC Educational Resources Information Center

Shultz, Thomas R.

2012-01-01

This article reviews a particular computational modeling approach to the study of psychological development--that of constructive neural networks. This approach is applied to a variety of developmental domains and issues, including Piagetian tasks, shift learning, language acquisition, number comparison, habituation of visual attention, concept…

Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain.

PubMed

Hou, Tingjun; Zhang, Wei; Case, David A; Wang, Wei

2008-02-29

Many important protein-protein interactions are mediated by peptide recognition modular domains, such as the Src homology 3 (SH3), SH2, PDZ, and WW domains. Characterizing the interaction interface of domain-peptide complexes and predicting binding specificity for modular domains are critical for deciphering protein-protein interaction networks. Here, we propose the use of an energetic decomposition analysis to characterize domain-peptide interactions and the molecular interaction energy components (MIECs), including van der Waals, electrostatic, and desolvation energy between residue pairs on the binding interface. We show a proof-of-concept study on the amphiphysin-1 SH3 domain interacting with its peptide ligands. The structures of the human amphiphysin-1 SH3 domain complexed with 884 peptides were first modeled using virtual mutagenesis and optimized by molecular mechanics (MM) minimization. Next, the MIECs between domain and peptide residues were computed using the MM/generalized Born decomposition analysis. We conducted two types of statistical analyses on the MIECs to demonstrate their usefulness for predicting binding affinities of peptides and for classifying peptides into binder and non-binder categories. First, combining partial least squares analysis and genetic algorithm, we fitted linear regression models between the MIECs and the peptide binding affinities on the training data set. These models were then used to predict binding affinities for peptides in the test data set; the predicted values have a correlation coefficient of 0.81 and an unsigned mean error of 0.39 compared with the experimentally measured ones. The partial least squares-genetic algorithm analysis on the MIECs revealed the critical interactions for the binding specificity of the amphiphysin-1 SH3 domain. Next, a support vector machine (SVM) was employed to build classification models based on the MIECs of peptides in the training set. A rigorous training-validation procedure was used to assess the performances of different kernel functions in SVM and different combinations of the MIECs. The best SVM classifier gave satisfactory predictions for the test set, indicated by average prediction accuracy rates of 78% and 91% for the binding and non-binding peptides, respectively. We also showed that the performance of our approach on both binding affinity prediction and binder/non-binder classification was superior to the performances of the conventional MM/Poisson-Boltzmann solvent-accessible surface area and MM/generalized Born solvent-accessible surface area calculations. Our study demonstrates that the analysis of the MIECs between peptides and the SH3 domain can successfully characterize the binding interface, and it provides a framework to derive integrated prediction models for different domain-peptide systems.

Field driven magnetic racetrack memory accompanied with the interfacial Dzyaloshinskii-Moriya interaction

NASA Astrophysics Data System (ADS)

Kim, June-Seo; Lee, Hyeon-Jun; Hong, Jung-Il; You, Chun-Yeol

2018-06-01

The in-plane magnetic field pulse driven domain wall motion on a perpendicularly magnetized nanowire is numerically investigated by performing micromagnetic simulations and magnetic domain wall dynamics are evaluated analytically with one-dimensional collective coordinate models including the interfacial Dzyaloshinskii-Moriya interaction. With the action of the precession torque, the chirality and the magnetic field direction dependent displacements of the magnetic domain walls are clearly observed. In order to move Bloch type and Neel type domain walls, a longitudinal and a transverse in-plane magnetic field pulse are required, respectively. The domain wall type (Bloch or Neel) can easily be determined by the dynamic motion of the domain walls under the applied pulse fields. By applying a temporally asymmetric in-plane field pulse and successive notches in the perpendicularly magnetized nanowire strip line with a proper interval, the concept of racetrack memory based on the synchronous displacements of the chirality dependent multiple domain walls is verified to be feasible. Requirement of multiple domain walls with homogeneous chirality is achieved with the help of Dzyaloshinskii-Moriya interaction.

Structure and regulatory role of the C-terminal winged helix domain of the archaeal minichromosome maintenance complex

PubMed Central

Wiedemann, Christoph; Szambowska, Anna; Häfner, Sabine; Ohlenschläger, Oliver; Gührs, Karl-Heinz; Görlach, Matthias

2015-01-01

The minichromosome maintenance complex (MCM) represents the replicative DNA helicase both in eukaryotes and archaea. Here, we describe the solution structure of the C-terminal domains of the archaeal MCMs of Sulfolobus solfataricus (Sso) and Methanothermobacter thermautotrophicus (Mth). Those domains consist of a structurally conserved truncated winged helix (WH) domain lacking the two typical ‘wings’ of canonical WH domains. A less conserved N-terminal extension links this WH module to the MCM AAA+ domain forming the ATPase center. In the Sso MCM this linker contains a short α-helical element. Using Sso MCM mutants, including chimeric constructs containing Mth C-terminal domain elements, we show that the ATPase and helicase activity of the Sso MCM is significantly modulated by the short α-helical linker element and by N-terminal residues of the first α-helix of the truncated WH module. Finally, based on our structural and functional data, we present a docking-derived model of the Sso MCM, which implies an allosteric control of the ATPase center by the C-terminal domain. PMID:25712103

Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?

PubMed

Karev, Georgy P; Wolf, Yuri I; Koonin, Eugene V

2003-10-12

The distributions of many genome-associated quantities, including the membership of paralogous gene families can be approximated with power laws. We are interested in developing mathematical models of genome evolution that adequately account for the shape of these distributions and describe the evolutionary dynamics of their formation. We show that simple stochastic models of genome evolution lead to power-law asymptotics of protein domain family size distribution. These models, called Birth, Death and Innovation Models (BDIM), represent a special class of balanced birth-and-death processes, in which domain duplication and deletion rates are asymptotically equal up to the second order. The simplest, linear BDIM shows an excellent fit to the observed distributions of domain family size in diverse prokaryotic and eukaryotic genomes. However, the stochastic version of the linear BDIM explored here predicts that the actual size of large paralogous families is reached on an unrealistically long timescale. We show that introduction of non-linearity, which might be interpreted as interaction of a particular order between individual family members, allows the model to achieve genome evolution rates that are much better compatible with the current estimates of the rates of individual duplication/loss events.

Serine protease-related proteins in the malaria mosquito, Anopheles gambiae.

PubMed

Cao, Xiaolong; Gulati, Mansi; Jiang, Haobo

2017-09-01

Insect serine proteases (SPs) and serine protease homologs (SPHs) participate in digestion, defense, development, and other physiological processes. In mosquitoes, some clip-domain SPs and SPHs (i.e. CLIPs) have been investigated for possible roles in antiparasitic responses. In a recent test aimed at improving quality of gene models in the Anopheles gambiae genome using RNA-seq data, we observed various discrepancies between gene models in AgamP4.5 and corresponding sequences selected from those modeled by Cufflinks, Trinity and Bridger. Here we report a comparative analysis of the 337 SP-related proteins in A. gambiae by examining their domain structures, sequence diversity, chromosomal locations, and expression patterns. One hundred and ten CLIPs contain 1 to 5 clip domains in addition to their protease domains (PDs) or non-catalytic, protease-like domains (PLDs). They are divided into five subgroups: CLIPAs (22) are clip 1-5 -PLD; CLIPBs (29), CLIPCs (12) and CLIPDs (14) are mainly clip-PD; most CLIPEs (33) have a domain structure of PD/PLD-PLD-clip-PLD 0-1 . While expression of the CLIP genes in group-1 is generally low and detected in various tissue- and stage-specific RNA-seq libraries, some putative GPs/GPHs (i.e. single domain gut SPs/SPHs) in group-2 are highly expressed in midgut, whole larva or whole adult libraries. In comparison, 46 SPs, 26 SPHs, and 37 multi-domain SPs/SPHs (i.e. PD/PLD-PLD ≥1 ) in group-3 do not seem to be specifically expressed in digestive tract. There are 16 SPs and 2 SPH containing other types of putative regulatory domains (e.g. LDLa, CUB, Gd). Of the 337 SP and SPH genes, 159 were sorted into 46 groups (2-8 members/group) based on similar phylogenetic tree position, chromosomal location, and expression profile. This information and analysis, including improved gene models and protein sequences, constitute a solid foundation for functional analysis of the SP-related proteins in A. gambiae. Copyright © 2017 Elsevier Ltd. All rights reserved.

A novel CFS-PML boundary condition for transient electromagnetic simulation using a fictitious wave domain method

NASA Astrophysics Data System (ADS)

Hu, Yanpu; Egbert, Gary; Ji, Yanju; Fang, Guangyou

2017-01-01

In this study, we apply fictitious wave domain (FWD) methods, based on the correspondence principle for the wave and diffusion fields, to finite difference (FD) modeling of transient electromagnetic (TEM) diffusion problems for geophysical applications. A novel complex frequency shifted perfectly matched layer (PML) boundary condition is adapted to the FWD to truncate the computational domain, with the maximum electromagnetic wave propagation velocity in the FWD used to set the absorbing parameters for the boundary layers. Using domains of varying spatial extent we demonstrate that these boundary conditions offer significant improvements over simpler PML approaches, which can result in spurious reflections and large errors in the FWD solutions, especially for low frequencies and late times. In our development, resistive air layers are directly included in the FWD, allowing simulation of TEM responses in the presence of topography, as is commonly encountered in geophysical applications. We compare responses obtained by our new FD-FWD approach and with the spectral Lanczos decomposition method on 3-D resistivity models of varying complexity. The comparisons demonstrate that our absorbing boundary condition in FWD for the TEM diffusion problems works well even in complex high-contrast conductivity models.

Triangular node for Transmission-Line Modeling (TLM) applied to bio-heat transfer.

PubMed

Milan, Hugo F M; Gebremedhin, Kifle G

2016-12-01

Transmission-Line Modeling (TLM) is a numerical method used to solve complex and time-domain bio-heat transfer problems. In TLM, rectangles are used to discretize two-dimensional problems. The drawback in using rectangular shapes is that instead of refining only the domain of interest, a large additional domain will also be refined in the x and y axes, which results in increased computational time and memory space. In this paper, we developed a triangular node for TLM applied to bio-heat transfer that does not have the drawback associated with the rectangular nodes. The model includes heat source, blood perfusion (advection), boundary conditions and initial conditions. The boundary conditions could be adiabatic, temperature, heat flux, or convection. A matrix equation for TLM, which simplifies the solution of time-domain problems or solves steady-state problems, was also developed. The predicted results were compared against results obtained from the solution of a simplified two-dimensional problem, and they agreed within 1% for a mesh length of triangular faces of 59µm±9µm (mean±standard deviation) and a time step of 1ms. Copyright © 2016 Elsevier Ltd. All rights reserved.

Generic domain models in software engineering

NASA Technical Reports Server (NTRS)

Maiden, Neil

1992-01-01

This paper outlines three research directions related to domain-specific software development: (1) reuse of generic models for domain-specific software development; (2) empirical evidence to determine these generic models, namely elicitation of mental knowledge schema possessed by expert software developers; and (3) exploitation of generic domain models to assist modelling of specific applications. It focuses on knowledge acquisition for domain-specific software development, with emphasis on tool support for the most important phases of software development.

Predicting health care utilization in marginalized populations: Black, female, street-based sex workers.

PubMed

Varga, Leah M; Surratt, Hilary L

2014-01-01

Patterns of social and structural factors experienced by vulnerable populations may negatively affect willingness and ability to seek out health care services, and ultimately, their health. The outcome variable was utilization of health care services in the previous 12 months. Using Andersen's Behavioral Model for Vulnerable Populations, we examined self-reported data on utilization of health care services among a sample of 546 Black, street-based, female sex workers in Miami, Florida. To evaluate the impact of each domain of the model on predicting health care utilization, domains were included in the logistic regression analysis by blocks using the traditional variables first and then adding the vulnerable domain variables. The most consistent variables predicting health care utilization were having a regular source of care and self-rated health. The model that included only enabling variables was the most efficient model in predicting health care utilization. Any type of resource, link, or connection to or with an institution, or any consistent point of care, contributes significantly to health care utilization behaviors. A consistent and reliable source for health care may increase health care utilization and subsequently decrease health disparities among vulnerable and marginalized populations, as well as contribute to public health efforts that encourage preventive health. Copyright © 2014 Jacobs Institute of Women's Health. Published by Elsevier Inc. All rights reserved.

The intrinsically disordered C-terminal domain of the measles virus nucleoprotein interacts with the C-terminal domain of the phosphoprotein via two distinct sites and remains predominantly unfolded

PubMed Central

Bourhis, Jean-Marie; Receveur-Bréchot, Véronique; Oglesbee, Michael; Zhang, Xinsheng; Buccellato, Matthew; Darbon, Hervé; Canard, Bruno; Finet, Stéphanie; Longhi, Sonia

2005-01-01

Measles virus is a negative-sense, single-stranded RNA virus within theMononegavirales order,which includes several human pathogens, including rabies, Ebola, Nipah, and Hendra viruses. Themeasles virus nucleoprotein consists of a structured N-terminal domain, and of an intrinsically disordered C-terminal domain, NTAIL (aa 401–525), which undergoes induced folding in the presence of the C-terminal domain (XD, aa 459–507) of the viral phosphoprotein. With in NTAIL, an α-helical molecular recognition element (α-MoRE, aa 488–499) involved in binding to P and in induced folding was identified and then observed in the crystal structure of XD. Using small-angle X-ray scattering, we have derived a low-resolution structural model of the complex between XD and NTAIL, which shows that most of NTAIL remains disordered in the complex despite P-induced folding within the α-MoRE. The model consists of an extended shape accommodating the multiple conformations adopted by the disordered N-terminal region of NTAIL, and of a bulky globular region, corresponding to XD and to the C terminus of NTAIL (aa 486–525). Using surface plasmon resonance, circular dichroism, fluorescence spectroscopy, and heteronuclear magnetic resonance, we show that NTAIL has an additional site (aa 517–525) involved in binding to XD but not in the unstructured-to-structured transition. This work provides evidence that intrinsically disordered domains can establish complex interactions with their partners, and can contact them through multiple sites that do not all necessarily gain regular secondary structure. PMID:16046624

Should Sensory Impairment Be Considered in Frailty Assessment? A Study in the GAZEL Cohort.

PubMed

Linard, M; Herr, M; Aegerter, P; Czernichow, S; Goldberg, M; Zins, M; Ankri, J

2016-01-01

The assessment of sensory difficulties is sometimes included in the screening of frailty in ageing population. This study aimed to compare the prevalence of frailty and associated risk of adverse outcomes depending on whether sensory difficulties participated in the definition of frailty. Prospective cohort study - GAZEL cohort. France. The 13,128 subjects who completed a questionnaire in 2012. According to the Strawbridge questionnaire, subjects were considered frail if they reported difficulties in two domains or more among physical, nutritive, cognitive and sensory domains. The risk of adverse health outcomes was assessed by using logistic regression models (hospitalisations, onset of difficulty in performing movements of everyday life) and multivariate Cox proportional hazards models (mortality). Mean age was 66.8 +/- 3.4 years and 73.8% were males. The prevalence of frailty varied from 4.4 to 14.2% depending on whether the sensory domain was excluded or included. During follow-up, 182 deaths (1.4%), 479 hospitalisations (3.6%) and 703 cases of new disability (8.0%) were observed. Both definitions of frailty predicted the onset of difficulties to perform everyday movements, with 2 to 3-fold increase in the risk. The inclusion of the sensory domain in the definition made frailty predictive of hospitalisations (Odds Ratio 1.31 [1.01-1.70]) but the association with mortality was only observed when sensory difficulties were ignored (Hazard Ratio 2.28 [1.32-3.92]). The inclusion of a sensory domain into a frailty screening instrument has a major impact in terms of prevalence and modifies the risk profile associated with frailty. In order to develop the use of frailty screening instruments in clinical practice, further researches will need to carefully evaluate the impact on risk prediction of the different domains involved.

Skill Acquisition in Ski Instruction and the Skill Model's Application to Treating Anorexia Nervosa

ERIC Educational Resources Information Center

Duesund, Liv; Jespersen, Ejgil

2004-01-01

The Dreyfus skill model has a wide range of applications to various domains, including sport, nursing, engineering, flying, and so forth. In this article, the authors discuss the skill model in connection with two different research projects concerning ski instruction and treating anorexia nervosa. The latter project has been published but not in…

Synergy of the Developed 6D BIM Framework and Conception of the nD BIM Framework and nD BIM Process Ontology

ERIC Educational Resources Information Center

O'Keeffe, Shawn Edward

2013-01-01

The author developed a unified nD framework and process ontology for Building Information Modeling (BIM). The research includes a framework developed for 6D BIM, nD BIM, and nD ontology that defines the domain and sub-domain constructs for future nD BIM dimensions. The nD ontology defines the relationships of kinds within any new proposed…

Modular System for Shelves and Coasts (MOSSCO v1.0) - a flexible and multi-component framework for coupled coastal ocean ecosystem modelling

NASA Astrophysics Data System (ADS)

Lemmen, Carsten; Hofmeister, Richard; Klingbeil, Knut; Hassan Nasermoaddeli, M.; Kerimoglu, Onur; Burchard, Hans; Kösters, Frank; Wirtz, Kai W.

2018-03-01

Shelf and coastal sea processes extend from the atmosphere through the water column and into the seabed. These processes reflect intimate interactions between physical, chemical, and biological states on multiple scales. As a consequence, coastal system modelling requires a high and flexible degree of process and domain integration; this has so far hardly been achieved by current model systems. The lack of modularity and flexibility in integrated models hinders the exchange of data and model components and has historically imposed the supremacy of specific physical driver models. We present the Modular System for Shelves and Coasts (MOSSCO; http://www.mossco.de), a novel domain and process coupling system tailored but not limited to the coupling challenges of and applications in the coastal ocean. MOSSCO builds on the Earth System Modeling Framework (ESMF) and on the Framework for Aquatic Biogeochemical Models (FABM). It goes beyond existing technologies by creating a unique level of modularity in both domain and process coupling, including a clear separation of component and basic model interfaces, flexible scheduling of several tens of models, and facilitation of iterative development at the lab and the station and on the coastal ocean scale. MOSSCO is rich in metadata and its concepts are also applicable outside the coastal domain. For coastal modelling, it contains dozens of example coupling configurations and tested set-ups for coupled applications. Thus, MOSSCO addresses the technology needs of a growing marine coastal Earth system community that encompasses very different disciplines, numerical tools, and research questions.

M-and-C Domain Map Maker: an environment complimenting MDE with M-and-C knowledge and ensuring solution completeness

NASA Astrophysics Data System (ADS)

Patwari, Puneet; Choudhury, Subhrojyoti R.; Banerjee, Amar; Swaminathan, N.; Pandey, Shreya

2016-07-01

Model Driven Engineering (MDE) as a key driver to reduce development cost of M&C systems is beginning to find acceptance across scientific instruments such as Radio Telescopes and Nuclear Reactors. Such projects are adopting it to reduce time to integrate, test and simulate their individual controllers and increase reusability and traceability in the process. The creation and maintenance of models is still a significant challenge to realizing MDE benefits. Creating domain-specific modelling environments reduces the barriers, and we have been working along these lines, creating a domain-specific language and environment based on an M&C knowledge model. However, large projects involve several such domains, and there is still a need to interconnect the domain models, in order to ensure modelling completeness. This paper presents a knowledge-centric approach to doing that, by creating a generic system model that underlies the individual domain knowledge models. We present our vision for M&C Domain Map Maker, a set of processes and tools that enables explication of domain knowledge in terms of domain models with mutual consistency relationships to aid MDE.

Global boundary flattening transforms for acoustic propagation under rough sea surfaces.

PubMed

Oba, Roger M

2010-07-01

This paper introduces a conformal transform of an acoustic domain under a one-dimensional, rough sea surface onto a domain with a flat top. This non-perturbative transform can include many hundreds of wavelengths of the surface variation. The resulting two-dimensional, flat-topped domain allows direct application of any existing, acoustic propagation model of the Helmholtz or wave equation using transformed sound speeds. Such a transform-model combination applies where the surface particle velocity is much slower than sound speed, such that the boundary motion can be neglected. Once the acoustic field is computed, the bijective (one-to-one and onto) mapping permits the field interpolation in terms of the original coordinates. The Bergstrom method for inverse Riemann maps determines the transform by iterated solution of an integral equation for a surface matching term. Rough sea surface forward scatter test cases provide verification of the method using a particular parabolic equation model of the Helmholtz equation.

A Pirate's Life: A Model and a Metaphor for Learning.

ERIC Educational Resources Information Center

Solomon, David L.

2002-01-01

Discusses various ways in which context may be interpreted to enhance learning and performance; illustrates domains of learning using a hockey team as an example; and suggests implications for learning, performance, and instructional design. Highlights include an ecological systems model; and examples of individual development, team learning, and…

A case Study of Applying Object-Relational Persistence in Astronomy Data Archiving

NASA Astrophysics Data System (ADS)

Yao, S. S.; Hiriart, R.; Barg, I.; Warner, P.; Gasson, D.

2005-12-01

The NOAO Science Archive (NSA) team is developing a comprehensive domain model to capture the science data in the archive. Java and an object model derived from the domain model weil address the application layer of the archive system. However, since RDBMS is the best proven technology for data management, the challenge is the paradigm mismatch between the object and the relational models. Transparent object-relational mapping (ORM) persistence is a successful solution to this challenge. In the data modeling and persistence implementation of NSA, we are using Hibernate, a well-accepted ORM tool, to bridge the object model in the business tier and the relational model in the database tier. Thus, the database is isolated from the Java application. The application queries directly on objects using a DBMS-independent object-oriented query API, which frees the application developers from the low level JDBC and SQL so that they can focus on the domain logic. We present the detailed design of the NSA R3 (Release 3) data model and object-relational persistence, including mapping, retrieving and caching. Persistence layer optimization and performance tuning will be analyzed. The system is being built on J2EE, so the integration of Hibernate into the EJB container and the transaction management are also explored.

Sexual Quality of Life and Aging: A Prospective Study of a Nationally Representative Sample

PubMed Central

Forbes, Miriam K.; Eaton, Nicholas R.; Krueger, Robert F.

2016-01-01

Unlike other life domains, sexual quality of life (SQoL) has a negative relationship with age. This study disentangled the effect of age in this relationship from confounding sociocultural influences (e.g., the period of time in which data were collected, and cohort differences), and aimed to understand the roles of other sexual domains (i.e., frequency, perceived control, thought and effort invested in sex, and number of sexual partners). We analyzed data from the longitudinal Midlife in the United States study (n = 6,278; age range 20–93), which were collected between 1995 and 2013. Repeated measures linear mixed-effects models showed that age was the most robust time-related predictor of declining SQoL. However, after the sexual domains were included in the model, age had a positive relationship with SQoL, and older adults’ SQoL was differentially influenced by the quality—not quantity—of sex. When partnership characteristics were included in the model, age was no longer related to SQoL. These findings suggest that aging may be associated with the acquisition of skills and strategies that can buffer age-related declines in SQoL, particularly in the context of a positive relationship. We summarize these findings as sexual wisdom. PMID:27798838

Sexual Quality of Life and Aging: A Prospective Study of a Nationally Representative Sample.

PubMed

Forbes, Miriam K; Eaton, Nicholas R; Krueger, Robert F

2017-02-01

Unlike other life domains, sexual quality of life (SQoL) has a negative relationship with age. This study disentangled the effect of age in this relationship from confounding sociocultural influences (e.g., the period of time in which data were collected, and cohort differences) and aimed to understand the roles of other sexual domains (i.e., frequency, perceived control, thought and effort invested in sex, and number of sexual partners). We analyzed data from the longitudinal Midlife in the United States study (n = 6,278; age range 20-93), which were collected between 1995 and 2013. Repeated measures linear mixed-effects models showed that age was the most robust time-related predictor of declining SQoL. However, after the sexual domains were included in the model, age had a positive relationship with SQoL and older adults' SQoL was differentially influenced by the quality-not quantity-of sex. When partnership characteristics were included in the model, age was no longer related to SQoL. These findings suggest that aging may be associated with the acquisition of skills and strategies that can buffer age-related declines in SQoL, particularly in the context of a positive relationship. We summarize these findings as sexual wisdom.

Interactions of the Auxilin-1 PTEN-like Domain with Model Membranes Result in Nanoclustering of Phosphatidyl Inositol Phosphates

PubMed Central

Kalli, Antreas C.; Morgan, Gareth; Sansom, Mark S.P.

2013-01-01

Auxilin-1 is a neuron-specific membrane-binding protein involved in a late stage of clathrin-mediated endocytosis. It recruits Hsc70, thus initiating uncoating of the clathrin-coated vesicles. Interactions of auxilin-1 with the vesicle membrane are crucial for this function and are mediated via an N-terminal PTEN-like domain. We have used multiscale molecular dynamics simulations to probe the interactions of the auxilin-1 PTEN-like domain with lipid bilayers containing differing phospholipid composition, including bilayers containing phosphatidyl inositol phosphates. Our results suggest a novel, to our knowledge, model for the auxilin/membrane encounter and subsequent interactions. Negatively charged lipids (especially PIP2) enhance binding of auxilin to lipid bilayers and facilitate its correct orientation relative to the membrane. Mutations in three basic residues (R301E/R307E/K311E) of the C2 subdomain of the PTEN-like domain perturbed its interaction with the bilayer, changing its orientation. The interaction of membrane-bound auxilin-1 PTEN-like domain with negatively charged lipid headgroups results in nanoclustering of PIP2 molecules in the adjacent bilayer leaflet. PMID:23823232

Identification and Characterization of C-type Lectins in Ostrinia furnacalis (Lepidoptera: Pyralidae)

PubMed Central

Shen, Dongxu; Wang, Lei; Ji, Jiayue; Liu, Qizhi; An, Chunju

2018-01-01

Abstract C-type lectins (CTLs) are a large family of calcium-dependent carbohydrate-binding proteins. They function primarily in cell adhesion and immunity by recognizing various glycoconjugates. We identified 14 transcripts encoding proteins with one or two CTL domains from the transcriptome from Asian corn borer, Ostrinia furnacalis (Guenée; Lepidoptera: Pyralidae). Among them, five (OfCTL-S1 through S5) only contain one CTL domain, the remaining nine (OfIML-1 through 9) have two tandem CTL domains. Five CTL-Ss and six OfIMLs have a signal peptide are likely extracellular while another two OfIMLs might be cytoplasmic. Phylogenetic analysis indicated that OfCTL-Ss had 1:1 orthologs in Lepidoptera, Diptera, Coleoptera and Hymenoptera species, but OfIMLs only clustered with immulectins (IMLs) from Lepidopteran. Structural modeling revealed that the 22 CTL domains adopt a similar double-loop fold consisting of β-sheets and α-helices. The key residues for calcium-dependent or independent binding of specific carbohydrates by CTL domains were predicted with homology modeling. Expression profiles assay showed distinct expression pattern of 14 CTLs: the expression and induction were related to the developmental stages and infected microorganisms. Overall, our work including the gene identification, sequence alignment, phylogenetic analysis, structural modeling, and expression profile assay would provide a valuable basis for the further functional studies of O. furnacalis CTLs. PMID:29718486

Comparison of patient perceived primary care quality in public clinics, public hospitals and private clinics in rural China.

PubMed

Wang, Wenhua; Maitland, Elizabeth; Nicholas, Stephen; Loban, Ekaterina; Haggerty, Jeannie

2017-10-03

In rural China, patients have free choice of health facilities for outpatient services. Comparison studies exploring the attributes of different health facilities can help identify optimal primary care service models. Using a representative sample of Chinese provinces, this study aimed to compare patients' rating of three primary care service models used by rural residents (public clinics, public hospitals and private clinics) on a range of health care attributes related to responsiveness. This was a secondary analysis using the household survey data from World Health Organization (WHO) Study on global AGEing and adult health (SAGE). Using a multistage cluster sampling strategy, eight provinces were selected and finally 3435 overall respondents reporting they had visited public clinics, public hospitals or private clinics during the last year, were included in our analysis. Five items were used to measure patient perceived quality in five domains including prompt attention, communication and autonomy, dignity and confidentiality. ANOVA and Turkey's post hoc tests were used to conduct comparative analysis of five domains. Separate multivariate linear regression models were estimated to examine the association of primary care service models with each domain after controlling for patient characteristics. The distribution of last health facilities visited was: 29.5% public clinics; 31.2% public hospitals and; 39.3% private clinics. Public clinics perform best in all five domains: prompt attention (4.15), dignity (4.17), communication (4.07), autonomy (4.05) and confidentiality (4.02). Public hospitals perform better than private clinics in dignity (4.03 vs 3.94), communication (3.97 vs 3.82), autonomy (3.92 vs 3.74) and confidentiality (3.94 vs 3.73), but equivalently in prompt attention (3.92 vs 3.93). Rural residents who are older, wealthier, and with higher self-rated health status have significantly higher patient perceived quality of care in all domains. Rural public clinics, which share many characteristics with the optimal primary care delivery model, should be strongly strengthened to respond to patients' needs. Better doctor-patient interaction training would improve respect, confidentiality, autonomy and, most importantly, health care quality for rural patients.

Stable static structures in models with higher-order derivatives

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

Bazeia, D., E-mail: bazeia@fisica.ufpb.br; Departamento de Física, Universidade Federal de Campina Grande, 58109-970 Campina Grande, PB; Lobão, A.S.

2015-09-15

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

Process-based model predictions of hurricane induced morphodynamic change on low-lying barrier islands

USGS Publications Warehouse

Plant, Nathaniel G.; Thompson, David M.; Elias, Edwin; Wang, Ping; Rosati, Julie D.; Roberts, Tiffany M.

2011-01-01

Using Delft3D, a Chandeleur Island model was constructed to examine the sediment-transport patterns and morphodynamic change caused by Hurricane Katrina and similar storm events. The model setup included a coarse Gulf of Mexico domain and a nested finer-resolution Chandeleur Island domain. The finer-resolution domain resolved morphodynamic processes driven by storms and tides. A sensitivity analysis of the simulated morphodynamic response was performed to investigate the effects of variations in surge levels. The Chandeleur morphodynamic model reproduced several important features that matched observed morphodynamic changes. A simulation of bathymetric change driven by storm surge alone (no waves) along the central portion of the Chandeleur Islands showed (1) a general landward retreat and lowering of the island chain and (2) multiple breaches that increased the degree of island dissection. The locations of many of the breaches correspond with the low-lying or narrow sections of the initial bathymetry. The major part of the morphological change occurred prior to the peak of the surge when overtopping of the islands produced a strong water-level gradient and induced significant flow velocities.

No-Reference Image Quality Assessment by Wide-Perceptual-Domain Scorer Ensemble Method.

PubMed

Liu, Tsung-Jung; Liu, Kuan-Hsien

2018-03-01

A no-reference (NR) learning-based approach to assess image quality is presented in this paper. The devised features are extracted from wide perceptual domains, including brightness, contrast, color, distortion, and texture. These features are used to train a model (scorer) which can predict scores. The scorer selection algorithms are utilized to help simplify the proposed system. In the final stage, the ensemble method is used to combine the prediction results from selected scorers. Two multiple-scale versions of the proposed approach are also presented along with the single-scale one. They turn out to have better performances than the original single-scale method. Because of having features from five different domains at multiple image scales and using the outputs (scores) from selected score prediction models as features for multi-scale or cross-scale fusion (i.e., ensemble), the proposed NR image quality assessment models are robust with respect to more than 24 image distortion types. They also can be used on the evaluation of images with authentic distortions. The extensive experiments on three well-known and representative databases confirm the performance robustness of our proposed model.

Performance Dependences of Multiplication Layer Thickness for InP/InGaAs Avalanche Photodiodes Based on Time Domain Modeling

NASA Technical Reports Server (NTRS)

Xiao, Yegao; Bhat, Ishwara; Abedin, M. Nurul

2005-01-01

InP/InGaAs avalanche photodiodes (APDs) are being widely utilized in optical receivers for modern long haul and high bit-rate optical fiber communication systems. The separate absorption, grading, charge, and multiplication (SAGCM) structure is an important design consideration for APDs with high performance characteristics. Time domain modeling techniques have been previously developed to provide better understanding and optimize design issues by saving time and cost for the APD research and development. In this work, performance dependences on multiplication layer thickness have been investigated by time domain modeling. These performance characteristics include breakdown field and breakdown voltage, multiplication gain, excess noise factor, frequency response and bandwidth etc. The simulations are performed versus various multiplication layer thicknesses with certain fixed values for the areal charge sheet density whereas the values for the other structure and material parameters are kept unchanged. The frequency response is obtained from the impulse response by fast Fourier transformation. The modeling results are presented and discussed, and design considerations, especially for high speed operation at 10 Gbit/s, are further analyzed.

Appropriate Domain Size for Groundwater Flow Modeling with a Discrete Fracture Network Model.

PubMed

Ji, Sung-Hoon; Koh, Yong-Kwon

2017-01-01

When a discrete fracture network (DFN) is constructed from statistical conceptualization, uncertainty in simulating the hydraulic characteristics of a fracture network can arise due to the domain size. In this study, the appropriate domain size, where less significant uncertainty in the stochastic DFN model is expected, was suggested for the Korea Atomic Energy Research Institute Underground Research Tunnel (KURT) site. The stochastic DFN model for the site was established, and the appropriate domain size was determined with the density of the percolating cluster and the percolation probability using the stochastically generated DFNs for various domain sizes. The applicability of the appropriate domain size to our study site was evaluated by comparing the statistical properties of stochastically generated fractures of varying domain sizes and estimating the uncertainty in the equivalent permeability of the generated DFNs. Our results show that the uncertainty of the stochastic DFN model is acceptable when the modeling domain is larger than the determined appropriate domain size, and the appropriate domain size concept is applicable to our study site. © 2016, National Ground Water Association.

Structural insights into SAM domain‐mediated tankyrase oligomerization

PubMed Central

DaRosa, Paul A.; Ovchinnikov, Sergey

2016-01-01

Abstract Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP‐ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain‐mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head‐to‐tail polymer that facilitates TNKS self‐association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM‐TNKS2 SAM) hetero‐oligomeric structures mediated by their SAM domains. Though wild‐type tankyrase proteins have very low solubility, model‐based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP‐ribosyl)ation (PARylation) and PARylation‐dependent ubiquitylation. PMID:27328430

Using domain knowledge and domain-inspired discourse model for coreference resolution for clinical narratives

PubMed Central

Roth, Dan

2013-01-01

Objective This paper presents a coreference resolution system for clinical narratives. Coreference resolution aims at clustering all mentions in a single document to coherent entities. Materials and methods A knowledge-intensive approach for coreference resolution is employed. The domain knowledge used includes several domain-specific lists, a knowledge intensive mention parsing, and task informed discourse model. Mention parsing allows us to abstract over the surface form of the mention and represent each mention using a higher-level representation, which we call the mention's semantic representation (SR). SR reduces the mention to a standard form and hence provides better support for comparing and matching. Existing coreference resolution systems tend to ignore discourse aspects and rely heavily on lexical and structural cues in the text. The authors break from this tradition and present a discourse model for “person” type mentions in clinical narratives, which greatly simplifies the coreference resolution. Results This system was evaluated on four different datasets which were made available in the 2011 i2b2/VA coreference challenge. The unweighted average of F1 scores (over B-cubed, MUC and CEAF) varied from 84.2% to 88.1%. These experiments show that domain knowledge is effective for different mention types for all the datasets. Discussion Error analysis shows that most of the recall errors made by the system can be handled by further addition of domain knowledge. The precision errors, on the other hand, are more subtle and indicate the need to understand the relations in which mentions participate for building a robust coreference system. Conclusion This paper presents an approach that makes an extensive use of domain knowledge to significantly improve coreference resolution. The authors state that their system and the knowledge sources developed will be made publicly available. PMID:22781192

Machine learning-based coreference resolution of concepts in clinical documents

PubMed Central

Ware, Henry; Mullett, Charles J; El-Rawas, Oussama

2012-01-01

Objective Coreference resolution of concepts, although a very active area in the natural language processing community, has not yet been widely applied to clinical documents. Accordingly, the 2011 i2b2 competition focusing on this area is a timely and useful challenge. The objective of this research was to collate coreferent chains of concepts from a corpus of clinical documents. These concepts are in the categories of person, problems, treatments, and tests. Design A machine learning approach based on graphical models was employed to cluster coreferent concepts. Features selected were divided into domain independent and domain specific sets. Training was done with the i2b2 provided training set of 489 documents with 6949 chains. Testing was done on 322 documents. Results The learning engine, using the un-weighted average of three different measurement schemes, resulted in an F measure of 0.8423 where no domain specific features were included and 0.8483 where the feature set included both domain independent and domain specific features. Conclusion Our machine learning approach is a promising solution for recognizing coreferent concepts, which in turn is useful for practical applications such as the assembly of problem and medication lists from clinical documents. PMID:22582205

Complex biomembrane mimetics on the sub-nanometer scale

DOE PAGES

Heberle, Frederick A.; Pabst, Georg

2017-07-17

Biomimetic lipid vesicles are indispensable tools for gaining insight into the biophysics of cell physiology on the molecular level. The level of complexity of these model systems has steadily increased, and now spans from domain forming lipid mixtures to asymmetric lipid bilayers. We review recent progress in the development and application of elastic neutron and X-ray scattering techniques for studying these systems in situ and under physiologically relevant conditions on the nanometer to sub-nanometer length scales. Particularly we focus on: (i) structural details of coexisting liquid-ordered and liquid-disordered domains, including their thickness and lipid packing mismatch as a function ofmore » a size transition from nanoscopic to macroscopic domains; (ii) membrane-mediated protein partitioning into lipid domains; (iii) the role of the aqueous medium in tuning interactions between membranes and domains; and (iv) leaflet specific structure in asymmetric bilayers and passive lipid flip-flop.« less

Complex biomembrane mimetics on the sub-nanometer scale

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

Heberle, Frederick A.; Pabst, Georg

Biomimetic lipid vesicles are indispensable tools for gaining insight into the biophysics of cell physiology on the molecular level. The level of complexity of these model systems has steadily increased, and now spans from domain forming lipid mixtures to asymmetric lipid bilayers. We review recent progress in the development and application of elastic neutron and X-ray scattering techniques for studying these systems in situ and under physiologically relevant conditions on the nanometer to sub-nanometer length scales. Particularly we focus on: (i) structural details of coexisting liquid-ordered and liquid-disordered domains, including their thickness and lipid packing mismatch as a function ofmore » a size transition from nanoscopic to macroscopic domains; (ii) membrane-mediated protein partitioning into lipid domains; (iii) the role of the aqueous medium in tuning interactions between membranes and domains; and (iv) leaflet specific structure in asymmetric bilayers and passive lipid flip-flop.« less

Domain and rim growth kinetics in stratifying foam films

NASA Astrophysics Data System (ADS)

Zhang, Yiran; Yilixiati, Subinuer; Sharma, Vivek

Foam films are freely standing thin liquid films that typically consist of two surfactant-laden surfaces that are ~5 nm - 10 micron apart. Sandwiched between these interfacial layers is a fluid that drains primarily under the influence of viscous and interfacial forces, including disjoining pressure. Interestingly, a layered ordering of micelles inside the foam films (thickness <100 nm) leads to a stepwise thinning phenomena called stratification, which results in a thickness-dependent variation in reflected light intensity, visualized as progressively darker shades of gray. Thinner, darker domains spontaneously grow within foam films. During the initial expansion, a rim forms near the contact line between the growing thinner domain and the surrounding region, which influences the dynamics of domain growth as well as stratification Using newly developed interferometry digitial imaging optical microscopy (IDIOM) technique, we capture the rim evolution dynamics. Finally, we also develop a theoretical model to describe both rim evolution and domain growth dynamics.

Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules.

PubMed

Schroeter, Timon Sebastian; Schwaighofer, Anton; Mika, Sebastian; Ter Laak, Antonius; Suelzle, Detlev; Ganzer, Ursula; Heinrich, Nikolaus; Müller, Klaus-Robert

2007-12-01

We investigate the use of different Machine Learning methods to construct models for aqueous solubility. Models are based on about 4000 compounds, including an in-house set of 632 drug discovery molecules of Bayer Schering Pharma. For each method, we also consider an appropriate method to obtain error bars, in order to estimate the domain of applicability (DOA) for each model. Here, we investigate error bars from a Bayesian model (Gaussian Process (GP)), an ensemble based approach (Random Forest), and approaches based on the Mahalanobis distance to training data (for Support Vector Machine and Ridge Regression models). We evaluate all approaches in terms of their prediction accuracy (in cross-validation, and on an external validation set of 536 molecules) and in how far the individual error bars can faithfully represent the actual prediction error.

Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules.

PubMed

Schroeter, Timon Sebastian; Schwaighofer, Anton; Mika, Sebastian; Ter Laak, Antonius; Suelzle, Detlev; Ganzer, Ursula; Heinrich, Nikolaus; Müller, Klaus-Robert

2007-09-01

We investigate the use of different Machine Learning methods to construct models for aqueous solubility. Models are based on about 4000 compounds, including an in-house set of 632 drug discovery molecules of Bayer Schering Pharma. For each method, we also consider an appropriate method to obtain error bars, in order to estimate the domain of applicability (DOA) for each model. Here, we investigate error bars from a Bayesian model (Gaussian Process (GP)), an ensemble based approach (Random Forest), and approaches based on the Mahalanobis distance to training data (for Support Vector Machine and Ridge Regression models). We evaluate all approaches in terms of their prediction accuracy (in cross-validation, and on an external validation set of 536 molecules) and in how far the individual error bars can faithfully represent the actual prediction error.

Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules

NASA Astrophysics Data System (ADS)

Schroeter, Timon Sebastian; Schwaighofer, Anton; Mika, Sebastian; Ter Laak, Antonius; Suelzle, Detlev; Ganzer, Ursula; Heinrich, Nikolaus; Müller, Klaus-Robert

2007-12-01

We investigate the use of different Machine Learning methods to construct models for aqueous solubility. Models are based on about 4000 compounds, including an in-house set of 632 drug discovery molecules of Bayer Schering Pharma. For each method, we also consider an appropriate method to obtain error bars, in order to estimate the domain of applicability (DOA) for each model. Here, we investigate error bars from a Bayesian model (Gaussian Process (GP)), an ensemble based approach (Random Forest), and approaches based on the Mahalanobis distance to training data (for Support Vector Machine and Ridge Regression models). We evaluate all approaches in terms of their prediction accuracy (in cross-validation, and on an external validation set of 536 molecules) and in how far the individual error bars can faithfully represent the actual prediction error.

Estimating the domain of applicability for machine learning QSAR models: a study on aqueous solubility of drug discovery molecules

NASA Astrophysics Data System (ADS)

Schroeter, Timon Sebastian; Schwaighofer, Anton; Mika, Sebastian; Ter Laak, Antonius; Suelzle, Detlev; Ganzer, Ursula; Heinrich, Nikolaus; Müller, Klaus-Robert

2007-09-01

We investigate the use of different Machine Learning methods to construct models for aqueous solubility. Models are based on about 4000 compounds, including an in-house set of 632 drug discovery molecules of Bayer Schering Pharma. For each method, we also consider an appropriate method to obtain error bars, in order to estimate the domain of applicability (DOA) for each model. Here, we investigate error bars from a Bayesian model (Gaussian Process (GP)), an ensemble based approach (Random Forest), and approaches based on the Mahalanobis distance to training data (for Support Vector Machine and Ridge Regression models). We evaluate all approaches in terms of their prediction accuracy (in cross-validation, and on an external validation set of 536 molecules) and in how far the individual error bars can faithfully represent the actual prediction error.

A cross-cultural comparison of the coexistence and domain superiority of individuating and relating autonomy.

PubMed

Yeh, Kuang-Hui; Bedford, Olwen; Yang, Yung-Jui

2009-06-01

The consensus definition of autonomy in the psychological literature emphasizes self-governance through free volition, not separation or independence from others. Since the concept of self may differ cross-culturally, several researchers have tried to incorporate types of self into the notion of autonomy; however, only the dual model of autonomy has been able to do this while retaining an emphasis on volition. The dual model describes two distinct forms of autonomy-individuating and relating-each with superior function in a specific domain of individual functioning. Individuating autonomy represents a volitional capacity to act against social constraints and offers a route to achieve an independent self-identity by expressing individualistic attributes and distinctions. Relating autonomy represents a volitional capacity to act by emphasizing the harmony of self-in-relation-to-others, the quality of interpersonal relationships, and self-transcendence. These two forms of autonomy have been shown to coexist at the individual level in a Taiwanese sample. This study takes the next step, with a cross-cultural test of the coexistence and domain superiority hypotheses of individuating and relating autonomy. Participants included 306 college students from Taiwan and 183 college students from the United States. Structural equation modelling by multigroup analyses confirmed the cross-cultural equivalence of the two-factor individuating autonomy and relating autonomy measurement model. Across both samples the two forms of autonomy were shown to be mutually inclusive and not exclusive or independent. The domain-superior function of each form of autonomy was also confirmed cross-culturally; each form of autonomy has a dominant, but not necessarily exclusive, domain of functioning. Specifically, individuating autonomy was more associated with intrapersonal than interpersonal domain dependent variables, while relating autonomy was more associated with interpersonal than intrapersonal domain dependent variables. Limitations of the study and considerations for future research are discussed.

Efficient calculation of full waveform time domain inversion for electromagnetic problem using fictitious wave domain method and cascade decimation decomposition

NASA Astrophysics Data System (ADS)

Imamura, N.; Schultz, A.

2016-12-01

Recently, a full waveform time domain inverse solution has been developed for the magnetotelluric (MT) and controlled-source electromagnetic (CSEM) methods. The ultimate goal of this approach is to obtain a computationally tractable direct waveform joint inversion to solve simultaneously for source fields and earth conductivity structure in three and four dimensions. This is desirable on several grounds, including the improved spatial resolving power expected from use of a multitude of source illuminations, the ability to operate in areas of high levels of source signal spatial complexity, and non-stationarity. This goal would not be obtainable if one were to adopt the pure time domain solution for the inverse problem. This is particularly true for the case of MT surveys, since an enormous number of degrees of freedom are required to represent the observed MT waveforms across a large frequency bandwidth. This means that for the forward simulation, the smallest time steps should be finer than that required to represent the highest frequency, while the number of time steps should also cover the lowest frequency. This leads to a sensitivity matrix that is computationally burdensome to solve a model update. We have implemented a code that addresses this situation through the use of cascade decimation decomposition to reduce the size of the sensitivity matrix substantially, through quasi-equivalent time domain decomposition. We also use a fictitious wave domain method to speed up computation time of the forward simulation in the time domain. By combining these refinements, we have developed a full waveform joint source field/earth conductivity inverse modeling method. We found that cascade decimation speeds computations of the sensitivity matrices dramatically, keeping the solution close to that of the undecimated case. For example, for a model discretized into 2.6x105 cells, we obtain model updates in less than 1 hour on a 4U rack-mounted workgroup Linux server, which is a practical computational time for the inverse problem.

An open-source software platform for data management, visualisation, model building and model sharing in water, energy and other resource modelling domains.

NASA Astrophysics Data System (ADS)

Knox, S.; Meier, P.; Mohammed, K.; Korteling, B.; Matrosov, E. S.; Hurford, A.; Huskova, I.; Harou, J. J.; Rosenberg, D. E.; Thilmant, A.; Medellin-Azuara, J.; Wicks, J.

2015-12-01

Capacity expansion on resource networks is essential to adapting to economic and population growth and pressures such as climate change. Engineered infrastructure systems such as water, energy, or transport networks require sophisticated and bespoke models to refine management and investment strategies. Successful modeling of such complex systems relies on good data management and advanced methods to visualize and share data.Engineered infrastructure systems are often represented as networks of nodes and links with operating rules describing their interactions. Infrastructure system management and planning can be abstracted to simulating or optimizing new operations and extensions of the network. By separating the data storage of abstract networks from manipulation and modeling we have created a system where infrastructure modeling across various domains is facilitated.We introduce Hydra Platform, a Free Open Source Software designed for analysts and modelers to store, manage and share network topology and data. Hydra Platform is a Python library with a web service layer for remote applications, called Apps, to connect. Apps serve various functions including network or results visualization, data export (e.g. into a proprietary format) or model execution. This Client-Server architecture allows users to manipulate and share centrally stored data. XML templates allow a standardised description of the data structure required for storing network data such that it is compatible with specific models.Hydra Platform represents networks in an abstract way and is therefore not bound to a single modeling domain. It is the Apps that create domain-specific functionality. Using Apps researchers from different domains can incorporate different models within the same network enabling cross-disciplinary modeling while minimizing errors and streamlining data sharing. Separating the Python library from the web layer allows developers to natively expand the software or build web-based apps in other languages for remote functionality. Partner CH2M is developing a commercial user-interface for Hydra Platform however custom interfaces and visualization tools can be built. Hydra Platform is available on GitHub while Apps will be shared on a central repository.

MIMO Sliding Mode Control for a Tailless Fighter Aircraft, An Alternative to Reconfigurable Architectures

NASA Technical Reports Server (NTRS)

Wells, S. R.; Hess, R. A.

2002-01-01

A frequency-domain procedure for the design of sliding mode controllers for multi-input, multi-output (MIMO) systems is presented. The methodology accommodates the effects of parasitic dynamics such as those introduced by unmodeled actuators through the introduction of multiple asymptotic observers and model reference hedging. The design procedure includes a frequency domain approach to specify the sliding manifold, the observer eigenvalues, and the hedge model. The procedure is applied to the development of a flight control system for a linear model of the Innovative Control Effector (ICE) fighter aircraft. The stability and performance robustness of the resulting design is demonstrated through the introduction of significant degradation in the control effector actuators and variation in vehicle dynamics.

New Inversion and Interpretation of Public-Domain Electromagnetic Survey Data from Selected Areas in Alaska

NASA Astrophysics Data System (ADS)

Smith, B. D.; Kass, A.; Saltus, R. W.; Minsley, B. J.; Deszcz-Pan, M.; Bloss, B. R.; Burns, L. E.

2013-12-01

Public-domain airborne geophysical surveys (combined electromagnetics and magnetics), mostly collected for and released by the State of Alaska, Division of Geological and Geophysical Surveys (DGGS), are a unique and valuable resource for both geologic interpretation and geophysical methods development. A new joint effort by the US Geological Survey (USGS) and the DGGS aims to add value to these data through the application of novel advanced inversion methods and through innovative and intuitive display of data: maps, profiles, voxel-based models, and displays of estimated inversion quality and confidence. Our goal is to make these data even more valuable for interpretation of geologic frameworks, geotechnical studies, and cryosphere studies, by producing robust estimates of subsurface resistivity that can be used by non-geophysicists. The available datasets, which are available in the public domain, include 39 frequency-domain electromagnetic datasets collected since 1993, and continue to grow with 5 more data releases pending in 2013. The majority of these datasets were flown for mineral resource purposes, with one survey designed for infrastructure analysis. In addition, several USGS datasets are included in this study. The USGS has recently developed new inversion methodologies for airborne EM data and have begun to apply these and other new techniques to the available datasets. These include a trans-dimensional Markov Chain Monte Carlo technique, laterally-constrained regularized inversions, and deterministic inversions which include calibration factors as a free parameter. Incorporation of the magnetic data as an additional constraining dataset has also improved the inversion results. Processing has been completed in several areas, including Fortymile and the Alaska Highway surveys, and continues in others such as the Styx River and Nome surveys. Utilizing these new techniques, we provide models beyond the apparent resistivity maps supplied by the original contractors, allowing us to produce a variety of products, such as maps of resistivity as a function of depth or elevation, cross section maps, and 3D voxel models, which have been treated consistently both in terms of processing and error analysis throughout the state. These products facilitate a more fruitful exchange between geologists and geophysicists and a better understanding of uncertainty, and the process results in iterative development and improvement of geologic models, both on small and large scales.

Model-based software design

NASA Technical Reports Server (NTRS)

Iscoe, Neil; Liu, Zheng-Yang; Feng, Guohui; Yenne, Britt; Vansickle, Larry; Ballantyne, Michael

1992-01-01

Domain-specific knowledge is required to create specifications, generate code, and understand existing systems. Our approach to automating software design is based on instantiating an application domain model with industry-specific knowledge and then using that model to achieve the operational goals of specification elicitation and verification, reverse engineering, and code generation. Although many different specification models can be created from any particular domain model, each specification model is consistent and correct with respect to the domain model.

Influence of spin creepage and contact angle on curve squeal: A numerical approach

NASA Astrophysics Data System (ADS)

Zenzerovic, I.; Kropp, W.; Pieringer, A.

2018-04-01

Curve squeal is a loud tonal sound that may arise when a railway vehicle negotiates a tight curve. Due to the nonlinear nature of squeal, time-domain models provide a higher degree of accuracy in comparison to frequency-domain models and also enable the determination of squeal amplitudes. In the present paper, a previously developed engineering time-domain model for curve squeal is extended to include the effects of the contact angle and spin creepage. The extensions enable the evaluation of more realistic squeal cases with the computationally efficient model. The model validation against Kalker's variational contact model shows good agreement between the models. Results of studies on the influence of spin creepage and contact angle show that the contact angle has a significant influence on the vertical-lateral dynamics coupling and, therefore, influences both squeal amplitude and frequency. Spin creepage mainly influences processes in the contact, therefore influencing the tangential contact force amplitude. In the combined spin-contact angle study the spin creepage value is kinematically related to the contact angle value. Results indicate that the influence of the contact angle is dominant over the influence of spin creepage. In general, results indicate that the most crucial factors in squeal are those that influence the dynamics coupling: the contact angle, wheel/rail contact positions and friction.

Multi-scale coupled modelling of waves and currents on the Catalan shelf.

NASA Astrophysics Data System (ADS)

Grifoll, M.; Warner, J. C.; Espino, M.; Sánchez-Arcilla, A.

2012-04-01

Catalan shelf circulation is characterized by a background along-shelf flow to the southwest (including some meso-scale features) plus episodic storm driven patterns. To investigate these dynamics, a coupled multi-scale modeling system is applied to the Catalan shelf (North-western Mediterranean Sea). The implementation consists of a set of increasing-resolution nested models, based on the circulation model ROMS and the wave model SWAN as part of the COAWST modeling system, covering from the slope and shelf region (~1 km horizontal resolution) down to a local area around Barcelona city (~40 m). The system is initialized with MyOcean products in the coarsest outer domain, and uses atmospheric forcing from other sources for the increasing resolution inner domains. Results of the finer resolution domains exhibit improved agreement with observations relative to the coarser model results. Several hydrodynamic configurations were simulated to determine dominant forcing mechanisms and hydrodynamic processes that control coastal scale processes. The numerical results reveal that the short term (hours to days) inner-shelf variability is strongly influenced by local wind variability, while sea-level slope, baroclinic effects, radiation stresses and regional circulation constitute second-order processes. Additional analysis identifies the significance of shelf/slope exchange fluxes, river discharge and the effect of the spatial resolution of the atmospheric fluxes.

Zipf’s Law Arises Naturally When There Are Underlying, Unobserved Variables

PubMed Central

Corradi, Nicola

2016-01-01

Zipf’s law, which states that the probability of an observation is inversely proportional to its rank, has been observed in many domains. While there are models that explain Zipf’s law in each of them, those explanations are typically domain specific. Recently, methods from statistical physics were used to show that a fairly broad class of models does provide a general explanation of Zipf’s law. This explanation rests on the observation that real world data is often generated from underlying causes, known as latent variables. Those latent variables mix together multiple models that do not obey Zipf’s law, giving a model that does. Here we extend that work both theoretically and empirically. Theoretically, we provide a far simpler and more intuitive explanation of Zipf’s law, which at the same time considerably extends the class of models to which this explanation can apply. Furthermore, we also give methods for verifying whether this explanation applies to a particular dataset. Empirically, these advances allowed us extend this explanation to important classes of data, including word frequencies (the first domain in which Zipf’s law was discovered), data with variable sequence length, and multi-neuron spiking activity. PMID:27997544

Modelling DNA origami self-assembly at the domain level.

PubMed

Dannenberg, Frits; Dunn, Katherine E; Bath, Jonathan; Kwiatkowska, Marta; Turberfield, Andrew J; Ouldridge, Thomas E

2015-10-28

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

Modelling DNA origami self-assembly at the domain level

NASA Astrophysics Data System (ADS)

Dannenberg, Frits; Dunn, Katherine E.; Bath, Jonathan; Kwiatkowska, Marta; Turberfield, Andrew J.; Ouldridge, Thomas E.

2015-10-01

We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each staple is associated with a free-energy change that depends on staple sequence, the possibility of coaxial stacking with neighbouring domains, and the entropic cost of constraining the scaffold by inserting staple crossovers. A rigorous thermodynamic model is difficult to implement as a result of the complex, multiply connected geometry of the scaffold: we present a solution to this problem for planar origami. Coaxial stacking of helices and entropic terms, particularly when loop closure exponents are taken to be larger than those for ideal chains, introduce interactions between staples. These cooperative interactions lead to the prediction of sharp assembly transitions with notable hysteresis that are consistent with experimental observations. We show that the model reproduces the experimentally observed consequences of reducing staple concentration, accelerated cooling, and absent staples. We also present a simpler methodology that gives consistent results and can be used to study a wider range of systems including non-planar origami.

Ontology for heart rate turbulence domain from the conceptual model of SNOMED-CT.

PubMed

Soguero-Ruiz, Cristina; Lechuga-Suárez, Luis; Mora-Jiménez, Inmaculada; Ramos-López, Javier; Barquero-Pérez, Óscar; García-Alberola, Arcadi; Rojo-Álvarez, José L

2013-07-01

Electronic health record (EHR) automates the clinician workflow, allowing evidence-based decision support and quality management. We aimed to start a framework for domain standardization of cardiovascular risk stratification into the EHR, including risk indices whose calculation involves ECG signal processing. We propose the use of biomedical ontologies completely based on the conceptual model of SNOMED-CT, which allows us to implement our domain in the EHR. In this setting, the present study focused on the heart rate turbulence (HRT) domain, according to its concise guidelines and clear procedures for parameter calculations. We used 289 concepts from SNOMED-CT, and generated 19 local extensions (new concepts) for the HRT specific concepts not present in the current version of SNOMED-CT. New concepts included averaged and individual ventricular premature complex tachograms, initial sinus acceleration for turbulence onset, or sinusal oscillation for turbulence slope. Two representative use studies were implemented: first, a prototype was inserted in the hospital information system for supporting HRT recordings and their simple follow up by medical societies; second, an advanced support for a prospective scientific research, involving standard and emergent signal processing algorithms in the HRT indices, was generated and then tested in an example database of 27 Holter patients. Concepts of the proposed HRT ontology are publicly available through a terminology server, hence their use in any information system will be straightforward due to the interoperability provided by SNOMED-CT.

Downscaling Soil Moisture in the Southern Great Plains Through a Calibrated Multifractal Model for Land Surface Modeling Applications

NASA Technical Reports Server (NTRS)

Mascaro, Giuseppe; Vivoni, Enrique R.; Deidda, Roberto

2010-01-01

Accounting for small-scale spatial heterogeneity of soil moisture (theta) is required to enhance the predictive skill of land surface models. In this paper, we present the results of the development, calibration, and performance evaluation of a downscaling model based on multifractal theory using aircraft!based (800 m) theta estimates collected during the southern Great Plains experiment in 1997 (SGP97).We first demonstrate the presence of scale invariance and multifractality in theta fields of nine square domains of size 25.6 x 25.6 sq km, approximately a satellite footprint. Then, we estimate the downscaling model parameters and evaluate the model performance using a set of different calibration approaches. Results reveal that small-scale theta distributions are adequately reproduced across the entire region when coarse predictors include a dynamic component (i.e., the spatial mean soil moisture ) and a stationary contribution accounting for static features (i.e., topography, soil texture, vegetation). For wet conditions, we found similar multifractal properties of soil moisture across all domains, which we ascribe to the signature of rainfall spatial variability. For drier states, the theta fields in the northern domains are more intermittent than in southern domains, likely because of differences in the distribution of vegetation coverage. Through our analyses, we propose a regional downscaling relation for coarse, satellite-based soil moisture estimates, based on ancillary information (static and dynamic landscape features), which can be used in the study area to characterize statistical properties of small-scale theta distribution required by land surface models and data assimilation systems.

Knowledge-based approach for generating target system specifications from a domain model

NASA Technical Reports Server (NTRS)

Gomaa, Hassan; Kerschberg, Larry; Sugumaran, Vijayan

1992-01-01

Several institutions in industry and academia are pursuing research efforts in domain modeling to address unresolved issues in software reuse. To demonstrate the concepts of domain modeling and software reuse, a prototype software engineering environment is being developed at George Mason University to support the creation of domain models and the generation of target system specifications. This prototype environment, which is application domain independent, consists of an integrated set of commercial off-the-shelf software tools and custom-developed software tools. This paper describes the knowledge-based tool that was developed as part of the environment to generate target system specifications from a domain model.

How to practice person-centred care: A conceptual framework.

PubMed

Santana, Maria J; Manalili, Kimberly; Jolley, Rachel J; Zelinsky, Sandra; Quan, Hude; Lu, Mingshan

2018-04-01

Globally, health-care systems and organizations are looking to improve health system performance through the implementation of a person-centred care (PCC) model. While numerous conceptual frameworks for PCC exist, a gap remains in practical guidance on PCC implementation. Based on a narrative review of the PCC literature, a generic conceptual framework was developed in collaboration with a patient partner, which synthesizes evidence, recommendations and best practice from existing frameworks and implementation case studies. The Donabedian model for health-care improvement was used to classify PCC domains into the categories of "Structure," "Process" and "Outcome" for health-care quality improvement. The framework emphasizes the structural domain, which relates to the health-care system or context in which care is delivered, providing the foundation for PCC, and influencing the processes and outcomes of care. Structural domains identified include: the creation of a PCC culture across the continuum of care; co-designing educational programs, as well as health promotion and prevention programs with patients; providing a supportive and accommodating environment; and developing and integrating structures to support health information technology and to measure and monitor PCC performance. Process domains describe the importance of cultivating communication and respectful and compassionate care; engaging patients in managing their care; and integration of care. Outcome domains identified include: access to care and Patient-Reported Outcomes. This conceptual framework provides a step-wise roadmap to guide health-care systems and organizations in the provision PCC across various health-care sectors. © 2017 The Authors Health Expectations published by John Wiley & Sons Ltd.

Domain-Adapted Convolutional Networks for Satellite Image Classification: A Large-Scale Interactive Learning Workflow

DOE PAGES

Lunga, Dalton D.; Yang, Hsiuhan Lexie; Reith, Andrew E.; ...

2018-02-06

Satellite imagery often exhibits large spatial extent areas that encompass object classes with considerable variability. This often limits large-scale model generalization with machine learning algorithms. Notably, acquisition conditions, including dates, sensor position, lighting condition, and sensor types, often translate into class distribution shifts introducing complex nonlinear factors and hamper the potential impact of machine learning classifiers. Here, this article investigates the challenge of exploiting satellite images using convolutional neural networks (CNN) for settlement classification where the class distribution shifts are significant. We present a large-scale human settlement mapping workflow based-off multiple modules to adapt a pretrained CNN to address themore » negative impact of distribution shift on classification performance. To extend a locally trained classifier onto large spatial extents areas we introduce several submodules: First, a human-in-the-loop element for relabeling of misclassified target domain samples to generate representative examples for model adaptation; second, an efficient hashing module to minimize redundancy and noisy samples from the mass-selected examples; and third, a novel relevance ranking module to minimize the dominance of source example on the target domain. The workflow presents a novel and practical approach to achieve large-scale domain adaptation with binary classifiers that are based-off CNN features. Experimental evaluations are conducted on areas of interest that encompass various image characteristics, including multisensors, multitemporal, and multiangular conditions. Domain adaptation is assessed on source–target pairs through the transfer loss and transfer ratio metrics to illustrate the utility of the workflow.« less

Domain-Adapted Convolutional Networks for Satellite Image Classification: A Large-Scale Interactive Learning Workflow

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

Lunga, Dalton D.; Yang, Hsiuhan Lexie; Reith, Andrew E.

Satellite imagery often exhibits large spatial extent areas that encompass object classes with considerable variability. This often limits large-scale model generalization with machine learning algorithms. Notably, acquisition conditions, including dates, sensor position, lighting condition, and sensor types, often translate into class distribution shifts introducing complex nonlinear factors and hamper the potential impact of machine learning classifiers. Here, this article investigates the challenge of exploiting satellite images using convolutional neural networks (CNN) for settlement classification where the class distribution shifts are significant. We present a large-scale human settlement mapping workflow based-off multiple modules to adapt a pretrained CNN to address themore » negative impact of distribution shift on classification performance. To extend a locally trained classifier onto large spatial extents areas we introduce several submodules: First, a human-in-the-loop element for relabeling of misclassified target domain samples to generate representative examples for model adaptation; second, an efficient hashing module to minimize redundancy and noisy samples from the mass-selected examples; and third, a novel relevance ranking module to minimize the dominance of source example on the target domain. The workflow presents a novel and practical approach to achieve large-scale domain adaptation with binary classifiers that are based-off CNN features. Experimental evaluations are conducted on areas of interest that encompass various image characteristics, including multisensors, multitemporal, and multiangular conditions. Domain adaptation is assessed on source–target pairs through the transfer loss and transfer ratio metrics to illustrate the utility of the workflow.« less

"Every Child Ready": Exposure to a Comprehensive Instructional Model Improves Students' Growth Trajectories in Multiple Early Learning Domains

ERIC Educational Resources Information Center

Carlson, Abby G.; Curby, Timothy W.; Brown, Chavaughn A.; Truong, Felicia R.

2017-01-01

The current study investigates the impact of Every Child Ready (ECR), a comprehensive instructional model that includes: "What to teach, how to teach and how to know instruction is effective." The ECR instructional model is designed to provide high quality instruction to children via a play-based, thematic curriculum. Participants…

Structure and Dynamics of Domains in Ferroelectric Nanostructures. In-situ TEM Studies

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

Pan, Xiaoqing

2015-06-30

The goal of this project was to explore the structure and dynamic behaviors of ferroelectric domains in ferroelectric thin films and nanostructures by advanced transmission electron microscopy (TEM) techniques in close collaboration with phase field modeling. The experimental techniques used include aberration-corrected sub-Å resolution TEM and in-situ TEM using a novel scanning tunneling microscopy (STM) - TEM holder that allows the direct observation of nucleation and dynamic evolution of ferroelectric domains under applied electric field. Specifically, this project was aimed to (1) to study the roles of static electrical boundary conditions and electrical charge in controlling the equilibrium domain structuresmore » of BiFeO 3 thin films with controlled substrate constraints, (2) to explore the fundamental mechanisms of ferroelectric domain nucleation, growth, and switching under an applied electric field in both uniform thin films and nanostructures, and to understand the roles of crystal defects such as dislocations and interfaces in these processes, (3) to understand the physics of ferroelectric domain walls and the influence of defects on the electrical switching of ferroelectric domains.« less

Analyzing and designing object-oriented missile simulations with concurrency

NASA Astrophysics Data System (ADS)

Randorf, Jeffrey Allen

2000-11-01

A software object model for the six degree-of-freedom missile modeling domain is presented. As a precursor, a domain analysis of the missile modeling domain was started, based on the Feature-Oriented Domain Analysis (FODA) technique described by the Software Engineering Institute (SEI). It was subsequently determined the FODA methodology is functionally equivalent to the Object Modeling Technique. The analysis used legacy software documentation and code from the ENDOSIM, KDEC, and TFrames 6-DOF modeling tools, including other technical literature. The SEI Object Connection Architecture (OCA) was the template for designing the object model. Three variants of the OCA were considered---a reference structure, a recursive structure, and a reference structure with augmentation for flight vehicle modeling. The reference OCA design option was chosen for maintaining simplicity while not compromising the expressive power of the OMT model. The missile architecture was then analyzed for potential areas of concurrent computing. It was shown how protected objects could be used for data passing between OCA object managers, allowing concurrent access without changing the OCA reference design intent or structure. The implementation language was the 1995 release of Ada. OCA software components were shown how to be expressed as Ada child packages. While acceleration of several low level and other high operations level are possible on proper hardware, there was a 33% degradation of 4th order Runge-Kutta integrator performance of two simultaneous ordinary differential equations using Ada tasking on a single processor machine. The Defense Department's High Level Architecture was introduced and explained in context with the OCA. It was shown the HLA and OCA were not mutually exclusive architectures, but complimentary. HLA was shown as an interoperability solution, with the OCA as an architectural vehicle for software reuse. Further directions for implementing a 6-DOF missile modeling environment are discussed.

Time Domain Tool Validation Using ARES I-X Flight Data

NASA Technical Reports Server (NTRS)

Hough, Steven; Compton, James; Hannan, Mike; Brandon, Jay

2011-01-01

The ARES I-X vehicle was launched from NASA's Kennedy Space Center (KSC) on October 28, 2009 at approximately 11:30 EDT. ARES I-X was the first test flight for NASA s ARES I launch vehicle, and it was the first non-Shuttle launch vehicle designed and flown by NASA since Saturn. The ARES I-X had a 4-segment solid rocket booster (SRB) first stage and a dummy upper stage (US) to emulate the properties of the ARES I US. During ARES I-X pre-flight modeling and analysis, six (6) independent time domain simulation tools were developed and cross validated. Each tool represents an independent implementation of a common set of models and parameters in a different simulation framework and architecture. Post flight data and reconstructed models provide the means to validate a subset of the simulations against actual flight data and to assess the accuracy of pre-flight dispersion analysis. Post flight data consists of telemetered Operational Flight Instrumentation (OFI) data primarily focused on flight computer outputs and sensor measurements as well as Best Estimated Trajectory (BET) data that estimates vehicle state information from all available measurement sources. While pre-flight models were found to provide a reasonable prediction of the vehicle flight, reconstructed models were generated to better represent and simulate the ARES I-X flight. Post flight reconstructed models include: SRB propulsion model, thrust vector bias models, mass properties, base aerodynamics, and Meteorological Estimated Trajectory (wind and atmospheric data). The result of the effort is a set of independently developed, high fidelity, time-domain simulation tools that have been cross validated and validated against flight data. This paper presents the process and results of high fidelity aerospace modeling, simulation, analysis and tool validation in the time domain.

Structural-Functional Analysis Reveals a Specific Domain Organization in Family GH20 Hexosaminidases.

PubMed

Val-Cid, Cristina; Biarnés, Xevi; Faijes, Magda; Planas, Antoni

2015-01-01

Hexosaminidases are involved in important biological processes catalyzing the hydrolysis of N-acetyl-hexosaminyl residues in glycosaminoglycans and glycoconjugates. The GH20 enzymes present diverse domain organizations for which we propose two minimal model architectures: Model A containing at least a non-catalytic GH20b domain and the catalytic one (GH20) always accompanied with an extra α-helix (GH20b-GH20-α), and Model B with only the catalytic GH20 domain. The large Bifidobacterium bifidum lacto-N-biosidase was used as a model protein to evaluate the minimal functional unit due to its interest and structural complexity. By expressing different truncated forms of this enzyme, we show that Model A architectures cannot be reduced to Model B. In particular, there are two structural requirements general to GH20 enzymes with Model A architecture. First, the non-catalytic domain GH20b at the N-terminus of the catalytic GH20 domain is required for expression and seems to stabilize it. Second, the substrate-binding cavity at the GH20 domain always involves a remote element provided by a long loop from the catalytic domain itself or, when this loop is short, by an element from another domain of the multidomain structure or from the dimeric partner. Particularly, the lacto-N-biosidase requires GH20b and the lectin-like domain at the N- and C-termini of the catalytic GH20 domain to be fully soluble and functional. The lectin domain provides this remote element to the active site. We demonstrate restoration of activity of the inactive GH20b-GH20-α construct (model A architecture) by a complementation assay with the lectin-like domain. The engineering of minimal functional units of multidomain GH20 enzymes must consider these structural requirements.

Three-dimensional finite elements for the analysis of soil contamination using a multiple-porosity approach

NASA Astrophysics Data System (ADS)

El-Zein, Abbas; Carter, John P.; Airey, David W.

2006-06-01

A three-dimensional finite-element model of contaminant migration in fissured clays or contaminated sand which includes multiple sources of non-equilibrium processes is proposed. The conceptual framework can accommodate a regular network of fissures in 1D, 2D or 3D and immobile solutions in the macro-pores of aggregated topsoils, as well as non-equilibrium sorption. A Galerkin weighted-residual statement for the three-dimensional form of the equations in the Laplace domain is formulated. Equations are discretized using linear and quadratic prism elements. The system of algebraic equations is solved in the Laplace domain and solution is inverted to the time domain numerically. The model is validated and its scope is illustrated through the analysis of three problems: a waste repository deeply buried in fissured clay, a storage tank leaking into sand and a sanitary landfill leaching into fissured clay over a sand aquifer.

What is eHealth (6)? Development of a Conceptual Model for eHealth: Qualitative Study with Key Informants

PubMed Central

Janssen, Anna; Barnet, Stewart

2017-01-01

Background Despite rapid growth in eHealth research, there remains a lack of consistency in defining and using terms related to eHealth. More widely cited definitions provide broad understanding of eHealth but lack sufficient conceptual clarity to operationalize eHealth and enable its implementation in health care practice, research, education, and policy. Definitions that are more detailed are often context or discipline specific, limiting ease of translation of these definitions across the breadth of eHealth perspectives and situations. A conceptual model of eHealth that adequately captures its complexity and potential overlaps is required. This model must also be sufficiently detailed to enable eHealth operationalization and hypothesis testing. Objective This study aimed to develop a conceptual practice-based model of eHealth to support health professionals in applying eHealth to their particular professional or discipline contexts. Methods We conducted semistructured interviews with key informants (N=25) from organizations involved in health care delivery, research, education, practice, governance, and policy to explore their perspectives on and experiences with eHealth. We used purposeful sampling for maximum diversity. Interviews were coded and thematically analyzed for emergent domains. Results Thematic analyses revealed 3 prominent but overlapping domains of eHealth: (1) health in our hands (using eHealth technologies to monitor, track, and inform health), (2) interacting for health (using digital technologies to enable health communication among practitioners and between health professionals and clients or patients), and (3) data enabling health (collecting, managing, and using health data). These domains formed a model of eHealth that addresses the need for clear definitions and a taxonomy of eHealth while acknowledging the fluidity of this area and the strengths of initiatives that span multiple eHealth domains. Conclusions This model extends current understanding of eHealth by providing clearly defined domains of eHealth while highlighting the benefits of using digital technologies in ways that cross several domains. It provides the depth of perspectives and examples of eHealth use that are lacking in previous research. On the basis of this model, we suggest that eHealth initiatives that are most impactful would include elements from all 3 domains. PMID:29066429

What is eHealth (6)? Development of a Conceptual Model for eHealth: Qualitative Study with Key Informants.

PubMed

Shaw, Tim; McGregor, Deborah; Brunner, Melissa; Keep, Melanie; Janssen, Anna; Barnet, Stewart

2017-10-24

Despite rapid growth in eHealth research, there remains a lack of consistency in defining and using terms related to eHealth. More widely cited definitions provide broad understanding of eHealth but lack sufficient conceptual clarity to operationalize eHealth and enable its implementation in health care practice, research, education, and policy. Definitions that are more detailed are often context or discipline specific, limiting ease of translation of these definitions across the breadth of eHealth perspectives and situations. A conceptual model of eHealth that adequately captures its complexity and potential overlaps is required. This model must also be sufficiently detailed to enable eHealth operationalization and hypothesis testing. This study aimed to develop a conceptual practice-based model of eHealth to support health professionals in applying eHealth to their particular professional or discipline contexts. We conducted semistructured interviews with key informants (N=25) from organizations involved in health care delivery, research, education, practice, governance, and policy to explore their perspectives on and experiences with eHealth. We used purposeful sampling for maximum diversity. Interviews were coded and thematically analyzed for emergent domains. Thematic analyses revealed 3 prominent but overlapping domains of eHealth: (1) health in our hands (using eHealth technologies to monitor, track, and inform health), (2) interacting for health (using digital technologies to enable health communication among practitioners and between health professionals and clients or patients), and (3) data enabling health (collecting, managing, and using health data). These domains formed a model of eHealth that addresses the need for clear definitions and a taxonomy of eHealth while acknowledging the fluidity of this area and the strengths of initiatives that span multiple eHealth domains. This model extends current understanding of eHealth by providing clearly defined domains of eHealth while highlighting the benefits of using digital technologies in ways that cross several domains. It provides the depth of perspectives and examples of eHealth use that are lacking in previous research. On the basis of this model, we suggest that eHealth initiatives that are most impactful would include elements from all 3 domains. ©Tim Shaw, Deborah McGregor, Melissa Brunner, Melanie Keep, Anna Janssen, Stewart Barnet. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 24.10.2017.

Documentation and verification of VST2D; a model for simulating transient, Variably Saturated, coupled water-heat-solute Transport in heterogeneous, anisotropic 2-Dimensional, ground-water systems with variable fluid density

USGS Publications Warehouse

Friedel, Michael J.

2001-01-01

This report describes a model for simulating transient, Variably Saturated, coupled water-heatsolute Transport in heterogeneous, anisotropic, 2-Dimensional, ground-water systems with variable fluid density (VST2D). VST2D was developed to help understand the effects of natural and anthropogenic factors on quantity and quality of variably saturated ground-water systems. The model solves simultaneously for one or more dependent variables (pressure, temperature, and concentration) at nodes in a horizontal or vertical mesh using a quasi-linearized general minimum residual method. This approach enhances computational speed beyond the speed of a sequential approach. Heterogeneous and anisotropic conditions are implemented locally using individual element property descriptions. This implementation allows local principal directions to differ among elements and from the global solution domain coordinates. Boundary conditions can include time-varying pressure head (or moisture content), heat, and/or concentration; fluxes distributed along domain boundaries and/or at internal node points; and/or convective moisture, heat, and solute fluxes along the domain boundaries; and/or unit hydraulic gradient along domain boundaries. Other model features include temperature and concentration dependent density (liquid and vapor) and viscosity, sorption and/or decay of a solute, and capability to determine moisture content beyond residual to zero. These features are described in the documentation together with development of the governing equations, application of the finite-element formulation (using the Galerkin approach), solution procedure, mass and energy balance considerations, input requirements, and output options. The VST2D model was verified, and results included solutions for problems of water transport under isohaline and isothermal conditions, heat transport under isobaric and isohaline conditions, solute transport under isobaric and isothermal conditions, and coupled water-heat-solute transport. The first three problems considered in model verification were compared to either analytical or numerical solutions, whereas the coupled problem was compared to measured laboratory results for which no known analytic solutions or numerical models are available. The test results indicate the model is accurate and applicable for a wide range of conditions, including when water (liquid and vapor), heat (sensible and latent), and solute are coupled in ground-water systems. The cumulative residual errors for the coupled problem tested was less than 10-8 cubic centimeter per cubic centimeter, 10-5 moles per kilogram, and 102 calories per cubic meter for liquid water content, solute concentration and heat content, respectively. This model should be useful to hydrologists, engineers, and researchers interested in studying coupled processes associated with variably saturated transport in ground-water systems.

Modeling of leachate generation from MSW landfills by a 2-dimensional 2-domain approach

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

Fellner, Johann, E-mail: j.fellner@tuwien.ac.a; Brunner, Paul H., E-mail: paul.h.brunner@tuwien.ac.a

2010-11-15

The flow of water through Municipal Solid Waste (MSW) landfills is highly non-uniform and dominated by preferential pathways. Thus, concepts to simulate landfill behavior require that a heterogeneous flow regime is considered. Recent models are based on a 2-domain approach, differentiating between channel domain with high hydraulic conductivity, and matrix domain of slow water movement with high water retention capacity. These models focus on the mathematical description of rapid water flow in channel domain. The present paper highlights the importance of water exchange between the two domains, and expands the 1-dimensional, 2-domain flow model by taking into account water flowsmore » in two dimensions. A flow field consisting of a vertical path (channel domain) surrounded by the waste mass (matrix domain) is defined using the software HYDRUS-2D. When the new model is calibrated using data sets from a MSW-landfill site the predicted leachate generation corresponds well with the observed leachate discharge. An overall model efficiency in terms of r{sup 2} of 0.76 was determined for a simulation period of almost 4 years. The results confirm that water in landfills follows a preferential path way characterized by high permeability (K{sub s} = 300 m/d) and zero retention capacity, while the bulk of the landfill (matrix domain) is characterized by low permeability (K{sub s} = 0.1 m/d) and high retention capacity. The most sensitive parameters of the model are the hydraulic conductivities of the channel domain and the matrix domain, and the anisotropy of the matrix domain.« less

Effect of membrane microheterogeneity and domain size on fluorescence resonance energy transfer.

PubMed

Towles, Kevin B; Brown, Angela C; Wrenn, Steven P; Dan, Nily

2007-07-15

Studies of multicomponent membranes suggest lateral inhomogeneity in the form of membrane domains, but the size of small (nanoscale) domains in situ cannot be determined with current techniques. In this article, we present a model that enables extraction of membrane domain size from time-resolved fluorescence resonance energy transfer (FRET) data. We expand upon a classic approach to the infinite phase separation limit and formulate a model that accounts for the presence of disklike domains of finite dimensions within a two-dimensional infinite planar bilayer. The model was tested against off-lattice Monte Carlo calculations of a model membrane in the liquid-disordered (l(d)) and liquid-ordered (l(o)) coexistence regime. Simulated domain size was varied from 5 to 50 nm, and two fluorophores, preferentially partitioning into opposite phases, were randomly mixed to obtain the simulated time-resolved FRET data. The Monte Carlo data show clear differences in the efficiency of energy transfer as a function of domain size. The model fit of the data yielded good agreement for the domain size, especially in cases where the domain diameter is <20 nm. Thus, data analysis using the proposed model enables measurement of nanoscale membrane domains using time-resolved FRET.

A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation

PubMed Central

Qin, Feng

2015-01-01

The transient receptor potential (TRP) channels act as key sensors of various chemical and physical stimuli in eukaryotic cells. Despite years of study, the molecular mechanisms of TRP channel activation remain unclear. To elucidate the structural, dynamic, and energetic basis of gating in TRPV1 (a founding member of the TRPV subfamily), we performed coarse-grained modeling and all-atom molecular dynamics (MD) simulation based on the recently solved high resolution structures of the open and closed form of TRPV1. Our coarse-grained normal mode analysis captures two key modes of collective motions involved in the TRPV1 gating transition, featuring a quaternary twist motion of the transmembrane domains (TMDs) relative to the intracellular domains (ICDs). Our transition pathway modeling predicts a sequence of structural movements that propagate from the ICDs to the TMDs via key interface domains (including the membrane proximal domain and the C-terminal domain), leading to sequential opening of the selectivity filter followed by the lower gate in the channel pore (confirmed by modeling conformational changes induced by the activation of ICDs). The above findings of coarse-grained modeling are robust to perturbation by lipids. Finally, our MD simulation of the ICD identifies key residues that contribute differently to the nonpolar energy of the open and closed state, and these residues are predicted to control the temperature sensitivity of TRPV1 gating. These computational predictions offer new insights to the mechanism for heat activation of TRPV1 gating, and will guide our future electrophysiology and mutagenesis studies. PMID:25918362

The reliability and validity of the English version of the Evaluation of Daily Activity Questionnaire for people with rheumatoid arthritis

PubMed Central

Tennant, Alan; Tyson, Sarah F.; Nordenskiöld, Ulla; Hawkins, Ruth; Prior, Yeliz

2015-01-01

Objectives. The Evaluation of Daily Activity Questionnaire (EDAQ) includes 138 items in 14 domains identified as important by people with RA. The aim of this study was to test the validity and reliability of the English EDAQ. Methods. A total of 502 participants completed two questionnaires 3 weeks apart. The first consisted of the EDAQ, HAQ, RA Quality of Life (RAQoL) and the Medical Outcomes Scale (MOS) 36-item Short-Form Health Survey (SF-36v2), and the second consisted of the EDAQ only. The 14 EDAQ domains were tested for: unidimensionality—using confirmatory factor analysis; fit, response dependency, invariance across groups (differential item functioning)—using Rasch analysis; internal consistency [Person Separation Index (PSI)]; concurrent validity—by correlations with the HAQ, SF-36v2 and RAQoL; and test–retest reliability (Spearman’s correlations). Results. Confirmatory factor analysis of the 14 EDAQ domains indicated unidimensionality, after adjustment for local dependency in each domain. All domains achieved a root mean square error of approximation <0.10 and satisfied Rasch model expectations for local dependency. DIF by age, gender and employment status was largely absent. The PSI was consistent with individual use (PSI = 0.94 for all 14 domains). For all domains, except Caring, concurrent validity was good: HAQ (rs = 0.72–0.91), RAQoL (rs = 0.67–0.82) and SF36v2 Physical Function scale (rs = −0.60 to −0.84) and test–retest reliability was good (rs = 0.70–0.89). Conclusion. Analysis supported a 14-domain, two-component structure (Self care and Mobility) of the EDAQ, where each domain, and both components, satisfied Rasch model requirements, and have robust reliability and validity. PMID:25863045

Fast-Running Aeroelastic Code Based on Unsteady Linearized Aerodynamic Solver Developed

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Bakhle, Milind A.; Keith, T., Jr.

2003-01-01

The NASA Glenn Research Center has been developing aeroelastic analyses for turbomachines for use by NASA and industry. An aeroelastic analysis consists of a structural dynamic model, an unsteady aerodynamic model, and a procedure to couple the two models. The structural models are well developed. Hence, most of the development for the aeroelastic analysis of turbomachines has involved adapting and using unsteady aerodynamic models. Two methods are used in developing unsteady aerodynamic analysis procedures for the flutter and forced response of turbomachines: (1) the time domain method and (2) the frequency domain method. Codes based on time domain methods require considerable computational time and, hence, cannot be used during the design process. Frequency domain methods eliminate the time dependence by assuming harmonic motion and, hence, require less computational time. Early frequency domain analyses methods neglected the important physics of steady loading on the analyses for simplicity. A fast-running unsteady aerodynamic code, LINFLUX, which includes steady loading and is based on the frequency domain method, has been modified for flutter and response calculations. LINFLUX, solves unsteady linearized Euler equations for calculating the unsteady aerodynamic forces on the blades, starting from a steady nonlinear aerodynamic solution. First, we obtained a steady aerodynamic solution for a given flow condition using the nonlinear unsteady aerodynamic code TURBO. A blade vibration analysis was done to determine the frequencies and mode shapes of the vibrating blades, and an interface code was used to convert the steady aerodynamic solution to a form required by LINFLUX. A preprocessor was used to interpolate the mode shapes from the structural dynamic mesh onto the computational dynamics mesh. Then, we used LINFLUX to calculate the unsteady aerodynamic forces for a given mode, frequency, and phase angle. A postprocessor read these unsteady pressures and calculated the generalized aerodynamic forces, eigenvalues, and response amplitudes. The eigenvalues determine the flutter frequency and damping. As a test case, the flutter of a helical fan was calculated with LINFLUX and compared with calculations from TURBO-AE, a nonlinear time domain code, and from ASTROP2, a code based on linear unsteady aerodynamics.

Comparison of Static and Dynamic Assessment Procedures and Their Relation to Independent Performance.

ERIC Educational Resources Information Center

Day, Jeanne D.; And Others

1997-01-01

Relationships between pretraining skills, learning, and posttest performance were studied in spatial and verbal tasks for 84 preschool children. The measurement model that fit the data best maintained separate verbal and spatial domains. The best structural model included paths from pretest and learning assessments to posttest performance within…

A mathematical model of the heat and fluid flows in direct-chill casting of aluminum sheet ingots and billets

NASA Astrophysics Data System (ADS)

Mortensen, Dag

1999-02-01

A finite-element method model for the time-dependent heat and fluid flows that develop during direct-chill (DC) semicontinuous casting of aluminium ingots is presented. Thermal convection and turbulence are included in the model formulation and, in the mushy zone, the momentum equations are modified with a Darcy-type source term dependent on the liquid fraction. The boundary conditions involve calculations of the air gap along the mold wall as well as the heat transfer to the falling water film with forced convection, nucleate boiling, and film boiling. The mold wall and the starting block are included in the computational domain. In the start-up period of the casting, the ingot domain expands over the starting-block level. The numerical method applies a fractional-step method for the dynamic Navier-Stokes equations and the “streamline upwind Petrov-Galerkin” (SUPG) method for mixed diffusion and convection in the momentum and energy equations. The modeling of the start-up period of the casting is demonstrated and compared to temperature measurements in an AA1050 200×600 mm sheet ingot.

Domain Growth Kinetics in Stratifying Foam Films

NASA Astrophysics Data System (ADS)

Zhang, Yiran; Sharma, Vivek

2015-03-01

Baking bread, brewing cappuccino, pouring beer, washing dishes, shaving, shampooing, whipping eggs and blowing bubbles all involve creation of aqueous foam films. Typical foam films consist of two surfactant-laden surfaces that are μ 5 nm - 10 micron apart. Sandwiched between these interfacial layers is a fluid that drains primarily under the influence of viscous and interfacial forces, including disjoining pressure. Interestingly, for certain low molecular weight surfactants, a layered ordering of micelles inside the foam films (thickness <100 nm) leads to a stepwise thinning phenomena called stratification. We experimentally elucidate the influence of these different driving forces, and confinement on drainage kinetics of horizontal stratifying foam films. Thinner, darker domains spontaneously grow within foam films. Quantitative characterization of domain growth visualized in a using Scheludko-type thin film cell and a theoretical model based on lubrication analysis, provide critical insights into hydrodynamics of thin foam films, and the strength and nature of surface forces, including supramolecular oscillatory structural forces.

Small and Robotic Telescopes in the Era of Massive Time-Domain Surveys

NASA Astrophysics Data System (ADS)

Bode, M. F.; Vestrand, W. T.

2012-04-01

We have entered an era in time-domain astronomy in which the detected rate of explosive transients and important ephemeral states in persistent objects threatens to overwhelm the world's supply of traditional follow-up telescopes. As new, comprehensive time-domain surveys become operational and wide-field multi-messenger observatories come on-line, that problem will become more acute. The goal of this workshop was to foster discussion about how autonomous robotic telescopes and small-aperture conventional telescopes can be employed in the most effective ways to help deal with the coming deluge of scientifically interesting follow-up opportunities. Discussion topics included the role of event brokers, automated event triage, the establishment of cooperative global telescope networks, and real-time coordination of observations at geographically diverse sites. It therefore included brief overviews of the current diverse landscape of telescopes and their interactions, and also considered planned and potential new facilities and operating models.

The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition

PubMed Central

Wienk, Hans; Slootweg, Jack C.; Speerstra, Sietske; Kaptein, Robert; Boelens, Rolf; Folkers, Gert E.

2013-01-01

To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition. PMID:23661679

Psychometric evaluation of the WHOQOL-BREF, Taiwan version, across five kinds of Taiwanese cancer survivors: Rasch analysis and confirmatory factor analysis.

PubMed

Lin, Chung-Ying; Hwang, Jing-Shiang; Wang, Wen-Chung; Lai, Wu-Wei; Su, Wu-Chou; Wu, Tzu-Yi; Yao, Grace; Wang, Jung-Der

2018-04-13

Quality of life (QoL) is important for clinicians to evaluate how cancer survivors judge their sense of well-being, and WHOQOL-BREF may be a good tool for clinical use. However, at least three issues remain unresolved: (1) the psychometric properties of the WHOQOL-BREF for cancer patients are insufficient; (2) the scoring method used for WHOQOL-BREF needs to be clarify; (3) whether different types of cancer patients interpret the WHOQOL-BREF similarly. We recruited 1000 outpatients with head/neck cancer, 1000 with colorectal cancer, 965 with liver cancer, 1438 with lung cancer and 1299 with gynecologic cancers in a medical center. Data analyses included Rasch models, confirmatory factor analysis (CFA), and Pearson correlations. The mean WHOQOL-BREF domain scores were between 13.34 and 14.77 among all participants. CFA supported construct validity; Rasch models revealed that almost all items were embedded in their expected domains and were interpreted similarly across five types of cancer patients; all correlation coefficients between Rasch scores and original domain scores were above 0.9. The linear relationship between Rasch scores and domain scores suggested that the current calculations for domain scores were applicable and without serious bias. Clinical practitioners may regularly collect and record the WHOQOL-BREF domain scores into electronic health records. Copyright © 2018. Published by Elsevier B.V.

Adapting Word Embeddings from Multiple Domains to Symptom Recognition from Psychiatric Notes

PubMed Central

Zhang, Yaoyun; Li, Hee-Jin; Wang, Jingqi; Cohen, Trevor; Roberts, Kirk; Xu, Hua

2018-01-01

Mental health is increasingly recognized an important topic in healthcare. Information concerning psychiatric symptoms is critical for the timely diagnosis of mental disorders, as well as for the personalization of interventions. However, the diversity and sparsity of psychiatric symptoms make it challenging for conventional natural language processing techniques to automatically extract such information from clinical text. To address this problem, this study takes the initiative to use and adapt word embeddings from four source domains – intensive care, biomedical literature, Wikipedia and Psychiatric Forum – to recognize symptoms in the target domain of psychiatry. We investigated four different approaches including 1) only using word embeddings of the source domain, 2) directly combining data of the source and target to generate word embeddings, 3) assigning different weights to word embeddings, and 4) retraining the word embedding model of the source domain using a corpus of the target domain. To the best of our knowledge, this is the first work of adapting multiple word embeddings of external domains to improve psychiatric symptom recognition in clinical text. Experimental results showed that the last two approaches outperformed the baseline methods, indicating the effectiveness of our new strategies to leverage embeddings from other domains. PMID:29888086

Federation of UML models for cyber physical use cases

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

This method employs the concept of federation, which is defined as the use of existing models that represent aspects of a system in specific domains (such as physical and cyber security domains) and building interfaces to link all of domain models. Federation seeks to build on existing bodies of work. Some examples include the Common Information Models (CIM) maintained by the International Electrotechnical Commission Technical Committee 57 (IEC TC 57) for the electric power industry. Another relevant model is the CIM maintained by the Distributed Management Task Force (DMTF)? this CIM defines a representation of the managed elements in anmore » Information Technology (IT) environment. The power system is an example of a cyber-physical system, where the cyber systems, consisting of computing infrastructure such as networks and devices, play a critical role in the operation of the underlying physical electricity delivery system. Measurements from remote field devices are relayed to control centers through computer networks, and the data is processed to determine suitable control actions. Control decisions are then relayed back to field devices. It has been observed that threat actors may be able to successfully compromise this cyber layer in order to impact power system operation. Therefore, future control center applications must be wary of potentially compromised measurements coming from field devices. In order to ensure the integrity of the field measurements, these applications could make use of compromise indicators from alternate sources of information such as cyber security. Thus, modern control applications may require access to data from sources that are not defined in the local information model. In such cases, software application interfaces will require integration of data objects from cross-domain data models. When incorporating or federating different domains, it is important to have subject matter experts work together, recognizing that not everyone has the same knowledge, responsibilities, focus, or skill set.« less

A New Formulation of the Filter-Error Method for Aerodynamic Parameter Estimation in Turbulence

NASA Technical Reports Server (NTRS)

Grauer, Jared A.; Morelli, Eugene A.

2015-01-01

A new formulation of the filter-error method for estimating aerodynamic parameters in nonlinear aircraft dynamic models during turbulence was developed and demonstrated. The approach uses an estimate of the measurement noise covariance to identify the model parameters, their uncertainties, and the process noise covariance, in a relaxation method analogous to the output-error method. Prior information on the model parameters and uncertainties can be supplied, and a post-estimation correction to the uncertainty was included to account for colored residuals not considered in the theory. No tuning parameters, needing adjustment by the analyst, are used in the estimation. The method was demonstrated in simulation using the NASA Generic Transport Model, then applied to the subscale T-2 jet-engine transport aircraft flight. Modeling results in different levels of turbulence were compared with results from time-domain output error and frequency- domain equation error methods to demonstrate the effectiveness of the approach.

WEC3: Wave Energy Converter Code Comparison Project: Preprint

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

Combourieu, Adrien; Lawson, Michael; Babarit, Aurelien

This paper describes the recently launched Wave Energy Converter Code Comparison (WEC3) project and present preliminary results from this effort. The objectives of WEC3 are to verify and validate numerical modelling tools that have been developed specifically to simulate wave energy conversion devices and to inform the upcoming IEA OES Annex VI Ocean Energy Modelling Verification and Validation project. WEC3 is divided into two phases. Phase 1 consists of a code-to-code verification and Phase II entails code-to-experiment validation. WEC3 focuses on mid-fidelity codes that simulate WECs using time-domain multibody dynamics methods to model device motions and hydrodynamic coefficients to modelmore » hydrodynamic forces. Consequently, high-fidelity numerical modelling tools, such as Navier-Stokes computational fluid dynamics simulation, and simple frequency domain modelling tools were not included in the WEC3 project.« less

Molecular and functional characterization of clathrin- and AP-2-binding determinants within a disordered domain of auxilin.

PubMed

Scheele, Urte; Alves, Jurgen; Frank, Ronald; Duwel, Michael; Kalthoff, Christoph; Ungewickell, Ernst

2003-07-11

Uncoating of clathrin-coated vesicles requires the J-domain protein auxilin for targeting hsc70 to the clathrin coats and for stimulating the hsc70 ATPase activity. This results in the release of hsc70-complexed clathrin triskelia and concomitant dissociation of the coat. To understand the complex role of auxilin in uncoating and clathrin assembly in more detail, we analyzed the molecular organization of its clathrin-binding domain (amino acids 547-813). CD spectroscopy of auxilin fragments revealed that the clathrin-binding domain is almost completely disordered in solution. By systematic mapping using synthetic peptides and by site-directed mutagenesis, we identified short peptide sequences involved in clathrin heavy chain and AP-2 binding and evaluated their significance for the function of auxilin. Some of the binding determinants, including those containing sequences 674DPF and 636WDW, showed dual specificity for both clathrin and AP-2. In contrast, the two DLL motifs within the clathrin-binding domain were exclusively involved in clathrin binding. Surprisingly, they interacted not only with the N-terminal domain of the heavy chain, but also with the distal domain. Moreover, both DLL peptides proved to be essential for clathrin assembly and uncoating. In addition, we found that the motif 726NWQ is required for efficient clathrin assembly activity. Auxilin shares a number of protein-protein interaction motifs with other endocytic proteins, including AP180. We demonstrate that AP180 and auxilin compete for binding to the alpha-ear domain of AP-2. Like AP180, auxilin also directly interacts with the ear domain of beta-adaptin. On the basis of our data, we propose a refined model for the uncoating mechanism of clathrin-coated vesicles.

Modeling Ignition of HMX with the Gibbs Formulation

NASA Astrophysics Data System (ADS)

Lee, Kibaek; Stewart, D. Scott

2017-06-01

We present a HMX model with the Gibbs formulation in which stress tensor and temperature are assumed to be in local equilibrium, but phase/chemical changes are not assumed to be in equilibrium. We assume multi-components for HMX including beta- and delta-phase, liquid, and gas phase of HMX and its gas products. Isotropic small strain solid model, modified Fried Howard liquid EOS, and ideal gas EOS are used for its relevant component. Phase/chemical changes are characterized as reactions and are in individual reaction rate. Maxwell-Stefan model is used for diffusion. Excited gas products in the local domain lead unreacted HMX solid to the ignition event. Density of the mixture, stress, strain, displacement, mass fractions, and temperature are considered in 1D domain with time histories. Office of Naval Research and Air Force Office of Scientific Research.

Transfer Function Identification Using Orthogonal Fourier Transform Modeling Functions

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

2013-01-01

A method for transfer function identification, including both model structure determination and parameter estimation, was developed and demonstrated. The approach uses orthogonal modeling functions generated from frequency domain data obtained by Fourier transformation of time series data. The method was applied to simulation data to identify continuous-time transfer function models and unsteady aerodynamic models. Model fit error, estimated model parameters, and the associated uncertainties were used to show the effectiveness of the method for identifying accurate transfer function models from noisy data.

Imaging-based biomarkers of cognitive performance in older adults constructed via high-dimensional pattern regression applied to MRI and PET.

PubMed

Wang, Ying; Goh, Joshua O; Resnick, Susan M; Davatzikos, Christos

2013-01-01

In this study, we used high-dimensional pattern regression methods based on structural (gray and white matter; GM and WM) and functional (positron emission tomography of regional cerebral blood flow; PET) brain data to identify cross-sectional imaging biomarkers of cognitive performance in cognitively normal older adults from the Baltimore Longitudinal Study of Aging (BLSA). We focused on specific components of executive and memory domains known to decline with aging, including manipulation, semantic retrieval, long-term memory (LTM), and short-term memory (STM). For each imaging modality, brain regions associated with each cognitive domain were generated by adaptive regional clustering. A relevance vector machine was adopted to model the nonlinear continuous relationship between brain regions and cognitive performance, with cross-validation to select the most informative brain regions (using recursive feature elimination) as imaging biomarkers and optimize model parameters. Predicted cognitive scores using our regression algorithm based on the resulting brain regions correlated well with actual performance. Also, regression models obtained using combined GM, WM, and PET imaging modalities outperformed models based on single modalities. Imaging biomarkers related to memory performance included the orbito-frontal and medial temporal cortical regions with LTM showing stronger correlation with the temporal lobe than STM. Brain regions predicting executive performance included orbito-frontal, and occipito-temporal areas. The PET modality had higher contribution to most cognitive domains except manipulation, which had higher WM contribution from the superior longitudinal fasciculus and the genu of the corpus callosum. These findings based on machine-learning methods demonstrate the importance of combining structural and functional imaging data in understanding complex cognitive mechanisms and also their potential usage as biomarkers that predict cognitive status.

CRT--Cascade Routing Tool to define and visualize flow paths for grid-based watershed models

USGS Publications Warehouse

Henson, Wesley R.; Medina, Rose L.; Mayers, C. Justin; Niswonger, Richard G.; Regan, R.S.

2013-01-01

The U.S. Geological Survey Cascade Routing Tool (CRT) is a computer application for watershed models that include the coupled Groundwater and Surface-water FLOW model, GSFLOW, and the Precipitation-Runoff Modeling System (PRMS). CRT generates output to define cascading surface and shallow subsurface flow paths for grid-based model domains. CRT requires a land-surface elevation for each hydrologic response unit (HRU) of the model grid; these elevations can be derived from a Digital Elevation Model raster data set of the area containing the model domain. Additionally, a list is required of the HRUs containing streams, swales, lakes, and other cascade termination features along with indices that uniquely define these features. Cascade flow paths are determined from the altitudes of each HRU. Cascade paths can cross any of the four faces of an HRU to a stream or to a lake within or adjacent to an HRU. Cascades can terminate at a stream, lake, or HRU that has been designated as a watershed outflow location.

Modeling procedures for handling qualities evaluation of flexible aircraft

NASA Technical Reports Server (NTRS)

Govindaraj, K. S.; Eulrich, B. J.; Chalk, C. R.

1981-01-01

This paper presents simplified modeling procedures to evaluate the impact of flexible modes and the unsteady aerodynamic effects on the handling qualities of Supersonic Cruise Aircraft (SCR). The modeling procedures involve obtaining reduced order transfer function models of SCR vehicles, including the important flexible mode responses and unsteady aerodynamic effects, and conversion of the transfer function models to time domain equations for use in simulations. The use of the modeling procedures is illustrated by a simple example.

Strategy for long-term 3D cloud-resolving simulations over the ARM SGP site and preliminary results

NASA Astrophysics Data System (ADS)

Lin, W.; Liu, Y.; Song, H.; Endo, S.

2011-12-01

Parametric representations of cloud/precipitation processes continue having to be adopted in climate simulations with increasingly higher spatial resolution or with emerging adaptive mesh framework; and it is only becoming more critical that such parameterizations have to be scale aware. Continuous cloud measurements at DOE's ARM sites have provided a strong observational basis for novel cloud parameterization research at various scales. Despite significant progress in our observational ability, there are important cloud-scale physical and dynamical quantities that are either not currently observable or insufficiently sampled. To complement the long-term ARM measurements, we have explored an optimal strategy to carry out long-term 3-D cloud-resolving simulations over the ARM SGP site using Weather Research and Forecasting (WRF) model with multi-domain nesting. The factors that are considered to have important influences on the simulated cloud fields include domain size, spatial resolution, model top, forcing data set, model physics and the growth of model errors. The hydrometeor advection that may play a significant role in hydrological process within the observational domain but is often lacking, and the limitations due to the constraint of domain-wide uniform forcing in conventional cloud system-resolving model simulations, are at least partly accounted for in our approach. Conventional and probabilistic verification approaches are employed first for selected cases to optimize the model's capability of faithfully reproducing the observed mean and statistical distributions of cloud-scale quantities. This then forms the basis of our setup for long-term cloud-resolving simulations over the ARM SGP site. The model results will facilitate parameterization research, as well as understanding and dissecting parameterization deficiencies in climate models.

Assessment of nutritional status in the elderly: a proposed function-driven model.

PubMed

Engelheart, Stina; Brummer, Robert

2018-01-01

There is no accepted or standardized definition of 'malnutrition'. Hence, there is also no definition of what constitutes an adequate nutritional status. In elderly people, assessment of nutritional status is complex and is complicated by multi-morbidity and disabilities combined with nutrition-related problems, such as dysphagia, decreased appetite, fatigue, and muscle weakness. We propose a nutritional status model that presents nutritional status from a comprehensive functional perspective. This model visualizes the complexity of the nutritional status in elderly people. The presented model could be interpreted as the nutritional status is conditional to a person's optimal function or situation. Another way of looking at it might be that a person's nutritional status affects his or her optimal situation. The proposed model includes four domains: (1) physical function and capacity; (2) health and somatic disorders; (3) food and nutrition; and (4) cognitive, affective, and sensory function. Each domain has a major impact on nutritional status, which in turn has a major impact on the outcome of each domain. Nutritional status is a multifaceted concept and there exist several knowledge gaps in the diagnosis, prevention, and optimization of treatment of inadequate nutritional status in elderly people. The nutritional status model may be useful in nutritional assessment research, as well as in the clinical setting.

Time and Frequency-Domain Cross-Verification of SLS 6DOF Trajectory Simulations

NASA Technical Reports Server (NTRS)

Johnson, Matthew; McCullough, John

2017-01-01

The Space Launch System (SLS) Guidance, Navigation, and Control (GNC) team and its partners have developed several time- and frequency-based simulations for development and analysis of the proposed SLS launch vehicle. The simulations differ in fidelity and some have unique functionality that allows them to perform specific analyses. Some examples of the purposes of the various models are: trajectory simulation, multi-body separation, Monte Carlo, hardware in the loop, loads, and frequency domain stability analyses. While no two simulations are identical, many of the models are essentially six degree-of-freedom (6DOF) representations of the SLS plant dynamics, hardware implementation, and flight software. Thus at a high level all of those models should be in agreement. Comparison of outputs from several SLS trajectory and stability analysis tools are ongoing as part of the program's current verification effort. The purpose of these comparisons is to highlight modeling and analysis differences, verify simulation data sources, identify inconsistencies and minor errors, and ultimately to verify output data as being a good representation of the vehicle and subsystem dynamics. This paper will show selected verification work in both the time and frequency domain from the current design analysis cycle of the SLS for several of the design and analysis simulations. In the time domain, the tools that will be compared are MAVERIC, CLVTOPS, SAVANT, STARS, ARTEMIS, and POST 2. For the frequency domain analysis, the tools to be compared are FRACTAL, SAVANT, and STARS. The paper will include discussion of these tools including their capabilities, configurations, and the uses to which they are put in the SLS program. Determination of the criteria by which the simulations are compared (matching criteria) requires thoughtful consideration, and there are several pitfalls that may occur that can severely punish a simulation if not considered carefully. The paper will discuss these considerations and will present a framework for responding to these issues when they arise. For example, small event timing differences can lead to large differences in mass properties if the criteria are to measure those properties at the same time, or large differences in altitude if the criteria are to measure those properties when the simulation experiences a staging event. Similarly, a tiny difference in phase can lead to large gain margin differences for frequency-domain comparisons of gain margins.

A Methodology for Cybercraft Requirement Definition and Initial System Design

DTIC Science & Technology

2008-06-01

the software development concepts of the SDLC , requirements, use cases and domain modeling . It ...collectively as Software Development 5 Life Cycle ( SDLC ) models . While there are numerous models that fit under the SDLC definition, all are based on... developed that provided expanded understanding of the domain, it is necessary to either update an existing domain model or create another domain

Interoperability challenges in river discharge modelling: A cross domain application scenario

NASA Astrophysics Data System (ADS)

Santoro, Mattia; Andres, Volker; Jirka, Simon; Koike, Toshio; Looser, Ulrich; Nativi, Stefano; Pappenberger, Florian; Schlummer, Manuela; Strauch, Adrian; Utech, Michael; Zsoter, Ervin

2018-06-01

River discharge is a critical water cycle variable, as it integrates all the processes (e.g. runoff and evapotranspiration) occurring within a river basin and provides a hydrological output variable that can be readily measured. Its prediction is of invaluable help for many water-related tasks including water resources assessment and management, flood protection, and disaster mitigation. Observations of river discharge are important to calibrate and validate hydrological or coupled land, atmosphere and ocean models. This requires using datasets from different scientific domains (Water, Weather, etc.). Typically, such datasets are provided using different technological solutions. This complicates the integration of new hydrological data sources into application systems. Therefore, a considerable effort is often spent on data access issues instead of the actual scientific question. This paper describes the work performed to address multidisciplinary interoperability challenges related to river discharge modeling and validation. This includes definition and standardization of domain specific interoperability standards for hydrological data sharing and their support in global frameworks such as the Global Earth Observation System of Systems (GEOSS). The research was developed in the context of the EU FP7-funded project GEOWOW (GEOSS Interoperability for Weather, Ocean and Water), which implemented a "River Discharge" application scenario. This scenario demonstrates the combination of river discharge observations data from the Global Runoff Data Centre (GRDC) database and model outputs produced by the European Centre for Medium-Range Weather Forecasts (ECMWF) predicting river discharge based on weather forecast information in the context of the GEOSS.

Functional Pathways of Social Support for Mental Health in Work and Family Domains Among Chinese Scientific and Technological Professionals.

PubMed

Gan, Yiqun; Gan, Tingting; Chen, Zhiyan; Miao, Miao; Zhang, Kan

2015-10-01

This study investigated the role of social support in the complex pattern of associations among stressors, work-family interferences and depression in the domains of work and family. A questionnaire was administered to a nationwide sample of 11,419 Chinese science and technology professionals. Several structural equation models were specified to determine whether social support functioned as a predictor or a mediator. Using Mplus 5.0, we compared the moderation model, the independence model, the antecedent model and the mediation model. The results revealed that the relationship between work-family interference and social support was domain specific. The independence model fit the data best in the work domain. Both the moderation model and the antecedent model fit the family domain data equally well. The current study was conducted to answer the need for comprehensive investigations of cultural uniqueness in the antecedents of work-family interference. The domain specificity, i.e. the multiple channels of the functions of support in the family domain and not in the work domain, ensures that this study is unique and culturally specific. Copyright © 2014 John Wiley & Sons, Ltd.

Electrical circuit modeling and analysis of microwave acoustic interaction with biological tissues.

PubMed

Gao, Fei; Zheng, Qian; Zheng, Yuanjin

2014-05-01

Numerical study of microwave imaging and microwave-induced thermoacoustic imaging utilizes finite difference time domain (FDTD) analysis for simulation of microwave and acoustic interaction with biological tissues, which is time consuming due to complex grid-segmentation and numerous calculations, not straightforward due to no analytical solution and physical explanation, and incompatible with hardware development requiring circuit simulator such as SPICE. In this paper, instead of conventional FDTD numerical simulation, an equivalent electrical circuit model is proposed to model the microwave acoustic interaction with biological tissues for fast simulation and quantitative analysis in both one and two dimensions (2D). The equivalent circuit of ideal point-like tissue for microwave-acoustic interaction is proposed including transmission line, voltage-controlled current source, envelop detector, and resistor-inductor-capacitor (RLC) network, to model the microwave scattering, thermal expansion, and acoustic generation. Based on which, two-port network of the point-like tissue is built and characterized using pseudo S-parameters and transducer gain. Two dimensional circuit network including acoustic scatterer and acoustic channel is also constructed to model the 2D spatial information and acoustic scattering effect in heterogeneous medium. Both FDTD simulation, circuit simulation, and experimental measurement are performed to compare the results in terms of time domain, frequency domain, and pseudo S-parameters characterization. 2D circuit network simulation is also performed under different scenarios including different sizes of tumors and the effect of acoustic scatterer. The proposed circuit model of microwave acoustic interaction with biological tissue could give good agreement with FDTD simulated and experimental measured results. The pseudo S-parameters and characteristic gain could globally evaluate the performance of tumor detection. The 2D circuit network enables the potential to combine the quasi-numerical simulation and circuit simulation in a uniform simulator for codesign and simulation of a microwave acoustic imaging system, bridging bioeffect study and hardware development seamlessly.

Dynamics and Predictability of The Eta Regional Model: The Role of Domain Size

NASA Astrophysics Data System (ADS)

Vannitsem, S.; Chomé, F.; Nicolis, C.

This paper investigates the dynamical properties of the Eta model, a state-of-the- art nested limited-area model, following the approach previously developed by the present authors. It is first shown that the intrinsic dynamics of the model depends crucially on the size of the domain, with a non-chaotic behavior for small domains, supporting earlier findings on the absence of sensitivity to the initial conditions in these models. The quality of the predictions of several Eta model versions differing by their domain size is next evaluated and compared with the Avn analyses on a targeted region, centered on France. Contrary to what is usually taken for granted, a non-trivial relation between predictability and domain size is found, the best model versions be- ing the ones integrated on the smallest and the largest domain sizes. An explanation in connection with the intrinsic dynamics of the model is advanced.

Cerebellar contributions to motor control and language comprehension: searching for common computational principles.

PubMed

Moberget, Torgeir; Ivry, Richard B

2016-04-01

The past 25 years have seen the functional domain of the cerebellum extend beyond the realm of motor control, with considerable discussion of how this subcortical structure contributes to cognitive domains including attention, memory, and language. Drawing on evidence from neuroanatomy, physiology, neuropsychology, and computational work, sophisticated models have been developed to describe cerebellar function in sensorimotor control and learning. In contrast, mechanistic accounts of how the cerebellum contributes to cognition have remained elusive. Inspired by the homogeneous cerebellar microanatomy and a desire for parsimony, many researchers have sought to extend mechanistic ideas from motor control to cognition. One influential hypothesis centers on the idea that the cerebellum implements internal models, representations of the context-specific dynamics of an agent's interactions with the environment, enabling predictive control. We briefly review cerebellar anatomy and physiology, to review the internal model hypothesis as applied in the motor domain, before turning to extensions of these ideas in the linguistic domain, focusing on speech perception and semantic processing. While recent findings are consistent with this computational generalization, they also raise challenging questions regarding the nature of cerebellar learning, and may thus inspire revisions of our views on the role of the cerebellum in sensorimotor control. © 2016 New York Academy of Sciences.

A dual process perspective on advances in cognitive science and alcohol use disorder.

PubMed

Lindgren, Kristen P; Hendershot, Christian S; Ramirez, Jason J; Bernat, Edward; Rangel-Gomez, Mauricio; Peterson, Kirsten P; Murphy, James G

2018-04-11

There is a tremendous global and national (US) burden associated with alcohol misuse and alcohol use disorder (AUD). Further, of the mental health disorders, AUD has the widest treatment gap. Thus, there is a critical need for improved understanding of the etiology, maintenance, and treatment of AUD. The application of cognitive science to the study of AUD has a longstanding history of attempting to meet this need. In this selective review, we identified and focused on four domains of recent (i.e., in the last decade) applications of cognitive science to the study of AUD: implicit cognitive biases, executive function, behavioral economic approaches to alcohol decision making, and functional connectivity neuroimaging. We highlighted advances within these four domains and considered them in the context of dual process models of addiction, which focus on the contribution and interplay of two complementary neurocognitive systems (impulsive and control systems). Findings across the domains were generally consistent with dual process models. They also suggest the need for further model refinements, including integrating behavioral economic approaches and findings from functional connectivity neuroimaging studies. Research evaluating candidate interventions associated with these domains is emergent but promising, suggesting important directions for future research. Copyright © 2018 Elsevier Ltd. All rights reserved.

Recombinant spider silk genetically functionalized with affinity domains.

PubMed

Jansson, Ronnie; Thatikonda, Naresh; Lindberg, Diana; Rising, Anna; Johansson, Jan; Nygren, Per-Åke; Hedhammar, My

2014-05-12

Functionalization of biocompatible materials for presentation of active protein domains is an area of growing interest. Herein, we describe a strategy for functionalization of recombinant spider silk via gene fusion to affinity domains of broad biotechnological use. Four affinity domains of different origin and structure; the IgG-binding domains Z and C2, the albumin-binding domain ABD, and the biotin-binding domain M4, were all successfully produced as soluble silk fusion proteins under nondenaturing purification conditions. Silk films and fibers produced from the fusion proteins were demonstrated to be chemically and thermally stable. Still, the bioactive domains are concluded to be folded and accessible, since their respective targets could be selectively captured from complex samples, including rabbit serum and human plasma. Interestingly, materials produced from mixtures of two different silk fusion proteins displayed combined binding properties, suggesting that tailor-made materials with desired stoichiometry and surface distributions of several binding domains can be produced. Further, use of the IgG binding ability as a general mean for presentation of desired biomolecules could be demonstrated for a human vascular endothelial growth factor (hVEGF) model system, via a first capture of anti-VEGF IgG to silk containing the Z-domain, followed by incubation with hVEGF. Taken together, this study demonstrates the potential of recombinant silk, genetically functionalized with affinity domains, for construction of biomaterials capable of presentation of almost any desired biomolecule.

Web portal on environmental sciences "ATMOS''

NASA Astrophysics Data System (ADS)

Gordov, E. P.; Lykosov, V. N.; Fazliev, A. Z.

2006-06-01

The developed under INTAS grant web portal ATMOS (http://atmos.iao.ru and http://atmos.scert.ru) makes available to the international research community, environmental managers, and the interested public, a bilingual information source for the domain of Atmospheric Physics and Chemistry, and the related application domain of air quality assessment and management. It offers access to integrated thematic information, experimental data, analytical tools and models, case studies, and related information and educational resources compiled, structured, and edited by the partners into a coherent and consistent thematic information resource. While offering the usual components of a thematic site such as link collections, user group registration, discussion forum, news section etc., the site is distinguished by its scientific information services and tools: on-line models and analytical tools, and data collections and case studies together with tutorial material. The portal is organized as a set of interrelated scientific sites, which addressed basic branches of Atmospheric Sciences and Climate Modeling as well as the applied domains of Air Quality Assessment and Management, Modeling, and Environmental Impact Assessment. Each scientific site is open for external access information-computational system realized by means of Internet technologies. The main basic science topics are devoted to Atmospheric Chemistry, Atmospheric Spectroscopy and Radiation, Atmospheric Aerosols, Atmospheric Dynamics and Atmospheric Models, including climate models. The portal ATMOS reflects current tendency of Environmental Sciences transformation into exact (quantitative) sciences and is quite effective example of modern Information Technologies and Environmental Sciences integration. It makes the portal both an auxiliary instrument to support interdisciplinary projects of regional environment and extensive educational resource in this important domain.

Linear modeling of human hand-arm dynamics relevant to right-angle torque tool interaction.

PubMed

Ay, Haluk; Sommerich, Carolyn M; Luscher, Anthony F

2013-10-01

A new protocol was evaluated for identification of stiffness, mass, and damping parameters employing a linear model for human hand-arm dynamics relevant to right-angle torque tool use. Powered torque tools are widely used to tighten fasteners in manufacturing industries. While these tools increase accuracy and efficiency of tightening processes, operators are repetitively exposed to impulsive forces, posing risk of upper extremity musculoskeletal injury. A novel testing apparatus was developed that closely mimics biomechanical exposure in torque tool operation. Forty experienced torque tool operators were tested with the apparatus to determine model parameters and validate the protocol for physical capacity assessment. A second-order hand-arm model with parameters extracted in the time domain met model accuracy criterion of 5% for time-to-peak displacement error in 93% of trials (vs. 75% for frequency domain). Average time-to-peak handle displacement and relative peak handle force errors were 0.69 ms and 0.21%, respectively. Model parameters were significantly affected by gender and working posture. Protocol and numerical calculation procedures provide an alternative method for assessing mechanical parameters relevant to right-angle torque tool use. The protocol more closely resembles tool use, and calculation procedures demonstrate better performance of parameter extraction using time domain system identification methods versus frequency domain. Potential future applications include parameter identification for in situ torque tool operation and equipment development for human hand-arm dynamics simulation under impulsive forces that could be used for assessing torque tools based on factors relevant to operator health (handle dynamics and hand-arm reaction force).

Modeling of Millimeter-Wave Modulation Characteristics of Semiconductor Lasers under Strong Optical Feedback

PubMed Central

Bakry, Ahmed

2014-01-01

This paper presents modeling and simulation on the characteristics of semiconductor laser modulated within a strong optical feedback (OFB-)induced photon-photon resonance over a passband of millimeter (mm) frequencies. Continuous wave (CW) operation of the laser under strong OFB is required to achieve the photon-photon resonance in the mm-wave band. The simulated time-domain characteristics of modulation include the waveforms of the intensity and frequency chirp as well as the associated distortions of the modulated mm-wave signal. The frequency domain characteristics include the intensity modulation (IM) and frequency modulation (FM) responses in addition to the associated relative intensity noise (RIN). The signal characteristics under modulations with both single and two mm-frequencies are considered. The harmonic distortion and the third order intermodulation distortion (IMD3) are examined and the spurious free dynamic range (SFDR) is calculated. PMID:25383381

Modeling and Analysis of Power Processing Systems (MAPPS), initial phase 2

NASA Technical Reports Server (NTRS)

Yu, Y.; Lee, F. C.; Wangenheim, H.; Warren, D.

1977-01-01

The overall objective of the program is to provide the engineering tools to reduce the analysis, design, and development effort, and thus the cost, in achieving the required performances for switching regulators and dc-dc converter systems. The program was both tutorial and application oriented. Various analytical methods were described in detail and supplemented with examples, and those with standardization appeals were reduced into computer-based subprograms. Major program efforts included those concerning small and large signal control-dependent performance analysis and simulation, control circuit design, power circuit design and optimization, system configuration study, and system performance simulation. Techniques including discrete time domain, conventional frequency domain, Lagrange multiplier, nonlinear programming, and control design synthesis were employed in these efforts. To enhance interactive conversation between the modeling and analysis subprograms and the user, a working prototype of the Data Management Program was also developed to facilitate expansion as future subprogram capabilities increase.

Theoretical domains framework to assess barriers to change for planning health care quality interventions: a systematic literature review.

PubMed

Mosavianpour, Mirkaber; Sarmast, Hamideh Helen; Kissoon, Niranjan; Collet, Jean-Paul

2016-01-01

Theoretical domains framework (TDF) provides an integrative model for assessing barriers to behavioral changes in order to suggest interventions for improvement in behavior and ultimately outcomes. However, there are other tools that are used to assess barriers. The objective of this study is to determine the degree of concordance between domains and constructs identified in two versions of the TDF including original (2005) and refined version (2012) and independent studies of other tools. We searched six databases for articles that studied barriers to health-related behavior changes of health care professionals or the general public. We reviewed quantitative papers published in English which included their questionnaires in the article. A table including the TDF domains of both original and refined versions and related constructs was developed to serve as a reference to describe the barriers assessed in the independent studies; descriptive statistics were used to express the results. Out of 552 papers retrieved, 50 were eligible to review. The barrier domains explored in these articles belonged to two to eleven domains of the refined TDF. Eighteen articles (36%) used constructs outside of the refined version. The spectrum of barrier constructs of the original TDF was broader and could meet the domains studied in 48 studies (96%). Barriers in domains of "environmental context and resources", "beliefs about consequences", and "social influences" were the most frequently explored in 42 (84%), 37 (74%), and 33 (66%) of the 50 articles, respectively. Both refined and original TDFs cataloged barriers measured by the other studies that did not use TDF as their framework. However, the original version of TDF explored a broader spectrum of barriers than the refined version. From this perspective, the original version of the TDF seems to be a more comprehensive tool for assessing barriers in practice.

Investigations into the triggered lightning response of the F106B thunderstorm research aircraft

NASA Technical Reports Server (NTRS)

Rudolph, Terence H.; Perala, Rodney A.; Mckenna, Paul M.; Parker, Steven L.

1985-01-01

An investigation has been conducted into the lightning characteristics of the NASA F106B thunderstorm research aircraft. The investigation includes analysis of measured data from the aircraft in the time and frequency domains. Linear and nonlinear computer modelling has also been performed. In addition, new computer tools have been developed, including a new enhanced nonlinear air breakdown model, and a subgrid model useful for analyzing fine details of the aircraft's geometry. Comparison of measured and calculated electromagnetic responses of the aircraft to a triggered lightning environment are presented.

Integrating HL7 RIM and ontology for unified knowledge and data representation in clinical decision support systems.

PubMed

Zhang, Yi-Fan; Tian, Yu; Zhou, Tian-Shu; Araki, Kenji; Li, Jing-Song

2016-01-01

The broad adoption of clinical decision support systems within clinical practice has been hampered mainly by the difficulty in expressing domain knowledge and patient data in a unified formalism. This paper presents a semantic-based approach to the unified representation of healthcare domain knowledge and patient data for practical clinical decision making applications. A four-phase knowledge engineering cycle is implemented to develop a semantic healthcare knowledge base based on an HL7 reference information model, including an ontology to model domain knowledge and patient data and an expression repository to encode clinical decision making rules and queries. A semantic clinical decision support system is designed to provide patient-specific healthcare recommendations based on the knowledge base and patient data. The proposed solution is evaluated in the case study of type 2 diabetes mellitus inpatient management. The knowledge base is successfully instantiated with relevant domain knowledge and testing patient data. Ontology-level evaluation confirms model validity. Application-level evaluation of diagnostic accuracy reaches a sensitivity of 97.5%, a specificity of 100%, and a precision of 98%; an acceptance rate of 97.3% is given by domain experts for the recommended care plan orders. The proposed solution has been successfully validated in the case study as providing clinical decision support at a high accuracy and acceptance rate. The evaluation results demonstrate the technical feasibility and application prospect of our approach. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

How culture shapes the body: cultural consonance and body mass in urban Brazil.

PubMed

Dressler, William W; Oths, Kathryn S; Balieiro, Mauro C; Ribeiro, Rosane P; Dos Santos, José Ernesto

2012-01-01

The aim of this article is to develop a model of how culture shapes the body, based on two studies conducted in urban Brazil. Research was conducted in 1991 and 2001 in four socioeconomically distinct neighborhoods. First, cultural domain analyses were conducted with samples of key informants. The cultural domains investigated included lifestyle, social support, family life, national identity, and food. Cultural consensus analysis was used to confirm shared knowledge in each domain and to derive measures of cultural consonance. Cultural consonance assesses how closely an individual matches the cultural consensus model for each domain. Second, body composition, cultural consonance, and related variables were assessed in community surveys. Multiple regression analysis was used to examine the association of cultural consonance and body composition, controlling for standard covariates and competing explanatory variables. In 1991, in a survey of 260 individuals, cultural consonance had a curvilinear association with the body mass index that differed for men and women, controlling for sociodemographic and dietary variables. In 2001, in a survey of 267 individuals, cultural consonance had a linear association with abdominal circumference that differed for men and women, controlling for sociodemographic and dietary variables. In general, as cultural consonance increases, body mass index and abdominal circumference decline, more strongly for women than men. As individuals, in their own beliefs and behaviors, more closely approximate shared cultural models in socially salient domains, body composition also more closely approximates the cultural prototype of the body. Copyright © 2012 Wiley Periodicals, Inc.

Comparison of the landslide susceptibility models in Taipei Water Source Domain, Taiwan

NASA Astrophysics Data System (ADS)

WU, C. Y.; Yeh, Y. C.; Chou, T. H.

2017-12-01

Taipei Water Source Domain, locating at the southeast of Taipei Metropolis, is the main source of water resource in this region. Recently, the downstream turbidity often soared significantly during the typhoon period because of the upstream landslides. The landslide susceptibilities should be analysed to assess the influence zones caused by different rainfall events, and to ensure the abilities of this domain to serve enough and quality water resource. Generally, the landslide susceptibility models can be established based on either a long-term landslide inventory or a specified landslide event. Sometimes, there is no long-term landslide inventory in some areas. Thus, the event-based landslide susceptibility models are established widely. However, the inventory-based and event-based landslide susceptibility models may result in dissimilar susceptibility maps in the same area. So the purposes of this study were to compare the landslide susceptibility maps derived from the inventory-based and event-based models, and to interpret how to select a representative event to be included in the susceptibility model. The landslide inventory from Typhoon Tim in July, 1994 and Typhoon Soudelor in August, 2015 was collected, and used to establish the inventory-based landslide susceptibility model. The landslides caused by Typhoon Nari and rainfall data were used to establish the event-based model. The results indicated the high susceptibility slope-units were located at middle upstream Nan-Shih Stream basin.

A strong pinning model for the coercivity of die-upset Pr-Fe-B magnets

NASA Astrophysics Data System (ADS)

Pinkerton, F. E.; fürst, C. D.

1991-04-01

We have measured the temperature dependence of the intrinsic coercivity Hci(T) between 5 and 565 K in a die-upset Pr-Fe-B magnet. Over a very wide temperature range up to 477 K, Hci(T) is in excellent agreement with a model for strong domain-wall pinning by a random array of pinning sites proposed by Gaunt [P. Gaunt, Philos. Mag. B 48, 261 (1983)]. The model includes both the temperature dependence of the intrinsic magnetic properties of the Pr2Fe14B phase and the effects of thermal activation of domain walls over the pinning barrier. The pinning sites are modeled as nonmagnetic planar inhomogeneities at the boundaries between platelet-shaped Pr2Fe14B grains. We develop an expression for the maximum pinning force per site, f, and derive the model prediction that (Hci/γHA)1/2 varies linearly with (T/γ)2/3, where HA and γ are the magnetocrystalline anisotropy field and the domain-wall energy per unit area of the Pr2Fe14B phase, respectively. Significant deviations from the model are observed only at high temperature, suggesting that the strong pinning model is no longer valid very close to the Curie temperature (565 K). The present result agrees with the model fit obtained for a die-upset Nd-Fe-B magnet.

Asymptotic modeling of transport phenomena at the interface between a fluid and a porous layer: Jump conditions

NASA Astrophysics Data System (ADS)

Angot, Philippe; Goyeau, Benoît; Ochoa-Tapia, J. Alberto

2017-06-01

We develop asymptotic modeling for two- or three-dimensional viscous fluid flow and convective transfer at the interface between a fluid and a porous layer. The asymptotic model is based on the fact that the thickness d of the interfacial transition region Ωfp of the one-domain representation is very small compared to the macroscopic length scale L . The analysis leads to an equivalent two-domain representation where transport phenomena in the transition layer of the one-domain approach are represented by algebraic jump boundary conditions at a fictive dividing interface Σ between the homogeneous fluid and porous regions. These jump conditions are thus stated up to first-order in O (d /L ) with d /L ≪1 . The originality and relevance of this asymptotic model lies in its general and multidimensional character. Indeed, it is shown that all the jump interface conditions derived for the commonly used 1D-shear flow are recovered by taking the tangential component of the asymptotic model. In that case, the comparison between the present model and the different models available in the literature gives explicit expressions of the effective jump coefficients and their associated scaling. In addition for multi-dimensional flows, the general asymptotic model yields the different components of the jump conditions including a new specific equation for the cross-flow pressure jump on Σ .

An evaluation of selected in silico models for the assessment ...

EPA Pesticide Factsheets

Skin sensitization remains an important endpoint for consumers, manufacturers and regulators. Although the development of alternative approaches to assess skin sensitization potential has been extremely active over many years, the implication of regulations such as REACH and the Cosmetics Directive in EU has provided a much stronger impetus to actualize this research into practical tools for decision making. Thus there has been considerable focus on the development, evaluation, and integration of alternative approaches for skin sensitization hazard and risk assessment. This includes in silico approaches such as (Q)SARs and expert systems. This study aimed to evaluate the predictive performance of a selection of in silico models and then to explore whether combining those models led to an improvement in accuracy. A dataset of 473 substances that had been tested in the local lymph node assay (LLNA) was compiled. This comprised 295 sensitizers and 178 non-sensitizers. Four freely available models were identified - 2 statistical models VEGA and MultiCASE model A33 for skin sensitization (MCASE A33) from the Danish National Food Institute and two mechanistic models Toxtree’s Skin sensitization Reaction domains (Toxtree SS Rxn domains) and the OASIS v1.3 protein binding alerts for skin sensitization from the OECD Toolbox (OASIS). VEGA and MCASE A33 aim to predict sensitization as a binary score whereas the mechanistic models identified reaction domains or structura

Asymptotic modeling of transport phenomena at the interface between a fluid and a porous layer: Jump conditions.

PubMed

Angot, Philippe; Goyeau, Benoît; Ochoa-Tapia, J Alberto

2017-06-01

We develop asymptotic modeling for two- or three-dimensional viscous fluid flow and convective transfer at the interface between a fluid and a porous layer. The asymptotic model is based on the fact that the thickness d of the interfacial transition region Ω_{fp} of the one-domain representation is very small compared to the macroscopic length scale L. The analysis leads to an equivalent two-domain representation where transport phenomena in the transition layer of the one-domain approach are represented by algebraic jump boundary conditions at a fictive dividing interface Σ between the homogeneous fluid and porous regions. These jump conditions are thus stated up to first-order in O(d/L) with d/L≪1. The originality and relevance of this asymptotic model lies in its general and multidimensional character. Indeed, it is shown that all the jump interface conditions derived for the commonly used 1D-shear flow are recovered by taking the tangential component of the asymptotic model. In that case, the comparison between the present model and the different models available in the literature gives explicit expressions of the effective jump coefficients and their associated scaling. In addition for multi-dimensional flows, the general asymptotic model yields the different components of the jump conditions including a new specific equation for the cross-flow pressure jump on Σ.

Analysis for Non-Traditional Security Challenges: Methods and Tools

DTIC Science & Technology

2006-11-20

PMESII Modeling Challenges modeling or where data is not available to support the model, would aid decision Domain is large, nebulous, complex, and...traditional challenges . This includes enlisting the aid of the inter-agency and alliance/coalition communities. Second, we need to realize this...20 November 2006 MILITARY OPERATIONS RESEARCH SOCIETY MIFh MORS Workshop Analysis for Non-Traditional Security Challenges : Methods and Tools 21-23

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

PubMed Central

Miller, Thomas F.

2017-01-01

We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency. PMID:28328943

Contrasting two models of academic self-efficacy--domain-specific versus cross-domain--in children receiving and not receiving special instruction in mathematics.

PubMed

Jungert, Tomas; Hesser, Hugo; Träff, Ulf

2014-10-01

In social cognitive theory, self-efficacy is domain-specific. An alternative model, the cross-domain influence model, would predict that self-efficacy beliefs in one domain might influence performance in other domains. Research has also found that children who receive special instruction are not good at estimating their performance. The aim was to test two models of how self-efficacy beliefs influence achievement, and to contrast children receiving special instruction in mathematics with normally-achieving children. The participants were 73 fifth-grade children who receive special instruction and 70 children who do not receive any special instruction. In year four and five, the children's skills in mathematics and reading were assessed by national curriculum tests, and in their fifth year, self-efficacy in mathematics and reading were measured. Structural equation modeling showed that in domains where children do not receive special instruction in mathematics, self-efficacy is a mediating variable between earlier and later achievement in the same domain. Achievement in mathematics was not mediated by self-efficacy in mathematics for children who receive special instruction. For normal achieving children, earlier achievement in the language domain had an influence on later self-efficacy in the mathematics domain, and self-efficacy beliefs in different domains were correlated. Self-efficacy is mostly domain specific, but may play a different role in academic performance depending on whether children receive special instruction. The results of the present study provided some support of the Cross-Domain Influence Model for normal achieving children. © 2014 Scandinavian Psychological Associations and John Wiley & Sons Ltd.

A Novel Domain Assembly Routine for Creating Full-Length Models of Membrane Proteins from Known Domain Structures.

PubMed

Koehler Leman, Julia; Bonneau, Richard

2018-04-03

Membrane proteins composed of soluble and membrane domains are often studied one domain at a time. However, to understand the biological function of entire protein systems and their interactions with each other and drugs, knowledge of full-length structures or models is required. Although few computational methods exist that could potentially be used to model full-length constructs of membrane proteins, none of these methods are perfectly suited for the problem at hand. Existing methods require an interface or knowledge of the relative orientations of the domains or are not designed for domain assembly, and none of them are developed for membrane proteins. Here we describe the first domain assembly protocol specifically designed for membrane proteins that assembles intra- and extracellular soluble domains and the transmembrane domain into models of the full-length membrane protein. Our protocol does not require an interface between the domains and samples possible domain orientations based on backbone dihedrals in the flexible linker regions, created via fragment insertion, while keeping the transmembrane domain fixed in the membrane. For five examples tested, our method mp_domain_assembly, implemented in RosettaMP, samples domain orientations close to the known structure and is best used in conjunction with experimental data to reduce the conformational search space.

Finite-element time-domain algorithms for modeling linear Debye and Lorentz dielectric dispersions at low frequencies.

PubMed

Stoykov, Nikolay S; Kuiken, Todd A; Lowery, Madeleine M; Taflove, Allen

2003-09-01

We present what we believe to be the first algorithms that use a simple scalar-potential formulation to model linear Debye and Lorentz dielectric dispersions at low frequencies in the context of finite-element time-domain (FETD) numerical solutions of electric potential. The new algorithms, which permit treatment of multiple-pole dielectric relaxations, are based on the auxiliary differential equation method and are unconditionally stable. We validate the algorithms by comparison with the results of a previously reported method based on the Fourier transform. The new algorithms should be useful in calculating the transient response of biological materials subject to impulsive excitation. Potential applications include FETD modeling of electromyography, functional electrical stimulation, defibrillation, and effects of lightning and impulsive electric shock.

Factor Structure of the Quality of Life Scale for Mental Disorders in Patients With Schizophrenia.

PubMed

Chiu, En-Chi; Lee, Shu-Chun

2018-06-01

The Quality of Life for Mental Disorders (QOLMD) scale was designed to measure health-related quality of life (HRQOL) in patients with mental illness, especially schizophrenia. The QOLMD contains 45 items, which are divided into eight domains. However, the factor structure of the QOLMD has not been evaluated, which restricts the interpretations of the results of this scale. The purpose of this study was to evaluate the factor structures (i.e., unidimensionality, eight-factor structure, and second-order model) of the QOLMD in patients with schizophrenia. Two hundred thirty-eight outpatients with schizophrenia participated. We first conducted confirmatory factor analysis to evaluate the unidimensionality of each domain. After the unidimensionality of the eight individual domains was supported, we examined the eight-factor structure and second-order model. The results of unidimensionality showed sufficient model fit in all of the domains with the exception of the autonomy domain. A good model fit was confirmed for the autonomy domain after deleting two of the original items. The eight-factor structure for the 43-item QOLMD showed an acceptable model fit, although the second-order model showed poor model fit. Our results supported the unidimensionality and eight-factor structure of the 43-item QOLMD. The sum score for each of the domains may be used to reflect its domain-specific function. We recommend using the 43-item QOLMD to capture the multiple domains of HRQOL. However, the second-order model showed an unsatisfactory model fit. Furthermore, caution is advised when interpreting overall HRQOL using the total score for the eight domains.

Requirements analysis, domain knowledge, and design

NASA Technical Reports Server (NTRS)

Potts, Colin

1988-01-01

Two improvements to current requirements analysis practices are suggested: domain modeling, and the systematic application of analysis heuristics. Domain modeling is the representation of relevant application knowledge prior to requirements specification. Artificial intelligence techniques may eventually be applicable for domain modeling. In the short term, however, restricted domain modeling techniques, such as that in JSD, will still be of practical benefit. Analysis heuristics are standard patterns of reasoning about the requirements. They usually generate questions of clarification or issues relating to completeness. Analysis heuristics can be represented and therefore systematically applied in an issue-based framework. This is illustrated by an issue-based analysis of JSD's domain modeling and functional specification heuristics. They are discussed in the context of the preliminary design of simple embedded systems.

Pulse analysis of acoustic emission signals. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Houghton, J. R.

1976-01-01

A method for the signature analysis of pulses in the frequency domain and the time domain is presented. Fourier spectrum, Fourier transfer function, shock spectrum and shock spectrum ratio are examined in the frequency domain analysis, and pulse shape deconvolution is developed for use in the time domain analysis. To demonstrate the relative sensitivity of each of the methods to small changes in the pulse shape, signatures of computer modeled systems with analytical pulses are presented. Optimization techniques are developed and used to indicate the best design parameters values for deconvolution of the pulse shape. Several experiments are presented that test the pulse signature analysis methods on different acoustic emission sources. These include acoustic emissions associated with: (1) crack propagation, (2) ball dropping on a plate, (3) spark discharge and (4) defective and good ball bearings.

Examining the Relations Among the DSM-5 Alternative Model of Personality, the Five-Factor Model, and Externalizing and Internalizing Behavior.

PubMed

Sleep, Chelsea E; Hyatt, Courtland S; Lamkin, Joanna; Maples-Keller, Jessica L; Miller, Joshua D

2017-01-26

Given long-standing criticisms of the DSM's reliance on categorical models of psychopathology, including the poor reliability and validity of personality-disorder diagnoses, the American Psychiatric Association (APA) published an alternative model (AM) of personality disorders in Section III of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5; APA, 2013), which, in part, comprises 5 pathological trait domains based on the 5-factor model (FFM). However, the empirical profiles and discriminant validity of the AM traits remain in question. We recruited a sample of undergraduates (N = 340) for the current study to compare the relations found between a measure of the DSM-5 AM traits (i.e., the Personality Inventory for DSM-5; PID-5; Krueger, Derringer, Markon, Watson, & Skodol, 2012) and a measure of the FFM (i.e., the International Personality Item Pool; IPIP; Goldberg, 1999) in relation to externalizing and internalizing symptoms. In general, the domains from the 2 measures were significantly related and demonstrated similar patterns of relations with these criteria, such that Antagonism/low Agreeableness and Disinhibition/low Conscientiousness were related to externalizing behaviors, whereas Negative Affectivity/Neuroticism was most significantly related to internalizing symptoms. However, the PID-5 demonstrated large interrelations among its domains and poorer discriminant validity than the IPIP. These results provide additional support that the conception of the trait model included in the DSM-5 AM is an extension of the FFM, but highlight some of the issues that arise due to the PID-5's more limited discriminant validity. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The elastic free energy of a tandem modular protein under force.

PubMed

Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

2015-05-01

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function.

PubMed

Banach, Mateusz; Konieczny, Leszek; Roterman, Irena

2014-10-21

In this paper we show that the fuzzy oil drop model represents a general framework for describing the generation of hydrophobic cores in proteins and thus provides insight into the influence of the water environment upon protein structure and stability. The model has been successfully applied in the study of a wide range of proteins, however this paper focuses specifically on domains representing immunoglobulin-like folds. Here we provide evidence that immunoglobulin-like domains, despite being structurally similar, differ with respect to their participation in the generation of hydrophobic core. It is shown that β-structural fragments in β-barrels participate in hydrophobic core formation in a highly differentiated manner. Quantitatively measured participation in core formation helps explain the variable stability of proteins and is shown to be related to their biological properties. This also includes the known tendency of immunoglobulin domains to form amyloids, as shown using transthyretin to reveal the clear relation between amyloidogenic properties and structural characteristics based on the fuzzy oil drop model. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Three-dimensional electrical impedance tomography: a topology optimization approach.

PubMed

Mello, Luís Augusto Motta; de Lima, Cícero Ribeiro; Amato, Marcelo Britto Passos; Lima, Raul Gonzalez; Silva, Emílio Carlos Nelli

2008-02-01

Electrical impedance tomography is a technique to estimate the impedance distribution within a domain, based on measurements on its boundary. In other words, given the mathematical model of the domain, its geometry and boundary conditions, a nonlinear inverse problem of estimating the electric impedance distribution can be solved. Several impedance estimation algorithms have been proposed to solve this problem. In this paper, we present a three-dimensional algorithm, based on the topology optimization method, as an alternative. A sequence of linear programming problems, allowing for constraints, is solved utilizing this method. In each iteration, the finite element method provides the electric potential field within the model of the domain. An electrode model is also proposed (thus, increasing the accuracy of the finite element results). The algorithm is tested using numerically simulated data and also experimental data, and absolute resistivity values are obtained. These results, corresponding to phantoms with two different conductive materials, exhibit relatively well-defined boundaries between them, and show that this is a practical and potentially useful technique to be applied to monitor lung aeration, including the possibility of imaging a pneumothorax.

The DSM-5 alternative model of personality disorders from the perspective of adult attachment: a study in community-dwelling adults.

PubMed

Fossati, Andrea; Krueger, Robert F; Markon, Kristian E; Borroni, Serena; Maffei, Cesare; Somma, Antonella

2015-04-01

To assess how the maladaptive personality domains and facets that were included in the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) Alternative Model of Personality Disorders relate to adult attachment styles, 480 Italian nonclinical adults were administered the Personality Inventory for DSM-5 (PID-5) and the Attachment Style Questionnaire (ASQ). To evaluate the uniqueness of the associations between the PID-5 scales and the ASQ scales, the participants were also administered the Big Five Inventory (BFI). Multiple regression analyses showed that the ASQ scales significantly predicted both PID-5 domain scales and BFI scales; however, the relationships were different both qualitatively and quantitatively. With the exception of the PID-5 risk taking scale (adjusted R(2) = 0.02), all other PID-5 trait scales were significantly predicted by the ASQ scales, median adjusted R(2) value = 0.25, all ps < 0.001. Our findings suggest that the maladaptive personality domains and traits listed in the DSM-5 Alternative Model of Personality Disorders show meaningful associations with adult attachment styles.

Portfolios: An Alternative Method of Student and Program Assessment

PubMed Central

Hannam, Susan E.

1995-01-01

The use of performance-based evaluation and alternative assessment techniques has become essential for curriculum programs seeking Commission of Accreditation of Allied Health Education Programs (CAAHEP) accreditation. In athletic training education, few assessment models exist to assess student performance over the entire course of their educational program. This article describes a model of assessment-a student athletic training portfolio of “best works.” The portfolio can serve as a method to assess student development and to assess program effectiveness. The goals of the program include purposes specific to the five NATA performance domains. In addition, four types of portfolio evidence are described: artifacts, attestations, productions, and reproductions. Quality assignments and projects completed by students as they progress through a six-semester program are identified relative to the type of evidence and the domain(s) they represent. The portfolio assists with student development, provides feedback for curriculum planning, allows for student/faculty collaboration and “coaching” of the student, and assists with job searching. This information will serve as a useful model for those athletic training programs looking for an alternative method of assessing student and program outcomes. PMID:16558359

Development, Validation, and Performance of a Scale to Measure Community Mobilization

PubMed Central

Lippman, Sheri A.; Neilands, Torsten B.; Leslie, Hannah H.; Maman, Suzanne; MacPhail, Catherine; Twine, Rhian; Peacock, Dean; Kahn, Kathleen; Pettifor, Audrey

2016-01-01

Rationale Community mobilization approaches (CMAs) are increasingly becoming key components of health programming. However, CMAs have been ill defined and poorly evaluated, largely due to the lack of measurement tools to assess mobilization processes and impact. Objective We developed the Community Mobilization Measure (CMM), composed of a set of scales to measure mobilization domains hypothesized to operate at the community-level. The six domains include: shared concerns, critical consciousness, leadership, collective action, social cohesion, and organizations and networks. We also included the domain of social control to explore synergies with the related construct of collective efficacy. Method A survey instrument was developed and pilot tested, then revised and administered to 1,181 young people, aged 18-35, in a community-based survey in rural South Africa. Item response modeling and exploratory factor analyses were conducted to assess model fit, dimensionality, reliability, and validity. Results Results indicate the seven-dimensional model, with linked domains but no higher order construct, fit the data best. Internal consistency reliability of the factors was strong, with ρ values ranging from .81 to .93. Six of seven scales were sufficiently correlated to represent linked concepts that comprise community mobilization; social control was less related to the other components. At the village level, CMM sub-scales were correlated with other metrics of village social capital and integrity, providing initial evidence of higher-level validity, however additional evaluation of the measure at the community-level is needed. Conclusion This is the first effort to develop and validate a comprehensive measure for community mobilization. The CMM was designed as an evaluation tool for health programming and should facilitate a more nuanced understanding of mechanisms of change associated with CM, ultimately making mobilizing approaches more effective. PMID:27085071

Bisphenol A (BPA) binding on full-length architectures of estrogen receptor.

PubMed

Liu, Yaquan; Qu, Kaili; Hai, Ying; Zhao, Chunyan

2018-08-01

Previous research has shown that the major toxicity mechanism for many environment chemicals is binding with estrogen receptor (ER) and blocking endogenous estrogen access, including bisphenol A (BPA). However, the molecular level understanding the global consequence of BPA binding on the full-length architectures of ER is largely unknown, which is a necessary stage to evaluate estrogen-like toxicity of BPA. In the present work, the consequence of BPA on full-length architectures of ER was firstly modeled based on molecular dynamics, focusing on the cross communication between multi-domains including ligand binding domain (LBD) and DNA binding domain (DBD). The study proved consequence of BPA upon full-length ER structure was dependent on long-range communications between multiple protein domains. The allosteric effects occurring in LBD units could alter dimerization formation through a crucial change in residue-residue connections, which resulted in relaxation of DBD. It indicated BPA could present consequence on the full-size receptor, not only on the separate domains, but also on the cross communication among LBD, DBD, and DNA molecules. It might provide detailed insight into the knowledge about the structural characteristics of ER and its role in gene regulation, which eventually helped us evaluate the estrogen-like toxicity upon BPA binding with full-length ER. © 2018 Wiley Periodicals, Inc.

Toward Development of a Fibromyalgia Responder Index and Disease Activity Score: OMERACT Module Update

PubMed Central

Mease, PJ; Clauw, DJ; Christensen, R; Crofford, L; Gendreau, M; Martin, SA; Simon, L; Strand, V; Williams, DA; Arnold, LM

2012-01-01

Following development of the core domain set for fibromyalgia (FM) in OMERACT 7–9, the FM working group has progressed toward the development of an FM responder index and a disease activity score based on these domains, utilizing outcome indices of these domains from archived randomized clinical trials (RCTs) in FM. Possible clinical domains that could be included in a responder index and disease activity score include: pain, fatigue, sleep disturbance, cognitive dysfunction, mood disturbance, tenderness, stiffness, and functional impairment. Outcome measures for these domains demonstrate good to adequate psychometric properties, although measures of cognitive dysfunction need to be further developed. The approach used in the development of responder indices and disease activity scores for rheumatoid arthritis and ankylosing spondylitis represent heuristic models for our work, but FM is challenging in that there is no clear algorithm of treatment that defines disease activity based on treatment decisions, nor are there objective markers that define thresholds of severity or response to treatment. The process of developing candidate dichotomous responder definitions and continuous quantitative disease activity measures is described, as is participant discussion that transpired at OMERACT 10. Final results of this work will be published in a separate manuscript pending completion of analyses. PMID:21724721

Focusing on Interactions between Content and Cognition: A New Perspective on Gender Differences in Mathematical Sub-Competencies

ERIC Educational Resources Information Center

George, Ann Cathrice; Robitzsch, Alexander

2018-01-01

This article presents a new perspective on measuring gender differences in the large-scale assessment study Trends in International Science Study (TIMSS). The suggested empirical model is directly based on the theoretical competence model of the domain mathematics and thus includes the interaction between content and cognitive sub-competencies.…

Self-Acceptance and Self-Disclosure of Sexual Orientation in Lesbian, Gay and Bisexual Adults: An Attachment Perspective

ERIC Educational Resources Information Center

Mohr, Jonathan J.; Fassinger, Ruth E.

2003-01-01

A model linking attachment variables with self-acceptance and self-disclosure of sexual orientation was tested using data from 489 lesbian, gay, and bisexual (LGB) adults. The model included the following 4 domains of variables: (a) representations of childhood attachment experiences with parents, (b) perceptions of parental support for sexual…

Engineering High Assurance Distributed Cyber Physical Systems

DTIC Science & Technology

2015-01-15

decisions: number of interacting agents and co-dependent decisions made in real-time without causing interference . To engineer a high assurance DART...environment specification, architecture definition, domain-specific languages, design patterns, code - generation, analysis, test-generation, and simulation...include synchronization between the models and source code , debugging at the model level, expression of the design intent, and quality of service

SLA Negotiation for VO Formation

NASA Astrophysics Data System (ADS)

Paurobally, Shamimabi

Resource management systems are changing from localized resources and services towards virtual organizations (VOs) sharing millions of heterogeneous resources across multiple organizations and domains. The virtual organizations and usage models include a variety of owners and consumers with different usage, access policies, cost models, varying loads, requirements and availability. The stakeholders have private utility functions that must be satisfied and possibly maximized.

Cross-Border Collaboration in History among Nordic Students: A Case Study about Creating Innovative ICT Didactic Models

ERIC Educational Resources Information Center

Spante, Maria; Karlsen, Asgjerd Vea; Nortvig, Anne-Mette; Christiansen, Rene B.

2014-01-01

Gränsöverskridande Nordisk Undervisning/Utdanelse (GNU, meaning Cross-Border Nordic Education), the larger Nordic project, under which this case study was carried out, aims at developing innovative, cross-border teaching models in different subject domains in elementary school, including mathematics, language, science, social studies and history.…

Statistics of opinion domains of the majority-vote model on a square lattice

NASA Astrophysics Data System (ADS)

Peres, Lucas R.; Fontanari, José F.

2010-10-01

The existence of juxtaposed regions of distinct cultures in spite of the fact that people’s beliefs have a tendency to become more similar to each other’s as the individuals interact repeatedly is a puzzling phenomenon in the social sciences. Here we study an extreme version of the frequency-dependent bias model of social influence in which an individual adopts the opinion shared by the majority of the members of its extended neighborhood, which includes the individual itself. This is a variant of the majority-vote model in which the individual retains its opinion in case there is a tie among the neighbors’ opinions. We assume that the individuals are fixed in the sites of a square lattice of linear size L and that they interact with their nearest neighbors only. Within a mean-field framework, we derive the equations of motion for the density of individuals adopting a particular opinion in the single-site and pair approximations. Although the single-site approximation predicts a single opinion domain that takes over the entire lattice, the pair approximation yields a qualitatively correct picture with the coexistence of different opinion domains and a strong dependence on the initial conditions. Extensive Monte Carlo simulations indicate the existence of a rich distribution of opinion domains or clusters, the number of which grows with L2 whereas the size of the largest cluster grows with lnL2 . The analysis of the sizes of the opinion domains shows that they obey a power-law distribution for not too large sizes but that they are exponentially distributed in the limit of very large clusters. In addition, similarly to other well-known social influence model—Axelrod’s model—we found that these opinion domains are unstable to the effect of a thermal-like noise.

Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex

PubMed Central

Coppola, David; White, Leonard E.; Wolf, Fred

2015-01-01

The architecture of iso-orientation domains in the primary visual cortex (V1) of placental carnivores and primates apparently follows species invariant quantitative laws. Dynamical optimization models assuming that neurons coordinate their stimulus preferences throughout cortical circuits linking millions of cells specifically predict these invariants. This might indicate that V1’s intrinsic connectome and its functional architecture adhere to a single optimization principle with high precision and robustness. To validate this hypothesis, it is critical to closely examine the quantitative predictions of alternative candidate theories. Random feedforward wiring within the retino-cortical pathway represents a conceptually appealing alternative to dynamical circuit optimization because random dimension-expanding projections are believed to generically exhibit computationally favorable properties for stimulus representations. Here, we ask whether the quantitative invariants of V1 architecture can be explained as a generic emergent property of random wiring. We generalize and examine the stochastic wiring model proposed by Ringach and coworkers, in which iso-orientation domains in the visual cortex arise through random feedforward connections between semi-regular mosaics of retinal ganglion cells (RGCs) and visual cortical neurons. We derive closed-form expressions for cortical receptive fields and domain layouts predicted by the model for perfectly hexagonal RGC mosaics. Including spatial disorder in the RGC positions considerably changes the domain layout properties as a function of disorder parameters such as position scatter and its correlations across the retina. However, independent of parameter choice, we find that the model predictions substantially deviate from the layout laws of iso-orientation domains observed experimentally. Considering random wiring with the currently most realistic model of RGC mosaic layouts, a pairwise interacting point process, the predicted layouts remain distinct from experimental observations and resemble Gaussian random fields. We conclude that V1 layout invariants are specific quantitative signatures of visual cortical optimization, which cannot be explained by generic random feedforward-wiring models. PMID:26575467

An ice-ocean coupled model for the Northern Hemisphere

NASA Technical Reports Server (NTRS)

Cheng, Abe; Preller, Ruth

1992-01-01

The Hibler ice model has been modified and adapted to a domain that includes most of the sea ice-covered areas in the Northern Hemisphere. This model, joined with the Cox ocean model, is developed as an enhancement to the U.S. Navy's sea ice forecasting, PIPS, and is termed PIPS2.0. Generally, the modeled ice edge is consistent with the Navy-NOAA Joint Ice Center weekly analysis, and the modeled ice thickness distribution agrees with submarine sonar data in the central Arctic basin.

Psychometric properties of the revised Malay version Medical Outcome Study Social Support Survey using confirmatory factor analysis among postpartum mothers.

PubMed

Norhayati, Mohd Noor; Aniza, Abd Aziz; Nik Hazlina, Nik Hussain; Azman, Mohd Yacob

2015-12-01

Social support is an essential component for the physical and emotional well-being of postpartum mothers. The objective of this study is to determine the psychometric properties of the revised Malay version Medical Outcome Study (MOS) Social Support Survey using a confirmatory validity approach. A cross-sectional study was conducted involving 144 postpartum mothers attending Obstetric and Gynecology Clinic, Universiti Sains Malaysia Hospital. Construct validity and internal consistency assessment was performed after the translation, content validity and face validity process. The data were analyzed using SPSS 20.0 (SPSS Inc., Chicago, IL, USA) and AMOS 20.0 (SPSS Inc., Chicago, IL, USA). The original questionnaire consists of four domains (emotional/informational support, tangible support, affectionate support and positive social interaction) and 19 items. Affectionate support domain with three items only was treated as a separate construct and was not included in the factor analysis. The final confirmatory model with three constructs and 13 items demonstrated acceptable factor loadings, domain to domain correlation and best fit; (χ2[df]=1.665 [61]; P-value=0.001; Tucker-Lewis Index=0.944; comparative fit index=0.956; root mean square error of approximation=0.068). Composite reliability, average variance extracted and Cronbach's α of the domains ranged from 0.649 to 0.903; 0.390 to 0.699; 0.616 to 0.902, respectively. The study suggested that the four-factor model with 16 items (including one separate factor of affectionate) of the revised Malay version MOS Social Support Survey was acceptable to be used to measure social support after childbirth because it is valid, reliable and simple. © 2015 Wiley Publishing Asia Pty Ltd.

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.

PubMed

Kobayashi, Chigusa; Matsunaga, Yasuhiro; Koike, Ryotaro; Ota, Motonori; Sugita, Yuji

2015-11-19

Large conformational changes of multidomain proteins are difficult to simulate using all-atom molecular dynamics (MD) due to the slow time scale. We show that a simple modification of the structure-based coarse-grained (CG) model enables a stable and efficient MD simulation of those proteins. "Motion Tree", a tree diagram that describes conformational changes between two structures in a protein, provides information on rigid structural units (domains) and the magnitudes of domain motions. In our new CG model, which we call the DoME (domain motion enhanced) model, interdomain interactions are defined as being inversely proportional to the magnitude of the domain motions in the diagram, whereas intradomain interactions are kept constant. We applied the DoME model in combination with the Go model to simulations of adenylate kinase (AdK). The results of the DoME-Go simulation are consistent with an all-atom MD simulation for 10 μs as well as known experimental data. Unlike the conventional Go model, the DoME-Go model yields stable simulation trajectories against temperature changes and conformational transitions are easily sampled despite domain rigidity. Evidently, identification of domains and their interfaces is useful approach for CG modeling of multidomain proteins.

Framework for Architecture Trade Study Using MBSE and Performance Simulation

NASA Technical Reports Server (NTRS)

Ryan, Jessica; Sarkani, Shahram; Mazzuchim, Thomas

2012-01-01

Increasing complexity in modern systems as well as cost and schedule constraints require a new paradigm of system engineering to fulfill stakeholder needs. Challenges facing efficient trade studies include poor tool interoperability, lack of simulation coordination (design parameters) and requirements flowdown. A recent trend toward Model Based System Engineering (MBSE) includes flexible architecture definition, program documentation, requirements traceability and system engineering reuse. As a new domain MBSE still lacks governing standards and commonly accepted frameworks. This paper proposes a framework for efficient architecture definition using MBSE in conjunction with Domain Specific simulation to evaluate trade studies. A general framework is provided followed with a specific example including a method for designing a trade study, defining candidate architectures, planning simulations to fulfill requirements and finally a weighted decision analysis to optimize system objectives.

Evaluation of an Impedance Model for Perforates Including the Effect of Bias Flow

NASA Technical Reports Server (NTRS)

Betts, J. F.; Follet, J. I.; Kelly, J. J.; Thomas, R. H.

2000-01-01

A new bias flow impedance model is developed for perforated plates from basic principles using as little empiricisms as possible. A quality experimental database was used to determine the predictive validity of the model. Results show that the model performs better for higher (15%) rather than lower (5%) percent open area (POA) samples. Based on the least squares ratio of numerical vs. experimental results, model predictions were on average within 20% and 30% for the higher and lower (POA), respectively. It is hypothesized on the work of other investigators that at lower POAs the higher fluid velocities in the perforate's orifices start forming unsteady vortices, which is not accounted for in our model. The numerical model, in general also underpredicts the experiments. It is theorized that the actual acoustic C(sub D) is lower than the measured raylometer C(sub D) used in the model. Using a larger C(sub D) makes the numerical model predict lower impedances. The frequency domain model derived in this paper shows very good agreement with another model derived using a time domain approach.

A digital computer program for the dynamic interaction simulation of controls and structure (DISCOS), volume 1

NASA Technical Reports Server (NTRS)

Bodley, C. S.; Devers, A. D.; Park, A. C.; Frisch, H. P.

1978-01-01

A theoretical development and associated digital computer program system for the dynamic simulation and stability analysis of passive and actively controlled spacecraft are presented. The dynamic system (spacecraft) is modeled as an assembly of rigid and/or flexible bodies not necessarily in a topological tree configuration. The computer program system is used to investigate total system dynamic characteristics, including interaction effects between rigid and/or flexible bodies, control systems, and a wide range of environmental loadings. In addition, the program system is used for designing attitude control systems and for evaluating total dynamic system performance, including time domain response and frequency domain stability analyses.

CD80 and CD86 IgC domains are important for quaternary structure, receptor binding and co-signaling function.

PubMed

Girard, Tanya; Gaucher, Denis; El-Far, Mohamed; Breton, Gaëlle; Sékaly, Rafick-Pierre

2014-09-01

CD86 and CD80, the ligands for the co-stimulatory molecules CD28 and CTLA-4, are members of the Ig superfamily. Their structure includes Ig variable-like (IgV) domains, Ig constant-like (IgC) domains and intracellular domains. Although crystallographic studies have clearly identified the IgV domain to be responsible for receptor interactions, earlier studies suggested that both Ig domains are required for full co-signaling function. Herein, we have used deletion and chimeric human CD80 and CD86 molecules in co-stimulation assays to study the impact of the multimeric state of IgV and IgC domains on receptor binding properties and on co-stimulatory function in a peptide-specific T cell activation model. We report for the first time the presence of CD80 dimers and CD86 monomers in living cells. Moreover, we show that the IgC domain of both molecules inhibits multimer formation and greatly affects binding to the co-receptors CD28 and CTLA-4. Finally, both IgC and intracellular domains are required for full co-signaling function. These findings reveal the distinct but complementary roles of CD80 and CD86 IgV and IgC domains in T cell activation. Copyright © 2014 Elsevier B.V. All rights reserved.

Are Some Technologies Beyond Regulatory Regimes?

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

Jones, Wendell B.; Kusnezov, Dimitri

Regulatory frameworks are a common tool in governance to incent and coerce behaviors supporting national or strategic stability. This includes domestic regulations and international agreements. Though regulation is always a challenge, the domain of fast evolving threats, like cyber, are proving much more difficult to control. Many discussions are underway searching for approaches that can provide national security in these domains. We use game theoretic learning models to explore the question of strategic stability with respect to the democratization of certain technologies (such as cyber). We suggest that such many-player games could inherently be chaotic with no corresponding (Nash) equilibria.more » In the absence of such equilibria, traditional approaches, as measures to achieve levels of overall security, may not be suitable approaches to support strategic stability in these domains. Altogether new paradigms may be needed for these issues. At the very least, regulatory regimes that fail to address the basic nature of the technology domains should not be pursued as a default solution, regardless of success in other domains. In addition, the very chaotic nature of these domains may hold the promise of novel approaches to regulation.« less

Structural Analysis of the GGDEF-EAL Domain-Containing c-di-GMP Receptor FimX

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

Navarro, M.; De, N; Bae, N

2009-01-01

Bacterial pathogenesis involves social behavior including biofilm formation and swarming, processes that are regulated by the bacterially unique second messenger cyclic di-GMP (c-di-GMP). Diguanylate cyclases containing GGDEF and phosphodiesterases containing EAL domains have been identified as the enzymes controlling cellular c-di-GMP levels, yet less is known regarding signal transmission and the targets of c-di-GMP. FimX, a protein from Pseudomonas aeruginosa that governs twitching motility, belongs to a large subfamily containing both GGDEF and EAL domains. Biochemical and structural analyses reveals its function as a high-affinity receptor for c-di-GMP. A model for full-length FimX was generated combining solution scattering data andmore » crystal structures of the degenerate GGDEF and EAL domains. Although FimX forms a dimer in solution via the N-terminal domains, a crystallographic EAL domain dimer suggests modes for the regulation of FimX by c-di-GMP binding. The results provide the structural basis for c-di-GMP sensing via degenerate phosphodiesterases.« less

Multiple Functional Domains of Enterococcus faecalis Aggregation Substance Asc10 Contribute to Endocarditis Virulence ▿ †

PubMed Central

Chuang, Olivia N.; Schlievert, Patrick M.; Wells, Carol L.; Manias, Dawn A.; Tripp, Timothy J.; Dunny, Gary M.

2009-01-01

Aggregation substance proteins encoded by sex pheromone plasmids increase the virulence of Enterococcus faecalis in experimental pathogenesis models, including infectious endocarditis models. These large surface proteins may contain multiple functional domains involved in various interactions with other bacterial cells and with the mammalian host. Aggregation substance Asc10, encoded by plasmid pCF10, is induced during growth in the mammalian bloodstream, and pCF10 carriage gives E. faecalis a significant selective advantage in this environment. We employed a rabbit model to investigate the role of various functional domains of Asc10 in endocarditis. The data suggested that the bacterial load of the infected tissue was the best indicator of virulence. Isogenic strains carrying either no plasmid, wild-type pCF10, a pCF10 derivative with an in-frame deletion of the prgB gene encoding Asc10, or pCF10 derivatives expressing other alleles of prgB were examined in this model. Previously identified aggregation domains contributed to the virulence associated with the wild-type protein, and a strain expressing an Asc10 derivative in which glycine residues in two RGD motifs were changed to alanine residues showed the greatest reduction in virulence. Remarkably, this strain and the strain carrying the pCF10 derivative with the in-frame deletion of prgB were both significantly less virulent than an isogenic plasmid-free strain. The data demonstrate that multiple functional domains are important in Asc10-mediated interactions with the host during the course of experimental endocarditis and that in the absence of a functional prgB gene, pCF10 carriage is actually disadvantageous in vivo. PMID:18955479

Analysis of the relationship between community characteristics and depression using geographically weighted regression.

PubMed

Choi, Hyungyun; Kim, Ho

2017-01-01

Achieving national health equity is currently a pressing issue. Large regional variations in the health determinants are observed. Depression, one of the most common mental disorders, has large variations in incidence among different populations, and thus must be regionally analyzed. The present study aimed at analyzing regional disparities in depressive symptoms and identifying the health determinants that require regional interventions. Using health indicators of depression in the Korea Community Health Survey 2011 and 2013, the Moran's I was calculated for each variable to assess spatial autocorrelation, and a validated geographically weighted regression analysis using ArcGIS version 10.1 of different domains: health behavior, morbidity, and the social and physical environments were created, and the final model included a combination of significant variables in these models. In the health behavior domain, the weekly breakfast intake frequency of 1-2 times was the most significantly correlated with depression in all regions, followed by exposure to secondhand smoke and the level of perceived stress in some regions. In the morbidity domain, the rate of lifetime diagnosis of myocardial infarction was the most significantly correlated with depression. In the social and physical environment domain, the trust environment within the local community was highly correlated with depression, showing that lower the level of trust, higher was the level of depression. A final model was constructed and analyzed using highly influential variables from each domain. The models were divided into two groups according to the significance of correlation of each variable with the experience of depression symptoms. The indicators of the regional health status are significantly associated with the incidence of depressive symptoms within a region. The significance of this correlation varied across regions.

Crystal structure at 2.8 A of Huntingtin-interacting protein 1 (HIP1) coiled-coil domain reveals a charged surface suitable for HIP1 protein interactor (HIPPI).

PubMed

Niu, Qian; Ybe, Joel A

2008-02-01

Huntington's disease is a genetic neurological disorder that is triggered by the dissociation of the huntingtin protein (htt) from its obligate interaction partner Huntingtin-interacting protein 1 (HIP1). The release of the huntingtin protein permits HIP1 protein interactor (HIPPI) to bind to its recognition site on HIP1 to form a HIPPI/HIP1 complex that recruits procaspase-8 to begin the process of apoptosis. The interaction module between HIPPI and HIP1 was predicted to resemble a death-effector domain. Our 2.8-A crystal structure of the HIP1 371-481 subfragment that includes F432 and K474, which is important for HIPPI binding, is not a death-effector domain but is a partially opened coiled coil. The HIP1 371-481 model reveals a basic surface that we hypothesize to be suitable for binding HIPPI. There is an opened region next to the putative HIPPI site that is highly negatively charged. The acidic residues in this region are highly conserved in HIP1 and a related protein, HIP1R, from different organisms but are not conserved in the yeast homologue of HIP1, sla2p. We have modeled approximately 85% of the coiled-coil domain by joining our new HIP1 371-481 structure to the HIP1 482-586 model (Protein Data Bank code: 2NO2). Finally, the middle of this coiled-coil domain may be intrinsically flexible and suggests a new interaction model where HIPPI binds to a U-shaped HIP1 molecule.

Conceptualising paediatric health disparities: a metanarrative systematic review and unified conceptual framework.

PubMed

Ridgeway, Jennifer L; Wang, Zhen; Finney Rutten, Lila J; van Ryn, Michelle; Griffin, Joan M; Murad, M Hassan; Asiedu, Gladys B; Egginton, Jason S; Beebe, Timothy J

2017-08-04

There exists a paucity of work in the development and testing of theoretical models specific to childhood health disparities even though they have been linked to the prevalence of adult health disparities including high rates of chronic disease. We conducted a systematic review and thematic analysis of existing models of health disparities specific to children to inform development of a unified conceptual framework. We systematically reviewed articles reporting theoretical or explanatory models of disparities on a range of outcomes related to child health. We searched Ovid Medline In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid Embase, Ovid Cochrane Central Register of Controlled Trials, Ovid Cochrane Database of Systematic Reviews, and Scopus (database inception to 9 July 2015). A metanarrative approach guided the analysis process. A total of 48 studies presenting 48 models were included. This systematic review found multiple models but no consensus on one approach. However, we did discover a fair amount of overlap, such that the 48 models reviewed converged into the unified conceptual framework. The majority of models included factors in three domains: individual characteristics and behaviours (88%), healthcare providers and systems (63%), and environment/community (56%), . Only 38% of models included factors in the health and public policies domain. A disease-agnostic unified conceptual framework may inform integration of existing knowledge of child health disparities and guide future research. This multilevel framework can focus attention among clinical, basic and social science research on the relationships between policy, social factors, health systems and the physical environment that impact children's health outcomes. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Effects of Working Memory Capacity and Domain Knowledge on Recall for Grocery Prices.

PubMed

Bermingham, Douglas; Gardner, Michael K; Woltz, Dan J

2016-01-01

Hambrick and Engle (2002) proposed 3 models of how domain knowledge and working memory capacity may work together to influence episodic memory: a "rich-get-richer" model, a "building blocks" model, and a "compensatory" model. Their results supported the rich-get-richer model, although later work by Hambrick and Oswald (2005) found support for a building blocks model. We investigated the effects of domain knowledge and working memory on recall of studied grocery prices. Working memory was measured with 3 simple span tasks. A contrast of realistic versus fictitious foods in the episodic memory task served as our manipulation of domain knowledge, because participants could not have domain knowledge of fictitious food prices. There was a strong effect for domain knowledge (realistic food-price pairs were easier to remember) and a moderate effect for working memory capacity (higher working memory capacity produced better recall). Furthermore, the interaction between domain knowledge and working memory produced a small but significant interaction in 1 measure of price recall. This supported the compensatory model and stands in contrast to previous research.

Interdependence of the rad50 hook and globular domain functions.

PubMed

Hohl, Marcel; Kochańczyk, Tomasz; Tous, Cristina; Aguilera, Andrés; Krężel, Artur; Petrini, John H J

2015-02-05

Rad50 contains a conserved Zn(2+) coordination domain (the Rad50 hook) that functions as a homodimerization interface. Hook ablation phenocopies Rad50 deficiency in all respects. Here, we focused on rad50 mutations flanking the Zn(2+)-coordinating hook cysteines. These mutants impaired hook-mediated dimerization, but recombination between sister chromatids was largely unaffected. This may reflect that cohesin-mediated sister chromatid interactions are sufficient for double-strand break repair. However, Mre11 complex functions specified by the globular domain, including Tel1 (ATM) activation, nonhomologous end joining, and DNA double-strand break end resection were affected, suggesting that dimerization exerts a broad influence on Mre11 complex function. These phenotypes were suppressed by mutations within the coiled-coil and globular ATPase domains, suggesting a model in which conformational changes in the hook and globular domains are transmitted via the extended coils of Rad50. We propose that transmission of spatial information in this manner underlies the regulation of Mre11 complex functions. Copyright © 2015 Elsevier Inc. All rights reserved.

Learning and Reasoning in Unknown Domains

NASA Astrophysics Data System (ADS)

Strannegård, Claes; Nizamani, Abdul Rahim; Juel, Jonas; Persson, Ulf

2016-12-01

In the story Alice in Wonderland, Alice fell down a rabbit hole and suddenly found herself in a strange world called Wonderland. Alice gradually developed knowledge about Wonderland by observing, learning, and reasoning. In this paper we present the system Alice In Wonderland that operates analogously. As a theoretical basis of the system, we define several basic concepts of logic in a generalized setting, including the notions of domain, proof, consistency, soundness, completeness, decidability, and compositionality. We also prove some basic theorems about those generalized notions. Then we model Wonderland as an arbitrary symbolic domain and Alice as a cognitive architecture that learns autonomously by observing random streams of facts from Wonderland. Alice is able to reason by means of computations that use bounded cognitive resources. Moreover, Alice develops her belief set by continuously forming, testing, and revising hypotheses. The system can learn a wide class of symbolic domains and challenge average human problem solvers in such domains as propositional logic and elementary arithmetic.

Modeling Patient Treatment With Medical Records: An Abstraction Hierarchy to Understand User Competencies and Needs.

PubMed

St-Maurice, Justin D; Burns, Catherine M

2017-07-28

Health care is a complex sociotechnical system. Patient treatment is evolving and needs to incorporate the use of technology and new patient-centered treatment paradigms. Cognitive work analysis (CWA) is an effective framework for understanding complex systems, and work domain analysis (WDA) is useful for understanding complex ecologies. Although previous applications of CWA have described patient treatment, due to their scope of work patients were previously characterized as biomedical machines, rather than patient actors involved in their own care. An abstraction hierarchy that characterizes patients as beings with complex social values and priorities is needed. This can help better understand treatment in a modern approach to care. The purpose of this study was to perform a WDA to represent the treatment of patients with medical records. The methods to develop this model included the analysis of written texts and collaboration with subject matter experts. Our WDA represents the ecology through its functional purposes, abstract functions, generalized functions, physical functions, and physical forms. Compared with other work domain models, this model is able to articulate the nuanced balance between medical treatment, patient education, and limited health care resources. Concepts in the analysis were similar to the modeling choices of other WDAs but combined them in as a comprehensive, systematic, and contextual overview. The model is helpful to understand user competencies and needs. Future models could be developed to model the patient's domain and enable the exploration of the shared decision-making (SDM) paradigm. Our work domain model links treatment goals, decision-making constraints, and task workflows. This model can be used by system developers who would like to use ecological interface design (EID) to improve systems. Our hierarchy is the first in a future set that could explore new treatment paradigms. Future hierarchies could model the patient as a controller and could be useful for mobile app development. ©Justin D St-Maurice, Catherine M Burns. Originally published in JMIR Human Factors (http://humanfactors.jmir.org), 28.07.2017.

Modeling Patient Treatment With Medical Records: An Abstraction Hierarchy to Understand User Competencies and Needs

PubMed Central

2017-01-01

Background Health care is a complex sociotechnical system. Patient treatment is evolving and needs to incorporate the use of technology and new patient-centered treatment paradigms. Cognitive work analysis (CWA) is an effective framework for understanding complex systems, and work domain analysis (WDA) is useful for understanding complex ecologies. Although previous applications of CWA have described patient treatment, due to their scope of work patients were previously characterized as biomedical machines, rather than patient actors involved in their own care. Objective An abstraction hierarchy that characterizes patients as beings with complex social values and priorities is needed. This can help better understand treatment in a modern approach to care. The purpose of this study was to perform a WDA to represent the treatment of patients with medical records. Methods The methods to develop this model included the analysis of written texts and collaboration with subject matter experts. Our WDA represents the ecology through its functional purposes, abstract functions, generalized functions, physical functions, and physical forms. Results Compared with other work domain models, this model is able to articulate the nuanced balance between medical treatment, patient education, and limited health care resources. Concepts in the analysis were similar to the modeling choices of other WDAs but combined them in as a comprehensive, systematic, and contextual overview. The model is helpful to understand user competencies and needs. Future models could be developed to model the patient’s domain and enable the exploration of the shared decision-making (SDM) paradigm. Conclusion Our work domain model links treatment goals, decision-making constraints, and task workflows. This model can be used by system developers who would like to use ecological interface design (EID) to improve systems. Our hierarchy is the first in a future set that could explore new treatment paradigms. Future hierarchies could model the patient as a controller and could be useful for mobile app development. PMID:28754650

Vitamin E Facilitates the Inactivation of the Kinase Akt by the Phosphatase PHLPP1

PubMed Central

Huang, Po-Hsien; Chuang, Hsiao-Ching; Chou, Chih-Chien; Wang, Huiling; Lee, Su-Lin; Yang, Hsiao-Ching; Chiu, Hao-Chieh; Kapuriya, Naval; Wang, Dasheng; Kulp, Samuel K.; Chen, Ching-Shih

2014-01-01

Vitamin E is a fat-soluble vitamin that includes isomers of tocopherols and tocotrienols which are known for their antioxidant properties. Tocopherols are the predominant form encountered in the diet and through supplementation, and have garnered interest for their potential cancer therapeutic and chemopreventive effects, which include the dephosphorylation of Akt, a serine/threonine kinase that plays a pivotal role in important cellular processes, such as cell growth, survival, metabolism and motility. Full catalytic activation of Akt requires phosphorylation at both Thr308 and Ser473. Dephosphorylation of Ser473 drastically reduces Akt catalytic activity and the number of downstream substrates it can regulate. The mechanism by which α- and γ-tocopherol facilitate the selective dephosphorylation of the kinase Akt at Ser473 was investigated. We showed that this site-specific Akt dephosphorylation was mediated through the pleckstrin homology (PH) domain-dependent recruitment to the plasma membrane of Akt and PHLPP1 (PH domain leucine-rich repeat protein phosphatase, isoform 1), a phosphatase that dephosphorylates Akt at Ser473. The ability of α- and γ-tocopherol to induce PHLPP-mediated Akt inhibition established PHLPP as a “druggable” target. We structurally optimized these tocopherols to obtain derivatives with greater in vitro potency and in vivo tumor-suppressive activity in two prostate xenograft tumor models. Binding affinities for the PH domains of Akt and PHLPP1 were greater than for other PH domain-containing proteins, which may underlie the preferential membrane recruitment of these proteins. Molecular modeling revealed the structural determinants of the interaction with the PH domain of Akt that may inform strategies for continued structural optimization. These findings describe a mechanism by which tocopherols facilitate the dephosphorylation of Akt at Ser473, thereby providing insights into the mode of antitumor action of tocopherols and a rationale for the translational development of tocopherols into novel PH domain-targeted Akt inhibitors. PMID:23512990

Orthologs in Arabidopsis thaliana of the Hsp70 interacting protein Hip

PubMed Central

Webb, Mary Alice; Cavaletto, John M.; Klanrit, Preekamol; Thompson, Gary A.

2001-01-01

The Hsp70-interacting protein Hip binds to the adenosine triphosphatase domain of Hsp70, stabilizing it in the adenosine 5′-diphosphate–ligated conformation and promoting binding of target polypeptides. In mammalian cells, Hip is a component of the cytoplasmic chaperone heterocomplex that regulates signal transduction via interaction with hormone receptors and protein kinases. Analysis of the complete genome sequence of the model flowering plant Arabidopsis thaliana revealed 2 genes encoding Hip orthologs. The deduced sequence of AtHip-1 consists of 441 amino acid residues and is 42% identical to human Hip. AtHip-1 contains the same functional domains characterized in mammalian Hip, including an N-terminal dimerization domain, an acidic domain, 3 tetratricopeptide repeats flanked by a highly charged region, a series of degenerate GGMP repeats, and a C-terminal region similar to the Sti1/Hop/p60 protein. The deduced amino acid sequence of AtHip-2 consists of 380 amino acid residues. AtHip-2 consists of a truncated Hip-like domain that is 46% identical to human Hip, followed by a C-terminal domain related to thioredoxin. AtHip-2 is 63% identical to another Hip-thioredoxin protein recently identified in Vitis labrusca (grape). The truncated Hip domain in AtHip-2 includes the amino terminus, the acidic domain, and tetratricopeptide repeats with flanking charged region. Analyses of expressed sequence tag databases indicate that both AtHip-1 and AtHip-2 are expressed in A thaliana and that orthologs of Hip are also expressed widely in other plants. The similarity between AtHip-1 and its mammalian orthologs is consistent with a similar role in plant cells. The sequence of AtHip-2 suggests the possibility of additional unique chaperone functions. PMID:11599566

The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

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

Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy G.

2011-06-18

CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despitemore » its potential role in retinoblastoma. Thus, here we have extensively characterized the CD147 Ig0 domain by elucidating its three-dimensional structure through crystallography and its solution behavior through several biophysical methods that include nuclear magnetic resonance. Furthermore, we have utilized this data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6, which is a well-known contributor to retinoblastoma and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Furthermore, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation.« less

Modelling the fate of the Tijuana River discharge plume

NASA Astrophysics Data System (ADS)

van Ormondt, M.; Terrill, E.; Hibler, L. F.; van Dongeren, A. R.

2010-12-01

After rainfall events, the Tijuana River discharges excess runoff into the ocean in a highly turbid plume. The runoff waters contain large suspended solids concentrations, as well as high levels of toxic contaminants, bacteria, and hepatitis and enteroviruses. Public health hazards posed by the effluent often result in beach closures for several kilometers northward along the U.S. shoreline. A Delft3D model has been set up to predict the fate of the Tijuana River plume. The model takes into account the effects of tides, wind, waves, salinity, and temperature stratification. Heat exchange with the atmosphere is also included. The model consists of a relatively coarse outer domain and a high-resolution surf zone domain that are coupled with Domain Decomposition. The offshore boundary conditions are obtained from the larger NCOM SoCal model (operated by the US Navy) that spans the entire Southern California Bight. A number of discharge events are investigated, in which model results are validated against a wide range of field measurements in the San Diego Bight. These include HF Radar surface currents, REMUS tracks, drifter deployments, satellite imagery, as well as current and temperature profile measurements at a number of locations. The model is able to reproduce the observed current and temperature patterns reasonably well. Under calm conditions, the model results suggest that the hydrodynamics in the San Diego Bight are largely governed by internal waves. During rainfall events, which are typically accompanied by strong winds and high waves, wind and wave driven currents become dominant. An analysis will be made of what conditions determine the trapping and mixing of the plume inside the surfzone and/or the propagation of the plume through the breakers and onto the coastal shelf. The model is now also running in operational mode. Three day forecasts are made every 24 hours. This study was funded by the Office of Naval Research.

Quality specifications in postgraduate medical e-learning: an integrative literature review leading to a postgraduate medical e-learning model.

PubMed

De Leeuw, R A; Westerman, Michiel; Nelson, E; Ket, J C F; Scheele, F

2016-07-08

E-learning is driving major shifts in medical education. Prioritizing learning theories and quality models improves the success of e-learning programs. Although many e-learning quality standards are available, few are focused on postgraduate medical education. We conducted an integrative review of the current postgraduate medical e-learning literature to identify quality specifications. The literature was thematically organized into a working model. Unique quality specifications (n = 72) were consolidated and re-organized into a six-domain model that we called the Postgraduate Medical E-learning Model (Postgraduate ME Model). This model was partially based on the ISO-19796 standard, and drew on cognitive load multimedia principles. The domains of the model are preparation, software design and system specifications, communication, content, assessment, and maintenance. This review clarified the current state of postgraduate medical e-learning standards and specifications. It also synthesized these specifications into a single working model. To validate our findings, the next-steps include testing the Postgraduate ME Model in controlled e-learning settings.

Schizophrenia and Depression Co-Morbidity: What We have Learned from Animal Models

PubMed Central

Samsom, James N.; Wong, Albert H. C.

2015-01-01

Patients with schizophrenia are at an increased risk for the development of depression. Overlap in the symptoms and genetic risk factors between the two disorders suggests a common etiological mechanism may underlie the presentation of comorbid depression in schizophrenia. Understanding these shared mechanisms will be important in informing the development of new treatments. Rodent models are powerful tools for understanding gene function as it relates to behavior. Examining rodent models relevant to both schizophrenia and depression reveals a number of common mechanisms. Current models which demonstrate endophenotypes of both schizophrenia and depression are reviewed here, including models of CUB and SUSHI multiple domains 1, PDZ and LIM domain 5, glutamate Delta 1 receptor, diabetic db/db mice, neuropeptide Y, disrupted in schizophrenia 1, and its interacting partners, reelin, maternal immune activation, and social isolation. Neurotransmission, brain connectivity, the immune system, the environment, and metabolism emerge as potential common mechanisms linking these models and potentially explaining comorbid depression in schizophrenia. PMID:25762938

IGMS: An Integrated ISO-to-Appliance Scale Grid Modeling System

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

Palmintier, Bryan; Hale, Elaine; Hansen, Timothy M.

This paper describes the Integrated Grid Modeling System (IGMS), a novel electric power system modeling platform for integrated transmission-distribution analysis that co-simulates off-the-shelf tools on high performance computing (HPC) platforms to offer unprecedented resolution from ISO markets down to appliances and other end uses. Specifically, the system simultaneously models hundreds or thousands of distribution systems in co-simulation with detailed Independent System Operator (ISO) markets and AGC-level reserve deployment. IGMS uses a new MPI-based hierarchical co-simulation framework to connect existing sub-domain models. Our initial efforts integrate opensource tools for wholesale markets (FESTIV), bulk AC power flow (MATPOWER), and full-featured distribution systemsmore » including physics-based end-use and distributed generation models (many instances of GridLAB-D[TM]). The modular IGMS framework enables tool substitution and additions for multi-domain analyses. This paper describes the IGMS tool, characterizes its performance, and demonstrates the impacts of the coupled simulations for analyzing high-penetration solar PV and price responsive load scenarios.« less

Membrane re-modelling by BAR domain superfamily proteins via molecular and non-molecular factors.

PubMed

Nishimura, Tamako; Morone, Nobuhiro; Suetsugu, Shiro

2018-04-17

Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane. BAR proteins co-operate with various molecular and non-molecular factors. The molecular factors include cytoskeletal proteins such as the regulators of actin filaments and the membrane scission protein dynamin. Lipid composition, including saturated or unsaturated fatty acid tails of phospholipids, also affects the ability of BAR proteins to mould the membrane. Non-molecular factors include the external physical forces applied to the membrane, such as tension and friction. In this mini-review, we will discuss how the BAR proteins orchestrate membrane dynamics together with various molecular and non-molecular factors. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Integrating language models into classifiers for BCI communication: a review

NASA Astrophysics Data System (ADS)

Speier, W.; Arnold, C.; Pouratian, N.

2016-06-01

Objective. The present review systematically examines the integration of language models to improve classifier performance in brain-computer interface (BCI) communication systems. Approach. The domain of natural language has been studied extensively in linguistics and has been used in the natural language processing field in applications including information extraction, machine translation, and speech recognition. While these methods have been used for years in traditional augmentative and assistive communication devices, information about the output domain has largely been ignored in BCI communication systems. Over the last few years, BCI communication systems have started to leverage this information through the inclusion of language models. Main results. Although this movement began only recently, studies have already shown the potential of language integration in BCI communication and it has become a growing field in BCI research. BCI communication systems using language models in their classifiers have progressed down several parallel paths, including: word completion; signal classification; integration of process models; dynamic stopping; unsupervised learning; error correction; and evaluation. Significance. Each of these methods have shown significant progress, but have largely been addressed separately. Combining these methods could use the full potential of language model, yielding further performance improvements. This integration should be a priority as the field works to create a BCI system that meets the needs of the amyotrophic lateral sclerosis population.

Integrating language models into classifiers for BCI communication: a review.

PubMed

Speier, W; Arnold, C; Pouratian, N

2016-06-01

The present review systematically examines the integration of language models to improve classifier performance in brain-computer interface (BCI) communication systems. The domain of natural language has been studied extensively in linguistics and has been used in the natural language processing field in applications including information extraction, machine translation, and speech recognition. While these methods have been used for years in traditional augmentative and assistive communication devices, information about the output domain has largely been ignored in BCI communication systems. Over the last few years, BCI communication systems have started to leverage this information through the inclusion of language models. Although this movement began only recently, studies have already shown the potential of language integration in BCI communication and it has become a growing field in BCI research. BCI communication systems using language models in their classifiers have progressed down several parallel paths, including: word completion; signal classification; integration of process models; dynamic stopping; unsupervised learning; error correction; and evaluation. Each of these methods have shown significant progress, but have largely been addressed separately. Combining these methods could use the full potential of language model, yielding further performance improvements. This integration should be a priority as the field works to create a BCI system that meets the needs of the amyotrophic lateral sclerosis population.

Opioid Prescribing After Curative-Intent Surgery: A Qualitative Study Using the Theoretical Domains Framework.

PubMed

Lee, Jay S; Parashar, Vartika; Miller, Jacquelyn B; Bremmer, Samantha M; Vu, Joceline V; Waljee, Jennifer F; Dossett, Lesly A

2018-07-01

Excessive opioid prescribing is common after curative-intent surgery, but little is known about what factors influence prescribing behaviors among surgeons. To identify targets for intervention, we performed a qualitative study of opioid prescribing after curative-intent surgery using the Theoretical Domains Framework, a well-established implementation science method for identifying factors influencing healthcare provider behavior. Prior to data collection, we constructed a semi-structured interview guide to explore decision making for opioid prescribing. We then conducted interviews with surgical oncology providers at a single comprehensive cancer center. Interviews were recorded, transcribed verbatim, then independently coded by two investigators using the Theoretical Domains Framework to identify theoretical domains relevant to opioid prescribing. Relevant domains were then linked to behavior models to select targeted interventions likely to improve opioid prescribing. Twenty-one subjects were interviewed from November 2016 to May 2017, including attending surgeons, resident surgeons, physician assistants, and nurses. Five theoretical domains emerged as relevant to opioid prescribing: environmental context and resources; social influences; beliefs about consequences; social/professional role and identity; and goals. Using these domains, three interventions were identified as likely to change opioid prescribing behavior: (1) enablement (deploy nurses during preoperative visits to counsel patients on opioid use); (2) environmental restructuring (provide on-screen prompts with normative data on the quantity of opioid prescribed); and (3) education (provide prescribing guidelines). Key determinants of opioid prescribing behavior after curative-intent surgery include environmental and social factors. Interventions targeting these factors are likely to improve opioid prescribing in surgical oncology.

Satellite based assessment of recent permafrost extent and active layer trends over Alaska and Northwest Canada

NASA Astrophysics Data System (ADS)

Kim, Y.; Kimball, J. S.; PARK, H.; Yi, Y.

2017-12-01

Climate change in the Boreal-Arctic region has experienced greater surface air temperature (SAT) warming than the global average in recent decades, which is promoting permafrost thawing and active layer deepening. Permafrost extent (PE) and active layer thickness (ALT) are key environmental indicators of recent climate change, and strongly impact other eco-hydrological processes including land-atmosphere carbon exchange. We developed a new approach for regional estimation and monitoring of PE using daily landscape freeze-thaw (FT) records derived from satellite microwave (37 GHz) brightness temperature (Tb) observations. ALT was estimated within the PE domain using empirical modeling of land cover dependent edaphic factors and an annual thawing index derived from MODIS land surface temperature (LST) observations and reanalysis based surface air temperatures (SAT). The PE and ALT estimates were derived over the 1980-2016 satellite record and NASA ABoVE (Arctic Boreal Vulnerability Experiment) domain encompassing Alaska and Northwest Canada. The baseline model estimates were derived at 25-km resolution consistent with the satellite FT global record. Our results show recent widespread PE decline and deepening ALT trends, with larger spatial variability and model uncertainty along the southern PE boundary. Larger PE and ALT variability occurs over heterogeneous permafrost subzones characterized by dense vegetation, and variable snow cover and organic layer conditions. We also tested alternative PE and ALT estimates derived using finer (6-km) scale satellite Tb (36.5 GHz) and FT retrievals from a calibrated AMSR-E and AMSR2 sensor record. The PE and ALT results were compared against other independent observations, including process model simulations, in situ measurements, and permafrost inventory records. A model sensitivity analysis was conducted to evaluate snow cover, soil organic layer, and vegetation composition impacts to ALT. The finer delineation of permafrost and active layer conditions provides enhanced regional monitoring of PE and ALT changes over the ABoVE domain, including heterogeneous permafrost subzones.

Coupling large scale hydrologic-reservoir-hydraulic models for impact studies in data sparse regions

NASA Astrophysics Data System (ADS)

O'Loughlin, Fiachra; Neal, Jeff; Wagener, Thorsten; Bates, Paul; Freer, Jim; Woods, Ross; Pianosi, Francesca; Sheffied, Justin

2017-04-01

As hydraulic modelling moves to increasingly large spatial domains it has become essential to take reservoirs and their operations into account. Large-scale hydrological models have been including reservoirs for at least the past two decades, yet they cannot explicitly model the variations in spatial extent of reservoirs, and many reservoirs operations in hydrological models are not undertaken during the run-time operation. This requires a hydraulic model, yet to-date no continental scale hydraulic model has directly simulated reservoirs and their operations. In addition to the need to include reservoirs and their operations in hydraulic models as they move to global coverage, there is also a need to link such models to large scale hydrology models or land surface schemes. This is especially true for Africa where the number of river gauges has consistently declined since the middle of the twentieth century. In this study we address these two major issues by developing: 1) a coupling methodology for the VIC large-scale hydrological model and the LISFLOOD-FP hydraulic model, and 2) a reservoir module for the LISFLOOD-FP model, which currently includes four sets of reservoir operating rules taken from the major large-scale hydrological models. The Volta Basin, West Africa, was chosen to demonstrate the capability of the modelling framework as it is a large river basin ( 400,000 km2) and contains the largest man-made lake in terms of area (8,482 km2), Lake Volta, created by the Akosombo dam. Lake Volta also experiences a seasonal variation in water levels of between two and six metres that creates a dynamic shoreline. In this study, we first run our coupled VIC and LISFLOOD-FP model without explicitly modelling Lake Volta and then compare these results with those from model runs where the dam operations and Lake Volta are included. The results show that we are able to obtain variation in the Lake Volta water levels and that including the dam operations and Lake Volta has significant impacts on the water levels across the domain.

An improved model for provision of rural community-based health rehabilitation services in Vhembe District, Limpopo Province of South Africa

PubMed Central

Netshandama, Vhonani O.; Francis, Joseph

2016-01-01

Background In 1991, Riakona Community Rehabilitation Programme initiated community-based rehabilitation (CBR) in the Vhembe District of Limpopo Province. Subsequently, the South African government adopted the programme. Aim The aim of the study was to suggest an improvement in the model of providing CBR services. Setting The study was conducted in six rehabilitation centres located in hospitals in the Vhembe District in Limpopo Province of South Africa. Method A mixed-mode research design with qualitative and quantitative elements was used to conduct the study. Content analysis, the chi-square test for Goodness of Fit and the Kruskal–Wallis and Mann–Whitney non-parametric tests were conducted. Results The key determinants of client satisfaction with the services that the community rehabilitation workers rendered included provision of assistive devices and the adoption of a holistic approach to their work. Overall, satisfaction per domain for each one of the five domains of satisfaction scored less than 90%. More than 80% of clients were satisfied with empathy (83%) and assurance (80%) domains. Tangibles, reliability and responsiveness domains had scores of 78%, 72% and 67%, respectively. These results, together with the reasoning map of conceptual framework description, were used as the building blocks of the CBR model. Conclusion The improved CBR model is useful for putting the programme into practice. This is particularly so for the CBR managers in the districts of the Limpopo Province. PMID:27380835

Reciprocal Exchange Patterned by Market Forces Helps Explain Cooperation in a Small-Scale Society.

PubMed

Jaeggi, Adrian V; Hooper, Paul L; Beheim, Bret A; Kaplan, Hillard; Gurven, Michael

2016-08-22

Social organisms sometimes depend on help from reciprocating partners to solve adaptive problems [1], and individual cooperation strategies should aim to offer high supply commodities at low cost to the donor in exchange for high-demand commodities with large return benefits [2, 3]. Although such market dynamics have been documented in some animals [4-7], naturalistic studies of human cooperation are often limited by focusing on single commodities [8]. We analyzed cooperation in five domains (meat sharing, produce sharing, field labor, childcare, and sick care) among 2,161 household dyads of Tsimane' horticulturalists, using Bayesian multilevel models and information-theoretic model comparison. Across domains, the best-fit models included kinship and residential proximity, exchanges in kind and across domains, measures of supply and demand and their interactions with exchange, and household-specific exchange slopes. In these best models, giving, receiving, and reciprocating were to some extent shaped by market forces, and reciprocal exchange across domains had a strong partial effect on cooperation independent of more exogenous factors like kinship and proximity. Our results support the view that reciprocal exchange can provide a reliable solution to adaptive problems [8-11]. Although individual strategies patterned by market forces may generate gains from trade in any species [3], humans' slow life history and skill-intensive foraging niche favor specialization and create interdependence [12, 13], thus stabilizing cooperation and fostering divisions of labor even in informal economies [14, 15]. Copyright © 2016 Elsevier Ltd. All rights reserved.

A mobile-mobile transport model for simulating reactive transport in connected heterogeneous fields

NASA Astrophysics Data System (ADS)

Lu, Chunhui; Wang, Zhiyuan; Zhao, Yue; Rathore, Saubhagya Singh; Huo, Jinge; Tang, Yuening; Liu, Ming; Gong, Rulan; Cirpka, Olaf A.; Luo, Jian

2018-05-01

Mobile-immobile transport models can be effective in reproducing heavily tailed breakthrough curves of concentration. However, such models may not adequately describe transport along multiple flow paths with intermediate velocity contrasts in connected fields. We propose using the mobile-mobile model for simulating subsurface flow and associated mixing-controlled reactive transport in connected fields. This model includes two local concentrations, one in the fast- and the other in the slow-flow domain, which predict both the concentration mean and variance. The normalized total concentration variance within the flux is found to be a non-monotonic function of the discharge ratio with a maximum concentration variance at intermediate values of the discharge ratio. We test the mobile-mobile model for mixing-controlled reactive transport with an instantaneous, irreversible bimolecular reaction in structured and connected random heterogeneous domains, and compare the performance of the mobile-mobile to the mobile-immobile model. The results indicate that the mobile-mobile model generally predicts the concentration breakthrough curves (BTCs) of the reactive compound better. Particularly, for cases of an elliptical inclusion with intermediate hydraulic-conductivity contrasts, where the travel-time distribution shows bimodal behavior, the prediction of both the BTCs and maximum product concentration is significantly improved. Our results exemplify that the conceptual model of two mobile domains with diffusive mass transfer in between is in general good for predicting mixing-controlled reactive transport, and particularly so in cases where the transfer in the low-conductivity zones is by slow advection rather than diffusion.

Field testing model predictions of foam coverage and bubble content in the surf zone

NASA Astrophysics Data System (ADS)

Shi, F.; Kirby, J. T.; Ma, G.; Holman, R. A.; Chickadel, C. C.

2012-12-01

Field-scale modeling of surfzone bubbles and foam coverage is challenging in terms of the computational intensity of multi-phase bubble models based on Navier-Stokes/VOF formulation. In this study, we developed the NHWAVE-bubble package, which includes a 3D non-hydrostatic wave model NHWAVE (Ma et al., 2012), a multi-phase bubble model and a foam model. NHWAVE uses a surface and bottom following sigma coordinate system, making it more applicable to 3D modeling of nearshore waves and circulation in a large-scale field domain. It has been extended to include a multiphase description of polydisperse bubble populations following the approach applied in a 3D VOF model by Ma et al. (2012). A model of a foam layer on the water surface is specified in the model package using a shallow water formulation based on a balance of drag forces due to wind and water column motion. Foam mass conservation includes source and sink terms representing outgassing of the water column, direct foam generation due to surface agitation, and erosion due to bubble bursting. The model is applied in a field scale domain at FRF, Duck, NC where optical data in either visible band (ARGUS) or infrared band were collected during 2010 Surf Zone Optics experiments. The decay of image brightness or intensity following the passage of wave crests is presumably tied to both decay of bubble populations and foam coverage after passage of a broken wave crest. Infrared imagery is likely to provide more detailed information which could separate active breaking from passive foam decay on the surface. Model results will be compared with the measurements with an attention to distinguishing between active generation and passive decay of the foam signature on the water surface.

Dynamical Downscaling of Typhoon Vera (1959) and related Storm Surge based on JRA-55 Reanalysis

NASA Astrophysics Data System (ADS)

Ninomiya, J.; Takemi, T.; Mori, N.; Shibutani, Y.; Kim, S.

2015-12-01

Typhoon Vera in 1959 is historical extreme typhoon that caused severest typhoon damage mainly due to the storm surge up to 389 cm in Japan. Vera developed 895 hPa on offshore and landed with 929.2 hPa. There are many studies of the dynamical downscaling of Vera but it is difficult to simulate accurately because of the lack of the accuracy of global reanalysis data. This study carried out dynamical downscaling experiment of Vera using WRF downscaling forced by JRA-55 that are latest atmospheric model and reanalysis data. In this study, the reproducibility of five global reanalysis data for Typhoon Vera were compered. Comparison shows that reanalysis data doesn't have strong typhoon information except for JRA-55, so that downscaling with conventional reanalysis data goes wrong. The dynamical downscaling method for storm surge is studied very much (e.g. choice of physical model, nudging, 4D-VAR, bogus and so on). In this study, domain size and resolution of the coarse domain were considered. The coarse domain size influences the typhoon route and central pressure, and larger domain restrains the typhoon strength. The results of simulations with different domain size show that the threshold of developing restrain is whether the coarse domain fully includes the area of wind speed more than 15 m/s around the typhoon. The results of simulations with different resolution show that the resolution doesn't affect the typhoon route, and higher resolution gives stronger typhoon simulation.

SECRET domain of variola virus CrmB protein can be a member of poxviral type II chemokine-binding proteins family

PubMed Central

2010-01-01

Background Variola virus (VARV) the causative agent of smallpox, eradicated in 1980, have wide spectrum of immunomodulatory proteins to evade host immunity. Recently additional biological activity was discovered for VARV CrmB protein, known to bind and inhibit tumour necrosis factor (TNF) through its N-terminal domain homologous to cellular TNF receptors. Besides binding TNF, this protein was also shown to bind with high affinity several chemokines which recruit B- and T-lymphocytes and dendritic cells to sites of viral entry and replication. Ability to bind chemokines was shown to be associated with unique C-terminal domain of CrmB protein. This domain named SECRET (Smallpox virus-Encoded Chemokine Receptor) is unrelated to the host proteins and lacks significant homology with other known viral chemokine-binding proteins or any other known protein. Findings De novo modelling of VARV-CrmB SECRET domain spatial structure revealed its apparent structural homology with cowpox virus CC-chemokine binding protein (vCCI) and vaccinia virus A41 protein, despite low sequence identity between these three proteins. Potential ligand-binding surface of modelled VARV-CrmB SECRET domain was also predicted to bear prominent electronegative charge which is characteristic to known orthopoxviral chemokine-binding proteins. Conclusions Our results suggest that SECRET should be included into the family of poxviral type II chemokine-binding proteins and that it might have been evolved from the vCCI-like predecessor protein. PMID:20979600

SECRET domain of variola virus CrmB protein can be a member of poxviral type II chemokine-binding proteins family.

PubMed

Antonets, Denis V; Nepomnyashchikh, Tatyana S; Shchelkunov, Sergei N

2010-10-27

Variola virus (VARV) the causative agent of smallpox, eradicated in 1980, have wide spectrum of immunomodulatory proteins to evade host immunity. Recently additional biological activity was discovered for VARV CrmB protein, known to bind and inhibit tumour necrosis factor (TNF) through its N-terminal domain homologous to cellular TNF receptors. Besides binding TNF, this protein was also shown to bind with high affinity several chemokines which recruit B- and T-lymphocytes and dendritic cells to sites of viral entry and replication. Ability to bind chemokines was shown to be associated with unique C-terminal domain of CrmB protein. This domain named SECRET (Smallpox virus-Encoded Chemokine Receptor) is unrelated to the host proteins and lacks significant homology with other known viral chemokine-binding proteins or any other known protein. De novo modelling of VARV-CrmB SECRET domain spatial structure revealed its apparent structural homology with cowpox virus CC-chemokine binding protein (vCCI) and vaccinia virus A41 protein, despite low sequence identity between these three proteins. Potential ligand-binding surface of modelled VARV-CrmB SECRET domain was also predicted to bear prominent electronegative charge which is characteristic to known orthopoxviral chemokine-binding proteins. Our results suggest that SECRET should be included into the family of poxviral type II chemokine-binding proteins and that it might have been evolved from the vCCI-like predecessor protein.

Ionic tethering contributes to the conformational stability and function of complement C3b.

PubMed

López-Perrote, Andrés; Harrison, Reed E S; Subías, Marta; Alcorlo, Martín; Rodríguez de Córdoba, Santiago; Morikis, Dimitrios; Llorca, Oscar

2017-05-01

C3b, the central component of the alternative pathway (AP) of the complement system, coexists as a mixture of conformations in solution. These conformational changes can affect interactions with other proteins and complement regulators. Here we combine a computational model for electrostatic interactions within C3b with molecular imaging to study the conformation of C3b. The computational analysis shows that the TED domain in C3b is tethered ionically to the macroglobulin (MG) ring. Monovalent counterion concentration affects the magnitude of electrostatic forces anchoring the TED domain to the rest of the C3b molecule in a thermodynamic model. This is confirmed by observing NaCl concentration dependent conformational changes using single molecule electron microscopy (EM). We show that the displacement of the TED domain is compatible with C3b binding to Factor B (FB), suggesting that the regulation of the C3bBb convertase could be affected by conditions that promote movement in the TED domain. Our molecular model also predicts mutations that could alter the positioning of the TED domain, including the common R102G polymorphism, a risk variant for developing age-related macular degeneration. The common C3b isoform, C3bS, and the risk isoform, C3bF, show distinct energetic barriers to displacement in the TED that are related to a network of electrostatic interactions at the interface of the TED and MG-ring domains of C3b. These computational predictions agree with experimental evidence that shows differences in conformation observed in C3b isoforms purified from homozygous donors. Altogether, we reveal an ionic, reversible attachment of the TED domain to the MG ring that may influence complement regulation in some mutations and polymorphisms of C3b. Copyright © 2016 Elsevier Ltd. All rights reserved.

The SIETTE Automatic Assessment Environment

ERIC Educational Resources Information Center

Conejo, Ricardo; Guzmán, Eduardo; Trella, Monica

2016-01-01

This article describes the evolution and current state of the domain-independent Siette assessment environment. Siette supports different assessment methods--including classical test theory, item response theory, and computer adaptive testing--and integrates them with multidimensional student models used by intelligent educational systems.…

Supporting Semantic Annotation of Educational Content by Automatic Extraction of Hierarchical Domain Relationships

ERIC Educational Resources Information Center

Vrablecová, Petra; Šimko, Marián

2016-01-01

The domain model is an essential part of an adaptive learning system. For each educational course, it involves educational content and semantics, which is also viewed as a form of conceptual metadata about educational content. Due to the size of a domain model, manual domain model creation is a challenging and demanding task for teachers or…

Mesoscale atmospheric modelling technology as a tool for the long-term meteorological dataset development

NASA Astrophysics Data System (ADS)

Platonov, Vladimir; Kislov, Alexander; Rivin, Gdaly; Varentsov, Mikhail; Rozinkina, Inna; Nikitin, Mikhail; Chumakov, Mikhail

2017-04-01

The detailed hydrodynamic modelling of meteorological parameters during the last 30 years (1985 - 2014) was performed for the Okhotsk Sea and the Sakhalin island regions. The regional non-hydrostatic atmospheric model COSMO-CLM used for this long-term simulation with 13.2, 6.6 and 2.2 km horizontal resolutions. The main objective of creation this dataset was the outlook of the investigation of statistical characteristics and the physical mechanisms of extreme weather events (primarily, wind speed extremes) on the small spatio-temporal scales. COSMO-CLM is the climate version of the well-known mesoscale COSMO model, including some modifications and extensions adapting to the long-term numerical experiments. The downscaling technique was realized and developed for the long-term simulations with three consequent nesting domains. ERA-Interim reanalysis ( 0.75 degrees resolution) used as global forcing data for the starting domain ( 13.2 km horizontal resolution), then these simulation data used as initial and boundary conditions for the next model runs over the domain with 6.6 km resolution, and similarly, for the next step to 2.2 km domain. Besides, the COSMO-CLM model configuration for 13.2 km run included the spectral nudging technique, i.e. an additional assimilation of reanalysis data not only at boundaries, but also inside the whole domain. Practically, this computational scheme realized on the SGI Altix 4700 supercomputer system in the Main Computer Center of Roshydromet and used 2,400 hours of CPU time total. According to modelling results, the verification of the obtained dataset was performed on the observation data. Estimations showed the mean error -0.5 0C, up to 2 - 3 0C RMSE in temperature, and overestimation in wind speed (RMSE is up to 2 m/s). Overall, analysis showed that the used downscaling technique with applying the COSMO-CLM model reproduced the meteorological conditions, spatial distribution, seasonal and synoptic variability of temperature and wind speed for the study area adequately. The dependences between reproduction quality of mesoscale atmospheric circulation features and the horizontal resolution of the model were revealed. In particular, it is shown that the use of 6 km resolution does not give any significant improvement comparing to 13 km resolution, whereas 2.2 km resolution provides an appreciable quality enhancement. Detailed synoptic analysis of extreme wind speed situations identified the main types of favorable to their genesis, associated with developing of cyclones over the Japan Islands or the Primorsky Kray of Russia, and penetration of intensified cyclones from Pacific Ocean through the Kamchatka peninsula, Kuril or Japan Islands. The obtained dataset will continue to be used for a full and comprehensive analysis of the reproduction quality of hydrometeorological fields, their statistical estimates, climatological trends and many other objectives.

Self-reported walking ability predicts functional mobility performance in frail older adults.

PubMed

Alexander, N B; Guire, K E; Thelen, D G; Ashton-Miller, J A; Schultz, A B; Grunawalt, J C; Giordani, B

2000-11-01

To determine how self-reported physical function relates to performance in each of three mobility domains: walking, stance maintenance, and rising from chairs. Cross-sectional analysis of older adults. University-based laboratory and community-based congregate housing facilities. Two hundred twenty-one older adults (mean age, 79.9 years; range, 60-102 years) without clinical evidence of dementia (mean Folstein Mini-Mental State score, 28; range, 24-30). We compared the responses of these older adults on a questionnaire battery used by the Established Populations for the Epidemiologic Study of the Elderly (EPESE) project, to performance on mobility tasks of graded difficulty. Responses to the EPESE battery included: (1) whether assistance was required to perform seven Katz activities of daily living (ADL) items, specifically with walking and transferring; (2) three Rosow-Breslau items, including the ability to walk up stairs and walk a half mile; and (3) five Nagi items, including difficulty stooping, reaching, and lifting objects. The performance measures included the ability to perform, and time taken to perform, tasks in three summary score domains: (1) walking ("Walking," seven tasks, including walking with an assistive device, turning, stair climbing, tandem walking); (2) stance maintenance ("Stance," six tasks, including unipedal, bipedal, tandem, and maximum lean); and (3) chair rise ("Chair Rise," six tasks, including rising from a variety of seat heights with and without the use of hands for assistance). A total score combines scores in each Walking, Stance, and Chair Rise domain. We also analyzed how cognitive/ behavioral factors such as depression and self-efficacy related to the residuals from the self-report and performance-based ANOVA models. Rosow-Breslau items have the strongest relationship with the three performance domains, Walking, Stance, and Chair Rise (eta-squared ranging from 0.21 to 0.44). These three performance domains are as strongly related to one Katz ADL item, walking (eta-squared ranging from 0.15 to 0.33) as all of the Katz ADL items combined (eta-squared ranging from 0.21 to 0.35). Tests of problem solving and psychomotor speed, the Trails A and Trails B tests, are significantly correlated with the residuals from the self-report and performance-based ANOVA models. Compared with the rest of the EPESE self-report items, self-report items related to walking (such as Katz walking and Rosow-Breslau items) are better predictors of functional mobility performance on tasks involving walking, stance maintenance, and rising from chairs. Compared with other self-report items, self-reported walking ability may be the best predictor of overall functional mobility.

The Loyal Opposition Comments on Plan Domain Description Languages

NASA Technical Reports Server (NTRS)

Frank, Jeremy; Golden, Keith; Jonsson, Ari

2003-01-01

In this paper we take a critical look at PDDL 2.1 as designers and users of plan domain description languages. We describe planning domains that have features which are hard to model using PDDL 2.1. We then offer some suggestions on domain description language design, and describe how these suggestions make modeling our chosen domains easier.

Assessing the uncertainty of soil moisture impacts on convective precipitation using a new ensemble approach

NASA Astrophysics Data System (ADS)

Henneberg, Olga; Ament, Felix; Grützun, Verena

2018-05-01

Soil moisture amount and distribution control evapotranspiration and thus impact the occurrence of convective precipitation. Many recent model studies demonstrate that changes in initial soil moisture content result in modified convective precipitation. However, to quantify the resulting precipitation changes, the chaotic behavior of the atmospheric system needs to be considered. Slight changes in the simulation setup, such as the chosen model domain, also result in modifications to the simulated precipitation field. This causes an uncertainty due to stochastic variability, which can be large compared to effects caused by soil moisture variations. By shifting the model domain, we estimate the uncertainty of the model results. Our novel uncertainty estimate includes 10 simulations with shifted model boundaries and is compared to the effects on precipitation caused by variations in soil moisture amount and local distribution. With this approach, the influence of soil moisture amount and distribution on convective precipitation is quantified. Deviations in simulated precipitation can only be attributed to soil moisture impacts if the systematic effects of soil moisture modifications are larger than the inherent simulation uncertainty at the convection-resolving scale. We performed seven experiments with modified soil moisture amount or distribution to address the effect of soil moisture on precipitation. Each of the experiments consists of 10 ensemble members using the deep convection-resolving COSMO model with a grid spacing of 2.8 km. Only in experiments with very strong modification in soil moisture do precipitation changes exceed the model spread in amplitude, location or structure. These changes are caused by a 50 % soil moisture increase in either the whole or part of the model domain or by drying the whole model domain. Increasing or decreasing soil moisture both predominantly results in reduced precipitation rates. Replacing the soil moisture with realistic fields from different days has an insignificant influence on precipitation. The findings of this study underline the need for uncertainty estimates in soil moisture studies based on convection-resolving models.

Experimentally validated multiphysics computational model of focusing and shock wave formation in an electromagnetic lithotripter.

PubMed

Fovargue, Daniel E; Mitran, Sorin; Smith, Nathan B; Sankin, Georgy N; Simmons, Walter N; Zhong, Pei

2013-08-01

A multiphysics computational model of the focusing of an acoustic pulse and subsequent shock wave formation that occurs during extracorporeal shock wave lithotripsy is presented. In the electromagnetic lithotripter modeled in this work the focusing is achieved via a polystyrene acoustic lens. The transition of the acoustic pulse through the solid lens is modeled by the linear elasticity equations and the subsequent shock wave formation in water is modeled by the Euler equations with a Tait equation of state. Both sets of equations are solved simultaneously in subsets of a single computational domain within the BEARCLAW framework which uses a finite-volume Riemann solver approach. This model is first validated against experimental measurements with a standard (or original) lens design. The model is then used to successfully predict the effects of a lens modification in the form of an annular ring cut. A second model which includes a kidney stone simulant in the domain is also presented. Within the stone the linear elasticity equations incorporate a simple damage model.

Experimentally validated multiphysics computational model of focusing and shock wave formation in an electromagnetic lithotripter

PubMed Central

Fovargue, Daniel E.; Mitran, Sorin; Smith, Nathan B.; Sankin, Georgy N.; Simmons, Walter N.; Zhong, Pei

2013-01-01

A multiphysics computational model of the focusing of an acoustic pulse and subsequent shock wave formation that occurs during extracorporeal shock wave lithotripsy is presented. In the electromagnetic lithotripter modeled in this work the focusing is achieved via a polystyrene acoustic lens. The transition of the acoustic pulse through the solid lens is modeled by the linear elasticity equations and the subsequent shock wave formation in water is modeled by the Euler equations with a Tait equation of state. Both sets of equations are solved simultaneously in subsets of a single computational domain within the BEARCLAW framework which uses a finite-volume Riemann solver approach. This model is first validated against experimental measurements with a standard (or original) lens design. The model is then used to successfully predict the effects of a lens modification in the form of an annular ring cut. A second model which includes a kidney stone simulant in the domain is also presented. Within the stone the linear elasticity equations incorporate a simple damage model. PMID:23927200

The electronic patient record: a strategic planning framework.

PubMed

Gordon, D B; Marafioti, S; Carter, M; Kunov, H; Dolan, A

1995-01-01

Sunnybrook Health Science Center (Sunnybrook) is a multifacility academic teaching center. In May 1994, Sunnybrook struck an electronic patient record taskforce to develop a strategic plan for the implementation of a comprehensive, facility wide electronic patient record (EPR). The taskforce sought to create a conceptual framework which provides context and integrates decision-making related to the comprehensive electronic patient record. The EPR is very much broader in scope than the traditional paper-based record. It is not restricted to simply reporting individual patient data. By the Institute of Medicine's definition, the electronic patient record resides in a system specifically designed to support users through availability of complete and accurate data, practitioner reminders and alerts, clinical decision support systems, links to bodies of medical knowledge, and other aids [1]. It is a comprehensive resource for patient care. The taskforce proposed a three domain model for determining how the EPR affects Sunnybrook. The EPR enables Sunnybrook to have a high performance team structure (domain 1), to function as an integrated organization (domain 2), and to reach out and develop new relationships with external organizations to become an extended enterprise (domain 3) [2]. Domain 1: Sunnybrook's high performance teams or patient service units' (PSUs) are decentralized, autonomous operating units that provide care to patients grouped by 'like' diagnosis and resource needs. The EPR must provide functions and applications which promote patient focused care, such as cross functional charting and care maps, group scheduling, clinical email, and a range of enabling technologies for multiskilled workers. Domain 2: In the integrated organization domain, the EPR should facilitate closer linkages between the arrangement of PSUs into clinical teams and with other facilities within the center in order to provide a longitudinal record that covers a continuum of care. Domain 3: In the inter-enterprise domain, the EPR must allow for patient information to be exchanged with external providers including referring doctors, laboratories, and other hospitals via community health information networks (CHINs). Sunnybrook will prioritize the development of first domain functionality within the corporate constraints imposed by the integrated organization domain. Inter-enterprise computing will be less of a priority until Sunnybrook has developed a critical mass of the electronic patient record internally. The three domain description is a useful model for describing the relationship between the electronic patient record enabling technologies and the Sunnybrook organizational structures. The taskforce has used this model to determine EPR development guidelines and implementation priorities.

Psychometric properties of WHOQOL-BREF in clinical and health Greek populations: incorporating new culture-relevant items.

PubMed

Ginieri-Coccossis, M; Triantafillou, E; Tomaras, V; Soldatos, C; Mavreas, V; Christodoulou, G

2012-01-01

Τhe present study examines main psychometric properties of the World Health Organisation (WHO) quality of life (QoL) instrument, the WHOQOL-BREF with the inclusion of four national items. Participants were 425 adult native Greek speaking, grouped into patients with physical disorders, psychiatric disorders and healthy individuals. Participants were administered WHOQOL-BREF and 23 national items, the General Health Questionnaire (GHQ-28) and the Life Satisfaction Index (LSI). Confirmatory factor analysis produced acceptable fit values for the original model of 26 items within the four WHOQOL domains: physical health, psychological health, social relationships and environment. Testing for the fit of national items within this model, the results indicated four new items with the most satisfactory fit indices and were thus included forming a 30-items version. The national items refer to: (a) nutrition, (b) satisfaction with work (both loaded in the physical health domain), (c) home life and (d) social life (both loaded in the social relationships domain). Statistical tests were applied to the 26- and 30-items versions producing satisfactory results, with the 30-items version showing slightly better values. Furthermore, results on the 30-items version included: (a) internal consistency, which was found satisfactory, with alpha values ranging from α=0.67-0.81, while the inclusion of new items produced higher alpha values in physical health and social relationships domains, (b) construct validity with good item-domain correlations, as well as strong correlations between domain scores, (c) convergent validity, which was very satisfactory, showing good correlations with GHQ-28 and LSI, (d) discriminant validity, showing instrument's ability to detect QoL differences between healthy and unhealthy participants, and between physically ill and psychiatric patients, and (e) test-retest reliability, with ICC scores in excess of 0.80 obtaining for all domains. The WHOQOL-BREF Greek version was found to perform well with sick and healthy participants, demonstrating satisfactory psychometric properties. Use of the instrument may be recommended for clinical and general populations, for service or intervention evaluation, as well as for cross-cultural clinical trials.

Modeling and Simulation Behavior Validation Methodology and Extension Model Validation for the Individual Soldier

DTIC Science & Technology

2015-03-01

domains. Major model functions include: • Ground combat: Light and heavy forces. • Air mobile forces. • Future forces. • Fixed-wing and rotary-wing...Constraints: • Study must be completed no later than 31 December 2014. • Entity behavior limited to select COMBATXXI Mobility , Unmanned Aerial System...and SQL backend , as well as any open application programming interface API. • Allows data transparency and data driven navigation through the model

Structural insight into the mechanism of synergistic autoinhibition of SAD kinases

PubMed Central

Wu, Jing-Xiang; Cheng, Yun-Sheng; Wang, Jue; Chen, Lei; Ding, Mei; Wu, Jia-Wei

2015-01-01

The SAD/BRSK kinases participate in various important life processes, including neural development, cell cycle and energy metabolism. Like other members of the AMPK family, SAD contains an N-terminal kinase domain followed by the characteristic UBA and KA1 domains. Here we identify a unique autoinhibitory sequence (AIS) in SAD kinases, which exerts autoregulation in cooperation with UBA. Structural studies of mouse SAD-A revealed that UBA binds to the kinase domain in a distinct mode and, more importantly, AIS nestles specifically into the KD-UBA junction. The cooperative action of AIS and UBA results in an ‘αC-out' inactive kinase, which is conserved across species and essential for presynaptic vesicle clustering in C. elegans. In addition, the AIS, along with the KA1 domain, is indispensable for phospholipid binding. Taken together, these data suggest a model for synergistic autoinhibition and membrane activation of SAD kinases. PMID:26626945

Structural insight into the mechanism of synergistic autoinhibition of SAD kinases.

PubMed

Wu, Jing-Xiang; Cheng, Yun-Sheng; Wang, Jue; Chen, Lei; Ding, Mei; Wu, Jia-Wei

2015-12-02

The SAD/BRSK kinases participate in various important life processes, including neural development, cell cycle and energy metabolism. Like other members of the AMPK family, SAD contains an N-terminal kinase domain followed by the characteristic UBA and KA1 domains. Here we identify a unique autoinhibitory sequence (AIS) in SAD kinases, which exerts autoregulation in cooperation with UBA. Structural studies of mouse SAD-A revealed that UBA binds to the kinase domain in a distinct mode and, more importantly, AIS nestles specifically into the KD-UBA junction. The cooperative action of AIS and UBA results in an 'αC-out' inactive kinase, which is conserved across species and essential for presynaptic vesicle clustering in C. elegans. In addition, the AIS, along with the KA1 domain, is indispensable for phospholipid binding. Taken together, these data suggest a model for synergistic autoinhibition and membrane activation of SAD kinases.

Cognitive Function and Vascular Risk Factors Among Older African American Adults

PubMed Central

Park, Moon Ho; Tsang, Siny; Sperling, Scott A.; Manning, Carol

2017-01-01

To evaluate the association between vascular risk factors and cognitive impairment among older African American (AA) adults in a primary care clinic. Participants included 96 AA adults aged 60 years or older who were evaluated for global and domain-specific cognition. Participants were interviewed using the Computerized Assessment of Memory and Cognitive Impairment (CAMCI). The relationship between CAMCI cognitive domain scores and vascular risk factors were examined using hierarchical regression models. Patients who smoked, those with higher SBP/DBP values had lower accuracy rates on CAMCI cognitive domains (attention, executive, memory).Those with higher BMI had better attention scores. Patients with higher HbA1C values had worse verbal memory. Patients with higher blood pressure were significantly faster in responding to tasks in the executive domain. Primary care providers working with older AA adults with these VRFs could implement cognitive screening earlier into their practice to reduce barriers of seeking treatment. PMID:28417319

Interacting particle systems in time-dependent geometries

NASA Astrophysics Data System (ADS)

Ali, A.; Ball, R. C.; Grosskinsky, S.; Somfai, E.

2013-09-01

Many complex structures and stochastic patterns emerge from simple kinetic rules and local interactions, and are governed by scale invariance properties in combination with effects of the global geometry. We consider systems that can be described effectively by space-time trajectories of interacting particles, such as domain boundaries in two-dimensional growth or river networks. We study trajectories embedded in time-dependent geometries, and the main focus is on uniformly expanding or decreasing domains for which we obtain an exact mapping to simple fixed domain systems while preserving the local scale invariance properties. This approach was recently introduced in Ali et al (2013 Phys. Rev. E 87 020102(R)) and here we provide a detailed discussion on its applicability for self-affine Markovian models, and how it can be adapted to self-affine models with memory or explicit time dependence. The mapping corresponds to a nonlinear time transformation which converges to a finite value for a large class of trajectories, enabling an exact analysis of asymptotic properties in expanding domains. We further provide a detailed discussion of different particle interactions and generalized geometries. All our findings are based on exact computations and are illustrated numerically for various examples, including Lévy processes and fractional Brownian motion.

In Situ Graphene Growth Dynamics on Polycrystalline Catalyst Foils

PubMed Central

2016-01-01

The dynamics of graphene growth on polycrystalline Pt foils during chemical vapor deposition (CVD) are investigated using in situ scanning electron microscopy and complementary structural characterization of the catalyst with electron backscatter diffraction. A general growth model is outlined that considers precursor dissociation, mass transport, and attachment to the edge of a growing domain. We thereby analyze graphene growth dynamics at different length scales and reveal that the rate-limiting step varies throughout the process and across different regions of the catalyst surface, including different facets of an individual graphene domain. The facets that define the domain shapes lie normal to slow growth directions, which are determined by the interfacial mobility when attachment to domain edges is rate-limiting, as well as anisotropy in surface diffusion as diffusion becomes rate-limiting. Our observations and analysis thus reveal that the structure of CVD graphene films is intimately linked to that of the underlying polycrystalline catalyst, with both interfacial mobility and diffusional anisotropy depending on the presence of step edges and grain boundaries. The growth model developed serves as a general framework for understanding and optimizing the growth of 2D materials on polycrystalline catalysts. PMID:27576749

[Modeling and experimental study on frequency-domain electricity properties of biological materials].

PubMed

Tian, Hua; Luo, Shiqiang; Zhang, Rui; Yang, Gang; Huang, Hua

2009-12-01

Frequency-domain electricity properties of four objects, including bullfrog skin, bullfrog muscle, triply distilled water and 0.9% NaCl, were tested in the range of 100Hz-10MHz using home-made electrode and measuring system. The experimental results showed that the resistance of 0.9% NaCl decreased dramatically, that the amplitude frequency characteristics of bullfrog's muscle and skin were similar, but that of triply distilled water did not change significantly. The frequency dependence of 0.9% NaCl showed that the electrode had great influence on the measuring system, so a new equivalent circuit model based on the electrode system was needed. These findings suggest that the new five-parameter equivalent circuit model, which embodies considerations on the interaction between electrodes and tissues, is a reasonable equivalent circuit for studying the electrical characteristics of biological materials.

Three Dimensional Reconstruction Workflows for Lost Cultural Heritage Monuments Exploiting Public Domain and Professional Photogrammetric Imagery

NASA Astrophysics Data System (ADS)

Wahbeh, W.; Nebiker, S.

2017-08-01

In our paper, we document experiments and results of image-based 3d reconstructions of famous heritage monuments which were recently damaged or completely destroyed by the so-called Islamic state in Syria and Iraq. The specific focus of our research is on the combined use of professional photogrammetric imagery and of publicly available imagery from the web for optimally 3d reconstructing those monuments. The investigated photogrammetric reconstruction techniques include automated bundle adjustment and dense multi-view 3d reconstruction using public domain and professional imagery on the one hand and an interactive polygonal modelling based on projected panoramas on the other. Our investigations show that the combination of these two image-based modelling techniques delivers better results in terms of model completeness, level of detail and appearance.

Multi-domain models of risk factors for depression and anxiety symptoms in preschoolers: evidence for common and specific factors.

PubMed

Hopkins, Joyce; Lavigne, John V; Gouze, Karen R; LeBailly, Susan A; Bryant, Fred B

2013-07-01

Relatively few studies have examined multiple pathways by which risk factors from different domains are related to symptoms of anxiety and depression in young children; even fewer have assessed risks for these symptoms specifically, rather than for internalizing symptoms in general. We examined a theoretically- and empirically-based model of variables associated with these symptom types in a diverse community sample of 796 4-year-olds (391 boys, 405 girls) that included factors from the following domains: contextual (SES, stress and family conflict); parent characteristics (parental depression); parenting (support/engagement, hostility and scaffolding); and child characteristics including negative affect (NA) effortful control (EC) sensory regulation (SR), inhibitory control (IC) and attachment. We also compared the models to determine which variables contribute to a common correlates of symptoms of anxiety or depression, and which correlates differentiate between those symptom types. In the best-fitting model for these symptom types (a) SES, stress and conflict had indirect effects on both symptom types via long-chain paths; (b) caregiver depression had direct effects and indirect ones (mediated through parenting and child effortful control) on both symptom types; (c) parenting had direct and indirect effects (via temperament and SR); and temperament had direct effects on both symptom types. These data provide evidence of common risk factors, as well as indicate some specific pathways/mediators for the different symptom types. EC was related to anxiety, but not depression symptoms, suggesting that strategies to improve child EC may be particularly effective for treatment of anxiety symptoms in young children.

Construct validity of the Swedish version of the revised piper fatigue scale in an oncology sample--a Rasch analysis.

PubMed

Lundgren-Nilsson, Asa; Dencker, Anna; Jakobsson, Sofie; Taft, Charles; Tennant, Alan

2014-06-01

Fatigue is a common and distressing symptom in cancer patients due to both the disease and its treatments. The concept of fatigue is multidimensional and includes both physical and mental components. The 22-item Revised Piper Fatigue Scale (RPFS) is a multidimensional instrument developed to assess cancer-related fatigue. This study reports on the construct validity of the Swedish version of the RPFS from the perspective of Rasch measurement. The Swedish version of the RPFS was answered by 196 cancer patients fatigued after 4 to 5 weeks of curative radiation therapy. Data from the scale were fitted to the Rasch measurement model. This involved testing a series of assumptions, including the stochastic ordering of items, local response dependency, and unidimensionality. A series of fit statistics were computed, differential item functioning (DIF) was tested, and local response dependency was accommodated through testlets. The Behavioral, Affective and Sensory domains all satisfied the Rasch model expectations. No DIF was observed, and all domains were found to be unidimensional. The Mood/Cognitive scale failed to fit the model, and substantial multidimensionality was found. Splitting the scale between Mood and Cognitive items resolved fit to the Rasch model, and new domains were unidimensional without DIF. The current Rasch analyses add to the evidence of measurement properties of the scale and show that the RPFS has good psychometric properties and works well to measure fatigue. The original four-factor structure, however, was not supported. Copyright © 2014 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Toward domain-specific design environments: Some representation ideas from the telecommunications domain

NASA Technical Reports Server (NTRS)

Greenspan, Sol; Feblowitz, Mark

1992-01-01

ACME is an experimental environment for investigating new approaches to modeling and analysis of system requirements and designs. ACME is built on and extends object-oriented conceptual modeling techniques and knowledge representation and reasoning (KRR) tools. The most immediate intended use for ACME is to help represent, understand, and communicate system designs during the early stages of system planning and requirements engineering. While our research is ostensibly aimed at software systems in general, we are particularly motivated to make an impact in the telecommunications domain, especially in the area referred to as Intelligent Networks (IN's). IN systems contain the software to provide services to users of a telecommunications network (e.g., call processing services, information services, etc.) as well as the software that provides the internal infrastructure for providing the services (e.g., resource management, billing, etc.). The software includes not only systems developed by the network proprietors but also by a growing group of independent service software providers.

Assessment of nutritional status in the elderly: a proposed function-driven model

PubMed Central

Engelheart, Stina; Brummer, Robert

2018-01-01

Background There is no accepted or standardized definition of ‘malnutrition’. Hence, there is also no definition of what constitutes an adequate nutritional status. In elderly people, assessment of nutritional status is complex and is complicated by multi-morbidity and disabilities combined with nutrition-related problems, such as dysphagia, decreased appetite, fatigue, and muscle weakness. Objective We propose a nutritional status model that presents nutritional status from a comprehensive functional perspective. This model visualizes the complexity of the nutritional status in elderly people. Design and results The presented model could be interpreted as the nutritional status is conditional to a person’s optimal function or situation. Another way of looking at it might be that a person’s nutritional status affects his or her optimal situation. The proposed model includes four domains: (1) physical function and capacity; (2) health and somatic disorders; (3) food and nutrition; and (4) cognitive, affective, and sensory function. Each domain has a major impact on nutritional status, which in turn has a major impact on the outcome of each domain. Conclusions Nutritional status is a multifaceted concept and there exist several knowledge gaps in the diagnosis, prevention, and optimization of treatment of inadequate nutritional status in elderly people. The nutritional status model may be useful in nutritional assessment research, as well as in the clinical setting. PMID:29720931

Use of Model-Based Design Methods for Enhancing Resiliency Analysis of Unmanned Aerial Vehicles

NASA Astrophysics Data System (ADS)

Knox, Lenora A.

The most common traditional non-functional requirement analysis is reliability. With systems becoming more complex, networked, and adaptive to environmental uncertainties, system resiliency has recently become the non-functional requirement analysis of choice. Analysis of system resiliency has challenges; which include, defining resilience for domain areas, identifying resilience metrics, determining resilience modeling strategies, and understanding how to best integrate the concepts of risk and reliability into resiliency. Formal methods that integrate all of these concepts do not currently exist in specific domain areas. Leveraging RAMSoS, a model-based reliability analysis methodology for Systems of Systems (SoS), we propose an extension that accounts for resiliency analysis through evaluation of mission performance, risk, and cost using multi-criteria decision-making (MCDM) modeling and design trade study variability modeling evaluation techniques. This proposed methodology, coined RAMSoS-RESIL, is applied to a case study in the multi-agent unmanned aerial vehicle (UAV) domain to investigate the potential benefits of a mission architecture where functionality to complete a mission is disseminated across multiple UAVs (distributed) opposed to being contained in a single UAV (monolithic). The case study based research demonstrates proof of concept for the proposed model-based technique and provides sufficient preliminary evidence to conclude which architectural design (distributed vs. monolithic) is most resilient based on insight into mission resilience performance, risk, and cost in addition to the traditional analysis of reliability.

Modelling biochemical reaction systems by stochastic differential equations with reflection.

PubMed

Niu, Yuanling; Burrage, Kevin; Chen, Luonan

2016-05-07

In this paper, we gave a new framework for modelling and simulating biochemical reaction systems by stochastic differential equations with reflection not in a heuristic way but in a mathematical way. The model is computationally efficient compared with the discrete-state Markov chain approach, and it ensures that both analytic and numerical solutions remain in a biologically plausible region. Specifically, our model mathematically ensures that species numbers lie in the domain D, which is a physical constraint for biochemical reactions, in contrast to the previous models. The domain D is actually obtained according to the structure of the corresponding chemical Langevin equations, i.e., the boundary is inherent in the biochemical reaction system. A variant of projection method was employed to solve the reflected stochastic differential equation model, and it includes three simple steps, i.e., Euler-Maruyama method was applied to the equations first, and then check whether or not the point lies within the domain D, and if not perform an orthogonal projection. It is found that the projection onto the closure D¯ is the solution to a convex quadratic programming problem. Thus, existing methods for the convex quadratic programming problem can be employed for the orthogonal projection map. Numerical tests on several important problems in biological systems confirmed the efficiency and accuracy of this approach. Copyright © 2016 Elsevier Ltd. All rights reserved.

Measuring the Performance and Intelligence of Systems: Proceedings of the 2002 PerMIS Workshop

NASA Technical Reports Server (NTRS)

Messina, E. R.; Meystel, A. M.

2002-01-01

Contents include the following: Performance Metrics; Performance of Multiple Agents; Performance of Mobility Systems; Performance of Planning Systems; General Discussion Panel 1; Uncertainty of Representation I; Performance of Robots in Hazardous Domains; Modeling Intelligence; Modeling of Mind; Measuring Intelligence; Grouping: A Core Procedure of Intelligence; Uncertainty in Representation II; Towards Universal Planning/Control Systems.

Psychometric Properties of an Abbreviated Instrument of the Five-Factor Model

ERIC Educational Resources Information Center

Mullins-Sweatt, Stephanie N.; Jamerson, Janetta E.; Samuel, Douglas B.; Olson, David R.; Widiger, Thomas A.

2006-01-01

Brief measures of the five-factor model (FFM) have been developed but none include an assessment of facets within each domain. The purpose of this study was to examine the validity of a simple, one-page, facet-level description of the FFM. Five data collections were completed to assess the reliability and the convergent and discriminant validity…

Domain-Invariant Partial-Least-Squares Regression.

PubMed

Nikzad-Langerodi, Ramin; Zellinger, Werner; Lughofer, Edwin; Saminger-Platz, Susanne

2018-05-11

Multivariate calibration models often fail to extrapolate beyond the calibration samples because of changes associated with the instrumental response, environmental condition, or sample matrix. Most of the current methods used to adapt a source calibration model to a target domain exclusively apply to calibration transfer between similar analytical devices, while generic methods for calibration-model adaptation are largely missing. To fill this gap, we here introduce domain-invariant partial-least-squares (di-PLS) regression, which extends ordinary PLS by a domain regularizer in order to align the source and target distributions in the latent-variable space. We show that a domain-invariant weight vector can be derived in closed form, which allows the integration of (partially) labeled data from the source and target domains as well as entirely unlabeled data from the latter. We test our approach on a simulated data set where the aim is to desensitize a source calibration model to an unknown interfering agent in the target domain (i.e., unsupervised model adaptation). In addition, we demonstrate unsupervised, semisupervised, and supervised model adaptation by di-PLS on two real-world near-infrared (NIR) spectroscopic data sets.

Opposing effects of stacking faults and antisite domain boundaries on the conduction band edge in kesterite quaternary semiconductors

NASA Astrophysics Data System (ADS)

Park, Ji-Sang; Kim, Sunghyun; Walsh, Aron

2018-01-01

We investigated stability and the electronic structure of extended defects including antisite domain boundaries and stacking faults in the kesterite-structured semiconductors, Cu2ZnSnS4 (CZTS) and Cu2ZnSnSe4 (CZTSe). Our hybrid density functional theory calculations show that stacking faults in CZTS and CZTSe induce a higher conduction band edge than the bulk counterparts, and thus the stacking faults act as electron barriers. Antisite domain boundaries, however, accumulate electrons as the conduction band edge is reduced in energy, having an opposite role. An Ising model was constructed to account for the stability of stacking faults, which shows the nearest-neighbor interaction is stronger in the case of the selenide.

Numerical Investigations of Two Typical Unsteady Flows in Turbomachinery Using the Multi-Passage Model

NASA Astrophysics Data System (ADS)

Zhou, Di; Lu, Zhiliang; Guo, Tongqing; Shen, Ennan

2016-06-01

In this paper, the research on two types of unsteady flow problems in turbomachinery including blade flutter and rotor-stator interaction is made by means of numerical simulation. For the former, the energy method is often used to predict the aeroelastic stability by calculating the aerodynamic work per vibration cycle. The inter-blade phase angle (IBPA) is an important parameter in computation and may have significant effects on aeroelastic behavior. For the latter, the numbers of blades in each row are usually not equal and the unsteady rotor-stator interactions could be strong. An effective way to perform multi-row calculations is the domain scaling method (DSM). These two cases share a common point that the computational domain has to be extended to multi passages (MP) considering their respective features. The present work is aimed at modeling these two issues with the developed MP model. Computational fluid dynamics (CFD) technique is applied to resolve the unsteady Reynolds-averaged Navier-Stokes (RANS) equations and simulate the flow fields. With the parallel technique, the additional time cost due to modeling more passages can be largely decreased. Results are presented on two test cases including a vibrating rotor blade and a turbine stage.

Numerical results for near surface time domain electromagnetic exploration: a full waveform approach

NASA Astrophysics Data System (ADS)

Sun, H.; Li, K.; Li, X., Sr.; Liu, Y., Sr.; Wen, J., Sr.

2015-12-01

Time domain or Transient electromagnetic (TEM) survey including types with airborne, semi-airborne and ground play important roles in applicants such as geological surveys, ground water/aquifer assess [Meju et al., 2000; Cox et al., 2010], metal ore exploration [Yang and Oldenburg, 2012], prediction of water bearing structures in tunnels [Xue et al., 2007; Sun et al., 2012], UXO exploration [Pasion et al., 2007; Gasperikova et al., 2009] etc. The common practice is introducing a current into a transmitting (Tx) loop and acquire the induced electromagnetic field after the current is cut off [Zhdanov and Keller, 1994]. The current waveforms are different depending on instruments. Rectangle is the most widely used excitation current source especially in ground TEM. Triangle and half sine are commonly used in airborne and semi-airborne TEM investigation. In most instruments, only the off time responses are acquired and used in later analysis and data inversion. Very few airborne instruments acquire the on time and off time responses together. Although these systems acquire the on time data, they usually do not use them in the interpretation.This abstract shows a novel full waveform time domain electromagnetic method and our recent modeling results. The benefits comes from our new algorithm in modeling full waveform time domain electromagnetic problems. We introduced the current density into the Maxwell's equation as the transmitting source. This approach allows arbitrary waveforms, such as triangle, half-sine, trapezoidal waves or scatter record from equipment, being used in modeling. Here, we simulate the establishing and induced diffusion process of the electromagnetic field in the earth. The traditional time domain electromagnetic with pure secondary fields can also be extracted from our modeling results. The real time responses excited by a loop source can be calculated using the algorithm. We analyze the full time gates responses of homogeneous half space and two layered models with half sine current waveform as examples. We find the on time responses are quite sensitive to resistivity or depth changes. The results show the potential use of full waveform responses in time domain electromagnetic surveys.

Toward an embedded training tool for Deep Space Network operations

NASA Technical Reports Server (NTRS)

Hill, Randall W., Jr.; Sturdevant, Kathryn F.; Johnson, W. L.

1993-01-01

There are three issues to consider when building an embedded training system for a task domain involving the operation of complex equipment: (1) how skill is acquired in the task domain; (2) how the training system should be designed to assist in the acquisition of the skill, and more specifically, how an intelligent tutor could aid in learning; and (3) whether it is feasible to incorporate the resulting training system into the operational environment. This paper describes how these issues have been addressed in a prototype training system that was developed for operations in NASA's Deep Space Network (DSN). The first two issues were addressed by building an executable cognitive model of problem solving and skill acquisition of the task domain and then using the model to design an intelligent tutor. The cognitive model was developed in Soar for the DSN's Link Monitor and Control (LMC) system; it led to several insights about learning in the task domain that were used to design an intelligent tutor called REACT that implements a method called 'impasse-driven tutoring'. REACT is one component of the LMC training system, which also includes a communications link simulator and a graphical user interface. A pilot study of the LMC training system indicates that REACT shows promise as an effective way for helping operators to quickly acquire expert skills.

Predicting skin sensitisation using a decision tree integrated testing strategy with an in silico model and in chemico/in vitro assays.

PubMed

Macmillan, Donna S; Canipa, Steven J; Chilton, Martyn L; Williams, Richard V; Barber, Christopher G

2016-04-01

There is a pressing need for non-animal methods to predict skin sensitisation potential and a number of in chemico and in vitro assays have been designed with this in mind. However, some compounds can fall outside the applicability domain of these in chemico/in vitro assays and may not be predicted accurately. Rule-based in silico models such as Derek Nexus are expert-derived from animal and/or human data and the mechanism-based alert domain can take a number of factors into account (e.g. abiotic/biotic activation). Therefore, Derek Nexus may be able to predict for compounds outside the applicability domain of in chemico/in vitro assays. To this end, an integrated testing strategy (ITS) decision tree using Derek Nexus and a maximum of two assays (from DPRA, KeratinoSens, LuSens, h-CLAT and U-SENS) was developed. Generally, the decision tree improved upon other ITS evaluated in this study with positive and negative predictivity calculated as 86% and 81%, respectively. Our results demonstrate that an ITS using an in silico model such as Derek Nexus with a maximum of two in chemico/in vitro assays can predict the sensitising potential of a number of chemicals, including those outside the applicability domain of existing non-animal assays. Copyright © 2016 Elsevier Inc. All rights reserved.

Flight-testing and frequency-domain analysis for rotorcraft handling qualities

NASA Technical Reports Server (NTRS)

Ham, Johnnie A.; Gardner, Charles K.; Tischler, Mark B.

1995-01-01

A demonstration of frequency-domain flight-testing techniques and analysis was performed on a U.S. Army OH-58D helicopter in support of the OH-58D Airworthiness and Flight Characteristics Evaluation and of the Army's development and ongoing review of Aeronautical Design Standard 33C, Handling Qualities Requirements for Military Rotorcraft. Hover and forward flight (60 kn) tests were conducted in 1 flight hour by Army experimental test pilots. Further processing of the hover data generated a complete database of velocity, angular-rate, and acceleration-frequency responses to control inputs. A joint effort was then undertaken by the Airworthiness Qualification Test Dirtectorate and the U.S. Army Aeroflightdynamics Directorate to derive handling-quality information from the frequency-domain database using a variety of approaches. This report documents numerous results that have been obtained from the simple frequency-domain tests; in many areas, these results provide more insight into the aircraft dynmamics that affect handling qualities than do traditional flight tests. The handling-quality results include ADS-33C bandwidth and phase-delay calculations, vibration spectral determinations, transfer-function models to examine single-axis results, and a six-degree-of-freedom fully coupled state-space model. The ability of this model to accurately predict responses was verified using data from pulse inputs. This report also documents the frequency-sweep flight-test technique and data analysis used to support the tests.

Archaeal “Dark Matter” and the Origin of Eukaryotes

PubMed Central

Williams, Tom A.; Embley, T. Martin

2014-01-01

Current hypotheses about the history of cellular life are mainly based on analyses of cultivated organisms, but these represent only a small fraction of extant biodiversity. The sequencing of new environmental lineages therefore provides an opportunity to test, revise, or reject existing ideas about the tree of life and the origin of eukaryotes. According to the textbook three domains hypothesis, the eukaryotes emerge as the sister group to a monophyletic Archaea. However, recent analyses incorporating better phylogenetic models and an improved sampling of the archaeal domain have generally supported the competing eocyte hypothesis, in which core genes of eukaryotic cells originated from within the Archaea, with important implications for eukaryogenesis. Given this trend, it was surprising that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree. Here, we show that this result was due in part to the use of a poorly fitting phylogenetic model and also to the inclusion by an automated pipeline of genes of putative bacterial origin rather than nucleocytosolic versions for some of the eukaryotes analyzed. When these issues were resolved, analyses including the new archaeal lineages placed core eukaryotic genes within the Archaea. These results are consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis. PMID:24532674

Archaeal "dark matter" and the origin of eukaryotes.

PubMed

Williams, Tom A; Embley, T Martin

2014-03-01

Current hypotheses about the history of cellular life are mainly based on analyses of cultivated organisms, but these represent only a small fraction of extant biodiversity. The sequencing of new environmental lineages therefore provides an opportunity to test, revise, or reject existing ideas about the tree of life and the origin of eukaryotes. According to the textbook three domains hypothesis, the eukaryotes emerge as the sister group to a monophyletic Archaea. However, recent analyses incorporating better phylogenetic models and an improved sampling of the archaeal domain have generally supported the competing eocyte hypothesis, in which core genes of eukaryotic cells originated from within the Archaea, with important implications for eukaryogenesis. Given this trend, it was surprising that a recent analysis incorporating new genomes from uncultivated Archaea recovered a strongly supported three domains tree. Here, we show that this result was due in part to the use of a poorly fitting phylogenetic model and also to the inclusion by an automated pipeline of genes of putative bacterial origin rather than nucleocytosolic versions for some of the eukaryotes analyzed. When these issues were resolved, analyses including the new archaeal lineages placed core eukaryotic genes within the Archaea. These results are consistent with a number of recent studies in which improved archaeal sampling and better phylogenetic models agree in supporting the eocyte tree over the three domains hypothesis.

Rating knowledge sharing in cross-domain collaborative filtering.

PubMed

Li, Bin; Zhu, Xingquan; Li, Ruijiang; Zhang, Chengqi

2015-05-01

Cross-domain collaborative filtering (CF) aims to share common rating knowledge across multiple related CF domains to boost the CF performance. In this paper, we view CF domains as a 2-D site-time coordinate system, on which multiple related domains, such as similar recommender sites or successive time-slices, can share group-level rating patterns. We propose a unified framework for cross-domain CF over the site-time coordinate system by sharing group-level rating patterns and imposing user/item dependence across domains. A generative model, say ratings over site-time (ROST), which can generate and predict ratings for multiple related CF domains, is developed as the basic model for the framework. We further introduce cross-domain user/item dependence into ROST and extend it to two real-world cross-domain CF scenarios: 1) ROST (sites) for alleviating rating sparsity in the target domain, where multiple similar sites are viewed as related CF domains and some items in the target domain depend on their correspondences in the related ones; and 2) ROST (time) for modeling user-interest drift over time, where a series of time-slices are viewed as related CF domains and a user at current time-slice depends on herself in the previous time-slice. All these ROST models are instances of the proposed unified framework. The experimental results show that ROST (sites) can effectively alleviate the sparsity problem to improve rating prediction performance and ROST (time) can clearly track and visualize user-interest drift over time.

Coercivity of die upset NdFeB magnets: A strong pinning model

NASA Astrophysics Data System (ADS)

Pinkerton, F. E.; Fuerst, C. D.

1990-09-01

We show that the temperature dependence of the intrinsic coercivity Hci( T) between 5 and 600 K in a die-upset NdFeB magnet is in good agreement with a model for strong domain wall pinning by a random array of pinning sites proposed by Gaunt [P. Gaunt, Phil. Mag. B48 (1983) 261]. The model includes both the temperature dependence of the intrinsic magnetic properties of the Nd 2Fe 14B phase and the effects of thermal activation of domain walls over the pinning barrier. The pinning sites are modeled as nonmagnetic planar inhomogeneities at the boundaries aetween platelet-shaped Nd 2Fe 14B grains. We develop an expression for the maximum pinning force per site, f, and derive the model prediction that (H ci/γH A) {1}/{2} varies linearly with (T/γ) {2}/{3}, where HA and γ are the magnetocrystalline anisotropy and the domain wall energy per unit area of the Nd 2Fe 14B phase, respectively. The model is in good agreement with the observed Hci values over a broad temperature range from 200 to 477 K. Deviations from the model below 200 K are an artifact of the axial-to-conical spin reorientation in Nd 2Fe 14B at low temperature. Deviations at high temperature most likely occur because the strong pinning model is no longer valid close to the Curie temperature (585 K).

Dopant profile modeling by rare event enhanced domain-following molecular dynamics

DOEpatents

Beardmore, Keith M.; Jensen, Niels G.

2002-01-01

A computer-implemented molecular dynamics-based process simulates a distribution of ions implanted in a semiconductor substrate. The properties of the semiconductor substrate and ion dose to be simulated are first initialized, including an initial set of splitting depths that contain an equal number of virtual ions implanted in each substrate volume determined by the splitting depths. A first ion with selected velocity is input onto an impact position of the substrate that defines a first domain for the first ion during a first timestep, where the first domain includes only those atoms of the substrate that exert a force on the ion. A first position and velocity of the first ion is determined after the first timestep and a second domain of the first ion is formed at the first position. The first ion is split into first and second virtual ions if the first ion has passed through a splitting interval. The process then follows each virtual ion until all of the virtual ions have come to rest. A new ion is input to the surface and the process repeats until all of the ion dose has been input. The resulting ion rest positions form the simulated implant distribution.

Merging Applicability Domains for in Silico Assessment of Chemical Mutagenicity

DTIC Science & Technology

2014-02-04

molecular fingerprints as descriptors for developing quantitative structure−activity relationship ( QSAR ) models and defining applicability domains with...used to define and quantify an applicability domain for either method. The importance of using applicability domains in QSAR modeling cannot be...domain from roughly 80% to 90%. These results indicated that the proposed QSAR protocol constituted a highly robust chemical mutagenicity prediction

SutraGUI, a graphical-user interface for SUTRA, a model for ground-water flow with solute or energy transport

USGS Publications Warehouse

Winston, Richard B.; Voss, Clifford I.

2004-01-01

This report describes SutraGUI, a flexible graphical user-interface (GUI) that supports two-dimensional (2D) and three-dimensional (3D) simulation with the U.S. Geological Survey (USGS) SUTRA ground-water-flow and transport model (Voss and Provost, 2002). SutraGUI allows the user to create SUTRA ground-water models graphically. SutraGUI provides all of the graphical functionality required for setting up and running SUTRA simulations that range from basic to sophisticated, but it is also possible for advanced users to apply programmable features within Argus ONE to meet the unique demands of particular ground-water modeling projects. SutraGUI is a public-domain computer program designed to run with the proprietary Argus ONE? package, which provides 2D Geographic Information System (GIS) and meshing support. For 3D simulation, GIS and meshing support is provided by programming contained within SutraGUI. When preparing a 3D SUTRA model, the model and all of its features are viewed within Argus 1 in 2D projection. For 2D models, SutraGUI is only slightly changed in functionality from the previous 2D-only version (Voss and others, 1997) and it provides visualization of simulation results. In 3D, only model preparation is supported by SutraGUI, and 3D simulation results may be viewed in SutraPlot (Souza, 1999) or Model Viewer (Hsieh and Winston, 2002). A comprehensive online Help system is included in SutraGUI. For 3D SUTRA models, the 3D model domain is conceptualized as bounded on the top and bottom by 2D surfaces. The 3D domain may also contain internal surfaces extending across the model that divide the domain into tabular units, which can represent hydrogeologic strata or other features intended by the user. These surfaces can be non-planar and non-horizontal. The 3D mesh is defined by one or more 2D meshes at different elevations that coincide with these surfaces. If the nodes in the 3D mesh are vertically aligned, only a single 2D mesh is needed. For nonaligned meshes, two or more 2D meshes of similar connectivity are used. Between each set of 2D meshes (and model surfaces), the vertical space in the 3D mesh is evenly divided into a user-specified number of layers of finite elements. Boundary conditions may be specified for 3D models in SutraGUI using a variety of geometric shapes that may be located freely within the 3D model domain. These shapes include points, lines, sheets, and solids. These are represented by 2D contours (within the vertically-projected Argus ONE view) with user-defined elevations. In addition, boundary conditions may be specified for 3D models as points, lines, and areas that are located exactly within the surfaces that define the model top and the bottoms of the tabular units. Aquifer properties may be specified separately for each tabular unit. If the aquifer properties vary vertically within a unit, SutraGUI provides the Sutra_Z function that can be used to specify such variation.

Clinic expert information extraction based on domain model and block importance model.

PubMed

Zhang, Yuanpeng; Wang, Li; Qian, Danmin; Geng, Xingyun; Yao, Dengfu; Dong, Jiancheng

2015-11-01

To extract expert clinic information from the Deep Web, there are two challenges to face. The first one is to make a judgment on forms. A novel method based on a domain model, which is a tree structure constructed by the attributes of query interfaces is proposed. With this model, query interfaces can be classified to a domain and filled in with domain keywords. Another challenge is to extract information from response Web pages indexed by query interfaces. To filter the noisy information on a Web page, a block importance model is proposed, both content and spatial features are taken into account in this model. The experimental results indicate that the domain model yields a precision 4.89% higher than that of the rule-based method, whereas the block importance model yields an F1 measure 10.5% higher than that of the XPath method. Copyright © 2015 Elsevier Ltd. All rights reserved.

Large-Signal Lyapunov-Based Stability Analysis of DC/AC Inverters and Inverter-Based Microgrids

NASA Astrophysics Data System (ADS)

Kabalan, Mahmoud

Microgrid stability studies have been largely based on small-signal linearization techniques. However, the validity and magnitude of the linearization domain is limited to small perturbations. Thus, there is a need to examine microgrids with large-signal nonlinear techniques to fully understand and examine their stability. Large-signal stability analysis can be accomplished by Lyapunov-based mathematical methods. These Lyapunov methods estimate the domain of asymptotic stability of the studied system. A survey of Lyapunov-based large-signal stability studies showed that few large-signal studies have been completed on either individual systems (dc/ac inverters, dc/dc rectifiers, etc.) or microgrids. The research presented in this thesis addresses the large-signal stability of droop-controlled dc/ac inverters and inverter-based microgrids. Dc/ac power electronic inverters allow microgrids to be technically feasible. Thus, as a prelude to examining the stability of microgrids, the research presented in Chapter 3 analyzes the stability of inverters. First, the 13 th order large-signal nonlinear model of a droop-controlled dc/ac inverter connected to an infinite bus is presented. The singular perturbation method is used to decompose the nonlinear model into 11th, 9th, 7th, 5th, 3rd and 1st order models. Each model ignores certain control or structural components of the full order model. The aim of the study is to understand the accuracy and validity of the reduced order models in replicating the performance of the full order nonlinear model. The performance of each model is studied in three different areas: time domain simulations, Lyapunov's indirect method and domain of attraction estimation. The work aims to present the best model to use in each of the three domains of study. Results show that certain reduced order models are capable of accurately reproducing the performance of the full order model while others can be used to gain insights into those three areas of study. This will enable future studies to save computational effort and produce the most accurate results according to the needs of the study being performed. Moreover, the effect of grid (line) impedance on the accuracy of droop control is explored using the 5th order model. Simulation results show that traditional droop control is valid up to R/X line impedance value of 2. Furthermore, the 3rd order nonlinear model improves the currently available inverter-infinite bus models by accounting for grid impedance, active power-frequency droop and reactive power-voltage droop. Results show the 3rd order model's ability to account for voltage and reactive power changes during a transient event. Finally, the large-signal Lyapunov-based stability analysis is completed for a 3 bus microgrid system (made up of 2 inverters and 1 linear load). The thesis provides a systematic state space large-signal nonlinear mathematical modeling method of inverter-based microgrids. The inverters include the dc-side dynamics associated with dc sources. The mathematical model is then used to estimate the domain of asymptotic stability of the 3 bus microgrid. The three bus microgrid system was used as a case study to highlight the design and optimization capability of a large-signal-based approach. The study explores the effect of system component sizing, load transient and generation variations on the asymptotic stability of the microgrid. Essentially, this advancement gives microgrid designers and engineers the ability to manipulate the domain of asymptotic stability depending on performance requirements. Especially important, this research was able to couple the domain of asymptotic stability of the ac microgrid with that of the dc side voltage source. Time domain simulations were used to demonstrate the mathematical nonlinear analysis results.

Learning Qualitative Differential Equation models: a survey of algorithms and applications.

PubMed

Pang, Wei; Coghill, George M

2010-03-01

Over the last two decades, qualitative reasoning (QR) has become an important domain in Artificial Intelligence. QDE (Qualitative Differential Equation) model learning (QML), as a branch of QR, has also received an increasing amount of attention; many systems have been proposed to solve various significant problems in this field. QML has been applied to a wide range of fields, including physics, biology and medical science. In this paper, we first identify the scope of this review by distinguishing QML from other QML systems, and then review all the noteworthy QML systems within this scope. The applications of QML in several application domains are also introduced briefly. Finally, the future directions of QML are explored from different perspectives.

Learning Qualitative Differential Equation models: a survey of algorithms and applications

PubMed Central

PANG, WEI; COGHILL, GEORGE M.

2013-01-01

Over the last two decades, qualitative reasoning (QR) has become an important domain in Artificial Intelligence. QDE (Qualitative Differential Equation) model learning (QML), as a branch of QR, has also received an increasing amount of attention; many systems have been proposed to solve various significant problems in this field. QML has been applied to a wide range of fields, including physics, biology and medical science. In this paper, we first identify the scope of this review by distinguishing QML from other QML systems, and then review all the noteworthy QML systems within this scope. The applications of QML in several application domains are also introduced briefly. Finally, the future directions of QML are explored from different perspectives. PMID:23704803

Theoretical Insights Reveal Novel Motions in Csk’s SH3 Domain That Control Kinase Activation

PubMed Central

Barkho, Sulyman; Pierce, Levi C. T.; Li, Sheng; Adams, Joseph A.; Jennings, Patricia A.

2015-01-01

The Src family of tyrosine kinases (SFKs) regulate numerous aspects of cell growth and differentiation and are under the principal control of the C-terminal Src Kinase (Csk). Although Csk and SFKs share conserved kinase, SH2 and SH3 domains, they differ considerably in three-dimensional structure, regulatory mechanism, and the intrinsic kinase activities. Although the SH2 and SH3 domains are known to up- or down-regulate tyrosine kinase function, little is known about the global motions in the full-length kinase that govern these catalytic variations. We use a combination of accelerated Molecular Dynamics (aMD) simulations and experimental methods to provide a new view of functional motions in the Csk scaffold. These computational studies suggest that high frequency vibrations in the SH2 domain are coupled through the N-terminal lobe of the kinase domain to motions in the SH3 domain. The effects of these reflexive movements on the kinase domain can be viewed using both Deuterium Exchange Mass Spectrometry (DXMS) and steady-state kinetic methods. Removal of several contacts, including a crystallographically unobserved N-terminal segment, between the SH3 and kinase domains short-circuit these coupled motions leading to reduced catalytic efficiency and stability of N-lobe motifs within the kinase domain. The data expands the model of Csk’s activation whereby separate domains productively interact with two diametrically opposed surfaces of the kinase domain. Such reversible transitions may organize the active structure of the tyrosine kinase domain of Csk. PMID:26030592

Calpain chronicle--an enzyme family under multidisciplinary characterization.

PubMed

Sorimachi, Hiroyuki; Hata, Shoji; Ono, Yasuko

2011-01-01

Calpain is an intracellular Ca2+-dependent cysteine protease (EC 3.4.22.17; Clan CA, family C02) discovered in 1964. It was also called CANP (Ca2+-activated neutral protease) as well as CASF, CDP, KAF, etc. until 1990. Calpains are found in almost all eukaryotes and a few bacteria, but not in archaebacteria. Calpains have a limited proteolytic activity, and function to transform or modulate their substrates' structures and activities; they are therefore called, "modulator proteases." In the human genome, 15 genes--CAPN1, CAPN2, etc.--encode a calpain-like protease domain. Their products are calpain homologs with divergent structures and various combinations of functional domains, including Ca2+-binding and microtubule-interaction domains. Genetic studies have linked calpain deficiencies to a variety of defects in many different organisms, including lethality, muscular dystrophies, gastropathy, and diabetes. This review of the study of calpains focuses especially on recent findings about their structure-function relationships. These discoveries have been greatly aided by the development of 3D structural studies and genetic models.

XFEL OSCILLATOR SIMULATION INCLUDING ANGLE-DEPENDENT CRYSTAL REFLECTIVITY

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

Fawley, William; Lindberg, Ryan; Kim, K-J

The oscillator package within the GINGER FEL simulation code has now been extended to include angle-dependent reflectivity properties of Bragg crystals. Previously, the package was modified to include frequencydependent reflectivity in order to model x-ray FEL oscillators from start-up from shot noise through to saturation. We present a summary of the algorithms used for modeling the crystal reflectivity and radiation propagation outside the undulator, discussing various numerical issues relevant to the domain of high Fresnel number and efficient Hankel transforms. We give some sample XFEL-O simulation results obtained with the angle-dependent reflectivity model, with particular attention directed to the longitudinalmore » and transverse coherence of the radiation output.« less

A Relational Metric, Its Application to Domain Analysis, and an Example Analysis and Model of a Remote Sensing Domain

DOT National Transportation Integrated Search

1995-07-01

An objective and quantitative method has been developed for deriving models of complex and specialized spheres of activity (domains) from domain-generated verbal data. The method was developed for analysis of interview transcripts, incident reports, ...

A Hierarchy of Management Training Requirements: The Competency Domain Model.

ERIC Educational Resources Information Center

Sandwith, Paul

1993-01-01

The Competency Domain Model has five domains of management competencies: conceptual/creative, leadership, interpersonal, administrative, and technical. Specific competencies and training plans can be identified in each domain for different levels--first line supervisor, field office manager, assistant manager, area manager, director of operations.…

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

DOE PAGES

Huang, Qiuhua; Vittal, Vijay

2018-05-09

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Advanced EMT and Phasor-Domain Hybrid Simulation with Simulation Mode Switching Capability for Transmission and Distribution Systems

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

Huang, Qiuhua; Vittal, Vijay

Conventional electromagnetic transient (EMT) and phasor-domain hybrid simulation approaches presently exist for trans-mission system level studies. Their simulation efficiency is generally constrained by the EMT simulation. With an increasing number of distributed energy resources and non-conventional loads being installed in distribution systems, it is imperative to extend the hybrid simulation application to include distribution systems and integrated transmission and distribution systems. Meanwhile, it is equally important to improve the simulation efficiency as the modeling scope and complexity of the detailed system in the EMT simulation increases. To meet both requirements, this paper introduces an advanced EMT and phasor-domain hybrid simulationmore » approach. This approach has two main features: 1) a comprehensive phasor-domain modeling framework which supports positive-sequence, three-sequence, three-phase and mixed three-sequence/three-phase representations and 2) a robust and flexible simulation mode switching scheme. The developed scheme enables simulation switching from hybrid simulation mode back to pure phasor-domain dynamic simulation mode to achieve significantly improved simulation efficiency. The proposed method has been tested on integrated transmission and distribution systems. In conclusion, the results show that with the developed simulation switching feature, the total computational time is significantly reduced compared to running the hybrid simulation for the whole simulation period, while maintaining good simulation accuracy.« less

Interactions between lipids and proteins are critical for organization of plasma membrane-ordered domains in tobacco BY-2 cells.

PubMed

Grosjean, Kevin; Der, Christophe; Robert, Franck; Thomas, Dominique; Mongrand, Sébastien; Simon-Plas, Françoise; Gerbeau-Pissot, Patricia

2018-06-27

The laterally heterogeneous plant plasma membrane (PM) is organized into finely controlled specialized areas that include membrane-ordered domains. Recently, the spatial distribution of such domains within the PM has been identified as playing a key role in cell responses to environmental challenges. To examine membrane order at a local level, BY-2 tobacco suspension cell PMs were labelled with an environment-sensitive probe (di-4-ANEPPDHQ). Four experimental models were compared to identify mechanisms and cell components involved in short-term (1 h) maintenance of the ordered domain organization in steady-state cell PMs: modulation of the cytoskeleton or the cell wall integrity of tobacco BY-2 cells; and formation of giant vesicles using either a lipid mixture of tobacco BY-2 cell PMs or the original lipid and protein combinations of the tobacco BY-2 cell PM. Whilst inhibiting phosphorylation or disrupting either the cytoskeleton or the cell wall had no observable effects, we found that lipids and proteins significantly modified both the abundance and spatial distribution of ordered domains. This indicates the involvement of intrinsic membrane components in the local physical state of the plant PM. Our findings support a major role for the 'lipid raft' model, defined as the sterol-dependent ordered assemblies of specific lipids and proteins in plant PM organization.

Modeling relationships between various domains of hearing aid provision.

PubMed

Meister, Hartmut; Lausberg, Isabel; Kiessling, Jürgen; von Wedel, Hasso; Walger, Martin

2003-01-01

Various inventories have been developed to quantify the success of hearing aid provision. Though numerous parameters including initial measures (hearing disability, handicap) or 'outcome measures' (e.g. benefit, satisfaction and usage) are recorded, relationships and interactions among them are still unclear. A study applying a questionnaire addressing 11 domains relevant to amplification was conducted in order to generate different psychometric models with the AMOS software package for structural equation modeling. The models expose easily interpretable interactions and are helpful in understanding effects occurring with commonly used outcome measures: benefit reflects the difference between the aided and unaided condition but additionally comprises the importance of the hearing aid within a specific situation. Satisfaction is highly reliant on benefit. Usage is strongly dependent on the severity of hearing problems and therefore not appropriate in assessing the success of amplification. Moreover, the models help to predict the outcome of clinically used inventories (i.e. the Glasgow Hearing Aid Benefit Profile). Copyright 2003 S. Karger AG, Basel

Machine learning models for lipophilicity and their domain of applicability.

PubMed

Schroeter, Timon; Schwaighofer, Anton; Mika, Sebastian; Laak, Antonius Ter; Suelzle, Detlev; Ganzer, Ursula; Heinrich, Nikolaus; Müller, Klaus-Robert

2007-01-01

Unfavorable lipophilicity and water solubility cause many drug failures; therefore these properties have to be taken into account early on in lead discovery. Commercial tools for predicting lipophilicity usually have been trained on small and neutral molecules, and are thus often unable to accurately predict in-house data. Using a modern Bayesian machine learning algorithm--a Gaussian process model--this study constructs a log D7 model based on 14,556 drug discovery compounds of Bayer Schering Pharma. Performance is compared with support vector machines, decision trees, ridge regression, and four commercial tools. In a blind test on 7013 new measurements from the last months (including compounds from new projects) 81% were predicted correctly within 1 log unit, compared to only 44% achieved by commercial software. Additional evaluations using public data are presented. We consider error bars for each method (model based error bars, ensemble based, and distance based approaches), and investigate how well they quantify the domain of applicability of each model.

A deep convolutional neural network with new training methods for bearing fault diagnosis under noisy environment and different working load

NASA Astrophysics Data System (ADS)

Zhang, Wei; Li, Chuanhao; Peng, Gaoliang; Chen, Yuanhang; Zhang, Zhujun

2018-02-01

In recent years, intelligent fault diagnosis algorithms using machine learning technique have achieved much success. However, due to the fact that in real world industrial applications, the working load is changing all the time and noise from the working environment is inevitable, degradation of the performance of intelligent fault diagnosis methods is very serious. In this paper, a new model based on deep learning is proposed to address the problem. Our contributions of include: First, we proposed an end-to-end method that takes raw temporal signals as inputs and thus doesn't need any time consuming denoising preprocessing. The model can achieve pretty high accuracy under noisy environment. Second, the model does not rely on any domain adaptation algorithm or require information of the target domain. It can achieve high accuracy when working load is changed. To understand the proposed model, we will visualize the learned features, and try to analyze the reasons behind the high performance of the model.

Agricultural Model for the Nile Basin Decision Support System

NASA Astrophysics Data System (ADS)

van der Bolt, Frank; Seid, Abdulkarim

2014-05-01

To analyze options for increasing food supply in the Nile basin the Nile Agricultural Model (AM) was developed. The AM includes state-of-the-art descriptions of biophysical, hydrological and economic processes and realizes a coherent and consistent integration of hydrology, agronomy and economics. The AM covers both the agro-ecological domain (water, crop productivity) and the economic domain (food supply, demand, and trade) and allows to evaluate the macro-economic and hydrological impacts of scenarios for agricultural development. Starting with the hydrological information from the NileBasin-DSS the AM calculates the available water for agriculture, the crop production and irrigation requirements with the FAO-model AquaCrop. With the global commodity trade model MAGNET scenarios for land development and conversion are evaluated. The AM predicts consequences for trade, food security and development based on soil and water availability, crop allocation, food demand and food policy. The model will be used as a decision support tool to contribute to more productive and sustainable agriculture in individual Nile countries and the whole region.

Evaluation of a computerized aid for creating human behavioral representations of human-computer interaction.

PubMed

Williams, Kent E; Voigt, Jeffrey R

2004-01-01

The research reported herein presents the results of an empirical evaluation that focused on the accuracy and reliability of cognitive models created using a computerized tool: the cognitive analysis tool for human-computer interaction (CAT-HCI). A sample of participants, expert in interacting with a newly developed tactical display for the U.S. Army's Bradley Fighting Vehicle, individually modeled their knowledge of 4 specific tasks employing the CAT-HCI tool. Measures of the accuracy and consistency of task models created by these task domain experts using the tool were compared with task models created by a double expert. The findings indicated a high degree of consistency and accuracy between the different "single experts" in the task domain in terms of the resultant models generated using the tool. Actual or potential applications of this research include assessing human-computer interaction complexity, determining the productivity of human-computer interfaces, and analyzing an interface design to determine whether methods can be automated.

Geostrophic Turbulence in the Frequency-Wavenumber Domain: Eddy-Driven Low-Frequency Variability

DTIC Science & Technology

2014-01-01

in ASFMRS. Previous studies of oceanic frequency– wavenumber spectra include Wunsch and Stammer (1995), Chelton and Schlax (1996), Farrar (2008...ASFMRS. However, the realistic eddying ocean model utilized here is the Hy- brid Coordinate Ocean Model (HYCOM; Chassignet et al. 2007 ), in place of...the Naval Research Laboratory (NRL) Layered Ocean Model (NLOM; Hurlburt and AUGUST 2014 ARB I C ET AL . 2051 Thompson 1980; Shriver et al. 2007 ) used

Evolution of GHF5 endoglucanase gene structure in plant-parasitic nematodes: no evidence for an early domain shuffling event.

PubMed

Kyndt, Tina; Haegeman, Annelies; Gheysen, Godelieve

2008-11-03

Endo-1,4-beta-glucanases or cellulases from the glycosyl hydrolase family 5 (GHF5) have been found in numerous bacteria and fungi, and recently also in higher eukaryotes, particularly in plant-parasitic nematodes (PPN). The origin of these genes has been attributed to horizontal gene transfer from bacteria, although there still is a lot of uncertainty about the origin and structure of the ancestral GHF5 PPN endoglucanase. It is not clear whether this ancestral endoglucanase consisted of the whole gene cassette, containing a catalytic domain and a carbohydrate-binding module (CBM, type 2 in PPN and bacteria) or only of the catalytic domain while the CBM2 was retrieved by domain shuffling later in evolution. Previous studies on the evolution of these genes have focused primarily on data of sedentary nematodes, while in this study, extra data from migratory nematodes were included. Two new endoglucanases from the migratory nematodes Pratylenchus coffeae and Ditylenchus africanus were included in this study. The latter one is the first gene isolated from a PPN of a different superfamily (Sphaerularioidea); all previously known nematode endoglucanases belong to the superfamily Tylenchoidea (order Rhabditida). Phylogenetic analyses were conducted with the PPN GHF5 endoglucanases and homologous endoglucanases from bacterial and other eukaryotic lineages such as beetles, fungi and plants. No statistical incongruence between the phylogenetic trees deduced from the catalytic domain and the CBM2 was found, which could suggest that both domains have evolved together. Furthermore, based on gene structure data, we inferred a model for the evolution of the GHF5 endoglucanase gene structure in plant-parasitic nematodes. Our data confirm a close relationship between Pratylenchus spp. and the root knot nematodes, while some Radopholus similis endoglucanases are more similar to cyst nematode genes. We conclude that the ancestral PPN GHF5 endoglucanase gene most probably consisted of the whole gene cassette, i.e. the GHF5 catalytic domain and the CBM2, rather than that it evolved by domain shuffling. Our evolutionary model for the gene structure in PPN GHF5 endoglucanases implies the occurrence of an early duplication event, and more recent gene duplications at genus or species level.

Phase-field model of domain structures in ferroelectric thin films

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

Li, Y. L.; Hu, S. Y.; Liu, Z. K.

A phase-field model for predicting the coherent microstructure evolution in constrained thin films is developed. It employs an analytical elastic solution derived for a constrained film with arbitrary eigenstrain distributions. The domain structure evolution during a cubic{r_arrow}tetragonal proper ferroelectric phase transition is studied. It is shown that the model is able to simultaneously predict the effects of substrate constraint and temperature on the volume fractions of domain variants, domain-wall orientations, domain shapes, and their temporal evolution. {copyright} 2001 American Institute of Physics.

The International development of PROQOL-HCV: An instrument to assess the health-related quality of life of patients treated for Hepatitis C virus.

PubMed

Armstrong, Andrew Richard; Herrmann, Susan Elizabeth; Chassany, Olivier; Lalanne, Christophe; Da Silva, Mariliza Henrique; Galano, Eliana; Carrieri, Patrizia M; Estellon, Vincent; Sogni, Philippe; Duracinsky, Martin

2016-08-23

Hepatitis C virus (HCV) compromises Health-related Quality of Life (HRQL) with detriments to Physical, Mental and Social health domains. Treatment with interferon and ribavirin is associated with side effects which further impair HRQL. New treatments appear potent, effective and tolerable. However, Patient Reported Outcomes instruments that capture the impact on HRQL for people with hepatitis C are largely non-specific and will be needed in the new treatment era. Therefore, we developed a conceptually valid multidimensional model of HCV-specific quality of life and pilot survey instrument, the Patient Reported Outcome Quality of Life survey for HCV (PROQOL-HCV). HCV patients from France (n = 30), Brazil (n = 20) and Australia (n = 20) were interviewed to investigate HCV-HRQL issues raised in the scientific literature and by treatment specialists. Interviews were recorded, transcribed and translated into English and French. Fifteen content dimensions were derived from the qualitative analysis, refined and fitted to four domains: (1) Physical Health included: fatigue, pain, sleep, sexual impairment and physical activity; (2) Mental Health: psychological distress, psychosocial impact, and cognition; (3) Social Health: support, stigma, social activity, substance use; (4) TREATMENT: management, side effects, and fear of treatment failure. The impact of some dimensions extended beyond their primary domain including: physical activity, cognition, sleep, sexual impairment, and the three treatment dimensions. A bank of 300 items was constructed to reflect patient reports and, following expert review, reduced to a 72-item pilot questionnaire. We present a conceptually valid multidimensional model of HCV-specific quality of life and the pilot survey instrument, PROQOL-HCV. The model is widely inclusive of the experience of hepatitis C and the first to include the treatment dimension.

A strand graph semantics for DNA-based computation

PubMed Central

Petersen, Rasmus L.; Lakin, Matthew R.; Phillips, Andrew

2015-01-01

DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure. PMID:27293306

PDS4 - Some Principles for Agile Data Curation

NASA Astrophysics Data System (ADS)

Hughes, J. S.; Crichton, D. J.; Hardman, S. H.; Joyner, R.; Algermissen, S.; Padams, J.

2015-12-01

PDS4, a research data management and curation system for NASA's Planetary Science Archive, was developed using principles that promote the characteristics of agile development. The result is an efficient system that produces better research data products while using less resources (time, effort, and money) and maximizes their usefulness for current and future scientists. The key principle is architectural. The PDS4 information architecture is developed and maintained independent of the infrastructure's process, application and technology architectures. The information architecture is based on an ontology-based information model developed to leverage best practices from standard reference models for digital archives, digital object registries, and metadata registries and capture domain knowledge from a panel of planetary science domain experts. The information model provides a sharable, stable, and formal set of information requirements for the system and is the primary source for information to configure most system components, including the product registry, search engine, validation and display tools, and production pipelines. Multi-level governance is also allowed for the effective management of the informational elements at the common, discipline, and project level. This presentation will describe the development principles, components, and uses of the information model and how an information model-driven architecture exhibits characteristics of agile curation including early delivery, evolutionary development, adaptive planning, continuous improvement, and rapid and flexible response to change.

Determination of the transmission coefficients for quantum structures using FDTD method.

PubMed

Peng, Yangyang; Wang, Xiaoying; Sui, Wenquan

2011-12-01

The purpose of this work is to develop a simple method to incorporate quantum effect in traditional finite-difference time-domain (FDTD) simulators. Witch could make it possible to co-simulate systems include quantum structures and traditional components. In this paper, tunneling transmission coefficient is calculated by solving time-domain Schrödinger equation with a developed FDTD technique, called FDTD-S method. To validate the feasibility of the method, a simple resonant tunneling diode (RTD) structure model has been simulated using the proposed method. The good agreement between the numerical and analytical results proves its accuracy. The effectness and accuracy of this approach makes it a potential method for analysis and design of hybrid systems includes quantum structures and traditional components.

Functional specialization in nucleotide sugar transporters occurred through differentiation of the gene cluster EamA (DUF6) before the radiation of Viridiplantae

PubMed Central

2011-01-01

Background The drug/metabolite transporter superfamily comprises a diversity of protein domain families with multiple functions including transport of nucleotide sugars. Drug/metabolite transporter domains are contained in both solute carrier families 30, 35 and 39 proteins as well as in acyl-malonyl condensing enzyme proteins. In this paper, we present an evolutionary analysis of nucleotide sugar transporters in relation to the entire superfamily of drug/metabolite transporters that considers crucial intra-protein duplication events that have shaped the transporters. We use a method that combines the strengths of hidden Markov models and maximum likelihood to find relationships between drug/metabolite transporter families, and branches within families. Results We present evidence that the triose-phosphate transporters, domain unknown function 914, uracil-diphosphate glucose-N-acetylglucosamine, and nucleotide sugar transporter families have evolved from a domain duplication event before the radiation of Viridiplantae in the EamA family (previously called domain unknown function 6). We identify previously unknown branches in the solute carrier 30, 35 and 39 protein families that emerged simultaneously as key physiological developments after the radiation of Viridiplantae, including the "35C/E" branch of EamA, which formed in the lineage of T. adhaerens (Animalia). We identify a second cluster of DMTs, called the domain unknown function 1632 cluster, which has non-cytosolic N- and C-termini, and thus appears to have been formed from a different domain duplication event. We identify a previously uncharacterized motif, G-X(6)-G, which is overrepresented in the fifth transmembrane helix of C-terminal domains. We present evidence that the family called fatty acid elongases are homologous to transporters, not enzymes as had previously been thought. Conclusions The nucleotide sugar transporters families were formed through differentiation of the gene cluster EamA (domain unknown function 6) before Viridiplantae, showing for the first time the significance of EamA. PMID:21569384

Cross-talk between the ligand- and DNA-binding domains of estrogen receptor.

PubMed

Huang, Wei; Greene, Geoffrey L; Ravikumar, Krishnakumar M; Yang, Sichun

2013-11-01

Estrogen receptor alpha (ERα) is a hormone-responsive transcription factor that contains several discrete functional domains, including a ligand-binding domain (LBD) and a DNA-binding domain (DBD). Despite a wealth of knowledge about the behaviors of individual domains, the molecular mechanisms of cross-talk between LBD and DBD during signal transduction from hormone to DNA-binding of ERα remain elusive. Here, we apply a multiscale approach combining coarse-grained (CG) and atomistically detailed simulations to characterize this cross-talk mechanism via an investigation of the ERα conformational landscape. First, a CG model of ERα is built based on crystal structures of individual LBDs and DBDs, with more emphasis on their interdomain interactions. Second, molecular dynamics simulations are implemented and enhanced sampling is achieved via the "push-pull-release" strategy in the search for different LBD-DBD orientations. Third, multiple energetically stable ERα conformations are identified on the landscape. A key finding is that estradiol-bound LBDs utilize the well-described activation helix H12 to pack and stabilize LBD-DBD interactions. Our results suggest that the estradiol-bound LBDs can serve as a scaffold to position and stabilize the DBD-DNA complex, consistent with experimental observations of enhanced DNA binding with the LBD. Final assessment using atomic-level simulations shows that these CG-predicted models are significantly stable within a 15-ns simulation window and that specific pairs of lysine residues in close proximity at the domain interfaces could serve as candidate sites for chemical cross-linking studies. Together, these simulation results provide a molecular view of the role of ERα domain interactions in response to hormone binding. Copyright © 2013 Wiley Periodicals, Inc.

Improvements to the ICRH antenna time-domain 3D plasma simulation model

NASA Astrophysics Data System (ADS)

Smithe, David N.; Jenkins, Thomas G.; King, J. R.

2015-12-01

We present a summary of ongoing improvements to the 3D time-domain plasma modeling software that has been used to look at ICRH antennas on Alcator C-Mod, NSTX, and ITER [1]. Our past investigations have shown that in low density cases where the slow wave is propagating, strong amplitude lower hybrid resonant fields can occur. Such a scenario could result in significant parasitic power loss in the SOL. The primary resonance broadening in this case is likely collisions with neutral gas, and thus we are upgrading the model to include realistic neutral gas in the SOL, in order to provide a better understanding of energy balance in these situations. Related to this, we are adding a temporal variation capability to the local plasma density in front of the antenna in order to investigate whether the near fields of the antenna could modify the local density sufficiently to initiate a low density situation. We will start with a simple scalar ponderomotive potential density expulsion model [2] for the density evolution, but are also looking to eventually couple to a more complex fluid treatment that would include tensor pressures and convective physics and sources of neutrals and ionization. We also review continued benchmarking efforts, and ongoing and planned improvements to the computational algorithms, resulting from experience gained during our recent supercomputing runs on the Titan supercomputer, including GPU operations.

Changes in language white matter tract microarchitecture associated with cognitive deficits in patients with presumed low-grade glioma.

PubMed

Incekara, Fatih; Satoer, Djaina; Visch-Brink, Evy; Vincent, Arnaud; Smits, Marion

2018-06-08

OBJECTIVE The authors conducted a study to determine whether cognitive functioning of patients with presumed low-grade glioma is associated with white matter (WM) tract changes. METHODS The authors included 77 patients with presumed low-grade glioma who underwent awake surgery between 2005 and 2013. Diffusion tensor imaging with deterministic tractography was performed preoperatively to identify the arcuate, inferior frontooccipital, and uncinate fasciculi and to obtain the mean fractional anisotropy (FA) and mean diffusivity per tract. All patients were evaluated preoperatively using an extensive neuropsychological protocol that included assessments of the language, memory, and attention/executive function domains. Linear regression models were used to analyze each cognitive domain and each diffusion tensor imaging metric of the 3 WM tracts. RESULTS Significant correlations (corrected for multiple testing) were found between FA of the arcuate fasciculus and results of the repetition test for the language domain (β = 0.59, p < 0.0001) and between FA of the inferior frontooccipital fasciculus and results of the imprinting test for the memory domain (β = -0.55, p = 0.002) and the attention test for the attention and executive function domain (β = -0.62, p = 0.006). CONCLUSIONS In patients with glioma, language deficits in repetition of speech, imprinting, and attention deficits are associated with changes in the microarchitecture of the arcuate and inferior frontooccipital fasciculi.

Evaluation of gas-particle partitioning in a regional air quality model for organic pollutants

NASA Astrophysics Data System (ADS)

Efstathiou, Christos I.; Matejovičová, Jana; Bieser, Johannes; Lammel, Gerhard

2016-12-01

Persistent organic pollutants (POPs) are of considerable concern due to their well-recognized toxicity and their potential to bioaccumulate and engage in long-range transport. These compounds are semi-volatile and, therefore, create a partition between vapour and condensed phases in the atmosphere, while both phases can undergo chemical reactions. This work describes the extension of the Community Multiscale Air Quality (CMAQ) modelling system to POPs with a focus on establishing an adaptable framework that accounts for gaseous chemistry, heterogeneous reactions, and gas-particle partitioning (GPP). The effect of GPP is assessed by implementing a set of independent parameterizations within the CMAQ aerosol module, including the Junge-Pankow (JP) adsorption model, the Harner-Bidleman (HB) organic matter (OM) absorption model, and the dual Dachs-Eisenreich (DE) black carbon (BC) adsorption and OM absorption model. Use of these descriptors in a modified version of CMAQ for benzo[a]pyrene (BaP) results in different fate and transport patterns as demonstrated by regional-scale simulations performed for a European domain during 2006. The dual DE model predicted 24.1 % higher average domain concentrations compared to the HB model, which was in turn predicting 119.2 % higher levels compared to the baseline JP model. Evaluation with measurements from the European Monitoring and Evaluation Programme (EMEP) reveals the capability of the more extensive DE model to better capture the ambient levels and seasonal behaviour of BaP. It is found that the heterogeneous reaction of BaP with O3 may decrease its atmospheric lifetime by 25.2 % (domain and annual average) and near-ground concentrations by 18.8 %. Marginally better model performance was found for one of the six EMEP stations (Košetice) when heterogeneous BaP reactivity was included. Further analysis shows that, for the rest of the EMEP locations, the model continues to underestimate BaP levels, an observation that can be attributed to low emission estimates for such remote areas. These findings suggest that, when modelling the fate and transport of organic pollutants on large spatio-temporal scales, the selection and parameterization of GPP can be as important as degradation (reactivity).

Assessing the contribution of different factors in RegCM4.3 regional climate model projections using the Factor Separation method over the Med-CORDEX domain

NASA Astrophysics Data System (ADS)

Zsolt Torma, Csaba; Giorgi, Filippo

2014-05-01

A set of regional climate model (RCM) simulations applying dynamical downscaling of global climate model (GCM) simulations over the Mediterranean domain specified by the international initiative Coordinated Regional Downscaling Experiment (CORDEX) were completed with the Regional Climate Model RegCM, version RegCM4.3. Two GCMs were selected from the Coupled Model Intercomparison Project Phase 5 (CMIP5) ensemble to provide the driving fields for the RegCM: HadGEM2-ES (HadGEM) and MPI-ESM-MR (MPI). The simulations consist of an ensemble including multiple physics configurations and different "Reference Concentration Pathways" (RCP4.5 and RCP8.5). In total 15 simulations were carried out with 7 model physics configurations with varying convection and land surface schemes. The horizontal grid spacing of the RCM simulations is 50 km and the simulated period in all cases is 1970-2100 (1970-2099 in case of HadGEM driven simulations). This ensemble includes a combination of experiments in which different model components are changed individually and in combination, and thus lends itself optimally to the application of the Factor Separation (FS) method. This study applies the FS method to investigate the contributions of different factors, along with their synergy, on a set of regional climate model (RCM) projections for the Mediterranean region. The FS method is applied to 6 projections for the period 1970-2100 performed with the regional model RegCM4.3 over the Med-CORDEX domain. Two different sets of factors are intercompared, namely the driving global climate model (HadGEM and MPI) boundary conditions against two model physics settings (convection scheme and irrigation). We find that both the GCM driving conditions and the model physics provide important contributions, depending on the variable analyzed (surface air temperature and precipitation), season (winter vs. summer) and time horizon into the future, while the synergy term mostly tends to counterbalance the contributions of the individual factors. We demonstrate the usefulness of the FS method to assess different sources of uncertainty in RCM-based regional climate projections.

Disentangling the Role of Domain-Specific Knowledge in Student Modeling

NASA Astrophysics Data System (ADS)

Ruppert, John; Duncan, Ravit Golan; Chinn, Clark A.

2017-08-01

This study explores the role of domain-specific knowledge in students' modeling practice and how this knowledge interacts with two domain-general modeling strategies: use of evidence and developing a causal mechanism. We analyzed models made by middle school students who had a year of intensive model-based instruction. These models were made to explain a familiar but unstudied biological phenomenon: late onset muscle pain. Students were provided with three pieces of evidence related to this phenomenon and asked to construct a model to account for this evidence. Findings indicate that domain-specific resources play a significant role in the extent to which the models accounted for provided evidence. On the other hand, familiarity with the situation appeared to contribute to the mechanistic character of models. Our results indicate that modeling strategies alone are insufficient for the development of a mechanistic model that accounts for provided evidence and that, while learners can develop a tentative model with a basic familiarity of the situation, scaffolding certain domain-specific knowledge is necessary to assist students with incorporating evidence in modeling tasks.

Monte Carlo simulation of ferroelectric domain growth

NASA Astrophysics Data System (ADS)

Li, B. L.; Liu, X. P.; Fang, F.; Zhu, J. L.; Liu, J.-M.

2006-01-01

The kinetics of two-dimensional isothermal domain growth in a quenched ferroelectric system is investigated using Monte Carlo simulation based on a realistic Ginzburg-Landau ferroelectric model with cubic-tetragonal (square-rectangle) phase transitions. The evolution of the domain pattern and domain size with annealing time is simulated, and the stability of trijunctions and tetrajunctions of domain walls is analyzed. It is found that in this much realistic model with strong dipole alignment anisotropy and long-range Coulomb interaction, the powerlaw for normal domain growth still stands applicable. Towards the late stage of domain growth, both the average domain area and reciprocal density of domain wall junctions increase linearly with time, and the one-parameter dynamic scaling of the domain growth is demonstrated.

Towards a Conceptual Design of a Cross-Domain Integrative Information System for the Geosciences

NASA Astrophysics Data System (ADS)

Zaslavsky, I.; Richard, S. M.; Valentine, D. W.; Malik, T.; Gupta, A.

2013-12-01

As geoscientists increasingly focus on studying processes that span multiple research domains, there is an increased need for cross-domain interoperability solutions that can scale to the entire geosciences, bridging information and knowledge systems, models, software tools, as well as connecting researchers and organization. Creating a community-driven cyberinfrastructure (CI) to address the grand challenges of integrative Earth science research and education is the focus of EarthCube, a new research initiative of the U.S. National Science Foundation. We are approaching EarthCube design as a complex socio-technical system of systems, in which communication between various domain subsystems, people and organizations enables more comprehensive, data-intensive research designs and knowledge sharing. In particular, we focus on integrating 'traditional' layered CI components - including information sources, catalogs, vocabularies, services, analysis and modeling tools - with CI components supporting scholarly communication, self-organization and social networking (e.g. research profiles, Q&A systems, annotations), in a manner that follows and enhances existing patterns of data, information and knowledge exchange within and across geoscience domains. We describe an initial architecture design focused on enabling the CI to (a) provide an environment for scientifically sound information and software discovery and reuse; (b) evolve by factoring in the impact of maturing movements like linked data, 'big data', and social collaborations, as well as experience from work on large information systems in other domains; (c) handle the ever increasing volume, complexity and diversity of geoscience information; (d) incorporate new information and analytical requirements, tools, and techniques, and emerging types of earth observations and models; (e) accommodate different ideas and approaches to research and data stewardship; (f) be responsive to the existing and anticipated needs of researchers and organizations representing both established and emerging CI users; and (g) make best use of NSF's current investment in the geoscience CI. The presentation will focus on the challenges and methodology of EarthCube CI design, in particular on supporting social engagement and interaction between geoscientists and computer scientists as a core function of EarthCube architecture. This capability must include mechanisms to not only locate and integrate available geoscience resources, but also engage individuals and projects, research products and publications, and enable efficient communication across many EarthCube stakeholders leading to long-term institutional alignment and trusted collaborations.

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

PubMed Central

Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

2015-01-01

Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

The chemistry side of AOP: implications for toxicity ...

EPA Pesticide Factsheets

An adverse outcome pathway (AOP) is a structured representation of the biological events that lead to adverse impacts following a molecular initiating event caused by chemical interaction with a macromolecule. AOPs have been proposed to facilitate toxicity extrapolation across species through understanding of species similarity in the sequence of molecular, cellular, organ and organismal level responses. However, AOPs are non-specific regarding the identity of the chemical initiators, and the range of structures for which an AOP is considered applicable has generally been poorly defined. Applicability domain has been widely understood in the field of QSAR as the response and chemical structure space in which the model makes predictions with a given reliability, and has been traditionally applied to define the similarity of query molecules within the training set. Three dimensional (3D) receptor modeling offers an approach to better define the applicability domain for selected AOPs through determination of the chemical space of the molecular initiating event. Universal 3D-QSAR models were developed for acetylcholinesterase inhibitors and estrogen receptor agonists and antagonists using a combination of fingerprint, molecular docking and structure-based pharmacophore approaches. The models were based on the critical molecular interactions within each receptor ligand binding domain, and included the key amino acid residues responsible for high binding affinity. T

The Hierarchical Data Format as a Foundation for Community Data Sharing

NASA Astrophysics Data System (ADS)

Habermann, T.

2017-12-01

Hierarchical Data Format (HDF) formats and libraries have been used by individual researchers and major science programs across many Earth and Space Science disciplines and sectors to provide high-performance information storage and access for several decades. Generic group, dataset, and attribute objects in HDF have been combined in many ways to form domain objects that scientists understand and use. Well-known applications of HDF in the Earth Sciences include thousands of global satellite observations and products produced by NASA's Earth Observing System using the HDF-EOS conventions, navigation quality bathymetry produced as Bathymetric Attributed Grids (BAGs) by the OpenNavigationSurface project and others, seismic wave collections written into the Adoptable Seismic Data Format (ASDF) and many oceanographic and atmospheric products produced using the climate-forecast conventions with the netCDF4 data model and API to HDF5. This is the modus operandi of these communities: 1) develop a model of scientific data objects and associated metadata used in a domain, 2) implement that model using HDF, 3) develop software libraries that connect that model to tools and 4) encourage adoption of those tools in the community. Understanding these domain object implementations and facilitating communication across communities is an important goal of The HDF Group. We will discuss these examples and approaches to community outreach during this session.

Tetrahedral node for Transmission-Line Modeling (TLM) applied to Bio-heat Transfer.

PubMed

Milan, Hugo F M; Gebremedhin, Kifle G

2016-12-01

Transmission-Line Modeling (TLM) is a numerical method used to solve complex and time-domain bio-heat transfer problems. In TLM, parallelepipeds are used to discretize three-dimensional problems. The drawback in using parallelepiped shapes is that instead of refining only the domain of interest, a large additional domain would also have to be refined, which results in increased computational time and memory space. In this paper, we developed a tetrahedral node for TLM applied to bio-heat transfer that does not have the drawback associated with the parallelepiped node. The model includes heat source, blood perfusion, boundary conditions and initial conditions. The boundary conditions could be adiabatic, temperature, heat flux, or convection. The predicted temperature and heat flux were compared against results from an analytical solution and the results agreed within 2% for a mesh size of 69,941 nodes and a time step of 5ms. The method was further validated against published results of maximum skin-surface temperature difference in a breast with and without tumor and the results agreed within 6%. The published results were obtained from a model that used parallelepiped TLM node. An open source software, TLMBHT, was written using the theory developed herein and is available for download free-of-charge. Copyright © 2016 Elsevier Ltd. All rights reserved.

Impact of joint statistical dual-energy CT reconstruction of proton stopping power images: Comparison to image- and sinogram-domain material decomposition approaches.

PubMed

Zhang, Shuangyue; Han, Dong; Politte, David G; Williamson, Jeffrey F; O'Sullivan, Joseph A

2018-05-01

The purpose of this study was to assess the performance of a novel dual-energy CT (DECT) approach for proton stopping power ratio (SPR) mapping that integrates image reconstruction and material characterization using a joint statistical image reconstruction (JSIR) method based on a linear basis vector model (BVM). A systematic comparison between the JSIR-BVM method and previously described DECT image- and sinogram-domain decomposition approaches is also carried out on synthetic data. The JSIR-BVM method was implemented to estimate the electron densities and mean excitation energies (I-values) required by the Bethe equation for SPR mapping. In addition, image- and sinogram-domain DECT methods based on three available SPR models including BVM were implemented for comparison. The intrinsic SPR modeling accuracy of the three models was first validated. Synthetic DECT transmission sinograms of two 330 mm diameter phantoms each containing 17 soft and bony tissues (for a total of 34) of known composition were then generated with spectra of 90 and 140 kVp. The estimation accuracy of the reconstructed SPR images were evaluated for the seven investigated methods. The impact of phantom size and insert location on SPR estimation accuracy was also investigated. All three selected DECT-SPR models predict the SPR of all tissue types with less than 0.2% RMS errors under idealized conditions with no reconstruction uncertainties. When applied to synthetic sinograms, the JSIR-BVM method achieves the best performance with mean and RMS-average errors of less than 0.05% and 0.3%, respectively, for all noise levels, while the image- and sinogram-domain decomposition methods show increasing mean and RMS-average errors with increasing noise level. The JSIR-BVM method also reduces statistical SPR variation by sixfold compared to other methods. A 25% phantom diameter change causes up to 4% SPR differences for the image-domain decomposition approach, while the JSIR-BVM method and sinogram-domain decomposition methods are insensitive to size change. Among all the investigated methods, the JSIR-BVM method achieves the best performance for SPR estimation in our simulation phantom study. This novel method is robust with respect to sinogram noise and residual beam-hardening effects, yielding SPR estimation errors comparable to intrinsic BVM modeling error. In contrast, the achievable SPR estimation accuracy of the image- and sinogram-domain decomposition methods is dominated by the CT image intensity uncertainties introduced by the reconstruction and decomposition processes. © 2018 American Association of Physicists in Medicine.

Modelling protein functional domains in signal transduction using Maude

NASA Technical Reports Server (NTRS)

Sriram, M. G.

2003-01-01

Modelling of protein-protein interactions in signal transduction is receiving increased attention in computational biology. This paper describes recent research in the application of Maude, a symbolic language founded on rewriting logic, to the modelling of functional domains within signalling proteins. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. In general, Maude models can simulate biological signalling networks and produce specific testable hypotheses at various levels of abstraction. Developing symbolic models of signalling proteins containing functional domains is important because of the potential to generate analyses of complex signalling networks based on structure-function relationships.

Description and evaluation of the Earth System Regional Climate Model (RegCM-ES)

NASA Astrophysics Data System (ADS)

Farneti, Riccardo; Sitz, Lina; Di Sante, Fabio; Fuentes-Franco, Ramon; Coppola, Erika; Mariotti, Laura; Reale, Marco; Sannino, Gianmaria; Barreiro, Marcelo; Nogherotto, Rita; Giuliani, Graziano; Graffino, Giorgio; Solidoro, Cosimo; Giorgi, Filippo

2017-04-01

The increasing availability of satellite remote sensing data, of high temporal frequency and spatial resolution, has provided a new and enhanced view of the global ocean and atmosphere, revealing strong air-sea coupling processes throughout the ocean basins. In order to obtain an accurate representation and better understanding of the climate system, its variability and change, the inclusion of all mechanisms of interaction among the different sub-components, at high temporal and spatial resolution, becomes ever more desirable. Recently, global coupled models have been able to progressively refine their horizontal resolution to attempt to resolve smaller-scale processes. However, regional coupled ocean-atmosphere models can achieve even finer resolutions and provide additional information on the mechanisms of air-sea interactions and feedbacks. Here we describe a new, state-of-the-art, Earth System Regional Climate Model (RegCM-ES). RegCM-ES presently includes the coupling between atmosphere, ocean, land surface and sea-ice components, as well as an hydrological and ocean biogeochemistry model. The regional coupled model has been implemented and tested over some of the COordinated Regional climate Downscaling Experiment (CORDEX) domains. RegCM-ES has shown improvements in the representation of precipitation and SST fields over the tested domains, as well as realistic representations of coupled air-sea processes and interactions. The RegCM-ES model, which can be easily implemented over any regional domain of interest, is open source making it suitable for usage by the large scientific community.

Modeling reactive transport processes in fractured rock using the time domain random walk approach within a dual-porosity framework

NASA Astrophysics Data System (ADS)

Roubinet, D.; Russian, A.; Dentz, M.; Gouze, P.

2017-12-01

Characterizing and modeling hydrodynamic reactive transport in fractured rock are critical challenges for various research fields and applications including environmental remediation, geological storage, and energy production. To this end, we consider a recently developed time domain random walk (TDRW) approach, which is adapted to reproduce anomalous transport behaviors and capture heterogeneous structural and physical properties. This method is also very well suited to optimize numerical simulations by memory-shared massive parallelization and provide numerical results at various scales. So far, the TDRW approach has been applied for modeling advective-diffusive transport with mass transfer between mobile and immobile regions and simple (theoretical) reactions in heterogeneous porous media represented as single continuum domains. We extend this approach to dual-continuum representations considering a highly permeable fracture network embedded into a poorly permeable rock matrix with heterogeneous geochemical reactions occurring in both geological structures. The resulting numerical model enables us to extend the range of the modeled heterogeneity scales with an accurate representation of solute transport processes and no assumption on the Fickianity of these processes. The proposed model is compared to existing particle-based methods that are usually used to model reactive transport in fractured rocks assuming a homogeneous surrounding matrix, and is used to evaluate the impact of the matrix heterogeneity on the apparent reaction rates for different 2D and 3D simple-to-complex fracture network configurations.

Vertically-Integrated Dual-Continuum Models for CO2 Injection in Fractured Aquifers

NASA Astrophysics Data System (ADS)

Tao, Y.; Guo, B.; Bandilla, K.; Celia, M. A.

2017-12-01

Injection of CO2 into a saline aquifer leads to a two-phase flow system, with supercritical CO2 and brine being the two fluid phases. Various modeling approaches, including fully three-dimensional (3D) models and vertical-equilibrium (VE) models, have been used to study the system. Almost all of that work has focused on unfractured formations. 3D models solve the governing equations in three dimensions and are applicable to generic geological formations. VE models assume rapid and complete buoyant segregation of the two fluid phases, resulting in vertical pressure equilibrium and allowing integration of the governing equations in the vertical dimension. This reduction in dimensionality makes VE models computationally more efficient, but the associated assumptions restrict the applicability of VE model to formations with moderate to high permeability. In this presentation, we extend the VE and 3D models for CO2 injection in fractured aquifers. This is done in the context of dual-continuum modeling, where the fractured formation is modeled as an overlap of two continuous domains, one representing the fractures and the other representing the rock matrix. Both domains are treated as porous media continua and can be modeled by either a VE or a 3D formulation. The transfer of fluid mass between rock matrix and fractures is represented by a mass transfer function connecting the two domains. We have developed a computational model that combines the VE and 3D models, where we use the VE model in the fractures, which typically have high permeability, and the 3D model in the less permeable rock matrix. A new mass transfer function is derived, which couples the VE and 3D models. The coupled VE-3D model can simulate CO2 injection and migration in fractured aquifers. Results from this model compare well with a full-3D model in which both the fractures and rock matrix are modeled with 3D models, with the hybrid VE-3D model having significantly reduced computational cost. In addition to the VE-3D model, we explore simplifications of the rock matrix domain by using sugar-cube and matchstick conceptualizations and develop VE-dual porosity and VE-matchstick models. These vertically-integrated dual-permeability and dual-porosity models provide a range of computationally efficient tools to model CO2 storage in fractured saline aquifers.

Influence of geologic layering on heat transport and storage in an aquifer thermal energy storage system

NASA Astrophysics Data System (ADS)

Bridger, D. W.; Allen, D. M.

2014-01-01

A modeling study was carried out to evaluate the influence of aquifer heterogeneity, as represented by geologic layering, on heat transport and storage in an aquifer thermal energy storage (ATES) system in Agassiz, British Columbia, Canada. Two 3D heat transport models were developed and calibrated using the flow and heat transport code FEFLOW including: a "non-layered" model domain with homogeneous hydraulic and thermal properties; and, a "layered" model domain with variable hydraulic and thermal properties assigned to discrete geological units to represent aquifer heterogeneity. The base model (non-layered) shows limited sensitivity for the ranges of all thermal and hydraulic properties expected at the site; the model is most sensitive to vertical anisotropy and hydraulic gradient. Simulated and observed temperatures within the wells reflect a combination of screen placement and layering, with inconsistencies largely explained by the lateral continuity of high permeability layers represented in the model. Simulation of heat injection, storage and recovery show preferential transport along high permeability layers, resulting in longitudinal plume distortion, and overall higher short-term storage efficiencies.

Handwriting Fluency and Visuospatial Generativity at Primary School

ERIC Educational Resources Information Center

Stievano, Paolo; Michetti, Silvia; McClintock, Shawn M.; Levi, Gabriel; Scalisi, Teresa Gloria

2016-01-01

Handwriting is a complex activity that involves continuous interaction between lowerlevel perceptual-motor and higher-level cognitive processes. All handwriting models describe involvement of executive functions (EF) in handwriting development. Particular EF domains associated with handwriting include maintenance of information in working memory,…

Gender and the Development of Wisdom.

ERIC Educational Resources Information Center

Orwoll, Lucinda; Achenbaum, W. Andrew

1993-01-01

Drawing on a model of wisdom that includes components in three domains (personality, cognition, and conation) and across three levels (intrapersonal, interpersonal, and transpersonal), highlights potential differences in the ways women and men attain and express wisdom; and examines interactive patterns across the components of wisdom. (BC)

Improving the process of process modelling by the use of domain process patterns

NASA Astrophysics Data System (ADS)

Koschmider, Agnes; Reijers, Hajo A.

2015-01-01

The use of business process models has become prevalent in a wide area of enterprise applications. But while their popularity is expanding, concerns are growing with respect to their proper creation and maintenance. An obvious way to boost the efficiency of creating high-quality business process models would be to reuse relevant parts of existing models. At this point, however, limited support exists to guide process modellers towards the usage of appropriate model content. In this paper, a set of content-oriented patterns is presented, which is extracted from a large set of process models from the order management and manufacturing production domains. The patterns are derived using a newly proposed set of algorithms, which are being discussed in this paper. The authors demonstrate how such Domain Process Patterns, in combination with information on their historic usage, can support process modellers in generating new models. To support the wider dissemination and development of Domain Process Patterns within and beyond the studied domains, an accompanying website has been set up.

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

TESP combines existing domain simulators in the electric power grid, with new transactive agents, growth models and evaluation scripts. The existing domain simulators include GridLAB-D for the distribution grid and single-family residential buildings, MATPOWER for transmission and bulk generation, and EnergyPlus for large buildings. More are planned for subsequent versions of TESP. The new elements are: TEAgents - simulate market participants and transactive systems for market clearing. Some of this functionality was extracted from GridLAB-D and implemented in Python for customization by PNNL and others; Growth Model - a means for simulating system changes over a multiyear period, including bothmore » normal load growth and specific investment decisions. Customizable in Python code; and Evaluation Script - a means of evaluating different transactive systems through customizable post-processing in Python code. TESP provides a method for other researchers and vendors to design transactive systems, and test them in a virtual environment. It allows customization of the key components by modifying Python code.« less

Additive Interaction between Heterogeneous Environmental Quality Domains (Air, Water, Land, Sociodemographic, and Built Environment) on Preterm Birth.

PubMed

Grabich, Shannon C; Rappazzo, Kristen M; Gray, Christine L; Jagai, Jyotsna S; Jian, Yun; Messer, Lynne C; Lobdell, Danelle T

2016-01-01

Environmental exposures often occur in tandem; however, epidemiological research often focuses on singular exposures. Statistical interactions among broad, well-characterized environmental domains have not yet been evaluated in association with health. We address this gap by conducting a county-level cross-sectional analysis of interactions between Environmental Quality Index (EQI) domain indices on preterm birth in the Unites States from 2000 to 2005. The EQI, a county-level index constructed for the 2000-2005 time period, was constructed from five domain-specific indices (air, water, land, built, and sociodemographic) using principal component analyses. County-level preterm birth rates ( n  = 3141) were estimated using live births from the National Center for Health Statistics. Linear regression was used to estimate prevalence differences (PDs) and 95% confidence intervals (CIs) comparing worse environmental quality to the better quality for each model for (a) each individual domain main effect, (b) the interaction contrast, and (c) the two main effects plus interaction effect (i.e., the "net effect") to show departure from additivity for the all U.S. counties. Analyses were also performed for subgroupings by four urban/rural strata. We found the suggestion of antagonistic interactions but no synergism, along with several purely additive (i.e., no interaction) associations. In the non-stratified model, we observed antagonistic interactions, between the sociodemographic/air domains [net effect (i.e., the association, including main effects and interaction effects) PD: -0.004 (95% CI: -0.007, 0.000), interaction contrast: -0.013 (95% CI: -0.020, -0.007)] and built/air domains [net effect PD: 0.008 (95% CI 0.004, 0.011), interaction contrast: -0.008 (95% CI: -0.015, -0.002)]. Most interactions were between the air domain and other respective domains. Interactions differed by urbanicity, with more interactions observed in non-metropolitan regions. Observed antagonistic associations may indicate that those living in areas with multiple detrimental domains may have other interfering factors reducing the burden of environmental exposure. This study is the first to explore interactions across different environmental domains and demonstrates the utility of the EQI to examine the relationship between environmental domain interactions and human health. While we did observe some departures from additivity, many observed effects were additive. This study demonstrated that interactions between environmental domains should be considered in future analyses.

Multiscale Multiphysics and Multidomain Models I: Basic Theory

PubMed Central

Wei, Guo-Wei

2013-01-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field. PMID:25382892

Multiscale Multiphysics and Multidomain Models I: Basic Theory.

PubMed

Wei, Guo-Wei

2013-12-01

This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.

A Conceptual Foundation for Measures of Physical Function and Behavioral Health Function for Social Security Work Disability Evaluation

PubMed Central

Marfeo, Elizabeth E.; Haley, Stephen M.; Jette, Alan M.; Eisen, Susan V.; Ni, Pengsheng; Bogusz, Kara; Meterko, Mark; McDonough, Christine M.; Chan, Leighton; Brandt, Diane E.; Rasch, Elizabeth K.

2014-01-01

Physical and mental impairments represent the two largest health condition categories for which workers receive Social Security disability benefits. Comprehensive assessment of physical and mental impairments should include aspects beyond medical conditions such as a person’s underlying capabilities as well as activity demands relevant to the context of work. The objective of this paper is to describe the initial conceptual stages of developing new measurement instruments of behavioral health and physical functioning relevant for Social Security work disability evaluation purposes. To outline a clear conceptualization of the constructs to be measured, two content models were developed using structured and informal qualitative approaches. We performed a structured literature review focusing on work disability and incorporating aspects of the International Classification of Functioning, Disability, and Health (ICF) as a unifying taxonomy for framework development. Expert interviews provided advice and consultation to enhance face validity of the resulting content models. The content model for work-related behavioral health function identifies five major domains (1) Behavior Control, (2) Basic Interactions, (3) Temperament and Personality, (4) Adaptability, and (5) Workplace Behaviors. The content model describing physical functioning includes three domains (1) Changing and Maintaining Body Position, (2) Whole Body Mobility, and (3) Carrying, Moving and Handling Objects. These content models informed subsequent measurement properties including item development, measurement scale construction, and provided conceptual coherence guiding future empirical inquiry. The proposed measurement approaches show promise to comprehensively and systematically assess physical and behavioral health functioning relevant to work. PMID:23548543

Initial development of a patient-reported outcome measure of experience with cognitive impairment associated with schizophrenia.

PubMed

Welch, Lisa C; Trudeau, Jeremiah J; Silverstein, Steven M; Sand, Michael; Henderson, David C; Rosen, Raymond C

2017-01-01

Cognitive impairment is a serious, often distressing aspect of schizophrenia that affects patients' day-to-day lives. Although several interview-based instruments exist to assess cognitive functioning, a reliable measure developed based on the experiences of patients facing cognitive difficulties is needed to complement the objective performance-based assessments. The present article describes the initial development of a patient-reported outcome (PRO) measure to assess the subjective experience of cognitive impairment among patients with schizophrenia, the Patient-Reported Experience of Cognitive Impairment in Schizophrenia (PRECIS). The phases of development included the construction of a conceptual model based on the existing knowledge and two sets of qualitative interviews with patients: 1) concept elicitation interviews to ensure face and content validity from the perspective of people with schizophrenia and 2) cognitive debriefing of the initial item pool. Input from experts was elicited throughout the process. The initial conceptual model included seven domains. The results from concept elicitation interviews (n=80) supported these domains but yielded substantive changes to concepts within domains and to terminology. Based on these results, an initial pool of 53 items was developed to reflect the most common descriptions and languages used by the study participants. Cognitive debriefing interviews (n=22) resulted in the removal of 18 items and modification of 22 other items. The remaining 35 items represented 23 concepts within six domains plus two items assessing bother. The draft PRO measure is currently undergoing psychometric testing as a precursor to broad-based clinical and research use.

Comparison of learning models based on mathematics logical intelligence in affective domain

NASA Astrophysics Data System (ADS)

Widayanto, Arif; Pratiwi, Hasih; Mardiyana

2018-04-01

The purpose of this study was to examine the presence or absence of different effects of multiple treatments (used learning models and logical-mathematical intelligence) on the dependent variable (affective domain of mathematics). This research was quasi experimental using 3x3 of factorial design. The population of this research was VIII grade students of junior high school in Karanganyar under the academic year 2017/2018. Data collected in this research was analyzed by two ways analysis of variance with unequal cells using 5% of significance level. The result of the research were as follows: (1) Teaching and learning with model TS lead to better achievement in affective domain than QSH, teaching and learning with model QSH lead to better achievement in affective domain than using DI; (2) Students with high mathematics logical intelligence have better achievement in affective domain than students with low mathematics logical intelligence have; (3) In teaching and learning mathematics using learning model TS, students with moderate mathematics logical intelligence have better achievement in affective domain than using DI; and (4) In teaching and learning mathematics using learning model TS, students with low mathematics logical intelligence have better achievement in affective domain than using QSH and DI.

Training Plan. Central Archive for Reusable Defense Software (CARDS)

DTIC Science & Technology

1994-01-29

Modeling Software Reuse Technology: Feature Oriented Domain Analysis ( FODA ). SEI, Carnegie Mellon University, May 1992. 8. Component Provider’s...events to the services of the domain. 4. Feature Oriented Domain Analysis ( FODA ) [COHEN92] The FODA method produces feature models. Feature models provide...Architecture FODA Feature-Oriented Domain Analysis GOTS Government-Off-The-Shelf Pap A-49 STARS-VC-B003/001/00 29 imaty 1994 MS Master of Science NEC

Improving Domain-specific Machine Translation by Constraining the Language Model

DTIC Science & Technology

2012-07-01

performance. To make up for the lack of parallel training data, one assumption is that more monolingual target language data should be used in building the...target language model. Prior work on domain-specific MT has focused on training target language models with monolingual 2 domain-specific data...showed that the using a large dictionary extracted from medical domain documents in a statistical MT system to generalize the training data significantly

Recovery-Oriented Mental Health Practice in a Community Care Unit: An Exploratory Study.

PubMed

McKenna, Brian; Oakes, Jane; Fourniotis, Niki; Toomey, Nigel; Furness, Trentham

A recovery-oriented model of care has become the major focus of mental health service delivery in the state of Victoria, Australia. However, there is a total absence of knowledge of recovery-oriented mental health practice in community care units (CCUs). Therefore, the aims of this exploratory study were to: (a) describe what aspects of the current model of care fit within the domains of recovery; and (b) describe the pragmatic processes that staff use to mold their care within the domains of recovery. Twenty-one key stakeholders provided informed voluntary consent to participate in one-to-one interviews. Six content domains evolved to include: (a) a common vision: "a continuous journey"; (b) promoting hope; (c) promoting autonomy and self-determination; (d) meaningful engagement; (e) holistic and personalized care; and (f) community participation and citizenship. The CCU appeared to be on a journey of transformation toward personal recovery. However, clinicians were grappling with an identified tension among personal recovery and clinical recovery. The tension among personal recovery and clinical recovery may be attributed to the psychosocial rehabilitation model of care, which was previously systemic in Victorian CCUs.

Pattern, growth, and aging in aggregation kinetics of a Vicsek-like active matter model

NASA Astrophysics Data System (ADS)

Das, Subir K.

2017-01-01

Via molecular dynamics simulations, we study kinetics in a Vicsek-like phase-separating active matter model. Quantitative results, for isotropic bicontinuous pattern, are presented on the structure, growth, and aging. These are obtained via the two-point equal-time density-density correlation function, the average domain length, and the two-time density autocorrelation function. Both the correlation functions exhibit basic scaling properties, implying self-similarity in the pattern dynamics, for which the average domain size exhibits a power-law growth in time. The equal-time correlation has a short distance behavior that provides reasonable agreement between the corresponding structure factor tail and the Porod law. The autocorrelation decay is a power-law in the average domain size. Apart from these basic similarities, the overall quantitative behavior of the above-mentioned observables is found to be vastly different from those of the corresponding passive limit of the model which also undergoes phase separation. The functional forms of these have been quantified. An exceptionally rapid growth in the active system occurs due to fast coherent motion of the particles, mean-squared-displacements of which exhibit multiple scaling regimes, including a long time ballistic one.