University Center, VA, United States
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Clausen R.,4400 University Drive | Shehu A.,4400 University Drive
2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 | Year: 2013

We present an algorithm to probe the conformational space of Ras, a critical enzyme that employs conformational switching for its biological activity. The algorithm is guided by experimental data on crystallographic structures of wildtype and mutant Ras. A principal component analysis (PCA) over these structures provides search directions, which are used in combination with energetic refinement to sample low-energy conformations of Ras. Our results show that experimental structures are reproduced, and the space is further populated with novel structures, warranting further investigation into structural characterization of Ras. Copyright © 2007 by the Association for Computing Machinery.

Hashmi I.,4400 University Drive | Shehu A.,4400 University Drive
2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 | Year: 2013

We present a probabilistic search algorithm for rigid-body protein-protein docking. The algorithm is a realization of the basin hopping framework for sampling low-energy local minima of a given energy function. To save computational resources, the algorithm employs a machine learning model to score bound configurations prior to subjecting promising configurations to local optimization with a sophisticated force field. The machine learning model is a decision tree trained on known native dimers to learn features that constitute true interaction interfaces. The FoldX force field is employed only on sampled dimeric configurations deter- mined by the decision tree model to contain true interaction interfaces. The preliminary results are promising and motivate us to further investigate such an informatics-driven approach to protein-protein docking. Copyright © 2007 by the Association for Computing Machinery.

Kennedy W.G.,4400 University Drive | Patterson R.E.,Air Force Research Lab
Proceedings of the 11th International Conference on Cognitive Modeling, ICCM 2012 | Year: 2012

One mode of human decision-making is considered intuitive, i.e., unconscious situational pattern recognition. Implicit statistical learning, which involves the sampling of invariances from the environment and is known to involve procedural (i.e., non-declarative) memory, has been shown to be a foundation of this mode of decision making. We present an ACT-R model of implicit learning whose implementation entailed a declarative memory-based learner of the classification of example strings of an artificial grammar. The model performed very well when compared to humans. The fact that the simulation of implicit learning could not be implemented in a straightforward way via a non-declarative memory approach, but rather required a declarative memorybased implementation, suggests that the conceptualization of procedural memory in the ACT-R framework may need to be expanded to include abstract representations of statistical regularities. Our approach to the development and testing of models in ACT-R can be used to predict the development of intuitive decision-making in humans.

Alizadeh M.,4400 University Drive | Cioffi-Revilla C.,George Mason University
JASSS | Year: 2015

Empirical evidences have supported the large heterogeneity in the timing of individuals' activities. Moreover, computational analysis of the agent-based models has shown the importance of the activation regimes. In this paper, we apply four different asynchronous updating schemes including random, uniform, and two state-driven Poisson updating schemes on an agent-based opinion dynamics model. We compare the effect of these activation regimes by measuring the appropriate opinion clustering statistics and also the number of emergent extremists. The results exhibit both qualitative and quantitative difference between different activation regimes which in some cases are counterintuitive. In particular, we find that exposing the radical/moderate agents to more encounters decreases/increases the average number of extremists compared to other types of activation regimes. The results also show that no specific updating scheme can always outperform the others in reaching to consensus. © 2015 JASSS.

Scafide K.N.,George Mason University | Scafide K.N.,4400 University Drive | Sheridan D.J.,Texas A&M University | Taylor L.A.,Uniformed Services University of the Health Sciences | Hayat M.J.,Georgia State University
Injury | Year: 2016

Background Bruising is one of the most common types of injury clinicians observe among victims of violence and other trauma patients. However, research has shown commonly used qualitative description of cutaneous bruise colour via the naked eye is subjective and unreliable. No published work has formally evaluated the reliability of tristimulus colourimetry as an alternative for assessing bruise colour, despite its clinical and research applications in accurately assessing skin colour. The purpose of this study was to systematically evaluate the test-retest and inter-observer reliability of tristimulus colourimetry in the assessment of cutaneous bruise colour. Methods Two researchers obtained repeated tristimulus colourimetry measures of cutaneous bruises with participants of diverse skin colour. Measures were obtained using the Minolta CR-400 Chomameter. Commission Internationale d'Eclairage (CIE) L∗a∗b∗colour space was used. Data was analysed using intraclass correlation coefficients (ICC), Cronbach's alpha, and minimal detectable change (MDC) on all three L∗a∗b∗values. Results The colorimeter demonstrated excellent test-retest or intra-rater reliability (L∗ICC = 0.999; a∗ICC = 0.973; b∗ICC = 0.892) and inter-rater reliability (L∗ICC = 0.997; a∗ICC = 0.976; b∗ICC = 0.982). Conclusions With consistent placement, the tristimulus colourimetry is reliable for the objective assessment and documentation of cutaneous bruise colour for purposes of clinical practice and research. Recommendations for use in practice/research are provided. © 2016 Elsevier Ltd. All rights reserved.

Shortle J.F.,4400 University Drive | Zhang Y.,George Mason University | Wang J.,George Mason University
Transportation Research Record | Year: 2010

The statistical characterization of flight tracks is a critical component of safety analysis models. This paper presents an analysis of multilateration data that uses an extension of an algorithm. Key results are as follows: the separation distribution does not appear to change much at different points along the approach path. The left tail of separation (corresponding to the smallest separation values) decays faster than a normal distribution. This is positive from a safety perspective. If this behavior is extrapolated beyond the observed data, one can conjecture that smaller separations have probabilities that rapidly decay to effectively zero. Lateral positions near the threshold do not appear to be heavy tailed, either. Finally, estimates of the final approach separation variability are consistent with previously published results.

Cioffi-Revilla C.,4400 University Drive | Cioffi-Revilla C.,George Mason University | de Jong K.,4400 University Drive | de Jong K.,George Mason University | And 2 more authors.
Computational and Mathematical Organization Theory | Year: 2012

Computational social science in general, and social agent-based modeling (ABM) simulation in particular, are challenged by modeling and analyzing complex adaptive social systems with emergent properties that are hard to understand in terms of components, even when the organization of component agents is know. Evolutionary computation (EC) is a mature field that provides a bio-inspired approach and a suite of techniques that are applicable to and provide new insights on complex adaptive social systems. This paper demonstrates a combined EC-ABM approach illustrated through the RebeLand model of a simple but complete polity system. Results highlight tax rates and frequency of public issue that stress society as significant features in phase transitions between stable and unstable governance regimes. These initial results suggest further applications of EC to ABM in terms of multi-population models with heterogeneous agents, multi-objective optimization, dynamic environments, and evolving executable objects for modeling social change. © 2012 Springer Science+Business Media, LLC.

Gulden T.R.,4400 University Drive
JASSS | Year: 2013

This paper makes use of an agent-based framework to extend traditional models of comparative advantage in international trade, illustrating several cases that make theoretical room for industrial policy and the regulation of trade. Using an agent based implementation of the Hecksher-Ohlin trade model; the paper confirms Samuelson's 2004 result demonstrating that the principle of comparative advantage does not ensure that technological progress in one country benefits its trading partners. It goes on to demonstrate that the presence of increasing returns leads to a situation with multiple equilibria, where free market trading policies can not be relied on to deliver an outcome which is efficient or equitable, with first movers in development enjoying permanent advantage over later developing nations. Finally, the paper examines the impact of relaxation of the Ricardian assumption of capital immobility on the principle of comparative advantage. It finds that the dynamics of factor trade are radically different from the dynamics of trade in goods and that factor mobility converts a regime of comparative advantage into a regime of absolute advantage, thus obviating the reassuring equity results that stem from comparative advantage. © JASSS.

Wang W.,4400 University Drive | Qu J.J.,4400 University Drive | Hao X.,4400 University Drive | Liu Y.,U.S. Department of Agriculture | Stanturf J.A.,U.S. Department of Agriculture
Agricultural and Forest Meteorology | Year: 2010

This study developed a rapid assessment algorithm for post-hurricane forest damage estimation using moderate resolution imaging spectroradiometer (MODIS) measurements. The performance of five commonly used vegetation indices as post-hurricane forest damage indicators was investigated through statistical analysis. The Normalized Difference Infrared Index (NDII) was identified as the optimal damage indicator among these vegetation indices. An approach for detecting forest damage at a regional scale, without relying on ground inventory or sampling, was designed and validated. The validation showed that the relative change of pre- and post-hurricane NDII was linearly related to the damage severity estimated by the ground inventory with the coefficient of determination 0.79. This approach was applied to evaluate forest damage severity and the impacted region caused by Hurricane Katrina.

Satinsky S.,University of Kansas | Satinsky S.,Indiana University Bloomington | Rosenberger J.G.,Indiana University Bloomington | Rosenberger J.G.,Indiana University | And 4 more authors.
International Journal of STD and AIDS | Year: 2011

HIV/AIDS disproportionately impacts men who have sex with men (MSM) in the USA. Most existing literature on MSM with HIV focuses on transmission risk, but does not acknowledge health-promoting sexual behaviours men may undertake. This study examined sex toy use within this population to describe the extent to which using toys is incorporated into their sexual repertoires as a risk reduction practice. Data regarding sociodemographics, sexual/health-related behaviours and sex toy use were collected from 2275 MSM using an online survey. Most participants reported being sexually active (88.5%), and the majority (70.2%) of participants reported sex toy use within the previous year. Sex toy users were more likely to be white, in sexual relationships with others, and reported higher levels of sexual satisfaction. Given that sex toy use is common among this population, room for discussion exists about sex toys as tools to enhance pleasure and reduce HIV/sexually transmitted infection (STI) transmission.

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