Science.gov

Sample records for sheds-wood model incorporation

  1. STOCHASTIC HUMAN EXPOSURE AND DOSE SIMULATION MODEL FOR THE WOOD PRESERVATIVE SCENARIO (SHEDS-WOOD), VERSION 2 MODEL SAS CODE

    EPA Science Inventory

    Concerns have been raised regarding the safety of young children contacting arsenic and chromium residues while playing on and around Chromated Copper Arsenate (CCA) treated wood playground structures and decks. Although CCA registrants voluntarily canceled treated wood for resi...

  2. Incorporating opponent models into adversary search

    SciTech Connect

    Carmel, D.; Markovitch, S.

    1996-12-31

    This work presents a generalized theoretical framework that allows incorporation of opponent models into adversary search. We present the M* algorithm, a generalization of minimax that uses an arbitrary opponent model to simulate the opponent`s search. The opponent model is a recursive structure consisting of the opponent`s evaluation function and its model of the player. We demonstrate experimentally the potential benefit of using an opponent model. Pruning in M* is impossible in the general case. We prove a sufficient condition for pruning and present the {alpha}{beta}* algorithm which returns the M* value of a tree while searching only necessary branches.

  3. Incorporating Plant Hydraulics Into Phenological Modeling

    NASA Astrophysics Data System (ADS)

    Savoy, P.; Mackay, D. S.

    2014-12-01

    Vegetation phenology is well studied in systems where temperature is the primary driver of change, such as temperate and boreal ecosystems. In order to accurately model phenology in water-limited systems it is necessary to consider the role of water stress on mediating phenology. While it is possible to use proxies for water stress, such as vapor pressure deficit (VPD), it is preferable to have a more direct link to the effects of water stress on plant physiology. One possible approach is to incorporate the physiological responses of plants to water stress into phenological models. The goal of this study is to examine the use of plant hydraulics to help predict phenology instead of using only meteorological variables. We used an ecosystem process model that incorporates plant hydraulics, the Terrestrial Regional Ecosystem Exchange Simulator (TREES), in order to model plant phenology based on hydraulic stress. Phenology submodels implemented within TREES included both those driven purely from environmental variables as well those modulated by plant hydraulics. Results showed that the use of plant hydraulics to predict phenology, instead of using VPD as a proxy of plant water stress, performed favorably in comparison to models driven by meteorological variables alone. The need for better representation of moisture stress on phenology was particularly apparent in water-limited systems and the inclusion of plant hydraulics into phenology models improved the predictions in these systems.

  4. Incorporating incorporating economic models into seasonal pool conservation planning

    USGS Publications Warehouse

    Loftin, Cyndy; Bell, Kathleen P.; Freeman, Robert C.; Calhoun, Aram J. K.

    2012-01-01

    Massachusetts, New Jersey, Connecticut, and Maine have adopted regulatory zones around seasonal (vernal) pools to conserve terrestrial habitat for pool-breeding amphibians. Most amphibians require access to distinct seasonal habitats in both terrestrial and aquatic ecosystems because of their complex life histories. These habitat requirements make them particularly vulnerable to land uses that destroy habitat or limit connectivity (or permeability) among habitats. Regulatory efforts focusing on breeding pools without consideration of terrestrial habitat needs will not ensure the persistence of pool-breeding amphibians. We used GIS to combine a discrete-choice, parcel-scale economic model of land conversion with a landscape permeability model based on known habitat requirements of wood frogs (Lithobates sylvaticus) in Maine (USA) to examine permeability among habitat elements for alternative future scenarios. The economic model predicts future landscapes under different subdivision open space and vernal pool regulatory requirements. Our model showed that even “no build” permit zones extending 76 m (250 ft) outward from the pool edge were insufficient to assure permeability among required habitat elements. Furthermore, effectiveness of permit zones may be inconsistent due to interactions with other growth management policies, highlighting the need for local and state planning for the long-term persistence of pool-breeding amphibians in developing landscapes.

  5. Incorporation of RAM techniques into simulation modeling

    SciTech Connect

    Nelson, S.C. Jr.; Haire, M.J.; Schryver, J.C.

    1995-07-01

    This work concludes that reliability, availability, and maintainability (RAM) analytical techniques can be incorporated into computer network simulation modeling to yield an important new analytical tool. This paper describes the incorporation of failure and repair information into network simulation to build a stochastic computer model represents the RAM Performance of two vehicles being developed for the US Army: The Advanced Field Artillery System (AFAS) and the Future Armored Resupply Vehicle (FARV). The AFAS is the US Army`s next generation self-propelled cannon artillery system. The FARV is a resupply vehicle for the AFAS. Both vehicles utilize automation technologies to improve the operational performance of the vehicles and reduce manpower. The network simulation model used in this work is task based. The model programmed in this application requirements a typical battle mission and the failures and repairs that occur during that battle. Each task that the FARV performs--upload, travel to the AFAS, refuel, perform tactical/survivability moves, return to logistic resupply, etc.--is modeled. Such a model reproduces a model reproduces operational phenomena (e.g., failures and repairs) that are likely to occur in actual performance. Simulation tasks are modeled as discrete chronological steps; after the completion of each task decisions are programmed that determine the next path to be followed. The result is a complex logic diagram or network. The network simulation model is developed within a hierarchy of vehicle systems, subsystems, and equipment and includes failure management subnetworks. RAM information and other performance measures are collected which have impact on design requirements. Design changes are evaluated through ``what if`` questions, sensitivity studies, and battle scenario changes.

  6. Incorporating neurophysiological concepts in mathematical thermoregulation models

    NASA Astrophysics Data System (ADS)

    Kingma, Boris R. M.; Vosselman, M. J.; Frijns, A. J. H.; van Steenhoven, A. A.; van Marken Lichtenbelt, W. D.

    2014-01-01

    Skin blood flow (SBF) is a key player in human thermoregulation during mild thermal challenges. Various numerical models of SBF regulation exist. However, none explicitly incorporates the neurophysiology of thermal reception. This study tested a new SBF model that is in line with experimental data on thermal reception and the neurophysiological pathways involved in thermoregulatory SBF control. Additionally, a numerical thermoregulation model was used as a platform to test the function of the neurophysiological SBF model for skin temperature simulation. The prediction-error of the SBF-model was quantified by root-mean-squared-residual (RMSR) between simulations and experimental measurement data. Measurement data consisted of SBF (abdomen, forearm, hand), core and skin temperature recordings of young males during three transient thermal challenges (1 development and 2 validation). Additionally, ThermoSEM, a thermoregulation model, was used to simulate body temperatures using the new neurophysiological SBF-model. The RMSR between simulated and measured mean skin temperature was used to validate the model. The neurophysiological model predicted SBF with an accuracy of RMSR < 0.27. Tskin simulation results were within 0.37 °C of the measured mean skin temperature. This study shows that (1) thermal reception and neurophysiological pathways involved in thermoregulatory SBF control can be captured in a mathematical model, and (2) human thermoregulation models can be equipped with SBF control functions that are based on neurophysiology without loss of performance. The neurophysiological approach in modelling thermoregulation is favourable over engineering approaches because it is more in line with the underlying physiology.

  7. Incorporating neurophysiological concepts in mathematical thermoregulation models.

    PubMed

    Kingma, Boris R M; Vosselman, M J; Frijns, A J H; van Steenhoven, A A; van Marken Lichtenbelt, W D

    2014-01-01

    Skin blood flow (SBF) is a key player in human thermoregulation during mild thermal challenges. Various numerical models of SBF regulation exist. However, none explicitly incorporates the neurophysiology of thermal reception. This study tested a new SBF model that is in line with experimental data on thermal reception and the neurophysiological pathways involved in thermoregulatory SBF control. Additionally, a numerical thermoregulation model was used as a platform to test the function of the neurophysiological SBF model for skin temperature simulation. The prediction-error of the SBF-model was quantified by root-mean-squared-residual (RMSR) between simulations and experimental measurement data. Measurement data consisted of SBF (abdomen, forearm, hand), core and skin temperature recordings of young males during three transient thermal challenges (1 development and 2 validation). Additionally, ThermoSEM, a thermoregulation model, was used to simulate body temperatures using the new neurophysiological SBF-model. The RMSR between simulated and measured mean skin temperature was used to validate the model. The neurophysiological model predicted SBF with an accuracy of RMSR < 0.27. Tskin simulation results were within 0.37 °C of the measured mean skin temperature. This study shows that (1) thermal reception and neurophysiological pathways involved in thermoregulatory SBF control can be captured in a mathematical model, and (2) human thermoregulation models can be equipped with SBF control functions that are based on neurophysiology without loss of performance. The neurophysiological approach in modelling thermoregulation is favourable over engineering approaches because it is more in line with the underlying physiology.

  8. Incorporation of salinity in Water Availability Modeling

    NASA Astrophysics Data System (ADS)

    Wurbs, Ralph A.; Lee, Chihun

    2011-10-01

    SummaryNatural salt pollution from geologic formations in the upper watersheds of several large river basins in the Southwestern United States severely constrains the use of otherwise available major water supply sources. The Water Rights Analysis Package modeling system has been routinely applied in Texas since the late 1990s in regional and statewide planning studies and administration of the state's water rights permit system, but without consideration of water quality. The modeling system was recently expanded to incorporate salinity considerations in assessments of river/reservoir system capabilities for supplying water for environmental, municipal, agricultural, and industrial needs. Salinity loads and concentrations are tracked through systems of river reaches and reservoirs to develop concentration frequency statistics that augment flow frequency and water supply reliability metrics at pertinent locations for alternative water management strategies. Flexible generalized capabilities are developed for using limited observed salinity data to model highly variable concentrations imposed upon complex river regulation infrastructure and institutional water allocation/management practices.

  9. Incorporating process variability into stormwater quality modelling.

    PubMed

    Wijesiri, Buddhi; Egodawatta, Prasanna; McGree, James; Goonetilleke, Ashantha

    2015-11-15

    Process variability in pollutant build-up and wash-off generates inherent uncertainty that affects the outcomes of stormwater quality models. Poor characterisation of process variability constrains the accurate accounting of the uncertainty associated with pollutant processes. This acts as a significant limitation to effective decision making in relation to stormwater pollution mitigation. The study undertaken developed three theoretical scenarios based on research findings that variations in particle size fractions <150 μm and >150 μm during pollutant build-up and wash-off primarily determine the variability associated with these processes. These scenarios, which combine pollutant build-up and wash-off processes that takes place on a continuous timeline, are able to explain process variability under different field conditions. Given the variability characteristics of a specific build-up or wash-off event, the theoretical scenarios help to infer the variability characteristics of the associated pollutant process that follows. Mathematical formulation of the theoretical scenarios enables the incorporation of variability characteristics of pollutant build-up and wash-off processes in stormwater quality models. The research study outcomes will contribute to the quantitative assessment of uncertainty as an integral part of the interpretation of stormwater quality modelling outcomes.

  10. Incorporating uncertainty in predictive species distribution modelling

    PubMed Central

    Beale, Colin M.; Lennon, Jack J.

    2012-01-01

    Motivated by the need to solve ecological problems (climate change, habitat fragmentation and biological invasions), there has been increasing interest in species distribution models (SDMs). Predictions from these models inform conservation policy, invasive species management and disease-control measures. However, predictions are subject to uncertainty, the degree and source of which is often unrecognized. Here, we review the SDM literature in the context of uncertainty, focusing on three main classes of SDM: niche-based models, demographic models and process-based models. We identify sources of uncertainty for each class and discuss how uncertainty can be minimized or included in the modelling process to give realistic measures of confidence around predictions. Because this has typically not been performed, we conclude that uncertainty in SDMs has often been underestimated and a false precision assigned to predictions of geographical distribution. We identify areas where development of new statistical tools will improve predictions from distribution models, notably the development of hierarchical models that link different types of distribution model and their attendant uncertainties across spatial scales. Finally, we discuss the need to develop more defensible methods for assessing predictive performance, quantifying model goodness-of-fit and for assessing the significance of model covariates. PMID:22144387

  11. A Financial Market Model Incorporating Herd Behaviour.

    PubMed

    Wray, Christopher M; Bishop, Steven R

    2016-01-01

    Herd behaviour in financial markets is a recurring phenomenon that exacerbates asset price volatility, and is considered a possible contributor to market fragility. While numerous studies investigate herd behaviour in financial markets, it is often considered without reference to the pricing of financial instruments or other market dynamics. Here, a trader interaction model based upon informational cascades in the presence of information thresholds is used to construct a new model of asset price returns that allows for both quiescent and herd-like regimes. Agent interaction is modelled using a stochastic pulse-coupled network, parametrised by information thresholds and a network coupling probability. Agents may possess either one or two information thresholds that, in each case, determine the number of distinct states an agent may occupy before trading takes place. In the case where agents possess two thresholds (labelled as the finite state-space model, corresponding to agents' accumulating information over a bounded state-space), and where coupling strength is maximal, an asymptotic expression for the cascade-size probability is derived and shown to follow a power law when a critical value of network coupling probability is attained. For a range of model parameters, a mixture of negative binomial distributions is used to approximate the cascade-size distribution. This approximation is subsequently used to express the volatility of model price returns in terms of the model parameter which controls the network coupling probability. In the case where agents possess a single pulse-coupling threshold (labelled as the semi-infinite state-space model corresponding to agents' accumulating information over an unbounded state-space), numerical evidence is presented that demonstrates volatility clustering and long-memory patterns in the volatility of asset returns. Finally, output from the model is compared to both the distribution of historical stock returns and the market

  12. A Financial Market Model Incorporating Herd Behaviour

    PubMed Central

    2016-01-01

    Herd behaviour in financial markets is a recurring phenomenon that exacerbates asset price volatility, and is considered a possible contributor to market fragility. While numerous studies investigate herd behaviour in financial markets, it is often considered without reference to the pricing of financial instruments or other market dynamics. Here, a trader interaction model based upon informational cascades in the presence of information thresholds is used to construct a new model of asset price returns that allows for both quiescent and herd-like regimes. Agent interaction is modelled using a stochastic pulse-coupled network, parametrised by information thresholds and a network coupling probability. Agents may possess either one or two information thresholds that, in each case, determine the number of distinct states an agent may occupy before trading takes place. In the case where agents possess two thresholds (labelled as the finite state-space model, corresponding to agents’ accumulating information over a bounded state-space), and where coupling strength is maximal, an asymptotic expression for the cascade-size probability is derived and shown to follow a power law when a critical value of network coupling probability is attained. For a range of model parameters, a mixture of negative binomial distributions is used to approximate the cascade-size distribution. This approximation is subsequently used to express the volatility of model price returns in terms of the model parameter which controls the network coupling probability. In the case where agents possess a single pulse-coupling threshold (labelled as the semi-infinite state-space model corresponding to agents’ accumulating information over an unbounded state-space), numerical evidence is presented that demonstrates volatility clustering and long-memory patterns in the volatility of asset returns. Finally, output from the model is compared to both the distribution of historical stock returns and the

  13. A Financial Market Model Incorporating Herd Behaviour.

    PubMed

    Wray, Christopher M; Bishop, Steven R

    2016-01-01

    Herd behaviour in financial markets is a recurring phenomenon that exacerbates asset price volatility, and is considered a possible contributor to market fragility. While numerous studies investigate herd behaviour in financial markets, it is often considered without reference to the pricing of financial instruments or other market dynamics. Here, a trader interaction model based upon informational cascades in the presence of information thresholds is used to construct a new model of asset price returns that allows for both quiescent and herd-like regimes. Agent interaction is modelled using a stochastic pulse-coupled network, parametrised by information thresholds and a network coupling probability. Agents may possess either one or two information thresholds that, in each case, determine the number of distinct states an agent may occupy before trading takes place. In the case where agents possess two thresholds (labelled as the finite state-space model, corresponding to agents' accumulating information over a bounded state-space), and where coupling strength is maximal, an asymptotic expression for the cascade-size probability is derived and shown to follow a power law when a critical value of network coupling probability is attained. For a range of model parameters, a mixture of negative binomial distributions is used to approximate the cascade-size distribution. This approximation is subsequently used to express the volatility of model price returns in terms of the model parameter which controls the network coupling probability. In the case where agents possess a single pulse-coupling threshold (labelled as the semi-infinite state-space model corresponding to agents' accumulating information over an unbounded state-space), numerical evidence is presented that demonstrates volatility clustering and long-memory patterns in the volatility of asset returns. Finally, output from the model is compared to both the distribution of historical stock returns and the market

  14. Incorporating evolutionary processes into population viability models.

    PubMed

    Pierson, Jennifer C; Beissinger, Steven R; Bragg, Jason G; Coates, David J; Oostermeijer, J Gerard B; Sunnucks, Paul; Schumaker, Nathan H; Trotter, Meredith V; Young, Andrew G

    2015-06-01

    We examined how ecological and evolutionary (eco-evo) processes in population dynamics could be better integrated into population viability analysis (PVA). Complementary advances in computation and population genomics can be combined into an eco-evo PVA to offer powerful new approaches to understand the influence of evolutionary processes on population persistence. We developed the mechanistic basis of an eco-evo PVA using individual-based models with individual-level genotype tracking and dynamic genotype-phenotype mapping to model emergent population-level effects, such as local adaptation and genetic rescue. We then outline how genomics can allow or improve parameter estimation for PVA models by providing genotypic information at large numbers of loci for neutral and functional genome regions. As climate change and other threatening processes increase in rate and scale, eco-evo PVAs will become essential research tools to evaluate the effects of adaptive potential, evolutionary rescue, and locally adapted traits on persistence.

  15. Incorporating 3-dimensional models in online articles

    PubMed Central

    Cevidanes, Lucia H. S.; Ruellasa, Antonio C. O.; Jomier, Julien; Nguyen, Tung; Pieper, Steve; Budin, Francois; Styner, Martin; Paniagua, Beatriz

    2015-01-01

    Introduction The aims of this article were to introduce the capability to view and interact with 3-dimensional (3D) surface models in online publications, and to describe how to prepare surface models for such online 3D visualizations. Methods Three-dimensional image analysis methods include image acquisition, construction of surface models, registration in a common coordinate system, visualization of overlays, and quantification of changes. Cone-beam computed tomography scans were acquired as volumetric images that can be visualized as 3D projected images or used to construct polygonal meshes or surfaces of specific anatomic structures of interest. The anatomic structures of interest in the scans can be labeled with color (3D volumetric label maps), and then the scans are registered in a common coordinate system using a target region as the reference. The registered 3D volumetric label maps can be saved in .obj, .ply, .stl, or .vtk file formats and used for overlays, quantification of differences in each of the 3 planes of space, or color-coded graphic displays of 3D surface distances. Results All registered 3D surface models in this study were saved in .vtk file format and loaded in the Elsevier 3D viewer. In this study, we describe possible ways to visualize the surface models constructed from cone-beam computed tomography images using 2D and 3D figures. The 3D surface models are available in the article’s online version for viewing and downloading using the reader’s software of choice. These 3D graphic displays are represented in the print version as 2D snapshots. Overlays and color-coded distance maps can be displayed using the reader’s software of choice, allowing graphic assessment of the location and direction of changes or morphologic differences relative to the structure of reference. The interpretation of 3D overlays and quantitative color-coded maps requires basic knowledge of 3D image analysis. Conclusions When submitting manuscripts, authors can

  16. Incorporating covariates in skewed functional data models.

    PubMed

    Li, Meng; Staicu, Ana-Maria; Bondell, Howard D

    2015-07-01

    We introduce a class of covariate-adjusted skewed functional models (cSFM) designed for functional data exhibiting location-dependent marginal distributions. We propose a semi-parametric copula model for the pointwise marginal distributions, which are allowed to depend on covariates, and the functional dependence, which is assumed covariate invariant. The proposed cSFM framework provides a unifying platform for pointwise quantile estimation and trajectory prediction. We consider a computationally feasible procedure that handles densely as well as sparsely observed functional data. The methods are examined numerically using simulations and is applied to a new tractography study of multiple sclerosis. Furthermore, the methodology is implemented in the R package cSFM, which is publicly available on CRAN.

  17. Incorporating parametric uncertainty into population viability analysis models

    USGS Publications Warehouse

    McGowan, Conor P.; Runge, Michael C.; Larson, Michael A.

    2011-01-01

    Uncertainty in parameter estimates from sampling variation or expert judgment can introduce substantial uncertainty into ecological predictions based on those estimates. However, in standard population viability analyses, one of the most widely used tools for managing plant, fish and wildlife populations, parametric uncertainty is often ignored in or discarded from model projections. We present a method for explicitly incorporating this source of uncertainty into population models to fully account for risk in management and decision contexts. Our method involves a two-step simulation process where parametric uncertainty is incorporated into the replication loop of the model and temporal variance is incorporated into the loop for time steps in the model. Using the piping plover, a federally threatened shorebird in the USA and Canada, as an example, we compare abundance projections and extinction probabilities from simulations that exclude and include parametric uncertainty. Although final abundance was very low for all sets of simulations, estimated extinction risk was much greater for the simulation that incorporated parametric uncertainty in the replication loop. Decisions about species conservation (e.g., listing, delisting, and jeopardy) might differ greatly depending on the treatment of parametric uncertainty in population models.

  18. Generating expansion model incorporating compact DC power flow equations

    SciTech Connect

    Nderitu, D.G.; Sparrow, F.T.; Yu, Z.

    1998-12-31

    This paper presents a compact method of incorporating the spatial dimension into the generation expansion problem. Compact DC power flow equations are used to provide real-power flow coordination equations. Using these equations the marginal contribution of a generator to th total system loss is formulated as a function of that generator`s output. Incorporating these flow equations directly into the MIP formulation of the generator expansion problem results in a model that captures a generator`s true net marginal cost, one that includes both the cost of generation and the cost of transport. This method contrasts with other methods that iterate between a generator expansion model and an optimal power flow model. The proposed model is very compact and has very good convergence performance. A case study with data from Kenya is used to provide a practical application to the model.

  19. Incorporating RTI in a Hybrid Model of Reading Disability

    ERIC Educational Resources Information Center

    Spencer, Mercedes; Wagner, Richard K.; Schatschneider, Christopher; Quinn, Jamie M.; Lopez, Danielle; Petscher, Yaacov

    2014-01-01

    The present study seeks to evaluate a hybrid model of identification that incorporates response to instruction and intervention (RTI) as one of the key symptoms of reading disability. The 1-year stability of alternative operational definitions of reading disability was examined in a large-scale sample of students who were followed longitudinally…

  20. Incorporating Women's Speeches as Models in the Basic Course.

    ERIC Educational Resources Information Center

    Jensen, Marvin D.

    Studies indicate that there is a general lack of availability and use of women's speeches in college speech curricula. By incorporating more women's speeches as models, instructors of the basic course in speech can present a more complete picture of American public speaking while also encouraging women in these classes to feel less muted in their…

  1. "Violent Intent Modeling: Incorporating Cultural Knowledge into the Analytical Process

    SciTech Connect

    Sanfilippo, Antonio P.; Nibbs, Faith G.

    2007-08-24

    While culture has a significant effect on the appropriate interpretation of textual data, the incorporation of cultural considerations into data transformations has not been systematic. Recognizing that the successful prevention of terrorist activities could hinge on the knowledge of the subcultures, Anthropologist and DHS intern Faith Nibbs has been addressing the need to incorporate cultural knowledge into the analytical process. In this Brown Bag she will present how cultural ideology is being used to understand how the rhetoric of group leaders influences the likelihood of their constituents to engage in violent or radicalized behavior, and how violent intent modeling can benefit from understanding that process.

  2. Methods improvements incorporated into the SAPHIRE ASP models

    SciTech Connect

    Sattison, M.B.; Blackman, H.S.; Novack, S.D.

    1995-04-01

    The Office for Analysis and Evaluation of Operational Data (AEOD) has sought the assistance of the Idaho National Engineering Laboratory (INEL) to make some significant enhancements to the SAPHIRE-based Accident Sequence Precursor (ASP) models recently developed by the INEL. The challenge of this project is to provide the features of a full-scale PRA within the framework of the simplified ASP models. Some of these features include: (1) uncertainty analysis addressing the standard PRA uncertainties and the uncertainties unique to the ASP models and methods, (2) incorporation and proper quantification of individual human actions and the interaction among human actions, (3) enhanced treatment of common cause failures, and (4) extension of the ASP models to more closely mimic full-scale PRAs (inclusion of more initiators, explicitly modeling support system failures, etc.). This paper provides an overview of the methods being used to make the above improvements.

  3. Incorporating Auditory Models in Speech/Audio Applications

    NASA Astrophysics Data System (ADS)

    Krishnamoorthi, Harish

    2011-12-01

    Following the success in incorporating perceptual models in audio coding algorithms, their application in other speech/audio processing systems is expanding. In general, all perceptual speech/audio processing algorithms involve minimization of an objective function that directly/indirectly incorporates properties of human perception. This dissertation primarily investigates the problems associated with directly embedding an auditory model in the objective function formulation and proposes possible solutions to overcome high complexity issues for use in real-time speech/audio algorithms. Specific problems addressed in this dissertation include: 1) the development of approximate but computationally efficient auditory model implementations that are consistent with the principles of psychoacoustics, 2) the development of a mapping scheme that allows synthesizing a time/frequency domain representation from its equivalent auditory model output. The first problem is aimed at addressing the high computational complexity involved in solving perceptual objective functions that require repeated application of auditory model for evaluation of different candidate solutions. In this dissertation, a frequency pruning and a detector pruning algorithm is developed that efficiently implements the various auditory model stages. The performance of the pruned model is compared to that of the original auditory model for different types of test signals in the SQAM database. Experimental results indicate only a 4-7% relative error in loudness while attaining up to 80-90 % reduction in computational complexity. Similarly, a hybrid algorithm is developed specifically for use with sinusoidal signals and employs the proposed auditory pattern combining technique together with a look-up table to store representative auditory patterns. The second problem obtains an estimate of the auditory representation that minimizes a perceptual objective function and transforms the auditory pattern back to

  4. Cirrus cloud model parameterizations: Incorporating realistic ice particle generation

    NASA Technical Reports Server (NTRS)

    Sassen, Kenneth; Dodd, G. C.; Starr, David OC.

    1990-01-01

    Recent cirrus cloud modeling studies have involved the application of a time-dependent, two dimensional Eulerian model, with generalized cloud microphysical parameterizations drawn from experimental findings. For computing the ice versus vapor phase changes, the ice mass content is linked to the maintenance of a relative humidity with respect to ice (RHI) of 105 percent; ice growth occurs both with regard to the introduction of new particles and the growth of existing particles. In a simplified cloud model designed to investigate the basic role of various physical processes in the growth and maintenance of cirrus clouds, these parametric relations are justifiable. In comparison, the one dimensional cloud microphysical model recently applied to evaluating the nucleation and growth of ice crystals in cirrus clouds explicitly treated populations of haze and cloud droplets, and ice crystals. Although these two modeling approaches are clearly incompatible, the goal of the present numerical study is to develop a parametric treatment of new ice particle generation, on the basis of detailed microphysical model findings, for incorporation into improved cirrus growth models. For example, the relation between temperature and the relative humidity required to generate ice crystals from ammonium sulfate haze droplets, whose probability of freezing through the homogeneous nucleation mode are a combined function of time and droplet molality, volume, and temperature. As an example of this approach, the results of cloud microphysical simulations are presented showing the rather narrow domain in the temperature/humidity field where new ice crystals can be generated. The microphysical simulations point out the need for detailed CCN studies at cirrus altitudes and haze droplet measurements within cirrus clouds, but also suggest that a relatively simple treatment of ice particle generation, which includes cloud chemistry, can be incorporated into cirrus cloud growth.

  5. USEPA SHEDS MODEL: METHODOLOGY FOR EXPOSURE ASSESSMENT FOR WOOD PRESERVATIVES

    EPA Science Inventory

    A physically-based, Monte Carlo probabilistic model (SHEDS-Wood: Stochastic Human Exposure and Dose Simulation model for wood preservatives) has been applied to assess the exposure and dose of children to arsenic (As) and chromium (Cr) from contact with chromated copper arsenat...

  6. Incorporating microbes into large-scale biogeochemical models

    NASA Astrophysics Data System (ADS)

    Allison, S. D.; Martiny, J. B.

    2008-12-01

    Micro-organisms, including Bacteria, Archaea, and Fungi, control major processes throughout the Earth system. Recent advances in microbial ecology and microbiology have revealed an astounding level of genetic and metabolic diversity in microbial communities. However, a framework for interpreting the meaning of this diversity has lagged behind the initial discoveries. Microbial communities have yet to be included explicitly in any major biogeochemical models in terrestrial ecosystems, and have only recently broken into ocean models. Although simplification of microbial communities is essential in complex systems, omission of community parameters may seriously compromise model predictions of biogeochemical processes. Two key questions arise from this tradeoff: 1) When and where must microbial community parameters be included in biogeochemical models? 2) If microbial communities are important, how should they be simplified, aggregated, and parameterized in models? To address these questions, we conducted a meta-analysis to determine if microbial communities are sensitive to four environmental disturbances that are associated with global change. In all cases, we found that community composition changed significantly following disturbance. However, the implications for ecosystem function were unclear in most of the published studies. Therefore, we developed a simple model framework to illustrate the situations in which microbial community changes would affect rates of biogeochemical processes. We found that these scenarios could be quite common, but powerful predictive models cannot be developed without much more information on the functions and disturbance responses of microbial taxa. Small-scale models that explicitly incorporate microbial communities also suggest that process rates strongly depend on microbial interactions and disturbance responses. The challenge is to scale up these models to make predictions at the ecosystem and global scales based on measurable

  7. Safety models incorporating graph theory based transit indicators.

    PubMed

    Quintero, Liliana; Sayed, Tarek; Wahba, Mohamed M

    2013-01-01

    There is a considerable need for tools to enable the evaluation of the safety of transit networks at the planning stage. One interesting approach for the planning of public transportation systems is the study of networks. Network techniques involve the analysis of systems by viewing them as a graph composed of a set of vertices (nodes) and edges (links). Once the transport system is visualized as a graph, various network properties can be evaluated based on the relationships between the network elements. Several indicators can be calculated including connectivity, coverage, directness and complexity, among others. The main objective of this study is to investigate the relationship between network-based transit indicators and safety. The study develops macro-level collision prediction models that explicitly incorporate transit physical and operational elements and transit network indicators as explanatory variables. Several macro-level (zonal) collision prediction models were developed using a generalized linear regression technique, assuming a negative binomial error structure. The models were grouped into four main themes: transit infrastructure, transit network topology, transit route design, and transit performance and operations. The safety models showed that collisions were significantly associated with transit network properties such as: connectivity, coverage, overlapping degree and the Local Index of Transit Availability. As well, the models showed a significant relationship between collisions and some transit physical and operational attributes such as the number of routes, frequency of routes, bus density, length of bus and 3+ priority lanes.

  8. Incorporation of shuttle CCT parameters in computer simulation models

    NASA Technical Reports Server (NTRS)

    Huntsberger, Terry

    1990-01-01

    Computer simulations of shuttle missions have become increasingly important during recent years. The complexity of mission planning for satellite launch and repair operations which usually involve EVA has led to the need for accurate visibility and access studies. The PLAID modeling package used in the Man-Systems Division at Johnson currently has the necessary capabilities for such studies. In addition, the modeling package is used for spatial location and orientation of shuttle components for film overlay studies such as the current investigation of the hydrogen leaks found in the shuttle flight. However, there are a number of differences between the simulation studies and actual mission viewing. These include image blur caused by the finite resolution of the CCT monitors in the shuttle and signal noise from the video tubes of the cameras. During the course of this investigation the shuttle CCT camera and monitor parameters are incorporated into the existing PLAID framework. These parameters are specific for certain camera/lens combinations and the SNR characteristics of these combinations are included in the noise models. The monitor resolution is incorporated using a Gaussian spread function such as that found in the screen phosphors in the shuttle monitors. Another difference between the traditional PLAID generated images and actual mission viewing lies in the lack of shadows and reflections of light from surfaces. Ray tracing of the scene explicitly includes the lighting and material characteristics of surfaces. The results of some preliminary studies using ray tracing techniques for the image generation process combined with the camera and monitor effects are also reported.

  9. Incorporation of multiple cloud layers for ultraviolet radiation modeling studies

    NASA Technical Reports Server (NTRS)

    Charache, Darryl H.; Abreu, Vincent J.; Kuhn, William R.; Skinner, Wilbert R.

    1994-01-01

    Cloud data sets compiled from surface observations were used to develop an algorithm for incorporating multiple cloud layers into a multiple-scattering radiative transfer model. Aerosol extinction and ozone data sets were also incorporated to estimate the seasonally averaged ultraviolet (UV) flux reaching the surface of the Earth in the Detroit, Michigan, region for the years 1979-1991, corresponding to Total Ozone Mapping Spectrometer (TOMS) version 6 ozone observations. The calculated UV spectrum was convolved with an erythema action spectrum to estimate the effective biological exposure for erythema. Calculations show that decreasing the total column density of ozone by 1% leads to an increase in erythemal exposure by approximately 1.1-1.3%, in good agreement with previous studies. A comparison of the UV radiation budget at the surface between a single cloud layer method and a multiple cloud layer method presented here is discussed, along with limitations of each technique. With improved parameterization of cloud properties, and as knowledge of biological effects of UV exposure increase, inclusion of multiple cloud layers may be important in accurately determining the biologically effective UV budget at the surface of the Earth.

  10. Incorporating Plant Phenology Dynamics in a Biophysical Canopy Model

    NASA Technical Reports Server (NTRS)

    Barata, Raquel A.; Drewry, Darren

    2012-01-01

    The Multi-Layer Canopy Model (MLCan) is a vegetation model created to capture plant responses to environmental change. Themodel vertically resolves carbon uptake, water vapor and energy exchange at each canopy level by coupling photosynthesis, stomatal conductance and leaf energy balance. The model is forced by incoming shortwave and longwave radiation, as well as near-surface meteorological conditions. The original formulation of MLCan utilized canopy structural traits derived from observations. This project aims to incorporate a plant phenology scheme within MLCan allowing these structural traits to vary dynamically. In the plant phenology scheme implemented here, plant growth is dependent on environmental conditions such as air temperature and soil moisture. The scheme includes functionality that models plant germination, growth, and senescence. These growth stages dictate the variation in six different vegetative carbon pools: storage, leaves, stem, coarse roots, fine roots, and reproductive. The magnitudes of these carbon pools determine land surface parameters such as leaf area index, canopy height, rooting depth and root water uptake capacity. Coupling this phenology scheme with MLCan allows for a more flexible representation of the structure and function of vegetation as it responds to changing environmental conditions.

  11. Tantalum strength model incorporating temperature, strain rate and pressure

    NASA Astrophysics Data System (ADS)

    Lim, Hojun; Battaile, Corbett; Brown, Justin; Lane, Matt

    Tantalum is a body-centered-cubic (BCC) refractory metal that is widely used in many applications in high temperature, strain rate and pressure environments. In this work, we propose a physically-based strength model for tantalum that incorporates effects of temperature, strain rate and pressure. A constitutive model for single crystal tantalum is developed based on dislocation kink-pair theory, and calibrated to measurements on single crystal specimens. The model is then used to predict deformations of single- and polycrystalline tantalum. In addition, the proposed strength model is implemented into Sandia's ALEGRA solid dynamics code to predict plastic deformations of tantalum in engineering-scale applications at extreme conditions, e.g. Taylor impact tests and Z machine's high pressure ramp compression tests, and the results are compared with available experimental data. Sandia National Laboratories is a multi program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

  12. A dengue model incorporating saturation incidence and human migration

    NASA Astrophysics Data System (ADS)

    Gakkhar, S.; Mishra, A.

    2015-03-01

    In this paper, a non-linear model has been proposed to investigate the effects of human migration on dengue dynamics. Human migration has been considered between two patches having different dengue strains. Due to migration secondary infection is possible. Further, the secondary infection is considered in patch-2 only as strain-2 in patch-2 is considered to be more severe than that of strain-1 in patch-1. The saturation incidence rate has been considered to incorporate the behavioral changes towards epidemic in human population. The basic reproduction number has been computed. Four Equilibrium states have been found and analyzed. Increasing saturation rate decreases the threshold thereby enhancing the stability of disease-free state in both the patches. Control on migration may lead to change in infection level of patches.

  13. An SIRS Epidemic Model Incorporating Media Coverage with Time Delay

    PubMed Central

    Lin, Yiping; Dai, Yunxian

    2014-01-01

    An SIRS epidemic model incorporating media coverage with time delay is proposed. The positivity and boundedness are studied firstly. The locally asymptotical stability of the disease-free equilibrium and endemic equilibrium is studied in succession. And then, the conditions on which periodic orbits bifurcate are given. Furthermore, we show that the local Hopf bifurcation implies the global Hopf bifurcation after the second critical value of the delay. The obtained results show that the time delay in media coverage can not affect the stability of the disease-free equilibrium when the basic reproduction number R0 < 1. However, when R0 > 1, the stability of the endemic equilibrium will be affected by the time delay; there will be a family of periodic orbits bifurcating from the endemic equilibrium when the time delay increases through a critical value. Finally, some examples for numerical simulations are also included. PMID:24723967

  14. Incorporation of molybdenum in rubredoxin: models for mononuclear molybdenum enzymes.

    PubMed

    Maiti, Biplab K; Maia, Luisa B; Silveira, Célia M; Todorovic, Smilja; Carreira, Cintia; Carepo, Marta S P; Grazina, Raquel; Moura, Isabel; Pauleta, Sofia R; Moura, José J G

    2015-07-01

    Molybdenum is found in the active site of enzymes usually coordinated by one or two pyranopterin molecules. Here, we mimic an enzyme with a mononuclear molybdenum-bis pyranopterin center by incorporating molybdenum in rubredoxin. In the molybdenum-substituted rubredoxin, the metal ion is coordinated by four sulfurs from conserved cysteine residues of the apo-rubredoxin and two other exogenous ligands, oxygen and thiol, forming a Mo((VI))-(S-Cys)4(O)(X) complex, where X represents -OH or -SR. The rubredoxin molybdenum center is stabilized in a Mo(VI) oxidation state, but can be reduced to Mo(IV) via Mo(V) by dithionite, being a suitable model for the spectroscopic properties of resting and reduced forms of molybdenum-bis pyranopterin-containing enzymes. Preliminary experiments indicate that the molybdenum site built in rubredoxin can promote oxo transfer reactions, as exemplified with the oxidation of arsenite to arsenate.

  15. Incorporating Phaeocystis into a Southern Ocean ecosystem model

    NASA Astrophysics Data System (ADS)

    Wang, Shanlin; Moore, J. Keith

    2011-01-01

    Phaeocystis antarctica is an important phytoplankton species in the Southern Ocean. We incorporated P. antarctica into the biogeochemical elemental cycling ocean model to study Southern Ocean ecosystem dynamics and biogeochemistry. The optimum values of ecological parameters for Phaeocystis were sought through synthesizing laboratory and field observations, and the model output was evaluated with observed chlorophyll a, carbon biomass, and nutrient distributions. Several factors have been proposed to control Southern Ocean ecosystem structure, including light adaptation, iron uptake capability, and loss processes. Optimum simulation results were obtained when P. antarctica had a relatively high α (P-I curve initial slope) value and a higher half-saturation constant for iron uptake than other phytoplankton. Simulation results suggested that P. antarctica had a competitive advantage under low irradiance levels, especially in the Ross Sea and Weddell Sea. However, the distributions of P. antarctica and diatoms were also strongly influenced by iron availability. Although grazing rates had an influence on total biomass, our simulations did not show a strong influence of grazing pressure in the competition between P. antarctica and diatoms. However, limited observations and the relative simplicity of zooplankton in our model suggest further research is needed. Overall, P. antarctica contributed ˜13% of annual primary production and ˜19% of sinking carbon export in the Southern Ocean (>40°S) in our best case simulation. At higher latitudes (>60°S) P. antarctica accounts for ˜23% of annual primary production and ˜30% of sinking carbon export.

  16. Incorporation of Helium Demixing in Interior Structure Models of Saturn

    NASA Astrophysics Data System (ADS)

    Tian, Bob; Stanley, Sabine; Valencia, Diana

    2015-04-01

    Experiments and ab initio calculations of hydrogen-helium mixtures predict a phase separation at pressure-temperature conditions relevant to Saturn's interior. At depths where this occurs, droplets of helium form out of the mixture and sink towards the deep interiors where it re-mixes again, thereby depleting the helium above the layer over time while enriching the concentration below the layer. In dynamo modelling, the axisymmetric nature of Saturn's magnetic field is so far best explained by the inclusion of a stably stratified layer just below the depth at which hydrogen metallizes (approximately 0.65RS). Stable stratification at that depth could occur if the compositional gradients produced by the helium rain process described above is great enough to suppress convection in the de-mixing layers. Thus, we first developed a range of interior structure models consistent with available constraints of the gravity field and atmospheric composition. The hydrogen-helium de-mixing curve was then incorporated in calculations of some of these models to assess its feasibility in compositionally stratifying the top of the dynamo source region. We found that when helium rain is taken into account, a stably stratified layer approximately 0.1 - 0.15RS in thickness can exist atop the dynamo source region, consistent with thicknesses needed in dynamo models to axisymmetrize the observable magnetic field. Furthermore, inertial gravity waves could be excited in such thick stably stratified regions. These may be detectable by asteroseismology techniques, or by analysis of wave modes' gravitational interaction with Saturn's ring particles. Thus, profiles of sound speed and Brunt-Vaisala frequencies were also calculated for all of the interior structures models studied to be used for comparison with possible seismic studies in the future.

  17. Digital terrain model generalization incorporating scale, semantic and cognitive constraints

    NASA Astrophysics Data System (ADS)

    Partsinevelos, Panagiotis; Papadogiorgaki, Maria

    2014-05-01

    Cartographic generalization is a well-known process accommodating spatial data compression, visualization and comprehension under various scales. In the last few years, there are several international attempts to construct tangible GIS systems, forming real 3D surfaces using a vast number of mechanical parts along a matrix formation (i.e., bars, pistons, vacuums). Usually, moving bars upon a structured grid push a stretching membrane resulting in a smooth visualization for a given surface. Most of these attempts suffer either in their cost, accuracy, resolution and/or speed. Under this perspective, the present study proposes a surface generalization process that incorporates intrinsic constrains of tangible GIS systems including robotic-motor movement and surface stretching limitations. The main objective is to provide optimized visualizations of 3D digital terrain models with minimum loss of information. That is, to minimize the number of pixels in a raster dataset used to define a DTM, while reserving the surface information. This neighborhood type of pixel relations adheres to the basics of Self Organizing Map (SOM) artificial neural networks, which are often used for information abstraction since they are indicative of intrinsic statistical features contained in the input patterns and provide concise and characteristic representations. Nevertheless, SOM remains more like a black box procedure not capable to cope with possible particularities and semantics of the application at hand. E.g. for coastal monitoring applications, the near - coast areas, surrounding mountains and lakes are more important than other features and generalization should be "biased"-stratified to fulfill this requirement. Moreover, according to the application objectives, we extend the SOM algorithm to incorporate special types of information generalization by differentiating the underlying strategy based on topologic information of the objects included in the application. The final

  18. Implementing the Standards: Incorporating Mathematical Modeling into the Curriculum.

    ERIC Educational Resources Information Center

    Swetz, Frank

    1991-01-01

    Following a brief historical review of the mechanism of mathematical modeling, examples are included that associate a mathematical model with given data (changes in sea level) and that model a real-life situation (process of parallel parking). Also provided is the rationale for the curricular implementation of mathematical modeling. (JJK)

  19. A Measurement Model for Likert Responses that Incorporates Response Time

    ERIC Educational Resources Information Center

    Ferrando, Pere J.; Lorenzo-Seva, Urbano

    2007-01-01

    This article describes a model for response times that is proposed as a supplement to the usual factor-analytic model for responses to graded or more continuous typical-response items. The use of the proposed model together with the factor model provides additional information about the respondent and can potentially increase the accuracy of the…

  20. A PROBABILISTIC EXPOSURE ASSESSMENT FOR CHILDREN WHO CONTACT CCA-TREATED PLAYSETS AND DECKS USING THE STOCHASTIC HUMAN EXPOSURE AND DOSE SIMULATION (SHEDS) MODEL FOR THE WOOD PRESERVATIVE EXPOSURE SCENARIO

    EPA Science Inventory

    The U.S. Environmental Protection Agency has conducted a probabilistic exposure and dose assessment on the arsenic (As) and chromium (Cr) components of Chromated Copper Arsenate (CCA) using the Stochastic Human Exposure and Dose Simulation model for wood preservatives (SHEDS-Wood...

  1. A new nonlinear Muskingum flood routing model incorporating lateral flow

    NASA Astrophysics Data System (ADS)

    Karahan, Halil; Gurarslan, Gurhan; Geem, Zong Woo

    2015-06-01

    A new nonlinear Muskingum flood routing model taking the contribution from lateral flow into consideration was developed in the present study. The cuckoo search algorithm, a quite novel and robust algorithm, was used in the calibration and verification of the model parameters. The success and the dependability of the proposed model were tested on five different sets of synthetic and real flood data. The optimal solutions for the test cases were determined by the currently proposed model rather than by different models taken from the literature, indicating that this model could be suitable for use in flood routing problems.

  2. Incorporating Temperature-driven Seasonal Variation in Survival, Growth, and Reproduction Models for Small Fish

    EPA Science Inventory

    Seasonal variation in survival and reproduction can be a large source of prediction uncertainty in models used for conservation and management. A seasonally varying matrix population model is developed that incorporates temperature-driven differences in mortality and reproduction...

  3. Incorporation of the planetary boundary layer in atmospheric models

    NASA Technical Reports Server (NTRS)

    Moeng, Chin-Hoh; Wyngaard, John; Pielke, Roger; Krueger, Steve

    1993-01-01

    The topics discussed include the following: perspectives on planetary boundary layer (PBL) measurements; current problems of PBL parameterization in mesoscale models; and convective cloud-PBL interactions.

  4. Progressive evaluation of incorporating information into a model building process

    NASA Astrophysics Data System (ADS)

    Gharari, Shervan; Hrachowitz, Markus; Fenicia, Fabrizio; Gao, Hongkai; Gupta, Hoshin; Savenije, Huub

    2014-05-01

    Catchments are open systems meaning that it is impossible to find out the exact boundary conditions of the real system spatially and temporarily. Therefore models are essential tools in capturing system behaviour spatially and extrapolating it temporarily for prediction. In recent years conceptual models have been in the center of attention rather than so called physically based models which are often over-parameterized and encounter difficulties for up-scaling of small scale processes. Conceptual models however are heavily dependent on calibration as one or more of their parameter values can typically not be physically measured at the catchment scale. The general understanding is based on the fact that increasing the complexity of conceptual model for better representation of hydrological process heterogeneity typically makes parameter identification more difficult however the evaluation of the amount of information given by each of the model elements, control volumes (so called buckets), interconnecting fluxes, parameterization (constitutive functions) and finally parameter values are rather unknown. Each of the mentioned components of a model contains information on the transformation of forcing (precipitation) into runoff, however the effect of each of them solely and together is not well understood. In this study we follow hierarchal steps for model building, firstly the model structure is built by its building blocks (control volumes) as well as interconnecting fluxes. The effect of adding every control volumes and the architecture of the model (formation of control volumes and fluxes) can be evaluated in this level. In the second layer the parameterization of model is evaluated. As an example the effect of a specific type of stage-discharge relation for a control volume can be explored. Finally in the last step of the model building the information gained by parameter values are quantified. In each development level the value of information which are added

  5. A Model for Library Book Circulations Incorporating Loan Periods.

    ERIC Educational Resources Information Center

    Burrell, Quentin L.; Fenton, Michael R.

    1994-01-01

    Proposes and explains a modification of the mixed Poisson model for library circulations which takes into account the periods when a book is out on loan and therefore unavailable for borrowing. Highlights include frequency of circulation distributions; negative binomial distribution; and examples of the model at two universities. (Contains 34…

  6. A transient stochastic weather generator incorporating climate model uncertainty

    NASA Astrophysics Data System (ADS)

    Glenis, Vassilis; Pinamonti, Valentina; Hall, Jim W.; Kilsby, Chris G.

    2015-11-01

    Stochastic weather generators (WGs), which provide long synthetic time series of weather variables such as rainfall and potential evapotranspiration (PET), have found widespread use in water resources modelling. When conditioned upon the changes in climatic statistics (change factors, CFs) predicted by climate models, WGs provide a useful tool for climate impacts assessment and adaption planning. The latest climate modelling exercises have involved large numbers of global and regional climate models integrations, designed to explore the implications of uncertainties in the climate model formulation and parameter settings: so called 'perturbed physics ensembles' (PPEs). In this paper we show how these climate model uncertainties can be propagated through to impact studies by testing multiple vectors of CFs, each vector derived from a different sample from a PPE. We combine this with a new methodology to parameterise the projected time-evolution of CFs. We demonstrate how, when conditioned upon these time-dependent CFs, an existing, well validated and widely used WG can be used to generate non-stationary simulations of future climate that are consistent with probabilistic outputs from the Met Office Hadley Centre's Perturbed Physics Ensemble. The WG enables extensive sampling of natural variability and climate model uncertainty, providing the basis for development of robust water resources management strategies in the context of a non-stationary climate.

  7. Incorporating measurement error in n = 1 psychological autoregressive modeling.

    PubMed

    Schuurman, Noémi K; Houtveen, Jan H; Hamaker, Ellen L

    2015-01-01

    Measurement error is omnipresent in psychological data. However, the vast majority of applications of autoregressive time series analyses in psychology do not take measurement error into account. Disregarding measurement error when it is present in the data results in a bias of the autoregressive parameters. We discuss two models that take measurement error into account: An autoregressive model with a white noise term (AR+WN), and an autoregressive moving average (ARMA) model. In a simulation study we compare the parameter recovery performance of these models, and compare this performance for both a Bayesian and frequentist approach. We find that overall, the AR+WN model performs better. Furthermore, we find that for realistic (i.e., small) sample sizes, psychological research would benefit from a Bayesian approach in fitting these models. Finally, we illustrate the effect of disregarding measurement error in an AR(1) model by means of an empirical application on mood data in women. We find that, depending on the person, approximately 30-50% of the total variance was due to measurement error, and that disregarding this measurement error results in a substantial underestimation of the autoregressive parameters.

  8. Markov modulated Poisson process models incorporating covariates for rainfall intensity.

    PubMed

    Thayakaran, R; Ramesh, N I

    2013-01-01

    Time series of rainfall bucket tip times at the Beaufort Park station, Bracknell, in the UK are modelled by a class of Markov modulated Poisson processes (MMPP) which may be thought of as a generalization of the Poisson process. Our main focus in this paper is to investigate the effects of including covariate information into the MMPP model framework on statistical properties. In particular, we look at three types of time-varying covariates namely temperature, sea level pressure, and relative humidity that are thought to be affecting the rainfall arrival process. Maximum likelihood estimation is used to obtain the parameter estimates, and likelihood ratio tests are employed in model comparison. Simulated data from the fitted model are used to make statistical inferences about the accumulated rainfall in the discrete time interval. Variability of the daily Poisson arrival rates is studied.

  9. Incorporating principal component analysis into air quality model evaluation

    EPA Science Inventory

    The efficacy of standard air quality model evaluation techniques is becoming compromised as the simulation periods continue to lengthen in response to ever increasing computing capacity. Accordingly, the purpose of this paper is to demonstrate a statistical approach called Princi...

  10. Viral dynamics model with CTL immune response incorporating antiretroviral therapy.

    PubMed

    Wang, Yan; Zhou, Yicang; Brauer, Fred; Heffernan, Jane M

    2013-10-01

    We present two HIV models that include the CTL immune response, antiretroviral therapy and a full logistic growth term for uninfected CD4+ T-cells. The difference between the two models lies in the inclusion or omission of a loss term in the free virus equation. We obtain critical conditions for the existence of one, two or three steady states, and analyze the stability of these steady states. Through numerical simulation we find substantial differences in the reproduction numbers and the behaviour at the infected steady state between the two models, for certain parameter sets. We explore the effect of varying the combination drug efficacy on model behaviour, and the possibility of reconstituting the CTL immune response through antiretroviral therapy. Furthermore, we employ Latin hypercube sampling to investigate the existence of multiple infected equilibria. PMID:22930342

  11. NEXT-GENERATION NUMERICAL MODELING: INCORPORATING ELASTICITY, ANISOTROPY AND ATTENUATION

    SciTech Connect

    S. LARSEN; ET AL

    2001-03-01

    A new effort has been initiated between the Department of Energy (DOE) and the Society of Exploration Geophysicists (SEG) to investigate what features the next generation of numerical seismic models should contain that will best address current technical problems encountered during exploration in increasingly complex geologies. This collaborative work is focused on designing and building these new models, generating synthetic seismic data through simulated surveys of various geometries, and using these data to test and validate new and improved seismic imaging algorithms. The new models will be both 2- and 3-dimensional and will include complex velocity structures as well as anisotropy and attenuation. Considerable attention is being focused on multi-component acoustic and elastic effects because it is now widely recognized that converted phases could play a vital role in improving the quality of seismic images. An existing, validated 3-D elastic modeling code is being used to generate the synthetic data. Preliminary elastic modeling results using this code are presented here along with a description of the proposed new models that will be built and tested.

  12. Stochastic modelling of landfill leachate and biogas production incorporating waste heterogeneity. Model formulation and uncertainty analysis.

    PubMed

    Zacharof, A I; Butler, A P

    2004-01-01

    A mathematical model simulating the hydrological and biochemical processes occurring in landfilled waste is presented and demonstrated. The model combines biochemical and hydrological models into an integrated representation of the landfill environment. Waste decomposition is modelled using traditional biochemical waste decomposition pathways combined with a simplified methodology for representing the rate of decomposition. Water flow through the waste is represented using a statistical velocity model capable of representing the effects of waste heterogeneity on leachate flow through the waste. Given the limitations in data capture from landfill sites, significant emphasis is placed on improving parameter identification and reducing parameter requirements. A sensitivity analysis is performed, highlighting the model's response to changes in input variables. A model test run is also presented, demonstrating the model capabilities. A parameter perturbation model sensitivity analysis was also performed. This has been able to show that although the model is sensitive to certain key parameters, its overall intuitive response provides a good basis for making reasonable predictions of the future state of the landfill system. Finally, due to the high uncertainty associated with landfill data, a tool for handling input data uncertainty is incorporated in the model's structure. It is concluded that the model can be used as a reasonable tool for modelling landfill processes and that further work should be undertaken to assess the model's performance. PMID:15120429

  13. GENERALIZED PARTIALLY LINEAR MIXED-EFFECTS MODELS INCORPORATING MISMEASURED COVARIATES

    PubMed Central

    Liang, Hua

    2009-01-01

    In this article we consider a semiparametric generalized mixed-effects model, and propose combining local linear regression, and penalized quasilikelihood and local quasilikelihood techniques to estimate both population and individual parameters and nonparametric curves. The proposed estimators take into account the local correlation structure of the longitudinal data. We establish normality for the estimators of the parameter and asymptotic expansion for the estimators of the nonparametric part. For practical implementation, we propose an appropriate algorithm. We also consider the measurement error problem in covariates in our model, and suggest a strategy for adjusting the effects of measurement errors. We apply the proposed models and methods to study the relation between virologic and immunologic responses in AIDS clinical trials, in which virologic response is classified into binary variables. A dataset from an AIDS clinical study is analyzed. PMID:20160899

  14. INCORPORATING CONCENTRATION DEPENDENCE IN STABLE ISOTOPE MIXING MODELS

    EPA Science Inventory

    Stable isotopes are frequently used to quantify the contributions of multiple sources to a mixture; e.g., C and N isotopic signatures can be used to determine the fraction of three food sources in a consumer's diet. The standard dual isotope, three source linear mixing model ass...

  15. Incorporating grassland management in a global vegetation model

    NASA Astrophysics Data System (ADS)

    Chang, Jinfeng; Viovy, Nicolas; Vuichard, Nicolas; Ciais, Philippe; Wang, Tao; Cozic, Anne; Lardy, Romain; Graux, Anne-Isabelle; Klumpp, Katja; Martin, Raphael; Soussana, Jean-François

    2013-04-01

    Grassland is a widespread vegetation type, covering nearly one-fifth of the world's land surface (24 million km2), and playing a significant role in the global carbon (C) cycle. Most of grasslands in Europe are cultivated to feed animals, either directly by grazing or indirectly by grass harvest (cutting). A better understanding of the C fluxes from grassland ecosystems in response to climate and management requires not only field experiments but also the aid of simulation models. ORCHIDEE process-based ecosystem model designed for large-scale applications treats grasslands as being unmanaged, where C / water fluxes are only subject to atmospheric CO2 and climate changes. Our study describes how management of grasslands is included in the ORCHIDEE, and how management affects modeled grassland-atmosphere CO2 fluxes. The new model, ORCHIDEE-GM (Grassland Management) is capable with a management module inspired from a grassland model (PaSim, version 5.0), of accounting for two grassland management practices (cutting and grazing). The evaluation of the results of ORCHIDEE-GM compared with those of ORCHIDEE at 11 European sites equipped with eddy covariance and biometric measurements, show that ORCHIDEE-GM can capture realistically the cut-induced seasonal variation in biometric variables (LAI: Leaf Area Index; AGB: Aboveground Biomass) and in CO2 fluxes (GPP: Gross Primary Productivity; TER: Total Ecosystem Respiration; and NEE: Net Ecosystem Exchange). But improvements at grazing sites are only marginal in ORCHIDEE-GM, which relates to the difficulty in accounting for continuous grazing disturbance and its induced complex animal-vegetation interactions. Both NEE and GPP on monthly to annual timescales can be better simulated in ORCHIDEE-GM than in ORCHIDEE without management. At some sites, the model-observation misfit in ORCHIDEE-GM is found to be more related to ill-constrained parameter values than to model structure. Additionally, ORCHIDEE-GM is able to simulate

  16. Incorporating Spatial Models in Visual Field Test Procedures

    PubMed Central

    Rubinstein, Nikki J.; McKendrick, Allison M.; Turpin, Andrew

    2016-01-01

    Purpose To introduce a perimetric algorithm (Spatially Weighted Likelihoods in Zippy Estimation by Sequential Testing [ZEST] [SWeLZ]) that uses spatial information on every presentation to alter visual field (VF) estimates, to reduce test times without affecting output precision and accuracy. Methods SWeLZ is a maximum likelihood Bayesian procedure, which updates probability mass functions at VF locations using a spatial model. Spatial models were created from empirical data, computational models, nearest neighbor, random relationships, and interconnecting all locations. SWeLZ was compared to an implementation of the ZEST algorithm for perimetry using computer simulations on 163 glaucomatous and 233 normal VFs (Humphrey Field Analyzer 24-2). Output measures included number of presentations and visual sensitivity estimates. Results There was no significant difference in accuracy or precision of SWeLZ for the different spatial models relative to ZEST, either when collated across whole fields or when split by input sensitivity. Inspection of VF maps showed that SWeLZ was able to detect localized VF loss. SWeLZ was faster than ZEST for normal VFs: median number of presentations reduced by 20% to 38%. The number of presentations was equivalent for SWeLZ and ZEST when simulated on glaucomatous VFs. Conclusions SWeLZ has the potential to reduce VF test times in people with normal VFs, without detriment to output precision and accuracy in glaucomatous VFs. Translational Relevance SWeLZ is a novel perimetric algorithm. Simulations show that SWeLZ can reduce the number of test presentations for people with normal VFs. Since many patients have normal fields, this has the potential for significant time savings in clinical settings. PMID:26981329

  17. Incorporating inheritance into models for understanding ventilatory behavior.

    PubMed

    Strohl, K P; Subramanian, S; Han, F; Principe, K; Dick, T E

    2001-01-01

    Ventilation and its components (frequency and tidal volume) appear to be determined to a significant extent by inheritance. Gene manipulation, gene identification, and functional genomics now offer powerful tools to identify the strength and mode of inheritance for ventilatory behavior under steady-state and non-steady-state conditions, in health and in disease. Conscious integration of genetic principles into existing explanatory models may increase the likelihood of detecting traits that correlate with protein systems responsible for the structures and the functional components of respiration.

  18. Design Protocols and Analytical Strategies that Incorporate Structural Reliability Models

    NASA Technical Reports Server (NTRS)

    Duffy, Stephen F.

    1997-01-01

    Ceramic matrix composites (CMC) and intermetallic materials (e.g., single crystal nickel aluminide) are high performance materials that exhibit attractive mechanical, thermal and chemical properties. These materials are critically important in advancing certain performance aspects of gas turbine engines. From an aerospace engineer's perspective the new generation of ceramic composites and intermetallics offers a significant potential for raising the thrust/weight ratio and reducing NO(x) emissions of gas turbine engines. These aspects have increased interest in utilizing these materials in the hot sections of turbine engines. However, as these materials evolve and their performance characteristics improve a persistent need exists for state-of-the-art analytical methods that predict the response of components fabricated from CMC and intermetallic material systems. This need provided the motivation for the technology developed under this research effort. Continuous ceramic fiber composites exhibit an increase in work of fracture, which allows for "graceful" rather than catastrophic failure. When loaded in the fiber direction, these composites retain substantial strength capacity beyond the initiation of transverse matrix cracking despite the fact that neither of its constituents would exhibit such behavior if tested alone. As additional load is applied beyond first matrix cracking, the matrix tends to break in a series of cracks bridged by the ceramic fibers. Any additional load is born increasingly by the fibers until the ultimate strength of the composite is reached. Thus modeling efforts supported under this research effort have focused on predicting this sort of behavior. For single crystal intermetallics the issues that motivated the technology development involved questions relating to material behavior and component design. Thus the research effort supported by this grant had to determine the statistical nature and source of fracture in a high strength, Ni

  19. Design Protocols and Analytical Strategies that Incorporate Structural Reliability Models

    NASA Technical Reports Server (NTRS)

    Duffy, Stephen F.

    1997-01-01

    Ceramic matrix composites (CMC) and intermetallic materials (e.g., single crystal nickel aluminide) are high performance materials that exhibit attractive mechanical, thermal, and chemical properties. These materials are critically important in advancing certain performance aspects of gas turbine engines. From an aerospace engineers perspective the new generation of ceramic composites and intermetallics offers a significant potential for raising the thrust/weight ratio and reducing NO(sub x) emissions of gas turbine engines. These aspects have increased interest in utilizing these materials in the hot sections of turbine engines. However, as these materials evolve and their performance characteristics improve a persistent need exists for state-of-the-art analytical methods that predict the response of components fabricated from CMC and intermetallic material systems. This need provided the motivation for the technology developed under this research effort. Continuous ceramic fiber composites exhibit an increase in work of fracture, which allows for 'graceful' rather than catastrophic failure. When loaded in the fiber direction these composites retain substantial strength capacity beyond the initiation of transverse matrix cracking despite the fact that neither of its constituents would exhibit such behavior if tested alone. As additional load is applied beyond first matrix cracking, the matrix tends to break in a series of cracks bridged by the ceramic fibers. Any additional load is born increasingly by the fibers until the ultimate strength of the composite is reached. Thus modeling efforts supported under this research effort have focused on predicting this sort of behavior. For single crystal intermetallics the issues that motivated the technology development involved questions relating to material behavior and component design. Thus the research effort supported by this grant had to determine the statistical nature and source of fracture in a high strength, Ni

  20. Incorporating affective bias in models of human decision making

    NASA Technical Reports Server (NTRS)

    Nygren, Thomas E.

    1991-01-01

    Research on human decision making has traditionally focused on how people actually make decisions, how good their decisions are, and how their decisions can be improved. Recent research suggests that this model is inadequate. Affective as well as cognitive components drive the way information about relevant outcomes and events is perceived, integrated, and used in the decision making process. The affective components include how the individual frames outcomes as good or bad, whether the individual anticipates regret in a decision situation, the affective mood state of the individual, and the psychological stress level anticipated or experienced in the decision situation. A focus of the current work has been to propose empirical studies that will attempt to examine in more detail the relationships between the latter two critical affective influences (mood state and stress) on decision making behavior.

  1. Incorporating tracer-tracee differences into models to improve accuracy

    SciTech Connect

    Schoeller, D.A. )

    1991-05-01

    The ideal tracer for metabolic studies is one that behaves exactly like the tracee. Compounds labeled with isotopes come the closest to this ideal because they are chemically identical to the tracee except for the substitution of a stable or radioisotope at one or more positions. Even this substitution, however, can introduce a difference in metabolism that may be quantitatively important with regard to the development of the mathematical model used to interpret the kinetic data. The doubly labeled water method for the measurement of carbon dioxide production and hence energy expenditure in free-living subjects is a good example of how differences between the metabolism of the tracers and the tracee can influence the accuracy of the carbon dioxide production rate determined from the kinetic data.

  2. Incorporating flood event analyses and catchment structures into model development

    NASA Astrophysics Data System (ADS)

    Oppel, Henning; Schumann, Andreas

    2016-04-01

    The space-time variability in catchment response results from several hydrological processes which differ in their relevance in an event-specific way. An approach to characterise this variance consists in comparisons between flood events in a catchment and between flood responses of several sub-basins in such an event. In analytical frameworks the impact of space and time variability of rainfall on runoff generation due to rainfall excess can be characterised. Moreover the effect of hillslope and channel network routing on runoff timing can be specified. Hence, a modelling approach is needed to specify the runoff generation and formation. Knowing the space-time variability of rainfall and the (spatial averaged) response of a catchment it seems worthwhile to develop new models based on event and catchment analyses. The consideration of spatial order and the distribution of catchment characteristics in their spatial variability and interaction with the space-time variability of rainfall provides additional knowledge about hydrological processes at the basin scale. For this purpose a new procedure to characterise the spatial heterogeneity of catchments characteristics in their succession along the flow distance (differentiated between river network and hillslopes) was developed. It was applied to study of flood responses at a set of nested catchments in a river basin in eastern Germany. In this study the highest observed rainfall-runoff events were analysed, beginning at the catchment outlet and moving upstream. With regard to the spatial heterogeneities of catchment characteristics, sub-basins were separated by new algorithms to attribute runoff-generation, hillslope and river network processes. With this procedure the cumulative runoff response at the outlet can be decomposed and individual runoff features can be assigned to individual aspects of the catchment. Through comparative analysis between the sub-catchments and the assigned effects on runoff dynamics new

  3. INCORPORATING CONCENTRATION DEPENDENCE IN STABLE ISOTOPE MIXING MODELS: A REPLY TO ROBBINS, HILDERBRAND AND FARLEY (2002)

    EPA Science Inventory

    Phillips & Koch (2002) outlined a new stable isotope mixing model which incorporates differences in elemental concentrations in the determinations of source proportions in a mixture. They illustrated their method with sensitivity analyses and two examples from the wildlife ecolog...

  4. Joint modelling of longitudinal and survival data: incorporating delayed entry and an assessment of model misspecification.

    PubMed

    Crowther, Michael J; Andersson, Therese M-L; Lambert, Paul C; Abrams, Keith R; Humphreys, Keith

    2016-03-30

    A now common goal in medical research is to investigate the inter-relationships between a repeatedly measured biomarker, measured with error, and the time to an event of interest. This form of question can be tackled with a joint longitudinal-survival model, with the most common approach combining a longitudinal mixed effects model with a proportional hazards survival model, where the models are linked through shared random effects. In this article, we look at incorporating delayed entry (left truncation), which has received relatively little attention. The extension to delayed entry requires a second set of numerical integration, beyond that required in a standard joint model. We therefore implement two sets of fully adaptive Gauss-Hermite quadrature with nested Gauss-Kronrod quadrature (to allow time-dependent association structures), conducted simultaneously, to evaluate the likelihood. We evaluate fully adaptive quadrature compared with previously proposed non-adaptive quadrature through a simulation study, showing substantial improvements, both in terms of minimising bias and reducing computation time. We further investigate, through simulation, the consequences of misspecifying the longitudinal trajectory and its impact on estimates of association. Our scenarios showed the current value association structure to be very robust, compared with the rate of change that we found to be highly sensitive showing that assuming a simpler trend when the truth is more complex can lead to substantial bias. With emphasis on flexible parametric approaches, we generalise previous models by proposing the use of polynomials or splines to capture the longitudinal trend and restricted cubic splines to model the baseline log hazard function. The methods are illustrated on a dataset of breast cancer patients, modelling mammographic density jointly with survival, where we show how to incorporate density measurements prior to the at-risk period, to make use of all the available

  5. Incorporating channel network information in hydrologic response modelling: model development and validation using ecologically relevant indicators

    NASA Astrophysics Data System (ADS)

    Biswal, B.; Singh, R.

    2015-12-01

    Many studies in the past have revealed that hydrologic response of a basin carries imprints of its channel network. However, accurate representation of channel networks in hydrologic models has been a challenge. In addition, dominating flow processes during high flow periods are not the same as those during recession periods, and there is a need for models that can represent these varying behaviors. In this study, we develop two model structures that aim to address the challenges above. The first model assumes that flow processes can be classified into two main categories: i) pure surface flow (PSF) and ii) mixed surface-subsurface flow (MSSF). The second model is a special case of the first model which neglects PSF. Using channel networks extracted from digital elevation models, we develop instantaneous unit hydrographs (IUHs) separately for PSF (PSFIUHs) and MSSF (MSSFIUHs). PSFIUH is descried by the channel 'network width function', whereas MSSFIUH is obtained by modifying a recently developed channel network morphology based recession flow model. To obtain the simulated streamflow time series for a basin, we convolute the PSFIUH and the MSSFIUH with the respective effective rainfall time series. The effective rainfall time series is obtained by using the probability distributed model (PDM). For comparison purposes, we also use a dual linear-bucket model for routing flow. Comparing model performance across 78 watersheds in the United States using the Nash Sutcliffe efficiency (NSE), we find that the two model structures that incorporate channel network information outperform the linear-bucket model in 56 watersheds. Further testing model performance using indicators that capture frequency and duration of low and high flows shows that the two developed models outperform the linear-bucket model in four out of five indicators.

  6. Models of Jupiter's growth incorporating thermal and hydrodynamic constraints

    NASA Astrophysics Data System (ADS)

    Lissauer, Jack J.; Hubickyj, Olenka; D'Angelo, Gennaro; Bodenheimer, Peter

    2009-02-01

    We model the growth of Jupiter via core nucleated accretion, applying constraints from hydrodynamical processes that result from the disk-planet interaction. We compute the planet's internal structure using a well tested planetary formation code that is based upon a Henyey-type stellar evolution code. The planet's interactions with the protoplanetary disk are calculated using 3-D hydrodynamic simulations. Previous models of Jupiter's growth have taken the radius of the planet to be approximately one Hill sphere radius, R. However, 3-D hydrodynamic simulations show that only gas within ˜0.25R remains bound to the planet, with the more distant gas eventually participating in the shear flow of the protoplanetary disk. Therefore in our new simulations, the planet's outer boundary is placed at the location where gas has the thermal energy to reach the portion of the flow not bound to the planet. We find that the smaller radius increases the time required for planetary growth by ˜5%. Thermal pressure limits the rate at which a planet less than a few dozen times as massive as Earth can accumulate gas from the protoplanetary disk, whereas hydrodynamics regulates the growth rate for more massive planets. Within a moderately viscous disk, the accretion rate peaks when the planet's mass is about equal to the mass of Saturn. In a less viscous disk hydrodynamical limits to accretion are smaller, and the accretion rate peaks at lower mass. Observations suggest that the typical lifetime of massive disks around young stellar objects is ˜3 Myr. To account for the dissipation of such disks, we perform some of our simulations of Jupiter's growth within a disk whose surface gas density decreases on this timescale. In all of the cases that we simulate, the planet's effective radiating temperature rises to well above 1000 K soon after hydrodynamic limits begin to control the rate of gas accretion and the planet's distended envelope begins to contract. According to our simulations

  7. Incorporating the life course model into MCH nutrition leadership education and training programs.

    PubMed

    Haughton, Betsy; Eppig, Kristen; Looney, Shannon M; Cunningham-Sabo, Leslie; Spear, Bonnie A; Spence, Marsha; Stang, Jamie S

    2013-01-01

    Life course perspective, social determinants of health, and health equity have been combined into one comprehensive model, the life course model (LCM), for strategic planning by US Health Resources and Services Administration's Maternal and Child Health Bureau. The purpose of this project was to describe a faculty development process; identify strategies for incorporation of the LCM into nutrition leadership education and training at the graduate and professional levels; and suggest broader implications for training, research, and practice. Nineteen representatives from 6 MCHB-funded nutrition leadership education and training programs and 10 federal partners participated in a one-day session that began with an overview of the models and concluded with guided small group discussions on how to incorporate them into maternal and child health (MCH) leadership training using obesity as an example. Written notes from group discussions were compiled and coded emergently. Content analysis determined the most salient themes about incorporating the models into training. Four major LCM-related themes emerged, three of which were about training: (1) incorporation by training grants through LCM-framed coursework and experiences for trainees, and similarly framed continuing education and skills development for professionals; (2) incorporation through collaboration with other training programs and state and community partners, and through advocacy; and (3) incorporation by others at the federal and local levels through policy, political, and prevention efforts. The fourth theme focused on anticipated challenges of incorporating the model in training. Multiple methods for incorporating the LCM into MCH training and practice are warranted. Challenges to incorporating include the need for research and related policy development.

  8. Efficiency improvement in a class of survival models through model-free covariate incorporation.

    PubMed

    Garcia, Tanya P; Ma, Yanyuan; Yin, Guosheng

    2011-10-01

    In randomized clinical trials, we are often concerned with comparing two-sample survival data. Although the log-rank test is usually suitable for this purpose, it may result in substantial power loss when the two groups have nonproportional hazards. In a more general class of survival models of Yang and Prentice (Biometrika 92:1-17, 2005), which includes the log-rank test as a special case, we improve model efficiency by incorporating auxiliary covariates that are correlated with the survival times. In a model-free form, we augment the estimating equation with auxiliary covariates, and establish the efficiency improvement using the semiparametric theories in Zhang et al. (Biometrics 64:707-715, 2008) and Lu and Tsiatis (Biometrics, 95:674-679, 2008). Under minimal assumptions, our approach produces an unbiased, asymptotically normal estimator with additional efficiency gain. Simulation studies and an application to a leukemia study show the satisfactory performance of the proposed method. PMID:21455700

  9. Incorporating phosphorus cycling into global modeling efforts: a worthwhile, tractable endeavor

    USGS Publications Warehouse

    Reed, Sasha C.; Yang, Xiaojuan; Thornton, Peter E.

    2015-01-01

    Myriad field, laboratory, and modeling studies show that nutrient availability plays a fundamental role in regulating CO2 exchange between the Earth's biosphere and atmosphere, and in determining how carbon pools and fluxes respond to climatic change. Accordingly, global models that incorporate coupled climate–carbon cycle feedbacks made a significant advance with the introduction of a prognostic nitrogen cycle. Here we propose that incorporating phosphorus cycling represents an important next step in coupled climate–carbon cycling model development, particularly for lowland tropical forests where phosphorus availability is often presumed to limit primary production. We highlight challenges to including phosphorus in modeling efforts and provide suggestions for how to move forward.

  10. A new car-following model with the consideration of incorporating timid and aggressive driving behaviors

    NASA Astrophysics Data System (ADS)

    Peng, Guanghan; He, Hongdi; Lu, Wei-Zhen

    2016-01-01

    In this paper, a new car-following model is proposed with the consideration of the incorporating timid and aggressive behaviors on single lane. The linear stability condition with the incorporating timid and aggressive behaviors term is obtained. Numerical simulation indicates that the new car-following model can estimate proper delay time of car motion and kinematic wave speed at jam density by considering the incorporating the timid and aggressive behaviors. The results also show that the aggressive behavior can improve traffic flow while the timid behavior deteriorates traffic stability, which means that the aggressive behavior is better than timid behavior since the aggressive driver makes rapid response to the variation of the velocity of the leading car. Snapshot of the velocities also shows that the new model can approach approximation to a wide moving jam.

  11. A vector auto-regressive model for onshore and offshore wind synthesis incorporating meteorological model information

    NASA Astrophysics Data System (ADS)

    Hill, D.; Bell, K. R. W.; McMillan, D.; Infield, D.

    2014-05-01

    The growth of wind power production in the electricity portfolio is striving to meet ambitious targets set, for example by the EU, to reduce greenhouse gas emissions by 20% by 2020. Huge investments are now being made in new offshore wind farms around UK coastal waters that will have a major impact on the GB electrical supply. Representations of the UK wind field in syntheses which capture the inherent structure and correlations between different locations including offshore sites are required. Here, Vector Auto-Regressive (VAR) models are presented and extended in a novel way to incorporate offshore time series from a pan-European meteorological model called COSMO, with onshore wind speeds from the MIDAS dataset provided by the British Atmospheric Data Centre. Forecasting ability onshore is shown to be improved with the inclusion of the offshore sites with improvements of up to 25% in RMS error at 6 h ahead. In addition, the VAR model is used to synthesise time series of wind at each offshore site, which are then used to estimate wind farm capacity factors at the sites in question. These are then compared with estimates of capacity factors derived from the work of Hawkins et al. (2011). A good degree of agreement is established indicating that this synthesis tool should be useful in power system impact studies.

  12. Physically-based strength model of tantalum incorporating effects of temperature, strain rate and pressure

    DOE PAGESBeta

    Lim, Hojun; Battaile, Corbett C.; Brown, Justin L.; Weinberger, Christopher R.

    2016-06-14

    In this work, we develop a tantalum strength model that incorporates e ects of temperature, strain rate and pressure. Dislocation kink-pair theory is used to incorporate temperature and strain rate e ects while the pressure dependent yield is obtained through the pressure dependent shear modulus. Material constants used in the model are parameterized from tantalum single crystal tests and polycrystalline ramp compression experiments. It is shown that the proposed strength model agrees well with the temperature and strain rate dependent yield obtained from polycrystalline tantalum experiments. Furthermore, the model accurately reproduces the pressure dependent yield stresses up to 250 GPa.more » The proposed strength model is then used to conduct simulations of a Taylor cylinder impact test and validated with experiments. This approach provides a physically-based multi-scale strength model that is able to predict the plastic deformation of polycrystalline tantalum through a wide range of temperature, strain and pressure regimes.« less

  13. Towards a new model of tumuli growth: Incorporating bending models and observations of active lava flows

    NASA Astrophysics Data System (ADS)

    Anderson, S. W.; Smrekar, S. E.; Stofan, E. R.; Sengstacken, A.

    2006-12-01

    Tumuli are the morphologic expression of pressure concentrating within an inflating lava flow. An existing model of tumuli growth (Rossi and Gudmundsson, 1996), suggests that approximately 40m of magmastic overpressure is needed to bend the surface crust of an active lava flow into the characteristic whale-back shape of a tumulus. This model assumes a small-deflection bending of a broken, rigid crust overlying a stronger viscoelastic layer, and uses reasonable values of tumuli dimensions and crustal thickness as boundary conditions. We measured the dimensions and crustal thicknesses of more than 100 tumuli on flows at Mount Etna and Kilauea volcanoes, and used the model to generate pressure estimates for each tumuli in an attempt to discover the nature and magnitude of pressure variations with active lava flow interiors. Although the model gives reasonable values of magmastic pressure for many of our measured tumuli, some values were unreasonably high (greater than 10m magmastic pressure) or low (less than 0.1m magmastic pressure). For those tumuli that have unreasonably low pressure estimates with the existing model, we find that more reasonable values are calculated if we consider whether the edges of the tumuli are clamped. Clamping requires greater magmastic overpressure to bend and break the edges than predicted by the current model. We also find that shape affects the pressure estimates. Tumuli are typically elliptical in plan view, and require greater pressure for bending than for circular features. For those tumuli that yield unreasonably large values of magmastic overpressure, a large-deflection bending model yields more reasonable values. Also, allowing the brittle crust to contribute to the strength of the bending layer improves the calculated values. We also incorporate observations of actively growing tumuli, and find that some are as wide as the entire flow lobe. Many also form at near constrictions in the flow lobe. Cracking of the flow surface may

  14. SPARC Groups: A Model for Incorporating Spiritual Psychoeducation into Group Work

    ERIC Educational Resources Information Center

    Christmas, Christopher; Van Horn, Stacy M.

    2012-01-01

    The use of spirituality as a resource for clients within the counseling field is growing; however, the primary focus has been on individual therapy. The purpose of this article is to provide counseling practitioners, administrators, and researchers with an approach for incorporating spiritual psychoeducation into group work. The proposed model can…

  15. Incorporating Eco-Evolutionary Processes into Population Models:Design and Applications

    EPA Science Inventory

    Eco-evolutionary population models are powerful new tools for exploring howevolutionary processes influence plant and animal population dynamics andvice-versa. The need to manage for climate change and other dynamicdisturbance regimes is creating a demand for the incorporation of...

  16. INCORPORATION OF MECHANISTIC INFORMATION IN THE ARSENIC PBPK MODEL DEVELOPMENT PROCESS

    EPA Science Inventory

    INCORPORATING MECHANISTIC INSIGHTS IN A PBPK MODEL FOR ARSENIC

    Elaina M. Kenyon, Michael F. Hughes, Marina V. Evans, David J. Thomas, U.S. EPA; Miroslav Styblo, University of North Carolina; Michael Easterling, Analytical Sciences, Inc.

    A physiologically based phar...

  17. Controllability and Optimal Harvesting of a Prey-Predator Model Incorporating a Prey Refuge

    ERIC Educational Resources Information Center

    Kar, Tapan Kumar

    2006-01-01

    This paper deals with a prey-predator model incorporating a prey refuge and harvesting of the predator species. A mathematical analysis shows that prey refuge plays a crucial role for the survival of the species and that the harvesting effort on the predator may be used as a control to prevent the cyclic behaviour of the system. The optimal…

  18. Nine challenges in incorporating the dynamics of behaviour in infectious diseases models.

    PubMed

    Funk, Sebastian; Bansal, Shweta; Bauch, Chris T; Eames, Ken T D; Edmunds, W John; Galvani, Alison P; Klepac, Petra

    2015-03-01

    Traditionally, the spread of infectious diseases in human populations has been modelled with static parameters. These parameters, however, can change when individuals change their behaviour. If these changes are themselves influenced by the disease dynamics, there is scope for mechanistic models of behaviour to improve our understanding of this interaction. Here, we present challenges in modelling changes in behaviour relating to disease dynamics, specifically: how to incorporate behavioural changes in models of infectious disease dynamics, how to inform measurement of relevant behaviour to parameterise such models, and how to determine the impact of behavioural changes on observed disease dynamics.

  19. Incorporating phosphorus cycling into global modeling efforts: a worthwhile, tractable endeavor.

    PubMed

    Reed, Sasha C; Yang, Xiaojuan; Thornton, Peter E

    2015-10-01

    324 I. 324 II. 325 III. 326 IV. 327 328 References 328 SUMMARY: Myriad field, laboratory, and modeling studies show that nutrient availability plays a fundamental role in regulating CO2 exchange between the Earth's biosphere and atmosphere, and in determining how carbon pools and fluxes respond to climatic change. Accordingly, global models that incorporate coupled climate-carbon cycle feedbacks made a significant advance with the introduction of a prognostic nitrogen cycle. Here we propose that incorporating phosphorus cycling represents an important next step in coupled climate-carbon cycling model development, particularly for lowland tropical forests where phosphorus availability is often presumed to limit primary production. We highlight challenges to including phosphorus in modeling efforts and provide suggestions for how to move forward. PMID:26115197

  20. Incorporating preferential flow into a 3D model of a forested headwater catchment

    NASA Astrophysics Data System (ADS)

    Glaser, Barbara; Jackisch, Conrad; Hopp, Luisa; Pfister, Laurent; Klaus, Julian

    2016-04-01

    Preferential flow plays an important role for water flow and solute transport. The inclusion of preferential flow, for example with dual porosity or dual permeability approaches, is a common feature in transport simulations at the plot scale. But at hillslope and catchment scales, incorporation of macropore and fracture flow into distributed hydrologic 3D models is rare, often due to limited data availability for model parameterisation. In this study, we incorporated preferential flow into an existing 3D integrated surface subsurface hydrologic model (HydroGeoSphere) of a headwater region (6 ha) of the forested Weierbach catchment in western Luxembourg. Our model philosophy was a strong link between measured data and the model setup. The model setup we used previously had been parameterised and validated based on various field data. But existing macropores and fractures had not been considered in this initial model setup. The multi-criteria validation revealed a good model performance but also suggested potential for further improvement by incorporating preferential flow as additional process. In order to pursue the data driven model philosophy for the implementation of preferential flow, we analysed the results of plot scale bromide sprinkling and infiltration experiments carried out in the vicinity of the Weierbach catchment. Three 1 sqm plots were sprinkled for one hour and excavated one day later for bromide depth profile sampling. We simulated these sprinkling experiments at the soil column scale, using the parameterisation of the base headwater model extended by a second permeability domain. Representing the bromide depth profiles was successful without changing this initial parameterisation. Moreover, to explain the variability between the three bromide depth profiles it was sufficient to adapt the dual permeability properties, indicating the spatial heterogeneity of preferential flow. Subsequently, we incorporated the dual permeability simulation in the

  1. Effect of incorporation of uncertainty in PCB bioaccumulation factors on modeled receptor doses

    SciTech Connect

    Welsh, C.; Duncan, J.; Purucker, S.; Richardson, N.; Redfearn, A.

    1995-12-31

    Bioaccumulation factors (BAFs) are regularly employed in ecological risk assessments to model contaminant transfer through ecological food chains. The authors compiled data on bioaccumulation of PCBs in plants, invertebrates, birds, and mammals from published literature and used these data to develop regression equations relating soil or food concentrations to bioaccumulation. They then used Latin Hypercube simulation techniques and simple food chain models to incorporate uncertainty in the BAF regressions into the derivation of exposure dose estimates for selected wildlife receptors. The authors present their preliminary results in this paper. Dose estimates ranged over several orders of magnitude for herbivorous, insectivorous, and carnivorous receptors. These results suggest incorporating the uncertainty in BAF values into food chain exposure models could provide risk assessors and risk managers with information on the probability of a given outcome that can be used in interpreting the potential risks at hazardous waste sites.

  2. Incorporating physically-based microstructures in materials modeling: Bridging phase field and crystal plasticity frameworks

    NASA Astrophysics Data System (ADS)

    Lim, Hojun; Abdeljawad, Fadi; Owen, Steven J.; Hanks, Byron W.; Foulk, James W.; Battaile, Corbett C.

    2016-05-01

    The mechanical properties of materials systems are highly influenced by various features at the microstructural level. The ability to capture these heterogeneities and incorporate them into continuum-scale frameworks of the deformation behavior is considered a key step in the development of complex non-local models of failure. In this study, we present a modeling framework that incorporates physically-based realizations of polycrystalline aggregates from a phase field (PF) model into a crystal plasticity finite element (CP-FE) framework. Simulated annealing via the PF model yields ensembles of materials microstructures with various grain sizes and shapes. With the aid of a novel FE meshing technique, FE discretizations of these microstructures are generated, where several key features, such as conformity to interfaces, and triple junction angles, are preserved. The discretizations are then used in the CP-FE framework to simulate the mechanical response of polycrystalline α-iron. It is shown that the conformal discretization across interfaces reduces artificial stress localization commonly observed in non-conformal FE discretizations. The work presented herein is a first step towards incorporating physically-based microstructures in lieu of the overly simplified representations that are commonly used. In broader terms, the proposed framework provides future avenues to explore bridging models of materials processes, e.g. additive manufacturing and microstructure evolution of multi-phase multi-component systems, into continuum-scale frameworks of the mechanical properties.

  3. Incorporating physically-based microstructures in materials modeling: Bridging phase field and crystal plasticity frameworks

    DOE PAGESBeta

    Lim, Hojun; Abdeljawad, Fadi; Owen, Steven J.; Hanks, Byron W.; Foulk, James W.; Battaile, Corbett C.

    2016-04-25

    Here, the mechanical properties of materials systems are highly influenced by various features at the microstructural level. The ability to capture these heterogeneities and incorporate them into continuum-scale frameworks of the deformation behavior is considered a key step in the development of complex non-local models of failure. In this study, we present a modeling framework that incorporates physically-based realizations of polycrystalline aggregates from a phase field (PF) model into a crystal plasticity finite element (CP-FE) framework. Simulated annealing via the PF model yields ensembles of materials microstructures with various grain sizes and shapes. With the aid of a novel FEmore » meshing technique, FE discretizations of these microstructures are generated, where several key features, such as conformity to interfaces, and triple junction angles, are preserved. The discretizations are then used in the CP-FE framework to simulate the mechanical response of polycrystalline α-iron. It is shown that the conformal discretization across interfaces reduces artificial stress localization commonly observed in non-conformal FE discretizations. The work presented herein is a first step towards incorporating physically-based microstructures in lieu of the overly simplified representations that are commonly used. In broader terms, the proposed framework provides future avenues to explore bridging models of materials processes, e.g. additive manufacturing and microstructure evolution of multi-phase multi-component systems, into continuum-scale frameworks of the mechanical properties.« less

  4. In silico investigation of the short QT syndrome, using human ventricle models incorporating electromechanical coupling

    PubMed Central

    Adeniran, Ismail; Hancox, Jules C.; Zhang, Henggui

    2013-01-01

    Introduction: Genetic forms of the Short QT Syndrome (SQTS) arise due to cardiac ion channel mutations leading to accelerated ventricular repolarization, arrhythmias and sudden cardiac death. Results from experimental and simulation studies suggest that changes to refractoriness and tissue vulnerability produce a substrate favorable to re-entry. Potential electromechanical consequences of the SQTS are less well-understood. The aim of this study was to utilize electromechanically coupled human ventricle models to explore electromechanical consequences of the SQTS. Methods and Results: The Rice et al. mechanical model was coupled to the ten Tusscher et al. ventricular cell model. Previously validated K+ channel formulations for SQT variants 1 and 3 were incorporated. Functional effects of the SQTS mutations on [Ca2+]i transients, sarcomere length shortening and contractile force at the single cell level were evaluated with and without the consideration of stretch-activated channel current (Isac). Without Isac, at a stimulation frequency of 1Hz, the SQTS mutations produced dramatic reductions in the amplitude of [Ca2+]i transients, sarcomere length shortening and contractile force. When Isac was incorporated, there was a considerable attenuation of the effects of SQTS-associated action potential shortening on Ca2+ transients, sarcomere shortening and contractile force. Single cell models were then incorporated into 3D human ventricular tissue models. The timing of maximum deformation was delayed in the SQTS setting compared to control. Conclusion: The incorporation of Isac appears to be an important consideration in modeling functional effects of SQT 1 and 3 mutations on cardiac electro-mechanical coupling. Whilst there is little evidence of profoundly impaired cardiac contractile function in SQTS patients, our 3D simulations correlate qualitatively with reported evidence for dissociation between ventricular repolarization and the end of mechanical systole. PMID

  5. A Cochlear Partition Model Incorporating Realistic Electrical and Mechanical Parameters for Outer Hair Cells

    NASA Astrophysics Data System (ADS)

    Nam, Jong-Hoon; Fettiplace, Robert

    2011-11-01

    The organ of Corti (OC) is believed to optimize the force transmission from the outer hair cell (OHC) to the basilar membrane and inner hair cell. Recent studies showed that the OC has complex modes of deformation. In an effort to understand the consequence of the OC deformation, we developed a fully deformable 3D finite element model of the OC. It incorporates hair bundle's mechano-transduction and the OHC electrical circuit. Geometric information was taken from the gerbil cochlea at locations with 18 and 0.7 kHz characteristic frequencies. Cochlear partitions of several hundred micrometers long were simulated. The model describes the signature 3D structural arrangement in the OC, especially the tilt of OHC and Deiters cell process. Transduction channel kinetics contributed to the system's mechanics through the hair bundle. The OHC electrical model incorporated the transduction channel conductance, nonlinear capacitance and piezoelectric properties. It also incorporated recent data on the voltage-dependent potassium conductance and membrane time constant. With the model we simulated (1) the limiting frequencies of mechano-transduction and OHC somatic motility and (2) OC transient response to impulse stimuli.

  6. Finite element analysis of structural engineering problems using a viscoplastic model incorporating two back stresses

    NASA Technical Reports Server (NTRS)

    Arya, Vinod K.; Halford, Gary R.

    1993-01-01

    The feasibility of a viscoplastic model incorporating two back stresses and a drag strength is investigated for performing nonlinear finite element analyses of structural engineering problems. To demonstrate suitability for nonlinear structural analyses, the model is implemented into a finite element program and analyses for several uniaxial and multiaxial problems are performed. Good agreement is shown between the results obtained using the finite element implementation and those obtained experimentally. The advantages of using advanced viscoplastic models for performing nonlinear finite element analyses of structural components are indicated.

  7. Dynamic modelling of a double-pendulum gantry crane system incorporating payload

    SciTech Connect

    Ismail, R. M. T. Raja; Ahmad, M. A.; Ramli, M. S.; Ishak, R.; Zawawi, M. A.

    2011-06-20

    The natural sway of crane payloads is detrimental to safe and efficient operation. Under certain conditions, the problem is complicated when the payloads create a double pendulum effect. This paper presents dynamic modelling of a double-pendulum gantry crane system based on closed-form equations of motion. The Lagrangian method is used to derive the dynamic model of the system. A dynamic model of the system incorporating payload is developed and the effects of payload on the response of the system are discussed. Extensive results that validate the theoretical derivation are presented in the time and frequency domains.

  8. Dynamic Modelling of a Double-Pendulum Gantry Crane System Incorporating Payload

    NASA Astrophysics Data System (ADS)

    Ismail, R. M. T. Raja; Ahmad, M. A.; Ramli, M. S.; Ishak, R.; Zawawi, M. A.

    2011-06-01

    The natural sway of crane payloads is detrimental to safe and efficient operation. Under certain conditions, the problem is complicated when the payloads create a double pendulum effect. This paper presents dynamic modelling of a double-pendulum gantry crane system based on closed-form equations of motion. The Lagrangian method is used to derive the dynamic model of the system. A dynamic model of the system incorporating payload is developed and the effects of payload on the response of the system are discussed. Extensive results that validate the theoretical derivation are presented in the time and frequency domains.

  9. Incorporating Mobility in Growth Modeling for Multilevel and Longitudinal Item Response Data.

    PubMed

    Choi, In-Hee; Wilson, Mark

    2016-01-01

    Multilevel data often cannot be represented by the strict form of hierarchy typically assumed in multilevel modeling. A common example is the case in which subjects change their group membership in longitudinal studies (e.g., students transfer schools; employees transition between different departments). In this study, cross-classified and multiple membership models for multilevel and longitudinal item response data (CCMM-MLIRD) are developed to incorporate such mobility, focusing on students' school change in large-scale longitudinal studies. Furthermore, we investigate the effect of incorrectly modeling school membership in the analysis of multilevel and longitudinal item response data. Two types of school mobility are described, and corresponding models are specified. Results of the simulation studies suggested that appropriate modeling of the two types of school mobility using the CCMM-MLIRD yielded good recovery of the parameters and improvement over models that did not incorporate mobility properly. In addition, the consequences of incorrectly modeling the school effects on the variance estimates of the random effects and the standard errors of the fixed effects depended upon mobility patterns and model specifications. Two sets of large-scale longitudinal data are analyzed to illustrate applications of the CCMM-MLIRD for each type of school mobility.

  10. Microfluidic vascularized bone tissue model with hydroxyapatite-incorporated extracellular matrix.

    PubMed

    Jusoh, Norhana; Oh, Soojung; Kim, Sudong; Kim, Jangho; Jeon, Noo Li

    2015-10-21

    Current in vitro systems mimicking bone tissues fail to fully integrate the three-dimensional (3D) microvasculature and bone tissue microenvironments, decreasing their similarity to in vivo conditions. Here, we propose 3D microvascular networks in a hydroxyapatite (HA)-incorporated extracellular matrix (ECM) for designing and manipulating a vascularized bone tissue model in a microfluidic device. Incorporation of HA of various concentrations resulted in ECM with varying mechanical properties. Sprouting angiogenesis was affected by mechanically modulated HA-extracellular matrix interactions, generating a model of vascularized bone microenvironment. Using this platform, we observed that hydroxyapatite enhanced angiogenic properties such as sprout length, sprouting speed, sprout number, and lumen diameter. This new platform integrates fibrin ECM with the synthetic bone mineral HA to provide in vivo-like microenvironments for bone vessel sprouting.

  11. Gold Incorporated Mesoporous Silica Thin Film Model Surface as a Robust SERS and Catalytically Active Substrate.

    PubMed

    Sunil Sekhar, Anandakumari Chandrasekharan; Vinod, Chathakudath Prabhakaran

    2016-01-01

    Ultra-small gold nanoparticles incorporated in mesoporous silica thin films with accessible pore channels perpendicular to the substrate are prepared by a modified sol-gel method. The simple and easy spin coating technique is applied here to make homogeneous thin films. The surface characterization using FESEM shows crack-free films with a perpendicular pore arrangement. The applicability of these thin films as catalysts as well as a robust SERS active substrate for model catalysis study is tested. Compared to bare silica film our gold incorporated silica, GSM-23F gave an enhancement factor of 10³ for RhB with a laser source 633 nm. The reduction reaction of p-nitrophenol with sodium borohydride from our thin films shows a decrease in peak intensity corresponding to -NO₂ group as time proceeds, confirming the catalytic activity. Such model surfaces can potentially bridge the material gap between a real catalytic system and surface science studies. PMID:27213321

  12. Incorporating Midbrain Adaptation to Mean Sound Level Improves Models of Auditory Cortical Processing

    PubMed Central

    Schoppe, Oliver; King, Andrew J.; Schnupp, Jan W.H.; Harper, Nicol S.

    2016-01-01

    Adaptation to stimulus statistics, such as the mean level and contrast of recently heard sounds, has been demonstrated at various levels of the auditory pathway. It allows the nervous system to operate over the wide range of intensities and contrasts found in the natural world. Yet current standard models of the response properties of auditory neurons do not incorporate such adaptation. Here we present a model of neural responses in the ferret auditory cortex (the IC Adaptation model), which takes into account adaptation to mean sound level at a lower level of processing: the inferior colliculus (IC). The model performs high-pass filtering with frequency-dependent time constants on the sound spectrogram, followed by half-wave rectification, and passes the output to a standard linear–nonlinear (LN) model. We find that the IC Adaptation model consistently predicts cortical responses better than the standard LN model for a range of synthetic and natural stimuli. The IC Adaptation model introduces no extra free parameters, so it improves predictions without sacrificing parsimony. Furthermore, the time constants of adaptation in the IC appear to be matched to the statistics of natural sounds, suggesting that neurons in the auditory midbrain predict the mean level of future sounds and adapt their responses appropriately. SIGNIFICANCE STATEMENT An ability to accurately predict how sensory neurons respond to novel stimuli is critical if we are to fully characterize their response properties. Attempts to model these responses have had a distinguished history, but it has proven difficult to improve their predictive power significantly beyond that of simple, mostly linear receptive field models. Here we show that auditory cortex receptive field models benefit from a nonlinear preprocessing stage that replicates known adaptation properties of the auditory midbrain. This improves their predictive power across a wide range of stimuli but keeps model complexity low as it

  13. Stochastic modelling of landfill processes incorporating waste heterogeneity and data uncertainty.

    PubMed

    Zacharof, A I; Butler, A P

    2004-01-01

    A landfill is a very complex heterogeneous environment and as such it presents many modelling challenges. Attempts to develop models that reproduce these complexities generally involve the use of large numbers of spatially dependent parameters that cannot be properly characterised in the face of data uncertainty. An alternative method is presented, which couples a simplified microbial degradation model with a stochastic hydrological and contaminant transport model. This provides a framework for incorporating the complex effects of spatial heterogeneity within the landfill in a simplified manner, along with other key variables. A methodology for handling data uncertainty is also integrated into the model structure. Illustrative examples of the model's output are presented to demonstrate effects of data uncertainty on leachate composition and gas volume prediction.

  14. Polychlorinated biphenyls in glaciers. 2. Model results of deposition and incorporation processes.

    PubMed

    Steinlin, Christine; Bogdal, Christian; Scheringer, Martin; Pavlova, Pavlina A; Schwikowski, Margit; Schmid, Peter; Hungerbühler, Konrad

    2014-07-15

    In previous work, Alpine glaciers have been identified as a secondary source of persistent organic pollutants (POPs). However, detailed understanding of the processes organic chemicals undergo in a glacial system was missing. Here, we present results from a chemical fate model describing deposition and incorporation of polychlorinated biphenyls (PCBs) into an Alpine glacier (Fiescherhorn, Switzerland) and an Arctic glacier (Lomonosovfonna, Norway). To understand PCB fate and dynamics, we investigate the interaction of deposition, sorption to ice and particles in the atmosphere and within the glacier, revolatilization, diffusion and degradation, and discuss the effects of these processes on the fate of individual PCB congeners. The model is able to reproduce measured absolute concentrations in the two glaciers for most PCB congeners. While the model generally predicts concentration profiles peaking in the 1970s, in the measurements, this behavior can only be seen for higher-chlorinated PCB congeners on Fiescherhorn glacier. We suspect seasonal melt processes are disturbing the concentration profiles of the lower-chlorinated PCB congeners. While a lower-chlorinated PCB congener is mainly deposited by dry deposition and almost completely revolatilized after deposition, a higher-chlorinated PCB congener is predominantly transferred to the glacier surface by wet deposition and then is incorporated into the glacier ice. The incorporated amounts of PCBs are higher on the Alpine glacier than on the Arctic glacier due to the higher precipitation rate and aerosol particle concentration on the former. Future studies should include the effects of seasonal melt processes, calculate the quantities of PCBs incorporated into the entire glacier surface, and estimate the quantity of chemicals released from glaciers to determine the importance of glaciers as a secondary source of organic chemicals to remote aquatic ecosystems. PMID:24999726

  15. Polychlorinated biphenyls in glaciers. 2. Model results of deposition and incorporation processes.

    PubMed

    Steinlin, Christine; Bogdal, Christian; Scheringer, Martin; Pavlova, Pavlina A; Schwikowski, Margit; Schmid, Peter; Hungerbühler, Konrad

    2014-07-15

    In previous work, Alpine glaciers have been identified as a secondary source of persistent organic pollutants (POPs). However, detailed understanding of the processes organic chemicals undergo in a glacial system was missing. Here, we present results from a chemical fate model describing deposition and incorporation of polychlorinated biphenyls (PCBs) into an Alpine glacier (Fiescherhorn, Switzerland) and an Arctic glacier (Lomonosovfonna, Norway). To understand PCB fate and dynamics, we investigate the interaction of deposition, sorption to ice and particles in the atmosphere and within the glacier, revolatilization, diffusion and degradation, and discuss the effects of these processes on the fate of individual PCB congeners. The model is able to reproduce measured absolute concentrations in the two glaciers for most PCB congeners. While the model generally predicts concentration profiles peaking in the 1970s, in the measurements, this behavior can only be seen for higher-chlorinated PCB congeners on Fiescherhorn glacier. We suspect seasonal melt processes are disturbing the concentration profiles of the lower-chlorinated PCB congeners. While a lower-chlorinated PCB congener is mainly deposited by dry deposition and almost completely revolatilized after deposition, a higher-chlorinated PCB congener is predominantly transferred to the glacier surface by wet deposition and then is incorporated into the glacier ice. The incorporated amounts of PCBs are higher on the Alpine glacier than on the Arctic glacier due to the higher precipitation rate and aerosol particle concentration on the former. Future studies should include the effects of seasonal melt processes, calculate the quantities of PCBs incorporated into the entire glacier surface, and estimate the quantity of chemicals released from glaciers to determine the importance of glaciers as a secondary source of organic chemicals to remote aquatic ecosystems.

  16. Dose convolution filter: Incorporating spatial dose information into tissue response modeling

    SciTech Connect

    Huang Yimei; Joiner, Michael; Zhao Bo; Liao Yixiang; Burmeister, Jay

    2010-03-15

    Purpose: A model is introduced to integrate biological factors such as cell migration and bystander effects into physical dose distributions, and to incorporate spatial dose information in plan analysis and optimization. Methods: The model consists of a dose convolution filter (DCF) with single parameter {sigma}. Tissue response is calculated by an existing NTCP model with DCF-applied dose distribution as input. The authors determined {sigma} of rat spinal cord from published data. The authors also simulated the GRID technique, in which an open field is collimated into many pencil beams. Results: After applying the DCF, the NTCP model successfully fits the rat spinal cord data with a predicted value of {sigma}=2.6{+-}0.5 mm, consistent with 2 mm migration distances of remyelinating cells. Moreover, it enables the appropriate prediction of a high relative seriality for spinal cord. The model also predicts the sparing of normal tissues by the GRID technique when the size of each pencil beam becomes comparable to {sigma}. Conclusions: The DCF model incorporates spatial dose information and offers an improved way to estimate tissue response from complex radiotherapy dose distributions. It does not alter the prediction of tissue response in large homogenous fields, but successfully predicts increased tissue tolerance in small or highly nonuniform fields.

  17. Velocity and Density Models Incorporating the Cascadia Subduction Zone for 3D Earthquake Ground Motion Simulations

    USGS Publications Warehouse

    Stephenson, William J.

    2007-01-01

    INTRODUCTION In support of earthquake hazards and ground motion studies in the Pacific Northwest, three-dimensional P- and S-wave velocity (3D Vp and Vs) and density (3D rho) models incorporating the Cascadia subduction zone have been developed for the region encompassed from about 40.2?N to 50?N latitude, and from about -122?W to -129?W longitude. The model volume includes elevations from 0 km to 60 km (elevation is opposite of depth in model coordinates). Stephenson and Frankel (2003) presented preliminary ground motion simulations valid up to 0.1 Hz using an earlier version of these models. The version of the model volume described here includes more structural and geophysical detail, particularly in the Puget Lowland as required for scenario earthquake simulations in the development of the Seattle Urban Hazards Maps (Frankel and others, 2007). Olsen and others (in press) used the model volume discussed here to perform a Cascadia simulation up to 0.5 Hz using a Sumatra-Andaman Islands rupture history. As research from the EarthScope Program (http://www.earthscope.org) is published, a wealth of important detail can be added to these model volumes, particularly to depths of the upper-mantle. However, at the time of development for this model version, no EarthScope-specific results were incorporated. This report is intended to be a reference for colleagues and associates who have used or are planning to use this preliminary model in their research. To this end, it is intended that these models will be considered a beginning template for a community velocity model of the Cascadia region as more data and results become available.

  18. Incorporation of UK Met Office's radiation scheme into CPTEC's global model

    NASA Astrophysics Data System (ADS)

    Chagas, Júlio C. S.; Barbosa, Henrique M. J.

    2009-03-01

    Current parameterization of radiation in the CPTEC's (Center for Weather Forecast and Climate Studies, Cachoeira Paulista, SP, Brazil) operational AGCM has its origins in the work of Harshvardhan et al. (1987) and uses the formulation of Ramaswamy and Freidenreich (1992) for the short-wave absorption by water vapor. The UK Met Office's radiation code (Edwards and Slingo, 1996) was incorporated into CPTEC's global model, initially for short-wave only, and some impacts of that were shown by Chagas and Barbosa (2006). Current paper presents some impacts of the complete incorporation (both short-wave and long-wave) of UK Met Office's scheme. Selected results from off-line comparisons with line-by-line benchmark calculations are shown. Impacts on the AGCM's climate are assessed by comparing output of climate runs of current and modified AGCM with products from GEWEX/SRB (Surface Radiation Budget) project.

  19. A Novel Approach of Understanding and Incorporating Error of Chemical Transport Models into a Geostatistical Framework

    NASA Astrophysics Data System (ADS)

    Reyes, J.; Vizuete, W.; Serre, M. L.; Xu, Y.

    2015-12-01

    The EPA employs a vast monitoring network to measure ambient PM2.5 concentrations across the United States with one of its goals being to quantify exposure within the population. However, there are several areas of the country with sparse monitoring spatially and temporally. One means to fill in these monitoring gaps is to use PM2.5 modeled estimates from Chemical Transport Models (CTMs) specifically the Community Multi-scale Air Quality (CMAQ) model. CMAQ is able to provide complete spatial coverage but is subject to systematic and random error due to model uncertainty. Due to the deterministic nature of CMAQ, often these uncertainties are not quantified. Much effort is employed to quantify the efficacy of these models through different metrics of model performance. Currently evaluation is specific to only locations with observed data. Multiyear studies across the United States are challenging because the error and model performance of CMAQ are not uniform over such large space/time domains. Error changes regionally and temporally. Because of the complex mix of species that constitute PM2.5, CMAQ error is also a function of increasing PM2.5 concentration. To address this issue we introduce a model performance evaluation for PM2.5 CMAQ that is regionalized and non-linear. This model performance evaluation leads to error quantification for each CMAQ grid. Areas and time periods of error being better qualified. The regionalized error correction approach is non-linear and is therefore more flexible at characterizing model performance than approaches that rely on linearity assumptions and assume homoscedasticity of CMAQ predictions errors. Corrected CMAQ data are then incorporated into the modern geostatistical framework of Bayesian Maximum Entropy (BME). Through cross validation it is shown that incorporating error-corrected CMAQ data leads to more accurate estimates than just using observed data by themselves.

  20. Simulations of chlorophyll fluorescence incorporated into the Community Land Model version 4.

    PubMed

    Lee, Jung-Eun; Berry, Joseph A; van der Tol, Christiaan; Yang, Xi; Guanter, Luis; Damm, Alexander; Baker, Ian; Frankenberg, Christian

    2015-09-01

    Several studies have shown that satellite retrievals of solar-induced chlorophyll fluorescence (SIF) provide useful information on terrestrial photosynthesis or gross primary production (GPP). Here, we have incorporated equations coupling SIF to photosynthesis in a land surface model, the National Center for Atmospheric Research Community Land Model version 4 (NCAR CLM4), and have demonstrated its use as a diagnostic tool for evaluating the calculation of photosynthesis, a key process in a land surface model that strongly influences the carbon, water, and energy cycles. By comparing forward simulations of SIF, essentially as a byproduct of photosynthesis, in CLM4 with observations of actual SIF, it is possible to check whether the model is accurately representing photosynthesis and the processes coupled to it. We provide some background on how SIF is coupled to photosynthesis, describe how SIF was incorporated into CLM4, and demonstrate that our simulated relationship between SIF and GPP values are reasonable when compared with satellite (Greenhouse gases Observing SATellite; GOSAT) and in situ flux-tower measurements. CLM4 overestimates SIF in tropical forests, and we show that this error can be corrected by adjusting the maximum carboxylation rate (Vmax ) specified for tropical forests in CLM4. Our study confirms that SIF has the potential to improve photosynthesis simulation and thereby can play a critical role in improving land surface and carbon cycle models. PMID:25881891

  1. Investigations of incorporating source directivity into room acoustics computer models to improve auralizations

    NASA Astrophysics Data System (ADS)

    Vigeant, Michelle C.

    Room acoustics computer modeling and auralizations are useful tools when designing or modifying acoustically sensitive spaces. In this dissertation, the input parameter of source directivity has been studied in great detail to determine first its effect in room acoustics computer models and secondly how to better incorporate the directional source characteristics into these models to improve auralizations. To increase the accuracy of room acoustics computer models, the source directivity of real sources, such as musical instruments, must be included in the models. The traditional method for incorporating source directivity into room acoustics computer models involves inputting the measured static directivity data taken every 10° in a sphere-shaped pattern around the source. This data can be entered into the room acoustics software to create a directivity balloon, which is used in the ray tracing algorithm to simulate the room impulse response. The first study in this dissertation shows that using directional sources over an omni-directional source in room acoustics computer models produces significant differences both in terms of calculated room acoustics parameters and auralizations. The room acoustics computer model was also validated in terms of accurately incorporating the input source directivity. A recently proposed technique for creating auralizations using a multi-channel source representation has been investigated with numerous subjective studies, applied to both solo instruments and an orchestra. The method of multi-channel auralizations involves obtaining multi-channel anechoic recordings of short melodies from various instruments and creating individual channel auralizations. These auralizations are then combined to create a total multi-channel auralization. Through many subjective studies, this process was shown to be effective in terms of improving the realism and source width of the auralizations in a number of cases, and also modeling different

  2. Lifetime growth in wild meerkats: incorporating life history and environmental factors into a standard growth model.

    PubMed

    English, Sinéad; Bateman, Andrew W; Clutton-Brock, Tim H

    2012-05-01

    Lifetime records of changes in individual size or mass in wild animals are scarce and, as such, few studies have attempted to model variation in these traits across the lifespan or to assess the factors that affect them. However, quantifying lifetime growth is essential for understanding trade-offs between growth and other life history parameters, such as reproductive performance or survival. Here, we used model selection based on information theory to measure changes in body mass over the lifespan of wild meerkats, and compared the relative fits of several standard growth models (monomolecular, von Bertalanffy, Gompertz, logistic and Richards). We found that meerkats exhibit monomolecular growth, with the best model incorporating separate growth rates before and after nutritional independence, as well as effects of season and total rainfall in the previous nine months. Our study demonstrates how simple growth curves may be improved by considering life history and environmental factors, which may be particularly relevant when quantifying growth patterns in wild populations.

  3. Modelling long-term deformation of granular soils incorporating the concept of fractional calculus

    NASA Astrophysics Data System (ADS)

    Sun, Yifei; Xiao, Yang; Zheng, Changjie; Hanif, Khairul Fikry

    2016-02-01

    Many constitutive models exist to characterise the cyclic behaviour of granular soils but can only simulate deformations for very limited cycles. Fractional derivatives have been regarded as one potential instrument for modelling memory-dependent phenomena. In this paper, the physical connection between the fractional derivative order and the fractal dimension of granular soils is investigated in detail. Then a modified elasto-plastic constitutive model is proposed for evaluating the long-term deformation of granular soils under cyclic loading by incorporating the concept of factional calculus. To describe the flow direction of granular soils under cyclic loading, a cyclic flow potential considering particle breakage is used. Test results of several types of granular soils are used to validate the model performance.

  4. Towards a functional model of mental disorders incorporating the laws of thermodynamics.

    PubMed

    Murray, George C; McKenzie, Karen

    2013-05-01

    The current paper presents the hypothesis that the understanding of mental disorders can be advanced by incorporating the laws of thermodynamics, specifically relating to energy conservation and energy transfer. These ideas, along with the introduction of the notion that entropic activities are symptomatic of inefficient energy transfer or disorder, were used to propose a model of understanding mental ill health as resulting from the interaction of entropy, capacity and work (environmental demands). The model was applied to Attention Deficit Hyperactivity Disorder, and was shown to be compatible with current thinking about this condition, as well as emerging models of mental disorders as complex networks. A key implication of the proposed model is that it argues that all mental disorders require a systemic functional approach, with the advantage that it offers a number of routes into the assessment, formulation and treatment for mental health problems.

  5. Modeling water scarcity over south Asia: Incorporating crop growth and irrigation models into the Variable Infiltration Capacity (VIC) model

    NASA Astrophysics Data System (ADS)

    Troy, Tara J.; Ines, Amor V. M.; Lall, Upmanu; Robertson, Andrew W.

    2013-04-01

    Large-scale hydrologic models, such as the Variable Infiltration Capacity (VIC) model, are used for a variety of studies, from drought monitoring to projecting the potential impact of climate change on the hydrologic cycle decades in advance. The majority of these models simulates the natural hydrological cycle and neglects the effects of human activities such as irrigation, which can result in streamflow withdrawals and increased evapotranspiration. In some parts of the world, these activities do not significantly affect the hydrologic cycle, but this is not the case in south Asia where irrigated agriculture has a large water footprint. To address this gap, we incorporate a crop growth model and irrigation model into the VIC model in order to simulate the impacts of irrigated and rainfed agriculture on the hydrologic cycle over south Asia (Indus, Ganges, and Brahmaputra basin and peninsular India). The crop growth model responds to climate signals, including temperature and water stress, to simulate the growth of maize, wheat, rice, and millet. For the primarily rainfed maize crop, the crop growth model shows good correlation with observed All-India yields (0.7) with lower correlations for the irrigated wheat and rice crops (0.4). The difference in correlation is because irrigation provides a buffer against climate conditions, so that rainfed crop growth is more tied to climate than irrigated crop growth. The irrigation water demands induce hydrologic water stress in significant parts of the region, particularly in the Indus, with the streamflow unable to meet the irrigation demands. Although rainfall can vary significantly in south Asia, we find that water scarcity is largely chronic due to the irrigation demands rather than being intermittent due to climate variability.

  6. Incorporating grazing into an eco-hydrologic model: Simulating coupled human and natural systems in rangelands

    NASA Astrophysics Data System (ADS)

    Reyes, J. J.; Liu, M.; Tague, C.; Choate, J. S.; Evans, R. D.; Johnson, K. A.; Adam, J. C.

    2013-12-01

    Rangelands provide an opportunity to investigate the coupled feedbacks between human activities and natural ecosystems. These areas comprise at least one-third of the Earth's surface and provide ecological support for birds, insects, wildlife and agricultural animals including grazing lands for livestock. Capturing the interactions among water, carbon, and nitrogen cycles within the context of regional scale patterns of climate and management is important to understand interactions, responses, and feedbacks between rangeland systems and humans, as well as provide relevant information to stakeholders and policymakers. The overarching objective of this research is to understand the full consequences, intended and unintended, of human activities and climate over time in rangelands by incorporating dynamics related to rangeland management into an eco-hydrologic model that also incorporates biogeochemical and soil processes. Here we evaluate our model over ungrazed and grazed sites for different rangeland ecosystems. The Regional Hydro-ecologic Simulation System (RHESSys) is a process-based, watershed-scale model that couples water with carbon and nitrogen cycles. Climate, soil, vegetation, and management effects within the watershed are represented in a nested landscape hierarchy to account for heterogeneity and the lateral movement of water and nutrients. We incorporated a daily time-series of plant biomass loss from rangeland to represent grazing. The TRY Plant Trait Database was used to parameterize genera of shrubs and grasses in different rangeland types, such as tallgrass prairie, Intermountain West cold desert, and shortgrass steppe. In addition, other model parameters captured the reallocation of carbon and nutrients after grass defoliation. Initial simulations were conducted at the Curlew Valley site in northern Utah, a former International Geosphere-Biosphere Programme Desert Biome site. We found that grasses were most sensitive to model parameters affecting

  7. A non-classical Mindlin plate model incorporating microstructure, surface energy and foundation effects

    NASA Astrophysics Data System (ADS)

    Gao, X.-L.; Zhang, G. Y.

    2016-07-01

    A non-classical model for a Mindlin plate resting on an elastic foundation is developed in a general form using a modified couple stress theory, a surface elasticity theory and a two-parameter Winkler-Pasternak foundation model. It includes all five kinematic variables possible for a Mindlin plate. The equations of motion and the complete boundary conditions are obtained simultaneously through a variational formulation based on Hamilton's principle, and the microstructure, surface energy and foundation effects are treated in a unified manner. The newly developed model contains one material length-scale parameter to describe the microstructure effect, three surface elastic constants to account for the surface energy effect, and two foundation parameters to capture the foundation effect. The current non-classical plate model reduces to its classical elasticity-based counterpart when the microstructure, surface energy and foundation effects are all suppressed. In addition, the new model includes the Mindlin plate models considering the microstructure dependence or the surface energy effect or the foundation influence alone as special cases, recovers the Kirchhoff plate model incorporating the microstructure, surface energy and foundation effects, and degenerates to the Timoshenko beam model including the microstructure effect. To illustrate the new Mindlin plate model, the static bending and free vibration problems of a simply supported rectangular plate are analytically solved by directly applying the general formulae derived.

  8. Non-Newtonian fluid model incorporated into elastohydrodynamic lubrication of rectangular contacts

    NASA Technical Reports Server (NTRS)

    Jacobson, B. O.; Hamrock, B. J.

    1984-01-01

    A procedure is outlined for the numerical solution of the complete elastohydrodynamic lubrication of rectangular contacts incorporating a non-Newtonian fluid model. The approach uses a Newtonian model as long as the shear stress is less than a limiting shear stress. If the shear stress exceeds the limiting value, the shear stress is set equal to the limiting value. The numerical solution requires the coupled solution of the pressure, film shape, and fluid rheology equations from the inlet to the outlet. Isothermal and no-side-leakage assumptions were imposed in the analysis. The influence of dimensionless speed, load, materials, and sliding velocity and limiting-shear-strength proportionality constant on dimensionless minimum film thickness was investigated. Fourteen cases were used in obtaining the minimum-film-thickness equation for an elastohydrodynamically lubricated rectangular contact incorporating a non-Newtonian fluid model. Computer plots are also presented that indicate in detail pressure distribution, film shape, shear stress at the surfaces, and flow throughout the conjunction.

  9. Non-Newtonian Fluid Model Incorporated into Elastohydrodynamic Lubrication of Rectangular Contacts

    NASA Technical Reports Server (NTRS)

    Jacobson, B. O.; Hamrock, B. J.

    1983-01-01

    A procedure is outlined for the numerical solution of the complete elastohydrodynamic lubrication of rectangular contacts incorporating a non-Newtonian fluid model. The approach uses a Newtonian model as long as the shear stress is less than a limiting shear stress. If the shear stress exceeds the limiting value, the shear stress is set equal to the limiting value. The numerical solution requires the coupled solution of the pressure, film shape, and fluid rheology equations from the inlet to the outlet. Isothermal and no-side-leakage assumptions were imposed in the analysis. The influence of dimensionless speed, load, materials, and sliding velocity and limiting-shear-strength proportionality constant on dimensionless minimum film thickness was investigated. Fourteen cases were used in obtaining the minimum-film-thickness equation for an elastohydrodynamically lubricated rectangular contact incorporating a non-Newtonian fluid model. Computer plots are also presented that indicate in detail pressure distribution, film shape, shear stress at the surfaces, and flow throughout the conjunction.

  10. Evolutionary demography of iteroparous plants: incorporating non-lethal costs of reproduction into integral projection models.

    PubMed

    Miller, Tom E X; Williams, Jennifer L; Jongejans, Eelke; Brys, Rein; Jacquemyn, Hans

    2012-07-22

    Understanding the selective forces that shape reproductive strategies is a central goal of evolutionary ecology. Selection on the timing of reproduction is well studied in semelparous organisms because the cost of reproduction (death) can be easily incorporated into demographic models. Iteroparous organisms also exhibit delayed reproduction and experience reproductive costs, although these are not necessarily lethal. How non-lethal costs shape iteroparous life histories remains unresolved. We analysed long-term demographic data for the iteroparous orchid Orchis purpurea from two habitat types (light and shade). In both the habitats, flowering plants had lower growth rates and this cost was greater for smaller plants. We detected an additional growth cost of fruit production in the light habitat. We incorporated these non-lethal costs into integral projection models to identify the flowering size that maximizes fitness. In both habitats, observed flowering sizes were well predicted by the models. We also estimated optimal parameters for size-dependent flowering effort, but found a strong mismatch with the observed flower production. Our study highlights the role of context-dependent non-lethal reproductive costs as selective forces in the evolution of iteroparous life histories, and provides a novel and broadly applicable approach to studying the evolutionary demography of iteroparous organisms.

  11. Three-dimensional numerical modelling of gas discharges at atmospheric pressure incorporating photoionization phenomena

    NASA Astrophysics Data System (ADS)

    Papageorgiou, L.; Metaxas, A. C.; Georghiou, G. E.

    2011-02-01

    A three-dimensional (3D) numerical model for the characterization of gas discharges in air at atmospheric pressure incorporating photoionization through the solution of the Helmholtz equation is presented. Initially, comparisons with a two-dimensional (2D) axi-symmetric model are performed in order to assess the validity of the model. Subsequently several discharge instabilities (plasma spots and low pressure inhomogeneities) are considered in order to study their effect on streamer branching and off-axis propagation. Depending on the magnitude and position of the plasma spot, deformations and off-axis propagation of the main discharge channel were obtained. No tendency for branching in small (of the order of 0.1 cm) overvolted discharge gaps was observed.

  12. Model for incorporating fuel swelling and clad shrinkage effects in diffusion theory calculations (LWBR Development Program)

    SciTech Connect

    Schick, W.C. Jr.; Milani, S.; Duncombe, E.

    1980-03-01

    A model has been devised for incorporating into the thermal feedback procedure of the PDQ few-group diffusion theory computer program the explicit calculation of depletion and temperature dependent fuel-rod shrinkage and swelling at each mesh point. The model determines the effect on reactivity of the change in hydrogen concentration caused by the variation in coolant channel area as the rods contract and expand. The calculation of fuel temperature, and hence of Doppler-broadened cross sections, is improved by correcting the heat transfer coefficient of the fuel-clad gap for the effects of clad creep, fuel densification and swelling, and release of fission-product gases into the gap. An approximate calculation of clad stress is also included in the model.

  13. Incorporating temporal EHR data in predictive models for risk stratification of renal function deterioration.

    PubMed

    Singh, Anima; Nadkarni, Girish; Gottesman, Omri; Ellis, Stephen B; Bottinger, Erwin P; Guttag, John V

    2015-02-01

    Predictive models built using temporal data in electronic health records (EHRs) can potentially play a major role in improving management of chronic diseases. However, these data present a multitude of technical challenges, including irregular sampling of data and varying length of available patient history. In this paper, we describe and evaluate three different approaches that use machine learning to build predictive models using temporal EHR data of a patient. The first approach is a commonly used non-temporal approach that aggregates values of the predictors in the patient's medical history. The other two approaches exploit the temporal dynamics of the data. The two temporal approaches vary in how they model temporal information and handle missing data. Using data from the EHR of Mount Sinai Medical Center, we learned and evaluated the models in the context of predicting loss of estimated glomerular filtration rate (eGFR), the most common assessment of kidney function. Our results show that incorporating temporal information in patient's medical history can lead to better prediction of loss of kidney function. They also demonstrate that exactly how this information is incorporated is important. In particular, our results demonstrate that the relative importance of different predictors varies over time, and that using multi-task learning to account for this is an appropriate way to robustly capture the temporal dynamics in EHR data. Using a case study, we also demonstrate how the multi-task learning based model can yield predictive models with better performance for identifying patients at high risk of short-term loss of kidney function. PMID:25460205

  14. Incorporating temporal EHR data in predictive models for risk stratification of renal function deterioration

    PubMed Central

    Singh, Anima; Nadkarni, Girish; Gottesman, Omri; Ellis, Stephen B.; Bottinger, Erwin P.; Guttag, John V.

    2015-01-01

    Predictive models built using temporal data in electronic health records (EHRs) can potentially play a major role in improving management of chronic diseases. However, these data present a multitude of technical challenges, including irregular sampling of data and varying length of available patient history. In this paper, we describe and evaluate three different approaches that use machine learning to build predictive models using temporal EHR data of a patient. The first approach is a commonly used non-temporal approach that aggregates values of the predictors in the patient’s medical history. The other two approaches exploit the temporal dynamics of the data. The two temporal approaches vary in how they model temporal information and handle missing data. Using data from the EHR of Mount Sinai Medical Center, we learned and evaluated the models in the context of predicting loss of estimated glomerular filtration rate (eGFR), the most common assessment of kidney function. Our results show that incorporating temporal information in patient’s medical history can lead to better prediction of loss of kidney function. They also demonstrate that exactly how this information is incorporated is important. In particular, our results demonstrate that the relative importance of different predictors varies over time, and that using multi-task learning to account for this is an appropriate way to robustly capture the temporal dynamics in EHR data. Using a case study, we also demonstrate how the multi-task learning based model can yield predictive models with better performance for identifying patients at high risk of short-term loss of kidney function. PMID:25460205

  15. A nonlinear biphasic fiber-reinforced porohyperviscoelastic model of articular cartilage incorporating fiber reorientation and dispersion.

    PubMed

    Seifzadeh, A; Wang, J; Oguamanam, D C D; Papini, M

    2011-08-01

    A nonlinear biphasic fiber-reinforced porohyperviscoelastic (BFPHVE) model of articular cartilage incorporating fiber reorientation effects during applied load was used to predict the response of ovine articular cartilage at relatively high strains (20%). The constitutive material parameters were determined using a coupled finite element-optimization algorithm that utilized stress relaxation indentation tests at relatively high strains. The proposed model incorporates the strain-hardening, tension-compression, permeability, and finite deformation nonlinearities that inherently exist in cartilage, and accounts for effects associated with fiber dispersion and reorientation and intrinsic viscoelasticity at relatively high strains. A new optimization cost function was used to overcome problems associated with large peak-to-peak differences between the predicted finite element and experimental loads that were due to the large strain levels utilized in the experiments. The optimized material parameters were found to be insensitive to the initial guesses. Using experimental data from the literature, the model was also able to predict both the lateral displacement and reaction force in unconfined compression, and the reaction force in an indentation test with a single set of material parameters. Finally, it was demonstrated that neglecting the effects of fiber reorientation and dispersion resulted in poorer agreement with experiments than when they were considered. There was an indication that the proposed BFPHVE model, which includes the intrinsic viscoelasticity of the nonfibrillar matrix (proteoglycan), might be used to model the behavior of cartilage up to relatively high strains (20%). The maximum percentage error between the indentation force predicted by the FE model using the optimized material parameters and that measured experimentally was 3%. PMID:21950897

  16. A coral polyp model of photosynthesis, respiration and calcification incorporating a transcellular ion transport mechanism

    NASA Astrophysics Data System (ADS)

    Nakamura, T.; Nadaoka, K.; Watanabe, A.

    2013-09-01

    A numerical simulation model of coral polyp photosynthesis, respiration and calcification was developed. The model is constructed with three components (ambient seawater, coelenteron and calcifying fluid), and incorporates photosynthesis, respiration and calcification processes with transcellular ion transport by Ca-ATPase activity and passive transmembrane CO2 transport and diffusion. The model calculates dissolved inorganic carbon and total alkalinity in the ambient seawater, coelenteron and calcifying fluid, dissolved oxygen (DO) in the seawater and coelenteron and stored organic carbon (CH2O). To reconstruct the drastic variation between light and dark respiration, respiration rate dependency on DO in the coelenteron is incorporated. The calcification rate depends on the aragonite saturation state in the calcifying fluid (Ω a cal). Our simulation result was a good approximation of "light-enhanced calcification." In our model, the mechanism is expressed as follows: (1) DO in the coelenteron is increased by photosynthesis, (2) respiration is stimulated by increased DO in the light (or respiration is limited by DO depletion in the dark), then (3) calcification increases due to Ca-ATPase, which is driven by the energy generated by respiration. The model simulation results were effective in reproducing the basic responses of the internal CO2 system and DO. The daily calcification rate, the gross photosynthetic rate and the respiration rate under a high-flow condition increased compared to those under the zero-flow condition, but the net photosynthetic rate decreased. The calculated calcification rate responses to variations in the ambient aragonite saturation state (Ω a amb) were nonlinear, and the responses agreed with experimental results of previous studies. Our model predicted that in response to ocean acidification (1) coral calcification will decrease, but will remain at a higher value until Ω a amb decreases to 1, by maintaining a higher Ω a cal due to

  17. Advanced Methods for Incorporating Solar Energy Technologies into Electric Sector Capacity-Expansion Models: Literature Review and Analysis

    SciTech Connect

    Sullivan, P.; Eurek, K.; Margolis, R.

    2014-07-01

    Because solar power is a rapidly growing component of the electricity system, robust representations of solar technologies should be included in capacity-expansion models. This is a challenge because modeling the electricity system--and, in particular, modeling solar integration within that system--is a complex endeavor. This report highlights the major challenges of incorporating solar technologies into capacity-expansion models and shows examples of how specific models address those challenges. These challenges include modeling non-dispatchable technologies, determining which solar technologies to model, choosing a spatial resolution, incorporating a solar resource assessment, and accounting for solar generation variability and uncertainty.

  18. Incorporating uncertainty of management costs in sensitivity analyses of matrix population models.

    PubMed

    Salomon, Yacov; McCarthy, Michael A; Taylor, Peter; Wintle, Brendan A

    2013-02-01

    The importance of accounting for economic costs when making environmental-management decisions subject to resource constraints has been increasingly recognized in recent years. In contrast, uncertainty associated with such costs has often been ignored. We developed a method, on the basis of economic theory, that accounts for the uncertainty in population-management decisions. We considered the case where, rather than taking fixed values, model parameters are random variables that represent the situation when parameters are not precisely known. Hence, the outcome is not precisely known either. Instead of maximizing the expected outcome, we maximized the probability of obtaining an outcome above a threshold of acceptability. We derived explicit analytical expressions for the optimal allocation and its associated probability, as a function of the threshold of acceptability, where the model parameters were distributed according to normal and uniform distributions. To illustrate our approach we revisited a previous study that incorporated cost-efficiency analyses in management decisions that were based on perturbation analyses of matrix population models. Incorporating derivations from this study into our framework, we extended the model to address potential uncertainties. We then applied these results to 2 case studies: management of a Koala (Phascolarctos cinereus) population and conservation of an olive ridley sea turtle (Lepidochelys olivacea) population. For low aspirations, that is, when the threshold of acceptability is relatively low, the optimal strategy was obtained by diversifying the allocation of funds. Conversely, for high aspirations, the budget was directed toward management actions with the highest potential effect on the population. The exact optimal allocation was sensitive to the choice of uncertainty model. Our results highlight the importance of accounting for uncertainty when making decisions and suggest that more effort should be placed on

  19. Incorporating biological pathways via a Markov random field model in genome-wide association studies.

    PubMed

    Chen, Min; Cho, Judy; Zhao, Hongyu

    2011-04-01

    Genome-wide association studies (GWAS) examine a large number of markers across the genome to identify associations between genetic variants and disease. Most published studies examine only single markers, which may be less informative than considering multiple markers and multiple genes jointly because genes may interact with each other to affect disease risk. Much knowledge has been accumulated in the literature on biological pathways and interactions. It is conceivable that appropriate incorporation of such prior knowledge may improve the likelihood of making genuine discoveries. Although a number of methods have been developed recently to prioritize genes using prior biological knowledge, such as pathways, most methods treat genes in a specific pathway as an exchangeable set without considering the topological structure of a pathway. However, how genes are related with each other in a pathway may be very informative to identify association signals. To make use of the connectivity information among genes in a pathway in GWAS analysis, we propose a Markov Random Field (MRF) model to incorporate pathway topology for association analysis. We show that the conditional distribution of our MRF model takes on a simple logistic regression form, and we propose an iterated conditional modes algorithm as well as a decision theoretic approach for statistical inference of each gene's association with disease. Simulation studies show that our proposed framework is more effective to identify genes associated with disease than a single gene-based method. We also illustrate the usefulness of our approach through its applications to a real data example.

  20. A semi-Lagrangian model incorporating a spectral method for pollutant transport and diffusion

    SciTech Connect

    Lee, H.N.

    1994-12-31

    To improve the semi-Lagrangian model, a spectral method was incorporated in the numerical calculations. This spectral method for solving nonperiodic boundary problems was based on a technique of decomposing a variable (i.e. pollutant concentration) into a polynomial and a periodic Fourier residual. A fifth-order polynomial was proposed. When performing the semi-Lagrangian calculation, the spectral intrapolation for estimating the transport of material between grid points was used. From this, a method for removing small negative masses without lossing mass conservation was developed. The numerical tests of the semi-Lagrangian scheme with the spectral interpolation on the advective transport of a mass under nonuniform and uniform winds in a limited computational domain were performed previously and published. In this study, the scheme was applied to solve the two-dimensional time-dependent advection-diffusion equation describing the transport and dispersion of atmospheric pollutants. The calculations demonstrated the efficiency and accuracy of the numerical solutions in a limited region by using this semi-Lagrangian technique incorporated with the spectral method. The main objective of this present study was to develop an advanced numerical modelling technique for air pollution studies on a regional scale.

  1. A methodology for incorporating geomechanically-based fault damage zones models into reservoir simulation

    NASA Astrophysics Data System (ADS)

    Paul, Pijush Kanti

    In the fault damage zone modeling study for a field in the Timor Sea, I present a methodology to incorporate geomechanically-based fault damage zones into reservoir simulation. In the studied field, production history suggests that the mismatch between actual production and model prediction is due to preferential fluid flow through the damage zones associated with the reservoir scale faults, which is not included in the baseline petrophysical model. I analyzed well data to estimate stress heterogeneity and fracture distributions in the reservoir. Image logs show that stress orientations are homogenous at the field scale with a strike-slip/normal faulting stress regime and maximum horizontal stress oriented in NE-SW direction. Observed fracture zones in wells are mostly associated with well scale fault and bed boundaries. These zones do not show any anomalies in production logs or well test data, because most of the fractures are not optimally oriented to the present day stress state, and matrix permeability is high enough to mask any small anomalies from the fracture zones. However, I found that fracture density increases towards the reservoir scale faults, indicating high fracture density zones or damage zones close to these faults, which is consistent with the preferred flow direction indicated by interference and tracer test done between the wells. It is well known from geologic studies that there is a concentration of secondary fractures and faults in a damage zone adjacent to larger faults. Because there is usually inadequate data to incorporate damage zone fractures and faults into reservoir simulation models, in this study I utilized the principles of dynamic rupture propagation from earthquake seismology to predict the nature of fractured/damage zones associated with reservoir scale faults. The implemented workflow can be used to more routinely incorporate damage zones into reservoir simulation models. Applying this methodology to a real reservoir utilizing

  2. Incorporating dose-rate effects in Markov radiation cell survival models.

    PubMed

    Sachs, R K; Hlatky, L; Hahnfeldt, P; Chen, P L

    1990-11-01

    Markov models for the survival of cells subjected to ionizing radiation take stochastic fluctuations into account more systematically than do non-Markov counterparts. Albright's Markov RMR (repair-misrepair) model (Radiat. Res. 118, 1-20, 1989) and Curtis's Markov LPL (lethal-potentially lethal) model [in Quantitative Mathematical Models in Radiation Biology (J. Kiefer, Ed.), pp. 127-146. Springer, New York, 1989], which assume acute irradiation, are here generalized to finite dose rates. Instead of treating irradiation as an instantaneous event we introduce an irradiation period T and analyze processes during the interval T as well as afterward. Albright's RMR transition matrix is used throughout for computing the time development of repair and misrepair. During irradiation an additional matrix is added to describe the evolving radiation damage. Albright's and Curtis's Markov models are recovered as limiting cases by taking T----0 with total dose fixed; the opposite limit, of low dose rates, is also analyzed. Deviations from Poisson behavior in the statistical distributions of lesions are calculated. Other continuous-time Markov chain models ("compartmental models") are discussed briefly, for example, models which incorporate cell proliferation and saturable repair models. It is found that for low dose rates the Markov RMR and LPL models give lower survivals compared to the original non-Markov versions. For acute irradiation and high doses, the Markov models predict higher survivals. In general, theoretical extrapolations which neglect some random fluctuations have a systematic bias toward overoptimism when damage to irradiated tumors is compared with damage to surrounding tissues. PMID:2247602

  3. Incorporating and Compensating Cerebrospinal Fluid in Surface-Based Forward Models of Magneto- and Electroencephalography

    PubMed Central

    Stenroos, Matti; Nummenmaa, Aapo

    2016-01-01

    MEG/EEG source imaging is usually done using a three-shell (3-S) or a simpler head model. Such models omit cerebrospinal fluid (CSF) that strongly affects the volume currents. We present a four-compartment (4-C) boundary-element (BEM) model that incorporates the CSF and is computationally efficient and straightforward to build using freely available software. We propose a way for compensating the omission of CSF by decreasing the skull conductivity of the 3-S model, and study the robustness of the 4-C and 3-S models to errors in skull conductivity. We generated dense boundary meshes using MRI datasets and automated SimNIBS pipeline. Then, we built a dense 4-C reference model using Galerkin BEM, and 4-C and 3-S test models using coarser meshes and both Galerkin and collocation BEMs. We compared field topographies of cortical sources, applying various skull conductivities and fitting conductivities that minimized the relative error in 4-C and 3-S models. When the CSF was left out from the EEG model, our compensated, unbiased approach improved the accuracy of the 3-S model considerably compared to the conventional approach, where CSF is neglected without any compensation (mean relative error < 20% vs. > 40%). The error due to the omission of CSF was of the same order in MEG and compensated EEG. EEG has, however, large overall error due to uncertain skull conductivity. Our results show that a realistic 4-C MEG/EEG model can be implemented using standard tools and basic BEM, without excessive workload or computational burden. If the CSF is omitted, compensated skull conductivity should be used in EEG. PMID:27472278

  4. Incorporating and Compensating Cerebrospinal Fluid in Surface-Based Forward Models of Magneto- and Electroencephalography.

    PubMed

    Stenroos, Matti; Nummenmaa, Aapo

    2016-01-01

    MEG/EEG source imaging is usually done using a three-shell (3-S) or a simpler head model. Such models omit cerebrospinal fluid (CSF) that strongly affects the volume currents. We present a four-compartment (4-C) boundary-element (BEM) model that incorporates the CSF and is computationally efficient and straightforward to build using freely available software. We propose a way for compensating the omission of CSF by decreasing the skull conductivity of the 3-S model, and study the robustness of the 4-C and 3-S models to errors in skull conductivity. We generated dense boundary meshes using MRI datasets and automated SimNIBS pipeline. Then, we built a dense 4-C reference model using Galerkin BEM, and 4-C and 3-S test models using coarser meshes and both Galerkin and collocation BEMs. We compared field topographies of cortical sources, applying various skull conductivities and fitting conductivities that minimized the relative error in 4-C and 3-S models. When the CSF was left out from the EEG model, our compensated, unbiased approach improved the accuracy of the 3-S model considerably compared to the conventional approach, where CSF is neglected without any compensation (mean relative error < 20% vs. > 40%). The error due to the omission of CSF was of the same order in MEG and compensated EEG. EEG has, however, large overall error due to uncertain skull conductivity. Our results show that a realistic 4-C MEG/EEG model can be implemented using standard tools and basic BEM, without excessive workload or computational burden. If the CSF is omitted, compensated skull conductivity should be used in EEG. PMID:27472278

  5. Incorporating headgroup structure into the Poisson-Boltzmann model of charged lipid membranes

    NASA Astrophysics Data System (ADS)

    Wang, Muyang; Chen, Er-Qiang; Yang, Shuang; May, Sylvio

    2013-07-01

    Charged lipids often possess a complex headgroup structure with several spatially separated charges and internal conformational degrees of freedom. We propose a headgroup model consisting of two rod-like segments of the same length that form a flexible joint, with three charges of arbitrary sign and valence located at the joint and the two terminal positions. One terminal charge is firmly anchored at the polar-apolar interface of the lipid layer whereas the other two benefit from the orientational degrees of freedom of the two headgroup segments. This headgroup model is incorporated into the mean-field continuum Poisson-Boltzmann formalism of the electric double layer. For sufficiently small lengths of the two rod-like segments a closed-form expression of the charging free energy is calculated. For three specific examples—a zwitterionic headgroup with conformational freedom and two headgroups that carry an excess charge—we analyze and discuss conformational properties and electrostatic free energies.

  6. Incorporation of experimentally-derived fiber orientation into a structural constitutive model for planar collagenous tissues.

    PubMed

    Sacks, Michael S

    2003-04-01

    Structural constitutive models integrate information on tissue composition and structure, avoiding ambiguities in material characterization. However, critical structural information (such as fiber orientation) must be modeled using assumed statistical distributions, with the distribution parameters estimated from fits to the mechanical test data. Thus, full realization of structural approaches continues to be limited without direct quantitative structural information for direct implementation or to validate model predictions. In the present study, fiber orientation information obtained using small angle light scattering (SALS) was directly incorporated into a structural constitutive model based on work by Lanir (J. Biomech., v. 16, pp. 1-12, 1983). Demonstration of the model was performed using existing biaxial mechanical and fiber orientation data for native bovine pericardium (Sacks and Chuong, ABME, v.26, pp. 892-902, 1998). The structural constitutive model accurately predicted the complete measured biaxial mechanical response. An important aspect of this approach is that only a single equibiaxial test to determine the effective fiber stress-strain response and the SALS-derived fiber orientation distribution were required to determine the complete planar biaxial mechanical response. Changes in collagen fiber crimp under equibiaxial strain suggest that, at the meso-scale, fiber deformations follow the global tissue strains. This result supports the assumption of affine strain to estimate the fiber strains. However, future evaluations will have to be performed for tissue subjected to a wider range of strain to more fully validate the current approach.

  7. An agent-based model of stock markets incorporating momentum investors

    NASA Astrophysics Data System (ADS)

    Wei, J. R.; Huang, J. P.; Hui, P. M.

    2013-06-01

    It has been widely accepted that there exist investors who adopt momentum strategies in real stock markets. Understanding the momentum behavior is of both academic and practical importance. For this purpose, we propose and study a simple agent-based model of trading incorporating momentum investors and random investors. The random investors trade randomly all the time. The momentum investors could be idle, buying or selling, and they decide on their action by implementing an action threshold that assesses the most recent price movement. The model is able to reproduce some of the stylized facts observed in real markets, including the fat-tails in returns, weak long-term correlation and scaling behavior in the kurtosis of returns. An analytic treatment of the model relates the model parameters to several quantities that can be extracted from real data sets. To illustrate how the model can be applied, we show that real market data can be used to constrain the model parameters, which in turn provide information on the behavior of momentum investors in different markets.

  8. Runoff Modelling of the Khumbu Glacier, Nepal: Incorporating Debris Cover and Retreat Dynamics.

    NASA Astrophysics Data System (ADS)

    Douglas, James; Huss, Matthias; Jones, Julie; Swift, Darrel; Salerno, Franco

    2016-04-01

    Detailed studies on the future evolution and runoff of glaciers in high mountain Asia are scarce considering the region is so reliant on on this essential water source. This study adapts a model well-proven in the European Alps, the Glacier Evolution and Runoff Model (GERM), to simulate the behaviour of the Khumbu glacier, Nepal. GERM calculates glacier mass balance and runoff using a distributed temperature index model which has been modified such that the unique dynamics of debris covered glaciers, namely stagnation, thinning, and melt-inhibiting debris surfaces, are incorporated. Debris thickness is derived from both remote sensing and model based approaches allowing a suite of experiments to be conducted using various levels of debris cover. The model is driven by CORDEX-South Asia regional climate model (RCM) simulations, bias corrected using a quantile mapping technique based on in-situ data from the Pyramid meteorological station. Here, results are presented showing the retreat of the Khumbu glacier and the corresponding changes for annual and seasonal discharge until 2100, using varying melt parameters and debris thicknesses to assess the impact of debris cover on glacier evolution and runoff.

  9. The dilemma of disappearing diatoms: Incorporating diatom dissolution data into palaeoenvironmental modelling and reconstruction

    NASA Astrophysics Data System (ADS)

    Ryves, David B.; Battarbee, Richard W.; Fritz, Sherilyn C.

    2009-01-01

    Taphonomic issues pose fundamental challenges for Quaternary scientists to recover environmental signals from biological proxies and make accurate inferences of past environments. The problem of microfossil preservation, specifically diatom dissolution, remains an important, but often overlooked, source of error in both qualitative and quantitative reconstructions of key variables from fossil samples, especially those using relative abundance data. A first step to tackling this complex issue is establishing an objective method of assessing preservation (here, diatom dissolution) that can be applied by different analysts and incorporated into routine counting strategies. Here, we establish a methodology for assessment of diatom dissolution under standard light microscopy (LM) illustrated with morphological criteria for a range of major diatom valve shapes. Dissolution data can be applied to numerical models (transfer functions) from contemporary samples, and to fossil material to aid interpretation of stratigraphic profiles and taphonomic pathways of individual taxa. Using a surface sediment diatom-salinity training set from the Northern Great Plains (NGP) as an example, we explore a variety of approaches to include dissolution data in salinity inference models indirectly and directly. Results show that dissolution data can improve models, with apparent dissolution-adjusted error (RMSE) up to 15% lower than their unadjusted counterparts. Internal validation suggests improvements are more modest, with bootstrapped prediction errors (RMSEP) up to 10% lower. When tested on a short core from Devils Lake, North Dakota, which has a historical record of salinity, dissolution-adjusted models infer higher values compared to unadjusted models during peak salinity of the 1930s-1940s Dust Bowl but nonetheless significantly underestimate peak values. Site-specific factors at Devils Lake associated with effects of lake level change on taphonomy (preservation and re

  10. Incorporating Student Mobility in Achievement Growth Modeling: A Cross-Classified Multiple Membership Growth Curve Model.

    PubMed

    Grady, Matthew W; Beretvas, S Natasha

    2010-05-28

    Multiple membership random effects models (MMREMs) have been developed for use in situations where individuals are members of multiple higher level organizational units. Despite their availability and the frequency with which multiple membership structures are encountered, no studies have extended the MMREM approach to hierarchical growth curve modeling (GCM). This study introduces a cross-classified multiple membership growth curve model (CCMM-GCM) for modeling, for example, academic achievement trajectories in the presence of student mobility. Real data are used to demonstrate and compare growth curve model estimates using the CCMM-GCM and a conventional GCM that ignores student mobility. Results indicate that the CCMM-GCM represents a promising option for modeling growth for multiple membership data structures.

  11. Progressive evaluation of incorporating information into a model building process: from scratch to FLEX-TOPO

    NASA Astrophysics Data System (ADS)

    Gharari, Shervan; Gupta, Hoshin; Hrachowitz, Markus; Fenicia, Fabrizio; Gao, Hongkai; Savenije, Hubert

    2015-04-01

    Although different strategies have demonstrated that incorporation of expert and a priori knowledge can help to improve the realism of models, no systematic strategy has been presented in the literature for constraining the model parameters to be consistent with the (sometimes) patchy understanding of a modeler regarding how the real system might work. Part of the difficulty in doing this is that expert knowledge may not always consist of explicitly quantifiable relationships between physical system characteristics and model parameters; rather, it may consist of conceptual understanding about consistency relationships that must exist between various model parameter or behavioral relationships that must exist among model state variables and/or fluxes. Apart from aforementioned constraints, a unified strategy for measurement of information content in hierarchal model building seems lacking. Firstly the model structure is built by its building blocks (control volumes or state variables) as well as interconnecting fluxes (formation of control volumes and fluxes). Secondly, parameterizations of model are designed, as an example the effect of a specific type of stage-discharge relation for a control volume can be explored. At the final stage the parameter values are quantified. In each step and based on assumptions made, more and more information is added to the model. In this study we try to construct (based on hierarchal model building scheme) and constrain parameters of different conceptual models built on landscape units classified according to their hydrological functions and based on our logical considerations and general lessons from previous studies across the globe for a Luxembourgish catchment. Based on the result, including our basic understanding of how a system may work into hydrological models appears to be a powerful tool to achieve higher model realism as it leads to models with higher performance. Progressive measurement of performance and uncertainty

  12. Progressive evaluation of incorporating information into a model building process: from scratch to FLEX-TOPO

    NASA Astrophysics Data System (ADS)

    Gharari, S.; Hrachowitz, M.; Fenicia, F.; Gao, H.; Gupta, H. V.; Savenije, H.

    2014-12-01

    Although different strategies have demonstrated that incorporation of expert and a priori knowledge can help to improve the realism of models, no systematic strategy has been presented in the literature for constraining the model parameters to be consistent with the (sometimes) patchy understanding of a modeler regarding how the real system might work. Part of the difficulty in doing this is that expert knowledge may not always consist of explicitly quantifiable relationships between physical system characteristics and model parameters; rather, it may consist of conceptual understanding about consistency relationships that must exist between various model parameter or behavioral relationships that must exist among model state variables and/or fluxes. Apart from aforementioned constraints, a unified strategy for measurement of information content in hierarchal model building seems lacking. Firstly the model structure is built by its building blocks (control volumes or state variables) as well as interconnecting fluxes (formation of control volumes and fluxes). Secondly, parameterizations of model are designed, as an example the effect of a specific type of stage-discharge relation for a control volume can be explored. At the final stage the parameter values are quantified. In each step and based on assumptions made, more and more information is added to the model. In this study we try to construct (based on hierarchal model building scheme) and constrain parameters of different conceptual models built on landscape units classified according to their hydrological functions and based on our logical considerations and general lessons from previous studies across the globe for a Luxembourgish catchment. Based on the result, including our basic understanding of how a system may work into hydrological models appears to be a powerful tool to achieve higher model realism as it leads to models with higher performance. Progressive measurement of performance and uncertainty

  13. Incorporating social groups' responses in a descriptive model for second- and higher-order impact identification

    SciTech Connect

    Sutheerawatthana, Pitch; Minato, Takayuki

    2010-02-15

    The response of a social group is a missing element in the formal impact assessment model. Previous discussion of the involvement of social groups in an intervention has mainly focused on the formation of the intervention. This article discusses the involvement of social groups in a different way. A descriptive model is proposed by incorporating a social group's response into the concept of second- and higher-order effects. The model is developed based on a cause-effect relationship through the observation of phenomena in case studies. The model clarifies the process by which social groups interact with a lower-order effect and then generate a higher-order effect in an iterative manner. This study classifies social groups' responses into three forms-opposing, modifying, and advantage-taking action-and places them in six pathways. The model is expected to be used as an analytical tool for investigating and identifying impacts in the planning stage and as a framework for monitoring social groups' responses during the implementation stage of a policy, plan, program, or project (PPPPs).

  14. Boosting probabilistic graphical model inference by incorporating prior knowledge from multiple sources.

    PubMed

    Praveen, Paurush; Fröhlich, Holger

    2013-01-01

    Inferring regulatory networks from experimental data via probabilistic graphical models is a popular framework to gain insights into biological systems. However, the inherent noise in experimental data coupled with a limited sample size reduces the performance of network reverse engineering. Prior knowledge from existing sources of biological information can address this low signal to noise problem by biasing the network inference towards biologically plausible network structures. Although integrating various sources of information is desirable, their heterogeneous nature makes this task challenging. We propose two computational methods to incorporate various information sources into a probabilistic consensus structure prior to be used in graphical model inference. Our first model, called Latent Factor Model (LFM), assumes a high degree of correlation among external information sources and reconstructs a hidden variable as a common source in a Bayesian manner. The second model, a Noisy-OR, picks up the strongest support for an interaction among information sources in a probabilistic fashion. Our extensive computational studies on KEGG signaling pathways as well as on gene expression data from breast cancer and yeast heat shock response reveal that both approaches can significantly enhance the reconstruction accuracy of Bayesian Networks compared to other competing methods as well as to the situation without any prior. Our framework allows for using diverse information sources, like pathway databases, GO terms and protein domain data, etc. and is flexible enough to integrate new sources, if available.

  15. a Maximum Entropy Model of the Bearded Capuchin Monkey Habitat Incorporating Topography and Spectral Unmixing Analysis

    NASA Astrophysics Data System (ADS)

    Howard, A. M.; Bernardes, S.; Nibbelink, N.; Biondi, L.; Presotto, A.; Fragaszy, D. M.; Madden, M.

    2012-07-01

    Movement patterns of bearded capuchin monkeys (Cebus (Sapajus) libidinosus) in northeastern Brazil are likely impacted by environmental features such as elevation, vegetation density, or vegetation type. Habitat preferences of these monkeys provide insights regarding the impact of environmental features on species ecology and the degree to which they incorporate these features in movement decisions. In order to evaluate environmental features influencing movement patterns and predict areas suitable for movement, we employed a maximum entropy modelling approach, using observation points along capuchin monkey daily routes as species presence points. We combined these presence points with spatial data on important environmental features from remotely sensed data on land cover and topography. A spectral mixing analysis procedure was used to generate fraction images that represent green vegetation, shade and soil of the study area. A Landsat Thematic Mapper scene of the area of study was geometrically and atmospherically corrected and used as input in a Minimum Noise Fraction (MNF) procedure and a linear spectral unmixing approach was used to generate the fraction images. These fraction images and elevation were the environmental layer inputs for our logistic MaxEnt model of capuchin movement. Our models' predictive power (test AUC) was 0.775. Areas of high elevation (>450 m) showed low probabilities of presence, and percent green vegetation was the greatest overall contributor to model AUC. This work has implications for predicting daily movement patterns of capuchins in our field site, as suitability values from our model may relate to habitat preference and facility of movement.

  16. Statistical integration of tracking and vessel survey data to incorporate life history differences in habitat models.

    PubMed

    Yamamoto, Takashi; Watanuki, Yutaka; Hazen, Elliott L; Nishizawa, Bungo; Sasaki, Hiroko; Takahashi, Akinori

    2015-12-01

    Habitat use is often examined at a species or population level, but patterns likely differ within a species, as a function of the sex, breeding colony, and current breeding status of individuals. Hence, within-species differences should be considered in habitat models when analyzing and predicting species distributions, such as predicted responses to expected climate change scenarios. Also, species' distribution data obtained by different methods (vessel-survey and individual tracking) are often analyzed separately rather than integrated to improve predictions. Here, we eventually fit generalized additive models for Streaked Shearwaters Calonectris leuconelas using tracking data from two different breeding colonies in the Northwestern Pacific and visual observer data collected during a research cruise off the coast of western Japan. The tracking-based models showed differences among patterns of relative density distribution as a function of life history category (colony, sex, and breeding conditions). The integrated tracking-based and vessel-based bird count model incorporated ecological states rather than predicting a single surface for the entire species. This study highlights both the importance of including ecological and life history data and integrating multiple data types (tag-based tracking and vessel count) when examining species-environment relationships, ultimately advancing the capabilities of species distribution models. PMID:26910963

  17. A transient electrochemical model incorporating the Donnan effect for all-vanadium redox flow batteries

    NASA Astrophysics Data System (ADS)

    Lei, Y.; Zhang, B. W.; Bai, B. F.; Zhao, T. S.

    2015-12-01

    In a typical all-vanadium redox flow battery (VRFB), the ion exchange membrane is directly exposed in the bulk electrolyte. Consequently, the Donnan effect occurs at the membrane/electrolyte (M/E) interfaces, which is critical for modeling of ion transport through the membrane and the prediction of cell performance. However, unrealistic assumptions in previous VRFB models, such as electroneutrality and discontinuities of ionic potential and ion concentrations at the M/E interfaces, lead to simulated results inconsistent with the theoretical analysis of ion adsorption in the membrane. To address this issue, this work proposes a continuous-Donnan effect-model using the Poisson equation coupled with the Nernst-Planck equation to describe variable distributions at the M/E interfaces. A one-dimensional transient VRFB model incorporating the Donnan effect is developed. It is demonstrated that the present model enables (i) a more realistic simulation of continuous distributions of ion concentrations and ionic potential throughout the membrane and (ii) a more comprehensive estimation for the effect of the fixed charge concentration on species crossover across the membrane and cell performance.

  18. Incorporating temporal features of repeatedly measured covariates into tree-structured survival models.

    PubMed

    Wallace, Meredith L; Anderson, Stewart J; Mazumdar, Sati; Kong, Lan; Mulsant, Benoit H

    2012-03-01

    Tree-structured survival methods empirically identify a series of covariate-based binary split points, resulting in an algorithm that can be used to classify new patients into risk groups and subsequently guide clinical treatment decisions. Traditionally, only fixed-time (e.g. baseline) values are used in tree-structured models. However, this manuscript considers the scenario where temporal features of a repeated measures polynomial model, such as the slope and/or curvature, are useful for distinguishing risk groups to predict future outcomes. Both fixed- and random-effects methods for estimating individual temporal features are discussed, and methods for including these features in a tree model and classifying new cases are proposed. A simulation study is performed to empirically compare the predictive accuracies of the proposed methods in a wide variety of model settings. For illustration, a tree-structured survival model incorporating the linear rate of change of depressive symptomatology during the first four weeks of treatment for late-life depression is used to identify subgroups of older adults who may benefit from an early change in treatment strategy. PMID:22522377

  19. Incorporating teleconnection information into reservoir operating policies using Stochastic Dynamic Programming and a Hidden Markov Model

    NASA Astrophysics Data System (ADS)

    Turner, Sean; Galelli, Stefano; Wilcox, Karen

    2015-04-01

    Water reservoir systems are often affected by recurring large-scale ocean-atmospheric anomalies, known as teleconnections, that cause prolonged periods of climatological drought. Accurate forecasts of these events -- at lead times in the order of weeks and months -- may enable reservoir operators to take more effective release decisions to improve the performance of their systems. In practice this might mean a more reliable water supply system, a more profitable hydropower plant or a more sustainable environmental release policy. To this end, climate indices, which represent the oscillation of the ocean-atmospheric system, might be gainfully employed within reservoir operating models that adapt the reservoir operation as a function of the climate condition. This study develops a Stochastic Dynamic Programming (SDP) approach that can incorporate climate indices using a Hidden Markov Model. The model simulates the climatic regime as a hidden state following a Markov chain, with the state transitions driven by variation in climatic indices, such as the Southern Oscillation Index. Time series analysis of recorded streamflow data reveals the parameters of separate autoregressive models that describe the inflow to the reservoir under three representative climate states ("normal", "wet", "dry"). These models then define inflow transition probabilities for use in a classic SDP approach. The key advantage of the Hidden Markov Model is that it allows conditioning the operating policy not only on the reservoir storage and the antecedent inflow, but also on the climate condition, thus potentially allowing adaptability to a broader range of climate conditions. In practice, the reservoir operator would effect a water release tailored to a specific climate state based on available teleconnection data and forecasts. The approach is demonstrated on the operation of a realistic, stylised water reservoir with carry-over capacity in South-East Australia. Here teleconnections relating

  20. Incorporating Single-nucleotide Polymorphisms Into the Lyman Model to Improve Prediction of Radiation Pneumonitis

    SciTech Connect

    Tucker, Susan L.; Li Minghuan; Xu Ting; Gomez, Daniel; Yuan Xianglin; Yu Jinming; Liu Zhensheng; Yin Ming; Guan Xiaoxiang; Wang Lie; Wei Qingyi; Mohan, Radhe; Vinogradskiy, Yevgeniy; Martel, Mary; Liao Zhongxing

    2013-01-01

    Purpose: To determine whether single-nucleotide polymorphisms (SNPs) in genes associated with DNA repair, cell cycle, transforming growth factor-{beta}, tumor necrosis factor and receptor, folic acid metabolism, and angiogenesis can significantly improve the fit of the Lyman-Kutcher-Burman (LKB) normal-tissue complication probability (NTCP) model of radiation pneumonitis (RP) risk among patients with non-small cell lung cancer (NSCLC). Methods and Materials: Sixteen SNPs from 10 different genes (XRCC1, XRCC3, APEX1, MDM2, TGF{beta}, TNF{alpha}, TNFR, MTHFR, MTRR, and VEGF) were genotyped in 141 NSCLC patients treated with definitive radiation therapy, with or without chemotherapy. The LKB model was used to estimate the risk of severe (grade {>=}3) RP as a function of mean lung dose (MLD), with SNPs and patient smoking status incorporated into the model as dose-modifying factors. Multivariate analyses were performed by adding significant factors to the MLD model in a forward stepwise procedure, with significance assessed using the likelihood-ratio test. Bootstrap analyses were used to assess the reproducibility of results under variations in the data. Results: Five SNPs were selected for inclusion in the multivariate NTCP model based on MLD alone. SNPs associated with an increased risk of severe RP were in genes for TGF{beta}, VEGF, TNF{alpha}, XRCC1 and APEX1. With smoking status included in the multivariate model, the SNPs significantly associated with increased risk of RP were in genes for TGF{beta}, VEGF, and XRCC3. Bootstrap analyses selected a median of 4 SNPs per model fit, with the 6 genes listed above selected most often. Conclusions: This study provides evidence that SNPs can significantly improve the predictive ability of the Lyman MLD model. With a small number of SNPs, it was possible to distinguish cohorts with >50% risk vs <10% risk of RP when they were exposed to high MLDs.

  1. Current plate velocities relative to the hotspots incorporating the NUVEL-1 global plate motion model

    SciTech Connect

    Gripp, A.E.; Gordon, R.G. )

    1990-07-01

    NUVEL-1 is a new global model of current relative plate velocities which differ significantly from those of prior models. Here the authors incorporate NUVEL-1 into HS2-NUVEL1, a new global model of plate velocities relative to the hotspots. HS2-NUVEL1 was determined from the hotspot data and errors used by Minster and Jordan (1978) to determine AM1-2, which is their model of plate velocities relative to the hotspots. AM1-2 is consistent with Minster and Jordan's relative plate velocity model RM2. Here the authors compare HS2-NUVEL1 with AM1-2 and examine how their differences relate to differences between NUVEL-1 and RM2. HS2-NUVEL1 plate velocities relative to the hotspots are mainly similar to those of AM1-2. Minor differences between the two models include the following: (1) in HS2-NUVEL1 the speed of the partly continental, apparently non-subducting Indian plate is greater than that of the purely oceanic, subducting Nazca plate; (2) in places the direction of motion of the African, Antarctic, Arabian, Australian, Caribbean, Cocos, Eurasian, North American, and South American plates differs between models by more than 10{degree}; (3) in places the speed of the Australian, Caribbean, Cocos, Indian, and Nazca plates differs between models by more than 8 mm/yr. Although 27 of the 30 RM2 Euler vectors differ with 95% confidence from those of NUVEL-1, only the AM1-2 Arabia-hotspot and India-hotspot Euler vectors differ with 95% confidence from those of HS2-NUVEL1. Thus, substituting NUVEL-1 for RM2 in the inversion for plate velocities relative to the hotspots changes few Euler vectors significantly, presumably because the uncertainty in the velocity of a plate relative to the hotspots is much greater than the uncertainty in its velocity relative to other plates.

  2. Incorporation of caffeine into a quantitative model of fatigue and sleep.

    PubMed

    Puckeridge, M; Fulcher, B D; Phillips, A J K; Robinson, P A

    2011-03-21

    A recent physiologically based model of human sleep is extended to incorporate the effects of caffeine on sleep-wake timing and fatigue. The model includes the sleep-active neurons of the hypothalamic ventrolateral preoptic area (VLPO), the wake-active monoaminergic brainstem populations (MA), their interactions with cholinergic/orexinergic (ACh/Orx) input to MA, and circadian and homeostatic drives. We model two effects of caffeine on the brain due to competitive antagonism of adenosine (Ad): (i) a reduction in the homeostatic drive and (ii) an increase in cholinergic activity. By comparing the model output to experimental data, constraints are determined on the parameters that describe the action of caffeine on the brain. In accord with experiment, the ranges of these parameters imply significant variability in caffeine sensitivity between individuals, with caffeine's effectiveness in reducing fatigue being highly dependent on an individual's tolerance, and past caffeine and sleep history. Although there are wide individual differences in caffeine sensitivity and thus in parameter values, once the model is calibrated for an individual it can be used to make quantitative predictions for that individual. A number of applications of the model are examined, using exemplar parameter values, including: (i) quantitative estimation of the sleep loss and the delay to sleep onset after taking caffeine for various doses and times; (ii) an analysis of the system's stable states showing that the wake state during sleep deprivation is stabilized after taking caffeine; and (iii) comparing model output successfully to experimental values of subjective fatigue reported in a total sleep deprivation study examining the reduction of fatigue with caffeine. This model provides a framework for quantitatively assessing optimal strategies for using caffeine, on an individual basis, to maintain performance during sleep deprivation.

  3. Petroacoustic Modelling of Heterolithic Sandstone Reservoirs: A Novel Approach to Gassmann Modelling Incorporating Sedimentological Constraints and NMR Porosity data

    NASA Astrophysics Data System (ADS)

    Matthews, S.; Lovell, M.; Davies, S. J.; Pritchard, T.; Sirju, C.; Abdelkarim, A.

    2012-12-01

    Heterolithic or 'shaly' sandstone reservoirs constitute a significant proportion of hydrocarbon resources. Petroacoustic models (a combination of petrophysics and rock physics) enhance the ability to extract reservoir properties from seismic data, providing a connection between seismic and fine-scale rock properties. By incorporating sedimentological observations these models can be better constrained and improved. Petroacoustic modelling is complicated by the unpredictable effects of clay minerals and clay-sized particles on geophysical properties. Such effects are responsible for erroneous results when models developed for "clean" reservoirs - such as Gassmann's equation (Gassmann, 1951) - are applied to heterolithic sandstone reservoirs. Gassmann's equation is arguably the most popular petroacoustic modelling technique in the hydrocarbon industry and is used to model elastic effects of changing reservoir fluid saturations. Successful implementation of Gassmann's equation requires well-constrained drained rock frame properties, which in heterolithic sandstones are heavily influenced by reservoir sedimentology, particularly clay distribution. The prevalent approach to categorising clay distribution is based on the Thomas - Stieber model (Thomas & Stieber, 1975), this approach is inconsistent with current understanding of 'shaly sand' sedimentology and omits properties such as sorting and grain size. The novel approach presented here demonstrates that characterising reservoir sedimentology constitutes an important modelling phase. As well as incorporating sedimentological constraints, this novel approach also aims to improve drained frame moduli estimates through more careful consideration of Gassmann's model assumptions and limitations. A key assumption of Gassmann's equation is a pore space in total communication with movable fluids. This assumption is often violated by conventional applications in heterolithic sandstone reservoirs where effective porosity, which

  4. Development of QTc prolongation model incorporating circadian rhythm using harmonic model.

    PubMed

    Back, Hyun-moon; Lee, Jong-Hwa; Yun, Hwi-yeol; Kwon, Kwang-il

    2015-05-01

    1. QT prolongation is one of the major safety tests used in the development of a new drug. The ICH guidelines for the evaluation of QT prolongation recommend the use of the in vitro hERG assay and the in vivo telemetry test. However, QT intervals change under normal conditions due to circadian rhythm and can affect the results of the tests. In this study, we developed a PK/PD model to describe the QT interval after the administration of astemizole allowing for the normal changes by circadian rhythm. 2. The typical PK parameters of absorption rate constant (ka), volume of distribution (Vc and Vm), metabolism (km), and elimination rate constant (kel and kel-m) were 0.49 h(-1), 4950 L, 20 L, 0.0127 h(-1), 0.0095 h(-1), and 0.95 h(-1), respectively. The final PK/PD model was the biophase model with the modified harmonic model. The typical PK/PD parameters, base QTc interval (QT0), amplitude (T1, T3), period of QTc interval changing (T2, T4), and EC50 were 233 ms, 3.31, 1.5, -9.24 h, 1.85 h, and 0.81 ng/ml, respectively. 3. The PK/PD model to explain the changes of the QT interval that allows normal changes in the circadian rhythm after the administration of astemizole was developed successfully. This final model can be applied to the development of a human model.

  5. Constraining Distributed Catchment Models by Incorporating Perceptual Understanding of Spatial Hydrologic Behaviour

    NASA Astrophysics Data System (ADS)

    Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei

    2016-04-01

    Distributed models offer the potential to resolve catchment systems in more detail, and therefore simulate the hydrological impacts of spatial changes in catchment forcing (e.g. landscape change). Such models tend to contain a large number of poorly defined and spatially varying model parameters which are therefore computationally expensive to calibrate. Insufficient data can result in model parameter and structural equifinality, particularly when calibration is reliant on catchment outlet discharge behaviour alone. Evaluating spatial patterns of internal hydrological behaviour has the potential to reveal simulations that, whilst consistent with measured outlet discharge, are qualitatively dissimilar to our perceptual understanding of how the system should behave. We argue that such understanding, which may be derived from stakeholder knowledge across different catchments for certain process dynamics, is a valuable source of information to help reject non-behavioural models, and therefore identify feasible model structures and parameters. The challenge, however, is to convert different sources of often qualitative and/or semi-qualitative information into robust quantitative constraints of model states and fluxes, and combine these sources of information together to reject models within an efficient calibration framework. Here we present the development of a framework to incorporate different sources of data to efficiently calibrate distributed catchment models. For each source of information, an interval or inequality is used to define the behaviour of the catchment system. These intervals are then combined to produce a hyper-volume in state space, which is used to identify behavioural models. We apply the methodology to calibrate the Penn State Integrated Hydrological Model (PIHM) at the Wye catchment, Plynlimon, UK. Outlet discharge behaviour is successfully simulated when perceptual understanding of relative groundwater levels between lowland peat, upland peat

  6. Roots, storms and soil pores: Incorporating key ecohydrological processes into Budyko's hydrological model

    NASA Astrophysics Data System (ADS)

    Donohue, Randall J.; Roderick, Michael L.; McVicar, Tim R.

    2012-05-01

    SummaryDue to its role in intercepting and evaporating water, vegetation is a key medium through which catchment water yields can be manipulated and may prove to be an important tool available to managers for mitigating the effects of climatic changes on yields. Understanding of the effects of vegetation on long-term catchment flows is growing, yet incorporation of these effects into hydrological models has typically been empirical and qualitative, or deterministic and quantitative - but at the cost of simplicity. Here we present a new ecohydrological model (the Budyko-Choudhury-Porporato, or BCP, model) that is the combination of two pre-existing models. It is simple, quantitative and process-based. As well as accounting for the well established roles played by average precipitation (P) and potential evaporation (Ep) on long-term catchment flows (R), the BCP model also provides estimates of n - a catchment-specific model parameter that alters the partitioning of P between R and evaporation - which is estimated as a function of plant-available soil water holding capacity (κ), mean storm depth (α) and effective rooting depth (Ze). After developing this model and testing results at several spatial scales across Australia, we used the model to analyse the sensitivity of R to changes in Ze and α (as well as P and Ep) in the high yield zones of the Murray-Darling Basin. The model performed well overall at both the coarse spatial scale (i.e., the Basin) and at the finer scales of sub-basin regions and of catchments, capturing ˜90% of the observed variability in R. At the regional scale, BCP-modelled R was more or less the same as when a default (constant) value of n was used to model R (that is, n = 1.8). This is due to the general aridity of these regions (under such conditions R is insensitive to small variations in n). However, at the catchment scale, use of the BCP model in 'wet' catchments (i.e., R > 500 mm y-1) increased the accuracy of predictions by

  7. Incorporating seismic phase correlations into a probabilistic model of global-scale seismology

    NASA Astrophysics Data System (ADS)

    Arora, Nimar

    2013-04-01

    We present a probabilistic model of seismic phases whereby the attributes of the body-wave phases are correlated to those of the first arriving P phase. This model has been incorporated into NET-VISA (Network processing Vertically Integrated Seismic Analysis) a probabilistic generative model of seismic events, their transmission, and detection on a global seismic network. In the earlier version of NET-VISA, seismic phase were assumed to be independent of each other. Although this didn't affect the quality of the inferred seismic bulletin, for the most part, it did result in a few instances of anomalous phase association. For example, an S phase with a smaller slowness than the corresponding P phase. We demonstrate that the phase attributes are indeed highly correlated, for example the uncertainty in the S phase travel time is significantly reduced given the P phase travel time. Our new model exploits these correlations to produce better calibrated probabilities for the events, as well as fewer anomalous associations.

  8. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism.

    PubMed

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model. PMID:26723613

  9. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    NASA Astrophysics Data System (ADS)

    Li, Zhen; Bian, Xin; Li, Xiantao; Karniadakis, George Em

    2015-12-01

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  10. Incorporation of memory effects in coarse-grained modeling via the Mori-Zwanzig formalism

    SciTech Connect

    Li, Zhen; Bian, Xin; Karniadakis, George Em; Li, Xiantao

    2015-12-28

    The Mori-Zwanzig formalism for coarse-graining a complex dynamical system typically introduces memory effects. The Markovian assumption of delta-correlated fluctuating forces is often employed to simplify the formulation of coarse-grained (CG) models and numerical implementations. However, when the time scales of a system are not clearly separated, the memory effects become strong and the Markovian assumption becomes inaccurate. To this end, we incorporate memory effects into CG modeling by preserving non-Markovian interactions between CG variables, and the memory kernel is evaluated directly from microscopic dynamics. For a specific example, molecular dynamics (MD) simulations of star polymer melts are performed while the corresponding CG system is defined by grouping many bonded atoms into single clusters. Then, the effective interactions between CG clusters as well as the memory kernel are obtained from the MD simulations. The constructed CG force field with a memory kernel leads to a non-Markovian dissipative particle dynamics (NM-DPD). Quantitative comparisons between the CG models with Markovian and non-Markovian approximations indicate that including the memory effects using NM-DPD yields similar results as the Markovian-based DPD if the system has clear time scale separation. However, for systems with small separation of time scales, NM-DPD can reproduce correct short-time properties that are related to how the system responds to high-frequency disturbances, which cannot be captured by the Markovian-based DPD model.

  11. Preliminary Assessment of Mercury Atmosphere-Surface Exchange Parameterizations for Incorporation into Chemical Transport Models

    NASA Astrophysics Data System (ADS)

    Khan, T.; Agnan, Y.; Obrist, D.; Selin, N. E.; Urban, N. R.; Wu, S.; Perlinger, J. A.

    2015-12-01

    Inadequate representation of process-based mechanisms of exchange behavior of elemental mercury (Hg0) and decoupled treatment of deposition and emission are two major limitations of parameterizations of atmosphere-surface exchange flux commonly incorporated into chemical transport models (CTMs). Of nineteen CTMs for Hg0 exchange we reviewed (ten global, nine regional), eight global and seven regional models have decoupled treatment of Hg0 deposition and emission, two global models include no parameterization to account for emission, and the remaining two regional models include coupled deposition and emission parameterizations (i.e., net atmosphere-surface exchange). The performance of atmosphere-surface exchange parameterizations in CTMs depends on parameterization uncertainty (in terms of both accuracy and precision) and feasibility of implementation. We provide a comparison of the performance of three available parameterizations of net atmosphere-surface exchange. To evaluate parameterization accuracy, we compare predicted exchange fluxes to field measurements conducted over a variety of surfaces compiled in a recently developed global database of terrestrial Hg0 surface-atmosphere exchange flux measurements. To assess precision, we estimate the sensitivity of predicted fluxes to the imprecision in parameter input values, and compare this sensitivity to that derived from analysis of the global Hg0 flux database. Feasibility of implementation is evaluated according to the availability of input parameters, computational requirements, and the adequacy of uncertainty representation. Based on this assessment, we provide suggestions for improved treatment of Hg0 net exchange processes in CTMs.

  12. Lifetime growth in wild meerkats: incorporating life history and environmental factors into a standard growth model.

    PubMed

    English, Sinéad; Bateman, Andrew W; Clutton-Brock, Tim H

    2012-05-01

    Lifetime records of changes in individual size or mass in wild animals are scarce and, as such, few studies have attempted to model variation in these traits across the lifespan or to assess the factors that affect them. However, quantifying lifetime growth is essential for understanding trade-offs between growth and other life history parameters, such as reproductive performance or survival. Here, we used model selection based on information theory to measure changes in body mass over the lifespan of wild meerkats, and compared the relative fits of several standard growth models (monomolecular, von Bertalanffy, Gompertz, logistic and Richards). We found that meerkats exhibit monomolecular growth, with the best model incorporating separate growth rates before and after nutritional independence, as well as effects of season and total rainfall in the previous nine months. Our study demonstrates how simple growth curves may be improved by considering life history and environmental factors, which may be particularly relevant when quantifying growth patterns in wild populations. PMID:22108854

  13. A non-classical Kirchhoff plate model incorporating microstructure, surface energy and foundation effects

    NASA Astrophysics Data System (ADS)

    Gao, X.-L.; Zhang, G. Y.

    2016-03-01

    A new non-classical Kirchhoff plate model is developed using a modified couple stress theory, a surface elasticity theory and a two-parameter elastic foundation model. A variational formulation based on Hamilton's principle is employed, which leads to the simultaneous determination of the equations of motion and the complete boundary conditions and provides a unified treatment of the microstructure, surface energy and foundation effects. The new plate model contains a material length scale parameter to account for the microstructure effect, three surface elastic constants to describe the surface energy effect, and two foundation moduli to represent the foundation effect. The current non-classical plate model reduces to its classical elasticity-based counterpart when the microstructure, surface energy and foundation effects are all suppressed. In addition, the newly developed plate model includes the models considering the microstructure dependence or the surface energy effect or the foundation influence alone as special cases and recovers the Bernoulli-Euler beam model incorporating the microstructure, surface energy and foundation effects. To illustrate the new model, the static bending and free vibration problems of a simply supported rectangular plate are analytically solved by directly applying the general formulas derived. For the static bending problem, the numerical results reveal that the deflection of the simply supported plate with or without the elastic foundation predicted by the current model is smaller than that predicted by the classical model. Also, it is observed that the difference in the deflection predicted by the new and classical plate models is very large when the plate thickness is sufficiently small, but it is diminishing with the increase of the plate thickness. For the free vibration problem, it is found that the natural frequency predicted by the new plate model with or without the elastic foundation is higher than that predicted by the

  14. Climate-informed stochastic hydrological modeling: Incorporating decadal-scale variability using paleo data

    NASA Astrophysics Data System (ADS)

    Henley, B.; Thyer, M.; Kuczera, G.

    2012-04-01

    A hierarchical framework for incorporating modes of climate variability into stochastic simulations of hydrological data is developed, termed the climate-informed multi-time scale stochastic (CIMSS) framework. To characterize long-term variability for the first level of the hierarchy, paleoclimate and instrumental data describing the Interdecadal Pacific Oscillation (IPO) and the Pacific Decadal Oscillation (PDO) are analyzed. A new paleo IPO-PDO time series dating back 440 yr is produced, combining seven IPO-PDO paleo sources using an objective smoothing procedure to fit low-pass filters to individual records. The paleo data analysis indicates that wet/dry IPO-PDO states have a broad range of run lengths, with 90% between 3 and 33 yr and a mean of 15 yr. Model selection techniques were used to determine a suitable stochastic model to simulate these run lengths. The Markov chain model, previously used to simulate oscillating wet/dry climate states, was found to underestimate the probability of wet/dry periods >5 yr, and was rejected in favor of a gamma distribution. For the second level of the hierarchy, a seasonal rainfall model is conditioned on the simulated IPO-PDO state. Application to two high quality rainfall sites close to water supply reservoirs found that mean seasonal rainfall in the IPO-PDO dry state was 15%-28% lower than the wet state. The model was able to replicate observed statistics such as seasonal and multi-year accumulated rainfall distributions and interannual autocorrelations for the case study sites. In comparison, an annual lag-one autoregressive AR(1) model was unable to adequately capture the observed rainfall distribution within separate IPO-PDO states. Furthermore, analysis of the impact of the CIMSS framework on drought risk analysis found that short-term drought risks conditional on IPO/PDO state were far higher than the traditional AR(1) model.

  15. Improving consumption rate estimates by incorporating wild activity into a bioenergetics model.

    PubMed

    Brodie, Stephanie; Taylor, Matthew D; Smith, James A; Suthers, Iain M; Gray, Charles A; Payne, Nicholas L

    2016-04-01

    Consumption is the basis of metabolic and trophic ecology and is used to assess an animal's trophic impact. The contribution of activity to an animal's energy budget is an important parameter when estimating consumption, yet activity is usually measured in captive animals. Developments in telemetry have allowed the energetic costs of activity to be measured for wild animals; however, wild activity is seldom incorporated into estimates of consumption rates. We calculated the consumption rate of a free-ranging marine predator (yellowtail kingfish, Seriola lalandi) by integrating the energetic cost of free-ranging activity into a bioenergetics model. Accelerometry transmitters were used in conjunction with laboratory respirometry trials to estimate kingfish active metabolic rate in the wild. These field-derived consumption rate estimates were compared with those estimated by two traditional bioenergetics methods. The first method derived routine swimming speed from fish morphology as an index of activity (a "morphometric" method), and the second considered activity as a fixed proportion of standard metabolic rate (a "physiological" method). The mean consumption rate for free-ranging kingfish measured by accelerometry was 152 J·g(-1)·day(-1), which lay between the estimates from the morphometric method (μ = 134 J·g(-1)·day(-1)) and the physiological method (μ = 181 J·g(-1)·day(-1)). Incorporating field-derived activity values resulted in the smallest variance in log-normally distributed consumption rates (σ = 0.31), compared with the morphometric (σ = 0.57) and physiological (σ = 0.78) methods. Incorporating field-derived activity into bioenergetics models probably provided more realistic estimates of consumption rate compared with the traditional methods, which may further our understanding of trophic interactions that underpin ecosystem-based fisheries management. The general methods used to estimate active metabolic rates of free-ranging fish

  16. Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions

    NASA Astrophysics Data System (ADS)

    Nielsen, Jens; d'Avezac, Mayeul; Hetherington, James; Stamatakis, Michail

    2013-12-01

    Ab initio kinetic Monte Carlo (KMC) simulations have been successfully applied for over two decades to elucidate the underlying physico-chemical phenomena on the surfaces of heterogeneous catalysts. These simulations necessitate detailed knowledge of the kinetics of elementary reactions constituting the reaction mechanism, and the energetics of the species participating in the chemistry. The information about the energetics is encoded in the formation energies of gas and surface-bound species, and the lateral interactions between adsorbates on the catalytic surface, which can be modeled at different levels of detail. The majority of previous works accounted for only pairwise-additive first nearest-neighbor interactions. More recently, cluster-expansion Hamiltonians incorporating long-range interactions and many-body terms have been used for detailed estimations of catalytic rate [C. Wu, D. J. Schmidt, C. Wolverton, and W. F. Schneider, J. Catal. 286, 88 (2012)]. In view of the increasing interest in accurate predictions of catalytic performance, there is a need for general-purpose KMC approaches incorporating detailed cluster expansion models for the adlayer energetics. We have addressed this need by building on the previously introduced graph-theoretical KMC framework, and we have developed Zacros, a FORTRAN2003 KMC package for simulating catalytic chemistries. To tackle the high computational cost in the presence of long-range interactions we introduce parallelization with OpenMP. We further benchmark our framework by simulating a KMC analogue of the NO oxidation system established by Schneider and co-workers [J. Catal. 286, 88 (2012)]. We show that taking into account only first nearest-neighbor interactions may lead to large errors in the prediction of the catalytic rate, whereas for accurate estimates thereof, one needs to include long-range terms in the cluster expansion.

  17. Development of QTc prolongation model incorporating circadian rhythm using harmonic model.

    PubMed

    Back, Hyun-moon; Lee, Jong-Hwa; Yun, Hwi-yeol; Kwon, Kwang-il

    2015-05-01

    1. QT prolongation is one of the major safety tests used in the development of a new drug. The ICH guidelines for the evaluation of QT prolongation recommend the use of the in vitro hERG assay and the in vivo telemetry test. However, QT intervals change under normal conditions due to circadian rhythm and can affect the results of the tests. In this study, we developed a PK/PD model to describe the QT interval after the administration of astemizole allowing for the normal changes by circadian rhythm. 2. The typical PK parameters of absorption rate constant (ka), volume of distribution (Vc and Vm), metabolism (km), and elimination rate constant (kel and kel-m) were 0.49 h(-1), 4950 L, 20 L, 0.0127 h(-1), 0.0095 h(-1), and 0.95 h(-1), respectively. The final PK/PD model was the biophase model with the modified harmonic model. The typical PK/PD parameters, base QTc interval (QT0), amplitude (T1, T3), period of QTc interval changing (T2, T4), and EC50 were 233 ms, 3.31, 1.5, -9.24 h, 1.85 h, and 0.81 ng/ml, respectively. 3. The PK/PD model to explain the changes of the QT interval that allows normal changes in the circadian rhythm after the administration of astemizole was developed successfully. This final model can be applied to the development of a human model. PMID:25475996

  18. Improving solar wind modeling at Mercury: Incorporating transient solar phenomena into the WSA-ENLIL model

    NASA Astrophysics Data System (ADS)

    Dewey, R. M.; Baker, D. N.; Anderson, B. J.; Benna, M.; Johnson, C. L.; Korth, H.; Gershman, D. J.; Ho, G. C.; McClintock, W. E.; Odstrcil, D.; Philpott, L. C.; Raines, J. M.; Schriver, D.; Slavin, J. A.; Solomon, S. C.; Winslow, R. M.; Zurbuchen, T.

    2014-12-01

    Coronal mass ejections (CMEs) and other transient solar phenomena play important roles in magnetospheric and exospheric dynamics. Although a planet may only occasionally interact with the products of these events, such transient phenomena can result in departures from the background solar wind that often involve more than an order of magnitude greater ram pressure and interplanetary electric field applied to the magnetosphere. For Mercury, an order of magnitude greater ram pressure can push the magnetopause to the planet's surface, exposing the surface directly to the solar wind. In order to understand how the solar wind interacts with Mercury's magnetosphere and exosphere, previous studies have used the Wang-Sheeley-Arge (WSA)-ENLIL solar wind modeling tool to calculate basic and composite solar wind parameters, such as solar wind velocity (V) and Alfvén Mach number (MA) at Mercury's orbital location. This model forecasts only the background solar wind, however, and does not include these transient events. The Cone extension permits the inclusion of CMEs and other phenomena, and thus enables characterization of the effect of strong solar wind perturbations on the Mercury system. The Cone extension is predicated on the assumption of constant angular and radial velocities of ejecta to integrate them into the WSA-ENLIL coupled model. Comparisons of the model results with the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft observations indicate that the WSA-ENLIL-Cone model more accurately forecasts total solar wind conditions at Mercury and has greater predictive power for magnetospheric and exospheric processes than the WSA-ENLIL model alone.

  19. Applying a Hypoxia-Incorporating TCP Model to Experimental Data on Rat Sarcoma

    SciTech Connect

    Ruggieri, Ruggero; Stavreva, Nadejda; Naccarato, Stefania; Stavrev, Pavel

    2012-08-01

    Purpose: To verify whether a tumor control probability (TCP) model which mechanistically incorporates acute and chronic hypoxia is able to describe animal in vivo dose-response data, exhibiting tumor reoxygenation. Methods and Materials: The investigated TCP model accounts for tumor repopulation, reoxygenation of chronic hypoxia, and fluctuating oxygenation of acute hypoxia. Using the maximum likelihood method, the model is fitted to Fischer-Moulder data on Wag/Rij rats, inoculated with rat rhabdomyosarcoma BA1112, and irradiated in vivo using different fractionation schemes. This data set is chosen because two of the experimental dose-response curves exhibit an inverse dose behavior, which is interpreted as due to reoxygenation. The tested TCP model is complex, and therefore, in vivo cell survival data on the same BA1112 cell line from Reinhold were added to Fischer-Moulder data and fitted simultaneously with a corresponding cell survival function. Results: The obtained fit to the combined Fischer-Moulder-Reinhold data was statistically acceptable. The best-fit values of the model parameters for which information exists were in the range of published values. The cell survival curves of well-oxygenated and hypoxic cells, computed using the best-fit values of the radiosensitivities and the initial number of clonogens, were in good agreement with the corresponding in vitro and in situ experiments of Reinhold. The best-fit values of most of the hypoxia-related parameters were used to recompute the TCP for non-small cell lung cancer patients as a function of the number of fractions, TCP(n). Conclusions: The investigated TCP model adequately describes animal in vivo data exhibiting tumor reoxygenation. The TCP(n) curve computed for non-small cell lung cancer patients with the best-fit values of most of the hypoxia-related parameters confirms previously obtained abrupt reduction in TCP for n < 10, thus warning against the adoption of severely hypofractionated schedules.

  20. An integrative model of the cardiac ventricular myocyte incorporating local control of Ca2+ release.

    PubMed Central

    Greenstein, Joseph L; Winslow, Raimond L

    2002-01-01

    The local control theory of excitation-contraction (EC) coupling in cardiac muscle asserts that L-type Ca(2+) current tightly controls Ca(2+) release from the sarcoplasmic reticulum (SR) via local interaction of closely apposed L-type Ca(2+) channels (LCCs) and ryanodine receptors (RyRs). These local interactions give rise to smoothly graded Ca(2+)-induced Ca(2+) release (CICR), which exhibits high gain. In this study we present a biophysically detailed model of the normal canine ventricular myocyte that conforms to local control theory. The model formulation incorporates details of microscopic EC coupling properties in the form of Ca(2+) release units (CaRUs) in which individual sarcolemmal LCCs interact in a stochastic manner with nearby RyRs in localized regions where junctional SR membrane and transverse-tubular membrane are in close proximity. The CaRUs are embedded within and interact with the global systems of the myocyte describing ionic and membrane pump/exchanger currents, SR Ca(2+) uptake, and time-varying cytosolic ion concentrations to form a model of the cardiac action potential (AP). The model can reproduce both the detailed properties of EC coupling, such as variable gain and graded SR Ca(2+) release, and whole-cell phenomena, such as modulation of AP duration by SR Ca(2+) release. Simulations indicate that the local control paradigm predicts stable APs when the L-type Ca(2+) current is adjusted in accord with the balance between voltage- and Ca(2+)-dependent inactivation processes as measured experimentally, a scenario where common pool models become unstable. The local control myocyte model provides a means for studying the interrelationship between microscopic and macroscopic behaviors in a manner that would not be possible in experiments. PMID:12496068

  1. Methodology for the Incorporation of Passive Component Aging Modeling into the RAVEN/ RELAP-7 Environment

    SciTech Connect

    Mandelli, Diego; Rabiti, Cristian; Cogliati, Joshua; Alfonsi, Andrea; Askin Guler; Tunc Aldemir

    2014-11-01

    Passive system, structure and components (SSCs) will degrade over their operation life and this degradation may cause to reduction in the safety margins of a nuclear power plant. In traditional probabilistic risk assessment (PRA) using the event-tree/fault-tree methodology, passive SSC failure rates are generally based on generic plant failure data and the true state of a specific plant is not reflected realistically. To address aging effects of passive SSCs in the traditional PRA methodology [1] does consider physics based models that account for the operating conditions in the plant, however, [1] does not include effects of surveillance/inspection. This paper represents an overall methodology for the incorporation of aging modeling of passive components into the RAVEN/RELAP-7 environment which provides a framework for performing dynamic PRA. Dynamic PRA allows consideration of both epistemic and aleatory uncertainties (including those associated with maintenance activities) in a consistent phenomenological and probabilistic framework and is often needed when there is complex process/hardware/software/firmware/ human interaction [2]. Dynamic PRA has gained attention recently due to difficulties in the traditional PRA modeling of aging effects of passive components using physics based models and also in the modeling of digital instrumentation and control systems. RAVEN (Reactor Analysis and Virtual control Environment) [3] is a software package under development at the Idaho National Laboratory (INL) as an online control logic driver and post-processing tool. It is coupled to the plant transient code RELAP-7 (Reactor Excursion and Leak Analysis Program) also currently under development at INL [3], as well as RELAP 5 [4]. The overall methodology aims to: • Address multiple aging mechanisms involving large number of components in a computational feasible manner where sequencing of events is conditioned on the physical conditions predicted in a simulation

  2. Incorporating Student Mobility in Achievement Growth Modeling: A Cross-Classified Multiple Membership Growth Curve Model

    ERIC Educational Resources Information Center

    Grady, Matthew W.; Beretvas, S. Natasha

    2010-01-01

    Multiple membership random effects models (MMREMs) have been developed for use in situations where individuals are members of multiple higher level organizational units. Despite their availability and the frequency with which multiple membership structures are encountered, no studies have extended the MMREM approach to hierarchical growth curve…

  3. Incorporating spatially explicit crown light competition into a model of canopy transpiration

    NASA Astrophysics Data System (ADS)

    Loranty, M. M.; Mackay, D. S.; Roberts, D. E.; Ewers, B. E.; Kruger, E. L.; Traver, E.

    2006-12-01

    Stomatal conductance parameterized in a transpiration model has been shown to vary spatially for aspen ( Populus tremuloides) and alder (Alnus incana) growing along a moisture gradient. We hypothesized that competition for light within the canopy would explain some of this variation. Sap flux data was collected over 10 days in 2004, and 30 days in 2005 at a 1.5 ha site near the WLEF AmeriFlux tower in the Chequmegon National Forest near Park Falls, Wisconsin. We used inverse modeling with the Terrestrial Regional Ecosystem Exchange Simulator (TREES) to estimate values of GSref for individual trees. Competition data for individual aspen sampled for sap flux was collected in August 2006. The number, height, DBH, and location of all competitors within 5 meters of each flux tree were recorded. Preliminary geostatistical analysis indicates that the number of competitor trees varies spatially for aspen. We hypothesize that height and species specific crown characteristics of competitor trees will have a spatially variable affect on transpiration via light attenuation. Furthermore, a simple light competition term will be able to incorporate this variability into the TREES transpiration model.

  4. EVOLUTIONARY MODELS OF SUPER-EARTHS AND MINI-NEPTUNES INCORPORATING COOLING AND MASS LOSS

    SciTech Connect

    Howe, Alex R.; Burrows, Adam E-mail: burrows@astro.princeton.edu

    2015-08-01

    We construct models of the structural evolution of super-Earth- and mini-Neptune-type exoplanets with H{sub 2}–He envelopes, incorporating radiative cooling and XUV-driven mass loss. We conduct a parameter study of these models, focusing on initial mass, radius, and envelope mass fractions, as well as orbital distance, metallicity, and the specific prescription for mass loss. From these calculations, we investigate how the observed masses and radii of exoplanets today relate to the distribution of their initial conditions. Orbital distance and the initial envelope mass fraction are the most important factors determining planetary evolution, particularly radius evolution. Initial mass also becomes important below a “turnoff mass,” which varies with orbital distance, with mass–radius curves being approximately flat for higher masses. Initial radius is the least important parameter we study, with very little difference between the hot start and cold start limits after an age of 100 Myr. Model sets with no mass loss fail to produce results consistent with observations, but a plausible range of mass-loss scenarios is allowed. In addition, we present scenarios for the formation of the Kepler-11 planets. Our best fit to observations of Kepler-11b and Kepler-11c involves formation beyond the snow line, after which they moved inward, circularized, and underwent a reduced degree of mass loss.

  5. Model-Based Detection of Radioactive Contraband for Harbor Defense Incorporating Compton Scattering Physics

    SciTech Connect

    Candy, J V; Chambers, D H; Breitfeller, E F; Guidry, B L; Verbeke, J M; Axelrod, M A; Sale, K E; Meyer, A M

    2010-03-02

    The detection of radioactive contraband is a critical problem is maintaining national security for any country. Photon emissions from threat materials challenge both detection and measurement technologies especially when concealed by various types of shielding complicating the transport physics significantly. This problem becomes especially important when ships are intercepted by U.S. Coast Guard harbor patrols searching for contraband. The development of a sequential model-based processor that captures both the underlying transport physics of gamma-ray emissions including Compton scattering and the measurement of photon energies offers a physics-based approach to attack this challenging problem. The inclusion of a basic radionuclide representation of absorbed/scattered photons at a given energy along with interarrival times is used to extract the physics information available from the noisy measurements portable radiation detection systems used to interdict contraband. It is shown that this physics representation can incorporated scattering physics leading to an 'extended' model-based structure that can be used to develop an effective sequential detection technique. The resulting model-based processor is shown to perform quite well based on data obtained from a controlled experiment.

  6. Incorporating ecological data and associated uncertainty in bioaccumulation modeling: methodology development and case study.

    PubMed

    De Laender, Frederik; Van Oevelen, Dick; Middelburg, Jack J; Soetaert, Karline

    2009-04-01

    Bioaccumulation models predict internal concentrations of hydrophobic chemicals by incorporating key gain/loss processes reflecting the ecology of the exposed species and the characteristics of the chemical. Here, we propose a new methodology that uses ecological data and the principle of mass balance in food webs to estimate bioaccumulation in food webs. To this end, we combine linear inverse models (LIMs) that estimate food web flows based on mass balance with a mechanistic bioaccumulation model (OMEGA). In a case study we show that uncertainty ranges on bioaccumulation predictions were on average estimated a factor of 4 lower by LIM-OMEGA than by an OMEGA application that does not consider mass balance within food webs, most notably for chemicals with log Kow > 5, reflecting an increasing importance of uptake through food ingestion for those chemicals. Ranges of internal concentrations predicted by LIM-OMEGA were smaller in enclosures with fish, as strong predation pressure from the latter on mesozooplankton constrains food web flows and thus bioaccumulation.

  7. Modelling of Dynamic Rock Fracture Process with a Rate-Dependent Combined Continuum Damage-Embedded Discontinuity Model Incorporating Microstructure

    NASA Astrophysics Data System (ADS)

    Saksala, Timo

    2016-10-01

    This paper deals with numerical modelling of rock fracture under dynamic loading. For this end, a combined continuum damage-embedded discontinuity model is applied in finite element modelling of crack propagation in rock. In this model, the strong loading rate sensitivity of rock is captured by the rate-dependent continuum scalar damage model that controls the pre-peak nonlinear hardening part of rock behaviour. The post-peak exponential softening part of the rock behaviour is governed by the embedded displacement discontinuity model describing the mode I, mode II and mixed mode fracture of rock. Rock heterogeneity is incorporated in the present approach by random description of the rock mineral texture based on the Voronoi tessellation. The model performance is demonstrated in numerical examples where the uniaxial tension and compression tests on rock are simulated. Finally, the dynamic three-point bending test of a semicircular disc is simulated in order to show that the model correctly predicts the strain rate-dependent tensile strengths as well as the failure modes of rock in this test. Special emphasis is laid on modelling the loading rate sensitivity of tensile strength of Laurentian granite.

  8. MIST: An Open Source Environmental Modelling Programming Language Incorporating Easy to Use Data Parallelism.

    NASA Astrophysics Data System (ADS)

    Bellerby, Tim

    2014-05-01

    Model Integration System (MIST) is open-source environmental modelling programming language that directly incorporates data parallelism. The language is designed to enable straightforward programming structures, such as nested loops and conditional statements to be directly translated into sequences of whole-array (or more generally whole data-structure) operations. MIST thus enables the programmer to use well-understood constructs, directly relating to the mathematical structure of the model, without having to explicitly vectorize code or worry about details of parallelization. A range of common modelling operations are supported by dedicated language structures operating on cell neighbourhoods rather than individual cells (e.g.: the 3x3 local neighbourhood needed to implement an averaging image filter can be simply accessed from within a simple loop traversing all image pixels). This facility hides details of inter-process communication behind more mathematically relevant descriptions of model dynamics. The MIST automatic vectorization/parallelization process serves both to distribute work among available nodes and separately to control storage requirements for intermediate expressions - enabling operations on very large domains for which memory availability may be an issue. MIST is designed to facilitate efficient interpreter based implementations. A prototype open source interpreter is available, coded in standard FORTRAN 95, with tools to rapidly integrate existing FORTRAN 77 or 95 code libraries. The language is formally specified and thus not limited to FORTRAN implementation or to an interpreter-based approach. A MIST to FORTRAN compiler is under development and volunteers are sought to create an ANSI-C implementation. Parallel processing is currently implemented using OpenMP. However, parallelization code is fully modularised and could be replaced with implementations using other libraries. GPU implementation is potentially possible.

  9. Incorporating dynamic collimator motion in Monte Carlo simulations: an application in modelling a dynamic wedge

    NASA Astrophysics Data System (ADS)

    Verhaegen, Frank; Liu, H. Helen

    2001-02-01

    In radiation therapy, new treatment modalities employing dynamic collimation and intensity modulation increase the complexity of dose calculation because a new dimension, time, has to be incorporated into the traditional three-dimensional problem. In this work, we investigated two classes of sampling technique to incorporate dynamic collimator motion in Monte Carlo simulation. The methods were initially evaluated for modelling enhanced dynamic wedges (EDWs) from Varian accelerators (Varian Medical Systems, Palo Alto, USA). In the position-probability-sampling or PPS method, a cumulative probability distribution function (CPDF) was computed for the collimator position, which could then be sampled during simulations. In the static-component-simulation or SCS method, a dynamic field is approximated by multiple static fields in a step-shoot fashion. The weights of the particles or the number of particles simulated for each component field are computed from the probability distribution function (PDF) of the collimator position. The CPDF and PDF were computed from the segmented treatment tables (STTs) for the EDWs. An output correction factor had to be applied in this calculation to account for the backscattered radiation affecting monitor chamber readings. Comparison of the phase-space data from the PPS method (with the step-shoot motion) with those from the SCS method showed excellent agreement. The accuracy of the PPS method was further verified from the agreement between the measured and calculated dose distributions. Compared to the SCS method, the PPS method is more automated and efficient from an operational point of view. The principle of the PPS method can be extended to simulate other dynamic motions, and in particular, intensity-modulated beams using multileaf collimators.

  10. Bias in diet determination: incorporating traditional methods in Bayesian mixing models.

    PubMed

    Franco-Trecu, Valentina; Drago, Massimiliano; Riet-Sapriza, Federico G; Parnell, Andrew; Frau, Rosina; Inchausti, Pablo

    2013-01-01

    There are not "universal methods" to determine diet composition of predators. Most traditional methods are biased because of their reliance on differential digestibility and the recovery of hard items. By relying on assimilated food, stable isotope and Bayesian mixing models (SIMMs) resolve many biases of traditional methods. SIMMs can incorporate prior information (i.e. proportional diet composition) that may improve the precision in the estimated dietary composition. However few studies have assessed the performance of traditional methods and SIMMs with and without informative priors to study the predators' diets. Here we compare the diet compositions of the South American fur seal and sea lions obtained by scats analysis and by SIMMs-UP (uninformative priors) and assess whether informative priors (SIMMs-IP) from the scat analysis improved the estimated diet composition compared to SIMMs-UP. According to the SIMM-UP, while pelagic species dominated the fur seal's diet the sea lion's did not have a clear dominance of any prey. In contrast, SIMM-IP's diets compositions were dominated by the same preys as in scat analyses. When prior information influenced SIMMs' estimates, incorporating informative priors improved the precision in the estimated diet composition at the risk of inducing biases in the estimates. If preys isotopic data allow discriminating preys' contributions to diets, informative priors should lead to more precise but unbiased estimated diet composition. Just as estimates of diet composition obtained from traditional methods are critically interpreted because of their biases, care must be exercised when interpreting diet composition obtained by SIMMs-IP. The best approach to obtain a near-complete view of predators' diet composition should involve the simultaneous consideration of different sources of partial evidence (traditional methods, SIMM-UP and SIMM-IP) in the light of natural history of the predator species so as to reliably ascertain and

  11. Bias in Diet Determination: Incorporating Traditional Methods in Bayesian Mixing Models

    PubMed Central

    Franco-Trecu, Valentina; Drago, Massimiliano; Riet-Sapriza, Federico G.; Parnell, Andrew; Frau, Rosina; Inchausti, Pablo

    2013-01-01

    There are not “universal methods” to determine diet composition of predators. Most traditional methods are biased because of their reliance on differential digestibility and the recovery of hard items. By relying on assimilated food, stable isotope and Bayesian mixing models (SIMMs) resolve many biases of traditional methods. SIMMs can incorporate prior information (i.e. proportional diet composition) that may improve the precision in the estimated dietary composition. However few studies have assessed the performance of traditional methods and SIMMs with and without informative priors to study the predators’ diets. Here we compare the diet compositions of the South American fur seal and sea lions obtained by scats analysis and by SIMMs-UP (uninformative priors) and assess whether informative priors (SIMMs-IP) from the scat analysis improved the estimated diet composition compared to SIMMs-UP. According to the SIMM-UP, while pelagic species dominated the fur seal’s diet the sea lion’s did not have a clear dominance of any prey. In contrast, SIMM-IP’s diets compositions were dominated by the same preys as in scat analyses. When prior information influenced SIMMs’ estimates, incorporating informative priors improved the precision in the estimated diet composition at the risk of inducing biases in the estimates. If preys isotopic data allow discriminating preys’ contributions to diets, informative priors should lead to more precise but unbiased estimated diet composition. Just as estimates of diet composition obtained from traditional methods are critically interpreted because of their biases, care must be exercised when interpreting diet composition obtained by SIMMs-IP. The best approach to obtain a near-complete view of predators’ diet composition should involve the simultaneous consideration of different sources of partial evidence (traditional methods, SIMM-UP and SIMM-IP) in the light of natural history of the predator species so as to reliably

  12. Incorporating H2 Dynamics and Inhibition into a Microbially Based Methanogenesis Model for Restored Wetland Sediments

    NASA Astrophysics Data System (ADS)

    Pal, David; Jaffe, Peter

    2015-04-01

    Estimates of global CH4 emissions from wetlands indicate that wetlands are the largest natural source of CH4 to the atmosphere. In this paper, we propose that there is a missing component to these models that should be addressed. CH4 is produced in wetland sediments from the microbial degradation of organic carbon through multiple fermentation steps and methanogenesis pathways. There are multiple sources of carbon for methananogenesis; in vegetated wetland sediments, microbial communities consume root exudates as a major source of organic carbon. In many methane models propionate is used as a model carbon molecule. This simple sugar is fermented into acetate and H2, acetate is transformed to methane and CO2, while the H2 and CO2 are used to form an additional CH4 molecule. The hydrogenotrophic pathway involves the equilibrium of two dissolved gases, CH4 and H2. In an effort to limit CH4 emissions from wetlands, there has been growing interest in finding ways to limit plant transport of soil gases through root systems. Changing planted species, or genetically modifying new species of plants may control this transport of soil gases. While this may decrease the direct emissions of methane, there is little understanding about how H2 dynamics may feedback into overall methane production. The results of an incubation study were combined with a new model of propionate degradation for methanogenesis that also examines other natural parameters (i.e. gas transport through plants). This presentation examines how we would expect this model to behave in a natural field setting with changing sulfate and carbon loading schemes. These changes can be controlled through new plant species and other management practices. Next, we compare the behavior of two variations of this model, with or without the incorporation of H2 interactions, with changing sulfate, carbon loading and root volatilization. Results show that while the models behave similarly there may be a discrepancy of nearly

  13. Incorporating an advanced aerosol activation parameterization into WRF-CAM5: Model evaluation and parameterization intercomparison

    SciTech Connect

    Zhang, Yang; Zhang, Xin; Wang, Kai; He, Jian; Leung, Lai-Yung R.; Fan, Jiwen; Nenes, Athanasios

    2015-07-22

    Aerosol activation into cloud droplets is an important process that governs aerosol indirect effects. The advanced treatment of aerosol activation by Fountoukis and Nenes (2005) and its recent updates, collectively called the FN series, have been incorporated into a newly developed regional coupled climate-air quality model based on the Weather Research and Forecasting model with the physics package of the Community Atmosphere Model version 5 (WRF-CAM5) to simulate aerosol-cloud interactions in both resolved and convective clouds. The model is applied to East Asia for two full years of 2005 and 2010. A comprehensive model evaluation is performed for model predictions of meteorological, radiative, and cloud variables, chemical concentrations, and column mass abundances against satellite data and surface observations from air quality monitoring sites across East Asia. The model performs overall well for major meteorological variables including near-surface temperature, specific humidity, wind speed, precipitation, cloud fraction, precipitable water, downward shortwave and longwave radiation, and column mass abundances of CO, SO2, NO2, HCHO, and O3 in terms of both magnitudes and spatial distributions. Larger biases exist in the predictions of surface concentrations of CO and NOx at all sites and SO2, O3, PM2.5, and PM10 concentrations at some sites, aerosol optical depth, cloud condensation nuclei over ocean, cloud droplet number concentration (CDNC), cloud liquid and ice water path, and cloud optical thickness. Compared with the default Abdul-Razzack Ghan (2000) parameterization, simulations with the FN series produce ~107–113% higher CDNC, with half of the difference attributable to the higher aerosol activation fraction by the FN series and the remaining half due to feedbacks in subsequent cloud microphysical processes. With the higher CDNC, the FN series are more skillful in simulating cloud water path, cloud optical thickness, downward shortwave radiation

  14. Incorporating an advanced aerosol activation parameterization into WRF-CAM5: Model evaluation and parameterization intercomparison

    NASA Astrophysics Data System (ADS)

    Zhang, Yang; Zhang, Xin; Wang, Kai; He, Jian; Leung, L. Ruby; Fan, Jiwen; Nenes, Athanasios

    2015-07-01

    Aerosol activation into cloud droplets is an important process that governs aerosol indirect effects. The advanced treatment of aerosol activation by Fountoukis and Nenes (2005) and its recent updates, collectively called the FN series, have been incorporated into a newly developed regional coupled climate-air quality model based on the Weather Research and Forecasting model with the physics package of the Community Atmosphere Model version 5 (WRF-CAM5) to simulate aerosol-cloud interactions in both resolved and convective clouds. The model is applied to East Asia for two full years of 2005 and 2010. A comprehensive model evaluation is performed for model predictions of meteorological, radiative, and cloud variables, chemical concentrations, and column mass abundances against satellite data and surface observations from air quality monitoring sites across East Asia. The model performs overall well for major meteorological variables including near-surface temperature, specific humidity, wind speed, precipitation, cloud fraction, precipitable water, downward shortwave and longwave radiation, and column mass abundances of CO, SO2, NO2, HCHO, and O3 in terms of both magnitudes and spatial distributions. Larger biases exist in the predictions of surface concentrations of CO and NOx at all sites and SO2, O3, PM2.5, and PM10 concentrations at some sites, aerosol optical depth, cloud condensation nuclei over ocean, cloud droplet number concentration (CDNC), cloud liquid and ice water path, and cloud optical thickness. Compared with the default Abdul-Razzack Ghan (2000) parameterization, simulations with the FN series produce ~107-113% higher CDNC, with half of the difference attributable to the higher aerosol activation fraction by the FN series and the remaining half due to feedbacks in subsequent cloud microphysical processes. With the higher CDNC, the FN series are more skillful in simulating cloud water path, cloud optical thickness, downward shortwave radiation

  15. Anisotropic constitutive model incorporating multiple damage mechanisms for multiscale simulation of dental enamel.

    PubMed

    Ma, Songyun; Scheider, Ingo; Bargmann, Swantje

    2016-09-01

    An anisotropic constitutive model is proposed in the framework of finite deformation to capture several damage mechanisms occurring in the microstructure of dental enamel, a hierarchical bio-composite. It provides the basis for a homogenization approach for an efficient multiscale (in this case: multiple hierarchy levels) investigation of the deformation and damage behavior. The influence of tension-compression asymmetry and fiber-matrix interaction on the nonlinear deformation behavior of dental enamel is studied by 3D micromechanical simulations under different loading conditions and fiber lengths. The complex deformation behavior and the characteristics and interaction of three damage mechanisms in the damage process of enamel are well captured. The proposed constitutive model incorporating anisotropic damage is applied to the first hierarchical level of dental enamel and validated by experimental results. The effect of the fiber orientation on the damage behavior and compressive strength is studied by comparing micro-pillar experiments of dental enamel at the first hierarchical level in multiple directions of fiber orientation. A very good agreement between computational and experimental results is found for the damage evolution process of dental enamel.

  16. Development and application of a mark-recapture model incorporating predicted sex and transitory behaviour

    USGS Publications Warehouse

    Conroy, M.J.; Senar, J.C.; Hines, J.E.; Domenech, J.

    1999-01-01

    We developed an extension of Cormack-Jolly-Seber models to handle a complex mark-recapture problem in which (a) the sex of birds cannot be determined prior to first moult, but can be predicted on the basis of body measurements, and (b) a significant portion of captured birds appear to be transients (i.e. are captured once but leave the area or otherwise become 'untrappable'). We applied this methodology to a data set of 4184 serins (Serinus serinus) trapped in northeastern Spain during 1985-96, in order to investigate age-, sex-, and time-specific variation in survival rates. Using this approach, we were able to successfully incorporate the majority of ringings of serins. Had we eliminated birds not previously captured (as has been advocated to avoid the problem of transience) we would have reduced our sample sizes by >2000 releases. In addition, we were able to include 1610 releases of birds of unknown (but predicted) sex; these data contributed to the precision of our estimates and the power of statistical tests. We discuss problems with data structure, encoding of the algorithms to compute parameter estimates, model selection, identifiability of parameters, and goodness-of-fit, and make recommendations for the design and analysis of future studies facing similar problems.

  17. Development and application of a mark-recapture model incorporating predicted sex and transitory behaviour

    USGS Publications Warehouse

    Conroy, M.J.; Senar, J.C.; Hines, J.E.; Domenech, J.

    1999-01-01

    We developed an extension of Cormack-Jolly-Seber models to handle a complex mark-recapture problem in which (a) the sex of birds cannot be determined prior to first moult, but can be predicted on the basis of body measurements, and (b) a significant portion of captured birds appear to be transients (i.e. are captured once but leave the area or otherwise become ' untrappable'). We applied this methodology to a data set of 4184 serins (Serinus serinus) trapped in northeastern Spain during 1985-96, in order to investigate age-, sex-, and time-specific variation in survival rates. Using this approach, we were able to successfully incorporate the majority of ringings of serins. Had we eliminated birds not previously captured (as has been advocated to avoid the problem of transience) we would have reduced our sample sizes by >2000 releases. In addition, we were able to include 1610 releases of birds of unknown (but predicted) sex; these data contributed to the precision of our estimates and the power of statistical tests. We discuss problems with data structure, encoding of the algorithms to compute parameter estimates, model selection, identifiability of parameters, and goodness-of-fit, and make recommendations for the design and analysis of future studies facing similar problems.

  18. Alternative Methods of Classifying Eating Disorders: Models Incorporating Comorbid Psychopathology and Associated Features

    PubMed Central

    Wildes, Jennifer E.; Marcus, Marsha D.

    2013-01-01

    There is increasing recognition of the limitations of current approaches to psychiatric classification. Nowhere is this more apparent than in the eating disorders (EDs). Several alternative methods of classifying EDs have been proposed, which can be divided into two major groups: 1) those that have classified individuals on the basis of disordered eating symptoms; and, 2) those that have classified individuals on the basis of comorbid psychopathology and associated features. Several reviews have addressed symptom-based approaches to ED classification, but we are aware of no paper that has critically examined comorbidity-based systems. Thus, in this paper, we review models of classifying EDs that incorporate information about comorbid psychopathology and associated features. Early approaches are described first, followed by more recent scholarly contributions to comorbidity-based ED classification. Importantly, several areas of overlap among the classification schemes are identified that may have implications for future research. In particular, we note similarities between early models and newer studies in the salience of impulsivity, compulsivity, distress, and inhibition versus risk taking. Finally, we close with directions for future work, with an emphasis on neurobiologically-informed research to elucidate basic behavioral and neuropsychological correlates of comorbidity-based ED classes, as well as implications for treatment. PMID:23416343

  19. A Bayesian model of lightness perception that incorporates spatial variation in the illumination

    PubMed Central

    Allred, Sarah R.; Brainard, David H.

    2013-01-01

    The lightness of a test stimulus depends in a complex manner on the context in which it is viewed. To predict lightness, it is necessary to leverage measurements of a feasible number of contextual configurations into predictions for a wider range of configurations. Here we pursue this goal, using the idea that lightness results from the visual system's attempt to provide stable information about object surface reflectance. We develop a Bayesian algorithm that estimates both illumination and reflectance from image luminance, and link perceived lightness to the algorithm's estimates of surface reflectance. The algorithm resolves ambiguity in the image through the application of priors that specify what illumination and surface reflectances are likely to occur in viewed scenes. The prior distributions were chosen to allow spatial variation in both illumination and surface reflectance. To evaluate our model, we compared its predictions to a data set of judgments of perceived lightness of test patches embedded in achromatic checkerboards (Allred, Radonjić, Gilchrist, & Brainard, 2012). The checkerboard stimuli incorporated the large variation in luminance that is a pervasive feature of natural scenes. In addition, the luminance profile of the checks both near to and remote from the central test patches was systematically manipulated. The manipulations provided a simplified version of spatial variation in illumination. The model can account for effects of overall changes in image luminance and the dependence of such changes on spatial location as well as some but not all of the more detailed features of the data. PMID:23814073

  20. Anisotropic constitutive model incorporating multiple damage mechanisms for multiscale simulation of dental enamel.

    PubMed

    Ma, Songyun; Scheider, Ingo; Bargmann, Swantje

    2016-09-01

    An anisotropic constitutive model is proposed in the framework of finite deformation to capture several damage mechanisms occurring in the microstructure of dental enamel, a hierarchical bio-composite. It provides the basis for a homogenization approach for an efficient multiscale (in this case: multiple hierarchy levels) investigation of the deformation and damage behavior. The influence of tension-compression asymmetry and fiber-matrix interaction on the nonlinear deformation behavior of dental enamel is studied by 3D micromechanical simulations under different loading conditions and fiber lengths. The complex deformation behavior and the characteristics and interaction of three damage mechanisms in the damage process of enamel are well captured. The proposed constitutive model incorporating anisotropic damage is applied to the first hierarchical level of dental enamel and validated by experimental results. The effect of the fiber orientation on the damage behavior and compressive strength is studied by comparing micro-pillar experiments of dental enamel at the first hierarchical level in multiple directions of fiber orientation. A very good agreement between computational and experimental results is found for the damage evolution process of dental enamel. PMID:27294283

  1. Incorporating measured valve properties into a numerical model of a lymphatic vessel

    PubMed Central

    Macaskill, C.; Moore, J.E.

    2015-01-01

    An existing lumped-parameter model of multiple lymphangions (lymphatic vascular segments) in series is adapted for the incorporation of recent physiological measurements of lymphatic vascular properties. The new data show very marked nonlinearity of the passive pressure-diameter relation during distension, relative to comparable blood vessels, and complex valve behaviour. Since lymph is transported as a result of either the active contraction or the passive squeezing of vascular segments situated between two one-way valves, the performance of these valves is of primary importance. The valves display hysteresis (the opening and closing pressure-drop thresholds differ), a bias to staying open (both state changes occur when the trans-valve pressure drop is adverse), and pressure-drop threshold dependence on transmural pressure. These properties, in combination with the strong nonlinearity that valve operation represents, have in turn caused intriguing numerical problems in the model, and we describe numerical stratagems by which we have overcome the problems. The principal problem is also generalised into a relatively simple mathematical example, for which solution detail is provided using two different solvers. PMID:23387996

  2. Conditional spectrum computation incorporating multiple causal earthquakes and ground-motion prediction models

    USGS Publications Warehouse

    Lin, Ting; Harmsen, Stephen C.; Baker, Jack W.; Luco, Nicolas

    2013-01-01

    The conditional spectrum (CS) is a target spectrum (with conditional mean and conditional standard deviation) that links seismic hazard information with ground-motion selection for nonlinear dynamic analysis. Probabilistic seismic hazard analysis (PSHA) estimates the ground-motion hazard by incorporating the aleatory uncertainties in all earthquake scenarios and resulting ground motions, as well as the epistemic uncertainties in ground-motion prediction models (GMPMs) and seismic source models. Typical CS calculations to date are produced for a single earthquake scenario using a single GMPM, but more precise use requires consideration of at least multiple causal earthquakes and multiple GMPMs that are often considered in a PSHA computation. This paper presents the mathematics underlying these more precise CS calculations. Despite requiring more effort to compute than approximate calculations using a single causal earthquake and GMPM, the proposed approach produces an exact output that has a theoretical basis. To demonstrate the results of this approach and compare the exact and approximate calculations, several example calculations are performed for real sites in the western United States. The results also provide some insights regarding the circumstances under which approximate results are likely to closely match more exact results. To facilitate these more precise calculations for real applications, the exact CS calculations can now be performed for real sites in the United States using new deaggregation features in the U.S. Geological Survey hazard mapping tools. Details regarding this implementation are discussed in this paper.

  3. Incorporating a Wheeled Vehicle Model in a New Monocular Visual Odometry Algorithm for Dynamic Outdoor Environments

    PubMed Central

    Jiang, Yanhua; Xiong, Guangming; Chen, Huiyan; Lee, Dah-Jye

    2014-01-01

    This paper presents a monocular visual odometry algorithm that incorporates a wheeled vehicle model for ground vehicles. The main innovation of this algorithm is to use the single-track bicycle model to interpret the relationship between the yaw rate and side slip angle, which are the two most important parameters that describe the motion of a wheeled vehicle. Additionally, the pitch angle is also considered since the planar-motion hypothesis often fails due to the dynamic characteristics of wheel suspensions and tires in real-world environments. Linearization is used to calculate a closed-form solution of the motion parameters that works as a hypothesis generator in a RAndom SAmple Consensus (RANSAC) scheme to reduce the complexity in solving equations involving trigonometric. All inliers found are used to refine the winner solution through minimizing the reprojection error. Finally, the algorithm is applied to real-time on-board visual localization applications. Its performance is evaluated by comparing against the state-of-the-art monocular visual odometry methods using both synthetic data and publicly available datasets over several kilometers in dynamic outdoor environments. PMID:25256109

  4. Climate-informed stochastic hydrological modeling: Incorporating decadal-scale variability using paleoclimate data

    NASA Astrophysics Data System (ADS)

    Henley, B. J.; Thyer, M. A.; Kuczera, G. A.

    2012-12-01

    A hierarchical framework for incorporating modes of climate variability into stochastic simulations of hydrological data is developed, termed the climate-informed multi-time scale stochastic (CIMSS) framework. To characterize long-term variability for the first level of the hierarchy, paleoclimate and instrumental data describing the Interdecadal Pacific Oscillation (IPO) and the Pacific Decadal Oscillation (PDO) are analyzed. A new paleo IPO-PDO time series dating back 440 yrs is produced, combining seven IPO-PDO paleo sources using an objective smoothing procedure to fit low-pass filters to individual records. The paleo data analysis indicates that wet/dry IPO-PDO states have a broad range of run-lengths, with 90% between 3 and 33 yr and a mean of 15 yr. Model selection techniques were used to determine a suitable stochastic model to simulate these run-lengths. The Markov chain model, previously used to simulate oscillating wet/dry climate states, was found to underestimate the probability of wet/dry periods >5 yr, and was rejected in favor of a gamma distribution. For the second level of the hierarchy, a seasonal rainfall model is conditioned on the simulated IPO-PDO state. Application to two high-quality rainfall sites close to water supply reservoirs found that mean seasonal rainfall in the IPO-PDO dry state was 15%-28% lower than the wet state. The model was able to replicate observed statistics such as seasonal and multi-year accumulated rainfall distributions and interannual autocorrelations for the case study sites. In comparison, an annual lag-one autoregressive AR(1) model was unable to adequately capture the observed rainfall distribution within separate IPO-PDO states. Furthermore, analysis of the impact of the CIMSS framework on drought risk analysis found that short-term drought risks conditional on IPO/PDO state were considerably higher than the traditional AR(1) model.hort-term conditional water supply drought risks for the CIMSS and AR(1) models

  5. Unsteady polynya flux model solutions incorporating a parameterization for the collection thickness of consolidated new ice

    NASA Astrophysics Data System (ADS)

    Biggs, Nicholas R. T.; Willmott, Andrew J.

    This paper develops a time-dependent, two-dimensional model for the opening of a coastal polynya. The model incorporates a parameterization for the collection thickness of frazil ice at the polynya edge that is given in terms of (a) the depth of frazil ice arriving at the polynya edge, (b) the component normal to the polynya edge of the frazil ice velocity relative to the consolidated new ice velocity, and (c) a constant depth term ( hw) associated with wave radiation stress. The last term depends upon the wavelength of surface waves that are most readily generated by the wind stress, and for coastal polynyas is shown to be of the order of 5 cm. The inclusion of hw also removes possible cases of the parameterization being non-robust in the unsteady problem. Polynya opening solutions are calculated adjacent to a straight coastal barrier of finite length D, by numerically integrating Charpit's equations, a generalisation of the method of characteristics. Polynya opening times are compared with those in a constant collection depth model, when both models open to polynyas with identical steady-state area. For "long" islands ( D≫alongshore adjustment length scale La), the opening time T obeys T> Tc, where Tc is the constant collection depth opening time; when D≪ La, the inequality is reversed. Finally, month by month simulations of the opening of the St. Lawrence Island Polynya (SLIP) are presented, for which satellite-derived steady-state areas are available. In most simulations, the simulated steady-state area falls within the 90% confidence limits of the observed area.

  6. A large-scale methane model by incorporating the surface water transport

    NASA Astrophysics Data System (ADS)

    Lu, Xiaoliang; Zhuang, Qianlai; Liu, Yaling; Zhou, Yuyu; Aghakouchak, Amir

    2016-06-01

    The effect of surface water movement on methane emissions is not explicitly considered in most of the current methane models. In this study, a surface water routing was coupled into our previously developed large-scale methane model. The revised methane model was then used to simulate global methane emissions during 2006-2010. From our simulations, the global mean annual maximum inundation extent is 10.6 ± 1.9 km2 and the methane emission is 297 ± 11 Tg C/yr in the study period. In comparison to the currently used TOPMODEL-based approach, we found that the incorporation of surface water routing leads to 24.7% increase in the annual maximum inundation extent and 30.8% increase in the methane emissions at the global scale for the study period, respectively. The effect of surface water transport on methane emissions varies in different regions: (1) the largest difference occurs in flat and moist regions, such as Eastern China; (2) high-latitude regions, hot spots in methane emissions, show a small increase in both inundation extent and methane emissions with the consideration of surface water movement; and (3) in arid regions, the new model yields significantly larger maximum flooded areas and a relatively small increase in the methane emissions. Although surface water is a small component in the terrestrial water balance, it plays an important role in determining inundation extent and methane emissions, especially in flat regions. This study indicates that future quantification of methane emissions shall consider the effects of surface water transport.

  7. Incorporating Geochemical And Microbial Kinetics In Reactive Transport Models For Generation Of Acid Rock Drainage

    NASA Astrophysics Data System (ADS)

    Andre, B. J.; Rajaram, H.; Silverstein, J.

    2010-12-01

    diffusion model at the scale of a single rock is developed incorporating the proposed kinetic rate expressions. Simulations of initiation, washout and AMD flows are discussed to gain a better understanding of the role of porosity, effective diffusivity and reactive surface area in generating AMD. Simulations indicate that flow boundary conditions control generation of acid rock drainage as porosity increases.

  8. A Model for Incorporating Lesson Study into the Student Teaching Placement: What Worked and What Did Not?

    ERIC Educational Resources Information Center

    Gurl, Theresa

    2011-01-01

    This article describes a model for incorporating lesson study into the student teaching placement and reports on the success of the implementation of such a model with student teachers and their cooperating teachers (CTs). Student teachers had the opportunity to discuss many important ideas with each other and their CTs, including "big ideas" of…

  9. Adolescent Decision-Making Processes regarding University Entry: A Model Incorporating Cultural Orientation, Motivation and Occupational Variables

    ERIC Educational Resources Information Center

    Jung, Jae Yup

    2013-01-01

    This study tested a newly developed model of the cognitive decision-making processes of senior high school students related to university entry. The model incorporated variables derived from motivation theory (i.e. expectancy-value theory and the theory of reasoned action), literature on cultural orientation and occupational considerations. A…

  10. Incorporation of Fine-Grained Sediment Erodibility Measurements into Sediment Transport Modeling, Capitol Lake, Washington

    USGS Publications Warehouse

    Stevens, Andrew W.; Gelfenbaum, Guy; Elias, Edwin; Jones, Craig

    2008-01-01

    lab with Sedflume, an apparatus for measuring sediment erosion-parameters. In this report, we present results of the characterization of fine-grained sediment erodibility within Capitol Lake. The erodibility data were incorporated into the previously developed hydrodynamic and sediment transport model. Model simulations using the measured erodibility parameters were conducted to provide more robust estimates of the overall magnitudes and spatial patterns of sediment transport resulting from restoration of the Deschutes Estuary.

  11. Paramagnetic isoprenoid carrier lipids. 1. Chemical synthesis and incorporation into model membranes.

    PubMed

    McCloskey, M A; Troy, F A

    1980-05-13

    The synthesis, purification, and characterization of two types of spin-labeled glycosyl carrier lipids and shorter chain isoprenols are described. As models for phosphorylated lipids intermediates, phosphodiesters of tempol and the prenols dolichol, ficaprenol, solanesol, phytol, and farnesol were prepared. For analogues of neutral species each prenol was esterified with a pyrrolidinecarboxylic acid based label. Tripropylbenzenesulfonyl chloride was used as the condensing agent in both cases. Phosphodiester yields ranged from 36% for the 55-carbon compound to greater than 66% for the 95-carbon prenol. Both types of probes were incorporated into phospholipid bilayers, where each became oriented with the artificial head group at, or very close to, the water--hydrocarbon interface. Electron spin resonance spectra of the phosphodiesters are matrix dependent, indicating rapid isotropic tumbling in chloroform but highly anisotropic reorientation in unsaturated phosphatidylcholine (PC) hosts. Rotation or large amplitude oscillation about either or both the tempo C4--O linkage and the P--O (chain) bond as well as whole molecule rotation within the bilayer could account for the observed x-axis anisotropy. Segmental motion within the polyprene chain does not appear to be a determinant.

  12. Incorporation of GRACE Data into a Bayesian Model for Groundwater Drought Monitoring

    NASA Astrophysics Data System (ADS)

    Slinski, K.; Hogue, T. S.; McCray, J. E.; Porter, A.

    2015-12-01

    Groundwater drought, defined as the sustained occurrence of below average availability of groundwater, is marked by below average water levels in aquifers and reduced flows to groundwater-fed rivers and wetlands. The impact of groundwater drought on ecosystems, agriculture, municipal water supply, and the energy sector is an increasingly important global issue. However, current drought monitors heavily rely on precipitation and vegetative stress indices to characterize the timing, duration, and severity of drought events. The paucity of in situ observations of aquifer levels is a substantial obstacle to the development of systems to monitor groundwater drought in drought-prone areas, particularly in developing countries. Observations from the NASA/German Space Agency's Gravity Recovery and Climate Experiment (GRACE) have been used to estimate changes in groundwater storage over areas with sparse point measurements. This study incorporates GRACE total water storage observations into a Bayesian framework to assess the performance of a probabilistic model for monitoring groundwater drought based on remote sensing data. Overall, it is hoped that these methods will improve global drought preparedness and risk reduction by providing information on groundwater drought necessary to manage its impacts on ecosystems, as well as on the agricultural, municipal, and energy sectors.

  13. The metabolic pace-of-life model: incorporating ectothermic organisms into the theory of vertebrate ecoimmunology.

    PubMed

    Sandmeier, Franziska C; Tracy, Richard C

    2014-09-01

    We propose a new heuristic model that incorporates metabolic rate and pace of life to predict a vertebrate species' investment in adaptive immune function. Using reptiles as an example, we hypothesize that animals with low metabolic rates will invest more in innate immunity compared with adaptive immunity. High metabolic rates and body temperatures should logically optimize the efficacy of the adaptive immune system--through rapid replication of T and B cells, prolific production of induced antibodies, and kinetics of antibody--antigen interactions. In current theory, the precise mechanisms of vertebrate immune function oft are inadequately considered as diverse selective pressures on the evolution of pathogens. We propose that the strength of adaptive immune function and pace of life together determine many of the important dynamics of host-pathogen evolution, namely, that hosts with a short lifespan and innate immunity or with a long lifespan and strong adaptive immunity are expected to drive the rapid evolution of their populations of pathogens. Long-lived hosts that rely primarily on innate immune functions are more likely to use defense mechanisms of tolerance (instead of resistance), which are not expected to act as a selection pressure for the rapid evolution of pathogens' virulence. PMID:24760792

  14. Global plate kinematic reconstructions and mantle flow models incorporating lithospheric deformation

    NASA Astrophysics Data System (ADS)

    Flament, N.; Williams, S.; Gurnis, M.; Seton, M.; Müller, R.; Heine, C.; Turner, M.

    2012-12-01

    The effect of mantle flow on surface topography has been the subject of considerable interest over the last few years. A common approach to the problem is to link plate tectonic reconstructions and global geodynamic models. An important limitation of this approach is that traditional plate tectonic reconstructions do not take the deformation of the lithosphere into account. Plates are represented as rigid blocks, resulting in continental overlap in full-fit reconstructions. Models that use topological polygons avoid continental overlaps, but plate velocities are still derived on the basis of Euler poles for rigid blocks. Our objective is to develop quantitative models of surface plate kinematics that include areas of deforming continental crust. We generated a series of global reconstructions including deforming plates in key areas, derived using tools developed within the open source reconstruction software GPlates. We used geological and geophysical data to define the areal and temporal extent of major crustal deformation phases. For convergent plate boundaries, we incorporated quantitative estimates of deformation to model the time-varying geometries of subduction zones such as the Andean margin of South America and east of the Lord Howe Rise. In reconstructions of continental breakup, for example between Australia and Antarctica or the opening of the South and Equatorial Atlantic, the timing and the intensity of continental extension is imposed by the progressive, diachronous breakup and initiation of seafloor spreading for each major margin system. We used these models as a boundary condition for geodynamic models. For each deforming domain, a topological mesh was generated such that surface velocity fields within the deforming regions are calculated by linear interpolation from velocities at the boundaries and from additional constraining points within the deforming regions. The velocity field derived from the plate reconstructions were used as a time

  15. Sensitivity studies for incorporating the direct effect of sulfate aerosols into climate models

    NASA Astrophysics Data System (ADS)

    Miller, Mary Rawlings Lamberton

    2000-09-01

    Aerosols have been identified as a major element of the climate system known to scatter and absorb solar and infrared radiation, but the development of procedures for representing them is still rudimentary. This study addresses the need to improve the treatment of sulfate aerosols in climate models by investigating how sensitive radiative particles are to varying specific sulfate aerosol properties. The degree to which sulfate particles absorb or scatter radiation, termed the direct effect, varies with the size distribution of particles, the aerosol mass density, the aerosol refractive indices, the relative humidity and the concentration of the aerosol. This study develops 504 case studies of altering sulfate aerosol chemistry, size distributions, refractive indices and densities at various ambient relative humidity conditions. Ammonium sulfate and sulfuric acid aerosols are studied with seven distinct size distributions at a given mode radius with three corresponding standard deviations implemented from field measurements. These test cases are evaluated for increasing relative humidity. As the relative humidity increases, the complex index of refraction and the mode radius for each distribution correspondingly change. Mie theory is employed to obtain the radiative properties for each case study. The case studies are then incorporated into a box model, the National Center of Atmospheric Research's (NCAR) column radiation model (CRM), and NCAR's community climate model version 3 (CCM3) to determine how sensitive the radiative properties and potential climatic effects are to altering sulfate properties. This study found the spatial variability of the sulfate aerosol leads to regional areas of intense aerosol forcing (W/m2). These areas are particularly sensitive to altering sulfate properties. Changes in the sulfate lognormal distribution standard deviation can lead to substantial regional differences in the annual aerosol forcing greater than 2 W/m 2. Changes in the

  16. NexGen PVAs: Incorporating Eco-Evolutionary Processes into Population Viability Models

    EPA Science Inventory

    We examine how the integration of evolutionary and ecological processes in population dynamics – an emerging framework in ecology – could be incorporated into population viability analysis (PVA). Driven by parallel, complementary advances in population genomics and computational ...

  17. Dynamic modeling of the servovalves incorporated in the servo hydraulic system of the 70-meter DSN antennas

    NASA Technical Reports Server (NTRS)

    Bartos, R. D.

    1992-01-01

    As the pointing accuracy and service life requirements of the DSN 70 meter antenna increase, it is necessary to gain a more complete understanding of the servo hydraulic system in order to improve system designs to meet the new requirements. A mathematical model is developed for the servovalve incorporated into the hydraulic system of the 70 meter antenna and uses experimental data to verify the validity of the model and to identify the model parameters.

  18. Convolution-Based Forced Detection Monte Carlo Simulation Incorporating Septal Penetration Modeling

    PubMed Central

    Liu, Shaoying; King, Michael A.; Brill, Aaron B.; Stabin, Michael G.; Farncombe, Troy H.

    2010-01-01

    In SPECT imaging, photon transport effects such as scatter, attenuation and septal penetration can negatively affect the quality of the reconstructed image and the accuracy of quantitation estimation. As such, it is useful to model these effects as carefully as possible during the image reconstruction process. Many of these effects can be included in Monte Carlo (MC) based image reconstruction using convolution-based forced detection (CFD). With CFD Monte Carlo (CFD-MC), often only the geometric response of the collimator is modeled, thereby making the assumption that the collimator materials are thick enough to completely absorb photons. However, in order to retain high collimator sensitivity and high spatial resolution, it is required that the septa be as thin as possible, thus resulting in a significant amount of septal penetration for high energy radionuclides. A method for modeling the effects of both collimator septal penetration and geometric response using ray tracing (RT) techniques has been performed and included into a CFD-MC program. Two look-up tables are pre-calculated based on the specific collimator parameters and radionuclides, and subsequently incorporated into the SIMIND MC program. One table consists of the cumulative septal thickness between any point on the collimator and the center location of the collimator. The other table presents the resultant collimator response for a point source at different distances from the collimator and for various energies. A series of RT simulations have been compared to experimental data for different radionuclides and collimators. Results of the RT technique matches experimental data of collimator response very well, producing correlation coefficients higher than 0.995. Reasonable values of the parameters in the lookup table and computation speed are discussed in order to achieve high accuracy while using minimal storage space for the look-up tables. In order to achieve noise-free projection images from MC, it

  19. Strategies for Incorporating Women-Specific Sexuality Education into Addiction Treatment Models

    ERIC Educational Resources Information Center

    James, Raven

    2007-01-01

    This paper advocates for the incorporation of a women-specific sexuality curriculum in the addiction treatment process to aid in sexual healing and provide for aftercare issues. Sexuality in addiction treatment modalities is often approached from a sex-negative stance, or that of sexual victimization. Sexual issues are viewed as addictive in and…

  20. Anticipating and Incorporating Stakeholder Feedback When Developing Value-Added Models

    ERIC Educational Resources Information Center

    Balch, Ryan; Koedel, Cory

    2014-01-01

    State and local education agencies across the United States are increasingly adopting rigorous teacher evaluation systems. Most systems formally incorporate teacher performance as measured by student test-score growth, sometimes by state mandate. An important consideration that will influence the long-term persistence and efficacy of these systems…

  1. The finite element absolute nodal coordinate formulation incorporated with surface stress effect to model elastic bending nanowires in large deformation

    NASA Astrophysics Data System (ADS)

    He, Jin; Lilley, Carmen M.

    2009-08-01

    Surface stress was incorporated into the finite element absolute nodal coordinate formulation in order to model elastic bending of nanowires in large deformation. The absolute nodal coordinate formulation is a numerical method to model bending structures in large deformation. The generalized Young-Laplace equation was employed to model the surface stress effect on bending nanowires. Effects from surface stress and large deformation on static bending nanowires are presented and discussed. The results calculated with the absolute nodal coordinate formulation incorporated with surface stress show that the surface stress effect makes the bending nanowires behave like softer or stiffer materials depending on the boundary condition. The surface stress effect diminishes as the dimensions of the bending structures increase beyond the nanoscale. The developed algorithm is consistent with the classical absolute nodal coordinate formulation at the macroscale.

  2. On the effects of circulation, sediment resuspension and biological incorporation by diatoms in an ocean model of aluminium*

    NASA Astrophysics Data System (ADS)

    van Hulten, M. M. P.; Sterl, A.; Middag, R.; de Baar, H. J. W.; Gehlen, M.; Dutay, J.-C.; Tagliabue, A.

    2014-07-01

    The distribution of dissolved aluminium in the West Atlantic Ocean shows a mirror image with that of dissolved silicic acid, hinting at intricate interactions between the ocean cycling of Al and Si. The marine biogeochemistry of Al is of interest because of its potential impact on diatom opal remineralisation, hence Si availability. Furthermore, the dissolved Al concentration at the surface ocean has been used as a tracer for dust input, dust being the most important source of the bio-essential trace element iron to the ocean. Previously, the dissolved concentration of Al was simulated reasonably well with only a dust source, and scavenging by adsorption on settling biogenic debris as the only removal process. Here we explore the impacts of (i) a sediment source of Al in the Northern Hemisphere (especially north of 40degree N), (ii) the imposed velocity field, and (iii) biological incorporation of Al on the modelled Al distribution in the ocean. The sediment source clearly improves the model results, and using a different velocity field shows the importance of advection on the simulated Al distribution. Biological incorporation appears to be a potentially important removal process. However, conclusive independent data to constrain the Al / Si incorporation ratio by growing diatoms are missing. Therefore, this study does not provide a definitive answer to the question of the relative importance of Al removal by incorporation compared to removal by adsorptive scavenging.

  3. An improved ocean model of aluminium: the effects of circulation, sediment resuspension and biological incorporation

    NASA Astrophysics Data System (ADS)

    van Hulten, M. M. P.; Sterl, A.; Middag, R.; de Baar, H. J. W.; Gehlen, M.; Dutay, J.-C.; Tagliabue, A.

    2013-09-01

    The distribution of dissolved aluminium (Al) in the ocean is of interest because of its potential impact on diatom remineralisation and the use of surface ocean Al as a tracer for dust. Previously, the ocean Al concentration has been simulated reasonably well with only a dust source and scavenging as the removal process. In this study the simulation has been significantly improved by a more refined circulation and the addition of a sediment resuspension source. The latter confirms that the most significant sources of Al to the ocean are dust deposition and sediment resuspension. Simulations with biological incorporation have been performed as well. These show that this can be an important removal process. However, this study does not provide a definitive answer to the question what the relative amount of incorporation is compared to scavenging.

  4. A Temperate Alpine Glacier as a Reservoir of Polychlorinated Biphenyls: Model Results of Incorporation, Transport, and Release.

    PubMed

    Steinlin, Christine; Bogdal, Christian; Lüthi, Martin P; Pavlova, Pavlina A; Schwikowski, Margit; Zennegg, Markus; Schmid, Peter; Scheringer, Martin; Hungerbühler, Konrad

    2016-06-01

    In previous studies, the incorporation of polychlorinated biphenyls (PCBs) has been quantified in the accumulation areas of Alpine glaciers. Here, we introduce a model framework that quantifies mass fluxes of PCBs in glaciers and apply it to the Silvretta glacier (Switzerland). The models include PCB incorporation into the entire surface of the glacier, downhill transport with the flow of the glacier ice, and chemical fate in the glacial lake. The models are run for the years 1900-2100 and validated by comparing modeled and measured PCB concentrations in an ice core, a lake sediment core, and the glacial streamwater. The incorporation and release fluxes, as well as the storage of PCBs in the glacier increase until the 1980s and decrease thereafter. After a temporary increase in the 2000s, the future PCB release and the PCB concentrations in the glacial stream are estimated to be small but persistent throughout the 21st century. This study quantifies all relevant PCB fluxes in and from a temperate Alpine glacier over two centuries, and concludes that Alpine glaciers are a small secondary source of PCBs, but that the aftermath of environmental pollution by persistent and toxic chemicals can endure for decades. PMID:27164482

  5. A Temperate Alpine Glacier as a Reservoir of Polychlorinated Biphenyls: Model Results of Incorporation, Transport, and Release.

    PubMed

    Steinlin, Christine; Bogdal, Christian; Lüthi, Martin P; Pavlova, Pavlina A; Schwikowski, Margit; Zennegg, Markus; Schmid, Peter; Scheringer, Martin; Hungerbühler, Konrad

    2016-06-01

    In previous studies, the incorporation of polychlorinated biphenyls (PCBs) has been quantified in the accumulation areas of Alpine glaciers. Here, we introduce a model framework that quantifies mass fluxes of PCBs in glaciers and apply it to the Silvretta glacier (Switzerland). The models include PCB incorporation into the entire surface of the glacier, downhill transport with the flow of the glacier ice, and chemical fate in the glacial lake. The models are run for the years 1900-2100 and validated by comparing modeled and measured PCB concentrations in an ice core, a lake sediment core, and the glacial streamwater. The incorporation and release fluxes, as well as the storage of PCBs in the glacier increase until the 1980s and decrease thereafter. After a temporary increase in the 2000s, the future PCB release and the PCB concentrations in the glacial stream are estimated to be small but persistent throughout the 21st century. This study quantifies all relevant PCB fluxes in and from a temperate Alpine glacier over two centuries, and concludes that Alpine glaciers are a small secondary source of PCBs, but that the aftermath of environmental pollution by persistent and toxic chemicals can endure for decades.

  6. Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization.

    PubMed

    Hasegawa, Takanori; Yamaguchi, Rui; Nagasaki, Masao; Miyano, Satoru; Imoto, Seiya

    2014-01-01

    Comprehensive understanding of gene regulatory networks (GRNs) is a major challenge in the field of systems biology. Currently, there are two main approaches in GRN analysis using time-course observation data, namely an ordinary differential equation (ODE)-based approach and a statistical model-based approach. The ODE-based approach can generate complex dynamics of GRNs according to biologically validated nonlinear models. However, it cannot be applied to ten or more genes to simultaneously estimate system dynamics and regulatory relationships due to the computational difficulties. The statistical model-based approach uses highly abstract models to simply describe biological systems and to infer relationships among several hundreds of genes from the data. However, the high abstraction generates false regulations that are not permitted biologically. Thus, when dealing with several tens of genes of which the relationships are partially known, a method that can infer regulatory relationships based on a model with low abstraction and that can emulate the dynamics of ODE-based models while incorporating prior knowledge is urgently required. To accomplish this, we propose a method for inference of GRNs using a state space representation of a vector auto-regressive (VAR) model with L1 regularization. This method can estimate the dynamic behavior of genes based on linear time-series modeling constructed from an ODE-based model and can infer the regulatory structure among several tens of genes maximizing prediction ability for the observational data. Furthermore, the method is capable of incorporating various types of existing biological knowledge, e.g., drug kinetics and literature-recorded pathways. The effectiveness of the proposed method is shown through a comparison of simulation studies with several previous methods. For an application example, we evaluated mRNA expression profiles over time upon corticosteroid stimulation in rats, thus incorporating corticosteroid

  7. Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization.

    PubMed

    Hasegawa, Takanori; Yamaguchi, Rui; Nagasaki, Masao; Miyano, Satoru; Imoto, Seiya

    2014-01-01

    Comprehensive understanding of gene regulatory networks (GRNs) is a major challenge in the field of systems biology. Currently, there are two main approaches in GRN analysis using time-course observation data, namely an ordinary differential equation (ODE)-based approach and a statistical model-based approach. The ODE-based approach can generate complex dynamics of GRNs according to biologically validated nonlinear models. However, it cannot be applied to ten or more genes to simultaneously estimate system dynamics and regulatory relationships due to the computational difficulties. The statistical model-based approach uses highly abstract models to simply describe biological systems and to infer relationships among several hundreds of genes from the data. However, the high abstraction generates false regulations that are not permitted biologically. Thus, when dealing with several tens of genes of which the relationships are partially known, a method that can infer regulatory relationships based on a model with low abstraction and that can emulate the dynamics of ODE-based models while incorporating prior knowledge is urgently required. To accomplish this, we propose a method for inference of GRNs using a state space representation of a vector auto-regressive (VAR) model with L1 regularization. This method can estimate the dynamic behavior of genes based on linear time-series modeling constructed from an ODE-based model and can infer the regulatory structure among several tens of genes maximizing prediction ability for the observational data. Furthermore, the method is capable of incorporating various types of existing biological knowledge, e.g., drug kinetics and literature-recorded pathways. The effectiveness of the proposed method is shown through a comparison of simulation studies with several previous methods. For an application example, we evaluated mRNA expression profiles over time upon corticosteroid stimulation in rats, thus incorporating corticosteroid

  8. Incorporating environmental attitudes in discrete choice models: an exploration of the utility of the awareness of consequences scale.

    PubMed

    Hoyos, David; Mariel, Petr; Hess, Stephane

    2015-02-01

    Environmental economists are increasingly interested in better understanding how people cognitively organise their beliefs and attitudes towards environmental change in order to identify key motives and barriers that stimulate or prevent action. In this paper, we explore the utility of a commonly used psychometric scale, the awareness of consequences (AC) scale, in order to better understand stated choices. The main contribution of the paper is that it provides a novel approach to incorporate attitudinal information into discrete choice models for environmental valuation: firstly, environmental attitudes are incorporated using a reinterpretation of the classical AC scale recently proposed by Ryan and Spash (2012); and, secondly, attitudinal data is incorporated as latent variables under a hybrid choice modelling framework. This novel approach is applied to data from a survey conducted in the Basque Country (Spain) in 2008 aimed at valuing land-use policies in a Natura 2000 Network site. The results are relevant to policy-making because choice models that are able to accommodate underlying environmental attitudes may help in designing more effective environmental policies.

  9. Incorporating three dimensional shapes of buildings and structures in tsunami inundation modeling of the 2011 Tohoku-oki earthquake

    NASA Astrophysics Data System (ADS)

    BABA, T.; Takahashi, N.; Kaneda, Y.; Inazawa, Y.; Kikkojin, M.

    2012-12-01

    The tsunami caused by the 2011 Tohoku-oki earthquake widely inundated destroying or passing the buildings and structures on land. Effect of buildings and structures on tsunami inundation is represented by a bottom friction in the conventional modeling solving non-linear shallow water theory in finite difference scheme, not included 3D shapes of those. But large strong buildings would be able to directly protect incoming tsunami like as seawalls, rather than bottom friction. While LiDAR measurements are recently being carried out along the Japan coast by Geospatial Information Authority of Japan, which collect reflected plus from the top of surface such as the building roof, road, bridge, and the top of trees. This is hereby called digital surface model (DSM). We extracted buildings and structures can be possible to affect tsunami inundation from DSM by comparing the Fundamental Geospatial Data which indicates locations of buildings and structures in the city. This is because we have to remove trees and river bridges in DSM where tsunami can pass through them. The 3D building data was incorporated as topography in tsunami computation of the 2011 Tohoku-oki earthquake (hereby, incorporated model) to compare the result from the conventional model. URSGA tsunami code (Jakeman et al. 2010) was used to include variable nesting system. The finest topographic grid interval was 0.22 arc-second (about 5m) along the longitude and latitude directions in coastal area. The initial sea-surface defamation was derived from the finite fault model version 1.1 provided by Tohoku University. In the incorporated model, the maximum inundation height at the front of coastal buildings and structures is higher than that in the conventional model. The inundation height is increased by 63 % (4.8 m) at the maximum. In the area back of the coastal buildings, the inundation height is inversely smaller than that in the conventional model. The tsunami inundation area becomes to be smaller in the

  10. [Incorporation of an organic MAGIC (Model of Acidification of Groundwater in Catchments) and testing of the revised model using independent data sources]. [MAGIC Model

    SciTech Connect

    Sullivan, T.J.

    1992-09-01

    A project was initiated in March, 1992 to (1) incorporate a rigorous organic acid representation, based on empirical data and geochemical considerations, into the MAGIC model of acidification response, and (2) test the revised model using three sets of independent data. After six months of performance, the project is on schedule and the majority of the tasks outlined for Year 1 have been successfully completed. Major accomplishments to data include development of the organic acid modeling approach, using data from the Adirondack Lakes Survey Corporation (ALSC), and coupling the organic acid model with MAGIC for chemical hindcast comparisons. The incorporation of an organic acid representation into MAGIC can account for much of the discrepancy earlier observed between MAGIC hindcasts and paleolimnological reconstructions of preindustrial pH and alkalinity for 33 statistically-selected Adirondack lakes. Additional work is on-going for model calibration and testing with data from two whole-catchment artificial acidification projects. Results obtained thus far are being prepared as manuscripts for submission to the peer-reviewed scientific literature.

  11. Computer simulation incorporating a helicopter model for evaluation of aircraft avionics systems

    NASA Technical Reports Server (NTRS)

    Ostroff, A. J.; Wood, R. B.

    1977-01-01

    A computer program was developed to integrate avionics research in navigation, guidance, controls, and displays with a realistic aircraft model. A user oriented program is described that allows a flexible combination of user supplied models to perform research in any avionics area. A preprocessor technique for selecting various models without significantly changing the memory storage is included. Also included are mathematical models for several avionics error models and for the CH-47 helicopter used in this program.

  12. Application of a Hierarchical Model Incorporating Intra-family Correlation and Cluster Effects

    PubMed Central

    Cheng, An-Lin; Kelly, Patricia J.

    2011-01-01

    Background Research interventions at the family level often include individual- and group-level data that can present an analytic challenge. The study that motivated this paper was an intervention study conducted with elementary school children and their parents. Randomization occurred at the school level, with families nested within schools. Repeated measurements collected from children and parents at different time points presented modeling challenges, including how to specify the covariance structure correctly among all measurements. Objectives To introduce a mixed model with random effects to model the correlations among family members, repeated measures, and the grouping effect. Method A hierarchical random-effect model was used that included both fixed and random effects; time and intervention-by-time variables were included as fixed effects, the school-specific variable was included as random effect, and the intrafamily correlation was modeled through a spatial autoregression covariance matrix. Comparisons were made between the performance of the proposed modeling method with other parsimony models using Akaike’s Information Criterion (AIC). Results The proposed modeling method produced a 3% and 9% reduction of AIC values, respectively, compared to the two other models. The likelihood ratio test further confirmed that the full model is better than the other two models (p < .0001 for both models). Discussion The data suggest that using the proposed mixed model technique will produce a significantly better model fit for intrafamily correlation with a nested study design. PMID:21317823

  13. A new general methodology for incorporating physico-chemical transformations into multi-phase wastewater treatment process models.

    PubMed

    Lizarralde, I; Fernández-Arévalo, T; Brouckaert, C; Vanrolleghem, P; Ikumi, D S; Ekama, G A; Ayesa, E; Grau, P

    2015-05-01

    This paper introduces a new general methodology for incorporating physico-chemical and chemical transformations into multi-phase wastewater treatment process models in a systematic and rigorous way under a Plant-Wide modelling (PWM) framework. The methodology presented in this paper requires the selection of the relevant biochemical, chemical and physico-chemical transformations taking place and the definition of the mass transport for the co-existing phases. As an example a mathematical model has been constructed to describe a system for biological COD, nitrogen and phosphorus removal, liquid-gas transfer, precipitation processes, and chemical reactions. The capability of the model has been tested by comparing simulated and experimental results for a nutrient removal system with sludge digestion. Finally, a scenario analysis has been undertaken to show the potential of the obtained mathematical model to study phosphorus recovery.

  14. A new general methodology for incorporating physico-chemical transformations into multi-phase wastewater treatment process models.

    PubMed

    Lizarralde, I; Fernández-Arévalo, T; Brouckaert, C; Vanrolleghem, P; Ikumi, D S; Ekama, G A; Ayesa, E; Grau, P

    2015-05-01

    This paper introduces a new general methodology for incorporating physico-chemical and chemical transformations into multi-phase wastewater treatment process models in a systematic and rigorous way under a Plant-Wide modelling (PWM) framework. The methodology presented in this paper requires the selection of the relevant biochemical, chemical and physico-chemical transformations taking place and the definition of the mass transport for the co-existing phases. As an example a mathematical model has been constructed to describe a system for biological COD, nitrogen and phosphorus removal, liquid-gas transfer, precipitation processes, and chemical reactions. The capability of the model has been tested by comparing simulated and experimental results for a nutrient removal system with sludge digestion. Finally, a scenario analysis has been undertaken to show the potential of the obtained mathematical model to study phosphorus recovery. PMID:25746499

  15. Nanofibers for drug delivery – incorporation and release of model molecules, influence of molecular weight and polymer structure

    PubMed Central

    Hrib, Jakub; Hobzova, Radka; Hampejsova, Zuzana; Bosakova, Zuzana; Munzarova, Marcela; Michalek, Jiri

    2015-01-01

    Summary Nanofibers were prepared from polycaprolactone, polylactide and polyvinyl alcohol using NanospiderTM technology. Polyethylene glycols with molecular weights of 2 000, 6 000, 10 000 and 20 000 g/mol, which can be used to moderate the release profile of incorporated pharmacologically active compounds, served as model molecules. They were terminated by aromatic isocyanate and incorporated into the nanofibers. The release of these molecules into an aqueous environment was investigated. The influences of the molecular length and chemical composition of the nanofibers on the release rate and the amount of released polyethylene glycols were evaluated. Longer molecules released faster, as evidenced by a significantly higher amount of released molecules after 72 hours. However, the influence of the chemical composition of nanofibers was even more distinct – the highest amount of polyethylene glycol molecules released from polyvinyl alcohol nanofibers, the lowest amount from polylactide nanofibers. PMID:26665065

  16. Incorporate Imaging Characteristics Into an Arteriovenous Malformation Radiosurgery Plan Evaluation Model

    SciTech Connect

    Zhang Pengpeng Wu, Leester; Liu Tian; Kutcher, Gerald J..; Isaacson, Steven

    2008-04-01

    Purpose: To integrate imaging performance characteristics, specifically sensitivity and specificity, of magnetic resonance angiography (MRA) and digital subtraction angiography (DSA) into arteriovenous malformation (AVM) radiosurgery planning and evaluation. Methods and Materials: Images of 10 patients with AVMs located in critical brain areas were analyzed in this retrospective planning study. The image findings were first used to estimate the sensitivity and specificity of MRA and DSA. Instead of accepting the imaging observation as a binary (yes or no) mapping of AVM location, our alternative is to translate the image into an AVM probability distribution map by incorporating imagers' sensitivity and specificity, and to use this map as a basis for planning and evaluation. Three sets of radiosurgery plans, targeting the MRA and DSA positive overlap, MRA positive, and DSA positive were optimized for best conformality. The AVM obliteration rate (ORAVM) and brain complication rate served as endpoints for plan comparison. Results: In our 10-patient study, the specificities and sensitivities of MRA and DSA were estimated to be (0.95, 0.74) and (0.71, 0.95), respectively. The positive overlap of MRA and DSA accounted for 67.8% {+-} 4.9% of the estimated true AVM volume. Compared with plans targeting MRA and DSA-positive overlap, plans targeting MRA-positive or DSA-positive improved ORAVM by 4.1% {+-} 1.9% and 15.7% {+-} 8.3%, while also increasing the complication rate by 1.0% {+-} 0.8% and 4.4% {+-} 2.3%, respectively. Conclusions: The impact of imagers' quality should be quantified and incorporated in AVM radiosurgery planning and evaluation to facilitate clinical decision making.

  17. Source-mask selection using computational lithography: further investigation incorporating rigorous resist models

    NASA Astrophysics Data System (ADS)

    Kapasi, Sanjay; Robertson, Stewart; Biafore, John; Smith, Mark D.

    2009-12-01

    Recent publications have emphasized the criticality of computational lithography in source-mask selection for 32 and 22 nm technology nodes. Lithographers often select the illuminator geometries based on analyzing aerial images for a limited set of structures using computational lithography tools. Last year, Biafore, et al1 demonstrated the divergence between aerial image models and resist models in computational lithography. In a follow-up study2, it was illustrated that optimal illuminator is different when selected based on resist model in contrast to aerial image model. In the study, optimal source shapes were evaluated for 1D logic patterns using aerial image model and two distinct commercial resist models. Physics based lumped parameter resist model (LPM) was used. Accurately calibrated full physical models are portable across imaging conditions compared to the lumped models. This study will be an extension of previous work. Full physical resist models (FPM) with calibrated resist parameters3,4,5,6 will be used in selecting optimum illumination geometries for 1D logic patterns. Several imaging parameters - like Numerical Aperture (NA), source geometries (Annular, Quadrupole, etc.), illumination configurations for different sizes and pitches will be explored in the study. Our goal is to compare and analyze the optimal source-shapes across various imaging conditions. In the end, the optimal source-mask solution for given set of designs based on all the models will be recommended.

  18. Incorporating Cold Cap Behavior in a Joule-heated Waste Glass Melter Model

    SciTech Connect

    Varija Agarwal; Donna Post Guillen

    2013-08-01

    In this paper, an overview of Joule-heated waste glass melters used in the vitrification of high level waste (HLW) is presented, with a focus on the cold cap region. This region, in which feed-to-glass conversion reactions occur, is critical in determining the melting properties of any given glass melter. An existing 1D computer model of the cold cap, implemented in MATLAB, is described in detail. This model is a standalone model that calculates cold cap properties based on boundary conditions at the top and bottom of the cold cap. Efforts to couple this cold cap model with a 3D STAR-CCM+ model of a Joule-heated melter are then described. The coupling is being implemented in ModelCenter, a software integration tool. The ultimate goal of this model is to guide the specification of melter parameters that optimize glass quality and production rate.

  19. A selenium-deficient Caco-2 cell model for assessing differential incorporation of chemical or food selenium into glutathione peroxidase.

    PubMed

    Zeng, Huawei; Botnen, James H; Johnson, Luann K

    2008-01-01

    Assessing the ability of a selenium (Se) sample to induce cellular glutathione peroxidase (GPx) activity in Se-deficient animals is the most commonly used method to determine Se bioavailability. Our goal is to establish a Se-deficient cell culture model with differential incorporation of Se chemical forms into GPx, which may complement the in vivo studies. In the present study, we developed a Se-deficient Caco-2 cell model with a serum gradual reduction method. It is well recognized that selenomethionine (SeMet) is the major nutritional source of Se; therefore, SeMet, selenite, or methylselenocysteine (SeMSC) was added to cell culture media with different concentrations and treatment time points. We found that selenite and SeMSC induced GPx more rapidly than SeMet. However, SeMet was better retained as it is incorporated into proteins in place of methionine; compared with 8-, 24-, or 48-h treatment, 72-h Se treatment was a more sensitive time point to measure the potential of GPx induction in all tested concentrations. Based on induction of GPx activity, the cellular bioavailability of Se from an extract of selenobroccoli after a simulated gastrointestinal digestion was comparable with that of SeMSC and SeMet. These in vitro data are, for the first time, consistent with previous published data regarding selenite and SeMet bioavailability in animal models and Se chemical speciation studies with broccoli. Thus, Se-deficient Caco-2 cell model with differential incorporation of chemical or food forms of Se into GPx provides a new tool to study the cellular mechanisms of Se bioavailability.

  20. Incorporating age at onset of smoking into genetic models for nicotine dependence: Evidence for interaction with multiple genes

    PubMed Central

    Grucza, Richard A.; Johnson, Eric O.; Krueger, Robert F.; Breslau, Naomi; Saccone, Nancy L.; Chen, Li-Shiun; Derringer, Jaime; Agrawal, Arpana; Lynskey, Micheal; Bierut, Laura J.

    2011-01-01

    Nicotine dependence is moderately heritable, but identified genetic associations explain only modest portions of this heritability. We analyzed 3,369 SNPs from 349 candidate genes, and investigated whether incorporation of SNP-by-environment interaction into association analyses might bolster gene discovery efforts and prediction of nicotine dependence. Specifically, we incorporated the interaction between allele count and age-at-onset of regular smoking (AOS) into association analyses of nicotine dependence. Subjects were from the Collaborative Genetic Study of Nicotine Dependence, and included 797 cases ascertained for Fagerström nicotine dependence, and 811 non-nicotine dependent smokers as controls, all of European descent. Compared with main-effect models, SNP x AOS interaction models resulted in higher numbers of nominally significant tests, increased predictive utility at individual SNPs, and higher predictive utility in a multi-locus model. Some SNPs previously documented in main-effect analyses exhibited improved fits in the joint-analysis, including rs16969968 from CHRNA5 and rs2314379 from MAP3K4. CHRNA5 exhibited larger effects in later-onset smokers, in contrast with a previous report that suggested the opposite interaction (Weiss et al, PLOS Genetics, 4: e1000125, 2008). However, a number of SNPs that did not emerge in main-effect analyses were among the strongest findings in the interaction analyses. These include SNPs located in GRIN2B (p=1.5 × 10−5), which encodes a subunit of the NMDA receptor channel, a key molecule in mediating age-dependent synaptic plasticity. Incorporation of logically chosen interaction parameters, such as AOS, into genetic models of substance-use disorders may increase the degree of explained phenotypic variation, and constitutes a promising avenue for gene-discovery. PMID:20624154

  1. A Model Incorporating Some of the Mechanical and Biochemical Factors Underlying Clot Formation and Dissolution in Flowing Blood

    DOE PAGESBeta

    Anand, M.; Rajagopal, K.; Rajagopal, K. R.

    2003-01-01

    Multiple interacting mechanisms control the formation and dissolution of clots to maintain blood in a state of delicate balance. In addition to a myriad of biochemical reactions, rheological factors also play a crucial role in modulating the response of blood to external stimuli. To date, a comprehensive model for clot formation and dissolution, that takes into account the biochemical, medical and rheological factors, has not been put into place, the existing models emphasizing either one or the other of the factors. In this paper, after discussing the various biochemical, physiologic and rheological factors at some length, we develop a modelmore » for clot formation and dissolution that incorporates many of the relevant crucial factors that have a bearing on the problem. The model, though just a first step towards understanding a complex phenomenon, goes further than previous models in integrating the biochemical, physiologic and rheological factors that come into play.« less

  2. Integrative modelling of animal movement: incorporating in situ habitat and behavioural information for a migratory marine predator.

    PubMed

    Bestley, Sophie; Jonsen, Ian D; Hindell, Mark A; Guinet, Christophe; Charrassin, Jean-Benoît

    2013-01-01

    A fundamental goal in animal ecology is to quantify how environmental (and other) factors influence individual movement, as this is key to understanding responsiveness of populations to future change. However, quantitative interpretation of individual-based telemetry data is hampered by the complexity of, and error within, these multi-dimensional data. Here, we present an integrative hierarchical Bayesian state-space modelling approach where, for the first time, the mechanistic process model for the movement state of animals directly incorporates both environmental and other behavioural information, and observation and process model parameters are estimated within a single model. When applied to a migratory marine predator, the southern elephant seal (Mirounga leonina), we find the switch from directed to resident movement state was associated with colder water temperatures, relatively short dive bottom time and rapid descent rates. The approach presented here can have widespread utility for quantifying movement-behaviour (diving or other)-environment relationships across species and systems. PMID:23135676

  3. A mathematical model for maximizing the value of phase 3 drug development portfolios incorporating budget constraints and risk.

    PubMed

    Patel, Nitin R; Ankolekar, Suresh; Antonijevic, Zoran; Rajicic, Natasa

    2013-05-10

    We describe a value-driven approach to optimizing pharmaceutical portfolios. Our approach incorporates inputs from research and development and commercial functions by simultaneously addressing internal and external factors. This approach differentiates itself from current practices in that it recognizes the impact of study design parameters, sample size in particular, on the portfolio value. We develop an integer programming (IP) model as the basis for Bayesian decision analysis to optimize phase 3 development portfolios using expected net present value as the criterion. We show how this framework can be used to determine optimal sample sizes and trial schedules to maximize the value of a portfolio under budget constraints. We then illustrate the remarkable flexibility of the IP model to answer a variety of 'what-if' questions that reflect situations that arise in practice. We extend the IP model to a stochastic IP model to incorporate uncertainty in the availability of drugs from earlier development phases for phase 3 development in the future. We show how to use stochastic IP to re-optimize the portfolio development strategy over time as new information accumulates and budget changes occur.

  4. Incorporation of Vegetation into Mountain Permafrost Distribution Models, Southern Yukon Territory

    NASA Astrophysics Data System (ADS)

    Kremer, Marian

    Three groups of variables (Digital Elevation Model [DEM]-derived variables, fieldwork-derived vegetation variables, and satellite imagery-derived vegetation variables) were combined in Classification and Regression Tree (CART) models to determine the utility of vegetation-based variables for mountain permafrost distribution modelling in the southern half of the Yukon Territory. Four variables were measured in the field: canopy openness, vegetation height, organic mat thickness, and dominant species. Using Landsat TM and ETM+ imagery, three variables were calculated: a Normalized Difference Vegetation Index (NDVI), a vegetation classification, and a canopy closure classification. Individual variables were also examined to determine the one most useful for representing vegetation when modelling permafrost presence or absence. Additionally, models for each of five study areas spread across 5° of latitude were compared to examine the transferability of each variable. The addition of vegetation variables to the CART models created with DEM-derived variables resulted in only a minimal increase in the overall accuracy. Dominant species proved to be the most useful variable, but the relationship between permafrost and each species differed among study areas. Only black spruce (Picea mariana) was consistently classified as permafrost probable and lodgepole pine (Pinus contorta var. latifolia) and trembling aspen (Populus tremuloides) were classified as permafrost improbable over all study areas. These results indicate that models of permafrost distribution across large areas are not likely to be enriched sufficiently by the inclusion of vegetation variables while models covering smaller areas may benefit from the inclusion of vegetation variables. The CART models tended to show a high accuracy in the prediction of areas with no permafrost which could be useful for the purposes of infrastructure development. CART models have not previously been used in permafrost modelling

  5. A strategy for residual error modeling incorporating scedasticity of variance and distribution shape.

    PubMed

    Dosne, Anne-Gaëlle; Bergstrand, Martin; Karlsson, Mats O

    2016-04-01

    Nonlinear mixed effects models parameters are commonly estimated using maximum likelihood. The properties of these estimators depend on the assumption that residual errors are independent and normally distributed with mean zero and correctly defined variance. Violations of this assumption can cause bias in parameter estimates, invalidate the likelihood ratio test and preclude simulation of real-life like data. The choice of error model is mostly done on a case-by-case basis from a limited set of commonly used models. In this work, two strategies are proposed to extend and unify residual error modeling: a dynamic transform-both-sides approach combined with a power error model (dTBS) capable of handling skewed and/or heteroscedastic residuals, and a t-distributed residual error model allowing for symmetric heavy tails. Ten published pharmacokinetic and pharmacodynamic models as well as stochastic simulation and estimation were used to evaluate the two approaches. dTBS always led to significant improvements in objective function value, with most examples displaying some degree of right-skewness and variances proportional to predictions raised to powers between 0 and 1. The t-distribution led to significant improvement for 5 out of 10 models with degrees of freedom between 3 and 9. Six models were most improved by the t-distribution while four models benefited more from dTBS. Changes in other model parameter estimates were observed. In conclusion, the use of dTBS and/or t-distribution models provides a flexible and easy-to-use framework capable of characterizing all commonly encountered residual error distributions.

  6. A Hall Thruster Performance Model Incorporating the Effects of a Multiply-Charged Plasma

    NASA Technical Reports Server (NTRS)

    Hofer, Richard R.; Jankovsky, Robert S.

    2002-01-01

    A Hall thruster performance model that predicts anode specific impulse, anode efficiency, and thrust is discussed. The model is derived as a function of a voltage loss parameter, an electron loss parameter, and the charge state of the plasma. Experimental data from SPT and TAL type thrusters up to discharge powers of 21.6 kW are used to determine the best fit for model parameters. General values for the model parameters are found, applicable to high power thrusters and irrespective of thruster type. Performance of a 50 kW thruster is calculated for an anode specific impulse of 2500 seconds or a discharge current of 100 A.

  7. From the simple to the sublime: incorporating surgical models into your surgical curriculum.

    PubMed

    Woodman, Patrick J; Nager, Charles W

    2006-06-01

    Financial and time constraints have limited graduating residents' operative experience, making the use of models a necessary adjunct to a complete surgical curriculum. Models are useful tools to teaching surgical skills outside the operating room. They can be very realistic and complex, or they can be simple and economical. Models are developed to represent the anatomic arrangements seen in human patients, and to reproduce the biomechanical tasks necessary to complete a surgical case. Bench model laboratories are well-received by trainees and steepen the learning curve in the operating room.

  8. Incorporating model quality information in climate change detection and attribution studies.

    PubMed

    Santer, B D; Taylor, K E; Gleckler, P J; Bonfils, C; Barnett, T P; Pierce, D W; Wigley, T M L; Mears, C; Wentz, F J; Brüggemann, W; Gillett, N P; Klein, S A; Solomon, S; Stott, P A; Wehner, M F

    2009-09-01

    In a recent multimodel detection and attribution (D&A) study using the pooled results from 22 different climate models, the simulated "fingerprint" pattern of anthropogenically caused changes in water vapor was identifiable with high statistical confidence in satellite data. Each model received equal weight in the D&A analysis, despite large differences in the skill with which they simulate key aspects of observed climate. Here, we examine whether water vapor D&A results are sensitive to model quality. The "top 10" and "bottom 10" models are selected with three different sets of skill measures and two different ranking approaches. The entire D&A analysis is then repeated with each of these different sets of more or less skillful models. Our performance metrics include the ability to simulate the mean state, the annual cycle, and the variability associated with El Niño. We find that estimates of an anthropogenic water vapor fingerprint are insensitive to current model uncertainties, and are governed by basic physical processes that are well-represented in climate models. Because the fingerprint is both robust to current model uncertainties and dissimilar to the dominant noise patterns, our ability to identify an anthropogenic influence on observed multidecadal changes in water vapor is not affected by "screening" based on model quality.

  9. Incorporating model quality information in climate change detection and attribution studies

    PubMed Central

    Santer, B. D.; Taylor, K. E.; Gleckler, P. J.; Bonfils, C.; Barnett, T. P.; Pierce, D. W.; Wigley, T. M. L.; Mears, C.; Wentz, F. J.; Brüggemann, W.; Gillett, N. P.; Klein, S. A.; Solomon, S.; Stott, P. A.; Wehner, M. F.

    2009-01-01

    In a recent multimodel detection and attribution (D&A) study using the pooled results from 22 different climate models, the simulated “fingerprint” pattern of anthropogenically caused changes in water vapor was identifiable with high statistical confidence in satellite data. Each model received equal weight in the D&A analysis, despite large differences in the skill with which they simulate key aspects of observed climate. Here, we examine whether water vapor D&A results are sensitive to model quality. The “top 10” and “bottom 10” models are selected with three different sets of skill measures and two different ranking approaches. The entire D&A analysis is then repeated with each of these different sets of more or less skillful models. Our performance metrics include the ability to simulate the mean state, the annual cycle, and the variability associated with El Niño. We find that estimates of an anthropogenic water vapor fingerprint are insensitive to current model uncertainties, and are governed by basic physical processes that are well-represented in climate models. Because the fingerprint is both robust to current model uncertainties and dissimilar to the dominant noise patterns, our ability to identify an anthropogenic influence on observed multidecadal changes in water vapor is not affected by “screening” based on model quality. PMID:19706477

  10. Incorporating NDVI in a gravity model setting to describe spatio-temporal patterns of Lyme borreliosis incidence

    NASA Astrophysics Data System (ADS)

    Barrios, J. M.; Verstraeten, W. W.; Farifteh, J.; Maes, P.; Aerts, J. M.; Coppin, P.

    2012-04-01

    Lyme borreliosis (LB) is the most common tick-borne disease in Europe and incidence growth has been reported in several European countries during the last decade. LB is caused by the bacterium Borrelia burgdorferi and the main vector of this pathogen in Europe is the tick Ixodes ricinus. LB incidence and spatial spread is greatly dependent on environmental conditions impacting habitat, demography and trophic interactions of ticks and the wide range of organisms ticks parasite. The landscape configuration is also a major determinant of tick habitat conditions and -very important- of the fashion and intensity of human interaction with vegetated areas, i.e. human exposure to the pathogen. Hence, spatial notions as distance and adjacency between urban and vegetated environments are related to human exposure to tick bites and, thus, to risk. This work tested the adequacy of a gravity model setting to model the observed spatio-temporal pattern of LB as a function of location and size of urban and vegetated areas and the seasonal and annual change in the vegetation dynamics as expressed by MODIS NDVI. Opting for this approach implies an analogy with Newton's law of universal gravitation in which the attraction forces between two bodies are directly proportional to the bodies mass and inversely proportional to distance. Similar implementations have proven useful in fields like trade modeling, health care service planning, disease mapping among other. In our implementation, the size of human settlements and vegetated systems and the distance separating these landscape elements are considered the 'bodies'; and the 'attraction' between them is an indicator of exposure to pathogen. A novel element of this implementation is the incorporation of NDVI to account for the seasonal and annual variation in risk. The importance of incorporating this indicator of vegetation activity resides in the fact that alterations of LB incidence pattern observed the last decade have been ascribed

  11. A rhenium tris-carbonyl derivative as a model molecule for incorporation into phospholipid assemblies for skin applications.

    PubMed

    Fernández, Estibalitz; Rodríguez, Gelen; Hostachy, Sarah; Clède, Sylvain; Cócera, Mercedes; Sandt, Christophe; Lambert, François; de la Maza, Alfonso; Policar, Clotilde; López, Olga

    2015-07-01

    A rhenium tris-carbonyl derivative (fac-[Re(CO)3Cl(2-(1-dodecyl-1H-1,2,3,triazol-4-yl)-pyridine)]) was incorporated into phospholipid assemblies, called bicosomes, and the penetration of this molecule into skin was monitored using Fourier-transform infrared microspectroscopy (FTIR). To evaluate the capacity of bicosomes to promote the penetration of this derivative, the skin penetration of the Re(CO)3 derivative dissolved in dimethyl sulfoxide (DMSO), a typical enhancer, was also studied. Dynamic light scattering results (DLS) showed an increase in the size of the bicosomes with the incorporation of the Re(CO)3 derivative, and the FTIR microspectroscopy showed that the Re(CO)3 derivative incorporated in bicosomes penetrated deeper into the skin than when dissolved in DMSO. When this molecule was applied on the skin using the bicosomes, 60% of the Re(CO)3 derivative was retained in the stratum corneum (SC) and 40% reached the epidermis (Epi). Otherwise, the application of this molecule via DMSO resulted in 95% of the Re(CO)3 derivative being in the SC and only 5% reaching the Epi. Using a Re(CO)3 derivative with a dodecyl-chain as a model molecule, it was possible to determine the distribution of molecules with similar physicochemical characteristics in the skin using bicosomes. This fact makes these nanostructures promising vehicles for the application of lipophilic molecules inside the skin.

  12. Anatomy-guided brain PET imaging incorporating a joint prior model

    NASA Astrophysics Data System (ADS)

    Lu, Lijun; Ma, Jianhua; Feng, Qianjin; Chen, Wufan; Rahmim, Arman

    2015-03-01

    We proposed a maximum a posterior (MAP) framework for incorporating information from co-registered anatomical images into PET image reconstruction through a novel anato-functional joint prior. The characteristic of the utilized hyperbolic potential function is determinate by the voxel intensity differences within the anatomical image, while the penalization is computed based on voxel intensity differences in reconstructed PET images. Using realistic simulated 18FDG PET scan data, we optimized the performance of the proposed MAP reconstruction with the joint prior (JP-MAP) and compared its performance with conventional 3D MLEM and 3D MAP reconstructions. The proposed JP-MAP reconstruction algorithm resulted in quantitatively enhanced reconstructed images, as demonstrated in extensive FDG PET simulation study. The proposed method was also tested on a 20 min Florbetapir patient study performed on the high-resolution research tomograph. It was shown to outperform conventional methods in visual as well as quantitative accuracy assessment (in terms of regional noise versus activity value performance). The JP-MAP method was also compared with another MR-guided MAP reconstruction method, utilizing the Bowsher prior and was seen to result in some quantitative enhancements, especially in the case of MR-PET mis-registrations, and a definitive improvement in computational performance.

  13. Model for the incorporation of plant detritus within clastic accumulating interdistributary bays

    SciTech Connect

    Gastaldo, R.A.; McCarroll, S.M.; Douglass, D.P.

    1985-01-01

    Plant-bearing clastic lithologies interpreted as interdistributary bay deposits are reported from rocks Devonian to Holocene in age. Often, these strata preserve accumulations of discrete, laterally continuous leaf beds or coaly horizons. Investigations within two modern inter-distributary bays in the lower delta plain of the Mobile Delta, Alabama have provided insight into the phytotaphonomic processes responsible for the generation of carbonaceous lithologies, coaly horizons and laterally continuous leaf beds. Delvan and Chacalooche Bays lie adjacent to the Tensaw River distributary channel and differ in the mode of clastic and plant detrital accumulation. Delvan Bay, lying west of the distributary channel, is accumulating detritus solely by overbank deposition. Chacaloochee Bay, lying east of the channel, presently is accumulating detritus by active crevasse-splay activity. Plant detritus is accumulating as transported assemblages in both bays, but the mode of preservation differs. In Delvan Bay, the organic component is highly degraded and incorporated within the clastic component resulting in a carbonaceous silt. Little identifiable plant detritus can be recovered. On the other hand, the organic component in Chacaloochee Bay is accumulating in locally restricted allochthonous peat deposits up to 2 m in thickness, and discrete leaf beds generated by flooding events. In addition, autochthonous plant accumulations occur on subaerially and aerially exposed portions of the crevasse. The resultant distribution of plant remains is a complicated array of transported and non-transported organics.

  14. Combined harvesting of a stage structured prey-predator model incorporating cannibalism in competitive environment.

    PubMed

    Chakraborty, Kunal; Das, Kunal; Kar, Tapan Kumar

    2013-01-01

    In this paper, we propose a prey-predator system with stage structure for predator. The proposed system incorporates cannibalism for predator populations in a competitive environment. The combined fishing effort is considered as control used to harvest the populations. The steady states of the system are determined and the dynamical behavior of the system is discussed. Local stability of the system is analyzed and sufficient conditions are derived for the global stability of the system at the positive equilibrium point. The existence of the Hopf bifurcation phenomenon is examined at the positive equilibrium point of the proposed system. We consider harvesting effort as a control parameter and subsequently, characterize the optimal control parameter in order to formulate the optimal control problem under the dynamic framework towards optimal utilization of the resource. Moreover, the optimal system is solved numerically to investigate the sustainability of the ecosystem using an iterative method with a Runge-Kutta fourth-order scheme. Simulation results show that the optimal control scheme can achieve sustainable ecosystem. Results are analyzed with the help of graphical illustrations. PMID:23537768

  15. Hearing Adults Ability to Transcribe Phrases Incorporating Homonyms Given Two Types of Models.

    ERIC Educational Resources Information Center

    Luetke-Stahlman, Barbara; Tyrrell, Amy J.

    1995-01-01

    Thirty-eight hearing adults' ability to comprehend English homonyms was evaluated from their transcriptions of two versions of a videotaped story, signed in either a literal sign model (Seeing Essential English 2) or a conceptual sign model (Pidgin Sign English). Participants' transcriptions were more successful after watching the literal version.…

  16. A simple 2-D inundation model for incorporating flood damage in urban drainage planning

    NASA Astrophysics Data System (ADS)

    Pathirana, A.; Tsegaye, S.; Gersonius, B.; Vairavamoorthy, K.

    2008-11-01

    In this paper a new inundation model code is developed and coupled with Storm Water Management Model, SWMM, to relate spatial information associated with urban drainage systems as criteria for planning of storm water drainage networks. The prime objective is to achive a model code that is simple and fast enough to be consistently be used in planning stages of urban drainage projects. The formulation for the two-dimensional (2-D) surface flow model algorithms is based on the Navier Stokes equation in two dimensions. An Alternating Direction Implicit (ADI) finite difference numerical scheme is applied to solve the governing equations. This numerical scheme is used to express the partial differential equations with time steps split into two halves. The model algorithm is written using C++ computer programming language. This 2-D surface flow model is then coupled with SWMM for simulation of both pipe flow component and surcharge induced inundation in urban areas. In addition, a damage calculation block is integrated within the inundation model code. The coupled model is shown to be capable of dealing with various flow conditions, as well as being able to simulate wetting and drying processes that will occur as the flood flows over an urban area. It has been applied under idealized and semi-hypothetical cases to determine detailed inundation zones, depths and velocities due to surcharged water on overland surface.

  17. A Dynamic Photovoltaic Model Incorporating Capacitive and Reverse-Bias Characteristics

    SciTech Connect

    Kim, KA; Xu, CY; Jin, L; Krein, PT

    2013-10-01

    Photovoltaics (PVs) are typically modeled only for their forward-biased dc characteristics, as in the commonly used single-diode model. While this approach accurately models the I-V curve under steady forward bias, it lacks dynamic and reverse-bias characteristics. The dynamic characteristics, primarily parallel capacitance and series inductance, affect operation when a PV cell or string interacts with switching converters or experiences sudden transients. Reverse-bias characteristics are often ignored because PV devices are not intended to operate in the reverse-biased region. However, when partial shading occurs on a string of PVs, the shaded cell can become reverse biased and develop into a hot spot that permanently degrades the cell. To fully examine PV behavior under hot spots and various other faults, reverse-bias characteristics must also be modeled. This study develops a comprehensive mathematical PV model based on circuit components that accounts for forward bias, reverse bias, and dynamic characteristics. Using a series of three experimental tests on an unilluminated PV cell, all required model parameters are determined. The model is implemented in MATLAB Simulink and accurately models the measured data.

  18. An Item Response Theory Model for Incorporating Response Time Data in Binary Personality Items

    ERIC Educational Resources Information Center

    Ferrando, Pere J.; Lorenzo-Seva, Urbano

    2007-01-01

    This article describes a general item response theory model for personality items that allows the information provided by the item response times to be used to estimate the individual trait levels. The submodel describing the item response times is a modification of Thissen's log-linear model and is based on the distance-difficulty hypothesis in…

  19. LINKING MICROBES TO CLIMATE: INCORPORATING MICROBIAL ACTIVITY INTO CLIMATE MODELS COLLOQUIUM

    SciTech Connect

    DeLong, Edward; Harwood, Caroline; Reid, Ann

    2011-01-01

    This report explains the connection between microbes and climate, discusses in general terms what modeling is and how it applied to climate, and discusses the need for knowledge in microbial physiology, evolution, and ecology to contribute to the determination of fluxes and rates in climate models. It recommends with a multi-pronged approach to address the gaps.

  20. On the importance of incorporating sampling weights in occupancy model estimation

    EPA Science Inventory

    Occupancy models are used extensively to assess wildlife-habitat associations and to predict species distributions across large geographic regions. Occupancy models were developed as a tool to properly account for imperfect detection of a species. Current guidelines on survey des...

  1. Building out a Measurement Model to Incorporate Complexities of Testing in the Language Domain

    ERIC Educational Resources Information Center

    Wilson, Mark; Moore, Stephen

    2011-01-01

    This paper provides a summary of a novel and integrated way to think about the item response models (most often used in measurement applications in social science areas such as psychology, education, and especially testing of various kinds) from the viewpoint of the statistical theory of generalized linear and nonlinear mixed models. In addition,…

  2. A Preventative Model of School Consultation: Incorporating Perspectives from Positive Psychology

    ERIC Educational Resources Information Center

    Akin-Little, K. Angeleque; Little, Steven G.; Delligatti, Nina

    2004-01-01

    Using the principles of mental health and behavioral consultation, combined with concepts from positive psychology, this paper generates a new preventative model of school consultation. This model has two steps: (1) the school psychologist aids the teacher in the development and use of his/her personal positive psychology (e.g., optimism,…

  3. Eco-Evo PVAs: Incorporating Eco-Evolutionary Processes into Population Viability Models

    EPA Science Inventory

    We synthesize how advances in computational methods and population genomics can be combined within an Ecological-Evolutionary (Eco-Evo) PVA model. Eco-Evo PVA models are powerful new tools for understanding the influence of evolutionary processes on plant and animal population pe...

  4. Incorporating Video Modeling into a School-Based Intervention for Students with Autism Spectrum Disorders

    ERIC Educational Resources Information Center

    Wilson, Kaitlyn P.

    2013-01-01

    Purpose: Video modeling is an intervention strategy that has been shown to be effective in improving the social and communication skills of students with autism spectrum disorders, or ASDs. The purpose of this tutorial is to outline empirically supported, step-by-step instructions for the use of video modeling by school-based speech-language…

  5. Augmenting watershed model calibration with incorporation of ancillary data sources and qualitative soft data sources

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Watershed simulation models can be calibrated using “hard data” such as temporal streamflow observations; however, users may find upon examination of detailed outputs that some of the calibrated models may not reflect summative actual watershed behavior. Thus, it is necessary to use “soft data” (i....

  6. Applications of explicitly-incorporated/post-processing measurement uncertainty in watershed modeling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The importance of measurement uncertainty in terms of calculation of model evaluation error statistics has been recently stated in the literature. The impact of measurement uncertainty on calibration results indicates the potential vague zone in the field of watershed modeling where the assumption ...

  7. The three-dimensional photochemical model CHARM. Incorporation of solar activity

    NASA Astrophysics Data System (ADS)

    Krivolutsky, A. A.; V'yushkova, T. Yu.; Cherepanova, L. A.; Kukoleva, A. A.; Repnev, A. I.; Banin, M. V.

    2015-01-01

    We describe the numerical global photochemical model CHARM (CHemical Atmospheric Research Model) and the results of a numerical simulation of climatological distributions of ozone and other atmospheric trace gases in a height range of up to 90 km. We also present the results of numerical scenarios of an impact induced by a change in UV radiation fluxes in the solar activity cycle and conditioned by ozone depletion in polar regions by high-energy particles of cosmic origin. The spatial transport of chemically active species is described in the model (the Prather scheme) on the basis of global fields of wind components and temperature calculated by the ARM (Atmospheric Research Model) general circulation model.

  8. Incorporating learning goals about modeling into an upper-division physics laboratory experiment

    NASA Astrophysics Data System (ADS)

    Zwickl, Benjamin M.; Finkelstein, Noah; Lewandowski, H. J.

    2014-09-01

    Implementing a laboratory activity involves a complex interplay among learning goals, available resources, feedback about the existing course, best practices for teaching, and an overall philosophy about teaching labs. Building on our previous work, which described a process of transforming an entire lab course, we now turn our attention to how an individual lab activity on the polarization of light was redesigned to include a renewed emphasis on one broad learning goal: modeling. By using this common optics lab as a concrete case study of a broadly applicable approach, we highlight many aspects of the activity development and show how modeling is used to integrate sophisticated conceptual and quantitative reasoning into the experimental process through the various aspects of modeling: constructing models, making predictions, interpreting data, comparing measurements with predictions, and refining models. One significant outcome is a natural way to integrate an analysis and discussion of systematic error into a lab activity.

  9. Incorporation of a Left Ventricle Finite Element Model Defining Infarction Into the XCAT Imaging Phantom

    PubMed Central

    Veress, Alexander I.; Segars, W. Paul; Tsui, Benjamin M. W.; Gullberg, Grant T.

    2011-01-01

    The 4D extended cardiac-torso (XCAT) phantom was developed to provide a realistic and flexible model of the human anatomy and cardiac and respiratory motions for use in medical imaging research. A prior limitation to the phantom was that it did not accurately simulate altered functions of the heart that result from cardiac pathologies such as coronary artery disease (CAD). We overcame this limitation in a previous study by combining the phantom with a finite-element (FE) mechanical model of the left ventricle (LV) capable of more realistically simulating regional defects caused by ischemia. In the present work, we extend this model giving it the ability to accurately simulate motion abnormalities caused by myocardial infarction (MI), a far more complex situation in terms of altered mechanics compared with the modeling of acute ischemia. The FE model geometry is based on high resolution CT images of a normal male subject. An anterior region was defined as infarcted and the material properties and fiber distribution were altered, according to the bio-physiological properties of two types of infarction, i.e., fibrous and remodeled infarction (30% thinner wall than fibrous case). Compared with the original, surface-based 4D beating heart model of the XCAT, where regional abnormalities are modeled by simply scaling down the motion in those regions, the FE model was found to provide a more accurate representation of the abnormal motion of the LV due to the effects of fibrous infarction as well as depicting the motion of remodeled infarction. In particular, the FE models allow for the accurate depiction of dyskinetic motion. The average circumferential strain results were found to be consistent with measured dyskinetic experimental results. Combined with the 4D XCAT phantom, the FE model can be used to produce realistic multimodality sets of imaging data from a variety of patients in which the normal or abnormal cardiac function is accurately represented. PMID:21041157

  10. A model for arsenic anti-site incorporation in GaAs grown by hydride vapor phase epitaxy

    SciTech Connect

    Schulte, K. L.; Kuech, T. F.

    2014-12-28

    GaAs growth by hydride vapor phase epitaxy (HVPE) has regained interest as a potential route to low cost, high efficiency thin film photovoltaics. In order to attain the highest efficiencies, deep level defect incorporation in these materials must be understood and controlled. The arsenic anti-site defect, As{sub Ga} or EL2, is the predominant deep level defect in HVPE-grown GaAs. In the present study, the relationships between HVPE growth conditions and incorporation of EL2 in GaAs epilayers were determined. Epitaxial n-GaAs layers were grown under a wide range of deposition temperatures (T{sub D}) and gallium chloride partial pressures (P{sub GaCl}), and the EL2 concentration, [EL2], was determined by deep level transient spectroscopy. [EL2] agreed with equilibrium thermodynamic predictions in layers grown under conditions in which the growth rate, R{sub G}, was controlled by conditions near thermodynamic equilibrium. [EL2] fell below equilibrium levels when R{sub G} was controlled by surface kinetic processes, with the disparity increasing as R{sub G} decreased. The surface chemical composition during growth was determined to have a strong influence on EL2 incorporation. Under thermodynamically limited growth conditions, e.g., high T{sub D} and/or low P{sub GaCl}, the surface vacancy concentration was high and the bulk crystal was close to equilibrium with the vapor phase. Under kinetically limited growth conditions, e.g., low T{sub D} and/or high P{sub GaCl}, the surface attained a high GaCl coverage, blocking As adsorption. This competitive adsorption process reduced the growth rate and also limited the amount of arsenic that incorporated as As{sub Ga}. A defect incorporation model which accounted for the surface concentration of arsenic as a function of the growth conditions, was developed. This model was used to identify optimal growth parameters for the growth of thin films for photovoltaics, conditions in which a high growth rate and low [EL2] could be

  11. Reconstruction of Biological Networks by Incorporating Prior Knowledge into Bayesian Network Models

    PubMed Central

    Shin, Dong-Guk

    2012-01-01

    Abstract Bayesian network model is widely used for reverse engineering of biological network structures. An advantage of this model is its capability to integrate prior knowledge into the model learning process, which can lead to improving the quality of the network reconstruction outcome. Some previous works have explored this area with focus on using prior knowledge of the direct molecular links, except for a few recent ones proposing to examine the effects of molecular orderings. In this study, we propose a Bayesian network model that can integrate both direct links and orderings into the model. Random weights are assigned to these two types of prior knowledge to alleviate bias toward certain types of information. We evaluate our model performance using both synthetic data and biological data for the RAF signaling network, and illustrate the significant improvement on network structure reconstruction of the proposing models over the existing methods. We also examine the correlation between the improvement and the abundance of ordering prior knowledge. To address the issue of generating prior knowledge, we propose an approach to automatically extract potential molecular orderings from knowledge resources such as Kyoto Encyclopedia of Genes and Genomes (KEGG) database and Gene Ontology (GO) annotation. PMID:23210479

  12. Incorporation of an Energy Equation into a Pulsed Inductive Thruster Performance Model

    NASA Technical Reports Server (NTRS)

    Polzin, Kurt A.; Reneau, Jarred P.; Sankaran, Kameshwaran

    2011-01-01

    A model for pulsed inductive plasma acceleration containing an energy equation to account for the various sources and sinks in such devices is presented. The model consists of a set of circuit equations coupled to an equation of motion and energy equation for the plasma. The latter two equations are obtained for the plasma current sheet by treating it as a one-element finite volume, integrating the equations over that volume, and then matching known terms or quantities already calculated in the model to the resulting current sheet-averaged terms in the equations. Calculations showing the time-evolution of the various sources and sinks in the system are presented to demonstrate the efficacy of the model, with two separate resistivity models employed to show an example of how the plasma transport properties can affect the calculation. While neither resistivity model is fully accurate, the demonstration shows that it is possible within this modeling framework to time-accurately update various plasma parameters.

  13. Development of a human eye model incorporated with intraocular scattering for visual performance assessment

    NASA Astrophysics Data System (ADS)

    Chen, Yi-Chun; Jiang, Chong-Jhih; Yang, Tsung-Hsun; Sun, Ching-Cherng

    2012-07-01

    A biometry-based human eye model was developed by using the empirical anatomic and optical data of ocular parameters. The gradient refractive index of the crystalline lens was modeled by concentric conicoid isoindical surfaces and was adaptive to accommodation and age. The chromatic dispersion of ocular media was described by Cauchy equations. The intraocular scattering model was composed of volumetric Mie scattering in the cornea and the crystalline lens, and a diffusive-surface model at the retina fundus. The retina was regarded as a Lambertian surface and was assigned its corresponding reflectance at each wavelength. The optical performance of the eye model was evaluated in CodeV and ASAP and presented by the modulation transfer functions at single and multiple wavelengths. The chromatic optical powers obtained from this model resembled that of the average physiological eyes. The scattering property was assessed by means of glare veiling luminance and compared with the CIE general disability glare equation. By replacing the transparent lens with a cataractous lens, the disability glare curve of cataracts was generated to compare with the normal disability glare curve. This model has high potential for investigating visual performance in ordinary lighting and display conditions and under the influence of glare sources.

  14. Reconstruction of biological networks by incorporating prior knowledge into Bayesian network models.

    PubMed

    Pei, Baikang; Shin, Dong-Guk

    2012-12-01

    Bayesian network model is widely used for reverse engineering of biological network structures. An advantage of this model is its capability to integrate prior knowledge into the model learning process, which can lead to improving the quality of the network reconstruction outcome. Some previous works have explored this area with focus on using prior knowledge of the direct molecular links, except for a few recent ones proposing to examine the effects of molecular orderings. In this study, we propose a Bayesian network model that can integrate both direct links and orderings into the model. Random weights are assigned to these two types of prior knowledge to alleviate bias toward certain types of information. We evaluate our model performance using both synthetic data and biological data for the RAF signaling network, and illustrate the significant improvement on network structure reconstruction of the proposing models over the existing methods. We also examine the correlation between the improvement and the abundance of ordering prior knowledge. To address the issue of generating prior knowledge, we propose an approach to automatically extract potential molecular orderings from knowledge resources such as Kyoto Encyclopedia of Genes and Genomes (KEGG) database and Gene Ontology (GO) annotation.

  15. A neural network model to predict the wastewater inflow incorporating rainfall events.

    PubMed

    El-Din, Ahmed Gamal; Smith, Daniel W

    2002-03-01

    Under steady-state conditions, a wastewater treatment plant usually has a satisfactory performance because these conditions are similar to design conditions. However, load variations constitute a large portion of the operating life of a treatment facility and most of the observed problems in complying with permit requirements occur during these load transients. During storm events upsets to the different physical and biological processes may take place in a wastewater treatment plant, and therefore, the ability to predict the hydraulic load to a treatment facility during such events is very beneficial for the optimization of the treatment process. Most of the hydrologic and hydraulic models describing sewage collection systems are deterministic. Such models require detailed knowledge of the system and usually rely on a large number of parameters, some of which are uncertain or difficult to determine. Presented in this paper, an artificial neural network (ANN) model that is used to make short-term predictions of wastewater inflow rate that enters the Gold Bar Wastewater Treatment Plant (GBWWTP), the largest plant in the Edmonton area (Alberta, Canada). The neural model uses rainfall data, observed in the collection system discharging to the plant, as inputs. The building process of the model was conducted in a systematic way that allowed the identification of a parsimonious model that is able to learn (and not memorize) from past data and generalize very well to unseen data that was used to validate the model. The neural network model gave excellent results. The potential of using the model as part of a real-time process control system is also discussed.

  16. Incorporating representation of agricultural ecosystems and management within a dynamic biosphere model: Approach, validation, and significance

    NASA Astrophysics Data System (ADS)

    Kucharik, C.

    2004-12-01

    At the scale of individual fields, crop models have long been used to examine the interactions between soils, vegetation, the atmosphere and human management, using varied levels of numerical sophistication. While previous efforts have contributed significantly towards the advancement of modeling tools, the models themselves are not typically applied across larger continental scales due to a lack of crucial data. Furthermore, many times crop models are used to study a single quantity, process, or cycle in isolation, limiting their value in considering the important tradeoffs between competing ecosystem services such as food production, water quality, and sequestered carbon. In response to the need for a more integrated agricultural modeling approach across the continental scale, an updated agricultural version of a dynamic biosphere model (IBIS) now integrates representations of land-surface physics and soil physics, canopy physiology, terrestrial carbon and nitrogen balance, crop phenology, solute transport, and farm management into a single framework. This version of the IBIS model (Agro-IBIS) uses a short 20 to 60-minute timestep to simulate the rapid exchange of energy, carbon, water, and momentum between soils, vegetative canopies, and the atmosphere. The model can be driven either by site-specific meteorological data or by gridded climate datasets. Mechanistic crop models for corn, soybean, and wheat use physiologically-based representations of leaf photosynthesis, stomatal conductance, and plant respiration. Model validation has been performed using a variety of temporal scale data collected at the following spatial scales: (1) the precision-agriculture scale (5 m), (2) the individual field experiment scale (AmeriFlux), and (3) regional and continental scales using annual USDA county-level yield data and monthly satellite (AVHRR) observations of vegetation characteristics at 0.5 degree resolution. To date, the model has been used with great success to

  17. Incorporation of NREL Solar Advisor Model Photovoltaic Capabilities with GridLAB-D

    SciTech Connect

    Tuffner, Francis K.; Hammerstrom, Janelle L.; Singh, Ruchi

    2012-10-19

    This report provides a summary of the work updating the photovoltaic model inside GridLAB-D. The National Renewable Energy Laboratory Solar Advisor Model (SAM) was utilized as a basis for algorithms and validation of the new implementation. Subsequent testing revealed that the two implementations are nearly identical in both solar impacts and power output levels. This synergized model aides the system-level impact studies of GridLAB-D, but also allows more specific details of a particular site to be explored via the SAM software.

  18. Simple model atmospheres incorporating new opacities of VO and TiO

    NASA Astrophysics Data System (ADS)

    Brett, J. M.

    1989-11-01

    The effect of the VO A-X, VO B-X and TiO-upsilon molecular band opacities upon the atmospheres of red giants is investigated by construction of plane-parallel straight mean opacity models. From these simple preliminary models a limited heating of the upper atmosphere is found producing a temperature rise of up to 100 K. This result and its effect upon computed bandstrengths suggests that these opacities should be included in more accurate model atmospheres of late M stars.

  19. Incorporation of Electrical Systems Models Into an Existing Thermodynamic Cycle Code

    NASA Technical Reports Server (NTRS)

    Freeh, Josh

    2003-01-01

    Integration of entire system includes: Fuel cells, motors, propulsors, thermal/power management, compressors, etc. Use of existing, pre-developed NPSS capabilities includes: 1) Optimization tools; 2) Gas turbine models for hybrid systems; 3) Increased interplay between subsystems; 4) Off-design modeling capabilities; 5) Altitude effects; and 6) Existing transient modeling architecture. Other factors inclde: 1) Easier transfer between users and groups of users; 2) General aerospace industry acceptance and familiarity; and 3) Flexible analysis tool that can also be used for ground power applications.

  20. A creep model for austenitic stainless steels incorporating cavitation and wedge cracking

    NASA Astrophysics Data System (ADS)

    Mahesh, S.; Alur, K. C.; Mathew, M. D.

    2011-01-01

    A model of damage evolution in austenitic stainless steels under creep loading at elevated temperatures is proposed. The initial microstructure is idealized as a space-tiling aggregate of identical rhombic dodecahedral grains, which undergo power-law creep deformation. Damage evolution in the form of cavitation and wedge cracking on grain-boundary facets is considered. Both diffusion- and deformation-driven grain-boundary cavity growth are treated. Cavity and wedge-crack length evolution are derived from an energy balance argument that combines and extends the models of Cottrell (1961 Trans. AIME 212 191-203), Williams (1967 Phil. Mag. 15 1289-91) and Evans (1971 Phil Mag. 23 1101-12). The time to rupture predicted by the model is in good agreement with published experimental data for a type 316 austenitic stainless steel under uniaxial creep loading. Deformation and damage evolution at the microscale predicted by the present model are also discussed.

  1. Incorporating Results of Avian Toxicity Tests into a Model of Annual Reproductive Success

    EPA Science Inventory

    This manuscript presents a modeling approach for translating results from laboratory avian reproduction tests into an estimate of pesticide-caused change in the annual reproductive success of birds, also known as fecundity rate.

  2. Incorporation of prior information on parameters into nonlinear regression groundwater flow models. l. Theory.

    USGS Publications Warehouse

    Cooley, R.L.

    1982-01-01

    Prior information on the parameters of a groundwater flow model can be used to improve parameter estimates obtained from nonlinear regression solution of a modeling problem. Two scales of prior information can be available: 1) prior information having known reliability (that is, bias and random error structure), and 2) prior information consisting of best available estimates of unknown reliability. It is shown that if both scales of prior information are available, then a combined regression analysis may be made. -from Author

  3. A modified capacitance model of RF MEMS shunt switch incorporating fringing field effects of perforated beam

    NASA Astrophysics Data System (ADS)

    Guha, Koushik; Kumar, Mithlesh; Agarwal, Saurabh; Baishya, Srimanta

    2015-12-01

    This paper deals with the approach to accurately model the capacitance of non-uniform meander based RF MEMS shunt switch with perforated structure. Here the general analytical model of capacitance is proposed for both up state and down state condition of the switch. The model also accounts for fringing capacitance due to beam thickness and etched holes on the beam. Calculated results are validated with the simulated results of full 3D FEM solver Coventorware in both the conditions of the switch. Variation of Up-state and Down-state capacitances with different dielectric thicknesses and voltages are plotted and error of analytical value is estimated and analyzed. Three benchmark models of parallel plate capacitance are modified for MEMS switch operation and their results are compared with the proposed model. Percentage contribution of fringing capacitance in up-state and down-state is approx. 25% and 2%, respectively, of the total capacitance. The model shows good accuracy with the mean error of -4.45% in up-state and -5.78% in down-state condition for a wide range of parameter variations and -2.13% for ligament efficiency of μ = 0.3.

  4. Incorporating GIS data into an agent-based model to support planning policy making for the development of creative industries

    NASA Astrophysics Data System (ADS)

    Liu, Helin; Silva, Elisabete A.; Wang, Qian

    2016-07-01

    This paper presents an extension to the agent-based model "Creative Industries Development-Urban Spatial Structure Transformation" by incorporating GIS data. Three agent classes, creative firms, creative workers and urban government, are considered in the model, and the spatial environment represents a set of GIS data layers (i.e. road network, key housing areas, land use). With the goal to facilitate urban policy makers to draw up policies locally and optimise the land use assignment in order to support the development of creative industries, the improved model exhibited its capacity to assist the policy makers conducting experiments and simulating different policy scenarios to see the corresponding dynamics of the spatial distributions of creative firms and creative workers across time within a city/district. The spatiotemporal graphs and maps record the simulation results and can be used as a reference by the policy makers to adjust land use plans adaptively at different stages of the creative industries' development process.

  5. A stoichiometric producer-grazer model incorporating the effects of excess food-nutrient content on consumer dynamics.

    PubMed

    Peace, Angela; Zhao, Yuqin; Loladze, Irakli; Elser, James J; Kuang, Yang

    2013-08-01

    There has been important progress in understanding ecological dynamics through the development of the theory of ecological stoichiometry. For example, modeling under this framework allows food quality to affect consumer dynamics. While the effects of nutrient deficiency on consumer growth are well understood, recent discoveries in ecological stoichiometry suggest that consumer dynamics are not only affected by insufficient food nutrient content (low phosphorus (P): carbon (C) ratio) but also by excess food nutrient content (high P:C). This phenomenon is known as the stoichiometric knife edge, in which animal growth is reduced not only by food with low P content but also by food with high P content, and needs to be incorporated into mathematical models. Here we present a Lotka-Volterra type model to investigate the growth response of Daphnia to algae of varying P:C ratios capturing the mechanism of the stoichiometric knife edge.

  6. Incorporating landslide erosion into the SWAT for modeling suspended sediment discharge from snowmelt-dependent watersheds in northern Japan

    NASA Astrophysics Data System (ADS)

    Mizugaki, S.; Kubo, M.; Tanise, A.; Hirai, Y.; Hamamoto, S.

    2015-12-01

    Landslide erosion is a key driver of sediment yield at the watershed scale. In snowy cold region, landslide is active especially in snowmelt season, leading to increase in lateral erosion during snowmelt floods. Then, snowmelt flood in spring season is crucial for water, sediment and nutrient cycles from mountain to coast. Common hydrological models such as SWAT and WEPP are useful tools to evaluate and/or predict hydrology and sediment dynamics at watershed scale in snowy cold region, but not include the landslide erosion process. To develop the SWAT model for modeling water and suspended sediment discharge in snowmelt-dependent watersheds, we investigated the suspended sediment yield using fingerprinting technique, and correlated with landslide distribution using GIS. Suspended sediment yield was determined and found to be varied with each lithological group in the watersheds, showing the highest sediment yield in the metamorphic rock area represented by serpentine rock. From this result, the suspended sediment yield at sub-basin scale was estimated according to the geological composition and correlated with landslide density. The correlation analysis showed that the suspended sediment yield increases in respond to the landslide area along the stream channel. To incorporate the landslide erosion process into the SWAT model, the parameter associated with channel bank erosion was weighted with landslide density along main channel, assuming the lateral erosion as a key driver of landslide erosion. In result of calibration for sediment discharge, the Nash-Sutcliffe coefficient was improved for the landslide-incorporated model from for the model with default parameter set.

  7. Incorporating Detailed Chemical Characterization of Biomass Burning Emissions into Air Quality Models

    NASA Astrophysics Data System (ADS)

    Barsanti, K.; Hatch, L. E.; Yokelson, R. J.; Stockwell, C.; Orlando, J. J.; Emmons, L. K.; Knote, C. J.; Wiedinmyer, C.

    2015-12-01

    Approximately 500 Tg/yr of non-methane organic compounds (NMOCs) are emitted by biomass burning (BB) to the global atmosphere, leading to the photochemical production of ozone (O3) and secondary particulate matter (PM). Until recently, in studies of BB emissions, a significant mass fraction of NMOCs (up to 80%) remained uncharacterized or unidentified. Models used to simulate the air quality impacts of BB thus have relied on very limited chemical characterization of the emitted compounds. During the Fourth Fire Lab at Missoula Experiment (FLAME-IV), an unprecedented fraction of emitted NMOCs were identified and quantified through the application of advanced analytical techniques. Here we use FLAME-IV data to improve BB emissions speciation profiles for individual fuel types. From box model simulations we evaluate the sensitivity of predicted precursor and pollutant concentrations (e.g., formaldehyde, acetaldehyde, and terpene oxidation products) to differences in the emission speciation profiles, for a range of ambient conditions (e.g., high vs. low NOx). Appropriate representation of emitted NMOCs in models is critical for the accurate prediction of downwind air quality. Explicit simulation of hundreds of NMOCs is not feasible; therefore we also investigate the consequences of using existing assumptions and lumping schemes to map individual NMOCs to model surrogates and we consider alternative strategies. The updated BB emissions speciation profiles lead to markedly different surrogate compound distributions than the default speciation profiles, and box model results suggest that these differences are likely to affect predictions of PM and important gas-phase species in chemical transport models. This study highlights the potential for further BB emissions characterization studies, with concerted model development efforts, to improve the accuracy of BB predictions using necessarily simplified mechanisms.

  8. Structural FE model updating of cavity systems incorporating vibro-acoustic coupling

    NASA Astrophysics Data System (ADS)

    Nehete, D. V.; Modak, S. V.; Gupta, K.

    2015-01-01

    Finite element model updating techniques are used to update the finite element model of a structure in order to improve its correlation with the experimental dynamic test data. These techniques are well developed and extensively studied for the case of purely structural dynamic systems. However, the cavities encountered in automotive, aerospace and other transportation applications represent a class of structures in which an elastic structure encloses an acoustic medium. In such systems the dynamic characteristics of the structure are influenced by the acoustic loading due to the acoustic response in the cavity. The existing structural FE model updating approaches assume the structure to be under in-vacuo condition and hence if used for updating cavity structural FE models would not allow taking into account the effect of acoustic loading on the structural dynamic characteristics. This may adversely affect the effectiveness of updating in yielding an accurate updated FE model. This paper addresses the above issue and presents a structural FE model updating method, called 'coupled inverse eigen-sensitivity method', which takes into account the acoustic loading on the structure. The method uses the experimentally identified coupled modal data on the structure as the reference data. A numerical case study of a 3D rectangular cavity backed by a flexible plate is presented to evaluate the effectiveness of the approach to obtain an accurate structural FE model. Updating is also carried out using the existing (uncoupled) inverse eigen-sensitivity method to study the influence of acoustic loading on the updating process and to study the accuracy with which the updating parameters are identified. The results obtained are also compared with those obtained by the proposed coupled inverse eigen-sensitivity method.

  9. Incorporating floating surface objects into a fully dispersive surface wave model

    NASA Astrophysics Data System (ADS)

    Orzech, Mark D.; Shi, Fengyan; Veeramony, Jayaram; Bateman, Samuel; Calantoni, Joseph; Kirby, James T.

    2016-06-01

    The shock-capturing, non-hydrostatic, three-dimensional (3D) finite-volume model NHWAVE was originally developed to simulate wave propagation and landslide-generated tsunamis in finite water depth (Ma, G., Shi, F., Kirby, J. T., 2012. Ocean Model. 43-44, 22-35). The model is based on the incompressible Navier-Stokes equations, in which the z-axis is transformed to a σ-coordinate that tracks the bed and surface. As part of an ongoing effort to simulate waves in polar marginal ice zones (MIZs), the model has now been adapted to allow objects of arbitrary shape and roughness to float on or near its water surface. The shape of the underside of each floating object is mapped onto an upper σ-level slightly below the surface. In areas without floating objects, this σ-level continues to track the surface and bed as before. Along the sides of each floating object, an immersed boundary method is used to interpolate the effects of the object onto the neighboring fluid volume. Provided with the object's shape, location, and velocity over time, NHWAVE determines the fluid fluxes and pressure variations from the corresponding accelerations at neighboring cell boundaries. The system was validated by comparison with analytical solutions and a VOF model for a 2D floating box and with laboratory measurements of wave generation by a vertically oscillating sphere. A steep wave simulation illustrated the high efficiency of NHWAVE relative to a VOF model. In a more realistic MIZ simulation, the adapted model produced qualitatively reasonable results for wave attenuation, diffraction, and scattering.

  10. Modeling mode choice behavior incorporating household and individual sociodemographics and travel attributes based on rough sets theory.

    PubMed

    Cheng, Long; Chen, Xuewu; Wei, Ming; Wu, Jingxian; Hou, Xianyao

    2014-01-01

    Most traditional mode choice models are based on the principle of random utility maximization derived from econometric theory. Alternatively, mode choice modeling can be regarded as a pattern recognition problem reflected from the explanatory variables of determining the choices between alternatives. The paper applies the knowledge discovery technique of rough sets theory to model travel mode choices incorporating household and individual sociodemographics and travel information, and to identify the significance of each attribute. The study uses the detailed travel diary survey data of Changxing county which contains information on both household and individual travel behaviors for model estimation and evaluation. The knowledge is presented in the form of easily understood IF-THEN statements or rules which reveal how each attribute influences mode choice behavior. These rules are then used to predict travel mode choices from information held about previously unseen individuals and the classification performance is assessed. The rough sets model shows high robustness and good predictive ability. The most significant condition attributes identified to determine travel mode choices are gender, distance, household annual income, and occupation. Comparative evaluation with the MNL model also proves that the rough sets model gives superior prediction accuracy and coverage on travel mode choice modeling.

  11. Incorporating harvest rates into the sex-age-kill model for white-tailed deer

    USGS Publications Warehouse

    Norton, Andrew S.; Diefenbach, Duane R.; Rosenberry, Christopher S.; Wallingford, Bret D.

    2013-01-01

    Although monitoring population trends is an essential component of game species management, wildlife managers rarely have complete counts of abundance. Often, they rely on population models to monitor population trends. As imperfect representations of real-world populations, models must be rigorously evaluated to be applied appropriately. Previous research has evaluated population models for white-tailed deer (Odocoileus virginianus); however, the precision and reliability of these models when tested against empirical measures of variability and bias largely is untested. We were able to statistically evaluate the Pennsylvania sex-age-kill (PASAK) population model using realistic error measured using data from 1,131 radiocollared white-tailed deer in Pennsylvania from 2002 to 2008. We used these data and harvest data (number killed, age-sex structure, etc.) to estimate precision of abundance estimates, identify the most efficient harvest data collection with respect to precision of parameter estimates, and evaluate PASAK model robustness to violation of assumptions. Median coefficient of variation (CV) estimates by Wildlife Management Unit, 13.2% in the most recent year, were slightly above benchmarks recommended for managing game species populations. Doubling reporting rates by hunters or doubling the number of deer checked by personnel in the field reduced median CVs to recommended levels. The PASAK model was robust to errors in estimates for adult male harvest rates but was sensitive to errors in subadult male harvest rates, especially in populations with lower harvest rates. In particular, an error in subadult (1.5-yr-old) male harvest rates resulted in the opposite error in subadult male, adult female, and juvenile population estimates. Also, evidence of a greater harvest probability for subadult female deer when compared with adult (≥2.5-yr-old) female deer resulted in a 9.5% underestimate of the population using the PASAK model. Because obtaining

  12. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    USGS Publications Warehouse

    He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, Anthony; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

    2015-01-01

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 Pg C yr−1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4–0.6) in the simulated spatial pattern of soil RHwith both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  13. Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

    NASA Astrophysics Data System (ADS)

    He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, Anthony D.; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

    2015-12-01

    Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil RH (7.5 ± 2.4 Pg C yr-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil RH with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

  14. A magnetospheric field model incorporating the OGO 3 and 5 magnetic field observations.

    NASA Technical Reports Server (NTRS)

    Sugiura, M.; Poros, D. J.

    1973-01-01

    A magnetospheric field model is presented in which the usually assumed toroidal ring current is replaced by a circular disk current of finite thickness that extends from the tail to geocentric distances less than 3 earth radii. The drastic departure of this model from the concept of the conventional ring current lies in that the current is continuous from the tail to the inner magnetosphere. This conceptual change was required to account for the recent results of analysis of the OGO 3 and 5 magnetic field observations. In the present model the cross-tail current flows along circular arcs concentric with the earth and completes circuit via surface currents on the magnetopause. Apart from these return currents in the tail magnetopause, Mead's (1964) model is used for the field from the magnetopause current. The difference scalar field, Delta B, defined as the difference between the scalar field calculated from the present model and the magnitude of the dipole field, is found to be in gross agreement with the observed Delta B.

  15. Ultrasonically assisted drilling: A finite-element model incorporating acoustic softening effects

    NASA Astrophysics Data System (ADS)

    Phadnis, V. A.; Roy, A.; Silberschmidt, V. V.

    2013-07-01

    Ultrasonically assisted drilling (UAD) is a novel machining technique suitable for drilling in hard-to-machine quasi-brittle materials such as carbon fibre reinforced polymer composites (CFRP). UAD has been shown to possess several advantages compared to conventional drilling (CD), including reduced thrust forces, diminished burr formation at drill exit and an overall improvement in roundness and surface finish of the drilled hole. Recently, our in-house experiments of UAD in CFRP composites demonstrated remarkable reductions in thrust-force and torque measurements (average force reductions in excess of 80%) when compared to CD with the same machining parameters. In this study, a 3D finite-element model of drilling in CFRP is developed. In order to model acoustic (ultrasonic) softening effects, a phenomenological model, which accounts for ultrasonically induced plastic strain, was implemented in ABAQUS/Explicit. The model also accounts for dynamic frictional effects, which also contribute to the overall improved machining characteristics in UAD. The model is validated with experimental findings, where an excellent correlation between the reduced thrust force and torque magnitude was achieved.

  16. Simulated masking of right whale sounds by shipping noise: incorporating a model of the auditory periphery.

    PubMed

    Cunningham, Kane A; Mountain, David C

    2014-03-01

    Many species of large, mysticete whales are known to produce low-frequency communication sounds. These low-frequency sounds are susceptible to communication masking by shipping noise, which also tends to be low frequency in nature. The size of these species makes behavioral assessment of auditory capabilities in controlled, captive environments nearly impossible, and field-based playback experiments are expensive and necessarily limited in scope. Hence, it is desirable to produce a masking model for these species that can aid in determining the potential effects of shipping and other anthropogenic noises on these protected animals. The aim of this study was to build a model that combines a sophisticated representation of the auditory periphery with a spectrogram-based decision stage to predict masking levels. The output of this model can then be combined with a habitat-appropriate propagation model to calculate the potential effects of noise on communication range. For this study, the model was tested on three common North Atlantic right whale communication sounds, both to demonstrate the method and to probe how shipping noise affects the detection of sounds with varying spectral and temporal characteristics.

  17. New systematic methodology for incorporating dynamic heat transfer modelling in multi-phase biochemical reactors.

    PubMed

    Fernández-Arévalo, T; Lizarralde, I; Grau, P; Ayesa, E

    2014-09-01

    This paper presents a new modelling methodology for dynamically predicting the heat produced or consumed in the transformations of any biological reactor using Hess's law. Starting from a complete description of model components stoichiometry and formation enthalpies, the proposed modelling methodology has integrated successfully the simultaneous calculation of both the conventional mass balances and the enthalpy change of reaction in an expandable multi-phase matrix structure, which facilitates a detailed prediction of the main heat fluxes in the biochemical reactors. The methodology has been implemented in a plant-wide modelling methodology in order to facilitate the dynamic description of mass and heat throughout the plant. After validation with literature data, as illustrative examples of the capability of the methodology, two case studies have been described. In the first one, a predenitrification-nitrification dynamic process has been analysed, with the aim of demonstrating the easy integration of the methodology in any system. In the second case study, the simulation of a thermal model for an ATAD has shown the potential of the proposed methodology for analysing the effect of ventilation and influent characterization. PMID:24852412

  18. New systematic methodology for incorporating dynamic heat transfer modelling in multi-phase biochemical reactors.

    PubMed

    Fernández-Arévalo, T; Lizarralde, I; Grau, P; Ayesa, E

    2014-09-01

    This paper presents a new modelling methodology for dynamically predicting the heat produced or consumed in the transformations of any biological reactor using Hess's law. Starting from a complete description of model components stoichiometry and formation enthalpies, the proposed modelling methodology has integrated successfully the simultaneous calculation of both the conventional mass balances and the enthalpy change of reaction in an expandable multi-phase matrix structure, which facilitates a detailed prediction of the main heat fluxes in the biochemical reactors. The methodology has been implemented in a plant-wide modelling methodology in order to facilitate the dynamic description of mass and heat throughout the plant. After validation with literature data, as illustrative examples of the capability of the methodology, two case studies have been described. In the first one, a predenitrification-nitrification dynamic process has been analysed, with the aim of demonstrating the easy integration of the methodology in any system. In the second case study, the simulation of a thermal model for an ATAD has shown the potential of the proposed methodology for analysing the effect of ventilation and influent characterization.

  19. Incorporating advanced language models into the P300 speller using particle filtering

    NASA Astrophysics Data System (ADS)

    Speier, W.; Arnold, C. W.; Deshpande, A.; Knall, J.; Pouratian, N.

    2015-08-01

    Objective. The P300 speller is a common brain-computer interface (BCI) application designed to communicate language by detecting event related potentials in a subject’s electroencephalogram signal. Information about the structure of natural language can be valuable for BCI communication, but attempts to use this information have thus far been limited to rudimentary n-gram models. While more sophisticated language models are prevalent in natural language processing literature, current BCI analysis methods based on dynamic programming cannot handle their complexity. Approach. Sampling methods can overcome this complexity by estimating the posterior distribution without searching the entire state space of the model. In this study, we implement sequential importance resampling, a commonly used particle filtering (PF) algorithm, to integrate a probabilistic automaton language model. Main result. This method was first evaluated offline on a dataset of 15 healthy subjects, which showed significant increases in speed and accuracy when compared to standard classification methods as well as a recently published approach using a hidden Markov model (HMM). An online pilot study verified these results as the average speed and accuracy achieved using the PF method was significantly higher than that using the HMM method. Significance. These findings strongly support the integration of domain-specific knowledge into BCI classification to improve system performance.

  20. Hybrid Cone-Beam Tomographic Reconstruction: Incorporation of Prior Anatomical Models to Compensate for Missing Data

    PubMed Central

    Sadowsky, Ofri; Lee, Junghoon; Sutter, E. Grant; Wall, Simon J.; Prince, Jerry L.; Taylor, Russell H.

    2012-01-01

    We propose a method for improving the quality of cone-beam tomographic reconstruction done with a C-arm. C-arm scans frequently suffer from incomplete information due to image truncation, limited scan length, or other limitations. Our proposed “hybrid reconstruction” method injects information from a prior anatomical model, derived from a subject-specific CT or from a statistical database (atlas), where the C-arm x-ray data is missing. This significantly reduces reconstruction artifacts with little loss of true information from the x-ray projections. The methods consist of constructing anatomical models, fast rendering of digitally reconstructed radiograph (DRR) projections of the models, rigid or deformable registration of the model and the x-ray images, and fusion of the DRR and x-ray projections, all prior to a conventional filtered back-projection algorithm. Our experiments, conducted with a mobile image intensifier C-arm, demonstrate visually and quantitatively the contribution of data fusion to image quality, which we assess through comparison to a “ground truth” CT. Importantly, we show that a significantly improved reconstruction can be obtained from a C-arm scan as short as 90° by complementing the observed projections with DRRs of two prior models, namely an atlas and a pre-operative same-patient CT. The hybrid reconstruction principles are applicable to other types of C-arms as well. PMID:20667807

  1. A new class of actuator surface models incorporating wind turbine blade and nacelle geometry effects

    NASA Astrophysics Data System (ADS)

    Yang, Xiaolei; Sotiropoulos, Fotis

    2015-11-01

    It was shown by Kang, Yang and Sotiropoulos that the nacelle has significant effects on the turbine wake even in the far wake region, which the standard actuator line model is not able to predict. We develop a new class of actuator surface models for the blades and nacelle, which is able to resolve the effects of both tip vortices and nacelle vortex. The new nacelle model, which is based on distributing forces from the actual nacelle geometry as in the diffused interface immersed boundary methods, is first tested by carrying out LES of the flow past a sphere and demonstrating good agreement with available in the literature DNS results. The proposed model is subsequently validated by simulating the flow past the hydrokinetic turbine used in the simulations of Kang et al. and good agreement with the measurements is demonstrated. Finally, the proposed model is applied to utility scale wind turbines to elucidate the role of nacelle vortex dynamics on turbine wake meandering. This work was supported by Department of Energy DOE (DE-EE0002980, DE-EE0005482 and DE-AC04-94AL85000), and Sandia National Laboratories. Computational resources were provided by SNL and MSI.

  2. Incorporating the eruptive history in a stochastic model for volcanic eruptions

    NASA Astrophysics Data System (ADS)

    Bebbington, Mark

    2008-08-01

    We show how a stochastic version of a general load-and-discharge model for volcanic eruptions can be implemented. The model tracks the history of the volcano through a quantity proportional to stored magma volume. Thus large eruptions can influence the activity rate for a considerable time following, rather than only the next repose as in the time-predictable model. The model can be fitted to data using point-process methods. Applied to flank eruptions of Mount Etna, it exhibits possible long-term quasi-cyclic behavior, and to Mauna Loa, a long-term decrease in activity. An extension to multiple interacting sources is outlined, which may be different eruption styles or locations, or different volcanoes. This can be used to identify an 'average interaction' between the sources. We find significant evidence that summit eruptions of Mount Etna are dependent on preceding flank eruptions, with both flank and summit eruptions being triggered by the other type. Fitted to Mauna Loa and Kilauea, the model had a marginally significant relationship between eruptions of Mauna Loa and Kilauea, consistent with the invasion of the latter's plumbing system by magma from the former.

  3. A Modeling Framework to Incorporate Effects of Infrastructure in Sociohydrological Systems

    NASA Astrophysics Data System (ADS)

    Muneepeerakul, R.

    2014-12-01

    In studying coupled natural-human systems, most modeling efforts focus on humans and the natural resources. In reality, however, humans rarely interact with these resources directly; the relationships between humans and resources are mediated by infrastructures. In sociohydrological systems, these include, for example, dams and irrigation canals. These infrastructures have important characteristics such as threshold behavior and a separate entity/organization tasked with maintaining them. These characteristics influence social dynamics within the system, which in turn determines the state of infrastructure and water usage, thereby exerting feedbacks onto the hydrological processes. Infrastructure is thus a necessary ingredient for modeling co-evolution of human and water in sociohydrological systems. A conceptual framework to address this gap has been proposed by Anderies, Janssen, and Ostrom (2004). Here we develop a model to operationalize the framework and report some preliminary results. Simple in its setup, the model highlights the structure of the social dilemmas and how it affects the system's sustainability. The model also offers a platform to explore how the system's sustainability may respond to external shocks from globalization and global climate change.

  4. Approximate world models: Incorporating qualitative and linguistic information into vision systems

    SciTech Connect

    Pinhanez, C.S.; Bobick, A.F.

    1996-12-31

    Approximate world models are coarse descriptions of the elements of a scene, and are intended to be used in the selection and control of vision routines in a vision system. In this paper we present a control architecture in which the approximate models represent the complex relationships among the objects in the world, allowing the vision routines to be situation or context specific. Moreover, because of their reduced accuracy requirements, approximate world models can employ qualitative information such as those provided by linguistic descriptions of the scene. The concept is demonstrated in the development of automatic cameras for a TV studio-SmartCams. Results are shown where SmartCams use vision processing of real imagery and information written in the script of a TV show to achieve TV-quality framing.

  5. Optimization of a rotating thermally conducting joint and incorporation in a laboratory model deployable radiator

    NASA Astrophysics Data System (ADS)

    Hinderer, B.

    1980-03-01

    A thermal and mechanical optimization of a thermally conducting joint and an attached heat pipe radiator was performed. A thermal node model was established to calculate different design configurations. The sealing-bearing concept was redesigned to minimize torque. Axially grooved heat pipe profiles were established for the design goal of this deployable radiator model. An engineering model deployable radiator was constructed and submitted to a thermal-vacuum test. Temperature drops from feeder to radiator closely met predictions, but measured torque exceeded expectations but was within an acceptable range for space applications. The heat pipe network comprising the heat pipes of the radiator and those integrated in the rotor profile was not entirely satisfactory. Evaluation of the results of thermal-vacuum test and previous heat pipe tests led to no definite explanation for the problems with some of the radiator heat pipes.

  6. ISG hybrid powertrain: a rule-based driver model incorporating look-ahead information

    NASA Astrophysics Data System (ADS)

    Shen, Shuiwen; Zhang, Junzhi; Chen, Xiaojiang; Zhong, Qing-Chang; Thornton, Roger

    2010-03-01

    According to European regulations, if the amount of regenerative braking is determined by the travel of the brake pedal, more stringent standards must be applied, otherwise it may adversely affect the existing vehicle safety system. The use of engine or vehicle speed to derive regenerative braking is one way to avoid strict design standards, but this introduces discontinuity in powertrain torque when the driver releases the acceleration pedal or applies the brake pedal. This is shown to cause oscillations in the pedal input and powertrain torque when a conventional driver model is adopted. Look-ahead information, together with other predicted vehicle states, are adopted to control the vehicle speed, in particular, during deceleration, and to improve the driver model so that oscillations can be avoided. The improved driver model makes analysis and validation of the control strategy for an integrated starter generator (ISG) hybrid powertrain possible.

  7. A Distributed Water Circulation Model Incorporating Large Irrigation Schemes for Paddy Areas

    NASA Astrophysics Data System (ADS)

    Yoshida, T.; Masumoto, T.; Kudo, R.; Horikawa, N.

    2010-12-01

    Water intake for paddy irrigation in Japan accounts for approximately 70% of total intake. Spatial and temporal variation of precipitation and river flow changes, likely to be caused by climate changes, directly affect paddy irrigation and its management schemes. Previous studies show that potential water stresses were estimated in the framework of grid-based distributed water circulation models, in which water availability and demand were roughly compared in large-scale grids of 10~100km. However, in mid and small-scale basins, where we carry out impact assessment studies of 1~10km grids, we need schemes to couple the irrigation intake and its allocation, because agricultural water is highly dependent on human decision making processes. Then, we have developed a model that couples natural hydrological behaviors of a basin and artificial irrigation systems. A distributed water circulation model, which explains natural hydrological behaviors of a basin, consists of approximately 1km square gridded meshes. Infiltration and saturation-excess flow and water requirements of irrigated paddy fields on any grid are calculated. The generated surface flow is routed by a kinematic wave equation so that daily flow rate can be calculated at any point of interest. The core of the model is water allocation and management scheme that exploit the spatial database of irrigation facilities and beneficiary areas. This analysis consists of new modeled plane for irrigation, which is calculated independently from the surface plain of the distributed water circulation model. Following the configuration of the water allocation and management schemes, the model is coupled with the distributed water circulation model. The reservoir operation scheme is an algorithm to determine the reservoir releases for irrigation based on requirement and flow rate at downstream diversion weirs. Diversion weirs intake water from associated rivers at the maximum rate, if water is available. The integrated

  8. On incorporating damping and gravity effects in models of structural dynamics of the SCOLE configuration

    NASA Technical Reports Server (NTRS)

    Taylor, Larry; Leary, Terry; Stewart, Eric

    1987-01-01

    The damping for structural dynamic models of flexible spacecraft is usually ignored and then added after modal frequencies and mode shapes are calculated. It is common practice to assume the same damping ratio for all modes, although it is known that damping due to bending and that due to torsion are sometimes ignored. Two methods of including damping in the modeling process from its onset are examined. First, the partial derivative equations of motion are analyzed for a pinned-pinned beam with damping. The end conditions are altered to handle bodies with mass and inertia for the Spacecraft Control Laboratory Experiment (SCOLE) configuration. Second, a massless beam approximation is used for the modes with low frequencies, and a clamped-clamped system is used to approximate the modes for arbitrarily high frequency. The model is then modified to include gravity effects and is compared with experimental results.

  9. Modeling ductile metals under large strain, pressure and high strain rates incorporating damage and microstructure evolution

    NASA Astrophysics Data System (ADS)

    Iannitti, Gianluca; Bonora, Nicola; Ruggiero, Andrew; Dichiaro, Simone

    2011-06-01

    In this work, a constitutive modeling that couples plasticity, grain size evolution (due to plastic deformation and dynamic recrystallization) and ductile damage has been developed. The effect of grain size on the material yield stress (Hall-Petch) and on the melting temperature has been considered. The model has been used to investigate computationally the behaviour of high purity copper in dynamic tensile extrusion test (DTE). An extensive numerical simulation work, using implicit finite element code with direct integration, has been performed and the results have been compared with available experimental data. The major finding is that the proposed model is capable to predict most of the observed features such as the increase of material ductility with the decreasing average grain size, the overall number and size of fragments and the average grain size distribution in the fragment trapped into the dime.

  10. Modeling ductile metals under large strain, pressure and high strain rate incorporating damage and microstructure evolution

    NASA Astrophysics Data System (ADS)

    Iannitti, Gianluca; Bonora, Nicola; Ruggiero, Andrew; Dichiaro, Simone

    2012-03-01

    In this work, a constitutive modeling that couples plasticity, grain size evolution (due to plastic deformation and dynamic recrystallization) and ductile damage has been developed. The effect of grain size on the material yield stress (Hall-Petch) and on the melting temperature has been considered. The model has been used to investigate computationally the behavior of high purity copper in dynamic tensile extrusion test (DTE). An extensive numerical simulation work, using implicit finite element code with direct integration, has been performed and the results have been compared with available experimental data. The major finding is that the proposed model is capable to predict most of the observed features such as the increase of material ductility with the decreasing average grain size, the overall number and size of fragments and the average grain size distribution in the fragment trapped into the dime.

  11. Incorporation of groundwater pumping in a global Land Surface Model with the representation of human impacts

    NASA Astrophysics Data System (ADS)

    Pokhrel, Yadu N.; Koirala, Sujan; Yeh, Pat J.-F.; Hanasaki, Naota; Longuevergne, Laurent; Kanae, Shinjiro; Oki, Taikan

    2015-01-01

    Observations indicate that groundwater levels are declining in many regions around the world. Simulating such depletion of groundwater at the global scale still remains a challenge because most global Land Surface Models (LSMs) lack the physical representation of groundwater dynamics in general and well pumping in particular. Here we present an integrated hydrologic model, which explicitly simulates groundwater dynamics and pumping within a global LSM that also accounts for human activities such as irrigation and reservoir operation. The model is used to simulate global water fluxes and storages with a particular focus on groundwater withdrawal and depletion in the High Plains Aquifer (HPA) and Central Valley Aquifer (CVA). Simulated global groundwater withdrawal and depletion for the year 2000 are 570 and 330 km3 yr-1, respectively; the depletion agrees better with observations than our previous model result without groundwater representation, but may still contain certain uncertainties and is on the higher side of other estimates. Groundwater withdrawals from the HPA and CVA are ˜22 and ˜9 km3 yr-1, respectively, which are also consistent with the observations of ˜24 and ˜13 km3 yr-1. The model simulates a significant decline in total terrestrial water storage in both regions as caused mainly by groundwater storage depletion. Groundwater table declined by ˜14 cm yr-1 in the HPA during 2003-2010; the rate is even higher (˜71 cm yr-1) in the CVA. These results demonstrate the potential of the developed model to study the dynamic relationship between human water use, groundwater storage, and the entire hydrologic cycle.

  12. Development of a used fuel cladding damage model incorporating circumferential and radial hydride responses

    NASA Astrophysics Data System (ADS)

    Chen, Qiushi; Ostien, Jakob T.; Hansen, Glen

    2014-04-01

    At the completion of the fuel drying process, used fuel Zry4 cladding typically exhibits a significant population of δ-hydride inclusions. These inclusions are in the form of small platelets that are generally oriented both circumferentially and radially within the cladding material. There is concern that radially-oriented hydride inclusions may weaken the cladding material and lead to issues during used fuel storage and transportation processes. A high fidelity model of the mechanical behavior of hydrides has utility in both designing fuel cladding to be more resistant to this hydride-induced weakening and also in suggesting modifications to drying, storage, and transport operations to reduce the impact of hydride formation and/or the avoidance of loading scenarios that could overly stress the radial inclusions. We develop a mechanical model for the Zry4-hydride system that, given a particular morphology of hydride inclusions, allows the calculation of the response of the hydrided cladding under various loading scenarios. The model treats the Zry4 matrix material as J2 elastoplastic, and treats the hydrides as platelets oriented in predefined directions (e.g., circumferentially and radially). The model is hosted by the Albany analysis framework, where a finite element approximation of the weak form of the cladding boundary value problem is solved using a preconditioned Newton-Krylov approach. Instead of forming the required system Jacobian operator directly or approximating its action with a differencing operation, Albany leverages the Trilinos Sacado package to form the Jacobian via automatic differentiation. We present results that describe the performance of the model in comparison with as-fabricated Zry4 as well as HB Robinson fuel cladding. Further, we also present performance results that demonstrate the efficacy of the overall solution method employed to host the model.

  13. Effect of Control-released Basic Fibroblast Growth Factor Incorporated in β-Tricalcium Phosphate for Murine Cranial Model

    PubMed Central

    Shimizu, Azusa; Tajima, Satoshi; Tobita, Morikuni; Tanaka, Rica; Tabata, Yasuhiko

    2014-01-01

    Background: β-Tricalcium phosphate (β-TCP) is used clinically as a bone substitute, but complete osteoinduction is slow. Basic fibroblast growth factor (bFGF) is important in bone regeneration, but the biological effects are very limited because of the short half-life of the free form. Incorporation in gelatin allows slow release of growth factors during degradation. The present study evaluated whether control-released bFGF incorporated in β-TCP can promote bone regeneration in a murine cranial defect model. Methods: Bilateral cranial defects of 4 mm in diameter were made in 10-week-old male Sprague-Dawley rats treated as follows: group 1, 20 μl saline as control; group 2, β-TCP disk in 20 μl saline; group 3, β-TCP disk in 50 μg bFGF solution; and group 4, β-TCP disk in 50 μg bFGF-containing gelatin hydrogel (n = 6 each). Histological and imaging analyses were performed at 1, 2, and 4 weeks after surgery. Results: The computed tomography value was lower in groups 3 and 4, whereas the rate of osteogenesis was higher histologically in group 4 than in the other groups. The appearance of tartrate-resistant acid phosphate–positive cells and osteocalcin-positive cells and disappearance of osteopontin-positive cells occurred earlier in group 4 than in the other groups. Conclusions: These findings suggest that control-released bFGF incorporated in β-TCP can accelerate bone regeneration in the murine cranial defect model and may be promising for the clinical treatment of cranial defects. PMID:25289319

  14. Absolute stability and Hopf bifurcation in a Plasmodium falciparum malaria model incorporating discrete immune response delay.

    PubMed

    Ncube, Israel

    2013-05-01

    We consider the absolute stability of the disease-free equilibrium of an intra-host Plasmodium falciparum malarial model allowing for antigenic variation within a single species. Antigenic variation can be viewed as an adaptation of the parasite to evade host defence [2]. The model was recently developed in [3-6]. The host's immune response is compartmentalised into reactions to major and minor epitopes. The immune response mounted by the human host is delayed, where, for simplicity, the delay is assumed to be discrete. We investigate the resulting characteristic equation, with a view to establishing absolute stability criteria and computing the Hopf bifurcation of the disease-free equilibrium.

  15. Incorporating photon recycling into the analytical drift-diffusion model of high efficiency solar cells

    SciTech Connect

    Lumb, Matthew P.; Steiner, Myles A.; Geisz, John F.; Walters, Robert J.

    2014-11-21

    The analytical drift-diffusion formalism is able to accurately simulate a wide range of solar cell architectures and was recently extended to include those with back surface reflectors. However, as solar cells approach the limits of material quality, photon recycling effects become increasingly important in predicting the behavior of these cells. In particular, the minority carrier diffusion length is significantly affected by the photon recycling, with consequences for the solar cell performance. In this paper, we outline an approach to account for photon recycling in the analytical Hovel model and compare analytical model predictions to GaAs-based experimental devices operating close to the fundamental efficiency limit.

  16. Process model for ammonia volatilization from anaerobic swine lagoons incorporating varying wind speeds and biogas bubbling

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ammonia volatilization from treatment lagoons varies widely with the total ammonia concentration, pH, temperature, suspended solids, atmospheric ammonia concentration above the water surface, and wind speed. Ammonia emissions were estimated with a process-based mechanistic model integrating ammonia ...

  17. A Model for Incorporating Content on Aging into the Curriculum: K-12.

    ERIC Educational Resources Information Center

    Blackwell, David L.; Hunt, Sara Stockard

    Following a statement of the problem of putting aging education in the elementary secondary curriculum, and a review of the relevant literature, a model for developing a curriculum on aging is presented. An overview of the 3-year project, developed in Baton Rouge, Louisiana schools for grades K-12, is offered, including activities and yearly…

  18. Numerical Computation of a Continuous-thrust State Transition Matrix Incorporating Accurate Hardware and Ephemeris Models

    NASA Technical Reports Server (NTRS)

    Ellison, Donald; Conway, Bruce; Englander, Jacob

    2015-01-01

    A significant body of work exists showing that providing a nonlinear programming (NLP) solver with expressions for the problem constraint gradient substantially increases the speed of program execution and can also improve the robustness of convergence, especially for local optimizers. Calculation of these derivatives is often accomplished through the computation of spacecraft's state transition matrix (STM). If the two-body gravitational model is employed as is often done in the context of preliminary design, closed form expressions for these derivatives may be provided. If a high fidelity dynamics model, that might include perturbing forces such as the gravitational effect from multiple third bodies and solar radiation pressure is used then these STM's must be computed numerically. We present a method for the power hardward model and a full ephemeris model. An adaptive-step embedded eight order Dormand-Prince numerical integrator is discussed and a method for the computation of the time of flight derivatives in this framework is presented. The use of these numerically calculated derivatieves offer a substantial improvement over finite differencing in the context of a global optimizer. Specifically the inclusion of these STM's into the low thrust missiondesign tool chain in use at NASA Goddard Spaceflight Center allows for an increased preliminary mission design cadence.

  19. A Probabilistic Model of Visual Working Memory: Incorporating Higher Order Regularities into Working Memory Capacity Estimates

    ERIC Educational Resources Information Center

    Brady, Timothy F.; Tenenbaum, Joshua B.

    2013-01-01

    When remembering a real-world scene, people encode both detailed information about specific objects and higher order information like the overall gist of the scene. However, formal models of change detection, like those used to estimate visual working memory capacity, assume observers encode only a simple memory representation that includes no…

  20. Scale and hierarchical relationships when incorporating observed data into fish models

    EPA Science Inventory

    Identifying correlations between environmental variables and fish presence or density is usually the main focus of efforts to model fish-habitat relationships. These relationships, however, can be confounded by scale and hierarchical effects. In particular the strength of fish –...

  1. A dimensional model of personality disorder: incorporating DSM Cluster A characteristics.

    PubMed

    Tackett, Jennifer L; Silberschmidt, Amy L; Krueger, Robert F; Sponheim, Scott R

    2008-05-01

    The authors articulate an expanded dimensional model of personality pathology to better account for symptoms of DSM-defined Cluster A personality disorders. Two hundred forty participants (98 first-degree relatives of probands with schizophrenia or schizoaffective disorder, 92 community control participants, and 50 first-degree relatives of probands with bipolar disorder) completed a dimensional personality pathology questionnaire, a measure of schizotypal characteristics, and Chapman measures of psychosis proneness. Scales from all questionnaires were subjected to an exploratory factor analysis with varimax rotation. A 5-factor structure of personality pathology emerged from the analyses, with Peculiarity forming an additional factor to the common 4-factor structure of personality pathology (consisting of Introversion, Emotional Dysregulation, Antagonism, and Compulsivity). These results support a 5-factor dimensional model of personality pathology that better accounts for phenomena encompassed by the Cluster A personality disorders in DSM-IV-TR (4th ed., text revised; American Psychiatric Association, 2000). This study has implications for the consideration of a dimensional model of personality disorder in DSM-V by offering a more comprehensive structural model that builds on previous work in this area.

  2. Incorporating Artificial Neural Networks in the dynamic thermal-hydraulic model of a controlled cryogenic circuit

    NASA Astrophysics Data System (ADS)

    Carli, S.; Bonifetto, R.; Savoldi, L.; Zanino, R.

    2015-09-01

    A model based on Artificial Neural Networks (ANNs) is developed for the heated line portion of a cryogenic circuit, where supercritical helium (SHe) flows and that also includes a cold circulator, valves, pipes/cryolines and heat exchangers between the main loop and a saturated liquid helium (LHe) bath. The heated line mimics the heat load coming from the superconducting magnets to their cryogenic cooling circuits during the operation of a tokamak fusion reactor. An ANN is trained, using the output from simulations of the circuit performed with the 4C thermal-hydraulic (TH) code, to reproduce the dynamic behavior of the heated line, including for the first time also scenarios where different types of controls act on the circuit. The ANN is then implemented in the 4C circuit model as a new component, which substitutes the original 4C heated line model. For different operational scenarios and control strategies, a good agreement is shown between the simplified ANN model results and the original 4C results, as well as with experimental data from the HELIOS facility confirming the suitability of this new approach which, extended to an entire magnet systems, can lead to real-time control of the cooling loops and fast assessment of control strategies for heat load smoothing to the cryoplant.

  3. Incorporating genomic information and predicting gene expression patterns in a simplified biogeochemical model

    NASA Astrophysics Data System (ADS)

    Wang, P.; Burd, A. B.; Moran, M. A.; Hood, R. R.; Coles, V. J.; Yager, P. L.

    2013-01-01

    We present results from a new marine plankton model that combines selective biogeochemical processes with genetic information. The model allows for phytoplankton to adapt to a changing environment by invoking different utilization pathways for acquisition of nutrients (nitrogen and phosphorus) in response to concentration changes. The simulations use simplified environmental conditions represented by a continuously stirred tank reactor, which is populated by 96 different types of phytoplankton that differ in their physiological characteristics and nutrient uptake/metabolism genes. The results show that the simulated phytoplankton community structure is conceptually consistent with observed regional and global phytoplankton biogeography, the genome content from the dominant types of phytoplankton reflects the imposed environmental constraints, and the transcription of the gene clusters is qualitatively simulated according to the environmental changes. The model shows the feasibility of including genomic knowledge into a biogeochemical model and is suited to understanding and predicting changes in marine microbial community structure and function, and to simulating the biological response to rapid environmental changes.

  4. Teaching Note--Incorporating Journal Clubs into Social Work Education: An Exploratory Model

    ERIC Educational Resources Information Center

    Moore, Megan; Fawley-King, Kya; Stone, Susan I.; Accomazzo, Sarah M.

    2013-01-01

    This article outlines the implementation of a journal club for master's and doctoral social work students interested in mental health practice. It defines educational journal clubs and discusses the history of journal clubs in medical education and the applicability of the model to social work education. The feasibility of implementing…

  5. Incorporating Biological, Chemical and Toxicological Knowledge into Predictive Models of Toxicity: Letter to the Editor

    EPA Science Inventory

    Thomas et al. (2012) recently published an evaluation of statistical models for classifying in vivo toxicity endpoints from ToxRefDB (Knudsen et al. 2009; Martin et al. 2009a and 2009b) using ToxCast in vitro bioactivity data (Judson et al. 2010) and chemical structure descriptor...

  6. Incorporating Retention Time to Refine Models Predicting Thermal Regimes of Stream Networks Across New England

    EPA Science Inventory

    Thermal regimes are a critical factor in models predicting effects of watershed management activities on fish habitat suitability. We have assembled a database of lotic temperature time series across New England (> 7000 station-year combinations) from state and Federal data s...

  7. A Theory and Model of Conflict Detection in Air Traffic Control: Incorporating Environmental Constraints

    ERIC Educational Resources Information Center

    Loft, Shayne; Bolland, Scott; Humphreys, Michael S.; Neal, Andrew

    2009-01-01

    A performance theory for conflict detection in air traffic control is presented that specifies how controllers adapt decisions to compensate for environmental constraints. This theory is then used as a framework for a model that can fit controller intervention decisions. The performance theory proposes that controllers apply safety margins to…

  8. Teaching for Art Criticism: Incorporating Feldman's Critical Analysis Learning Model in Students' Studio Practice

    ERIC Educational Resources Information Center

    Subramaniam, Maithreyi; Hanafi, Jaffri; Putih, Abu Talib

    2016-01-01

    This study adopted 30 first year graphic design students' artwork, with critical analysis using Feldman's model of art criticism. Data were analyzed quantitatively; descriptive statistical techniques were employed. The scores were viewed in the form of mean score and frequencies to determine students' performances in their critical ability.…

  9. Incorporating Stakeholder Decision Support Needs into an Integrated Regional Earth System Model

    SciTech Connect

    Rice, Jennie S.; Moss, Richard H.; Runci, Paul J.; Anderson, K. L.; Malone, Elizabeth L.

    2012-03-21

    A new modeling effort exploring the opportunities, constraints, and interactions between mitigation and adaptation at regional scale is utilizing stakeholder engagement in an innovative approach to guide model development and demonstration, including uncertainty characterization, to effectively inform regional decision making. This project, the integrated Regional Earth System Model (iRESM), employs structured stakeholder interactions and literature reviews to identify the most relevant adaptation and mitigation alternatives and decision criteria for each regional application of the framework. The information is used to identify important model capabilities and to provide a focus for numerical experiments. This paper presents the stakeholder research results from the first iRESM pilot region. The pilot region includes the Great Lakes Basin in the Midwest portion of the United States as well as other contiguous states. This geographic area (14 states in total) permits cohesive modeling of hydrologic systems while also providing gradients in climate, demography, land cover/land use, and energy supply and demand. The results from the stakeholder research indicate that iRESM should prioritize addressing adaptation alternatives in the water resources, urban infrastructure, and agriculture sectors, such as water conservation, expanded water quality monitoring, altered reservoir releases, lowered water intakes, urban infrastructure upgrades, increased electric power reserves in urban areas, and land use management/crop selection changes. Regarding mitigation alternatives, the stakeholder research shows a need for iRESM to focus on policies affecting the penetration of renewable energy technologies, and the costs and effectiveness of energy efficiency, bioenergy production, wind energy, and carbon capture and sequestration.

  10. Incorporating Stage-Specific Drug Action into Pharmacological Modeling of Antimalarial Drug Treatment

    PubMed Central

    2016-01-01

    Pharmacological modeling of antiparasitic treatment based on a drug's pharmacokinetic and pharmacodynamic properties plays an increasingly important role in identifying optimal drug dosing regimens and predicting their potential impact on control and elimination programs. Conventional modeling of treatment relies on methods that do not distinguish between parasites at different developmental stages. This is problematic for malaria parasites, as their sensitivity to drugs varies substantially during their 48-h developmental cycle. We investigated four drug types (short or long half-lives with or without stage-specific killing) to quantify the accuracy of the standard methodology. The treatment dynamics of three drug types were well characterized with standard modeling. The exception were short-half-life drugs with stage-specific killing (i.e., artemisinins) because, depending on time of treatment, parasites might be in highly drug-sensitive stages or in much less sensitive stages. We describe how to bring such drugs into pharmacological modeling by including additional variation into the drug's maximal killing rate. Finally, we show that artemisinin kill rates may have been substantially overestimated in previous modeling studies because (i) the parasite reduction ratio (PRR) (generally estimated to be 104) is based on observed changes in circulating parasite numbers, which generally overestimate the “true” PRR, which should include both circulating and sequestered parasites, and (ii) the third dose of artemisinin at 48 h targets exactly those stages initially hit at time zero, so it is incorrect to extrapolate the PRR measured over 48 h to predict the impact of doses at 48 h and later. PMID:26902760

  11. The three-dimensional global numerical model CHARM-I: The incorporation of processes in the ionospheric D-region

    NASA Astrophysics Data System (ADS)

    Krivolutsky, A. A.; Cherepanova, L. A.; V'yushkova, T. Yu.; Repnev, A. I.

    2015-07-01

    We describe the three-dimensional numerical global photochemical model CHARM-I (CHemical Atmospheric Research Model with Ions) and the results of numerical calculations of global distributions of neutral and charged atmospheric trace gases (in the height range of up to 90 km), such as ozone, nitrogen oxides, electrons, and positive and negative ions. This model is an improved version of the CHARM three-dimensional photochemical model of neutral components with additional reactions with the involvement of ions (a total of 200 photochemical reactions). The model incorporates UV-radiation fluxes on the Lyman-α line and galactic cosmic rays as ionizing factors. The neutral components are calculated with the method of "chemical families" and the concentrations of charged components are calculated by the electroneutrality condition at each time step. The spatial transport of chemically active species is described in the model by the Prather scheme. The developed model makes it also possible to take into account solar flares and particle precipitations in the ionospheric D-region.

  12. Incorporating imperfect detection into joint models of communites: A response to Warton et al.

    USGS Publications Warehouse

    Beissinger, Steven R.; Iknayan, Kelly J.; Guillera-Arroita, Gurutzeta; Zipkin, Elise; Dorazio, Robert; Royle, Andy; Kery, Marc

    2016-01-01

    Warton et al. [1] advance community ecology by describing a statistical framework that can jointly model abundances (or distributions) across many taxa to quantify how community properties respond to environmental variables. This framework specifies the effects of both measured and unmeasured (latent) variables on the abundance (or occurrence) of each species. Latent variables are random effects that capture the effects of both missing environmental predictors and correlations in parameter values among different species. As presented in Warton et al., however, the joint modeling framework fails to account for the common problem of detection or measurement errors that always accompany field sampling of abundance or occupancy, and are well known to obscure species- and community-level inferences.

  13. SAI (Systems Applications, Incorporated) airshed model operations manuals. Volume 2: Systems manual

    NASA Astrophysics Data System (ADS)

    Ames, J.; Hayes, S. R.; Myers, T. C.; Whitney, D. C.

    1985-04-01

    The SAI Airshed Model System is described fro a programmer's point of view. Included are discussions of all subroutines and how they fit together, run-time core allocation techniques, internal methods of segment handling using secondary storage, and detailed definitions of the structure of each file in the ystem. This manual also includes suggestions for implementing the programs on different computers. The SAI Airshed Model System consists of 17 programs that communicate with each other through 17; data files; both the programs and files are described in detail in this manual. An overview briefly describing the programs used to perform each of the five system functions is presented. Guidelines for implementing the programs, detailed descriptions of the programs by function, including hierarchical subroutine tables and short module descriptions, and detailed file structure definitions for each file in the system are given.

  14. A sliding microtubule model incorporating axonemal twist and compatible with three-dimensional ciliary bending.

    PubMed

    Holwill, M E; Cohen, H J; Satir, P

    1979-02-01

    1. Equations are developed to calculate the relative displacements of the doublet microtubules at the tip of a cilium when the microtubules twist about the axis of the organelle. 2. Displacements measured from electron micrographs show asymmetry (or skew) which can be matched quantitatively by the theoretical model with the appropriate selection of twist angle and orientation of the axoneme with respect to the plane of beat. 3. For Elliptio cilia the experimental results are consistent with a planar effective stroke and a recovery stroke involving a three-dimensional bend. The plane of the effective stroke is not normal to a surface containing the central pair of microtubules but contains microtubule 2 to produce the observed skew. 4. This model for the beat also explains the range of orientations of axoneme observed in sections through the metachronal wave.

  15. Time dependent reliability model incorporating continuum damage mechanics for high-temperature ceramics

    NASA Technical Reports Server (NTRS)

    Duffy, Stephen F.; Gyekenyesi, John P.

    1989-01-01

    Presently there are many opportunities for the application of ceramic materials at elevated temperatures. In the near future ceramic materials are expected to supplant high temperature metal alloys in a number of applications. It thus becomes essential to develop a capability to predict the time-dependent response of these materials. The creep rupture phenomenon is discussed, and a time-dependent reliability model is outlined that integrates continuum damage mechanics principles and Weibull analysis. Several features of the model are presented in a qualitative fashion, including predictions of both reliability and hazard rate. In addition, a comparison of the continuum and the microstructural kinetic equations highlights a strong resemblance in the two approaches.

  16. Finite-volume model for chemical vapor infiltration incorporating radiant heat transfer. Interim report

    SciTech Connect

    Smith, A.W.; Starr, T.L.

    1995-05-01

    Most finite-volume thermal models account for the diffusion and convection of heat and may include volume heating. However, for certain simulation geometries, a large percentage of heat flux is due to thermal radiation. In this paper a finite-volume computational procedure for the simulation of heat transfer by conduction, convection and radiation in three dimensional complex enclosures is developed. The radiant heat transfer is included as a source term in each volume element which is derived by Monte Carlo ray tracing from all possible radiating and absorbing faces. The importance of radiative heat transfer is illustrated in the modeling of chemical vapor infiltration (CVI) of tubes. The temperature profile through the tube preform matches experimental measurements only when radiation is included. An alternative, empirical approach using an {open_quotes}effective{close_quotes} thermal conductivity for the gas space can match the initial temperature profile but does not match temperature changes that occur during preform densification.

  17. Towards an improvement of carbon accounting for wildfires: incorporation of charcoal production into carbon emission models

    NASA Astrophysics Data System (ADS)

    Doerr, Stefan H.; Santin, Cristina; de Groot, Bill

    2015-04-01

    Every year fires release to the atmosphere the equivalent to 20-30% of the carbon (C) emissions from fossil fuel consumption, with future emissions from wildfires expected to increase under a warming climate. Critically, however, part of the biomass C affected by fire is not emitted during burning, but converted into charcoal, which is very resistant to environmental degradation and, thus, contributes to long-term C sequestration. The magnitude of charcoal production from wildfires as a long-term C sink remains essentially unknown and, to the date, charcoal production has not been included in wildfire emission and C budget models. Here we present complete inventories of charcoal production in two fuel-rich, but otherwise very different ecosystems: i) a boreal conifer forest (experimental stand-replacing crown fire; Canada, 2012) and a dry eucalyptus forest (high-intensity fuel reduction burn; Australia 2014). Our data show that, when considering all the fuel components and quantifying all the charcoal produced from each (i.e. bark, dead wood debris, fine fuels), the overall amount of charcoal produced is significant: up to a third of the biomass C affected by fire. These findings indicate that charcoal production from wildfires could represent a major and currently unaccounted error in the estimation of the effects of wildfires in the global C balance. We suggest an initial approach to include charcoal production in C emission models, by using our case study of a boreal forest fire and the Canadian Fire Effects Model (CanFIRE). We also provide recommendations of how a 'conversion factor' for charcoal production could be relatively easily estimated when emission factors for different types of fuels and fire conditions are experimentally obtained. Ultimately, this presentation is a call for integrative collaboration between the fire emission modelling community and the charcoal community to work together towards the improvement of C accounting for wildfires.

  18. Incorporating biologically based models into assessments of risk from chemical contaminants

    NASA Technical Reports Server (NTRS)

    Bull, R. J.; Conolly, R. B.; De Marini, D. M.; MacPhail, R. C.; Ohanian, E. V.; Swenberg, J. A.

    1993-01-01

    The general approach to assessment of risk from chemical contaminants in drinking water involves three steps: hazard identification, exposure assessment, and dose-response assessment. Traditionally, the risks to humans associated with different levels of a chemical have been derived from the toxic responses observed in animals. It is becoming increasingly clear, however, that further information is needed if risks to humans are to be assessed accurately. Biologically based models help clarify the dose-response relationship and reduce uncertainty.

  19. Terrestrial Feedbacks Incorporated in Global Vegetation Models through Observed Trait-Environment Responses

    NASA Astrophysics Data System (ADS)

    Bodegom, P. V.

    2015-12-01

    Most global vegetation models used to evaluate climate change impacts rely on plant functional types to describe vegetation responses to environmental stresses. In a traditional set-up in which vegetation characteristics are considered constant within a vegetation type, the possibility to implement and infer feedback mechanisms are limited as feedback mechanisms will likely involve a changing expression of community trait values. Based on community assembly concepts, we implemented functional trait-environment relationships into a global dynamic vegetation model to quantitatively assess this feature. For the current climate, a different global vegetation distribution was calculated with and without the inclusion of trait variation, emphasizing the importance of feedbacks -in interaction with competitive processes- for the prevailing global patterns. These trait-environmental responses do, however, not necessarily imply adaptive responses of vegetation to changing conditions and may locally lead to a faster turnover in vegetation upon climate change. Indeed, when running climate projections, simulations with trait variation did not yield a more stable or resilient vegetation than those without. Through the different feedback expressions, global and regional carbon and water fluxes were -however- strongly altered. At a global scale, model projections suggest an increased productivity and hence an increased carbon sink in the next decades to come, when including trait variation. However, by the end of the century, a reduced carbon sink is projected. This effect is due to a downregulation of photosynthesis rates, particularly in the tropical regions, even when accounting for CO2-fertilization effects. Altogether, the various global model simulations suggest the critical importance of including vegetation functional responses to changing environmental conditions to grasp terrestrial feedback mechanisms at global scales in the light of climate change.

  20. A microstructurally based continuum model of cartilage viscoelasticity and permeability incorporating measured statistical fiber orientations.

    PubMed

    Pierce, David M; Unterberger, Michael J; Trobin, Werner; Ricken, Tim; Holzapfel, Gerhard A

    2016-02-01

    The remarkable mechanical properties of cartilage derive from an interplay of isotropically distributed, densely packed and negatively charged proteoglycans; a highly anisotropic and inhomogeneously oriented fiber network of collagens; and an interstitial electrolytic fluid. We propose a new 3D finite strain constitutive model capable of simultaneously addressing both solid (reinforcement) and fluid (permeability) dependence of the tissue's mechanical response on the patient-specific collagen fiber network. To represent fiber reinforcement, we integrate the strain energies of single collagen fibers-weighted by an orientation distribution function (ODF) defined over a unit sphere-over the distributed fiber orientations in 3D. We define the anisotropic intrinsic permeability of the tissue with a structure tensor based again on the integration of the local ODF over all spatial fiber orientations. By design, our modeling formulation accepts structural data on patient-specific collagen fiber networks as determined via diffusion tensor MRI. We implement our new model in 3D large strain finite elements and study the distributions of interstitial fluid pressure, fluid pressure load support and shear stress within a cartilage sample under indentation. Results show that the fiber network dramatically increases interstitial fluid pressure and focuses it near the surface. Inhomogeneity in the tissue's composition also increases fluid pressure and reduces shear stress in the solid. Finally, a biphasic neo-Hookean material model, as is available in commercial finite element codes, does not capture important features of the intra-tissue response, e.g., distributions of interstitial fluid pressure and principal shear stress. PMID:26001349

  1. Incorporation of Advanced Activation Treatments into CESM/CAM5: Model Evaluation and Impacts on Aerosol Indirect Forcing

    NASA Astrophysics Data System (ADS)

    Gantt, B.; He, J.; Zhang, X.; Zhang, Y.; Nenes, A.

    2013-12-01

    One of the greatest sources of uncertainty in climate science is the influence of aerosols on clouds through indirect effects, especially processes affecting the activation of aerosols into cloud droplets. Aerosol activation parameterizations incorporate much of the complexity of these processes, but the small differences between parameterizations can have a large impact on the spatiotemporal distribution of activated aerosols and the resulting cloud properties. Currently, most models simulate aerosol activation using the Abdul-Razzak and Ghan [2000] (AR-G00) scheme which derives an empiric calculation of the maximum parcel supersaturation based on the regression of numerical parcel calculations. The Community Atmosphere Model version 5.1.1 within the Community Earth Systems Model version 1.0.5 (CESM/CAM5) is an online-coupled Earth Systems model that simulates the interactions among aerosols, clouds, and radiation. CESM/CAM5 uses the AR-G00 scheme to simulate aerosol activation. In this work, we update CESM/CAM5 by incorporating a series of explicit aerosol activation schemes (Fountoukis and Nenes [2005]; Barahona and Nenes [2007]; Kumar et al. [2009]; and Barahona et al. [2010]) which account for the impacts of insoluble aerosol adsorption, giant cloud condensation nuclei activation kinetics, and entrainment on cloud droplet number concentrations (CDNC). CESM/CAM5 results with the empiric and explicit aerosol activation schemes are evaluated against several global datasets including observed low-level CDNC and satellite-derived cloud optical thickness (COT), liquid water path (LWP), and shortwave cloud forcing (SWCF). Globally, the incorporation of all explicit schemes leads to an average increase in column CDNC of 155%, increase (more negative) in SWCF of 13%, and decrease in surface shortwave radiation of -4%. In terms of climate impacts, these schemes result in an annual mean decrease in surface temperature and precipitation of -0.9 K (~0.2%) and -0.04 mm day

  2. Incorporating single-side sparing in models for predicting parotid dose sparing in head and neck IMRT

    SciTech Connect

    Yuan, Lulin Wu, Q. Jackie; Yin, Fang-Fang; Yoo, David; Jiang, Yuliang; Ge, Yaorong

    2014-02-15

    Purpose: Sparing of single-side parotid gland is a common practice in head-and-neck (HN) intensity modulated radiation therapy (IMRT) planning. It is a special case of dose sparing tradeoff between different organs-at-risk. The authors describe an improved mathematical model for predicting achievable dose sparing in parotid glands in HN IMRT planning that incorporates single-side sparing considerations based on patient anatomy and learning from prior plan data. Methods: Among 68 HN cases analyzed retrospectively, 35 cases had physician prescribed single-side parotid sparing preferences. The single-side sparing model was trained with cases which had single-side sparing preferences, while the standard model was trained with the remainder of cases. A receiver operating characteristics (ROC) analysis was performed to determine the best criterion that separates the two case groups using the physician's single-side sparing prescription as ground truth. The final predictive model (combined model) takes into account the single-side sparing by switching between the standard and single-side sparing models according to the single-side sparing criterion. The models were tested with 20 additional cases. The significance of the improvement of prediction accuracy by the combined model over the standard model was evaluated using the Wilcoxon rank-sum test. Results: Using the ROC analysis, the best single-side sparing criterion is (1) the predicted median dose of one parotid is higher than 24 Gy; and (2) that of the other is higher than 7 Gy. This criterion gives a true positive rate of 0.82 and a false positive rate of 0.19, respectively. For the bilateral sparing cases, the combined and the standard models performed equally well, with the median of the prediction errors for parotid median dose being 0.34 Gy by both models (p = 0.81). For the single-side sparing cases, the standard model overestimates the median dose by 7.8 Gy on average, while the predictions by the combined

  3. Finite Element Surface Registration Incorporating Curvature, Volume Preservation, and Statistical Model Information

    PubMed Central

    Lüthi, Marcel; Vetter, Thomas

    2013-01-01

    We present a novel method for nonrigid registration of 3D surfaces and images. The method can be used to register surfaces by means of their distance images, or to register medical images directly. It is formulated as a minimization problem of a sum of several terms representing the desired properties of a registration result: smoothness, volume preservation, matching of the surface, its curvature, and possible other feature images, as well as consistency with previous registration results of similar objects, represented by a statistical deformation model. While most of these concepts are already known, we present a coherent continuous formulation of these constraints, including the statistical deformation model. This continuous formulation renders the registration method independent of its discretization. The finite element discretization we present is, while independent of the registration functional, the second main contribution of this paper. The local discontinuous Galerkin method has not previously been used in image registration, and it provides an efficient and general framework to discretize each of the terms of our functional. Computational efficiency and modest memory consumption are achieved thanks to parallelization and locally adaptive mesh refinement. This allows for the first time the use of otherwise prohibitively large 3D statistical deformation models. PMID:24187581

  4. Finite element surface registration incorporating curvature, volume preservation, and statistical model information.

    PubMed

    Albrecht, Thomas; Dedner, Andreas; Lüthi, Marcel; Vetter, Thomas

    2013-01-01

    We present a novel method for nonrigid registration of 3D surfaces and images. The method can be used to register surfaces by means of their distance images, or to register medical images directly. It is formulated as a minimization problem of a sum of several terms representing the desired properties of a registration result: smoothness, volume preservation, matching of the surface, its curvature, and possible other feature images, as well as consistency with previous registration results of similar objects, represented by a statistical deformation model. While most of these concepts are already known, we present a coherent continuous formulation of these constraints, including the statistical deformation model. This continuous formulation renders the registration method independent of its discretization. The finite element discretization we present is, while independent of the registration functional, the second main contribution of this paper. The local discontinuous Galerkin method has not previously been used in image registration, and it provides an efficient and general framework to discretize each of the terms of our functional. Computational efficiency and modest memory consumption are achieved thanks to parallelization and locally adaptive mesh refinement. This allows for the first time the use of otherwise prohibitively large 3D statistical deformation models.

  5. Incorporating level set methods in Geographical Information Systems (GIS) for land-surface process modeling

    NASA Astrophysics Data System (ADS)

    Pullar, D.

    2005-08-01

    Land-surface processes include a broad class of models that operate at a landscape scale. Current modelling approaches tend to be specialised towards one type of process, yet it is the interaction of processes that is increasing seen as important to obtain a more integrated approach to land management. This paper presents a technique and a tool that may be applied generically to landscape processes. The technique tracks moving interfaces across landscapes for processes such as water flow, biochemical diffusion, and plant dispersal. Its theoretical development applies a Lagrangian approach to motion over a Eulerian grid space by tracking quantities across a landscape as an evolving front. An algorithm for this technique, called level set method, is implemented in a geographical information system (GIS). It fits with a field data model in GIS and is implemented as operators in map algebra. The paper describes an implementation of the level set methods in a map algebra programming language, called MapScript, and gives example program scripts for applications in ecology and hydrology.

  6. A partition-based active contour model incorporating local information for image segmentation.

    PubMed

    Shi, Jiao; Wu, Jiaji; Paul, Anand; Jiao, Licheng; Gong, Maoguo

    2014-01-01

    Active contour models are always designed on the assumption that images are approximated by regions with piecewise-constant intensities. This assumption, however, cannot be satisfied when describing intensity inhomogeneous images which frequently occur in real world images and induced considerable difficulties in image segmentation. A milder assumption that the image is statistically homogeneous within different local regions may better suit real world images. By taking local image information into consideration, an enhanced active contour model is proposed to overcome difficulties caused by intensity inhomogeneity. In addition, according to curve evolution theory, only the region near contour boundaries is supposed to be evolved in each iteration. We try to detect the regions near contour boundaries adaptively for satisfying the requirement of curve evolution theory. In the proposed method, pixels within a selected region near contour boundaries have the opportunity to be updated in each iteration, which enables the contour to be evolved gradually. Experimental results on synthetic and real world images demonstrate the advantages of the proposed model when dealing with intensity inhomogeneity images.

  7. Incorporating temporal heterogeneity in environmental conditions into a somatic growth model

    USGS Publications Warehouse

    Dzul, Maria C.; Yackulic, Charles B.; Korman, Josh; Yard, Michael D.; Muehlbauer, Jeffrey D.

    2016-01-01

    Evaluating environmental effects on fish growth can be challenging because environmental conditions may vary at relatively fine temporal scales compared to sampling occasions. Here we develop a Bayesian state-space growth model to evaluate effects of monthly environmental data on growth of fish that are observed less frequently (e.g., from mark-recapture data where time between captures can range from months to years). We assess effects of temperature, turbidity duration, food availability, flow variability, and trout abundance on subadult humpback chub (Gila cypha) growth in two rivers, the Colorado River (CR) and the Little Colorado River (LCR), and we use out-of-sample prediction to rank competing models. Environmental covariates explained a high proportion of the variation in growth in both rivers; however, the best growth models were river-specific and included either positive temperature and turbidity duration effects (CR) or positive temperature and food availability effects (LCR). Our approach to analyzing environmental controls on growth should be applicable in other systems where environmental data vary over relatively short time scales compared to animal observations.

  8. Incorporation of SemiSpan SuperSonic Transport (S4T) Aeroservoelastic Models into SAREC-ASV Simulation

    NASA Technical Reports Server (NTRS)

    Christhilf, David M.; Pototzky, Anthony S.; Stevens, William L.

    2010-01-01

    The Simulink-based Simulation Architecture for Evaluating Controls for Aerospace Vehicles (SAREC-ASV) was modified to incorporate linear models representing aeroservoelastic characteristics of the SemiSpan SuperSonic Transport (S4T) wind-tunnel model. The S4T planform is for a Technology Concept Aircraft (TCA) design from the 1990s. The model has three control surfaces and is instrumented with accelerometers and strain gauges. Control laws developed for wind-tunnel testing for Ride Quality Enhancement, Gust Load Alleviation, and Flutter Suppression System functions were implemented in the simulation. The simulation models open- and closed-loop response to turbulence and to control excitation. It provides time histories for closed-loop stable conditions above the open-loop flutter boundary. The simulation is useful for assessing the potential impact of closed-loop control rate and position saturation. It also provides a means to assess fidelity of system identification procedures by providing time histories for a known plant model, with and without unmeasured turbulence as a disturbance. Sets of linear models representing different Mach number and dynamic pressure conditions were implemented as MATLAB Linear Time Invariant (LTI) objects. Configuration changes were implemented by selecting which LTI object to use in a Simulink template block. A limited comparison of simulation versus wind-tunnel results is shown.

  9. Incorporating Satellite Remote Sensing Data into Hydrologic Models: Towards Improved Performance in Modeling the Past and Reduced Uncertainty in Predicting the Future

    NASA Astrophysics Data System (ADS)

    Parr, D.; Wang, G.

    2014-12-01

    In many regions of the worlds, studies of past hydrological variability have to rely on hydrological models either because river gauge measurement is not available or because measurements do not reflect the natural flow due to water diversion or reservoir regulation. However, results from these studies are subject to major uncertainty related to the challenges in quantifying vegetation conditions and evapotranspiration, both of which are important for surface water and energy budgets. This study incorporates satellite remote sensing data for ET and vegetation into the VIC model to improve the model performance in simulating the surface water budget, hydrological seasonality, and timing of hydrological extremes. Using the Connecticut River Basin as an example, and driven with the NASA NLDAS-2 meteorological forcing data, the VIC model has been modified to read in LAI and ET data derived from MODIS among others. The MODIS LAI data provides VIC with the inter-annually varying seasonal cycle of vegetation, and the MODIS ET data replaces the model simulated ET. The data-enhanced model performs significantly better in simulating river discharge, its magnitude, seasonality, timing, soil moisture and its temporal variation. Incorporation of the ET data led to an increase of stream flow correlations between model and observations on the daily and biweekly temporal scales, and the seasonality is better represented on a monthly scale with particular magnitude improvements during the summer when ET is greatest. Incorporation of the LAI data led to improved simulation of inter-annual variability. This joint application of remote sensing and modeling helps quantify the extent to which remote sensing data improves model performance, facilitates a more accurate understanding and attribution of past hydrological variability/changes, and helps characterize the range of model-related uncertainties in future predictions.

  10. Improving Public Health DSSs by Including Saharan Dust Forecasts Through Incorporation of NASA's GOCART Model Results

    NASA Technical Reports Server (NTRS)

    Berglund, Judith

    2007-01-01

    Approximately 2-3 billion metric tons of soil dust are estimated to be transported in the Earth's atmosphere each year. Global transport of desert dust is believed to play an important role in many geochemical, climatological, and environmental processes. This dust carries minerals and nutrients, but it has also been shown to carry pollutants and viable microorganisms capable of harming human, animal, plant, and ecosystem health. Saharan dust, which impacts the eastern United States (especially Florida and the southeast) and U.S. Territories in the Caribbean primarily during the summer months, has been linked to increases in respiratory illnesses in this region and has been shown to carry other human, animal, and plant pathogens. For these reasons, this candidate solution recommends integrating Saharan dust distribution and concentration forecasts from the NASA GOCART global dust cycle model into a public health DSS (decision support system), such as the CDC's (Centers for Disease Control and Prevention's) EPHTN (Environmental Public Health Tracking Network), for the eastern United States and Caribbean for early warning purposes regarding potential increases in respiratory illnesses or asthma attacks, potential disease outbreaks, or bioterrorism. This candidate solution pertains to the Public Health National Application but also has direct connections to Air Quality and Homeland Security. In addition, the GOCART model currently uses the NASA MODIS aerosol product as an input and uses meteorological forecasts from the NASA GEOS-DAS (Goddard Earth Observing System Data Assimilation System) GEOS-4 AGCM. In the future, VIIRS aerosol products and perhaps CALIOP aerosol products could be assimilated into the GOCART model to improve the results.

  11. A 3-D probabilistic stability model incorporating the variability of root reinforcement

    NASA Astrophysics Data System (ADS)

    Cislaghi, Alessio; Chiaradia, Enrico; Battista Bischetti, Gian

    2016-04-01

    Process-oriented models of hillslope stability have a great potentiality to improve spatially-distributed landslides hazard analyses. At the same time, they may have severe limitations and among them the variability and uncertainty of the parameters play a key role. In this context, the application of a probabilistic approach through Monte Carlo techniques can be the right practice to deal with the variability of each input parameter by considering a proper probability distribution. In forested areas an additional point must be taken into account: the reinforcement due to roots permeating the soil and its variability and uncertainty. While the probability distributions of geotechnical and hydrological parameters have been widely investigated, little is known concerning the variability and the spatial heterogeneity of root reinforcement. Moreover, there are still many difficulties in measuring and in evaluating such a variable. In our study we aim to: i) implement a robust procedure to evaluate the variability of root reinforcement as a probabilistic distribution, according to the stand characteristics of forests, such as the trees density, the average diameter at breast height, the minimum distance among trees, and (ii) combine a multidimensional process-oriented model with a Monte Carlo Simulation technique, to obtain a probability distribution of the Factor of Safety. The proposed approach has been applied to a small Alpine area, mainly covered by a coniferous forest and characterized by steep slopes and a high landslide hazard. The obtained results show a good reliability of the model according to the landslide inventory map. At the end, our findings contribute to improve the reliability of landslide hazard mapping in forested areas and help forests managers to evaluate different management scenarios.

  12. Approximate solution of a model of biological immune responses incorporating delay.

    PubMed

    Fowler, A C

    1981-01-01

    A model of the humoral immune response, proposed by Dibrov, Livshits and Volkenstein (1977b), in which the antibody production by a constant target cell population depends on the antigenic stimulation at earlier times, is considered from an analytic standpoint. A method of approximation based on a consideration of the asymptotic limit of "large" delay in the antibody response is shown to be applicable, and to give results similar to those obtained numerically by the above authors. The relevance of this type of approximation to other systems exhibiting "outbreak" phenomena is discussed.

  13. Two-site adsolubilization model of incorporation of fluoromonomers into fluorosurfactants formed on cotton fabric.

    PubMed

    Hanumansetty, Srinivas; O'Rear, Edgar

    2014-04-01

    The adsorption of surfactants and adsolubilization of organic compounds on knit cotton fabric are fundamentally important in admicellar polymerization to impart characteristics like water repellency, stain resistance, and flame retardancy. The main objective of this research is to study adsorption and adsolubilization of fluororsurfactants and fluoromonomers used to obtain water repellency characteristics. Adsorption of nonionic (fluoroaliphatic amine oxide) and cationic (fluoroaliphatic quaternary ammonium surfactant) fluororsurfactants at the interface of cotton is investigated with and without fluoroacrylate monomers. A two-site adsolubilization model was used to predict the aggregation number of fluorosurfactant.

  14. An Expanded Notch-Delta Model Exhibiting Long-Range Patterning and Incorporating MicroRNA Regulation

    PubMed Central

    Chen, Jerry S.; Gumbayan, Abygail M.; Zeller, Robert W.; Mahaffy, Joseph M.

    2014-01-01

    Notch-Delta signaling is a fundamental cell-cell communication mechanism that governs the differentiation of many cell types. Most existing mathematical models of Notch-Delta signaling are based on a feedback loop between Notch and Delta leading to lateral inhibition of neighboring cells. These models result in a checkerboard spatial pattern whereby adjacent cells express opposing levels of Notch and Delta, leading to alternate cell fates. However, a growing body of biological evidence suggests that Notch-Delta signaling produces other patterns that are not checkerboard, and therefore a new model is needed. Here, we present an expanded Notch-Delta model that builds upon previous models, adding a local Notch activity gradient, which affects long-range patterning, and the activity of a regulatory microRNA. This model is motivated by our experiments in the ascidian Ciona intestinalis showing that the peripheral sensory neurons, whose specification is in part regulated by the coordinate activity of Notch-Delta signaling and the microRNA miR-124, exhibit a sparse spatial pattern whereby consecutive neurons may be spaced over a dozen cells apart. We perform rigorous stability and bifurcation analyses, and demonstrate that our model is able to accurately explain and reproduce the neuronal pattern in Ciona. Using Monte Carlo simulations of our model along with miR-124 transgene over-expression assays, we demonstrate that the activity of miR-124 can be incorporated into the Notch decay rate parameter of our model. Finally, we motivate the general applicability of our model to Notch-Delta signaling in other animals by providing evidence that microRNAs regulate Notch-Delta signaling in analogous cell types in other organisms, and by discussing evidence in other organisms of sparse spatial patterns in tissues where Notch-Delta signaling is active. PMID:24945987

  15. On the tectonics and metallogenesis of West Africa: a model incorporating new geophysical data

    USGS Publications Warehouse

    Hastings, David A.

    1982-01-01

    The gold, diamond and manganese deposits of Ghana have attracted commercial interest, but appropriate geophysical data to delineate the tectonic setting of these and other deposits have been lacking until recently. Recent gravity surveys, however, now cover about 75% of the country. When used in a synthesis of the sometimes contradictory existing theories about the geology and metallogenesis of West Africa, the available gravity, magnetic, and seismic data lead to a preliminary tectonic model that postulates rifting at the time of the (1800-2000 m.y. old) Eburnean orogeny and is consistent with the occurrences of mineral deposits in the region. In this model, diamond-bearing kimberlites formed during the commencement of rifting during the Eburnean orogenesis. Later emplacement of kimberlites was associated with the initiation of Mesozoic rifting of Gondwanaland. Primary gold vein deposits were probably formed by the migration of hydrothermal fluids (associated with the formation of granitoids) into dilatant zones, such as rift-related faults and anticlinal axial areas, toward the end of the Eburnean orogeny. At this time, the major concordant granitoids were formed, with smaller plutonic granitoids forming on the fringes of the concordant masses as partial melting fractions of the latter. Sedimentary manganese deposits were formed along the margins of rift lakes toward the end of the orogeny.

  16. Quantifying the regional water footprint of biofuel production by incorporating hydrologic modeling

    NASA Astrophysics Data System (ADS)

    Wu, M.; Chiu, Y.; Demissie, Y.

    2012-10-01

    A spatially explicit life cycle water analysis framework is proposed, in which a standardized water footprint methodology is coupled with hydrologic modeling to assess blue water, green water (rainfall), and agricultural grey water discharge in the production of biofuel feedstock at county-level resolution. Grey water is simulated via SWAT, a watershed model. Evapotranspiration (ET) estimates generated with the Penman-Monteith equation and crop parameters were verified by using remote sensing results, a satellite-imagery-derived data set, and other field measurements. Crop irrigation survey data are used to corroborate the estimate of irrigation ET. An application of the concept is presented in a case study for corn-stover-based ethanol grown in Iowa (United States) within the Upper Mississippi River basin. Results show vast spatial variations in the water footprint of stover ethanol from county to county. Producing 1 L of ethanol from corn stover growing in the Iowa counties studied requires from 4.6 to 13.1 L of blue water (with an average of 5.4 L), a majority (86%) of which is consumed in the biorefinery. The county-level green water (rainfall) footprint ranges from 760 to 1000 L L-1. The grey water footprint varies considerably, ranging from 44 to 1579 L, a 35-fold difference, with a county average of 518 L. This framework can be a useful tool for watershed- or county-level biofuel sustainability metric analysis to address the heterogeneity of the water footprint for biofuels.

  17. A process-based evapotranspiration model incorporating coupled soil water-atmospheric controls

    NASA Astrophysics Data System (ADS)

    Haghighi, Erfan; Kirchner, James

    2016-04-01

    Despite many efforts to develop evapotranspiration models (in the framework of the Penman-Monteith equation) with improved parametrizations of various resistance terms to water vapor transfer into the atmosphere, evidence suggests that estimates of evapotranspiration and its partitioning are prone to bias. Much of this bias could arise from the exclusion of surface hydro-thermal properties and of physical interactions close to the surface where heat and water vapor fluxes originate. Recent progress has been made in mechanistic modeling of surface-turbulence interactions, accounting for localized heat and mass exchange rates from bare soil surfaces covered by protruding obstacles. We seek to extend these results partially vegetated surfaces, to improve predictive capabilities and accuracy of remote sensing techniques quantifying evapotranspiration fluxes. The governing equations of liquid water, water vapor, and energy transport dynamics in the soil-plant-atmosphere system are coupled to resolve diffusive vapor fluxes from isolated pores (plant stomata and soil pores) across a near-surface viscous sublayer, explicitly accounting for pore-scale transport mechanisms and environmental forcing. Preliminary results suggest that this approach offers unique opportunities for directly linking transport properties in plants and adjacent bare soil with resulting plant transpiration and localized bare soil evaporation rates. It thus provides an essential building block for interpreting and upscaling results to field and landscape scales for a range of vegetation cover and atmospheric conditions.

  18. Study of an intraurban travel demand model incorporating commuter preference variables

    NASA Technical Reports Server (NTRS)

    Holligan, P. E.; Coote, M. A.; Rushmer, C. R.; Fanning, M. L.

    1971-01-01

    The model is based on the substantial travel data base for the nine-county San Francisco Bay Area, provided by the Metropolitan Transportation Commission. The model is of the abstract type, and makes use of commuter attitudes towards modes and simple demographic characteristics of zones in a region to predict interzonal travel by mode for the region. A characterization of the STOL/VTOL mode was extrapolated by means of a subjective comparison of its expected characteristics with those of modes characterized by the survey. Predictions of STOL demand were made for the Bay Area and an aircraft network was developed to serve this demand. When this aircraft system is compared to the base case system, the demand for STOL service has increased five fold and the resulting economics show considerable benefit from the increased scale of operations. In the previous study all systems required subsidy in varying amounts. The new system shows a substantial profit at an average fare of $3.55 per trip.

  19. Incorporating Information on (micro)Topography when Modelling Soil Erosion at the Watershed Scale

    NASA Astrophysics Data System (ADS)

    Cerdan, O.

    2015-12-01

    In the context of shallow flows, the spatial distribution of the flow is highly influenced by the micro-topography. For instance, local oriented depressions may exist in which the flow depth and velocity may exceed the threshold for soil erosion initiation. If a mean uniform flow shear stress is used to characterize the area, it would be smaller and therefore may not initiate erosion. However, management of water and sediment fluxes requires analysis and modeling at the watershed scale in order to integrate the relations between upstream and downstream areas. At this scale, high resolution information on the microtopography is usually not always available and would anyway require too extensive computation resources to be explicitly integrated in modelling attempt. Moreover, in agricultural context, this information is likely to change during the year depending on the agricultural practices. In this context, the objective of this study is to propose a parameterisation of the influence of microtopography on erosion into the framework of the shallow water equation. For each cell, the proportion of wetted area is used as a microtopography indicator. For the case of erosion, the system is coupled to the sediment transport equations. In such context, an additional equation describing the micro-topography evolution caused by erosion is introduced. Different case study will be presented to investigate the potential of the approach.

  20. Incorporating Religiosity into a Developmental Model of Positive Family Functioning across Generations

    PubMed Central

    Spilman, Sarah K.; Neppl, Tricia K.; Donnellan, M. Brent; Schofield, Thomas J.; Conger, Rand D.

    2012-01-01

    This study evaluated a developmental model of intergenerational continuity in religiosity and its association with observed competency in romantic and parent-child relationships across two generations. Using multi-informant data from the Family Transitions Project, a 20-year longitudinal study of families that began during early adolescence (N = 451), we found that parental religiosity assessed during the youth’s adolescence was positively related to the youth’s own religiosity during adolescence which, in turn, predicted their religiosity after the transition to adulthood. The findings also supported the theoretical model guiding the study, which proposes that religiosity acts as a personal resource that will be uniquely and positively associated with the quality of family relationships. Especially important, the findings demonstrate support for the role of religiosity in a developmental process that promotes positive family functioning after addressing earlier methodological limitations in this area of study, such as cross-sectional research designs, single informant measurement, retrospective reports, and the failure to control for other individual differences. PMID:22545832

  1. Constitutive Modeling and Testing of Polymer Matrix Composites Incorporating Physical Aging at Elevated Temperatures

    NASA Technical Reports Server (NTRS)

    Veazie, David R.

    1998-01-01

    Advanced polymer matrix composites (PMC's) are desirable for structural materials in diverse applications such as aircraft, civil infrastructure and biomedical implants because of their improved strength-to-weight and stiffness-to-weight ratios. For example, the next generation military and commercial aircraft requires applications for high strength, low weight structural components subjected to elevated temperatures. A possible disadvantage of polymer-based composites is that the physical and mechanical properties of the matrix often change significantly over time due to the exposure of elevated temperatures and environmental factors. For design, long term exposure (i.e. aging) of PMC's must be accounted for through constitutive models in order to accurately assess the effects of aging on performance, crack initiation and remaining life. One particular aspect of this aging process, physical aging, is considered in this research.

  2. A phase field model incorporating strain gradient viscoplasticity: Application to rafting in Ni-base superalloys

    NASA Astrophysics Data System (ADS)

    Cottura, M.; Le Bouar, Y.; Finel, A.; Appolaire, B.; Ammar, K.; Forest, S.

    2012-07-01

    The first formulation of a phase field model accounting for size-dependent viscoplasticity is developed to study materials in which microstructure evolution and viscoplastic behavior are strongly coupled. Plasticity is introduced using a continuum strain gradient formalism which captures the size effect of the viscoplastic behavior. First, the influence of this size effect on the mechanical behavior of the material is discussed in static microstructures. Then, the dynamic coupling between microstructure evolution and viscoplastic activity is addressed and illustrated by the rafting of the microstructure observed in Ni-base superalloys under creep conditions. It is found that the plastic size effect has only a moderate impact on the shape of the rafts but is crucial to reproduce the macroscopic mechanical behavior of that particular material.

  3. An ecosystem modelling framework for incorporating climate regime shifts into fisheries management

    NASA Astrophysics Data System (ADS)

    Fu, Caihong; Perry, R. Ian; Shin, Yunne-Jai; Schweigert, Jake; Liu, Huizhu

    2013-08-01

    Ecosystem-based approaches to fisheries management (EBM) attempt to account for fishing, climate variability and species interactions when formulating fisheries management advice. Ecosystem models that investigate the combined effects of ecological processes are vital to support the implementation of EBM by assessing the effectiveness of management strategies in an ecosystem context. In this study, an individual-based ecosystem model was used to demonstrate how species at different trophic levels and of different life histories responded to climate regimes and how well different single- or various multi-species fisheries at different intensities perform in terms of human benefits (yield) and trade-offs (fishery closures) as well as their impacts on the ecosystem. In addition, other performance indicators were also used to evaluate management strategies. The simulations indicated that under no fishing, each species responded to the regimes differently due to different life history traits and different trophic interactions. Fishing at the level of natural mortality (F = M) produced the highest yields within each fishery, however, an F adjusted for the current productivity conditions (regime) resulted in much fewer fishery closures compared with F = M, indicating the advantage of implementing a policy of a regime-specific F from the stand point of conservation and fishery stability. Furthermore, a regime-specific F strategy generally resulted in higher yield and fewer fishery closures compared with F = 0.5M. Other performance indicators also pointed to the advantage of using a regime-specific F strategy in terms of the stability of both ecosystem and fishery production. As a specific example, fishing the predators of Pacific herring under all multi-species fisheries scenarios increased the yield of Pacific herring and reduced the number of herring fishery closures. This supports the conclusion that an exploitation strategy which is balanced across all trophic levels

  4. Incorporating plasticity of the interfibrillar matrix in shear lag models is necessary to replicate the multiscale mechanics of tendon fascicles.

    PubMed

    Szczesny, Spencer E; Elliott, Dawn M

    2014-12-01

    Despite current knowledge of tendon structure, the fundamental deformation mechanisms underlying tendon mechanics and failure are unknown. We recently showed that a shear lag model, which explicitly assumed plastic interfibrillar load transfer between discontinuous fibrils, could explain the multiscale fascicle mechanics, suggesting that fascicle yielding is due to plastic deformation of the interfibrillar matrix. However, it is unclear whether alternative physical mechanisms, such as elastic interfibrillar deformation or fibril yielding, also contribute to fascicle mechanical behavior. The objective of the current work was to determine if plasticity of the interfibrillar matrix is uniquely capable of explaining the multiscale mechanics of tendon fascicles including the tissue post-yield behavior. This was examined by comparing the predictions of a continuous fibril model and three separate shear lag models incorporating an elastic, plastic, or elastoplastic interfibrillar matrix with multiscale experimental data. The predicted effects of fibril yielding on each of these models were also considered. The results demonstrated that neither the continuous fibril model nor the elastic shear lag model can successfully predict the experimental data, even if fibril yielding is included. Only the plastic or elastoplastic shear lag models were capable of reproducing the multiscale tendon fascicle mechanics. Differences between these two models were small, although the elastoplastic model did improve the fit of the experimental data at low applied tissue strains. These findings suggest that while interfibrillar elasticity contributes to the initial stress response, plastic deformation of the interfibrillar matrix is responsible for tendon fascicle post-yield behavior. This information sheds light on the physical processes underlying tendon failure, which is essential to improve our understanding of tissue pathology and guide the development of successful repair. PMID:25262202

  5. Incorporating Plasticity of the Interfibrillar Matrix in Shear Lag Models is Necessary to Replicate the Multiscale Mechanics of Tendon Fascicles

    PubMed Central

    Szczesny, Spencer E.; Elliott, Dawn M.

    2015-01-01

    Despite current knowledge of tendon structure, the fundamental deformation mechanisms underlying tendon mechanics and failure are unknown. We recently showed that a shear lag model, which explicitly assumed plastic interfibrillar load transfer between discontinuous fibrils, could explain the multiscale fascicle mechanics, suggesting that fascicle yielding is due to plastic deformation of the interfibrillar matrix. However, it is unclear whether alternative physical mechanisms, such as elastic interfibrillar deformation or fibril yielding, also contribute to fascicle mechanical behavior. The objective of the current work was to determine if plasticity of the interfibrillar matrix is uniquely capable of explaining the multiscale mechanics of tendon fascicles including the tissue post-yield behavior. This was examined by comparing the predictions of a continuous fibril model and three separate shear lag models incorporating an elastic, plastic, or elastoplastic interfibrillar matrix with multiscale experimental data. The predicted effects of fibril yielding on each of these models were also considered. The results demonstrated that neither the continuous fibril model nor the elastic shear lag model can successfully predict the experimental data, even if fibril yielding is included. Only the plastic or elastoplastic shear lag models were capable of reproducing the multiscale tendon fascicle mechanics. Differences between these two models were small, although the elastoplastic model did improve the fit of the experimental data at low applied tissue strains. These findings suggest that while interfibrillar elasticity contributes to the initial stress response, plastic deformation of the interfibrillar matrix is responsible for tendon fascicle post-yield behavior. This information sheds light on the physical processes underlying tendon failure, which is essential to improve our understanding of tissue pathology and guide the development of successful repair. PMID:25262202

  6. Incorporation of advanced aerosol activation treatments into CESM/CAM5: model evaluation and impacts on aerosol indirect effects

    NASA Astrophysics Data System (ADS)

    Gantt, B.; He, J.; Zhang, X.; Zhang, Y.; Nenes, A.

    2014-07-01

    One of the greatest sources of uncertainty in the science of anthropogenic climate change is from aerosol-cloud interactions. The activation of aerosols into cloud droplets is a direct microphysical linkage between aerosols and clouds; parameterizations of this process link aerosol with cloud condensation nuclei (CCN) and the resulting indirect effects. Small differences between parameterizations can have a large impact on the spatiotemporal distributions of activated aerosols and the resulting cloud properties. In this work, we incorporate a series of aerosol activation schemes into the Community Atmosphere Model version 5.1.1 within the Community Earth System Model version 1.0.5 (CESM/CAM5) which include factors such as insoluble aerosol adsorption and giant cloud condensation nuclei (CCN) activation kinetics to understand their individual impacts on global-scale cloud droplet number concentration (CDNC). Compared to the existing activation scheme in CESM/CAM5, this series of activation schemes increase the computation time by ~10% but leads to predicted CDNC in better agreement with satellite-derived/in situ values in many regions with high CDNC but in worse agreement for some regions with low CDNC. Large percentage changes in predicted CDNC occur over desert and oceanic regions, owing to the enhanced activation of dust from insoluble aerosol adsorption and reduced activation of sea spray aerosol after accounting for giant CCN activation kinetics. Comparison of CESM/CAM5 predictions against satellite-derived cloud optical thickness and liquid water path shows that the updated activation schemes generally improve the low biases. Globally, the incorporation of all updated schemes leads to an average increase in column CDNC of 150% and an increase (more negative) in shortwave cloud forcing of 12%. With the improvement of model-predicted CDNCs and better agreement with most satellite-derived cloud properties in many regions, the inclusion of these aerosol activation

  7. Microbial Community Evolution as Evidenced by Isotopic Incorporation into Phospholipid Fatty Acids in a Model Aquifer System

    NASA Astrophysics Data System (ADS)

    Morrison, L.; Mailloux, B. J.; Kujawinski, E. B.

    2004-12-01

    Stable isotope probing (SIP) of biomarkers such as phospholipid fatty acids (PLFAs) has been used successfully to identify active microbial communities in a variety of environments. We are interested in extending this approach to examine the evolution of microbial communities over time. We tested this capability within the context of a larger experiment examining the role of microbes in mediating transformations of organic matter within an aquifer system. A laboratory flow-through column experiment was conducted with sediment collected from a pristine, shallow, coastal plain aquifer. The groundwater medium was amended with low levels of an isotopically labeled substrate, 13C-acetate, for approximately one month and then with non-labeled acetate for one month. PLFAs were extracted from sediments prior to and after labeled-acetate addition. In addition, PLFAs were isolated from effluent samples during selected time points within the two-month experiment. Incorporation of the 13C label into the PLFAs was monitored using isotope-ratio GC/MS. Because some PLFAs can be used to infer the presence of specific microbial groups, we used the relative concentration of different PLFAs and the timing and degree of isotopic incorporation (or loss) to examine the progression of different microbial communities within our model system. This powerful method can be used to untangle the complex interactions within microbial systems and can be extended to a variety of ecosystems.

  8. Incorporation of cooling-induced crystallization into a 2-dimensional axisymmetric conduit heat flow model

    NASA Astrophysics Data System (ADS)

    Heptinstall, David; Bouvet de Maisonneuve, Caroline; Neuberg, Jurgen; Taisne, Benoit; Collinson, Amy

    2016-04-01

    Heat flow models can bring new insights into the thermal and rheological evolution of volcanic 3 systems. We shall investigate the thermal processes and timescales in a crystallizing, static 4 magma column, with a heat flow model of Soufriere Hills Volcano (SHV), Montserrat. The latent heat of crystallization is initially computed with MELTS, as a function of pressure and temperature for an andesitic melt (SHV groundmass starting composition). Three fractional crystallization simulations are performed; two with initial pressures of 34MPa (runs 1 & 2) and one of 25MPa (run 3). Decompression rate was varied between 0.1MPa/° C (runs 1 & 3) and 0.2MPa/° C (run 2). Natural and experimental matrix glass compositions are accurately reproduced by all MELTS runs. The cumulative latent heat released for runs 1, 2 and 3 differs by less than 9% (8.69E5 J/kg*K, 9.32E5 J/kg*K, and 9.49E5 J/kg*K respectively). The 2D axisymmetric conductive cooling simulations consider a 30m-diameter conduit that extends from the surface to a depth of 1500m (34MPa). The temporal evolution of temperature is closely tracked at depths of 10m, 750m and 1400m in the centre of the conduit, at the conduit walls, and 20m from the walls into the host rock. Following initial cooling by 7-15oC at 10m depth inside the conduit, the magma temperature rebounds through latent heat release by 32-35oC over 85-123 days to a maximum temperature of 1002-1005oC. At 10m depth, it takes 4.1-9.2 years for the magma column to cool by 108-131oC and crystallize to 75wt%, at which point it cannot be easily remobilized. It takes 11-31.5 years to reach the same crystallinity at 750-1400m depth. We find a wide range in cooling timescales, particularly at depths of 750m or greater, attributed to the initial run pressure and the dominant latent heat producing crystallizing phase, Albite-rich Plagioclase Feldspar. Run 1 is shown to cool fastest and run 3 cool the slowest, with surface emissivity having the strongest cooling

  9. A method for incorporating equilibrium chemical reactions into multiphase flow models for CO2 storage

    NASA Astrophysics Data System (ADS)

    Saaltink, Maarten W.; Vilarrasa, Victor; De Gaspari, Francesca; Silva, Orlando; Carrera, Jesús; Rötting, Tobias S.

    2013-12-01

    CO2 injection and storage in deep saline aquifers involves many coupled processes, including multiphase flow, heat and mass transport, rock deformation and mineral precipitation and dissolution. Coupling is especially critical in carbonate aquifers, where minerals will tend to dissolve in response to the dissolution of CO2 into the brine. The resulting neutralization will drive further dissolution of both CO2 and calcite. This suggests that large cavities may be formed and that proper simulation may require full coupling of reactive transport and multiphase flow. We show that solving the latter may suffice whenever two requirements are met: (1) all reactions can be assumed to occur in equilibrium and (2) the chemical system can be calculated as a function of the state variables of the multiphase flow model (i.e., liquid and gas pressure, and temperature). We redefine the components of multiphase flow codes (traditionally, water and CO2), so that they are conservative for all reactions of the chemical system. This requires modifying the traditional constitutive relationships of the multiphase flow codes, but yields the concentrations of all species and all reaction rates by simply performing speciation and mass balance calculations at the end of each time step. We applied this method to the H2O-CO2-Na-Cl-CaCO3 system, so as to model CO2 injection into a carbonate aquifer containing brine. Results were very similar to those obtained with traditional formulations, which implies that full coupling of reactive transport and multi-phase flow is not really needed for this kind of systems, but the resulting simplifications may make it advisable even for cases where the above requirements are not met. Regarding the behavior of carbonate rocks, we find that porosity development near the injection well is small because of the low solubility of calcite. Moreover, dissolution concentrates at the front of the advancing CO2 plume because the brine below the plume tends to reach

  10. Incorporating covariates into fisheries stock assessment models with application to Pacific herring.

    PubMed

    Deriso, Richard B; Maunder, Mark N; Pearson, Walter H

    2008-07-01

    We present a framework for evaluating the cause of fishery declines by integrating covariates into a fisheries stock assessment model. This allows the evaluation of fisheries' effects vs. natural and other human impacts. The analyses presented are based on integrating ecological science and statistics and form the basis for environmental decision-making advice. Hypothesis tests are described to rank hypotheses and determine the size of a multiple covariate model. We extend recent developments in integrated analysis and use novel methods to produce effect size estimates that are relevant to policy makers and include estimates of uncertainty. Results can be directly applied to evaluate trade-offs among alternative management decisions. The methods and results are also broadly applicable outside fisheries stock assessment. We show that multiple factors influence populations and that analysis of factors in isolation can be misleading. We illustrate the framework by applying it to Pacific herring of Prince William Sound, Alaska (USA). The Pacific herring stock that spawns in Prince William Sound is a stock that has collapsed, but there are several competing or alternative hypotheses to account for the initial collapse and subsequent lack of recovery. Factors failing the initial screening tests for statistical significance included indicators of the 1989 Exxon Valdez oil spill, coho salmon predation, sea lion predation, Pacific Decadal Oscillation, Northern Oscillation Index, and effects of containment in the herring egg-on-kelp pound fishery. The overall results indicate that the most statistically significant factors related to the lack of recovery of the herring stock involve competition or predation by juvenile hatchery pink salmon on herring juveniles. Secondary factors identified in the analysis were poor nutrition in the winter, ocean (Gulf of Alaska) temperature in the winter, the viral hemorrhagic septicemia virus, and the pathogen Ichthyophonus hoferi. The

  11. Incorporating induced seismicity in the 2014 United States National Seismic Hazard Model: results of the 2014 workshop and sensitivity studies

    USGS Publications Warehouse

    Petersen, Mark D.; Mueller, Charles S.; Moschetti, Morgan P.; Hoover, Susan M.; Rubinstein, Justin L.; Llenos, Andrea L.; Michael, Andrew J.; Ellsworth, William L.; McGarr, Arthur F.; Holland, Austin A.; Anderson, John G.

    2015-01-01

    The U.S. Geological Survey National Seismic Hazard Model for the conterminous United States was updated in 2014 to account for new methods, input models, and data necessary for assessing the seismic ground shaking hazard from natural (tectonic) earthquakes. The U.S. Geological Survey National Seismic Hazard Model project uses probabilistic seismic hazard analysis to quantify the rate of exceedance for earthquake ground shaking (ground motion). For the 2014 National Seismic Hazard Model assessment, the seismic hazard from potentially induced earthquakes was intentionally not considered because we had not determined how to properly treat these earthquakes for the seismic hazard analysis. The phrases “potentially induced” and “induced” are used interchangeably in this report, however it is acknowledged that this classification is based on circumstantial evidence and scientific judgment. For the 2014 National Seismic Hazard Model update, the potentially induced earthquakes were removed from the NSHM’s earthquake catalog, and the documentation states that we would consider alternative models for including induced seismicity in a future version of the National Seismic Hazard Model. As part of the process of incorporating induced seismicity into the seismic hazard model, we evaluate the sensitivity of the seismic hazard from induced seismicity to five parts of the hazard model: (1) the earthquake catalog, (2) earthquake rates, (3) earthquake locations, (4) earthquake Mmax (maximum magnitude), and (5) earthquake ground motions. We describe alternative input models for each of the five parts that represent differences in scientific opinions on induced seismicity characteristics. In this report, however, we do not weight these input models to come up with a preferred final model. Instead, we present a sensitivity study showing uniform seismic hazard maps obtained by applying the alternative input models for induced seismicity. The final model will be released after

  12. Modelling how incorporation of divalent cations affects calcite wettability-implications for biomineralisation and oil recovery.

    PubMed

    Andersson, M P; Dideriksen, K; Sakuma, H; Stipp, S L S

    2016-01-01

    Using density functional theory and geochemical speciation modelling, we predicted how solid-fluid interfacial energy is changed, when divalent cations substitute into a calcite surface. The effect on wettability can be dramatic. Trace metal uptake can impact organic compound adsorption, with effects for example, on the ability of organisms to control crystal growth and our ability to predict the wettability of pore surfaces. Wettability influences how easily an organic phase can be removed from a surface, either organic compounds from contaminated soil or crude oil from a reservoir. In our simulations, transition metals substituted exothermically into calcite and more favourably into sites at the surface than in the bulk, meaning that surface properties are more strongly affected than results from bulk experiments imply. As a result of divalent cation substitution, calcite-fluid interfacial energy is significantly altered, enough to change macroscopic contact angle by tens of degrees. Substitution of Sr, Ba and Pb makes surfaces more hydrophobic. With substitution of Mg and the transition metals, calcite becomes more hydrophilic, weakening organic compound adsorption. For biomineralisation, this provides a switch for turning on and off the activity of organic crystal growth inhibitors, thereby controlling the shape of the associated mineral phase. PMID:27352933

  13. Searching for the True Diet of Marine Predators: Incorporating Bayesian Priors into Stable Isotope Mixing Models

    PubMed Central

    Chiaradia, André; Forero, Manuela G.; McInnes, Julie C.; Ramírez, Francisco

    2014-01-01

    Reconstructing the diet of top marine predators is of great significance in several key areas of applied ecology, requiring accurate estimation of their true diet. However, from conventional stomach content analysis to recent stable isotope and DNA analyses, no one method is bias or error free. Here, we evaluated the accuracy of recent methods to estimate the actual proportion of a controlled diet fed to a top-predator seabird, the Little penguin (Eudyptula minor). We combined published DNA data of penguins scats with blood plasma δ15N and δ13C values to reconstruct the diet of individual penguins fed experimentally. Mismatch between controlled (true) ingested diet and dietary estimates obtained through the separately use of stable isotope and DNA data suggested some degree of differences in prey assimilation (stable isotope) and digestion rates (DNA analysis). In contrast, combined posterior isotope mixing model with DNA Bayesian priors provided the closest match to the true diet. We provided the first evidence suggesting that the combined use of these complementary techniques may provide better estimates of the actual diet of top marine predators- a powerful tool in applied ecology in the search for the true consumed diet. PMID:24667296

  14. Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.

    PubMed

    Amato, Katherine R

    2016-01-01

    The mammalian gut is home to a diverse community of microbes. Advances in technology over the past two decades have allowed us to examine this community, the gut microbiota, in more detail, revealing a wide range of influences on host nutrition, health, and behavior. These host-gut microbe interactions appear to shape host plasticity and fitness in a variety of contexts, and therefore represent a key factor missing from existing models of human and non-human primate ecology and evolution. However, current studies of the gut microbiota tend to include limited contextual data or are clinical, making it difficult to directly test broad anthropological hypotheses. Here, I review what is known about the animal gut microbiota and provide examples of how gut microbiota research can be integrated into the study of human and non-human primate ecology and evolution with targeted data collection. Specifically, I examine how the gut microbiota may impact primate diet, energetics, disease resistance, and cognition. While gut microbiota research is proliferating rapidly, especially in the context of humans, there remain important gaps in our understanding of host-gut microbe interactions that will require an anthropological perspective to fill. Likewise, gut microbiota research will be an important tool for filling remaining gaps in anthropological research. PMID:26808106

  15. Incorporating Vibration Test Results for the Advanced Stirling Convertor into the System Dynamic Model

    NASA Technical Reports Server (NTRS)

    Meer, David W.; Lewandowski, Edward J.

    2010-01-01

    The U.S. Department of Energy (DOE), Lockheed Martin Corporation (LM), and NASA Glenn Research Center (GRC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. As part of the extended operation testing of this power system, the Advanced Stirling Convertors (ASC) at NASA GRC undergo a vibration test sequence intended to simulate the vibration history that an ASC would experience when used in an ASRG for a space mission. During these tests, a data system collects several performance-related parameters from the convertor under test for health monitoring and analysis. Recently, an additional sensor recorded the slip table position during vibration testing to qualification level. The System Dynamic Model (SDM) integrates Stirling cycle thermodynamics, heat flow, mechanical mass, spring, damper systems, and electrical characteristics of the linear alternator and controller. This Paper presents a comparison of the performance of the ASC when exposed to vibration to that predicted by the SDM when exposed to the same vibration.

  16. Development and Validation of a Hierarchical Memory Model Incorporating CPU- and Memory-Operation Overlap

    SciTech Connect

    Lubeck, Olaf M.; Luo, Yong; Wasserman, Harvey J.; Bassetti, Federico

    1997-12-31

    Distributed shared memory architectures (DSM`s) such as the Origin 2000 are being implemented which extend the concept of single-processor cache hierarchies across an entire physically-distributed multiprocessor machine. The scalability of a DSM machine is inherently tied to memory hierarchy performance, including such issues as latency hiding techniques in the architecture, global cache-coherence protocols, memory consistency models and, of course, the inherent locality of reference in algorithms of interest. In this paper, we characterize application performance with a {open_quotes}memory-centric{close_quotes} view. Using a simple mean value analysis (MVA) strategy and empirical performance data, we infer the contribution of each level in the memory system to the application`s overall cycles per instruction (cpi). We account for the overlap of processor execution with memory accesses - a key parameter which is not directly measurable on the Origin systems. We infer the separate contributions of three major architecture features in the memory subsystem of the Origin 2000: cache size, outstanding loads-under-miss, and memory latency.

  17. Modelling how incorporation of divalent cations affects calcite wettability-implications for biomineralisation and oil recovery

    NASA Astrophysics Data System (ADS)

    Andersson, M. P.; Dideriksen, K.; Sakuma, H.; Stipp, S. L. S.

    2016-06-01

    Using density functional theory and geochemical speciation modelling, we predicted how solid-fluid interfacial energy is changed, when divalent cations substitute into a calcite surface. The effect on wettability can be dramatic. Trace metal uptake can impact organic compound adsorption, with effects for example, on the ability of organisms to control crystal growth and our ability to predict the wettability of pore surfaces. Wettability influences how easily an organic phase can be removed from a surface, either organic compounds from contaminated soil or crude oil from a reservoir. In our simulations, transition metals substituted exothermically into calcite and more favourably into sites at the surface than in the bulk, meaning that surface properties are more strongly affected than results from bulk experiments imply. As a result of divalent cation substitution, calcite-fluid interfacial energy is significantly altered, enough to change macroscopic contact angle by tens of degrees. Substitution of Sr, Ba and Pb makes surfaces more hydrophobic. With substitution of Mg and the transition metals, calcite becomes more hydrophilic, weakening organic compound adsorption. For biomineralisation, this provides a switch for turning on and off the activity of organic crystal growth inhibitors, thereby controlling the shape of the associated mineral phase.

  18. Modelling how incorporation of divalent cations affects calcite wettability–implications for biomineralisation and oil recovery

    PubMed Central

    Andersson, M. P.; Dideriksen, K.; Sakuma, H.; Stipp, S. L. S.

    2016-01-01

    Using density functional theory and geochemical speciation modelling, we predicted how solid-fluid interfacial energy is changed, when divalent cations substitute into a calcite surface. The effect on wettability can be dramatic. Trace metal uptake can impact organic compound adsorption, with effects for example, on the ability of organisms to control crystal growth and our ability to predict the wettability of pore surfaces. Wettability influences how easily an organic phase can be removed from a surface, either organic compounds from contaminated soil or crude oil from a reservoir. In our simulations, transition metals substituted exothermically into calcite and more favourably into sites at the surface than in the bulk, meaning that surface properties are more strongly affected than results from bulk experiments imply. As a result of divalent cation substitution, calcite-fluid interfacial energy is significantly altered, enough to change macroscopic contact angle by tens of degrees. Substitution of Sr, Ba and Pb makes surfaces more hydrophobic. With substitution of Mg and the transition metals, calcite becomes more hydrophilic, weakening organic compound adsorption. For biomineralisation, this provides a switch for turning on and off the activity of organic crystal growth inhibitors, thereby controlling the shape of the associated mineral phase. PMID:27352933

  19. Incorporating pattern identification of Chinese medicine into precision medicine: An integrative model for individualized medicine.

    PubMed

    Li, Jin-gen; Xu, Hao

    2015-11-01

    On 20 January, 2015, U.S. President Obama announced an ambitious plan called "Precision Medicine (PM) Initiative", aiming to deliver genetics-based medical treatments. PM has shown a promising prospect by tailoring disease treatments and preventions to individuals. However, a predominantly genetics-based method restricts its benefit and applicability in most chronic and complex diseases. Pattern identification (PI) is one of the representative characteristics of Chinese medicine implying the concept of holism and individualized treatment. It is another classification method taking environmental, psychosocial and other individual factors into account. Integrating PI with disease diagnosis of Western medicine will provide a strong complement to genetics-based PM, thus establish an integrative model for individualized medicine. PI provides new perspectives for PM, not only in clinical practice, but also in new drug development and clinical trial design. It is for sure that the integrative approach will ultimately lead to a safer, more convenient and effective patient-centered healthcare and most patients will benefit in the era of PM.

  20. Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.

    PubMed

    Amato, Katherine R

    2016-01-01

    The mammalian gut is home to a diverse community of microbes. Advances in technology over the past two decades have allowed us to examine this community, the gut microbiota, in more detail, revealing a wide range of influences on host nutrition, health, and behavior. These host-gut microbe interactions appear to shape host plasticity and fitness in a variety of contexts, and therefore represent a key factor missing from existing models of human and non-human primate ecology and evolution. However, current studies of the gut microbiota tend to include limited contextual data or are clinical, making it difficult to directly test broad anthropological hypotheses. Here, I review what is known about the animal gut microbiota and provide examples of how gut microbiota research can be integrated into the study of human and non-human primate ecology and evolution with targeted data collection. Specifically, I examine how the gut microbiota may impact primate diet, energetics, disease resistance, and cognition. While gut microbiota research is proliferating rapidly, especially in the context of humans, there remain important gaps in our understanding of host-gut microbe interactions that will require an anthropological perspective to fill. Likewise, gut microbiota research will be an important tool for filling remaining gaps in anthropological research.

  1. Modelling how incorporation of divalent cations affects calcite wettability–implications for biomineralisation and oil recovery

    NASA Astrophysics Data System (ADS)

    Andersson, M. P.; Dideriksen, K.; Sakuma, H.; Stipp, S. L. S.

    2016-06-01

    Using density functional theory and geochemical speciation modelling, we predicted how solid-fluid interfacial energy is changed, when divalent cations substitute into a calcite surface. The effect on wettability can be dramatic. Trace metal uptake can impact organic compound adsorption, with effects for example, on the ability of organisms to control crystal growth and our ability to predict the wettability of pore surfaces. Wettability influences how easily an organic phase can be removed from a surface, either organic compounds from contaminated soil or crude oil from a reservoir. In our simulations, transition metals substituted exothermically into calcite and more favourably into sites at the surface than in the bulk, meaning that surface properties are more strongly affected than results from bulk experiments imply. As a result of divalent cation substitution, calcite-fluid interfacial energy is significantly altered, enough to change macroscopic contact angle by tens of degrees. Substitution of Sr, Ba and Pb makes surfaces more hydrophobic. With substitution of Mg and the transition metals, calcite becomes more hydrophilic, weakening organic compound adsorption. For biomineralisation, this provides a switch for turning on and off the activity of organic crystal growth inhibitors, thereby controlling the shape of the associated mineral phase.

  2. An innovative land use regression model incorporating meteorology for exposure analysis.

    PubMed

    Su, Jason G; Brauer, Michael; Ainslie, Bruce; Steyn, Douw; Larson, Timothy; Buzzelli, Michael

    2008-02-15

    The advent of spatial analysis and geographic information systems (GIS) has led to studies of chronic exposure and health effects based on the rationale that intra-urban variations in ambient air pollution concentrations are as great as inter-urban differences. Such studies typically rely on local spatial covariates (e.g., traffic, land use type) derived from circular areas (buffers) to predict concentrations/exposures at receptor sites, as a means of averaging the annual net effect of meteorological influences (i.e., wind speed, wind direction and insolation). This is the approach taken in the now popular land use regression (LUR) method. However spatial studies of chronic exposures and temporal studies of acute exposures have not been adequately integrated. This paper presents an innovative LUR method implemented in a GIS environment that reflects both temporal and spatial variability and considers the role of meteorology. The new source area LUR integrates wind speed, wind direction and cloud cover/insolation to estimate hourly nitric oxide (NO) and nitrogen dioxide (NO(2)) concentrations from land use types (i.e., road network, commercial land use) and these concentrations are then used as covariates to regress against NO and NO(2) measurements at various receptor sites across the Vancouver region and compared directly with estimates from a regular LUR. The results show that, when variability in seasonal concentration measurements is present, the source area LUR or SA-LUR model is a better option for concentration estimation.

  3. TOWARD MORE REALISTIC ANALYTIC MODELS OF THE HELIOTAIL: INCORPORATING MAGNETIC FLATTENING VIA DISTORTION FLOWS

    SciTech Connect

    Kleimann, Jens; Fichtner, Horst; Röken, Christian; Heerikhuisen, Jacob E-mail: hf@tp4.rub.de E-mail: jacob.heerikhuisen@uah.edu

    2016-01-01

    Both physical arguments and simulations of the global heliosphere indicate that the tailward heliopause is flattened considerably in the direction perpendicular to both the incoming flow and the large-scale interstellar magnetic field. Despite this fact, all of the existing global analytical models of the outer heliosheath's magnetic field assume a circular cross section of the heliotail. To eliminate this inconsistency, we introduce a mathematical procedure by which any analytically or numerically given magnetic field can be deformed in such a way that the cross sections along the heliotail axis attain freely prescribed, spatially dependent values for their total area and aspect ratio. The distorting transformation of this method honors both the solenoidality condition and the stationary induction equation with respect to an accompanying flow field, provided that both constraints were already satisfied for the original magnetic and flow fields prior to the transformation. In order to obtain realistic values for the above parameters, we present the first quantitative analysis of the heliotail's overall distortion as seen in state-of-the-art three-dimensional hybrid MHD–kinetic simulations.

  4. Classifying Multifunctional Enzymes by Incorporating Three Different Models into Chou's General Pseudo Amino Acid Composition.

    PubMed

    Zou, Hong-Liang; Xiao, Xuan

    2016-08-01

    With the avalanche of the newly found protein sequences in the post-genomic epoch, there is an increasing trend for annotating a number of newly discovered enzyme sequences. Among the various proteins, enzyme was considered as the one of the largest kind of proteins. It takes part in most of the biochemical reactions and plays a key role in metabolic pathways. Multifunctional enzyme is enzyme that plays multiple physiological roles. Given a multifunctional enzyme sequence, how can we identify its class? Especially, how can we deal with the multi-classes problem since an enzyme may simultaneously belong to two or more functional classes? To address these problems, which are obviously very important both to basic research and drug development, a multi-label classifier was developed via three different prediction models with multi-label K-nearest algorithm. Experimental results obtained on a stringent benchmark dataset of enzymes by jackknife cross-validation test show that the predicting results were exciting, indicating that the current method could be an effective and promising high throughput method in the enzyme research. We hope it could play an important complementary role to the existing predictors in identifying the classes of enzymes. PMID:27113936

  5. Toward More Realistic Analytic Models of the Heliotail: Incorporating Magnetic Flattening via Distortion Flows

    NASA Astrophysics Data System (ADS)

    Kleimann, Jens; Röken, Christian; Fichtner, Horst; Heerikhuisen, Jacob

    2016-01-01

    Both physical arguments and simulations of the global heliosphere indicate that the tailward heliopause is flattened considerably in the direction perpendicular to both the incoming flow and the large-scale interstellar magnetic field. Despite this fact, all of the existing global analytical models of the outer heliosheath's magnetic field assume a circular cross section of the heliotail. To eliminate this inconsistency, we introduce a mathematical procedure by which any analytically or numerically given magnetic field can be deformed in such a way that the cross sections along the heliotail axis attain freely prescribed, spatially dependent values for their total area and aspect ratio. The distorting transformation of this method honors both the solenoidality condition and the stationary induction equation with respect to an accompanying flow field, provided that both constraints were already satisfied for the original magnetic and flow fields prior to the transformation. In order to obtain realistic values for the above parameters, we present the first quantitative analysis of the heliotail's overall distortion as seen in state-of-the-art three-dimensional hybrid MHD-kinetic simulations.

  6. A heat transfer model for incorporating carbon foam fabrics in firefighter's garment

    NASA Astrophysics Data System (ADS)

    Elgafy, Ahmed; Mishra, Sarthak

    2014-04-01

    In the present work, a numerical study was performed to predict and investigate the performance of a thermal protection system for firefighter's garment consisting of carbon foam fabric in both the outer shell and the thermal liner elements. Several types of carbon foam with different thermal conductivity, porosity, and density were introduced to conduct a parametric study. Additionally, the thickness of the introduced carbon foam fabrics was varied to acquire optimum design. Simulation was conducted for a square planar 2D geometry of the clothing comprising of different fabric layers and a double precision pressure-based implicit solver, under transient state condition was used. The new anticipated thermal protection system was tested under harsh thermal environmental conditions that firefighters are exposed to. The parametric study showed that employing carbon foam fabric with one set of designed parameters, weight reduction of 33 % in the outer shell, 56 % in the thermal liner and a temperature reduction of 2 % at the inner edge of the garment was achieved when compared to the traditional firefighter garment model used by Song et al. (Int J Occup Saf Ergon 14:89-106, 2008). Also, carbon foam fabric with another set of designed parameters resulted in a weight reduction of 25 % in the outer shell, 28 % in the thermal liner and a temperature reduction of 6 % at the inner edge of the garment. As a result, carbon foam fabrics make the firefighter's garment more protective, durable, and lighter in weight.

  7. Incorporating pattern identification of Chinese medicine into precision medicine: An integrative model for individualized medicine.

    PubMed

    Li, Jin-gen; Xu, Hao

    2015-11-01

    On 20 January, 2015, U.S. President Obama announced an ambitious plan called "Precision Medicine (PM) Initiative", aiming to deliver genetics-based medical treatments. PM has shown a promising prospect by tailoring disease treatments and preventions to individuals. However, a predominantly genetics-based method restricts its benefit and applicability in most chronic and complex diseases. Pattern identification (PI) is one of the representative characteristics of Chinese medicine implying the concept of holism and individualized treatment. It is another classification method taking environmental, psychosocial and other individual factors into account. Integrating PI with disease diagnosis of Western medicine will provide a strong complement to genetics-based PM, thus establish an integrative model for individualized medicine. PI provides new perspectives for PM, not only in clinical practice, but also in new drug development and clinical trial design. It is for sure that the integrative approach will ultimately lead to a safer, more convenient and effective patient-centered healthcare and most patients will benefit in the era of PM. PMID:26519373

  8. New Direction in Hydrogeochemical Transport Modeling: Incorporating Multiple Kinetic and Equilibrium Reaction Pathways

    SciTech Connect

    Steefel, C.I.

    2000-02-02

    At least two distinct kinds of hydrogeochemical models have evolved historically for use in analyzing contaminant transport, but each has important limitations. One kind, focusing on organic contaminants, treats biodegradation reactions as parts of relatively simple kinetic reaction networks with no or limited coupling to aqueous and surface complexation and mineral dissolution/precipitation reactions. A second kind, evolving out of the speciation and reaction path codes, is capable of handling a comprehensive suite of multicomponent complexation (aqueous and surface) and mineral precipitation and dissolution reactions, but has not been able to treat reaction networks characterized by partial redox disequilibrium and multiple kinetic pathways. More recently, various investigators have begun to consider biodegradation reactions in the context of comprehensive equilibrium and kinetic reaction networks (e.g. Hunter et al. 1998, Mayer 1999). Here we explore two examples of multiple equilibrium and kinetic reaction pathways using the reactive transport code GIMRT98 (Steefel, in prep.): (1) a computational example involving the generation of acid mine drainage due to oxidation of pyrite, and (2) a computational/field example where the rates of chlorinated VOC degradation are linked to the rates of major redox processes occurring in organic-rich wetland sediments overlying a contaminated aerobic aquifer.

  9. Development of Advanced Continuum Models that Incorporate Nanomechanical Deformation into Engineering Analysis.

    SciTech Connect

    Zimmerman, Jonathan A.; Jones, Reese E.; Templeton, Jeremy Alan; McDowell, David L.; Mayeur, Jason R.; Tucker, Garritt J.; Bammann, Douglas J.; Gao, Huajian

    2008-09-01

    Materials with characteristic structures at nanoscale sizes exhibit significantly different mechani-cal responses from those predicted by conventional, macroscopic continuum theory. For example,nanocrystalline metals display an inverse Hall-Petch effect whereby the strength of the materialdecreases with decreasing grain size. The origin of this effect is believed to be a change in defor-mation mechanisms from dislocation motion across grains and pileup at grain boundaries at mi-croscopic grain sizes to rotation of grains and deformation within grain boundary interface regionsfor nanostructured materials. These rotational defects are represented by the mathematical conceptof disclinations. The ability to capture these effects within continuum theory, thereby connectingnanoscale materials phenomena and macroscale behavior, has eluded the research community.The goal of our project was to develop a consistent theory to model both the evolution ofdisclinations and their kinetics. Additionally, we sought to develop approaches to extract contin-uum mechanical information from nanoscale structure to verify any developed continuum theorythat includes dislocation and disclination behavior. These approaches yield engineering-scale ex-pressions to quantify elastic and inelastic deformation in all varieties of materials, even those thatpossess highly directional bonding within their molecular structures such as liquid crystals, cova-lent ceramics, polymers and biological materials. This level of accuracy is critical for engineeringdesign and thermo-mechanical analysis is performed in micro- and nanosystems. The researchproposed here innovates on how these nanoscale deformation mechanisms should be incorporatedinto a continuum mechanical formulation, and provides the foundation upon which to develop ameans for predicting the performance of advanced engineering materials.4 AcknowledgmentThe authors acknowledge helpful discussions with Farid F. Abraham, Youping Chen, Terry J

  10. Photocatalytic degradation and reactor modeling of 17α-ethynylestradiol employing titanium dioxide-incorporated foam concrete.

    PubMed

    Wang, Yuming; Li, Yi; Zhang, Wenlong; Wang, Qing; Wang, Dawei

    2015-03-01

    Photocatalytic degradation of 17α-ethynylestradiol (EE2) using TiO2 photocatalysts incorporated with foam concrete (TiO2/FC) was investigated for the first time. Scanning electron microscopy (SEM) study of the samples revealed a narrow air void size distribution on the surface of FC cubes on with 5 wt% addition of P25 TiO2, and TiO2 particles were distributed heterogeneously on the surface of TiO2/FC samples. The sorption and photocatalytic degradation of EE2 with UV-light irradiation by TiO2/FC cubes were investigated. Adsorption capacity of EE2 by the TiO2/FC and blank foam concrete (FC) samples were similar, while the degradation rates showed a great difference. More than 50 % of EE2 was removed by TiO2/FC within 3.5 h, compared with 5 % by blank FC. The EE2 removal process was then studied in a photoreactor modified from ultraviolet disinfection pool and constructed with TiO2/FC materials. An integrated model including a plate adsorption-scattering model and a modified flow diffusion model was established to simulate the photocatalytic degradation process with different radiation fields, contaminant load, and flow velocity. A satisfactory agreement was observed between the model simulations and experimental results, showing a potential for the design and scale-up of the modified photocatalytic reactor.

  11. Global Hopf bifurcation analysis of an susceptible-infective-removed epidemic model incorporating media coverage with time delay.

    PubMed

    Zhao, Huitao; Zhao, Miaochan

    2017-12-01

    An susceptible-infective-removed epidemic model incorporating media coverage with time delay is proposed. The stability of the disease-free equilibrium and endemic equilibrium is studied. And then, the conditions which guarantee the existence of local Hopf bifurcation are given. Furthermore, we show that the local Hopf bifurcation implies the global Hopf bifurcation after the second critical value of delay. The obtained results show that the time delay in media coverage can not affect the stability of the disease-free equilibrium when the basic reproduction number is less than unity. However, the time delay affects the stability of the endemic equilibrium and produces limit cycle oscillations while the basic reproduction number is greater than unity. Finally, some examples for numerical simulations are included to support the theoretical prediction. PMID:27627694

  12. Global Hopf bifurcation analysis of an susceptible-infective-removed epidemic model incorporating media coverage with time delay.

    PubMed

    Zhao, Huitao; Zhao, Miaochan

    2017-12-01

    An susceptible-infective-removed epidemic model incorporating media coverage with time delay is proposed. The stability of the disease-free equilibrium and endemic equilibrium is studied. And then, the conditions which guarantee the existence of local Hopf bifurcation are given. Furthermore, we show that the local Hopf bifurcation implies the global Hopf bifurcation after the second critical value of delay. The obtained results show that the time delay in media coverage can not affect the stability of the disease-free equilibrium when the basic reproduction number is less than unity. However, the time delay affects the stability of the endemic equilibrium and produces limit cycle oscillations while the basic reproduction number is greater than unity. Finally, some examples for numerical simulations are included to support the theoretical prediction.

  13. Incorporating target-mediated drug disposition in a minimal physiologically-based pharmacokinetic model for monoclonal antibodies

    PubMed Central

    Cao, Yanguang

    2014-01-01

    Target-mediated drug disposition (TMDD) usually accounts for nonlinear pharmacokinetics (PK) of drugs whose distribution and/or clearance are affected by their targets owing to high affinity and limited capacity. TMDD is frequently reported for monoclonal antibodies (mAb) for such reason. Minimal physiologically-based pharmacokinetic models (mPBPK), which accommodate the unique PK behaviors of mAb, provide a general approach for analyzing mAbs PK and predicting mAb interstitial concentrations in two groups of tissues. This study assessed the feasibility of incorporating TMDD into mPBPK models to consider target-binding in either plasma (cTMDD) or interstitial fluid (ISF) (pTMDD). The dose-related signature profiles of the pTMDD model reveal a parallel early decay phase, in contrast with the cTMDD model that exhibits a faster initial decline for low doses. The parallel early phase in the pTMDD model is associated with the slow perivascular extravasation of mAb, which restricts the initial decline regardless of interstitial target-mediated elimination. The cTMDD and pTMDD models both preserve the long terminal phase that is typically perceived in conventional two-compartment (2CM) and TMDD models. Having TMDD in ISF impacts the typical relationships between plasma concentrations and receptor occupancy, and between saturation of apparent nonlinear clearance and saturation of receptors. The vascular reflection coefficient (σv) was found to affect receptor occupancy in ISF. In the cTMDD model, saturation of nonlinear clearance is equivalent to saturation of receptors. However, in the pTMDD model, they are no longer equal and all parameters pertaining to receptors or receptor binding (Rtotal, KD, Kss, kint) shifts such relationships. Different TMDD models were utilized in analyzing PK for seven mAbs from digitized literature data. When the target is in plasma, the cTMDD model performed similarly to the 2CM and TMDD models, but with one less system parameter. When the

  14. A New Paradigm For Modeling Fault Zone Inelasticity: A Multiscale Continuum Framework Incorporating Spontaneous Localization and Grain Fragmentation.

    NASA Astrophysics Data System (ADS)

    Elbanna, A. E.

    2015-12-01

    The brittle portion of the crust contains structural features such as faults, jogs, joints, bends and cataclastic zones that span a wide range of length scales. These features may have a profound effect on earthquake nucleation, propagation and arrest. Incorporating these existing features in modeling and the ability to spontaneously generate new one in response to earthquake loading is crucial for predicting seismicity patterns, distribution of aftershocks and nucleation sites, earthquakes arrest mechanisms, and topological changes in the seismogenic zone structure. Here, we report on our efforts in modeling two important mechanisms contributing to the evolution of fault zone topology: (1) Grain comminution at the submeter scale, and (2) Secondary faulting/plasticity at the scale of few to hundreds of meters. We use the finite element software Abaqus to model the dynamic rupture. The constitutive response of the fault zone is modeled using the Shear Transformation Zone theory, a non-equilibrium statistical thermodynamic framework for modeling plastic deformation and localization in amorphous materials such as fault gouge. The gouge layer is modeled as 2D plane strain region with a finite thickness and heterogeenous distribution of porosity. By coupling the amorphous gouge with the surrounding elastic bulk, the model introduces a set of novel features that go beyond the state of the art. These include: (1) self-consistent rate dependent plasticity with a physically-motivated set of internal variables, (2) non-locality that alleviates mesh dependence of shear band formation, (3) spontaneous evolution of fault roughness and its strike which affects ground motion generation and the local stress fields, and (4) spontaneous evolution of grain size and fault zone fabric.

  15. Incorporation of ABCB1-mediated transport into a physiologically-based pharmacokinetic model of docetaxel in mice

    PubMed Central

    Hudachek, Susan F.

    2015-01-01

    Docetaxel is one of the most widely used anticancer agents. While this taxane has proven to be an effective chemotherapeutic drug, noteworthy challenges exist in relation to docetaxel administration due to the considerable interindividual variability in efficacy and toxicity associated with the use of this compound, largely attributable to differences between individuals in their ability to metabolize and eliminate docetaxel. Regarding the latter, the ATP-binding cassette transporter B1 (ABCB1, PGP, MDR1) is primarily responsible for docetaxel elimination. To further understand the role of ABCB1 in the biodistribution of docetaxel in mice, we utilized physiologically-based pharmacokinetic (PBPK) modeling that included ABCB1-mediated transport in relevant tissues. Transporter function was evaluated by studying docetaxel pharmacokinetics in wild-type FVB and Mdr1a/b constitutive knockout (KO) mice and incorporating this concentration–time data into a PBPK model comprised of eight tissue compartments (plasma, brain, heart, lung, kidney, intestine, liver and slowly perfused tissues) and, in addition to ABCB1-mediated transport, included intravenous drug administration, specific binding to intracellular tubulin, intestinal and hepatic metabolism, glomerular filtration and tubular reabsorption. For all tissues in both the FVB and KO cohorts, the PBPK model simulations closely mirrored the observed data. Furthermore, both models predicted AUC values that were with 15 % of the observed AUC values, indicating that our model-simulated drug exposures accurately reflected the observed tissue exposures. Overall, our PBPK model furthers the understanding of the role of ABCB1 in the biodistribution of docetaxel. Additionally, this exemplary model structure can be applied to investigate the pharmacokinetics of other ABCB1 transporter substrates. PMID:23616082

  16. Towards a Predictive Thermodynamic Model of Oxidation States of Uranium Incorporated in Fe (hydr) oxides

    SciTech Connect

    Bagus, Paul S.

    2013-01-01

    -Level Excited States: Consequences For X-Ray Absorption Spectroscopy”, J. Elec. Spectros. and Related Phenom., 200, 174 (2015) describes our first application of these methods. As well as applications to problems and materials of direct interest for our PNNL colleagues, we have pursued applications of fundamental theoretical significance for the analysis and interpretation of XPS and XAS spectra. These studies are important for the development of the fields of core-level spectroscopies as well as to advance our capabilities for applications of interest to our PNNL colleagues. An excellent example is our study of the surface core-level shifts, SCLS, for the surface and bulk atoms of an oxide that provides a new approach to understanding how the surface electronic of oxides differs from that in the bulk of the material. This work has the potential to lead to a new key to understanding the reactivity of oxide surfaces. Our theoretical studies use cluster models with finite numbers of atoms to describe the properties of condensed phases and crystals. This approach has allowed us to focus on the local atomistic, chemical interactions. For these clusters, we obtain orbitals and spinors through the solution of the Hartree-Fock, HF, and the fully relativistic Dirac HF equations. These orbitals are used to form configuration mixing wavefunctions which treat the many-body effects responsible for the open shell angular momentum coupling and for the satellites of the core-level spectra. Our efforts have been in two complementary directions. As well as the applications described above, we have placed major emphasis on the enhancement and extension of our theoretical and computational capabilities so that we can treat complex systems with a greater range of many-body effects. Noteworthy accomplishments in terms of method development and enhancement have included: (1) An improvement in our treatment of the large matrices that must be handled when many-body effects are treated. (2

  17. KINETIC MODELING OF A FISCHER-TROPSCH REACTION OVER A COBALT CATALYST IN A SLURRY BUBBLE COLUMN REACTOR FOR INCORPORATION INTO A COMPUTATIONAL MULTIPHASE FLUID DYNAMICS MODEL

    SciTech Connect

    Anastasia Gribik; Doona Guillen, PhD; Daniel Ginosar, PhD

    2008-09-01

    Currently multi-tubular fixed bed reactors, fluidized bed reactors, and slurry bubble column reactors (SBCRs) are used in commercial Fischer Tropsch (FT) synthesis. There are a number of advantages of the SBCR compared to fixed and fluidized bed reactors. The main advantage of the SBCR is that temperature control and heat recovery are more easily achieved. The SBCR is a multiphase chemical reactor where a synthesis gas, comprised mainly of H2 and CO, is bubbled through a liquid hydrocarbon wax containing solid catalyst particles to produce specialty chemicals, lubricants, or fuels. The FT synthesis reaction is the polymerization of methylene groups [-(CH2)-] forming mainly linear alkanes and alkenes, ranging from methane to high molecular weight waxes. The Idaho National Laboratory is developing a computational multiphase fluid dynamics (CMFD) model of the FT process in a SBCR. This paper discusses the incorporation of absorption and reaction kinetics into the current hydrodynamic model. A phased approach for incorporation of the reaction kinetics into a CMFD model is presented here. Initially, a simple kinetic model is coupled to the hydrodynamic model, with increasing levels of complexity added in stages. The first phase of the model includes incorporation of the absorption of gas species from both large and small bubbles into the bulk liquid phase. The driving force for the gas across the gas liquid interface into the bulk liquid is dependent upon the interfacial gas concentration in both small and large bubbles. However, because it is difficult to measure the concentration at the gas-liquid interface, coefficients for convective mass transfer have been developed for the overall driving force between the bulk concentrations in the gas and liquid phases. It is assumed that there are no temperature effects from mass transfer of the gas phases to the bulk liquid phase, since there are only small amounts of dissolved gas in the liquid phase. The product from the

  18. An efficient Bayesian framework incorporating the Stochastic Response Surface Method for the uncertainty analysis of subsurface and multimedia transport models

    NASA Astrophysics Data System (ADS)

    Balakrishnan, S.; Roy, A.; Ierapetritou, M. G.; Flach, G. P.; Georgopoulos, P. G.

    2002-05-01

    Comprehensive uncertainty analyses of complex models of environmental and biological systems are essential but often not feasible due to the computational resources they require. Traditional Monte Carlo methods, e.g. involving standard or Latin Hypercube sampling, for propagating uncertainty and developing probability densities of model outputs, may require performing a large number of model simulations that can be prohibitive in the case of 3D dynamic finite element or finite difference models. An alternative approach is provided by the Stochastic Response Surface Method (SRSM), which is a computationally efficient framework that facilitates uncertainty analysis through the determination of statistically equivalent reduced models; SRSM is applied here to subsurface transport modeling. Past applications of SRSM included the uncertainty analysis of atmospheric chemistry and transport models, groundwater models, and physiologically based pharmacokinetic models [Isukapalli et al., 1998, Risk Analysis, 18(3), 351-363;Isukapalli et al., 2000, Risk Analysis, 20(5), 591-602]. The present work further demonstrates how the SRSM framework can be used in a Bayesian manner not only to characterize but also to reduce uncertainties, by incorporating observational information in estimates of model parameters. This is achieved by the combined application of the SRSM and Markov Chain Monte Carlo (MCMC) methods. Current and ongoing work includes the application of this novel framework to the groundwater and unsaturated zone modeling of the General Separations Area (GSA) of the US DOE Savannah River Site. Subsurface processes are simulated with the Flow And Contaminant Transport (FACT) code [Flach, G.P. and M.K. Harris, 2000, WSRC-TR-96-00399]. FACT is transient three-dimensional, finite element code designed to simulate isothermal groundwater flow, moisture movement, and solute transport in variably saturated and fully saturated subsurface porous media. Furthermore, FACT is designed

  19. A two-scale non-local model of swelling porous media incorporating ion size correlation effects

    NASA Astrophysics Data System (ADS)

    Le, T. D.; Moyne, C.; Murad, M. A.; Lima, S. A.

    2013-12-01

    A new two-scale model is proposed for derivation of the macroscopic modified effective stress principle for swelling porous media saturated by an electrolyte solution containing finite size ions. A non-local pore-scale model is developed within the framework of Statistical Mechanics in conjunction with the thermodynamic approach based on Density Functional Theory leading to a nonlinear integral Fredholm equation of second kind for the ion/nanopore correlation function coupled with Poisson problem for the electric double layer potential. When combined with the fluid equilibrium condition such non-local electrochemical problem gives rise to a constitutive law for the fluid stress tensor in terms of the disjoining pressure which is decomposed into several components of different nature. The homogenization procedure based on formal asymptotic expansions is applied to up-scale the model to the macroscale leading to a two-scale constitutive law for the swelling pressure appearing in the modified effective stress principle with improved accuracy incorporating the deviations from the Gouy-Chapman Poisson-Boltzmann-based theory due to the finite size short-range ion-ion correlation effects. The integro-differential problem posed in a periodic cell is discretized by collocation schemes. Numerical results are obtained for a stratified arrangement of parallel macromolecules showing that the effects of ion-ion correlation forces give rise to anomalous attraction patterns between the particles for divalent ions.

  20. Oculomotor learning revisited: a model of reinforcement learning in the basal ganglia incorporating an efference copy of motor actions

    PubMed Central

    Fee, Michale S.

    2012-01-01

    In its simplest formulation, reinforcement learning is based on the idea that if an action taken in a particular context is followed by a favorable outcome, then, in the same context, the tendency to produce that action should be strengthened, or reinforced. While reinforcement learning forms the basis of many current theories of basal ganglia (BG) function, these models do not incorporate distinct computational roles for signals that convey context, and those that convey what action an animal takes. Recent experiments in the songbird suggest that vocal-related BG circuitry receives two functionally distinct excitatory inputs. One input is from a cortical region that carries context information about the current “time” in the motor sequence. The other is an efference copy of motor commands from a separate cortical brain region that generates vocal variability during learning. Based on these findings, I propose here a general model of vertebrate BG function that combines context information with a distinct motor efference copy signal. The signals are integrated by a learning rule in which efference copy inputs gate the potentiation of context inputs (but not efference copy inputs) onto medium spiny neurons in response to a rewarded action. The hypothesis is described in terms of a circuit that implements the learning of visually guided saccades. The model makes testable predictions about the anatomical and functional properties of hypothesized context and efference copy inputs to the striatum from both thalamic and cortical sources. PMID:22754501

  1. Early-stage hypogene karstification in a mountain hydrologic system: A coupled thermohydrochemical model incorporating buoyant convection

    NASA Astrophysics Data System (ADS)

    Chaudhuri, A.; Rajaram, H.; Viswanathan, H.

    2013-09-01

    The early stage of hypogene karstification is investigated using a coupled thermohydrochemical model of a mountain hydrologic system, in which water enters along a water table and descends to significant depth (˜1 km) before ascending through a central high-permeability fracture. The model incorporates reactive alteration driven by dissolution/precipitation of limestone in a carbonic acid system, due to both temperature- and pressure-dependent solubility, and kinetics. Simulations were carried out for homogeneous and heterogeneous initial fracture aperture fields, using the FEHM (Finite Element Heat and Mass Transfer) code. Initially, retrograde solubility is the dominant mechanism of fracture aperture growth. As the fracture transmissivity increases, a critical Rayleigh number value is exceeded at some stage. Buoyant convection is then initiated and controls the evolution of the system thereafter. For an initially homogeneous fracture aperture field, deep well-organized buoyant convection rolls form. For initially heterogeneous aperture fields, preferential flow suppresses large buoyant convection rolls, although a large number of smaller rolls form. Even after the onset of buoyant convection, dissolution in the fracture is sustained along upward flow paths by retrograde solubility and by additional "mixing corrosion" effects closer to the surface. Aperture growth patterns in the fracture are very different from those observed in simulations of epigenic karst systems, and retain imprints of both buoyant convection and preferential flow. Both retrograde solubility and buoyant convection contribute to these differences. The paper demonstrates the potential value of coupled models as tools for understanding the evolution and behavior of hypogene karst systems.

  2. Incorporating fault tolerance in distributed agent based systems by simulating bio-computing model of stress pathways

    NASA Astrophysics Data System (ADS)

    Bansal, Arvind K.

    2006-05-01

    Bio-computing model of 'Distributed Multiple Intelligent Agents Systems' (BDMIAS) models agents as genes, a cooperating group of agents as operons - commonly regulated groups of genes, and the complex task as a set of interacting pathways such that the pathways involve multiple cooperating operons. The agents (or groups of agents) interact with each other using message passing and pattern based bindings that may reconfigure agent's function temporarily. In this paper, a technique has been described for incorporating fault tolerance in BDMIAS. The scheme is based upon simulating BDMIAS, exploiting the modeling of biological stress pathways, integration of fault avoidance, and distributed fault recovery of the crashed agents. Stress pathways are latent pathways in biological system that gets triggered very quickly, regulate the complex biological system by temporarily regulating or inactivating the undesirable pathways, and are essential to avoid catastrophic failures. Pattern based interaction between messages and agents allow multiple agents to react concurrently in response to single condition change represented by a message broadcast. The fault avoidance exploits the integration of the intelligent processing rate control using message based loop feedback and temporary reconfiguration that alters the data flow between functional modules within an agent, and may alter. The fault recovery exploits the concept of semi passive shadow agents - one on the local machine and other on the remote machine, dynamic polling of machines, logically time stamped messages to avoid message losses, and distributed archiving of volatile part of agent state on distributed machines. Various algorithms have been described.

  3. Thermal remote sensing of surface soil water content with partial vegetation cover for incorporation into climate models

    NASA Technical Reports Server (NTRS)

    Gillies, Robert R.; Carlson, Toby N.

    1995-01-01

    This study outlines a method for the estimation of regional patterns of surface moisture availability (M(sub 0)) and fractional vegetation (Fr) in the presence of spatially variable vegetation cover. The method requires relating variations in satellite-derived (NOAA, Advanced Very High Resolution Radiometer (AVHRR)) surface radiant temperature to a vegetation index (computed from satellite visible and near-infrared data) while coupling this association to an inverse modeling scheme. More than merely furnishing surface soil moisture values, the method constitues a new conceptual and practical approach for combining thermal infrared and vegetation index measurements for incorporating the derived values of M(sub 0) into hydrologic and atmospheric prediction models. Application of the technique is demonstrated for a region in and around the city of Newcastle upon Tyne situated in the northeast of England. A regional estimate of M(sub 0) is derived and is probabbly good for fractional vegetation cover up to 80% before errors in the estimated soil water content become unacceptably large. Moreover, a normalization scheme is suggested from which a nomogram, `universal triangle,' is constructed and is seen to fit the observed data well. The universal triangle also simplifies the inclusion of remotely derived M(sub 0) in hydrology and meteorological models and is perhaps a practicable step toward integrating derived data from satellite measurements in weather forecasting.

  4. Incorporating Field Studies into Species Distribution and Climate Change Modelling: A Case Study of the Koomal Trichosurus vulpecula hypoleucus (Phalangeridae).

    PubMed

    Molloy, Shaun W; Davis, Robert A; van Etten, Eddie J B

    2016-01-01

    Species distribution models (SDMs) are an effective way of predicting the potential distribution of species and their response to environmental change. Most SDMs apply presence data to a relatively generic set of predictive variables such as climate. However, this weakens the modelling process by overlooking the responses to more cryptic predictive variables. In this paper we demonstrate a means by which data gathered from an intensive animal trapping study can be used to enhance SDMs by combining field data with bioclimatic modelling techniques to determine the future potential distribution for the koomal (Trichosurus vulpecula hypoleucus). The koomal is a geographically isolated subspecies of the common brushtail possum, endemic to south-western Australia. Since European settlement this taxon has undergone a significant reduction in distribution due to its vulnerability to habitat fragmentation, introduced predators and tree/shrub dieback caused by a virulent group of plant pathogens of the genus Phytophthora. An intensive field study found: 1) the home range for the koomal rarely exceeded 1 km in in length at its widest point; 2) areas heavily infested with dieback were not occupied; 3) gap crossing between patches (>400 m) was common behaviour; 4) koomal presence was linked to the extent of suitable vegetation; and 5) where the needs of koomal were met, populations in fragments were demographically similar to those found in contiguous landscapes. We used this information to resolve a more accurate SDM for the koomal than that created from bioclimatic data alone. Specifically, we refined spatial coverages of remnant vegetation and dieback, to develop a set of variables that we combined with selected bioclimatic variables to construct models. We conclude that the utility value of an SDM can be enhanced and given greater resolution by identifying variables that reflect observed, species-specific responses to landscape parameters and incorporating these responses

  5. Incorporating Field Studies into Species Distribution and Climate Change Modelling: A Case Study of the Koomal Trichosurus vulpecula hypoleucus (Phalangeridae)

    PubMed Central

    Davis, Robert A.; van Etten, Eddie J. B.

    2016-01-01

    Species distribution models (SDMs) are an effective way of predicting the potential distribution of species and their response to environmental change. Most SDMs apply presence data to a relatively generic set of predictive variables such as climate. However, this weakens the modelling process by overlooking the responses to more cryptic predictive variables. In this paper we demonstrate a means by which data gathered from an intensive animal trapping study can be used to enhance SDMs by combining field data with bioclimatic modelling techniques to determine the future potential distribution for the koomal (Trichosurus vulpecula hypoleucus). The koomal is a geographically isolated subspecies of the common brushtail possum, endemic to south-western Australia. Since European settlement this taxon has undergone a significant reduction in distribution due to its vulnerability to habitat fragmentation, introduced predators and tree/shrub dieback caused by a virulent group of plant pathogens of the genus Phytophthora. An intensive field study found: 1) the home range for the koomal rarely exceeded 1 km in in length at its widest point; 2) areas heavily infested with dieback were not occupied; 3) gap crossing between patches (>400 m) was common behaviour; 4) koomal presence was linked to the extent of suitable vegetation; and 5) where the needs of koomal were met, populations in fragments were demographically similar to those found in contiguous landscapes. We used this information to resolve a more accurate SDM for the koomal than that created from bioclimatic data alone. Specifically, we refined spatial coverages of remnant vegetation and dieback, to develop a set of variables that we combined with selected bioclimatic variables to construct models. We conclude that the utility value of an SDM can be enhanced and given greater resolution by identifying variables that reflect observed, species-specific responses to landscape parameters and incorporating these responses

  6. Incorporation of advanced aerosol activation treatments into CESM/CAM5: model evaluation and impacts on aerosol indirect effects

    NASA Astrophysics Data System (ADS)

    Gantt, B.; He, J.; Zhang, X.; Zhang, Y.; Nenes, A.

    2013-12-01

    One of the greatest sources of uncertainty in the science of anthropogenic climate change is from aerosol-cloud interactions. The activation of aerosols into cloud droplets is a direct microphysical link between aerosols and clouds; parameterizations of this process realistically link aerosol with cloud condensation nuclei (CCN) and the resulting indirect effects. Small differences between parameterizations can have a large impact on the spatiotemporal distributions of activated aerosols and the resulting cloud properties. In this work, we incorporate a series of aerosol activation schemes into the Community Atmosphere Model version 5.1.1 within the Community Earth System Model version 1.0.5 (CESM/CAM5), which include factors such as insoluble aerosol adsorption, giant cloud condensation nuclei (CCN) activation kinetics, and entrainment to understand their individual impacts on global scale cloud droplet number concentrations (CDNCs). Compared to the existing simple activation scheme in CESM/CAM5, this series of schemes predict CDNCs that are typically in better agreement with satellite-derived and observed values. The largest changes in predicted CDNCs occur over desert and oceanic regions, owing to the enhanced activation of dust from insoluble aerosol adsorption and reductions in cloud supersaturation from the intense absorption of water vapor in regions of strong giant CCN emissions (e.g., sea-salt). Comparison of CESM/CAM5 against satellite-derived cloud optical thickness and liquid water path shows that the updated activation schemes improve the low biases in their predictions. Globally, the incorporation of all updated schemes leads to an average increase in column CDNCs of 155%, an increase in shortwave cloud forcing of 13%, and a decrease in surface shortwave radiation of 4%. In terms of meteorological impacts, these updated aerosol activation schemes result in a slight decrease in near-surface temperature of 0.9 °C and precipitation of 0.04 mm day-1

  7. Electrochemical measurement of lateral diffusion coefficients of ubiquinones and plastoquinones of various isoprenoid chain lengths incorporated in model bilayers.

    PubMed Central

    Marchal, D; Boireau, W; Laval, J M; Moiroux, J; Bourdillon, C

    1998-01-01

    The long-range diffusion coefficients of isoprenoid quinones in a model of lipid bilayer were determined by a method avoiding fluorescent probe labeling of the molecules. The quinone electron carriers were incorporated in supported dimyristoylphosphatidylcholine layers at physiological molar fractions (<3 mol%). The elaborate bilayer template contained a built-in gold electrode at which the redox molecules solubilized in the bilayer were reduced or oxidized. The lateral diffusion coefficient of a natural quinone like UQ10 or PQ9 was 2.0 +/- 0.4 x 10(-8) cm2 s(-1) at 30 degrees C, two to three times smaller than the diffusion coefficient of a lipid analog in the same artificial bilayer. The lateral mobilities of the oxidized or reduced forms could be determined separately and were found to be identical in the 4-13 pH range. For a series of isoprenoid quinones, UQ2 or PQ2 to UQ10, the diffusion coefficient exhibited a marked dependence on the length of the isoprenoid chain. The data fit very well the quantitative behavior predicted by a continuum fluid model in which the isoprenoid chains are taken as rigid particles moving in the less viscous part of the bilayer and rubbing against the more viscous layers of lipid heads. The present study supports the concept of a homogeneous pool of quinone located in the less viscous region of the bilayer. PMID:9545054

  8. Incorporation of diffusion-weighted magnetic resonance imaging data into a simple mathematical model of tumor growth

    NASA Astrophysics Data System (ADS)

    Atuegwu, N. C.; Colvin, D. C.; Loveless, M. E.; Xu, L.; Gore, J. C.; Yankeelov, T. E.

    2012-01-01

    We build on previous work to show how serial diffusion-weighted MRI (DW-MRI) data can be used to estimate proliferation rates in a rat model of brain cancer. Thirteen rats were inoculated intracranially with 9L tumor cells; eight rats were treated with the chemotherapeutic drug 1,3-bis(2-chloroethyl)-1-nitrosourea and five rats were untreated controls. All animals underwent DW-MRI immediately before, one day and three days after treatment. Values of the apparent diffusion coefficient (ADC) were calculated from the DW-MRI data and then used to estimate the number of cells in each voxel and also for whole tumor regions of interest. The data from the first two imaging time points were then used to estimate the proliferation rate of each tumor. The proliferation rates were used to predict the number of tumor cells at day three, and this was correlated with the corresponding experimental data. The voxel-by-voxel analysis yielded Pearson's correlation coefficients ranging from -0.06 to 0.65, whereas the region of interest analysis provided Pearson's and concordance correlation coefficients of 0.88 and 0.80, respectively. Additionally, the ratio of positive to negative proliferation values was used to separate the treated and control animals (p <0.05) at an earlier point than the mean ADC values. These results further illustrate how quantitative measurements of tumor state obtained non-invasively by imaging can be incorporated into mathematical models that predict tumor growth.

  9. Patient-derived xenograft models for pancreatic adenocarcinoma demonstrate retention of tumor morphology through incorporation of murine stromal elements.

    PubMed

    Delitto, Daniel; Pham, Kien; Vlada, Adrian C; Sarosi, George A; Thomas, Ryan M; Behrns, Kevin E; Liu, Chen; Hughes, Steven J; Wallet, Shannon M; Trevino, Jose G

    2015-05-01

    Direct implantation of viable surgical specimens provides a representative preclinical platform in pancreatic adenocarcinoma. Patient-derived xenografts consistently demonstrate retained tumor morphology and genetic stability. However, the evolution of the tumor microenvironment over time remains poorly characterized in these models. This work specifically addresses the recruitment and incorporation of murine stromal elements into expanding patient-derived pancreatic adenocarcinoma xenografts, establishing the integration of murine cells into networks of invading cancer cells. In addition, we provide methods and observations in the establishment and maintenance of a patient-derived pancreatic adenocarcinoma xenograft model. A total of 25 histologically confirmed pancreatic adenocarcinoma specimens were implanted subcutaneously into nonobese diabetic severe combined immunodeficiency mice. Patient demographics, staging, pathological analysis, and outcomes were analyzed. After successful engraftment of tumors, histological and immunofluorescence analyses were performed on explanted tumors. Pancreatic adenocarcinoma specimens were successfully engrafted in 15 (60%) of 25 attempts. Successful engraftment does not appear to correlate with clinicopathologic factors or patient survival. Tumor morphology is conserved through multiple passages, and tumors retain metastatic potential. Interestingly, despite morphological similarity between passages, human stromal elements do not appear to expand with invading cancer cells. Rather, desmoplastic murine stroma dominates the xenograft microenvironment after the initial implantation. Recruitment of stromal elements in this manner to support and maintain tumor growth represents a novel avenue for investigation into tumor-stromal interactions.

  10. A modified Wright-Fisher model that incorporates Ne: A variant of the standard model with increased biological realism and reduced computational complexity.

    PubMed

    Zhao, Lei; Gossmann, Toni I; Waxman, David

    2016-03-21

    The Wright-Fisher model is an important model in evolutionary biology and population genetics. It has been applied in numerous analyses of finite populations with discrete generations. It is recognised that real populations can behave, in some key aspects, as though their size that is not the census size, N, but rather a smaller size, namely the effective population size, Ne. However, in the Wright-Fisher model, there is no distinction between the effective and census population sizes. Equivalently, we can say that in this model, Ne coincides with N. The Wright-Fisher model therefore lacks an important aspect of biological realism. Here, we present a method that allows Ne to be directly incorporated into the Wright-Fisher model. The modified model involves matrices whose size is determined by Ne. Thus apart from increased biological realism, the modified model also has reduced computational complexity, particularly so when Ne⪡N. For complex problems, it may be hard or impossible to numerically analyse the most commonly-used approximation of the Wright-Fisher model that incorporates Ne, namely the diffusion approximation. An alternative approach is simulation. However, the simulations need to be sufficiently detailed that they yield an effective size that is different to the census size. Simulations may also be time consuming and have attendant statistical errors. The method presented in this work may then be the only alternative to simulations, when Ne differs from N. We illustrate the straightforward application of the method to some problems involving allele fixation and the determination of the equilibrium site frequency spectrum. We then apply the method to the problem of fixation when three alleles are segregating in a population. This latter problem is significantly more complex than a two allele problem and since the diffusion equation cannot be numerically solved, the only other way Ne can be incorporated into the analysis is by simulation. We have

  11. Incorporating moisture content in modeling the surface energy balance of debris-covered Changri Nup Glacier, Nepal

    NASA Astrophysics Data System (ADS)

    Giese, Alexandra; Boone, Aaron; Morin, Samuel; Lejeune, Yves; Wagnon, Patrick; Dumont, Marie; Hawley, Robert

    2016-04-01

    Glaciers whose ablation zones are covered in supraglacial debris comprise a significant portion of glaciers in High Mountain Asia and two-thirds in the South Central Himalaya. Such glaciers evade traditional proxies for mass balance because they are difficult to delineate remotely and because they lose volume via thinning rather than via retreat. Additionally, their surface energy balance is significantly more complicated than their clean counterparts' due to a conductive heat flux from the debris-air interface to the ice-debris boundary, where melt occurs. This flux is a function of the debris' thickness; thermal, radiative, and physical properties; and moisture content. To date, few surface energy balance models have accounted for debris moisture content and phase changes despite the fact that they are well-known to affect fluxes of mass, latent heat, and conduction. In this study, we introduce a new model, ISBA-DEB, which is capable of solving not only the heat equation but also moisture transport and retention in the debris. The model is based upon Meteo-France's Interactions between Soil, Biosphere, and Atmosphere (ISBA) soil and vegetation model, significantly adapted for debris and coupled with the snowpack model Crocus within the SURFEX platform. We drive the model with continuous ERA-Interim reanalysis data, adapted to the local topography (i.e. considering local elevation and shadowing) and downscaled and de-biased using 5 years of in-situ meteorological data at Changri Nup glacier [(27.859N, 86.847E)] in the Khumbu Himal. The 1-D model output is then evaluated through comparison with measured temperature in and ablation under a 10-cm thick debris layer on Changri Nup. We have found that introducing a non-equilibrium model for water flow, rather than using the mixed-form Richard's equation alone, promotes greater consistency with moisture observations. This explicit incorporation of moisture processes improves simulation of the snow-debris-ice column

  12. Evaluating the Capacity of Global CO2 Flux and Atmospheric Transport Models to Incorporate New Satellite Observations

    NASA Technical Reports Server (NTRS)

    Kawa, S. R.; Collatz, G. J.; Erickson, D. J.; Denning, A. S.; Wofsy, S. C.; Andrews, A. E.

    2007-01-01

    As we enter the new era of satellite remote sensing for CO2 and other carbon cyclerelated quantities, advanced modeling and analysis capabilities are required to fully capitalize on the new observations. Model estimates of CO2 surface flux and atmospheric transport are required for initial constraints on inverse analyses, to connect atmospheric observations to the location of surface sources and sinks, and ultimately for future projections of carbon-climate interactions. For application to current, planned, and future remotely sensed CO2 data, it is desirable that these models are accurate and unbiased at time scales from less than daily to multi-annual and at spatial scales from several kilometers or finer to global. Here we focus on simulated CO2 fluxes from terrestrial vegetation and atmospheric transport mutually constrained by analyzed meteorological fields from the Goddard Modeling and Assimilation Office for the period 1998 through 2006. Use of assimilated meteorological data enables direct model comparison to observations across a wide range of scales of variability. The biospheric fluxes are produced by the CASA model at lxi degrees on a monthly mean basis, modulated hourly with analyzed temperature and sunlight. Both physiological and biomass burning fluxes are derived using satellite observations of vegetation, burned area (as in GFED-2), and analyzed meteorology. For the purposes of comparison to CO2 data, fossil fuel and ocean fluxes are also included in the transport simulations. In this presentation we evaluate the model's ability to simulate CO2 flux and mixing ratio variability in comparison to in situ observations at sites in Northern mid latitudes and the continental tropics. The influence of key process representations is inferred. We find that the model can resolve much of the hourly to synoptic variability in the observations, although there are limits imposed by vertical resolution of boundary layer processes. The seasonal cycle and its

  13. Recent Progresses in Incorporating Human Land-Water Management into Global Land Surface Models Toward Their Integration into Earth System Models

    NASA Technical Reports Server (NTRS)

    Pokhrel, Yadu N.; Hanasaki, Naota; Wada, Yoshihide; Kim, Hyungjun

    2016-01-01

    The global water cycle has been profoundly affected by human land-water management. As the changes in the water cycle on land can affect the functioning of a wide range of biophysical and biogeochemical processes of the Earth system, it is essential to represent human land-water management in Earth system models (ESMs). During the recent past, noteworthy progress has been made in large-scale modeling of human impacts on the water cycle but sufficient advancements have not yet been made in integrating the newly developed schemes into ESMs. This study reviews the progresses made in incorporating human factors in large-scale hydrological models and their integration into ESMs. The study focuses primarily on the recent advancements and existing challenges in incorporating human impacts in global land surface models (LSMs) as a way forward to the development of ESMs with humans as integral components, but a brief review of global hydrological models (GHMs) is also provided. The study begins with the general overview of human impacts on the water cycle. Then, the algorithms currently employed to represent irrigation, reservoir operation, and groundwater pumping are discussed. Next, methodological deficiencies in current modeling approaches and existing challenges are identified. Furthermore, light is shed on the sources of uncertainties associated with model parameterizations, grid resolution, and datasets used for forcing and validation. Finally, representing human land-water management in LSMs is highlighted as an important research direction toward developing integrated models using ESM frameworks for the holistic study of human-water interactions within the Earths system.

  14. First steps in incorporating data-driven modelling to flood early warning in Norway's Flood Forecasting Service

    NASA Astrophysics Data System (ADS)

    Borsányi, Péter; Hamududu, Byman; Wong Kwok, Wai; Magnusson, Jan; Shi, Min

    2016-04-01

    -describers will be refined to help identifying seasonal, geographical or other physical or temporal features, which will allow the preparation for hybrid use of data-driven and conceptual models. This way low forecast performance is expected to be improved by incorporating DDM to the existing conceptual modelling framework.

  15. In Situ Measurement, Characterization, and Modeling of Two-Phase Pressure Drop Incorporating Local Water Saturation in PEMFC Gas Channels

    NASA Astrophysics Data System (ADS)

    See, Evan J.

    Proton Exchange Membrane Fuel Cells (PEMFCs) have been an area of focus as an alternative for internal combustion engines in the transportation sector. Water and thermal management techniques remain as one of the key roadblocks in PEMFC development. The ability to model two-phase flow and pressure drop in PEMFCs is of significant importance to the performance and optimization of PEMFCs. This work provides a perspective on the numerous factors that affect the two-phase flow in the gas channels and presents a comprehensive pressure drop model through an extensive in situ fuel cell investigation. The study focused on low current density and low temperature operation of the cell, as these conditions present the most challenging scenario for water transport in the PEMFC reactant channels. Tests were conducted using two PEMFCs that were representative of the actual full scale commercial automotive geometry. The design of the flow fields allowed visual access to both cathode and anode sides for correlating the visual observations to the two-phase flow patterns and pressure drop. A total of 198 tests were conducted varying gas diffusion layer (GDL), inlet humidity, current density, and stoichiometry; this generated over 1500 average pressure drop measurements to develop and validate two-phase models. A two-phase 1+1 D modeling scheme is proposed that incorporates an elemental approach and control volume analysis to provide a comprehensive methodology and correlation for predicting two-phase pressure drop in PEMFC conditions. Key considerations, such as condensation within the channel, consumption of reactant gases, water transport across the membrane, and thermal gradients within the fuel cell, are reviewed and their relative importance illustrated. The modeling scheme is shown to predict channel pressure drop with a mean error of 10% over the full range of conditions and with a mean error of 5% for the primary conditions of interest. The model provides a unique and

  16. Incorporating Uncertainty Into the Ranking of SPARROW Model Nutrient Yields From Mississippi/Atchafalaya River Basin Watersheds1

    PubMed Central

    Robertson, Dale M; Schwarz, Gregory E; Saad, David A; Alexander, Richard B

    2009-01-01

    Excessive loads of nutrients transported by tributary rivers have been linked to hypoxia in the Gulf of Mexico. Management efforts to reduce the hypoxic zone in the Gulf of Mexico and improve the water quality of rivers and streams could benefit from targeting nutrient reductions toward watersheds with the highest nutrient yields delivered to sensitive downstream waters. One challenge is that most conventional watershed modeling approaches (e.g., mechanistic models) used in these management decisions do not consider uncertainties in the predictions of nutrient yields and their downstream delivery. The increasing use of parameter estimation procedures to statistically estimate model coefficients, however, allows uncertainties in these predictions to be reliably estimated. Here, we use a robust bootstrapping procedure applied to the results of a previous application of the hybrid statistical/mechanistic watershed model SPARROW (Spatially Referenced Regression On Watershed attributes) to develop a statistically reliable method for identifying “high priority” areas for management, based on a probabilistic ranking of delivered nutrient yields from watersheds throughout a basin. The method is designed to be used by managers to prioritize watersheds where additional stream monitoring and evaluations of nutrient-reduction strategies could be undertaken. Our ranking procedure incorporates information on the confidence intervals of model predictions and the corresponding watershed rankings of the delivered nutrient yields. From this quantified uncertainty, we estimate the probability that individual watersheds are among a collection of watersheds that have the highest delivered nutrient yields. We illustrate the application of the procedure to 818 eight-digit Hydrologic Unit Code watersheds in the Mississippi/Atchafalaya River basin by identifying 150 watersheds having the highest delivered nutrient yields to the Gulf of Mexico. Highest delivered yields were from

  17. Incorporating uncertainty into the ranking of SPARROW model nutrient yields from Mississippi/Atchafalaya River basin watersheds

    USGS Publications Warehouse

    Robertson, Dale M.; Schwarz, Gregory E.; Saad, David A.; Alexander, Richard B.

    2009-01-01

    Excessive loads of nutrients transported by tributary rivers have been linked to hypoxia in the Gulf of Mexico. Management efforts to reduce the hypoxic zone in the Gulf of Mexico and improve the water quality of rivers and streams could benefit from targeting nutrient reductions toward watersheds with the highest nutrient yields delivered to sensitive downstream waters. One challenge is that most conventional watershed modeling approaches (e.g., mechanistic models) used in these management decisions do not consider uncertainties in the predictions of nutrient yields and their downstream delivery. The increasing use of parameter estimation procedures to statistically estimate model coefficients, however, allows uncertainties in these predictions to be reliably estimated. Here, we use a robust bootstrapping procedure applied to the results of a previous application of the hybrid statistical/mechanistic watershed model SPARROW (Spatially Referenced Regression On Watershed attributes) to develop a statistically reliable method for identifying “high priority” areas for management, based on a probabilistic ranking of delivered nutrient yields from watersheds throughout a basin. The method is designed to be used by managers to prioritize watersheds where additional stream monitoring and evaluations of nutrient-reduction strategies could be undertaken. Our ranking procedure incorporates information on the confidence intervals of model predictions and the corresponding watershed rankings of the delivered nutrient yields. From this quantified uncertainty, we estimate the probability that individual watersheds are among a collection of watersheds that have the highest delivered nutrient yields. We illustrate the application of the procedure to 818 eight-digit Hydrologic Unit Code watersheds in the Mississippi/Atchafalaya River basin by identifying 150 watersheds having the highest delivered nutrient yields to the Gulf of Mexico. Highest delivered yields were from

  18. Erosion Modeling in Central China - Soil Data Acquisition by Conditioned Latin Hypercube Sampling and Incorporation of Legacy Data

    NASA Astrophysics Data System (ADS)

    Stumpf, Felix; Schönbrodt-Stitt, Sarah; Schmidt, Karsten; Behrens, Thorsten; Scholten, Thomas

    2013-04-01

    The Three Gorges Dam at the Yangtze River in Central China outlines a prominent example of human-induced environmental impacts. Throughout one year the water table at the main river fluctuates about 30m due to impoundment and drainage activities. The dynamic water table implicates a range of georisks such as soil erosion, mass movements, sediment transport and diffuse matter inputs into the reservoir. Within the framework of the joint Sino-German project YANGTZE GEO, the subproject "Soil Erosion" deals with soil erosion risks and sediment transport pathways into the reservoir. The study site is a small catchment (4.8 km²) in Badong, approximately 100 km upstream the dam. It is characterized by scattered plots of agricultural landuse and resettlements in a largely wooded, steep sloping and mountainous area. Our research is focused on data acquisition and processing to develop a process-oriented erosion model. Hereby, area-covering knowledge of specific soil properties in the catchment is an intrinsic input parameter. This will be acquired by means of digital soil mapping (DSM). Thereby, soil properties are estimated by covariates. The functions are calibrated by soil property samples. The DSM approach is based on an appropriate sample design, which reflects the heterogeneity of the catchment, regarding the covariates with influence on the relevant soil properties. In this approach the covariates, processed by a digital terrain analysis, are outlined by the slope, altitude, profile curvature, plane curvature, and the aspect. For the development of the sample design, we chose the Conditioned Latin Hypercube Sampling (cLHS) procedure (Minasny and McBratney, 2006). It provides an efficient method of sampling variables from their multivariate distribution. Thereby, a sample size n from multiple variables is drawn such that for each variable the sample is marginally maximally stratified. The method ensures the maximal stratification by two features: First, number of

  19. A flexible automatically adaptive surface nuclear magnetic resonance modelling and inversion framework incorporating complex data and static dephasing dynamics

    NASA Astrophysics Data System (ADS)

    Irons, Trevor P.

    Surface nuclear magnetic resonance (sNMR) is the only geophysical technique that can directly and non-invasively detect the presence of subsurface liquid water. The method has established itself as valuable tool for hydrologists and groundwater managers owing to the fact that both porosity and hydraulic conductivity estimates can be made using this technique. Although sNMR has enormous potential, there are many challenges with the technique which hinder it's more widespread adoption. For these reasons sNMR has primarily been used as a 1D groundwater sounding tool, although there exist myriad other applications for a method directly sensitive to liquid water. Simultaneously inverting the entire complex dataset as well as the employment of arrays of separated transmitter and receiver coils and integration with other geophysical methods can help to overcome these limitations. This requires modelling algorithms that can accommodate a widely varying set of survey configurations and scenarios. I present the innovative use of sNMR applied to two geotechnical problems: volcanic landslide hazard characterization on Mt. Baker, Washington and the monitoring of internal erosion in earthen embankments. These applications necessitated the development of a general modelling framework capable of handling arbitrary positioned transmitter and receiver coils as well as 3D water distribution. The advantages of comprehensive (whole dataset) inversion of the entire sNMR record have been established for time-domain inversions. However, these inversions are memory intensive and struggle to fit the phase portion of the dataset-necessitating the regretful dismissal of this valuable information. I instead consider the sNMR inversion problem in the frequency-domain for the first time. There are several benefits: effectively lossless compression, and the ability to easily incorporate and solve for static dephasing dynamics caused by magnetic field inhomogeneities. This has allowed for the

  20. A Robust Model-free Approach for Rare Variants Association Studies Incorporating Gene-Gene and Gene-Environmental Interactions

    PubMed Central

    Fan, Ruixue; Lo, Shaw-Hwa

    2013-01-01

    Recently more and more evidence suggest that rare variants with much lower minor allele frequencies play significant roles in disease etiology. Advances in next-generation sequencing technologies will lead to many more rare variants association studies. Several statistical methods have been proposed to assess the effect of rare variants by aggregating information from multiple loci across a genetic region and testing the association between the phenotype and aggregated genotype. One limitation of existing methods is that they only look into the marginal effects of rare variants but do not systematically take into account effects due to interactions among rare variants and between rare variants and environmental factors. In this article, we propose the summation of partition approach (SPA), a robust model-free method that is designed specifically for detecting both marginal effects and effects due to gene-gene (G×G) and gene-environmental (G×E) interactions for rare variants association studies. SPA has three advantages. First, it accounts for the interaction information and gains considerable power in the presence of unknown and complicated G×G or G×E interactions. Secondly, it does not sacrifice the marginal detection power; in the situation when rare variants only have marginal effects it is comparable with the most competitive method in current literature. Thirdly, it is easy to extend and can incorporate more complex interactions; other practitioners and scientists can tailor the procedure to fit their own study friendly. Our simulation studies show that SPA is considerably more powerful than many existing methods in the presence of G×G and G×E interactions. PMID:24358248

  1. Predicting Secretory Proteins of Malaria Parasite by Incorporating Sequence Evolution Information into Pseudo Amino Acid Composition via Grey System Model

    PubMed Central

    Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

    2012-01-01

    The malaria disease has become a cause of poverty and a major hindrance to economic development. The culprit of the disease is the parasite, which secretes an array of proteins within the host erythrocyte to facilitate its own survival. Accordingly, the secretory proteins of malaria parasite have become a logical target for drug design against malaria. Unfortunately, with the increasing resistance to the drugs thus developed, the situation has become more complicated. To cope with the drug resistance problem, one strategy is to timely identify the secreted proteins by malaria parasite, which can serve as potential drug targets. However, it is both expensive and time-consuming to identify the secretory proteins of malaria parasite by experiments alone. To expedite the process for developing effective drugs against malaria, a computational predictor called “iSMP-Grey” was developed that can be used to identify the secretory proteins of malaria parasite based on the protein sequence information alone. During the prediction process a protein sample was formulated with a 60D (dimensional) feature vector formed by incorporating the sequence evolution information into the general form of PseAAC (pseudo amino acid composition) via a grey system model, which is particularly useful for solving complicated problems that are lack of sufficient information or need to process uncertain information. It was observed by the jackknife test that iSMP-Grey achieved an overall success rate of 94.8%, remarkably higher than those by the existing predictors in this area. As a user-friendly web-server, iSMP-Grey is freely accessible to the public at http://www.jci-bioinfo.cn/iSMP-Grey. Moreover, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematical equations involved in this paper. PMID:23189138

  2. Predicting secretory proteins of malaria parasite by incorporating sequence evolution information into pseudo amino acid composition via grey system model.

    PubMed

    Lin, Wei-Zhong; Fang, Jian-An; Xiao, Xuan; Chou, Kuo-Chen

    2012-01-01

    The malaria disease has become a cause of poverty and a major hindrance to economic development. The culprit of the disease is the parasite, which secretes an array of proteins within the host erythrocyte to facilitate its own survival. Accordingly, the secretory proteins of malaria parasite have become a logical target for drug design against malaria. Unfortunately, with the increasing resistance to the drugs thus developed, the situation has become more complicated. To cope with the drug resistance problem, one strategy is to timely identify the secreted proteins by malaria parasite, which can serve as potential drug targets. However, it is both expensive and time-consuming to identify the secretory proteins of malaria parasite by experiments alone. To expedite the process for developing effective drugs against malaria, a computational predictor called "iSMP-Grey" was developed that can be used to identify the secretory proteins of malaria parasite based on the protein sequence information alone. During the prediction process a protein sample was formulated with a 60D (dimensional) feature vector formed by incorporating the sequence evolution information into the general form of PseAAC (pseudo amino acid composition) via a grey system model, which is particularly useful for solving complicated problems that are lack of sufficient information or need to process uncertain information. It was observed by the jackknife test that iSMP-Grey achieved an overall success rate of 94.8%, remarkably higher than those by the existing predictors in this area. As a user-friendly web-server, iSMP-Grey is freely accessible to the public at http://www.jci-bioinfo.cn/iSMP-Grey. Moreover, for the convenience of most experimental scientists, a step-by-step guide is provided on how to use the web-server to get the desired results without the need to follow the complicated mathematical equations involved in this paper.

  3. From Numerical Problem Solving to Model-Based Experimentation Incorporating Computer-Based Tools of Various Scales into the ChE Curriculum

    ERIC Educational Resources Information Center

    Shacham, Mordechai; Cutlip, Michael B.; Brauner, Neima

    2009-01-01

    A continuing challenge to the undergraduate chemical engineering curriculum is the time-effective incorporation and use of computer-based tools throughout the educational program. Computing skills in academia and industry require some proficiency in programming and effective use of software packages for solving 1) single-model, single-algorithm…

  4. Molecular view modeling of atmospheric organic particulate matter: Incorporating molecular structure and co-condensation of water

    NASA Astrophysics Data System (ADS)

    Pankow, James F.; Marks, Marguerite C.; Barsanti, Kelley C.; Mahmud, Abdullah; Asher, William E.; Li, Jingyi; Ying, Qi; Jathar, Shantanu H.; Kleeman, Michael J.

    2015-12-01

    Most urban and regional models used to predict levels of organic particulate matter (OPM) are based on fundamental equations for gas/particle partitioning, but make the highly simplifying, anonymized-view (AV) assumptions that OPM levels are not affected by either: a) the molecular characteristics of the condensing organic compounds (other than simple volatility); or b) co-condensation of water as driven by non-zero relative humidity (RH) values. The simplifying assumptions have allowed parameterized chamber results for formation of secondary organic aerosol (SOA) (e.g., "two-product" (2p) coefficients) to be incorporated in chemical transport models. However, a return towards a less simplistic (and more computationally demanding) molecular view (MV) is needed that acknowledges that atmospheric OPM is a mixture of organic compounds with differing polarities, water, and in some cases dissolved salts. The higher computational cost of MV modeling results from a need for iterative calculations of the composition-dependent gas/particle partition coefficient values. MV modeling of OPM that considered water uptake (but not dissolved salts) was carried out for the southeast United States for the period August 29 through September 7, 2006. Three model variants were used at three universities: CMAQ-RH-2p (at PSU), UCD/CIT-RH-2p (at UCD), and CMAQ-RH-MCM (at TAMU). With the first two, MV structural characteristics (carbon number and numbers of functional groups) were assigned to each of the 2p products used in CMAQv.4.7.1 such that resulting predicted Kp,i values matched those in CMAQv.4.7.1. When water uptake was allowed, most runs assumed that uptake occurred only into the SOA portion, and imposed immiscibility of SOA with primary organic aerosol (POA). (POA is often viewed as rather non-polar, while SOA is commonly viewed as moderately-to-rather polar. Some runs with UCD/CIT-RH-2p were used to investigate the effects of POA/SOA miscibility.) CMAQ-RH-MCM used MCM to

  5. Optimizing stem cell functions and antibacterial properties of TiO2 nanotubes incorporated with ZnO nanoparticles: experiments and modeling.

    PubMed

    Liu, Wenwen; Su, Penglei; Gonzales, Arthur; Chen, Su; Wang, Na; Wang, Jinshu; Li, Hongyi; Zhang, Zhenting; Webster, Thomas J

    2015-01-01

    To optimize mesenchymal stem cell differentiation and antibacterial properties of titanium (Ti), nano-sized zinc oxide (ZnO) particles with tunable concentrations were incorporated into TiO2 nanotubes (TNTs) using a facile hydrothermal strategy. It is revealed here for the first time that the TNTs incorporated with ZnO nanoparticles exhibited better biocompatibility compared with pure Ti samples (controls) and that the amount of ZnO (tailored by the concentration of Zn(NO3)2 in the precursor) introduced into TNTs played a crucial role on their osteogenic properties. Not only was the alkaline phosphatase activity improved to about 13.8 U/g protein, but the osterix, collagen-I, and osteocalcin gene expressions was improved from mesenchymal stem cells compared to controls. To further explore the mechanism of TNTs decorated with ZnO on cell functions, a response surface mathematical model was used to optimize the concentration of ZnO incorporation into the Ti nanotubes for stem cell differentiation and antibacterial properties for the first time. Both experimental and modeling results confirmed (R (2) values of 0.8873-0.9138 and 0.9596-0.9941, respectively) that Ti incorporated with appropriate concentrations (with an initial concentration of Zn(NO3)2 at 0.015 M) of ZnO can provide exceptional osteogenic properties for stem cell differentiation in bone cells with strong antibacterial effects, properties important for improving dental and orthopedic implant efficacy. PMID:25792833

  6. Ameliorative effects of telmisartan on the inflammatory response and impaired spatial memory in a rat model of Alzheimer's disease incorporating additional cerebrovascular disease factors.

    PubMed

    Shindo, Taro; Takasaki, Kotaro; Uchida, Kanako; Onimura, Rika; Kubota, Kaori; Uchida, Naoki; Irie, Keiichi; Katsurabayashi, Shutaro; Mishima, Kenichi; Nishimura, Ryoji; Fujiwara, Michihiro; Iwasaki, Katsunori

    2012-01-01

    Telmisartan, an angiotensin type 1 receptor blocker, is used in the management of hypertension to control blood pressure. In addition, telmisartan has a partial agonistic effect on peroxisome proliferator activated receptor γ (PPARγ). Recently, the effects of telmisartan on spatial memory or the inflammatory response were monitored in a mouse model of Alzheimer's disease (AD). However, to date, no studies have investigated the ameliorative effects of telmisartan on impaired spatial memory and the inflammatory response in an AD animal model incorporating additional cerebrovascular disease factors. In this study, we examined the effect of telmisartan on spatial memory impairment and the inflammatory response in a rat model of AD incorporating additional cerebrovascular disease factors. Rats were subjected to cerebral ischemia and an intracerebroventricular injection of oligomeric or aggregated amyloid-β (Aβ). Oral administration of telmisartan (0.3, 1, 3 mg/kg/d) seven days after ischemia and Aβ treatment resulted in better performance in the eight arm radial maze task in a dose-dependent manner. Telmisartan also reduced tumor necrosis factor α mRNA expression in the hippocampal region of rats with impaired spatial memory. These effects of telmisartan were antagonized by GW9662, an antagonist of PPARγ. These results suggest that telmisartan has ameliorative effects on the impairment of spatial memory in a rat model of AD incorporating additional cerebrovascular disease factors via its anti-inflammatory effect.

  7. Incorporation model of N into GaInNAs alloys grown by radio-frequency plasma-assisted molecular beam epitaxy

    SciTech Connect

    Aho, A.; Korpijärvi, V.-M.; Tukiainen, A.; Puustinen, J.; Guina, M.

    2014-12-07

    We present a Maxwell-Boltzmann electron energy distribution based model for the incorporation rate of nitrogen into GaInNAs grown by molecular beam epitaxy (MBE) using a radio frequency plasma source. Nitrogen concentration is predicted as a function of radio-frequency system primary resistance, N flow, and RF power, and group III growth rate. The semi-empirical model is shown to be repeatable with a maximum error of 6%. The model was validated for two different MBE systems by growing GaInNAs on GaAs(100) with variable nitrogen composition of 0%–6%.

  8. Quantitative measurements of regional glucose utilization and rate of valine incorporation into proteins by double-tracer autoradiography in the rat brain tumor model

    SciTech Connect

    Kirikae, M.; Diksic, M.; Yamamoto, Y.L.

    1989-02-01

    We examined the rate of glucose utilization and the rate of valine incorporation into proteins using 2-(/sup 18/F)fluoro-2-deoxyglucose and L-(1-14C)-valine in a rat brain tumor model by quantitative double-tracer autoradiography. We found that in the implanted tumor the rate of valine incorporation into proteins was about 22 times and the rate of glucose utilization was about 1.5 times that in the contralateral cortex. (In the ipsilateral cortex, the tumor had a profound effect on glucose utilization but no effect on the rate of valine incorporation into proteins.) Our findings suggest that it is more useful to measure protein synthesis than glucose utilization to assess the effectiveness of antitumor agents and their toxicity to normal brain tissue. We compared two methods to estimate the rate of valine incorporation: kinetic (quantitation done using an operational equation and the average brain rate coefficients) and washed slices (unbound labeled valine removed by washing brain slices in 10% trichloroacetic acid). The results were the same using either method. It would seem that the kinetic method can thus be used for quantitative measurement of protein synthesis in brain tumors and normal brain tissue using (/sup 11/C)-valine with positron emission tomography.

  9. The Internal/External Frame of Reference Model Revisited: Incorporating General Cognitive Ability and General Academic Self-Concept

    ERIC Educational Resources Information Center

    Brunner, Martin; Ludtke, Oliver; Trautwein, Ulrich

    2008-01-01

    The internal/external frame of reference model (I/E model; Marsh, 1986) is a highly influential model of self-concept formation, which predicts that domain-specific abilities have positive effects on academic self-concepts in the corresponding domain and negative effects across domains. Investigations of the I/E model do not typically incorporate…

  10. Modification of a method-of-characteristics solute-transport model to incorporate decay and equilibrium-controlled sorption or ion exchange

    USGS Publications Warehouse

    Goode, D.J.; Konikow, L.F.

    1989-01-01

    The U.S. Geological Survey computer model of two-dimensional solute transport and dispersion in ground water (Konikow and Bredehoeft, 1978) has been modified to incorporate the following types of chemical reactions: (1) first-order irreversible rate-reaction, such as radioactive decay; (2) reversible equilibrium-controlled sorption with linear, Freundlich, or Langmuir isotherms; and (3) reversible equilibrium-controlled ion exchange for monovalent or divalent ions. Numerical procedures are developed to incorporate these processes in the general solution scheme that uses method-of- characteristics with particle tracking for advection and finite-difference methods for dispersion. The first type of reaction is accounted for by an exponential decay term applied directly to the particle concentration. The second and third types of reactions are incorporated through a retardation factor, which is a function of concentration for nonlinear cases. The model is evaluated and verified by comparison with analytical solutions for linear sorption and decay, and by comparison with other numerical solutions for nonlinear sorption and ion exchange.

  11. Macro-level pedestrian and bicycle crash analysis: Incorporating spatial spillover effects in dual state count models.

    PubMed

    Cai, Qing; Lee, Jaeyoung; Eluru, Naveen; Abdel-Aty, Mohamed

    2016-08-01

    This study attempts to explore the viability of dual-state models (i.e., zero-inflated and hurdle models) for traffic analysis zones (TAZs) based pedestrian and bicycle crash frequency analysis. Additionally, spatial spillover effects are explored in the models by employing exogenous variables from neighboring zones. The dual-state models such as zero-inflated negative binomial and hurdle negative binomial models (with and without spatial effects) are compared with the conventional single-state model (i.e., negative binomial). The model comparison for pedestrian and bicycle crashes revealed that the models that considered observed spatial effects perform better than the models that did not consider the observed spatial effects. Across the models with spatial spillover effects, the dual-state models especially zero-inflated negative binomial model offered better performance compared to single-state models. Moreover, the model results clearly highlighted the importance of various traffic, roadway, and sociodemographic characteristics of the TAZ as well as neighboring TAZs on pedestrian and bicycle crash frequency.

  12. Macro-level pedestrian and bicycle crash analysis: Incorporating spatial spillover effects in dual state count models.

    PubMed

    Cai, Qing; Lee, Jaeyoung; Eluru, Naveen; Abdel-Aty, Mohamed

    2016-08-01

    This study attempts to explore the viability of dual-state models (i.e., zero-inflated and hurdle models) for traffic analysis zones (TAZs) based pedestrian and bicycle crash frequency analysis. Additionally, spatial spillover effects are explored in the models by employing exogenous variables from neighboring zones. The dual-state models such as zero-inflated negative binomial and hurdle negative binomial models (with and without spatial effects) are compared with the conventional single-state model (i.e., negative binomial). The model comparison for pedestrian and bicycle crashes revealed that the models that considered observed spatial effects perform better than the models that did not consider the observed spatial effects. Across the models with spatial spillover effects, the dual-state models especially zero-inflated negative binomial model offered better performance compared to single-state models. Moreover, the model results clearly highlighted the importance of various traffic, roadway, and sociodemographic characteristics of the TAZ as well as neighboring TAZs on pedestrian and bicycle crash frequency. PMID:27153525

  13. A survival model for unthinned loblolly pine plantations that incorporates non-planted tree competition, site quality, and incidence of fusiform rust.

    PubMed

    Lee, Young-Jin; Coble, Dean W

    2002-12-01

    Future biomass yields are functionally related to the number of trees surviving at a given age. A stand level survival model was developed that incorporates competition of non-planted trees, site quality, and the incidence of fusiform rust (Cronartium quercuum [Berk.] Miyabe ex Shirai f. sp. fusiforme). The model consists of a system of two equations, one of which represents the number of surviving trees infected by fusiform rust while the other represents the number of trees not infected by fusiform rust. Data from unthinned loblolly pine (Pinus taeda L.) plantations in East Texas were used to fit and evaluate the survival model and illustrate its use. The model successfully predicted that the number of surviving loblolly pine trees decreased as the number of non-planted trees increased. The model also successfully predicted the transition of loblolly pine trees from an uninfected to an infected status by fusiform rust.

  14. Optimizing stem cell functions and antibacterial properties of TiO2 nanotubes incorporated with ZnO nanoparticles: experiments and modeling

    PubMed Central

    Liu, Wenwen; Su, Penglei; Gonzales, Arthur; Chen, Su; Wang, Na; Wang, Jinshu; Li, Hongyi; Zhang, Zhenting; Webster, Thomas J

    2015-01-01

    To optimize mesenchymal stem cell differentiation and antibacterial properties of titanium (Ti), nano-sized zinc oxide (ZnO) particles with tunable concentrations were incorporated into TiO2 nanotubes (TNTs) using a facile hydrothermal strategy. It is revealed here for the first time that the TNTs incorporated with ZnO nanoparticles exhibited better biocompatibility compared with pure Ti samples (controls) and that the amount of ZnO (tailored by the concentration of Zn(NO3)2 in the precursor) introduced into TNTs played a crucial role on their osteogenic properties. Not only was the alkaline phosphatase activity improved to about 13.8 U/g protein, but the osterix, collagen-I, and osteocalcin gene expressions was improved from mesenchymal stem cells compared to controls. To further explore the mechanism of TNTs decorated with ZnO on cell functions, a response surface mathematical model was used to optimize the concentration of ZnO incorporation into the Ti nanotubes for stem cell differentiation and antibacterial properties for the first time. Both experimental and modeling results confirmed (R2 values of 0.8873–0.9138 and 0.9596–0.9941, respectively) that Ti incorporated with appropriate concentrations (with an initial concentration of Zn(NO3)2 at 0.015 M) of ZnO can provide exceptional osteogenic properties for stem cell differentiation in bone cells with strong antibacterial effects, properties important for improving dental and orthopedic implant efficacy. PMID:25792833

  15. Incorporating autoregulatory mechanisms of the cardiovascular system in three-dimensional finite element models of arterial blood flow.

    PubMed

    Kim, H J; Jansen, K E; Taylor, C A

    2010-07-01

    The cardiovascular system is a closed-loop system in which billions of vessels interact with each other, and it enables the control of the systemic arterial pressure and varying organ flow through autoregulatory mechanisms. In this study, we describe the development of mathematical models of autoregulatory mechanisms for systemic arterial pressure and coronary flow and discuss the connection of these models to a hybrid numerical/analytic closed-loop model of the cardiovascular system. The closed-loop model consists of two lumped parameter heart models representing the left and right sides of the heart, a three-dimensional finite element model of the aorta with coronary arteries, three-element Windkessel models and lumped parameter coronary vascular models that represent the systemic circulation, and a three-element Windkessel model to approximate the pulmonary circulation. Using the connection between the systemic arterial pressure and coronary flow regulation systems, and the hybrid closed-loop model, we studied how the heart, coronary vascular beds, and arterial system respond to physiologic changes during light exercise and showed that these models can realistically simulate temporal behaviors of the heart, coronary vascular beds, and arterial system during exercise of healthy subjects. These models can be used to study temporal changes occurring in the heart, coronary vascular beds, and arterial system during cardiovascular intervention or changes in physiological states.

  16. Evaluation of Boundless Biogeochemical Cycle through Development of Process-Based Eco-Hydrological and Biogeochemical Cycle Model to Incorporate Terrestrial-Aquatic Continuum

    NASA Astrophysics Data System (ADS)

    Nakayama, T.; Maksyutov, S. S.

    2014-12-01

    Inland water might act as important transport pathway for continental biogeochemical cycle although its contribution has remained uncertain yet due to a paucity of data (Battin et al. 2009). The author has developed process-based National Integrated Catchment-based Eco-hydrology (NICE) model (Nakayama, 2008a-b, 2010, 2011a-b, 2012a-c, 2013; Nakayama and Fujita, 2010; Nakayama and Hashimoto, 2011; Nakayama and Shankman, 2013a-b; Nakayama and Watanabe, 2004, 2006, 2008a-b; Nakayama et al., 2006, 2007, 2010, 2012), which incorporates surface-groundwater interactions, includes up- and down-scaling processes between local-regional-global scales, and can simulate iteratively nonlinear feedback between hydrologic-geomorphic-ecological processes. Because NICE incorporates 3-D groundwater sub-model and expands from previous 1- or 2-D or steady state, the model can simulate the lateral transport pronounced at steeper-slope or riparian/floodplain with surface-groundwater connectivity. River discharge and groundwater level simulated by NICE agreed reasonably with those in previous researches (Niu et al., 2007; Fan et al., 2013) and extended to clarify lateral subsurface also has important role on global hydrologic cycle (Nakayama, 2011b; Nakayama and Shankman, 2013b) though the resolution was coarser. NICE was further developed to incorporate biogeochemical cycle including reaction between inorganic and organic carbons in terrestrial and aquatic ecosystems. The missing role of carbon cycle simulated by NICE, for example, CO2 evasion from inland water (global total flux was estimated as about 1.0 PgC/yr), was relatively in good agreement in that estimated by empirical relation using previous pCO2 data (Aufdenkampe et al., 2011; Laruelle et al., 2013). The model would play important role in identification of greenhouse gas balance of the biosphere and spatio-temporal hot spots, and bridging gap between top-down and bottom-up approaches (Cole et al. 2007; Frei et al. 2012).

  17. Modeling responses of large-river fish populations to global climate change through downscaling and incorporation of predictive uncertainty

    USGS Publications Warehouse

    Wildhaber, Mark L.; Wikle, Christopher K.; Anderson, Christopher J.; Franz, Kristie J.; Moran, Edward H.; Dey, Rima; Mader, Helmut; Kraml, Julia

    2012-01-01

    Climate change operates over a broad range of spatial and temporal scales. Understanding its effects on ecosystems requires multi-scale models. For understanding effects on fish populations of riverine ecosystems, climate predicted by coarse-resolution Global Climate Models must be downscaled to Regional Climate Models to watersheds to river hydrology to population response. An additional challenge is quantifying sources of uncertainty given the highly nonlinear nature of interactions between climate variables and community level processes. We present a modeling approach for understanding and accomodating uncertainty by applying multi-scale climate models and a hierarchical Bayesian modeling framework to Midwest fish population dynamics and by linking models for system components together by formal rules of probability. The proposed hierarchical modeling approach will account for sources of uncertainty in forecasts of community or population response. The goal is to evaluate the potential distributional changes in an ecological system, given distributional changes implied by a series of linked climate and system models under various emissions/use scenarios. This understanding will aid evaluation of management options for coping with global climate change. In our initial analyses, we found that predicted pallid sturgeon population responses were dependent on the climate scenario considered.

  18. Incorporating landscape depressions and tile drainages of a northern German lowland catchment into a semi-distributed model

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Hydrological models need to be adapted to specific hydrological characteristics of the catchment in which they are applied. In the lowland region of northern Germany, tile drains and depressions are prominent features of the landscape though are often neglected in hydrological modelling on the catch...

  19. A Multidisciplinary Model of Health Promotion Incorporating Spirituality into a Successful Aging Intervention with African American and White Elderly Groups.

    ERIC Educational Resources Information Center

    Parker, Michael W.; Bellis, Jeffrey M.; Bishop, Phillip; Harper, Mary; Allman, Richard M.; Moore, Cynthia; Thompson, Paula

    2002-01-01

    Faculty from academic, medical, state, and religious institutions presented workshops at a community and faith-based conference attended by seniors. Lifestyle changes and forms of spirituality were affirmed using a model of successful aging. Model has the potential to help unify the religious community around promoting successful aging. African…

  20. Incorporation of Reaction Kinetics into a Multiphase, Hydrodynamic Model of a Fischer Tropsch Slurry Bubble Column Reactor

    SciTech Connect

    Donna Guillen, PhD; Anastasia Gribik; Daniel Ginosar, PhD; Steven P. Antal, PhD

    2008-11-01

    This paper describes the development of a computational multiphase fluid dynamics (CMFD) model of the Fischer Tropsch (FT) process in a Slurry Bubble Column Reactor (SBCR). The CMFD model is fundamentally based which allows it to be applied to different industrial processes and reactor geometries. The NPHASE CMFD solver [1] is used as the robust computational platform. Results from the CMFD model include gas distribution, species concentration profiles, and local temperatures within the SBCR. This type of model can provide valuable information for process design, operations and troubleshooting of FT plants. An ensemble-averaged, turbulent, multi-fluid solution algorithm for the multiphase, reacting flow with heat transfer was employed. Mechanistic models applicable to churn turbulent flow have been developed to provide a fundamentally based closure set for the equations. In this four-field model formulation, two of the fields are used to track the gas phase (i.e., small spherical and large slug/cap bubbles), and the other two fields are used for the liquid and catalyst particles. Reaction kinetics for a cobalt catalyst is based upon values reported in the published literature. An initial, reaction kinetics model has been developed and exercised to demonstrate viability of the overall solution scheme. The model will continue to be developed with improved physics added in stages.

  1. A model model: a commentary on DiFrancesco and Noble (1985) ‘A model of cardiac electrical activity incorporating ionic pumps and concentration changes’

    PubMed Central

    Dibb, Katharine; Trafford, Andrew; Zhang, Henggui; Eisner, David

    2015-01-01

    This paper summarizes the advances made by the DiFrancesco and Noble (DFN) model of cardiac cellular electrophysiology, which was published in Philosophical Transactions B in 1985. This model was developed at a time when the introduction of new techniques and provision of experimental data had resulted in an explosion of knowledge about the cellular and biophysical properties of the heart. It advanced the cardiac modelling field from a period when computer models considered only the voltage-dependent channels in the surface membrane. In particular, it included a consideration of changes of both intra- and extracellular ionic concentrations. In this paper, we summarize the most important contributions of the DiFrancesco and Noble paper. We also describe how computer modelling has developed subsequently with the extension from the single cell to the whole heart as well as its use in understanding disease and predicting the effects of pharmaceutical interventions. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society. PMID:25750236

  2. An Ultrasound-Driven Kinematic Model for Deformation of the Infarcted Mouse Left Ventricle Incorporating A Near-Incompressibility Constraint

    PubMed Central

    Lin, Dan; French, Brent A.; Xu, Yaqin; Hossack, John A.; Holmes, Jeffrey W.

    2014-01-01

    Mathematical models of varying complexity have proved useful in fitting and interpreting regional cardiac displacements obtained from imaging methods such as ultrasound speckle tracking or MRI tagging. Simpler models, such as the classic thick-walled cylinder model of the left ventricle (LV), solve quickly and are easy to implement, but they ignore regional geometric variations and are difficult to adapt to the study of regional pathologies such as myocardial infarction. Complex, anatomically accurate finite-element models work well but are computationally intensive and require specialized expertise to implement. We developed a kinematic model that offers a compromise between these two traditional approaches, assuming only that displacements in the left ventricle are polynomial functions of initial position and that the myocardium is nearly incompressible, while allowing myocardial motion to vary spatially as would be expected in an ischemic or dyssynchronous left ventricle. Model parameters were determined using an objective function with adjustable weights to account for confidence in individual displacement components and desired strength of the incompressibility constraint. The model accurately represented the motion of both normal and infarcted mouse left ventricles during the cardiac cycle, with normalized root mean square errors in predicted deformed positions of 8.2 ± 2.3% and 7.4 ± 2.1% for normal and infarcted hearts, respectively. PMID:25542490

  3. A statistical model for measurement error that incorporates variation over time in the target measure, with application to nutritional epidemiology.

    PubMed

    Freedman, Laurence S; Midthune, Douglas; Dodd, Kevin W; Carroll, Raymond J; Kipnis, Victor

    2015-11-30

    Most statistical methods that adjust analyses for measurement error assume that the target exposure T is a fixed quantity for each individual. However, in many applications, the value of T for an individual varies with time. We develop a model that accounts for such variation, describing the model within the framework of a meta-analysis of validation studies of dietary self-report instruments, where the reference instruments are biomarkers. We demonstrate that in this application, the estimates of the attenuation factor and correlation with true intake, key parameters quantifying the accuracy of the self-report instrument, are sometimes substantially modified under the time-varying exposure model compared with estimates obtained under a traditional fixed-exposure model. We conclude that accounting for the time element in measurement error problems is potentially important.

  4. Incorporation of measured photosynthetic rate in a mathematical model for calculation of non-structural saccharide concentration

    NASA Technical Reports Server (NTRS)

    Lim, J. T.; Raper, C. D. Jr; Gold, H. J.; Wilkerson, G. G.; Raper CD, J. r. (Principal Investigator)

    1989-01-01

    A simple mathematical model for calculating the concentration of mobile carbon skeletons in the shoot of soya bean plants [Glycine max (L.) Merrill cv. Ransom] was built to examine the suitability of measured net photosynthetic rates (PN) for calculation of saccharide flux into the plant. The results suggest that either measurement of instantaneous PN overestimated saccharide influx or respiration rates utilized in the model were underestimated. If neither of these is the case, end-product inhibition of photosynthesis or waste respiration through the alternative pathway should be included in modelling of CH2O influx or efflux; and even if either of these is the case, the model output at a low coefficient of leaf activity indicates that PN still may be controlled by either end-product inhibition or alternative respiration.

  5. Incorporation of measured photosynthetic rate in a mathematical model for calculation of non-structural saccharide concentration.

    PubMed

    Lim, J T; Raper, C D; Gold, H J; Wilkerson, G G

    1989-01-01

    A simple mathematical model for calculating the concentration of mobile carbon skeletons in the shoot of soya bean plants [Glycine max (L.) Merrill cv. Ransom] was built to examine the suitability of measured net photosynthetic rates (PN) for calculation of saccharide flux into the plant. The results suggest that either measurement of instantaneous PN overestimated saccharide influx or respiration rates utilized in the model were underestimated. If neither of these is the case, end-product inhibition of photosynthesis or waste respiration through the alternative pathway should be included in modelling of CH2O influx or efflux; and even if either of these is the case, the model output at a low coefficient of leaf activity indicates that PN still may be controlled by either end-product inhibition or alternative respiration.

  6. Dynamics of a producer-grazer model incorporating the effects of excess food nutrient content on grazer's growth.

    PubMed

    Peace, Angela; Wang, Hao; Kuang, Yang

    2014-09-01

    Modeling under the framework of ecological stoichiometric allows the investigation of the effects of food quality on food web population dynamics. Recent discoveries in ecological stoichiometry suggest that grazer dynamics are affected by insufficient food nutrient content (low phosphorus (P)/carbon (C) ratio) as well as excess food nutrient content (high P:C). This phenomenon is known as the "stoichiometric knife edge." While previous models have captured this phenomenon, they do not explicitly track P in the producer or in the media that supports the producer, which brings questions to the validity of their predictions. Here, we extend a Lotka-Volterra-type stoichiometric model by mechanistically deriving and tracking P in the producer and free P in the environment in order to investigate the growth response of Daphnia to algae of varying P:C ratios. Bifurcation analysis and numerical simulations of the full model, that explicitly tracks phosphorus, lead to quantitative different predictions than previous models that neglect to track free nutrients. The full model shows that the fate of the grazer population can be very sensitive to excess nutrient concentrations. Dynamical free nutrient pool seems to induce extreme grazer population density changes when total nutrient is in an intermediate range. PMID:25124765

  7. Incorporating Anthropogenic Influences into Fire Probability Models: Effects of Human Activity and Climate Change on Fire Activity in California.

    PubMed

    Mann, Michael L; Batllori, Enric; Moritz, Max A; Waller, Eric K; Berck, Peter; Flint, Alan L; Flint, Lorraine E; Dolfi, Emmalee

    2016-01-01

    The costly interactions between humans and wildfires throughout California demonstrate the need to understand the relationships between them, especially in the face of a changing climate and expanding human communities. Although a number of statistical and process-based wildfire models exist for California, there is enormous uncertainty about the location and number of future fires, with previously published estimates of increases ranging from nine to fifty-three percent by the end of the century. Our goal is to assess the role of climate and anthropogenic influences on the state's fire regimes from 1975 to 2050. We develop an empirical model that integrates estimates of biophysical indicators relevant to plant communities and anthropogenic influences at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of explanatory power in the model. We also find that the total area burned is likely to increase, with burned area expected to increase by 2.2 and 5.0 percent by 2050 under climatic bookends (PCM and GFDL climate models, respectively). Our two climate models show considerable agreement, but due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid inland deserts and coastal areas of the south. Given the strength of human-related variables in some regions, however, it is clear that comprehensive projections of future fire activity should include both anthropogenic and biophysical influences. Previous findings of substantially increased numbers of fires and burned area for California may be tied to omitted variable bias from the exclusion of human influences. The omission of anthropogenic variables in our model would overstate the importance of climatic ones by at least 24%. As such, the failure to include anthropogenic effects in many models likely overstates the response of wildfire to climatic change.

  8. Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data

    USGS Publications Warehouse

    Buderman, Frances E.; Diefenbach, Duane R.; Casalena, Mary Jo; Rosenberry, Christopher S.; Wallingford, Bret D.

    2014-01-01

    The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward-tagged animals in a Brownie tag-recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging-to-harvest survival rates from >20 individuals with radio transmitters combined with 50–100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo,to estimate harvest rates, and data from white-tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known-fate tag-recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior.

  9. Incorporating Anthropogenic Influences into Fire Probability Models: Effects of Human Activity and Climate Change on Fire Activity in California

    PubMed Central

    Batllori, Enric; Moritz, Max A.; Waller, Eric K.; Berck, Peter; Flint, Alan L.; Flint, Lorraine E.; Dolfi, Emmalee

    2016-01-01

    The costly interactions between humans and wildfires throughout California demonstrate the need to understand the relationships between them, especially in the face of a changing climate and expanding human communities. Although a number of statistical and process-based wildfire models exist for California, there is enormous uncertainty about the location and number of future fires, with previously published estimates of increases ranging from nine to fifty-three percent by the end of the century. Our goal is to assess the role of climate and anthropogenic influences on the state’s fire regimes from 1975 to 2050. We develop an empirical model that integrates estimates of biophysical indicators relevant to plant communities and anthropogenic influences at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of explanatory power in the model. We also find that the total area burned is likely to increase, with burned area expected to increase by 2.2 and 5.0 percent by 2050 under climatic bookends (PCM and GFDL climate models, respectively). Our two climate models show considerable agreement, but due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid inland deserts and coastal areas of the south. Given the strength of human-related variables in some regions, however, it is clear that comprehensive projections of future fire activity should include both anthropogenic and biophysical influences. Previous findings of substantially increased numbers of fires and burned area for California may be tied to omitted variable bias from the exclusion of human influences. The omission of anthropogenic variables in our model would overstate the importance of climatic ones by at least 24%. As such, the failure to include anthropogenic effects in many models likely overstates the response of wildfire to climatic change. PMID:27124597

  10. Incorporating Anthropogenic Influences into Fire Probability Models: Effects of Human Activity and Climate Change on Fire Activity in California.

    PubMed

    Mann, Michael L; Batllori, Enric; Moritz, Max A; Waller, Eric K; Berck, Peter; Flint, Alan L; Flint, Lorraine E; Dolfi, Emmalee

    2016-01-01

    The costly interactions between humans and wildfires throughout California demonstrate the need to understand the relationships between them, especially in the face of a changing climate and expanding human communities. Although a number of statistical and process-based wildfire models exist for California, there is enormous uncertainty about the location and number of future fires, with previously published estimates of increases ranging from nine to fifty-three percent by the end of the century. Our goal is to assess the role of climate and anthropogenic influences on the state's fire regimes from 1975 to 2050. We develop an empirical model that integrates estimates of biophysical indicators relevant to plant communities and anthropogenic influences at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of explanatory power in the model. We also find that the total area burned is likely to increase, with burned area expected to increase by 2.2 and 5.0 percent by 2050 under climatic bookends (PCM and GFDL climate models, respectively). Our two climate models show considerable agreement, but due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid inland deserts and coastal areas of the south. Given the strength of human-related variables in some regions, however, it is clear that comprehensive projections of future fire activity should include both anthropogenic and biophysical influences. Previous findings of substantially increased numbers of fires and burned area for California may be tied to omitted variable bias from the exclusion of human influences. The omission of anthropogenic variables in our model would overstate the importance of climatic ones by at least 24%. As such, the failure to include anthropogenic effects in many models likely overstates the response of wildfire to climatic change. PMID:27124597

  11. Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data

    PubMed Central

    Buderman, Frances E; Diefenbach, Duane R; Casalena, Mary Jo; Rosenberry, Christopher S; Wallingford, Bret D

    2014-01-01

    The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward-tagged animals in a Brownie tag-recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging-to-harvest survival rates from >20 individuals with radio transmitters combined with 50–100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo, to estimate harvest rates, and data from white-tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known-fate tag-recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior. PMID:24834339

  12. Accounting for tagging-to-harvest mortality in a Brownie tag-recovery model by incorporating radio-telemetry data.

    PubMed

    Buderman, Frances E; Diefenbach, Duane R; Casalena, Mary Jo; Rosenberry, Christopher S; Wallingford, Bret D

    2014-04-01

    The Brownie tag-recovery model is useful for estimating harvest rates but assumes all tagged individuals survive to the first hunting season; otherwise, mortality between time of tagging and the hunting season will cause the Brownie estimator to be negatively biased. Alternatively, fitting animals with radio transmitters can be used to accurately estimate harvest rate but may be more costly. We developed a joint model to estimate harvest and annual survival rates that combines known-fate data from animals fitted with transmitters to estimate the probability of surviving the period from capture to the first hunting season, and data from reward-tagged animals in a Brownie tag-recovery model. We evaluated bias and precision of the joint estimator, and how to optimally allocate effort between animals fitted with radio transmitters and inexpensive ear tags or leg bands. Tagging-to-harvest survival rates from >20 individuals with radio transmitters combined with 50-100 reward tags resulted in an unbiased and precise estimator of harvest rates. In addition, the joint model can test whether transmitters affect an individual's probability of being harvested. We illustrate application of the model using data from wild turkey, Meleagris gallapavo, to estimate harvest rates, and data from white-tailed deer, Odocoileus virginianus, to evaluate whether the presence of a visible radio transmitter is related to the probability of a deer being harvested. The joint known-fate tag-recovery model eliminates the requirement to capture and mark animals immediately prior to the hunting season to obtain accurate and precise estimates of harvest rate. In addition, the joint model can assess whether marking animals with radio transmitters affects the individual's probability of being harvested, caused by hunter selectivity or changes in a marked animal's behavior. PMID:24834339

  13. Computational model of the fathead minnow hypothalamic-pituitary-gonadal axis: Incorporating protein synthesis in improving predictability of responses to endocrine active chemicals.

    PubMed

    Breen, Miyuki; Villeneuve, Daniel L; Ankley, Gerald T; Bencic, David; Breen, Michael S; Watanabe, Karen H; Lloyd, Alun L; Conolly, Rory B

    2016-01-01

    There is international concern about chemicals that alter endocrine system function in humans and/or wildlife and subsequently cause adverse effects. We previously developed a mechanistic computational model of the hypothalamic-pituitary-gonadal (HPG) axis in female fathead minnows exposed to a model aromatase inhibitor, fadrozole (FAD), to predict dose-response and time-course behaviors for apical reproductive endpoints. Initial efforts to develop a computational model describing adaptive responses to endocrine stress providing good fits to empirical plasma 17β-estradiol (E2) data in exposed fish were only partially successful, which suggests that additional regulatory biology processes need to be considered. In this study, we addressed short-comings of the previous model by incorporating additional details concerning CYP19A (aromatase) protein synthesis. Predictions based on the revised model were evaluated using plasma E2 concentrations and ovarian cytochrome P450 (CYP) 19A aromatase mRNA data from two fathead minnow time-course experiments with FAD, as well as from a third 4-day study. The extended model provides better fits to measured E2 time-course concentrations, and the model accurately predicts CYP19A mRNA fold changes and plasma E2 dose-response from the 4-d concentration-response study. This study suggests that aromatase protein synthesis is an important process in the biological system to model the effects of FAD exposure.

  14. Development of a New Analog Test System Capable of Modeling Tectonic Deformation Incorporating the Effects of Pore Fluid Pressure

    NASA Astrophysics Data System (ADS)

    Zhang, M.; Nakajima, H.; Takeda, M.; Aung, T. T.

    2005-12-01

    Understanding and predicting the tectonic deformation within geologic strata has been a very important research subject in many fields such as structural geology and petroleum geology. In recent years, such research has also become a fundamental necessity for the assessment of active fault migration, site selection for geological disposal of radioactive nuclear waste and exploration for methane hydrate. Although analog modeling techniques have played an important role in the elucidation of the tectonic deformation mechanisms, traditional approaches have typically used dry materials and ignored the effects of pore fluid pressure. In order for analog models to properly depict the tectonic deformation of the targeted, large-prototype system within a small laboratory-scale configuration, physical properties of the models, including geometry, force, and time, must be correctly scaled. Model materials representing brittle rock behavior require an internal friction identical to the prototype rock and virtually zero cohesion. Granular materials such as sand, glass beads, or steel beads of dry condition have been preferably used for this reason in addition to their availability and ease of handling. Modeling protocols for dry granular materials have been well established but such model tests cannot account for the pore fluid effects. Although the concept of effective stress has long been recognized and the role of pore-fluid pressure in tectonic deformation processes is evident, there have been few analog model studies that consider the effects of pore fluid movement. Some new applications require a thorough understanding of the coupled deformation and fluid flow processes within the strata. Taking the field of waste management as an example, deep geological disposal of radioactive waste has been thought to be an appropriate methodology for the safe isolation of the wastes from the human environment until the toxicity of the wastes decays to non-hazardous levels. For the

  15. Incorporating positive body image into the treatment of eating disorders: A model for attunement and mindful self-care.

    PubMed

    Cook-Cottone, Catherine P

    2015-06-01

    This article provides a model for understanding the role positive body image can play in the treatment of eating disorders and methods for guiding patients away from symptoms and toward flourishing. The Attuned Representational Model of Self (Cook-Cottone, 2006) and a conceptual model detailing flourishing in the context of body image and eating behavior (Cook-Cottone et al., 2013) are discussed. The flourishing inherent in positive body image comes hand-in-hand with two critical ways of being: (a) having healthy, embodied awareness of the internal and external aspects of self (i.e., attunement) and (b) engaging in mindful self-care. Attunement and mindful self-care thus are considered as potential targets of actionable therapeutic work in the cultivation of positive body image among those with disordered eating. For context, best-practices in eating disorder treatment are also reviewed. Limitations in current research are detailed and directions for future research are explicated. PMID:25886712

  16. Incorporating positive body image into the treatment of eating disorders: A model for attunement and mindful self-care.

    PubMed

    Cook-Cottone, Catherine P

    2015-06-01

    This article provides a model for understanding the role positive body image can play in the treatment of eating disorders and methods for guiding patients away from symptoms and toward flourishing. The Attuned Representational Model of Self (Cook-Cottone, 2006) and a conceptual model detailing flourishing in the context of body image and eating behavior (Cook-Cottone et al., 2013) are discussed. The flourishing inherent in positive body image comes hand-in-hand with two critical ways of being: (a) having healthy, embodied awareness of the internal and external aspects of self (i.e., attunement) and (b) engaging in mindful self-care. Attunement and mindful self-care thus are considered as potential targets of actionable therapeutic work in the cultivation of positive body image among those with disordered eating. For context, best-practices in eating disorder treatment are also reviewed. Limitations in current research are detailed and directions for future research are explicated.

  17. A model for incorporating computation without changing the course: An example from middle-division classical mechanics

    NASA Astrophysics Data System (ADS)

    Caballero, Marcos D.; Pollock, Steven J.

    2014-03-01

    Although much of the research done by modern physicists would be impossible without the use of computers, today's physics curricula do not generally reflect their importance and utility. To more tightly connect undergraduate preparation with professional practice, we integrated computational instruction into middle-division classical mechanics at the University of Colorado Boulder. Our model for integration works with the constraints of faculty who do not specialize in computation by placing a strong emphasis on an adaptable curriculum. It also includes the construction of learning goals and the design of activities consistent with those goals, including assessment of student computational fluency. We present critiques of our model as we work to develop an effective and sustainable model for computational instruction in the undergraduate curriculum.

  18. A cortical folding model incorporating stress-dependent growth explains gyral wavelengths and stress patterns in the developing brain

    NASA Astrophysics Data System (ADS)

    Bayly, P. V.; Okamoto, R. J.; Xu, G.; Shi, Y.; Taber, L. A.

    2013-02-01

    In humans and many other mammals, the cortex (the outer layer of the brain) folds during development. The mechanics of folding are not well understood; leading explanations are either incomplete or at odds with physical measurements. We propose a mathematical model in which (i) folding is driven by tangential expansion of the cortex and (ii) deeper layers grow in response to the resulting stress. In this model the wavelength of cortical folds depends predictably on the rate of cortical growth relative to the rate of stress-induced growth. We show analytically and in simulations that faster cortical expansion leads to shorter gyral wavelengths; slower cortical expansion leads to long wavelengths or even smooth (lissencephalic) surfaces. No inner or outer (skull) constraint is needed to produce folding, but initial shape and mechanical heterogeneity influence the final shape. The proposed model predicts patterns of stress in the tissue that are consistent with experimental observations.

  19. Incorporating 3-D Subsurface Hydrologic Processes within the Community Land Surface Model (CLM): Coupling PFLOTRAN and CLM

    NASA Astrophysics Data System (ADS)

    Bisht, G.; Mills, R. T.; Hoffman, F. M.; Thornton, P. E.; Lichtner, P. C.; Hammond, G. E.

    2011-12-01

    Numerous studies have shown a positive soil moisture-rainfall feedback through observational data, as well as, modeling studies. Spatial variability of topography, soils, and vegetation play a significant role in determining the response of land surface states (soil moisture) and fluxes (runoff, evapotranspirtiaon); but their explicit accounting within Land Surface Models (LSMs) is computa- tionally expensive. Additionally, anthropogenic climate change is altering the hydrologic cycle at global and regional scales. Characterizing the sensitivity of groundwater recharge is critical for understanding the effects of climate change on water resources. In order to explicitly represent lateral redistribution of soil moisture and unified treatment of the unsaturated-saturated zone in the subsurface within the CLM, we propose coupling PFLOTRAN and CLM. PFLOTRAN is a parallel multiphase-multicomponent subsurface reactive flow and transport code for modeling subsurface processes and has been devel- oped under a DOE SciDAC-2 project. PFLOTRAN is written in Fortran 90 using a modular, object-oriented approach. PFLOTRAN utilizes fully implicit time-stepping and is built on top of the Portable, Extensible Toolkit for Scientific Computation (PETSc). The PFLOTRAN model is capable of simulating fluid flow through porous media with fluid phases of air, water, and supercritical CO2. PFLOTRAN has been successfully employed on up to 131,072 cores on Jaguar, the massively parallel Cray XT4/XT5 at ORNL, for problems composed of up to 2 billion degrees of freedom. In this work, we will present a strategy of coupling the two models, CLM and PFLOTRAN, along with a few preliminary results obtained from the coupled model.

  20. Incorporating cold-air pooling into downscaled climate models increases potential refugia for snow-dependent species within the Sierra Nevada Ecoregion, CA.

    PubMed

    Curtis, Jennifer A; Flint, Lorraine E; Flint, Alan L; Lundquist, Jessica D; Hudgens, Brian; Boydston, Erin E; Young, Julie K

    2014-01-01

    We present a unique water-balance approach for modeling snowpack under historic, current and future climates throughout the Sierra Nevada Ecoregion. Our methodology uses a finer scale (270 m) than previous regional studies and incorporates cold-air pooling, an atmospheric process that sustains cooler temperatures in topographic depressions thereby mitigating snowmelt. Our results are intended to support management and conservation of snow-dependent species, which requires characterization of suitable habitat under current and future climates. We use the wolverine (Gulo gulo) as an example species and investigate potential habitat based on the depth and extent of spring snowpack within four National Park units with proposed wolverine reintroduction programs. Our estimates of change in spring snowpack conditions under current and future climates are consistent with recent studies that generally predict declining snowpack. However, model development at a finer scale and incorporation of cold-air pooling increased the persistence of April 1st snowpack. More specifically, incorporation of cold-air pooling into future climate projections increased April 1st snowpack by 6.5% when spatially averaged over the study region and the trajectory of declining April 1st snowpack reverses at mid-elevations where snow pack losses are mitigated by topographic shading and cold-air pooling. Under future climates with sustained or increased precipitation, our results indicate a high likelihood for the persistence of late spring snowpack at elevations above approximately 2,800 m and identify potential climate refugia sites for snow-dependent species at mid-elevations, where significant topographic shading and cold-air pooling potential exist. PMID:25188379

  1. Incorporating Cold-Air Pooling into Downscaled Climate Models Increases Potential Refugia for Snow-Dependent Species within the Sierra Nevada Ecoregion, CA

    PubMed Central

    Curtis, Jennifer A.; Flint, Lorraine E.; Flint, Alan L.; Lundquist, Jessica D.; Hudgens, Brian; Boydston, Erin E.; Young, Julie K.

    2014-01-01

    We present a unique water-balance approach for modeling snowpack under historic, current and future climates throughout the Sierra Nevada Ecoregion. Our methodology uses a finer scale (270 m) than previous regional studies and incorporates cold-air pooling, an atmospheric process that sustains cooler temperatures in topographic depressions thereby mitigating snowmelt. Our results are intended to support management and conservation of snow-dependent species, which requires characterization of suitable habitat under current and future climates. We use the wolverine (Gulo gulo) as an example species and investigate potential habitat based on the depth and extent of spring snowpack within four National Park units with proposed wolverine reintroduction programs. Our estimates of change in spring snowpack conditions under current and future climates are consistent with recent studies that generally predict declining snowpack. However, model development at a finer scale and incorporation of cold-air pooling increased the persistence of April 1st snowpack. More specifically, incorporation of cold-air pooling into future climate projections increased April 1st snowpack by 6.5% when spatially averaged over the study region and the trajectory of declining April 1st snowpack reverses at mid-elevations where snow pack losses are mitigated by topographic shading and cold-air pooling. Under future climates with sustained or increased precipitation, our results indicate a high likelihood for the persistence of late spring snowpack at elevations above approximately 2,800 m and identify potential climate refugia sites for snow-dependent species at mid-elevations, where significant topographic shading and cold-air pooling potential exist. PMID:25188379

  2. Incorporating cold-air pooling into downscaled climate models increases potential refugia for snow-dependent species within the Sierra Nevada Ecoregion, CA

    USGS Publications Warehouse

    Curtis, Jennifer A.; Flint, Lorraine E.; Flint, Alan L.; Lundquist, Jessica D.; Hudgens, Brian; Boydston, Erin E.; Young, Julie K.

    2014-01-01

    We present a unique water-balance approach for modeling snowpack under historic, current and future climates throughout the Sierra Nevada Ecoregion. Our methodology uses a finer scale (270 m) than previous regional studies and incorporates cold-air pooling, an atmospheric process that sustains cooler temperatures in topographic depressions thereby mitigating snowmelt. Our results are intended to support management and conservation of snow-dependent species, which requires characterization of suitable habitat under current and future climates. We use the wolverine (Gulo gulo) as an example species and investigate potential habitat based on the depth and extent of spring snowpack within four National Park units with proposed wolverine reintroduction programs. Our estimates of change in spring snowpack conditions under current and future climates are consistent with recent studies that generally predict declining snowpack. However, model development at a finer scale and incorporation of cold-air pooling increased the persistence of April 1st snowpack. More specifically, incorporation of cold-air pooling into future climate projections increased April 1st snowpack by 6.5% when spatially averaged over the study region and the trajectory of declining April 1st snowpack reverses at mid-elevations where snow pack losses are mitigated by topographic shading and cold-air pooling. Under future climates with sustained or increased precipitation, our results indicate a high likelihood for the persistence of late spring snowpack at elevations above approximately 2,800 m and identify potential climate refugia sites for snow-dependent species at mid-elevations, where significant topographic shading and cold-air pooling potential exist.

  3. Parameterizing Spatial Models of Infectious Disease Transmission that Incorporate Infection Time Uncertainty Using Sampling-Based Likelihood Approximations.

    PubMed

    Malik, Rajat; Deardon, Rob; Kwong, Grace P S

    2016-01-01

    A class of discrete-time models of infectious disease spread, referred to as individual-level models (ILMs), are typically fitted in a Bayesian Markov chain Monte Carlo (MCMC) framework. These models quantify probabilistic outcomes regarding the risk of infection of susceptible individuals due to various susceptibility and transmissibility factors, including their spatial distance from infectious individuals. The infectious pressure from infected individuals exerted on susceptible individuals is intrinsic to these ILMs. Unfortunately, quantifying this infectious pressure for data sets containing many individuals can be computationally burdensome, leading to a time-consuming likelihood calculation and, thus, computationally prohibitive MCMC-based analysis. This problem worsens when using data augmentation to allow for uncertainty in infection times. In this paper, we develop sampling methods that can be used to calculate a fast, approximate likelihood when fitting such disease models. A simple random sampling approach is initially considered followed by various spatially-stratified schemes. We test and compare the performance of our methods with both simulated data and data from the 2001 foot-and-mouth disease (FMD) epidemic in the U.K. Our results indicate that substantial computation savings can be obtained--albeit, of course, with some information loss--suggesting that such techniques may be of use in the analysis of very large epidemic data sets. PMID:26731666

  4. Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift

    PubMed Central

    Greenbaum, Gili; Templeton, Alan R.; Zarmi, Yair; Bar-David, Shirli

    2014-01-01

    Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution. PMID:25526062

  5. Parameterizing Spatial Models of Infectious Disease Transmission that Incorporate Infection Time Uncertainty Using Sampling-Based Likelihood Approximations

    PubMed Central

    Malik, Rajat; Deardon, Rob; Kwong, Grace P. S.

    2016-01-01

    A class of discrete-time models of infectious disease spread, referred to as individual-level models (ILMs), are typically fitted in a Bayesian Markov chain Monte Carlo (MCMC) framework. These models quantify probabilistic outcomes regarding the risk of infection of susceptible individuals due to various susceptibility and transmissibility factors, including their spatial distance from infectious individuals. The infectious pressure from infected individuals exerted on susceptible individuals is intrinsic to these ILMs. Unfortunately, quantifying this infectious pressure for data sets containing many individuals can be computationally burdensome, leading to a time-consuming likelihood calculation and, thus, computationally prohibitive MCMC-based analysis. This problem worsens when using data augmentation to allow for uncertainty in infection times. In this paper, we develop sampling methods that can be used to calculate a fast, approximate likelihood when fitting such disease models. A simple random sampling approach is initially considered followed by various spatially-stratified schemes. We test and compare the performance of our methods with both simulated data and data from the 2001 foot-and-mouth disease (FMD) epidemic in the U.K. Our results indicate that substantial computation savings can be obtained—albeit, of course, with some information loss—suggesting that such techniques may be of use in the analysis of very large epidemic data sets. PMID:26731666

  6. Incorporating human activities into an earth system model of the Northeastern United States: socio-hydrology at the regional scale

    NASA Astrophysics Data System (ADS)

    Rosenzweig, B.; Vorosmarty, C. J.; Miara, A.; Stewart, R.; Wollheim, W. M.; Lu, X.; Kicklighter, D. W.; Ehsani, N.; Shikhmacheva, K.; Yang, P.

    2013-12-01

    The Northeastern United States is one of the most urbanized regions of the world and its 70 million residents will be challenged by climate change as well as competing demands for land and water through the remainder of the 21st Century. The strategic management decisions made in the next few years will have major impacts on the region's future water resources, but planners have had limited quantitative information to support their decision-making. We have developed a Northeast Regional Earth System Model (NE-RESM), which allows for the testing of future scenarios of climate change, land use change and infrastructure management to better understand their implications for the region's water resources and ecosystem services. Human features of the water cycle - including thermoelectric power plants, wastewater treatment plants interbasin transfers and changes in impervious cover with different patterns of urban development - are explicitly represented in our modeling. We are currently engaged in a novel, participatory scenario design process with regional stakeholders to ensure the policy relevancy of our modeling experiments. The NE-RESM hydrologic modeling domain. Figure by Stanley Glidden and Rob Stewart

  7. Allelic richness following population founding events--a stochastic modeling framework incorporating gene flow and genetic drift.

    PubMed

    Greenbaum, Gili; Templeton, Alan R; Zarmi, Yair; Bar-David, Shirli

    2014-01-01

    Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the "One Migrant per Generation" rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.

  8. Learning-Goals-Driven Design Model: Developing Curriculum Materials that Align with National Standards and Incorporate Project-Based Pedagogy

    ERIC Educational Resources Information Center

    Krajcik, Joseph; McNeill, Katherine L.; Reiser, Brian J.

    2008-01-01

    Reform efforts in science education emphasize the importance of rigorous treatment of science standards and use of innovative pedagogical approaches to make science more meaningful and successful. In this paper, we present a learning-goals-driven design model for developing curriculum materials, which combines national standards and a…

  9. Incorporating Modeling and Simulations in Undergraduate Biophysical Chemistry Course to Promote Understanding of Structure-Dynamics-Function Relationships in Proteins

    ERIC Educational Resources Information Center

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-01-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and…

  10. Incorporation of Predictive Population Modeling into the AOP Famework: A Case Study with White Suckers Exposed to Pulp Effluent

    EPA Science Inventory

    A need in ecological risk assessment is the ability to create linkages between chemically-induced alterations at molecular and biochemical levels of organization with adverse outcomes in whole organisms and populations. A predictive model was developed to translate changes in th...

  11. Development of a Quantitative Model Incorporating Key Events in a Hepatoxic Mode of Action to Predict Tumor Incidence

    EPA Science Inventory

    Biologically-Based Dose Response (BBDR) modeling of environmental pollutants can be utilized to inform the mode of action (MOA) by which compounds elicit adverse health effects. Chemicals that produce tumors are typically described as either genotoxic or non-genotoxic. One common...

  12. Imaging the lithosphere beneath NE Tibet: teleseismic P and S body wave tomography incorporating surface wave starting models

    NASA Astrophysics Data System (ADS)

    Nunn, Ceri; Roecker, Steven W.; Tilmann, Frederik J.; Priestley, Keith F.; Heyburn, Ross; Sandvol, Eric A.; Ni, James F.; Chen, Yongshun John; Zhao, Wenjin; Team, The Indepth

    2014-03-01

    The northeastern margin of the Tibetan Plateau, which includes the Qiangtang and Songpan-Ganzi terranes as well as the Kunlun Shan and the Qaidam Basin, continues to deform in response to the ongoing India-Eurasia collision. To test competing hypotheses concerning the mechanisms for this deformation, we assembled a high-quality data set of approximately 14 000 P- and 4000 S-wave arrival times from earthquakes at teleseismic distances from the International Deep Profiling of Tibet and the Himalaya, Phase IV broad-band seismometer deployments. We analyse these arrival times to determine tomographic images of P- and S-wave velocities in the upper mantle beneath this part of the plateau. To account for the effects of major heterogeneity in crustal and uppermost mantle wave velocities in Tibet, we use recent surface wave models to construct a starting model for our teleseismic body wave inversion. We compare the results from our model with those from simpler starting models, and find that while the reduction in residuals and results for deep structure are similar between models, the results for shallow structure are different. Checkerboard tests indicate that features of ˜125 km length scale are reliably imaged throughout the study region. Using synthetic tests, we show that the best recovery is below ˜300 km, and that broad variations in shallow structure can also be recovered. We also find that significant smearing can occur, especially at the edges of the model. We observe a shallow dipping seismically fast structure at depths of ˜140-240 km, which dies out gradually between 33°N and 35°N. Based on the lateral continuity of this structure (from the surface waves) we interpret it as Indian lithosphere. Alternatively, the entire area could be thickened by pure shear, or the northern part could be an underthrust Lhasa Terrane lithospheric slab with only the southern part from India. We see a deep fast wave velocity anomaly (below 300 km), that is consistent with

  13. Incorporating Cancer Stem Cells in Radiation Therapy Treatment Response Modeling and the Implication in Glioblastoma Multiforme Treatment Resistance

    SciTech Connect

    Yu, Victoria Y.; Nguyen, Dan; Pajonk, Frank; Kupelian, Patrick; Kaprealian, Tania; Selch, Michael; Low, Daniel A.; Sheng, Ke

    2015-03-15

    Purpose: To perform a preliminary exploration with a simplistic mathematical cancer stem cell (CSC) interaction model to determine whether the tumor-intrinsic heterogeneity and dynamic equilibrium between CSCs and differentiated cancer cells (DCCs) can better explain radiation therapy treatment response with a dual-compartment linear-quadratic (DLQ) model. Methods and Materials: The radiosensitivity parameters of CSCs and DCCs for cancer cell lines including glioblastoma multiforme (GBM), non–small cell lung cancer, melanoma, osteosarcoma, and prostate, cervical, and breast cancer were determined by performing robust least-square fitting using the DLQ model on published clonogenic survival data. Fitting performance was compared with the single-compartment LQ (SLQ) and universal survival curve models. The fitting results were then used in an ordinary differential equation describing the kinetics of DCCs and CSCs in response to 2- to 14.3-Gy fractionated treatments. The total dose to achieve tumor control and the fraction size that achieved the least normal biological equivalent dose were calculated. Results: Smaller cell survival fitting errors were observed using DLQ, with the exception of melanoma, which had a low α/β = 0.16 in SLQ. Ordinary differential equation simulation indicated lower normal tissue biological equivalent dose to achieve the same tumor control with a hypofractionated approach for 4 cell lines for the DLQ model, in contrast to SLQ, which favored 2 Gy per fraction for all cells except melanoma. The DLQ model indicated greater tumor radioresistance than SLQ, but the radioresistance was overcome by hypofractionation, other than the GBM cells, which responded poorly to all fractionations. Conclusion: The distinct radiosensitivity and dynamics between CSCs and DCCs in radiation therapy response could perhaps be one possible explanation for the heterogeneous intertumor response to hypofractionation and in some cases superior outcome from

  14. Implications of incorporating N cycling and N limitations on primary production in an individual-based dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Smith, B.; Wårlind, D.; Arneth, A.; Hickler, T.; Leadley, P.; Siltberg, J.; Zaehle, S.

    2014-04-01

    The LPJ-GUESS dynamic vegetation model uniquely combines an individual- and patch-based representation of vegetation dynamics with ecosystem biogeochemical cycling from regional to global scales. We present an updated version that includes plant and soil N dynamics, analysing the implications of accounting for C-N interactions on predictions and performance of the model. Stand structural dynamics and allometric scaling of tree growth suggested by global databases of forest stand structure and development were well reproduced by the model in comparison to an earlier multi-model study. Accounting for N cycle dynamics improved the goodness of fit for broadleaved forests. N limitation associated with low N-mineralisation rates reduces productivity of cold-climate and dry-climate ecosystems relative to mesic temperate and tropical ecosystems. In a model experiment emulating free-air CO2 enrichment (FACE) treatment for forests globally, N limitation associated with low N-mineralisation rates of colder soils reduces CO2 enhancement of net primary production (NPP) for boreal forests, while some temperate and tropical forests exhibit increased NPP enhancement. Under a business-as-usual future climate and emissions scenario, ecosystem C storage globally was projected to increase by ca. 10%; additional N requirements to match this increasing ecosystem C were within the high N supply limit estimated on stoichiometric grounds in an earlier study. Our results highlight the importance of accounting for C-N interactions in studies of global terrestrial N cycling, and as a basis for understanding mechanisms on local scales and in different regional contexts.

  15. Implications of incorporating N cycling and N limitations on primary production in an individual-based dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Smith, B.; Wårlind, D.; Arneth, A.; Hickler, T.; Leadley, P.; Siltberg, J.; Zaehle, S.

    2013-11-01

    The LPJ-GUESS dynamic vegetation model uniquely combines an individual- and patch-based representation of vegetation dynamics with ecosystem biogeochemical cycling from regional to global scales. We present an updated version that includes plant and soil N dynamics, analysing the implications of accounting for C-N interactions on predictions and performance of the model. Stand structural dynamics and allometric scaling of tree growth suggested by global databases of forest stand structure and development were well-reproduced by the model in comparison to an earlier multi-model study. Accounting for N cycle dynamics improved the goodness-of-fit for broadleaved forests. N limitation associated with low N mineralisation rates reduces productivity of cold-climate and dry-climate ecosystems relative to mesic temperate and tropical ecosystems. In a model experiment emulating free-air CO2 enrichment (FACE) treatment for forests globally, N-limitation associated with low N mineralisation rates of colder soils reduces CO2-enhancement of NPP for boreal forests, while some temperate and tropical forests exhibit increased NPP enhancement. Under a business-as-usual future climate and emissions scenario, ecosystem C storage globally was projected to increase by c. 10%; additional N requirements to match this increasing ecosystem C were within the high N supply limit estimated on stoichiometric grounds in an earlier study. Our results highlight the importance of accounting for C-N interactions not only in studies of global terrestrial C cycling, but to understand underlying mechanisms on local scales and in different regional contexts.

  16. Incorporating the Role of Nitrogen in the Noah-MP Land Surface Model for Climate and Environmental Studies

    NASA Astrophysics Data System (ADS)

    Cai, X.; Yang, Z. L.; Fisher, J. B.

    2014-12-01

    Noah-MP (Niu et al., 2011; Yang et al., 2011) is the next generation land surface model for the Weather Research and Forecasting (WRF) meteorological model and the Climate Forecast Systems in the National Centers for Environmental Prediction. While Noah-MP does not currently contain a dynamic nitrogen cycle, this can readily be updated with the interactive vegetation canopy option. In this study, Noah-MP is coupled with the Fixation & Uptake of Nitrogen (FUN) model (Fisher et al., 2010) for the above ground processes and the soil nitrogen model from the Soil and Water Assessment Tool (SWAT) for the below ground processes. This combines FUN's state-of-the-art concept of the carbon cost theory and SWAT's strength in representing the anthropogenic effects on the nitrogen cycle. The processes employed from FUN are the nitrogen uptake and fixation of plants, both of which are directly linked to the plant productivity. If passive nitrogen uptake cannot meet the nitrogen demand, plants have to spend part of the photosynthesized carbon production on nitrogen acquisition. The processes employed from SWAT are nitrogen mineralization, nitrification, immobilization, volatilization, atmospheric deposition, and leaching. In addition, the modified universal soil loss equation is used to more accurately account for the nitrogen removal in sediment caused by surface runoff. Because human input of nitrogen greatly changes the nitrogen cycle, a simple nitrogen fertilization approach is also applied to crops. Preliminary results show that Noah-MP is capable of simulating the dynamics of the major nitrogen pools. Further comprehensive evaluation of the new model will be conducted at one or more experimental sites.

  17. A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

    SciTech Connect

    Lim, H.; Hale, L. M.; Zimmerman, J. A.; Battaile, C. C.; Weinberger, C. R.

    2015-01-05

    In this study, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equation is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.

  18. A multi-scale model of dislocation plasticity in α-Fe: Incorporating temperature, strain rate and non-Schmid effects

    DOE PAGESBeta

    Lim, H.; Hale, L. M.; Zimmerman, J. A.; Battaile, C. C.; Weinberger, C. R.

    2015-01-05

    In this study, we develop an atomistically informed crystal plasticity finite element (CP-FE) model for body-centered-cubic (BCC) α-Fe that incorporates non-Schmid stress dependent slip with temperature and strain rate effects. Based on recent insights obtained from atomistic simulations, we propose a new constitutive model that combines a generalized non-Schmid yield law with aspects from a line tension (LT) model for describing activation enthalpy required for the motion of dislocation kinks. Atomistic calculations are conducted to quantify the non-Schmid effects while both experimental data and atomistic simulations are used to assess the temperature and strain rate effects. The parameterized constitutive equationmore » is implemented into a BCC CP-FE model to simulate plastic deformation of single and polycrystalline Fe which is compared with experimental data from the literature. This direct comparison demonstrates that the atomistically informed model accurately captures the effects of crystal orientation, temperature and strain rate on the flow behavior of siangle crystal Fe. Furthermore, our proposed CP-FE model exhibits temperature and strain rate dependent flow and yield surfaces in polycrystalline Fe that deviate from conventional CP-FE models based on Schmid's law.« less

  19. A reduced-dimensionality quantum model which incorporates the full-dimensional energy of the system: Application to the vibrational predissociation of Cl2-Ne2

    NASA Astrophysics Data System (ADS)

    Ceotto, M.; García-Vela, A.

    2001-08-01

    A reduced-dimensionality quantum model is proposed which incorporates the zero-point energy of the neglected modes in a systematic, natural way. In this model the reduced-dimensionality Hamiltonian is obtained by averaging the exact Hamiltonian over the dependence of the full-dimensional initial state of the neglected modes. The reduced Hamiltonian conserves all the terms of the full Hamiltonian, providing a more flexible description of the couplings between the modes considered explicitly in the model. The model is applied to simulate the vibrational predissociation dynamics of Cl2-Ne2, considering the three stretching modes of the complex. The results are compared to experimental data and to previous calculations using a reduced-dimensionality quantum model and a full-dimensional quantum-classical approach. The Cl2-Ne2 resonance lifetimes obtained agree only qualitatively with the experimental and previously calculated ones. By contrast, the present model predicts more correctly than previous calculations the behavior of the Cl2 fragment vibrational distributions observed experimentally. The applicability of the model is discussed and further refinements are suggested.

  20. Mathematical modelling of oil spill fate and transport in the marine environment incorporating biodegradation kinetics of oil droplets

    NASA Astrophysics Data System (ADS)

    Spanoudaki, Katerina

    2016-04-01

    Oil biodegradation by native bacteria is one of the most important natural processes that can attenuate the environmental impacts of marine oil spills. However, very few numerical models of oil spill fate and transport include biodegradation kinetics of spilled oil. Furthermore, in models where biodegradation is included amongst the oil transformation processes simulated, it is mostly represented as a first order decay process neglecting the effect of several important parameters that can limit biodegradation rate, such as oil composition and oil droplets-water interface. To this end, the open source numerical model MEDSKIL-II, which simulates oil spill fate and transport in the marine environment, has been modified to include biodegradation kinetics of oil droplets dispersed in the water column. MEDSLIK-II predicts the transport and weathering of oil spills following a Lagrangian approach for the solution of the advection-diffusion equation. Transport is governed by the 3D sea currents and wave field provided by ocean circulation models. In addition to advective and diffusive displacements, the model simulates several physical and chemical processes that transform the oil (evaporation, emulsification, dispersion in the water column, adhesion to coast). The fate algorithms employed in MEDSLIK-II consider the oil as a uniform substance whose properties change as the slick weathers, an approach that can lead to reduced accuracy, especially in the estimation of oil evaporation and biodegradation. Therefore MEDSLIK-II has been modified by adopting the "pseudo-component" approach for simulating weathering processes. Spilled oil is modelled as a relatively small number of discrete, non-interacting components (pseudo-components). Chemicals in the oil mixture are grouped by physical-chemical properties and the resulting pseudo-component behaves as if it were a single substance with characteristics typical of the chemical group. The fate (evaporation, dispersion

  1. Incorporating topography in a cellular automata model to simulate residents evacuation in a mountain area in China

    NASA Astrophysics Data System (ADS)

    Wang, Li; Liu, Mao; Meng, Bo

    2013-02-01

    In China, both the mountainous areas and the number of people who live in mountain areas occupy a significant proportion. When production accidents or natural disasters happen, the residents in mountain areas should be evacuated and the evacuation is of obvious importance to public safety. But it is a pity that there are few studies on safety evacuation in rough terrain. The particularity of the complex terrain in mountain areas, however, makes it difficult to study pedestrian evacuation. In this paper, a three-dimensional surface cellular automata model is proposed to numerically simulate the real time dynamic evacuation of residents. The model takes into account topographic characteristics (the slope gradient) of the environment and the biomechanics characteristics (weight and leg extensor power) of the residents to calculate the walking speed. This paper only focuses on the influence of topography and the physiological parameters are defined as constants according to a statistical report. Velocity varies with the topography. In order to simulate the behavior of a crowd with varying movement velocities, and a numerical algorithm is used to determine the time step of iteration. By doing so, a numerical simulation can be conducted in a 3D surface CA model. Moreover, considering residents evacuation around a gas well in a mountain area as a case, a visualization system for a three-dimensional simulation of pedestrian evacuation is developed. In the simulation process, population behaviors of congestion, queuing and collision avoidance can be observed. The simulation results are explained reasonably. Therefore, the model presented in this paper can realize a 3D dynamic simulation of pedestrian evacuation vividly in complex terrain and predict the evacuation procedure and evacuation time required, which can supply some valuable information for emergency management.

  2. Incorporating anthropogenic influences into fire probability models: Effects of development and climate change on fire activity in California

    NASA Astrophysics Data System (ADS)

    Mann, M.; Moritz, M.; Batllori, E.; Waller, E.; Krawchuk, M.; Berck, P.

    2014-12-01

    The costly interactions between humans and natural fire regimes throughout California demonstrate the need to understand the uncertainties surrounding wildfire, especially in the face of a changing climate and expanding human communities. Although a number of statistical and process-based wildfire models exist for California, there is enormous uncertainty about the location and number of future fires. Models estimate an increase in fire occurrence between nine and fifty-three percent by the end of the century. Our goal is to assess the role of uncertainty in climate and anthropogenic influences on the state's fire regime from 2000-2050. We develop an empirical model that integrates novel information about the distribution and characteristics of future plant communities without assuming a particular distribution, and improve on previous efforts by integrating dynamic estimates of population density at each forecast time step. Historically, we find that anthropogenic influences account for up to fifty percent of the total fire count, and that further housing development will incite or suppress additional fires according to their intensity. We also find that the total area burned is likely to increase but at a slower than historical rate. Previous findings of substantially increased numbers of fires may be tied to the assumption of static fuel loadings, and the use of proxy variables not relevant to plant community distributions. We also find considerable agreement between GFDL and PCM model A2 runs, with decreasing fire counts expected only in areas of coastal influence below San Francisco and above Los Angeles. Due to potential shifts in rainfall patterns, substantial uncertainty remains for the semiarid deserts of the inland south. The broad shifts of wildfire between California's climatic regions forecast in this study point to dramatic shifts in the pressures plant and human communities will face by midcentury. The information provided by this study reduces the

  3. The interconnection of wet and dry deposition and the alteration of deposition budgets due to incorporation of new process understanding in regional models

    NASA Astrophysics Data System (ADS)

    Dennis, R. L.; Bash, J. O.; Foley, K. M.; Gilliam, R.; Pinder, R. W.

    2013-12-01

    Deposition is affected by the chemical and physical processes represented in the regional models as well as source strength. The overall production and loss budget (wet and dry deposition) is dynamically connected and adjusts internally to changes in process representation. In addition, the scrubbing of pollutants from the atmosphere by precipitation is one of several processes that remove pollutants, creating a coupling with the atmospheric aqueous and gas phase chemistry that can influence wet deposition rates in a nonlinear manner. We explore through model sensitivities with the regional Community Multiscale Air Quality (CMAQ) model the influence on wet and dry deposition, and the overall continental nitrogen budget, of changes in three process representations in the model: (1) incorporation of lightning generated NO, (2) improved representation of convective precipitation, and (3) replacement of the typical unidirectional dry deposition of NH3 with a state of the science representation of NH3 bi-directional air-surface exchange. Results of the sensitivity studies will be presented. (1) Incorporation of lightning generated NO significantly reduces a negative bias in summer wet nitrate deposition, but is sensitive to the choice of convective parameterization. (2) Use of a less active trigger of convective precipitation in the WRF meteorological model to reduce summertime precipitation over prediction bias reduces the generation of NO from lightning. It also reduces the wet deposition of nitrate and increases the dry deposition of oxidized nitrogen, as well as changing (reducing) the surface level exposure to ozone. Improvements in the convective precipitation processes also result in more non-precipitating clouds leading to an increase in SO4 production through the aqueous pathway resulting in improvements in summertime SO4 ambient aerosol estimates.(3) Incorporation of state of the science ammonia bi-directional air surface exchange affects both the dry

  4. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement.

    PubMed

    Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

    2016-04-01

    To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains. PMID:26860200

  5. Incorporating modeling and simulations in undergraduate biophysical chemistry course to promote understanding of structure-dynamics-function relationships in proteins.

    PubMed

    Hati, Sanchita; Bhattacharyya, Sudeep

    2016-01-01

    A project-based biophysical chemistry laboratory course, which is offered to the biochemistry and molecular biology majors in their senior year, is described. In this course, the classroom study of the structure-function of biomolecules is integrated with the discovery-guided laboratory study of these molecules using computer modeling and simulations. In particular, modern computational tools are employed to elucidate the relationship between structure, dynamics, and function in proteins. Computer-based laboratory protocols that we introduced in three modules allow students to visualize the secondary, super-secondary, and tertiary structures of proteins, analyze non-covalent interactions in protein-ligand complexes, develop three-dimensional structural models (homology model) for new protein sequences and evaluate their structural qualities, and study proteins' intrinsic dynamics to understand their functions. In the fourth module, students are assigned to an authentic research problem, where they apply their laboratory skills (acquired in modules 1-3) to answer conceptual biophysical questions. Through this process, students gain in-depth understanding of protein dynamics-the missing link between structure and function. Additionally, the requirement of term papers sharpens students' writing and communication skills. Finally, these projects result in new findings that are communicated in peer-reviewed journals.

  6. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

    PubMed Central

    Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

    2016-01-01

    To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains. PMID:26860200

  7. Modelling of the interaction between chemical and mechanical behaviour of ion exchange resins incorporated into a cement-based matrix

    NASA Astrophysics Data System (ADS)

    Neji, M.; Bary, B.; Burlion, N.; Le Bescop, P.

    2013-07-01

    In this paper, we present a predictive model, based on experimental data, to determine the macroscopic mechanical behavior of a material made up of ion exchange resins solidified into a CEM III cement paste. Some observations have shown that in some cases, a significant macroscopic expansion of this composite material may be expected, due to internal pressures generated in the resin. To build the model, we made the choice to break down the problem in two scale's studies. The first deals with the mechanical behavior of the different heterogeneities of the composite, i.e. the resin and the cement paste. The second upscales the information from the heterogeneities to the Representative Elementary Volume (REV) of the composite. The heterogeneities effects are taken into account in the REV by applying a homogenization method derived from the Eshelby theory combined with an interaction coefficient drawn from the poroelasticity theory. At the first scale, from the second thermodynamic law, a formulation is developed to estimate the resin microscopic swelling. The model response is illustrated on a simple example showing the impact of the calculated internal pressure, on the macroscopic strain.

  8. Incorporating Ecosystem Experiments and Observations into Process Models of Forest Carbon and Water Cycles: Challenges and Solutions

    NASA Astrophysics Data System (ADS)

    Ward, E. J.; Thomas, R. Q.; Sun, G.; McNulty, S. G.; Domec, J. C.; Noormets, A.; King, J. S.

    2015-12-01

    Numerous studies, both experimental and observational, have been conducted over the past two decades in an attempt to understand how water and carbon cycling in terrestrial ecosystems may respond to changes in climatic conditions. These studies have produced a wealth of detailed data on key processes driving these cycles. In parallel, sophisticated models of these processes have been formulated to answer a variety of questions relevant to natural resource management. Recent advances in data assimilation techniques offer exciting new possibilities to combine this wealth of ecosystem data with process models of ecosystem function to improve prediction and quantify associated uncertainty. Using forests of the southeastern United States as our focus, we will specify how fine-scale physiological (e.g. half-hourly sap flux) can be scaled up with quantified error for use in models of stand growth and hydrology. This approach represents an opportunity to leverage current and past research from experiments including throughfall displacement × fertilization (PINEMAP), irrigation × fertilization (SETRES), elevated CO­2­ (Duke and ORNL FACE) and a variety of observational studies in both conifer and hardwood forests throughout the region, using a common platform for data assimilation and prediction. As part of this discussion, we will address variation in dominant species, stand structure, site age, management practices, soils and climate that represent both challenges to the development of a common analytical approach and opportunities to address questions of interest to policy makers and natural resource managers.

  9. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement.

    PubMed

    Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

    2016-04-01

    To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association